diff --git a/.gitignore b/.gitignore
index 8f718aea18f8228889f4966d3e05d98422a63c57..5a12c9f6778a0f6d3d7e41243a29ccdc903a43d4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -166,7 +166,7 @@ Desktop.ini
.tags
.tags_sorted_by_file
-Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h
+Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h
# Make sure Third_Party doesn't get checked into the main repository
diff --git a/Framework/API/CMakeLists.txt b/Framework/API/CMakeLists.txt
index cbaec9de9b5cdf93e075d3f1aab6cf62ee14d592..f847f9e46ddb9db9caf008d904bce4d838d64efd 100644
--- a/Framework/API/CMakeLists.txt
+++ b/Framework/API/CMakeLists.txt
@@ -18,6 +18,7 @@ set ( SRC_FILES
src/ChopperModel.cpp
src/Column.cpp
src/ColumnFactory.cpp
+ src/CommonBinsValidator.cpp
src/CompositeCatalog.cpp
src/CompositeDomainMD.cpp
src/CompositeFunction.cpp
@@ -45,6 +46,7 @@ set ( SRC_FILES
src/FunctionValues.cpp
src/GridDomain.cpp
src/GridDomain1D.cpp
+ src/HistogramValidator.cpp
src/HistoryItem.cpp
src/HistoryView.cpp
src/IDomainCreator.cpp
@@ -74,7 +76,9 @@ set ( SRC_FILES
src/ImplicitFunctionFactory.cpp
src/ImplicitFunctionParameterParserFactory.cpp
src/ImplicitFunctionParserFactory.cpp
+ src/IncreasingAxisValidator.cpp
src/InstrumentDataService.cpp
+ src/InstrumentValidator.cpp
src/JointDomain.cpp
src/LatticeDomain.cpp
src/LinearScale.cpp
@@ -92,10 +96,11 @@ set ( SRC_FILES
src/MultiPeriodGroupWorker.cpp
src/MultipleExperimentInfos.cpp
src/MultipleFileProperty.cpp
+ src/NotebookBuilder.cpp
+ src/NotebookWriter.cpp
src/NullCoordTransform.cpp
- src/NotebookBuilder.cpp
- src/NotebookWriter.cpp
src/NumericAxis.cpp
+ src/NumericAxisValidator.cpp
src/ParamFunction.cpp
src/ParameterReference.cpp
src/ParameterTie.cpp
@@ -104,17 +109,20 @@ set ( SRC_FILES
src/Projection.cpp
src/PropertyManagerDataService.cpp
src/PropertyNexus.cpp
+ src/RawCountValidator.cpp
src/RefAxis.cpp
src/RemoteJobManagerFactory.cpp
src/Run.cpp
src/Sample.cpp
src/SampleEnvironment.cpp
src/SampleShapeValidator.cpp
+ src/SampleValidator.cpp
src/ScopedWorkspace.cpp
src/ScriptBuilder.cpp
src/ScriptRepository.cpp
src/ScriptRepositoryFactory.cpp
src/SpectraAxis.cpp
+ src/SpectraAxisValidator.cpp
src/SpectrumDetectorMapping.cpp
src/TableRow.cpp
src/TextAxis.cpp
@@ -125,7 +133,7 @@ set ( SRC_FILES
src/WorkspaceHistory.cpp
src/WorkspaceOpOverloads.cpp
src/WorkspaceProperty.cpp
- src/WorkspaceValidators.cpp
+ src/WorkspaceUnitValidator.cpp
)
set ( SRC_UNITY_IGNORE_FILES src/CompositeFunction.cpp
@@ -158,6 +166,7 @@ set ( INC_FILES
inc/MantidAPI/ChopperModel.h
inc/MantidAPI/Column.h
inc/MantidAPI/ColumnFactory.h
+ inc/MantidAPI/CommonBinsValidator.h
inc/MantidAPI/CompositeCatalog.h
inc/MantidAPI/CompositeDomain.h
inc/MantidAPI/CompositeDomainMD.h
@@ -189,6 +198,7 @@ set ( INC_FILES
inc/MantidAPI/FunctionValues.h
inc/MantidAPI/GridDomain.h
inc/MantidAPI/GridDomain1D.h
+ inc/MantidAPI/HistogramValidator.h
inc/MantidAPI/HistoryItem.h
inc/MantidAPI/HistoryView.h
inc/MantidAPI/IAlgorithm.h
@@ -242,7 +252,9 @@ set ( INC_FILES
inc/MantidAPI/ImplicitFunctionParameterParserFactory.h
inc/MantidAPI/ImplicitFunctionParser.h
inc/MantidAPI/ImplicitFunctionParserFactory.h
+ inc/MantidAPI/IncreasingAxisValidator.h
inc/MantidAPI/InstrumentDataService.h
+ inc/MantidAPI/InstrumentValidator.h
inc/MantidAPI/Jacobian.h
inc/MantidAPI/JointDomain.h
inc/MantidAPI/LatticeDomain.h
@@ -253,8 +265,9 @@ set ( INC_FILES
inc/MantidAPI/MDGeometry.h
inc/MantidAPI/MatrixWSIndexCalculator.h
inc/MantidAPI/MatrixWorkspace.h
- inc/MantidAPI/MatrixWorkspace_fwd.h
inc/MantidAPI/MatrixWorkspaceMDIterator.h
+ inc/MantidAPI/MatrixWorkspaceValidator.h
+ inc/MantidAPI/MatrixWorkspace_fwd.h
inc/MantidAPI/MemoryManager.h
inc/MantidAPI/ModeratorModel.h
inc/MantidAPI/MultiDomainFunction.h
@@ -262,10 +275,11 @@ set ( INC_FILES
inc/MantidAPI/MultiPeriodGroupWorker.h
inc/MantidAPI/MultipleExperimentInfos.h
inc/MantidAPI/MultipleFileProperty.h
- inc/MantidAPI/NotebookBuilder.h
- inc/MantidAPI/NotebookWriter.h
+ inc/MantidAPI/NotebookBuilder.h
+ inc/MantidAPI/NotebookWriter.h
inc/MantidAPI/NullCoordTransform.h
inc/MantidAPI/NumericAxis.h
+ inc/MantidAPI/NumericAxisValidator.h
inc/MantidAPI/ParamFunction.h
inc/MantidAPI/ParameterReference.h
inc/MantidAPI/ParameterTie.h
@@ -274,12 +288,14 @@ set ( INC_FILES
inc/MantidAPI/Projection.h
inc/MantidAPI/PropertyManagerDataService.h
inc/MantidAPI/PropertyNexus.h
+ inc/MantidAPI/RawCountValidator.h
inc/MantidAPI/RefAxis.h
inc/MantidAPI/RemoteJobManagerFactory.h
inc/MantidAPI/Run.h
inc/MantidAPI/Sample.h
inc/MantidAPI/SampleEnvironment.h
inc/MantidAPI/SampleShapeValidator.h
+ inc/MantidAPI/SampleValidator.h
inc/MantidAPI/ScopedWorkspace.h
inc/MantidAPI/ScriptBuilder.h
inc/MantidAPI/ScriptRepository.h
@@ -287,6 +303,7 @@ set ( INC_FILES
inc/MantidAPI/SingleValueParameter.h
inc/MantidAPI/SingleValueParameterParser.h
inc/MantidAPI/SpectraAxis.h
+ inc/MantidAPI/SpectraAxisValidator.h
inc/MantidAPI/SpectrumDetectorMapping.h
inc/MantidAPI/TableRow.h
inc/MantidAPI/TextAxis.h
@@ -294,14 +311,14 @@ set ( INC_FILES
inc/MantidAPI/VectorParameter.h
inc/MantidAPI/VectorParameterParser.h
inc/MantidAPI/Workspace.h
- inc/MantidAPI/Workspace_fwd.h
inc/MantidAPI/WorkspaceFactory.h
inc/MantidAPI/WorkspaceGroup.h
inc/MantidAPI/WorkspaceGroup_fwd.h
inc/MantidAPI/WorkspaceHistory.h
inc/MantidAPI/WorkspaceOpOverloads.h
inc/MantidAPI/WorkspaceProperty.h
- inc/MantidAPI/WorkspaceValidators.h
+ inc/MantidAPI/WorkspaceUnitValidator.h
+ inc/MantidAPI/Workspace_fwd.h
)
set ( TEST_FILES
@@ -317,6 +334,7 @@ set ( TEST_FILES
AsynchronousTest.h
BinEdgeAxisTest.h
BoxControllerTest.h
+ CommonBinsValidatorTest.h
CompositeFunctionTest.h
CoordTransformTest.h
CostFunctionFactoryTest.h
@@ -337,6 +355,7 @@ set ( TEST_FILES
FunctionPropertyTest.h
FunctionTest.h
FunctionValuesTest.h
+ HistogramValidatorTest.h
HistoryItemTest.h
HistoryViewTest.h
IEventListTest.h
@@ -352,6 +371,7 @@ set ( TEST_FILES
ImplicitFunctionParserFactoryTest.h
IncreasingAxisValidatorTest.h
InstrumentDataServiceTest.h
+ InstrumentValidatorTest.h
LatticeDomainTest.h
LiveListenerFactoryTest.h
LogManagerTest.h
@@ -367,6 +387,7 @@ set ( TEST_FILES
NotebookBuilderTest.h
NotebookWriterTest.h
NumericAxisTest.h
+ NumericAxisValidatorTest.h
ParamFunctionAttributeHolderTest.h
ParameterReferenceTest.h
ParameterTieTest.h
@@ -374,14 +395,17 @@ set ( TEST_FILES
ProjectionTest.h
PropertyManagerDataServiceTest.h
PropertyNexusTest.h
+ RawCountValidatorTest.h
RemoteJobManagerFactoryTest.h
RunTest.h
SampleEnvironmentTest.h
SampleShapeValidatorTest.h
SampleTest.h
+ SampleValidatorTest.h
ScopedWorkspaceTest.h
ScriptBuilderTest.h
SpectraAxisTest.h
+ SpectraAxisValidatorTest.h
SpectrumDetectorMappingTest.h
TextAxisTest.h
VectorParameterParserTest.h
@@ -392,6 +416,7 @@ set ( TEST_FILES
WorkspaceHistoryTest.h
WorkspaceOpOverloadsTest.h
WorkspacePropertyTest.h
+ WorkspaceUnitValidatorTest.h
)
set ( GMOCK_TEST_FILES
diff --git a/Framework/API/inc/MantidAPI/AlgorithmProxy.h b/Framework/API/inc/MantidAPI/AlgorithmProxy.h
index ef45cafbbf59b8bce4303063b7ae87fb6a73fa05..cc2c06272044a8d3aee5889ffdb1da9975de73aa 100644
--- a/Framework/API/inc/MantidAPI/AlgorithmProxy.h
+++ b/Framework/API/inc/MantidAPI/AlgorithmProxy.h
@@ -116,6 +116,8 @@ public:
void setPropertyValue(const std::string &name, const std::string &value);
/// Do something after a property was set
void afterPropertySet(const std::string &);
+ /// Make m_properties point to the same PropertyManager as po.
+ void copyPropertiesFrom(const PropertyManagerOwner &po);
//@}
void cancel();
diff --git a/Framework/API/inc/MantidAPI/CommonBinsValidator.h b/Framework/API/inc/MantidAPI/CommonBinsValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..491e1fb63f0be05d84dc65edf01712a834195f4b
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/CommonBinsValidator.h
@@ -0,0 +1,52 @@
+#ifndef MANTID_API_COMMONBINSVALIDATOR_H_
+#define MANTID_API_COMMONBINSVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which provides a <I>TENTATIVE</I> check that a workspace
+ contains common bins in each spectrum.
+ For efficiency reasons, it only checks that the first and last spectra have
+ common bins, so it is important to carry out a full check within the
+ algorithm itself.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL CommonBinsValidator : public MatrixWorkspaceValidator {
+public:
+ /// Gets the type of the validator
+ std::string getType() const { return "commonbins"; }
+ /// Clone the current state
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_COMMONBINSVALIDATOR_H_ */
\ No newline at end of file
diff --git a/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h b/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h
index 68c8250521e5bb0c2d476a682a009ac44c851898..f48837d236cb6925ef562a70ff597d62b28fc7db 100644
--- a/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h
+++ b/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h
@@ -52,7 +52,7 @@ private:
/// Replacement version, -1 indicates latest
int m_replacementVersion;
/// The date that the algorithm was first deprecated.
- std::string m_deprecatdDate;
+ std::string m_deprecatedDate;
};
} // namespace API
diff --git a/Framework/API/inc/MantidAPI/HistogramValidator.h b/Framework/API/inc/MantidAPI/HistogramValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..a576d266ab28b1e245530d693cfeb04cb16b4f80
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/HistogramValidator.h
@@ -0,0 +1,55 @@
+#ifndef MANTID_API_HISTOGRAMVALIDATOR_H_
+#define MANTID_API_HISTOGRAMVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which checks that a workspace contains histogram data (the
+ default) or point data as required.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL HistogramValidator : public MatrixWorkspaceValidator {
+public:
+ explicit HistogramValidator(const bool &mustBeHistogram = true);
+
+ /// Gets the type of the validator
+ std::string getType() const { return "histogram"; }
+ /// Clone the current state
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+
+ /// A flag indicating whether this validator requires that the workspace be a
+ /// histogram (true) or not
+ const bool m_mustBeHistogram;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_HISTOGRAMVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/IncreasingAxisValidator.h b/Framework/API/inc/MantidAPI/IncreasingAxisValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..95965219c77caeaf436903e4c4daba4a470940cd
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/IncreasingAxisValidator.h
@@ -0,0 +1,49 @@
+#ifndef MANTID_API_INCREASINGAXISVALIDATOR_H_
+#define MANTID_API_INCREASINGAXISVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which checks that the X axis of a workspace is increasing from
+ left to right.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL IncreasingAxisValidator : public MatrixWorkspaceValidator {
+public:
+ /// Get the type of the validator
+ std::string getType() const { return "IncreasingAxis"; }
+ /// Clone the current state
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_INCREASINGAXISVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/InstrumentValidator.h b/Framework/API/inc/MantidAPI/InstrumentValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..3362f8c80ce5ce06cd966bd0bdaab282e7b5d558
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/InstrumentValidator.h
@@ -0,0 +1,57 @@
+#ifndef MANTID_API_INSTRUMENTVALIDATOR_H_
+#define MANTID_API_INSTRUMENTVALIDATOR_H_
+
+#include "MantidAPI/DllConfig.h"
+#include "MantidAPI/ExperimentInfo.h"
+#include "MantidKernel/TypedValidator.h"
+
+namespace Mantid {
+namespace API {
+
+class ExperimentInfo;
+
+/**
+ A validator which checks that a workspace has a valid instrument.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL InstrumentValidator
+ : public Kernel::TypedValidator<boost::shared_ptr<ExperimentInfo>> {
+public:
+ /// Enumeration describing requirements
+ enum Requirements { SourcePosition = 0x1, SamplePosition = 0x2 };
+
+ // The default is historical so I don't break a lot of user code
+ InstrumentValidator(const unsigned int flags = SamplePosition);
+ std::string getType() const;
+ Kernel::IValidator_sptr clone() const;
+ std::string
+ checkValidity(const boost::shared_ptr<ExperimentInfo> &value) const;
+
+private:
+ unsigned int m_requires;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_INSTRUMENTVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/MatrixWorkspaceValidator.h b/Framework/API/inc/MantidAPI/MatrixWorkspaceValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..6c3cbea5d0d74875d1513478d8404ba2a423d307
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/MatrixWorkspaceValidator.h
@@ -0,0 +1,42 @@
+#ifndef MANTID_API_MATRIXWORKSPACEVALIDATOR_H_
+#define MANTID_API_MATRIXWORKSPACEVALIDATOR_H_
+
+#include "MantidAPI/DllConfig.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidKernel/TypedValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ An interface for those validators that require the MatrixWorkspace interface
+
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL MatrixWorkspaceValidator
+ : public Kernel::TypedValidator<MatrixWorkspace_sptr> {};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_MATRIXWORKSPACEVALIDATOR_H_ */
\ No newline at end of file
diff --git a/Framework/API/inc/MantidAPI/NumericAxisValidator.h b/Framework/API/inc/MantidAPI/NumericAxisValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..e33deb71603395a8004fea88f9a049a9c2a8c14f
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/NumericAxisValidator.h
@@ -0,0 +1,53 @@
+#ifndef MANTID_API_NUMERICAXISVALIDATOR_H_
+#define MANTID_API_NUMERICAXISVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which checks whether the input workspace has the Numeric data in
+ the axis.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL NumericAxisValidator : public MatrixWorkspaceValidator {
+public:
+ explicit NumericAxisValidator(const int &axisNumber = 1);
+
+ /// Gets the type of the validator
+ std::string getType() const { return "numericaaxis"; }
+ /// Clone the current state
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+ /// Axis number to check on, defaults to 1
+ const int m_axisNumber;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_NUMERICAXISVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/RawCountValidator.h b/Framework/API/inc/MantidAPI/RawCountValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..fe3e2655ee66e7d611a2f2155281e3da5166451f
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/RawCountValidator.h
@@ -0,0 +1,53 @@
+#ifndef MANTID_API_RAWCOUNTVALIDATOR_H_
+#define MANTID_API_RAWCOUNTVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/** A validator which checks that a workspace contains raw counts in its bins.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL RawCountValidator : public MatrixWorkspaceValidator {
+public:
+ explicit RawCountValidator(const bool &mustNotBeDistribution = true);
+
+ /// Gets the type of the validator
+ std::string getType() const { return "rawcount"; }
+ /// Clone the current state
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+
+ /// A flag indicating whether this validator requires that the workspace must
+ /// be a distribution (false) or not (true, the default)
+ const bool m_mustNotBeDistribution;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_RAWCOUNTVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/SampleValidator.h b/Framework/API/inc/MantidAPI/SampleValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..38685e032578314d1dad514b881a7df534630b1f
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/SampleValidator.h
@@ -0,0 +1,50 @@
+#ifndef MANTID_API_SAMPLEVALIDATOR_H_
+#define MANTID_API_SAMPLEVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which checks that sample has the required properties.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL SampleValidator : public MatrixWorkspaceValidator {
+public:
+ /// Enumeration describing requirements
+ enum Requirements { Shape = 0x1, Material = 0x2 };
+
+ SampleValidator(const unsigned int flags = (Shape | Material));
+ std::string getType() const;
+ Kernel::IValidator_sptr clone() const;
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+
+private:
+ unsigned int m_requires;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_SAMPLEVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/SpectraAxisValidator.h b/Framework/API/inc/MantidAPI/SpectraAxisValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..bb96d2e5a3c0ce8784bdb79c94882c1db5472018
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/SpectraAxisValidator.h
@@ -0,0 +1,53 @@
+#ifndef MANTID_API_SPECTRAAXISVALIDATOR_H_
+#define MANTID_API_SPECTRAAXISVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which checks whether the input workspace has the Spectra number
+ in the axis.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL SpectraAxisValidator : public MatrixWorkspaceValidator {
+public:
+ explicit SpectraAxisValidator(const int &axisNumber = 1);
+
+ /// Gets the type of the validator
+ std::string getType() const { return "spectraaxis"; }
+ /// Clone the current validator
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+ /// Axis number to check on, defaults to 1
+ const int m_axisNumber;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_SPECTRAAXISVALIDATOR_H_ */
diff --git a/Framework/API/inc/MantidAPI/WorkspaceUnitValidator.h b/Framework/API/inc/MantidAPI/WorkspaceUnitValidator.h
new file mode 100644
index 0000000000000000000000000000000000000000..f4ddf3a9133d3e3434e7c26c3c4510c4a95968e6
--- /dev/null
+++ b/Framework/API/inc/MantidAPI/WorkspaceUnitValidator.h
@@ -0,0 +1,53 @@
+#ifndef MANTID_API_WORKSPACEUNITVALIDATOR_H_
+#define MANTID_API_WORKSPACEUNITVALIDATOR_H_
+
+#include "MantidAPI/MatrixWorkspaceValidator.h"
+
+namespace Mantid {
+namespace API {
+
+/**
+ A validator which checks that the unit of the workspace referred to
+ by a WorkspaceProperty is the expected one.
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_API_DLL WorkspaceUnitValidator : public MatrixWorkspaceValidator {
+public:
+ explicit WorkspaceUnitValidator(const std::string &unitID = "");
+ /// Gets the type of the validator
+ std::string getType() const { return "workspaceunit"; }
+ /// Clone the current state
+ Kernel::IValidator_sptr clone() const;
+
+private:
+ /// Check for validity.
+ std::string checkValidity(const MatrixWorkspace_sptr &value) const;
+
+ /// The name of the required unit
+ const std::string m_unitID;
+};
+
+} // namespace API
+} // namespace Mantid
+
+#endif /* MANTID_API_WORKSPACEUNITVALIDATOR_H_ */
\ No newline at end of file
diff --git a/Framework/API/inc/MantidAPI/WorkspaceValidators.h b/Framework/API/inc/MantidAPI/WorkspaceValidators.h
deleted file mode 100644
index f6bf5308cb4dac8dd5a9f6e6bc8c5363dcbcdccf..0000000000000000000000000000000000000000
--- a/Framework/API/inc/MantidAPI/WorkspaceValidators.h
+++ /dev/null
@@ -1,409 +0,0 @@
-#ifndef MANTID_API_WORKSPACEVALIDATORS_H_
-#define MANTID_API_WORKSPACEVALIDATORS_H_
-
-//----------------------------------------------------------------------
-// Includes
-//----------------------------------------------------------------------
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidKernel/TypedValidator.h"
-#include "MantidKernel/CompositeValidator.h"
-#include <numeric>
-#include <vector>
-
-namespace Mantid {
-namespace API {
-
-//===============================================================================================
-/** A validator for workspaces which can contain a number of individual
- validators,
- all of which must pass for the overall validator to do so.
-
- @author Russell Taylor, Tessella Support Services plc
- @date 16/09/2008
-
- Copyright © 2008-2010 ISIS Rutherford Appleton Laboratory, NScD Oak
- Ridge National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- File change history is stored at: <https://github.com/mantidproject/mantid>.
- Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-
-//==============================================================================================
-/**
- * An interface for those validators that require the MatrixWorkspace interface
- */
-class MatrixWorkspaceValidator
- : public Kernel::TypedValidator<MatrixWorkspace_sptr> {};
-
-//===============================================================================================
-/** A validator which checks that the unit of the workspace referred to
- * by a WorkspaceProperty is the expected one.
- *
- * @author Russell Taylor, Tessella Support Services plc
- * @date 16/09/2008
- */
-class DLLExport WorkspaceUnitValidator : public MatrixWorkspaceValidator {
-public:
- /** Constructor
- * @param unitID :: The name of the unit that the workspace must have. If
- * left empty,
- * the validator will simply check that the workspace is not
- * unitless.
- */
- explicit WorkspaceUnitValidator(const std::string &unitID = "")
- : MatrixWorkspaceValidator(), m_unitID(unitID) {}
-
- /// Gets the type of the validator
- std::string getType() const { return "workspaceunit"; }
- /// Clone the current state
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<WorkspaceUnitValidator>(*this);
- }
-
-private:
- /** Checks that the units of the workspace data are declared match any
- *required units
- *
- * @param value :: The workspace to test
- * @return A user level description of the error or "" for no error
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- // This effectively checks for single-valued workspaces
- if (value->axes() == 0)
- return "A single valued workspace has no unit, which is required for "
- "this algorithm";
-
- Kernel::Unit_const_sptr unit = value->getAxis(0)->unit();
- // If m_unitID is empty it means that the workspace must have units, which
- // can be anything
- if (m_unitID.empty()) {
- return (unit && (!boost::dynamic_pointer_cast<const Kernel::Units::Empty>(
- unit))
- ? ""
- : "The workspace must have units");
- }
- // now check if the units of the workspace is correct
- else {
- if ((!unit) || (unit->unitID().compare(m_unitID))) {
- return "The workspace must have units of " +
- m_unitID; //+ "; its unit is: " + unit->caption();
- } else
- return "";
- }
- }
-
- /// The name of the required unit
- const std::string m_unitID;
-};
-
-//===============================================================================================
-/** A validator which checks that a workspace contains histogram data (the
- *default)
- * or point data as required.
- *
- * @author Russell Taylor, Tessella Support Services plc
- * @date 16/09/2008
- */
-class DLLExport HistogramValidator : public MatrixWorkspaceValidator {
-public:
- /** Constructor
- * @param mustBeHistogram :: Flag indicating whether the check is that a
- * workspace should
- * contain histogram data (true, default) or shouldn't
- * (false).
- */
- explicit HistogramValidator(const bool &mustBeHistogram = true)
- : MatrixWorkspaceValidator(), m_mustBeHistogram(mustBeHistogram) {}
-
- /// Gets the type of the validator
- std::string getType() const { return "histogram"; }
- /// Clone the current state
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<HistogramValidator>(*this);
- }
-
-private:
- /** Checks if the workspace contains a histogram when it shouldn't and
- * vice-versa
- * @param value :: The workspace to test
- * @return A user level description if a problem exists or ""
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- if (m_mustBeHistogram) {
- if (value->isHistogramData())
- return "";
- else
- return "The workspace must contain histogram data";
- } else {
- if (!value->isHistogramData())
- return "";
- else
- return "The workspace must not contain histogram data";
- }
- }
-
- /// A flag indicating whether this validator requires that the workspace be a
- /// histogram (true) or not
- const bool m_mustBeHistogram;
-};
-
-//===============================================================================================
-/** A validator which checks that a workspace contains raw counts in its bins
- *
- * @author Russell Taylor, Tessella Support Services plc
- * @date 16/09/2008
- */
-class DLLExport RawCountValidator : public MatrixWorkspaceValidator {
-public:
- /** Constructor
- * @param mustNotBeDistribution :: Flag indicating whether the check is that
- * a workspace should
- * not be a distribution (true, default) or
- * should be (false).
- */
- RawCountValidator(const bool &mustNotBeDistribution = true)
- : m_mustNotBeDistribution(mustNotBeDistribution) {}
-
- /// Gets the type of the validator
- std::string getType() const { return "rawcount"; }
- /// Clone the current state
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<RawCountValidator>(*this);
- }
-
-private:
- /** Checks if the workspace must be a distribution but isn't and vice-versa
- * @param value :: The workspace to test
- * @return A user level description of any problem that exists or "" no
- * problem
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- if (m_mustNotBeDistribution) {
- if (!value->isDistribution())
- return "";
- else
- return "A workspace containing numbers of counts is required here";
- } else {
- if (value->isDistribution())
- return "";
- else
- return "A workspace of numbers of counts is not allowed here";
- }
- }
-
- /// A flag indicating whether this validator requires that the workspace must
- /// be a distribution (false) or not (true, the default)
- const bool m_mustNotBeDistribution;
-};
-
-//===============================================================================================
-/** A validator which provides a <I>TENTATIVE</I> check that a workspace
- *contains
- * common bins in each spectrum.
- * For efficiency reasons, it only checks that the first and last spectra have
- * common bins, so it is important to carry out a full check within the
- *algorithm
- * itself.
- *
- * @author Russell Taylor, Tessella Support Services plc
- * @date 18/09/2008
- */
-class DLLExport CommonBinsValidator : public MatrixWorkspaceValidator {
-public:
- /// Gets the type of the validator
- std::string getType() const { return "commonbins"; }
- /// Clone the current state
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<CommonBinsValidator>(*this);
- }
-
-private:
- /** Checks that the bin boundaries of each histogram in the workspace are the
- * same
- * @param value :: The workspace to test
- * @return A message for users saying that bins are different, otherwise ""
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- if (!value)
- return "Enter an existing workspace";
- if (value->isCommonBins())
- return "";
- else
- return "The workspace must have common bin boundaries for all histograms";
- }
-};
-//===============================================================================================
-/** A validator which checks whether the input workspace has the Spectra number
- * in the axis.
- * @author Michael Whitty, STFC
- * @date 15/09/2010
- */
-class DLLExport SpectraAxisValidator : public MatrixWorkspaceValidator {
-public:
- /** Class constructor with parameter.
- * @param axisNumber :: set the axis number to validate
- */
- SpectraAxisValidator(const int &axisNumber = 1) : m_axisNumber(axisNumber) {}
-
- /// Gets the type of the validator
- std::string getType() const { return "spectraaxis"; }
- /// Clone the current validator
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<SpectraAxisValidator>(*this);
- }
-
-private:
- /** Checks that the axis stated
- * @param value :: The workspace to test
- * @return A message for users with negative results, otherwise ""
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- Mantid::API::Axis *axis = value->getAxis(m_axisNumber);
- if (axis->isSpectra())
- return "";
- else
- return "A workspace with axis being Spectra Number is required here.";
- }
- const int m_axisNumber; ///< axis number to check on, defaults to 1
-};
-//===============================================================================================
-/** A validator which checks whether the input workspace has the Numeric data in
- * the axis.
- * @author Michael Whitty, STFC
- * @date 15/09/2010
- */
-class DLLExport NumericAxisValidator : public MatrixWorkspaceValidator {
-public:
- /** Class constructor with parameter.
- * @param axisNumber :: set the axis number to validate
- */
- NumericAxisValidator(const int &axisNumber = 1) : m_axisNumber(axisNumber) {}
-
- /// Gets the type of the validator
- std::string getType() const { return "numericaaxis"; }
- /// Clone the current state
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<NumericAxisValidator>(*this);
- }
-
-private:
- /** Checks that the axis stated
- * @param value :: The workspace to test
- * @return A message for users with negative results, otherwise ""
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- Mantid::API::Axis *axis = value->getAxis(m_axisNumber);
- if (axis->isNumeric())
- return "";
- else
- return "A workspace with axis being a Numeric Axis is required here.";
- }
- const int m_axisNumber; ///< axis number to check on, defaults to 1
-};
-
-//===============================================================================================
-/** A validator which checks that a workspace has a valid instrument
- * or point data as required.
- *
- * @author Russell Taylor, Tessella
- * @date 17/12/2010
- */
-class DLLExport InstrumentValidator
- : public Kernel::TypedValidator<boost::shared_ptr<ExperimentInfo>> {
-public:
- /// Enumeration describing requirements
- enum Requirements { SourcePosition = 0x1, SamplePosition = 0x2 };
-
- // The default is historical so I don't break a lot of user code
- InstrumentValidator(const unsigned int flags = SamplePosition);
- std::string getType() const;
- Kernel::IValidator_sptr clone() const;
- std::string
- checkValidity(const boost::shared_ptr<ExperimentInfo> &value) const;
-
-private:
- unsigned int m_requires;
-};
-
-//==============================================================================
-/**
- @class SampleShapeValidator
-
- A validator which checks that sample has the required properties
- */
-class DLLExport SampleValidator : public MatrixWorkspaceValidator {
-public:
- /// Enumeration describing requirements
- enum Requirements { Shape = 0x1, Material = 0x2 };
-
- SampleValidator(const unsigned int flags = (Shape | Material));
- std::string getType() const;
- Kernel::IValidator_sptr clone() const;
- std::string checkValidity(const MatrixWorkspace_sptr &value) const;
-
-private:
- unsigned int m_requires;
-};
-
-//==============================================================================
-/**
- @class IncreasingAxisValidator
-
- A validator which checks that the X axis of a workspace is increasing from
- left to right.
-
- @author Arturs Bekasovs [arturs.bekasovs@stfc.ac.uk]
- @date 08/07/2013
-
- TODO: Move out to the different file.
- */
-class DLLExport IncreasingAxisValidator : public MatrixWorkspaceValidator {
-public:
- /// Get the type of the validator
- std::string getType() const { return "IncreasingAxis"; }
- /// Clone the current state
- Kernel::IValidator_sptr clone() const {
- return boost::make_shared<IncreasingAxisValidator>(*this);
- }
-
-private:
- /**
- * Checks that X axis is in the right direction.
- *
- * @param value The workspace to check
- * @return "" if is valid, otherwise a user level description of a problem
- */
- std::string checkValidity(const MatrixWorkspace_sptr &value) const {
- // 0 for X axis
- Axis *xAxis = value->getAxis(0);
-
- // Left-most axis value should be less than the right-most, if ws has
- // more than one X axis value
- if (xAxis->length() > 1 &&
- xAxis->getValue(0) >= xAxis->getValue(xAxis->length() - 1))
- return "X axis of the workspace should be increasing from left to "
- "right";
- else
- return "";
- }
-};
-
-} // namespace API
-} // namespace Mantid
-
-#endif /* MANTID_API_WORKSPACEVALIDATORS_H_ */
diff --git a/Framework/API/src/Algorithm.cpp b/Framework/API/src/Algorithm.cpp
index e95b083c084a4db9beba993a20643fbb9c1f1d85..860a17a3d66cb681fd368d2f87a4f69347f5af71 100644
--- a/Framework/API/src/Algorithm.cpp
+++ b/Framework/API/src/Algorithm.cpp
@@ -1278,11 +1278,13 @@ bool Algorithm::processGroups() {
// ---------- Create all the output workspaces ----------------------------
for (size_t owp = 0; owp < m_pureOutputWorkspaceProps.size(); owp++) {
Property *prop = dynamic_cast<Property *>(m_pureOutputWorkspaceProps[owp]);
- WorkspaceGroup_sptr outWSGrp = WorkspaceGroup_sptr(new WorkspaceGroup());
- outGroups.push_back(outWSGrp);
- // Put the GROUP in the ADS
- AnalysisDataService::Instance().addOrReplace(prop->value(), outWSGrp);
- outWSGrp->observeADSNotifications(false);
+ if (prop) {
+ WorkspaceGroup_sptr outWSGrp = WorkspaceGroup_sptr(new WorkspaceGroup());
+ outGroups.push_back(outWSGrp);
+ // Put the GROUP in the ADS
+ AnalysisDataService::Instance().addOrReplace(prop->value(), outWSGrp);
+ outWSGrp->observeADSNotifications(false);
+ }
}
// Go through each entry in the input group(s)
diff --git a/Framework/API/src/AlgorithmProxy.cpp b/Framework/API/src/AlgorithmProxy.cpp
index a400d76b3943ccaab4a31a82474c523b4be6f1b9..c1a77746b23d389a16f10c89c606aaa192430d24 100644
--- a/Framework/API/src/AlgorithmProxy.cpp
+++ b/Framework/API/src/AlgorithmProxy.cpp
@@ -218,6 +218,17 @@ void AlgorithmProxy::afterPropertySet(const std::string &name) {
copyPropertiesFrom(*m_alg);
}
+/**
+ * Copy properties from another property manager
+ * Making sure that the concrete alg is kept in sync
+ * @param po :: The property manager to copy
+ */
+void AlgorithmProxy::copyPropertiesFrom(const PropertyManagerOwner &po) {
+ PropertyManagerOwner::copyPropertiesFrom(po);
+ createConcreteAlg(true);
+ m_alg->copyPropertiesFrom(*this);
+}
+
//----------------------------------------------------------------------
// Private methods
//----------------------------------------------------------------------
diff --git a/Framework/API/src/CommonBinsValidator.cpp b/Framework/API/src/CommonBinsValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..86871c6be5121ffff037b111437adb95d1c73725
--- /dev/null
+++ b/Framework/API/src/CommonBinsValidator.cpp
@@ -0,0 +1,28 @@
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid {
+namespace API {
+
+/// Clone the current state
+Kernel::IValidator_sptr CommonBinsValidator::clone() const {
+ return boost::make_shared<CommonBinsValidator>(*this);
+}
+
+/** Checks that the bin boundaries of each histogram in the workspace are the
+ * same
+ * @param value :: The workspace to test
+ * @return A message for users saying that bins are different, otherwise ""
+ */
+std::string
+CommonBinsValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ if (!value)
+ return "Enter an existing workspace";
+ if (value->isCommonBins())
+ return "";
+ else
+ return "The workspace must have common bin boundaries for all histograms";
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/DeprecatedAlgorithm.cpp b/Framework/API/src/DeprecatedAlgorithm.cpp
index 095b870de6dce2c5493b60e1b42277f86d52a730..804e2e0ca5c0caa89d57d3944d32415fcfd7f188 100644
--- a/Framework/API/src/DeprecatedAlgorithm.cpp
+++ b/Framework/API/src/DeprecatedAlgorithm.cpp
@@ -13,7 +13,7 @@ Kernel::Logger g_log("DeprecatedAlgorithm");
/// Does nothing other than make the compiler happy.
DeprecatedAlgorithm::DeprecatedAlgorithm()
- : m_replacementAlgorithm(), m_replacementVersion(-1), m_deprecatdDate() {}
+ : m_replacementAlgorithm(), m_replacementVersion(-1), m_deprecatedDate() {}
/// Does nothing other than make the compiler happy.
DeprecatedAlgorithm::~DeprecatedAlgorithm() {}
@@ -37,7 +37,7 @@ void DeprecatedAlgorithm::useAlgorithm(const std::string &replacement,
/// The date the algorithm was deprecated on
void DeprecatedAlgorithm::deprecatedDate(const std::string &date) {
- this->m_deprecatdDate = "";
+ this->m_deprecatedDate = "";
if (date.empty()) {
// TODO warn people that it wasn't set
return;
@@ -46,7 +46,7 @@ void DeprecatedAlgorithm::deprecatedDate(const std::string &date) {
// TODO warn people that it wasn't set
return;
}
- this->m_deprecatdDate = date;
+ this->m_deprecatedDate = date;
}
/// This merely prints the deprecation error for people to see.
@@ -57,8 +57,8 @@ const std::string DeprecatedAlgorithm::deprecationMsg(const IAlgorithm *algo) {
msg << "deprecated";
- if (!this->m_deprecatdDate.empty())
- msg << " (on " << this->m_deprecatdDate << ")";
+ if (!this->m_deprecatedDate.empty())
+ msg << " (on " << this->m_deprecatedDate << ")";
if (this->m_replacementAlgorithm.empty()) {
msg << " and has no replacement.";
diff --git a/Framework/API/src/ExperimentInfo.cpp b/Framework/API/src/ExperimentInfo.cpp
index 26a61864f6b9927aad85b761c5e985a894de8ce7..3ddd52bfdf0bbefe09fb0864bbf10fd4f1ba0e93 100644
--- a/Framework/API/src/ExperimentInfo.cpp
+++ b/Framework/API/src/ExperimentInfo.cpp
@@ -1149,7 +1149,7 @@ void ExperimentInfo::readParameterMap(const std::string ¶meterStr) {
// if( comp_name == prev_name ) continue; this blocks reading in different
// parameters of the same component. RNT
// prev_name = comp_name;
- const Geometry::IComponent *comp = 0;
+ const Geometry::IComponent *comp = NULL;
if (comp_name.find("detID:") != std::string::npos) {
int detID = atoi(comp_name.substr(6).c_str());
comp = instr->getDetector(detID).get();
@@ -1164,8 +1164,7 @@ void ExperimentInfo::readParameterMap(const std::string ¶meterStr) {
continue;
}
}
- if (!comp)
- continue;
+
// create parameter's value as a sum of all tokens with index 3 or larger
// this allow a parameter's value to contain ";"
std::string paramValue = tokens[3];
diff --git a/Framework/API/src/FunctionFactory.cpp b/Framework/API/src/FunctionFactory.cpp
index 5d2a0a1aad401f3cebf7326d1219a3edf99798c1..29a5ec54767c1b593c9cf2e3c028f262707968d6 100644
--- a/Framework/API/src/FunctionFactory.cpp
+++ b/Framework/API/src/FunctionFactory.cpp
@@ -192,6 +192,9 @@ CompositeFunction_sptr FunctionFactoryImpl::createComposite(
inputError(expr.str());
}
+ if (!cfun)
+ inputError(expr.str());
+
for (; it != terms.end(); ++it) {
const Expression &term = it->bracketsRemoved();
IFunction_sptr fun;
diff --git a/Framework/API/src/HistogramValidator.cpp b/Framework/API/src/HistogramValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..603eedde2e6fe60bbc5c401a826780e58732de44
--- /dev/null
+++ b/Framework/API/src/HistogramValidator.cpp
@@ -0,0 +1,42 @@
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid {
+namespace API {
+
+/** Constructor
+ *
+ * @param mustBeHistogram :: Flag indicating whether the check is that a
+ * workspace should contain histogram data (true, default) or shouldn't
+ * (false).
+ */
+HistogramValidator::HistogramValidator(const bool &mustBeHistogram)
+ : MatrixWorkspaceValidator(), m_mustBeHistogram(mustBeHistogram) {}
+
+/// Clone the current state
+Kernel::IValidator_sptr HistogramValidator::clone() const {
+ return boost::make_shared<HistogramValidator>(*this);
+}
+
+/** Checks if the workspace contains a histogram when it shouldn't and
+ * vice-versa
+ * @param value :: The workspace to test
+ * @return A user level description if a problem exists or ""
+ */
+std::string
+HistogramValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ if (m_mustBeHistogram) {
+ if (value->isHistogramData())
+ return "";
+ else
+ return "The workspace must contain histogram data";
+ } else {
+ if (!value->isHistogramData())
+ return "";
+ else
+ return "The workspace must not contain histogram data";
+ }
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/IncreasingAxisValidator.cpp b/Framework/API/src/IncreasingAxisValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6d653af5335b0494dc6630dadf2bb2d73b9c0449
--- /dev/null
+++ b/Framework/API/src/IncreasingAxisValidator.cpp
@@ -0,0 +1,34 @@
+#include "MantidAPI/IncreasingAxisValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid {
+namespace API {
+
+/// Clone the current state
+Kernel::IValidator_sptr IncreasingAxisValidator::clone() const {
+ return boost::make_shared<IncreasingAxisValidator>(*this);
+}
+
+/**
+ * Checks that X axis is in the right direction.
+ *
+ * @param value The workspace to check
+ * @return "" if is valid, otherwise a user level description of a problem
+ */
+std::string IncreasingAxisValidator::checkValidity(
+ const MatrixWorkspace_sptr &value) const {
+ // 0 for X axis
+ Axis *xAxis = value->getAxis(0);
+
+ // Left-most axis value should be less than the right-most, if ws has
+ // more than one X axis value
+ if (xAxis->length() > 1 &&
+ xAxis->getValue(0) >= xAxis->getValue(xAxis->length() - 1))
+ return "X axis of the workspace should be increasing from left to "
+ "right";
+ else
+ return "";
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/InstrumentValidator.cpp b/Framework/API/src/InstrumentValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a8fc0b0e146b71e357a07bae0b4371a9d0610afd
--- /dev/null
+++ b/Framework/API/src/InstrumentValidator.cpp
@@ -0,0 +1,56 @@
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/ExperimentInfo.h"
+#include "MantidKernel/Strings.h"
+
+namespace Mantid {
+namespace API {
+using Kernel::Strings::join;
+
+/**
+ * Construct a validator with requirements (default = SamplePosition)
+ * @param flags A combination of flags to specify requirements
+ */
+InstrumentValidator::InstrumentValidator(const unsigned int flags)
+ : m_requires(flags) {}
+
+/**
+ * @return A string type identifier for the object
+ */
+std::string InstrumentValidator::getType() const { return "Instrument"; }
+
+/**
+ * @return A copy of the current state of the object
+ */
+Kernel::IValidator_sptr InstrumentValidator::clone() const {
+ return boost::make_shared<InstrumentValidator>(*this);
+}
+
+/** Checks that the workspace has an instrument defined
+ * @param value :: The workspace to test
+ * @return A user-level description if a problem exists or ""
+ */
+std::string InstrumentValidator::checkValidity(
+ const boost::shared_ptr<ExperimentInfo> &value) const {
+ const auto inst = value->getInstrument();
+ if (!inst)
+ return "The workspace must have an instrument defined";
+
+ std::list<std::string> missing;
+ if ((m_requires & SourcePosition) && !inst->getSource()) {
+ missing.emplace_back("source");
+ }
+ if ((m_requires & SamplePosition) && !inst->getSample()) {
+ missing.emplace_back("sample holder");
+ }
+
+ if (missing.empty())
+ return "";
+ else {
+ return "The instrument is missing the following "
+ "components: " +
+ join(missing.begin(), missing.end(), ",");
+ }
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/NumericAxis.cpp b/Framework/API/src/NumericAxis.cpp
index 819ad1a5445b13c0a0415db954d2b2650bfe0d60..d609325a2397082f50219cfd5610807e58ae826c 100644
--- a/Framework/API/src/NumericAxis.cpp
+++ b/Framework/API/src/NumericAxis.cpp
@@ -191,9 +191,9 @@ std::string NumericAxis::label(const std::size_t &index) const {
auto it = numberLabel.end() - 1;
for (; it != numberLabel.begin(); --it) {
if (*it == '0') {
- numberLabel.erase(it);
+ it = numberLabel.erase(it);
} else if (*it == '.') {
- numberLabel.erase(it);
+ it = numberLabel.erase(it);
break;
} else {
break;
diff --git a/Framework/API/src/NumericAxisValidator.cpp b/Framework/API/src/NumericAxisValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..1273e248df1b5813a3a7a402a806313b558a2e1c
--- /dev/null
+++ b/Framework/API/src/NumericAxisValidator.cpp
@@ -0,0 +1,32 @@
+#include "MantidAPI/NumericAxisValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid {
+namespace API {
+
+/** Class constructor with parameter.
+ * @param axisNumber :: set the axis number to validate
+ */
+NumericAxisValidator::NumericAxisValidator(const int &axisNumber)
+ : m_axisNumber(axisNumber) {}
+
+/// Clone the current state
+Kernel::IValidator_sptr NumericAxisValidator::clone() const {
+ return boost::make_shared<NumericAxisValidator>(*this);
+}
+
+/** Checks that the axis stated
+* @param value :: The workspace to test
+* @return A message for users with negative results, otherwise ""
+*/
+std::string
+NumericAxisValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ Mantid::API::Axis *axis = value->getAxis(m_axisNumber);
+ if (axis->isNumeric())
+ return "";
+ else
+ return "A workspace with axis being a Numeric Axis is required here.";
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/RawCountValidator.cpp b/Framework/API/src/RawCountValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..1ab11c81051199aaecd51a7113b999cb187ac811
--- /dev/null
+++ b/Framework/API/src/RawCountValidator.cpp
@@ -0,0 +1,41 @@
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid {
+namespace API {
+
+/** Constructor
+ * @param mustNotBeDistribution :: Flag indicating whether the check is that
+ * a workspace should not be a distribution (true, default) or should be
+ * (false).
+ */
+RawCountValidator::RawCountValidator(const bool &mustNotBeDistribution)
+ : m_mustNotBeDistribution(mustNotBeDistribution) {}
+
+/// Clone the current state
+Kernel::IValidator_sptr RawCountValidator::clone() const {
+ return boost::make_shared<RawCountValidator>(*this);
+}
+
+/** Checks if the workspace must be a distribution but isn't and vice-versa
+ * @param value :: The workspace to test
+ * @return A user level description of any problem that exists or "" no
+ * problem
+ */
+std::string
+RawCountValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ if (m_mustNotBeDistribution) {
+ if (!value->isDistribution())
+ return "";
+ else
+ return "A workspace containing numbers of counts is required here";
+ } else {
+ if (value->isDistribution())
+ return "";
+ else
+ return "A workspace of numbers of counts is not allowed here";
+ }
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/SampleValidator.cpp b/Framework/API/src/SampleValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6e85c719da2b27a8c1116a42af84ce2c3f25b81a
--- /dev/null
+++ b/Framework/API/src/SampleValidator.cpp
@@ -0,0 +1,54 @@
+#include "MantidAPI/SampleValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidKernel/Strings.h"
+
+namespace Mantid {
+namespace API {
+using Kernel::Strings::join;
+
+/**
+ * Construct a validator with a set of requirements
+ * @param flags A combination of SampleValidator::Requirements flags. Defaults
+ * to requiring both a shape and material
+ */
+SampleValidator::SampleValidator(const unsigned int flags)
+ : m_requires(flags) {}
+
+/**
+ * @return A string type identifier for the object
+ */
+std::string SampleValidator::getType() const { return "Sample"; }
+
+/**
+ * @return A copy of the current state of the object
+ */
+Kernel::IValidator_sptr SampleValidator::clone() const {
+ return boost::make_shared<SampleValidator>(*this);
+}
+
+/**
+ * Check if the workspace satisfies the validation requirements
+ * @param value A pointer to a MatrixWorkspace object
+ * @return An empty string if the requirements are satisfied otherwise
+ * a string containing a message indicating the problem(s)
+ */
+std::string
+SampleValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ const auto &shape = value->sample().getShape();
+ std::list<std::string> missing;
+ if ((m_requires & Shape) && !shape.hasValidShape())
+ missing.emplace_back("shape");
+ const auto &material = shape.material();
+ if ((m_requires & Material) && material.name().empty())
+ missing.emplace_back("material");
+
+ if (missing.empty())
+ return "";
+ else {
+ return "The sample is missing the following properties: " +
+ join(missing.begin(), missing.end(), ",");
+ }
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/SpectraAxisValidator.cpp b/Framework/API/src/SpectraAxisValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..312c8dabd9a2e931fca08b50e51a1828f4bdf0b3
--- /dev/null
+++ b/Framework/API/src/SpectraAxisValidator.cpp
@@ -0,0 +1,32 @@
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid {
+namespace API {
+
+/** Class constructor with parameter.
+ * @param axisNumber :: set the axis number to validate
+ */
+SpectraAxisValidator::SpectraAxisValidator(const int &axisNumber)
+ : m_axisNumber(axisNumber) {}
+
+/// Clone the current validator
+Kernel::IValidator_sptr SpectraAxisValidator::clone() const {
+ return boost::make_shared<SpectraAxisValidator>(*this);
+}
+
+/** Checks that the axis stated
+* @param value :: The workspace to test
+* @return A message for users with negative results, otherwise ""
+*/
+std::string
+SpectraAxisValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ Mantid::API::Axis *axis = value->getAxis(m_axisNumber);
+ if (axis->isSpectra())
+ return "";
+ else
+ return "A workspace with axis being Spectra Number is required here.";
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/WorkspaceFactory.cpp b/Framework/API/src/WorkspaceFactory.cpp
index e2f890671126a479d732b36c980a5f9a530496d7..2eaca592865c4e520599f043bdb02b4c632c5acd 100644
--- a/Framework/API/src/WorkspaceFactory.cpp
+++ b/Framework/API/src/WorkspaceFactory.cpp
@@ -86,7 +86,7 @@ WorkspaceFactoryImpl::create(const MatrixWorkspace_const_sptr &parent,
return ws;
}
-/** Initialise a workspace from its parent
+/** Initialize a workspace from its parent
* This sets values such as title, instrument, units, sample, spectramap.
* This does NOT copy any data.
*
diff --git a/Framework/API/src/WorkspaceHistory.cpp b/Framework/API/src/WorkspaceHistory.cpp
index c7bf7a9d6ce737665f837c8f59ac8f0d00afaad1..94bb24122e2785c1ab04d21948990c75739d15ef 100644
--- a/Framework/API/src/WorkspaceHistory.cpp
+++ b/Framework/API/src/WorkspaceHistory.cpp
@@ -370,7 +370,7 @@ WorkspaceHistory::parseAlgorithmHistory(const std::string &rawData) {
// Get the duration
getWordsInString(info[EXEC_DUR], dummy, dummy, temp, dummy);
double dur = boost::lexical_cast<double>(temp);
- if (dur < 0.0) {
+ if (dur < -1.0) {
g_log.warning() << "Error parsing duration in algorithm history entry."
<< "\n";
dur = -1.0;
diff --git a/Framework/API/src/WorkspaceOpOverloads.cpp b/Framework/API/src/WorkspaceOpOverloads.cpp
index cfd3595724a9d60b327e5565606e1b504442491d..f29bca1ca5fe27a3bd029a203c5169e2eb8c3897 100644
--- a/Framework/API/src/WorkspaceOpOverloads.cpp
+++ b/Framework/API/src/WorkspaceOpOverloads.cpp
@@ -5,11 +5,11 @@
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidKernel/Property.h"
-#include "MantidKernel/Exception.h"
+//#include "MantidKernel/Exception.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/IWorkspaceProperty.h"
#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidAPI/SpectraAxis.h"
+//#include "MantidAPI/SpectraAxis.h"
#include "MantidAPI/IMDWorkspace.h"
#include "MantidAPI/IMDHistoWorkspace.h"
#include "MantidAPI/WorkspaceGroup_fwd.h"
@@ -67,30 +67,20 @@ ResultType executeBinaryOperation(const std::string &algorithmName,
alg->execute();
- if (alg->isExecuted()) {
- // Get the output workspace property
- if (child) {
- return alg->getProperty("OutputWorkspace");
- } else {
- API::Workspace_sptr result =
- API::AnalysisDataService::Instance().retrieve(
- alg->getPropertyValue("OutputWorkspace"));
- return boost::dynamic_pointer_cast<typename ResultType::element_type>(
- result);
- }
- } else {
+ if (!alg->isExecuted()) {
std::string message = "Error while executing operation: " + algorithmName;
throw std::runtime_error(message);
}
- throw Kernel::Exception::NotFoundError(
- "Required output workspace property not found on Child Algorithm",
- "OutputWorkspace");
-
- // Horendous code inclusion to satisfy compilers that all code paths return a
- // value
- // in reality the above code should either throw or return successfully.
- return ResultType();
+ // Get the output workspace property
+ if (child) {
+ return alg->getProperty("OutputWorkspace");
+ } else {
+ API::Workspace_sptr result = API::AnalysisDataService::Instance().retrieve(
+ alg->getPropertyValue("OutputWorkspace"));
+ return boost::dynamic_pointer_cast<typename ResultType::element_type>(
+ result);
+ }
}
template DLLExport MatrixWorkspace_sptr
@@ -169,14 +159,12 @@ bool equals(const MatrixWorkspace_sptr lhs, const MatrixWorkspace_sptr rhs,
// Rest: use default
alg->execute();
- if (alg->isExecuted()) {
- return (alg->getPropertyValue("Result") == "Success!");
- } else {
+ if (!alg->isExecuted()) {
std::string message =
"Error while executing operation: CheckWorkspacesMatch";
throw std::runtime_error(message);
}
- return false;
+ return (alg->getPropertyValue("Result") == "Success!");
}
/** Creates a temporary single value workspace the error is set to zero
@@ -512,17 +500,18 @@ bool WorkspaceHelpers::matchingBins(const MatrixWorkspace_const_sptr ws1,
if (!step)
step = 1;
for (size_t i = step; i < numHist; i += step) {
- const double firstWS =
+ const double firstWSLoop =
std::accumulate(ws1->readX(i).begin(), ws1->readX(i).end(), 0.);
- const double secondWS =
+ const double secondWSLoop =
std::accumulate(ws2->readX(i).begin(), ws2->readX(i).end(), 0.);
- if (std::abs(firstWS) < 1.0E-7 && std::abs(secondWS) < 1.0E-7) {
+ if (std::abs(firstWSLoop) < 1.0E-7 && std::abs(secondWSLoop) < 1.0E-7) {
for (size_t j = 0; j < ws1->readX(i).size(); j++) {
if (std::abs(ws1->readX(i)[j] - ws2->readX(i)[j]) > 1.0E-7)
return false;
}
- } else if (std::abs(firstWS - secondWS) /
- std::max<double>(std::abs(firstWS), std::abs(secondWS)) >
+ } else if (std::abs(firstWSLoop - secondWSLoop) /
+ std::max<double>(std::abs(firstWSLoop),
+ std::abs(secondWSLoop)) >
1.0E-7)
return false;
}
diff --git a/Framework/API/src/WorkspaceUnitValidator.cpp b/Framework/API/src/WorkspaceUnitValidator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..23be6cc30aef9f4a7666df856d68da63d3246037
--- /dev/null
+++ b/Framework/API/src/WorkspaceUnitValidator.cpp
@@ -0,0 +1,57 @@
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidKernel/Unit.h"
+
+namespace Mantid {
+namespace API {
+
+/** Constructor
+ *
+ * @param unitID :: The name of the unit that the workspace must have. If
+ * left empty, the validator will simply check that the workspace is not
+ * unitless.
+ */
+WorkspaceUnitValidator::WorkspaceUnitValidator(const std::string &unitID)
+ : MatrixWorkspaceValidator(), m_unitID(unitID) {}
+
+/**
+ * Clone the current state
+ */
+Kernel::IValidator_sptr WorkspaceUnitValidator::clone() const {
+ return boost::make_shared<WorkspaceUnitValidator>(*this);
+}
+
+/** Checks that the units of the workspace data are declared match any
+ * required units
+ *
+ * @param value :: The workspace to test
+ * @return A user level description of the error or "" for no error
+ */
+std::string
+WorkspaceUnitValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
+ // This effectively checks for single-valued workspaces
+ if (value->axes() == 0)
+ return "A single valued workspace has no unit, which is required for "
+ "this algorithm";
+
+ Kernel::Unit_const_sptr unit = value->getAxis(0)->unit();
+ // If m_unitID is empty it means that the workspace must have units, which
+ // can be anything
+ if (m_unitID.empty()) {
+ return (
+ unit && (!boost::dynamic_pointer_cast<const Kernel::Units::Empty>(unit))
+ ? ""
+ : "The workspace must have units");
+ }
+ // now check if the units of the workspace is correct
+ else {
+ if ((!unit) || (unit->unitID().compare(m_unitID))) {
+ return "The workspace must have units of " +
+ m_unitID; //+ "; its unit is: " + unit->caption();
+ } else
+ return "";
+ }
+}
+
+} // namespace API
+} // namespace Mantid
diff --git a/Framework/API/src/WorkspaceValidators.cpp b/Framework/API/src/WorkspaceValidators.cpp
deleted file mode 100644
index d6d6efa3460f052e0e5ec983e197b4ce63f7618f..0000000000000000000000000000000000000000
--- a/Framework/API/src/WorkspaceValidators.cpp
+++ /dev/null
@@ -1,107 +0,0 @@
-//------------------------------------------------------------------------------
-// Includes
-//------------------------------------------------------------------------------
-#include "MantidAPI/WorkspaceValidators.h"
-
-namespace Mantid {
-using Kernel::Strings::join;
-
-namespace API {
-
-//------------------------------------------------------------------------------
-// InstrumentValidator
-//------------------------------------------------------------------------------
-/**
- * Construct a validator with requirements (default = SamplePosition)
- * @param flags A combination of flags to specify requirements
- */
-InstrumentValidator::InstrumentValidator(const unsigned int flags)
- : m_requires(flags) {}
-
-/**
- * @return A string type identifier for the object
- */
-std::string InstrumentValidator::getType() const { return "Instrument"; }
-
-/**
- * @return A copy of the current state of the object
- */
-Kernel::IValidator_sptr InstrumentValidator::clone() const {
- return boost::make_shared<InstrumentValidator>(*this);
-}
-
-/** Checks that the workspace has an instrument defined
- * @param value :: The workspace to test
- * @return A user-level description if a problem exists or ""
- */
-std::string InstrumentValidator::checkValidity(
- const boost::shared_ptr<ExperimentInfo> &value) const {
- const auto inst = value->getInstrument();
- if (!inst)
- return "The workspace must have an instrument defined";
-
- std::list<std::string> missing;
- if ((m_requires & SourcePosition) && !inst->getSource()) {
- missing.emplace_back("source");
- }
- if ((m_requires & SamplePosition) && !inst->getSample()) {
- missing.emplace_back("sample holder");
- }
-
- if (missing.empty())
- return "";
- else {
- return "The instrument is missing the following "
- "components: " +
- join(missing.begin(), missing.end(), ",");
- }
-}
-
-//------------------------------------------------------------------------------
-// SampleValidator
-//------------------------------------------------------------------------------
-/**
- * Construct a validator with a set of requirements
- * @param flags A combination of SampleValidator::Requirements flags. Defaults
- * to requiring both a shape and material
- */
-SampleValidator::SampleValidator(const unsigned int flags)
- : m_requires(flags) {}
-
-/**
- * @return A string type identifier for the object
- */
-std::string SampleValidator::getType() const { return "Sample"; }
-
-/**
- * @return A copy of the current state of the object
- */
-Kernel::IValidator_sptr SampleValidator::clone() const {
- return boost::make_shared<SampleValidator>(*this);
-}
-
-/**
- * Check if the workspace satisfies the validation requirements
- * @param value A pointer to a MatrixWorkspace object
- * @return An empty string if the requirements are satisfied otherwise
- * a string containing a message indicating the problem(s)
- */
-std::string
-SampleValidator::checkValidity(const MatrixWorkspace_sptr &value) const {
- const auto &shape = value->sample().getShape();
- std::list<std::string> missing;
- if ((m_requires & Shape) && !shape.hasValidShape())
- missing.emplace_back("shape");
- const auto &material = shape.material();
- if ((m_requires & Material) && material.name().empty())
- missing.emplace_back("material");
-
- if (missing.empty())
- return "";
- else {
- return "The sample is missing the following properties: " +
- join(missing.begin(), missing.end(), ",");
- }
-}
-}
-}
diff --git a/Framework/API/test/AlgorithmProxyTest.h b/Framework/API/test/AlgorithmProxyTest.h
index 8c50e2e0dcd53e09f3d9ce26df5d78dd7f952dd2..6e8cafd780007d1caedf0087baf6c4936736b8c6 100644
--- a/Framework/API/test/AlgorithmProxyTest.h
+++ b/Framework/API/test/AlgorithmProxyTest.h
@@ -212,6 +212,30 @@ public:
}
TS_ASSERT_EQUALS("InputWorkspace", alg->workspaceMethodInputProperty());
}
+
+ void test_copyPropertiesFrom() {
+ IAlgorithm_sptr alg =
+ AlgorithmManager::Instance().create("ToyAlgorithmProxy");
+ alg->initialize();
+ alg->setPropertyValue("prop1", "string");
+ alg->setPropertyValue("prop2", "1");
+ IAlgorithm_sptr algCopy =
+ AlgorithmManager::Instance().create("ToyAlgorithmProxy");
+
+ auto algProxy = boost::dynamic_pointer_cast<AlgorithmProxy>(alg);
+ auto algCopyProxy = boost::dynamic_pointer_cast<AlgorithmProxy>(algCopy);
+ algCopyProxy->copyPropertiesFrom(*algProxy);
+
+ int val = boost::lexical_cast<int>(algCopy->getPropertyValue("prop2"));
+
+ TS_ASSERT_EQUALS(val, 1);
+
+ // set another value and check the other value is unaffected
+ algCopy->setPropertyValue("prop1", "A difference");
+ int val2 = boost::lexical_cast<int>(algCopy->getPropertyValue("prop2"));
+
+ TS_ASSERT_EQUALS(val, val2);
+ }
};
#endif /*ALGORITHMPROXYTEST_H_*/
diff --git a/Framework/API/test/CommonBinsValidatorTest.h b/Framework/API/test/CommonBinsValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..da9f44d52b3b905dc3291534d0f5bf2e15849302
--- /dev/null
+++ b/Framework/API/test/CommonBinsValidatorTest.h
@@ -0,0 +1,60 @@
+#ifndef MANTID_API_COMMONBINSVALIDATORTEST_H_
+#define MANTID_API_COMMONBINSVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+
+using Mantid::API::CommonBinsValidator;
+
+class CommonBinsValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static CommonBinsValidatorTest *createSuite() {
+ return new CommonBinsValidatorTest();
+ }
+ static void destroySuite(CommonBinsValidatorTest *suite) { delete suite; }
+
+ void test_empty() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ CommonBinsValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+
+ void test_zero_length_bins() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ CommonBinsValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+
+ void test_common_bins() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(3, 11, 10);
+ for (size_t k = 0; k < 3; ++k)
+ for (size_t i = 0; i < 11; ++i) {
+ auto di = double(i);
+ ws->dataX(k)[i] = di * (1.0 + 0.001 * di);
+ }
+ CommonBinsValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+
+ void test_diff_bins() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(3, 11, 10);
+ for (size_t k = 0; k < 3; ++k)
+ for (size_t i = 0; i < 11; ++i) {
+ auto di = double(i + k);
+ ws->dataX(k)[i] = di * (1.0 + 0.001 * di);
+ }
+ CommonBinsValidator validator;
+ TS_ASSERT_EQUALS(
+ validator.isValid(ws),
+ "The workspace must have common bin boundaries for all histograms");
+ }
+};
+
+#endif /* MANTID_API_COMMONBINSVALIDATORTEST_H_ */
diff --git a/Framework/API/test/HistogramValidatorTest.h b/Framework/API/test/HistogramValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..d916627aee046d72a71fbdae5e05ccc7cea69901
--- /dev/null
+++ b/Framework/API/test/HistogramValidatorTest.h
@@ -0,0 +1,36 @@
+#ifndef MANTID_API_HISTOGRAMVALIDATORTEST_H_
+#define MANTID_API_HISTOGRAMVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+
+using Mantid::API::HistogramValidator;
+
+class HistogramValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static HistogramValidatorTest *createSuite() {
+ return new HistogramValidatorTest();
+ }
+ static void destroySuite(HistogramValidatorTest *suite) { delete suite; }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ HistogramValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 10, 10);
+ HistogramValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws),
+ "The workspace must contain histogram data");
+ }
+};
+
+#endif /* MANTID_API_HISTOGRAMVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/API/test/IncreasingAxisValidatorTest.h b/Framework/API/test/IncreasingAxisValidatorTest.h
index baca926a97e89efa645552d3684e716eabd55e5d..cb7ca28992fd94fcd3faeff6c5fb3d604b46ea8b 100644
--- a/Framework/API/test/IncreasingAxisValidatorTest.h
+++ b/Framework/API/test/IncreasingAxisValidatorTest.h
@@ -3,7 +3,7 @@
#include <cxxtest/TestSuite.h>
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/IncreasingAxisValidator.h"
#include "MantidTestHelpers/FakeObjects.h"
#include "MantidAPI/NumericAxis.h"
diff --git a/Framework/API/test/InstrumentValidatorTest.h b/Framework/API/test/InstrumentValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..3edaddca83aa70324e9fa179fae8492a85d41f67
--- /dev/null
+++ b/Framework/API/test/InstrumentValidatorTest.h
@@ -0,0 +1,49 @@
+#ifndef MANTID_API_INSTRUMENTVALIDATORTEST_H_
+#define MANTID_API_INSTRUMENTVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidGeometry/Instrument/ObjComponent.h"
+#include "MantidTestHelpers/FakeObjects.h"
+#include "MantidTestHelpers/ComponentCreationHelper.h"
+
+using Mantid::API::InstrumentValidator;
+
+class InstrumentValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static InstrumentValidatorTest *createSuite() {
+ return new InstrumentValidatorTest();
+ }
+ static void destroySuite(InstrumentValidatorTest *suite) { delete suite; }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ auto instr =
+ boost::make_shared<Mantid::Geometry::Instrument>("TestInstrument");
+ ws->setInstrument(instr);
+ // Define a sample as a simple sphere
+ auto sample = new Mantid::Geometry::ObjComponent(
+ "samplePos",
+ ComponentCreationHelper::createSphere(0.1, V3D(0, 0, 0), "1"),
+ instr.get());
+ instr->setPos(0.0, 0.0, 0.0);
+ instr->add(sample);
+ instr->markAsSamplePos(sample);
+
+ InstrumentValidator validator;
+ TS_ASSERT_EQUALS(validator.checkValidity(ws), "");
+ }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ InstrumentValidator validator;
+ TS_ASSERT_EQUALS(
+ validator.checkValidity(ws),
+ "The instrument is missing the following components: sample holder");
+ }
+};
+
+#endif /* MANTID_API_INSTRUMENTVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/API/test/NumericAxisValidatorTest.h b/Framework/API/test/NumericAxisValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..d33e9c5948abfbd590e5f38257edaad1d30a5c06
--- /dev/null
+++ b/Framework/API/test/NumericAxisValidatorTest.h
@@ -0,0 +1,39 @@
+#ifndef MANTID_API_NUMERICAXISVALIDATORTEST_H_
+#define MANTID_API_NUMERICAXISVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/NumericAxisValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+
+using Mantid::API::NumericAxisValidator;
+
+class NumericAxisValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static NumericAxisValidatorTest *createSuite() {
+ return new NumericAxisValidatorTest();
+ }
+ static void destroySuite(NumericAxisValidatorTest *suite) { delete suite; }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ auto newAxis = new NumericAxis(2);
+ ws->replaceAxis(1, newAxis);
+ NumericAxisValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ NumericAxisValidator validator;
+ TS_ASSERT_EQUALS(
+ validator.isValid(ws),
+ "A workspace with axis being a Numeric Axis is required here.");
+ }
+};
+
+#endif /* MANTID_API_NUMERICAXISVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/API/test/RawCountValidatorTest.h b/Framework/API/test/RawCountValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..5b8692dcb0d23081a011b69607ffee2fcea4a846
--- /dev/null
+++ b/Framework/API/test/RawCountValidatorTest.h
@@ -0,0 +1,36 @@
+#ifndef MANTID_API_RAWCOUNTVALIDATORTEST_H_
+#define MANTID_API_RAWCOUNTVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+
+using Mantid::API::RawCountValidator;
+
+class RawCountValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static RawCountValidatorTest *createSuite() {
+ return new RawCountValidatorTest();
+ }
+ static void destroySuite(RawCountValidatorTest *suite) { delete suite; }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ RawCountValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->isDistribution(true);
+ RawCountValidator validator;
+ TS_ASSERT_EQUALS(
+ validator.isValid(ws),
+ "A workspace containing numbers of counts is required here");
+ }
+};
+
+#endif /* MANTID_API_RAWCOUNTVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/API/test/SampleValidatorTest.h b/Framework/API/test/SampleValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..abb1dcd897ff8c091f14bddb21d7a754af1bd47c
--- /dev/null
+++ b/Framework/API/test/SampleValidatorTest.h
@@ -0,0 +1,43 @@
+#ifndef MANTID_API_SAMPLEVALIDATORTEST_H_
+#define MANTID_API_SAMPLEVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/SampleValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+#include "MantidTestHelpers/ComponentCreationHelper.h"
+
+using Mantid::API::SampleValidator;
+
+class SampleValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static SampleValidatorTest *createSuite() {
+ return new SampleValidatorTest();
+ }
+ static void destroySuite(SampleValidatorTest *suite) { delete suite; }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ SampleValidator validator;
+ TS_ASSERT_EQUALS(
+ validator.isValid(ws),
+ "The sample is missing the following properties: shape,material");
+ }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ auto sphere = ComponentCreationHelper::createSphere(1.0, V3D(), "sphere");
+ Mantid::Kernel::Material material(
+ "stuff", Mantid::PhysicalConstants::NeutronAtom(), 10);
+ sphere->setMaterial(material);
+ ws->mutableSample().setShape(*sphere);
+
+ SampleValidator validator;
+ TS_ASSERT_EQUALS(validator.checkValidity(ws), "");
+ }
+};
+
+#endif /* MANTID_API_SAMPLEVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/API/test/SpectraAxisValidatorTest.h b/Framework/API/test/SpectraAxisValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..c1cdc4ca28170885f8e9f87a2d32171a73f6d080
--- /dev/null
+++ b/Framework/API/test/SpectraAxisValidatorTest.h
@@ -0,0 +1,39 @@
+#ifndef MANTID_API_SPECTRAAXISVALIDATORTEST_H_
+#define MANTID_API_SPECTRAAXISVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+
+using Mantid::API::SpectraAxisValidator;
+
+class SpectraAxisValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static SpectraAxisValidatorTest *createSuite() {
+ return new SpectraAxisValidatorTest();
+ }
+ static void destroySuite(SpectraAxisValidatorTest *suite) { delete suite; }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ auto newAxis = new NumericAxis(2);
+ ws->replaceAxis(1, newAxis);
+ SpectraAxisValidator validator;
+ TS_ASSERT_EQUALS(
+ validator.isValid(ws),
+ "A workspace with axis being Spectra Number is required here.");
+ }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ SpectraAxisValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+};
+
+#endif /* MANTID_API_SPECTRAAXISVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/API/test/WorkspaceUnitValidatorTest.h b/Framework/API/test/WorkspaceUnitValidatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..d2e86987bdd4a6ff7eddbaae445081d3b076fc2f
--- /dev/null
+++ b/Framework/API/test/WorkspaceUnitValidatorTest.h
@@ -0,0 +1,36 @@
+#ifndef MANTID_API_WORKSPACEUNITVALIDATORTEST_H_
+#define MANTID_API_WORKSPACEUNITVALIDATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidTestHelpers/FakeObjects.h"
+
+using Mantid::API::WorkspaceUnitValidator;
+
+class WorkspaceUnitValidatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static WorkspaceUnitValidatorTest *createSuite() {
+ return new WorkspaceUnitValidatorTest();
+ }
+ static void destroySuite(WorkspaceUnitValidatorTest *suite) { delete suite; }
+
+ void test_fail() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ WorkspaceUnitValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "The workspace must have units");
+ }
+
+ void test_success() {
+ auto ws = boost::make_shared<WorkspaceTester>();
+ ws->init(2, 11, 10);
+ ws->getAxis(0)->setUnit("TOF");
+ WorkspaceUnitValidator validator;
+ TS_ASSERT_EQUALS(validator.isValid(ws), "");
+ }
+};
+
+#endif /* MANTID_API_WORKSPACEUNITVALIDATORTEST_H_ */
\ No newline at end of file
diff --git a/Framework/Algorithms/CMakeLists.txt b/Framework/Algorithms/CMakeLists.txt
index 445f1c602b5a55ebdbf14fe468ff005ace9d28bc..9231a99e1f936d0aeae54af68af3dcbb6cf7b0f6 100644
--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -128,8 +128,10 @@ set ( SRC_FILES
src/GenerateEventsFilter.cpp
src/GeneratePeaks.cpp
src/GeneratePythonScript.cpp
+ src/GetAllEi.cpp
src/GetDetOffsetsMultiPeaks.cpp
src/GetDetectorOffsets.cpp
+ src/GetAllEi.cpp
src/GetEi.cpp
src/GetEi2.cpp
src/GetTimeSeriesLogInformation.cpp
@@ -399,6 +401,7 @@ set ( INC_FILES
inc/MantidAlgorithms/FixGSASInstrumentFile.h
inc/MantidAlgorithms/FlatPlateAbsorption.h
inc/MantidAlgorithms/GSLFunctions.h
+ inc/MantidAlgorithms/GetAllEi.h
inc/MantidAlgorithms/GeneralisedSecondDifference.h
inc/MantidAlgorithms/GenerateEventsFilter.h
inc/MantidAlgorithms/GeneratePeaks.h
@@ -684,6 +687,7 @@ set ( TEST_FILES
GenerateIPythonNotebookTest.h
GeneratePeaksTest.h
GeneratePythonScriptTest.h
+ GetAllEiTest.h
GetDetOffsetsMultiPeaksTest.h
GetDetectorOffsetsTest.h
GetEiTest.h
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/CreateSampleWorkspace.h b/Framework/Algorithms/inc/MantidAlgorithms/CreateSampleWorkspace.h
index 4a74b3b6a95bf4bd3076f123cf20baf15b8ff2ee..cef126ba1c1e1e557da6b0708b2930960bd8d1e4 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/CreateSampleWorkspace.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/CreateSampleWorkspace.h
@@ -76,6 +76,7 @@ private:
double noiseScale);
void replaceAll(std::string &str, const std::string &from,
const std::string &to);
+ void addChopperParameters(API::MatrixWorkspace_sptr &ws);
/// A pointer to the random number generator
Kernel::PseudoRandomNumberGenerator *m_randGen;
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/GetAllEi.h b/Framework/Algorithms/inc/MantidAlgorithms/GetAllEi.h
new file mode 100644
index 0000000000000000000000000000000000000000..155d8fc2d45d2c6bfa0310962dcfe8cef81e6614
--- /dev/null
+++ b/Framework/Algorithms/inc/MantidAlgorithms/GetAllEi.h
@@ -0,0 +1,126 @@
+#ifndef MANTID_ALGORITHMS_GETALLEI_H_
+#define MANTID_ALGORITHMS_GETALLEI_H_
+
+#include "MantidKernel/System.h"
+#include "MantidKernel/cow_ptr.h"
+#include "MantidAPI/Algorithm.h"
+#include "MantidAPI/MatrixWorkspace.h"
+//#include "MantidAPI/IAlgorithm.h"
+
+namespace Mantid {
+
+namespace Algorithms {
+
+/** Estimate all incident energies, used by chopper instrument.
+
+ Copyright © 2008-9 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>.
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class DLLExport GetAllEi : public API::Algorithm {
+public:
+ GetAllEi();
+ virtual ~GetAllEi(){};
+
+ /// Algorithms name for identification. @see Algorithm::name
+ virtual const std::string name() const { return "GetAllEi"; };
+ /// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
+ virtual const std::string summary() const {
+ return "Analyze the chopper logs and the signal registered by the monitors "
+ "to identify energies used as incident energies in an inelastic "
+ "experiment.";
+ }
+ /// Algorithm's version for identification. @see Algorithm::version
+ virtual int version() const { return 1; };
+ /// Algorithm's category for identification. @see Algorithm::category
+ virtual const std::string category() const { return "Inelastic"; };
+ /// Cross-check properties with each other @see IAlgorithm::validateInputs
+ virtual std::map<std::string, std::string> validateInputs();
+
+private:
+ // Implement abstract Algorithm methods
+ void init();
+ void exec();
+ Kernel::Property *getPLogForProperty(const API::MatrixWorkspace_sptr &inputWS,
+ const std::string &name);
+ void setFilterLog(const API::MatrixWorkspace_sptr &inputWS);
+ // former lambda function exposed as not evry compiler support this yet
+ bool peakGuess(const API::MatrixWorkspace_sptr &inputWS, size_t index,
+ double Ei, const std::vector<size_t> &monsRangeMin,
+ const std::vector<size_t> &monsRangeMax, double &peakPos,
+ double &peakHeight, double &peakTwoSigma);
+
+protected: // for testing, private otherwise.
+ // prepare working workspace with appropriate monitor spectra for fitting
+ API::MatrixWorkspace_sptr
+ // prepare matrix workspace to analyze monitor signal
+ buildWorkspaceToFit(const API::MatrixWorkspace_sptr &inputWS,
+ size_t &wsIndex0);
+
+ /**Return average time series log value for the appropriately filtered log*/
+ double getAvrgLogValue(const API::MatrixWorkspace_sptr &inputWS,
+ const std::string &propertyName,
+ std::vector<Kernel::SplittingInterval> &splitter);
+ /**process logs and retrieve chopper speed and chopper delay*/
+ void findChopSpeedAndDelay(const API::MatrixWorkspace_sptr &inputWS,
+ double &chop_speed, double &chop_delay);
+ void findGuessOpeningTimes(const std::pair<double, double> &TOF_range,
+ double ChopDelay, double Period,
+ std::vector<double> &guess_opening_times);
+ /**Get energy of monitor peak if one is present*/
+ bool findMonitorPeak(const API::MatrixWorkspace_sptr &inputWS, double Ei,
+ const std::vector<size_t> &monsRangeMin,
+ const std::vector<size_t> &monsRangeMax, double &energy,
+ double &height, double &width);
+ /**Find indexes of each expected peak intervals */
+ void findBinRanges(const MantidVec &eBins, const MantidVec &signal,
+ const std::vector<double> &guess_energies,
+ double Eresolution, std::vector<size_t> &irangeMin,
+ std::vector<size_t> &irangeMax,
+ std::vector<bool> &guessValid);
+
+ size_t calcDerivativeAndCountZeros(const std::vector<double> &bins,
+ const std::vector<double> &signal,
+ std::vector<double> &deriv,
+ std::vector<double> &zeros);
+
+ /// if true, take derivate of the filter log to identify interval when
+ /// instrument is running.
+ bool m_FilterWithDerivative;
+ /// maximal relative peak width to consider acceptable. Defined by minimal
+ /// instrument resolution
+ /// and does not exceed 0.08
+ double m_min_Eresolution;
+ // set as half max LET resolution at 20mev at 5e-4
+ double m_max_Eresolution;
+ double m_peakEnergyRatio2reject;
+ // the value of constant phase shift on the chopper used to calculate
+ // tof at chopper from recorded delay.
+ double m_phase;
+ // internal pointer to access to chopper
+ boost::shared_ptr<const Geometry::IComponent> m_chopper;
+ // internal pointer to access log, used for filtering
+ Kernel::TimeSeriesProperty<double> *m_pFilterLog;
+};
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif /* MANTID_ALGORITHMS_GETALLEI_H_ */
diff --git a/Framework/Algorithms/src/AbsorptionCorrection.cpp b/Framework/Algorithms/src/AbsorptionCorrection.cpp
index b80ec8b19e19433f7ec078c2fb612f4b9537d8c9..70903dcf3d193cf3f527a6a774439b6142389e40 100644
--- a/Framework/Algorithms/src/AbsorptionCorrection.cpp
+++ b/Framework/Algorithms/src/AbsorptionCorrection.cpp
@@ -2,13 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/AbsorptionCorrection.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/Fast_Exponential.h"
-#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/Fast_Exponential.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/VectorHelper.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/AlignDetectors.cpp b/Framework/Algorithms/src/AlignDetectors.cpp
index de941aea91cf913e25be29eb8cb537a740f617e7..742f56343e698b4fae2c524d7927248922e68e0c 100644
--- a/Framework/Algorithms/src/AlignDetectors.cpp
+++ b/Framework/Algorithms/src/AlignDetectors.cpp
@@ -4,11 +4,13 @@
#include "MantidAlgorithms/AlignDetectors.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/ITableWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
-#include "MantidKernel/V3D.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/V3D.h"
#include "MantidKernel/UnitFactory.h"
#include <fstream>
#include <sstream>
@@ -151,7 +153,9 @@ const std::string AlignDetectors::summary() const {
}
/// (Empty) Constructor
-AlignDetectors::AlignDetectors() { this->tofToDmap = NULL; }
+AlignDetectors::AlignDetectors() : m_numberOfSpectra(0) {
+ this->tofToDmap = NULL;
+}
/// Destructor
AlignDetectors::~AlignDetectors() { delete this->tofToDmap; }
diff --git a/Framework/Algorithms/src/AnnularRingAbsorption.cpp b/Framework/Algorithms/src/AnnularRingAbsorption.cpp
index f38414c7f7ff268684cfba3b1fc1c937479def57..58b80dc9d919f8726012fee0940fa1bd44549655 100644
--- a/Framework/Algorithms/src/AnnularRingAbsorption.cpp
+++ b/Framework/Algorithms/src/AnnularRingAbsorption.cpp
@@ -1,7 +1,8 @@
#include "MantidAlgorithms/AnnularRingAbsorption.h"
#include "MantidAPI/SampleEnvironment.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument/ObjComponent.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
@@ -9,10 +10,11 @@
#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidKernel/Atom.h"
-#include "MantidKernel/NeutronAtom.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/Material.h"
#include "MantidKernel/MandatoryValidator.h"
+#include "MantidKernel/NeutronAtom.h"
#include "MantidKernel/V3D.h"
#include <boost/format.hpp>
diff --git a/Framework/Algorithms/src/AppendSpectra.cpp b/Framework/Algorithms/src/AppendSpectra.cpp
index 4efa279245915d7c63bcb81534a1c786ab5824bd..14cfa7656af6558b06c4743dff44fc79880ebd84 100644
--- a/Framework/Algorithms/src/AppendSpectra.cpp
+++ b/Framework/Algorithms/src/AppendSpectra.cpp
@@ -1,6 +1,5 @@
#include "MantidAlgorithms/AppendSpectra.h"
-#include "MantidKernel/System.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/BoundedValidator.h"
diff --git a/Framework/Algorithms/src/ApplyDeadTimeCorr.cpp b/Framework/Algorithms/src/ApplyDeadTimeCorr.cpp
index dc16356c68ae91486b5b8bd4ef90c9de1f890ca2..e50710997d9036191e5d48c42fd5114e05d33743 100644
--- a/Framework/Algorithms/src/ApplyDeadTimeCorr.cpp
+++ b/Framework/Algorithms/src/ApplyDeadTimeCorr.cpp
@@ -6,7 +6,6 @@
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/PropertyWithValue.h"
#include "boost/lexical_cast.hpp"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/TableRow.h"
diff --git a/Framework/Algorithms/src/ApplyDetailedBalance.cpp b/Framework/Algorithms/src/ApplyDetailedBalance.cpp
index c5fdf2865461f3cc9e980fff8852b5752c050111..6fd2dc79cbd60860112bb005fc02713ebe7cf145 100644
--- a/Framework/Algorithms/src/ApplyDetailedBalance.cpp
+++ b/Framework/Algorithms/src/ApplyDetailedBalance.cpp
@@ -1,11 +1,12 @@
#include "MantidAlgorithms/ApplyDetailedBalance.h"
-#include "MantidKernel/System.h"
-#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/PropertyWithValue.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+
#include "boost/lexical_cast.hpp"
#include <cmath>
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/PhysicalConstants.h"
using std::string;
using namespace Mantid::Kernel;
diff --git a/Framework/Algorithms/src/ApplyTransmissionCorrection.cpp b/Framework/Algorithms/src/ApplyTransmissionCorrection.cpp
index c41ee0b23c4569dd0692bf4cd362b9bc9bac5a09..89a09d77008e3a0969d7715a0a225ee3e7694613 100644
--- a/Framework/Algorithms/src/ApplyTransmissionCorrection.cpp
+++ b/Framework/Algorithms/src/ApplyTransmissionCorrection.cpp
@@ -2,9 +2,11 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ApplyTransmissionCorrection.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/BinaryOperateMasks.cpp b/Framework/Algorithms/src/BinaryOperateMasks.cpp
index 4ff720334961749c18cff5412052f3f9e359b3bd..6ebc7dc2068cd3644d46ae35ac4324aaf8069a64 100644
--- a/Framework/Algorithms/src/BinaryOperateMasks.cpp
+++ b/Framework/Algorithms/src/BinaryOperateMasks.cpp
@@ -1,7 +1,5 @@
#include "MantidAlgorithms/BinaryOperateMasks.h"
-#include "MantidKernel/System.h"
#include "MantidDataObjects/MaskWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/ListValidator.h"
using namespace Mantid::Kernel;
diff --git a/Framework/Algorithms/src/CalculateEfficiency.cpp b/Framework/Algorithms/src/CalculateEfficiency.cpp
index 24814cd4f45e6d47c872ea6acc54a0875a1e30c7..7dba05e6e247cdcc3fc1c9b450d2fa51d014664e 100644
--- a/Framework/Algorithms/src/CalculateEfficiency.cpp
+++ b/Framework/Algorithms/src/CalculateEfficiency.cpp
@@ -2,11 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CalculateEfficiency.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
-#include <vector>
#include "MantidKernel/BoundedValidator.h"
+#include <vector>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/CalculateFlatBackground.cpp b/Framework/Algorithms/src/CalculateFlatBackground.cpp
index 34b3f5a8ba418043878fcef208d96f97c787fa75..3f7be3751b51ef6911c03095757686b99ee99043 100644
--- a/Framework/Algorithms/src/CalculateFlatBackground.cpp
+++ b/Framework/Algorithms/src/CalculateFlatBackground.cpp
@@ -2,17 +2,18 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CalculateFlatBackground.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/WorkspaceOpOverloads.h"
#include "MantidAPI/FunctionFactory.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/IFunction.h"
+#include "MantidAPI/WorkspaceOpOverloads.h"
+#include "MantidDataObjects/TableWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidDataObjects/TableWorkspace.h"
#include <algorithm>
#include <climits>
-#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/MandatoryValidator.h"
+#include <numeric>
#include <boost/lexical_cast.hpp>
namespace Mantid {
diff --git a/Framework/Algorithms/src/CalculateResolution.cpp b/Framework/Algorithms/src/CalculateResolution.cpp
index a0a8980966416a5a744c5026214cf3c2935a9db1..558bdf5db4fd5e9d01bbc1486dabce632990474f 100644
--- a/Framework/Algorithms/src/CalculateResolution.cpp
+++ b/Framework/Algorithms/src/CalculateResolution.cpp
@@ -1,6 +1,6 @@
#include "MantidAlgorithms/CalculateResolution.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/Instrument.h"
#include "MantidKernel/TimeSeriesProperty.h"
diff --git a/Framework/Algorithms/src/CalculateTransmission.cpp b/Framework/Algorithms/src/CalculateTransmission.cpp
index 072c2fa66a3840bfccd507170a85fefca3e48a65..752472e915a9f0646ec23e497332e469dbcdbdc2 100644
--- a/Framework/Algorithms/src/CalculateTransmission.cpp
+++ b/Framework/Algorithms/src/CalculateTransmission.cpp
@@ -3,14 +3,17 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CalculateTransmission.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/FunctionFactory.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/IFunction.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
-#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/IFunction.h"
+#include "MantidKernel/VectorHelper.h"
#include <algorithm>
#include <cassert>
diff --git a/Framework/Algorithms/src/CalculateTransmissionBeamSpreader.cpp b/Framework/Algorithms/src/CalculateTransmissionBeamSpreader.cpp
index 9696ed78ff77fca1a3a11095af172da6a476421b..c397d05a368bbb521b43f21a8e2e88b720b39135 100644
--- a/Framework/Algorithms/src/CalculateTransmissionBeamSpreader.cpp
+++ b/Framework/Algorithms/src/CalculateTransmissionBeamSpreader.cpp
@@ -2,10 +2,12 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CalculateTransmissionBeamSpreader.h"
-#include "MantidAlgorithms/SumSpectra.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/ChopData.cpp b/Framework/Algorithms/src/ChopData.cpp
index 3e7fc4fc7bba029f77cb06ddc3e9565e75beb973..28f221746db9966337f4b0c4a113da604ff9fff8 100644
--- a/Framework/Algorithms/src/ChopData.cpp
+++ b/Framework/Algorithms/src/ChopData.cpp
@@ -1,5 +1,8 @@
#include "MantidAlgorithms/ChopData.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MultiThreaded.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/ClearInstrumentParameters.cpp b/Framework/Algorithms/src/ClearInstrumentParameters.cpp
index 04c3f06953c48b941a9bc5f62214ff9483e010b1..3d906b174ae338f195bfdd2de8f6fd1f06ce8895 100644
--- a/Framework/Algorithms/src/ClearInstrumentParameters.cpp
+++ b/Framework/Algorithms/src/ClearInstrumentParameters.cpp
@@ -1,6 +1,6 @@
#include "MantidAlgorithms/ClearInstrumentParameters.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
diff --git a/Framework/Algorithms/src/ConjoinWorkspaces.cpp b/Framework/Algorithms/src/ConjoinWorkspaces.cpp
index 9084f32bd316c8f5f1d72a90ee4b3bdbdaed0d42..6c9534667016d823b41472bd3e0286bf5c575e80 100644
--- a/Framework/Algorithms/src/ConjoinWorkspaces.cpp
+++ b/Framework/Algorithms/src/ConjoinWorkspaces.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConjoinWorkspaces.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/SpectraAxis.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/ConvertAxesToRealSpace.cpp b/Framework/Algorithms/src/ConvertAxesToRealSpace.cpp
index 5d3fea10458bb9ce29ab3ae9b86afd8a38b395ca..eb31dc324bc890430ec12db758ff1a343bc1d57b 100644
--- a/Framework/Algorithms/src/ConvertAxesToRealSpace.cpp
+++ b/Framework/Algorithms/src/ConvertAxesToRealSpace.cpp
@@ -1,5 +1,4 @@
#include "MantidAlgorithms/ConvertAxesToRealSpace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/NumericAxis.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/ListValidator.h"
diff --git a/Framework/Algorithms/src/ConvertAxisByFormula.cpp b/Framework/Algorithms/src/ConvertAxisByFormula.cpp
index ba63602625758b78e34e024b2f4f0fdc21ff4b87..7ca2d86629a6e93fdfd086a19cc17abc42858a5f 100644
--- a/Framework/Algorithms/src/ConvertAxisByFormula.cpp
+++ b/Framework/Algorithms/src/ConvertAxisByFormula.cpp
@@ -1,8 +1,9 @@
#include "MantidAlgorithms/ConvertAxisByFormula.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidGeometry/muParser_Silent.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/IncreasingAxisValidator.h"
#include "MantidAPI/RefAxis.h"
+#include "MantidGeometry/muParser_Silent.h"
+#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitFactory.h"
#include <boost/shared_ptr.hpp>
diff --git a/Framework/Algorithms/src/ConvertEmptyToTof.cpp b/Framework/Algorithms/src/ConvertEmptyToTof.cpp
index 144171a08a4da4024893ff6003757e3e2ecbf8ee..85319960217c8f758a3a2344eb42e2716224cc89 100644
--- a/Framework/Algorithms/src/ConvertEmptyToTof.cpp
+++ b/Framework/Algorithms/src/ConvertEmptyToTof.cpp
@@ -3,13 +3,13 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConvertEmptyToTof.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ArrayProperty.h"
+#include "MantidAPI/ConstraintFactory.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/IPeakFunction.h"
-#include "MantidAPI/ConstraintFactory.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/UnitFactory.h"
#include <cmath>
#include <map>
@@ -54,8 +54,7 @@ const std::string ConvertEmptyToTof::category() const {
*/
void ConvertEmptyToTof::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("Empty");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("Empty");
declareProperty(new WorkspaceProperty<DataObjects::Workspace2D>(
"InputWorkspace", "", Direction::Input, wsValidator),
"Name of the input workspace");
diff --git a/Framework/Algorithms/src/ConvertFromDistribution.cpp b/Framework/Algorithms/src/ConvertFromDistribution.cpp
index 9c881e02b9e957e8c8a3a9877e04535333ec0117..3f39c2030f0f8d8161c19af7879972959907eee7 100644
--- a/Framework/Algorithms/src/ConvertFromDistribution.cpp
+++ b/Framework/Algorithms/src/ConvertFromDistribution.cpp
@@ -2,8 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConvertFromDistribution.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/RawCountValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
+#include "MantidKernel/CompositeValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ConvertSpectrumAxis.cpp b/Framework/Algorithms/src/ConvertSpectrumAxis.cpp
index cfa92ffabf5d20b7c7c6db8102cb6973d002203e..d9cca8541838325f4875209f8c13755c20e3d4b2 100644
--- a/Framework/Algorithms/src/ConvertSpectrumAxis.cpp
+++ b/Framework/Algorithms/src/ConvertSpectrumAxis.cpp
@@ -2,15 +2,20 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConvertSpectrumAxis.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/NumericAxis.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/Run.h"
-#include <boost/function.hpp>
-#include <boost/bind.hpp>
-#include <cfloat>
+#include "MantidAPI/SpectraAxisValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/UnitFactory.h"
+
+#include <boost/bind.hpp>
+#include <boost/function.hpp>
+
+#include <cfloat>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ConvertSpectrumAxis2.cpp b/Framework/Algorithms/src/ConvertSpectrumAxis2.cpp
index 58fe670a884249e4395a2a2843925c8b84fdc9e0..fd072bbea71a381fd2ea7299b3ea4a6ea185c3cf 100644
--- a/Framework/Algorithms/src/ConvertSpectrumAxis2.cpp
+++ b/Framework/Algorithms/src/ConvertSpectrumAxis2.cpp
@@ -2,16 +2,21 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConvertSpectrumAxis2.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/NumericAxis.h"
+#include "MantidAPI/Run.h"
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitConversion.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/Run.h"
-#include <boost/function.hpp>
+
#include <boost/bind.hpp>
+#include <boost/function.hpp>
+
#include <cfloat>
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/ListValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ConvertToDistribution.cpp b/Framework/Algorithms/src/ConvertToDistribution.cpp
index c5a18d9594af5fe4e71e84111d583476bebeeb61..4c17fe561cb243fe925d45b3794eb1c21f3a4194 100644
--- a/Framework/Algorithms/src/ConvertToDistribution.cpp
+++ b/Framework/Algorithms/src/ConvertToDistribution.cpp
@@ -2,7 +2,9 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConvertToDistribution.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidKernel/CompositeValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ConvertToHistogram.cpp b/Framework/Algorithms/src/ConvertToHistogram.cpp
index 37acbb1439ea3462532815b25831d0052ef30db2..d72f63685baa09ea2566efed985846f9240e6430 100644
--- a/Framework/Algorithms/src/ConvertToHistogram.cpp
+++ b/Framework/Algorithms/src/ConvertToHistogram.cpp
@@ -2,7 +2,6 @@
// Includes
//------------------------------------------------------------------------------
#include "MantidAlgorithms/ConvertToHistogram.h"
-#include "MantidAPI/WorkspaceValidators.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ConvertUnits.cpp b/Framework/Algorithms/src/ConvertUnits.cpp
index 5a3012b50bf12fd6d09b9c2ec60fa77d618e4450..43d213c3a6c8972cf2592e40755b08aa57766444 100644
--- a/Framework/Algorithms/src/ConvertUnits.cpp
+++ b/Framework/Algorithms/src/ConvertUnits.cpp
@@ -2,19 +2,24 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ConvertUnits.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/AlgorithmFactory.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/Run.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include <boost/function.hpp>
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/UnitFactory.h"
+
#include <boost/bind.hpp>
+#include <boost/function.hpp>
#include <boost/math/special_functions/fpclassify.hpp>
+
#include <cfloat>
#include <limits>
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/ListValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ConvertUnitsUsingDetectorTable.cpp b/Framework/Algorithms/src/ConvertUnitsUsingDetectorTable.cpp
index 33c06ad4900fe13d0916b6ad17ddba9f0de2b792..a97fdd6433e02909ae3d290f4dbba4672ff00575 100644
--- a/Framework/Algorithms/src/ConvertUnitsUsingDetectorTable.cpp
+++ b/Framework/Algorithms/src/ConvertUnitsUsingDetectorTable.cpp
@@ -1,30 +1,24 @@
#include "MantidAlgorithms/ConvertUnitsUsingDetectorTable.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/ITableWorkspace.h"
-#include "MantidDataObjects/TableWorkspace.h"
-#include "MantidAPI/AlgorithmFactory.h"
+#include "MantidAPI/Run.h"
#include "MantidAPI/TableRow.h"
+#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidDataObjects/TableWorkspace.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidAlgorithms/ConvertUnitsUsingDetectorTable.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/AlgorithmFactory.h"
-#include "MantidAPI/Run.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidDataObjects/Workspace2D.h"
-#include "MantidDataObjects/TableWorkspace.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include <boost/function.hpp>
#include <boost/bind.hpp>
+#include <boost/function.hpp>
#include <boost/math/special_functions/fpclassify.hpp>
+
+#include <algorithm>
#include <cfloat>
#include <limits>
-#include <vector>
-#include <algorithm>
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/ListValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/CopyInstrumentParameters.cpp b/Framework/Algorithms/src/CopyInstrumentParameters.cpp
index 2eacc15ba853740c203f3637ffc7799c849f1eb8..61e350ee9654cdd2eb621216924f905a33944665 100644
--- a/Framework/Algorithms/src/CopyInstrumentParameters.cpp
+++ b/Framework/Algorithms/src/CopyInstrumentParameters.cpp
@@ -2,10 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CopyInstrumentParameters.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/MemoryManager.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
+#include <iostream>
+
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/CorelliCrossCorrelate.cpp b/Framework/Algorithms/src/CorelliCrossCorrelate.cpp
index a6e0cb33adfc00ecba56d322c2c4855662b143b7..75bfd01219154690408f807d50bf75f27aa7cc33 100644
--- a/Framework/Algorithms/src/CorelliCrossCorrelate.cpp
+++ b/Framework/Algorithms/src/CorelliCrossCorrelate.cpp
@@ -1,10 +1,12 @@
#include "MantidAlgorithms/CorelliCrossCorrelate.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidGeometry/IComponent.h"
+#include "MantidGeometry/muParser_Silent.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
-#include "MantidGeometry/muParser_Silent.h"
namespace Mantid {
namespace Algorithms {
@@ -168,6 +170,11 @@ void CorelliCrossCorrelate::exec() {
// Determine period from chopper frequency.
auto motorSpeed = dynamic_cast<TimeSeriesProperty<double> *>(
inputWS->run().getProperty("BL9:Chop:Skf4:MotorSpeed"));
+ if (!motorSpeed) {
+ throw Exception::NotFoundError(
+ "Could not find a log value for the motor speed",
+ "BL9:Chop:Skf4:MotorSpeed");
+ }
double period = 1e9 / static_cast<double>(motorSpeed->timeAverageValue());
g_log.information() << "Frequency = " << 1e9 / period
<< "Hz Period = " << period << "ns\n";
diff --git a/Framework/Algorithms/src/CorrectFlightPaths.cpp b/Framework/Algorithms/src/CorrectFlightPaths.cpp
index 75608fd98addc548316097cac8d9e5b3730015e7..b6b8cbb2eaf3b3775dc4bf4d1d27eb29e4475e40 100644
--- a/Framework/Algorithms/src/CorrectFlightPaths.cpp
+++ b/Framework/Algorithms/src/CorrectFlightPaths.cpp
@@ -2,14 +2,14 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CorrectFlightPaths.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Workspace2D.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/ListValidator.h"
+#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument/ComponentHelper.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/UnitFactory.h"
#include <cmath>
diff --git a/Framework/Algorithms/src/CorrectKiKf.cpp b/Framework/Algorithms/src/CorrectKiKf.cpp
index bea4c9556cfbee0bfc0edf9e93a8e7841721c986..44c11cb2c03d2446d3276629a2feb88b2339926d 100644
--- a/Framework/Algorithms/src/CorrectKiKf.cpp
+++ b/Framework/Algorithms/src/CorrectKiKf.cpp
@@ -2,12 +2,12 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CorrectKiKf.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/UnitFactory.h"
namespace Mantid {
namespace Algorithms {
@@ -29,8 +29,7 @@ CorrectKiKf::~CorrectKiKf() {}
/// Initialisation method
void CorrectKiKf::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("DeltaE");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("DeltaE");
this->declareProperty(
new WorkspaceProperty<API::MatrixWorkspace>(
diff --git a/Framework/Algorithms/src/CreateCalFileByNames.cpp b/Framework/Algorithms/src/CreateCalFileByNames.cpp
index 67e006535d12ca43b1fb4eafdb6e54221b0039fc..5fce447687eb61314466cdaa481a316473960879 100644
--- a/Framework/Algorithms/src/CreateCalFileByNames.cpp
+++ b/Framework/Algorithms/src/CreateCalFileByNames.cpp
@@ -4,12 +4,13 @@
#include "MantidAlgorithms/CreateCalFileByNames.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/InstrumentDataService.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ConfigService.h"
+
#include <boost/algorithm/string/detail/classification.hpp>
#include <boost/algorithm/string/split.hpp>
+
#include <fstream>
#include <queue>
diff --git a/Framework/Algorithms/src/CreateDummyCalFile.cpp b/Framework/Algorithms/src/CreateDummyCalFile.cpp
index d7c9020aaf9ecfded65339768e765ff11d20f89b..a13e9ba5626e143f39053f6c44d5f3dea6f87ca6 100644
--- a/Framework/Algorithms/src/CreateDummyCalFile.cpp
+++ b/Framework/Algorithms/src/CreateDummyCalFile.cpp
@@ -111,7 +111,7 @@ void CreateDummyCalFile::exec() {
std::string filename = getProperty("CalFilename");
// Plan to overwrite file, so do not check if it exists
- bool overwrite = false;
+ const bool overwrite = false;
int number = 0;
Progress prog(this, 0.0, 0.8, assemblies.size());
diff --git a/Framework/Algorithms/src/CreateLogTimeCorrection.cpp b/Framework/Algorithms/src/CreateLogTimeCorrection.cpp
index 61264770e98c0f19d4d10fa338cb55089cdc61cc..4652655b238a0dd0130e7c75e78c0219e19a592f 100644
--- a/Framework/Algorithms/src/CreateLogTimeCorrection.cpp
+++ b/Framework/Algorithms/src/CreateLogTimeCorrection.cpp
@@ -2,7 +2,7 @@
#include "MantidAPI/WorkspaceProperty.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/TableRow.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include <fstream>
diff --git a/Framework/Algorithms/src/CreatePSDBleedMask.cpp b/Framework/Algorithms/src/CreatePSDBleedMask.cpp
index 1b5b6df6565838f359379c38f9ac336ebc4675d0..719cc8654ee67f937e723436c004863a442afc04 100644
--- a/Framework/Algorithms/src/CreatePSDBleedMask.cpp
+++ b/Framework/Algorithms/src/CreatePSDBleedMask.cpp
@@ -2,17 +2,16 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CreatePSDBleedMask.h"
-#include "MantidKernel/MultiThreaded.h"
#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/MultiThreaded.h"
#include "MantidKernel/NullValidator.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
-#include <map>
-#include <list>
#include <cfloat>
#include <iterator>
+#include <list>
+#include <map>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/CreateSampleWorkspace.cpp b/Framework/Algorithms/src/CreateSampleWorkspace.cpp
index 8d3585304e8c43cf9d972af12777e7adeb20ae92..4976102fe9062d9729b35fd29b8bb71cf05e25f1 100644
--- a/Framework/Algorithms/src/CreateSampleWorkspace.cpp
+++ b/Framework/Algorithms/src/CreateSampleWorkspace.cpp
@@ -203,7 +203,6 @@ void CreateSampleWorkspace::exec() {
}
m_randGen = new Kernel::MersenneTwister(seedValue);
}
-
// Create an instrument with one or more rectangular banks.
Instrument_sptr inst = createTestInstrumentRectangular(
numBanks, bankPixelWidth, pixelSpacing, bankDistanceFromSample,
@@ -221,6 +220,8 @@ void CreateSampleWorkspace::exec() {
numBanks * bankPixelWidth * bankPixelWidth, num_bins, xMin, binWidth,
bankPixelWidth * bankPixelWidth, inst, functionString, isRandom);
}
+ // add chopper
+ this->addChopperParameters(ws);
// Set the Unit of the X Axis
try {
@@ -249,6 +250,34 @@ void CreateSampleWorkspace::exec() {
setProperty("OutputWorkspace", ws);
;
}
+/** Add chopper to the existing matrix workspace
+@param ws -- shared pointer to existing matrix workspace which has instrument
+and chopper
+
+@returns workspace modified to have Fermi chopper added to it.
+*/
+void CreateSampleWorkspace::addChopperParameters(
+ API::MatrixWorkspace_sptr &ws) {
+
+ auto testInst = ws->getInstrument();
+ auto chopper = testInst->getComponentByName("chopper-position");
+
+ // add chopper parameters
+ auto ¶mMap = ws->instrumentParameters();
+ const std::string description(
+ "The initial rotation phase of the disk used to calculate the time"
+ " for neutrons arriving at the chopper according to the formula time = "
+ "delay + initial_phase/Speed");
+ paramMap.add<double>("double", chopper.get(), "initial_phase", -3000.,
+ &description);
+ paramMap.add<std::string>("string", chopper.get(), "ChopperDelayLog",
+ "fermi_delay");
+ paramMap.add<std::string>("string", chopper.get(), "ChopperSpeedLog",
+ "fermi_speed");
+ paramMap.add<std::string>("string", chopper.get(), "FilterBaseLog",
+ "is_running");
+ paramMap.add<bool>("bool", chopper.get(), "filter_with_derivative", false);
+}
/** Create histogram workspace
*/
@@ -479,6 +508,12 @@ Instrument_sptr CreateSampleWorkspace::createTestInstrumentRectangular(
testInst->add(source);
testInst->markAsSource(source);
+ // Add chopper
+ ObjComponent *chopper = new ObjComponent(
+ "chopper-position", Object_sptr(new Object), testInst.get());
+ chopper->setPos(V3D(0.0, 0.0, -0.25 * sourceSampleDistance));
+ testInst->add(chopper);
+
// Define a sample as a simple sphere
Object_sptr sampleSphere =
createSphere(0.001, V3D(0.0, 0.0, 0.0), "sample-shape");
diff --git a/Framework/Algorithms/src/CreateTransmissionWorkspace.cpp b/Framework/Algorithms/src/CreateTransmissionWorkspace.cpp
index 2b7b6da122750c306b499535f4028362fcaf0a29..b18f7639e859f4df8176c559a0cb48f08e565c60 100644
--- a/Framework/Algorithms/src/CreateTransmissionWorkspace.cpp
+++ b/Framework/Algorithms/src/CreateTransmissionWorkspace.cpp
@@ -1,12 +1,8 @@
#include "MantidAlgorithms/CreateTransmissionWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/MandatoryValidator.h"
-#include "MantidKernel/ArrayProperty.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/BoundedValidator.h"
-#include <boost/make_shared.hpp>
+
#include <boost/assign/list_of.hpp>
using namespace Mantid::Kernel;
@@ -48,9 +44,7 @@ const std::string CreateTransmissionWorkspace::category() const {
/** Initialize the algorithm's properties.
*/
void CreateTransmissionWorkspace::init() {
- boost::shared_ptr<CompositeValidator> inputValidator =
- boost::make_shared<CompositeValidator>();
- inputValidator->add(boost::make_shared<WorkspaceUnitValidator>("TOF"));
+ auto inputValidator = boost::make_shared<WorkspaceUnitValidator>("TOF");
declareProperty(new WorkspaceProperty<MatrixWorkspace>(
"FirstTransmissionRun", "", Direction::Input,
diff --git a/Framework/Algorithms/src/CreateTransmissionWorkspaceAuto.cpp b/Framework/Algorithms/src/CreateTransmissionWorkspaceAuto.cpp
index f9c02b1c52857b591126eabbd164dd77ee760613..f1800493a048d9f836da08ac1465c0bf0b6b41ca 100644
--- a/Framework/Algorithms/src/CreateTransmissionWorkspaceAuto.cpp
+++ b/Framework/Algorithms/src/CreateTransmissionWorkspaceAuto.cpp
@@ -9,12 +9,11 @@
*WIKI*/
#include "MantidAlgorithms/CreateTransmissionWorkspaceAuto.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ListValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
-#include "MantidAPI/AlgorithmManager.h"
+#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/RebinParamsValidator.h"
using namespace Mantid::Kernel;
using namespace Mantid::API;
diff --git a/Framework/Algorithms/src/CropWorkspace.cpp b/Framework/Algorithms/src/CropWorkspace.cpp
index 3107951ca432f29feac24ceccab5fc3f58e8f14e..8f11aeb64f9920361f8da933cf35ab1fed6c1fe5 100644
--- a/Framework/Algorithms/src/CropWorkspace.cpp
+++ b/Framework/Algorithms/src/CropWorkspace.cpp
@@ -2,12 +2,6 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/CropWorkspace.h"
-
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/NumericAxis.h"
-#include "MantidAPI/TextAxis.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/MemoryManager.h"
#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/CrossCorrelate.cpp b/Framework/Algorithms/src/CrossCorrelate.cpp
index 46e222a1a1c6b85958521c285ef290939dd3f5ee..d6d5138ac023799cec4189fdd9c504078c0804dd 100644
--- a/Framework/Algorithms/src/CrossCorrelate.cpp
+++ b/Framework/Algorithms/src/CrossCorrelate.cpp
@@ -1,14 +1,15 @@
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
-
-#include <fstream>
-#include <sstream>
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/VectorHelper.h"
#include "MantidAlgorithms/CrossCorrelate.h"
-#include <numeric>
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/VectorHelper.h"
+
+#include <numeric>
+#include <sstream>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/DetectorEfficiencyCor.cpp b/Framework/Algorithms/src/DetectorEfficiencyCor.cpp
index 367403ea41f0f49a24819e644c2cb5ad862f08c9..1f54beb297d1d194a8649c56590e155aebb0b7de 100644
--- a/Framework/Algorithms/src/DetectorEfficiencyCor.cpp
+++ b/Framework/Algorithms/src/DetectorEfficiencyCor.cpp
@@ -1,11 +1,15 @@
#include "MantidAlgorithms/DetectorEfficiencyCor.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+
#include <algorithm>
-#include <functional>
#include <cmath>
-#include "MantidKernel/BoundedValidator.h"
+#include <functional>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp b/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp
index 8350ba3e3180264519d696f5adf90436c39096df..88085ac6165e01bc82d870d1f087876049b6f9a2 100644
--- a/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp
+++ b/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp
@@ -1,9 +1,10 @@
#include "MantidAlgorithms/DetectorEfficiencyCorUser.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidGeometry/muParser_Silent.h"
-#include <ctime>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/DetectorEfficiencyVariation.cpp b/Framework/Algorithms/src/DetectorEfficiencyVariation.cpp
index 1028ee9ad56469fc4175e35cb8b5f27324185b56..011b562de726798e6589ff05826220931998a34b 100644
--- a/Framework/Algorithms/src/DetectorEfficiencyVariation.cpp
+++ b/Framework/Algorithms/src/DetectorEfficiencyVariation.cpp
@@ -2,10 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/DetectorEfficiencyVariation.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidKernel/BoundedValidator.h"
#include <boost/math/special_functions/fpclassify.hpp>
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp b/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp
index 050b93edf61f6f0828e8575212e2fef0bb6385f9..d1d9cbaf304cecfe0db193f78e39aa8965d55ff0 100644
--- a/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp
+++ b/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp
@@ -4,27 +4,27 @@
#include "MantidAlgorithms/DiffractionEventCalibrateDetectors.h"
#include "MantidAlgorithms/GSLFunctions.h"
#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/IFunction.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/TableRow.h"
#include "MantidAPI/TextAxis.h"
-#include "MantidAPI/IFunction.h"
#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidDataObjects/GroupingWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/CPUTimer.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/BoundedValidator.h"
+
+#include <Poco/File.h>
#include <cmath>
#include <numeric>
-#include <Poco/File.h>
-#include <sstream>
#include <fstream>
-#include "MantidDataObjects/GroupingWorkspace.h"
-#include "MantidAPI/AlgorithmFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidAPI/MatrixWorkspace.h"
+#include <sstream>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/DiffractionFocussing2.cpp b/Framework/Algorithms/src/DiffractionFocussing2.cpp
index cf0cd5a42c1cb15a7e4aabe38408d5c39eef1977..eee96f03c7f86d667169fe809434f4554daded7a 100644
--- a/Framework/Algorithms/src/DiffractionFocussing2.cpp
+++ b/Framework/Algorithms/src/DiffractionFocussing2.cpp
@@ -2,21 +2,19 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/DiffractionFocussing2.h"
+#include "MantidAPI/Axis.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/MemoryManager.h"
+#include "MantidAPI/ISpectrum.h"
+#include "MantidAPI/RawCountValidator.h"
#include "MantidAPI/SpectraAxis.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/GroupingWorkspace.h"
-#include "MantidDataObjects/Workspace2D.h"
-#include "MantidKernel/CPUTimer.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/Axis.h"
+
#include <cfloat>
-#include <fstream>
#include <iterator>
#include <numeric>
-#include "MantidAPI/ISpectrum.h"
using namespace Mantid::Kernel;
using namespace Mantid::API;
@@ -43,9 +41,7 @@ DiffractionFocussing2::~DiffractionFocussing2() {}
*/
void DiffractionFocussing2::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- // wsValidator->add<wsValidator->add>("dSpacing");
- wsValidator->add<API::RawCountValidator>();
+ auto wsValidator = boost::make_shared<API::RawCountValidator>();
declareProperty(new API::WorkspaceProperty<MatrixWorkspace>(
"InputWorkspace", "", Direction::Input, wsValidator),
"A 2D workspace with X values of d-spacing/Q-spacing");
diff --git a/Framework/Algorithms/src/EQSANSResolution.cpp b/Framework/Algorithms/src/EQSANSResolution.cpp
index df4eb5d3308435b42f8caae7cffc4293127bdd2d..d2c958d7d5f5e5e2e4716ca97395d08e2c38f148 100644
--- a/Framework/Algorithms/src/EQSANSResolution.cpp
+++ b/Framework/Algorithms/src/EQSANSResolution.cpp
@@ -2,12 +2,6 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/EQSANSResolution.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidDataObjects/EventList.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/VectorHelper.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/EQSANSTofStructure.cpp b/Framework/Algorithms/src/EQSANSTofStructure.cpp
index 0ec55d511661c82fe6c7b5a0635098f570dc569b..d129fb4032dbe0e1c115724342becccd8decd2bb 100644
--- a/Framework/Algorithms/src/EQSANSTofStructure.cpp
+++ b/Framework/Algorithms/src/EQSANSTofStructure.cpp
@@ -2,12 +2,12 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/EQSANSTofStructure.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/Events.h"
#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidGeometry/Instrument.h"
+#include "MantidKernel/TimeSeriesProperty.h"
#include <vector>
diff --git a/Framework/Algorithms/src/ElasticWindow.cpp b/Framework/Algorithms/src/ElasticWindow.cpp
index f6cda7ece96c1971072bf27da87f5412b90f0194..3496acff080b5560b08bd434ff05118829adfebf 100644
--- a/Framework/Algorithms/src/ElasticWindow.cpp
+++ b/Framework/Algorithms/src/ElasticWindow.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ElasticWindow.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/MandatoryValidator.h"
diff --git a/Framework/Algorithms/src/ExtractSpectra.cpp b/Framework/Algorithms/src/ExtractSpectra.cpp
index c797b9b7bcc98937545883f26f19445063a055fe..b3530855cb3effad9bb21c1d1760dd0c4eefbbc5 100644
--- a/Framework/Algorithms/src/ExtractSpectra.cpp
+++ b/Framework/Algorithms/src/ExtractSpectra.cpp
@@ -3,7 +3,6 @@
#include "MantidAPI/MemoryManager.h"
#include "MantidAPI/NumericAxis.h"
#include "MantidAPI/TextAxis.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/VectorHelper.h"
diff --git a/Framework/Algorithms/src/FFT.cpp b/Framework/Algorithms/src/FFT.cpp
index f8e6db3c74314b67a7c712256543b0733b55e805..1d6f94e2bf38fe60405370cd002df6453f65d240 100644
--- a/Framework/Algorithms/src/FFT.cpp
+++ b/Framework/Algorithms/src/FFT.cpp
@@ -172,7 +172,7 @@ void FFT::exec() {
// centerShift == true means that the zero on the x axis is assumed to be in
// the data centre
// at point with index i = ySize/2. If shift == false the zero is at i = 0
- bool centerShift = true;
+ const bool centerShift = true;
API::TextAxis *tAxis = new API::TextAxis(nOut);
int iRe = 0;
diff --git a/Framework/Algorithms/src/FilterBadPulses.cpp b/Framework/Algorithms/src/FilterBadPulses.cpp
index 262111e5bdf0a986eb661f43a985dbb2df12feb4..1a437b32dfc0395a9adaaf9803eb62f6573811ed 100644
--- a/Framework/Algorithms/src/FilterBadPulses.cpp
+++ b/Framework/Algorithms/src/FilterBadPulses.cpp
@@ -2,17 +2,14 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/FilterBadPulses.h"
+#include "MantidAPI/FileProperty.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/TimeSeriesProperty.h"
-#include "MantidAPI/FileProperty.h"
+#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/V3D.h"
-#include <fstream>
-#include "MantidKernel/BoundedValidator.h"
-
namespace Mantid {
namespace Algorithms {
// Register the algorithm into the algorithm factory
diff --git a/Framework/Algorithms/src/FilterByTime.cpp b/Framework/Algorithms/src/FilterByTime.cpp
index 6cdec5b56de6b60379e9459e476a1468508bf91b..474224de5fbae7b709002159704cac3034423921 100644
--- a/Framework/Algorithms/src/FilterByTime.cpp
+++ b/Framework/Algorithms/src/FilterByTime.cpp
@@ -3,14 +3,10 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/FilterByTime.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
-#include "MantidKernel/DateAndTime.h"
-#include "MantidAPI/FileProperty.h"
-
-#include <fstream>
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/DateAndTime.h"
+#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/UnitFactory.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/FindCenterOfMassPosition.cpp b/Framework/Algorithms/src/FindCenterOfMassPosition.cpp
index 20964f31e5edb860cb8fe394702e34a10fd2bf40..aa74da68d4ec9f51afd070ed185bcbda651b092d 100644
--- a/Framework/Algorithms/src/FindCenterOfMassPosition.cpp
+++ b/Framework/Algorithms/src/FindCenterOfMassPosition.cpp
@@ -2,17 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/FindCenterOfMassPosition.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/TableRow.h"
-#include <vector>
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/NullValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/FindCenterOfMassPosition2.cpp b/Framework/Algorithms/src/FindCenterOfMassPosition2.cpp
index 76bb448c085867c580f713ca6f2cac06bf06b5d0..09fc7ac018094ec8ed1c1efb25daec2819c8529b 100644
--- a/Framework/Algorithms/src/FindCenterOfMassPosition2.cpp
+++ b/Framework/Algorithms/src/FindCenterOfMassPosition2.cpp
@@ -2,18 +2,16 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/FindCenterOfMassPosition2.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/TableRow.h"
-#include <vector>
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
+#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/FindPeakBackground.cpp b/Framework/Algorithms/src/FindPeakBackground.cpp
index f5de226028bff2fb6f34e25ccc26c37f68d85f66..047bb0748a29536e74291b11089fd189ca149331 100644
--- a/Framework/Algorithms/src/FindPeakBackground.cpp
+++ b/Framework/Algorithms/src/FindPeakBackground.cpp
@@ -157,7 +157,7 @@ void FindPeakBackground::exec() {
Statistics stats = getStatistics(maskedY);
Ymean = stats.mean;
Yvariance = stats.standard_deviation * stats.standard_deviation;
- Ysigma = std::sqrt((moment4(maskedY, n - l0, Ymean) -
+ Ysigma = std::sqrt((moment4(maskedY, static_cast<size_t>(xn), Ymean) -
(xn - 3.0) / (xn - 1.0) * Yvariance) /
xn);
MantidVec::const_iterator it =
diff --git a/Framework/Algorithms/src/FindPeaks.cpp b/Framework/Algorithms/src/FindPeaks.cpp
index 5273c255ad5a789f30717cbfeeecadd6d5e8a8ba..67fd790e406c8bf64bd03f63717d3ab4d602638b 100644
--- a/Framework/Algorithms/src/FindPeaks.cpp
+++ b/Framework/Algorithms/src/FindPeaks.cpp
@@ -8,7 +8,6 @@
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/FuncMinimizerFactory.h"
#include "MantidAPI/TableRow.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/StartsWithValidator.h"
diff --git a/Framework/Algorithms/src/FitPeak.cpp b/Framework/Algorithms/src/FitPeak.cpp
index 5a8f34e8eb8dc6a096bccab2c3789419c5e8bac7..831efbb6eeee6d3c66d2fc978891c605bb54ae40 100644
--- a/Framework/Algorithms/src/FitPeak.cpp
+++ b/Framework/Algorithms/src/FitPeak.cpp
@@ -502,10 +502,19 @@ void FitOneSinglePeak::highBkgdFit() {
g_log.warning(outss.str());
size_t numpts = i_maxFitX - i_minFitX;
- i_minPeakX += static_cast<size_t>(static_cast<double>(numpts) / 6.);
- m_minPeakX = m_dataWS->readX(m_wsIndex)[i_minPeakX];
- i_maxPeakX -= static_cast<size_t>(static_cast<double>(numpts) / 6.);
- m_maxPeakX = m_dataWS->readX(m_wsIndex)[i_maxPeakX];
+ size_t shift = static_cast<size_t>(static_cast<double>(numpts) / 6.);
+ i_minPeakX += shift;
+ auto Xdata = m_dataWS->readX(m_wsIndex);
+ if (i_minPeakX >= Xdata.size())
+ i_minPeakX = Xdata.size() - 1;
+ m_minPeakX = Xdata[i_minPeakX];
+
+ if (i_maxPeakX < shift) {
+ i_maxPeakX = 0;
+ } else {
+ i_maxPeakX -= shift;
+ }
+ m_maxPeakX = Xdata[i_maxPeakX];
}
m_bkgdFunc = fitBackground(m_bkgdFunc);
@@ -1288,7 +1297,8 @@ void FitPeak::processProperties() {
// Peak range
vector<double> peakrange = getProperty("PeakRange");
if (peakrange.size() != 2) {
- throw runtime_error("Must enter 2 and only 2 items in fit window. ");
+ throw runtime_error(
+ "Must enter 2 and only 2 items for PeakRange in fit window. ");
}
m_minPeakX = peakrange[0];
m_maxPeakX = peakrange[1];
diff --git a/Framework/Algorithms/src/GetAllEi.cpp b/Framework/Algorithms/src/GetAllEi.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..60418d5071ea437e50237e3f826e2d099efadc9e
--- /dev/null
+++ b/Framework/Algorithms/src/GetAllEi.cpp
@@ -0,0 +1,1255 @@
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include <boost/format.hpp>
+#include <boost/algorithm/string.hpp>
+#include <string>
+
+#include "MantidAlgorithms/GetAllEi.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/FilteredTimeSeriesProperty.h"
+#include "MantidKernel/EnabledWhenProperty.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/Unit.h"
+#include "MantidKernel/VectorHelper.h"
+#include "MantidDataObjects/TableWorkspace.h"
+
+namespace Mantid {
+namespace Algorithms {
+
+DECLARE_ALGORITHM(GetAllEi)
+
+/// Empty default constructor
+GetAllEi::GetAllEi()
+ : Algorithm(), m_FilterWithDerivative(true),
+ // minimal resolution for all instruments
+ m_min_Eresolution(0.08),
+ // half maximal resolution for LET
+ m_max_Eresolution(0.5e-3), m_peakEnergyRatio2reject(0.1), m_phase(0),
+ m_chopper(), m_pFilterLog(NULL) {}
+
+/// Initialization method.
+void GetAllEi::init() {
+
+ declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>(
+ "Workspace", "", Kernel::Direction::Input),
+ "The input workspace containing the monitor's spectra "
+ "measured after the last chopper");
+ auto nonNegative = boost::make_shared<Kernel::BoundedValidator<int>>();
+ nonNegative->setLower(0);
+
+ declareProperty(
+ "Monitor1SpecID", EMPTY_INT(), nonNegative,
+ "The workspace index (ID) of the spectra, containing first monitor's"
+ " signal to analyze.");
+ declareProperty(
+ "Monitor2SpecID", EMPTY_INT(), nonNegative,
+ "The workspace index (ID) of the spectra, containing second monitor's"
+ " signal to analyze.");
+
+ declareProperty("ChopperSpeedLog", "Defined in IDF",
+ "Name of the instrument log, "
+ "containing chopper angular velocity. If 'Defined in IDF' "
+ "option is specified, "
+ "the log name is obtained from the IDF");
+ declareProperty(
+ "ChopperDelayLog", "Defined in IDF",
+ "Name of the instrument log, "
+ "containing chopper delay time or chopper phase v.r.t. the pulse time. "
+ "If 'Defined in IDF' option is specified, "
+ "the log name is obtained from IDF");
+ declareProperty(
+ "FilterBaseLog", "Defined in IDF",
+ "Name of the instrument log, "
+ "with positive values indicating that instrument is running\n "
+ "and 0 or negative that it is not.\n"
+ "The log is used to identify time interval to evaluate"
+ " chopper speed and chopper delay which matter.\n"
+ "If such log is not present, average log values are calculated "
+ "within experiment start&end time range.");
+ declareProperty(
+ "FilterWithDerivative", true,
+ "Use derivative of 'FilterBaseLog' "
+ "rather then log values itself to filter invalid time intervals.\n"
+ "Invalid values are then the "
+ "values where the derivative of the log turns zero.\n"
+ "E.g. the 'proton_chage' log grows for each frame "
+ "when instrument is counting and is constant otherwise.");
+ setPropertySettings(
+ "FilterWithDerivative",
+ new Kernel::EnabledWhenProperty("FilterBaseLog",
+ Kernel::ePropertyCriterion::IS_EQUAL_TO,
+ "Defined in IDF"));
+
+ auto maxInRange = boost::make_shared<Kernel::BoundedValidator<double>>();
+ maxInRange->setLower(1.e-6);
+ maxInRange->setUpper(0.1);
+
+ declareProperty("MaxInstrResolution", 0.0005, maxInRange,
+ "The maximal energy resolution possible for an "
+ "instrument at working energies (full width at half "
+ "maximum). \nPeaks, sharper then "
+ "this width are rejected. Accepted limits are: 1e^(-6)-0.1");
+
+ auto minInRange = boost::make_shared<Kernel::BoundedValidator<double>>();
+ minInRange->setLower(0.001);
+ minInRange->setUpper(0.5);
+ declareProperty(
+ "MinInstrResolution", 0.08, minInRange,
+ "The minimal energy resolution possible for an "
+ "instrument at working energies (full width at half maximum).\n"
+ "Peaks broader then this width are rejected. Accepted limits are: "
+ "0.001-0.5");
+
+ auto peakInRange = boost::make_shared<Kernel::BoundedValidator<double>>();
+ peakInRange->setLower(0.0);
+ minInRange->setUpper(1.);
+ declareProperty(
+ "PeaksRatioToReject", 0.1, peakInRange,
+ "Ratio of a peak energy to the maximal energy among all peaks. "
+ "If the ratio is lower then the value specified here, "
+ "peak is treated as insignificant and rejected.\n"
+ "Accepted limits are:0.0 (All accepted) to 1 -- only one peak \n"
+ "(or peaks with max and equal intensity) are accepted.");
+ declareProperty(
+ "IgnoreSecondMonitor", false,
+ "Usually peaks are analyzed and accepted "
+ "only if identified on both monitors. If this property is set to true, "
+ "only first monitor peaks are analyzed.\n"
+ "This is debugging option as getEi has to use both monitors.");
+
+ declareProperty(
+ new API::WorkspaceProperty<API::Workspace>("OutputWorkspace", "",
+ Kernel::Direction::Output),
+ "Name of the output matrix workspace, containing single spectra with"
+ " monitor peaks energies\n"
+ "together with total intensity within each peak.");
+}
+
+// unnamed namespace for auxiliary file-based compilation units
+namespace {
+
+/**Simple template function to remove invalid data from vector
+*@param guessValid -- boolean vector of indicating if each particular guess is
+*valid
+*@param guess -- vector guess values at input and values with removing
+* invalid parameters at output
+*/
+template <class T>
+void removeInvalidValues(const std::vector<bool> &guessValid,
+ std::vector<T> &guess) {
+ std::vector<T> new_guess;
+ new_guess.reserve(guess.size());
+
+ for (size_t i = 0; i < guessValid.size(); i++) {
+ if (guessValid[i]) {
+ new_guess.push_back(guess[i]);
+ }
+ }
+ new_guess.swap(guess);
+}
+/**Internal class to contain peak information */
+struct peakKeeper {
+ double position;
+ double height;
+ double sigma;
+ double energy;
+
+ peakKeeper(double pos, double heigh, double sig)
+ : position(pos), height(heigh), sigma(sig) {
+ this->energy = std::sqrt(2 * M_PI) * height * sigma;
+ }
+ // to sort peaks
+ bool operator<(const peakKeeper &str) const { return (energy > str.energy); }
+};
+
+} // END unnamed namespace for auxiliary file-based compilation units
+
+/** Executes the algorithm -- found all existing monitor peaks. */
+void GetAllEi::exec() {
+ // Get pointers to the workspace, parameter map and table
+ API::MatrixWorkspace_sptr inputWS = getProperty("Workspace");
+ m_min_Eresolution = getProperty("MinInstrResolution");
+ m_max_Eresolution = getProperty("MaxInstrResolution");
+ m_peakEnergyRatio2reject = getProperty("PeaksRatioToReject");
+
+ ////---> recalculate chopper delay to monitor position:
+ auto pInstrument = inputWS->getInstrument();
+ // auto lastChopPositionComponent =
+ // pInstrument->getComponentByName("chopper-position");
+ // auto chopPoint1 = pInstrument->getChopperPoint(0); ->TODO: BUG! this
+ // operation loses parameters map.
+ m_chopper = pInstrument->getComponentByName("chopper-position");
+ if (!m_chopper)
+ throw std::runtime_error("Instrument " + pInstrument->getName() +
+ " does not have 'chopper-position' component");
+
+ auto phase = m_chopper->getNumberParameter("initial_phase");
+
+ if (phase.size() == 0) {
+ throw std::runtime_error("Can not find initial_phase parameter"
+ " attached to the chopper-position component");
+ }
+ if (phase.size() > 1) {
+ throw std::runtime_error(
+ "Can not deal with multiple phases for initial_phase"
+ " parameter attached to the chopper-position component");
+ }
+ m_phase = phase[0];
+
+ this->setFilterLog(inputWS);
+
+ // auto chopPoint1 = pInstrument->getComponentByName("fermi-chopper");
+ // auto par = chopPoint1->getDoubleParameter("Delay (us)");
+ double chopSpeed, chopDelay;
+ findChopSpeedAndDelay(inputWS, chopSpeed, chopDelay);
+ g_log.debug() << boost::str(
+ boost::format("*Identified avrg ChopSpeed: %8.2f and Delay: %8.2f\n") %
+ chopSpeed % chopDelay);
+
+ auto moderator = pInstrument->getSource();
+ double chopDistance = m_chopper->getDistance(
+ *moderator); // location[0].distance(moderator->getPos());
+ double velocity = chopDistance / chopDelay;
+
+ // build workspace to find monitor's peaks
+ size_t det1WSIndex;
+ auto monitorWS = buildWorkspaceToFit(inputWS, det1WSIndex);
+
+ // recalculate delay time from chopper position to monitor position
+ auto detector1 = inputWS->getDetector(det1WSIndex);
+ double mon1Distance = detector1->getDistance(*moderator);
+ double TOF0 = mon1Distance / velocity;
+
+ //--->> below is reserved until full chopper's implementation is available;
+ // auto nChoppers = pInstrument->getNumberOfChopperPoints();
+ // get last chopper.
+ /*
+ if( nChoppers==0)throw std::runtime_error("Instrument does not have any
+ choppers defined");
+
+ auto lastChopper = pInstrument->getChopperPoint(nChoppers-1);
+ ///<---------------------------------------------------
+ */
+ auto baseSpectrum = inputWS->getSpectrum(det1WSIndex);
+ std::pair<double, double> TOF_range = baseSpectrum->getXDataRange();
+
+ double Period =
+ (0.5 * 1.e+6) / chopSpeed; // 0.5 because some choppers open twice.
+ // Would be nice to have it 1 or 0.5 depending on chopper type, but
+ // it looks like not enough information on what chopper is available on ws;
+ std::vector<double> guess_opening;
+ this->findGuessOpeningTimes(TOF_range, TOF0, Period, guess_opening);
+ if (guess_opening.size() == 0) {
+ throw std::runtime_error(
+ "Can not find any chopper opening time within TOF range: " +
+ boost::lexical_cast<std::string>(TOF_range.first) + ':' +
+ boost::lexical_cast<std::string>(TOF_range.second));
+ } else {
+ g_log.debug() << "*Found : " << guess_opening.size()
+ << " chopper prospective opening within time frame: "
+ << TOF_range.first << " to: " << TOF_range.second
+ << std::endl;
+ g_log.debug() << " Timings are:\n";
+ for (size_t i = 0; i < guess_opening.size(); i++) {
+ g_log.debug() << boost::str(boost::format(" %8.2f; ") % guess_opening[i]);
+ }
+ g_log.debug() << std::endl;
+ }
+ std::pair<double, double> Mon1_Erange =
+ monitorWS->getSpectrum(0)->getXDataRange();
+ std::pair<double, double> Mon2_Erange =
+ monitorWS->getSpectrum(1)->getXDataRange();
+ double eMin = std::max(Mon1_Erange.first, Mon2_Erange.first);
+ double eMax = std::min(Mon1_Erange.second, Mon2_Erange.second);
+ g_log.debug() << boost::str(
+ boost::format(
+ "Monitors record data in energy range Emin=%8.2f; Emax=%8.2f\n") %
+ eMin % eMax);
+
+ // convert to energy
+ std::vector<double> guess_ei;
+ guess_ei.reserve(guess_opening.size());
+ double unused(0.0);
+ auto destUnit = Kernel::UnitFactory::Instance().create("Energy");
+ destUnit->initialize(mon1Distance, 0., 0.,
+ static_cast<int>(Kernel::DeltaEMode::Elastic), 0.,
+ unused);
+ for (size_t i = 0; i < guess_opening.size(); i++) {
+ double eGuess = destUnit->singleFromTOF(guess_opening[i]);
+ if (eGuess > eMin && eGuess < eMax) {
+ guess_ei.push_back(eGuess);
+ }
+ }
+ g_log.debug() << "*From all chopper opening only: " +
+ boost::lexical_cast<std::string>(guess_ei.size()) +
+ " fell within both monitor's recording energy range\n";
+ g_log.debug() << " Guess Energies are:\n";
+ for (size_t i = 0; i < guess_ei.size(); i++) {
+ g_log.debug() << boost::str(boost::format(" %8.2f; ") % guess_ei[i]);
+ }
+ g_log.debug() << std::endl;
+
+ std::sort(guess_ei.begin(), guess_ei.end());
+
+ std::vector<size_t> irange_min, irange_max;
+ std::vector<bool> guessValid;
+ // preprocess first monitors peaks;
+ g_log.debug() << "*Looking for real energy peaks on first monitor\n";
+ findBinRanges(monitorWS->readX(0), monitorWS->readY(0), guess_ei,
+ this->m_min_Eresolution / (2 * std::sqrt(2 * std::log(2.))),
+ irange_min, irange_max, guessValid);
+
+ // remove invalid guess values
+ removeInvalidValues<double>(guessValid, guess_ei);
+
+ // preprocess second monitors peaks
+ std::vector<size_t> irange1_min, irange1_max;
+ if (!this->getProperty("IgnoreSecondMonitor")) {
+ g_log.debug() << "*Looking for real energy peaks on second monitor\n";
+ findBinRanges(monitorWS->readX(1), monitorWS->readY(1), guess_ei,
+ this->m_min_Eresolution / (2 * std::sqrt(2 * std::log(2.))),
+ irange1_min, irange1_max, guessValid);
+ removeInvalidValues<double>(guessValid, guess_ei);
+ removeInvalidValues<size_t>(guessValid, irange_min);
+ removeInvalidValues<size_t>(guessValid, irange_max);
+ } else {
+ // this is wrong but will not be used anyway
+ // (except formally looping through vector)
+ irange1_min.assign(irange_min.begin(), irange_min.end());
+ irange1_max.assign(irange_max.begin(), irange_max.end());
+ }
+ g_log.debug()
+ << "*Identified: " + boost::lexical_cast<std::string>(guess_ei.size()) +
+ " peaks with sufficient signal around guess chopper opening\n";
+
+ std::vector<peakKeeper> peaks;
+
+ double maxPeakEnergy(0);
+ std::vector<size_t> monsRangeMin(2), monsRangeMax(2);
+ for (size_t i = 0; i < guess_ei.size(); i++) {
+ monsRangeMin[0] = irange_min[i];
+ monsRangeMax[0] = irange_max[i];
+ monsRangeMin[1] = irange1_min[i];
+ monsRangeMax[1] = irange1_max[i];
+
+ double energy, height, twoSigma;
+ bool found = findMonitorPeak(monitorWS, guess_ei[i], monsRangeMin,
+ monsRangeMax, energy, height, twoSigma);
+ if (found) {
+ peaks.push_back(peakKeeper(energy, height, 0.5 * twoSigma));
+ if (peaks.back().energy > maxPeakEnergy)
+ maxPeakEnergy = peaks.back().energy;
+ }
+ }
+ monitorWS.reset();
+
+ size_t nPeaks = peaks.size();
+ if (nPeaks == 0) {
+ throw std::runtime_error("Can not identify any energy peaks");
+ }
+ // sort peaks and remove invalid one
+ guessValid.resize(nPeaks);
+ bool needsRemoval(false);
+ for (size_t i = 0; i < nPeaks; i++) {
+ peaks[i].energy /= maxPeakEnergy;
+ if (peaks[i].energy < m_peakEnergyRatio2reject) {
+ guessValid[i] = false;
+ g_log.debug() << "*Rejecting peak at Ei=" +
+ boost::lexical_cast<std::string>(peaks[i].position) +
+ " as its total energy lower then the threshold\n";
+ needsRemoval = true;
+ } else {
+ guessValid[i] = true;
+ }
+ }
+ if (needsRemoval)
+ removeInvalidValues<peakKeeper>(guessValid, peaks);
+ nPeaks = peaks.size();
+ // sort by energy decreasing -- see class definition
+ std::sort(peaks.begin(), peaks.end());
+
+ // finalize output
+ auto result_ws = API::WorkspaceFactory::Instance().create("Workspace2D", 1,
+ nPeaks, nPeaks);
+
+ MantidVec peaks_positions;
+ MantidVec &Signal = result_ws->dataY(0);
+ MantidVec &Error = result_ws->dataE(0);
+ for (size_t i = 0; i < nPeaks; i++) {
+ peaks_positions.push_back(peaks[i].position);
+ Signal[i] = peaks[i].height;
+ Error[i] = peaks[i].sigma;
+ }
+ result_ws->setX(0, peaks_positions);
+
+ setProperty("OutputWorkspace", result_ws);
+}
+
+// unnamed namespace for auxiliary file-based functions, converted from lambda
+// as not all Mantid compilers support lambda yet.
+
+/**The internal procedure to set filter log from properties,
+ defining it.
+* @param inputWS -- shared pointer to the input workspace with
+ logs to analyze
+*/
+void GetAllEi::setFilterLog(const API::MatrixWorkspace_sptr &inputWS) {
+
+ std::string filerLogName;
+ std::string filterBase = getProperty("FilterBaseLog");
+ if (boost::iequals(filterBase, "Defined in IDF")) {
+ filerLogName = m_chopper->getStringParameter("FilterBaseLog")[0];
+ m_FilterWithDerivative =
+ m_chopper->getBoolParameter("filter_with_derivative")[0];
+ } else {
+ filerLogName = filterBase;
+ m_FilterWithDerivative = getProperty("FilterWithDerivative");
+ }
+ try {
+ m_pFilterLog = dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
+ inputWS->run().getProperty(filerLogName));
+ } catch (std::runtime_error &) {
+ g_log.warning() << " Can not retrieve (double) filtering log: " +
+ filerLogName +
+ " from current workspace\n"
+ " Using total experiment range to "
+ "find logs averages for chopper parameters\n";
+ m_FilterWithDerivative = false;
+ }
+}
+/**Former lambda to identify guess values for a peak at given index
+* and set up these parameters as input for fitting algorithm
+*
+*@param inputWS -- the workspace to process
+*@param index -- the number of the workspace spectra to process
+*@param Ei -- incident energy
+*@param monsRangeMin -- vector of left boundaries for the subintervals to look
+*for peak
+*@param monsRangeMax -- vector of right boundaries for the subintervals to look
+*for peak
+*
+*@param peakPos -- output energy of the peak
+*@param peakHeight -- output height of the peak assuming Gaussian shape
+*@param peakTwoSigma -- output width of the peak assuming Gaussian shape
+*/
+bool GetAllEi::peakGuess(const API::MatrixWorkspace_sptr &inputWS, size_t index,
+ double Ei, const std::vector<size_t> &monsRangeMin,
+ const std::vector<size_t> &monsRangeMax,
+ double &peakPos, double &peakHeight,
+ double &peakTwoSigma) {
+
+ // calculate sigma from half-width parameters
+ double maxSigma = Ei * m_min_Eresolution / (2 * std::sqrt(2 * std::log(2.)));
+
+ double sMin(std::numeric_limits<double>::max());
+ double sMax(-sMin);
+ double xOfMax(0), dXmax(0);
+ double Intensity(0);
+
+ auto X = inputWS->readX(index);
+ auto S = inputWS->readY(index);
+ size_t ind_min = monsRangeMin[index];
+ size_t ind_max = monsRangeMax[index];
+ // interval too small -- not interested in a peak there
+ if (std::fabs(double(ind_max - ind_min)) < 5)
+ return false;
+
+ // double xMin = X[ind_min];
+ // double xMax = X[ind_max];
+ // size_t ind_Ofmax(ind_min);
+
+ for (size_t i = ind_min; i < ind_max; i++) {
+ double dX = X[i + 1] - X[i];
+ double signal = S[i] / dX;
+ if (signal < sMin)
+ sMin = signal;
+ if (signal > sMax) {
+ sMax = signal;
+ dXmax = dX;
+ xOfMax = X[i];
+ // ind_Ofmax=i;
+ }
+ Intensity += S[i];
+ }
+ // monitor peak should not have just two counts in it.
+ if (sMax * dXmax <= 2)
+ return false;
+ //
+ // size_t SearchAreaSize = ind_max - ind_min;
+
+ double SmoothRange = 2 * maxSigma;
+
+ std::vector<double> SAvrg, binsAvrg;
+ Kernel::VectorHelper::smoothInRange(S, SAvrg, SmoothRange, &X, ind_min,
+ ind_max, &binsAvrg);
+
+ double realPeakPos(xOfMax); // this position is less shifted
+ // due to the skew in averaging formula
+ bool foundRealPeakPos(false);
+ std::vector<double> der1Avrg, der2Avrg, peaks, hillsPos, SAvrg1, binsAvrg1;
+ size_t nPeaks =
+ this->calcDerivativeAndCountZeros(binsAvrg, SAvrg, der1Avrg, peaks);
+ size_t nHills =
+ this->calcDerivativeAndCountZeros(binsAvrg, der1Avrg, der2Avrg, hillsPos);
+ size_t nPrevHills = 2 * nHills;
+ if (nPeaks == 1) {
+ foundRealPeakPos = true;
+ realPeakPos = peaks[0];
+ }
+
+ size_t ic(0), stay_still_count(0);
+ bool iterations_fail(false);
+ while ((nPeaks > 1 || nHills > 2) && (!iterations_fail)) {
+ Kernel::VectorHelper::smoothInRange(SAvrg, SAvrg1, SmoothRange, &binsAvrg,
+ 0, ind_max - ind_min, &binsAvrg1);
+ nPrevHills = nHills;
+
+ nPeaks =
+ this->calcDerivativeAndCountZeros(binsAvrg1, SAvrg1, der1Avrg, peaks);
+ nHills = this->calcDerivativeAndCountZeros(binsAvrg1, der1Avrg, der2Avrg,
+ hillsPos);
+ SAvrg.swap(SAvrg1);
+ binsAvrg.swap(binsAvrg1);
+ if (nPeaks == 1 && !foundRealPeakPos) { // fix first peak position found
+ foundRealPeakPos = true; // as averaging shift peaks on
+ realPeakPos = peaks[0]; // irregular grid.
+ }
+ ic++;
+ if (nPrevHills <= nHills) {
+ stay_still_count++;
+ } else {
+ stay_still_count = 0;
+ }
+ if (ic > 50 || stay_still_count > 3)
+ iterations_fail = true;
+ }
+ if (iterations_fail) {
+ g_log.information() << "*No peak search convergence after " +
+ boost::lexical_cast<std::string>(ic) +
+ " smoothing iterations at still_count: " +
+ boost::lexical_cast<std::string>(
+ stay_still_count) +
+ " Wrong energy or noisy peak at Ei=" +
+ boost::lexical_cast<std::string>(Ei)
+ << std::endl;
+ }
+ g_log.debug() << "*Performed: " + boost::lexical_cast<std::string>(ic) +
+ " averages for spectra " +
+ boost::lexical_cast<std::string>(index) +
+ " at energy: " + boost::lexical_cast<std::string>(Ei) +
+ "\n and found: " +
+ boost::lexical_cast<std::string>(nPeaks) + "peaks and " +
+ boost::lexical_cast<std::string>(nHills) + " hills\n";
+ if (nPeaks != 1) {
+ g_log.debug() << "*Peak rejected as n-peaks !=1 after averaging\n";
+ return false;
+ }
+
+ peakPos = peaks[0];
+ if (nHills > 2) {
+ size_t peakIndex = Kernel::VectorHelper::getBinIndex(hillsPos, peaks[0]);
+ peakTwoSigma = hillsPos[peakIndex + 1] - hillsPos[peakIndex];
+ } else {
+ if (hillsPos.size() == 2) {
+ peakTwoSigma = hillsPos[1] - hillsPos[0];
+ } else {
+ g_log.debug() << "*Peak rejected as averaging gives: " +
+ boost::lexical_cast<std::string>(nPeaks) +
+ " peaks and " +
+ boost::lexical_cast<std::string>(nHills) +
+ " heals\n";
+
+ return false;
+ }
+ }
+ // assuming that averaging conserves intensity and removing linear
+ // background:
+ peakHeight = Intensity / (0.5 * std::sqrt(2. * M_PI) * peakTwoSigma) - sMin;
+ peakPos = realPeakPos;
+
+ return true;
+}
+
+/**Get energy of monitor peak if one is present
+*@param inputWS -- the workspace to process
+*@param Ei -- incident energy
+*@param monsRangeMin -- vector of indexes of left boundaries
+* for the subintervals to look for peak
+*@param monsRangeMax -- vector of indexes of right boundaries
+* for the subintervals to look for peak
+*
+*@param position -- output energy of the peak center.
+*@param height -- output height of the peak assuming Gaussian shape
+*@param twoSigma -- output width of the peak assuming Gaussian shape
+*/
+bool GetAllEi::findMonitorPeak(const API::MatrixWorkspace_sptr &inputWS,
+ double Ei,
+ const std::vector<size_t> &monsRangeMin,
+ const std::vector<size_t> &monsRangeMax,
+ double &position, double &height,
+ double &twoSigma) {
+ // calculate sigma from half-width parameters
+ double maxSigma = Ei * m_min_Eresolution / (2 * std::sqrt(2 * std::log(2.)));
+ double minSigma = Ei * m_max_Eresolution / (2 * std::sqrt(2 * std::log(2.)));
+ //--------------------------------------------------------------------
+ double peak1Pos, peak1TwoSigma, peak1Height;
+ if (!peakGuess(inputWS, 0, Ei, monsRangeMin, monsRangeMax, peak1Pos,
+ peak1Height, peak1TwoSigma))
+ return false;
+ if (0.25 * peak1TwoSigma > maxSigma || peak1TwoSigma < minSigma) {
+ g_log.debug() << "*Rejecting due to width: Peak at mon1 Ei=" +
+ boost::lexical_cast<std::string>(peak1Pos) +
+ " with Height:" +
+ boost::lexical_cast<std::string>(peak1Height) +
+ " and 2*Sigma: " +
+ boost::lexical_cast<std::string>(peak1TwoSigma)
+ << std::endl;
+ return false;
+ }
+
+ if (!this->getProperty("IgnoreSecondMonitor")) {
+ double peak2Pos, peak2TwoSigma, peak2Height;
+ if (!peakGuess(inputWS, 1, Ei, monsRangeMin, monsRangeMax, peak2Pos,
+ peak2Height, peak2TwoSigma))
+ return false;
+ // Let's not check anything except peak position for monitor2, as
+ // its intensity may be very low for some instruments.
+ // if(0.25*peak2TwoSigma>maxSigma||peak2TwoSigma<minSigma)return false;
+
+ // peak in first and second monitors are too far from each other. May be the
+ // instrument
+ // is ill-calibrated but GetEi will probably not find this peak anyway.
+ if (std::fabs(peak1Pos - peak2Pos) >
+ 0.25 * (peak1TwoSigma + peak2TwoSigma)) {
+ g_log.debug()
+ << "*Rejecting due to displacement between Peak at mon1: Ei=" +
+ boost::lexical_cast<std::string>(peak1Pos) + " with Height:" +
+ boost::lexical_cast<std::string>(peak1Height) +
+ " and 2*Sigma: " +
+ boost::lexical_cast<std::string>(peak1TwoSigma) +
+ "\n and Peak at mon2: Ei= " +
+ boost::lexical_cast<std::string>(peak2Pos) + "and height: " +
+ boost::lexical_cast<std::string>(peak1Height) << std::endl;
+
+ return false;
+ }
+ }
+
+ position = peak1Pos;
+ twoSigma = peak1TwoSigma;
+ height = peak1Height;
+
+ return true;
+}
+namespace { // for lambda extracted from calcDerivativeAndCountZeros
+ /**former lambda from calcDerivativeAndCountZeros
+ *estimating if sign have changed from its previous value
+ *@param val -- current function value
+ *@param prevSign -- the sign of the function at previous value
+ */
+bool signChanged(double val, int &prevSign) {
+ int curSign = (val >= 0 ? 1 : -1);
+ bool changed = curSign != prevSign;
+ prevSign = curSign;
+ return changed;
+}
+}
+
+/**Bare-bone function to calculate numerical derivative, and estimate number of
+* zeros this derivative has. The function is assumed to be defined on the
+* the left of a bin range so the derivative is calculated in the same point.
+* No checks are performed for simplicity so data have to be correct
+* form at input.
+*@param bins -- vector of bin boundaries.
+*@param signal -- vector of signal size of bins.size()-1
+*@param deriv -- output vector of numerical derivative
+*@param zeros -- coordinates of found zeros
+
+*@return -- number of zeros, the derivative has in the interval provided.
+*/
+size_t GetAllEi::calcDerivativeAndCountZeros(const std::vector<double> &bins,
+ const std::vector<double> &signal,
+ std::vector<double> &deriv,
+ std::vector<double> &zeros) {
+ size_t nPoints = signal.size();
+ deriv.resize(nPoints);
+ zeros.resize(0);
+
+ std::list<double> funVal;
+ double bin0 = bins[1] - bins[0];
+ double f0 = signal[0] / bin0;
+ double bin1 = bins[2] - bins[1];
+ double f1 = signal[1] / bin1;
+
+ size_t nZeros(0);
+
+ funVal.push_front(f1);
+ deriv[0] = 2 * (f1 - f0) / (bin0 + bin1);
+ int prevSign = (deriv[0] >= 0 ? 1 : -1);
+
+ for (size_t i = 1; i < nPoints - 1; i++) {
+ bin1 = (bins[i + 2] - bins[i + 1]);
+ f1 = signal[i + 1] / bin1;
+ deriv[i] = (f1 - f0) / (bins[i + 2] - bins[i]);
+ f0 = funVal.back();
+ funVal.pop_back();
+ funVal.push_front(f1);
+
+ if (signChanged(deriv[i], prevSign)) {
+ nZeros++;
+ zeros.push_back(0.5 * (bins[i - 1] + bins[i]));
+ }
+ }
+ deriv[nPoints - 1] = 2 * (f1 - f0) / (bin1 + bin0);
+ if (signChanged(deriv[nPoints - 1], prevSign)) {
+ zeros.push_back(bins[nPoints - 1]);
+ nZeros++;
+ }
+
+ return nZeros;
+}
+namespace { // for lambda extracted from findBinRanges
+// get bin range corresponding to the energy range
+void getBinRange(const MantidVec &eBins, double eMin, double eMax,
+ size_t &index_min, size_t &index_max) {
+
+ size_t nBins = eBins.size();
+ if (eMin <= eBins[0]) {
+ index_min = 0;
+ } else {
+ index_min = Kernel::VectorHelper::getBinIndex(eBins, eMin);
+ }
+
+ if (eMax >= eBins[nBins - 1]) {
+ index_max = nBins - 1;
+ } else {
+ index_max = Kernel::VectorHelper::getBinIndex(eBins, eMax) + 1;
+ if (index_max >= nBins)
+ index_max = nBins - 1; // last bin range anyway. Should not happen
+ }
+}
+
+// refine bin range. May need better procedure for this.
+bool refineEGuess(const MantidVec &eBins, const MantidVec &signal,
+ double &eGuess, size_t index_min, size_t index_max) {
+
+ size_t ind_Emax = index_min;
+ double SMax(0);
+ for (size_t i = index_min; i < index_max; i++) {
+ double dX = eBins[i + 1] - eBins[i];
+ double sig = signal[i] / dX;
+ if (sig > SMax) {
+ SMax = sig;
+ ind_Emax = i;
+ }
+ }
+ if (ind_Emax == index_min || ind_Emax == index_max) {
+ return false;
+ }
+ eGuess = 0.5 * (eBins[ind_Emax] + eBins[ind_Emax + 1]);
+ return true;
+}
+
+struct peakKeeper2 {
+ double left_rng;
+ double right_rng;
+ peakKeeper2(){};
+ peakKeeper2(double left, double right) : left_rng(left), right_rng(right) {}
+};
+}
+
+/**Find indexes of each expected peak intervals from monotonous array of ranges.
+*@param eBins -- bin ranges to look through
+*@param signal -- vector of signal in the bins
+*@param guess_energy -- vector of guess energies to look for
+*@param eResolution -- instrument resolution in energy units
+*@param irangeMin -- start indexes of energy intervals in the guess_energies
+* vector.
+*@param irangeMax -- final indexes of energy intervals in the guess_energies
+* vector.
+*@param guessValid -- output boolean vector, which specifies if guess energies
+* in guess_energy vector are valid or not
+*/
+void GetAllEi::findBinRanges(const MantidVec &eBins, const MantidVec &signal,
+ const std::vector<double> &guess_energy,
+ double eResolution, std::vector<size_t> &irangeMin,
+ std::vector<size_t> &irangeMax,
+ std::vector<bool> &guessValid) {
+
+ // size_t nBins = eBins.size();
+ guessValid.resize(guess_energy.size());
+
+ // Do the job
+ size_t ind_min, ind_max;
+ irangeMin.resize(0);
+ irangeMax.resize(0);
+
+ // identify guess bin ranges
+ std::vector<peakKeeper2> guess_peak(guess_energy.size());
+ for (size_t nGuess = 0; nGuess < guess_energy.size(); nGuess++) {
+ double eGuess = guess_energy[nGuess];
+ getBinRange(eBins, eGuess * (1 - 4 * eResolution),
+ eGuess * (1 + 4 * eResolution), ind_min, ind_max);
+ guess_peak[nGuess] = peakKeeper2(eBins[ind_min], eBins[ind_max]);
+ }
+ // verify that the ranges not intercept and refine interceptions
+ for (size_t i = 1; i < guess_energy.size(); i++) {
+ if (guess_peak[i - 1].right_rng > guess_peak[i].left_rng) {
+ double mid_pnt =
+ 0.5 * (guess_peak[i - 1].right_rng + guess_peak[i].left_rng);
+ guess_peak[i - 1].right_rng = mid_pnt;
+ guess_peak[i].left_rng = mid_pnt;
+ }
+ }
+ // identify final bin ranges
+ for (size_t nGuess = 0; nGuess < guess_energy.size(); nGuess++) {
+
+ double eGuess = guess_energy[nGuess];
+ getBinRange(eBins, guess_peak[nGuess].left_rng,
+ guess_peak[nGuess].right_rng, ind_min, ind_max);
+
+ if (refineEGuess(eBins, signal, eGuess, ind_min, ind_max)) {
+ getBinRange(eBins, std::max(guess_peak[nGuess].left_rng,
+ eGuess * (1 - 3 * eResolution)),
+ std::max(guess_peak[nGuess].right_rng,
+ eGuess * (1 + 3 * eResolution)),
+ ind_min, ind_max);
+ irangeMin.push_back(ind_min);
+ irangeMax.push_back(ind_max);
+ guessValid[nGuess] = true;
+ } else {
+ guessValid[nGuess] = false;
+ g_log.debug() << "*Incorrect guess energy: "
+ << boost::lexical_cast<std::string>(eGuess)
+ << " no energy peak found in 4*Sigma range\n";
+ }
+ }
+ // if array decreasing rather then increasing, indexes behave differently.
+ // Will it still work?
+ if (irangeMax.size() > 0) {
+ if (irangeMax[0] < irangeMin[0]) {
+ irangeMax.swap(irangeMin);
+ }
+ }
+}
+
+/**Build 2-spectra workspace in units of energy, used as source
+*to identify actual monitors spectra
+*@param inputWS shared pointer to initial workspace
+*@param wsIndex0 -- returns workspace index for first detector.
+*@return shared pointer to intermediate workspace, in units of energy
+* used to fit monitor's spectra.
+*/
+API::MatrixWorkspace_sptr
+GetAllEi::buildWorkspaceToFit(const API::MatrixWorkspace_sptr &inputWS,
+ size_t &wsIndex0) {
+
+ // at this stage all properties are validated so its safe to access them
+ // without
+ // additional checks.
+ specid_t specNum1 = getProperty("Monitor1SpecID");
+ wsIndex0 = inputWS->getIndexFromSpectrumNumber(specNum1);
+ specid_t specNum2 = getProperty("Monitor2SpecID");
+ size_t wsIndex1 = inputWS->getIndexFromSpectrumNumber(specNum2);
+ auto pSpectr1 = inputWS->getSpectrum(wsIndex0);
+ auto pSpectr2 = inputWS->getSpectrum(wsIndex1);
+ // assuming equally binned ws.
+ // auto bins = inputWS->dataX(wsIndex0);
+ auto bins = pSpectr1->dataX();
+ size_t XLength = bins.size();
+ size_t YLength = inputWS->dataY(wsIndex0).size();
+ auto working_ws =
+ API::WorkspaceFactory::Instance().create(inputWS, 2, XLength, YLength);
+ // copy data --> very bad as implicitly assigns pointer
+ // to bins array and bins array have to exist out of this routine
+ // scope.
+ // This does not matter in this case as below we convert units
+ // which should decouple cow_pointer but very scary operation in
+ // general.
+ working_ws->setX(0, bins);
+ working_ws->setX(1, bins);
+ MantidVec &Signal1 = working_ws->dataY(0);
+ MantidVec &Error1 = working_ws->dataE(0);
+ MantidVec &Signal2 = working_ws->dataY(1);
+ MantidVec &Error2 = working_ws->dataE(1);
+ for (size_t i = 0; i < YLength; i++) {
+ Signal1[i] = inputWS->dataY(wsIndex0)[i];
+ Error1[i] = inputWS->dataE(wsIndex0)[i];
+ Signal2[i] = inputWS->dataY(wsIndex1)[i];
+ Error2[i] = inputWS->dataE(wsIndex1)[i];
+ }
+ // copy detector mapping
+ API::ISpectrum *spectrum = working_ws->getSpectrum(0);
+ spectrum->setSpectrumNo(specNum1);
+ spectrum->clearDetectorIDs();
+ spectrum->addDetectorIDs(pSpectr1->getDetectorIDs());
+ spectrum = working_ws->getSpectrum(1);
+ spectrum->setSpectrumNo(specNum2);
+ spectrum->clearDetectorIDs();
+ spectrum->addDetectorIDs(pSpectr2->getDetectorIDs());
+
+ if (inputWS->getAxis(0)->unit()->caption() != "Energy") {
+ API::IAlgorithm_sptr conv = createChildAlgorithm("ConvertUnits");
+ conv->initialize();
+ conv->setProperty("InputWorkspace", working_ws);
+ conv->setProperty("OutputWorkspace", working_ws);
+ conv->setPropertyValue("Target", "Energy");
+ conv->setPropertyValue("EMode", "Elastic");
+ // conv->setProperty("AlignBins",true); --> throws due to bug in
+ // ConvertUnits
+ conv->execute();
+ }
+
+ return working_ws;
+}
+/**function calculates list of provisional chopper opening times.
+*@param TOF_range -- std::pair containing min and max time, of signal
+* measured on monitors
+*@param ChopDelay -- the time of flight neutrons travel from source
+* to the chopper opening.
+*@param Period -- period of chopper openings
+
+*@param guess_opening_times -- output vector with time values
+* at which neutrons may pass through the chopper.
+*/
+void GetAllEi::findGuessOpeningTimes(const std::pair<double, double> &TOF_range,
+ double ChopDelay, double Period,
+ std::vector<double> &guess_opening_times) {
+
+ if (ChopDelay >= TOF_range.second) {
+ std::string chop = boost::str(boost::format("%.2g") % ChopDelay);
+ std::string t_min = boost::str(boost::format("%.2g") % TOF_range.first);
+ std::string t_max = boost::str(boost::format("%.2g") % TOF_range.second);
+ throw std::runtime_error("Logical error: Chopper opening time: " + chop +
+ " is outside of time interval: " + t_min + ":" +
+ t_max + " of the signal, measured on monitors.");
+ }
+
+ // number of times chopper with specified rotation period opens.
+ size_t n_openings =
+ static_cast<size_t>((TOF_range.second - ChopDelay) / Period) + 1;
+ // number of periods falling outside of the time period, measuring on monitor.
+ size_t n_start(0);
+ if (ChopDelay < TOF_range.first) {
+ n_start = static_cast<size_t>((TOF_range.first - ChopDelay) / Period) + 1;
+ n_openings -= n_start;
+ }
+
+ guess_opening_times.resize(n_openings);
+ for (size_t i = n_start; i < n_openings + n_start; i++) {
+ guess_opening_times[i - n_start] =
+ ChopDelay + static_cast<double>(i) * Period;
+ }
+}
+/**Finds pointer to log value for the property with the name provided
+*
+*@param inputWS -- workspace with logs attached
+*@param propertyName -- name of the property to find log for
+*
+*@return -- pointer to property which contain the log requested or nullptr if
+* no log found or other errors identified. */
+Kernel::Property *
+GetAllEi::getPLogForProperty(const API::MatrixWorkspace_sptr &inputWS,
+ const std::string &propertyName) {
+
+ std::string LogName = this->getProperty(propertyName);
+ if (boost::iequals(LogName, "Defined in IDF")) {
+ auto AllNames = m_chopper->getStringParameter(propertyName);
+ if (AllNames.size() != 1)
+ return NULL;
+ LogName = AllNames[0];
+ }
+ auto pIProperty = (inputWS->run().getProperty(LogName));
+
+ return pIProperty;
+}
+
+/**Return average time series log value for the appropriately filtered log
+* @param inputWS -- shared pointer to the input workspace containing
+* the log to process
+* @param propertyName -- log name
+* @param splitter -- array of Kernel::splittingInterval data, used to
+* filter input events or empty array to use
+* experiment start/end times.
+*/
+double
+GetAllEi::getAvrgLogValue(const API::MatrixWorkspace_sptr &inputWS,
+ const std::string &propertyName,
+ std::vector<Kernel::SplittingInterval> &splitter) {
+
+ auto pIProperty = getPLogForProperty(inputWS, propertyName);
+
+ // this will always provide a defined pointer as this has been verified in
+ // validator.
+ auto pTimeSeries =
+ dynamic_cast<Kernel::TimeSeriesProperty<double> *>(pIProperty);
+
+ if (splitter.size() == 0) {
+ auto TimeStart = inputWS->run().startTime();
+ auto TimeEnd = inputWS->run().endTime();
+ pTimeSeries->filterByTime(TimeStart, TimeEnd);
+ } else {
+ pTimeSeries->filterByTimes(splitter);
+ }
+ if (pTimeSeries->size() == 0) {
+ throw std::runtime_error(
+ "Can not find average value for log defined by property" +
+ propertyName + " As no valid log values are found.");
+ }
+
+ return pTimeSeries->getStatistics().mean;
+}
+namespace { // former lambda function for findChopSpeedAndDelay
+
+/**Select time interval on the basis of previous time interval
+* selection and check if current value gets in the selection
+*
+* @param t_beg -- initial time for current time interval
+* @param t_end -- final time for current time interval
+* @param inSelection -- the boolean indicating if previous interval
+* was selected on input and current selected on
+* output
+* @param startTime -- total selection time start moment
+* @param endTime -- total selection time final moments
+*
+*@return true if selection interval is completed
+* (current interval is not selected) and false otherwise
+*/
+bool SelectInterval(const Kernel::DateAndTime &t_beg,
+ const Kernel::DateAndTime &t_end, double value,
+ bool &inSelection, Kernel::DateAndTime &startTime,
+ Kernel::DateAndTime &endTime) {
+
+ if (value > 0) {
+ if (!inSelection) {
+ startTime = t_beg;
+ }
+ inSelection = true;
+ } else {
+ if (inSelection) {
+ inSelection = false;
+ if (endTime > startTime)
+ return true;
+ }
+ }
+ endTime = t_end;
+ return false;
+}
+}
+/**Analyze chopper logs and identify chopper speed and delay
+@param inputWS -- sp to workspace with attached logs.
+@param chop_speed -- output value for chopper speed in uSec
+@param chop_delay -- output value for chopper delay in uSec
+*/
+void GetAllEi::findChopSpeedAndDelay(const API::MatrixWorkspace_sptr &inputWS,
+ double &chop_speed, double &chop_delay) {
+
+ // TODO: Make it dependent on inputWS time range
+
+ std::vector<Kernel::SplittingInterval> splitter;
+ if (m_pFilterLog) {
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> pDerivative;
+
+ // Define selecting function
+ bool inSelection(false);
+ // time interval to select (start-end)
+ Kernel::DateAndTime startTime, endTime;
+ //
+ // Analyze filtering log
+ auto dateAndTimes = m_pFilterLog->valueAsCorrectMap();
+ auto it = dateAndTimes.begin();
+ auto next = it;
+ next++;
+ std::map<Kernel::DateAndTime, double> derivMap;
+ auto itder = it;
+ if (m_FilterWithDerivative) {
+ pDerivative = m_pFilterLog->getDerivative();
+ derivMap = pDerivative->valueAsCorrectMap();
+ itder = derivMap.begin();
+ }
+
+ // initialize selection log
+ if (dateAndTimes.size() <= 1) {
+ SelectInterval(it->first, it->first, itder->second, inSelection,
+ startTime, endTime);
+ if (inSelection) {
+ startTime = inputWS->run().startTime();
+ endTime = inputWS->run().endTime();
+ Kernel::SplittingInterval interval(startTime, endTime, 0);
+ splitter.push_back(interval);
+ } else {
+ throw std::runtime_error("filtered all data points. Nothing to do");
+ }
+ } else {
+ SelectInterval(it->first, next->first, itder->second, inSelection,
+ startTime, endTime);
+ }
+
+ // if its filtered using log, both iterator walk through the same values
+ // if use derivative, derivative's values are used for filtering
+ // and derivative assumed in a center of an interval
+ for (; next != dateAndTimes.end(); ++next, ++itder) {
+ if (SelectInterval(it->first, next->first, itder->second, inSelection,
+ startTime, endTime)) {
+ Kernel::SplittingInterval interval(startTime, endTime, 0);
+ splitter.push_back(interval);
+ }
+ it = next;
+ }
+ // final interval
+ if (inSelection && (endTime > startTime)) {
+ Kernel::SplittingInterval interval(startTime, endTime, 0);
+ splitter.push_back(interval);
+ }
+ } // End of USE filter log.
+
+ chop_speed = this->getAvrgLogValue(inputWS, "ChopperSpeedLog", splitter);
+ chop_speed = std::fabs(chop_speed);
+ if (chop_speed < 1.e-7) {
+ throw std::runtime_error("Chopper speed can not be zero ");
+ }
+ chop_delay =
+ std::fabs(this->getAvrgLogValue(inputWS, "ChopperDelayLog", splitter));
+
+ // process chopper delay in the units of degree (phase)
+ auto pProperty = getPLogForProperty(inputWS, "ChopperDelayLog");
+ if (!pProperty)
+ throw std::runtime_error("ChopperDelayLog has been removed from workspace "
+ "during the algorithm execution");
+ std::string units = pProperty->units();
+ // its chopper phase provided
+ if (units == "deg" ||
+ units.c_str()[0] ==
+ -80) { //<- userd in ISIS ASCII representation of o(deg)
+ chop_delay *= 1.e+6 / (360. * chop_speed); // convert in uSec
+ }
+ chop_delay += m_phase / chop_speed;
+}
+
+namespace { // namespace for lambda functions, used in validators
+
+/* former Lambda to validate if appropriate log is present in workspace
+and if it's present, it is a time-series property
+* @param prop_name -- the name of the log to check
+* @param err_presence -- core error message to return if no log found
+* @param err_type -- core error message to return if
+* log is of incorrect type
+* @param fail -- fail or warn if appropriate log is not available.
+*
+* @param result -- map to add the result of check for errors
+* if no error found the map is not modified and remains
+* empty.
+
+
+* @return -- false if all checks are fine, or true if check is
+* failed
+*/
+bool check_time_series_property(
+ const GetAllEi *algo, const API::MatrixWorkspace_sptr &inputWS,
+ const boost::shared_ptr<const Geometry::IComponent> &chopper,
+ const std::string &prop_name, const std::string &err_presence,
+ const std::string &err_type, bool fail,
+ std::map<std::string, std::string> &result) {
+
+ std::string LogName = algo->getProperty(prop_name);
+ if (boost::iequals(LogName, "Defined in IDF")) {
+ try {
+ auto theLogs = chopper->getStringParameter(prop_name);
+ if (theLogs.size() == 0) {
+ if (fail)
+ result[prop_name] = "Can not retrieve parameter " + prop_name +
+ " from the instrument definition file.";
+ return true;
+ }
+ LogName = theLogs[0];
+ } catch (...) {
+ result[prop_name] = "Can not retrieve parameter " + prop_name +
+ " from the instrument definition file.";
+ return true;
+ }
+ }
+ try {
+ Kernel::Property *pProp = inputWS->run().getProperty(LogName);
+ auto pTSProp = dynamic_cast<Kernel::TimeSeriesProperty<double> *>(pProp);
+ if (!pTSProp) {
+ if (fail)
+ result[prop_name] = "Workspace contains " + err_type + LogName +
+ " But its type is not a timeSeries property";
+ return true;
+ }
+ } catch (std::runtime_error &) {
+ if (fail)
+ result[prop_name] = "Workspace has to contain " + err_presence + LogName;
+ return true;
+ }
+ return false;
+}
+}
+
+/**Validates if input workspace contains all necessary logs and if all
+* these logs are the logs of appropriate type
+@return list of invalid logs or empty list if no errors is found.
+*/
+std::map<std::string, std::string> GetAllEi::validateInputs() {
+
+ // Do Validation
+ std::map<std::string, std::string> result;
+
+ API::MatrixWorkspace_sptr inputWS = getProperty("Workspace");
+ if (!inputWS) {
+ result["Workspace"] = "Input workspace can not be identified";
+ return result;
+ }
+ if (!inputWS->isHistogramData()) {
+ result["Workspace"] = "Only histogram workspaces are currently supported. "
+ "Rebin input workspace first.";
+ }
+
+ specid_t specNum1 = getProperty("Monitor1SpecID");
+ try {
+ inputWS->getIndexFromSpectrumNumber(specNum1);
+ } catch (std::runtime_error &) {
+ result["Monitor1SpecID"] =
+ "Input workspace does not contain spectra with ID: " +
+ boost::lexical_cast<std::string>(specNum1);
+ }
+ specid_t specNum2 = getProperty("Monitor2SpecID");
+ try {
+ inputWS->getIndexFromSpectrumNumber(specNum2);
+ } catch (std::runtime_error &) {
+ result["Monitor2SpecID"] =
+ "Input workspace does not contain spectra with ID: " +
+ boost::lexical_cast<std::string>(specNum2);
+ }
+ // check chopper and initiate it if present (for debugging)
+ m_chopper = inputWS->getInstrument()->getComponentByName("chopper-position");
+ if (!m_chopper) {
+ result["Workspace_chopper"] =
+ " For this algorithm to work workspace has"
+ " to contain well defined 'chopper-position' component";
+ return result;
+ }
+
+ check_time_series_property(this, inputWS, m_chopper, "ChopperSpeedLog",
+ "chopper speed log with name: ",
+ "chopper speed log ", true, result);
+ check_time_series_property(
+ this, inputWS, m_chopper, "ChopperDelayLog",
+ "property related to chopper delay log with name: ", "chopper delay log ",
+ true, result);
+ bool failed = check_time_series_property(
+ this, inputWS, m_chopper, "FilterBaseLog", "filter base log named: ",
+ "filter base log: ", false, result);
+ if (failed) {
+ g_log.warning()
+ << " Can not find a log to identify good DAE operations.\n"
+ " Assuming that good operations start from experiment time=0";
+ } else {
+ this->setFilterLog(inputWS);
+ }
+ return result;
+}
+
+} // namespace Algorithms
+} // namespace Mantid
diff --git a/Framework/Algorithms/src/GetDetOffsetsMultiPeaks.cpp b/Framework/Algorithms/src/GetDetOffsetsMultiPeaks.cpp
index 07e9673ba2151c55e0ce2beec63f3c18a07106b6..ed6fedd46ee75042c300526e89d281f43395ebad 100644
--- a/Framework/Algorithms/src/GetDetOffsetsMultiPeaks.cpp
+++ b/Framework/Algorithms/src/GetDetOffsetsMultiPeaks.cpp
@@ -1,24 +1,23 @@
#include "MantidAlgorithms/GetDetOffsetsMultiPeaks.h"
#include "MantidAlgorithms/GSLFunctions.h"
+#include "MantidAPI/CompositeFunction.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/IPeakFunction.h"
#include "MantidAPI/IBackgroundFunction.h"
-#include "MantidAPI/CompositeFunction.h"
#include "MantidAPI/TableRow.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/VectorHelper.h"
+#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/MaskWorkspace.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
+#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/ListValidator.h"
#include "MantidKernel/Statistics.h"
+#include "MantidKernel/VectorHelper.h"
+
#include <boost/math/special_functions/fpclassify.hpp>
-#include <fstream>
-#include <ostream>
#include <sstream>
namespace Mantid {
diff --git a/Framework/Algorithms/src/GetDetectorOffsets.cpp b/Framework/Algorithms/src/GetDetectorOffsets.cpp
index 86b595c4c5f14faae0dbdcaa28a8cc7e20b7390b..5af130be47dc42589c73a119d8910ff94ba8dbb3 100644
--- a/Framework/Algorithms/src/GetDetectorOffsets.cpp
+++ b/Framework/Algorithms/src/GetDetectorOffsets.cpp
@@ -1,19 +1,17 @@
#include "MantidAlgorithms/GetDetectorOffsets.h"
+#include "MantidAPI/CompositeFunction.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/IPeakFunction.h"
-#include "MantidAPI/IBackgroundFunction.h"
-#include "MantidAPI/CompositeFunction.h"
-#include "MantidDataObjects/OffsetsWorkspace.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/MaskWorkspace.h"
-#include <boost/math/special_functions/fpclassify.hpp>
-#include <fstream>
-#include <ostream>
-#include <sstream>
+#include "MantidDataObjects/OffsetsWorkspace.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
+#include <boost/math/special_functions/fpclassify.hpp>
+#include <sstream>
+
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/GetEi.cpp b/Framework/Algorithms/src/GetEi.cpp
index 040830fa3dcec6de114074a44b87a887fa3701d7..2447bd9b0e91055c8360395399d0845c1545cb20 100644
--- a/Framework/Algorithms/src/GetEi.cpp
+++ b/Framework/Algorithms/src/GetEi.cpp
@@ -1,12 +1,14 @@
#include "MantidAlgorithms/GetEi.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/Exception.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/PhysicalConstants.h"
-#include "MantidAPI/WorkspaceValidators.h"
+
#include <boost/lexical_cast.hpp>
-#include "MantidKernel/Exception.h"
#include <cmath>
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/GetEi2.cpp b/Framework/Algorithms/src/GetEi2.cpp
index 03cf0741b494e38c4c752a53d3a6b52d9fcdd723..e01d556106a5c727e34e267fb89018964f2b181d 100644
--- a/Framework/Algorithms/src/GetEi2.cpp
+++ b/Framework/Algorithms/src/GetEi2.cpp
@@ -1,18 +1,21 @@
#include "MantidAlgorithms/GetEi2.h"
-#include "MantidKernel/PhysicalConstants.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/IEventWorkspace.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
#include "MantidGeometry/IObjComponent.h"
+#include "MantidGeometry/muParser_Silent.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/VectorHelper.h"
#include <boost/lexical_cast.hpp>
#include <cmath>
#include <algorithm>
#include <sstream>
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidGeometry/muParser_Silent.h"
using namespace Mantid::Kernel;
using namespace Mantid::API;
diff --git a/Framework/Algorithms/src/He3TubeEfficiency.cpp b/Framework/Algorithms/src/He3TubeEfficiency.cpp
index 0b82d45efee51204131cd80fb26212b20702965b..b8e5d300845d397c8b7a8e18436825100890634f 100644
--- a/Framework/Algorithms/src/He3TubeEfficiency.cpp
+++ b/Framework/Algorithms/src/He3TubeEfficiency.cpp
@@ -1,10 +1,13 @@
#include "MantidAlgorithms/He3TubeEfficiency.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/ArrayBoundedValidator.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/cow_ptr.h"
+#include "MantidKernel/CompositeValidator.h"
+
#include <algorithm>
#include <cmath>
#include <stdexcept>
diff --git a/Framework/Algorithms/src/IQTransform.cpp b/Framework/Algorithms/src/IQTransform.cpp
index c2a5c506de78480e335546ce81b2db2cf9885327..d0484e12012ee7ed4563f64fbc68824149d58715 100644
--- a/Framework/Algorithms/src/IQTransform.cpp
+++ b/Framework/Algorithms/src/IQTransform.cpp
@@ -2,12 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/IQTransform.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/IncreasingAxisValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/VectorHelper.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp b/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp
index 0f4fd9d60e98339411cf48c23418c0cc3340e78a..8970268ec6e453b2326086689c3977de04cf60a3 100644
--- a/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp
+++ b/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp
@@ -1,5 +1,9 @@
#include "MantidAlgorithms/IdentifyNoisyDetectors.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/CompositeValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/IntegrateByComponent.cpp b/Framework/Algorithms/src/IntegrateByComponent.cpp
index 3736939ef44d5308342132576d077262bd22c1a5..104713732b2aefb44f91e81125f1483a752da01d 100644
--- a/Framework/Algorithms/src/IntegrateByComponent.cpp
+++ b/Framework/Algorithms/src/IntegrateByComponent.cpp
@@ -1,5 +1,5 @@
#include "MantidAlgorithms/IntegrateByComponent.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/BoundedValidator.h"
#include <gsl/gsl_statistics.h>
#include <boost/math/special_functions/fpclassify.hpp>
diff --git a/Framework/Algorithms/src/Integration.cpp b/Framework/Algorithms/src/Integration.cpp
index 302661368b18d6047887914f40a7587d2a8ad4a5..eca1ce5afd3fd9a789892d7a4f843637a3071059 100644
--- a/Framework/Algorithms/src/Integration.cpp
+++ b/Framework/Algorithms/src/Integration.cpp
@@ -2,16 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Integration.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidDataObjects/RebinnedOutput.h"
-#include "MantidAPI/Progress.h"
-#include <cmath>
-
#include "MantidAPI/NumericAxis.h"
#include "MantidAPI/TextAxis.h"
+#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidDataObjects/RebinnedOutput.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/VectorHelper.h"
+
+#include <cmath>
+#include <numeric>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/LorentzCorrection.cpp b/Framework/Algorithms/src/LorentzCorrection.cpp
index 2d42cd4b7ccfccc6e28dfd1c2dbd4103ab9fb745..b83c575d271cfecb3d9583b4fa27a821a738e865 100644
--- a/Framework/Algorithms/src/LorentzCorrection.cpp
+++ b/Framework/Algorithms/src/LorentzCorrection.cpp
@@ -1,7 +1,7 @@
#include "MantidAlgorithms/LorentzCorrection.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/Progress.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/MultiThreaded.h"
#include <boost/make_shared.hpp>
#include <boost/shared_ptr.hpp>
diff --git a/Framework/Algorithms/src/MaskBins.cpp b/Framework/Algorithms/src/MaskBins.cpp
index 47358a6f69b014f5270851122da89df4e6f17b28..3c0992086a7da82b4a9afd29028d3d287af94f55 100644
--- a/Framework/Algorithms/src/MaskBins.cpp
+++ b/Framework/Algorithms/src/MaskBins.cpp
@@ -2,12 +2,13 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/MaskBins.h"
-#include <limits>
-#include <sstream>
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include <limits>
+#include <sstream>
+
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/MaskBinsFromTable.cpp b/Framework/Algorithms/src/MaskBinsFromTable.cpp
index afae3bc3632b3890d2c22ca7c134ef4d3a13283f..9f3c80a35ee0dc4ab3370c52807f3464a0db8855 100644
--- a/Framework/Algorithms/src/MaskBinsFromTable.cpp
+++ b/Framework/Algorithms/src/MaskBinsFromTable.cpp
@@ -1,7 +1,7 @@
#include "MantidAlgorithms/MaskBinsFromTable.h"
#include "MantidKernel/System.h"
#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/TableRow.h"
#include "MantidKernel/ArrayProperty.h"
diff --git a/Framework/Algorithms/src/MaskDetectorsIf.cpp b/Framework/Algorithms/src/MaskDetectorsIf.cpp
index 209f7a9873e4ecf268d92c43d65b3c901946a116..803f1008d76317cb96a3fd17fc3ba4c193cf401d 100644
--- a/Framework/Algorithms/src/MaskDetectorsIf.cpp
+++ b/Framework/Algorithms/src/MaskDetectorsIf.cpp
@@ -3,10 +3,10 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/MaskDetectorsIf.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include <fstream>
#include "MantidKernel/ListValidator.h"
+#include <fstream>
+
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/Max.cpp b/Framework/Algorithms/src/Max.cpp
index 7546fcac717306d23c913dc0d9047dae82bff790..fba42c21fb13c5a991c5e792564faccf16a3af66 100644
--- a/Framework/Algorithms/src/Max.cpp
+++ b/Framework/Algorithms/src/Max.cpp
@@ -2,9 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Max.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/Progress.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/MaxMin.cpp b/Framework/Algorithms/src/MaxMin.cpp
index d6273ea22f5311bde5b5919a938a4692341b43e5..c4011d80b83eb22b4587736aee53c8a05081b4f7 100644
--- a/Framework/Algorithms/src/MaxMin.cpp
+++ b/Framework/Algorithms/src/MaxMin.cpp
@@ -2,9 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/MaxMin.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/Progress.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/MedianDetectorTest.cpp b/Framework/Algorithms/src/MedianDetectorTest.cpp
index 77aacd341507f67e1eb3e63aed54a1482291d817..c79c0eb1e07eb0923179fc162f93dc320b7223e2 100644
--- a/Framework/Algorithms/src/MedianDetectorTest.cpp
+++ b/Framework/Algorithms/src/MedianDetectorTest.cpp
@@ -1,6 +1,5 @@
#include "MantidAlgorithms/MedianDetectorTest.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/Exception.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/BoundedValidator.h"
#include <boost/math/special_functions/fpclassify.hpp>
diff --git a/Framework/Algorithms/src/Min.cpp b/Framework/Algorithms/src/Min.cpp
index 3a5308b3830f57c758d63fad0fcd83e4bcffdac7..9ef64db2439bff35c23ae087e21e5f88c3b2730e 100644
--- a/Framework/Algorithms/src/Min.cpp
+++ b/Framework/Algorithms/src/Min.cpp
@@ -2,9 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Min.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/Progress.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/ModeratorTzero.cpp b/Framework/Algorithms/src/ModeratorTzero.cpp
index 3363a67a67c6678cb115b142ad170536863f036f..91b979561b8520185f438b0a7f20898d60d681cc 100644
--- a/Framework/Algorithms/src/ModeratorTzero.cpp
+++ b/Framework/Algorithms/src/ModeratorTzero.cpp
@@ -2,14 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ModeratorTzero.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Workspace2D.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidGeometry/muParser_Silent.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidGeometry/muParser_Silent.h"
+
#include <boost/lexical_cast.hpp>
-#include "MantidDataObjects/EventList.h"
namespace Mantid {
namespace Algorithms {
@@ -35,8 +36,7 @@ void ModeratorTzero::setFormula(const std::string &formula) {
void ModeratorTzero::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("TOF");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("TOF");
declareProperty(new WorkspaceProperty<MatrixWorkspace>(
"InputWorkspace", "", Direction::Input, wsValidator),
"The name of the input workspace, containing events and/or "
diff --git a/Framework/Algorithms/src/ModeratorTzeroLinear.cpp b/Framework/Algorithms/src/ModeratorTzeroLinear.cpp
index e05fb167d709390118651e08c1601cad936ae1ef..8e2820e42e81c4f6804659a9d5caf3b79d196830 100644
--- a/Framework/Algorithms/src/ModeratorTzeroLinear.cpp
+++ b/Framework/Algorithms/src/ModeratorTzeroLinear.cpp
@@ -2,9 +2,9 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/ModeratorTzeroLinear.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Workspace2D.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/UnitFactory.h"
#include <boost/lexical_cast.hpp>
diff --git a/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp b/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp
index 6b04c6163b6b0eb648f952a3611da0105d343efd..5278427de9e61d573a00f6cdee0ed2b5462857e7 100644
--- a/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp
+++ b/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp
@@ -1,10 +1,7 @@
#include "MantidAlgorithms/MonitorEfficiencyCorUser.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/CompositeValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidGeometry/muParser_Silent.h"
#include "MantidKernel/MultiThreaded.h"
-#include <ctime>
namespace Mantid {
namespace Algorithms {
@@ -19,7 +16,8 @@ DECLARE_ALGORITHM(MonitorEfficiencyCorUser)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
-MonitorEfficiencyCorUser::MonitorEfficiencyCorUser() {}
+MonitorEfficiencyCorUser::MonitorEfficiencyCorUser()
+ : m_inputWS(), m_outputWS(), m_Ei(.0), m_monitorCounts(0) {}
//----------------------------------------------------------------------------------------------
/** Destructor
diff --git a/Framework/Algorithms/src/MonteCarloAbsorption.cpp b/Framework/Algorithms/src/MonteCarloAbsorption.cpp
index 0252a5bcd827c2cc9880b84ff1e4b3c1b0cbba3b..229285ea32c5d9657b1dc3698d050015afa5c314 100644
--- a/Framework/Algorithms/src/MonteCarloAbsorption.cpp
+++ b/Framework/Algorithms/src/MonteCarloAbsorption.cpp
@@ -2,13 +2,14 @@
// Includes
//------------------------------------------------------------------------------
#include "MantidAlgorithms/MonteCarloAbsorption.h"
-#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/SampleEnvironment.h"
+#include "MantidAPI/WorkspaceProperty.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/IDetector.h"
#include "MantidGeometry/Objects/Track.h"
#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/NeutronAtom.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/VectorHelper.h"
#include <boost/random/uniform_int.hpp>
diff --git a/Framework/Algorithms/src/MultipleScatteringCylinderAbsorption.cpp b/Framework/Algorithms/src/MultipleScatteringCylinderAbsorption.cpp
index 5008df1b96ebf2bd8e1614d101794a1e297f951d..89ba570077bdf3a054c899ad7a2ecadde78e8430 100644
--- a/Framework/Algorithms/src/MultipleScatteringCylinderAbsorption.cpp
+++ b/Framework/Algorithms/src/MultipleScatteringCylinderAbsorption.cpp
@@ -2,9 +2,8 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/MultipleScatteringCylinderAbsorption.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidKernel/Exception.h"
#include "MantidKernel/PhysicalConstants.h"
#include <stdexcept>
diff --git a/Framework/Algorithms/src/NormaliseByDetector.cpp b/Framework/Algorithms/src/NormaliseByDetector.cpp
index 97e2ee6a72ee2c4ce3bddd1cb8b9f1af6f8a61b9..b06f40a2629a20cc0e6ff65cb37e1ac333000a01 100644
--- a/Framework/Algorithms/src/NormaliseByDetector.cpp
+++ b/Framework/Algorithms/src/NormaliseByDetector.cpp
@@ -1,18 +1,18 @@
#include "MantidAlgorithms/NormaliseByDetector.h"
-#include "MantidKernel/System.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/IFunction.h"
#include "MantidAPI/FunctionDomain1D.h"
+#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/FunctionValues.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/Progress.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/IFunction.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
#include "MantidGeometry/Instrument/Component.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
#include "MantidGeometry/Instrument/FitParameter.h"
#include "MantidGeometry/muParser_Silent.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/UnitFactory.h"
using namespace Mantid::Kernel;
using namespace Mantid::API;
diff --git a/Framework/Algorithms/src/NormaliseToMonitor.cpp b/Framework/Algorithms/src/NormaliseToMonitor.cpp
index d870469b1b28ec7a149c662388c9c2b5a19582f4..f8592f395175e7cacce6eaa1900828a11475a4dc 100644
--- a/Framework/Algorithms/src/NormaliseToMonitor.cpp
+++ b/Framework/Algorithms/src/NormaliseToMonitor.cpp
@@ -2,17 +2,19 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/NormaliseToMonitor.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/RawCountValidator.h"
#include "MantidAPI/SpectraAxis.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
-#include "MantidKernel/VectorHelper.h"
+#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/VectorHelper.h"
#include <cfloat>
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidKernel/IPropertyManager.h"
+#include <numeric>
using namespace Mantid::DataObjects;
using Mantid::Kernel::IPropertyManager;
diff --git a/Framework/Algorithms/src/NormaliseToUnity.cpp b/Framework/Algorithms/src/NormaliseToUnity.cpp
index 97edb9ce4fd2b1833a050d350419f22894c0e0f0..eb23f1cd5f3957c1429bee36a38a8ac50ee7bf49 100644
--- a/Framework/Algorithms/src/NormaliseToUnity.cpp
+++ b/Framework/Algorithms/src/NormaliseToUnity.cpp
@@ -2,9 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/NormaliseToUnity.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/Progress.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/PDFFourierTransform.cpp b/Framework/Algorithms/src/PDFFourierTransform.cpp
index 41219d20557743ef17e89f324f9d373a48fc65cf..c535813ba1e16eb49cdb089c19f3a28d6dbf4c1e 100644
--- a/Framework/Algorithms/src/PDFFourierTransform.cpp
+++ b/Framework/Algorithms/src/PDFFourierTransform.cpp
@@ -1,6 +1,5 @@
#include "MantidAlgorithms/PDFFourierTransform.h"
-#include "MantidKernel/System.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/PhysicalConstants.h"
diff --git a/Framework/Algorithms/src/PointByPointVCorrection.cpp b/Framework/Algorithms/src/PointByPointVCorrection.cpp
index 6e001cfd900f4eaf4b31f68a7efac9aa6e57c44d..19bddb05cf7ace8ece1a461699194653f5970e58 100644
--- a/Framework/Algorithms/src/PointByPointVCorrection.cpp
+++ b/Framework/Algorithms/src/PointByPointVCorrection.cpp
@@ -3,9 +3,9 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/PointByPointVCorrection.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include <cfloat>
#include <cmath>
+#include <numeric>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/Q1D2.cpp b/Framework/Algorithms/src/Q1D2.cpp
index 78d913910c8e30a7bd7bd92c18ffff9d5a56914d..495d921058017d3549c8ac020d8ff4d9e06df281 100644
--- a/Framework/Algorithms/src/Q1D2.cpp
+++ b/Framework/Algorithms/src/Q1D2.cpp
@@ -2,16 +2,19 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Q1D2.h"
+#include "MantidAlgorithms/Qhelper.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/ISpectrum.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/Histogram1D.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Histogram1D.h"
-#include "MantidAlgorithms/Qhelper.h"
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidAPI/ISpectrum.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/Q1DWeighted.cpp b/Framework/Algorithms/src/Q1DWeighted.cpp
index daa445af929575b29064d677926b51b6809aef40..806211eb597b8216f7990a6479d90949cbd6e5e7 100644
--- a/Framework/Algorithms/src/Q1DWeighted.cpp
+++ b/Framework/Algorithms/src/Q1DWeighted.cpp
@@ -2,15 +2,17 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Q1DWeighted.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/Histogram1D.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Histogram1D.h"
-#include <vector>
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/Qhelper.cpp b/Framework/Algorithms/src/Qhelper.cpp
index f8fb50ce236bacab30b4a38c0d5092c714b9b282..aad22cc3df354532788b013f50bced1db5f0205d 100644
--- a/Framework/Algorithms/src/Qhelper.cpp
+++ b/Framework/Algorithms/src/Qhelper.cpp
@@ -2,13 +2,6 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Qhelper.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Histogram1D.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/Qxy.cpp b/Framework/Algorithms/src/Qxy.cpp
index d2609396a111e48832bc26e97db790e89d511937..b791d857ac10d6f6c45cc217d95f3feb626bfebd 100644
--- a/Framework/Algorithms/src/Qxy.cpp
+++ b/Framework/Algorithms/src/Qxy.cpp
@@ -4,10 +4,13 @@
#include "MantidAlgorithms/Qxy.h"
#include "MantidAlgorithms/Qhelper.h"
#include "MantidAPI/BinEdgeAxis.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidKernel/BoundedValidator.h"
#include <boost/math/special_functions/fpclassify.hpp>
namespace Mantid {
diff --git a/Framework/Algorithms/src/ReadGroupsFromFile.cpp b/Framework/Algorithms/src/ReadGroupsFromFile.cpp
index c355b8564e8dc78c40cccbfa5be5849ffc8299cd..fdfdf7844f95a19980f3b108f068962e7798a6d2 100644
--- a/Framework/Algorithms/src/ReadGroupsFromFile.cpp
+++ b/Framework/Algorithms/src/ReadGroupsFromFile.cpp
@@ -1,18 +1,14 @@
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
-#include <fstream>
-
#include "MantidAlgorithms/ReadGroupsFromFile.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/InstrumentDataService.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/Workspace2D.h"
-#include "MantidKernel/ConfigService.h"
#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/System.h"
// Poco XML Headers for Grouping File
#include <Poco/DOM/Document.h>
@@ -20,6 +16,8 @@
#include <Poco/DOM/Element.h>
#include <Poco/DOM/NodeList.h>
+#include <fstream>
+
using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
diff --git a/Framework/Algorithms/src/Rebin.cpp b/Framework/Algorithms/src/Rebin.cpp
index c1acf075fa22c0536aba77c1cd2d12d499b52fd0..678c303e3f1cd727b9fa5eca42004f28725cd96b 100644
--- a/Framework/Algorithms/src/Rebin.cpp
+++ b/Framework/Algorithms/src/Rebin.cpp
@@ -3,15 +3,11 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/Rebin.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/VisibleWhenProperty.h"
-
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
+#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/RebinParamsValidator.h"
+#include "MantidKernel/VectorHelper.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/ReflectometryReductionOne.cpp b/Framework/Algorithms/src/ReflectometryReductionOne.cpp
index 430b9bf0c34bd19130093c35b65752f6773f0d17..4cd3d8f4e0c6db52a5be356d80c44a3e39320f29 100644
--- a/Framework/Algorithms/src/ReflectometryReductionOne.cpp
+++ b/Framework/Algorithms/src/ReflectometryReductionOne.cpp
@@ -1,12 +1,11 @@
#include "MantidAlgorithms/ReflectometryReductionOne.h"
-#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/EnabledWhenProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
#include <boost/make_shared.hpp>
#include <boost/assign/list_of.hpp>
diff --git a/Framework/Algorithms/src/ReflectometryReductionOneAuto.cpp b/Framework/Algorithms/src/ReflectometryReductionOneAuto.cpp
index fcd4c481b612503e401b7d0f1d7ba2ec32581097..9f1ccdc743b5dff2c71919c6cbd687805997abf2 100644
--- a/Framework/Algorithms/src/ReflectometryReductionOneAuto.cpp
+++ b/Framework/Algorithms/src/ReflectometryReductionOneAuto.cpp
@@ -1,9 +1,9 @@
#include "MantidAlgorithms/ReflectometryReductionOneAuto.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ListValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/EnabledWhenProperty.h"
+#include "MantidKernel/ListValidator.h"
#include "MantidKernel/RebinParamsValidator.h"
#include <boost/optional.hpp>
#include <boost/assign/list_of.hpp>
@@ -110,9 +110,8 @@ void ReflectometryReductionOneAuto::init() {
"I0 monitor workspace index");
declareProperty(new PropertyWithValue<std::string>("ProcessingInstructions",
"", Direction::Input),
- "Processing commands to select and add spectrum to make a "
- "detector workspace. See [[PeformIndexOperations]] for "
- "syntax.");
+ "Grouping pattern of workspace indices to yield only the"
+ " detectors of interest. See GroupDetectors for syntax.");
declareProperty("WavelengthMin", Mantid::EMPTY_DBL(),
"Wavelength Min in angstroms", Direction::Input);
declareProperty("WavelengthMax", Mantid::EMPTY_DBL(),
diff --git a/Framework/Algorithms/src/ReflectometryWorkflowBase.cpp b/Framework/Algorithms/src/ReflectometryWorkflowBase.cpp
index 38522663a8796941adaa4650ccfff4bf01f2df63..94bb19678628d45155eabc132cbe78404505d4bd 100644
--- a/Framework/Algorithms/src/ReflectometryWorkflowBase.cpp
+++ b/Framework/Algorithms/src/ReflectometryWorkflowBase.cpp
@@ -1,9 +1,10 @@
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/MandatoryValidator.h"
+#include "MantidAlgorithms/ReflectometryWorkflowBase.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/BoundedValidator.h"
-#include "MantidAlgorithms/ReflectometryWorkflowBase.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/MandatoryValidator.h"
+#include "MantidKernel/RebinParamsValidator.h"
#include <boost/assign/list_of.hpp>
diff --git a/Framework/Algorithms/src/Regroup.cpp b/Framework/Algorithms/src/Regroup.cpp
index b3997f78f68c2899f31e85d3f23a45da697091dc..4abbbff1d039d7f1c053344fd272e4376f712315 100644
--- a/Framework/Algorithms/src/Regroup.cpp
+++ b/Framework/Algorithms/src/Regroup.cpp
@@ -2,11 +2,12 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Regroup.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/RebinParamsValidator.h"
-#include <sstream>
#include <numeric>
#include <algorithm>
#include <functional>
diff --git a/Framework/Algorithms/src/RemoveBackground.cpp b/Framework/Algorithms/src/RemoveBackground.cpp
index 76e10a78de8a04f7bae2ebe5ae3ec52c7f9aff19..c958ccedccdba37732122f297b3ac1c6255a2968 100644
--- a/Framework/Algorithms/src/RemoveBackground.cpp
+++ b/Framework/Algorithms/src/RemoveBackground.cpp
@@ -3,16 +3,18 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/RemoveBackground.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/EventList.h"
+#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/VectorHelper.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/RebinParamsValidator.h"
+#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/VisibleWhenProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidDataObjects/EventList.h"
-
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/RemoveBins.cpp b/Framework/Algorithms/src/RemoveBins.cpp
index 48b633d5abc8382b5561401feb1ccb754ec5452b..9e8f74ede8b0fa0731859b299e06ab29430fe2df 100644
--- a/Framework/Algorithms/src/RemoveBins.cpp
+++ b/Framework/Algorithms/src/RemoveBins.cpp
@@ -2,11 +2,13 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/RemoveBins.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/MandatoryValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/MandatoryValidator.h"
+#include "MantidKernel/UnitFactory.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/RemoveLowResTOF.cpp b/Framework/Algorithms/src/RemoveLowResTOF.cpp
index 621db894fb1fd07f891f55f06bcdeedf848e6ff4..47c65f788a2dcedd00454e6deedd04158edf912f 100644
--- a/Framework/Algorithms/src/RemoveLowResTOF.cpp
+++ b/Framework/Algorithms/src/RemoveLowResTOF.cpp
@@ -1,8 +1,11 @@
-#include "MantidAlgorithms/AlignDetectors.h"
#include "MantidAlgorithms/RemoveLowResTOF.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/UnitFactory.h"
#include <limits>
diff --git a/Framework/Algorithms/src/RemovePromptPulse.cpp b/Framework/Algorithms/src/RemovePromptPulse.cpp
index ceaecb85d4746b238478623d474eab6efed925c3..ae43e1db8dbe835485aa5c68b3b806afb63fd5b4 100644
--- a/Framework/Algorithms/src/RemovePromptPulse.cpp
+++ b/Framework/Algorithms/src/RemovePromptPulse.cpp
@@ -1,9 +1,8 @@
#include "MantidAlgorithms/RemovePromptPulse.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidKernel/System.h"
-#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/TimeSeriesProperty.h"
using std::string;
namespace Mantid {
@@ -72,7 +71,7 @@ void getTofRange(MatrixWorkspace_const_sptr wksp, double &tmin, double &tmax) {
DataObjects::EventWorkspace_const_sptr eventWksp =
boost::dynamic_pointer_cast<const DataObjects::EventWorkspace>(wksp);
- bool isEvent = false;
+ const bool isEvent = false;
if (isEvent) {
eventWksp->getEventXMinMax(tmin, tmax);
} else {
diff --git a/Framework/Algorithms/src/ResampleX.cpp b/Framework/Algorithms/src/ResampleX.cpp
index c8386e5d6f7f132218aa7d9168f3f42864788c4d..78f2267942ebe3790e4ab791a99014d348b07654 100644
--- a/Framework/Algorithms/src/ResampleX.cpp
+++ b/Framework/Algorithms/src/ResampleX.cpp
@@ -1,11 +1,11 @@
-#include <sstream>
#include "MantidAlgorithms/ResampleX.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/VectorHelper.h"
+#include <sstream>
+
namespace Mantid {
namespace Algorithms {
using namespace API;
diff --git a/Framework/Algorithms/src/SANSDirectBeamScaling.cpp b/Framework/Algorithms/src/SANSDirectBeamScaling.cpp
index f603aaed91cd7ed1293125ae4dbe3e8ff5713713..1ae0064a116eb8db2c871ee87dadfd1c1ad68cdd 100644
--- a/Framework/Algorithms/src/SANSDirectBeamScaling.cpp
+++ b/Framework/Algorithms/src/SANSDirectBeamScaling.cpp
@@ -2,15 +2,16 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/SANSDirectBeamScaling.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/Histogram1D.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/VectorHelper.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/Histogram1D.h"
-#include <vector>
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SampleCorrections/MayersSampleCorrection.cpp b/Framework/Algorithms/src/SampleCorrections/MayersSampleCorrection.cpp
index a849986bdc52fb2d29c473ef6a9088feed22e869..071b81d604bafcf800a4cd353e4bb2c00a84297c 100644
--- a/Framework/Algorithms/src/SampleCorrections/MayersSampleCorrection.cpp
+++ b/Framework/Algorithms/src/SampleCorrections/MayersSampleCorrection.cpp
@@ -3,9 +3,9 @@
//------------------------------------------------------------------------------
#include "MantidAlgorithms/SampleCorrections/MayersSampleCorrection.h"
#include "MantidAlgorithms/SampleCorrections/MayersSampleCorrectionStrategy.h"
-#include "MantidAPI/Progress.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/SampleValidator.h"
#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidKernel/CompositeValidator.h"
diff --git a/Framework/Algorithms/src/SetInstrumentParameter.cpp b/Framework/Algorithms/src/SetInstrumentParameter.cpp
index e06d9b1f72eb441cf90572f88ff4e4551f7db4a2..63a006dedbee290d5530be631171b8a8d01aae8c 100644
--- a/Framework/Algorithms/src/SetInstrumentParameter.cpp
+++ b/Framework/Algorithms/src/SetInstrumentParameter.cpp
@@ -1,10 +1,10 @@
#include "MantidAlgorithms/SetInstrumentParameter.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidGeometry/Instrument.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/Strings.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidGeometry/Instrument.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SmoothNeighbours.cpp b/Framework/Algorithms/src/SmoothNeighbours.cpp
index ad39fb1d85c8c6b396edca2267188b3f0ff4f828..ef6a97273b595673dbf46a1c111856a2c73b887d 100644
--- a/Framework/Algorithms/src/SmoothNeighbours.cpp
+++ b/Framework/Algorithms/src/SmoothNeighbours.cpp
@@ -1,5 +1,5 @@
#include "MantidAlgorithms/SmoothNeighbours.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
@@ -8,11 +8,12 @@
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
+#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
+#include "MantidKernel/ListValidator.h"
+
#include <boost/algorithm/string.hpp>
#include <boost/regex.hpp>
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/ListValidator.h"
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
diff --git a/Framework/Algorithms/src/SofQW.cpp b/Framework/Algorithms/src/SofQW.cpp
index 8c6480f1954dfbe560ce3fab319cda5af791acbd..e56ce439f3a85ca4ced59d16ae7d9fd0ef11aa0d 100644
--- a/Framework/Algorithms/src/SofQW.cpp
+++ b/Framework/Algorithms/src/SofQW.cpp
@@ -4,17 +4,22 @@
#include <stdexcept>
#include "MantidAlgorithms/SofQW.h"
-#include "MantidDataObjects/Histogram1D.h"
#include "MantidAPI/BinEdgeAxis.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/SpectrumDetectorMapping.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/Histogram1D.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
+#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/RebinParamsValidator.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/VectorHelper.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SofQWCentre.cpp b/Framework/Algorithms/src/SofQWCentre.cpp
index d6763d7a59eaa9639a97f3eb6420ee91c4f86812..34c28e07a785dd55c560fc2412dbdd80fbf5208b 100644
--- a/Framework/Algorithms/src/SofQWCentre.cpp
+++ b/Framework/Algorithms/src/SofQWCentre.cpp
@@ -1,20 +1,26 @@
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
-#include <stdexcept>
-
#include "MantidAlgorithms/SofQWCentre.h"
#include "MantidDataObjects/Histogram1D.h"
#include "MantidAPI/BinEdgeAxis.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/SpectraAxisValidator.h"
#include "MantidAPI/SpectrumDetectorMapping.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
-#include "MantidKernel/VectorHelper.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
+#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/RebinParamsValidator.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/VectorHelper.h"
+
+#include <numeric>
+#include <stdexcept>
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SolidAngle.cpp b/Framework/Algorithms/src/SolidAngle.cpp
index 43b76ee1ee8f49476722d268e6d5b66e4a705ed5..b1d092b70bab0ec7f549ca54fa2b3af6d9c040a3 100644
--- a/Framework/Algorithms/src/SolidAngle.cpp
+++ b/Framework/Algorithms/src/SolidAngle.cpp
@@ -2,11 +2,11 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/SolidAngle.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/AlgorithmFactory.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/UnitFactory.h"
+
#include <cfloat>
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SortEvents.cpp b/Framework/Algorithms/src/SortEvents.cpp
index fef7295a185d1c2c80208dbb24a81fcdce4e4d00..77b619f5a277e119f59bec706dda1d063faf21e9 100644
--- a/Framework/Algorithms/src/SortEvents.cpp
+++ b/Framework/Algorithms/src/SortEvents.cpp
@@ -2,7 +2,6 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/SortEvents.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/ListValidator.h"
diff --git a/Framework/Algorithms/src/SpecularReflectionPositionCorrect.cpp b/Framework/Algorithms/src/SpecularReflectionPositionCorrect.cpp
index 3497a23d437b317b942c9f2da90897a1a40f95f5..bf1dc7ae29423ab0ccef331b3deca16b4f3367b5 100644
--- a/Framework/Algorithms/src/SpecularReflectionPositionCorrect.cpp
+++ b/Framework/Algorithms/src/SpecularReflectionPositionCorrect.cpp
@@ -1,12 +1,10 @@
#include "MantidAlgorithms/SpecularReflectionPositionCorrect.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidGeometry/Instrument/ComponentHelper.h"
+#include "MantidGeometry/Instrument/DetectorGroup.h"
+#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MandatoryValidator.h"
-#include "MantidGeometry/Instrument/DetectorGroup.h"
-#include "MantidGeometry/Instrument/ReferenceFrame.h"
-#include "MantidGeometry/Instrument/ComponentHelper.h"
-#include <boost/make_shared.hpp>
using namespace Mantid::API;
using namespace Mantid::Geometry;
diff --git a/Framework/Algorithms/src/SphericalAbsorption.cpp b/Framework/Algorithms/src/SphericalAbsorption.cpp
index 9449eb51b422f88ac99edf0969c46e844da18d9b..73fd77e14af619b155f3a136cd1755cd36b66307 100644
--- a/Framework/Algorithms/src/SphericalAbsorption.cpp
+++ b/Framework/Algorithms/src/SphericalAbsorption.cpp
@@ -2,14 +2,16 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/SphericalAbsorption.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidGeometry/Objects/ShapeFactory.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/Fast_Exponential.h"
-#include "MantidKernel/VectorHelper.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
+#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/Fast_Exponential.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/VectorHelper.h"
using namespace Mantid::PhysicalConstants;
diff --git a/Framework/Algorithms/src/Stitch1D.cpp b/Framework/Algorithms/src/Stitch1D.cpp
index 813bfdb825de1e19bbd158d85666eb04843e10a3..6ee41612d24897405c9e5928f9038edfd67fc6d5 100644
--- a/Framework/Algorithms/src/Stitch1D.cpp
+++ b/Framework/Algorithms/src/Stitch1D.cpp
@@ -1,19 +1,17 @@
#include "MantidAlgorithms/Stitch1D.h"
#include "MantidAPI/WorkspaceProperty.h"
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/PropertyWithValue.h"
#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/MultiThreaded.h"
#include "MantidKernel/BoundedValidator.h"
-#include <boost/make_shared.hpp>
#include <boost/tuple/tuple.hpp>
#include <boost/format.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/math/special_functions.hpp>
-#include <vector>
#include <algorithm>
using namespace Mantid::Kernel;
diff --git a/Framework/Algorithms/src/Stitch1DMany.cpp b/Framework/Algorithms/src/Stitch1DMany.cpp
index 8611b757ee9372acc8d756c7727534fc5312364a..da43501fa7b14433aa4c573525dd0a9656726c54 100644
--- a/Framework/Algorithms/src/Stitch1DMany.cpp
+++ b/Framework/Algorithms/src/Stitch1DMany.cpp
@@ -1,11 +1,9 @@
#include "MantidAlgorithms/Stitch1DMany.h"
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/WorkspaceProperty.h"
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceProperty.h"
#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/RebinParamsValidator.h"
#include <boost/make_shared.hpp>
diff --git a/Framework/Algorithms/src/StripVanadiumPeaks.cpp b/Framework/Algorithms/src/StripVanadiumPeaks.cpp
index a50de4c62c0e6fb950dd1969e43b69944d38a9fb..491687e7948474a92a65822acc7f9722abe98c79 100644
--- a/Framework/Algorithms/src/StripVanadiumPeaks.cpp
+++ b/Framework/Algorithms/src/StripVanadiumPeaks.cpp
@@ -1,10 +1,9 @@
#include "MantidAlgorithms/StripVanadiumPeaks.h"
-#include "MantidKernel/PhysicalConstants.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/TableRow.h"
-#include "MantidKernel/VectorHelper.h"
+#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/VectorHelper.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SumNeighbours.cpp b/Framework/Algorithms/src/SumNeighbours.cpp
index dcdb670b48c38eb86bf590ba2691095f4af6d23e..f029f7fa5714f5c359dccf703c146416eebdb92b 100644
--- a/Framework/Algorithms/src/SumNeighbours.cpp
+++ b/Framework/Algorithms/src/SumNeighbours.cpp
@@ -2,15 +2,16 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/SumNeighbours.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/ICompAssembly.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include <boost/algorithm/string.hpp>
#include "MantidKernel/BoundedValidator.h"
+#include <boost/algorithm/string.hpp>
+
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/SumSpectra.cpp b/Framework/Algorithms/src/SumSpectra.cpp
index 7388ab59c7f2e88fa2bee3e86cdbc770f386f2ba..612141dab3fa7cc3a3bfe4e75dded4cb76441bbf 100644
--- a/Framework/Algorithms/src/SumSpectra.cpp
+++ b/Framework/Algorithms/src/SumSpectra.cpp
@@ -2,10 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/SumSpectra.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidDataObjects/RebinnedOutput.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
-#include "MantidDataObjects/RebinnedOutput.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/TOFSANSResolution.cpp b/Framework/Algorithms/src/TOFSANSResolution.cpp
index 342c6719e5e37dcd02738da33a7841cd53d8dfdd..18cb26fd59f926325adfc7c879ffc1c25baf1b25 100644
--- a/Framework/Algorithms/src/TOFSANSResolution.cpp
+++ b/Framework/Algorithms/src/TOFSANSResolution.cpp
@@ -2,16 +2,16 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/TOFSANSResolution.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventList.h"
+#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
-#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/VectorHelper.h"
#include "boost/math/special_functions/fpclassify.hpp"
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
@@ -34,8 +34,7 @@ void TOFSANSResolution::init() {
boost::make_shared<WorkspaceUnitValidator>("MomentumTransfer")),
"Name the workspace to calculate the resolution for");
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("Wavelength");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("Wavelength");
declareProperty(new WorkspaceProperty<>("ReducedWorkspace", "",
Direction::Input, wsValidator),
"I(Q) workspace");
diff --git a/Framework/Algorithms/src/TOFSANSResolutionByPixel.cpp b/Framework/Algorithms/src/TOFSANSResolutionByPixel.cpp
index d405f9179ba1c08486d26d4a218ecf6c61762f2c..51071266677504efc8e7763dd1bc05b4d44b00c2 100644
--- a/Framework/Algorithms/src/TOFSANSResolutionByPixel.cpp
+++ b/Framework/Algorithms/src/TOFSANSResolutionByPixel.cpp
@@ -2,12 +2,10 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/TOFSANSResolutionByPixel.h"
+#include "MantidAlgorithms/GravitySANSHelper.h"
#include "MantidAlgorithms/TOFSANSResolutionByPixelCalculator.h"
#include "MantidAlgorithms/SANSCollimationLengthEstimator.h"
-#include "MantidAlgorithms/GravitySANSHelper.h"
-#include "MantidAlgorithms/CloneWorkspace.h"
-#include "MantidAlgorithms/RebinToWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
diff --git a/Framework/Algorithms/src/Transpose.cpp b/Framework/Algorithms/src/Transpose.cpp
index af9019a8b8a3a8dde651495e86b89e786cfb8f26..194f41ee9e0f85dfb35137b00fd02de8eb264966 100644
--- a/Framework/Algorithms/src/Transpose.cpp
+++ b/Framework/Algorithms/src/Transpose.cpp
@@ -3,8 +3,8 @@
//----------------------------------------------------------------------
#include "MantidAlgorithms/Transpose.h"
#include "MantidAPI/BinEdgeAxis.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/NumericAxis.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/RebinnedOutput.h"
namespace Mantid {
diff --git a/Framework/Algorithms/src/UnwrapMonitor.cpp b/Framework/Algorithms/src/UnwrapMonitor.cpp
index df3d8df8104a2f16cb93ebb85d2263a742d9716b..59f85033b655d16ef9701a79348e9725cbaa0bc2 100644
--- a/Framework/Algorithms/src/UnwrapMonitor.cpp
+++ b/Framework/Algorithms/src/UnwrapMonitor.cpp
@@ -2,10 +2,14 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/UnwrapMonitor.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/PhysicalConstants.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/UnitFactory.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/src/UnwrapSNS.cpp b/Framework/Algorithms/src/UnwrapSNS.cpp
index eac769d4381f6a6f460f32a373cc4c33d1d808f2..0c9a7eb777777fa8d7519ea6f15dc8c119f43bb0 100644
--- a/Framework/Algorithms/src/UnwrapSNS.cpp
+++ b/Framework/Algorithms/src/UnwrapSNS.cpp
@@ -2,12 +2,17 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/UnwrapSNS.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventList.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/UnitFactory.h"
+
#include <limits>
-#include "MantidKernel/BoundedValidator.h"
namespace Mantid {
namespace Algorithms {
diff --git a/Framework/Algorithms/test/GetAllEiTest.h b/Framework/Algorithms/test/GetAllEiTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..9dfadd5311c1761101143bc1832f02b64436d75e
--- /dev/null
+++ b/Framework/Algorithms/test/GetAllEiTest.h
@@ -0,0 +1,584 @@
+#ifndef GETALLEI_TEST_H_
+#define GETALLEI_TEST_H_
+
+#include <memory>
+#include <boost/math/special_functions/fpclassify.hpp>
+#include <cxxtest/TestSuite.h>
+#include "MantidAlgorithms/GetAllEi.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidTestHelpers/WorkspaceCreationHelper.h"
+
+using namespace Mantid;
+using namespace Mantid::Algorithms;
+using namespace Mantid::API;
+
+class GetAllEiTester : public GetAllEi {
+public:
+ void find_chop_speed_and_delay(const API::MatrixWorkspace_sptr &inputWS,
+ double &chop_speed, double &chop_delay) {
+ GetAllEi::findChopSpeedAndDelay(inputWS, chop_speed, chop_delay);
+ }
+ void findGuessOpeningTimes(const std::pair<double, double> &TOF_range,
+ double ChopDelay, double Period,
+ std::vector<double> &guess_opening_times) {
+ GetAllEi::findGuessOpeningTimes(TOF_range, ChopDelay, Period,
+ guess_opening_times);
+ }
+ bool filterLogProvided() const { return (m_pFilterLog != NULL); }
+ double getAvrgLogValue(const API::MatrixWorkspace_sptr &inputWS,
+ const std::string &propertyName) {
+ std::vector<Kernel::SplittingInterval> splitter;
+ return GetAllEi::getAvrgLogValue(inputWS, propertyName, splitter);
+ }
+ API::MatrixWorkspace_sptr
+ buildWorkspaceToFit(const API::MatrixWorkspace_sptr &inputWS,
+ size_t &wsIndex0) {
+ return GetAllEi::buildWorkspaceToFit(inputWS, wsIndex0);
+ }
+ void findBinRanges(const MantidVec &eBins, const MantidVec &signal,
+ const std::vector<double> &guess_energies,
+ double Eresolution, std::vector<size_t> &irangeMin,
+ std::vector<size_t> &irangeMax,
+ std::vector<bool> &guessValid) {
+ GetAllEi::findBinRanges(eBins, signal, guess_energies, Eresolution,
+ irangeMin, irangeMax, guessValid);
+ }
+ void setResolution(double newResolution) {
+ this->m_max_Eresolution = newResolution;
+ }
+ size_t calcDerivativeAndCountZeros(const std::vector<double> &bins,
+ const std::vector<double> &signal,
+ std::vector<double> &deriv,
+ std::vector<double> &zeros) {
+ return GetAllEi::calcDerivativeAndCountZeros(bins, signal, deriv, zeros);
+ }
+};
+
+class GetAllEiTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static GetAllEiTest *createSuite() { return new GetAllEiTest(); }
+ static void destroySuite(GetAllEiTest *suite) { delete suite; }
+
+ GetAllEiTest() {}
+
+public:
+ void testName() { TS_ASSERT_EQUALS(m_getAllEi.name(), "GetAllEi"); }
+
+ void testVersion() { TS_ASSERT_EQUALS(m_getAllEi.version(), 1); }
+
+ void testInit() {
+ TS_ASSERT_THROWS_NOTHING(m_getAllEi.initialize());
+ TS_ASSERT(m_getAllEi.isInitialized());
+ }
+ //
+ void test_validators_work() {
+
+ MatrixWorkspace_sptr ws = this->createTestingWS(true);
+
+ m_getAllEi.initialize();
+ m_getAllEi.setProperty("Workspace", ws);
+ m_getAllEi.setProperty("OutputWorkspace", "monitor_peaks");
+ TSM_ASSERT_THROWS(
+ "should throw runtime error on as spectra ID should be positive",
+ m_getAllEi.setProperty("Monitor1SpecID", -1), std::invalid_argument);
+
+ m_getAllEi.setProperty("Monitor1SpecID", 1);
+ m_getAllEi.setProperty("Monitor2SpecID", 2);
+ m_getAllEi.setProperty("ChopperSpeedLog", "Chopper_Speed");
+ m_getAllEi.setProperty("ChopperDelayLog", "Chopper_Delay");
+ m_getAllEi.setProperty("FilterBaseLog", "proton_charge");
+ m_getAllEi.setProperty("FilterWithDerivative", false);
+
+ TSM_ASSERT_THROWS("should throw runtime error on validation as no "
+ "appropriate logs are defined",
+ m_getAllEi.execute(), std::runtime_error);
+ auto log_messages = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("Two logs should fail", log_messages.size(), 2);
+ // add invalid property type
+ ws->mutableRun().addLogData(
+ new Kernel::PropertyWithValue<double>("Chopper_Speed", 10.));
+ auto log_messages2 = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("Two logs should fail", log_messages2.size(), 2);
+
+ TSM_ASSERT_DIFFERS("should fail for different reason ",
+ log_messages["ChopperSpeedLog"],
+ log_messages2["ChopperSpeedLog"]);
+ // add correct property type:
+ ws->mutableRun().clearLogs();
+ ws->mutableRun().addLogData(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Speed"));
+ log_messages = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("One log should fail", log_messages.size(), 1);
+ TSM_ASSERT("Filter log is not provided ", !m_getAllEi.filterLogProvided());
+ ws->mutableRun().addLogData(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Delay"));
+ ws->mutableRun().addLogData(
+ new Kernel::TimeSeriesProperty<double>("proton_charge"));
+ log_messages = m_getAllEi.validateInputs();
+
+ TSM_ASSERT_EQUALS("All logs are defined", log_messages.size(), 0);
+ TSM_ASSERT("Filter log is provided ", m_getAllEi.filterLogProvided());
+
+ m_getAllEi.setProperty("Monitor1SpecID", 3);
+ log_messages = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("Workspace should not have spectra with ID=3",
+ log_messages.size(), 1);
+ }
+ //
+ void test_get_chopper_speed() {
+
+ MatrixWorkspace_sptr ws = this->createTestingWS(true);
+
+ m_getAllEi.initialize();
+ m_getAllEi.setProperty("Workspace", ws);
+ m_getAllEi.setProperty("OutputWorkspace", "monitor_peaks");
+ m_getAllEi.setProperty("Monitor1SpecID", 1);
+ m_getAllEi.setProperty("Monitor2SpecID", 2);
+ m_getAllEi.setProperty("ChopperSpeedLog", "Chopper_Speed");
+ m_getAllEi.setProperty("ChopperDelayLog", "Chopper_Delay");
+ m_getAllEi.setProperty("FilterBaseLog", "proton_charge");
+ m_getAllEi.setProperty("FilterWithDerivative", false);
+
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> chopSpeed(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Speed"));
+ for (int i = 0; i < 10; i++) {
+ chopSpeed->addValue(Kernel::DateAndTime(10000 + 10 * i, 0), 1.);
+ }
+ for (int i = 0; i < 10; i++) {
+ chopSpeed->addValue(Kernel::DateAndTime(100 + 10 * i, 0), 10.);
+ }
+ for (int i = 0; i < 10; i++) {
+ chopSpeed->addValue(Kernel::DateAndTime(10 * i, 0), 100.);
+ }
+ ws->mutableRun().addLogData(chopSpeed.release());
+
+ // Test sort log by run time.
+ TSM_ASSERT_THROWS(
+ "Attempt to get log without start/stop time set should fail",
+ m_getAllEi.getAvrgLogValue(ws, "ChopperSpeedLog"), std::runtime_error);
+
+ ws->mutableRun().setStartAndEndTime(Kernel::DateAndTime(90, 0),
+ Kernel::DateAndTime(10000, 0));
+ double val = m_getAllEi.getAvrgLogValue(ws, "ChopperSpeedLog");
+ TS_ASSERT_DELTA(val, (10 * 10 + 100.) / 11., 1.e-6);
+
+ ws->mutableRun().setStartAndEndTime(Kernel::DateAndTime(100, 0),
+ Kernel::DateAndTime(10000, 0));
+ val = m_getAllEi.getAvrgLogValue(ws, "ChopperSpeedLog");
+ TS_ASSERT_DELTA(val, 10., 1.e-6);
+
+ // Test sort log by log.
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> chopDelay(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Delay"));
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> goodFram(
+ new Kernel::TimeSeriesProperty<double>("proton_charge"));
+
+ for (int i = 0; i < 10; i++) {
+ auto time = Kernel::DateAndTime(200 + 10 * i, 0);
+ chopDelay->addValue(time, 10.);
+ if (i < 2) {
+ goodFram->addValue(time, 1);
+ } else {
+ goodFram->addValue(time, 0);
+ }
+ }
+ for (int i = 0; i < 10; i++) {
+ auto time = Kernel::DateAndTime(100 + 10 * i, 0);
+ chopDelay->addValue(time, 0.1);
+ goodFram->addValue(time, 1);
+ }
+ for (int i = 0; i < 10; i++) {
+ auto time = Kernel::DateAndTime(10 * i, 0);
+ chopDelay->addValue(time, 1.);
+ goodFram->addValue(time, 0);
+ }
+ ws->mutableRun().addLogData(chopDelay.release());
+ ws->mutableRun().addLogData(goodFram.release());
+
+ // Run validate as this will set up property, which indicates filter log
+ // presence
+ auto errors = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("All logs are defined now", errors.size(), 0);
+
+ double chop_speed, chop_delay;
+ m_getAllEi.find_chop_speed_and_delay(ws, chop_speed, chop_delay);
+ TSM_ASSERT_DELTA("Chopper delay should have special speed ",
+ (10 * 0.1 + 20) / 12., chop_delay, 1.e-6);
+
+ goodFram.reset(new Kernel::TimeSeriesProperty<double>("proton_charge"));
+ for (int i = 0; i < 10; i++) {
+ auto time = Kernel::DateAndTime(100 + 10 * i, 0);
+ goodFram->addValue(time, 1);
+ }
+
+ ws->mutableRun().addProperty(goodFram.release(), true);
+ errors = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("All logs are defined now", errors.size(), 0);
+
+ m_getAllEi.find_chop_speed_and_delay(ws, chop_speed, chop_delay);
+ TSM_ASSERT_DELTA("Chopper delay should have special speed", 0.1, chop_delay,
+ 1.e-6);
+ }
+ void test_get_chopper_speed_filter_derivative() {
+
+ MatrixWorkspace_sptr ws = this->createTestingWS(true);
+
+ m_getAllEi.initialize();
+ m_getAllEi.setProperty("Workspace", ws);
+ m_getAllEi.setProperty("OutputWorkspace", "monitor_peaks");
+ m_getAllEi.setProperty("Monitor1SpecID", 1);
+ m_getAllEi.setProperty("Monitor2SpecID", 2);
+ m_getAllEi.setProperty("ChopperSpeedLog", "Chopper_Speed");
+ m_getAllEi.setProperty("ChopperDelayLog", "Chopper_Delay");
+ m_getAllEi.setProperty("FilterBaseLog", "proton_charge");
+ m_getAllEi.setProperty("FilterWithDerivative", true);
+
+ // Test select log by log derivative
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> chopDelay(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Delay"));
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> chopSpeed(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Speed"));
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> protCharge(
+ new Kernel::TimeSeriesProperty<double>("proton_charge"));
+
+ double gf(0);
+ for (int i = 0; i < 50; i++) {
+ auto time = Kernel::DateAndTime(10 * i, 0);
+ if (i > 10 && i < 20) {
+ chopDelay->addValue(time, 100.);
+ chopSpeed->addValue(time, 0.);
+ protCharge->addValue(time, gf);
+ } else {
+ chopDelay->addValue(time, 10.);
+ chopSpeed->addValue(time, 50.);
+ protCharge->addValue(time, gf);
+ gf++;
+ }
+ }
+ ws->mutableRun().addLogData(chopSpeed.release());
+ ws->mutableRun().addLogData(chopDelay.release());
+ ws->mutableRun().addLogData(protCharge.release());
+
+ // Run validate as this will set up property, which indicates filter log
+ // presence
+ auto errors = m_getAllEi.validateInputs();
+ TSM_ASSERT_EQUALS("All logs are defined now", errors.size(), 0);
+
+ double chop_speed, chop_delay;
+ m_getAllEi.find_chop_speed_and_delay(ws, chop_speed, chop_delay);
+ TSM_ASSERT_DELTA("Chopper delay should have defined value ", 10.,
+ chop_delay, 1.e-6);
+ TSM_ASSERT_DELTA("Chopper speed should have defined speed", 50., chop_speed,
+ 1.e-6);
+ }
+
+ void test_guess_opening_times() {
+
+ std::pair<double, double> TOF_range(5, 100);
+ double t0(6), Period(10);
+ std::vector<double> guess_tof;
+ m_getAllEi.findGuessOpeningTimes(TOF_range, t0, Period, guess_tof);
+ TSM_ASSERT_EQUALS("should have 10 periods within the specified interval",
+ guess_tof.size(), 10);
+
+ guess_tof.resize(0);
+ t0 = TOF_range.first;
+ m_getAllEi.findGuessOpeningTimes(TOF_range, t0, Period, guess_tof);
+ TSM_ASSERT_EQUALS(
+ "Still should be 10 periods within the specified interval",
+ guess_tof.size(), 10);
+
+ t0 = TOF_range.second;
+ TSM_ASSERT_THROWS(
+ "Should throw out of range",
+ m_getAllEi.findGuessOpeningTimes(TOF_range, t0, Period, guess_tof),
+ std::runtime_error);
+
+ t0 = 1;
+ guess_tof.resize(0);
+ m_getAllEi.findGuessOpeningTimes(TOF_range, t0, Period, guess_tof);
+ TSM_ASSERT_EQUALS(" should be 9 periods within the specified interval",
+ guess_tof.size(), 9);
+
+ guess_tof.resize(0);
+ t0 = 21;
+ TOF_range.first = 20;
+ m_getAllEi.findGuessOpeningTimes(TOF_range, t0, Period, guess_tof);
+ TSM_ASSERT_EQUALS(" should be 8 periods within the specified interval",
+ guess_tof.size(), 8);
+ }
+ //
+ void test_internalWS_to_fit() {
+ Mantid::DataObjects::Workspace2D_sptr tws =
+ WorkspaceCreationHelper::create2DWorkspaceWithFullInstrument(5, 100,
+ true);
+ auto det1 = tws->getDetector(0);
+ auto det2 = tws->getDetector(4);
+ auto spec1 = tws->getSpectrum(0);
+ auto spec2 = tws->getSpectrum(4);
+ auto detID1 = spec1->getDetectorIDs();
+ auto detID2 = spec2->getDetectorIDs();
+
+ m_getAllEi.initialize();
+ m_getAllEi.setProperty("Workspace", tws);
+ m_getAllEi.setProperty("OutputWorkspace", "monitor_peaks");
+ m_getAllEi.setProperty("Monitor1SpecID", 1);
+ m_getAllEi.setProperty("Monitor2SpecID", 5);
+
+ size_t wsIndex0;
+ auto wws = m_getAllEi.buildWorkspaceToFit(tws, wsIndex0);
+
+ auto det1p = wws->getDetector(0);
+ auto det2p = wws->getDetector(1);
+ TSM_ASSERT_EQUALS("should be the same first detector position",
+ det1p->getRelativePos(), det1->getRelativePos());
+ TSM_ASSERT_EQUALS("should be the same second detector position",
+ det2p->getRelativePos(), det2->getRelativePos());
+
+ TSM_ASSERT_EQUALS("Detector's ID for the first spectrum and new workspace "
+ "should coincide",
+ *(detID1.begin()),
+ (*wws->getSpectrum(0)->getDetectorIDs().begin()));
+ TSM_ASSERT_EQUALS("Detector's ID for the second spectrum and new workspace "
+ "should coincide",
+ *(detID2.begin()),
+ (*wws->getSpectrum(1)->getDetectorIDs().begin()));
+ auto pSpec1 = wws->getSpectrum(0);
+ auto pSpec2 = wws->getSpectrum(1);
+ auto Xsp1 = pSpec1->dataX();
+ auto Xsp2 = pSpec2->dataX();
+ size_t nSpectra = Xsp2.size();
+ TS_ASSERT_EQUALS(nSpectra, 101);
+ TS_ASSERT(boost::math::isinf(Xsp1[nSpectra - 1]));
+ TS_ASSERT(boost::math::isinf(Xsp2[nSpectra - 1]));
+
+ // for(size_t i=0;i<Xsp1.size();i++){
+ // TS_ASSERT_DELTA(Xsp1[i],Xsp2[i],1.e-6);
+ //}
+ }
+ void test_calcDerivative() {
+ double sig[] = {1, 2, 3, 4, 5, 6};
+ std::vector<double> signal(sig, sig + sizeof(sig) / sizeof(double));
+ double bin[] = {2, 3, 4, 5, 6, 7, 8};
+ std::vector<double> bins(bin, bin + sizeof(bin) / sizeof(double));
+ std::vector<double> zeros;
+
+ std::vector<double> deriv;
+ size_t nZer =
+ m_getAllEi.calcDerivativeAndCountZeros(bins, signal, deriv, zeros);
+ TS_ASSERT_EQUALS(nZer, 0);
+ TS_ASSERT_DELTA(deriv[0], deriv[1], 1.e-9);
+ TS_ASSERT_DELTA(deriv[0], deriv[5], 1.e-9);
+ TS_ASSERT_DELTA(deriv[0], deriv[2], 1.e-9);
+ TS_ASSERT_DELTA(deriv[0], 1., 1.e-9);
+
+ double bin1[] = {0, 1, 3, 6, 10, 15, 21};
+ std::vector<double> bins1(bin1, bin1 + sizeof(bin1) / sizeof(double));
+ nZer = m_getAllEi.calcDerivativeAndCountZeros(bins1, signal, deriv, zeros);
+ TS_ASSERT_EQUALS(nZer, 0);
+ TS_ASSERT_DELTA(deriv[0], deriv[1], 1.e-9);
+ TS_ASSERT_DELTA(deriv[0], deriv[5], 1.e-9);
+ TS_ASSERT_DELTA(deriv[0], deriv[2], 1.e-9);
+ TS_ASSERT_DELTA(deriv[0], 0, 1.e-9);
+
+ bins.resize(101);
+ signal.resize(100);
+ for (size_t i = 0; i < 101; i++) {
+ bins[i] = double(i) * 0.1;
+ }
+ for (size_t i = 0; i < 100; i++) {
+ signal[i] = std::sin(0.5 * (bins[i] + bins[i + 1]));
+ }
+ nZer = m_getAllEi.calcDerivativeAndCountZeros(bins, signal, deriv, zeros);
+ TS_ASSERT_EQUALS(nZer, 3);
+ for (size_t i = 0; i < 99; i++) { // intentionally left boundary point --
+ // its accuracy is much lower
+ TSM_ASSERT_DELTA("At i=" + boost::lexical_cast<std::string>(i), deriv[i],
+ 10. * std::cos(0.5 * (bins[i] + bins[i + 1])), 1.e-1);
+ }
+ TS_ASSERT_DELTA(zeros[0], 1.55, 1.e-3);
+ TS_ASSERT_DELTA(zeros[1], 4.65, 1.e-3);
+ TS_ASSERT_DELTA(zeros[2], 7.85, 1.e-3);
+ }
+ void test_binRanges() {
+ std::vector<size_t> bin_min, bin_max, zeros;
+ // Index 0 1 2 3 4 5 6 7 8 9 10 11 12 13
+ double debin[] = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15};
+ std::vector<double> ebin(debin, debin + sizeof(debin) / sizeof(double));
+ // Not yet supported in VC 2012
+ // std::vector<double> ebin={1,2,3,4,5,6,7,8,9,10,11,12,13,15};
+ // Ind 0 1 2 3 4 5 6 7 8 9 10 11 12 13
+ double sig[] = {0, 0, 0, 3, 0, 0, 4, 0, 0, 0, 11, 0, 0};
+ std::vector<double> signal(sig, sig + sizeof(sig) / sizeof(double));
+
+ double dguess[] = {1, 6, 10, 12};
+ std::vector<double> guess(dguess, dguess + sizeof(dguess) / sizeof(double));
+ std::vector<bool> guessValid;
+
+ m_getAllEi.findBinRanges(ebin, signal, guess, 0.1, bin_min, bin_max,
+ guessValid);
+
+ TS_ASSERT_EQUALS(bin_min.size(), 2)
+ TS_ASSERT_EQUALS(bin_max.size(), 2)
+ TS_ASSERT_EQUALS(guessValid.size(), 4)
+ TS_ASSERT_EQUALS(bin_min[0], 4)
+ TS_ASSERT_EQUALS(bin_max[0], 9)
+ TS_ASSERT_EQUALS(bin_min[1], 7)
+ TS_ASSERT_EQUALS(bin_max[1], 13)
+
+ signal[10] = 0;
+ signal[11] = 11;
+ guess[1] = 3;
+ guess[2] = 6;
+ guess[3] = 11;
+ m_getAllEi.findBinRanges(ebin, signal, guess, 0.01, bin_min, bin_max,
+ guessValid);
+ TS_ASSERT_EQUALS(bin_min.size(), 3)
+ TS_ASSERT_EQUALS(bin_max.size(), 3)
+ TS_ASSERT_EQUALS(guessValid.size(), 4)
+
+ TS_ASSERT_EQUALS(bin_min[0], 3);
+ TS_ASSERT_EQUALS(bin_max[0], 4);
+ TS_ASSERT(guessValid[1]);
+
+ TS_ASSERT_EQUALS(bin_min[1], 6);
+ TS_ASSERT_EQUALS(bin_max[1], 7);
+ TS_ASSERT(guessValid[2]);
+
+ TS_ASSERT_EQUALS(bin_min[2], 11);
+ TS_ASSERT_EQUALS(bin_max[2], 12);
+ TS_ASSERT(guessValid[3]);
+
+ TS_ASSERT(!guessValid[0]);
+ }
+
+ void test_getAllEi() {
+ auto ws = createTestingWS();
+
+ m_getAllEi.initialize();
+ m_getAllEi.setProperty("Workspace", ws);
+ m_getAllEi.setProperty("OutputWorkspace", "monitor_peaks");
+ m_getAllEi.setProperty("Monitor1SpecID", 1);
+ m_getAllEi.setProperty("Monitor2SpecID", 2);
+ m_getAllEi.setProperty("ChopperSpeedLog", "Chopper_Speed");
+ m_getAllEi.setProperty("ChopperDelayLog", "Chopper_Delay");
+ m_getAllEi.setProperty("FilterBaseLog", "is_running");
+ m_getAllEi.setProperty("FilterWithDerivative", false);
+ m_getAllEi.setProperty("OutputWorkspace", "allEiWs");
+
+ TS_ASSERT_THROWS_NOTHING(m_getAllEi.execute());
+ API::MatrixWorkspace_sptr out_ws;
+ TS_ASSERT_THROWS_NOTHING(
+ out_ws = API::AnalysisDataService::Instance()
+ .retrieveWS<API::MatrixWorkspace>("allEiWs"));
+
+ TSM_ASSERT("Should be able to retrieve workspace", out_ws);
+ auto wso = dynamic_cast<DataObjects::Workspace2D *>(out_ws.get());
+ TS_ASSERT(wso);
+ if (!wso)
+ return;
+
+ auto &x = wso->dataX(0);
+ TSM_ASSERT_EQUALS("Second peak should be filtered by monitor ranges",
+ x.size(), 1);
+ TS_ASSERT_DELTA(x[0], 134.316, 1.e-3)
+ }
+
+private:
+ GetAllEiTester m_getAllEi;
+
+ DataObjects::Workspace2D_sptr createTestingWS(bool noLogs = false) {
+ double delay(2000), chopSpeed(100), inital_chop_phase(-3000);
+ auto ws = WorkspaceCreationHelper::create2DWorkspaceWithFullInstrument(
+ 2, 1000, true);
+ auto pInstrument = ws->getInstrument();
+ auto chopper = pInstrument->getComponentByName("chopper-position");
+
+ // add chopper parameters
+ auto ¶mMap = ws->instrumentParameters();
+ const std::string description(
+ "The initial rotation phase of the disk used to calculate the time"
+ " for neutrons arriving at the chopper according to the formula time = "
+ "delay + initial_phase/Speed");
+ paramMap.add<double>("double", chopper.get(), "initial_phase",
+ inital_chop_phase, &description);
+ paramMap.add<std::string>("string", chopper.get(), "ChopperDelayLog",
+ "fermi_delay");
+ paramMap.add<std::string>("string", chopper.get(), "ChopperSpeedLog",
+ "fermi_speed");
+ paramMap.add<std::string>("string", chopper.get(), "FilterBaseLog",
+ "is_running");
+ paramMap.add<bool>("bool", chopper.get(), "filter_with_derivative", false);
+
+ // test instrument parameters (obtained from workspace):
+ auto moderator = pInstrument->getSource();
+ auto detector1 = ws->getDetector(0);
+ auto detector2 = ws->getDetector(1);
+ double l_chop = chopper->getDistance(*moderator);
+ double l_mon1 = detector1->getDistance(*moderator);
+ double l_mon2 = detector2->getDistance(*moderator);
+ //,l_mon1(20-9),l_mon2(20-2);
+ double t_chop(delay + inital_chop_phase / chopSpeed);
+ double Period =
+ (0.5 * 1.e+6) / chopSpeed; // 0.5 because some choppers open twice.
+ auto &x = ws->dataX(0);
+ for (size_t i = 0; i < x.size(); i++) {
+ x[i] = 5 + double(i) * 10;
+ }
+ // signal at first monitor
+ double t1 = t_chop * l_mon1 / l_chop;
+ double t2 = (t_chop + Period) * l_mon1 / l_chop;
+ {
+ auto &y = ws->dataY(0);
+ for (size_t i = 0; i < y.size(); i++) {
+ double t = 0.5 * (x[i] + x[i + 1]);
+ double tm1 = t - t1;
+ double tm2 = t - t2;
+ y[i] = (10000 * std::exp(-tm1 * tm1 / 1000.) +
+ 20000 * std::exp(-tm2 * tm2 / 1000.));
+ // std::cout<<"t="<<t<<" signal="<<y[i]<<" ind="<<i<<std::endl;
+ }
+ }
+ // signal at second monitor
+ t1 = t_chop * l_mon2 / l_chop;
+ t2 = (t_chop + Period) * l_mon2 / l_chop;
+ {
+ auto &y = ws->dataY(1);
+ for (size_t i = 0; i < y.size(); i++) {
+ double t = 0.5 * (x[i] + x[i + 1]);
+ double tm1 = t - t1;
+ double tm2 = t - t2;
+ y[i] = (100 * std::exp(-tm1 * tm1 / 1000.) +
+ 200 * std::exp(-tm2 * tm2 / 1000.));
+ // std::cout<<"t="<<t<<" signal="<<y[i]<<" ind="<<i<<std::endl;
+ }
+ }
+
+ if (noLogs)
+ return ws;
+
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> chopDelayLog(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Delay"));
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> chopSpeedLog(
+ new Kernel::TimeSeriesProperty<double>("Chopper_Speed"));
+ std::unique_ptr<Kernel::TimeSeriesProperty<double>> isRunning(
+ new Kernel::TimeSeriesProperty<double>("is_running"));
+
+ for (int i = 0; i < 10; i++) {
+ auto time = Kernel::DateAndTime(10 * i, 0);
+ chopDelayLog->addValue(time, delay);
+ chopSpeedLog->addValue(time, chopSpeed);
+ isRunning->addValue(time, 1.);
+ }
+
+ ws->mutableRun().addLogData(chopSpeedLog.release());
+ ws->mutableRun().addLogData(chopDelayLog.release());
+ ws->mutableRun().addLogData(isRunning.release());
+
+ return ws;
+ }
+};
+
+#endif
diff --git a/Framework/Algorithms/test/RemoveExpDecayTest.h b/Framework/Algorithms/test/RemoveExpDecayTest.h
index e4d20a3f95e44748f4f7128fdadcd112f6d298f5..136e48cf707bef934f0138026a1ad26eebee85b7 100644
--- a/Framework/Algorithms/test/RemoveExpDecayTest.h
+++ b/Framework/Algorithms/test/RemoveExpDecayTest.h
@@ -3,11 +3,11 @@
#include <cxxtest/TestSuite.h>
#include "MantidAPI/FrameworkManager.h"
-#include "MantidAlgorithms/RemoveExpDecay.h"
+#include "MantidAPI/AlgorithmManager.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
-using namespace Mantid::Algorithms;
using namespace Mantid::API;
+using Mantid::MantidVec;
const std::string outputName = "MuonRemoveExpDecay_Output";
@@ -21,52 +21,165 @@ public:
RemoveExpDecayTest() { FrameworkManager::Instance(); }
void testInit() {
- MuonRemoveExpDecay alg;
- alg.initialize();
- TS_ASSERT(alg.isInitialized())
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("RemoveExpDecay");
+ alg->initialize();
+ TS_ASSERT(alg->isInitialized())
}
- void testExecute() {
- auto ws = WorkspaceCreationHelper::Create2DWorkspace(1, 1);
-
- MuonRemoveExpDecay alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT(alg.isInitialized());
- alg.setChild(true);
- alg.setProperty("InputWorkspace", ws);
- alg.setPropertyValue("OutputWorkspace", outputName);
- alg.setPropertyValue("Spectra", "0");
- TS_ASSERT_THROWS_NOTHING(alg.execute());
- TS_ASSERT(alg.isExecuted())
+ void test_Execute() {
+
+ auto ws = createWorkspace(1, 50);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("RemoveExpDecay");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setPropertyValue("OutputWorkspace", outputName);
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+ TS_ASSERT(alg->isExecuted());
+
+ MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
}
- void testExecuteWhereSepctraNotSet() {
- auto ws = WorkspaceCreationHelper::Create2DWorkspace(1, 1);
-
- MuonRemoveExpDecay alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT(alg.isInitialized());
- alg.setChild(true);
- alg.setProperty("InputWorkspace", ws);
- alg.setPropertyValue("OutputWorkspace", outputName);
- TS_ASSERT_THROWS_NOTHING(alg.execute());
- TS_ASSERT(alg.isExecuted())
+ void test_EmptySpectrumList() {
+
+ auto ws = createWorkspace(2, 50);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("RemoveExpDecay");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setPropertyValue("OutputWorkspace", outputName);
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+ TS_ASSERT(alg->isExecuted());
+
+ MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
+
+ // First spectrum
+ // Test some X values
+ TS_ASSERT_DELTA(outWS->readX(0)[10], 0.2000, 0.0001);
+ TS_ASSERT_DELTA(outWS->readX(0)[19], 0.3800, 0.0001);
+ TS_ASSERT_DELTA(outWS->readX(0)[49], 0.9800, 0.0001);
+ // Test some Y values
+ TS_ASSERT_DELTA(outWS->readY(0)[10], -0.0992, 0.0001);
+ TS_ASSERT_DELTA(outWS->readY(0)[19], -0.0111, 0.0001);
+ TS_ASSERT_DELTA(outWS->readY(0)[49], -0.0622, 0.0001);
+ // Test some E values
+ TS_ASSERT_DELTA(outWS->readE(0)[10], 0.0054, 0.0001);
+ TS_ASSERT_DELTA(outWS->readE(0)[19], 0.0059, 0.0001);
+ TS_ASSERT_DELTA(outWS->readE(0)[49], 0.0077, 0.0001);
+
+ // Second spectrum
+ // Test some X values
+ TS_ASSERT_DELTA(outWS->readX(1)[10], 0.2000, 0.0001);
+ TS_ASSERT_DELTA(outWS->readX(1)[19], 0.3800, 0.0001);
+ TS_ASSERT_DELTA(outWS->readX(1)[49], 0.9800, 0.0001);
+ // Test some Y values
+ TS_ASSERT_DELTA(outWS->readY(1)[10], 0.0274, 0.0001);
+ TS_ASSERT_DELTA(outWS->readY(1)[19], -0.1003, 0.0001);
+ TS_ASSERT_DELTA(outWS->readY(1)[49], 0.0802, 0.0001);
+ // Test some E values
+ TS_ASSERT_DELTA(outWS->readE(1)[10], 0.0054, 0.0001);
+ TS_ASSERT_DELTA(outWS->readE(1)[19], 0.0059, 0.0001);
+ TS_ASSERT_DELTA(outWS->readE(1)[49], 0.0078, 0.0001);
+ }
+
+ void test_SpectrumList() {
+
+ auto ws = createWorkspace(2, 50);
+
+ // First, run the algorithm without specifying any spectrum
+ IAlgorithm_sptr alg1 =
+ AlgorithmManager::Instance().create("RemoveExpDecay");
+ alg1->initialize();
+ alg1->setChild(true);
+ alg1->setProperty("InputWorkspace", ws);
+ alg1->setPropertyValue("OutputWorkspace", outputName);
+ TS_ASSERT_THROWS_NOTHING(alg1->execute());
+ TS_ASSERT(alg1->isExecuted());
+ MatrixWorkspace_sptr out1 = alg1->getProperty("OutputWorkspace");
+
+ // Then run the algorithm on the second spectrum only
+ IAlgorithm_sptr alg2 =
+ AlgorithmManager::Instance().create("RemoveExpDecay");
+ alg2->initialize();
+ alg2->setChild(true);
+ alg2->setProperty("InputWorkspace", ws);
+ alg2->setPropertyValue("OutputWorkspace", outputName);
+ alg2->setPropertyValue("Spectra", "1");
+ TS_ASSERT_THROWS_NOTHING(alg2->execute());
+ TS_ASSERT(alg2->isExecuted());
+ MatrixWorkspace_sptr out2 = alg2->getProperty("OutputWorkspace");
+
+ // Both output workspaces should have 2 spectra
+ TS_ASSERT_EQUALS(out1->getNumberHistograms(), ws->getNumberHistograms());
+ TS_ASSERT_EQUALS(out2->getNumberHistograms(), ws->getNumberHistograms());
+
+ // Compare results, they should match for the selected spectrum
+ TS_ASSERT_EQUALS(out1->readX(1), out2->readX(1));
+ TS_ASSERT_EQUALS(out1->readY(1), out2->readY(1));
+ TS_ASSERT_EQUALS(out1->readE(1), out2->readE(1));
+
+ // Compare non-selected spectra, the should match the input ones
+ TS_ASSERT_EQUALS(ws->readX(0), out2->readX(0));
+ TS_ASSERT_EQUALS(ws->readY(0), out2->readY(0));
+ TS_ASSERT_EQUALS(ws->readE(0), out2->readE(0));
}
void test_yUnitLabel() {
- auto ws = WorkspaceCreationHelper::Create2DWorkspace(1, 1);
- MuonRemoveExpDecay alg;
- alg.initialize();
- alg.setChild(true);
- alg.setProperty("InputWorkspace", ws);
- alg.setProperty("OutputWorkspace", outputName);
- alg.execute();
+ auto ws = createWorkspace(4, 50);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("RemoveExpDecay");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setPropertyValue("OutputWorkspace", outputName);
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+ TS_ASSERT(alg->isExecuted())
- MatrixWorkspace_sptr result = alg.getProperty("OutputWorkspace");
+ MatrixWorkspace_sptr result = alg->getProperty("OutputWorkspace");
TS_ASSERT(result);
TS_ASSERT_EQUALS(result->YUnitLabel(), "Asymmetry");
}
+
+ MatrixWorkspace_sptr createWorkspace(size_t nspec, size_t maxt) {
+
+ // Create a fake muon dataset
+ double a = 0.1; // Amplitude of the oscillations
+ double w = 25.; // Frequency of the oscillations
+ double tau = 2.2; // Muon life time
+
+ MantidVec X;
+ MantidVec Y;
+ MantidVec E;
+ for (size_t s = 0; s < nspec; s++) {
+ for (size_t t = 0; t < maxt; t++) {
+ double x = static_cast<double>(t) / static_cast<double>(maxt);
+ double e = exp(-x / tau);
+ X.push_back(x);
+ Y.push_back(a * sin(w * x +
+ static_cast<double>(s) * M_PI /
+ static_cast<double>(nspec)) *
+ e +
+ e);
+ E.push_back(0.005);
+ }
+ }
+
+ auto createWS = AlgorithmManager::Instance().create("CreateWorkspace");
+ createWS->initialize();
+ createWS->setChild(true);
+ createWS->setProperty("DataX", X);
+ createWS->setProperty("DataY", Y);
+ createWS->setProperty("DataE", E);
+ createWS->setProperty("NSpec", static_cast<int>(nspec));
+ createWS->setPropertyValue("OutputWorkspace", "ws");
+ createWS->execute();
+ MatrixWorkspace_sptr ws = createWS->getProperty("OutputWorkspace");
+
+ return ws;
+ }
};
#endif /*MUONREMOVEEXPDECAYTEST_H_*/
diff --git a/Framework/Crystal/inc/MantidCrystal/LoadIsawPeaks.h b/Framework/Crystal/inc/MantidCrystal/LoadIsawPeaks.h
index f5f08d514683494a3c4327d930e392068240de3e..f051bc0a419caa4d5082e0b14bdc4c526ff882c6 100644
--- a/Framework/Crystal/inc/MantidCrystal/LoadIsawPeaks.h
+++ b/Framework/Crystal/inc/MantidCrystal/LoadIsawPeaks.h
@@ -8,7 +8,8 @@
namespace Mantid {
namespace Crystal {
-/** LoadIsawPeaks : Load an ISAW-style .peaks file
+/**
+ * Load an ISAW-style .peaks or .integrate file
* into a PeaksWorkspace
*
* @author Janik Zikovsky, SNS
@@ -21,14 +22,16 @@ public:
virtual ~LoadIsawPeaks();
/// Algorithm's name for identification
- virtual const std::string name() const { return "LoadIsawPeaks"; };
+ virtual const std::string name() const { return "LoadIsawPeaks"; }
+
/// Summary of algorithms purpose
virtual const std::string summary() const {
return "Load an ISAW-style .peaks file into a PeaksWorkspace.";
}
/// Algorithm's version for identification
- virtual int version() const { return 1; };
+ virtual int version() const { return 1; }
+
/// Algorithm's category for identification
virtual const std::string category() const {
return "Crystal;DataHandling\\Isaw";
@@ -36,26 +39,52 @@ public:
/// Returns a confidence value that this algorithm can load a file
virtual int confidence(Kernel::FileDescriptor &descriptor) const;
- int findPixelID(Geometry::Instrument_const_sptr inst, std::string bankName,
- int col, int row);
private:
/// Initialise the properties
void init();
+
/// Run the algorithm
void exec();
+ /// Reads calibration/detector section and returns first word of next line
std::string ApplyCalibInfo(std::ifstream &in, std::string startChar,
Geometry::Instrument_const_sptr instr_old,
Geometry::Instrument_const_sptr instr, double &T0);
+ /// Reads first line of peaks file and returns first word of next line
std::string readHeader(Mantid::DataObjects::PeaksWorkspace_sptr outWS,
std::ifstream &in, double &T0);
+ /// Read a single peak from peaks file
+ DataObjects::Peak readPeak(DataObjects::PeaksWorkspace_sptr outWS,
+ std::string &lastStr, std::ifstream &in,
+ int &seqNum, std::string bankName);
+
+ int findPixelID(Geometry::Instrument_const_sptr inst, std::string bankName,
+ int col, int row);
+
+ /// Read the header of a peak block section, returns first word of next line
+ std::string readPeakBlockHeader(std::string lastStr, std::ifstream &in,
+ int &run, int &detName, double &chi,
+ double &phi, double &omega, double &monCount);
+
+ /// Append peaks from given file to given workspace
void appendFile(Mantid::DataObjects::PeaksWorkspace_sptr outWS,
std::string filename);
+
+ /// Compare number of peaks in given file to given workspace
+ /// Throws std::length_error on mismatch
void checkNumberPeaks(Mantid::DataObjects::PeaksWorkspace_sptr outWS,
std::string filename);
+
+ /// Local cache of bank IComponents used in file
+ std::map<std::string, boost::shared_ptr<const Geometry::IComponent>> m_banks;
+
+ /// Retrieve cached bank (or load and cache for next time)
+ boost::shared_ptr<const Geometry::IComponent> getCachedBankByName(
+ std::string bankname,
+ const boost::shared_ptr<const Geometry::Instrument> &inst);
};
} // namespace Mantid
diff --git a/Framework/Crystal/src/AnvredCorrection.cpp b/Framework/Crystal/src/AnvredCorrection.cpp
index 31667b090362ea9d0168778db58460b94573120c..3f49fb8f31e249c413db7af989bb4df0f6715e8b 100644
--- a/Framework/Crystal/src/AnvredCorrection.cpp
+++ b/Framework/Crystal/src/AnvredCorrection.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidCrystal/AnvredCorrection.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/UnitFactory.h"
@@ -78,9 +78,7 @@ AnvredCorrection::AnvredCorrection()
void AnvredCorrection::init() {
// The input workspace must have an instrument and units of wavelength
- boost::shared_ptr<CompositeValidator> wsValidator =
- boost::make_shared<CompositeValidator>();
- wsValidator->add(boost::make_shared<InstrumentValidator>());
+ auto wsValidator = boost::make_shared<InstrumentValidator>();
declareProperty(new WorkspaceProperty<>("InputWorkspace", "",
Direction::Input, wsValidator),
diff --git a/Framework/Crystal/src/FilterPeaks.cpp b/Framework/Crystal/src/FilterPeaks.cpp
index 8e398c2b0de67a54cfba1205285caa2be5a0808c..f60acecea9586ca7449801c11b174ecdbefd7e16 100644
--- a/Framework/Crystal/src/FilterPeaks.cpp
+++ b/Framework/Crystal/src/FilterPeaks.cpp
@@ -98,6 +98,8 @@ void FilterPeaks::exec() {
filterFunction = &intensity;
else if (FilterVariable == "Signal/Noise")
filterFunction = &SN;
+ else
+ throw std::invalid_argument("Unknown FilterVariable: " + FilterVariable);
const double FilterValue = getProperty("FilterValue");
const std::string Operator = getProperty("Operator");
diff --git a/Framework/Crystal/src/FindSXPeaks.cpp b/Framework/Crystal/src/FindSXPeaks.cpp
index 456d0c022b62f578840185a6f89974c1d9bac922..a2cdbc16f408aba18adec1153b38260ee6183580 100644
--- a/Framework/Crystal/src/FindSXPeaks.cpp
+++ b/Framework/Crystal/src/FindSXPeaks.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidCrystal/FindSXPeaks.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/BoundedValidator.h"
diff --git a/Framework/Crystal/src/IndexSXPeaks.cpp b/Framework/Crystal/src/IndexSXPeaks.cpp
index 00cb0dd4f10e97bc6f856833adfc8afcea4be027..0409b1dd4e5ed9ccdb0e8bc04ef7ede55cb4a457 100644
--- a/Framework/Crystal/src/IndexSXPeaks.cpp
+++ b/Framework/Crystal/src/IndexSXPeaks.cpp
@@ -2,7 +2,6 @@
// Includes
//----------------------------------------------------------------------
#include "MantidCrystal/IndexSXPeaks.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidGeometry/Crystal/IPeak.h"
diff --git a/Framework/Crystal/src/IntegratePeakTimeSlices.cpp b/Framework/Crystal/src/IntegratePeakTimeSlices.cpp
index 70e398ef3d65ea8c30d3b112373b7e929153f56e..9828bea2f54bfa54db588459eca4c19b2d772842 100644
--- a/Framework/Crystal/src/IntegratePeakTimeSlices.cpp
+++ b/Framework/Crystal/src/IntegratePeakTimeSlices.cpp
@@ -587,6 +587,12 @@ void IntegratePeakTimeSlices::exec() {
// Now set up the center for this peak
int i = find("Mrow", names);
+ if (i < 0) {
+ throw std::runtime_error("Inconsistency found in algorithm "
+ "execution. The index for the parameter "
+ "Mrow is negative.");
+ }
+
lastRow = (int)(params[i] + .5);
i = find("Mcol", names);
lastCol = (int)(params[i] + .5);
@@ -2220,7 +2226,16 @@ bool IntegratePeakTimeSlices::isGoodFit(std::vector<double> const ¶ms,
std::vector<std::string> const &names,
double chisqOverDOF) {
int Ibk = find("Background", names);
+ if (Ibk < 0)
+ throw std::runtime_error(
+ "Irrecoverable inconsistency found. The index for the "
+ "parameter 'Background' is lower than zero.");
+
int IIntensity = find("Intensity", names);
+ if (IIntensity < 0)
+ throw std::runtime_error(
+ "Irrecoverable inconsistency found. The index for the "
+ "parameter 'Intensity' is lower than zero.");
if (chisqOverDOF < 0) {
@@ -2498,6 +2513,15 @@ int IntegratePeakTimeSlices::UpdateOutputWS(
int Irow = find("Mrow", names);
int Icol = find("Mcol", names);
+ if (Ibk < 0 || IIntensity < 0 || IVx < 0 || IVy < 0 || IVxy < 0 || Irow < 0 ||
+ Icol < 0) {
+ throw std::runtime_error("Inconsistency found when updating output "
+ "workspace. None of the indices for the "
+ "parameters 'Background', 'Intensity', 'SScol', "
+ "'SSrow', 'SSrc', 'Mrow', 'Mcol' can be "
+ "negative.");
+ }
+
int newRowIndex = 0;
if (dir > 0)
diff --git a/Framework/Crystal/src/LoadHKL.cpp b/Framework/Crystal/src/LoadHKL.cpp
index 0a2cdd3331a2f06b44acfe61f5341eee67f450c7..01bd724729514325c5ab87c8f4ca8491a9e6f251 100644
--- a/Framework/Crystal/src/LoadHKL.cpp
+++ b/Framework/Crystal/src/LoadHKL.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/LoadHKL.h"
#include "MantidCrystal/AnvredCorrection.h"
#include "MantidGeometry/Instrument/Detector.h"
diff --git a/Framework/Crystal/src/LoadIsawPeaks.cpp b/Framework/Crystal/src/LoadIsawPeaks.cpp
index 4dc4b229cef31411c56aaf270075ecd24b75a52f..bec1b06a5a50a931294dcd83d625d172b7c28841 100644
--- a/Framework/Crystal/src/LoadIsawPeaks.cpp
+++ b/Framework/Crystal/src/LoadIsawPeaks.cpp
@@ -29,8 +29,9 @@ LoadIsawPeaks::LoadIsawPeaks() {}
*/
LoadIsawPeaks::~LoadIsawPeaks() {}
+//----------------------------------------------------------------------------------------------
/**
- * Return the confidence with with this algorithm can load the file
+ * Determine the confidence with which this algorithm can load a given file
* @param descriptor A descriptor for the file
* @returns An integer specifying the confidence level. 0 indicates it will not
* be used
@@ -78,12 +79,10 @@ int LoadIsawPeaks::confidence(Kernel::FileDescriptor &descriptor) const {
confidence = 95;
} catch (std::exception &) {
}
+
return confidence;
}
-//----------------------------------------------------------------------------------------------
-//----------------------------------------------------------------------------------------------
-
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm's properties.
*/
@@ -99,6 +98,23 @@ void LoadIsawPeaks::init() {
"Name of the output workspace.");
}
+//----------------------------------------------------------------------------------------------
+/** Execute the algorithm.
+ */
+void LoadIsawPeaks::exec() {
+ // Create the workspace
+ PeaksWorkspace_sptr ws(new PeaksWorkspace());
+
+ // This loads (appends) the peaks
+ this->appendFile(ws, getPropertyValue("Filename"));
+
+ // Save it in the output
+ setProperty("OutputWorkspace", boost::dynamic_pointer_cast<Workspace>(ws));
+
+ this->checkNumberPeaks(ws, getPropertyValue("Filename"));
+}
+
+//----------------------------------------------------------------------------------------------
std::string
LoadIsawPeaks::ApplyCalibInfo(std::ifstream &in, std::string startChar,
Geometry::Instrument_const_sptr instr_old,
@@ -113,7 +129,6 @@ LoadIsawPeaks::ApplyCalibInfo(std::ifstream &in, std::string startChar,
startChar = getWord(in, false);
}
if (!(in.good())) {
- // g_log.error()<<"Peaks file has no time shift and L0 info"<<std::endl;
throw std::invalid_argument("Peaks file has no time shift and L0 info");
}
std::string L1s = getWord(in, false);
@@ -190,7 +205,7 @@ LoadIsawPeaks::ApplyCalibInfo(std::ifstream &in, std::string startChar,
}
bankName += SbankNum;
boost::shared_ptr<const Geometry::IComponent> bank =
- instr_old->getComponentByName(bankName);
+ getCachedBankByName(bankName, instr_old);
if (!bank) {
g_log.error() << "There is no bank " << bankName << " in the instrument"
@@ -291,15 +306,11 @@ std::string LoadIsawPeaks::readHeader(PeaksWorkspace_sptr outWS,
Geometry::Instrument_const_sptr instr(
new Geometry::Instrument(instr_old->baseInstrument(), map));
- // std::string s;
std::string s = ApplyCalibInfo(in, "", instr_old, instr, T0);
outWS->setInstrument(instr);
// Now skip all lines on L1, detector banks, etc. until we get to a block of
// peaks. They start with 0.
- // readToEndOfLine( in , true );
- // readToEndOfLine( in , true );
- // s = getWord(in, false);
while (s != "0" && in.good()) {
readToEndOfLine(in, true);
s = getWord(in, false);
@@ -318,9 +329,10 @@ std::string LoadIsawPeaks::readHeader(PeaksWorkspace_sptr outWS,
* @param bankName :: the bank number from the ISAW file.
* @return the Peak the Peak object created
*/
-Mantid::DataObjects::Peak readPeak(PeaksWorkspace_sptr outWS,
- std::string &lastStr, std::ifstream &in,
- int &seqNum, std::string bankName) {
+DataObjects::Peak LoadIsawPeaks::readPeak(PeaksWorkspace_sptr outWS,
+ std::string &lastStr,
+ std::ifstream &in, int &seqNum,
+ std::string bankName) {
double h;
double k;
double l;
@@ -387,9 +399,9 @@ Mantid::DataObjects::Peak readPeak(PeaksWorkspace_sptr outWS,
Instrument_const_sptr inst = outWS->getInstrument();
if (!inst)
throw std::runtime_error("No instrument in PeaksWorkspace!");
- LoadIsawPeaks u;
- int pixelID = u.findPixelID(inst, bankName, static_cast<int>(col),
- static_cast<int>(row));
+
+ int pixelID =
+ findPixelID(inst, bankName, static_cast<int>(col), static_cast<int>(row));
// Create the peak object
Peak peak(outWS->getInstrument(), pixelID, wl);
@@ -402,10 +414,12 @@ Mantid::DataObjects::Peak readPeak(PeaksWorkspace_sptr outWS,
return peak;
}
+//----------------------------------------------------------------------------------------------
int LoadIsawPeaks::findPixelID(Instrument_const_sptr inst, std::string bankName,
int col, int row) {
boost::shared_ptr<const IComponent> parent =
- inst->getComponentByName(bankName);
+ getCachedBankByName(bankName, inst);
+
if (parent->type().compare("RectangularDetector") == 0) {
boost::shared_ptr<const RectangularDetector> RDet =
boost::dynamic_pointer_cast<const RectangularDetector>(parent);
@@ -441,9 +455,11 @@ int LoadIsawPeaks::findPixelID(Instrument_const_sptr inst, std::string bankName,
//-----------------------------------------------------------------------------------------------
/** Read the header of each peak block section */
-std::string readPeakBlockHeader(std::string lastStr, std::ifstream &in,
- int &run, int &detName, double &chi,
- double &phi, double &omega, double &monCount) {
+std::string LoadIsawPeaks::readPeakBlockHeader(std::string lastStr,
+ std::ifstream &in, int &run,
+ int &detName, double &chi,
+ double &phi, double &omega,
+ double &monCount) {
std::string s = lastStr;
if (s.length() < 1 && in.good()) // blank line
@@ -491,6 +507,11 @@ void LoadIsawPeaks::appendFile(PeaksWorkspace_sptr outWS,
// Open the file
std::ifstream in(filename.c_str());
+ // Calculate filesize
+ in.seekg(0, in.end);
+ auto filelen = in.tellg();
+ in.seekg(0, in.beg);
+
// Read the header, load the instrument
double T0;
std::string s = readHeader(outWS, in, T0);
@@ -514,8 +535,8 @@ void LoadIsawPeaks::appendFile(PeaksWorkspace_sptr outWS,
Mantid::Geometry::Goniometer uniGonio;
uniGonio.makeUniversalGoniometer();
- // TODO: Can we find the number of peaks to get better progress reporting?
- Progress prog(this, 0.0, 1.0, 100);
+ // Progress is reported based on how much of the file we've read
+ Progress prog(this, 0.0, 1.0, filelen);
while (in.good()) {
// Read the header if necessary
@@ -565,9 +586,10 @@ void LoadIsawPeaks::appendFile(PeaksWorkspace_sptr outWS,
<< e.what() << std::endl;
}
- prog.report();
+ prog.report(in.tellg());
}
}
+
//-----------------------------------------------------------------------------------------------
/** Count the peaks from a .peaks file and compare with the workspace
* @param outWS :: the workspace in which to place the information
@@ -592,19 +614,29 @@ void LoadIsawPeaks::checkNumberPeaks(PeaksWorkspace_sptr outWS,
}
//----------------------------------------------------------------------------------------------
-/** Execute the algorithm.
+/** Retrieves pointer to given bank from local cache.
+ *
+ * When the bank isn't in the local cache, it is loaded and
+ * added to the cache for later use. Lifetime of the cache
+ * is bound to the lifetime of this instance of the algorithm
+ * (typically, the instance should be destroyed once exec()
+ * finishes).
+ *
+ * Note that while this is used only for banks here, it would
+ * work for caching any component without modification.
+ *
+ * @param bankname :: the name of the requested bank
+ * @param inst :: the instrument from which to load the bank if it is not yet
+ *cached
+ * @return A shared pointer to the request bank (empty shared pointer if not
+ *found)
*/
-void LoadIsawPeaks::exec() {
- // Create the workspace
- PeaksWorkspace_sptr ws(new PeaksWorkspace());
-
- // This loads (appends) the peaks
- this->appendFile(ws, getPropertyValue("Filename"));
-
- // Save it in the output
- setProperty("OutputWorkspace", boost::dynamic_pointer_cast<Workspace>(ws));
-
- this->checkNumberPeaks(ws, getPropertyValue("Filename"));
+boost::shared_ptr<const IComponent> LoadIsawPeaks::getCachedBankByName(
+ std::string bankname,
+ const boost::shared_ptr<const Geometry::Instrument> &inst) {
+ if (m_banks.count(bankname) == 0)
+ m_banks[bankname] = inst->getComponentByName(bankname);
+ return m_banks[bankname];
}
} // namespace Mantid
diff --git a/Framework/Crystal/src/LoadIsawSpectrum.cpp b/Framework/Crystal/src/LoadIsawSpectrum.cpp
index 1020210a59d8f48c1c261685b9a4e787d7427f38..2c5a6da66ba1706e9aa415a2cdbd27c3755d84ad 100644
--- a/Framework/Crystal/src/LoadIsawSpectrum.cpp
+++ b/Framework/Crystal/src/LoadIsawSpectrum.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/LoadIsawSpectrum.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
@@ -69,38 +68,24 @@ void LoadIsawSpectrum::exec() {
std::vector<std::vector<double>> spectra;
std::vector<std::vector<double>> time;
int iSpec = 0;
- if (iSpec == 1) {
- while (!infile.eof()) // To get you all the lines.
- {
- // Set up sizes. (HEIGHT x WIDTH)
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- infile >> spec[0] >> spec[1] >> spec[2] >> spec[3] >> spec[4] >>
- spec[5] >> spec[6] >> spec[7] >> spec[8] >> spec[9] >> spec[10];
- for (int i = 0; i < 11; i++)
- spectra[a].push_back(spec[i]);
- a++;
- }
- } else {
- for (int wi = 0; wi < 8; wi++)
- getline(infile, STRING); // Saves the line in STRING.
- while (!infile.eof()) // To get you all the lines.
- {
- time.resize(a + 1);
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- if (infile.eof())
- break;
- std::stringstream ss(STRING);
- if (STRING.find("Bank") == std::string::npos) {
- double time0, spectra0;
- ss >> time0 >> spectra0;
- time[a].push_back(time0);
- spectra[a].push_back(spectra0);
+ for (int wi = 0; wi < 8; wi++)
+ getline(infile, STRING); // Saves the line in STRING.
+ while (!infile.eof()) // To get you all the lines.
+ {
+ time.resize(a + 1);
+ spectra.resize(a + 1);
+ getline(infile, STRING); // Saves the line in STRING.
+ if (infile.eof())
+ break;
+ std::stringstream ss(STRING);
+ if (STRING.find("Bank") == std::string::npos) {
+ double time0, spectra0;
+ ss >> time0 >> spectra0;
+ time[a].push_back(time0);
+ spectra[a].push_back(spectra0);
- } else {
- a++;
- }
+ } else {
+ a++;
}
}
infile.close();
diff --git a/Framework/Crystal/src/MaskPeaksWorkspace.cpp b/Framework/Crystal/src/MaskPeaksWorkspace.cpp
index 173c6877ede1aba29f3b21f045c73e8b67b54684..eccab7700967e20f1772efe0c842d64b30fb3866 100644
--- a/Framework/Crystal/src/MaskPeaksWorkspace.cpp
+++ b/Framework/Crystal/src/MaskPeaksWorkspace.cpp
@@ -3,13 +3,12 @@
//----------------------------------------------------------------------
#include "MantidCrystal/MaskPeaksWorkspace.h"
#include "MantidDataObjects/PeaksWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/IPeakFunction.h"
#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/ArrayProperty.h"
-#include <fstream>
namespace Mantid {
namespace Crystal {
diff --git a/Framework/Crystal/src/NormaliseVanadium.cpp b/Framework/Crystal/src/NormaliseVanadium.cpp
index dd7b026f1c4a54171729bd101e1a436d104b9caa..cc42991e91367cbaa260fc5dcbe71aa58e7792cc 100644
--- a/Framework/Crystal/src/NormaliseVanadium.cpp
+++ b/Framework/Crystal/src/NormaliseVanadium.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidCrystal/NormaliseVanadium.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/Fast_Exponential.h"
@@ -26,8 +26,7 @@ NormaliseVanadium::NormaliseVanadium() : API::Algorithm() {}
void NormaliseVanadium::init() {
// The input workspace must have an instrument and units of wavelength
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<InstrumentValidator>();
+ auto wsValidator = boost::make_shared<InstrumentValidator>();
declareProperty(new WorkspaceProperty<>("InputWorkspace", "",
Direction::Input, wsValidator),
diff --git a/Framework/Crystal/src/OptimizeExtinctionParameters.cpp b/Framework/Crystal/src/OptimizeExtinctionParameters.cpp
index 5cb88b11706a63b570e70bf636db0d70b0f9b9f5..f52313952078931c092fb49f01d12b1a1282f2d5 100644
--- a/Framework/Crystal/src/OptimizeExtinctionParameters.cpp
+++ b/Framework/Crystal/src/OptimizeExtinctionParameters.cpp
@@ -2,7 +2,6 @@
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/IPeakFunction.h"
#include "MantidAPI/IBackgroundFunction.h"
#include "MantidAPI/CompositeFunction.h"
diff --git a/Framework/Crystal/src/OptimizeLatticeForCellType.cpp b/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
index b5b60609b2b08f3c6317cb9f80da1a5a6791e14f..26327af7378dc145c9d3314000aaa430c311d330 100644
--- a/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
+++ b/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
@@ -2,7 +2,6 @@
#include "MantidCrystal/GSLFunctions.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/IPeakFunction.h"
#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/ListValidator.h"
diff --git a/Framework/Crystal/src/PeakIntegration.cpp b/Framework/Crystal/src/PeakIntegration.cpp
index 8c4a5f1f5bb8f897cee60688ec9d068bd584be3c..9da094c81196f2cf68705daf25cc447ba8d85a8d 100644
--- a/Framework/Crystal/src/PeakIntegration.cpp
+++ b/Framework/Crystal/src/PeakIntegration.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAPI/MemoryManager.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/IPeakFunction.h"
@@ -14,7 +14,6 @@
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/VisibleWhenProperty.h"
#include <boost/math/special_functions/fpclassify.hpp>
-#include <fstream>
namespace Mantid {
namespace Crystal {
diff --git a/Framework/Crystal/src/PredictPeaks.cpp b/Framework/Crystal/src/PredictPeaks.cpp
index d6b2032d12e760b89565e9047123393622ca34fd..c9a4014e0e6201c05c8ab193f9c80f7d1d48099e 100644
--- a/Framework/Crystal/src/PredictPeaks.cpp
+++ b/Framework/Crystal/src/PredictPeaks.cpp
@@ -1,7 +1,6 @@
#include "MantidCrystal/PredictPeaks.h"
#include "MantidGeometry/Objects/InstrumentRayTracer.h"
#include "MantidKernel/ListValidator.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidAPI/IMDEventWorkspace.h"
diff --git a/Framework/Crystal/src/SaveHKL.cpp b/Framework/Crystal/src/SaveHKL.cpp
index 531893ebf5181eaacb538ee2eb25602000c59645..0892660f75417fbe9b98815157a12693a1a32eba 100644
--- a/Framework/Crystal/src/SaveHKL.cpp
+++ b/Framework/Crystal/src/SaveHKL.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/SaveHKL.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidKernel/Utils.h"
@@ -230,37 +229,23 @@ void SaveHKL::exec() {
infile.open(spectraFile.c_str());
if (infile.is_open()) {
size_t a = 0;
- if (iSpec == 1) {
- while (!infile.eof()) // To get you all the lines.
- {
- // Set up sizes. (HEIGHT x WIDTH)
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- infile >> spec[0] >> spec[1] >> spec[2] >> spec[3] >> spec[4] >>
- spec[5] >> spec[6] >> spec[7] >> spec[8] >> spec[9] >> spec[10];
- for (int i = 0; i < 11; i++)
- spectra[a].push_back(spec[i]);
+ for (int wi = 0; wi < 8; wi++)
+ getline(infile, STRING); // Saves the line in STRING.
+ while (!infile.eof()) // To get you all the lines.
+ {
+ time.resize(a + 1);
+ spectra.resize(a + 1);
+ getline(infile, STRING); // Saves the line in STRING.
+ std::stringstream ss(STRING);
+ if (STRING.find("Bank") == std::string::npos) {
+ double time0, spectra0;
+ ss >> time0 >> spectra0;
+ time[a].push_back(time0);
+ spectra[a].push_back(spectra0);
+
+ } else {
a++;
}
- } else {
- for (int wi = 0; wi < 8; wi++)
- getline(infile, STRING); // Saves the line in STRING.
- while (!infile.eof()) // To get you all the lines.
- {
- time.resize(a + 1);
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- std::stringstream ss(STRING);
- if (STRING.find("Bank") == std::string::npos) {
- double time0, spectra0;
- ss >> time0 >> spectra0;
- time[a].push_back(time0);
- spectra[a].push_back(spectra0);
-
- } else {
- a++;
- }
- }
}
infile.close();
}
diff --git a/Framework/Crystal/src/SaveIsawPeaks.cpp b/Framework/Crystal/src/SaveIsawPeaks.cpp
index 9d8754c9ce9c8fb4e47f910fd854e7f69128d7a4..eb5403151890cc03f04798f5d73f622bbd9e0d42 100644
--- a/Framework/Crystal/src/SaveIsawPeaks.cpp
+++ b/Framework/Crystal/src/SaveIsawPeaks.cpp
@@ -1,5 +1,5 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidCrystal/SaveIsawPeaks.h"
#include "MantidDataObjects/Peak.h"
#include "MantidDataObjects/PeaksWorkspace.h"
diff --git a/Framework/Crystal/src/SaveLauenorm.cpp b/Framework/Crystal/src/SaveLauenorm.cpp
index 927a86d07c8a9797dfd8a0df0164c71fc6268431..339c05f661de42f35bec75af98fde98ee01a4000 100644
--- a/Framework/Crystal/src/SaveLauenorm.cpp
+++ b/Framework/Crystal/src/SaveLauenorm.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/SaveLauenorm.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidKernel/Utils.h"
diff --git a/Framework/Crystal/src/SetSpecialCoordinates.cpp b/Framework/Crystal/src/SetSpecialCoordinates.cpp
index 492e5840cb752bdfaa8a8f22491f577611482007..05b5d9b518e062c79c30c9f312309ad1cd464587 100644
--- a/Framework/Crystal/src/SetSpecialCoordinates.cpp
+++ b/Framework/Crystal/src/SetSpecialCoordinates.cpp
@@ -1,5 +1,4 @@
#include "MantidCrystal/SetSpecialCoordinates.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/IPeaksWorkspace.h"
#include "MantidAPI/IMDEventWorkspace.h"
#include "MantidAPI/IMDHistoWorkspace.h"
diff --git a/Framework/Crystal/src/SortHKL.cpp b/Framework/Crystal/src/SortHKL.cpp
index 019bb2e8507fe323848e1eefcba552df6f5a3a51..7e1d9cadcc29f23a6ea860af189c12c1d92002d1 100644
--- a/Framework/Crystal/src/SortHKL.cpp
+++ b/Framework/Crystal/src/SortHKL.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/SortHKL.h"
#include "MantidDataObjects/Peak.h"
#include "MantidDataObjects/PeaksWorkspace.h"
diff --git a/Framework/Crystal/src/StatisticsOfPeaksWorkspace.cpp b/Framework/Crystal/src/StatisticsOfPeaksWorkspace.cpp
index 4bf0b39255b41d08655309b985dd74dac3336407..07d090b008bde9a419d3272f6856c3080ea02631 100644
--- a/Framework/Crystal/src/StatisticsOfPeaksWorkspace.cpp
+++ b/Framework/Crystal/src/StatisticsOfPeaksWorkspace.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/StatisticsOfPeaksWorkspace.h"
#include "MantidKernel/Utils.h"
#include "MantidKernel/BoundedValidator.h"
diff --git a/Framework/Crystal/src/TOFExtinction.cpp b/Framework/Crystal/src/TOFExtinction.cpp
index 609acdfb5cc0844652119b074ce47eda9c7c9e38..19fb13381c3df3d8ade2d6d7e8f7de99fe05b004 100644
--- a/Framework/Crystal/src/TOFExtinction.cpp
+++ b/Framework/Crystal/src/TOFExtinction.cpp
@@ -1,5 +1,4 @@
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidCrystal/TOFExtinction.h"
#include "MantidDataObjects/Peak.h"
#include "MantidDataObjects/PeaksWorkspace.h"
diff --git a/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h b/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h
index ae51ee6bc546147d19ee3d365b728512e0bf0641..9d3eeba57a4f02f257190c767a07f51f4f6f6df0 100644
--- a/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h
+++ b/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h
@@ -152,43 +152,43 @@ private:
//--------------- Class Variables -------------------
/// Output Workspace containing the dspacing ~ TOF peak positions
- DataObjects::Workspace2D_sptr dataWS;
+ DataObjects::Workspace2D_sptr m_dataWS;
/// Map for all peaks to fit individually
- std::map<std::vector<int>, Functions::BackToBackExponential_sptr> mPeaks;
+ std::map<std::vector<int>, Functions::BackToBackExponential_sptr> m_Peaks;
/// Map for all peaks' error (fitted vs. experimental): [HKL]: Chi^2
- std::map<std::vector<int>, double> mPeakErrors;
+ std::map<std::vector<int>, double> m_PeakErrors;
/// Map for function (instrument parameter)
- std::map<std::string, double> mFuncParameters;
+ std::map<std::string, double> m_FuncParameters;
/// Map to store the original (input) parameters
- std::map<std::string, double> mOrigParameters;
+ std::map<std::string, double> m_OrigParameters;
/// Peak function parameter names
- std::vector<std::string> mPeakFunctionParameterNames;
+ std::vector<std::string> m_PeakFunctionParameterNames;
/// N sets of the peak parameter values for the best N chi2 for MC. It is
/// paired with mPeakFunctionParameterNames
- std::vector<std::pair<double, std::vector<double>>> mBestMCParameters;
+ std::vector<std::pair<double, std::vector<double>>> m_BestMCParameters;
/// N sets of the peak parameter values for the best N chi2 for MC. It is
/// paired with mPeakFunctionParameterNames
- std::vector<std::pair<double, std::vector<double>>> mBestFitParameters;
+ std::vector<std::pair<double, std::vector<double>>> m_BestFitParameters;
/// N sets of the homemade chi2 and gsl chi2
- std::vector<std::pair<double, double>> mBestFitChi2s;
+ std::vector<std::pair<double, double>> m_BestFitChi2s;
/// Best Chi2 ever
- double mBestGSLChi2;
+ double m_BestGSLChi2;
/// Minimum allowed sigma of a peak
- double mMinSigma;
+ double m_MinSigma;
/// Minimum number of fitted peaks for refinement
- size_t mMinNumFittedPeaks;
+ size_t m_MinNumFittedPeaks;
/// Maximum number of data stored
- size_t mMaxNumberStoredParameters;
+ size_t m_MaxNumberStoredParameters;
/// Modelling function
- Functions::ThermalNeutronDtoTOFFunction_sptr mFunction;
+ Functions::ThermalNeutronDtoTOFFunction_sptr m_Function;
};
/** Formular for linear iterpolation: X = [(xf-x0)*Y - (xf*y0-x0*yf)]/(yf-y0)
diff --git a/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h b/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h
index e9e35f7ac6e9d915984bba1aa8a17d91f7c10955..9add0ff7f666e5946222020673c31a24eb6c58d6 100644
--- a/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h
+++ b/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h
@@ -241,6 +241,7 @@ inline GSLMatrixMult3 operator*(const GSLMatrixMult2 &mm, const Tr &m) {
/// The << operator. Prints a matrix in rows.
inline std::ostream &operator<<(std::ostream &ostr, const GSLMatrix &m) {
+ std::ios::fmtflags fflags(ostr.flags());
ostr << std::scientific << std::setprecision(6);
for (size_t i = 0; i < m.size1(); ++i) {
for (size_t j = 0; j < m.size2(); ++j) {
@@ -248,6 +249,7 @@ inline std::ostream &operator<<(std::ostream &ostr, const GSLMatrix &m) {
}
ostr << std::endl;
}
+ ostr.flags(fflags);
return ostr;
}
diff --git a/Framework/CurveFitting/src/Algorithms/CalculateGammaBackground.cpp b/Framework/CurveFitting/src/Algorithms/CalculateGammaBackground.cpp
index a6281e12576ea6a561de2189adf28c38e98ac59f..0daa71f91663bea98e7a610601556e78d77aa205 100644
--- a/Framework/CurveFitting/src/Algorithms/CalculateGammaBackground.cpp
+++ b/Framework/CurveFitting/src/Algorithms/CalculateGammaBackground.cpp
@@ -6,9 +6,11 @@
#include "MantidAPI/CompositeFunction.h"
#include "MantidAPI/FunctionProperty.h"
#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/PhysicalConstants.h"
diff --git a/Framework/CurveFitting/src/Algorithms/CalculateMSVesuvio.cpp b/Framework/CurveFitting/src/Algorithms/CalculateMSVesuvio.cpp
index c34d6b66b7caf69f416a7fb04af6a6f341c9a881..c0aab6f4f53fad24963adeb9762cd707836a1e7b 100644
--- a/Framework/CurveFitting/src/Algorithms/CalculateMSVesuvio.cpp
+++ b/Framework/CurveFitting/src/Algorithms/CalculateMSVesuvio.cpp
@@ -8,7 +8,7 @@
#include "MantidCurveFitting/Functions/VesuvioResolution.h"
#include "MantidAPI/SampleShapeValidator.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
diff --git a/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp b/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp
index 1124ff0504e39bf341dc6e2d45f958ec507eeda8..1f2ba6bfb145c5dc580e11219a74c281bbb5966b 100644
--- a/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp
+++ b/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp
@@ -1,10 +1,11 @@
#include "MantidCurveFitting/Algorithms/ConvertToYSpace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
#include "MantidKernel/BoundedValidator.h"
-
-#include <boost/make_shared.hpp>
+#include "MantidKernel/CompositeValidator.h"
namespace Mantid {
namespace CurveFitting {
diff --git a/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp b/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
index b69b92fdba2ae6bc11c07eaadbd5e5c46d75924d..87801460543315e7aaccd4501e43e74facf27e8f 100644
--- a/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
+++ b/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
@@ -2021,7 +2021,6 @@ bool FitPowderDiffPeaks::doFitMultiplePeaks(
// 1. Fit peaks intensities first
const size_t numpeaks = peakfuncs.size();
map<string, double> peaksfuncparams;
- bool evergood = true;
// a) Set up fit/fix
vector<string> peakparnames = peakfuncs[0]->getParameterNames();
@@ -2045,7 +2044,7 @@ bool FitPowderDiffPeaks::doFitMultiplePeaks(
double chi2;
bool fitgood = doFitNPeaksSimple(dataws, wsindex, peaksfunc, peakfuncs,
"Levenberg-MarquardtMD", 1000, chi2);
- evergood = evergood || fitgood;
+ bool evergood = fitgood;
// c) Process result
if (!fitgood) {
diff --git a/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp b/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp
index 60e3d731b21978a1bb9b3ed92ab4deb36575ab06..21d6e9af3d6c32ae3b6a07aa2cd14487ad0aac60 100644
--- a/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp
+++ b/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp
@@ -341,7 +341,7 @@ void LeBailFit::exec() {
case FIT:
// LeBail Fit
g_log.notice() << "Function: Do LeBail Fit ==> Monte Carlo.\n";
-
+ // fall through
case MONTECARLO:
// Monte carlo Le Bail refinement
g_log.notice("Function: Do LeBail Fit By Monte Carlo Random Walk.");
diff --git a/Framework/CurveFitting/src/Algorithms/NormaliseByPeakArea.cpp b/Framework/CurveFitting/src/Algorithms/NormaliseByPeakArea.cpp
index 780f0feb4261bf251d0c137fae577124e818ec44..320b0e0a634c02a01930dc8823504a199c8202a3 100644
--- a/Framework/CurveFitting/src/Algorithms/NormaliseByPeakArea.cpp
+++ b/Framework/CurveFitting/src/Algorithms/NormaliseByPeakArea.cpp
@@ -1,10 +1,13 @@
#include "MantidCurveFitting/Algorithms/NormaliseByPeakArea.h"
-#include "MantidAPI/IFunction.h"
#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/IFunction.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
#include <boost/make_shared.hpp>
diff --git a/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp b/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp
index 98a64f0b76769673b79f16fcf1fab4ce31aea6d1..80d4fdec61c340ed49b564399931f1824e76dc26 100644
--- a/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp
+++ b/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp
@@ -48,7 +48,9 @@ DECLARE_ALGORITHM(RefinePowderInstrumentParameters)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
-RefinePowderInstrumentParameters::RefinePowderInstrumentParameters() {}
+RefinePowderInstrumentParameters::RefinePowderInstrumentParameters()
+ : m_BestGSLChi2(0.0), m_MinSigma(0.0), m_MinNumFittedPeaks(0),
+ m_MaxNumberStoredParameters(0) {}
//----------------------------------------------------------------------------------------------
/** Destructor
@@ -145,7 +147,7 @@ void RefinePowderInstrumentParameters::exec() {
DataObjects::TableWorkspace_sptr parameterWS =
this->getProperty("InstrumentParameterWorkspace");
- mMinSigma = getProperty("MinSigma");
+ m_MinSigma = getProperty("MinSigma");
int tempint = getProperty("MinNumberFittedPeaks");
if (tempint <= 1) {
@@ -153,13 +155,13 @@ void RefinePowderInstrumentParameters::exec() {
<< " is too small. " << endl;
throw std::invalid_argument("Input MinNumberFittedPeaks is too small.");
}
- mMinNumFittedPeaks = static_cast<size_t>(tempint);
+ m_MinNumFittedPeaks = static_cast<size_t>(tempint);
tempint = getProperty("NumberBestFitRecorded");
if (tempint <= 0)
throw runtime_error(
"Input NumberBestFitRecorded cannot be less and equal to 0. ");
- mMaxNumberStoredParameters = static_cast<size_t>(tempint);
+ m_MaxNumberStoredParameters = static_cast<size_t>(tempint);
string algoption = getProperty("RefinementAlgorithm");
if (algoption.compare("DirectFit") == 0)
@@ -172,14 +174,14 @@ void RefinePowderInstrumentParameters::exec() {
// 2. Parse input table workspace
genPeaksFromTable(peakWS);
- importParametersFromTable(parameterWS, mFuncParameters);
- mOrigParameters = mFuncParameters;
+ importParametersFromTable(parameterWS, m_FuncParameters);
+ m_OrigParameters = m_FuncParameters;
// 3. Generate a cener workspace as function of d-spacing.
bool usemc = false;
if (refinealgorithm == MonteCarlo)
usemc = true;
- genPeakCentersWorkspace(usemc, mMaxNumberStoredParameters);
+ genPeakCentersWorkspace(usemc, m_MaxNumberStoredParameters);
// 4. Fit instrument geometry function
stringstream errss;
@@ -208,7 +210,7 @@ void RefinePowderInstrumentParameters::exec() {
}
// 5. Set output workspace
- this->setProperty("OutputWorkspace", dataWS);
+ this->setProperty("OutputWorkspace", m_dataWS);
// 6. Output new instrument parameters
DataObjects::TableWorkspace_sptr fitparamws =
@@ -228,16 +230,16 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
// 1. Initialize the fitting function
ThermalNeutronDtoTOFFunction rawfunc;
- mFunction = boost::make_shared<ThermalNeutronDtoTOFFunction>(rawfunc);
- mFunction->initialize();
+ m_Function = boost::make_shared<ThermalNeutronDtoTOFFunction>(rawfunc);
+ m_Function->initialize();
- API::FunctionDomain1DVector domain(dataWS->readX(1));
+ API::FunctionDomain1DVector domain(m_dataWS->readX(1));
API::FunctionValues values(domain);
- const MantidVec &rawY = dataWS->readY(0);
- const MantidVec &rawE = dataWS->readE(0);
+ const MantidVec &rawY = m_dataWS->readY(0);
+ const MantidVec &rawE = m_dataWS->readE(0);
// 2. Set up parameters values
- std::vector<std::string> funparamnames = mFunction->getParameterNames();
+ std::vector<std::string> funparamnames = m_Function->getParameterNames();
std::vector<std::string> paramtofit = getProperty("ParametersToFit");
std::sort(paramtofit.begin(), paramtofit.end());
@@ -247,22 +249,22 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
std::map<std::string, double>::iterator paramiter;
for (size_t i = 0; i < funparamnames.size(); ++i) {
string parname = funparamnames[i];
- paramiter = mFuncParameters.find(parname);
- if (paramiter == mFuncParameters.end()) {
+ paramiter = m_FuncParameters.find(parname);
+ if (paramiter == m_FuncParameters.end()) {
// Not found and thus skip
continue;
}
double parvalue = paramiter->second;
- mFunction->setParameter(parname, parvalue);
+ m_Function->setParameter(parname, parvalue);
msgss << setw(10) << parname << " = " << parvalue << endl;
}
cout << msgss.str();
// 2b. Calculate the statistic of the starting values
- double gslchi2 = calculateFunctionStatistic(mFunction, dataWS, 0);
+ double gslchi2 = calculateFunctionStatistic(m_Function, m_dataWS, 0);
double homchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
cout << "Fit Starting Value: Chi^2 (GSL) = " << gslchi2
<< ", Chi2^2 (Home) = " << homchi2 << endl;
@@ -274,9 +276,9 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
vsiter = std::find(paramtofit.begin(), paramtofit.end(), parname);
if (vsiter == paramtofit.end())
- mFunction->fix(i);
+ m_Function->fix(i);
else
- mFunction->unfix(i);
+ m_Function->unfix(i);
}
// 4. Select minimizer. Use Simplex for more than 1 parameters to fit.
@@ -288,13 +290,13 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
g_log.information() << "Fit use minizer: " << minimizer << endl;
// 5. Create and setup fit algorithm
- g_log.information() << "Fit instrument geometry: " << mFunction->asString()
+ g_log.information() << "Fit instrument geometry: " << m_Function->asString()
<< std::endl;
stringstream outss;
- for (size_t i = 0; i < dataWS->readX(0).size(); ++i)
- outss << dataWS->readX(0)[i] << "\t\t" << dataWS->readY(0)[i] << "\t\t"
- << dataWS->readE(0)[i] << endl;
+ for (size_t i = 0; i < m_dataWS->readX(0).size(); ++i)
+ outss << m_dataWS->readX(0)[i] << "\t\t" << m_dataWS->readY(0)[i] << "\t\t"
+ << m_dataWS->readE(0)[i] << endl;
cout << "Input Peak Position Workspace To Fit: " << endl
<< outss.str() << endl;
@@ -302,8 +304,8 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
fitalg->initialize();
fitalg->setProperty("Function",
- boost::dynamic_pointer_cast<API::IFunction>(mFunction));
- fitalg->setProperty("InputWorkspace", dataWS);
+ boost::dynamic_pointer_cast<API::IFunction>(m_Function));
+ fitalg->setProperty("InputWorkspace", m_dataWS);
fitalg->setProperty("WorkspaceIndex", 0);
fitalg->setProperty("Minimizer", minimizer);
fitalg->setProperty("CostFunction", "Least squares");
@@ -326,31 +328,31 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
API::IFunction_sptr fitfunc = fitalg->getProperty("Function");
// 4. Set the output data (model and diff)
- mFunction->function(domain, values);
+ m_Function->function(domain, values);
for (size_t i = 0; i < domain.size(); ++i) {
- dataWS->dataY(1)[i] = values[i];
- dataWS->dataY(2)[i] = dataWS->readY(0)[i] - values[i];
+ m_dataWS->dataY(1)[i] = values[i];
+ m_dataWS->dataY(2)[i] = m_dataWS->readY(0)[i] - values[i];
}
double selfchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
cout << "Homemade Chi^2 = " << selfchi2 << endl;
// 5. Update fitted parameters
for (size_t i = 0; i < funparamnames.size(); ++i) {
std::string parname = funparamnames[i];
double parvalue = fitfunc->getParameter(parname);
- mFuncParameters[parname] = parvalue;
+ m_FuncParameters[parname] = parvalue;
}
// 6. Pretty screen output
stringstream dbss;
dbss << "************ Fit Parameter Result *************" << std::endl;
- for (paramiter = mFuncParameters.begin(); paramiter != mFuncParameters.end();
- ++paramiter) {
+ for (paramiter = m_FuncParameters.begin();
+ paramiter != m_FuncParameters.end(); ++paramiter) {
std::string parname = paramiter->first;
- double inpparvalue = mOrigParameters[parname];
+ double inpparvalue = m_OrigParameters[parname];
double parvalue = paramiter->second;
dbss << setw(20) << parname << " = " << setw(15) << setprecision(6)
<< parvalue << "\t\tFrom " << setw(15) << setprecision(6)
@@ -362,18 +364,18 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
// 7. Play with Zscore: template<typename TYPE>
// std::vector<double> getZscore(const std::vector<TYPE>& data, const bool
// sorted=false);
- vector<double> z0 = Kernel::getZscore(dataWS->readY(0));
- vector<double> z1 = Kernel::getZscore(dataWS->readY(1));
- vector<double> z2 = Kernel::getZscore(dataWS->readY(2));
+ vector<double> z0 = Kernel::getZscore(m_dataWS->readY(0));
+ vector<double> z1 = Kernel::getZscore(m_dataWS->readY(1));
+ vector<double> z2 = Kernel::getZscore(m_dataWS->readY(2));
stringstream zss;
zss << setw(20) << "d_h" << setw(20) << "Z DataY" << setw(20) << "Z ModelY"
<< setw(20) << "Z DiffY" << setw(20) << "DiffY" << endl;
for (size_t i = 0; i < z0.size(); ++i) {
- double d_h = dataWS->readX(0)[i];
+ double d_h = m_dataWS->readX(0)[i];
double zdatay = z0[i];
double zmodely = z1[i];
double zdiffy = z2[i];
- double diffy = dataWS->readY(2)[i];
+ double diffy = m_dataWS->readY(2)[i];
zss << setw(20) << d_h << setw(20) << zdatay << setw(20) << zmodely
<< setw(20) << zdiffy << setw(20) << diffy << endl;
}
@@ -392,7 +394,7 @@ bool RefinePowderInstrumentParameters::fitFunction(IFunction_sptr func,
fitalg->setProperty("Function",
boost::dynamic_pointer_cast<API::IFunction>(func));
- fitalg->setProperty("InputWorkspace", dataWS);
+ fitalg->setProperty("InputWorkspace", m_dataWS);
fitalg->setProperty("WorkspaceIndex", 0);
fitalg->setProperty("Minimizer", "Simplex");
fitalg->setProperty("CostFunction", "Least squares");
@@ -462,19 +464,20 @@ double RefinePowderInstrumentParameters::calculateFunctionStatistic(
void RefinePowderInstrumentParameters::refineInstrumentParametersMC(
TableWorkspace_sptr parameterWS, bool fit2) {
// 1. Get function's parameter names
- getD2TOFFuncParamNames(mPeakFunctionParameterNames);
+ getD2TOFFuncParamNames(m_PeakFunctionParameterNames);
// 2. Parse parameter (table) workspace
vector<double> stepsizes, lowerbounds, upperbounds;
- importMonteCarloParametersFromTable(parameterWS, mPeakFunctionParameterNames,
+ importMonteCarloParametersFromTable(parameterWS, m_PeakFunctionParameterNames,
stepsizes, lowerbounds, upperbounds);
stringstream dbss;
- for (size_t i = 0; i < mPeakFunctionParameterNames.size(); ++i) {
- dbss << setw(20) << mPeakFunctionParameterNames[i] << ": Min = " << setw(15)
- << setprecision(6) << lowerbounds[i] << ", Max = " << setw(15)
- << setprecision(6) << upperbounds[i] << ", Step Size = " << setw(15)
- << setprecision(6) << stepsizes[i] << endl;
+ for (size_t i = 0; i < m_PeakFunctionParameterNames.size(); ++i) {
+ dbss << setw(20) << m_PeakFunctionParameterNames[i]
+ << ": Min = " << setw(15) << setprecision(6) << lowerbounds[i]
+ << ", Max = " << setw(15) << setprecision(6) << upperbounds[i]
+ << ", Step Size = " << setw(15) << setprecision(6) << stepsizes[i]
+ << endl;
}
g_log.notice() << "Monte Carlo Parameters: " << endl
<< dbss.str();
@@ -494,33 +497,33 @@ void RefinePowderInstrumentParameters::refineInstrumentParametersMC(
double stepsizescalefactor = 1.1;
// 5. Monte Carlo simulation
- doParameterSpaceRandomWalk(mPeakFunctionParameterNames, lowerbounds,
+ doParameterSpaceRandomWalk(m_PeakFunctionParameterNames, lowerbounds,
upperbounds, stepsizes, maxsteps,
stepsizescalefactor, fit2);
// 6. Record the result
- const MantidVec &X = dataWS->readX(0);
- const MantidVec &Y = dataWS->readY(0);
- const MantidVec &E = dataWS->readE(0);
+ const MantidVec &X = m_dataWS->readX(0);
+ const MantidVec &Y = m_dataWS->readY(0);
+ const MantidVec &E = m_dataWS->readE(0);
FunctionDomain1DVector domain(X);
FunctionValues values(domain);
- for (size_t i = 0; i < mBestFitParameters.size(); ++i) {
+ for (size_t i = 0; i < m_BestFitParameters.size(); ++i) {
// a. Set the function with the
- for (size_t j = 0; j < mPeakFunctionParameterNames.size(); ++j) {
- mFunction->setParameter(mPeakFunctionParameterNames[j],
- mBestFitParameters[i].second[j]);
+ for (size_t j = 0; j < m_PeakFunctionParameterNames.size(); ++j) {
+ m_Function->setParameter(m_PeakFunctionParameterNames[j],
+ m_BestFitParameters[i].second[j]);
}
// b. Calculate
- calculateD2TOFFunction(mFunction, domain, values, Y, E);
+ calculateD2TOFFunction(m_Function, domain, values, Y, E);
vector<double> vec_n;
- calculateThermalNeutronSpecial(mFunction, X, vec_n);
+ calculateThermalNeutronSpecial(m_Function, X, vec_n);
// c. Put the data to output workspace
- MantidVec &newY = dataWS->dataY(3 * i + 1);
- MantidVec &newD = dataWS->dataY(3 * i + 2);
- MantidVec &newN = dataWS->dataY(3 * i + 3);
+ MantidVec &newY = m_dataWS->dataY(3 * i + 1);
+ MantidVec &newD = m_dataWS->dataY(3 * i + 2);
+ MantidVec &newN = m_dataWS->dataY(3 * i + 3);
for (size_t j = 0; j < newY.size(); ++j) {
newY[j] = values[j];
newD[j] = Y[j] - values[j];
@@ -548,30 +551,30 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
<< setw(20) << "Upper Boundary" << setw(20) << "Step Size" << endl;
for (size_t i = 0; i < parnames.size(); ++i)
inpinfo << setw(20) << parnames[i] << setw(20) <<
- mFuncParameters[parnames[i]]
+ m_FuncParameters[parnames[i]]
<< setw(20) << lowerbounds[i]
<< setw(20) << upperbounds[i] << setw(20) << stepsizes[i] << endl;
cout << inpinfo.str();
------------*/
- // 1. Set up starting values, esp. to mFunction
+ // 1. Set up starting values, esp. to m_Function
size_t numparameters = parnames.size();
vector<double> paramvalues;
for (size_t i = 0; i < numparameters; ++i) {
string parname = parnames[i];
- double parvalue = mFuncParameters[parname];
+ double parvalue = m_FuncParameters[parname];
paramvalues.push_back(parvalue);
- mFunction->setParameter(parname, parvalue);
+ m_Function->setParameter(parname, parvalue);
}
// Calcualte the function's initial statistic
- mBestGSLChi2 = calculateFunctionStatistic(mFunction, dataWS, 0);
- cout << "Function with starting values has Chi2 = " << mBestGSLChi2
+ m_BestGSLChi2 = calculateFunctionStatistic(m_Function, m_dataWS, 0);
+ cout << "Function with starting values has Chi2 = " << m_BestGSLChi2
<< " (GSL L.M) " << endl;
- const MantidVec &X = dataWS->readX(0);
- const MantidVec &rawY = dataWS->readY(0);
- const MantidVec &rawE = dataWS->readE(0);
+ const MantidVec &X = m_dataWS->readX(0);
+ const MantidVec &rawY = m_dataWS->readY(0);
+ const MantidVec &rawE = m_dataWS->readE(0);
FunctionDomain1DVector domain(X);
FunctionValues values(domain);
@@ -623,7 +626,7 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// 4. Do MC loops
double curchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
g_log.notice() << "Monte Carlo Random Walk Starting Chi^2 = " << curchi2
<< endl;
@@ -656,7 +659,7 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
}
try {
- mFunction->setParameter(parnames[paramindex], newvalue);
+ m_Function->setParameter(parnames[paramindex], newvalue);
} catch (runtime_error &) {
stringstream errss;
errss << "New Value = " << newvalue
@@ -669,13 +672,13 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// b. Calcualte the new
double newchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
// Optionally fit
if (fit2) {
// i. Copy the parameters
for (size_t i = 0; i < numparameters; ++i) {
- double parvalue = mFunction->getParameter(i);
+ double parvalue = m_Function->getParameter(i);
func4fit->setParameter(i, parvalue);
}
@@ -688,8 +691,8 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
double homchi2 =
calculateD2TOFFunction(func4fit, domain, values, rawY, rawE);
- if (gslchi2 < mBestGSLChi2)
- mBestGSLChi2 = gslchi2;
+ if (gslchi2 < m_BestGSLChi2)
+ m_BestGSLChi2 = gslchi2;
// iv. Archive
vector<double> newparvalues;
@@ -697,15 +700,15 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
double parvalue = func4fit->getParameter(i);
newparvalues.push_back(parvalue);
}
- mBestFitParameters.push_back(make_pair(homchi2, newparvalues));
- mBestFitChi2s.push_back(make_pair(homchi2, gslchi2));
+ m_BestFitParameters.push_back(make_pair(homchi2, newparvalues));
+ m_BestFitChi2s.push_back(make_pair(homchi2, gslchi2));
// v. Sort and keep in size
- sort(mBestFitParameters.begin(), mBestFitParameters.end());
- sort(mBestFitChi2s.begin(), mBestFitChi2s.end());
- if (mBestFitParameters.size() > mMaxNumberStoredParameters) {
- mBestFitParameters.pop_back();
- mBestFitChi2s.pop_back();
+ sort(m_BestFitParameters.begin(), m_BestFitParameters.end());
+ sort(m_BestFitChi2s.begin(), m_BestFitChi2s.end());
+ if (m_BestFitParameters.size() > m_MaxNumberStoredParameters) {
+ m_BestFitParameters.pop_back();
+ m_BestFitChi2s.pop_back();
}
// cout << "\tHomemade Chi^2 = " << homchi2 << endl;
@@ -752,12 +755,12 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// ii. Add the new values to vector
vector<double> parametervalues = paramvalues;
- mBestMCParameters.push_back(make_pair(newchi2, parametervalues));
+ m_BestMCParameters.push_back(make_pair(newchi2, parametervalues));
// iii. Sort and delete the last if necessary
- sort(mBestMCParameters.begin(), mBestMCParameters.end());
- if (mBestMCParameters.size() > mMaxNumberStoredParameters)
- mBestMCParameters.pop_back();
+ sort(m_BestMCParameters.begin(), m_BestMCParameters.end());
+ if (m_BestMCParameters.size() > m_MaxNumberStoredParameters)
+ m_BestMCParameters.pop_back();
// iv. Update chi2 and ...
curchi2 = newchi2;
@@ -773,24 +776,24 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// 3. Debug output
stringstream mcresult;
- mcresult << "Monte Carlo Result for " << mBestMCParameters.size()
+ mcresult << "Monte Carlo Result for " << m_BestMCParameters.size()
<< " Best Results" << endl;
mcresult << "Number of acceptance = " << numacceptance << ", out of "
<< maxsteps << " MC steps."
<< "Accept ratio = "
<< static_cast<double>(numacceptance) / static_cast<double>(maxsteps)
<< endl;
- mcresult << "Best " << mBestMCParameters.size()
+ mcresult << "Best " << m_BestMCParameters.size()
<< " Monte Carlo (no fit) results: " << endl;
- for (size_t i = 0; i < mBestMCParameters.size(); ++i) {
- mcresult << setw(3) << i << ": Chi^2 = " << mBestMCParameters[i].first
+ for (size_t i = 0; i < m_BestMCParameters.size(); ++i) {
+ mcresult << setw(3) << i << ": Chi^2 = " << m_BestMCParameters[i].first
<< endl;
}
- mcresult << "Best " << mBestMCParameters.size()
- << " fitting results. Best Chi^2 = " << mBestGSLChi2 << endl;
- for (size_t i = 0; i < mBestFitParameters.size(); ++i) {
- mcresult << setw(3) << i << ": Chi^2 = " << mBestFitParameters[i].first
- << ", GSL Chi^2 = " << mBestFitChi2s[i].second << endl;
+ mcresult << "Best " << m_BestMCParameters.size()
+ << " fitting results. Best Chi^2 = " << m_BestGSLChi2 << endl;
+ for (size_t i = 0; i < m_BestFitParameters.size(); ++i) {
+ mcresult << setw(3) << i << ": Chi^2 = " << m_BestFitParameters[i].first
+ << ", GSL Chi^2 = " << m_BestFitChi2s[i].second << endl;
}
g_log.notice() << mcresult.str();
@@ -809,7 +812,7 @@ void RefinePowderInstrumentParameters::getD2TOFFuncParamNames(
d2toffunc.initialize();
std::vector<std::string> funparamnames = d2toffunc.getParameterNames();
- mFunction = boost::make_shared<ThermalNeutronDtoTOFFunction>(d2toffunc);
+ m_Function = boost::make_shared<ThermalNeutronDtoTOFFunction>(d2toffunc);
// 3. Copy
parnames = funparamnames;
@@ -824,14 +827,14 @@ double RefinePowderInstrumentParameters::calculateD2TOFFunction(
const MantidVec &rawY, const MantidVec &rawE) {
// 1. Check validity
if (!func) {
- throw std::runtime_error("mFunction has not been initialized!");
+ throw std::runtime_error("m_Function has not been initialized!");
} else {
/*
- vector<string> parnames = mFunction->getParameterNames();
+ vector<string> parnames = m_Function->getParameterNames();
for (size_t i = 0; i < parnames.size(); ++i)
{
cout << "DBx1125 " << parnames[i] << " = " <<
- mFunction->getParameter(parnames[i]) << endl;
+ m_Function->getParameter(parnames[i]) << endl;
}
*/
;
@@ -861,7 +864,7 @@ double RefinePowderInstrumentParameters::calculateD2TOFFunction(
//------------------------------- Processing Inputs
//----------------------------------------
/** Genearte peaks from input workspace
- * Peaks are stored in a map. (HKL) is the key
+ * m_Peaks are stored in a map. (HKL) is the key
*/
void RefinePowderInstrumentParameters::genPeaksFromTable(
DataObjects::TableWorkspace_sptr peakparamws) {
@@ -873,7 +876,7 @@ void RefinePowderInstrumentParameters::genPeaksFromTable(
"Invalid input table workspace for peak parameters");
}
- mPeaks.clear();
+ m_Peaks.clear();
// 2. Parse table workspace rows to generate peaks
vector<string> colnames = peakparamws->getColumnNames();
@@ -940,12 +943,12 @@ void RefinePowderInstrumentParameters::genPeaksFromTable(
hkl.push_back(k);
hkl.push_back(l);
- mPeaks.insert(std::make_pair(hkl, newpeakptr));
+ m_Peaks.insert(std::make_pair(hkl, newpeakptr));
- mPeakErrors.insert(make_pair(hkl, chi2));
+ m_PeakErrors.insert(make_pair(hkl, chi2));
- g_log.information() << "[GeneratePeaks] Peak " << ir << " HKL = [" << hkl[0]
- << ", " << hkl[1] << ", " << hkl[2]
+ g_log.information() << "[Generatem_Peaks] Peak " << ir << " HKL = ["
+ << hkl[0] << ", " << hkl[1] << ", " << hkl[2]
<< "], Input Center = " << setw(10) << setprecision(6)
<< newpeak.centre() << endl;
@@ -1118,17 +1121,17 @@ hkl, double lattice)
/** Calcualte value n for thermal neutron peak profile
*/
void RefinePowderInstrumentParameters::calculateThermalNeutronSpecial(
- IFunction_sptr mFunction, vector<double> vec_d, vector<double> &vec_n) {
- if (mFunction->name().compare("ThermalNeutronDtoTOFFunction") != 0) {
- g_log.warning() << "Function (" << mFunction->name()
+ IFunction_sptr m_Function, vector<double> vec_d, vector<double> &vec_n) {
+ if (m_Function->name().compare("ThermalNeutronDtoTOFFunction") != 0) {
+ g_log.warning() << "Function (" << m_Function->name()
<< " is not ThermalNeutronDtoTOFFunction. And it is not "
"required to calculate n." << endl;
for (size_t i = 0; i < vec_d.size(); ++i)
vec_n.push_back(0);
}
- double width = mFunction->getParameter("Width");
- double tcross = mFunction->getParameter("Tcross");
+ double width = m_Function->getParameter("Width");
+ double tcross = m_Function->getParameter("Tcross");
for (size_t i = 0; i < vec_d.size(); ++i) {
double dh = vec_d[i];
@@ -1149,7 +1152,7 @@ void RefinePowderInstrumentParameters::calculateThermalNeutronSpecial(
void RefinePowderInstrumentParameters::genPeakCentersWorkspace(
bool montecarlo, size_t numbestfit) {
// 1. Collect values in a vector for sorting
- double lattice = mFuncParameters["LatticeConstant"];
+ double lattice = m_FuncParameters["LatticeConstant"];
if (lattice < 1.0E-5) {
std::stringstream errmsg;
errmsg << "Input Lattice constant = " << lattice
@@ -1176,12 +1179,12 @@ void RefinePowderInstrumentParameters::genPeakCentersWorkspace(
Geometry::UnitCell unitcell(lattice, lattice, lattice, 90.0, 90.0, 90.0);
- for (peakiter = mPeaks.begin(); peakiter != mPeaks.end(); ++peakiter) {
+ for (peakiter = m_Peaks.begin(); peakiter != m_Peaks.end(); ++peakiter) {
vector<int> hkl = peakiter->first;
BackToBackExponential_sptr peak = peakiter->second;
double sigma = peak->getParameter("S");
- if (sigma < mMinSigma) {
+ if (sigma < m_MinSigma) {
g_log.information() << "Peak (" << hkl[0] << ", " << hkl[1] << ", "
<< hkl[2]
<< ") has unphysically small Sigma = " << sigma
@@ -1222,18 +1225,18 @@ void RefinePowderInstrumentParameters::genPeakCentersWorkspace(
nspec = 1 + 3;
}
- dataWS = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
+ m_dataWS = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", nspec, size,
size));
- dataWS->getAxis(0)->setUnit("dSpacing");
+ m_dataWS->getAxis(0)->setUnit("dSpacing");
// 4. Put data to output workspace
for (size_t i = 0; i < peakcenters.size(); ++i) {
for (size_t j = 0; j < nspec; ++j) {
- dataWS->dataX(j)[i] = peakcenters[i].first;
+ m_dataWS->dataX(j)[i] = peakcenters[i].first;
}
- dataWS->dataY(0)[i] = peakcenters[i].second.first;
- dataWS->dataE(0)[i] = peakcenters[i].second.second;
+ m_dataWS->dataY(0)[i] = peakcenters[i].second.first;
+ m_dataWS->dataE(0)[i] = peakcenters[i].second.second;
}
return;
@@ -1250,18 +1253,18 @@ RefinePowderInstrumentParameters::genMCResultTable() {
tablews->addColumn("double", "Chi2");
tablews->addColumn("double", "GSLChi2");
- for (size_t i = 0; i < mPeakFunctionParameterNames.size(); ++i) {
- tablews->addColumn("double", mPeakFunctionParameterNames[i]);
+ for (size_t i = 0; i < m_PeakFunctionParameterNames.size(); ++i) {
+ tablews->addColumn("double", m_PeakFunctionParameterNames[i]);
}
// 2. Put values in
- for (size_t ib = 0; ib < mBestFitParameters.size(); ++ib) {
+ for (size_t ib = 0; ib < m_BestFitParameters.size(); ++ib) {
TableRow newrow = tablews->appendRow();
- double chi2 = mBestFitParameters[ib].first;
- double gslchi2 = mBestFitChi2s[ib].second;
+ double chi2 = m_BestFitParameters[ib].first;
+ double gslchi2 = m_BestFitChi2s[ib].second;
newrow << chi2 << gslchi2;
- for (size_t ip = 0; ip < mPeakFunctionParameterNames.size(); ++ip) {
- double tempdbl = mBestFitParameters[ib].second[ip];
+ for (size_t ip = 0; ip < m_PeakFunctionParameterNames.size(); ++ip) {
+ double tempdbl = m_BestFitParameters[ib].second[ip];
newrow << tempdbl;
}
} // ENDFOR 1 Best Answer
@@ -1290,7 +1293,7 @@ RefinePowderInstrumentParameters::genOutputInstrumentParameterTable() {
std::map<std::string, double>::iterator pariter;
- for (pariter = mFuncParameters.begin(); pariter != mFuncParameters.end();
+ for (pariter = m_FuncParameters.begin(); pariter != m_FuncParameters.end();
++pariter) {
API::TableRow newrow = newtablews->appendRow();
std::string parname = pariter->first;
diff --git a/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters3.cpp b/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters3.cpp
index a5c35c1f331d71bca31643d8fc85b77d7bf7b2fd..f87a83a0013f454452b40c588a6b9787401d477a 100644
--- a/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters3.cpp
+++ b/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters3.cpp
@@ -870,8 +870,15 @@ double RefinePowderInstrumentParameters3::calculateFunctionError(
// 2. Fit with zero iteration
double chi2;
string fitstatus;
- doFitFunction(function, dataws, wsindex, "Levenberg-MarquardtMD", 0, chi2,
- fitstatus);
+ const std::string minimizer = "Levenberg-MarquardtMD";
+ bool fitOK =
+ doFitFunction(function, dataws, wsindex, minimizer, 0, chi2, fitstatus);
+
+ if (!fitOK) {
+ g_log.warning() << "Fit by " << minimizer
+ << " with 0 iterations failed, with reason: " << fitstatus
+ << "\n";
+ }
// 3. Restore the fit/fix setup
for (size_t i = 0; i < parnames.size(); ++i) {
diff --git a/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp b/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
index 93b2e86016a7320e17d3ae657789ec49ad86da6f..a19fa51061060d39206dd760f8a1d8db453d9fb0 100644
--- a/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
+++ b/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
@@ -66,8 +66,7 @@ void SplineBackground::exec() {
bool isMasked = inWS->hasMaskedBins(spec);
std::vector<int> masked(Y.size());
if (isMasked) {
- for (API::MatrixWorkspace::MaskList::const_iterator it =
- inWS->maskedBins(spec).begin();
+ for (auto it = inWS->maskedBins(spec).begin();
it != inWS->maskedBins(spec).end(); ++it)
masked[it->first] = 1;
n -= static_cast<int>(inWS->maskedBins(spec).size());
diff --git a/Framework/CurveFitting/src/GSLVector.cpp b/Framework/CurveFitting/src/GSLVector.cpp
index 6c7c341cf7d4f0f9f158ba91e7ebffe771a3cce0..cdbc2a12db0e7f571b5a8703754af69f1805cfd1 100644
--- a/Framework/CurveFitting/src/GSLVector.cpp
+++ b/Framework/CurveFitting/src/GSLVector.cpp
@@ -157,10 +157,12 @@ double GSLVector::dot(const GSLVector &v) const {
/// The << operator.
std::ostream &operator<<(std::ostream &ostr, const GSLVector &v) {
+ std::ios::fmtflags fflags(ostr.flags());
ostr << std::scientific << std::setprecision(6);
for (size_t j = 0; j < v.size(); ++j) {
ostr << std::setw(13) << v[j] << ' ';
}
+ ostr.flags(fflags);
return ostr;
}
diff --git a/Framework/CurveFitting/src/IFittingAlgorithm.cpp b/Framework/CurveFitting/src/IFittingAlgorithm.cpp
index de562d920cb7ca6961c07095663dd03ce53bc28c..4984b1edc74ed77ea305da877eece95d140f407f 100644
--- a/Framework/CurveFitting/src/IFittingAlgorithm.cpp
+++ b/Framework/CurveFitting/src/IFittingAlgorithm.cpp
@@ -216,9 +216,10 @@ void IFittingAlgorithm::addWorkspace(const std::string &workspacePropertyName,
boost::shared_ptr<MultiDomainCreator> multiCreator =
boost::dynamic_pointer_cast<MultiDomainCreator>(m_domainCreator);
if (!multiCreator) {
+ auto &reference = *m_domainCreator.get();
throw std::runtime_error(
std::string("MultiDomainCreator expected, found ") +
- typeid(*m_domainCreator.get()).name());
+ typeid(reference).name());
}
if (!multiCreator->hasCreator(index)) {
creator->declareDatasetProperties(suffix, addProperties);
@@ -283,4 +284,4 @@ void IFittingAlgorithm::exec() {
}
} // namespace CurveFitting
-} // namespace Mantid
\ No newline at end of file
+} // namespace Mantid
diff --git a/Framework/CurveFitting/src/ParameterEstimator.cpp b/Framework/CurveFitting/src/ParameterEstimator.cpp
index 93c46fd68fbb9ae0690fbf296458a5f3bb20b7c4..db682fa12c32e3fce6170d9e4ca8c7a28725dfcd 100644
--- a/Framework/CurveFitting/src/ParameterEstimator.cpp
+++ b/Framework/CurveFitting/src/ParameterEstimator.cpp
@@ -7,6 +7,8 @@
#include "MantidKernel/Logger.h"
+#include <Poco/Mutex.h>
+
#include <cmath>
namespace Mantid {
@@ -18,20 +20,44 @@ using namespace Functions;
/// The logger.
Kernel::Logger g_log("ParameterEstimator");
+namespace {
+/// Mutex to prevent simultaneous access to functionMap
+Poco::Mutex FUNCTION_MAP_MUTEX;
+}
+
enum Function { None, Gaussian, Lorentzian, BackToBackExponential };
typedef std::map<std::string, std::pair<size_t, Function>> FunctionMapType;
//----------------------------------------------------------------------------------------------
+
+/// Initializes a FunctionMapType object
+/// @param functionMapType :: the function map to initialize
+void initFunctionLookup(FunctionMapType &functionMapType) {
+ assert(functionMapType.empty());
+
+ functionMapType["Gaussian"] = std::make_pair(2, Gaussian);
+ functionMapType["Lorentzian"] = std::make_pair(2, Lorentzian);
+ functionMapType["BackToBackExponential"] =
+ std::make_pair(4, BackToBackExponential);
+}
+
+/// Returns a reference to the static functionMapType
+/// @returns :: a const reference to the functionMapType
+const FunctionMapType &getFunctionMapType() {
+
+ Poco::Mutex::ScopedLock lock(FUNCTION_MAP_MUTEX);
+
+ static FunctionMapType functionMapType;
+
+ if (functionMapType.empty())
+ initFunctionLookup(functionMapType);
+ return functionMapType;
+}
+
/// Return a function code for a function if it needs setting values or None
/// otherwise.
Function whichFunction(const API::IFunction &function) {
- static FunctionMapType functionMap;
- if (functionMap.empty()) {
- functionMap["Gaussian"] = std::make_pair(2, Gaussian);
- functionMap["Lorentzian"] = std::make_pair(2, Lorentzian);
- functionMap["BackToBackExponential"] =
- std::make_pair(4, BackToBackExponential);
- }
+ const FunctionMapType &functionMap = getFunctionMapType();
auto index = functionMap.find(function.name());
if (index != functionMap.end()) {
if (!function.isExplicitlySet(index->second.first))
diff --git a/Framework/CurveFitting/src/SimplexMinimizer.cpp b/Framework/CurveFitting/src/SimplexMinimizer.cpp
index b0c5ba671041eaada2fdb2979a8abb0249bd05dc..694b344296ef6cb9944ff1f1932b6950cc8bd19e 100644
--- a/Framework/CurveFitting/src/SimplexMinimizer.cpp
+++ b/Framework/CurveFitting/src/SimplexMinimizer.cpp
@@ -55,6 +55,9 @@ void SimplexMinimizer::initialize(API::ICostFunction_sptr function, size_t) {
size_t np = function->nParams();
// step size for simplex
m_simplexStepSize = gsl_vector_alloc(np);
+ if (m_simplexStepSize == NULL) {
+ throw std::runtime_error("Simplex step size initialized to NULL pointer");
+ }
gsl_vector_set_all(m_simplexStepSize, m_size);
// setup simplex container
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h b/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h
index 44e695b5bcd1d3a08be0c73641950774822fbbb9..cf495c009be312933a224018d34b0deb1079edab 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h
@@ -5,6 +5,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAPI/IFileLoader.h"
+#include "MantidAPI/DeprecatedAlgorithm.h"
namespace Mantid {
namespace DataHandling {
@@ -45,7 +46,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
File change history is stored at: <https://github.com/mantidproject/mantid>.
Code Documentation is available at: <http://doxygen.mantidproject.org>
*/
-class DLLExport LoadAscii : public API::IFileLoader<Kernel::FileDescriptor> {
+class DLLExport LoadAscii : public API::IFileLoader<Kernel::FileDescriptor>,
+ public API::DeprecatedAlgorithm {
public:
/// Default constructor
LoadAscii();
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h b/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h
index c3f14b233810c5a14e3082ea5bc88725df2ef0ed..328be8a18896d921be8e0a25bd1c6ff8f0185c86 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h
@@ -5,6 +5,7 @@
#include <string>
#include <vector>
#include "MantidAPI/IFileLoader.h"
+#include "MantidAPI/DeprecatedAlgorithm.h"
#include "MantidKernel/BinaryFile.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Events.h"
@@ -88,7 +89,8 @@ struct Pulse {
#pragma pack(pop)
class DLLExport LoadEventPreNexus
- : public API::IFileLoader<Kernel::FileDescriptor> {
+ : public API::IFileLoader<Kernel::FileDescriptor>,
+ public API::DeprecatedAlgorithm {
public:
/// Constructor
LoadEventPreNexus();
diff --git a/Framework/DataHandling/src/CheckMantidVersion.cpp b/Framework/DataHandling/src/CheckMantidVersion.cpp
index 30a620c6079eaca94651b3e22d92d059b72a93cf..01776379510adfeda238fd768ab2a72cf9949863 100644
--- a/Framework/DataHandling/src/CheckMantidVersion.cpp
+++ b/Framework/DataHandling/src/CheckMantidVersion.cpp
@@ -107,11 +107,35 @@ void CheckMantidVersion::exec() {
if (!json.empty()) {
Json::Reader r;
Json::Value root;
- r.parse(json, root);
+ bool parseOK = r.parse(json, root);
+ if (!parseOK) {
+ // just warning. The parser is able to get relevant info even if there are
+ // formatting issues like missing quotes or brackets.
+ g_log.warning() << "Error found when parsing version information "
+ "retrieved from GitHub as a JSON string. "
+ "Error trying to parse this JSON string: " << json
+ << std::endl
+ << ". Parsing error details: "
+ << r.getFormattedErrorMessages() << std::endl;
+ }
- std::string gitHubVersionTag = root["tag_name"].asString();
- mostRecentVersion = cleanVersionTag(gitHubVersionTag);
+ std::string gitHubVersionTag;
+ try {
+ gitHubVersionTag = root["tag_name"].asString();
+ } catch (std::runtime_error &re) {
+ g_log.error()
+ << "Error while trying to get the field 'tag_name' from "
+ "the version information retrieved from GitHub. This "
+ "algorithm cannot continue and will stop now. Error details: "
+ << re.what() << std::endl;
+
+ mostRecentVersion = "Could not get information from GitHub";
+ setProperty("MostRecentVersion", mostRecentVersion);
+ setProperty("IsNewVersionAvailable", isNewVersionAvailable);
+ return;
+ }
+ mostRecentVersion = cleanVersionTag(gitHubVersionTag);
isNewVersionAvailable =
isVersionMoreRecent(currentVersion, mostRecentVersion);
if (isNewVersionAvailable) {
diff --git a/Framework/DataHandling/src/CompressEvents.cpp b/Framework/DataHandling/src/CompressEvents.cpp
index 581ac3d877a23a594b99f2e011abda62550c0d55..3597a53930144170a37c23bccc2b7270269cb700 100644
--- a/Framework/DataHandling/src/CompressEvents.cpp
+++ b/Framework/DataHandling/src/CompressEvents.cpp
@@ -2,9 +2,8 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/CompressEvents.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/MemoryManager.h"
+#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include <set>
diff --git a/Framework/DataHandling/src/FindDetectorsPar.cpp b/Framework/DataHandling/src/FindDetectorsPar.cpp
index ebf13530cb10af84b215944a36f5ec26b906d378..54a55db21733e1805eef52f48f2c924e01370b45 100644
--- a/Framework/DataHandling/src/FindDetectorsPar.cpp
+++ b/Framework/DataHandling/src/FindDetectorsPar.cpp
@@ -1,16 +1,19 @@
#include "MantidDataHandling/FindDetectorsPar.h"
-#include "MantidGeometry/Objects/BoundingBox.h"
-#include "MantidKernel/Logger.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/Exception.h"
-#include "MantidKernel/MultiThreaded.h"
-#include "MantidAPI/FileProperty.h"
-#include "MantidGeometry/Instrument/DetectorGroup.h"
-#include "MantidAPI/WorkspaceValidators.h"
+
#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/TableRow.h"
+#include "MantidGeometry/Instrument/DetectorGroup.h"
+#include "MantidGeometry/Objects/BoundingBox.h"
+
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/Exception.h"
+#include "MantidKernel/MultiThreaded.h"
+
#include <Poco/File.h>
#include <limits>
diff --git a/Framework/DataHandling/src/GroupDetectors.cpp b/Framework/DataHandling/src/GroupDetectors.cpp
index a116a4e05c564dc93be1ad0734a52373617c27fc..5ff3c1c1b7d2b4ecf235f9a8a1c9d7ae0058d6a0 100644
--- a/Framework/DataHandling/src/GroupDetectors.cpp
+++ b/Framework/DataHandling/src/GroupDetectors.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/GroupDetectors.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
#include "MantidKernel/ArrayProperty.h"
#include <set>
diff --git a/Framework/DataHandling/src/GroupDetectors2.cpp b/Framework/DataHandling/src/GroupDetectors2.cpp
index 060f54bee77e172c5cfa3da87e6294c5f0aea2c2..7567cc8e6da22794430ce706cb97c7f5d4c1aeca 100644
--- a/Framework/DataHandling/src/GroupDetectors2.cpp
+++ b/Framework/DataHandling/src/GroupDetectors2.cpp
@@ -3,14 +3,14 @@
//----------------------------------------------------------------------
#include "MantidDataHandling/GroupDetectors2.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidAPI/SpectraAxis.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/SpectraAxis.h"
#include "MantidDataHandling/LoadDetectorsGroupingFile.h"
+#include "MantidGeometry/Instrument/DetectorGroup.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/ListValidator.h"
-#include "MantidGeometry/Instrument/DetectorGroup.h"
#include <boost/regex.hpp>
@@ -353,7 +353,7 @@ void GroupDetectors2::getGroups(API::MatrixWorkspace_const_sptr workspace,
}
// check we don't have an index that is too high for the workspace
size_t maxIn = static_cast<size_t>(workspace->getNumberHistograms() - 1);
- std::vector<size_t>::const_iterator it = m_GroupSpecInds[0].begin();
+ auto it = m_GroupSpecInds[0].begin();
for (; it != m_GroupSpecInds[0].end(); ++it) {
if (*it > maxIn) {
g_log.error() << "Spectra index " << *it
@@ -375,7 +375,7 @@ void GroupDetectors2::getGroups(API::MatrixWorkspace_const_sptr workspace,
// up date unUsedSpec, this is used to find duplicates and when the user has
// set KeepUngroupedSpectra
- std::vector<size_t>::const_iterator index = m_GroupSpecInds[0].begin();
+ auto index = m_GroupSpecInds[0].begin();
for (; index != m_GroupSpecInds[0].end();
++index) { // the vector<int> m_GroupSpecInds[0] must not index contain
// numbers that don't exist in the workspaace
@@ -804,6 +804,10 @@ void GroupDetectors2::readFile(spec2index_map &specs2index, std::istream &File,
numberOfSpectra = readInt(thisLine);
} while (numberOfSpectra == EMPTY_LINE);
+ if (numberOfSpectra <= 0) {
+ throw std::invalid_argument("The number of spectra is zero or negative");
+ }
+
// the value of this map is the list of spectra numbers that will be
// combined into a group
m_GroupSpecInds[spectrumNo].reserve(numberOfSpectra);
diff --git a/Framework/DataHandling/src/LoadANSTOHelper.cpp b/Framework/DataHandling/src/LoadANSTOHelper.cpp
index 2e539fb756adc0e48415746d9fcd9bbb5229d2e1..17d5c6f83bc20f1c59b77a4438e693e512e6d135 100644
--- a/Framework/DataHandling/src/LoadANSTOHelper.cpp
+++ b/Framework/DataHandling/src/LoadANSTOHelper.cpp
@@ -2,7 +2,6 @@
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
diff --git a/Framework/DataHandling/src/LoadAscii.cpp b/Framework/DataHandling/src/LoadAscii.cpp
index 747bd5422b98555db8ceb6e6bff37a5245f66abe..74dda663af566b72c71ca5209a90493ddff03af7 100644
--- a/Framework/DataHandling/src/LoadAscii.cpp
+++ b/Framework/DataHandling/src/LoadAscii.cpp
@@ -24,7 +24,9 @@ using namespace Kernel;
using namespace API;
/// Empty constructor
-LoadAscii::LoadAscii() : m_columnSep(), m_separatorIndex() {}
+LoadAscii::LoadAscii() : m_columnSep(), m_separatorIndex() {
+ this->useAlgorithm("LoadAscii", 2);
+}
/**
* Return the confidence with with this algorithm can load the file
diff --git a/Framework/DataHandling/src/LoadBBY.cpp b/Framework/DataHandling/src/LoadBBY.cpp
index 5c670badbacd110171d22b117186b3d4f9f54c32..2db849718f279c461ff19ee9bb8f792f10345342 100644
--- a/Framework/DataHandling/src/LoadBBY.cpp
+++ b/Framework/DataHandling/src/LoadBBY.cpp
@@ -1,13 +1,12 @@
#include "MantidDataHandling/LoadBBY.h"
-#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidKernel/PropertyWithValue.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/UnitFactory.h"
+#include "MantidDataObjects/EventWorkspace.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
+#include "MantidKernel/PropertyWithValue.h"
+#include "MantidKernel/UnitFactory.h"
#include "MantidNexus/NexusClasses.h"
#include <Poco/TemporaryFile.h>
@@ -405,6 +404,7 @@ void LoadBBY::exec() {
createChildAlgorithm("LoadInstrument");
loadInstrumentAlg->setProperty("Workspace", eventWS);
loadInstrumentAlg->setPropertyValue("InstrumentName", "BILBY");
+ loadInstrumentAlg->setProperty("RewriteSpectraMap", false);
loadInstrumentAlg->executeAsChildAlg();
setProperty("OutputWorkspace", eventWS);
@@ -826,4 +826,4 @@ void BbyDetectorBankFactory::createAndAssign(size_t startIndex,
}
} // DataHandling
-} // Mantid
\ No newline at end of file
+} // Mantid
diff --git a/Framework/DataHandling/src/LoadDspacemap.cpp b/Framework/DataHandling/src/LoadDspacemap.cpp
index bbbf5cc6c878a555eb1ddb45f9fafcac52a51baa..751343163fff9bd27f8f21ff75109295bc040e25 100644
--- a/Framework/DataHandling/src/LoadDspacemap.cpp
+++ b/Framework/DataHandling/src/LoadDspacemap.cpp
@@ -1,17 +1,15 @@
+#include "MantidDataHandling/LoadDspacemap.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataHandling/LoadCalFile.h"
-#include "MantidDataHandling/LoadDspacemap.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/GroupingWorkspace.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
-#include "MantidKernel/V3D.h"
+#include "MantidGeometry/IDetector.h"
#include "MantidKernel/BinaryFile.h"
+#include "MantidKernel/ListValidator.h"
#include "MantidKernel/PhysicalConstants.h"
-#include "MantidKernel/System.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidGeometry/IDetector.h"
-#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/V3D.h"
using namespace Mantid::Kernel;
using namespace Mantid::API;
diff --git a/Framework/DataHandling/src/LoadEventPreNexus.cpp b/Framework/DataHandling/src/LoadEventPreNexus.cpp
index 43f73c8f10abe5c91fba36406380bfab82c5570c..e6687146f3fab3f327e3d18c3213dddf8b786999 100644
--- a/Framework/DataHandling/src/LoadEventPreNexus.cpp
+++ b/Framework/DataHandling/src/LoadEventPreNexus.cpp
@@ -84,7 +84,9 @@ LoadEventPreNexus::LoadEventPreNexus()
num_good_events(0), num_error_events(0), num_ignored_events(0),
first_event(0), max_events(0), using_mapping_file(false),
loadOnlySomeSpectra(false), spectraLoadMap(), longest_tof(0),
- shortest_tof(0), parallelProcessing(false) {}
+ shortest_tof(0), parallelProcessing(false) {
+ this->useAlgorithm("LoadEventPreNexus", 2);
+}
LoadEventPreNexus::~LoadEventPreNexus() { delete this->eventfile; }
diff --git a/Framework/DataHandling/src/LoadGSS.cpp b/Framework/DataHandling/src/LoadGSS.cpp
index eb228a845fad9e75f85288cf57e9aac4b2626faf..86192ed9b42ab11bfa661fd3b81051edde09121d 100644
--- a/Framework/DataHandling/src/LoadGSS.cpp
+++ b/Framework/DataHandling/src/LoadGSS.cpp
@@ -5,7 +5,6 @@
#include "MantidAPI/ISpectrum.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/Detector.h"
diff --git a/Framework/DataHandling/src/LoadIsawDetCal.cpp b/Framework/DataHandling/src/LoadIsawDetCal.cpp
index 5a7ddf61096bc0e18243b50d626eb116159d9055..2fc3168b716430b093a5fd2da80f0ef2f1aa17fa 100644
--- a/Framework/DataHandling/src/LoadIsawDetCal.cpp
+++ b/Framework/DataHandling/src/LoadIsawDetCal.cpp
@@ -2,26 +2,26 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/LoadIsawDetCal.h"
+
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/TableRow.h"
+#include "MantidAPI/InstrumentValidator.h"
+
#include "MantidDataObjects/Workspace2D.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/PeaksWorkspace.h"
-#include "MantidAPI/TextAxis.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/Exception.h"
+
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidGeometry/Instrument/ObjCompAssembly.h"
#include "MantidGeometry/Instrument/ComponentHelper.h"
+
#include "MantidKernel/V3D.h"
+
#include <Poco/File.h>
#include <sstream>
#include <fstream>
#include <numeric>
#include <cmath>
-#include "MantidAPI/WorkspaceValidators.h"
namespace Mantid {
namespace DataHandling {
diff --git a/Framework/DataHandling/src/LoadQKK.cpp b/Framework/DataHandling/src/LoadQKK.cpp
index 316cffc185ab4b6e02656661ef7d28664ddee6ac..61b45a8cb2b559b5ef5946cee55f665b52c347d9 100644
--- a/Framework/DataHandling/src/LoadQKK.cpp
+++ b/Framework/DataHandling/src/LoadQKK.cpp
@@ -2,14 +2,16 @@
// Includes
//---------------------------------------------------
#include "MantidDataHandling/LoadQKK.h"
+
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include "MantidKernel/UnitFactory.h"
+
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
+#include "MantidKernel/UnitFactory.h"
+
#include "MantidNexus/NexusClasses.h"
#include <boost/math/special_functions/fpclassify.hpp>
diff --git a/Framework/DataHandling/src/LoadRaw/isisraw.cpp b/Framework/DataHandling/src/LoadRaw/isisraw.cpp
index 6037ec23a60ae12f7ffbcacb65f8b3695f64bbac..475c96358d3637d62e0030ac41939bca61816f33 100644
--- a/Framework/DataHandling/src/LoadRaw/isisraw.cpp
+++ b/Framework/DataHandling/src/LoadRaw/isisraw.cpp
@@ -460,7 +460,17 @@ int ISISRAW::ioRAW(FILE *file, bool from_file, bool read_data) {
// ioRAW(file, &u_len, 1, from_file);
if (from_file) {
u_len = add.ad_data - add.ad_user - 2;
+
+ if (u_len < 0 || (add.ad_data < add.ad_user + 2)) {
+ // this will/would be used for memory allocation
+ std::cerr << "Error in u_len value read from file, it would be " << u_len
+ << "; where it is calculated as "
+ "u_len = ad_data - ad_user - 2, where ad_data: "
+ << add.ad_data << ", ad_user: " << add.ad_user << std::endl;
+ return 0;
+ }
}
+
ioRAW(file, &u_dat, u_len, from_file);
ioRAW(file, &ver8, 1, from_file);
fgetpos(file, &dhdr_pos);
@@ -474,8 +484,12 @@ int ISISRAW::ioRAW(FILE *file, bool from_file, bool read_data) {
if (from_file) {
ndes = t_nper * (t_nsp1 + 1);
ioRAW(file, &ddes, ndes, from_file);
- for (i = 0; i < ndes; i++)
- fseek(file, 4 * ddes[i].nwords, SEEK_CUR);
+ for (i = 0; i < ndes; i++) {
+ int zero = fseek(file, 4 * ddes[i].nwords, SEEK_CUR);
+ if (0 != zero)
+ std::cerr << "Failed to seek position in file for index: " << i
+ << "\n";
+ }
}
} else if (dhdr.d_comp == 0) {
ndata = t_nper * (t_nsp1 + 1) * (t_ntc1 + 1);
@@ -527,15 +541,38 @@ int ISISRAW::ioRAW(FILE *file, bool from_file, bool read_data) {
dhdr.d_exp_filesize =
uncomp_filesize /
128; // in 512 byte blocks (vms default allocation unit)
- fgetpos(file, &keep_pos);
+ int zero = fgetpos(file, &keep_pos);
+ if (!zero) {
+ std::cerr << "Error when getting file position: " << strerror(errno)
+ << std::endl;
+ return -1;
+ }
+
// update section addresses
- fsetpos(file, &add_pos);
+ zero = fsetpos(file, &add_pos);
+ if (!zero) {
+ std::cerr << "Error when setting file position: " << strerror(errno)
+ << std::endl;
+ return -1;
+ }
+
ioRAW(file, &add, 1, from_file);
// update data header and descriptors etc.
- fsetpos(file, &dhdr_pos);
+ zero = fsetpos(file, &dhdr_pos);
+ if (!zero) {
+ std::cerr << "Error when setting file position to header: "
+ << strerror(errno) << std::endl;
+ return -1;
+ }
+
ioRAW(file, &dhdr, 1, from_file);
ioRAW(file, &ddes, ndes, from_file);
- fsetpos(file, &keep_pos);
+ zero = fsetpos(file, &keep_pos);
+ if (!zero) {
+ std::cerr << "Error when restoring file position: " << strerror(errno)
+ << std::endl;
+ return -1;
+ }
}
return 0;
}
@@ -669,16 +706,18 @@ int ISISRAW::ioRAW(FILE *file, LOG_LINE *s, int len, bool from_file) {
/// stuff
int ISISRAW::ioRAW(FILE *file, char *s, int len, bool from_file) {
- size_t n;
if ((len <= 0) || (s == 0)) {
return 0;
}
+
+ size_t n;
if (from_file) {
n = fread(s, sizeof(char), len, file);
return static_cast<int>(n - len);
} else {
n = fwrite(s, sizeof(char), len, file);
}
+
return 0;
}
@@ -687,11 +726,15 @@ int ISISRAW::ioRAW(FILE *file, int *s, int len, bool from_file) {
if ((len <= 0) || (s == 0)) {
return 0;
}
+
+ size_t n;
if (from_file) {
- fread(s, sizeof(int), len, file);
+ n = fread(s, sizeof(int), len, file);
+ return static_cast<int>(n - len);
} else {
- fwrite(s, sizeof(int), len, file);
+ n = fwrite(s, sizeof(int), len, file);
}
+
return 0;
}
@@ -700,10 +743,13 @@ int ISISRAW::ioRAW(FILE *file, uint32_t *s, int len, bool from_file) {
if ((len <= 0) || (s == 0)) {
return 0;
}
+
+ size_t n;
if (from_file) {
- fread(s, sizeof(uint32_t), len, file);
+ n = fread(s, sizeof(uint32_t), len, file);
+ return static_cast<int>(n - len);
} else {
- fwrite(s, sizeof(uint32_t), len, file);
+ n = fwrite(s, sizeof(uint32_t), len, file);
}
return 0;
}
@@ -714,12 +760,15 @@ int ISISRAW::ioRAW(FILE *file, float *s, int len, bool from_file) {
if ((len <= 0) || (s == 0)) {
return 0;
}
+
+ size_t n;
if (from_file) {
- fread(s, sizeof(float), len, file);
+ n = fread(s, sizeof(float), len, file);
vaxf_to_local(s, &len, &errcode);
+ return static_cast<int>(n - len);
} else {
local_to_vaxf(s, &len, &errcode);
- fwrite(s, sizeof(float), len, file);
+ n = fwrite(s, sizeof(float), len, file);
vaxf_to_local(s, &len, &errcode);
}
return 0;
@@ -900,36 +949,6 @@ int ISISRAW::readFromFile(const char *filename, bool read_data) {
}
}
-/// stuff
-int ISISRAW::writeToFile(const char *filename) {
- unsigned char zero_pad[512];
- memset(zero_pad, 0, sizeof(zero_pad));
- remove(filename);
-#ifdef MS_VISUAL_STUDIO
- FILE *output_file = NULL;
- if (fopen_s(&output_file, filename, "w+bc") != 0) {
- return -1;
- }
-#else //_WIN32
- FILE *output_file = fopen(filename, "w+bc");
-#endif //_WIN32
- if (output_file != NULL) {
- ioRAW(output_file, false, 0);
- fflush(output_file);
- // we need to pad to a multiple of 512 bytes for VMS compatibility
- fseek(output_file, 0, SEEK_END);
- long pos = ftell(output_file);
- if (pos % 512 > 0) {
- int npad = 512 - pos % 512;
- fwrite(zero_pad, 1, npad, output_file);
- }
- fclose(output_file);
- return 0;
- } else {
- return -1;
- }
-}
-
/// stuff
int ISISRAW::printInfo(std::ostream &os) {
int i;
diff --git a/Framework/DataHandling/src/LoadRaw/isisraw.h b/Framework/DataHandling/src/LoadRaw/isisraw.h
index c7c419aac95c38cfaaefb20c7d6f262499901955..84d82a06fe282a491b652c79e9f084d907683ecc 100644
--- a/Framework/DataHandling/src/LoadRaw/isisraw.h
+++ b/Framework/DataHandling/src/LoadRaw/isisraw.h
@@ -373,7 +373,6 @@ public:
int ioRAW(FILE *file, DDES_STRUCT **s, int len, bool from_file);
int ioRAW(FILE *file, LOG_LINE **s, int len, bool from_file);
int readFromFile(const char *filename, bool read_data = true);
- int writeToFile(const char *filename);
int printInfo(std::ostream &os);
int getTimeChannels(float *rtcb1, int n);
};
diff --git a/Framework/DataHandling/src/LoadRaw/isisraw2.cpp b/Framework/DataHandling/src/LoadRaw/isisraw2.cpp
index f4bbb1f41873c6d09032e9d21c667cd829995d36..331b26bb1f8bb3a6758834da87dc064b47ac0d5a 100644
--- a/Framework/DataHandling/src/LoadRaw/isisraw2.cpp
+++ b/Framework/DataHandling/src/LoadRaw/isisraw2.cpp
@@ -95,7 +95,17 @@ int ISISRAW2::ioRAW(FILE *file, bool from_file, bool read_data) {
// ISISRAW::ioRAW(file, &u_len, 1, from_file);
if (from_file) {
u_len = add.ad_data - add.ad_user - 2;
+
+ if (u_len < 0 || (add.ad_data < add.ad_user + 2)) {
+ // this will/would be used for memory allocation
+ g_log.error() << "Error in u_len value read from file, it would be "
+ << u_len << "; where it is calculated as "
+ "u_len = ad_data - ad_user - 2, where ad_data: "
+ << add.ad_data << ", ad_user: " << add.ad_user << "\n";
+ throw std::runtime_error("Inconsistent value for the field u_len found");
+ }
}
+
ISISRAW::ioRAW(file, &u_dat, u_len, from_file);
ISISRAW::ioRAW(file, &ver8, 1, from_file);
fgetpos(file, &dhdr_pos);
@@ -115,8 +125,13 @@ int ISISRAW2::ioRAW(FILE *file, bool from_file, bool read_data) {
/// @param file :: The file pointer
/// @param i :: The amount of data to skip
void ISISRAW2::skipData(FILE *file, int i) {
- if (i < ndes)
- fseek(file, 4 * ddes[i].nwords, SEEK_CUR);
+ if (i < ndes) {
+ int zero = fseek(file, 4 * ddes[i].nwords, SEEK_CUR);
+ if (0 != zero) {
+ g_log.warning() << "Failed to skip data from file, with value: " << i
+ << "\n";
+ }
+ }
}
/// Read data
diff --git a/Framework/DataHandling/src/MaskDetectors.cpp b/Framework/DataHandling/src/MaskDetectors.cpp
index 141acf5d0c8369fac89d6292a3cff3b889ac7ca3..cde8d9af47d06e555f8c80b64d2a9304121163dd 100644
--- a/Framework/DataHandling/src/MaskDetectors.cpp
+++ b/Framework/DataHandling/src/MaskDetectors.cpp
@@ -2,11 +2,11 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/MaskDetectors.h"
-#include "MantidAPI/FrameworkManager.h"
+
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/MaskWorkspace.h"
+
#include "MantidKernel/ArrayProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/BoundedValidator.h"
#include <set>
diff --git a/Framework/DataHandling/src/SaveCanSAS1D.cpp b/Framework/DataHandling/src/SaveCanSAS1D.cpp
index 65ebb1ea446a059ba762d29d4220728f29836823..33224957650f863d5769dd05b9fe56101ccf9eb4 100644
--- a/Framework/DataHandling/src/SaveCanSAS1D.cpp
+++ b/Framework/DataHandling/src/SaveCanSAS1D.cpp
@@ -2,13 +2,17 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/SaveCanSAS1D.h"
+
#include "MantidAPI/FileProperty.h"
-#include "MantidKernel/Exception.h"
+#include "MantidAPI/Run.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+
#include "MantidGeometry/IComponent.h"
-#include "MantidAPI/WorkspaceValidators.h"
+
+#include "MantidKernel/Exception.h"
#include "MantidKernel/MantidVersion.h"
#include "MantidKernel/ListValidator.h"
-#include "MantidAPI/Run.h"
+
#include <boost/shared_ptr.hpp>
//-----------------------------------------------------------------------------
diff --git a/Framework/DataHandling/src/SaveCanSAS1D2.cpp b/Framework/DataHandling/src/SaveCanSAS1D2.cpp
index 49a9bb0a4f8ce1e8a9ebec32452525d66e7dd3b1..df414fa039447c4febfc5e44d9cc6a9f8a54cea0 100644
--- a/Framework/DataHandling/src/SaveCanSAS1D2.cpp
+++ b/Framework/DataHandling/src/SaveCanSAS1D2.cpp
@@ -2,14 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/SaveCanSAS1D2.h"
+
#include "MantidAPI/FileProperty.h"
-#include "MantidKernel/Exception.h"
+#include "MantidAPI/Run.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+
#include "MantidGeometry/IComponent.h"
-#include "MantidAPI/WorkspaceValidators.h"
+
+#include "MantidKernel/Exception.h"
#include "MantidKernel/MantidVersion.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidAPI/Run.h"
-#include <boost/shared_ptr.hpp>
//-----------------------------------------------------------------------------
using namespace Mantid::Kernel;
diff --git a/Framework/DataHandling/src/SaveDiffCal.cpp b/Framework/DataHandling/src/SaveDiffCal.cpp
index 66259ba0ad274d6856f16180cc48240a99e183ca..96c2cbe07747c32a9b817a67505126fa137752eb 100644
--- a/Framework/DataHandling/src/SaveDiffCal.cpp
+++ b/Framework/DataHandling/src/SaveDiffCal.cpp
@@ -30,7 +30,8 @@ DECLARE_ALGORITHM(SaveDiffCal)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
-SaveDiffCal::SaveDiffCal() {}
+SaveDiffCal::SaveDiffCal()
+ : m_numValues(0), m_calibrationWS(), m_detidToIndex() {}
//----------------------------------------------------------------------------------------------
/** Destructor
diff --git a/Framework/DataHandling/src/SaveGSS.cpp b/Framework/DataHandling/src/SaveGSS.cpp
index 460f326f800f6ccb0538b63aa49f9b59740bf633..af536d1977a0afa2330f7b899b36a42d6e2c2031 100644
--- a/Framework/DataHandling/src/SaveGSS.cpp
+++ b/Framework/DataHandling/src/SaveGSS.cpp
@@ -2,11 +2,14 @@
// Includes
//---------------------------------------------------
#include "MantidDataHandling/SaveGSS.h"
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+
#include "MantidAPI/AlgorithmHistory.h"
+#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/ListValidator.h"
+
#include <boost/math/special_functions/fpclassify.hpp>
#include <Poco/File.h>
#include <Poco/Path.h>
@@ -410,6 +413,7 @@ void writeLogValue(std::ostream &os, const Run &runinfo,
void SaveGSS::writeHeaders(const std::string &format, std::stringstream &os,
double primaryflightpath) const {
const Run &runinfo = inputWS->run();
+ std::ios::fmtflags fflags(os.flags());
// Run number
if (format.compare(SLOG) == 0) {
@@ -483,6 +487,8 @@ void SaveGSS::writeHeaders(const std::string &format, std::stringstream &os,
os << "\n";
}
+ os.flags(fflags);
+
return;
}
@@ -491,10 +497,12 @@ void SaveGSS::writeHeaders(const std::string &format, std::stringstream &os,
*/
inline void writeBankLine(std::stringstream &out, const std::string &bintype,
const int banknum, const size_t datasize) {
+ std::ios::fmtflags fflags(out.flags());
out << "BANK " << std::fixed << std::setprecision(0)
<< banknum // First bank should be 1 for GSAS; this can be changed
<< std::fixed << " " << datasize << std::fixed << " " << datasize
<< std::fixed << " " << bintype;
+ out.flags(fflags);
}
//----------------------------------------------------------------------------------------------
diff --git a/Framework/DataHandling/src/SaveNISTDAT.cpp b/Framework/DataHandling/src/SaveNISTDAT.cpp
index 0b32dc7d6dcf8e41fed88f6c0715e9cdc582aa21..8df313f51064c5a4d544940865572342e636778e 100644
--- a/Framework/DataHandling/src/SaveNISTDAT.cpp
+++ b/Framework/DataHandling/src/SaveNISTDAT.cpp
@@ -3,7 +3,10 @@
//----------------------------------------------------------------------
#include "MantidDataHandling/SaveNISTDAT.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+
#include <fstream> // used to get ofstream
namespace Mantid {
diff --git a/Framework/DataHandling/src/SaveNXSPE.cpp b/Framework/DataHandling/src/SaveNXSPE.cpp
index e07c856189d1a7392aed34a9b1ac945f6799dbb3..3d9a6397fdb37ff36251547c39e9e6d997b68d89 100644
--- a/Framework/DataHandling/src/SaveNXSPE.cpp
+++ b/Framework/DataHandling/src/SaveNXSPE.cpp
@@ -1,10 +1,15 @@
#include "MantidDataHandling/SaveNXSPE.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
-#include "MantidGeometry/Instrument/Detector.h"
+
#include "MantidDataHandling/FindDetectorsPar.h"
+#include "MantidGeometry/Instrument/Detector.h"
+
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MantidVersion.h"
#include <boost/scoped_array.hpp>
diff --git a/Framework/DataHandling/src/SaveNXTomo.cpp b/Framework/DataHandling/src/SaveNXTomo.cpp
index fb1ae0d02f6d4c633699088fee09857121afb6de..efd42c3346d85889cac94edd6aaaf1ec4b2ec4db 100644
--- a/Framework/DataHandling/src/SaveNXTomo.cpp
+++ b/Framework/DataHandling/src/SaveNXTomo.cpp
@@ -1,8 +1,14 @@
+#include "MantidDataHandling/SaveNXTomo.h"
+
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+
#include "MantidDataHandling/FindDetectorsPar.h"
-#include "MantidDataHandling/SaveNXTomo.h"
+
#include "MantidGeometry/IComponent.h"
+
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MantidVersion.h"
#include <nexus/NeXusException.hpp>
diff --git a/Framework/DataHandling/src/SaveNexus.cpp b/Framework/DataHandling/src/SaveNexus.cpp
index a65dac9a97dd1f00b7a695c49fad098da15badd1..06c047463739c04cc2c116afbc7a47d1b33cbc6c 100644
--- a/Framework/DataHandling/src/SaveNexus.cpp
+++ b/Framework/DataHandling/src/SaveNexus.cpp
@@ -147,7 +147,7 @@ void SaveNexus::runSaveNexusProcessed() {
// If we're tracking history, add the entry before we save it to file
if (trackingHistory()) {
m_history->fillAlgorithmHistory(
- this, Mantid::Kernel::DateAndTime::getCurrentTime(), -1,
+ this, Mantid::Kernel::DateAndTime::getCurrentTime(), 0,
Algorithm::g_execCount);
if (!isChild()) {
m_inputWorkspace->history().addHistory(m_history);
diff --git a/Framework/DataHandling/src/SaveNexusProcessed.cpp b/Framework/DataHandling/src/SaveNexusProcessed.cpp
index 20c6890c5bf3ab6ce715c2295aab85b86d11eaaf..261eb8079c01e9f164beb9f53ca1e13ab22833b9 100644
--- a/Framework/DataHandling/src/SaveNexusProcessed.cpp
+++ b/Framework/DataHandling/src/SaveNexusProcessed.cpp
@@ -291,7 +291,7 @@ void SaveNexusProcessed::doExec(Workspace_sptr inputWorkspace,
// Switch to the Cpp API for the algorithm history
if (trackingHistory()) {
m_history->fillAlgorithmHistory(
- this, Mantid::Kernel::DateAndTime::getCurrentTime(), -1,
+ this, Mantid::Kernel::DateAndTime::getCurrentTime(), 0,
Algorithm::g_execCount);
if (!isChild()) {
inputWorkspace->history().addHistory(m_history);
diff --git a/Framework/DataHandling/src/SavePAR.cpp b/Framework/DataHandling/src/SavePAR.cpp
index bf4ea3d2395a941f182cc0b72ebe719a69d24fa9..858d42a4487f7217908c3672e669a8c1a9e93f60 100644
--- a/Framework/DataHandling/src/SavePAR.cpp
+++ b/Framework/DataHandling/src/SavePAR.cpp
@@ -1,10 +1,13 @@
#include "MantidDataHandling/SavePAR.h"
-#include "MantidDataHandling/FindDetectorsPar.h"
+
#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/InstrumentValidator.h"
+
+#include "MantidDataHandling/FindDetectorsPar.h"
+
#include "MantidGeometry/Instrument/Detector.h"
#include "MantidGeometry/Instrument/ObjComponent.h"
#include "MantidGeometry/Objects/Object.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include <cstdio>
#include <fstream>
diff --git a/Framework/DataHandling/src/SavePHX.cpp b/Framework/DataHandling/src/SavePHX.cpp
index 579ba691415232329674dca274aee32009a4a907..12564c28e1524eca7c709d1275ada6f2d1eaf001 100644
--- a/Framework/DataHandling/src/SavePHX.cpp
+++ b/Framework/DataHandling/src/SavePHX.cpp
@@ -1,10 +1,13 @@
#include "MantidDataHandling/SavePHX.h"
-#include "MantidDataHandling/FindDetectorsPar.h"
+
#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/InstrumentValidator.h"
+
+#include "MantidDataHandling/FindDetectorsPar.h"
+
#include "MantidGeometry/Instrument/Detector.h"
#include "MantidGeometry/Instrument/ObjComponent.h"
#include "MantidGeometry/Objects/Object.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include <cstdio>
#include <fstream>
diff --git a/Framework/DataHandling/src/SaveParameterFile.cpp b/Framework/DataHandling/src/SaveParameterFile.cpp
index 931538cbb9488116d9dcb0211b5061077e7df773..226e00665a2f41a939e8c3fea80d86ef7cfec0d6 100644
--- a/Framework/DataHandling/src/SaveParameterFile.cpp
+++ b/Framework/DataHandling/src/SaveParameterFile.cpp
@@ -1,6 +1,8 @@
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataHandling/SaveParameterFile.h"
+
+#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/InstrumentValidator.h"
+
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
diff --git a/Framework/DataHandling/src/SaveSPE.cpp b/Framework/DataHandling/src/SaveSPE.cpp
index f455a0c15d2db3d19efc421176c8a8e5f3cf2052..58902124d4daab9a15db5e4d357fd4a0e30eafc2 100644
--- a/Framework/DataHandling/src/SaveSPE.cpp
+++ b/Framework/DataHandling/src/SaveSPE.cpp
@@ -2,13 +2,17 @@
// Includes
//---------------------------------------------------
#include "MantidDataHandling/SaveSPE.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/WorkspaceOpOverloads.h"
+#include "MantidKernel/CompositeValidator.h"
+
#include "Poco/File.h"
+#include <boost/math/special_functions/fpclassify.hpp>
+
#include <cstdio>
#include <cmath>
-#include <boost/math/special_functions/fpclassify.hpp>
#include <stdexcept>
namespace Mantid {
diff --git a/Framework/DataHandling/src/SetScalingPSD.cpp b/Framework/DataHandling/src/SetScalingPSD.cpp
index c977d3fad5df2c23771be8425438380a21b86f9a..3affb36b8cb1625621dd640030ab6ac6697faf87 100644
--- a/Framework/DataHandling/src/SetScalingPSD.cpp
+++ b/Framework/DataHandling/src/SetScalingPSD.cpp
@@ -4,14 +4,14 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/SetScalingPSD.h"
+#include "MantidAPI/FileProperty.h"
+#include "MantidGeometry/Instrument/ComponentHelper.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
-#include "MantidGeometry/Instrument/ComponentHelper.h"
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "LoadRaw/isisraw.h"
+
#include <cmath>
#include <fstream>
-#include "LoadRaw/isisraw.h"
namespace Mantid {
namespace DataHandling {
diff --git a/Framework/DataHandling/test/CheckMantidVersionTest.h b/Framework/DataHandling/test/CheckMantidVersionTest.h
index d6c1e17a95dc93acdedd0d93979488ee0e964ce3..d7cf6155fca679d6c730a2f7b7f5e55354adddb4 100644
--- a/Framework/DataHandling/test/CheckMantidVersionTest.h
+++ b/Framework/DataHandling/test/CheckMantidVersionTest.h
@@ -77,7 +77,8 @@ private:
"\"https://api.github.com/users/peterfpeterson/received_events\",\n"
" \"type\": \"User\",\n"
" \"site_admin\": false\n"
- " }";
+ " }\n"
+ "}";
return outputString;
}
diff --git a/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h b/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h
index 2656b0085f6924d57618e626b151cacf0d9d1508..7256f47e3bbb7c5b3a8a1936b742f8c057749b9f 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h
+++ b/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h
@@ -22,7 +22,8 @@ public:
/**
Constructor
*/
- CalculateReflectometryQxQz() : m_dirQx(0.0), m_dirQz(0.0) {}
+ CalculateReflectometryQxQz()
+ : m_cos_theta_i(0.0), m_sin_theta_i(0.0), m_dirQx(0.0), m_dirQz(0.0) {}
/**
Setter for the incident theta value require for the calculation. Internally
diff --git a/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc b/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
index d03eb54542a77ee0bdd2b9cd5f04adcf3020215a..4de121711232aa6c6a24fd477c7118097ca62778 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
+++ b/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
@@ -40,10 +40,10 @@ namespace DataObjects {
*/
TMDE(MDGridBox)::MDGridBox(
BoxController *const bc, const uint32_t depth,
- const std::vector<
- Mantid::Geometry::MDDimensionExtents<coord_t>> &extentsVector)
- : MDBoxBase<MDE, nd>(bc, depth, UNDEF_SIZET, extentsVector),
- numBoxes(0), m_Children(), diagonalSquared(0.f), nPoints(0) {
+ const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t>> &
+ extentsVector)
+ : MDBoxBase<MDE, nd>(bc, depth, UNDEF_SIZET, extentsVector), numBoxes(0),
+ m_Children(), diagonalSquared(0.f), nPoints(0) {
initGridBox();
}
@@ -55,8 +55,8 @@ TMDE(MDGridBox)::MDGridBox(
*/
TMDE(MDGridBox)::MDGridBox(
boost::shared_ptr<API::BoxController> &bc, const uint32_t depth,
- const std::vector<
- Mantid::Geometry::MDDimensionExtents<coord_t>> &extentsVector)
+ const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t>> &
+ extentsVector)
: MDBoxBase<MDE, nd>(bc.get(), depth, UNDEF_SIZET, extentsVector),
numBoxes(0), m_Children(), diagonalSquared(0.f), nPoints(0) {
initGridBox();
@@ -68,17 +68,16 @@ template <typename MDE, size_t nd> size_t MDGridBox<MDE, nd>::initGridBox() {
"MDGridBox::ctor(): No BoxController specified in box.");
// How many is it split?
- // If we are at the top level and we have a specific top level split, then set it.
- boost::optional<std::vector<size_t>> splitTopInto = this->m_BoxController->getSplitTopInto();
- if (this->getDepth() == 0 && splitTopInto)
- {
+ // If we are at the top level and we have a specific top level split, then set
+ // it.
+ boost::optional<std::vector<size_t>> splitTopInto =
+ this->m_BoxController->getSplitTopInto();
+ if (this->getDepth() == 0 && splitTopInto) {
for (size_t d = 0; d < nd; d++)
split[d] = splitTopInto.get()[d];
- }
- else
- {
- for (size_t d = 0; d < nd; d++)
- split[d] = this->m_BoxController->getSplitInto(d);
+ } else {
+ for (size_t d = 0; d < nd; d++)
+ split[d] = this->m_BoxController->getSplitInto(d);
}
// Compute sizes etc.
@@ -94,10 +93,9 @@ template <typename MDE, size_t nd> size_t MDGridBox<MDE, nd>::initGridBox() {
* @param box :: MDBox containing the events to split
*/
TMDE(MDGridBox)::MDGridBox(MDBox<MDE, nd> *box)
- : MDBoxBase<MDE, nd>(*box, box->getBoxController()), split(),
- splitCumul(), m_SubBoxSize(), numBoxes(0), m_Children(),
- diagonalSquared(0.f), nPoints(0)
-{
+ : MDBoxBase<MDE, nd>(*box, box->getBoxController()), split(), splitCumul(),
+ m_SubBoxSize(), numBoxes(0), m_Children(), diagonalSquared(0.f),
+ nPoints(0) {
size_t totalSize = initGridBox();
double ChildVol(1);
@@ -188,10 +186,10 @@ void MDGridBox<MDE, nd>::fillBoxShell(const size_t tot,
*/
TMDE(MDGridBox)::MDGridBox(const MDGridBox<MDE, nd> &other,
Mantid::API::BoxController *const otherBC)
- : MDBoxBase<MDE, nd>(other, otherBC), numBoxes(other.numBoxes), m_Children(),
- diagonalSquared(other.diagonalSquared), nPoints(other.nPoints) {
- for (size_t d = 0; d < nd; d++)
- {
+ : MDBoxBase<MDE, nd>(other, otherBC), numBoxes(other.numBoxes),
+ m_Children(), diagonalSquared(other.diagonalSquared),
+ nPoints(other.nPoints) {
+ for (size_t d = 0; d < nd; d++) {
split[d] = other.split[d];
splitCumul[d] = other.splitCumul[d];
m_SubBoxSize[d] = other.m_SubBoxSize[d];
@@ -415,7 +413,7 @@ TMDE(std::vector<MDE> *MDGridBox)::getEventsCopy() {
*/
TMDE(void MDGridBox)::getBoxes(std::vector<API::IMDNode *> &outBoxes,
size_t maxDepth, bool leafOnly) {
- //Add this box, unless we only want the leaves
+ // Add this box, unless we only want the leaves
if (!leafOnly)
outBoxes.push_back(this);
@@ -1465,8 +1463,9 @@ TMDE(void MDGridBox)::integrateCylinder(
coord_t out[nd];
radiusTransform.apply(boxCenter, out);
if (out[0] < std::sqrt(diagonalSquared * 0.72 + radius * radius) &&
- std::fabs(out[1]) <
- std::sqrt(diagonalSquared * 0.72 + 0.25 * length * length)) {
+ (nd >= 1 &&
+ std::fabs(out[1]) <
+ std::sqrt(diagonalSquared * 0.72 + 0.25 * length * length))) {
// If the center is closer than the size of the box, then it MIGHT be
// touching.
// (We multiply by 0.72 (about sqrt(2)) to look for half the diagonal).
diff --git a/Framework/DataObjects/src/EventList.cpp b/Framework/DataObjects/src/EventList.cpp
index efb6e74c71354d9c2d6207883c39d49a6e1e95f2..8dfbd6d9421904169c2016b3f5f11279c626469a 100644
--- a/Framework/DataObjects/src/EventList.cpp
+++ b/Framework/DataObjects/src/EventList.cpp
@@ -548,6 +548,7 @@ EventList &EventList::operator-=(const EventList &more_events) {
minusHelper(this->weightedEvents, more_events.weightedEventsNoTime);
break;
}
+ break;
case WEIGHTED_NOTIME:
switch (more_events.getEventType()) {
@@ -561,6 +562,7 @@ EventList &EventList::operator-=(const EventList &more_events) {
minusHelper(this->weightedEventsNoTime, more_events.weightedEventsNoTime);
break;
}
+ break;
}
// No guaranteed order
diff --git a/Framework/DataObjects/src/MDHistoWorkspaceIterator.cpp b/Framework/DataObjects/src/MDHistoWorkspaceIterator.cpp
index 9965a7d050731a517612282a0975edcaa791e746..87ad5e25ccdc9c2f2b6a49f9bee92cd90d46debd 100644
--- a/Framework/DataObjects/src/MDHistoWorkspaceIterator.cpp
+++ b/Framework/DataObjects/src/MDHistoWorkspaceIterator.cpp
@@ -199,8 +199,17 @@ void MDHistoWorkspaceIterator::init(
for (size_t d = 0; d < m_nd; d++)
m_center[d] = m_origin[d] + 0.5f * m_binWidth[d];
// Skip on if the first point is NOT contained
- if (!m_function->isPointContained(m_center))
- next();
+ if (!m_function->isPointContained(m_center)) {
+ bool didNext = next();
+ if (!didNext && this->valid()) {
+ throw std::runtime_error(
+ "Inconsistency found initializing "
+ "MDHistoWorkspace iterator: this iterator should be valid, but "
+ "when tried to skip the "
+ "first point (not contained) could not iterate to "
+ "next point.");
+ }
+ }
}
// --- Calculate index permutations for neighbour finding face touching ---
@@ -293,9 +302,11 @@ bool MDHistoWorkspaceIterator::valid() const { return (m_pos < m_max); }
/// @return true if you can continue iterating
bool MDHistoWorkspaceIterator::next() {
if (m_function) {
+ bool allIncremented = false;
do {
m_pos++;
- Utils::NestedForLoop::Increment(m_nd, m_index, m_indexMax);
+ allIncremented =
+ Utils::NestedForLoop::Increment(m_nd, m_index, m_indexMax);
// Calculate the center
for (size_t d = 0; d < m_nd; d++) {
m_center[d] =
@@ -304,7 +315,8 @@ bool MDHistoWorkspaceIterator::next() {
}
// std::cout<<std::endl;
// Keep incrementing until you are in the implicit function
- } while (!m_function->isPointContained(m_center) && m_pos < m_max);
+ } while (!allIncremented && !m_function->isPointContained(m_center) &&
+ m_pos < m_max);
} else {
++m_pos;
}
diff --git a/Framework/DataObjects/src/PeakColumn.cpp b/Framework/DataObjects/src/PeakColumn.cpp
index b3d7e129cc927636043721605c3517a80c4892a8..7554f7f04ab8fa95178afe9f906f3cfffa88caf6 100644
--- a/Framework/DataObjects/src/PeakColumn.cpp
+++ b/Framework/DataObjects/src/PeakColumn.cpp
@@ -80,7 +80,13 @@ PeakColumn::PeakColumn(std::vector<Peak> &peaks, const std::string &name)
this->m_name = name;
this->m_type = typeFromName(name); // Throws if the name is unknown
this->m_hklPrec = 2;
- ConfigService::Instance().getValue("PeakColumn.hklPrec", this->m_hklPrec);
+ const std::string key = "PeakColumn.hklPrec";
+ int gotit = ConfigService::Instance().getValue(key, this->m_hklPrec);
+ if (!gotit)
+ g_log.information()
+ << "In PeakColumn constructor, did not find any value for '" << key
+ << "' from the Config Service. Using default: " << this->m_hklPrec
+ << "\n";
}
//----------------------------------------------------------------------------------------------
@@ -134,6 +140,7 @@ const std::type_info &PeakColumn::get_pointer_type_info() const {
void PeakColumn::print(size_t index, std::ostream &s) const {
Peak &peak = m_peaks[index];
+ std::ios::fmtflags fflags(s.flags());
if (m_name == "RunNumber")
s << peak.getRunNumber();
else if (m_name == "DetID")
@@ -152,6 +159,7 @@ void PeakColumn::print(size_t index, std::ostream &s) const {
s << std::fixed << std::setprecision(m_hklPrec) << peak.getL();
} else
s << peak.getValueByColName(m_name);
+ s.flags(fflags);
}
//-------------------------------------------------------------------------------------
diff --git a/Framework/DataObjects/test/WorkspaceValidatorsTest.h b/Framework/DataObjects/test/WorkspaceValidatorsTest.h
index 4182d305bc8ce58a3053f687223432fd1afd6e71..90af5914fb69ce2ad7443690c3308f5b32f04595 100644
--- a/Framework/DataObjects/test/WorkspaceValidatorsTest.h
+++ b/Framework/DataObjects/test/WorkspaceValidatorsTest.h
@@ -2,7 +2,12 @@
#define WORKSPACEVALIDATORSTEST_H_
#include <cxxtest/TestSuite.h>
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/SampleValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/WorkspaceProperty.h"
#include "MantidKernel/Material.h"
#include "MantidKernel/NeutronAtom.h"
diff --git a/Framework/Geometry/CMakeLists.txt b/Framework/Geometry/CMakeLists.txt
index ed3948fe974248bc96432c9dd109bf0af5f5395c..9ec241cd5176b287923763d9a86807c85ab503da 100644
--- a/Framework/Geometry/CMakeLists.txt
+++ b/Framework/Geometry/CMakeLists.txt
@@ -1,6 +1,7 @@
set ( SRC_FILES
${SRC_FILES} ${OPENCASCADE_SRC}
src/ComponentParser.cpp
+ src/Crystal/BasicHKLFilters.cpp
src/Crystal/BraggScatterer.cpp
src/Crystal/BraggScattererFactory.cpp
src/Crystal/BraggScattererInCrystalStructure.cpp
@@ -10,6 +11,8 @@ set ( SRC_FILES
src/Crystal/CrystalStructure.cpp
src/Crystal/CyclicGroup.cpp
src/Crystal/Group.cpp
+ src/Crystal/HKLFilter.cpp
+ src/Crystal/HKLGenerator.cpp
src/Crystal/IPeak.cpp
src/Crystal/IndexingUtils.cpp
src/Crystal/IsotropicAtomBraggScatterer.cpp
@@ -25,9 +28,12 @@ set ( SRC_FILES
src/Crystal/ProductOfCyclicGroups.cpp
src/Crystal/ReducedCell.cpp
src/Crystal/ReflectionCondition.cpp
+ src/Crystal/ReflectionGenerator.cpp
src/Crystal/ScalarUtils.cpp
src/Crystal/SpaceGroup.cpp
src/Crystal/SpaceGroupFactory.cpp
+ src/Crystal/StructureFactorCalculator.cpp
+ src/Crystal/StructureFactorCalculatorSummation.cpp
src/Crystal/SymmetryElement.cpp
src/Crystal/SymmetryElementFactory.cpp
src/Crystal/SymmetryOperation.cpp
@@ -130,6 +136,7 @@ set ( SRC_UNITY_IGNORE_FILES src/Instrument/CompAssembly.cpp
set ( INC_FILES
inc/MantidGeometry/ComponentParser.h
+ inc/MantidGeometry/Crystal/BasicHKLFilters.h
inc/MantidGeometry/Crystal/BraggScatterer.h
inc/MantidGeometry/Crystal/BraggScattererFactory.h
inc/MantidGeometry/Crystal/BraggScattererInCrystalStructure.h
@@ -140,6 +147,8 @@ set ( INC_FILES
inc/MantidGeometry/Crystal/CrystalStructure.h
inc/MantidGeometry/Crystal/CyclicGroup.h
inc/MantidGeometry/Crystal/Group.h
+ inc/MantidGeometry/Crystal/HKLFilter.h
+ inc/MantidGeometry/Crystal/HKLGenerator.h
inc/MantidGeometry/Crystal/IPeak.h
inc/MantidGeometry/Crystal/IndexingUtils.h
inc/MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h
@@ -157,9 +166,12 @@ set ( INC_FILES
inc/MantidGeometry/Crystal/ProductOfCyclicGroups.h
inc/MantidGeometry/Crystal/ReducedCell.h
inc/MantidGeometry/Crystal/ReflectionCondition.h
+ inc/MantidGeometry/Crystal/ReflectionGenerator.h
inc/MantidGeometry/Crystal/ScalarUtils.h
inc/MantidGeometry/Crystal/SpaceGroup.h
inc/MantidGeometry/Crystal/SpaceGroupFactory.h
+ inc/MantidGeometry/Crystal/StructureFactorCalculator.h
+ inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h
inc/MantidGeometry/Crystal/SymmetryElement.h
inc/MantidGeometry/Crystal/SymmetryElementFactory.h
inc/MantidGeometry/Crystal/SymmetryOperation.h
@@ -256,6 +268,7 @@ set ( INC_FILES
set ( TEST_FILES
AcompTest.h
AlgebraTest.h
+ BasicHKLFiltersTest.h
BnIdTest.h
BoundingBoxTest.h
BraggScattererFactoryTest.h
@@ -282,6 +295,8 @@ set ( TEST_FILES
GeneralTest.h
GoniometerTest.h
GroupTest.h
+ HKLFilterTest.h
+ HKLGeneratorTest.h
HKLTest.h
IDFObjectTest.h
IMDDimensionFactoryTest.h
@@ -337,6 +352,7 @@ set ( TEST_FILES
ReducedCellTest.h
ReferenceFrameTest.h
ReflectionConditionTest.h
+ ReflectionGeneratorTest.h
RotCounterTest.h
RulesBoolValueTest.h
RulesCompGrpTest.h
@@ -350,6 +366,8 @@ set ( TEST_FILES
SpaceGroupFactoryTest.h
SpaceGroupTest.h
SphereTest.h
+ StructureFactorCalculatorSummationTest.h
+ StructureFactorCalculatorTest.h
SurfaceFactoryTest.h
SurfaceTest.h
SymmetryElementFactoryTest.h
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h b/Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h
new file mode 100644
index 0000000000000000000000000000000000000000..8081a3ebe33d623b95637c87a4995dfab5e02f74
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h
@@ -0,0 +1,162 @@
+#ifndef MANTID_GEOMETRY_BASICHKLFILTERS_H_
+#define MANTID_GEOMETRY_BASICHKLFILTERS_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/HKLFilter.h"
+#include "MantidGeometry/Crystal/ReflectionCondition.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+#include "MantidGeometry/Crystal/SpaceGroup.h"
+#include "MantidGeometry/Crystal/UnitCell.h"
+
+#include <strstream>
+
+namespace Mantid {
+namespace Geometry {
+
+/** BasicHKLFilters
+
+ This file contains some implementations of HKLFilter that
+ provide filtering based on things like d-value, space group
+ or centering.
+
+ A common use would be to generate a specific list of HKLs,
+ for example all reflections that are allowed according to a certain
+ range of d-values and the reflection conditions of a space group:
+
+ HKLFilter_const_sptr filter =
+ boost::make_shared<HKLFilterDRange>(unitCell, 0.5)
+ & boost::make_shared<HKLFilterSpaceGroup>(spaceGroup);
+
+ HKLGenerator gen(unitCell, 0.5);
+ std::vector<V3D> hkls;
+
+ std::remove_copy_if(gen.begin(), gen.end(), std::back_inserter(hkls),
+ (~filter)->fn());
+
+ An existing list of HKLs could be checked for indices that match the
+ reflection conditions of a space group:
+
+ HKLFilter_const_sptr sgFilter =
+ boost::make_shared<HKLFilterSpaceGroup>(spaceGroup);
+
+ auto matchingHKLCount = std::count_if(hkls.begin(), hkls.end(),
+ sgFilter->fn());
+
+ auto violatingHKLCount = std::count_if(hkls.begin(), hkls.end(),
+ (~sgFilter)->fn());
+
+ Combining HKLGenerator and different HKLFilters provides a very flexible
+ system for creating and processing specific sets of Miller indices that
+ is easy to expand by adding other HKLFilters.
+
+ @author Michael Wedel, ESS
+ @date 23/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+
+/**
+ * A class to filter HKLs by their d-values
+ *
+ * This class takes a UnitCell object and calculates the spacing of
+ * the lattice planes for each HKL. If the lattice spacing is within
+ * the spcified range of values, the reflection is allowed.
+ *
+ * If the first constructor with only dMin is used, dMax is taken to
+ * be the lattice parameter with the largest value. There can not be
+ * a greater interplanar spacing than that value.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterDRange : public HKLFilter {
+public:
+ HKLFilterDRange(const UnitCell &cell, double dMin);
+ HKLFilterDRange(const UnitCell &cell, double dMin, double dMax);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+private:
+ void checkProperDRangeValues();
+
+ UnitCell m_cell;
+ double m_dmin, m_dmax;
+};
+
+/**
+ * A class to filter HKLs according to a space group
+ *
+ * HKLFilterSpaceGroup stores a SpaceGroup object and marks those
+ * reflections as allowed that are allowed according to the
+ * reflection conditions of the space group.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterSpaceGroup : public HKLFilter {
+public:
+ HKLFilterSpaceGroup(const SpaceGroup_const_sptr &spaceGroup);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+protected:
+ SpaceGroup_const_sptr m_spaceGroup;
+};
+
+/**
+ * A class to filter HKLs according to structure factor magnitudes
+ *
+ * This filter takes a StructureFactorCalculator and calculates the
+ * structure factor for each HKL. If F^2 is larger than the specified
+ * minimum, the reflection is considered allowed. The default minimum
+ * is 1e-6.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterStructureFactor : public HKLFilter {
+public:
+ HKLFilterStructureFactor(const StructureFactorCalculator_sptr &calculator,
+ double fSquaredMin = 1.0e-6);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+protected:
+ StructureFactorCalculator_sptr m_calculator;
+ double m_fSquaredMin;
+};
+
+/**
+ * A class to filter HKLs according to a lattice centering
+ *
+ * HKLFilterCentering is a filter that stores a ReflectionCondition object
+ * internally and filters the HKLs according to that.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterCentering : public HKLFilter {
+public:
+ HKLFilterCentering(const ReflectionCondition_sptr ¢ering);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+protected:
+ ReflectionCondition_sptr m_centering;
+};
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_BASICHKLFILTERS_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererFactory.h b/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererFactory.h
index 1b98b0eacd299f18d22ffa93b35166fa0f4b1721..2203f878b2c33329bf6d66cc46e3b51b21196a55 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererFactory.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererFactory.h
@@ -4,7 +4,9 @@
#include "MantidGeometry/DllConfig.h"
#include "MantidKernel/DynamicFactory.h"
#include "MantidKernel/SingletonHolder.h"
+
#include "MantidGeometry/Crystal/BraggScatterer.h"
+#include "MantidGeometry/Crystal/CompositeBraggScatterer.h"
namespace Mantid {
namespace Geometry {
@@ -67,7 +69,7 @@ class MANTID_GEOMETRY_DLL BraggScattererFactoryImpl
: public Kernel::DynamicFactory<BraggScatterer> {
public:
BraggScatterer_sptr createScatterer(const std::string &name,
- const std::string &properties = "");
+ const std::string &properties = "") const;
/// Subscribes a scatterer class into the factory.
template <class C> void subscribeScatterer() {
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererInCrystalStructure.h b/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererInCrystalStructure.h
index 9cbb27cd64be109ea50e3f12d2fe40bd887ffeb1..abd137481536e20b60610d266e22fc81be6f754a 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererInCrystalStructure.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/BraggScattererInCrystalStructure.h
@@ -14,12 +14,10 @@ namespace Geometry {
This class provides an extension of BraggScatterer, suitable
for scatterers that are part of a crystal structure. Information about
- the unit cell and space group can be set. The space group information
- is used to calculate equivalent positions in the structure.
+ the unit cell can be set.
- Both space group and unit cell are exposed marked as exposed to
- BraggScattererComposite, so all members of one composite will
- have the same unit cell and space group.
+ The unit cell is marked as exposed to BraggScattererComposite, so all
+ members of one composite will have the same unit cell.
@author Michael Wedel, Paul Scherrer Institut - SINQ
@date 04/11/2014
@@ -51,9 +49,7 @@ public:
virtual ~BraggScattererInCrystalStructure() {}
Kernel::V3D getPosition() const;
- std::vector<Kernel::V3D> getEquivalentPositions() const;
UnitCell getCell() const;
- SpaceGroup_const_sptr getSpaceGroup() const;
protected:
virtual void afterPropertySet(const std::string &propertyName);
@@ -68,18 +64,13 @@ protected:
virtual void setPosition(const Kernel::V3D &position);
virtual void setCell(const UnitCell &cell);
- virtual void setSpaceGroup(const SpaceGroup_const_sptr &spaceGroup);
virtual void declareProperties();
Kernel::V3D getPositionFromString(const std::string &positionString) const;
- void recalculateEquivalentPositions();
Kernel::V3D m_position;
- std::vector<Kernel::V3D> m_equivalentPositions;
-
UnitCell m_cell;
- SpaceGroup_const_sptr m_spaceGroup;
};
typedef boost::shared_ptr<BraggScattererInCrystalStructure>
@@ -99,6 +90,9 @@ protected:
virtual std::string checkValidity(const std::string &unitCellString) const;
};
+MANTID_GEOMETRY_DLL std::vector<std::string>
+getTokenizedPositionString(const std::string &position);
+
} // namespace Geometry
} // namespace Mantid
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/CompositeBraggScatterer.h b/Framework/Geometry/inc/MantidGeometry/Crystal/CompositeBraggScatterer.h
index d1e23c735bba3d934b2d65cc15068487c12c318b..58ced2a99a06a94d745b7f0419097c77530ebfde 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/CompositeBraggScatterer.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/CompositeBraggScatterer.h
@@ -73,7 +73,8 @@ public:
std::string name() const { return "CompositeBraggScatterer"; }
BraggScatterer_sptr clone() const;
- void addScatterer(const BraggScatterer_sptr &scatterer);
+ virtual void addScatterer(const BraggScatterer_sptr &scatterer);
+ void setScatterers(const std::vector<BraggScatterer_sptr> &scatterers);
size_t nScatterers() const;
BraggScatterer_sptr getScatterer(size_t i) const;
void removeScatterer(size_t i);
@@ -88,6 +89,9 @@ protected:
const std::string &propertyName,
const std::string &propertyValue);
+ void addScattererImplementation(const BraggScatterer_sptr &scatterer);
+ void removeScattererImplementation(size_t i);
+
void redeclareProperties();
std::map<std::string, size_t> getPropertyCountMap() const;
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/CrystalStructure.h b/Framework/Geometry/inc/MantidGeometry/Crystal/CrystalStructure.h
index 24d279a0d68867f21a7aadccab7a3894963df011..96eeb35286bef35cdc4e57d9230f0de170a5c15f 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/CrystalStructure.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/CrystalStructure.h
@@ -8,12 +8,16 @@
#include "MantidGeometry/Crystal/SpaceGroup.h"
#include "MantidGeometry/Crystal/ReflectionCondition.h"
#include "MantidGeometry/Crystal/CompositeBraggScatterer.h"
+#include "MantidGeometry/Crystal/HKLFilter.h"
#include <boost/make_shared.hpp>
namespace Mantid {
namespace Geometry {
+// Forward declaration
+class StructureFactorCalculator;
+
/**
@class CrystalStructure
@@ -28,90 +32,30 @@ namespace Geometry {
them in order to provide some useful calculations that are
common when working with crystal structures.
- A common task is to calculate lattice plane spacings for a
- given list of HKL-values. For this calculation, only the unit
- cell has to be known:
-
- CrystalStructure structure(someUnitCell);
-
- std::vector<double> dValues = structure.getDValues(hklList);
-
- Where did 'hklList' come from? For this, CrystalStructure offers
- a method as well. Provided a unit cell, it's possible to get all
- HKLs within a given d range:
-
- CrystalStructure structure(someUnitCell);
- std::vector<V3D> hklList = structure.getHKLs(0.5, 10.0);
-
- If the lattice is centered, not all combinations of h, k and l are
- allowed. The first method to provide a centering is to use
- one of the ReflectionCondition-classes directly:
-
- ReflectionCondition_sptr fCentering =
- boost::make_shared<ReflectionConditionAllFaceCentred>();
-
- structure.setCentering(fCentering);
-
- Now, only reflections that fulfill the centering condition are
- returned by getHKLs. For powder diffraction it's not very
- useful to get all reflections, because symmetrically equivalent
- reflections can not be distinguished. Which reflections are
- equivalent is determined by the point group. Again, one possibility
- is to directly assign a point group:
-
- PointGroup_sptr pointGroup =
- PointGroupFactory::Instance().createPointGroup("m-3m");
-
- structure.setPointGroup(pointGroup);
-
- std::vector<V3D> uniqueHKLs = structure.getUniqueHKLs(0.5, 10.0);
-
- The list uniqueHKLs contains only symmetrically independent
- reflections. Both point group and centering may be provided
- to the constructor of CrystalStructure as well:
-
- CrystalStructure structure(someUnitCell, pointGroup, centering);
-
- According to the list given above, this is not a complete description
- of a crystal structure - indeed, the information only describes
- the crystal lattice. As demonstrated by the examples, this is already
- enough information for knowing which reflections are present in
- a given d-range for many cases.
-
- An example where more information is required can be found in a very
- common crystal structure, the structure of Silicon. Silicon crystallizes
- in the space group Fd-3m (No. 227) and the asymmetric unit consists of
- one Si-atom at the position (1/8, 1/8, 1/8) (for origin choice 2, with the
- inversion at the origin). Looking up this space group in the International
- Tables for Crystallography A reveals that placing a scatterer at this
- position introduces a new reflection condition for general reflections hkl:
-
- h = 2n + 1 (reflections with odd h are allowed)
- or h + k + l = 4n
+ Besides construction from actual objects, a CrystalStructure object can be
+ constructed from three strings that contain the corresponding information.
- This means that for example the reflection family {2 2 2} is not allowed,
- even though the F-centering would allow it. In other words, guessing
- existing reflections of silicon only using lattice information does not lead
- to the correct result. Besides that, there are also glide planes in that
- space group, which come with additional reflection conditions as well.
+ The unit cell string must consist of 3 or 6 floating point numbers, which
+ are 3 lenghts in Angström and 3 angles in degree. If the angles are not
+ supplied, they are assumed to be 90 degrees.
- One way to obtain the correct result for this case is to calculate
- structure factors for each HKL and check whether |F|^2 is non-zero. Of
- course, to perform this calculation, all three items mentioned in the list
- at the beginning must be present. CrystalStructure offers an additional
- constructor for this purpose:
+ The space group string must be a valid space group that is registered into
+ the factory. Lastly, specification of the atoms in the asymmetric unit is
+ required. The format is as follows:
- CrystalStructure silicon(unitcell, spaceGroup, scatterers);
+ Element x y z Occupancy U_iso;
+ Element x y z Occupancy U_iso;
+ ...
- After constructing the object like this, it's no longer possible to set
- point group and centering, because this is determined by the space group.
- Now, a different method for checking allowed reflections is available:
+ Element has to be a valid NeutronAtom, x, y and z are fractional coordinates
+ between 0 and 1 (other coordinates will be transformed to that range). It is
+ allowed (and encouraged) to use proper fractions in the coordinates, for
+ example:
- std::vector<V3D> uniqueHKLs = silicon.getUniqueHKLs(0.5, 10.0,
- CrystalStructure::UseStructureFactors);
+ Mg 1/3 2/3 1/4 1.0 0.05;
- By supplying the extra argument, |F|^2 is calculated for each reflection
- and if it's greater than 1e-9, it's considered to be allowed.
+ Occupancy must be given as values between 0 and 1 and U_iso is the isotropic
+ thermal displacement parameter, given in Angrström^2.
@author Michael Wedel, Paul Scherrer Institut - SINQ
@date 05/08/2014
@@ -138,20 +82,18 @@ namespace Geometry {
*/
class DLLExport CrystalStructure {
public:
- enum ReflectionConditionMethod { UseCentering, UseStructureFactor };
-
- CrystalStructure(
- const UnitCell &unitCell,
- const PointGroup_sptr &pointGroup =
- PointGroupFactory::Instance().createPointGroup("-1"),
- const ReflectionCondition_sptr ¢ering =
- ReflectionCondition_sptr(new ReflectionConditionPrimitive));
-
CrystalStructure(const UnitCell &unitCell,
const SpaceGroup_const_sptr &spaceGroup,
const CompositeBraggScatterer_sptr &scatterers);
- virtual ~CrystalStructure() {}
+ CrystalStructure(const std::string &unitCellString,
+ const std::string &spaceGroupString,
+ const std::string &scattererString);
+
+ CrystalStructure(const CrystalStructure &other);
+ CrystalStructure &operator=(const CrystalStructure &other);
+
+ ~CrystalStructure() {}
UnitCell cell() const;
void setCell(const UnitCell &cell);
@@ -159,55 +101,24 @@ public:
SpaceGroup_const_sptr spaceGroup() const;
void setSpaceGroup(const SpaceGroup_const_sptr &spaceGroup);
- void setPointGroup(const PointGroup_sptr &pointGroup);
- PointGroup_sptr pointGroup() const;
- PointGroup::CrystalSystem crystalSystem() const;
-
- void setCentering(const ReflectionCondition_sptr ¢ering);
- ReflectionCondition_sptr centering() const;
+ ReflectionCondition_sptr centering() const { return m_centering; }
CompositeBraggScatterer_sptr getScatterers() const;
void setScatterers(const CompositeBraggScatterer_sptr &scatterers);
void addScatterers(const CompositeBraggScatterer_sptr &scatterers);
- std::vector<Kernel::V3D>
- getHKLs(double dMin, double dMax,
- ReflectionConditionMethod method = UseCentering) const;
- std::vector<Kernel::V3D>
- getUniqueHKLs(double dMin, double dMax,
- ReflectionConditionMethod method = UseCentering) const;
-
- std::vector<double> getDValues(const std::vector<Kernel::V3D> &hkls) const;
- std::vector<double> getFSquared(const std::vector<Kernel::V3D> &hkls) const;
-
protected:
- void setPointGroupFromSpaceGroup(const SpaceGroup_const_sptr &spaceGroup);
+ void assignUnitCellToScatterers(const UnitCell &unitCell);
+
void
setReflectionConditionFromSpaceGroup(const SpaceGroup_const_sptr &spaceGroup);
- void assignSpaceGroupToScatterers(const SpaceGroup_const_sptr &spaceGroup);
- void assignUnitCellToScatterers(const UnitCell &unitCell);
-
void initializeScatterers();
- bool
- isStateSufficientForHKLGeneration(ReflectionConditionMethod method) const;
- bool isStateSufficientForUniqueHKLGeneration(
- ReflectionConditionMethod method) const;
-
- void throwIfRangeUnacceptable(double dMin, double dMax) const;
-
- bool isAllowed(const Kernel::V3D &hkl,
- ReflectionConditionMethod method) const;
-
- double getDValue(const Kernel::V3D &hkl) const;
- double getFSquared(const Kernel::V3D &hkl) const;
-
UnitCell m_cell;
SpaceGroup_const_sptr m_spaceGroup;
- CompositeBraggScatterer_sptr m_scatterers;
- PointGroup_sptr m_pointGroup;
ReflectionCondition_sptr m_centering;
+ CompositeBraggScatterer_sptr m_scatterers;
};
typedef boost::shared_ptr<CrystalStructure> CrystalStructure_sptr;
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..ca812aebdefeb7fdaa31219407f718d6becdfa2b
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h
@@ -0,0 +1,175 @@
+#ifndef MANTID_GEOMETRY_HKLFILTER_H_
+#define MANTID_GEOMETRY_HKLFILTER_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidKernel/V3D.h"
+
+#include <boost/shared_ptr.hpp>
+#include <functional>
+
+namespace Mantid {
+namespace Geometry {
+
+/** HKLFilter
+
+ There are many ways to filter lists of Miller indices HKL. In order
+ to be able to use HKLGenerator with arbitrary filters, HKLFilter provides
+ a general interface for such filters.
+
+ The abstract base class HKLFilter defines a pure virtual method
+ HKLFilter::isAllowed(), which takes a V3D as argument and returns a boolean.
+ Implementing classes can then implement this method, wrapping very different
+ concepts of checking HKLs for certain characteristics.
+
+ There are two general ways of using HKLFilters. When used "standalone",
+ the isAllowed()-function can be used directly:
+
+ if(filter->isAllowed(hkl)) {
+ // do something
+ }
+
+ For interoperability with STL-algorithms, HKLFilter provides a method that
+ returns a function-object with the filter:
+
+ std::copy_if(generator.begin(), generator.end(),
+ hkls.begin(), filter->fn());
+
+ Often, it's not enough to filter a list by one criterion. To this end,
+ there are two implementations of HKLFilter that provide binary logic
+ operations
+ "and" (HKLFilterAnd) and "or" (HKLFilterOr). They can be constructed from two
+ HKLFilter_const_sptrs, or, more conveniently, by using the operators & and |
+ directly with those types. This makes it possible to combine filters in many
+ ways:
+
+ HKLFilter_const_sptr filter = (filter1 | filter2) & filter3;
+
+ Lastly, the unary logic operation "not" (HKLFilterNot) is implemented. This is
+ important for usability with the pre-C++11 algorithm std::remove_copy_if that
+ works logically reversed compared to std::copy_if:
+
+ std::remove_copy_if(generator.begin(), generator.end(), hkls.begin(),
+ (~filter)->fn());
+
+ For actual implementations of HKLFilter, check out BasicHKLFilters, where some
+ important filters are defined.
+
+ @author Michael Wedel, ESS
+ @date 06/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL HKLFilter {
+public:
+ virtual ~HKLFilter() {}
+
+ std::function<bool(const Kernel::V3D &)> fn() const;
+
+ virtual std::string getDescription() const = 0;
+ virtual bool isAllowed(const Kernel::V3D &hkl) const = 0;
+};
+
+typedef boost::shared_ptr<const HKLFilter> HKLFilter_const_sptr;
+
+/// Base class for unary logic operations for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterUnaryLogicOperation : public HKLFilter {
+public:
+ HKLFilterUnaryLogicOperation(const HKLFilter_const_sptr &filter);
+ ~HKLFilterUnaryLogicOperation() {}
+
+ /// Returns the operand of the function.
+ const HKLFilter_const_sptr &getOperand() const { return m_operand; }
+
+protected:
+ HKLFilter_const_sptr m_operand;
+};
+
+/// Logical "Not"-operation for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterNot : public HKLFilterUnaryLogicOperation {
+public:
+ /// Constructor, calls base class constructor, throws exception if filter is a
+ /// null pointer.
+ HKLFilterNot(const HKLFilter_const_sptr &filter)
+ : HKLFilterUnaryLogicOperation(filter) {}
+ ~HKLFilterNot() {}
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+};
+
+/// Base class for binary logic operations for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterBinaryLogicOperation : public HKLFilter {
+public:
+ HKLFilterBinaryLogicOperation(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs);
+ virtual ~HKLFilterBinaryLogicOperation() {}
+
+ /// Returns the left-hand side operand of the operation.
+ const HKLFilter_const_sptr &getLHS() const { return m_lhs; }
+
+ /// Returns the right-hand side operand of the operation.
+ const HKLFilter_const_sptr &getRHS() const { return m_rhs; }
+
+protected:
+ HKLFilter_const_sptr m_lhs;
+ HKLFilter_const_sptr m_rhs;
+};
+
+/// Logical "And"-operation for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterAnd : public HKLFilterBinaryLogicOperation {
+public:
+ /// Constructor, calls base class constructor, throws exception if either of
+ /// the operands is null.
+ HKLFilterAnd(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs)
+ : HKLFilterBinaryLogicOperation(lhs, rhs) {}
+ ~HKLFilterAnd() {}
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+};
+
+/// Logical "Or"-operation for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterOr : public HKLFilterBinaryLogicOperation {
+public:
+ /// Constructor, calls base class constructor, throws exception if either of
+ /// the operands is null.
+ HKLFilterOr(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs)
+ : HKLFilterBinaryLogicOperation(lhs, rhs) {}
+ ~HKLFilterOr() {}
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+};
+
+MANTID_GEOMETRY_DLL const HKLFilter_const_sptr
+operator~(const HKLFilter_const_sptr &filter);
+
+MANTID_GEOMETRY_DLL const HKLFilter_const_sptr
+operator&(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs);
+
+MANTID_GEOMETRY_DLL const HKLFilter_const_sptr
+operator|(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs);
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_HKLFILTER_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h
new file mode 100644
index 0000000000000000000000000000000000000000..bbfde3fc99b3695b9b254245c192691d762ce50c
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h
@@ -0,0 +1,186 @@
+#ifndef MANTID_GEOMETRY_HKLGENERATOR_H_
+#define MANTID_GEOMETRY_HKLGENERATOR_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/UnitCell.h"
+#include "MantidKernel/V3D.h"
+
+#include <boost/iterator/iterator_facade.hpp>
+
+namespace Mantid {
+namespace Geometry {
+
+/** HKLGenerator
+
+ HKLGenerator is a pseudo-container that helps in generating actual
+ containers with V3D-objects representing Miller indices (HKL).
+
+ It's a common task to generate lists of Miller indices. The simplest
+ way of doing that is to simply create a nested loop structure that
+ goes through all combinations of H, K, L within some limits and then
+ put them into a container (vector, list, set, ...):
+
+ for(int h = -hmin; h <= hmax; ++h) {
+ for(int k = -kmin; k <= kmax; ++k) {
+ for(int l = -lmin; l <= lmax; ++l) {
+ hkls.push_back(V3D(h, k, l));
+ }
+ }
+ }
+
+ In most cases the list is not used like that, instead it's filtered
+ using some criteria, for example a certain range of d-spacings or
+ others, so the reflection needs to be checked first:
+
+ ...
+ hkl = V3D(h, k, l)
+ if(isOk(hkl)) {
+ hkls.push_back(hkl);
+ }
+ ...
+
+ Instead of explicitly stating the triple-loop, HKLGenerator provides
+ a shorter way for this process using a const_iterator. The first code
+ example then becomes this:
+
+ HKLGenerator generator(V3D(hmin, kmin, lmin), V3D(hmax, kmax, lmax));
+ for(auto hkl = generator.begin(); hkl != generator.end(); ++hkl) {
+ hkls.push_back(*hkl);
+ }
+
+ Or even shorter, using std::copy:
+
+ HKLGenerator generator(V3D(hmin, kmin, lmin), V3D(hmax, kmax, lmax));
+ std::copy(generator.begin(), generator.end(), std::back_inserter(hkls));
+
+ It's also possible to use filters this way, but in a much easier fashion,
+ using std::copy_remove_if (pre C++11) or std::copy_if (C++11):
+
+ // pre C++11
+ std::copy_remove_if(generator.begin(), generator.end(),
+ std::back_inserter(hkls), isNotOk)
+
+ // C++11
+ std::copy_if(generator.begin(), generator.end(), std::back_inserter(hkls),
+ isOk)
+
+ See the documentation for HKLFilter for more details on how to perform
+ actual filtering.
+
+ Please be aware that the iterator increments infinitely if it passes the
+ specified maximimum HKL. In that case K and L remain constant while H is
+ incremented (until it overflows).
+
+ @author Michael Wedel, ESS
+ @date 23/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL HKLGenerator {
+public:
+ /**
+ * @brief The const_iterator class
+ *
+ * This class uses boost::iterator_facade to provide a const_iterator
+ * interface to HKLGenerator. This makes it very easy to use the standard
+ * library algorithms. It's a forward iterator, so it's not possible to use
+ * operator[] for random access of specific HKLs (this would have to be
+ * done on the generated container if that supports it).
+ *
+ * While the iterators can be instantiated directly, the intention is to
+ * use HKLGenerator::begin() and HKLGenerator::end().
+ */
+ class MANTID_GEOMETRY_DLL const_iterator
+ : public boost::iterator_facade<const_iterator, const Kernel::V3D &,
+ boost::forward_traversal_tag> {
+ public:
+ const_iterator();
+
+ explicit const_iterator(const Kernel::V3D ¤t);
+
+ explicit const_iterator(const Kernel::V3D &hklMin,
+ const Kernel::V3D &hklMax);
+
+ private:
+ // Required for boost::iterator_facade to work
+ friend class boost::iterator_core_access;
+
+ void increment();
+
+ /// Returns true if other is at the same position
+ inline bool equal(const const_iterator &other) const {
+ return this->m_h == other.m_h && this->m_k == other.m_k &&
+ this->m_l == other.m_l;
+ }
+
+ /// Returns a const reference to the currently pointed at HKL.
+ inline const Kernel::V3D &dereference() const { return m_hkl; }
+
+ /// Required for compilation in VS. Forward iterator can not be used
+ /// that way, so the implementation does nothing.
+ inline void advance(difference_type) {}
+ inline void decrement() {}
+
+ int m_h, m_k, m_l;
+ Kernel::V3D m_hkl;
+
+ int m_hMin, m_hMax;
+ int m_kMin, m_kMax;
+ int m_lMin, m_lMax;
+ };
+
+ HKLGenerator(const Kernel::V3D &hklMin, const Kernel::V3D &hklMax);
+ HKLGenerator(const Kernel::V3D &hklMinMax);
+ HKLGenerator(int hMinMax, int kMinMax, int lMinMax);
+ HKLGenerator(const UnitCell &unitCell, double dMin);
+
+ virtual ~HKLGenerator() {}
+
+ /// Returns the number of HKLs to be generated.
+ inline size_t size() const { return m_size; }
+
+ /// Returns an iterator to the beginning of the sequence.
+ inline const const_iterator &begin() const { return m_begin; }
+
+ /// Returns an iterator which "points at" one element past the end.
+ inline const const_iterator &end() const { return m_end; }
+
+private:
+ size_t getSize(const Kernel::V3D &min, const Kernel::V3D &max) const;
+
+ const_iterator getBeginIterator() const;
+ const_iterator getEndIterator() const;
+ Kernel::V3D getEndHKL() const;
+
+ Kernel::V3D m_hklMin;
+ Kernel::V3D m_hklMax;
+
+ size_t m_size;
+
+ const_iterator m_begin;
+ const_iterator m_end;
+};
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_HKLGENERATOR_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h b/Framework/Geometry/inc/MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h
index 0a243f40c6a964250adddfd185533c9bee325f4f..24dd9e30aa59263162745d0d4a7bd426855025c1 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h
@@ -60,26 +60,11 @@ typedef boost::shared_ptr<IsotropicAtomBraggScatterer>
(hence the class name), which may be insufficient depending on the crystal
structure, but as a first approximation it is often enough.
- This class is designed to handle atoms in a unit cell. When a position is
- set, the internally stored space group is used to generate all positions
- that are symmetrically equivalent. In the structure factor calculation
- method all contributions are summed.
+ This class is designed to handle atoms in the asymmetric unit of the cell,
+ creation of symmetrically equivalent atoms in the entire unit cell has to
+ be handled elsewhere.
- Easiest is demonstration by example. Copper crystallizes in the space group
- \f$Fm\bar{3}m\f$, Cu atoms occupy the position (0,0,0) and, because
- of the F-centering, also 3 additional positions.
-
- BraggScatterer_sptr cu =
- BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer",
- "Element=Cu; SpaceGroup=F m -3 m")
-
- cu->setProperty("UnitCell", unitCellToStr(cellCu));
- StructureFactor F = cu->calculateStructureFactor(V3D(1, 1, 1));
-
- The structure factor F contains contributions from all 4 copper atoms in the
- cell. This is convenient especially for general positions.
- The general position of \f$Fm\bar{3}m\f$ for example has 192 equivalents.
+ One example where this is done can be found in CrystalStructure.
[1] http://ww1.iucr.org/comm/cnom/adp/finrep/finrep.html
@@ -139,6 +124,23 @@ protected:
typedef boost::shared_ptr<IsotropicAtomBraggScatterer>
IsotropicAtomBraggScatterer_sptr;
+class MANTID_GEOMETRY_DLL IsotropicAtomBraggScattererParser {
+public:
+ IsotropicAtomBraggScattererParser(const std::string &scattererString);
+
+ std::vector<BraggScatterer_sptr> operator()() const;
+
+private:
+ BraggScatterer_sptr getScatterer(const std::string &singleScatterer) const;
+ std::vector<std::string>
+ getCleanScattererTokens(const std::vector<std::string> &tokens) const;
+
+ std::string m_scattererString;
+};
+
+MANTID_GEOMETRY_DLL std::string
+getIsotropicAtomBraggScattererString(const BraggScatterer_sptr &scatterer);
+
} // namespace Geometry
} // namespace Mantid
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h b/Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h
new file mode 100644
index 0000000000000000000000000000000000000000..439fcfa162daeee23ff22469fd2f258932b7ad74
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h
@@ -0,0 +1,144 @@
+#ifndef MANTID_GEOMETRY_REFLECTIONGENERATOR_H_
+#define MANTID_GEOMETRY_REFLECTIONGENERATOR_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/CrystalStructure.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+#include "MantidGeometry/Crystal/HKLFilter.h"
+
+namespace Mantid {
+namespace Geometry {
+
+enum struct ReflectionConditionFilter {
+ None,
+ Centering,
+ SpaceGroup,
+ StructureFactor
+};
+
+/** ReflectionGenerator
+
+ ReflectionGenerator is a class that provides the means to perform some
+ common tasks involving generation of reflections. While the combination
+ of HKLGenerator and HKLFilter is very flexible, very often a limited set
+ of operations has to be performed repeatedly, involving the crystal
+ structure.
+
+ ReflectionGenerator is constructed from a CrystalStructure object, which
+ is then stored internally. Additionally, a default filter for reflection
+ conditions can be set, which is applied for HKL-generation in addition
+ to a DRangeFilter. For more flexibility, a method is provided that accepts
+ an HKLFilter as additional argument, this filter is then added to the
+ DRangeFilter.
+
+ This way it's very simple to obtain for example a list of unique reflections
+ for a given crystal structure:
+
+ CrystalStructure structure("5.43 5.43 5.43",
+ "F d -3 m", "Si 0 0 0 1.0 0.05");
+ ReflectionGenerator generator(structure);
+
+ // Get all unique HKLs between 0.5 and 5.0 Angstrom
+ std::vector<V3D> hkls = generator.getUniqueHKLs(0.5, 5.0);
+
+ Additionally there are methods to obtain structure factors and d-values
+ for a given list of HKLs.
+
+ The generated reflection lists can be filtered by several criteria to remove
+ reflections that are not allowed. In the default case, the reflection
+ conditions of the space group are used. Alternatively, the reflections can be
+ filtered according to the centering of the lattice or, with some more
+ computational effort, by their structure factors.
+
+ The default filter method can be supplied to the constructor in the form of
+ the enum ReflectionConditionFilter. Furthermore, it's possible to provide
+ self-defined filters in overloaded versions of the HKL generation methods.
+ These can also be generated by using a small helper method that creates
+ the filters and populates them with values associated to the stored crystal
+ structure:
+
+
+ ReflectionGenerator generator(
+ CrystalStructure("5.43 5.43 5.43",
+ "F d -3 m", "Si 0 0 0 1.0 0.05"));
+ auto filter = generator.getReflectionConditionFilter(
+ ReflectionConditionFilter::StructureFactor);
+
+ The filter can then be used in connection with HKLGenerator or the HKL-
+ generation methods of ReflectionGenerator.
+
+ An example where structure factors are required can be found in a very
+ common crystal structure, the structure of Silicon. Silicon crystallizes
+ in the space group Fd-3m (No. 227) and the asymmetric unit consists of
+ one Si-atom at the position (1/8, 1/8, 1/8) (for origin choice 2, with the
+ inversion at the origin). Looking up this space group in the International
+ Tables for Crystallography A reveals that placing a scatterer at this
+ position introduces a new reflection condition for general reflections hkl:
+
+ h = 2n + 1 (reflections with odd h are allowed)
+ or h + k + l = 4n
+
+ This means that for example the reflection family {2 2 2} is not allowed,
+ even though the F-centering would allow it. Using the structure factor
+ calculation filter solves this problem.
+
+ @author Michael Wedel, ESS
+ @date 30/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL ReflectionGenerator {
+public:
+ ReflectionGenerator(const CrystalStructure &crystalStructure,
+ ReflectionConditionFilter defaultFilter =
+ ReflectionConditionFilter::SpaceGroup);
+ ~ReflectionGenerator() {}
+
+ const CrystalStructure &getCrystalStructure() const;
+
+ HKLFilter_const_sptr getDRangeFilter(double dMin, double dMax) const;
+ HKLFilter_const_sptr
+ getReflectionConditionFilter(ReflectionConditionFilter filter);
+
+ std::vector<Kernel::V3D> getHKLs(double dMin, double dMax) const;
+ std::vector<Kernel::V3D>
+ getHKLs(double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const;
+
+ std::vector<Kernel::V3D> getUniqueHKLs(double dMin, double dMax) const;
+ std::vector<Kernel::V3D>
+ getUniqueHKLs(double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const;
+
+ std::vector<double> getDValues(const std::vector<Kernel::V3D> &hkls) const;
+ std::vector<double> getFsSquared(const std::vector<Kernel::V3D> &hkls) const;
+
+private:
+ CrystalStructure m_crystalStructure;
+ StructureFactorCalculator_sptr m_sfCalculator;
+ HKLFilter_const_sptr m_defaultHKLFilter;
+};
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_REFLECTIONGENERATOR_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h
new file mode 100644
index 0000000000000000000000000000000000000000..04b51ff0b49f016817b43884dd822c9c59e09041
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h
@@ -0,0 +1,82 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATOR_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATOR_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/CrystalStructure.h"
+
+namespace Mantid {
+namespace Geometry {
+
+/** StructureFactorCalculator
+
+ This is a base class for concrete structure factor calculators. It is used
+ to logically separate this calculation from CrystalStructure so that different
+ methods of calculation can be used. For actual implementations please consult
+ the available sub-classes.
+
+ @author Michael Wedel, ESS
+ @date 05/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL StructureFactorCalculator {
+public:
+ StructureFactorCalculator();
+ virtual ~StructureFactorCalculator() {}
+
+ void setCrystalStructure(const CrystalStructure &crystalStructure);
+
+ /// In implementations this method should return the structure factor for the
+ /// specified HKL.
+ virtual StructureFactor getF(const Kernel::V3D &hkl) const = 0;
+ virtual double getFSquared(const Kernel::V3D &hkl) const;
+
+ virtual std::vector<StructureFactor>
+ getFs(const std::vector<Kernel::V3D> &hkls) const;
+ virtual std::vector<double>
+ getFsSquared(const std::vector<Kernel::V3D> &hkls) const;
+
+protected:
+ virtual void
+ crystalStructureSetHook(const CrystalStructure &crystalStructure);
+};
+
+typedef boost::shared_ptr<StructureFactorCalculator>
+ StructureFactorCalculator_sptr;
+
+namespace StructureFactorCalculatorFactory {
+/// Small templated factory function that creates the desired calculator
+/// and initializes it by setting the crystal structure.
+template <typename T>
+StructureFactorCalculator_sptr
+create(const CrystalStructure &crystalStructure) {
+ boost::shared_ptr<T> calculator = boost::make_shared<T>();
+ calculator->setCrystalStructure(crystalStructure);
+
+ return calculator;
+}
+}
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATOR_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h
new file mode 100644
index 0000000000000000000000000000000000000000..5cfed836be0c671fee66916460800dcfc735911f
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h
@@ -0,0 +1,64 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATION_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATION_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+
+namespace Mantid {
+namespace Geometry {
+
+/** StructureFactorCalculatorSummation
+
+ This implementation of StructureFactorCalculator uses the summation method
+ provided by BraggScatterer and its sub-classes. It obtains all scatterers in
+ the unit cell by combining the space group and the scatterers located in the
+ asymmetric unit (both taken from CrystalStructure) and stores them.
+
+ @author Michael Wedel, ESS
+ @date 05/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL StructureFactorCalculatorSummation
+ : public StructureFactorCalculator {
+public:
+ StructureFactorCalculatorSummation();
+ virtual ~StructureFactorCalculatorSummation() {}
+
+ StructureFactor getF(const Kernel::V3D &hkl) const;
+
+protected:
+ void crystalStructureSetHook(const CrystalStructure &crystalStructure);
+
+ void updateUnitCellScatterers(const CrystalStructure &crystalStructure);
+ std::string getV3DasString(const Kernel::V3D &point) const;
+
+ CompositeBraggScatterer_sptr m_unitCellScatterers;
+};
+
+typedef boost::shared_ptr<StructureFactorCalculatorSummation>
+ StructureFactorSummation_sptr;
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATION_H_ */
diff --git a/Framework/Geometry/src/Crystal/BasicHKLFilters.cpp b/Framework/Geometry/src/Crystal/BasicHKLFilters.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..9dfec3038a8b7d458404e4ea5490392e80bc2182
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/BasicHKLFilters.cpp
@@ -0,0 +1,120 @@
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+
+namespace Mantid {
+namespace Geometry {
+
+/// Constructor, dMax is set to the largest lattice parameter.
+HKLFilterDRange::HKLFilterDRange(const UnitCell &cell, double dMin)
+ : m_cell(cell), m_dmin(dMin) {
+ m_dmax = std::max(m_cell.a(), std::max(m_cell.b(), m_cell.c()));
+
+ checkProperDRangeValues();
+}
+
+/// Constructor with explicit dMax.
+HKLFilterDRange::HKLFilterDRange(const UnitCell &cell, double dMin, double dMax)
+ : m_cell(cell), m_dmin(dMin), m_dmax(dMax) {
+ checkProperDRangeValues();
+}
+
+/// Returns a description containing the parameters of the filter.
+std::string HKLFilterDRange::getDescription() const {
+ std::ostringstream strm;
+ strm << "(" << m_dmin << " <= d <= " << m_dmax << ")";
+
+ return strm.str();
+}
+
+/// Returns true if the d-value of the HKL is within the specified range.
+bool HKLFilterDRange::isAllowed(const Kernel::V3D &hkl) const {
+ double d = m_cell.d(hkl);
+
+ return d >= m_dmin && d <= m_dmax;
+}
+
+/// Throws exception if m_dMin or m_dMax is <= 0 or if m_dMax < m_dMin.
+void HKLFilterDRange::checkProperDRangeValues() {
+ if (m_dmin <= 0.0) {
+ throw std::range_error("dMin cannot be <= 0.");
+ }
+
+ if (m_dmax <= 0.0) {
+ throw std::range_error("dMax cannot be <= 0.");
+ }
+
+ if (m_dmax <= m_dmin) {
+ throw std::range_error("dMax cannot be smaller than dMin.");
+ }
+}
+
+/// Constructor, throws exception if the supplied pointer is invalid.
+HKLFilterSpaceGroup::HKLFilterSpaceGroup(
+ const SpaceGroup_const_sptr &spaceGroup)
+ : m_spaceGroup(spaceGroup) {
+ if (!m_spaceGroup) {
+ throw std::runtime_error(
+ "Cannot construct HKLFilterSpaceGroup from null space group.");
+ }
+}
+
+/// Returns a description of the filter that contains the space group symbol.
+std::string HKLFilterSpaceGroup::getDescription() const {
+ std::ostringstream strm;
+ strm << "(Space group: " << m_spaceGroup->hmSymbol() << ")";
+
+ return strm.str();
+}
+
+/// Returns true if the reflection is allowed by the space group reflection
+/// conditions.
+bool HKLFilterSpaceGroup::isAllowed(const Kernel::V3D &hkl) const {
+ return m_spaceGroup->isAllowedReflection(hkl);
+}
+
+/// Constructor, throws exception if the calculator pointer is invalid.
+HKLFilterStructureFactor::HKLFilterStructureFactor(
+ const StructureFactorCalculator_sptr &calculator, double fSquaredMin)
+ : m_calculator(calculator), m_fSquaredMin(fSquaredMin) {
+ if (!m_calculator) {
+ throw std::runtime_error(
+ "Cannot construct HKLFilterStructureFactor from null calculator.");
+ }
+}
+
+/// Returns a description for the filter that contains the minimum F^2.
+std::string HKLFilterStructureFactor::getDescription() const {
+ std::ostringstream strm;
+ strm << "(F^2 > " << m_fSquaredMin << ")";
+
+ return strm.str();
+}
+
+/// Returns true if F^2(hkl) is larger than the stored minimum.
+bool HKLFilterStructureFactor::isAllowed(const Kernel::V3D &hkl) const {
+ return m_calculator->getFSquared(hkl) > m_fSquaredMin;
+}
+
+/// Constructor, throws exception if pointer is null.
+HKLFilterCentering::HKLFilterCentering(
+ const ReflectionCondition_sptr ¢ering)
+ : m_centering(centering) {
+ if (!m_centering) {
+ throw std::runtime_error(
+ "Cannot construct HKLFilterCentering from null centering.");
+ }
+}
+
+/// Returns a description with the centering symbol.
+std::string HKLFilterCentering::getDescription() const {
+ return "(Centering: " + m_centering->getSymbol() + ")";
+}
+
+/// Returns true if the HKL is allowed according to the lattice centering.
+bool HKLFilterCentering::isAllowed(const Kernel::V3D &hkl) const {
+ return m_centering->isAllowed(static_cast<int>(hkl.X()),
+ static_cast<int>(hkl.Y()),
+ static_cast<int>(hkl.Z()));
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/BraggScattererFactory.cpp b/Framework/Geometry/src/Crystal/BraggScattererFactory.cpp
index 14a4e4bd97f51c4935e6c1e9c48066474d52abf4..d873b535249ea0df0c2c5e3b505f3c8a76fd587b 100644
--- a/Framework/Geometry/src/Crystal/BraggScattererFactory.cpp
+++ b/Framework/Geometry/src/Crystal/BraggScattererFactory.cpp
@@ -19,9 +19,8 @@ namespace Geometry {
* @param properties :: Semi-colon separated "name=value"-pairs.
* @return Initialized scatterer object.
*/
-BraggScatterer_sptr
-BraggScattererFactoryImpl::createScatterer(const std::string &name,
- const std::string &properties) {
+BraggScatterer_sptr BraggScattererFactoryImpl::createScatterer(
+ const std::string &name, const std::string &properties) const {
BraggScatterer_sptr scatterer = create(name);
scatterer->initialize();
diff --git a/Framework/Geometry/src/Crystal/BraggScattererInCrystalStructure.cpp b/Framework/Geometry/src/Crystal/BraggScattererInCrystalStructure.cpp
index a9046162022c4c0faaad4ff4010b0013275ffae8..7ae70b86507cf844dd2b9db530615ea3a21a4158 100644
--- a/Framework/Geometry/src/Crystal/BraggScattererInCrystalStructure.cpp
+++ b/Framework/Geometry/src/Crystal/BraggScattererInCrystalStructure.cpp
@@ -25,16 +25,13 @@ using namespace Kernel;
/// Default constructor.
BraggScattererInCrystalStructure::BraggScattererInCrystalStructure()
- : BraggScatterer(), m_position(), m_cell(UnitCell(1, 1, 1, 90, 90, 90)),
- m_spaceGroup() {}
+ : BraggScatterer(), m_position(), m_cell(UnitCell(1, 1, 1, 90, 90, 90)) {}
/// Sets the position of the scatterer to the supplied coordinates - vector is
-/// wrapped to [0, 1) and equivalent positions are recalculated.
+/// wrapped to [0, 1).
void BraggScattererInCrystalStructure::setPosition(
const Kernel::V3D &position) {
m_position = getWrappedVector(position);
-
- recalculateEquivalentPositions();
}
/// Returns the position of the scatterer.
@@ -42,44 +39,17 @@ Kernel::V3D BraggScattererInCrystalStructure::getPosition() const {
return m_position;
}
-/// Returns all equivalent positions of the scatterer according to the assigned
-/// space group.
-std::vector<Kernel::V3D>
-BraggScattererInCrystalStructure::getEquivalentPositions() const {
- return m_equivalentPositions;
-}
-
/// Returns the cell which is currently set.
UnitCell BraggScattererInCrystalStructure::getCell() const { return m_cell; }
-/// Returns the assigned space group.
-SpaceGroup_const_sptr BraggScattererInCrystalStructure::getSpaceGroup() const {
- return m_spaceGroup;
-}
-
/// Assigns a unit cell, which may be required for certain calculations.
void BraggScattererInCrystalStructure::setCell(const UnitCell &cell) {
m_cell = cell;
}
-/// Sets the space group, which is required for calculation of equivalent
-/// positions.
-void BraggScattererInCrystalStructure::setSpaceGroup(
- const SpaceGroup_const_sptr &spaceGroup) {
- m_spaceGroup = spaceGroup;
-
- recalculateEquivalentPositions();
-}
-
/// Declares basic properties, should not be overridden by subclasses, use
/// declareScattererProperties instead.
void BraggScattererInCrystalStructure::declareProperties() {
- /* This is required for default behavior. It's not possible to call it
- * from the constructure, because it's not guaranteed that the space group
- * factory has been filled at the time the ScattererFactory is filled.
- */
- setSpaceGroup(SpaceGroupFactory::Instance().createSpaceGroup("P 1"));
-
declareProperty(
new Kernel::PropertyWithValue<std::string>("Position", "[0, 0, 0]"),
"Position of the scatterer");
@@ -92,32 +62,13 @@ void BraggScattererInCrystalStructure::declareProperties() {
"Unit cell.");
exposePropertyToComposite("UnitCell");
- IValidator_sptr spaceGroupValidator =
- boost::make_shared<ListValidator<std::string>>(
- SpaceGroupFactory::Instance().subscribedSpaceGroupSymbols());
- declareProperty(new Kernel::PropertyWithValue<std::string>(
- "SpaceGroup", "P 1", spaceGroupValidator),
- "Space group.");
- exposePropertyToComposite("SpaceGroup");
-
declareScattererProperties();
}
V3D BraggScattererInCrystalStructure::getPositionFromString(
const std::string &positionString) const {
- std::string positionStringClean = positionString;
- positionStringClean.erase(std::remove_if(positionStringClean.begin(),
- positionStringClean.end(),
- boost::is_any_of("[]")),
- positionStringClean.end());
-
- std::vector<std::string> numberParts;
- boost::split(numberParts, positionStringClean, boost::is_any_of(","));
-
- if (numberParts.size() != 3) {
- throw std::invalid_argument("Cannot parse '" + positionString +
- "' as a position.");
- }
+ std::vector<std::string> numberParts =
+ getTokenizedPositionString(positionString);
mu::Parser parser;
@@ -133,8 +84,7 @@ V3D BraggScattererInCrystalStructure::getPositionFromString(
/**
* Additional property processing
*
- * Takes care of handling new property values, for example for construction of a
- * space group from string and so on.
+ * Takes care of handling new property values.
*
* Please note that derived classes should not re-implement this method, as
* the processing for the base properties is absolutely necessary. Instead, all
@@ -147,9 +97,6 @@ void BraggScattererInCrystalStructure::afterPropertySet(
std::string position = getProperty("Position");
setPosition(getPositionFromString(position));
- } else if (propertyName == "SpaceGroup") {
- setSpaceGroup(SpaceGroupFactory::Instance().createSpaceGroup(
- getProperty("SpaceGroup")));
} else if (propertyName == "UnitCell") {
setCell(strToUnitCell(getProperty("UnitCell")));
}
@@ -157,18 +104,6 @@ void BraggScattererInCrystalStructure::afterPropertySet(
afterScattererPropertySet(propertyName);
}
-/// Uses the stored space group to calculate all equivalent positions or if
-/// present.
-void BraggScattererInCrystalStructure::recalculateEquivalentPositions() {
- m_equivalentPositions.clear();
-
- if (m_spaceGroup) {
- m_equivalentPositions = m_spaceGroup->getEquivalentPositions(m_position);
- } else {
- m_equivalentPositions.push_back(m_position);
- }
-}
-
/// Return a clone of the validator.
IValidator_sptr UnitCellStringValidator::clone() const {
return boost::make_shared<UnitCellStringValidator>(*this);
@@ -187,5 +122,25 @@ std::string UnitCellStringValidator::checkValidity(
return "";
}
+/// Returns components of comma-separated position string, cleaned from [ and ].
+std::vector<std::string>
+getTokenizedPositionString(const std::string &position) {
+ std::string positionStringClean = position;
+ positionStringClean.erase(std::remove_if(positionStringClean.begin(),
+ positionStringClean.end(),
+ boost::is_any_of("[]")),
+ positionStringClean.end());
+
+ std::vector<std::string> numberParts;
+ boost::split(numberParts, positionStringClean, boost::is_any_of(","));
+
+ if (numberParts.size() != 3) {
+ throw std::invalid_argument("Cannot parse '" + position +
+ "' as a position.");
+ }
+
+ return numberParts;
+}
+
} // namespace Geometry
} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/CompositeBraggScatterer.cpp b/Framework/Geometry/src/Crystal/CompositeBraggScatterer.cpp
index d004bde9faa304e63834e65c2db28dcee6819568..7a58df47252a25f6fffaca657c66a6f8cc00c81d 100644
--- a/Framework/Geometry/src/Crystal/CompositeBraggScatterer.cpp
+++ b/Framework/Geometry/src/Crystal/CompositeBraggScatterer.cpp
@@ -27,9 +27,7 @@ CompositeBraggScatterer_sptr CompositeBraggScatterer::create(
const std::vector<BraggScatterer_sptr> &scatterers) {
CompositeBraggScatterer_sptr collection = CompositeBraggScatterer::create();
- for (auto it = scatterers.begin(); it != scatterers.end(); ++it) {
- collection->addScatterer(*it);
- }
+ collection->setScatterers(scatterers);
return collection;
}
@@ -41,9 +39,7 @@ BraggScatterer_sptr CompositeBraggScatterer::clone() const {
boost::make_shared<CompositeBraggScatterer>();
clone->initialize();
- for (auto it = m_scatterers.begin(); it != m_scatterers.end(); ++it) {
- clone->addScatterer(*it);
- }
+ clone->setScatterers(m_scatterers);
clone->setProperties(this->asString(false, ';'));
@@ -54,13 +50,18 @@ BraggScatterer_sptr CompositeBraggScatterer::clone() const {
/// cell to the clone and adds it to the composite.
void CompositeBraggScatterer::addScatterer(
const BraggScatterer_sptr &scatterer) {
- if (!scatterer) {
- throw std::invalid_argument("Cannot process null-scatterer.");
- }
+ addScattererImplementation(scatterer);
+ redeclareProperties();
+}
- BraggScatterer_sptr localScatterer = scatterer->clone();
+/// Clears all scatterers and assigns clones of the supplied ones.
+void CompositeBraggScatterer::setScatterers(
+ const std::vector<BraggScatterer_sptr> &scatterers) {
+ removeAllScatterers();
- m_scatterers.push_back(localScatterer);
+ for (auto it = scatterers.begin(); it != scatterers.end(); ++it) {
+ addScattererImplementation(*it);
+ }
redeclareProperties();
}
@@ -82,20 +83,27 @@ BraggScatterer_sptr CompositeBraggScatterer::getScatterer(size_t i) const {
/// Removes the i-th scatterer from the composite or throws an std::out_of_range
/// exception.
void CompositeBraggScatterer::removeScatterer(size_t i) {
+ removeScattererImplementation(i);
+
+ redeclareProperties();
+}
+
+/// This method performs the actual removal of the i-th scatterer.
+void CompositeBraggScatterer::removeScattererImplementation(size_t i) {
if (i >= nScatterers()) {
throw std::out_of_range("Index is out of range.");
}
m_scatterers.erase(m_scatterers.begin() + i);
-
- redeclareProperties();
}
/// Removes all scatterers.
void CompositeBraggScatterer::removeAllScatterers() {
while (nScatterers() > 0) {
- removeScatterer(0);
+ removeScattererImplementation(0);
}
+
+ redeclareProperties();
}
/// Calculates the structure factor for the given HKL by summing all
@@ -139,6 +147,17 @@ void CompositeBraggScatterer::propagatePropertyToScatterer(
}
}
+/// This method performs the actual cloning and adding of a new scatterer.
+void CompositeBraggScatterer::addScattererImplementation(
+ const BraggScatterer_sptr &scatterer) {
+ if (!scatterer) {
+ throw std::invalid_argument("Cannot process null-scatterer.");
+ }
+
+ BraggScatterer_sptr localScatterer = scatterer->clone();
+ m_scatterers.push_back(localScatterer);
+}
+
/**
* Synchronize properties with scatterer members
*
diff --git a/Framework/Geometry/src/Crystal/CrystalStructure.cpp b/Framework/Geometry/src/Crystal/CrystalStructure.cpp
index 05963caaae393496b769669cf8c8c3bc5eeec581..d40ffe8bf0a99e95b075b1b3a8b04658be403e31 100644
--- a/Framework/Geometry/src/Crystal/CrystalStructure.cpp
+++ b/Framework/Geometry/src/Crystal/CrystalStructure.cpp
@@ -1,26 +1,23 @@
#include "MantidGeometry/Crystal/CrystalStructure.h"
#include <boost/bind.hpp>
#include <stdexcept>
+#include <algorithm>
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+#include "MantidGeometry/Crystal/HKLGenerator.h"
#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
#include "MantidGeometry/Crystal/PointGroupFactory.h"
+#include "MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+
+#include <iostream>
+#include <iomanip>
namespace Mantid {
namespace Geometry {
using namespace Mantid::Kernel;
-/// PointGroup/Centering based constructor
-CrystalStructure::CrystalStructure(const UnitCell &unitCell,
- const PointGroup_sptr &pointGroup,
- const ReflectionCondition_sptr ¢ering) {
- initializeScatterers();
-
- setCell(unitCell);
- setPointGroup(pointGroup);
- setCentering(centering);
-}
-
/// SpaceGroup/Scatterers constructor
CrystalStructure::CrystalStructure(
const UnitCell &unitCell, const SpaceGroup_const_sptr &spaceGroup,
@@ -32,6 +29,38 @@ CrystalStructure::CrystalStructure(
setSpaceGroup(spaceGroup);
}
+/// String-based constructor
+CrystalStructure::CrystalStructure(const std::string &unitCellString,
+ const std::string &spaceGroupString,
+ const std::string &scattererString) {
+ initializeScatterers();
+
+ addScatterers(CompositeBraggScatterer::create(
+ IsotropicAtomBraggScattererParser(scattererString)()));
+ setCell(strToUnitCell(unitCellString));
+ setSpaceGroup(
+ SpaceGroupFactory::Instance().createSpaceGroup(spaceGroupString));
+}
+
+/// Copy constructor
+CrystalStructure::CrystalStructure(const CrystalStructure &other) {
+ initializeScatterers();
+ setScatterers(other.getScatterers());
+ setCell(other.cell());
+ setSpaceGroup(other.spaceGroup());
+}
+
+/// Assignment operator
+CrystalStructure &CrystalStructure::operator=(const CrystalStructure &other) {
+ if (&other != this) {
+ setScatterers(other.getScatterers());
+ setCell(other.cell());
+ setSpaceGroup(other.spaceGroup());
+ }
+
+ return *this;
+}
+
/// Returns the unit cell of the structure
UnitCell CrystalStructure::cell() const { return m_cell; }
@@ -50,62 +79,12 @@ SpaceGroup_const_sptr CrystalStructure::spaceGroup() const {
/**
* Assigns a new space group to the crystal structure
*
- * Setting a new space group on a crystal structure causes several effects:
- * - The space group is propagated to the scatterers
- * - A new point group is assigned
- * - A change in point group can also mean change in crystal system
- * - A new reflection condition object is assigned
- * After this operation, the crystal structure object may be in a state
- * where it does not have a valid point group or centering.
- *
* @param spaceGroup :: New space group of the crystal structure
*/
void CrystalStructure::setSpaceGroup(const SpaceGroup_const_sptr &spaceGroup) {
m_spaceGroup = spaceGroup;
- setPointGroupFromSpaceGroup(m_spaceGroup);
setReflectionConditionFromSpaceGroup(m_spaceGroup);
- assignSpaceGroupToScatterers(m_spaceGroup);
-}
-
-/// Assigns the point group or throws std::runtime_error if the space group has
-/// been set before.
-void CrystalStructure::setPointGroup(const PointGroup_sptr &pointGroup) {
- if (m_spaceGroup) {
- throw std::runtime_error(
- "Cannot set point group if a space group has been set.");
- }
-
- m_pointGroup = pointGroup;
-}
-
-/// Returns the structure's point group
-PointGroup_sptr CrystalStructure::pointGroup() const { return m_pointGroup; }
-
-/// Convenience method to get the PointGroup's crystal system
-PointGroup::CrystalSystem CrystalStructure::crystalSystem() const {
- if (!m_pointGroup) {
- throw std::invalid_argument(
- "Cannot determine crystal system from null-PointGroup.");
- }
-
- return m_pointGroup->crystalSystem();
-}
-
-/// Sets the centering or throws std::runtime_error if a space group has been
-/// assigned to the crystal structure
-void CrystalStructure::setCentering(const ReflectionCondition_sptr ¢ering) {
- if (m_spaceGroup) {
- throw std::runtime_error(
- "Cannot set centering if a space group has been set.");
- }
-
- m_centering = centering;
-}
-
-/// Returns the centering of the structure
-ReflectionCondition_sptr CrystalStructure::centering() const {
- return m_centering;
}
/// Return a clone of the internal CompositeBraggScatterer instance.
@@ -134,125 +113,6 @@ void CrystalStructure::addScatterers(
}
assignUnitCellToScatterers(m_cell);
- assignSpaceGroupToScatterers(m_spaceGroup);
-}
-
-/// Returns a vector with all allowed HKLs in the given d-range
-std::vector<Kernel::V3D>
-CrystalStructure::getHKLs(double dMin, double dMax,
- ReflectionConditionMethod method) const {
- if (!isStateSufficientForHKLGeneration(method)) {
- throw std::invalid_argument("Insufficient data for creation of a "
- "reflection list, need at least centering and "
- "unit cell.");
- }
-
- throwIfRangeUnacceptable(dMin, dMax);
-
- std::vector<V3D> hkls;
-
- /* There's an estimation for the number of reflections from the unit cell
- * volume
- * and the minimum d-value. This should speed up insertion into the vector.
- */
- size_t estimatedReflectionCount = static_cast<size_t>(
- ceil(32.0 * M_PI * m_cell.volume()) / (3.0 * pow(2.0 * dMin, 3.0)));
- hkls.reserve(estimatedReflectionCount);
-
- int hMax = static_cast<int>(m_cell.a() / dMin);
- int kMax = static_cast<int>(m_cell.b() / dMin);
- int lMax = static_cast<int>(m_cell.c() / dMin);
-
- for (int h = -hMax; h <= hMax; ++h) {
- for (int k = -kMax; k <= kMax; ++k) {
- for (int l = -lMax; l <= lMax; ++l) {
- V3D hkl(h, k, l);
- double d = getDValue(hkl);
-
- if (d <= dMax && d >= dMin && isAllowed(hkl, method)) {
- hkls.push_back(hkl);
- }
- }
- }
- }
-
- return hkls;
-}
-
-/// Returns a vector with all allowed symmetry independent HKLs (depends on
-/// point group) in the given d-range
-std::vector<Kernel::V3D>
-CrystalStructure::getUniqueHKLs(double dMin, double dMax,
- ReflectionConditionMethod method) const {
- if (!isStateSufficientForUniqueHKLGeneration(method)) {
- throw std::invalid_argument("Insufficient data for creation of a "
- "reflection list, need at least centering, "
- "unit cell and point group.");
- }
-
- throwIfRangeUnacceptable(dMin, dMax);
-
- std::set<V3D> uniqueHKLs;
-
- int hMax = static_cast<int>(m_cell.a() / dMin);
- int kMax = static_cast<int>(m_cell.b() / dMin);
- int lMax = static_cast<int>(m_cell.c() / dMin);
-
- for (int h = -hMax; h <= hMax; ++h) {
- for (int k = -kMax; k <= kMax; ++k) {
- for (int l = -lMax; l <= lMax; ++l) {
- V3D hkl(h, k, l);
- double d = getDValue(hkl);
-
- if (d <= dMax && d >= dMin && isAllowed(hkl, method)) {
- uniqueHKLs.insert(m_pointGroup->getReflectionFamily(hkl));
- }
- }
- }
- }
-
- return std::vector<V3D>(uniqueHKLs.begin(), uniqueHKLs.end());
-}
-
-/// Maps a vector of hkls to d-values using the internal cell
-std::vector<double>
-CrystalStructure::getDValues(const std::vector<V3D> &hkls) const {
-
- std::vector<double> dValues(hkls.size());
- std::transform(hkls.begin(), hkls.end(), dValues.begin(),
- boost::bind(&CrystalStructure::getDValue, this, _1));
-
- return dValues;
-}
-
-/// Returns |F(hkl)|^2 for all supplied hkls.
-std::vector<double>
-CrystalStructure::getFSquared(const std::vector<V3D> &hkls) const {
- std::vector<double> fSquared;
- fSquared.reserve(hkls.size());
-
- for (auto hkl = hkls.begin(); hkl != hkls.end(); ++hkl) {
- fSquared.push_back(getFSquared(*hkl));
- }
-
- return fSquared;
-}
-
-/// Tries to set the point group from the space group symbol or removes the
-/// current point group if creation fails.
-void CrystalStructure::setPointGroupFromSpaceGroup(
- const SpaceGroup_const_sptr &spaceGroup) {
- m_pointGroup.reset();
-
- if (spaceGroup) {
- try {
- m_pointGroup =
- PointGroupFactory::Instance().createPointGroupFromSpaceGroup(
- spaceGroup);
- } catch (...) {
- // do nothing - point group will be null
- }
- }
}
/// Tries to set the centering from the space group symbol or removes the
@@ -279,19 +139,6 @@ void CrystalStructure::setReflectionConditionFromSpaceGroup(
}
}
-/// Assigns the space group to all scatterers
-void CrystalStructure::assignSpaceGroupToScatterers(
- const SpaceGroup_const_sptr &spaceGroup) {
- if (!m_scatterers) {
- throw std::runtime_error(
- "Scatterer collection is a null pointer. Aborting.");
- }
-
- if (m_spaceGroup && m_scatterers->existsProperty("SpaceGroup")) {
- m_scatterers->setProperty("SpaceGroup", spaceGroup->hmSymbol());
- }
-}
-
/// Assigns the cell to all scatterers
void CrystalStructure::assignUnitCellToScatterers(const UnitCell &unitCell) {
if (!m_scatterers) {
@@ -311,58 +158,5 @@ void CrystalStructure::initializeScatterers() {
}
}
-/// Check that the internal state is sufficient for generating a list of HKLs
-bool CrystalStructure::isStateSufficientForHKLGeneration(
- CrystalStructure::ReflectionConditionMethod method) const {
- switch (method) {
- case UseStructureFactor:
- return m_scatterers->nScatterers() > 0;
- default:
- return static_cast<bool>(m_centering);
- }
-}
-
-/// Check that the internal state is sufficient for generating a list of
-/// symmetry independent HKLs
-bool CrystalStructure::isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::ReflectionConditionMethod method) const {
- return isStateSufficientForHKLGeneration(method) && m_pointGroup;
-}
-
-/// Throws std::invalid_argument if dMin <= 0 or dMax >= dMin
-void CrystalStructure::throwIfRangeUnacceptable(double dMin,
- double dMax) const {
- if (dMin <= 0.0) {
- throw std::invalid_argument("dMin is <= 0.0, not a valid spacing.");
- }
-
- if (dMax <= dMin) {
- throw std::invalid_argument("dMax must be larger than dMin.");
- }
-}
-
-/// Checks whether a reflection is allowed, using the specified method
-bool CrystalStructure::isAllowed(
- const V3D &hkl, CrystalStructure::ReflectionConditionMethod method) const {
- switch (method) {
- case UseStructureFactor:
- return getFSquared(hkl) > 1e-9;
- default:
- return m_centering->isAllowed(static_cast<int>(hkl.X()),
- static_cast<int>(hkl.Y()),
- static_cast<int>(hkl.Z()));
- }
-}
-
-/// Returns the lattice plane spacing for the given HKL.
-double CrystalStructure::getDValue(const V3D &hkl) const {
- return m_cell.d(hkl);
-}
-
-/// Returns |F|^2 for the given HKL.
-double CrystalStructure::getFSquared(const V3D &hkl) const {
- return m_scatterers->calculateFSquared(hkl);
-}
-
} // namespace Geometry
} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/HKLFilter.cpp b/Framework/Geometry/src/Crystal/HKLFilter.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ed218cb7fdb2f3fce2bdeaa204efc113e8479009
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/HKLFilter.cpp
@@ -0,0 +1,117 @@
+#include "MantidGeometry/Crystal/HKLFilter.h"
+#include <boost/make_shared.hpp>
+#include <stdexcept>
+
+namespace Mantid {
+namespace Geometry {
+
+/**
+ * Returns a function object that wraps HKLFilter::isAllowed
+ *
+ * This method uses std::bind to create a function object that
+ * represents the HKLFilter::isAllowed() method. This way it's
+ * possible to pass the function to STL-algorithms easily (see
+ * class documentation).
+ *
+ * @return Function object with filter function for V3D.s
+ */
+std::function<bool(const Kernel::V3D &)> HKLFilter::fn() const {
+ return std::bind(&HKLFilter::isAllowed, this, std::placeholders::_1);
+}
+
+/// Stores the supplied filter, throws exception if filter is null.
+HKLFilterUnaryLogicOperation::HKLFilterUnaryLogicOperation(
+ const HKLFilter_const_sptr &filter)
+ : m_operand(filter) {
+ if (!m_operand) {
+ throw std::runtime_error(
+ "Cannot create HKLFilterUnaryLogicOperation from null operand.");
+ }
+}
+
+/// Returns a description of the HKLFilterNot.
+std::string HKLFilterNot::getDescription() const {
+ return "!" + m_operand->getDescription();
+}
+
+/// Returns true if the wrapped filter returns false and false otherwise.
+bool HKLFilterNot::isAllowed(const Kernel::V3D &hkl) const {
+ return !(m_operand->isAllowed(hkl));
+}
+
+/// Stores the left-hand and right-hand side operators, throws exception if
+/// either is null.
+HKLFilterBinaryLogicOperation::HKLFilterBinaryLogicOperation(
+ const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs)
+ : m_lhs(lhs), m_rhs(rhs) {
+ if (!m_lhs || !m_rhs) {
+ throw std::runtime_error("Cannot construct HKLFilterBinaryLogicOperation "
+ "with one or more null-operands.");
+ }
+}
+
+/// Returns a description of the HKLFilterAnd.
+std::string HKLFilterAnd::getDescription() const {
+ return "(" + m_lhs->getDescription() + " & " + m_rhs->getDescription() + ")";
+}
+
+/// Returns true if both wrapped filters return true.
+bool HKLFilterAnd::isAllowed(const Kernel::V3D &hkl) const {
+ return m_lhs->isAllowed(hkl) && m_rhs->isAllowed(hkl);
+}
+
+/// Returns a description of the HKLFilterOr.
+std::string HKLFilterOr::getDescription() const {
+ return "(" + m_lhs->getDescription() + " | " + m_rhs->getDescription() + ")";
+}
+
+/// Returns true if either of the wrapped filters returns true.
+bool HKLFilterOr::isAllowed(const Kernel::V3D &hkl) const {
+ return m_lhs->isAllowed(hkl) || m_rhs->isAllowed(hkl);
+}
+
+/**
+ * Constructs an HKLFilterNot from the operand
+ *
+ * This function makes it easy to construct HKLFilterNot by using the
+ * operator ~, which inverts the wrapped filter.
+ *
+ * @param filter :: HKLFilter to invert.
+ * @return HKLFilterNot with the wrapped filter.
+ */
+const HKLFilter_const_sptr operator~(const HKLFilter_const_sptr &filter) {
+ return boost::make_shared<const HKLFilterNot>(filter);
+}
+
+/**
+ * Constructs an HKLFilterAnd from the operands
+ *
+ * This function makes it easy to construct HKLFilterAnd by using the
+ * operator & directly on HKLFilter_const_sptr.
+ *
+ * @param lhs :: Left-hand side HKLFilter operand.
+ * @param rhs :: Right-hand side HKLFilter operand.
+ * @return HKLFilterAnd with two wrapped filters.
+ */
+const HKLFilter_const_sptr operator&(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs) {
+ return boost::make_shared<const HKLFilterAnd>(lhs, rhs);
+}
+
+/**
+ * Constructs an HKLFilterOr from the operands
+ *
+ * This function makes it easy to construct HKLFilterOr by using the
+ * operator | directly on HKLFilter_const_sptr.
+ *
+ * @param lhs :: Left-hand side HKLFilter operand.
+ * @param rhs :: Right-hand side HKLFilter operand.
+ * @return HKLFilterOr with two wrapped filters.
+ */
+const HKLFilter_const_sptr operator|(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs) {
+ return boost::make_shared<HKLFilterOr>(lhs, rhs);
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/HKLGenerator.cpp b/Framework/Geometry/src/Crystal/HKLGenerator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..05a153674c612074fa06a4dd936f6285092284da
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/HKLGenerator.cpp
@@ -0,0 +1,101 @@
+#include "MantidGeometry/Crystal/HKLGenerator.h"
+
+namespace Mantid {
+namespace Geometry {
+
+using namespace Kernel;
+
+/// Constructs a generator that creates all indices from hklMin to hklMax.
+HKLGenerator::HKLGenerator(const Kernel::V3D &hklMin, const Kernel::V3D &hklMax)
+ : m_hklMin(hklMin), m_hklMax(hklMax), m_size(getSize(m_hklMin, m_hklMax)),
+ m_begin(getBeginIterator()), m_end(getEndIterator()) {}
+
+/// Constructs a generator that creates all indices from -hklMinMax to
+/// hklMinMax.
+HKLGenerator::HKLGenerator(const Kernel::V3D &hklMinMax)
+ : m_hklMin(hklMinMax * -1), m_hklMax(hklMinMax),
+ m_size(getSize(m_hklMin, m_hklMax)), m_begin(getBeginIterator()),
+ m_end(getEndIterator()) {}
+
+/// Constructs a generator that creates all indices from -h,-k,-l to h,k,l.
+HKLGenerator::HKLGenerator(int hMinMax, int kMinMax, int lMinMax) {
+ m_hklMax = V3D(hMinMax, kMinMax, lMinMax);
+ m_hklMin = m_hklMax * -1;
+ m_size = getSize(m_hklMin, m_hklMax);
+
+ m_begin = getBeginIterator();
+ m_end = getEndIterator();
+}
+
+/// Constructs a generator that creates all indices for the given cell up to
+/// dMin.
+HKLGenerator::HKLGenerator(const UnitCell &unitCell, double dMin) {
+ m_hklMax = V3D(unitCell.a() / dMin, unitCell.b() / dMin, unitCell.c() / dMin);
+ m_hklMin = m_hklMax * -1;
+ m_size = getSize(m_hklMin, m_hklMax);
+
+ m_begin = getBeginIterator();
+ m_end = getEndIterator();
+}
+
+/// Returns the number of indices between min and max.
+size_t HKLGenerator::getSize(const V3D &min, const V3D &max) const {
+ V3D diff = (max - min) + V3D(1, 1, 1);
+ return static_cast<size_t>(diff.X() * diff.Y() * diff.Z());
+}
+
+/// Constructs an iterator that points to the beginning of the sequence.
+HKLGenerator::const_iterator HKLGenerator::getBeginIterator() const {
+ return HKLGenerator::const_iterator(m_hklMin, m_hklMax);
+}
+
+/// Constructs an iterator that points to an HKL one past the maximum.
+HKLGenerator::const_iterator HKLGenerator::getEndIterator() const {
+ return HKLGenerator::const_iterator(getEndHKL());
+}
+
+/// Returns the HKL "one past the maximum".
+V3D HKLGenerator::getEndHKL() const {
+ return V3D(m_hklMax.X() + 1, m_hklMin.Y(), m_hklMin.Z());
+}
+
+/// Default constructor, requirement from boost::iterator_facade
+HKLGenerator::const_iterator::const_iterator()
+ : m_h(0), m_k(0), m_l(0), m_hkl(V3D(0, 0, 0)), m_hMin(0), m_hMax(0),
+ m_kMin(0), m_kMax(0), m_lMin(0), m_lMax(0) {}
+
+/// Return an iterator with min = max = current.
+HKLGenerator::const_iterator::const_iterator(const V3D ¤t)
+ : m_h(static_cast<int>(current.X())), m_k(static_cast<int>(current.Y())),
+ m_l(static_cast<int>(current.Z())), m_hkl(current), m_hMin(m_h),
+ m_hMax(m_h), m_kMin(m_k), m_kMax(m_k), m_lMin(m_l), m_lMax(m_l) {}
+
+/// Return an iterator that can move from min to max, with current = min
+HKLGenerator::const_iterator::const_iterator(const V3D &hklMin,
+ const V3D &hklMax)
+ : m_h(static_cast<int>(hklMin.X())), m_k(static_cast<int>(hklMin.Y())),
+ m_l(static_cast<int>(hklMin.Z())), m_hkl(hklMin), m_hMin(m_h),
+ m_hMax(static_cast<int>(hklMax.X())), m_kMin(m_k),
+ m_kMax(static_cast<int>(hklMax.Y())), m_lMin(m_l),
+ m_lMax(static_cast<int>(hklMax.Z())) {}
+
+/// Increments HKL, l moves fastest, h moves slowest, wrapping around at the max
+/// for each index.
+void HKLGenerator::const_iterator::increment() {
+ ++m_l;
+
+ if (m_l > m_lMax) {
+ m_l = m_lMin;
+
+ ++m_k;
+ if (m_k > m_kMax) {
+ m_k = m_kMin;
+ ++m_h;
+ }
+ }
+
+ m_hkl = V3D(m_h, m_k, m_l);
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/IsotropicAtomBraggScatterer.cpp b/Framework/Geometry/src/Crystal/IsotropicAtomBraggScatterer.cpp
index 80e8f54eebf9e9ee47577303faec65ba32b13883..6797299f9b47dfe25d63f7db5c9fa6b834d8f244 100644
--- a/Framework/Geometry/src/Crystal/IsotropicAtomBraggScatterer.cpp
+++ b/Framework/Geometry/src/Crystal/IsotropicAtomBraggScatterer.cpp
@@ -7,6 +7,10 @@
#include "MantidGeometry/Crystal/BraggScattererFactory.h"
+#include <boost/tokenizer.hpp>
+#include <boost/algorithm/string.hpp>
+#include <boost/assign.hpp>
+
namespace Mantid {
namespace Geometry {
@@ -56,9 +60,7 @@ double IsotropicAtomBraggScatterer::getU() const { return getProperty("U"); }
/**
* Calculates the structure factor
*
- * This method calculates the structure factor, taking into account
- * contributions from all atoms on the stored position
- * _and all symmetrically equivalent_.
+ * This method calculates the structure factor.
* For details, please refer to the class documentation in the header file.
*
* @param hkl :: HKL for which the structure factor should be calculated
@@ -69,16 +71,9 @@ IsotropicAtomBraggScatterer::calculateStructureFactor(const V3D &hkl) const {
double amplitude =
getOccupancy() * getDebyeWallerFactor(hkl) * getScatteringLength();
- StructureFactor sum(0.0, 0.0);
-
- std::vector<V3D> equivalentPositions = getEquivalentPositions();
- for (auto pos = equivalentPositions.begin(); pos != equivalentPositions.end();
- ++pos) {
- double phase = 2.0 * M_PI * (*pos).scalar_prod(hkl);
- sum += amplitude * StructureFactor(cos(phase), sin(phase));
- }
+ double phase = 2.0 * M_PI * m_position.scalar_prod(hkl);
- return sum;
+ return amplitude * StructureFactor(cos(phase), sin(phase));
}
/**
@@ -136,5 +131,105 @@ double IsotropicAtomBraggScatterer::getScatteringLength() const {
DECLARE_BRAGGSCATTERER(IsotropicAtomBraggScatterer)
+/**
+ * Constructor for vector with IsotropicAtomBraggScatterers from a string
+ *
+ * The functor expects to be constructed from a string in the following format:
+ *
+ * Element x y z occupancy u_iso; Element x y z occupancy u_iso; ...
+ *
+ * It generates an IsotropicAtomBraggScatterer for each specified atom.
+ *
+ * @param scattererString :: String in the format specified above
+ */
+IsotropicAtomBraggScattererParser::IsotropicAtomBraggScattererParser(
+ const std::string &scattererString)
+ : m_scattererString(scattererString) {}
+
+/// Operator that returns vector of IsotropicAtomBraggScatterers.
+std::vector<BraggScatterer_sptr> IsotropicAtomBraggScattererParser::
+operator()() const {
+ boost::char_separator<char> atomSep(";");
+ boost::tokenizer<boost::char_separator<char>> tokens(m_scattererString,
+ atomSep);
+ std::vector<BraggScatterer_sptr> scatterers;
+
+ for (auto it = tokens.begin(); it != tokens.end(); ++it) {
+ scatterers.push_back(getScatterer(boost::trim_copy(*it)));
+ }
+
+ return scatterers;
+}
+
+/// Returns IsotropicAtomBraggScatterer for string with format "Element x y z
+/// occupancy u_iso".
+BraggScatterer_sptr IsotropicAtomBraggScattererParser::getScatterer(
+ const std::string &singleScatterer) const {
+ std::vector<std::string> tokens;
+ boost::split(tokens, singleScatterer, boost::is_any_of(" "));
+
+ if (tokens.size() < 4 || tokens.size() > 6) {
+ throw std::invalid_argument("Could not parse scatterer string: " +
+ singleScatterer);
+ }
+
+ std::vector<std::string> cleanScattererTokens =
+ getCleanScattererTokens(tokens);
+ std::vector<std::string> properties =
+ boost::assign::list_of("Element")("Position")("Occupancy")("U")
+ .convert_to_container<std::vector<std::string>>();
+
+ std::string initString;
+ for (size_t i = 0; i < cleanScattererTokens.size(); ++i) {
+ initString += properties[i] + "=" + cleanScattererTokens[i] + ";";
+ }
+
+ return BraggScattererFactory::Instance().createScatterer(
+ "IsotropicAtomBraggScatterer", initString);
+}
+
+/// Converts tokens for getScatterer method so they can be processed by factory.
+std::vector<std::string>
+IsotropicAtomBraggScattererParser::getCleanScattererTokens(
+ const std::vector<std::string> &tokens) const {
+ std::vector<std::string> cleanTokens;
+
+ // Element
+ cleanTokens.push_back(tokens[0]);
+
+ // X, Y, Z
+ cleanTokens.push_back("[" + tokens[1] + "," + tokens[2] + "," + tokens[3] +
+ "]");
+
+ for (size_t i = 4; i < tokens.size(); ++i) {
+ cleanTokens.push_back(tokens[i]);
+ }
+
+ return cleanTokens;
+}
+
+std::string
+getIsotropicAtomBraggScattererString(const BraggScatterer_sptr &scatterer) {
+ IsotropicAtomBraggScatterer_sptr isotropicAtom =
+ boost::dynamic_pointer_cast<IsotropicAtomBraggScatterer>(scatterer);
+
+ if (!isotropicAtom) {
+ throw std::invalid_argument(
+ "Printing function can only process IsotropicAtomBraggScatterer.");
+ }
+
+ std::string rawPositionString = isotropicAtom->getProperty("Position");
+ std::vector<std::string> positionComponents =
+ getTokenizedPositionString(rawPositionString);
+
+ std::stringstream outStream;
+ outStream << isotropicAtom->getElement() << " " << positionComponents[0]
+ << " " << positionComponents[1] << " " << positionComponents[2]
+ << " " << isotropicAtom->getOccupancy() << " "
+ << isotropicAtom->getU();
+
+ return outStream.str();
+}
+
} // namespace Geometry
} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/ReflectionGenerator.cpp b/Framework/Geometry/src/Crystal/ReflectionGenerator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..59fd597ef216ad55f5d601c3a8f688c5e443738d
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/ReflectionGenerator.cpp
@@ -0,0 +1,146 @@
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+#include "MantidGeometry/Crystal/HKLGenerator.h"
+
+namespace Mantid {
+namespace Geometry {
+
+using namespace Kernel;
+
+/// Small helper functor to calculate d-Values from a unit cell.
+class LatticeSpacingCalculator {
+public:
+ LatticeSpacingCalculator(const UnitCell &cell) : m_cell(cell) {}
+
+ double operator()(const V3D &hkl) { return m_cell.d(hkl); }
+
+private:
+ UnitCell m_cell;
+};
+
+/// Constructor
+ReflectionGenerator::ReflectionGenerator(
+ const CrystalStructure &crystalStructure,
+ ReflectionConditionFilter defaultFilter)
+ : m_crystalStructure(crystalStructure),
+ m_sfCalculator(StructureFactorCalculatorFactory::create<
+ StructureFactorCalculatorSummation>(m_crystalStructure)),
+ m_defaultHKLFilter(getReflectionConditionFilter(defaultFilter)) {}
+
+/// Returns the internally stored crystal structure
+const CrystalStructure &ReflectionGenerator::getCrystalStructure() const {
+ return m_crystalStructure;
+}
+
+/// Returns a DRangeFilter from the supplied d-limits and the internally stored
+/// cell.
+HKLFilter_const_sptr ReflectionGenerator::getDRangeFilter(double dMin,
+ double dMax) const {
+ return boost::make_shared<const HKLFilterDRange>(m_crystalStructure.cell(),
+ dMin, dMax);
+}
+
+/// Returns a reflection condition HKLFilter based on the supplied enum.
+HKLFilter_const_sptr ReflectionGenerator::getReflectionConditionFilter(
+ ReflectionConditionFilter filter) {
+ switch (filter) {
+ case ReflectionConditionFilter::Centering:
+ return boost::make_shared<const HKLFilterCentering>(
+ m_crystalStructure.centering());
+ break;
+ case ReflectionConditionFilter::SpaceGroup:
+ return boost::make_shared<const HKLFilterSpaceGroup>(
+ m_crystalStructure.spaceGroup());
+ break;
+ case ReflectionConditionFilter::StructureFactor:
+ return boost::make_shared<const HKLFilterStructureFactor>(m_sfCalculator);
+ default:
+ return HKLFilter_const_sptr();
+ }
+}
+
+/// Returns a list of HKLs within the specified d-limits using the default
+/// reflection condition filter.
+std::vector<V3D> ReflectionGenerator::getHKLs(double dMin, double dMax) const {
+ return getHKLs(dMin, dMax, m_defaultHKLFilter);
+}
+
+/// Returns a list of HKLs within the specified d-limits using the specified
+/// filter. If the pointer is null, it's ignored.
+std::vector<Kernel::V3D> ReflectionGenerator::getHKLs(
+ double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const {
+ HKLGenerator generator(m_crystalStructure.cell(), dMin);
+
+ HKLFilter_const_sptr filter = getDRangeFilter(dMin, dMax);
+ if (reflectionConditionFilter) {
+ filter = filter & reflectionConditionFilter;
+ }
+
+ std::vector<V3D> hkls;
+ hkls.reserve(generator.size());
+
+ std::remove_copy_if(generator.begin(), generator.end(),
+ std::back_inserter(hkls), (~filter)->fn());
+ return hkls;
+}
+
+/// Returns a list of symetrically independent HKLs within the specified
+/// d-limits using the default reflection condition filter.
+std::vector<V3D> ReflectionGenerator::getUniqueHKLs(double dMin,
+ double dMax) const {
+ return getUniqueHKLs(dMin, dMax, m_defaultHKLFilter);
+}
+
+/// Returns a list of symetrically independent HKLs within the specified
+/// d-limits using the specified reflection condition filter.
+std::vector<V3D> ReflectionGenerator::getUniqueHKLs(
+ double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const {
+ HKLGenerator generator(m_crystalStructure.cell(), dMin);
+
+ HKLFilter_const_sptr filter = getDRangeFilter(dMin, dMax);
+ if (reflectionConditionFilter) {
+ filter = filter & reflectionConditionFilter;
+ }
+
+ std::vector<V3D> hkls;
+ hkls.reserve(generator.size());
+
+ PointGroup_sptr pg = m_crystalStructure.spaceGroup()->getPointGroup();
+
+ for (auto hkl = generator.begin(); hkl != generator.end(); ++hkl) {
+ if (filter->isAllowed(*hkl)) {
+ hkls.push_back(pg->getReflectionFamily(*hkl));
+ }
+ }
+
+ std::sort(hkls.begin(), hkls.end());
+ hkls.erase(std::unique(hkls.begin(), hkls.end()), hkls.end());
+
+ return hkls;
+}
+
+/// Returns a list of d-values that correspond to the supplied hkl list, using
+/// the unit cell of the stored crystal structure.
+std::vector<double>
+ReflectionGenerator::getDValues(const std::vector<V3D> &hkls) const {
+ std::vector<double> dValues;
+ dValues.reserve(hkls.size());
+
+ std::transform(hkls.begin(), hkls.end(), std::back_inserter(dValues),
+ LatticeSpacingCalculator(m_crystalStructure.cell()));
+
+ return dValues;
+}
+
+/// Returns a list of squared structure factor amplitudes corresponding to the
+/// supplied list of HKLs.
+std::vector<double>
+ReflectionGenerator::getFsSquared(const std::vector<V3D> &hkls) const {
+ return m_sfCalculator->getFsSquared(hkls);
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/ScalarUtils.cpp b/Framework/Geometry/src/Crystal/ScalarUtils.cpp
index 096cbabf474a832b4b82a10cd92da237707671aa..e92b977edef531ba35d5a1092e8df1dc1ffe07e4 100644
--- a/Framework/Geometry/src/Crystal/ScalarUtils.cpp
+++ b/Framework/Geometry/src/Crystal/ScalarUtils.cpp
@@ -229,7 +229,7 @@ ConventionalCell ScalarUtils::GetCellForForm(const DblMatrix &UB,
if (allowPermutations) {
double angle_tolerance = 2.0;
double length_factor = 1.05;
- UB_list = GetRelatedUBs(UB, angle_tolerance, length_factor);
+ UB_list = GetRelatedUBs(UB, length_factor, angle_tolerance);
} else {
// Get exact form requested and not permutations
UB_list.push_back(UB);
diff --git a/Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp b/Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..df4cb44ed97825cee453bb450b2be33a9b5be755
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp
@@ -0,0 +1,83 @@
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+
+#include <boost/bind.hpp>
+
+namespace Mantid {
+namespace Geometry {
+
+StructureFactorCalculator::StructureFactorCalculator() {}
+
+/**
+ * Sets the crystal structure for which to calculate structure factors
+ *
+ * Additionally StructureFactorCalculator::crystalStructureSetHook() is called
+ * with the CrystalStructure. This function may be re-implemented
+ * by concrete structure factor calculators to perform other necessary actions
+ * that involve the crystal structure (for example extracting and storing
+ * members of it).
+ *
+ * @param crystalStructure :: Crystal structure for calculations.
+ */
+void StructureFactorCalculator::setCrystalStructure(
+ const CrystalStructure &crystalStructure) {
+ crystalStructureSetHook(crystalStructure);
+}
+
+/// Returns F^2 for the given HKL, calling StructureFactorCalculator::getF().
+double StructureFactorCalculator::getFSquared(const Kernel::V3D &hkl) const {
+ StructureFactor sf = getF(hkl);
+
+ return sf.real() * sf.real() + sf.imag() * sf.imag();
+}
+
+/**
+ * Returns structure factors for each HKL in the container
+ *
+ * The default implementation uses StructureFactorCalculator::getF() to get
+ * the structure factor for each HKL. This behavior can be overriden in
+ * sub-classes for example to implement this in a more efficient way.
+ *
+ * @param hkls :: Vector of HKLs.
+ * @return :: Vector of structure factors for the given HKLs.
+ */
+std::vector<StructureFactor>
+StructureFactorCalculator::getFs(const std::vector<Kernel::V3D> &hkls) const {
+ std::vector<StructureFactor> structureFactors(hkls.size());
+
+ std::transform(hkls.begin(), hkls.end(), structureFactors.begin(),
+ boost::bind(&StructureFactorCalculator::getF, this, _1));
+
+ return structureFactors;
+}
+
+/**
+ * Returns structure factors for each HKL in the container
+ *
+ * The default implementation uses StructureFactorCalculator::getFSquared() with
+ * each HKL. This behavior can be overriden in
+ * sub-classes for example to implement this in a more efficient way.
+ *
+ * @param hkls :: Vector of HKLs.
+ * @return :: Vector of squared structure factors for the given HKLs.
+ */
+std::vector<double> StructureFactorCalculator::getFsSquared(
+ const std::vector<Kernel::V3D> &hkls) const {
+ std::vector<double> fSquareds(hkls.size());
+
+ std::transform(
+ hkls.begin(), hkls.end(), fSquareds.begin(),
+ boost::bind(&StructureFactorCalculator::getFSquared, this, _1));
+
+ return fSquareds;
+}
+
+/// This function is called from
+/// StructureFactorCalculator::setCrystalStructure() and can be overriden to
+/// perform additional actions.
+void StructureFactorCalculator::crystalStructureSetHook(
+ const CrystalStructure &crystalStructure) {
+ UNUSED_ARG(crystalStructure)
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp b/Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..eabc22952cbd37217570255a766d4f023f170d83
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp
@@ -0,0 +1,82 @@
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+#include "MantidGeometry/Crystal/BraggScattererInCrystalStructure.h"
+
+#include <iomanip>
+
+namespace Mantid {
+namespace Geometry {
+
+using namespace Kernel;
+
+StructureFactorCalculatorSummation::StructureFactorCalculatorSummation()
+ : StructureFactorCalculator(),
+ m_unitCellScatterers(CompositeBraggScatterer::create()) {}
+
+/// Returns the structure factor obtained from the stored scatterers.
+StructureFactor
+StructureFactorCalculatorSummation::getF(const Kernel::V3D &hkl) const {
+ return m_unitCellScatterers->calculateStructureFactor(hkl);
+}
+
+/// Calls updateUnitCellScatterers() to rebuild the complete list of scatterers.
+void StructureFactorCalculatorSummation::crystalStructureSetHook(
+ const CrystalStructure &crystalStructure) {
+ updateUnitCellScatterers(crystalStructure);
+}
+
+/**
+ * Rebuilds the internal list of scatterers
+ *
+ * This method extracts two items from the supplied CrystalStructure object, the
+ * list of scatterers in the asymmetric unit and the space group. Then it
+ * generates all equivalent positions and creates a complete list of scatterers.
+ *
+ * @param crystalStructure :: CrystalStructure for structure factor calculation.
+ */
+void StructureFactorCalculatorSummation::updateUnitCellScatterers(
+ const CrystalStructure &crystalStructure) {
+ m_unitCellScatterers->removeAllScatterers();
+
+ CompositeBraggScatterer_sptr scatterersInAsymmetricUnit =
+ crystalStructure.getScatterers();
+ SpaceGroup_const_sptr spaceGroup = crystalStructure.spaceGroup();
+
+ if (spaceGroup) {
+ std::vector<BraggScatterer_sptr> braggScatterers;
+ braggScatterers.reserve(scatterersInAsymmetricUnit->nScatterers() *
+ spaceGroup->order());
+
+ for (size_t i = 0; i < scatterersInAsymmetricUnit->nScatterers(); ++i) {
+ BraggScattererInCrystalStructure_sptr current =
+ boost::dynamic_pointer_cast<BraggScattererInCrystalStructure>(
+ scatterersInAsymmetricUnit->getScatterer(i));
+
+ if (current) {
+ std::vector<V3D> positions =
+ spaceGroup->getEquivalentPositions(current->getPosition());
+
+ for (auto pos = positions.begin(); pos != positions.end(); ++pos) {
+ BraggScatterer_sptr clone = current->clone();
+ clone->setProperty("Position", getV3DasString(*pos));
+
+ braggScatterers.push_back(clone);
+ }
+ }
+ }
+
+ m_unitCellScatterers->setScatterers(braggScatterers);
+ }
+}
+
+/// Return V3D as string without losing precision.
+std::string
+StructureFactorCalculatorSummation::getV3DasString(const V3D &point) const {
+ std::ostringstream posStream;
+ posStream << std::setprecision(17);
+ posStream << point;
+
+ return posStream.str();
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Instrument.cpp b/Framework/Geometry/src/Instrument.cpp
index 8841dfdceac65fa7349966abb79781c368247339..0990d31e19b2e3d79b816f62485c16a9f91b945f 100644
--- a/Framework/Geometry/src/Instrument.cpp
+++ b/Framework/Geometry/src/Instrument.cpp
@@ -1258,6 +1258,11 @@ Instrument::ContainsState Instrument::containsRectDetectors() const {
if (detector && detector->isMonitor())
continue;
+ // skip choppers HACK!
+ if (comp->getName() == "chopper-position") {
+ continue;
+ }
+
if (dynamic_cast<const RectangularDetector *>(comp.get())) {
if (!foundRect)
foundRect = true;
diff --git a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
index cdc50169d55ad5ab98597068d3a5a4ced1b04ddb..f4c9afef815111745fea386715ae9a79b4d531ea 100644
--- a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
+++ b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
@@ -1554,7 +1554,15 @@ void InstrumentDefinitionParser::populateIdList(Poco::XML::Element *pE,
increment = atoi((pIDElem->getAttribute("step")).c_str());
// check the start end and increment values are sensible
- if (((endID - startID) / increment) < 0) {
+ if (0 == increment) {
+ std::stringstream ss;
+ ss << "The step element cannot be zero, found step: " << increment;
+
+ throw Kernel::Exception::InstrumentDefinitionError(ss.str(),
+ filename);
+ }
+ int numSteps = (endID - startID) / increment;
+ if (numSteps < 0) {
std::stringstream ss;
ss << "The start, end, and step elements do not allow a single id "
"in the idlist entry - ";
@@ -1565,7 +1573,7 @@ void InstrumentDefinitionParser::populateIdList(Poco::XML::Element *pE,
filename);
}
- idList.vec.reserve((endID - startID) / increment);
+ idList.vec.reserve(numSteps);
for (int i = startID; i != endID + increment; i += increment) {
idList.vec.push_back(i);
}
@@ -2301,7 +2309,9 @@ void InstrumentDefinitionParser::createNeutronicInstrument() {
mapTypeNameToShape.find(shapeName);
if (shapeIt != mapTypeNameToShape.end()) {
// Change the shape on the current component to the one requested
- dynamic_cast<ObjComponent *>(it->first)->setShape(shapeIt->second);
+ auto objCmpt = dynamic_cast<ObjComponent *>(it->first);
+ if (objCmpt)
+ objCmpt->setShape(shapeIt->second);
} else {
throw Exception::InstrumentDefinitionError(
"Requested type " + shapeName + " not defined in IDF");
diff --git a/Framework/Geometry/src/Math/Acomp.cpp b/Framework/Geometry/src/Math/Acomp.cpp
index 0788103182bd08ed8d4202180f43ed171f722ee3..75c5fb5fe2be6d8d76bc081899ffbf8b4e10774a 100644
--- a/Framework/Geometry/src/Math/Acomp.cpp
+++ b/Framework/Geometry/src/Math/Acomp.cpp
@@ -366,7 +366,8 @@ Assumes that the component is sorted and inserts appropiately.
for (acp = AX.Comp.begin(); acp != AX.Comp.end(); ++acp) {
std::vector<Acomp>::iterator cpt;
cpt = std::lower_bound(Comp.begin(), Comp.end(), *acp);
- if (cpt == Comp.end() || *cpt != *aup) // Only insert if new
+ if (cpt == Comp.end() ||
+ (AX.Units.end() != aup && *cpt != *aup)) // Only insert if new
Comp.insert(cpt, *acp);
}
return;
@@ -981,6 +982,9 @@ It is set on exit (to the EPI)
break;
}
+ if (PIactive.end() == px)
+ continue;
+
EPI.push_back(PIform[*px]);
// remove all minterm that the EPI covered
for (ddx = DNFactive.begin(); ddx != DNFactive.end(); ++ddx)
diff --git a/Framework/Geometry/src/Objects/Object.cpp b/Framework/Geometry/src/Objects/Object.cpp
index e6ab975dda916bb686a74b0efc4530155844cac6..d7bccf922d68d8ae460d4ef200e57dec7ee257a5 100644
--- a/Framework/Geometry/src/Objects/Object.cpp
+++ b/Framework/Geometry/src/Objects/Object.cpp
@@ -221,11 +221,13 @@ int Object::complementaryObject(const int Cnum, std::string &Ln) {
std::string::size_type posB;
posB = Ln.find_first_of("()", posA);
if (posB == std::string::npos)
- throw std::runtime_error("Object::complemenet :: " + Ln);
+ throw std::runtime_error("Object::complement :: " + Ln);
brackCnt = (Ln[posB] == '(') ? 1 : 0;
while (posB != std::string::npos && brackCnt) {
posB = Ln.find_first_of("()", posB);
+ if (posB == std::string::npos)
+ break;
brackCnt += (Ln[posB] == '(') ? 1 : -1;
posB++;
}
@@ -242,7 +244,7 @@ int Object::complementaryObject(const int Cnum, std::string &Ln) {
return 1;
}
- throw std::runtime_error("Object::complemenet :: " + Part);
+ throw std::runtime_error("Object::complement :: " + Part);
return 0;
}
diff --git a/Framework/Geometry/test/BasicHKLFiltersTest.h b/Framework/Geometry/test/BasicHKLFiltersTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..7295290c09a156062be0e9cd70d3c2308ef2bead
--- /dev/null
+++ b/Framework/Geometry/test/BasicHKLFiltersTest.h
@@ -0,0 +1,146 @@
+#ifndef MANTID_GEOMETRY_BASICHKLFILTERSTEST_H_
+#define MANTID_GEOMETRY_BASICHKLFILTERSTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+
+#include <strstream>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+using ::testing::_;
+using ::testing::Return;
+using ::testing::Mock;
+
+class BasicHKLFiltersTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static BasicHKLFiltersTest *createSuite() {
+ return new BasicHKLFiltersTest();
+ }
+ static void destroySuite(BasicHKLFiltersTest *suite) { delete suite; }
+
+ void testHKLFilterDRangeConstructors() {
+ UnitCell cell(10., 10., 10.);
+
+ TS_ASSERT_THROWS_NOTHING(HKLFilterDRange dFilter(cell, 1.0));
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, -1.0), std::range_error);
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, 0.0), std::range_error);
+
+ TS_ASSERT_THROWS_NOTHING(HKLFilterDRange dFilter(cell, 1.0, 2.0));
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, 1.0, 0.5), std::range_error);
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, 1.0, -0.5),
+ std::range_error);
+ }
+
+ void testHKLFilterDRangeDescription() {
+ UnitCell cell(10., 10., 10.);
+
+ std::ostringstream reference;
+ reference << "(" << 1.0 << " <= d <= " << 10.0 << ")";
+
+ HKLFilterDRange dFilter(cell, 1.0);
+ TS_ASSERT_EQUALS(dFilter.getDescription(), reference.str());
+ }
+
+ void testHKLFilterDRangeIsAllowed() {
+ UnitCell cell(10., 10., 10.);
+ HKLFilterDRange dFilter(cell, 1.0, 9.0);
+
+ TS_ASSERT(dFilter.isAllowed(V3D(1, 2, 3)));
+
+ TS_ASSERT(dFilter.isAllowed(V3D(2, 0, 0)));
+ TS_ASSERT(!dFilter.isAllowed(V3D(1, 0, 0)));
+
+ TS_ASSERT(dFilter.isAllowed(V3D(10, 0, 0)));
+ TS_ASSERT(!dFilter.isAllowed(V3D(11, 0, 0)));
+ }
+
+ void testHKLFilterSpaceGroupConstructor() {
+ SpaceGroup_const_sptr invalid;
+ TS_ASSERT_THROWS(HKLFilterSpaceGroup sgFilter(invalid), std::runtime_error);
+
+ SpaceGroup_const_sptr sg =
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m");
+ TS_ASSERT_THROWS_NOTHING(HKLFilterSpaceGroup sgFilter(sg));
+ }
+
+ void testHKLFilterSpaceGroupDescription() {
+ SpaceGroup_const_sptr sg =
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m");
+
+ HKLFilterSpaceGroup sgFilter(sg);
+
+ TS_ASSERT_EQUALS(sgFilter.getDescription(),
+ "(Space group: " + sg->hmSymbol() + ")");
+ }
+
+ void testHKLFilterSpaceGroupIsAllowed() {
+ SpaceGroup_const_sptr sg =
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m");
+
+ HKLFilterSpaceGroup sgFilter(sg);
+
+ TS_ASSERT(!sgFilter.isAllowed(V3D(1, 0, 0)));
+ TS_ASSERT(!sgFilter.isAllowed(V3D(1, 1, 0)));
+ TS_ASSERT(sgFilter.isAllowed(V3D(1, 1, 1)));
+
+ TS_ASSERT(!sgFilter.isAllowed(V3D(2, 0, 0)));
+ TS_ASSERT(!sgFilter.isAllowed(V3D(3, 0, 0)));
+ TS_ASSERT(sgFilter.isAllowed(V3D(4, 0, 0)));
+ }
+
+ void testHKLFilterStructureFactorConstructor() {
+ StructureFactorCalculator_sptr invalid;
+ TS_ASSERT_THROWS(HKLFilterStructureFactor sfFilter(invalid),
+ std::runtime_error);
+
+ StructureFactorCalculator_sptr mock =
+ boost::make_shared<MockStructureFactorCalculator>();
+ TS_ASSERT_THROWS_NOTHING(HKLFilterStructureFactor sfFilter(mock));
+ TS_ASSERT_THROWS_NOTHING(HKLFilterStructureFactor sfFilter(mock, 12.0));
+ }
+
+ void testHKLFilterStructureFactorDescription() {
+ std::ostringstream reference;
+ reference << "(F^2 > " << 1.0 << ")";
+
+ StructureFactorCalculator_sptr mock =
+ boost::make_shared<MockStructureFactorCalculator>();
+ HKLFilterStructureFactor sfFilter(mock, 1.0);
+ TS_ASSERT_EQUALS(sfFilter.getDescription(), reference.str());
+ }
+
+ void testHKLFilterStructureFactorIsAllowed() {
+ boost::shared_ptr<MockStructureFactorCalculator> mock =
+ boost::make_shared<MockStructureFactorCalculator>();
+
+ EXPECT_CALL(*mock, getFSquared(_))
+ .WillOnce(Return(2.0))
+ .WillOnce(Return(0.5))
+ .WillOnce(Return(1.0));
+
+ HKLFilterStructureFactor sfFilter(mock, 1.0);
+ TS_ASSERT(sfFilter.isAllowed(V3D(1, 1, 1)));
+ TS_ASSERT(!sfFilter.isAllowed(V3D(1, 1, 1)));
+ TS_ASSERT(!sfFilter.isAllowed(V3D(1, 1, 1)));
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(mock.get()))
+ }
+
+private:
+ class MockStructureFactorCalculator : public StructureFactorCalculator {
+ public:
+ MOCK_CONST_METHOD1(getF, StructureFactor(const V3D &));
+ MOCK_CONST_METHOD1(getFSquared, double(const V3D &));
+ };
+};
+
+#endif /* MANTID_GEOMETRY_BASICHKLFILTERSTEST_H_ */
diff --git a/Framework/Geometry/test/BraggScattererInCrystalStructureTest.h b/Framework/Geometry/test/BraggScattererInCrystalStructureTest.h
index 2f66f592ca71d10a57eb76f584560cad042cb040..fe58dd10a1d43c22e7212cb8dfee451150a3558d 100644
--- a/Framework/Geometry/test/BraggScattererInCrystalStructureTest.h
+++ b/Framework/Geometry/test/BraggScattererInCrystalStructureTest.h
@@ -33,7 +33,6 @@ public:
TS_ASSERT(scatterer->existsProperty("Position"));
TS_ASSERT(scatterer->existsProperty("UnitCell"));
- TS_ASSERT(scatterer->existsProperty("SpaceGroup"));
}
void testAfterScattererPropertySet() {
@@ -72,47 +71,6 @@ public:
TS_ASSERT_EQUALS(scatterer->getCell().getG(), cell.getG());
}
- void testGetSetSpaceGroup() {
- BraggScattererInCrystalStructure_sptr scatterer = getInitializedScatterer();
-
- SpaceGroup_const_sptr testGroup =
- SpaceGroupFactory::Instance().createSpaceGroup("P m -3 m");
-
- TS_ASSERT_THROWS_NOTHING(scatterer->setProperty("SpaceGroup", "P m -3 m"));
- TS_ASSERT_EQUALS(scatterer->getSpaceGroup()->hmSymbol(),
- testGroup->hmSymbol());
- }
-
- void testEquivalentPositions() {
- BraggScattererInCrystalStructure_sptr scatterer = getInitializedScatterer();
-
- V3D generalPosition(0.3, 0.32, 0.45);
-
- // No space group set - no equivalent positions
- scatterer->setProperty("Position", "[0.3, 0.32, 0.45]");
- TS_ASSERT_EQUALS(scatterer->getEquivalentPositions().size(), 1);
- TS_ASSERT_EQUALS(scatterer->getEquivalentPositions().front(),
- generalPosition);
-
- // Assigning a space group must cause recalculation of equivalent positions
- SpaceGroup_const_sptr testGroup =
- SpaceGroupFactory::Instance().createSpaceGroup("P m -3 m");
- scatterer->setProperty("SpaceGroup", "P m -3 m");
-
- TS_ASSERT_EQUALS(scatterer->getEquivalentPositions().size(),
- testGroup->order());
-
- // Re-setting the position also recalculates
- V3D specialPosition(0.0, 0.0, 0.0);
-
- scatterer->setProperty("Position", "[0, 0, 0]");
- // Pm-3m does not contain translations, so (0,0,0) is not transformed by any
- // symmetry operation of the group
- TS_ASSERT_EQUALS(scatterer->getEquivalentPositions().size(), 1);
- TS_ASSERT_EQUALS(scatterer->getEquivalentPositions().front(),
- specialPosition);
- }
-
void testUnitCellStringValidator() {
IValidator_sptr validator = boost::make_shared<UnitCellStringValidator>();
diff --git a/Framework/Geometry/test/CompositeBraggScattererTest.h b/Framework/Geometry/test/CompositeBraggScattererTest.h
index f5c45156900d5a7fac250eed7109010787ecc007..618c86120f6765301577d1116d4831617bb9bd95 100644
--- a/Framework/Geometry/test/CompositeBraggScattererTest.h
+++ b/Framework/Geometry/test/CompositeBraggScattererTest.h
@@ -9,6 +9,7 @@
#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
#include "MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h"
+#include <iostream>
#include <map>
using namespace Mantid::Geometry;
@@ -68,38 +69,16 @@ public:
}
void testAddGetScatterer() {
- UnitCell cell(5.43, 5.43, 5.43);
- SpaceGroup_const_sptr spaceGroup =
- SpaceGroupFactory::Instance().createSpaceGroup("P 1 2/m 1");
-
CompositeBraggScatterer_sptr scatterer = CompositeBraggScatterer::create();
TS_ASSERT_EQUALS(scatterer->propertyCount(), 0);
IsotropicAtomBraggScatterer_sptr siOne =
getInitializedScatterer("Si", "[0, 0, 0]");
- TS_ASSERT_DIFFERS(siOne->getSpaceGroup()->hmSymbol(),
- spaceGroup->hmSymbol());
-
size_t oldCount = scatterer->nScatterers();
scatterer->addScatterer(siOne);
- TS_ASSERT_EQUALS(scatterer->propertyCount(), 2);
+ TS_ASSERT_EQUALS(scatterer->propertyCount(), 1);
TS_ASSERT_EQUALS(scatterer->nScatterers(), oldCount + 1);
-
- // Properties are propagated.
- scatterer->setProperty("UnitCell", unitCellToStr(cell));
- scatterer->setProperty("SpaceGroup", spaceGroup->hmSymbol());
-
- // The scatterer is cloned, so the new space group is not in siOne
- TS_ASSERT_EQUALS(
- boost::dynamic_pointer_cast<BraggScattererInCrystalStructure>(
- scatterer->getScatterer(0))
- ->getSpaceGroup()
- ->hmSymbol(),
- spaceGroup->hmSymbol());
- TS_ASSERT_DIFFERS(siOne->getSpaceGroup()->hmSymbol(),
- spaceGroup->hmSymbol());
-
TS_ASSERT_THROWS(scatterer->getScatterer(2), std::out_of_range);
}
@@ -147,12 +126,16 @@ public:
UnitCell cell(5.43, 6.43, 7.43, 90.0, 103.0, 90.0);
SpaceGroup_const_sptr spaceGroup =
SpaceGroupFactory::Instance().createSpaceGroup("P 1 2/m 1");
+ std::vector<V3D> positions =
+ spaceGroup->getEquivalentPositions(V3D(0.2, 0.3, 0.4));
CompositeBraggScatterer_sptr coll = CompositeBraggScatterer::create();
- coll->addScatterer(
- getInitializedScatterer("Si", "[0.2, 0.3, 0.4]", 0.01267));
+ for (auto pos = positions.begin(); pos != positions.end(); ++pos) {
+ std::ostringstream strm;
+ strm << (*pos);
+ coll->addScatterer(getInitializedScatterer("Si", strm.str(), 0.01267));
+ }
- coll->setProperty("SpaceGroup", spaceGroup->hmSymbol());
coll->setProperty("UnitCell", unitCellToStr(cell));
// Load reference data, obtained with SHELXL-2014.
diff --git a/Framework/Geometry/test/CrystalStructureTest.h b/Framework/Geometry/test/CrystalStructureTest.h
index 307106f56182291db5fe7eda0ec513887011d847..80fa1f63d0a5dfc9a391edbeb314c014b3fdda83 100644
--- a/Framework/Geometry/test/CrystalStructureTest.h
+++ b/Framework/Geometry/test/CrystalStructureTest.h
@@ -22,10 +22,7 @@ public:
}
static void destroySuite(CrystalStructureTest *suite) { delete suite; }
- CrystalStructureTest()
- : m_CsCl(4.126, 4.126, 4.126),
- m_pg(PointGroupFactory::Instance().createPointGroup("m-3m")),
- m_centering(new ReflectionConditionPrimitive) {
+ CrystalStructureTest() : m_CsCl(4.126, 4.126, 4.126) {
m_spaceGroup = SpaceGroupFactory::Instance().createSpaceGroup("I m -3 m");
m_scatterers = CompositeBraggScatterer::create();
@@ -34,30 +31,10 @@ public:
"IsotropicAtomBraggScatterer", "Element=Si;Position=[0,0,0]"));
}
- void testConstructionDefault() {
- // Only cell is really required, for the others there's a default value
- CrystalStructure structure(m_CsCl);
-
- TS_ASSERT_EQUALS(structure.cell().a(), m_CsCl.a());
- // TS_ASSERT(boost::dynamic_pointer_cast<PointGroupLaue1>(structure.pointGroup()));
- TS_ASSERT(boost::dynamic_pointer_cast<ReflectionConditionPrimitive>(
- structure.centering()));
- TS_ASSERT_THROWS_NOTHING(structure.crystalSystem());
- TS_ASSERT_EQUALS(structure.crystalSystem(), PointGroup::Triclinic);
-
- CrystalStructure structurePg(m_CsCl, m_pg);
- TS_ASSERT_EQUALS(structurePg.pointGroup(), m_pg);
- TS_ASSERT(boost::dynamic_pointer_cast<ReflectionConditionPrimitive>(
- structurePg.centering()));
- TS_ASSERT_EQUALS(structurePg.crystalSystem(), m_pg->crystalSystem());
-
- CrystalStructure structureAll(m_CsCl, m_pg, m_centering);
- TS_ASSERT_EQUALS(structureAll.centering(), m_centering);
- }
-
void testConstructionSpaceGroup() {
TS_ASSERT_THROWS_NOTHING(
CrystalStructure structure(m_CsCl, m_spaceGroup, m_scatterers));
+
CrystalStructure structure(m_CsCl, m_spaceGroup, m_scatterers);
TS_ASSERT_EQUALS(structure.cell().getG(), m_CsCl.getG());
TS_ASSERT_EQUALS(structure.spaceGroup(), m_spaceGroup);
@@ -66,52 +43,20 @@ public:
}
void testSetSpaceGroup() {
- CrystalStructure structure(m_CsCl, m_pg, m_centering);
-
- // Space group is null
- TS_ASSERT(!structure.spaceGroup());
- TS_ASSERT_THROWS(std::string sg =
- structure.getScatterers()->getProperty("SpaceGroup"),
- Exception::NotFoundError);
+ CrystalStructure structure(m_CsCl, m_spaceGroup, m_scatterers);
- TS_ASSERT_THROWS_NOTHING(structure.setSpaceGroup(m_spaceGroup));
+ TS_ASSERT_EQUALS(structure.spaceGroup()->hmSymbol(),
+ m_spaceGroup->hmSymbol());
+ TS_ASSERT_THROWS_NOTHING(structure.setSpaceGroup(
+ SpaceGroupFactory::Instance().createSpaceGroup("I a -3 d")));
// Not null anymore
- TS_ASSERT(structure.spaceGroup())
-
- // No Scatterers present, so space group is not set.
- TS_ASSERT_THROWS(std::string sg =
- structure.getScatterers()->getProperty("SpaceGroup"),
- Exception::NotFoundError);
-
- // Adding a scatterer should set space group for all scatterers.
- std::vector<BraggScatterer_sptr> scatterer(
- 1, BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer", "Element=Si;Position=[0,0,0]"));
- structure.addScatterers(CompositeBraggScatterer::create(scatterer));
-
- std::string sg;
- TS_ASSERT_THROWS_NOTHING(
- sg = structure.getScatterers()->getPropertyValue("SpaceGroup"));
-
- // Symbol of test space group is I m -3 m
- TS_ASSERT_EQUALS(sg, "I m -3 m")
-
- // pointers are different
- TS_ASSERT_DIFFERS(structure.pointGroup(), m_pg);
- // symbol is the same
- TS_ASSERT_EQUALS(structure.pointGroup()->getSymbol(), "m-3m");
-
- // pointers are different
- TS_ASSERT_DIFFERS(structure.centering(), m_centering);
- // symbols as well
- TS_ASSERT_DIFFERS(structure.centering()->getSymbol(),
- m_centering->getSymbol());
- TS_ASSERT_EQUALS(structure.centering()->getSymbol(), "I");
+ TS_ASSERT(structure.spaceGroup());
+ TS_ASSERT_EQUALS(structure.spaceGroup()->hmSymbol(), "I a -3 d")
}
void testCellGetSet() {
- CrystalStructure structure(m_CsCl);
+ CrystalStructure structure(m_CsCl, m_spaceGroup, m_scatterers);
TS_ASSERT_EQUALS(structure.cell().a(), m_CsCl.a());
UnitCell Si(5.43, 5.43, 5.43);
@@ -120,313 +65,45 @@ public:
TS_ASSERT_EQUALS(structure.cell().a(), Si.a());
}
- void testPointGroupGetSet() {
- CrystalStructure structure(m_CsCl, m_pg);
- TS_ASSERT_EQUALS(structure.pointGroup(), m_pg);
- TS_ASSERT_EQUALS(structure.crystalSystem(), m_pg->crystalSystem());
-
- // PointGroup_sptr newPg = boost::make_shared<PointGroupLaue3>();
- // structure.setPointGroup(newPg);
-
- // TS_ASSERT_EQUALS(structure.pointGroup(), newPg);
- // TS_ASSERT_EQUALS(structure.crystalSystem(), newPg->crystalSystem());
-
- // setting a space group makes setting a point group impossible
- structure.setSpaceGroup(m_spaceGroup);
- // TS_ASSERT_DIFFERS(structure.crystalSystem(), newPg->crystalSystem());
-
- // TS_ASSERT_THROWS(structure.setPointGroup(newPg), std::runtime_error);
- }
-
- void testCenteringGetSet() {
- CrystalStructure structure(m_CsCl, m_pg, m_centering);
- TS_ASSERT_EQUALS(structure.centering(), m_centering);
-
- ReflectionCondition_sptr newCentering =
- boost::make_shared<ReflectionConditionAFaceCentred>();
- structure.setCentering(newCentering);
-
- TS_ASSERT_EQUALS(structure.centering(), newCentering);
-
- // setting a space group makes setting a centering impossible
- structure.setSpaceGroup(m_spaceGroup);
- TS_ASSERT_DIFFERS(structure.centering()->getSymbol(),
- newCentering->getSymbol());
-
- TS_ASSERT_THROWS(structure.setCentering(newCentering), std::runtime_error);
- }
-
- void testSufficientStateForHKLGeneration() {
- TestableCrystalStructure structure;
-
- // Default is "UseCentering"
- ReflectionCondition_sptr nullCentering;
- structure.setCentering(nullCentering);
- TS_ASSERT(!structure.isStateSufficientForHKLGeneration(
- CrystalStructure::UseCentering));
- structure.setCentering(m_centering);
- TS_ASSERT(structure.isStateSufficientForHKLGeneration(
- CrystalStructure::UseCentering));
-
- // Structure factor requires at least one scatterer - otherwise all hkl are
- // "forbidden"
- TS_ASSERT(!structure.isStateSufficientForHKLGeneration(
- CrystalStructure::UseStructureFactor));
- structure.addScatterers(m_scatterers);
- TS_ASSERT(structure.isStateSufficientForHKLGeneration(
- CrystalStructure::UseStructureFactor));
-
- // centering does not matter for this
- structure.setCentering(nullCentering);
- TS_ASSERT(structure.isStateSufficientForHKLGeneration(
- CrystalStructure::UseStructureFactor));
- }
-
- void testSufficientStateForUniqueHKLGeneration() {
- TestableCrystalStructure structure;
-
- // Default is "UseCentering"
- ReflectionCondition_sptr nullCentering;
- PointGroup_sptr nullPointGroup;
-
- structure.setCentering(nullCentering);
- structure.setPointGroup(nullPointGroup);
-
- // Does not work with null point group
- TS_ASSERT(!structure.isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::UseCentering));
-
- // not even when centering is set
- structure.setCentering(m_centering);
- TS_ASSERT(!structure.isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::UseCentering));
-
- // now it's okay
- structure.setPointGroup(m_pg);
- TS_ASSERT(structure.isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::UseCentering));
-
- // Structure factor requires at least one scatterer - otherwise all hkl are
- // "forbidden"
- TS_ASSERT(!structure.isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::UseStructureFactor));
- structure.addScatterers(m_scatterers);
- TS_ASSERT(structure.isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::UseStructureFactor));
-
- // point group is required anyway
- structure.setPointGroup(nullPointGroup);
- TS_ASSERT(!structure.isStateSufficientForUniqueHKLGeneration(
- CrystalStructure::UseStructureFactor));
- }
-
- void testThrowIfRangeUnacceptable() {
- TestableCrystalStructure structure;
+ void testCrystalStructureFromStrings() {
+ CrystalStructure structure("5.431 5.431 5.431", "F d -3 m",
+ "Si 0 0 0 1.0 0.02");
- TS_ASSERT_THROWS(structure.throwIfRangeUnacceptable(0.0, 1.0),
- std::invalid_argument);
- TS_ASSERT_THROWS(structure.throwIfRangeUnacceptable(-10.0, 1.0),
- std::invalid_argument);
- TS_ASSERT_THROWS(structure.throwIfRangeUnacceptable(1.0, 0.0),
- std::invalid_argument);
- TS_ASSERT_THROWS(structure.throwIfRangeUnacceptable(1.0, -1.0),
- std::invalid_argument);
- TS_ASSERT_THROWS(structure.throwIfRangeUnacceptable(2.0, 1.0),
- std::invalid_argument);
+ TS_ASSERT_EQUALS(structure.cell().a(), 5.431);
+ TS_ASSERT_EQUALS(structure.cell().b(), 5.431);
+ TS_ASSERT_EQUALS(structure.cell().c(), 5.431);
- TS_ASSERT_THROWS_NOTHING(structure.throwIfRangeUnacceptable(1.0, 2.0))
+ TS_ASSERT_EQUALS(structure.spaceGroup()->hmSymbol(), "F d -3 m");
+ TS_ASSERT_EQUALS(structure.getScatterers()->nScatterers(), 1);
}
- void testGetUniqueHKLsHappyCase() {
- double dMin = 0.55;
- double dMax = 4.0;
-
- CrystalStructure structure(m_CsCl, m_pg, m_centering);
-
- TS_ASSERT_THROWS_NOTHING(structure.getUniqueHKLs(dMin, dMax));
-
- std::vector<V3D> peaks = structure.getUniqueHKLs(dMin, dMax);
-
- TS_ASSERT_EQUALS(peaks.size(), 68);
- TS_ASSERT_EQUALS(peaks[0], V3D(1, 1, 0));
- TS_ASSERT_EQUALS(peaks[11], V3D(3, 2, 0));
- TS_ASSERT_EQUALS(peaks[67], V3D(7, 2, 1));
+ void testCopyConstructor() {
+ CrystalStructure one("1.2 2.3 3.4", "F d d d", "Fe 1/8 1/8 1/8 1.0 0.001");
- // make d-value list and check that peaks are within limits
- std::vector<double> peaksD = structure.getDValues(peaks);
-
- std::sort(peaksD.begin(), peaksD.end());
-
- TS_ASSERT_LESS_THAN_EQUALS(dMin, peaksD.front());
- TS_ASSERT_LESS_THAN_EQUALS(peaksD.back(), dMax);
+ CrystalStructure two(one);
+ TS_ASSERT_EQUALS(two.getScatterers()->nScatterers(),
+ one.getScatterers()->nScatterers());
+ TS_ASSERT_EQUALS(two.spaceGroup()->hmSymbol(),
+ one.spaceGroup()->hmSymbol());
+ TS_ASSERT_EQUALS(unitCellToStr(two.cell()), unitCellToStr(one.cell()));
}
- void testGetHKLsHappyCase() {
- double dMin = 0.55;
- double dMax = 4.0;
-
- // make a structure with P-1
- CrystalStructure structure(
- m_CsCl, PointGroupFactory::Instance().createPointGroup("-1"));
+ void testAssignmentOperator() {
+ CrystalStructure one("1.2 2.3 3.4", "F d d d", "Fe 1/8 1/8 1/8 1.0 0.001");
- std::vector<V3D> unique = structure.getUniqueHKLs(dMin, dMax);
- std::vector<V3D> peaks = structure.getHKLs(dMin, dMax);
+ CrystalStructure two = one;
- // Because of symmetry -1, each reflection has multiplicity 2.
- TS_ASSERT_EQUALS(peaks.size(), 2 * unique.size());
- }
-
- void testGetDValues() {
- std::vector<V3D> hkls;
- hkls.push_back(V3D(1, 0, 0));
- hkls.push_back(V3D(0, 1, 0));
- hkls.push_back(V3D(0, 0, 1));
-
- UnitCell ortho(2.0, 3.0, 5.0);
- CrystalStructure structure(ortho);
-
- std::vector<double> dValues = structure.getDValues(hkls);
-
- TS_ASSERT_EQUALS(dValues.size(), hkls.size());
- TS_ASSERT_EQUALS(dValues[0], 2.0);
- TS_ASSERT_EQUALS(dValues[1], 3.0);
- TS_ASSERT_EQUALS(dValues[2], 5.0);
- }
-
- void testReflectionConditionMethods() {
- /* This test compares the two methods that are available
- * for testing if a reflection is allowed.
- */
-
- UnitCell cellSi(5.43, 5.43, 5.43);
- PointGroup_sptr pgSi =
- PointGroupFactory::Instance().createPointGroup("m-3m");
- ReflectionCondition_sptr centeringSi =
- boost::make_shared<ReflectionConditionAllFaceCentred>();
-
- // Crystal structure with cell, point group, centering
- CrystalStructure siUseCentering(cellSi, pgSi, centeringSi);
- std::vector<V3D> hklsCentering =
- siUseCentering.getUniqueHKLs(0.6, 10.0, CrystalStructure::UseCentering);
-
- // Crystal structure with cell, space group, scatterers - must be a space
- // group without glides/screws.
- SpaceGroup_const_sptr sgSi =
- SpaceGroupFactory::Instance().createSpaceGroup("F m -3 m");
- // With an atom at (x, x, x) there are no extra conditions.
- CompositeBraggScatterer_sptr scatterers = CompositeBraggScatterer::create();
- scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer",
- "Element=Si;Position=[0.3,0.3,0.3];U=0.05"));
-
- CrystalStructure siUseStructureFactors(cellSi, sgSi, scatterers);
- std::vector<V3D> hklsStructureFactors = siUseStructureFactors.getUniqueHKLs(
- 0.6, 10.0, CrystalStructure::UseStructureFactor);
- std::vector<V3D> hklsCenteringAlternative =
- siUseStructureFactors.getUniqueHKLs(0.6, 10.0,
- CrystalStructure::UseCentering);
-
- TS_ASSERT_EQUALS(hklsCentering.size(), hklsStructureFactors.size());
- TS_ASSERT_EQUALS(hklsCentering.size(), hklsCenteringAlternative.size());
-
- for (size_t i = 0; i < hklsCentering.size(); ++i) {
- TS_ASSERT_EQUALS(hklsCentering[i], hklsStructureFactors[i]);
- TS_ASSERT_EQUALS(hklsCentering[i], hklsCenteringAlternative[i]);
- }
-
- /* Add another scatterer and use setScatterers to replace old scatterers of
- *siUseStructureFactors
- *
- * At this point the advantage of using the structure factor method is very
- *clear. When an atom is
- * added at a different position (for example [0.4, 0.4, 0.4]), some
- *reflections become 0.
- *
- * When the atom is slightly shifted like in the case below, the same
- *reflections as above are
- * allowed.
- */
- scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer",
- "Element=Si;Position=[0.42,0.42,0.42];U=0.05"));
- siUseStructureFactors.setScatterers(scatterers);
-
- TS_ASSERT_EQUALS(
- siUseStructureFactors.getScatterers()->getPropertyValue("SpaceGroup"),
- "F m -3 m");
-
- hklsStructureFactors = siUseStructureFactors.getUniqueHKLs(
- 0.6, 10.0, CrystalStructure::UseStructureFactor);
-
- for (size_t i = 0; i < hklsCentering.size(); ++i) {
- TS_ASSERT_EQUALS(hklsCentering[i], hklsStructureFactors[i]);
- }
- }
-
- void testHexagonal() {
- UnitCell cellMg(3.2094, 3.2094, 5.2108, 90.0, 90.0, 120.0);
- CompositeBraggScatterer_sptr scatterers = CompositeBraggScatterer::create();
- scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer",
- "Element=Mg;Position=[0.333333,0.666667,0.25];U=0.005"));
- SpaceGroup_const_sptr sgMg =
- SpaceGroupFactory::Instance().createSpaceGroup("P 63/m m c");
-
- CrystalStructure mg(cellMg, sgMg, scatterers);
-
- std::vector<V3D> hkls =
- mg.getUniqueHKLs(0.5, 10.0, CrystalStructure::UseStructureFactor);
- for (size_t i = 0; i < hkls.size(); ++i) {
- TS_ASSERT_LESS_THAN(0.5, cellMg.d(hkls[i]));
- }
-
- std::vector<double> dValues = mg.getDValues(hkls);
- for (size_t i = 0; i < hkls.size(); ++i) {
- TS_ASSERT_LESS_THAN(0.5, dValues[i]);
- }
- }
-
- void testTrigonal() {
- UnitCell cellAl2O3(4.759355, 4.759355, 12.99231, 90.0, 90.0, 120.0);
- CompositeBraggScatterer_sptr scatterers = CompositeBraggScatterer::create();
- scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer",
- "Element=Al;Position=[0,0,0.35217];U=0.005"));
- scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer",
- "Element=O;Position=[0.69365,0,0.25];U=0.005"));
- SpaceGroup_const_sptr sgAl2O3 =
- SpaceGroupFactory::Instance().createSpaceGroup("R -3 c");
-
- std::cout << sgAl2O3->order() << std::endl;
-
- // O is on the 18e wyckoff position
- std::vector<V3D> positions = sgAl2O3 * V3D(0.69365000, 0, 0.25000);
- TS_ASSERT_EQUALS(positions.size(), 18);
-
- CrystalStructure mg(cellAl2O3, sgAl2O3, scatterers);
-
- std::vector<V3D> hkls =
- mg.getUniqueHKLs(0.885, 10.0, CrystalStructure::UseStructureFactor);
-
- TS_ASSERT_EQUALS(hkls.size(), 44);
+ TS_ASSERT_EQUALS(two.getScatterers()->nScatterers(),
+ one.getScatterers()->nScatterers());
+ TS_ASSERT_EQUALS(two.spaceGroup()->hmSymbol(),
+ one.spaceGroup()->hmSymbol());
+ TS_ASSERT_EQUALS(unitCellToStr(two.cell()), unitCellToStr(one.cell()));
}
private:
UnitCell m_CsCl;
- PointGroup_sptr m_pg;
- ReflectionCondition_sptr m_centering;
-
SpaceGroup_const_sptr m_spaceGroup;
CompositeBraggScatterer_sptr m_scatterers;
-
- class TestableCrystalStructure : public CrystalStructure {
- friend class CrystalStructureTest;
-
- public:
- TestableCrystalStructure() : CrystalStructure(UnitCell()) {}
- ~TestableCrystalStructure() {}
- };
};
#endif /* MANTID_GEOMETRY_CRYSTALSTRUCTURETEST_H_ */
diff --git a/Framework/Geometry/test/HKLFilterTest.h b/Framework/Geometry/test/HKLFilterTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..c0ef32dde759a8601d65ffdfd9fae6adc7e001e8
--- /dev/null
+++ b/Framework/Geometry/test/HKLFilterTest.h
@@ -0,0 +1,209 @@
+#ifndef MANTID_GEOMETRY_HKLFILTERTEST_H_
+#define MANTID_GEOMETRY_HKLFILTERTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+
+#include "MantidGeometry/Crystal/HKLFilter.h"
+#include "MantidKernel/V3D.h"
+
+#include <boost/make_shared.hpp>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+using ::testing::_;
+using ::testing::Return;
+using ::testing::Mock;
+
+class HKLFilterTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static HKLFilterTest *createSuite() { return new HKLFilterTest(); }
+ static void destroySuite(HKLFilterTest *suite) { delete suite; }
+
+ void testFn() {
+ MockHKLFilter filter;
+ EXPECT_CALL(filter, isAllowed(_))
+ .Times(2)
+ .WillOnce(Return(true))
+ .WillRepeatedly(Return(false));
+
+ std::function<bool(const V3D &)> f = filter.fn();
+
+ TS_ASSERT_EQUALS(f(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(f(V3D(1, 1, 1)), false);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&filter));
+ }
+
+ void testUnaryLogicOperation() {
+ HKLFilter_const_sptr filter = boost::make_shared<MockHKLFilter>();
+
+ TS_ASSERT_THROWS_NOTHING(MockHKLFilterUnaryLogicOperation op(filter));
+
+ MockHKLFilterUnaryLogicOperation op(filter);
+ TS_ASSERT_EQUALS(op.getOperand(), filter);
+
+ HKLFilter_const_sptr invalid;
+ TS_ASSERT_THROWS(MockHKLFilterUnaryLogicOperation op(invalid),
+ std::runtime_error);
+ }
+
+ void testBinaryLogicOperation() {
+ HKLFilter_const_sptr lhs = boost::make_shared<MockHKLFilter>();
+ HKLFilter_const_sptr rhs = boost::make_shared<MockHKLFilter>();
+
+ TS_ASSERT_THROWS_NOTHING(MockHKLFilterBinaryLogicOperation op(lhs, rhs));
+
+ MockHKLFilterBinaryLogicOperation op(lhs, rhs);
+ TS_ASSERT_EQUALS(op.getLHS(), lhs);
+ TS_ASSERT_EQUALS(op.getRHS(), rhs);
+
+ HKLFilter_const_sptr invalid;
+ TS_ASSERT_THROWS(MockHKLFilterBinaryLogicOperation op(invalid, rhs),
+ std::runtime_error);
+ TS_ASSERT_THROWS(MockHKLFilterBinaryLogicOperation op(lhs, invalid),
+ std::runtime_error);
+ TS_ASSERT_THROWS(MockHKLFilterBinaryLogicOperation op(invalid, invalid),
+ std::runtime_error);
+ }
+
+ void testHKLFilterNot() {
+ boost::shared_ptr<const MockHKLFilter> filter(new MockHKLFilter);
+
+ EXPECT_CALL(*filter, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false));
+
+ HKLFilterNot notFilter(filter);
+
+ TS_ASSERT_EQUALS(notFilter.isAllowed(V3D(1, 1, 1)), false);
+ TS_ASSERT_EQUALS(notFilter.isAllowed(V3D(1, 1, 1)), true);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(filter).get()));
+ }
+
+ void testHKLFilterNotOperator() {
+ HKLFilter_const_sptr filter = boost::make_shared<MockHKLFilter>();
+
+ HKLFilter_const_sptr notFilter = ~filter;
+
+ boost::shared_ptr<const HKLFilterNot> notFilterCasted =
+ boost::dynamic_pointer_cast<const HKLFilterNot>(notFilter);
+ TS_ASSERT(notFilterCasted);
+
+ TS_ASSERT_EQUALS(notFilterCasted->getOperand(), filter);
+ }
+
+ void testHKLFilterAnd() {
+ boost::shared_ptr<const MockHKLFilter> lhs(new MockHKLFilter);
+ EXPECT_CALL(*lhs, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false))
+ .WillOnce(Return(true));
+
+ boost::shared_ptr<const MockHKLFilter> rhs(new MockHKLFilter);
+ EXPECT_CALL(*rhs, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false));
+
+ HKLFilterAnd andFilter(lhs, rhs);
+
+ TS_ASSERT_EQUALS(andFilter.isAllowed(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(andFilter.isAllowed(V3D(1, 1, 1)), false);
+ TS_ASSERT_EQUALS(andFilter.isAllowed(V3D(1, 1, 1)), false);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(lhs).get()));
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(rhs).get()));
+ }
+
+ void testHKLFilterAndOperator() {
+ HKLFilter_const_sptr lhs = boost::make_shared<MockHKLFilter>();
+ HKLFilter_const_sptr rhs = boost::make_shared<MockHKLFilter>();
+
+ HKLFilter_const_sptr andFilter = lhs & rhs;
+
+ boost::shared_ptr<const HKLFilterAnd> andFilterCasted =
+ boost::dynamic_pointer_cast<const HKLFilterAnd>(andFilter);
+
+ TS_ASSERT(andFilterCasted);
+
+ TS_ASSERT_EQUALS(andFilterCasted->getLHS(), lhs);
+ TS_ASSERT_EQUALS(andFilterCasted->getRHS(), rhs);
+ }
+
+ void testHKLFilterOr() {
+ boost::shared_ptr<const MockHKLFilter> lhs(new MockHKLFilter);
+ EXPECT_CALL(*lhs, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false));
+
+ boost::shared_ptr<const MockHKLFilter> rhs(new MockHKLFilter);
+ EXPECT_CALL(*rhs, isAllowed(_))
+ .WillOnce(Return(false))
+ .WillOnce(Return(true));
+
+ HKLFilterOr orFilter(lhs, rhs);
+
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), false);
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), true);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(lhs).get()));
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(rhs).get()));
+ }
+
+ void testHKLFilterOrOperator() {
+ HKLFilter_const_sptr lhs = boost::make_shared<MockHKLFilter>();
+ HKLFilter_const_sptr rhs = boost::make_shared<MockHKLFilter>();
+
+ HKLFilter_const_sptr orFilter = lhs | rhs;
+
+ boost::shared_ptr<const HKLFilterOr> orFilterCasted =
+ boost::dynamic_pointer_cast<const HKLFilterOr>(orFilter);
+
+ TS_ASSERT(orFilterCasted);
+
+ TS_ASSERT_EQUALS(orFilterCasted->getLHS(), lhs);
+ TS_ASSERT_EQUALS(orFilterCasted->getRHS(), rhs);
+ }
+
+private:
+ class MockHKLFilter : public HKLFilter {
+ public:
+ MOCK_CONST_METHOD0(getDescription, std::string());
+ MOCK_CONST_METHOD1(isAllowed, bool(const V3D &));
+ };
+
+ class MockHKLFilterUnaryLogicOperation : public HKLFilterUnaryLogicOperation {
+ public:
+ MockHKLFilterUnaryLogicOperation(const HKLFilter_const_sptr &filter)
+ : HKLFilterUnaryLogicOperation(filter) {}
+
+ MOCK_CONST_METHOD0(getDescription, std::string());
+ MOCK_CONST_METHOD1(isAllowed, bool(const V3D &));
+ };
+
+ class MockHKLFilterBinaryLogicOperation
+ : public HKLFilterBinaryLogicOperation {
+ public:
+ MockHKLFilterBinaryLogicOperation(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs)
+ : HKLFilterBinaryLogicOperation(lhs, rhs) {}
+
+ MOCK_CONST_METHOD0(getDescription, std::string());
+ MOCK_CONST_METHOD1(isAllowed, bool(const V3D &));
+ };
+};
+#endif /* MANTID_GEOMETRY_HKLFILTERTEST_H_ */
diff --git a/Framework/Geometry/test/HKLGeneratorTest.h b/Framework/Geometry/test/HKLGeneratorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..f6cffd236d46002b8dac782b7defd1f04d12bc89
--- /dev/null
+++ b/Framework/Geometry/test/HKLGeneratorTest.h
@@ -0,0 +1,98 @@
+#ifndef MANTID_GEOMETRY_HKLGENERATORTEST_H_
+#define MANTID_GEOMETRY_HKLGENERATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include "MantidGeometry/Crystal/HKLGenerator.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+class HKLGeneratorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static HKLGeneratorTest *createSuite() { return new HKLGeneratorTest(); }
+ static void destroySuite(HKLGeneratorTest *suite) { delete suite; }
+
+ void test_HKLGeneratorReturnsCorrectSizeSymmetricInt() {
+ HKLGenerator gen(2, 2, 2);
+
+ TS_ASSERT_EQUALS(gen.size(), 125);
+ }
+
+ void test_HKLGeneratorReturnsCorrectSizeSymmetricV3D() {
+ HKLGenerator gen(V3D(2, 2, 2));
+
+ TS_ASSERT_EQUALS(gen.size(), 125);
+ }
+
+ void test_HKLGeneratorReturnsCorrectSizeAsymmetricV3D() {
+ HKLGenerator gen(V3D(-2, -1, -5), V3D(3, 4, -2));
+
+ TS_ASSERT_EQUALS(gen.size(), 144);
+ }
+
+ void test_HKLGeneratorReturnsCorrectSizeOne() {
+ HKLGenerator gen(V3D(-2, -1, -5), V3D(-2, -1, -5));
+ TS_ASSERT_EQUALS(gen.size(), 1);
+ }
+
+ void test_beginIterator() {
+ HKLGenerator gen(V3D(-2, -2, -3), V3D(1, 1, 0));
+
+ HKLGenerator::const_iterator it = gen.begin();
+ TS_ASSERT_EQUALS(*it, V3D(-2, -2, -3));
+ }
+
+ void test_endIterator() {
+ HKLGenerator gen(V3D(-2, -2, -3), V3D(1, 1, 0));
+
+ HKLGenerator::const_iterator it = gen.end();
+ TS_ASSERT_EQUALS(*it, V3D(2, -2, -3));
+ }
+
+ void test_iterator_dereference() {
+ HKLGenerator::const_iterator it;
+ TS_ASSERT_EQUALS(*it, V3D(0, 0, 0));
+ }
+
+ void test_comparison() {
+ HKLGenerator::const_iterator it1(V3D(-2, -3, 1));
+ HKLGenerator::const_iterator it2(V3D(-2, -3, 1));
+ HKLGenerator::const_iterator it3(V3D(-2, -3, 0));
+
+ TS_ASSERT_EQUALS(it1, it2);
+ TS_ASSERT_DIFFERS(it1, it3);
+ }
+
+ void test_iterator_increment() {
+ HKLGenerator::const_iterator defaultIterator;
+ TS_ASSERT_THROWS_NOTHING(++defaultIterator);
+ }
+
+ void test_iterator_dereference_range() {
+ HKLGenerator::const_iterator it(V3D(-1, -1, -1), V3D(1, 1, 1));
+ TS_ASSERT_EQUALS(*it, V3D(-1, -1, -1));
+ ++it;
+ TS_ASSERT_EQUALS(*it, V3D(-1, -1, 0));
+ }
+
+ void test_hkl_range() {
+ HKLGenerator::const_iterator it(V3D(-1, -1, -1), V3D(1, 1, 1));
+ HKLGenerator::const_iterator end(V3D(2, -1, -1));
+
+ std::vector<V3D> hkls;
+ std::copy(it, end, std::back_inserter(hkls));
+
+ TS_ASSERT_EQUALS(hkls.size(), 27);
+ TS_ASSERT_EQUALS(hkls[0], V3D(-1, -1, -1));
+ TS_ASSERT_EQUALS(hkls[1], V3D(-1, -1, 0));
+ TS_ASSERT_EQUALS(hkls[2], V3D(-1, -1, 1));
+ TS_ASSERT_EQUALS(hkls[3], V3D(-1, 0, -1));
+ TS_ASSERT_EQUALS(hkls[26], V3D(1, 1, 1));
+
+ TS_ASSERT_EQUALS(std::distance(it, end), 27);
+ }
+};
+
+#endif /* MANTID_GEOMETRY_HKLGENERATORTEST_H_ */
diff --git a/Framework/Geometry/test/IsotropicAtomBraggScattererTest.h b/Framework/Geometry/test/IsotropicAtomBraggScattererTest.h
index 446c8b567157fc0972d92ccd3a8e92837069577e..0854c3a3d7d39509a1f8f77b10668c28b0920379 100644
--- a/Framework/Geometry/test/IsotropicAtomBraggScattererTest.h
+++ b/Framework/Geometry/test/IsotropicAtomBraggScattererTest.h
@@ -4,7 +4,6 @@
#include <cxxtest/TestSuite.h>
#include "MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h"
-#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
using namespace Mantid::Geometry;
using namespace Mantid::Kernel;
@@ -31,7 +30,6 @@ public:
TS_ASSERT_THROWS_NOTHING(scatterer->initialize());
TS_ASSERT(scatterer->existsProperty("Position"));
- TS_ASSERT(scatterer->existsProperty("SpaceGroup"));
TS_ASSERT(scatterer->existsProperty("UnitCell"));
TS_ASSERT(scatterer->existsProperty("U"));
TS_ASSERT(scatterer->existsProperty("Element"));
@@ -88,27 +86,22 @@ public:
void testClone() {
UnitCell cell(5.43, 5.43, 5.43);
- SpaceGroup_const_sptr spaceGroup =
- SpaceGroupFactory::Instance().createSpaceGroup("P m -3 m");
IsotropicAtomBraggScatterer_sptr scatterer =
getInitializedScatterer("H", "[1, 0, 0]", 0.0);
scatterer->setProperty("U", 3.04);
scatterer->setProperty("Occupancy", 0.5);
scatterer->setProperty("UnitCell", unitCellToStr(cell));
- scatterer->setProperty("SpaceGroup", spaceGroup->hmSymbol());
BraggScatterer_sptr baseclone = scatterer->clone();
BraggScattererInCrystalStructure_sptr clone =
boost::dynamic_pointer_cast<BraggScattererInCrystalStructure>(
baseclone);
- TS_ASSERT(clone)
+ TS_ASSERT(clone);
TS_ASSERT_EQUALS(clone->getPosition(), scatterer->getPosition());
TS_ASSERT_EQUALS(clone->getCell().getG(), scatterer->getCell().getG());
- TS_ASSERT_EQUALS(clone->getSpaceGroup()->hmSymbol(),
- scatterer->getSpaceGroup()->hmSymbol());
IsotropicAtomBraggScatterer_sptr scattererClone =
boost::dynamic_pointer_cast<IsotropicAtomBraggScatterer>(clone);
@@ -154,50 +147,70 @@ public:
TS_ASSERT_EQUALS(structureFactor.real(),
bSi * 0.5 * 0.96708061593352515459);
- // Set a space group with F-centering
- SpaceGroup_const_sptr spaceGroup =
- SpaceGroupFactory::Instance().createSpaceGroup("F m -3 m");
- scatterer->setProperty("SpaceGroup", spaceGroup->hmSymbol());
-
- /* Now there are 4 equivalent positions, the contributions cancel out for
- *(1, 0, 0)
- * scalar products are:
- * (1,0,0) * (0,0,0) = (1*0 + 1*0 + 1*0) = 0 cos(0) = 1, sin(0)
- *= 0
- * (1,0,0) * (0,0.5,0.5) = (1*0 + 0*0.5 + 0*0.5) = 0 cos(0) = 1, sin(0)
- *= 0
+ /* Assume a space group with F centering.
+ *
+ * Now there are 4 equivalent positions, the contributions cancel out for
+ * (1, 0, 0)
+ * The scalar products are:
+ * (1,0,0) * (0,0,0) = (1*0 + 1*0 + 1*0) = 0 cos(0) = 1,
+ * sin(0) = 0
+ * (1,0,0) * (0,0.5,0.5) = (1*0 + 0*0.5 + 0*0.5) = 0 cos(0) = 1,
+ * sin(0) = 0
* (1,0,0) * (0.5,0,0.5) = (1*0.5 + 0*0 + 0*0.5) = 0.5 cos(pi) = -1,
- *sin(pi) = 0
+ * sin(pi) = 0
* (1,0,0) * (0.5,0.5,0) = (1*0.5 + 0*0.5 + 0*0) = 0.5 cos(pi) = -1,
- *sin(pi) = 0
+ * sin(pi) = 0
*
* That means 1 * real + 1 * real + (-1 * real) + (-1 * real) = 0
*/
- structureFactor = scatterer->calculateStructureFactor(hkl);
+ StructureFactor totalStructureFactorForbidden;
+
+ scatterer->setProperty("Position", "[0, 0, 0]");
+ totalStructureFactorForbidden += scatterer->calculateStructureFactor(hkl);
+
+ scatterer->setProperty("Position", "[0, 0.5, 0.5]");
+ totalStructureFactorForbidden += scatterer->calculateStructureFactor(hkl);
+
+ scatterer->setProperty("Position", "[0.5, 0, 0.5]");
+ totalStructureFactorForbidden += scatterer->calculateStructureFactor(hkl);
+
+ scatterer->setProperty("Position", "[0.5, 0.5, 0]");
+ totalStructureFactorForbidden += scatterer->calculateStructureFactor(hkl);
// It's not always exactly 0 (floating point math), but should not be less
- // than 0
- TS_ASSERT_LESS_THAN(structureFactor.real(), 1e-9);
- TS_ASSERT_LESS_THAN_EQUALS(0, structureFactor.real());
+ TS_ASSERT_LESS_THAN(totalStructureFactorForbidden.real(), 1e-9);
+ TS_ASSERT_LESS_THAN_EQUALS(0, totalStructureFactorForbidden.real());
// For (1, 1, 1), the value is defined
hkl = V3D(1, 1, 1);
- structureFactor = scatterer->calculateStructureFactor(hkl);
+
+ StructureFactor totalStructureFactorAllowed;
+ scatterer->setProperty("Position", "[0, 0, 0]");
+ totalStructureFactorAllowed += scatterer->calculateStructureFactor(hkl);
+
+ scatterer->setProperty("Position", "[0, 0.5, 0.5]");
+ totalStructureFactorAllowed += scatterer->calculateStructureFactor(hkl);
+
+ scatterer->setProperty("Position", "[0.5, 0, 0.5]");
+ totalStructureFactorAllowed += scatterer->calculateStructureFactor(hkl);
+
+ scatterer->setProperty("Position", "[0.5, 0.5, 0]");
+ totalStructureFactorAllowed += scatterer->calculateStructureFactor(hkl);
/* scalar products are:
- * (1,1,1) * (0,0,0) = (1*0 + 1*0 + 1*0) = 0 cos(0) = 1, sin(0) =
- *0
+ * (1,1,1) * (0,0,0) = (1*0 + 1*0 + 1*0) = 0 cos(0) = 1
+ * sin(0) = 0
* (1,1,1) * (0,0.5,0.5) = (1*0 + 1*0.5 + 1*0.5) = 1 cos(2pi) = 1,
- *sin(2pi) = 0
+ * sin(2pi) = 0
* (1,1,1) * (0.5,0,0.5) = (1*0.5 + 1*0 + 1*0.5) = 1 cos(2pi) = 1,
- *sin(2pi) = 0
+ * sin(2pi) = 0
* (1,1,1) * (0.5,0.5,0) = (1*0.5 + 1*0.5 + 1*0) = 1 cos(2pi) = 1,
- *sin(2pi) = 0
+ * sin(2pi) = 0
*
* That means 4 * real * debye waller * occupation. d = 3.13...
*/
- TS_ASSERT_DELTA(structureFactor.real(),
- 4.0 * bSi * 0.90445723107190849637 * 0.5, 5e-16)
+ TS_ASSERT_DELTA(totalStructureFactorAllowed.real(),
+ 4.0 * bSi * 0.90445723107190849637 * 0.5, 5e-16);
}
private:
diff --git a/Framework/Geometry/test/ReflectionGeneratorTest.h b/Framework/Geometry/test/ReflectionGeneratorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..9c3da2883aa0664fbd38315122247b895a5123cf
--- /dev/null
+++ b/Framework/Geometry/test/ReflectionGeneratorTest.h
@@ -0,0 +1,126 @@
+#ifndef MANTID_GEOMETRY_REFLECTIONGENERATORTEST_H_
+#define MANTID_GEOMETRY_REFLECTIONGENERATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+class ReflectionGeneratorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static ReflectionGeneratorTest *createSuite() {
+ return new ReflectionGeneratorTest();
+ }
+ static void destroySuite(ReflectionGeneratorTest *suite) { delete suite; }
+
+ void test_getUniqueHKLs() {
+ double dMin = 0.55;
+ double dMax = 4.0;
+
+ ReflectionGenerator generator(
+ CrystalStructure("4.126 4.126 4.126", "P m -3 m", "Si 0 0 0 1.0 0.01"),
+ ReflectionConditionFilter::Centering);
+
+ TS_ASSERT_THROWS_NOTHING(generator.getUniqueHKLs(dMin, dMax));
+
+ std::vector<V3D> peaks = generator.getUniqueHKLs(dMin, dMax);
+
+ TS_ASSERT_EQUALS(peaks.size(), 68);
+ TS_ASSERT_EQUALS(peaks[0], V3D(1, 1, 0));
+ TS_ASSERT_EQUALS(peaks[11], V3D(3, 2, 0));
+ TS_ASSERT_EQUALS(peaks[67], V3D(7, 2, 1));
+
+ // make d-value list and check that peaks are within limits
+ std::vector<double> peaksD = generator.getDValues(peaks);
+
+ std::sort(peaksD.begin(), peaksD.end());
+
+ TS_ASSERT_LESS_THAN_EQUALS(dMin, peaksD.front());
+ TS_ASSERT_LESS_THAN_EQUALS(peaksD.back(), dMax);
+ }
+
+ void test_getHKLs() {
+ double dMin = 0.55;
+ double dMax = 4.0;
+
+ // make a structure with P-1
+ ReflectionGenerator generator(
+ CrystalStructure("4.126 4.126 4.126", "P -1", "Si 0 0 0 1.0 0.01"),
+ ReflectionConditionFilter::Centering);
+
+ std::vector<V3D> unique = generator.getUniqueHKLs(dMin, dMax);
+ std::vector<V3D> peaks = generator.getHKLs(dMin, dMax);
+
+ // Because of symmetry -1, each reflection has multiplicity 2.
+ TS_ASSERT_EQUALS(peaks.size(), 2 * unique.size());
+ }
+
+ void test_getDValues() {
+ std::vector<V3D> hkls;
+ hkls.push_back(V3D(1, 0, 0));
+ hkls.push_back(V3D(0, 1, 0));
+ hkls.push_back(V3D(0, 0, 1));
+
+ ReflectionGenerator generator(
+ CrystalStructure("2 3 5", "P -1", "Si 0 0 0 1.0 0.01"));
+ std::vector<double> dValues = generator.getDValues(hkls);
+
+ TS_ASSERT_EQUALS(dValues.size(), hkls.size());
+ TS_ASSERT_EQUALS(dValues[0], 2.0);
+ TS_ASSERT_EQUALS(dValues[1], 3.0);
+ TS_ASSERT_EQUALS(dValues[2], 5.0);
+ }
+
+ void test_getUniqueHKLsStructureFactor() {
+ CrystalStructure si("5.43 5.43 5.43", "F m -3 m",
+ "Si 0.3 0.3 0.3 1.0 0.05");
+
+ ReflectionGenerator generator(si,
+ ReflectionConditionFilter::StructureFactor);
+
+ std::vector<V3D> hklsCentering = generator.getUniqueHKLs(
+ 0.6, 10.0, boost::make_shared<HKLFilterCentering>(si.centering()));
+
+ std::vector<V3D> hklsStructureFactors = generator.getUniqueHKLs(0.6, 10.0);
+
+ TS_ASSERT_EQUALS(hklsCentering.size(), hklsStructureFactors.size());
+
+ for (size_t i = 0; i < hklsCentering.size(); ++i) {
+ TS_ASSERT_EQUALS(hklsCentering[i], hklsStructureFactors[i]);
+ }
+ }
+
+ void test_getUniqueHKLsHexagonal() {
+ ReflectionGenerator generator(
+ CrystalStructure("3.2094 3.2094 5.2108 90.0 90.0 120.0", "P 63/m m c",
+ "Mg 1/3 2/3 1/4 1.0 0.005"),
+ ReflectionConditionFilter::StructureFactor);
+
+ std::vector<V3D> hkls = generator.getUniqueHKLs(0.5, 10.0);
+
+ TS_ASSERT_EQUALS(hkls.size(), 88);
+
+ std::vector<double> dValues = generator.getDValues(hkls);
+ for (size_t i = 0; i < hkls.size(); ++i) {
+ TS_ASSERT_LESS_THAN(0.5, dValues[i]);
+ }
+ }
+
+ void test_getUniqueHKLsTrigonal() {
+ ReflectionGenerator generator(
+ CrystalStructure("4.759355 4.759355 12.99231 90.0 90.0 120.0", "R -3 c",
+ "Al 0 0 0.35217 1.0 0.005; O 0.69365 0 1/4 1.0 0.005"),
+ ReflectionConditionFilter::StructureFactor);
+
+ std::vector<V3D> hkls = generator.getUniqueHKLs(0.885, 10.0);
+
+ TS_ASSERT_EQUALS(hkls.size(), 44);
+ }
+};
+
+#endif /* MANTID_GEOMETRY_REFLECTIONGENERATORTEST_H_ */
diff --git a/Framework/Geometry/test/StructureFactorCalculatorSummationTest.h b/Framework/Geometry/test/StructureFactorCalculatorSummationTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..a1ce3c9670a57b3edd0cd2dd6302d8c27c3a33bf
--- /dev/null
+++ b/Framework/Geometry/test/StructureFactorCalculatorSummationTest.h
@@ -0,0 +1,75 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATIONTEST_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATIONTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+
+#include "MantidGeometry/Crystal/BraggScattererFactory.h"
+#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+class StructureFactorCalculatorSummationTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static StructureFactorCalculatorSummationTest *createSuite() {
+ return new StructureFactorCalculatorSummationTest();
+ }
+ static void destroySuite(StructureFactorCalculatorSummationTest *suite) {
+ delete suite;
+ }
+
+ void testEquivalentPositionsAreUsed() {
+ // Approximate crystal structure of Silicon
+ CrystalStructure si = getCrystalStructure();
+
+ StructureFactorCalculatorSummation calculator;
+ calculator.setCrystalStructure(si);
+
+ // {1 0 0} reflections are not allowed because of F centering
+ TS_ASSERT_LESS_THAN(calculator.getFSquared(V3D(1, 0, 0)), 1e-9);
+
+ // {2 2 2} is forbidden because of Si on special position
+ TS_ASSERT_LESS_THAN(calculator.getFSquared(V3D(2, 2, 2)), 1e-9);
+
+ // With space group P-1, those are allowed.
+ si.setSpaceGroup(SpaceGroupFactory::Instance().createSpaceGroup("P -1"));
+
+ calculator.setCrystalStructure(si);
+ // {1 0 0} reflections are not allowed because of F centering
+ TS_ASSERT_LESS_THAN(1e-9, calculator.getFSquared(V3D(1, 0, 0)));
+
+ // {2 2 2} is forbidden because of Si on special position
+ TS_ASSERT_LESS_THAN(1e-9, calculator.getFSquared(V3D(2, 2, 2)));
+ }
+
+ void testCreateWithFactory() {
+ CrystalStructure si = getCrystalStructure();
+
+ StructureFactorCalculator_sptr calculator =
+ StructureFactorCalculatorFactory::create<
+ StructureFactorCalculatorSummation>(si);
+
+ // same reflections as in testEquivalentPositionsAreUsed
+ TS_ASSERT_LESS_THAN(calculator->getFSquared(V3D(1, 0, 0)), 1e-9);
+ TS_ASSERT_LESS_THAN(calculator->getFSquared(V3D(2, 2, 2)), 1e-9);
+ }
+
+private:
+ CrystalStructure getCrystalStructure() {
+ CompositeBraggScatterer_sptr scatterers = CompositeBraggScatterer::create();
+ scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
+ "IsotropicAtomBraggScatterer", "Element=Si;Position=[0,0,0];U=0.05"));
+
+ CrystalStructure si(
+ UnitCell(5.43, 5.43, 5.43),
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m"), scatterers);
+
+ return si;
+ }
+};
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATIONTEST_H_ */
diff --git a/Framework/Geometry/test/StructureFactorCalculatorTest.h b/Framework/Geometry/test/StructureFactorCalculatorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..72421449f7132c3b281a0f7873be91431a052d59
--- /dev/null
+++ b/Framework/Geometry/test/StructureFactorCalculatorTest.h
@@ -0,0 +1,107 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORTEST_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using ::testing::Mock;
+using ::testing::_;
+using ::testing::Return;
+
+class StructureFactorCalculatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static StructureFactorCalculatorTest *createSuite() {
+ return new StructureFactorCalculatorTest();
+ }
+ static void destroySuite(StructureFactorCalculatorTest *suite) {
+ delete suite;
+ }
+
+ void testCrystalStructureSetHookIsCalled() {
+ CrystalStructure cs(UnitCell(1, 2, 3),
+ SpaceGroupFactory::Instance().createSpaceGroup("P -1"),
+ CompositeBraggScatterer::create());
+
+ MockStructureFactorCalculator calculator;
+ EXPECT_CALL(calculator, crystalStructureSetHook(_)).Times(1);
+
+ calculator.setCrystalStructure(cs);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+ void testGetFSquared() {
+ MockStructureFactorCalculator calculator;
+
+ EXPECT_CALL(calculator, getF(_))
+ .WillRepeatedly(Return(StructureFactor(2.21, 3.1)));
+
+ // Check that the square of 2.21 + i * 3.1 is returned
+ TS_ASSERT_DELTA(calculator.getFSquared(V3D()), 14.4941, 1e-15);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+ void testGetFs() {
+ MockStructureFactorCalculator calculator;
+
+ int numHKLs = 10;
+ EXPECT_CALL(calculator, getF(_))
+ .Times(numHKLs)
+ .WillRepeatedly(Return(StructureFactor(2.0, 2.0)));
+
+ std::vector<V3D> hkls(numHKLs);
+ std::vector<StructureFactor> sfs = calculator.getFs(hkls);
+
+ TS_ASSERT_EQUALS(sfs.size(), hkls.size());
+
+ for (auto sf = sfs.begin(); sf != sfs.end(); ++sf) {
+ TS_ASSERT_EQUALS(*sf, StructureFactor(2.0, 2.0));
+ }
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+ void testGetFsSquared() {
+ MockStructureFactorCalculator calculator;
+
+ int numHKLs = 10;
+ EXPECT_CALL(calculator, getF(_))
+ .Times(numHKLs)
+ .WillRepeatedly(Return(StructureFactor(2.0, 2.0)));
+
+ std::vector<V3D> hkls(numHKLs);
+ std::vector<double> sfsSquared = calculator.getFsSquared(hkls);
+
+ TS_ASSERT_EQUALS(sfsSquared.size(), hkls.size());
+
+ for (auto sf = sfsSquared.begin(); sf != sfsSquared.end(); ++sf) {
+ TS_ASSERT_EQUALS(*sf, 8.0);
+ }
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+private:
+ /* This MockStructureFactorCalculator helps to test whether the
+ * default implementations of the virtual methods work correctly.
+ * Furthermore it is used to confirm that crystalStructureSetHook
+ * is called appropriately.
+ */
+ class MockStructureFactorCalculator : public StructureFactorCalculator {
+ public:
+ MOCK_CONST_METHOD1(getF, StructureFactor(const V3D &hkl));
+ MOCK_METHOD1(crystalStructureSetHook,
+ void(const CrystalStructure &crystalStructure));
+ };
+};
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORTEST_H_ */
diff --git a/Framework/ICat/src/GSoap/stdsoap2.cpp b/Framework/ICat/src/GSoap/stdsoap2.cpp
index ec26daa1e2e5e4ba9c1137565e6c2f1d5d763e28..252bc7ae6514f1f8380bd35f9c89fcc5e46abd54 100644
--- a/Framework/ICat/src/GSoap/stdsoap2.cpp
+++ b/Framework/ICat/src/GSoap/stdsoap2.cpp
@@ -2348,7 +2348,7 @@ int SOAP_FMAC2 soap_resolve(struct soap *soap) {
} else if (*ip->id == '#') {
DBGLOG(TEST,
SOAP_MESSAGE(fdebug, "Missing data for id='%s'\n", ip->id));
- strcpy(soap->id, ip->id + 1);
+ strncpy(soap->id, ip->id + 1, sizeof(soap->id));
return soap->error = SOAP_MISSING_ID;
}
}
@@ -2386,7 +2386,7 @@ int SOAP_FMAC2 soap_resolve(struct soap *soap) {
"location=%p level=%u,%u id='%s'\n",
ip->type, p, ip->level, fp->level, ip->id));
while (ip->level < k) {
- void **q = (void **)soap_malloc(soap, sizeof(q));
+ void **q = (void **)soap_malloc(soap, sizeof(*q));
if (!q)
return soap->error;
*q = p;
@@ -3207,7 +3207,7 @@ const char *SOAP_FMAC2 soap_ssl_error(struct soap *soap, int ret) {
int err = SSL_get_error(soap->ssl, ret);
const char *msg = soap_code_str(h_ssl_error_codes, err);
if (msg)
- strcpy(soap->msgbuf, msg);
+ strncpy(soap->msgbuf, msg, sizeof(soap->msgbuf));
else
return ERR_error_string(err, soap->msgbuf);
if (ERR_peek_error()) {
@@ -6049,7 +6049,7 @@ static int http_post(struct soap *soap, const char *endpoint, const char *host,
sprintf(soap->tmpbuf, "[%s]", host); /* RFC 2732 */
else
#endif
- strcpy(soap->tmpbuf, host);
+ strncpy(soap->tmpbuf, host, sizeof(soap->tmpbuf));
}
if ((err = soap->fposthdr(soap, "Host", soap->tmpbuf)))
return err;
@@ -8161,7 +8161,7 @@ void *SOAP_FMAC2 soap_id_lookup(struct soap *soap, const char *id, void **p,
"Resolved href='%s' type=%d location=%p (%u bytes)\n",
id, t, ip->ptr, (unsigned int)n));
if (ip->type != t) {
- strcpy(soap->id, id);
+ strncpy(soap->id, id, sizeof(soap->id));
soap->error = SOAP_HREF;
DBGLOG(TEST,
SOAP_MESSAGE(
@@ -8188,9 +8188,11 @@ void *SOAP_FMAC2 soap_id_lookup(struct soap *soap, const char *id, void **p,
void *s, **r = &ip->link;
q = (void **)ip->link;
while (q) {
- *r = (void *)soap_malloc(soap, sizeof(void *));
- if (!*r)
+ void **tmp = (void **)soap_malloc(soap, sizeof(void *));
+ if (!tmp)
return NULL;
+ *r = (void *)tmp;
+
s = *q;
*q = *r;
r = (void **)*r;
@@ -8263,7 +8265,7 @@ void *SOAP_FMAC2 soap_id_forward(struct soap *soap, const char *href, void *p,
"size=%lu level=%u got type=%d size=%lu\n",
href, ip->type, (unsigned long)ip->size, k, st,
(unsigned long)n));
- strcpy(soap->id, href);
+ strncpy(soap->id, href, sizeof(soap->id));
soap->error = SOAP_HREF;
return NULL;
}
@@ -8355,12 +8357,12 @@ soap_id_enter(struct soap *soap, const char *id, void *p, int t, size_t n,
"size=%lu level=%u got type=%d size=%lu\n",
id, ip->type, (unsigned long)ip->size, k, t,
(unsigned long)n));
- strcpy(soap->id, id);
+ strncpy(soap->id, id, sizeof(soap->id));
soap->error = SOAP_HREF;
return NULL;
} else if (ip->ptr) {
DBGLOG(TEST, SOAP_MESSAGE(fdebug, "Multiply defined id='%s'\n", id));
- strcpy(soap->id, id);
+ strncpy(soap->id, id, sizeof(soap->id));
soap->error = SOAP_DUPLICATE_ID;
return NULL;
} else {
@@ -10040,7 +10042,7 @@ int SOAP_FMAC2 soap_element_start_end_out(struct soap *soap, const char *tag) {
if (soap->mode & SOAP_XML_CANONICAL) {
struct soap_nlist *np;
for (tp = soap->attributes; tp; tp = tp->next) {
- if (tp->visible && tp->name)
+ if (tp->visible && tp->name[0])
soap_utilize_ns(soap, tp->name);
}
for (np = soap->nlist; np; np = np->next) {
@@ -11048,7 +11050,7 @@ int SOAP_FMAC2 soap_peek_element(struct soap *soap) {
soap->arraySize[sizeof(soap->arrayType) - 1] = '\0';
soap->arrayType[sizeof(soap->arrayType) - 1] = '\0';
} else if (!soap_match_tag(soap, tp->name, "SOAP-ENC:offset"))
- strncpy(soap->arrayOffset, tp->value, sizeof(soap->arrayOffset));
+ strncpy(soap->arrayOffset, tp->value, sizeof(soap->arrayOffset) - 1);
else if (!soap_match_tag(soap, tp->name, "SOAP-ENC:position"))
soap->position = soap_getposition(tp->value, soap->positions);
else if (!soap_match_tag(soap, tp->name, "SOAP-ENC:root"))
@@ -16060,18 +16062,24 @@ int SOAP_FMAC2 soap_puthttphdr(struct soap *soap, int status, size_t count) {
} else
strcat(soap->tmpbuf, s);
if (soap->mime.start) {
- strcat(soap->tmpbuf, "\"; start=\"");
- strcat(soap->tmpbuf, soap->mime.start);
+ const char startStr[] = "\"; start=\"";
+ strcat(soap->tmpbuf, startStr);
+ strncat(soap->tmpbuf, soap->mime.start,
+ sizeof(soap->tmpbuf) - sizeof(startStr));
}
strcat(soap->tmpbuf, "\"");
if (r) {
- strcat(soap->tmpbuf, "; start-info=\"");
- strcat(soap->tmpbuf, r);
- strcat(soap->tmpbuf, "\"");
+ const char startInfoStr[] = "; start-info=\"";
+ size_t lenStart = sizeof(soap->tmpbuf) - sizeof(startInfoStr);
+ strncat(soap->tmpbuf, startInfoStr, lenStart);
+ size_t lenR = lenStart - strnlen(r, lenStart);
+ strncat(soap->tmpbuf, r, lenR);
+ size_t lenEnd = lenR - 1;
+ strncat(soap->tmpbuf, "\"", lenEnd);
}
s = soap->tmpbuf;
} else
- s = strcpy(soap->tmpbuf, s);
+ s = strncpy(soap->tmpbuf, s, sizeof(soap->tmpbuf));
if (status == SOAP_OK && soap->version == 2 && soap->action &&
strlen(soap->action) + strlen(s) < sizeof(soap->tmpbuf) - 80)
sprintf(soap->tmpbuf + strlen(s), "; action=\"%s\"", soap->action);
diff --git a/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h b/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h
index 7a095862e9ce2aad426bcb01da21b7910b545aa2..ada32918cb12d35a2b41a9359cce28e8c18ca112 100644
--- a/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h
+++ b/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h
@@ -65,7 +65,9 @@ public:
void setPropertyOrdinal(const int &index, const std::string &value);
/// Make m_properties point to the same PropertyManager as po.
- void copyPropertiesFrom(const PropertyManagerOwner &po) { *this = po; }
+ virtual void copyPropertiesFrom(const PropertyManagerOwner &po) {
+ *this = po;
+ }
bool existsProperty(const std::string &name) const;
bool validateProperties() const;
diff --git a/Framework/Kernel/inc/MantidKernel/TimeSeriesProperty.h b/Framework/Kernel/inc/MantidKernel/TimeSeriesProperty.h
index 46177e23dcdaaccdd8236528af0aacc35c87d13a..cf1df3f3df0a80b93e127d1c0f38b4778ef017c9 100644
--- a/Framework/Kernel/inc/MantidKernel/TimeSeriesProperty.h
+++ b/Framework/Kernel/inc/MantidKernel/TimeSeriesProperty.h
@@ -116,6 +116,11 @@ public:
virtual ~TimeSeriesProperty();
/// "Virtual" copy constructor
TimeSeriesProperty<TYPE> *clone() const;
+ //
+ /// Return time series property, containing time derivative of current
+ /// property
+ std::unique_ptr<TimeSeriesProperty<double>> getDerivative() const;
+
/// "Virtual" copy constructor with a time shift in seconds
virtual Property *cloneWithTimeShift(const double timeShift) const;
/// Return the memory used by the property, in bytes
@@ -273,6 +278,11 @@ public:
/// Stringize the property
std::string toString() const;
+ /**Reserve memory for efficient adding values to existing property
+ * makes sense only when you have reasonably precise estimate of the
+ * total size you'll need easily available in advance. */
+ void reserve(size_t size) { m_values.reserve(size); };
+
private:
/// Sort the property into increasing times
void sort() const;
diff --git a/Framework/Kernel/inc/MantidKernel/VectorHelper.h b/Framework/Kernel/inc/MantidKernel/VectorHelper.h
index b1643b23acca49c8d9be328558d7e745338d3f79..489b6d1864b0407af065d5b6301f97c7d0980607 100644
--- a/Framework/Kernel/inc/MantidKernel/VectorHelper.h
+++ b/Framework/Kernel/inc/MantidKernel/VectorHelper.h
@@ -59,7 +59,7 @@ rebinHistogram(const std::vector<double> &xold, const std::vector<double> &yold,
std::vector<double> &ynew, std::vector<double> &enew,
bool addition);
-/// Convert an array of bin boundaries to bin centre values.
+/// Convert an array of bin boundaries to bin center values.
void MANTID_KERNEL_DLL convertToBinCentre(const std::vector<double> &bin_edges,
std::vector<double> &bin_centres);
@@ -81,6 +81,15 @@ MANTID_KERNEL_DLL int getBinIndex(const std::vector<double> &bins,
MANTID_KERNEL_DLL void linearlyInterpolateY(const std::vector<double> &x,
std::vector<double> &y,
const double stepSize);
+// Do running average of input vector within specified range, considering
+// heterogeneous bin-boundaries
+// if such boundaries are provided
+MANTID_KERNEL_DLL void
+smoothInRange(const std::vector<double> &input, std::vector<double> &output,
+ double avrgInterval,
+ std::vector<double> const *const binBoundaris = NULL,
+ size_t startIndex = 0, size_t endIndex = 0,
+ std::vector<double> *const outputBinBoundaries = NULL);
//-------------------------------------------------------------------------------------
/** Return the length of the vector (in the physical sense),
@@ -102,7 +111,7 @@ template <typename T>
T scalar_prod(const std::vector<T> &v1, const std::vector<T> &v2) {
if (v1.size() != v2.size())
throw std::invalid_argument(" scalar product is defined only for the "
- "vectors of the equivalient length");
+ "vectors of the equivalent length");
T total = 0;
for (size_t i = 0; i < v1.size(); i++)
total += v1[i] * v2[i];
@@ -153,7 +162,7 @@ template <class T> struct SumGaussError : public std::binary_function<T, T, T> {
};
/**
- * Functor to deal with the increase in the error when adding (or substracting)
+ * Functor to deal with the increase in the error when adding (or subtracting)
* a number of counts.
* More generally add errors in quadrature using the square of one of the errors
* (variance = error^2)
diff --git a/Framework/Kernel/src/ANN/kd_dump.cpp b/Framework/Kernel/src/ANN/kd_dump.cpp
index 203a443249f79c5ed1a24aa84dcac9c33ae2d1b0..eb99a37d414ff2aaefaad18ba3f2f46450b7553c 100644
--- a/Framework/Kernel/src/ANN/kd_dump.cpp
+++ b/Framework/Kernel/src/ANN/kd_dump.cpp
@@ -34,6 +34,8 @@
#include "kd_tree.h" // kd-tree declarations
#include "bd_tree.h" // bd-tree declarations
+#include <limits>
+
using namespace std; // make std:: available
//----------------------------------------------------------------------
@@ -332,6 +334,15 @@ annReadDump(istream &in, // input stream
for (j = 0; j < the_dim; j++) { // read bounding box low
in >> the_bnd_box_hi[j];
}
+
+ if (0 > the_n_pts ||
+ static_cast<size_t>(std::numeric_limits<int>::max()) <=
+ static_cast<size_t>(the_n_pts / sizeof(ANNidx))) {
+ annError("Too big number of elements for the point index array. This "
+ "would cause an overflow when allocating memory",
+ ANNabort);
+ }
+
the_pidx = new ANNidx[the_n_pts]; // allocate point index array
int next_idx = 0; // number of indices filled
// read the tree and indices
@@ -429,6 +440,16 @@ static ANNkd_ptr annReadTree(istream &in, // input stream
int n_bnds; // number of bounding sides
in >> n_bnds; // number of bounding sides
// allocate bounds array
+
+ if (0 > n_bnds ||
+ static_cast<size_t>(std::numeric_limits<int>::max()) <=
+ static_cast<size_t>(n_bnds / sizeof(ANNorthHalfSpace))) {
+ annError("Too big number of bounding sides, would cause overflow when "
+ "allocating memory",
+ ANNabort);
+ exit(0);
+ }
+
ANNorthHSArray bds = new ANNorthHalfSpace[n_bnds];
for (int i = 0; i < n_bnds; i++) {
int sd; // which side
diff --git a/Framework/Kernel/src/DateValidator.cpp b/Framework/Kernel/src/DateValidator.cpp
index 2ff99628903731dcf38e75d971c67852a1f8c550..5362fb247e217211a577736781841c1057ccacfe 100644
--- a/Framework/Kernel/src/DateValidator.cpp
+++ b/Framework/Kernel/src/DateValidator.cpp
@@ -28,6 +28,9 @@ struct tm getTimeValue(const std::string &sDate, std::string &error) {
timeinfo.tm_wday = 0;
timeinfo.tm_yday = 0;
timeinfo.tm_isdst = -1;
+#ifndef _WIN32
+ timeinfo.tm_gmtoff = 0;
+#endif
std::basic_string<char>::size_type index, off = 0;
int day, month, year;
diff --git a/Framework/Kernel/src/Matrix.cpp b/Framework/Kernel/src/Matrix.cpp
index f4e1adc13197297776e06c33da66c50614498298..014284f04c4da6b769c33f2d1157cb0390e3f336 100644
--- a/Framework/Kernel/src/Matrix.cpp
+++ b/Framework/Kernel/src/Matrix.cpp
@@ -158,17 +158,20 @@ Matrix<T>::Matrix(const Matrix<T> &A, const size_t nrow, const size_t ncol)
throw Kernel::Exception::IndexError(ncol, A.ny,
"Matrix::Constructor without col");
setMem(nx, ny);
- size_t iR(0);
- for (size_t i = 0; i <= nx; i++) {
- if (i != nrow) {
- size_t jR(0);
- for (size_t j = 0; j <= ny; j++) {
- if (j != ncol) {
- V[iR][jR] = A.V[i][j];
- jR++;
+ if (V) {
+ size_t iR(0);
+ for (size_t i = 0; i <= nx; i++) {
+ if (i != nrow) {
+ size_t jR(0);
+ for (size_t j = 0; j <= ny; j++) {
+ if (j != ncol) {
+
+ V[iR][jR] = A.V[i][j];
+ jR++;
+ }
}
+ iR++;
}
- iR++;
}
}
}
diff --git a/Framework/Kernel/src/Strings.cpp b/Framework/Kernel/src/Strings.cpp
index c2bf98bd5ac359c668662ad04aab5db601603e03..44225dc1dbceae906bef58ab08bda5b599d093aa 100644
--- a/Framework/Kernel/src/Strings.cpp
+++ b/Framework/Kernel/src/Strings.cpp
@@ -865,34 +865,49 @@ int setValues(const std::string &Line, const std::vector<int> &Index,
* @return a string with the word read in
*/
std::string getWord(std::istream &in, bool consumeEOL) {
- std::string s;
- char c = 0;
- if (in.good())
- for (c = static_cast<char>(in.get()); c == ' ' && in.good();
- c = static_cast<char>(in.get())) {
+ std::string ret;
+ char nextch = 0;
+
+ // Skip leading spaces
+ do {
+ nextch = static_cast<char>(in.get());
+ } while (nextch == ' ');
+
+ // Return an empty string on EOL; optionally consume it
+ if (nextch == '\n' || nextch == '\r') {
+ if (!consumeEOL) {
+ in.unget();
+ } else if ((nextch == '\n' && in.peek() == '\r') ||
+ (nextch == '\r' && in.peek() == '\n')) {
+ // Handle CRLF and LFCR on Unix by consuming both
+ in.ignore();
}
- else
- return std::string();
-
- if (c == '\n') {
- if (!consumeEOL)
- in.putback(c);
- return std::string();
+ return ret;
+ } else { // Non-EOL and non-space character
+ in.unget(); // Put it back on stream
}
- s.push_back(c);
-
+ // Get next word if stream is still valid
if (in.good())
- for (c = static_cast<char>(in.get());
- in.good() && c != ' ' && c != '\n' && c != '\r';
- c = static_cast<char>(in.get()))
- s.push_back(c);
+ in >> ret;
+
+ // Optionally consume EOL character
+ if (consumeEOL) {
+ nextch = static_cast<char>(in.get());
- if (((c == '\n') || (c == '\r')) && !consumeEOL)
- in.putback(c);
+ // Handle CRLF and LFCR on Unix by consuming both
+ if (nextch == '\n' || nextch == '\r') {
+ if ((nextch == '\n' && in.peek() == '\r') ||
+ (nextch == '\r' && in.peek() == '\n')) {
+ in.ignore();
+ }
+ } else {
+ in.unget();
+ }
+ }
- return s;
+ return ret;
}
//-----------------------------------------------------------------------------------------------
diff --git a/Framework/Kernel/src/TimeSeriesProperty.cpp b/Framework/Kernel/src/TimeSeriesProperty.cpp
index 3cc831022f25f516b30603ebccbaca119f83f68f..f1a10e4b434adeb6455e9f99648ed6ac8673f76f 100644
--- a/Framework/Kernel/src/TimeSeriesProperty.cpp
+++ b/Framework/Kernel/src/TimeSeriesProperty.cpp
@@ -57,6 +57,54 @@ TimeSeriesProperty<TYPE>::cloneWithTimeShift(const double timeShift) const {
return timeSeriesProperty;
}
+/** Return time series property, containing time derivative of current property.
+* The property itself and the returned time derivative become sorted by time and
+* the derivative is calculated in seconds^-1.
+* (e.g. dValue/dT where dT=t2-t1 is time difference in seconds
+* for subsequent time readings and dValue=Val1-Val2 is difference in
+* subsequent values)
+*
+*/
+template <typename TYPE>
+std::unique_ptr<TimeSeriesProperty<double>>
+TimeSeriesProperty<TYPE>::getDerivative() const {
+
+ if (this->m_values.size() < 2) {
+ throw std::runtime_error("Derivative is not defined for a time-series "
+ "property with less then two values");
+ }
+
+ this->sort();
+ auto it = this->m_values.begin();
+ int64_t t0 = it->time().totalNanoseconds();
+ TYPE v0 = it->value();
+
+ it++;
+ auto timeSeriesDeriv = std::unique_ptr<TimeSeriesProperty<double>>(
+ new TimeSeriesProperty<double>(this->name() + "_derivative"));
+ timeSeriesDeriv->reserve(this->m_values.size() - 1);
+ for (; it != m_values.end(); it++) {
+ TYPE v1 = it->value();
+ int64_t t1 = it->time().totalNanoseconds();
+ if (t1 != t0) {
+ double deriv = 1.e+9 * (double(v1 - v0) / double(t1 - t0));
+ int64_t tm = static_cast<int64_t>((t1 + t0) / 2);
+ timeSeriesDeriv->addValue(Kernel::DateAndTime(tm), deriv);
+ }
+ t0 = t1;
+ v0 = v1;
+ }
+ return timeSeriesDeriv;
+}
+/** time series derivative specialization for string type */
+template <>
+std::unique_ptr<TimeSeriesProperty<double>>
+TimeSeriesProperty<std::string>::getDerivative() const {
+ throw std::runtime_error(
+ "Time series property derivative is not defined for strings");
+ // return nullptr;
+}
+
/**
* Return the memory used by the property, in bytes
* */
diff --git a/Framework/Kernel/src/VectorHelper.cpp b/Framework/Kernel/src/VectorHelper.cpp
index 61aedadfc83fefb11da536e3229170dc378d050e..52144d225aa4f454563c018cefb3c214ad817445 100644
--- a/Framework/Kernel/src/VectorHelper.cpp
+++ b/Framework/Kernel/src/VectorHelper.cpp
@@ -533,6 +533,164 @@ void linearlyInterpolateY(const std::vector<double> &x, std::vector<double> &y,
step++;
}
}
+namespace {
+/** internal function converted from Lambda to identify interval around
+* specified point and run average around this point
+*
+*@param index -- index to average around
+*@param startIndex -- index in the array of data (input to start average
+* from) should be: index>=startIndex>=0
+*@param endIndex -- index in the array of data (input to end average at)
+* should be: index<=endIndex<=input.size()
+*@param halfWidth -- half width of the interval to integrate.
+*@param input -- vector of input signal
+*@param binBndrs -- pointer to vector of bin boundaries or NULL pointer.
+ */
+double runAverage(size_t index, size_t startIndex, size_t endIndex,
+ const double halfWidth, const std::vector<double> &input,
+ std::vector<double> const *const binBndrs) {
+
+ size_t iStart, iEnd;
+ double weight0(0), weight1(0), start, end;
+ //
+ if (binBndrs) {
+ // identify initial and final bins to
+ // integrate over. Notice the difference
+ // between start and end bin and shift of
+ // the interpolating function into the center
+ // of each bin
+ auto &rBndrs = *binBndrs;
+ // bin0 = binBndrs->operator[](index + 1) - binBndrs->operator[](index);
+
+ double binC = 0.5 * (rBndrs[index + 1] + rBndrs[index]);
+ start = binC - halfWidth;
+ end = binC + halfWidth;
+ if (start <= rBndrs[startIndex]) {
+ iStart = startIndex;
+ start = rBndrs[iStart];
+ } else {
+ iStart = getBinIndex(*binBndrs, start);
+ weight0 =
+ (rBndrs[iStart + 1] - start) / (rBndrs[iStart + 1] - rBndrs[iStart]);
+ iStart++;
+ }
+ if (end >= rBndrs[endIndex]) {
+ iEnd = endIndex; // the signal defined up to i<iEnd
+ end = rBndrs[endIndex];
+ } else {
+ iEnd = getBinIndex(*binBndrs, end);
+ weight1 = (end - rBndrs[iEnd]) / (rBndrs[iEnd + 1] - rBndrs[iEnd]);
+ }
+ if (iStart > iEnd) { // start and end get into the same bin
+ weight1 = 0;
+ weight0 = (end - start) / (rBndrs[iStart] - rBndrs[iStart - 1]);
+ }
+ } else { // integer indexes and functions defined in the bin centers
+ auto iHalfWidth = static_cast<size_t>(halfWidth);
+ iStart = index - iHalfWidth;
+ if (startIndex + iHalfWidth > index)
+ iStart = startIndex;
+ iEnd = index + iHalfWidth;
+ if (iEnd > endIndex)
+ iEnd = endIndex;
+ }
+
+ double avrg = 0;
+ size_t ic = 0;
+ for (size_t j = iStart; j < iEnd; j++) {
+ avrg += input[j];
+ ic++;
+ }
+ if (binBndrs) { // add values at edges
+ if (iStart != startIndex)
+ avrg += input[iStart - 1] * weight0;
+ if (iEnd != endIndex)
+ avrg += input[iEnd] * weight1;
+
+ return avrg / (end - start);
+ } else {
+ return avrg / double(ic);
+ }
+}
+}
+/** Basic running average of input vector within specified range, considering
+* variable bin-boundaries if such boundaries are provided.
+* The algorithm performs trapezium integration, so some peak shift
+* related to the first derivative of the integrated function can be observed.
+*
+* @param input:: input vector to smooth
+* @param output:: resulting vector (can not coincide with input)
+* @param avrgInterval:: the interval to average function in.
+* the function is averaged within +-0.5*avrgInterval
+* @param binBndrs :: pointer to the vector, containing bin boundaries.
+* If provided, its length has to be input.size()+1,
+* if not, equal size bins of size 1 are assumed,
+* so avrgInterval becomes the number of points
+* to average over. Bin boundaries array have to
+* increase and can not contain equal boundaries.
+* @param startIndex:: if provided, its start index to run averaging from.
+* if not, averaging starts from the index 0
+* @param endIndex :: final index to run average to, if provided. If
+* not, or higher then number of elements in input array,
+* averaging is performed to the end point of the input
+* array
+* @param outBins :: if present, pointer to a vector to return
+* bin boundaries for output array.
+*/
+void smoothInRange(const std::vector<double> &input,
+ std::vector<double> &output, const double avrgInterval,
+ std::vector<double> const *const binBndrs, size_t startIndex,
+ size_t endIndex, std::vector<double> *const outBins) {
+
+ if (endIndex == 0)
+ endIndex = input.size();
+ if (endIndex > input.size())
+ endIndex = input.size();
+
+ if (endIndex <= startIndex) {
+ output.resize(0);
+ return;
+ }
+
+ size_t max_size = input.size();
+ if (binBndrs) {
+ if (binBndrs->size() != max_size + 1) {
+ throw std::invalid_argument(
+ "Array of bin boundaries, "
+ "if present, have to be one bigger then the input array");
+ }
+ }
+
+ size_t length = endIndex - startIndex;
+ output.resize(length);
+
+ double halfWidth = avrgInterval / 2;
+ if (!binBndrs) {
+ if (std::floor(halfWidth) * 2 - avrgInterval > 1.e-6) {
+ halfWidth = std::floor(halfWidth) + 1;
+ }
+ }
+
+ if (outBins)
+ outBins->resize(length + 1);
+
+ // Run averaging
+ double binSize = 1;
+ for (size_t i = startIndex; i < endIndex; i++) {
+ if (binBndrs) {
+ binSize = binBndrs->operator[](i + 1) - binBndrs->operator[](i);
+ }
+ output[i - startIndex] =
+ runAverage(i, startIndex, endIndex, halfWidth, input, binBndrs) *
+ binSize;
+ if (outBins) {
+ outBins->operator[](i - startIndex) = binBndrs->operator[](i);
+ }
+ }
+ if (outBins) {
+ outBins->operator[](endIndex - startIndex) = binBndrs->operator[](endIndex);
+ }
+}
/// Declare all version of this
template DLLExport std::vector<int32_t>
diff --git a/Framework/Kernel/test/TimeSeriesPropertyTest.h b/Framework/Kernel/test/TimeSeriesPropertyTest.h
index 284bfb9bc6f55d75e19630a1788b1839afbb4727..87a1480b405e3035e1babbded9d0a4469e34a2c5 100644
--- a/Framework/Kernel/test/TimeSeriesPropertyTest.h
+++ b/Framework/Kernel/test/TimeSeriesPropertyTest.h
@@ -122,7 +122,36 @@ public:
TS_ASSERT_EQUALS(twoVals[1], threeVals[2]);
TS_ASSERT_EQUALS(newVal, threeVals[1]);
}
+ void test_GetDerivative() {
+ dProp->addValue("2007-11-30T16:17:10", 10);
+ dProp->addValue("2007-11-30T16:17:12", 12);
+ dProp->addValue("2007-11-30T16:17:01", 01);
+ dProp->addValue("2007-11-30T16:17:05", 05);
+ auto derProp = dProp->getDerivative();
+ TS_ASSERT(dynamic_cast<TimeSeriesProperty<double> *>(derProp.get()))
+
+ TS_ASSERT_EQUALS(derProp->size(), 3);
+ auto derValues = derProp->valuesAsVector();
+
+ TS_ASSERT_EQUALS(derValues[0], 1);
+ TS_ASSERT_EQUALS(derValues[1], 1);
+ TS_ASSERT_EQUALS(derValues[2], 1);
+
+ TSM_ASSERT_THROWS("derivative undefined for string property",
+ sProp->getDerivative(), std::runtime_error);
+
+ iProp->addValue("2007-11-30T16:17:10", 10);
+ TSM_ASSERT_THROWS(
+ "derivative undefined for property with less then 2 values",
+ iProp->getDerivative(), std::runtime_error);
+ iProp->addValue("2007-11-30T16:17:12", 12);
+
+ derProp = iProp->getDerivative();
+ TS_ASSERT_EQUALS(derProp->size(), 1);
+ derValues = derProp->valuesAsVector();
+ TS_ASSERT_EQUALS(derValues[0], 1);
+ }
void test_timesAsVector() {
TimeSeriesProperty<double> *p =
new TimeSeriesProperty<double>("doubleProp");
diff --git a/Framework/Kernel/test/VectorHelperTest.h b/Framework/Kernel/test/VectorHelperTest.h
index 16f9f4b86a2f79e2fe41a07dc55323e44066e000..36ac636a8f3644be183ca269644490a15f7f741e 100644
--- a/Framework/Kernel/test/VectorHelperTest.h
+++ b/Framework/Kernel/test/VectorHelperTest.h
@@ -5,6 +5,7 @@
#include "MantidKernel/Timer.h"
#include "MantidKernel/VectorHelper.h"
#include <cxxtest/TestSuite.h>
+#include <cstdlib>
#include <boost/assign/list_of.hpp>
using namespace Mantid::Kernel;
@@ -266,6 +267,121 @@ public:
index = VectorHelper::getBinIndex(m_test_bins, testValue));
TS_ASSERT_EQUALS(index, 2);
}
+ void test_RunningAveraging() {
+ double id[] = {1, 2, 3, 4, 5, 6};
+ std::vector<double> inputData(id, id + sizeof(id) / sizeof(double));
+ double ib[] = {0, 1, 2, 3, 4, 5};
+ std::vector<double> inputBoundaries(ib, ib + sizeof(ib) / sizeof(double));
+
+ std::vector<double> output;
+ TS_ASSERT_THROWS(
+ VectorHelper::smoothInRange(inputData, output, 6, &inputBoundaries),
+ std::invalid_argument);
+ inputBoundaries.push_back(6);
+ VectorHelper::smoothInRange(inputData, output, 6, &inputBoundaries);
+
+ TS_ASSERT_DELTA(output[1] - output[0], 0.492, 1.e-3);
+ TS_ASSERT_DELTA(output[3] - output[2], 0.4545, 1.e-3);
+ TS_ASSERT_DELTA(output[5] - output[4], 0.492, 1.e-3);
+ inputBoundaries[1] = 1;
+ inputBoundaries[2] = 3;
+ inputBoundaries[3] = 6;
+ inputBoundaries[4] = 10;
+ inputBoundaries[5] = 15;
+ inputBoundaries[6] = 21;
+ VectorHelper::smoothInRange(inputData, output, 6, &inputBoundaries);
+ TS_ASSERT_DELTA(output[2], 3, 1.e-8);
+ TS_ASSERT_DELTA(output[0], 1, 1.e-8);
+ TS_ASSERT_DELTA(output[5], 6, 1.e-8);
+
+ std::vector<double> out_bins;
+ VectorHelper::smoothInRange(inputData, output, 3, &inputBoundaries, 1, 5,
+ &out_bins);
+ TS_ASSERT_EQUALS(output.size(), 4);
+ TS_ASSERT_DELTA(output[1], 3, 1.e-8);
+ }
+
+ void test_Smooth_keeps_peakPosition() {
+
+ std::vector<double> output;
+ std::vector<double> inputBoundaries(21);
+ inputBoundaries[0] = 0;
+ double step(1);
+ for (size_t i = 1; i < 21; i++) {
+ inputBoundaries[i] = inputBoundaries[i - 1] + step;
+ step *= 1.1;
+ }
+ double norm = 100 / inputBoundaries[20];
+ for (size_t i = 0; i < 21; i++) {
+ inputBoundaries[i] *= norm;
+ }
+
+ std::vector<double> inputData(20);
+ for (size_t i = 0; i < 20; i++) {
+ double dev = 0.5 * (inputBoundaries[i] + inputBoundaries[i + 1]) - 50;
+ inputData[i] =
+ exp(-dev * dev / 100) * (inputBoundaries[i + 1] - inputBoundaries[i]);
+ }
+ int indOfMax = VectorHelper::getBinIndex(inputBoundaries, 50.);
+ double fMax = inputData[indOfMax] /
+ (inputBoundaries[indOfMax + 1] - inputBoundaries[indOfMax]);
+ double iLeft = inputData[indOfMax - 1] /
+ (inputBoundaries[indOfMax] - inputBoundaries[indOfMax - 1]);
+ double iRight = inputData[indOfMax + 1] / (inputBoundaries[indOfMax + 2] -
+ inputBoundaries[indOfMax + 1]);
+
+ TS_ASSERT(iLeft < fMax);
+ TS_ASSERT(iRight < fMax);
+ VectorHelper::smoothInRange(inputData, output, 10, &inputBoundaries);
+ fMax = output[indOfMax] /
+ (inputBoundaries[indOfMax + 1] - inputBoundaries[indOfMax]);
+ iLeft = inputData[indOfMax - 1] /
+ (inputBoundaries[indOfMax] - inputBoundaries[indOfMax - 1]);
+ iRight = inputData[indOfMax + 1] /
+ (inputBoundaries[indOfMax + 2] - inputBoundaries[indOfMax + 1]);
+
+ TS_ASSERT(iLeft < fMax);
+ TS_ASSERT(iRight < fMax);
+
+ output.swap(inputData);
+ VectorHelper::smoothInRange(inputData, output, 10, &inputBoundaries);
+
+ fMax = output[indOfMax] /
+ (inputBoundaries[indOfMax + 1] - inputBoundaries[indOfMax]);
+ iLeft = inputData[indOfMax - 1] /
+ (inputBoundaries[indOfMax] - inputBoundaries[indOfMax - 1]);
+ iRight = inputData[indOfMax + 1] /
+ (inputBoundaries[indOfMax + 2] - inputBoundaries[indOfMax + 1]);
+
+ // TS_ASSERT(iLeft<fMax);
+ TS_ASSERT(iRight < fMax);
+
+ output.swap(inputData);
+ VectorHelper::smoothInRange(inputData, output, 10, &inputBoundaries);
+
+ fMax = output[indOfMax] /
+ (inputBoundaries[indOfMax + 1] - inputBoundaries[indOfMax]);
+ iLeft = inputData[indOfMax - 1] /
+ (inputBoundaries[indOfMax] - inputBoundaries[indOfMax - 1]);
+ iRight = inputData[indOfMax + 1] /
+ (inputBoundaries[indOfMax + 2] - inputBoundaries[indOfMax + 1]);
+
+ // TS_ASSERT(iLeft<fMax);
+ TS_ASSERT(iRight < fMax);
+
+ output.swap(inputData);
+ VectorHelper::smoothInRange(inputData, output, 10, &inputBoundaries);
+
+ fMax = output[indOfMax] /
+ (inputBoundaries[indOfMax + 1] - inputBoundaries[indOfMax]);
+ iLeft = inputData[indOfMax - 1] /
+ (inputBoundaries[indOfMax] - inputBoundaries[indOfMax - 1]);
+ iRight = inputData[indOfMax + 1] /
+ (inputBoundaries[indOfMax + 2] - inputBoundaries[indOfMax + 1]);
+
+ TS_ASSERT(inputData[indOfMax - 1] < output[indOfMax]);
+ TS_ASSERT(inputData[indOfMax + 1] < output[indOfMax]);
+ }
private:
/// Testing bins
diff --git a/Framework/LiveData/src/ADARA/ADARAParser.cpp b/Framework/LiveData/src/ADARA/ADARAParser.cpp
index 8fe1652ecb61c1985e1538b85869fc1c8d029b3f..1fe48e4b00b4755d3c0e3a73e5c25c8caf289e86 100644
--- a/Framework/LiveData/src/ADARA/ADARAParser.cpp
+++ b/Framework/LiveData/src/ADARA/ADARAParser.cpp
@@ -9,7 +9,7 @@ using namespace ADARA;
Parser::Parser(unsigned int initial_buffer_size, unsigned int max_pkt_size)
: m_size(initial_buffer_size), m_max_size(max_pkt_size), m_len(0),
- m_restart_offset(0), m_oversize_len(0) {
+ m_restart_offset(0), m_oversize_len(0), m_oversize_offset(0) {
m_buffer = new uint8_t[initial_buffer_size];
m_discarded_packets.clear();
}
diff --git a/Framework/LiveData/src/ISISHistoDataListener.cpp b/Framework/LiveData/src/ISISHistoDataListener.cpp
index d962ecea3eafff1aabb5550675c27bf898669eba..b211f601a4eb5dd334c87e053d597a875164d35d 100644
--- a/Framework/LiveData/src/ISISHistoDataListener.cpp
+++ b/Framework/LiveData/src/ISISHistoDataListener.cpp
@@ -181,6 +181,10 @@ boost::shared_ptr<Workspace> ISISHistoDataListener::extractData() {
getFloatArray("RRPB", floatBuffer, 32);
const double protonCharge = floatBuffer[8];
+ if (m_timeRegime < 0)
+ throw std::runtime_error("The value of the time regime variable is "
+ "negative. This is an Internal inconsistency.");
+
// find out the number of histograms in the output workspace
const size_t numberOfHistograms =
m_specList.empty() ? m_numberOfSpectra[m_timeRegime] : m_specList.size();
diff --git a/Framework/LiveData/src/LoadDAE/isisds_command.cpp b/Framework/LiveData/src/LoadDAE/isisds_command.cpp
index 790c2391b29ba8394be8f545f77d2e4e4fa1eeb6..b54ea2c9781699874f8f7b5c3b9b3cc1ba9209b8 100644
--- a/Framework/LiveData/src/LoadDAE/isisds_command.cpp
+++ b/Framework/LiveData/src/LoadDAE/isisds_command.cpp
@@ -145,8 +145,14 @@ SOCKET isisds_send_open(const char *host, ISISDSAccessMode access_type,
if (s == INVALID_SOCKET) {
return INVALID_SOCKET;
}
- setsockopt(s, SOL_SOCKET, SO_KEEPALIVE, (char *)&setkeepalive,
- sizeof(setkeepalive));
+
+ int zero = setsockopt(s, SOL_SOCKET, SO_KEEPALIVE, (char *)&setkeepalive,
+ sizeof(setkeepalive));
+ if (0 != zero) {
+ closesocket(s);
+ return INVALID_SOCKET;
+ }
+
if (connect(s, (struct sockaddr *)&address, sizeof(address)) == -1) {
closesocket(s);
return INVALID_SOCKET;
diff --git a/Framework/MDAlgorithms/CMakeLists.txt b/Framework/MDAlgorithms/CMakeLists.txt
index f3e9e4d04a2db2271f828af463f363f2364f2462..8725b21a5ce0ae0f8beeca48f7506a054beffeb4 100644
--- a/Framework/MDAlgorithms/CMakeLists.txt
+++ b/Framework/MDAlgorithms/CMakeLists.txt
@@ -12,6 +12,7 @@ set ( SRC_FILES
src/CentroidPeaksMD.cpp
src/CentroidPeaksMD2.cpp
src/CloneMDWorkspace.cpp
+ src/CompactMD.cpp
src/CompareMDWorkspaces.cpp
src/ConvToMDBase.cpp
src/ConvToMDEventsWS.cpp
@@ -136,6 +137,7 @@ set ( INC_FILES
inc/MantidMDAlgorithms/CentroidPeaksMD2.h
inc/MantidMDAlgorithms/CloneMDWorkspace.h
inc/MantidMDAlgorithms/CompareMDWorkspaces.h
+ inc/MantidMDAlgorithms/CompactMD.h
inc/MantidMDAlgorithms/ConvToMDBase.h
inc/MantidMDAlgorithms/ConvertCWPDMDToSpectra.h
inc/MantidMDAlgorithms/ConvertCWSDExpToMomentum.h
@@ -257,6 +259,7 @@ set ( TEST_FILES
CentroidPeaksMDTest.h
CloneMDWorkspaceTest.h
CompareMDWorkspacesTest.h
+ CompactMDTest.h
ConvertCWPDMDToSpectraTest.h
ConvertCWSDExpToMomentumTest.h
ConvertCWSDMDtoHKLTest.h
diff --git a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/CompactMD.h b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/CompactMD.h
new file mode 100644
index 0000000000000000000000000000000000000000..c206f73b5409e0178a836f0d32a3a30d67014c16
--- /dev/null
+++ b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/CompactMD.h
@@ -0,0 +1,65 @@
+#ifndef MANTID_MDALGORITHMS_COMPACTMD_H_
+#define MANTID_MDALGORITHMS_COMPACTMD_H_
+
+/** An algorithm used to crop an MDHistoWorkspace based on the first
+ non-zero signals found in each dimension.
+
+ @author Matt King
+ @date 02-10-2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+
+#include "MantidAPI/IMDHistoWorkspace.h"
+#include "MantidDataObjects/MDHistoWorkspace.h"
+#include "MantidMDAlgorithms/CutMD.h"
+#include "MantidAPI/Algorithm.h"
+#include "boost/shared_ptr.hpp"
+namespace Mantid {
+namespace MDAlgorithms {
+class DLLExport CompactMD : public API::Algorithm {
+public:
+ CompactMD(){};
+ ~CompactMD(){};
+
+ virtual void init();
+ virtual void exec();
+ /// Algorithm's name for identification
+ const std::string name() const { return "CompactMD"; }
+ /// Summary of algorithms purpose
+ const std::string summary() const {
+ return "Crops an MDHistoWorkspace based on the first non-zero signals "
+ "giving a more focussed area of interest.";
+ }
+ const std::string category() const { return "MDAlgorithms"; }
+ /// Algorithm's version for identification
+ int version() const { return 1; }
+ /// Finding the extents of the first non-zero signals.
+ void
+ findFirstNonZeroMinMaxExtents(Mantid::API::IMDHistoWorkspace_sptr inputWs,
+ std::vector<Mantid::coord_t> &minVec,
+ std::vector<Mantid::coord_t> &maxVec);
+};
+}
+}
+
+#endif // MANTID_MDALGORITHMS_COMPACTMD_H_
\ No newline at end of file
diff --git a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h
index 2d2b6398fcbc13ef8930008df57da0b01eb015e7..d5a3c71fc66da3866275f0cd6a87bf0c4b5050e5 100644
--- a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h
+++ b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h
@@ -127,10 +127,10 @@ private:
double detectorQ(std::vector<Kernel::V3D> E1Vec,
const Mantid::Kernel::V3D QLabFrame, std::vector<double> &r);
// Private data members
- PeakQMap peak_qs; // hashtable with peak Q-vectors
- EventListMap event_lists; // hashtable with lists of events for each peak
- Kernel::DblMatrix UBinv; // matrix mapping from Q to h,k,l
- double radius; // size of sphere to use for events around a peak
+ PeakQMap m_peak_qs; // hashtable with peak Q-vectors
+ EventListMap m_event_lists; // hashtable with lists of events for each peak
+ Kernel::DblMatrix m_UBinv; // matrix mapping from Q to h,k,l
+ double m_radius; // size of sphere to use for events around a peak
};
} // namespace MDAlgorithms
diff --git a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/PreprocessDetectorsToMD.h b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/PreprocessDetectorsToMD.h
index 7464a55bd76b1e3209a19e205b493542fbaa5642..f139433836d5c9fe001ec8fae65aff65db29325b 100644
--- a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/PreprocessDetectorsToMD.h
+++ b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/PreprocessDetectorsToMD.h
@@ -6,7 +6,6 @@
//----------------------------------------------------------------------
#include "MantidAPI/Algorithm.h"
#include "MantidDataObjects/TableWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidMDAlgorithms/DllConfig.h"
namespace Mantid {
diff --git a/Framework/MDAlgorithms/src/CalculateCoverageDGS.cpp b/Framework/MDAlgorithms/src/CalculateCoverageDGS.cpp
index b08e5a46ea2e45b5d4819401618fde18945c48b5..d9e2a957b1f7411b3848390a8cbe22415ea1609b 100644
--- a/Framework/MDAlgorithms/src/CalculateCoverageDGS.cpp
+++ b/Framework/MDAlgorithms/src/CalculateCoverageDGS.cpp
@@ -1,5 +1,5 @@
#include "MantidMDAlgorithms/CalculateCoverageDGS.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidDataObjects/MDHistoWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/ArrayLengthValidator.h"
diff --git a/Framework/MDAlgorithms/src/CompactMD.cpp b/Framework/MDAlgorithms/src/CompactMD.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7c815d5277ff64361e8487fe54f330c038b1f0bd
--- /dev/null
+++ b/Framework/MDAlgorithms/src/CompactMD.cpp
@@ -0,0 +1,140 @@
+#include "MantidMDAlgorithms/CompactMD.h"
+#include "MantidAPI/IMDIterator.h"
+using namespace Mantid::API;
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+namespace {
+/**
+ * helper method to create a string from min and max extents (with non-zero
+ * signals) ready to be used as the PBins for IntegrateMDHistoWorkspace
+ * algorithm in
+ * exec
+ * @param minVector : Vector containing the minimum extents that we will crop
+ * to.
+ * @param maxVector : Vector containing the maximum extents that we will crop
+ * to.
+ * @param inputWs : Used in the calculation from centre to bin edges
+ * @return : a string vector of binning parameters for IntegrateMDHistoWorkspace
+ * to take as input.
+*/
+std::vector<std::string>
+createPBinStringVector(std::vector<Mantid::coord_t> minVector,
+ std::vector<Mantid::coord_t> maxVector,
+ IMDHistoWorkspace_sptr inputWs) {
+ size_t numDims = inputWs->getNumDims();
+ std::vector<std::string> pBinStrVector;
+ for (size_t iter = 0; iter < numDims; iter++) {
+ if (minVector[iter] >= maxVector[iter]) {
+ std::cerr << "Minimum extent of non-zero signal must be LESS than the "
+ "maximum extent with non-zero signal" << std::endl;
+ }
+ // creating pbin string using Min and Max Centre positions
+ auto pBinStr = boost::lexical_cast<std::string>(
+ minVector[iter] -
+ (inputWs->getDimension(iter)->getBinWidth() * 0.5)) +
+ ",0," +
+ boost::lexical_cast<std::string>(
+ maxVector[iter] +
+ (inputWs->getDimension(iter)->getBinWidth() * 0.5));
+ pBinStrVector.push_back(pBinStr);
+ }
+ return pBinStrVector;
+}
+}
+
+namespace Mantid {
+namespace MDAlgorithms {
+
+DECLARE_ALGORITHM(CompactMD)
+
+/**
+* Finding the centre points of Bins with non-zero signal values
+* we then compare this centre to minimum and maximum centres we have
+* to get the minimum and maximum extents of the workspace that has non-zero
+* signal values in the Bins.
+* @param inputWs : The workspace that will be iterated over to find the extents.
+* @param minVec : Vector used to stored the minimum extent in each dimension
+* @param maxVec : Vector used to stored the maximum extents in each dimension
+*/
+
+void CompactMD::findFirstNonZeroMinMaxExtents(
+ IMDHistoWorkspace_sptr inputWs, std::vector<Mantid::coord_t> &minVec,
+ std::vector<Mantid::coord_t> &maxVec) {
+ auto ws_iter = inputWs->createIterator();
+ do {
+ if (ws_iter->getSignal() == 0) {
+ // if signal is 0 then go to next index
+ continue;
+ } else {
+ // we have found a non-zero signal we need to compare
+ // the position of the bin with our Min and Max values
+ auto current_index = ws_iter->getLinearIndex();
+ auto current_center = inputWs->getCenter(current_index);
+ for (size_t index = 0; index < inputWs->getNumDims(); index++) {
+ if (current_center[index] > maxVec[index]) {
+ // set new maximum
+ maxVec[index] = current_center[index];
+ }
+ if (current_center[index] < minVec[index]) {
+ // set new minimum
+ minVec[index] = current_center[index];
+ }
+ }
+ }
+ } while (ws_iter->next());
+}
+
+/**
+* Initiliase the algorithm's properties.
+*/
+void CompactMD::init() {
+ // input workspace to compact
+ declareProperty(new WorkspaceProperty<IMDHistoWorkspace>("InputWorkspace", "",
+ Direction::Input),
+ "MDHistoWorkspace to compact");
+ // output workspace that will have been compacted
+ declareProperty(new WorkspaceProperty<IMDHistoWorkspace>(
+ "OutputWorkspace", "", Direction::Output),
+ "Output compacted workspace");
+}
+/**
+* Execute the algorithm.
+*/
+void CompactMD::exec() {
+ const IMDHistoWorkspace_sptr input_ws = this->getProperty("InputWorkspace");
+ IMDWorkspace_sptr out_ws;
+
+ const size_t nDimensions = input_ws->getNumDims();
+ std::vector<Mantid::coord_t> minVector;
+ std::vector<Mantid::coord_t> maxVector;
+
+ // fill the min/max vectors with values per dimension.
+ for (size_t index = 0; index < nDimensions; index++) {
+ minVector.push_back(input_ws->getDimension(index)->getMaximum());
+ maxVector.push_back(input_ws->getDimension(index)->getMinimum());
+ }
+ // start our search for the first non-zero signal index.
+ findFirstNonZeroMinMaxExtents(input_ws, minVector, maxVector);
+ auto pBinStrings = createPBinStringVector(minVector, maxVector, input_ws);
+ // creating IntegrateMDHistoWorkspace algorithm to crop our workspace.
+ auto cut_alg = this->createChildAlgorithm("IntegrateMDHistoWorkspace");
+ cut_alg->setProperty("InputWorkspace", input_ws);
+ cut_alg->setProperty("OutputWorkspace", "temp");
+ // setting property PxBin depending on the number of dimensions the
+ // input workspace has.
+ for (size_t iter = 0; iter < input_ws->getNumDims(); iter++) {
+ std::string propertyString =
+ "P" + boost::lexical_cast<std::string>(iter + 1) + "Bin";
+ cut_alg->setProperty(propertyString, pBinStrings[iter]);
+ }
+ cut_alg->execute();
+
+ // retrieve the output workspace from IntegrateMDHistoWorkspace
+ IMDHistoWorkspace_sptr temp = cut_alg->getProperty("OutputWorkspace");
+ out_ws = temp;
+ // set output workspace of CompactMD to output of IntegrateMDHistoWorkspace
+ this->setProperty("OutputWorkspace", out_ws);
+}
+}
+}
\ No newline at end of file
diff --git a/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp b/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
index 091f8322f9c4d7c99a96fa07b0daa3bf8bbe0e49..746eb498bc4ad870cb81ff6452f4c2cce3ab69e5 100644
--- a/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
+++ b/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
@@ -25,7 +25,8 @@ DECLARE_ALGORITHM(ConvertCWSDExpToMomentum)
/** Constructor
*/
ConvertCWSDExpToMomentum::ConvertCWSDExpToMomentum()
- : m_iColFilename(2), m_iColStartDetID(3), m_setQRange(true) {}
+ : m_iColFilename(2), m_iColStartDetID(3), m_setQRange(true),
+ m_isBaseName(false) {}
//----------------------------------------------------------------------------------------------
/** Destructor
@@ -204,13 +205,15 @@ void ConvertCWSDExpToMomentum::addMDEvents(bool usevirtual) {
// Check whether to add / or \ to m_dataDir
std::string sep("");
if (m_dataDir.size() > 0) {
- // Determine system
- bool isWindows(false);
+// Determine system
#if _WIN64
- isWindows = true;
-#elif _WIND32
- isWindows = true;
+ const bool isWindows = true;
+#elif _WIN32
+ const bool isWindows = true;
+#else
+ const bool isWindows = false;
#endif
+
if (isWindows && *m_dataDir.rbegin() != '\\') {
sep = "\\";
} else if (!isWindows && *m_dataDir.rbegin() != '/')
@@ -415,6 +418,13 @@ void ConvertCWSDExpToMomentum::convertSpiceMatrixToMomentumMDEvents(
}
expinfo->mutableRun().setGoniometer(dataws->run().getGoniometer(), false);
expinfo->mutableRun().addProperty("run_number", runnumber);
+ // Add all the other propertys from original data workspace
+ const std::vector<Kernel::Property *> vec_property =
+ dataws->run().getProperties();
+ for (size_t i = 0; i < vec_property.size(); ++i) {
+ expinfo->mutableRun().addProperty(vec_property[i]->clone());
+ }
+
m_outputWS->addExperimentInfo(expinfo);
return;
diff --git a/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace.cpp b/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace.cpp
index 3135b45ca53cba893ee347f0b150591e75017cb9..4f6bf32e23452dd2ec1d8b6ba2a0ed9ec04cddb4 100644
--- a/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace.cpp
@@ -1,6 +1,6 @@
#include "MantidAPI/IMDEventWorkspace.h"
#include "MantidAPI/Progress.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
diff --git a/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace2.cpp b/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace2.cpp
index adf27e22bfebf50acca9eacb400cba07ea5bcdd8..4fc927b7a231e5905c4c3276c43eb69f2ddffed8 100644
--- a/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace2.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace2.cpp
@@ -1,8 +1,6 @@
#include "MantidMDAlgorithms/ConvertToDiffractionMDWorkspace2.h"
#include "MantidAPI/IMDEventWorkspace.h"
-#include "MantidAPI/Progress.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/MDEventWorkspace.h"
diff --git a/Framework/MDAlgorithms/src/ConvertToMD.cpp b/Framework/MDAlgorithms/src/ConvertToMD.cpp
index 84a87c0a76fd3627fa1430df9aadcf29461b29a3..375e4467d683893bf65dd0f2a736b58f3bb5cf2c 100644
--- a/Framework/MDAlgorithms/src/ConvertToMD.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToMD.cpp
@@ -3,8 +3,6 @@
#include <algorithm>
#include "MantidAPI/IMDEventWorkspace.h"
-#include "MantidAPI/Progress.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/ArrayLengthValidator.h"
diff --git a/Framework/MDAlgorithms/src/ConvertToMDMinMaxGlobal.cpp b/Framework/MDAlgorithms/src/ConvertToMDMinMaxGlobal.cpp
index 13dbd0d43c1e6a5dc66babc5ee38b05245c03ae1..c344b7c1b0bdd0b7bfb65af1b7cc759baea6c074 100644
--- a/Framework/MDAlgorithms/src/ConvertToMDMinMaxGlobal.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToMDMinMaxGlobal.cpp
@@ -1,7 +1,10 @@
#include "MantidMDAlgorithms/ConvertToMDMinMaxGlobal.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/VisibleWhenProperty.h"
diff --git a/Framework/MDAlgorithms/src/ConvertToMDParent.cpp b/Framework/MDAlgorithms/src/ConvertToMDParent.cpp
index d41e435fa5f888ed795ead18e6d8fdfbd2aeaa80..2c19786b0a51263b0022ff4bc0b347ebabbed181 100644
--- a/Framework/MDAlgorithms/src/ConvertToMDParent.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToMDParent.cpp
@@ -1,9 +1,11 @@
#include "MantidMDAlgorithms/ConvertToMDParent.h"
#include "MantidAPI/IMDEventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/VisibleWhenProperty.h"
diff --git a/Framework/MDAlgorithms/src/ConvertToReflectometryQ.cpp b/Framework/MDAlgorithms/src/ConvertToReflectometryQ.cpp
index cd2a8bff145221be83b4ab299bb36c53a428059d..399b1c3e426f90ed072a1c1ff80c4dc0d94a1ced 100644
--- a/Framework/MDAlgorithms/src/ConvertToReflectometryQ.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToReflectometryQ.cpp
@@ -2,7 +2,8 @@
#include "MantidAPI/IEventWorkspace.h"
#include "MantidAPI/ITableWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/Progress.h"
#include "MantidDataObjects/EventWorkspace.h"
@@ -10,6 +11,7 @@
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
diff --git a/Framework/MDAlgorithms/src/FindPeaksMD.cpp b/Framework/MDAlgorithms/src/FindPeaksMD.cpp
index 1e94707a155f447cab458f8d4b2e3528fef25294..ba70dd4bedd2239fcf40c699cdac43d92045abe3 100644
--- a/Framework/MDAlgorithms/src/FindPeaksMD.cpp
+++ b/Framework/MDAlgorithms/src/FindPeaksMD.cpp
@@ -215,12 +215,15 @@ FindPeaksMD::createPeak(const Mantid::Kernel::V3D &Q, const double binCount) {
boost::shared_ptr<DataObjects::Peak> p;
if (dimType == QLAB) {
// Build using the Q-lab-frame constructor
- p = boost::shared_ptr<DataObjects::Peak>(new Peak(inst, Q));
+ p = boost::make_shared<Peak>(inst, Q);
// Save gonio matrix for later
p->setGoniometerMatrix(m_goniometer);
} else if (dimType == QSAMPLE) {
// Build using the Q-sample-frame constructor
- p = boost::shared_ptr<DataObjects::Peak>(new Peak(inst, Q, m_goniometer));
+ p = boost::make_shared<Peak>(inst, Q, m_goniometer);
+ } else {
+ throw std::invalid_argument(
+ "Cannot Integrate peaks unless the dimension is QLAB or QSAMPLE");
}
try { // Look for a detector
diff --git a/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp b/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp
index 9bb7c6d1a1723019e115ccda352ef3039a6dccee..8aab04ee8dbf02e05f695e30c90b2100fb472a3a 100644
--- a/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp
+++ b/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp
@@ -266,7 +266,13 @@ void ImportMDEventWorkspace::exec() {
m_nDimensions + 4; // signal, error, run_no, detector_no
m_IsFullDataObjects = (nActualColumns == columnsForFullEvents);
- m_nDataObjects = posDiffMDEvent / nActualColumns;
+ if (0 == nActualColumns) {
+ m_nDataObjects = 0;
+ g_log.warning() << "The number of actual columns found in the file "
+ "(exlcuding comments) is zero" << std::endl;
+ } else {
+ m_nDataObjects = posDiffMDEvent / nActualColumns;
+ }
// Get the min and max extents in each dimension.
std::vector<double> extentMins(m_nDimensions);
diff --git a/Framework/MDAlgorithms/src/Integrate3DEvents.cpp b/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
index f3db57b5fd7b3652e27e4bf5187cbf8311c872e5..372e9b1ad95a59e2852b7522d4b4e3602fc6a41b 100644
--- a/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
+++ b/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
@@ -35,14 +35,14 @@ using Mantid::Kernel::V3D;
Integrate3DEvents::Integrate3DEvents(
std::vector<std::pair<double, V3D>> const &peak_q_list,
DblMatrix const &UBinv, double radius) {
- this->UBinv = UBinv;
- this->radius = radius;
+ m_UBinv = UBinv;
+ m_radius = radius;
int64_t hkl_key;
for (size_t it = 0; it != peak_q_list.size(); ++it) {
hkl_key = getHklKey(peak_q_list[it].second);
if (hkl_key != 0) // only save if hkl != (0,0,0)
- peak_qs[hkl_key] = peak_q_list[it].second;
+ m_peak_qs[hkl_key] = peak_q_list[it].second;
}
}
@@ -124,7 +124,12 @@ Integrate3DEvents::ellipseIntegrateEvents(
return boost::make_shared<NoShape>();
}
- std::vector<std::pair<double, V3D>> &some_events = event_lists[hkl_key];
+ auto pos = m_event_lists.find(hkl_key);
+ if (m_event_lists.end() == pos)
+ return boost::make_shared<NoShape>();
+ ;
+
+ std::vector<std::pair<double, V3D>> &some_events = pos->second;
if (some_events.size() < 3) // if there are not enough events to
{ // find covariance matrix, return
@@ -132,14 +137,14 @@ Integrate3DEvents::ellipseIntegrateEvents(
}
DblMatrix cov_matrix(3, 3);
- makeCovarianceMatrix(some_events, cov_matrix, radius);
+ makeCovarianceMatrix(some_events, cov_matrix, m_radius);
std::vector<V3D> eigen_vectors;
getEigenVectors(cov_matrix, eigen_vectors);
std::vector<double> sigmas;
for (int i = 0; i < 3; i++) {
- sigmas.push_back(stdDev(some_events, eigen_vectors[i], radius));
+ sigmas.push_back(stdDev(some_events, eigen_vectors[i], m_radius));
}
bool invalid_peak = false;
@@ -392,7 +397,7 @@ int64_t Integrate3DEvents::getHklKey2(V3D const &hkl) {
* @param q_vector The q_vector to be mapped to h,k,l
*/
int64_t Integrate3DEvents::getHklKey(V3D const &q_vector) {
- V3D hkl = UBinv * q_vector;
+ V3D hkl = m_UBinv * q_vector;
int h = boost::math::iround<double>(hkl[0]);
int k = boost::math::iround<double>(hkl[1]);
int l = boost::math::iround<double>(hkl[2]);
@@ -424,15 +429,15 @@ void Integrate3DEvents::addEvent(std::pair<double, V3D> event_Q,
if (hkl_key == 0) // don't keep events associated with 0,0,0
return;
- auto peak_it = peak_qs.find(hkl_key);
- if (peak_it != peak_qs.end()) {
+ auto peak_it = m_peak_qs.find(hkl_key);
+ if (peak_it != m_peak_qs.end()) {
if (!peak_it->second.nullVector()) {
if (hkl_integ)
- event_Q.second = event_Q.second - UBinv * peak_it->second;
+ event_Q.second = event_Q.second - m_UBinv * peak_it->second;
else
event_Q.second = event_Q.second - peak_it->second;
- if (event_Q.second.norm() < radius) {
- event_lists[hkl_key].push_back(event_Q);
+ if (event_Q.second.norm() < m_radius) {
+ m_event_lists[hkl_key].push_back(event_Q);
}
}
}
@@ -511,8 +516,8 @@ PeakShapeEllipsoid_const_sptr Integrate3DEvents::ellipseIntegrateEvents(
// if necessary restrict the background ellipsoid
// to lie within the specified sphere, and adjust
// the other sizes, proportionally
- if (r3 * max_sigma > radius) {
- r3 = radius / max_sigma;
+ if (r3 * max_sigma > m_radius) {
+ r3 = m_radius / max_sigma;
r1 = r3 * 0.79370053f; // This value for r1 and r2 makes the background
r2 = r1; // shell volume equal to the peak region volume.
}
diff --git a/Framework/MDAlgorithms/src/IntegrateEllipsoids.cpp b/Framework/MDAlgorithms/src/IntegrateEllipsoids.cpp
index ad7bec8a36395a171beca37f96c453a9fcbd9780..ca721437fce6cc96906887af9a14d2ff4436022c 100644
--- a/Framework/MDAlgorithms/src/IntegrateEllipsoids.cpp
+++ b/Framework/MDAlgorithms/src/IntegrateEllipsoids.cpp
@@ -1,7 +1,8 @@
#include "MantidMDAlgorithms/IntegrateEllipsoids.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidDataObjects/PeakShapeEllipsoid.h"
diff --git a/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp b/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp
index 711de48f4bf03d29ae298d0aaebf6c47f0f01693..ee80f5f9e527c13dde9b8612a768c4c3cde20b58 100644
--- a/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp
+++ b/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp
@@ -104,7 +104,7 @@ Mantid::coord_t getPrecisionCorrectedCoordinate(Mantid::coord_t position,
// Check if the relative deviation is larger than 1e-6
const auto deviation = fabs((nearest - position) / binWidth);
- const auto tolerance = 1e-6;
+ const auto tolerance = 1e-5;
Mantid::coord_t coordinate(position);
if (deviation < tolerance) {
coordinate = nearest;
@@ -195,6 +195,7 @@ MDHistoWorkspace_sptr createShapedOutput(IMDHistoWorkspace const *const inWS,
binning.back()) /*max*/); // Set custom min, max and nbins.
} else if (i < pbins.size() && similarBinning(pbins[i])) {
auto binning = pbins[i];
+
Mantid::coord_t pMin = static_cast<Mantid::coord_t>(binning.front());
Mantid::coord_t pMax = static_cast<Mantid::coord_t>(binning.back());
size_t numberOfBins;
@@ -386,6 +387,10 @@ void IntegrateMDHistoWorkspace::exec() {
// Create a thread-local input iterator.
boost::scoped_ptr<MDHistoWorkspaceIterator> inIterator(
dynamic_cast<MDHistoWorkspaceIterator *>(inWS->createIterator()));
+ if (!inIterator) {
+ throw std::runtime_error(
+ "Could not convert IMDIterator to a MDHistoWorkspaceIterator");
+ }
/*
We jump to the iterator position which is closest in the model
diff --git a/Framework/MDAlgorithms/src/MDNormDirectSC.cpp b/Framework/MDAlgorithms/src/MDNormDirectSC.cpp
index bf6d76d02d1724504ed5d16bbf289e37863b4adf..20336f562b787a80af15e6326eef4524a1a21aca 100644
--- a/Framework/MDAlgorithms/src/MDNormDirectSC.cpp
+++ b/Framework/MDAlgorithms/src/MDNormDirectSC.cpp
@@ -1,9 +1,11 @@
#include "MantidMDAlgorithms/MDNormDirectSC.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/MDEventWorkspace.h"
#include "MantidDataObjects/MDHistoWorkspace.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/VectorHelper.h"
diff --git a/Framework/MDAlgorithms/src/MDNormSCD.cpp b/Framework/MDAlgorithms/src/MDNormSCD.cpp
index 31a69c5e9f109de3ab85d46f7945ac4052789a5b..b5141d1c6261d84c96796d48326a0fe63c580c57 100644
--- a/Framework/MDAlgorithms/src/MDNormSCD.cpp
+++ b/Framework/MDAlgorithms/src/MDNormSCD.cpp
@@ -1,9 +1,12 @@
#include "MantidMDAlgorithms/MDNormSCD.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/MDEventWorkspace.h"
#include "MantidDataObjects/MDHistoWorkspace.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/VectorHelper.h"
diff --git a/Framework/MDAlgorithms/src/PreprocessDetectorsToMD.cpp b/Framework/MDAlgorithms/src/PreprocessDetectorsToMD.cpp
index 837827c91fa24209572bb3781af4ef48a4d974d5..c3aa0a51f81f48e0ed42730b7d8ef8a14a1f45b3 100644
--- a/Framework/MDAlgorithms/src/PreprocessDetectorsToMD.cpp
+++ b/Framework/MDAlgorithms/src/PreprocessDetectorsToMD.cpp
@@ -1,7 +1,8 @@
#include "MantidMDAlgorithms/PreprocessDetectorsToMD.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/NumericAxis.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/PropertyWithValue.h"
-#include "MantidAPI/NumericAxis.h"
using namespace Mantid;
using namespace Mantid::API;
diff --git a/Framework/MDAlgorithms/src/ReplicateMD.cpp b/Framework/MDAlgorithms/src/ReplicateMD.cpp
index f97a4822c388c378ffdd2bc9e9b495baa2345632..f60b7c005638cc174503903508972036d78f8528 100644
--- a/Framework/MDAlgorithms/src/ReplicateMD.cpp
+++ b/Framework/MDAlgorithms/src/ReplicateMD.cpp
@@ -152,7 +152,7 @@ const std::string ReplicateMD::category() const { return "MDAlgorithms"; }
/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
const std::string ReplicateMD::summary() const {
- return "This is a algorithm to create a higher dimensional dataset by "
+ return "This is an algorithm to create a higher dimensional dataset by "
"replicating along an additional axis";
}
diff --git a/Framework/MDAlgorithms/src/SaveIsawQvector.cpp b/Framework/MDAlgorithms/src/SaveIsawQvector.cpp
index 46f3d0f66fea322d216dd1e1d4afe0431acf4214..3f871f0992e8f7e6d672e93ebb565fcc826c4715 100644
--- a/Framework/MDAlgorithms/src/SaveIsawQvector.cpp
+++ b/Framework/MDAlgorithms/src/SaveIsawQvector.cpp
@@ -3,7 +3,8 @@
#include <fstream>
#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidMDAlgorithms/MDTransfFactory.h"
diff --git a/Framework/MDAlgorithms/test/CompactMDTest.h b/Framework/MDAlgorithms/test/CompactMDTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..c902a63bd606528350418ca3664b634d0314e4bd
--- /dev/null
+++ b/Framework/MDAlgorithms/test/CompactMDTest.h
@@ -0,0 +1,289 @@
+#ifndef MANTID_MDALGORITHMS_COMPACTMDTEST_H_
+#define MANTID_MDALGORITHMS_COMPACTMDTEST_H_
+#include <cxxtest/TestSuite.h>
+
+#include "MantidMDAlgorithms/CompactMD.h"
+#include "MantidDataObjects/MDHistoWorkspace.h"
+#include "MantidTestHelpers/MDEventsTestHelper.h"
+
+using Mantid::MDAlgorithms::CompactMD;
+using namespace Mantid::API;
+
+//==================
+// Functional Tests
+//==================
+class CompactMDTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static CompactMDTest *createSuite() { return new CompactMDTest(); }
+ static void destroySuite(CompactMDTest *suite) { delete suite; }
+
+ void test_Init() {
+ CompactMD alg;
+ TSM_ASSERT_THROWS_NOTHING("Instance of CompactMD threw: ",
+ alg.initialize());
+ TSM_ASSERT("Instance of CompactMD was not initialised: ",
+ alg.isInitialized());
+ }
+ void
+ test_all_non_zero_signals_are_kept_with_data_concentrated_in_the_centre() {
+ /*
+ *testing the effectiveness of CompactMD when the data looks like this:
+ *------------------
+ * Input structure:
+ *------------------
+ * -------------
+ * | | |///| | |
+ * ---------------------
+ * -5-4-3 2-1 0 1 2 3 4 5
+ *---------------------------
+ * Expected output structure:
+ *----------------------------
+ * should trim until the first non-zero value.
+ * -----
+ * |///|
+ * -----
+ * -1 0 1
+ */
+
+ using namespace Mantid::DataObjects;
+ const size_t numDims = 1;
+ const double signal = 0.0;
+ const double errorSquared = 1.3;
+ size_t numBins[static_cast<int>(numDims)] = {5};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-5};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {5};
+ const std::string name("test");
+ auto inWS = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
+ numDims, signal, errorSquared, numBins, min, max, name);
+ inWS->setSignalAt(2, 1.0); // set middle bin signal to one
+ CompactMD alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", inWS);
+ alg.setProperty("OutputWorkspace", "out");
+ alg.execute();
+ // output workspace should be cropped so extents ~ [-1,1]
+ IMDHistoWorkspace_sptr outputWorkspace = alg.getProperty("OutputWorkspace");
+ TSM_ASSERT_EQUALS("Should have a signal of 1.0: ",
+ outputWorkspace->getSignalAt(0), 1);
+ TSM_ASSERT_EQUALS("Minimum should be cropped to -1: ",
+ outputWorkspace->getDimension(0)->getMinimum(), -1.0);
+ TSM_ASSERT_EQUALS("Maximum should be cropped to 1: ",
+ outputWorkspace->getDimension(0)->getMaximum(), 1.0);
+ TSM_ASSERT_EQUALS("Number of Bins should be 1 : ",
+ outputWorkspace->getDimension(0)->getNBins(), 1.0);
+ TSM_ASSERT_EQUALS("Bin width should be consistent: ",
+ outputWorkspace->getDimension(0)->getBinWidth(),
+ inWS->getDimension(0)->getBinWidth());
+ }
+ void test_all_non_zero_signals_are_kept_with_data_in_each_corner() {
+ /*
+ *testing the effectiveness of CompactMD when the data looks like this:
+ *-----------------------------------
+ * Input structure: 2D HistoWorkspace
+ *-----------------------------------
+ * ------------- -3
+ * |/a/| |/b/| -2
+ * ------------- -1
+ * | | | | 0
+ * ------------- 1
+ * |/c/| |/d/| 2
+ * ------------- 3
+ * -3-2-1 0 1 2 3
+ *----------------------------
+ * Expected output structure:
+ *----------------------------
+ * should not trim the workspace at all.
+ * ------------- -3
+ * |/a/| |/b/| -2
+ * ------------- -1
+ * | | | | 0
+ * ------------- 1
+ * |/c/| |/d/| 2
+ * ------------- 3
+ * -3-2-1 0 1 2 3
+ */
+ using namespace Mantid::DataObjects;
+ const size_t numDims = 2;
+ const double signal = 0.0;
+ const double errorSquared = 1.2;
+ size_t numBins[static_cast<int>(numDims)] = {3, 3};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-3, -3};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {3, 3};
+ const std::string name("test");
+ auto inWS = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
+ numDims, signal, errorSquared, numBins, min, max, name);
+ inWS->setSignalAt(0, 1.0); // cell a
+ inWS->setSignalAt(2, 1.0); // cell b
+ inWS->setSignalAt(6, 1.0); // cell c
+ inWS->setSignalAt(8, 1.0); // cell d
+
+ CompactMD alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", inWS);
+ alg.setProperty("OutputWorkspace", "out");
+ alg.execute();
+ IMDHistoWorkspace_sptr outputWorkspace = alg.getProperty("OutputWorkspace");
+ TSM_ASSERT_EQUALS("Should have a signal of 1.0: ",
+ outputWorkspace->getSignalAt(0), 1);
+ TSM_ASSERT_EQUALS("Should have a signal of 1.0: ",
+ outputWorkspace->getSignalAt(2), 1);
+ TSM_ASSERT_EQUALS("Should have a signal of 1.0: ",
+ outputWorkspace->getSignalAt(6), 1);
+ TSM_ASSERT_EQUALS("Should have a signal of 1.0: ",
+ outputWorkspace->getSignalAt(8), 1);
+ TSM_ASSERT_EQUALS("Minimum for dim 0 should be consistent: ",
+ outputWorkspace->getDimension(0)->getMinimum(),
+ inWS->getDimension(0)->getMinimum());
+ TSM_ASSERT_EQUALS("Maximum for dim 0 should be consistent: ",
+ outputWorkspace->getDimension(0)->getMaximum(),
+ inWS->getDimension(0)->getMaximum());
+ TSM_ASSERT_EQUALS("Minimum for dim 1 should be consistent:",
+ outputWorkspace->getDimension(1)->getMinimum(),
+ inWS->getDimension(1)->getMinimum());
+ TSM_ASSERT_EQUALS("Maximum for dim 1 should be consistent: ",
+ outputWorkspace->getDimension(1)->getMaximum(),
+ inWS->getDimension(1)->getMaximum());
+ TSM_ASSERT_EQUALS("Number of Bins for dim 0 should be consistent : ",
+ outputWorkspace->getDimension(0)->getNBins(),
+ inWS->getDimension(0)->getNBins());
+ TSM_ASSERT_EQUALS("Number of Bins for dim 1 should be consistent : ",
+ outputWorkspace->getDimension(1)->getNBins(),
+ inWS->getDimension(1)->getNBins());
+ TSM_ASSERT_EQUALS("Bin width for dim 0 should be consistent: ",
+ outputWorkspace->getDimension(0)->getBinWidth(),
+ inWS->getDimension(0)->getBinWidth());
+ TSM_ASSERT_EQUALS("Bin width for dim 1 should be consistent: ",
+ outputWorkspace->getDimension(1)->getBinWidth(),
+ inWS->getDimension(1)->getBinWidth());
+ }
+
+ void
+ test_all_non_zero_signals_are_kept_when_data_is_concentrated_in_one_half_of_the_workspace() {
+ /*
+ *testing the effectiveness of CompactMD when the data looks like this:
+ *------------------
+ * Input structure:
+ *------------------
+ * -------------
+ * |///| | |
+ * -------------
+ * -3-2-1 0 1 2 3
+ *---------------------------
+ * Expected output structure:
+ *----------------------------
+ * should trim until the first non-zero value.
+ * -----
+ * |///|
+ * -----
+ * 1 2 3
+ */
+
+ using namespace Mantid::DataObjects;
+ const size_t numDims = 1;
+ const double signal = 0.0;
+ const double errorSquared = 1.3;
+ size_t numBins[static_cast<int>(numDims)] = {3};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-3};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {3};
+ const std::string name("test");
+ auto inWS = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
+ numDims, signal, errorSquared, numBins, min, max, name);
+ inWS->setSignalAt(0, 1.0); // set right-most bin signal to one
+ CompactMD alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", inWS);
+ alg.setProperty("OutputWorkspace", "out");
+ TS_ASSERT_THROWS_NOTHING(alg.execute());
+ IMDHistoWorkspace_sptr outputWorkspace = alg.getProperty("OutputWorkspace");
+ TS_ASSERT(outputWorkspace);
+ TSM_ASSERT_EQUALS("Should have a signal of 1.0: ",
+ outputWorkspace->getSignalAt(0), 1);
+ TSM_ASSERT_EQUALS("Minimum should be cut to 1: ",
+ outputWorkspace->getDimension(0)->getMinimum(), -3.0);
+ TSM_ASSERT_EQUALS("Maximum should still be 3: ",
+ outputWorkspace->getDimension(0)->getMaximum(), -1.0);
+ TSM_ASSERT_EQUALS("Number of Bins should be 1 : ",
+ outputWorkspace->getDimension(0)->getNBins(), 1);
+ TSM_ASSERT_EQUALS("Bin width should be consistent: ",
+ outputWorkspace->getDimension(0)->getBinWidth(),
+ inWS->getDimension(0)->getBinWidth());
+ }
+ void test_compact_md_throws_when_loading_empty_workspace() {
+ using namespace Mantid::DataObjects;
+ const size_t numDims = 1;
+ const double signal = 0.0;
+ const double errorSquared = 1.3;
+ size_t numBins[static_cast<int>(numDims)] = {3};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-3};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {3};
+ const std::string name("test");
+ auto inWS = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
+ numDims, signal, errorSquared, numBins, min, max, name);
+ CompactMD alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", inWS);
+ alg.setProperty("OutputWorkspace", "out");
+ TS_ASSERT_THROWS(alg.execute(), std::runtime_error &);
+ }
+};
+
+//===================
+// Performance Tests
+//===================
+using namespace Mantid::DataObjects;
+class CompactMDTestPerformance : public CxxTest::TestSuite {
+
+private:
+ MDHistoWorkspace_sptr m_ws;
+
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static CompactMDTestPerformance *createSuite() {
+ return new CompactMDTestPerformance();
+ }
+ static void destroySuite(CompactMDTestPerformance *suite) { delete suite; }
+ void setUp() {
+ // Create a 4D workspace.
+ const size_t numDims = 4;
+ const double signal = 0.0;
+ const double errorSquared = 1.2;
+ size_t numBins[static_cast<int>(numDims)] = {10, 20, 10, 20};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-5, -10, -5, -10};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {5, 10, 5, 10};
+ const std::string name("test");
+ m_ws = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
+ numDims, signal, errorSquared, numBins, min, max, name);
+ // setting signals like this for variety
+ auto iter = m_ws->createIterator();
+ do {
+ auto index = iter->getLinearIndex();
+ if (index % 2 == 0) {
+ m_ws->setSignalAt(index, 1.0);
+ }
+ } while (iter->next());
+ }
+ void test_execute_4d() {
+ CompactMD alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", m_ws);
+ alg.setProperty("OutputWorkspace", "out");
+ alg.execute();
+ IMDHistoWorkspace_sptr outWS = alg.getProperty("OutputWorkspace");
+ TS_ASSERT(outWS);
+ }
+};
+
+#endif // !MANTID_MDALGORITHMS_COMPACTMDTEST_H_
diff --git a/Framework/Properties/Mantid.properties.template b/Framework/Properties/Mantid.properties.template
index 27e669d1d7ff7c2297397b120797a006c97aa4b6..9b160ba84bb9860cdd4b2237dc08e7576198f65b 100644
--- a/Framework/Properties/Mantid.properties.template
+++ b/Framework/Properties/Mantid.properties.template
@@ -16,7 +16,7 @@ default.facility = ISIS
default.instrument =
# Set of PyQt interfaces to add to the Interfaces menu, separated by a space. Interfaces are seperated from their respective categories by a "/".
-mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py SANS/ORNL_SANS.py Reflectometry/REFL_Reduction.py Reflectometry/REFL_SF_Calculator.py Reflectometry/REFM_Reduction.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_Powder_Diffraction_Reduction.py
+mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py SANS/ORNL_SANS.py Reflectometry/REFL_Reduction.py Reflectometry/REFL_SF_Calculator.py Reflectometry/REFM_Reduction.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_Powder_Diffraction_Reduction.py Diffraction/HFIR_4Circle_Reduction.py
mantidqt.python_interfaces_directory = @MANTID_ROOT@/scripts
diff --git a/Framework/PythonInterface/inc/MantidPythonInterface/api/WorkspacePropertyExporter.h b/Framework/PythonInterface/inc/MantidPythonInterface/api/WorkspacePropertyExporter.h
index f28cb82152330306db9044da42922b1e994284c0..aff1c6a9507ca2431c3838f5558181fc7933a5b9 100644
--- a/Framework/PythonInterface/inc/MantidPythonInterface/api/WorkspacePropertyExporter.h
+++ b/Framework/PythonInterface/inc/MantidPythonInterface/api/WorkspacePropertyExporter.h
@@ -134,10 +134,10 @@ template <typename WorkspaceType> struct WorkspacePropertyExporter {
API::PropertyMode::Type, API::LockMode::Type>(
args("name", "defaultValue", "direction", "optional", "locking")))
// These variants require the validator object to be cloned
- .def("__init__",
- make_constructor(
- &createPropertyWithValidator, default_call_policies(),
- args("name", "defaultValue", "direction", "validator")))
+ .def("__init__", make_constructor(&createPropertyWithValidator,
+ default_call_policies(),
+ (arg("name"), arg("defaultValue"),
+ arg("direction"), arg("validator"))))
.def("__init__",
make_constructor(&createPropertyWithOptionalFlag,
default_call_policies(),
@@ -148,7 +148,7 @@ template <typename WorkspaceType> struct WorkspacePropertyExporter {
default_call_policies(),
args("name", "defaultValue", "direction",
"optional", "locking", "validator")))
- .def("isOptional", &TypedWorkspaceProperty::isOptional,
+ .def("isOptional", &TypedWorkspaceProperty::isOptional, arg("self"),
"Returns true if the property has been marked as optional")
.add_property("value", &value);
diff --git a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h
index 5de200f77772535379d80f49cc8303345a0d4aba..90679c67007c4a433a9654ac8c4b214633f45354 100644
--- a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h
+++ b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h
@@ -66,30 +66,37 @@ template <typename SvcType, typename SvcPtrType> struct DataServiceExporter {
auto classType =
PythonType(pythonClassName, no_init)
.def("add", &DataServiceExporter::addItem,
+ (arg("self"), arg("name"), arg("item")),
"Adds the given object to the service with the given name. If "
"the name/object exists it will raise an error.")
.def("addOrReplace", &DataServiceExporter::addOrReplaceItem,
+ (arg("self"), arg("name"), arg("item")),
"Adds the given object to the service with the given name. "
"The the name exists the object is replaced.")
- .def("doesExist", &SvcType::doesExist,
+ .def("doesExist", &SvcType::doesExist, (arg("self"), arg("name")),
"Returns True if the object is found in the service.")
.def("retrieve", &DataServiceExporter::retrieveOrKeyError,
+ (arg("self"), arg("name")),
"Retrieve the named object. Raises an exception if the name "
"does not exist")
- .def("remove", &SvcType::remove, "Remove a named object")
- .def("clear", &SvcType::clear,
+ .def("remove", &SvcType::remove, (arg("self"), arg("name")),
+ "Remove a named object")
+ .def("clear", &SvcType::clear, arg("self"),
"Removes all objects managed by the service.")
- .def("size", &SvcType::size,
+ .def("size", &SvcType::size, arg("self"),
"Returns the number of objects within the service")
.def("getObjectNames", &DataServiceExporter::getObjectNamesAsList,
+ arg("self"),
"Return the list of names currently known to the ADS")
// Make it act like a dictionary
- .def("__len__", &SvcType::size)
- .def("__getitem__", &DataServiceExporter::retrieveOrKeyError)
- .def("__setitem__", &DataServiceExporter::addOrReplaceItem)
- .def("__contains__", &SvcType::doesExist)
- .def("__delitem__", &SvcType::remove);
+ .def("__len__", &SvcType::size, arg("self"))
+ .def("__getitem__", &DataServiceExporter::retrieveOrKeyError,
+ (arg("self"), arg("name")))
+ .def("__setitem__", &DataServiceExporter::addOrReplaceItem,
+ (arg("self"), arg("name"), arg("item")))
+ .def("__contains__", &SvcType::doesExist, arg("self"))
+ .def("__delitem__", &SvcType::remove, (arg("self"), arg("name")));
return classType;
}
diff --git a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/TypedValidatorExporter.h b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/TypedValidatorExporter.h
index e876486b65ce12d54ea8a1a57c5e651db2a7a722..aed38b70fe762cec3f5f3df0fa9c7fc1038125f5 100644
--- a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/TypedValidatorExporter.h
+++ b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/TypedValidatorExporter.h
@@ -39,7 +39,7 @@ template <typename Type> struct TypedValidatorExporter {
class_<TypedValidator<Type>, bases<IValidator>, boost::noncopyable>(
pythonClassName, no_init)
- .def("isValid", &IValidator::isValid<Type>,
+ .def("isValid", &IValidator::isValid<Type>, (arg("self"), arg("value")),
"Returns an empty string if the value is considered valid, "
"otherwise a string defining the error is returned.");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp
index 0aa43a5125cda02fbee15246c8a18a000b34103e..44b07a508d7484ec85fd0d0b15371ab40f1f85c4 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp
@@ -42,7 +42,11 @@ typedef void (*declarePropertyType3)(boost::python::object &self,
typedef void (*declarePropertyType4)(boost::python::object &self,
const std::string &,
const boost::python::object &, const int);
-
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Overload types
BOOST_PYTHON_FUNCTION_OVERLOADS(declarePropertyType1_Overload,
PythonAlgorithm::declarePyAlgProperty, 2, 3)
@@ -50,7 +54,9 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(declarePropertyType2_Overload,
PythonAlgorithm::declarePyAlgProperty, 3, 6)
BOOST_PYTHON_FUNCTION_OVERLOADS(declarePropertyType3_Overload,
PythonAlgorithm::declarePyAlgProperty, 4, 5)
-
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
/**
* Map a CancelException to a Python KeyboardInterupt
* @param exc A cancel exception to translate. Unused here as the message is
@@ -77,22 +83,19 @@ void export_leaf_classes() {
.def("fromString", &Algorithm::fromString,
"Initialize the algorithm from a string representation")
.staticmethod("fromString")
-
.def("createChildAlgorithm", &Algorithm::createChildAlgorithm,
- (arg("name"), arg("startProgress") = -1.0, arg("endProgress") = -1.0,
- arg("enableLogging") = true, arg("version") = -1),
+ (arg("self"), arg("name"), arg("startProgress") = -1.0,
+ arg("endProgress") = -1.0, arg("enableLogging") = true,
+ arg("version") = -1),
"Creates and intializes a named child algorithm. Output workspaces "
"are given a dummy name.")
-
.def("declareProperty",
(declarePropertyType1)&PythonAlgorithm::declarePyAlgProperty,
declarePropertyType1_Overload(
(arg("self"), arg("prop"), arg("doc") = "")))
-
.def("enableHistoryRecordingForChild",
- &Algorithm::enableHistoryRecordingForChild, (args("on")),
+ &Algorithm::enableHistoryRecordingForChild, (arg("self"), arg("on")),
"Turns history recording on or off for an algorithm.")
-
.def("declareProperty",
(declarePropertyType2)&PythonAlgorithm::declarePyAlgProperty,
declarePropertyType2_Overload(
@@ -102,7 +105,6 @@ void export_leaf_classes() {
"Declares a named property where the type is taken from "
"the type of the defaultValue and mapped to an appropriate C++ "
"type"))
-
.def("declareProperty",
(declarePropertyType3)&PythonAlgorithm::declarePyAlgProperty,
declarePropertyType3_Overload(
@@ -111,23 +113,22 @@ void export_leaf_classes() {
"Declares a named property where the type is taken from the "
"type "
"of the defaultValue and mapped to an appropriate C++ type"))
-
.def("declareProperty",
(declarePropertyType4)&PythonAlgorithm::declarePyAlgProperty,
(arg("self"), arg("name"), arg("defaultValue"),
arg("direction") = Direction::Input),
"Declares a named property where the type is taken from the type "
"of the defaultValue and mapped to an appropriate C++ type")
-
- .def("getLogger", &PythonAlgorithm::getLogger,
+ .def("getLogger", &PythonAlgorithm::getLogger, arg("self"),
return_value_policy<reference_existing_object>(),
"Returns a reference to this algorithm's logger")
- .def("log", &PythonAlgorithm::getLogger,
+ .def("log", &PythonAlgorithm::getLogger, arg("self"),
return_value_policy<reference_existing_object>(),
"Returns a reference to this algorithm's logger") // Traditional name
// deprecated methods
.def("setWikiSummary", &PythonAlgorithm::setWikiSummary,
+ (arg("self"), arg("summary")),
"(Deprecated.) Set summary for the help.");
// Prior to version 3.2 there was a separate C++ PythonAlgorithm class that
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp
index 48b3811552796c151162c47efb7a013fbd5415aa..16596444d5052301e09371c9ef001fdf29eb5665 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp
@@ -99,8 +99,15 @@ void subscribe(AlgorithmFactoryImpl &self, const boost::python::object &obj) {
// from the FileLoaderRegistry
FileLoaderRegistry::Instance().unsubscribe(descr.first, descr.second);
}
-
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(existsOverloader, exists, 1, 2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
///@endcond
}
@@ -118,12 +125,15 @@ void export_AlgorithmFactory() {
"an option to specify the version"))
.def("getRegisteredAlgorithms", &getRegisteredAlgorithms,
+ (arg("self"), arg("include_hidden")),
"Returns a Python dictionary of currently registered algorithms")
.def("highestVersion", &AlgorithmFactoryImpl::highestVersion,
+ (arg("self"), arg("algorithm_name")),
"Returns the highest version of the named algorithm. Throws "
"ValueError if no algorithm can be found")
- .def("subscribe", &subscribe, "Register a Python class derived from "
- "PythonAlgorithm into the factory")
+ .def("subscribe", &subscribe, (arg("self"), arg("object")),
+ "Register a Python class derived from "
+ "PythonAlgorithm into the factory")
.def("Instance", &AlgorithmFactory::Instance,
return_value_policy<reference_existing_object>(),
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp
index 8c886db7e8e024996dfda59da964188d8b61eb96..05a5f7045434a46b2bbd1ba14e0f7e9a2b35ec6a 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp
@@ -58,40 +58,42 @@ void export_AlgorithmHistory() {
register_ptr_to_python<Mantid::API::AlgorithmHistory_sptr>();
class_<AlgorithmHistory>("AlgorithmHistory", no_init)
- .def("name", &AlgorithmHistory::name,
+ .def("name", &AlgorithmHistory::name, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns the name of the algorithm.")
- .def("version", &AlgorithmHistory::version,
+ .def("version", &AlgorithmHistory::version, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns the version of the algorithm.")
.def("executionDuration", &AlgorithmHistory::executionDuration,
- "Returns the execution duration of the algorithm.")
+ arg("self"), "Returns the execution duration of the algorithm.")
- .def("executionDate", &AlgorithmHistory::executionDate,
+ .def("executionDate", &AlgorithmHistory::executionDate, arg("self"),
"Returns the execution date of the algorithm.")
- .def("execCount", &AlgorithmHistory::execCount,
+ .def("execCount", &AlgorithmHistory::execCount, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns the execution number of the algorithm.")
- .def("childHistorySize", &AlgorithmHistory::childHistorySize,
+ .def("childHistorySize", &AlgorithmHistory::childHistorySize, arg("self"),
"Returns the number of the child algorithms.")
.def("getChildAlgorithmHistory",
- &AlgorithmHistory::getChildAlgorithmHistory, arg("index"),
+ &AlgorithmHistory::getChildAlgorithmHistory,
+ (arg("self"), arg("index")),
"Returns the child algorithm at the given index in the history")
- .def("getChildHistories", &getChildrenAsList, "Returns a list of child "
- "algorithm histories for "
- "this algorithm history.")
+ .def("getChildHistories", &getChildrenAsList, arg("self"),
+ "Returns a list of child "
+ "algorithm histories for "
+ "this algorithm history.")
- .def("getProperties", &getPropertiesAsList,
+ .def("getProperties", &getPropertiesAsList, arg("self"),
"Returns properties for this algorithm history.")
.def("getChildAlgorithm", &AlgorithmHistory::getChildAlgorithm,
- arg("index"),
+ (arg("self"), arg("index")),
"Returns the algorithm at the given index in the history")
// ----------------- Operators --------------------------------------
.def(self_ns::str(self));
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp
index f827fd3728ba1ebccc8943358a1da9c8f7a28563..283b71e128e716988c2c52cc63c09f788932503f 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp
@@ -57,12 +57,20 @@ boost::python::list runningInstancesOf(AlgorithmManagerImpl &self,
///@cond
//------------------------------------------------------------------------------------------------------
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
/// Define overload generators
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(create_overloads,
AlgorithmManagerImpl::create, 1, 2)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(createUnmanaged_overloads,
AlgorithmManagerImpl::createUnmanaged, 1,
2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
///@endcond
}
@@ -78,22 +86,25 @@ void export_AlgorithmManager() {
.def("createUnmanaged", &AlgorithmManagerImpl::createUnmanaged,
createUnmanaged_overloads((arg("name"), arg("version")),
"Creates an unmanaged algorithm."))
- .def("size", &AlgorithmManagerImpl::size,
+ .def("size", &AlgorithmManagerImpl::size, arg("self"),
"Returns the number of managed algorithms")
.def("setMaxAlgorithms", &AlgorithmManagerImpl::setMaxAlgorithms,
+ (arg("self"), arg("n")),
"Set the maximum number of allowed managed algorithms")
- .def("getAlgorithm", &getAlgorithm,
+ .def("getAlgorithm", &getAlgorithm, (arg("self"), arg("id_holder")),
"Return the algorithm instance identified by the given id.")
- .def("removeById", &removeById,
+ .def("removeById", &removeById, (arg("self"), arg("id_holder")),
"Remove an algorithm from the managed list")
.def("newestInstanceOf", &AlgorithmManagerImpl::newestInstanceOf,
+ (arg("self"), arg("algorithm_name")),
"Returns the newest created instance of the named algorithm")
.def("runningInstancesOf", &runningInstancesOf,
+ (arg("self"), arg("algorithm_name")),
"Returns a list of managed algorithm instances that are "
"currently executing")
- .def("clear", &AlgorithmManagerImpl::clear,
+ .def("clear", &AlgorithmManagerImpl::clear, arg("self"),
"Clears the current list of managed algorithms")
- .def("cancelAll", &AlgorithmManagerImpl::cancelAll,
+ .def("cancelAll", &AlgorithmManagerImpl::cancelAll, arg("self"),
"Requests that all currently running algorithms be cancelled");
// Instance method
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp
index 0df0e6417b49f3a387dacbd0df445430981119e2..664da1fb0da97aea7d9a3bfca91669d1b2683fa9 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp
@@ -25,9 +25,19 @@ namespace {
namespace bpl = boost::python;
//------------------------------- Overload macros ---------------------------
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
+
// Overloads for operator() function which has 1 optional argument
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(Axis_getValue, Axis::getValue, 1, 2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
+
/**
* Extract the axis values as a sequence. A numpy array is used if the
* data is numerical or a simple python list is used if the data is a string
@@ -73,33 +83,41 @@ void export_Axis() {
// Class
class_<Axis, boost::noncopyable>("MantidAxis", no_init)
- .def("length", &Axis::length, "Returns the length of the axis")
+ .def("length", &Axis::length, arg("self"),
+ "Returns the length of the axis")
.def("title", (const std::string &(Axis::*)() const) & Axis::title,
- return_value_policy<copy_const_reference>(), "Get the axis title")
- .def("isSpectra", &Axis::isSpectra,
+ arg("self"), return_value_policy<copy_const_reference>(),
+ "Get the axis title")
+ .def("isSpectra", &Axis::isSpectra, arg("self"),
"Returns true if this is a SpectraAxis")
- .def("isNumeric", &Axis::isNumeric,
+ .def("isNumeric", &Axis::isNumeric, arg("self"),
"Returns true if this is a NumericAxis")
- .def("isText", &Axis::isText, "Returns true if this is a TextAxis")
- .def("label", &Axis::label, "Return the axis label")
+ .def("isText", &Axis::isText, arg("self"),
+ "Returns true if this is a TextAxis")
+ .def("label", &Axis::label, (arg("self"), arg("index")),
+ "Return the axis label")
.def("getUnit", (const Unit_sptr &(Axis::*)() const) & Axis::unit,
- return_value_policy<copy_const_reference>(),
+ arg("self"), return_value_policy<copy_const_reference>(),
"Returns the unit object for the axis")
.def("getValue", &Axis::getValue,
- Axis_getValue(args("index", "vertical_index"),
+ Axis_getValue((arg("self"), arg("index"), arg("vertical_index")),
"Returns the value at the given point on the Axis. "
"The vertical axis index [default=0]"))
- .def("extractValues", &extractAxisValues,
+ .def("extractValues", &extractAxisValues, arg("self"),
"Return a numpy array of the axis values")
- .def("setUnit", &Axis::setUnit,
+ .def("setUnit", &Axis::setUnit, (arg("self"), arg("unit_name")),
return_value_policy<copy_const_reference>(),
"Set the unit for this axis by name.")
- .def("setValue", &Axis::setValue, "Set a value at the given index")
- .def("getMin", &Axis::getMin, "Get min value specified on the axis")
- .def("getMax", &Axis::getMax, "Get max value specified on the axis")
+ .def("setValue", &Axis::setValue,
+ (arg("self"), arg("index"), arg("value")),
+ "Set a value at the given index")
+ .def("getMin", &Axis::getMin, arg("self"),
+ "Get min value specified on the axis")
+ .def("getMax", &Axis::getMax, arg("self"),
+ "Get max value specified on the axis")
//------------------------------------ Special methods
//------------------------------------
- .def("__len__", &Axis::length);
+ .def("__len__", &Axis::length, arg("self"));
}
// --------------------------------------------------------------------------------------------
@@ -118,7 +136,8 @@ void export_NumericAxis() {
/// Exported so that Boost.Python can give back a NumericAxis class when an
/// Axis* is returned
class_<NumericAxis, bases<Axis>, boost::noncopyable>("NumericAxis", no_init)
- .def("create", &createNumericAxis, return_internal_reference<>(),
+ .def("create", &createNumericAxis, arg("length"),
+ return_internal_reference<>(),
"Creates a new NumericAxis of a specified length")
.staticmethod("create");
}
@@ -141,7 +160,8 @@ void export_BinEdgeAxis() {
/// Axis* is returned
class_<BinEdgeAxis, bases<NumericAxis>, boost::noncopyable>("BinEdgeAxis",
no_init)
- .def("create", &createBinEdgeAxis, return_internal_reference<>(),
+ .def("create", &createBinEdgeAxis, arg("length"),
+ return_internal_reference<>(),
"Creates a new BinEdgeAxis of a specified length")
.staticmethod("create");
}
@@ -159,9 +179,13 @@ Axis *createTextAxis(int length) { return new Mantid::API::TextAxis(length); }
void export_TextAxis() {
class_<TextAxis, bases<Axis>, boost::noncopyable>("TextAxis", no_init)
- .def("setLabel", &TextAxis::setLabel, "Set the label at the given entry")
- .def("label", &TextAxis::label, "Return the label at the given position")
- .def("create", &createTextAxis, return_internal_reference<>(),
+ .def("setLabel", &TextAxis::setLabel,
+ (arg("self"), arg("index"), arg("label")),
+ "Set the label at the given entry")
+ .def("label", &TextAxis::label, (arg("self"), arg("index")),
+ "Return the label at the given position")
+ .def("create", &createTextAxis, arg("length"),
+ return_internal_reference<>(),
"Creates a new TextAxis of a specified length")
.staticmethod("create");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/BoxController.cpp b/Framework/PythonInterface/mantid/api/src/Exports/BoxController.cpp
index 7caf592a3ea586aad1dc6544bb2b80c7024c543b..af6debd38bd7864bcda9671f74e9e7979deeeed6 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/BoxController.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/BoxController.cpp
@@ -11,24 +11,28 @@ void export_BoxController() {
register_ptr_to_python<boost::shared_ptr<BoxController>>();
class_<BoxController, boost::noncopyable>("BoxController", no_init)
- .def("getNDims", &BoxController::getNDims, "Get # of dimensions")
- .def("getSplitThreshold", &BoxController::getSplitThreshold,
+ .def("getNDims", &BoxController::getNDims, arg("self"),
+ "Get # of dimensions")
+ .def("getSplitThreshold", &BoxController::getSplitThreshold, arg("self"),
"Return the splitting threshold, in # of events")
.def("getSplitInto", &BoxController::getSplitInto,
+ (arg("self"), arg("dim")),
"Return into how many to split along a dimension")
- .def("getMaxDepth", &BoxController::getMaxDepth,
+ .def("getMaxDepth", &BoxController::getMaxDepth, arg("self"),
"Return the max recursion depth allowed for grid box splitting.")
.def("getTotalNumMDBoxes", &BoxController::getTotalNumMDBoxes,
+ arg("self"),
"Return the total number of MD Boxes, irrespective of depth")
.def("getTotalNumMDGridBoxes", &BoxController::getTotalNumMDGridBoxes,
+ arg("self"),
"Return the total number of MDGridBox'es, irrespective of depth")
- .def("getAverageDepth", &BoxController::getAverageDepth,
+ .def("getAverageDepth", &BoxController::getAverageDepth, arg("self"),
"Return the average recursion depth of gridding.")
- .def("isFileBacked", &BoxController::isFileBacked,
+ .def("isFileBacked", &BoxController::isFileBacked, arg("self"),
"Return True if the MDEventWorkspace is backed by a file ")
- .def("getFilename", &BoxController::getFilename,
+ .def("getFilename", &BoxController::getFilename, arg("self"),
"Return the full path to the file open as the file-based back or "
"empty string if no file back-end is initiated")
- .def("useWriteBuffer", &BoxController::useWriteBuffer,
+ .def("useWriteBuffer", &BoxController::useWriteBuffer, arg("self"),
"Return true if the MRU should be used");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/DataProcessorAlgorithm.cpp b/Framework/PythonInterface/mantid/api/src/Exports/DataProcessorAlgorithm.cpp
index 1dacf9c7bc503e3455d541b358f1beb3dac72b61..00c8a38090785a1306a40883c221b28f3dffbcd5 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/DataProcessorAlgorithm.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/DataProcessorAlgorithm.cpp
@@ -25,61 +25,72 @@ void export_DataProcessorAlgorithm() {
"DataProcessorAlgorithm", "Base class workflow-type algorithms")
.def("setLoadAlg", &DataProcessorAdapter::setLoadAlgProxy,
+ (arg("self"), arg("alg")),
"Set the name of the algorithm called using the load() method "
"[Default=Load]")
.def("setLoadAlgFileProp", &DataProcessorAdapter::setLoadAlgFilePropProxy,
+ (arg("self"), arg("file_prop_name")),
"Set the name of the file property for the load algorithm when "
"using "
"the load() method [Default=Filename]")
.def("setAccumAlg", &DataProcessorAdapter::setAccumAlgProxy,
+ (arg("self"), arg("alg")),
"Set the name of the algorithm called to accumulate a chunk of "
"processed data [Default=Plus]")
.def("determineChunk", &DataProcessorAdapter::determineChunkProxy,
+ (arg("self"), arg("file_name")),
"Return a TableWorkspace containing the information on how to split "
"the "
"input file when processing in chunks")
.def("loadChunk", &DataProcessorAdapter::loadChunkProxy,
- "Load a chunk of data")
+ (arg("self"), arg("row_index")), "Load a chunk of data")
.def("load", (loadOverload1)&DataProcessorAdapter::loadProxy,
+ (arg("self"), arg("input_data")),
"Loads the given file or workspace data and returns the workspace. "
"The output is not stored in the AnalysisDataService.")
.def("load", (loadOverload2)&DataProcessorAdapter::loadProxy,
+ (arg("self"), arg("input_data"), arg("load_quite")),
"Loads the given file or workspace data and returns the workspace. "
"If loadQuiet=True then output is not stored in the "
"AnalysisDataService.")
.def("splitInput", &DataProcessorAdapter::splitInputProxy,
- return_value_policy<VectorToNumpy>())
+ (arg("self"), arg("input")), return_value_policy<VectorToNumpy>())
- .def("forwardProperties", &DataProcessorAdapter::forwardPropertiesProxy)
+ .def("forwardProperties", &DataProcessorAdapter::forwardPropertiesProxy,
+ arg("self"))
.def("getProcessProperties",
&DataProcessorAdapter::getProcessPropertiesProxy,
+ (arg("self"), arg("property_manager")),
"Returns the named property manager from the service or creates "
"a new one if it does not exist")
.def("assemble", &DataProcessorAdapter::assembleProxy,
+ (arg("self"), arg("partial_wsname"), arg("output_wsname")),
"If an MPI build, assemble the partial workspaces from all MPI "
"processes. "
"Otherwise, simply returns the input workspace")
.def("saveNexus", &DataProcessorAdapter::saveNexusProxy,
+ (arg("self"), arg("output_wsname"), arg("output_filename")),
"Save a workspace as a nexus file. If this is an MPI build then "
"saving only "
"happens for the main thread.")
.def("isMainThread", &DataProcessorAdapter::isMainThreadProxy,
+ arg("self"),
"Returns true if this algorithm is the main thread for an MPI "
"build. For "
"non-MPI build it always returns true")
- .def("getNThreads", &DataProcessorAdapter::getNThreadsProxy,
+ .def("getNThreads", &DataProcessorAdapter::getNThreadsProxy, arg("self"),
"Returns the number of running MPI processes in an MPI build or 1 "
"for "
"a non-MPI build");
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp
index 758c1c8e2a933bc2f15a62470d37281966dac503..926a6d0b31e49e4e9970553c29118e819f30f7fd 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp
@@ -10,9 +10,17 @@ using Mantid::API::ExperimentInfo;
using Mantid::PythonInterface::Policies::RemoveConstSharedPtr;
using namespace boost::python;
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
/// Overload generator for getInstrumentFilename
BOOST_PYTHON_FUNCTION_OVERLOADS(getInstrumentFilename_Overload,
ExperimentInfo::getInstrumentFilename, 1, 2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
void export_ExperimentInfo() {
register_ptr_to_python<boost::shared_ptr<ExperimentInfo>>();
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp b/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp
index f762919cdf1a63339a14da24330e4208426b954c..6d216cc065028263cc2edb49956b08f50b7456bc 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp
@@ -8,18 +8,26 @@ using Mantid::API::FileFinderImpl;
using namespace boost::python;
namespace {
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(getFullPathOverloader, getFullPath, 1, 2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
}
void export_FileFinder() {
class_<FileFinderImpl, boost::noncopyable>("FileFinderImpl", no_init)
.def("getFullPath", &FileFinderImpl::getFullPath,
getFullPathOverloader(
- (arg("path"), arg("ignoreDirs") = false),
+ (arg("self"), arg("path"), arg("ignoreDirs") = false),
"Return a full path to the given file if it can be found within "
"datasearch.directories paths. Directories can be ignored with "
"ignoreDirs=True. An empty string is returned otherwise."))
- .def("findRuns", &FileFinderImpl::findRuns,
+ .def("findRuns", &FileFinderImpl::findRuns, (arg("self"), arg("hintstr")),
"Find a list of files file given a hint. "
"The hint can be a comma separated list of run numbers and can also "
"include ranges of runs, e.g. 123-135 or equivalently 123-35"
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/FileLoaderRegistry.cpp b/Framework/PythonInterface/mantid/api/src/Exports/FileLoaderRegistry.cpp
index 5935cb7aae9932ac57f2f9c6f8ce18203e867f2d..baa9c3e8a188627728b20dfa745d7dd2cdfbaee7 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/FileLoaderRegistry.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/FileLoaderRegistry.cpp
@@ -10,9 +10,10 @@ void export_FileLoaderRegistry() {
class_<FileLoaderRegistryImpl, boost::noncopyable>("FileLoaderRegistryImpl",
no_init)
.def("canLoad", &FileLoaderRegistryImpl::canLoad,
+ (arg("self"), arg("algorithm_name"), arg("file_name")),
"Perform a check that that the given algorithm can load the file")
.def("Instance", &FileLoaderRegistry::Instance,
return_value_policy<reference_existing_object>(),
"Returns a reference to the FileLoaderRegistry singleton instance")
.staticmethod("Instance");
-}
\ No newline at end of file
+}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/FrameworkManager.cpp b/Framework/PythonInterface/mantid/api/src/Exports/FrameworkManager.cpp
index 1e31d32096f1b312b05f7f5cfff115ab486ccf85..d6df442a862bd0060019dd70b7ef395c26ec8a73 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/FrameworkManager.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/FrameworkManager.cpp
@@ -12,31 +12,34 @@ void export_FrameworkManager() {
class_<FrameworkManagerImpl, boost::noncopyable>("FrameworkManagerImpl",
no_init)
.def("setNumOMPThreadsToConfigValue",
- &FrameworkManagerImpl::setNumOMPThreadsToConfigValue,
+ &FrameworkManagerImpl::setNumOMPThreadsToConfigValue, arg("self"),
"Sets the number of OpenMP threads to the value specified in the "
"config file")
.def("setNumOMPThreads", &FrameworkManagerImpl::setNumOMPThreads,
+ (arg("self"), arg("nthread")),
"Set the number of OpenMP threads to the given value")
.def("getNumOMPThreads", &FrameworkManagerImpl::getNumOMPThreads,
+ arg("self"),
"Returns the number of OpenMP threads that will be used.")
- .def("clear", &FrameworkManagerImpl::clear,
+ .def("clear", &FrameworkManagerImpl::clear, arg("self"),
"Clear all memory held by Mantid")
.def("clearAlgorithms", &FrameworkManagerImpl::clearAlgorithms,
+ arg("self"),
"Clear memory held by algorithms (does not include workspaces)")
- .def("clearData", &FrameworkManagerImpl::clearData,
+ .def("clearData", &FrameworkManagerImpl::clearData, arg("self"),
"Clear memory held by the data service (essentially all workspaces, "
"including hidden)")
.def("clearInstruments", &FrameworkManagerImpl::clearInstruments,
- "Clear memory held by the cached instruments")
+ arg("self"), "Clear memory held by the cached instruments")
.def("clearPropertyManagers",
- &FrameworkManagerImpl::clearPropertyManagers,
+ &FrameworkManagerImpl::clearPropertyManagers, arg("self"),
"Clear memory held by the PropertyManagerDataService")
.def("Instance", &FrameworkManager::Instance,
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/FunctionFactory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/FunctionFactory.cpp
index 2d94e8f7aea8f4484f240f8b13488aa68e7a6d44..7735fc15decf7418218e07c3b204f3235ef4774c 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/FunctionFactory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/FunctionFactory.cpp
@@ -89,15 +89,15 @@ void export_FunctionFactory() {
class_<FunctionFactoryImpl, boost::noncopyable>("FunctionFactoryImpl",
no_init)
- .def("getFunctionNames", &getFunctionNames,
+ .def("getFunctionNames", &getFunctionNames, arg("self"),
"Returns a list of the currently available functions")
.def("createFunction", &FunctionFactoryImpl::createFunction,
+ (arg("self"), arg("type")),
"Return a pointer to the requested function")
- .def("subscribe", &subscribe,
+ .def("subscribe", &subscribe, (arg("self"), arg("object")),
"Register a Python class derived from IFunction into the factory")
.def("unsubscribe", &FunctionFactoryImpl::unsubscribe,
- "Remove a type from the factory")
-
+ (arg("self"), arg("class_name")), "Remove a type from the factory")
.def("Instance", &FunctionFactory::Instance,
return_value_policy<reference_existing_object>(),
"Returns a reference to the FunctionFactory singleton")
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
index e2be117bf9a2e743ff79c79dfc3e2a0e5843cf51..009ca30fb110ff5ede255104d493cfe8e16fcbdf 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
@@ -302,89 +302,102 @@ void export_ialgorithm() {
class_<IAlgorithm, bases<IPropertyManager>, boost::noncopyable>(
"IAlgorithm", "Interface for all algorithms", no_init)
- .def("name", &IAlgorithm::name, "Returns the name of the algorithm")
- .def("alias", &IAlgorithm::alias, "Return the aliases for the algorithm")
- .def("version", &IAlgorithm::version,
+ .def("name", &IAlgorithm::name, arg("self"),
+ "Returns the name of the algorithm")
+ .def("alias", &IAlgorithm::alias, arg("self"),
+ "Return the aliases for the algorithm")
+ .def("version", &IAlgorithm::version, arg("self"),
"Returns the version number of the algorithm")
- .def("cancel", &IAlgorithm::cancel,
+ .def("cancel", &IAlgorithm::cancel, arg("self"),
"Request that the algorithm stop running")
- .def("category", &IAlgorithm::category,
+ .def("category", &IAlgorithm::category, arg("self"),
"Returns the category containing the algorithm")
- .def("categories", &IAlgorithm::categories,
+ .def("categories", &IAlgorithm::categories, arg("self"),
"Returns the list of categories this algorithm belongs to")
- .def("summary", &IAlgorithm::summary,
+ .def("summary", &IAlgorithm::summary, arg("self"),
"Returns a summary message describing the algorithm")
- .def("workspaceMethodName", &IAlgorithm::workspaceMethodName,
+ .def("workspaceMethodName", &IAlgorithm::workspaceMethodName, arg("self"),
"Returns a name that will be used when attached as a workspace "
"method. Empty string indicates do not attach")
- .def("workspaceMethodOn", &IAlgorithm::workspaceMethodOn,
+ .def("workspaceMethodOn", &IAlgorithm::workspaceMethodOn, arg("self"),
return_value_policy<VectorToNumpy>(), // creates a list for strings
"Returns a set of class names that will have the method attached. "
"Empty list indicates all types")
.def("workspaceMethodInputProperty",
- &IAlgorithm::workspaceMethodInputProperty,
+ &IAlgorithm::workspaceMethodInputProperty, arg("self"),
"Returns the name of the input workspace property used by the "
"calling object")
- .def("getAlgorithmID", &getAlgorithmID,
+ .def("getAlgorithmID", &getAlgorithmID, arg("self"),
"Returns a unique identifier for this algorithm object")
- .def("docString", &createDocString,
+ .def("docString", &createDocString, arg("self"),
"Returns a doc string for the algorithm")
.def("mandatoryProperties", &getInputPropertiesWithMandatoryFirst,
+ arg("self"),
"Returns a list of input and in/out property names that is ordered "
"such that the mandatory properties are first followed by the "
"optional ones.")
- .def("orderedProperties", &getAlgorithmPropertiesOrdered,
+ .def("orderedProperties", &getAlgorithmPropertiesOrdered, arg("self"),
"Return a list of input, in/out and output properties "
"such that the mandatory properties are first followed by the "
"optional ones.")
- .def("outputProperties", &getOutputProperties,
+ .def("outputProperties", &getOutputProperties, arg("self"),
"Returns a list of the output properties on the algorithm")
- .def("isInitialized", &IAlgorithm::isInitialized,
+ .def("isInitialized", &IAlgorithm::isInitialized, arg("self"),
"Returns True if the algorithm is initialized, False otherwise")
- .def("isExecuted", &IAlgorithm::isExecuted,
+ .def("isExecuted", &IAlgorithm::isExecuted, arg("self"),
"Returns True if the algorithm has been executed successfully, "
"False otherwise")
- .def("isLogging", &IAlgorithm::isLogging, "Returns True if the "
- "algorithm's logger is turned "
- "on, False otherwise")
- .def("isRunning", &IAlgorithm::isRunning, "Returns True if the algorithm "
- "is considered to be running, "
- "False otherwise")
- .def("setChild", &IAlgorithm::setChild,
+ .def("isLogging", &IAlgorithm::isLogging, arg("self"),
+ "Returns True if the "
+ "algorithm's logger is turned "
+ "on, False otherwise")
+ .def("isRunning", &IAlgorithm::isRunning, arg("self"),
+ "Returns True if the algorithm "
+ "is considered to be running, "
+ "False otherwise")
+ .def("setChild", &IAlgorithm::setChild, (arg("self"), arg("is_child")),
"If true this algorithm is run as a child algorithm. There will be "
"no logging and nothing is stored in the Analysis Data Service")
.def("enableHistoryRecordingForChild",
&IAlgorithm::enableHistoryRecordingForChild,
+ (arg("self"), arg("on")),
"If true then history will be recorded regardless of the child "
"status")
.def("setAlgStartupLogging", &IAlgorithm::setAlgStartupLogging,
+ (arg("self"), arg("enabled")),
"If true then allow logging of start and end messages")
.def("getAlgStartupLogging", &IAlgorithm::getAlgStartupLogging,
- "Returns true if logging of start and end messages")
+ arg("self"), "Returns true if logging of start and end messages")
.def("setAlwaysStoreInADS", &IAlgorithm::setAlwaysStoreInADS,
+ (arg("self"), arg("do_store")),
"If true then even child algorithms will have their workspaces "
"stored in the ADS.")
- .def("isChild", &IAlgorithm::isChild,
+ .def("isChild", &IAlgorithm::isChild, arg("self"),
"Returns True if the algorithm has been marked to run as a child. "
"If True then Output workspaces "
"are NOT stored in the Analysis Data Service but must be retrieved "
"from the property.")
- .def("setLogging", &IAlgorithm::setLogging, "Toggle logging on/off.")
- .def("setRethrows", &IAlgorithm::setRethrows)
- .def("initialize", &IAlgorithm::initialize, "Initializes the algorithm")
- .def("validateInputs", &IAlgorithm::validateInputs,
+ .def("setLogging", &IAlgorithm::setLogging, (arg("self"), arg("value")),
+ "Toggle logging on/off.")
+ .def("setRethrows", &IAlgorithm::setRethrows,
+ (arg("self"), arg("rethrow")), "To query whether an algorithm "
+ "should rethrow exceptions when "
+ "executing.")
+ .def("initialize", &IAlgorithm::initialize, arg("self"),
+ "Initializes the algorithm")
+ .def("validateInputs", &IAlgorithm::validateInputs, arg("self"),
"Cross-check all inputs and return any errors as a dictionary")
- .def("execute", &executeProxy,
+ .def("execute", &executeProxy, arg("self"),
"Runs the algorithm and returns whether it has been successful")
// 'Private' static methods
- .def("_algorithmInThread", &_algorithmInThread)
+ .def("_algorithmInThread", &_algorithmInThread, arg("thread_id"))
.staticmethod("_algorithmInThread")
// Special methods
- .def("__str__", &IAlgorithm::toString)
+ .def("__str__", &IAlgorithm::toString, arg("self"))
// deprecated methods
- .def("getOptionalMessage", &getOptionalMessage,
+ .def("getOptionalMessage", &getOptionalMessage, arg("self"),
"Returns the optional user message attached to the algorithm")
- .def("getWikiSummary", &getWikiSummary,
+ .def("getWikiSummary", &getWikiSummary, arg("self"),
"Returns the summary found on the wiki page");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp
index 77761eb93936d24f8948d8cb9c6fdd1604d6f813..4805e9a712f33945ff66e444d5968e5cd0d0e139 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp
@@ -34,6 +34,11 @@ PyObject *getCategories(IFunction &self) {
// -- Set property overloads --
// setProperty(index,value,explicit)
typedef void (IFunction::*setParameterType1)(size_t, const double &value, bool);
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(setParameterType1_Overloads,
setParameter, 2, 3)
// setProperty(index,value,explicit)
@@ -41,7 +46,9 @@ typedef void (IFunction::*setParameterType2)(const std::string &,
const double &value, bool);
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(setParameterType2_Overloads,
setParameter, 2, 3)
-
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
///@endcond
}
@@ -51,82 +58,96 @@ void export_IFunction() {
class_<IFunction, IFunctionAdapter, boost::noncopyable>(
"IFunction", "Base class for all functions", no_init)
- .def("name", &IFunction::name, "Return the name of the function")
+ .def("name", &IFunction::name, arg("self"),
+ "Return the name of the function")
- .def("category", &IFunctionAdapter::category,
+ .def("category", &IFunctionAdapter::category, arg("self"),
"Return a semi-colon(;) separated string for the categories this "
"class should belong to. For sub-categories use a \\ separator")
- .def("initialize", &IFunction::initialize,
+ .def("initialize", &IFunction::initialize, arg("self"),
"Declares any parameters and attributes on the function")
- .def("getCategories", &getCategories,
+ .def("getCategories", &getCategories, arg("self"),
"Returns a list of the categories for an algorithm")
- .def("nAttributes", &IFunction::nAttributes,
+ .def("nAttributes", &IFunction::nAttributes, arg("self"),
"Return the number of attributes (non-fitting arguments)")
- .def("attributeNames", &IFunction::getAttributeNames,
+ .def("attributeNames", &IFunction::getAttributeNames, arg("self"),
"The names of all the attributes")
- .def("nParams", &IFunction::nParams, "Return the number of parameters")
+ .def("nParams", &IFunction::nParams, arg("self"),
+ "Return the number of parameters")
- .def("parameterName", &IFunction::parameterName,
+ .def("parameterName", &IFunction::parameterName, (arg("self"), arg("i")),
"Return the name of the ith parameter")
.def("paramDescription", &IFunction::parameterDescription,
- "Return a description of the ith parameter")
+ (arg("self"), arg("i")), "Return a description of the ith parameter")
.def("isExplicitlySet", &IFunction::isExplicitlySet,
+ (arg("self"), arg("i")),
"Return whether the ith parameter needs to be explicitely set")
.def("getParameterValue",
(double (IFunction::*)(size_t) const) & IFunction::getParameter,
- "Get the value of the ith parameter")
+ (arg("self"), arg("i")), "Get the value of the ith parameter")
.def("getParameterValue",
(double (IFunction::*)(const std::string &) const) &
IFunction::getParameter,
- "Get the value of the named parameter")
+ (arg("self"), arg("name")), "Get the value of the named parameter")
.def("setParameter", (setParameterType1)&IFunction::setParameter,
- setParameterType1_Overloads("Sets the value of the ith parameter"))
+ setParameterType1_Overloads(
+ (arg("self"), arg("i"), arg("value"), arg("explicitlySet")),
+ "Sets the value of the ith parameter"))
.def("setParameter", (setParameterType2)&IFunction::setParameter,
- setParameterType2_Overloads("Sets the value of the named parameter"))
+ setParameterType2_Overloads(
+ (arg("self"), arg("name"), arg("value"), arg("explicitlySet")),
+ "Sets the value of the named parameter"))
.def("declareAttribute", &IFunctionAdapter::declareAttribute,
+ (arg("self"), arg("name"), arg("default_value")),
"Declare an attribute with an initial value")
.def("getAttributeValue",
(PyObject * (IFunctionAdapter::*)(const std::string &)) &
IFunctionAdapter::getAttributeValue,
+ (arg("self"), arg("name")),
"Return the value of the named attribute")
.def("declareParameter", &IFunctionAdapter::declareFitParameter,
+ (arg("self"), arg("name"), arg("init_value"), arg("description")),
"Declare a fitting parameter settings its default value & "
"description")
.def("declareParameter", &IFunctionAdapter::declareFitParameterNoDescr,
+ (arg("self"), arg("name"), arg("init_value")),
"Declare a fitting parameter settings its default value")
.def("declareParameter", &IFunctionAdapter::declareFitParameterZeroInit,
+ (arg("self"), arg("name")),
"Declare a fitting parameter settings its default value to 0.0")
//-- Deprecated functions that have the wrong names --
- .def("categories", &getCategories,
+ .def("categories", &getCategories, arg("self"),
"Returns a list of the categories for an algorithm")
- .def("numParams", &IFunction::nParams, "Return the number of parameters")
- .def("getParamName", &IFunction::parameterName,
+ .def("numParams", &IFunction::nParams, arg("self"),
+ "Return the number of parameters")
+ .def("getParamName", &IFunction::parameterName, (arg("self"), arg("i")),
"Return the name of the ith parameter")
.def("getParamDescr", &IFunction::parameterDescription,
- "Return a description of the ith parameter")
+ (arg("self"), arg("i")), "Return a description of the ith parameter")
.def("getParamExplicit", &IFunction::isExplicitlySet,
+ (arg("self"), arg("i")),
"Return whether the ith parameter needs to be explicitely set")
.def("getParamValue",
(double (IFunction::*)(std::size_t) const) & IFunction::getParameter,
- "Get the value of the ith parameter")
+ (arg("self"), arg("i")), "Get the value of the ith parameter")
//-- Python special methods --
- .def("__repr__", &IFunction::asString,
+ .def("__repr__", &IFunction::asString, arg("self"),
"Return a string representation of the function");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IFunction1D.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IFunction1D.cpp
index b610b945ffb3ccb664e1fd82870631607349008c..a435fc7b192eadaad8060c02817d251d5bd2cf59 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IFunction1D.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IFunction1D.cpp
@@ -18,6 +18,7 @@ void export_IFunction1D() {
.def("function1D",
(object (IFunction1DAdapter::*)(const object &) const) &
IFunction1DAdapter::function1D,
+ (arg("self"), arg("xvals")),
"Calculate the values of the function for the given x values and "
"returns them");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IMDEventWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IMDEventWorkspace.cpp
index bd69cd0dab31b54c2ede7e5b609a0471b05bdde8..4bd404f62e4b60fe2af7038ce00b91a43326241e 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IMDEventWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IMDEventWorkspace.cpp
@@ -12,15 +12,15 @@ void export_IMDEventWorkspace() {
// IMDEventWorkspace class
class_<IMDEventWorkspace, bases<IMDWorkspace, MultipleExperimentInfos>,
boost::noncopyable>("IMDEventWorkspace", no_init)
- .def("getNPoints", &IMDEventWorkspace::getNPoints,
+ .def("getNPoints", &IMDEventWorkspace::getNPoints, arg("self"),
"Returns the total number of points (events) in this workspace")
- .def("getNumDims", &IMDEventWorkspace::getNumDims,
+ .def("getNumDims", &IMDEventWorkspace::getNumDims, arg("self"),
"Returns the number of dimensions in this workspace")
.def("getBoxController", (BoxController_sptr (IMDEventWorkspace::*)()) &
IMDEventWorkspace::getBoxController,
- "Returns the BoxController used in this workspace");
+ arg("self"), "Returns the BoxController used in this workspace");
RegisterWorkspacePtrToPython<IMDEventWorkspace>();
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IMDHistoWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IMDHistoWorkspace.cpp
index 3852f7080de7fc94c761795836bf827b22994e65..f64840efaf7bd9f7a3266ade3d528054fdb18aa4 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IMDHistoWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IMDHistoWorkspace.cpp
@@ -167,55 +167,65 @@ void export_IMDHistoWorkspace() {
// IMDHistoWorkspace class
class_<IMDHistoWorkspace, bases<IMDWorkspace, MultipleExperimentInfos>,
boost::noncopyable>("IMDHistoWorkspace", no_init)
- .def("getSignalArray", &getSignalArrayAsNumpyArray,
+ .def("getSignalArray", &getSignalArrayAsNumpyArray, arg("self"),
"Returns a read-only numpy array containing the signal values")
.def("getErrorSquaredArray", &getErrorSquaredArrayAsNumpyArray,
+ arg("self"),
"Returns a read-only numpy array containing the square of the error "
"values")
- .def("getNumEventsArray", &getNumEventsArrayAsNumpyArray,
+ .def("getNumEventsArray", &getNumEventsArrayAsNumpyArray, arg("self"),
"Returns a read-only numpy array containing the number of MD events "
"in each bin")
.def("signalAt", &IMDHistoWorkspace::signalAt,
+ (arg("self"), arg("index")),
return_value_policy<copy_non_const_reference>(),
"Return a reference to the signal at the linear index")
.def("errorSquaredAt", &IMDHistoWorkspace::errorSquaredAt,
+ (arg("self"), arg("index")),
return_value_policy<copy_non_const_reference>(),
"Return the squared-errors at the linear index")
.def("setSignalAt", &IMDHistoWorkspace::setSignalAt,
+ (arg("self"), arg("index"), arg("value")),
"Sets the signal at the specified index.")
.def("setErrorSquaredAt", &IMDHistoWorkspace::setErrorSquaredAt,
+ (arg("self"), arg("index"), arg("value")),
"Sets the squared-error at the specified index.")
.def("setSignalArray", &setSignalArray,
+ (arg("self"), arg("signalValues")),
"Sets the signal from a numpy array. The sizes must match the "
"current workspace sizes. A ValueError is thrown if not")
- .def("setErrorSquaredArray", &setErrorSquaredArray,
+ .def("setErrorSquaredArray", &setErrorSquaredArray, arg("self"),
"Sets the square of the errors from a numpy array. The sizes must "
"match the current workspace sizes. A ValueError is thrown if not")
.def("setTo", &IMDHistoWorkspace::setTo,
+ (arg("self"), arg("signal"), arg("error_squared"),
+ arg("num_events")),
"Sets all signals/errors in the workspace to the given values")
.def("getInverseVolume", &IMDHistoWorkspace::getInverseVolume,
- return_value_policy<return_by_value>(),
+ arg("self"), return_value_policy<return_by_value>(),
"Return the inverse of volume of EACH cell in the workspace.")
.def("getLinearIndex",
(size_t (IMDHistoWorkspace::*)(size_t, size_t) const) &
IMDHistoWorkspace::getLinearIndex,
+ (arg("self"), arg("index1"), arg("index2")),
return_value_policy<return_by_value>(),
"Get the 1D linear index from the 2D array")
.def("getLinearIndex",
(size_t (IMDHistoWorkspace::*)(size_t, size_t, size_t) const) &
IMDHistoWorkspace::getLinearIndex,
+ (arg("self"), arg("index1"), arg("index2"), arg("index3")),
return_value_policy<return_by_value>(),
"Get the 1D linear index from the 3D array")
@@ -223,10 +233,13 @@ void export_IMDHistoWorkspace() {
(size_t (IMDHistoWorkspace::*)(size_t, size_t, size_t, size_t)
const) &
IMDHistoWorkspace::getLinearIndex,
+ (arg("self"), arg("index1"), arg("index2"), arg("index3"),
+ arg("index4")),
return_value_policy<return_by_value>(),
"Get the 1D linear index from the 4D array")
.def("getCenter", &IMDHistoWorkspace::getCenter,
+ (arg("self"), arg("linear_index")),
return_value_policy<return_by_value>(),
"Return the position of the center of a bin at a given position");
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IMDWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IMDWorkspace.cpp
index 3c8921df6623a7b4dee6c9abeb6324acb7341798..989089801c34318f3e7087c81f2a3221bd553a33 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IMDWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IMDWorkspace.cpp
@@ -25,17 +25,17 @@ void export_IMDWorkspace() {
// EventWorkspace class
class_<IMDWorkspace, bases<Workspace, MDGeometry>, boost::noncopyable>(
"IMDWorkspace", no_init)
- .def("getNPoints", &IMDWorkspace::getNPoints, args("self"),
+ .def("getNPoints", &IMDWorkspace::getNPoints, arg("self"),
"Returns the total number of points within the workspace")
- .def("getNEvents", &IMDWorkspace::getNEvents, args("self"),
+ .def("getNEvents", &IMDWorkspace::getNEvents, arg("self"),
"Returns the total number of events, contributed to the workspace")
.def("getSpecialCoordinateSystem",
- &IMDWorkspace::getSpecialCoordinateSystem, args("self"),
+ &IMDWorkspace::getSpecialCoordinateSystem, arg("self"),
"Returns the special coordinate system of the workspace")
.def("displayNormalization", &IMDWorkspace::displayNormalization,
args("self"), "Returns the visual normalization of the workspace.")
.def("displayNormalizationHisto",
- &IMDWorkspace::displayNormalizationHisto, args("self"),
+ &IMDWorkspace::displayNormalizationHisto, arg("self"),
"For MDEventWorkspaces returns the visual normalization of dervied "
"MDHistoWorkspaces."
"For all others returns the same as displayNormalization.");
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IMaskWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IMaskWorkspace.cpp
index 66affb607c0e136f9da7bbfb99b7d421020880b1..7090972a851786d4d7cf28c5e48773cfe1146485 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IMaskWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IMaskWorkspace.cpp
@@ -28,12 +28,13 @@ bool isMaskedFromList(const IMaskWorkspace &self,
void export_IMaskWorkspace() {
class_<IMaskWorkspace, boost::noncopyable>("IMaskWorkspace", no_init)
- .def("getNumberMasked", &IMaskWorkspace::getNumberMasked,
+ .def("getNumberMasked", &IMaskWorkspace::getNumberMasked, arg("self"),
"Returns the number of masked pixels in the workspace")
.def("isMasked", (bool (IMaskWorkspace::*)(const Mantid::detid_t) const) &
IMaskWorkspace::isMasked,
+ (arg("self"), arg("detector_id")),
"Returns whether the given detector ID is masked")
- .def("isMasked", isMaskedFromList,
+ .def("isMasked", isMaskedFromList, (arg("self"), arg("detector_id_list")),
"Returns whether all of the given detector ID list are masked");
// register pointers
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IPeak.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IPeak.cpp
index 13ace3dced290717e05e3ff3888be2e1c5603115..f3e42c14c3f26423d58cb51961c44b632746c78a 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IPeak.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IPeak.cpp
@@ -36,95 +36,111 @@ void export_IPeak() {
register_ptr_to_python<IPeak *>();
class_<IPeak, boost::noncopyable>("IPeak", no_init)
- .def("getDetectorID", &IPeak::getDetectorID,
+ .def("getDetectorID", &IPeak::getDetectorID, arg("self"),
"Get the ID of the detector at the center of the peak")
- .def("setDetectorID", &IPeak::setDetectorID,
+ .def("setDetectorID", &IPeak::setDetectorID, (arg("self"), arg("det_id")),
"Set the detector ID and look up and cache values related to it.")
- .def("getRunNumber", &IPeak::getRunNumber,
+ .def("getRunNumber", &IPeak::getRunNumber, arg("self"),
"Return the run number this peak was measured at")
.def("setRunNumber", &IPeak::setRunNumber,
+ (arg("self"), arg("run_number")),
"Set the run number that measured this peak")
- .def("getMonitorCount", &IPeak::getMonitorCount,
+ .def("getMonitorCount", &IPeak::getMonitorCount, arg("self"),
"Get the monitor count set for this peak")
.def("setMonitorCount", &IPeak::setMonitorCount,
+ (arg("self"), arg("monitor_count")),
"Set the monitor count for this peak")
- .def("getH", &IPeak::getH, "Get the H index of the peak")
- .def("getK", &IPeak::getK, "Get the K index of the peak")
- .def("getL", &IPeak::getL, "Get the L index of the peak")
- .def("getHKL", &IPeak::getHKL, "Get HKL as a V3D object")
+ .def("getH", &IPeak::getH, arg("self"), "Get the H index of the peak")
+ .def("getK", &IPeak::getK, arg("self"), "Get the K index of the peak")
+ .def("getL", &IPeak::getL, arg("self"), "Get the L index of the peak")
+ .def("getHKL", &IPeak::getHKL, arg("self"), "Get HKL as a V3D object")
.def("setHKL", (void (IPeak::*)(double, double, double)) & IPeak::setHKL,
+ (arg("self"), arg("h"), arg("k"), arg("l")),
"Set the HKL values of this peak")
- .def("setH", &IPeak::setH, "Get the H index of the peak")
- .def("setK", &IPeak::setK, "Get the K index of the peak")
- .def("setL", &IPeak::setL, "Get the L index of the peak")
- .def("getQLabFrame", &IPeak::getQLabFrame,
+ .def("setH", &IPeak::setH, (arg("self"), arg("h")),
+ "Get the H index of the peak")
+ .def("setK", &IPeak::setK, (arg("self"), arg("k")),
+ "Get the K index of the peak")
+ .def("setL", &IPeak::setL, (arg("self"), arg("l")),
+ "Get the L index of the peak")
+ .def("getQLabFrame", &IPeak::getQLabFrame, arg("self"),
"Return the Q change (of the lattice, k_i - k_f) for this peak.\n"
"The Q is in the Lab frame: the goniometer rotation was NOT taken "
"out.\n"
"Note: There is no 2*pi factor used, so \\|Q| = 1/wavelength.")
- .def("findDetector", &IPeak::findDetector,
+ .def("findDetector", &IPeak::findDetector, arg("self"),
"Using the instrument set in the peak, perform ray tracing to find "
"the exact detector.")
- .def("getQSampleFrame", &IPeak::getQSampleFrame,
+ .def("getQSampleFrame", &IPeak::getQSampleFrame, arg("self"),
"Return the Q change (of the lattice, k_i - k_f) for this peak."
"The Q is in the Sample frame: the goniometer rotation WAS taken "
"out. ")
- .def("setQLabFrame", setQLabFrame1, "Set the peak using the peak's "
- "position in reciprocal space, in "
- "the lab frame.")
+ .def("setQLabFrame", setQLabFrame1, (arg("self"), arg("qlab_frame")),
+ "Set the peak using the peak's "
+ "position in reciprocal space, in "
+ "the lab frame.")
.def("setQLabFrame", setQLabFrame2,
+ (arg("self"), arg("qlab_frame"), arg("distance")),
"Set the peak using the peak's position in reciprocal space, in the "
"lab frame. Detector distance explicitly supplied.") // two argument
// overload
- .def("setQSampleFrame", setQSampleFrame1, "Set the peak using the peak's "
+ .def("setQSampleFrame", setQSampleFrame1,
+ (arg("self"), arg("qsample_frame")), "Set the peak using the peak's "
"position in reciprocal space, "
"in the sample frame.")
.def("setQSampleFrame", setQSampleFrame2,
+ (arg("self"), arg("qsample_frame"), arg("distance")),
"Set the peak using the peak's position in reciprocal space, in the "
"sample frame. Detector distance explicitly supplied.")
.def("setWavelength", &IPeak::setWavelength,
+ (arg("self"), arg("wave_length")),
"Set the incident wavelength of the neutron. Calculates the energy "
"from this assuming elastic scattering.")
- .def("getWavelength", &IPeak::getWavelength,
+ .def("getWavelength", &IPeak::getWavelength, arg("self"),
"Return the incident wavelength")
- .def("getScattering", &IPeak::getScattering,
+ .def("getScattering", &IPeak::getScattering, arg("self"),
"Calculate the scattering angle of the peak")
- .def("getDSpacing", &IPeak::getDSpacing,
+ .def("getDSpacing", &IPeak::getDSpacing, arg("self"),
"Calculate the d-spacing of the peak, in 1/Angstroms")
- .def("getTOF", &IPeak::getTOF, "Calculate the time of flight (in "
- "microseconds) of the neutrons for this "
- "peak")
- .def("getInitialEnergy", &IPeak::getInitialEnergy,
+ .def("getTOF", &IPeak::getTOF, arg("self"),
+ "Calculate the time of flight (in "
+ "microseconds) of the neutrons for this "
+ "peak")
+ .def("getInitialEnergy", &IPeak::getInitialEnergy, arg("self"),
"Get the initial (incident) neutron energy")
- .def("getFinalEnergy", &IPeak::getFinalEnergy,
+ .def("getFinalEnergy", &IPeak::getFinalEnergy, arg("self"),
"Get the final neutron energy")
.def("setInitialEnergy", &IPeak::setInitialEnergy,
+ (arg("self"), arg("initial_energy")),
"Set the initial (incident) neutron energy")
.def("setFinalEnergy", &IPeak::setFinalEnergy,
- "Set the final neutron energy")
- .def("getIntensity", &IPeak::getIntensity,
+ (arg("self"), arg("final_energy")), "Set the final neutron energy")
+ .def("getIntensity", &IPeak::getIntensity, arg("self"),
"Return the integrated peak intensity")
- .def("getSigmaIntensity", &IPeak::getSigmaIntensity,
+ .def("getSigmaIntensity", &IPeak::getSigmaIntensity, arg("self"),
"Return the error on the integrated peak intensity")
.def("setIntensity", &IPeak::setIntensity,
- "Set the integrated peak intensity")
+ (arg("self"), arg("intensity")), "Set the integrated peak intensity")
.def("setSigmaIntensity", &IPeak::setSigmaIntensity,
+ (arg("self"), arg("sigma_intensity")),
"Set the error on the integrated peak intensity")
- .def("getBinCount", &IPeak::getBinCount,
+ .def("getBinCount", &IPeak::getBinCount, arg("self"),
"Return the # of counts in the bin at its peak")
- .def("setBinCount", &IPeak::setBinCount,
+ .def("setBinCount", &IPeak::setBinCount, (arg("self"), arg("bin_count")),
"Set the # of counts in the bin at its peak")
- .def("getRow", &IPeak::getRow, "For RectangularDetectors only, returns "
- "the row (y) of the pixel of the "
- "detector.")
- .def("getCol", &IPeak::getCol, "For RectangularDetectors only, returns "
- "the column (x) of the pixel of the "
- "detector.")
- .def("getDetPos", &IPeak::getDetPos,
+ .def("getRow", &IPeak::getRow, arg("self"),
+ "For RectangularDetectors only, returns "
+ "the row (y) of the pixel of the "
+ "detector.")
+ .def("getCol", &IPeak::getCol, arg("self"),
+ "For RectangularDetectors only, returns "
+ "the column (x) of the pixel of the "
+ "detector.")
+ .def("getDetPos", &IPeak::getDetPos, arg("self"),
"Return the detector position vector")
- .def("getL1", &IPeak::getL1,
+ .def("getL1", &IPeak::getL1, arg("self"),
"Return the L1 flight path length (source to sample), in meters. ")
- .def("getL2", &IPeak::getL2,
+ .def("getL2", &IPeak::getL2, arg("self"),
"Return the L2 flight path length (sample to detector), in meters.")
- .def("getPeakShape", getPeakShape, "Get the peak shape");
+ .def("getPeakShape", getPeakShape, arg("self"), "Get the peak shape");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IPeakFunction.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IPeakFunction.cpp
index f98e84fb8ec7b29d732c1f0626a252e2a9604872..3ac4f6332732a278c3b3ffaa9371cdb41d21edf9 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IPeakFunction.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IPeakFunction.cpp
@@ -14,11 +14,13 @@ void export_IPeakFunction() {
.def("functionLocal",
(object (IPeakFunctionAdapter::*)(const object &) const) &
IPeakFunction::functionLocal,
+ (arg("self"), arg("vec_x")),
"Calculate the values of the function for the given x values. The "
"output should be stored in the out array")
- .def("intensity", &IPeakFunction::intensity,
+ .def("intensity", &IPeakFunction::intensity, arg("self"),
"Returns the integral intensity of the peak function.")
.def("setIntensity", &IPeakFunction::setIntensity,
+ (arg("self"), arg("new_intensity")),
"Changes the integral intensity of the peak function by setting its "
"height.");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IPeaksWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IPeaksWorkspace.cpp
index cedd6732c37158cc1c9d6e074d721bd5203735f8..392d246c8fc1f0b33b63ddbeb98e747aabadd1de 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IPeaksWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IPeaksWorkspace.cpp
@@ -40,29 +40,33 @@ void export_IPeaksWorkspace() {
// IPeaksWorkspace class
class_<IPeaksWorkspace, bases<ITableWorkspace, ExperimentInfo>,
boost::noncopyable>("IPeaksWorkspace", no_init)
- .def("getNumberPeaks", &IPeaksWorkspace::getNumberPeaks,
+ .def("getNumberPeaks", &IPeaksWorkspace::getNumberPeaks, arg("self"),
"Returns the number of peaks within the workspace")
- .def("addPeak", &IPeaksWorkspace::addPeak, "Add a peak to the workspace")
+ .def("addPeak", &IPeaksWorkspace::addPeak, (arg("self"), arg("peak")),
+ "Add a peak to the workspace")
.def("removePeak", &IPeaksWorkspace::removePeak,
- "Remove a peak from the workspace")
+ (arg("self"), arg("peak_num")), "Remove a peak from the workspace")
.def("getPeak", &IPeaksWorkspace::getPeakPtr,
- return_internal_reference<>(), "Returns a peak at the given index")
- .def("createPeak", createPeakQLab,
+ (arg("self"), arg("peak_num")), return_internal_reference<>(),
+ "Returns a peak at the given index")
+ .def("createPeak", createPeakQLab, (arg("self"), arg("data")),
return_value_policy<manage_new_object>(),
"Create a Peak and return it from its coordinates in the QLab frame")
.def("createPeak", createPeakQLabWithDistance,
+ (arg("self"), arg("data"), arg("detector_distance")),
return_value_policy<manage_new_object>(),
"Create a Peak and return it from its coordinates in the QLab "
"frame, detector-sample distance explicitly provided")
- .def("createPeakHKL", createPeakHKL,
+ .def("createPeakHKL", createPeakHKL, (arg("self"), arg("data")),
return_value_policy<manage_new_object>(),
"Create a Peak and return it from its coordinates in the HKL frame")
.def("hasIntegratedPeaks", &IPeaksWorkspace::hasIntegratedPeaks,
- "Determine if the peaks have been integrated")
- .def("getRun", &IPeaksWorkspace::mutableRun,
+ arg("self"), "Determine if the peaks have been integrated")
+ .def("getRun", &IPeaksWorkspace::mutableRun, arg("self"),
return_internal_reference<>(),
"Return the Run object for this workspace")
.def("peakInfoNumber", &IPeaksWorkspace::peakInfoNumber,
+ (arg("self"), arg("qlab_frame"), arg("lab_coordinate")),
"Peak info number at Q vector for this workspace");
//-------------------------------------------------------------------------------------------------
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ISpectrum.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ISpectrum.cpp
index 1e27e7f78036b3a1a341ac103b9f1a0c747bec1f..3afbf36902caa3b24d84fadceb531e4cddd67ca3 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ISpectrum.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ISpectrum.cpp
@@ -12,21 +12,24 @@ void export_ISpectrum() {
class_<ISpectrum, boost::noncopyable>("ISpectrum", no_init)
.def("hasDetectorID", &ISpectrum::hasDetectorID,
+ (arg("self"), arg("det_id")),
"Returns True if the spectrum contain the given spectrum number")
- .def("getSpectrumNo", &ISpectrum::getSpectrumNo,
+ .def("getSpectrumNo", &ISpectrum::getSpectrumNo, arg("self"),
"Returns the spectrum number of this spectrum")
.def("getDetectorIDs", (const std::set<detid_t> &(ISpectrum::*)() const) &
ISpectrum::getDetectorIDs,
- return_value_policy<copy_const_reference>(),
+ arg("self"), return_value_policy<copy_const_reference>(),
"Returns a list of detector IDs for this spectrum")
.def("addDetectorID", &ISpectrum::addDetectorID,
- "Add a detector ID to this spectrum")
+ (arg("self"), arg("det_id")), "Add a detector ID to this spectrum")
.def("setDetectorID", &ISpectrum::setDetectorID,
- "Set the given ID has the only")
- .def("clearDetectorIDs", &ISpectrum::clearDetectorIDs,
+ (arg("self"), arg("det_id")), "Set the given ID has the only")
+ .def("clearDetectorIDs", &ISpectrum::clearDetectorIDs, arg("self"),
"Clear the set of detector IDs")
.def("setSpectrumNo", &ISpectrum::setSpectrumNo,
+ (arg("self"), arg("num")),
"Set the spectrum number for this spectrum")
- .def("hasDx", &ISpectrum::hasDx, "Returns True if the spectrum uses the "
- "DX (X Error) array, else False.");
+ .def("hasDx", &ISpectrum::hasDx, arg("self"),
+ "Returns True if the spectrum uses the "
+ "DX (X Error) array, else False.");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ISplittersWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ISplittersWorkspace.cpp
index 55585283456e84176d06a1bc53b33b0f37a287a1..2ace16a65bb1aac998660d10ba45565d1a2e88c1 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ISplittersWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ISplittersWorkspace.cpp
@@ -11,7 +11,7 @@ void export_ISplittersWorkspace() {
class_<ISplittersWorkspace, boost::noncopyable>("ISplittersWorkspace",
no_init)
.def("getNumberSplitters", &ISplittersWorkspace::getNumberSplitters,
- "Returns the number of splitters within the workspace");
+ arg("self"), "Returns the number of splitters within the workspace");
// register pointers
RegisterWorkspacePtrToPython<ISplittersWorkspace>();
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ITableWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ITableWorkspace.cpp
index 8280d0fb2512acd690f46edcfa72fcfb2ede005a..853166f3094888aba80258dd77e561a5fbfe564b 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ITableWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ITableWorkspace.cpp
@@ -338,51 +338,55 @@ void export_ITableWorkspace() {
class_<ITableWorkspace, bases<Workspace>, boost::noncopyable>(
"ITableWorkspace", iTableWorkspace_docstring.c_str(), no_init)
- .def("addColumn", &addColumn, (arg("type"), arg("name")),
+ .def("addColumn", &addColumn, (arg("self"), arg("type"), arg("name")),
"Add a named column with the given type. Recognized types are: "
"int,float,double,bool,str,V3D,long64")
- .def("removeColumn", &ITableWorkspace::removeColumn, (arg("name")),
- "Remove the named column")
+ .def("removeColumn", &ITableWorkspace::removeColumn,
+ (arg("self"), arg("name")), "Remove the named column")
- .def("columnCount", &ITableWorkspace::columnCount,
+ .def("columnCount", &ITableWorkspace::columnCount, arg("self"),
"Returns the number of columns in the workspace")
- .def("rowCount", &ITableWorkspace::rowCount,
+ .def("rowCount", &ITableWorkspace::rowCount, arg("self"),
"Returns the number of rows within the workspace")
- .def("setRowCount", &ITableWorkspace::setRowCount, (arg("count")),
+ .def("setRowCount", &ITableWorkspace::setRowCount,
+ (arg("self"), arg("count")),
"Resize the table to contain count rows")
- .def("__len__", &ITableWorkspace::rowCount,
+ .def("__len__", &ITableWorkspace::rowCount, arg("self"),
"Returns the number of rows within the workspace")
- .def("getColumnNames", &ITableWorkspace::getColumnNames,
+ .def("getColumnNames", &ITableWorkspace::getColumnNames, arg("self"),
boost::python::return_value_policy<VectorToNumpy>(),
"Return a list of the column names")
- .def("keys", &ITableWorkspace::getColumnNames,
+ .def("keys", &ITableWorkspace::getColumnNames, arg("self"),
boost::python::return_value_policy<VectorToNumpy>(),
"Return a list of the column names")
- .def("column", &column,
+ .def("column", &column, (arg("self"), arg("column")),
"Return all values of a specific column as a list")
- .def("row", &row, "Return all values of a specific row as a dict")
+ .def("row", &row, (arg("self"), arg("row")),
+ "Return all values of a specific row as a dict")
- .def("addRow", &addRowFromDict,
+ .def("addRow", &addRowFromDict, (arg("self"), arg("row_items_dict")),
"Appends a row with the values from the dictionary")
- .def("addRow", &addRowFromList,
+ .def("addRow", &addRowFromList, (arg("self"), arg("row_items_list")),
"Appends a row with the values from the given list. "
"It it assumed that the items are in the correct order for the "
"defined columns")
- .def("cell", &cell, "Return the given cell. If the first argument is a "
- "number then it is interpreted as a row otherwise it "
- "is interpreted as a column name")
+ .def("cell", &cell, (arg("self"), arg("value"), arg("row_or_column")),
+ "Return the given cell. If the first argument is a "
+ "number then it is interpreted as a row otherwise it "
+ "is interpreted as a column name")
- .def("setCell", &setCell,
+ .def("setCell", &setCell, (arg("self"), arg("row_or_column"),
+ arg("column_or_row"), arg("value")),
"Sets the value of a given cell. If the first argument is a "
"number then it is interpreted as a row otherwise it is interpreted "
"as a column name");
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IWorkspaceProperty.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IWorkspaceProperty.cpp
index 525d92c8448be014be0f277607eff7b2593beeb8..8e50a5b573226ff8e8a6707bca688bf8555f6c7b 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IWorkspaceProperty.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IWorkspaceProperty.cpp
@@ -6,8 +6,8 @@ void export_IWorkspaceProperty() {
using Mantid::API::IWorkspaceProperty;
class_<IWorkspaceProperty, boost::noncopyable>("IWorkspaceProperty", no_init)
- .def("isOptional", &IWorkspaceProperty::isOptional,
+ .def("isOptional", &IWorkspaceProperty::isOptional, arg("self"),
"Is the input workspace property optional")
- .def("isLocking", &IWorkspaceProperty::isLocking,
+ .def("isLocking", &IWorkspaceProperty::isLocking, arg("self"),
"Will the workspace be locked when starting an algorithm");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/InstrumentValidator.cpp b/Framework/PythonInterface/mantid/api/src/Exports/InstrumentValidator.cpp
index b4985d71e60f31150577b8ed4fbd20f6b908bd90..651b725701c3c8d379f2f6e3276748a25c22b60c 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/InstrumentValidator.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/InstrumentValidator.cpp
@@ -1,4 +1,4 @@
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/InstrumentValidator.h"
#include "MantidPythonInterface/kernel/TypedValidatorExporter.h"
#include <boost/python/class.hpp>
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Jacobian.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Jacobian.cpp
index 732cae6fca5c6feaec3b64c6d969d5ffbaa4067f..e9d0eb07cfbfb1e91c8151f51e009ff885a90daf 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Jacobian.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Jacobian.cpp
@@ -9,11 +9,12 @@ void export_Jacobian() {
register_ptr_to_python<Jacobian *>();
class_<Jacobian, boost::noncopyable>("Jacobian", no_init)
- .def("set", &Jacobian::set, (arg("iy"), arg("ip"), arg("value")),
+ .def("set", &Jacobian::set,
+ (arg("self"), arg("iy"), arg("ip"), arg("value")),
"Set an element of the Jacobian matrix where iy=index of data "
"point, ip=index of parameter.")
- .def("get", &Jacobian::get, (arg("iy"), arg("ip")),
+ .def("get", &Jacobian::get, (arg("self"), arg("iy"), arg("ip")),
"Return the given element of the Jacobian matrix where iy=index of "
"data point, ip=index of parameter.");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/MDGeometry.cpp b/Framework/PythonInterface/mantid/api/src/Exports/MDGeometry.cpp
index 2c62473353409541efc3e8d1a815ac758c4ad425..c739bc51666f77b172acb054c3266249488ec7d7 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/MDGeometry.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/MDGeometry.cpp
@@ -35,88 +35,94 @@ boost::python::list getNonIntegratedDimensionsAsPyList(const MDGeometry &self) {
void export_MDGeometry() {
class_<MDGeometry, boost::noncopyable>("MDGeometry", no_init)
- .def("getNumDims", &MDGeometry::getNumDims,
+ .def("getNumDims", &MDGeometry::getNumDims, arg("self"),
"Returns the number of dimensions present")
- .def("getDimension", &MDGeometry::getDimension, (args("index")),
+ .def("getDimension", &MDGeometry::getDimension,
+ (arg("self"), arg("index")),
return_value_policy<RemoveConstSharedPtr>(),
"Returns the description of the dimension at the given index "
"(starts from 0). Raises RuntimeError if index is out of range.")
- .def("getDimensionWithId", &MDGeometry::getDimensionWithId, (args("id")),
+ .def("getDimensionWithId", &MDGeometry::getDimensionWithId,
+ (arg("self"), arg("id")),
return_value_policy<RemoveConstSharedPtr>(),
"Returns the description of the dimension with the given id string. "
"Raises ValueError if the string is not a known id.")
.def("getDimensionIndexByName", &MDGeometry::getDimensionIndexByName,
- (args("name")), "Returns the index of the dimension with the given "
- "name. Raises RuntimeError if the name does not "
- "exist.")
+ (arg("self"), arg("name")),
+ "Returns the index of the dimension with the given "
+ "name. Raises RuntimeError if the name does not "
+ "exist.")
.def("getDimensionIndexById", &MDGeometry::getDimensionIndexById,
- (args("id")), "Returns the index of the dimension with the given "
- "ID. Raises RuntimeError if the name does not exist.")
+ (arg("self"), arg("id")),
+ "Returns the index of the dimension with the given "
+ "ID. Raises RuntimeError if the name does not exist.")
.def("getNonIntegratedDimensions", &getNonIntegratedDimensionsAsPyList,
+ arg("self"),
"Returns the description objects of the non-integrated dimension as "
"a python list of IMDDimension.")
- .def("estimateResolution", &MDGeometry::estimateResolution,
+ .def("estimateResolution", &MDGeometry::estimateResolution, arg("self"),
return_value_policy<VectorToNumpy>(),
"Returns a numpy array containing the width of the smallest bin in "
"each dimension")
- .def("getXDimension", &MDGeometry::getXDimension,
+ .def("getXDimension", &MDGeometry::getXDimension, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Returns the dimension description mapped to X")
- .def("getYDimension", &MDGeometry::getYDimension,
+ .def("getYDimension", &MDGeometry::getYDimension, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Returns the dimension description mapped to Y")
- .def("getZDimension", &MDGeometry::getZDimension,
+ .def("getZDimension", &MDGeometry::getZDimension, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Returns the dimension description mapped to Z")
- .def("getTDimension", &MDGeometry::getTDimension,
+ .def("getTDimension", &MDGeometry::getTDimension, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Returns the dimension description mapped to time")
- .def("getGeometryXML", &MDGeometry::getGeometryXML,
+ .def("getGeometryXML", &MDGeometry::getGeometryXML, arg("self"),
"Returns an XML representation, as a string, of the geometry of the "
"workspace")
.def("getBasisVector",
(const Mantid::Kernel::VMD &(MDGeometry::*)(size_t) const) &
MDGeometry::getBasisVector,
- (args("index")), return_value_policy<copy_const_reference>(),
+ (arg("self"), arg("index")),
+ return_value_policy<copy_const_reference>(),
"Returns a VMD object defining the basis vector for the specified "
"dimension")
.def("hasOriginalWorkspace", &MDGeometry::hasOriginalWorkspace,
- (args("index")),
+ (arg("self"), arg("index")),
"Returns True if there is a source workspace at the given index")
.def("numOriginalWorkspaces", &MDGeometry::numOriginalWorkspaces,
- "Returns the number of source workspaces attached")
+ arg("self"), "Returns the number of source workspaces attached")
.def("getOriginalWorkspace", &MDGeometry::getOriginalWorkspace,
- (args("index")),
+ (arg("self"), arg("index")),
"Returns the source workspace attached at the given index")
.def("getOrigin", (const Mantid::Kernel::VMD &(MDGeometry::*)() const) &
MDGeometry::getOrigin,
- return_value_policy<copy_const_reference>(),
+ arg("self"), return_value_policy<copy_const_reference>(),
"Returns the vector of the origin (in the original workspace) that "
"corresponds to 0,0,0... in this workspace")
.def("getNumberTransformsFromOriginal",
- &MDGeometry::getNumberTransformsFromOriginal,
+ &MDGeometry::getNumberTransformsFromOriginal, arg("self"),
"Returns the number of transformations from original workspace "
"coordinate systems")
.def("getNumberTransformsToOriginal",
- &MDGeometry::getNumberTransformsToOriginal,
+ &MDGeometry::getNumberTransformsToOriginal, arg("self"),
"Returns the number of transformations to original workspace "
"coordinate systems")
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp
index 0047015ad1c0e5fb397956107fe4ec08d21411c4..fbb754ab25819191b32321b6a3133e9441408f20 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp
@@ -34,10 +34,17 @@ typedef return_value_policy<VectorRefToNumpy<WrapReadWrite>>
return_readwrite_numpy;
//------------------------------- Overload macros ---------------------------
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Overloads for binIndexOf function which has 1 optional argument
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(MatrixWorkspace_binIndexOfOverloads,
MatrixWorkspace::binIndexOf, 1, 2)
-
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
/**
* Set the values from an python array-style object into the given spectrum in
* the workspace
@@ -150,10 +157,10 @@ void export_MatrixWorkspace() {
boost::noncopyable>("MatrixWorkspace", no_init)
//--------------------------------------- Meta information
//-----------------------------------------------------------------------
- .def("blocksize", &MatrixWorkspace::blocksize, args("self"),
+ .def("blocksize", &MatrixWorkspace::blocksize, arg("self"),
"Returns size of the Y data array")
.def("getNumberHistograms", &MatrixWorkspace::getNumberHistograms,
- args("self"), "Returns the number of spectra in the workspace")
+ arg("self"), "Returns the number of spectra in the workspace")
.def("binIndexOf", &MatrixWorkspace::binIndexOf,
MatrixWorkspace_binIndexOfOverloads(
(arg("self"), arg("xvalue"), arg("workspaceIndex")),
@@ -161,73 +168,79 @@ void export_MatrixWorkspace() {
"workspace_index is optional [default=0]"))
.def("detectorTwoTheta",
(getDetectorSignature)&MatrixWorkspace::detectorTwoTheta,
- args("self", "det"),
+ (arg("self"), arg("det")),
"Returns the two theta value for a given detector")
.def("detectorSignedTwoTheta",
(getDetectorSignature)&MatrixWorkspace::detectorSignedTwoTheta,
- args("self", "det"),
+ (arg("self"), arg("det")),
"Returns the signed two theta value for given detector")
.def("getSpectrum", (ISpectrum * (MatrixWorkspace::*)(const size_t)) &
MatrixWorkspace::getSpectrum,
- return_internal_reference<>(), args("self", "workspaceIndex"),
+ (arg("self"), arg("workspaceIndex")), return_internal_reference<>(),
"Return the spectra at the given workspace index.")
.def("getIndexFromSpectrumNumber",
- &MatrixWorkspace::getIndexFromSpectrumNumber, args("self"),
+ &MatrixWorkspace::getIndexFromSpectrumNumber,
+ (arg("self"), arg("spec_no")),
"Returns workspace index correspondent to the given spectrum "
"number. Throws if no such spectrum is present in the workspace")
.def("getDetector", &MatrixWorkspace::getDetector,
return_value_policy<RemoveConstSharedPtr>(),
- args("self", "workspaceIndex"), "Return the Detector or "
- "DetectorGroup that is linked to "
- "the given workspace index")
- .def("getRun", &MatrixWorkspace::mutableRun,
- return_internal_reference<>(), args("self"),
+ (arg("self"), arg("workspaceIndex")),
+ "Return the Detector or "
+ "DetectorGroup that is linked to "
+ "the given workspace index")
+ .def("getRun", &MatrixWorkspace::mutableRun, arg("self"),
+ return_internal_reference<>(),
"Return the Run object for this workspace")
- .def("axes", &MatrixWorkspace::axes, args("self"),
+ .def("axes", &MatrixWorkspace::axes, arg("self"),
"Returns the number of axes attached to the workspace")
- .def("getAxis", &MatrixWorkspace::getAxis, return_internal_reference<>(),
- args("self", "axis_index"))
- .def("isHistogramData", &MatrixWorkspace::isHistogramData, args("self"),
+ .def("getAxis", &MatrixWorkspace::getAxis,
+ (arg("self"), arg("axis_index")), return_internal_reference<>(),
+ "Get a pointer to a workspace axis")
+ .def("isHistogramData", &MatrixWorkspace::isHistogramData, arg("self"),
"Returns True if this is considered to be binned data.")
.def("isDistribution", (const bool &(MatrixWorkspace::*)() const) &
MatrixWorkspace::isDistribution,
- return_value_policy<copy_const_reference>(), args("self"),
+ arg("self"), return_value_policy<copy_const_reference>(),
"Returns the status of the distribution flag")
- .def("YUnit", &MatrixWorkspace::YUnit, args("self"),
+ .def("YUnit", &MatrixWorkspace::YUnit, arg("self"),
"Returns the current Y unit for the data (Y axis) in the workspace")
- .def("YUnitLabel", &MatrixWorkspace::YUnitLabel, args("self"),
+ .def("YUnitLabel", &MatrixWorkspace::YUnitLabel, arg("self"),
"Returns the caption for the Y axis")
// Deprecated
- .def("getNumberBins", &getNumberBinsDeprecated, args("self"),
+ .def("getNumberBins", &getNumberBinsDeprecated, arg("self"),
"Returns size of the Y data array (deprecated, use blocksize "
"instead)")
- .def("getSampleDetails", &getSampleDetailsDeprecated,
- return_internal_reference<>(), args("self"),
+ .def("getSampleDetails", &getSampleDetailsDeprecated, arg("self"),
+ return_internal_reference<>(),
"Return the Run object for this workspace (deprecated, use getRun "
"instead)")
//--------------------------------------- Setters
//------------------------------------
.def("setYUnitLabel", &MatrixWorkspace::setYUnitLabel,
- args("self", "newLabel"),
+ (arg("self"), arg("newLabel")),
"Sets a new caption for the data (Y axis) in the workspace")
- .def("setYUnit", &MatrixWorkspace::setYUnit, args("self", "newUnit"),
+ .def("setYUnit", &MatrixWorkspace::setYUnit,
+ (arg("self"), arg("newUnit")),
"Sets a new unit for the data (Y axis) in the workspace")
.def("setDistribution", (bool &(MatrixWorkspace::*)(const bool)) &
MatrixWorkspace::isDistribution,
- return_value_policy<return_by_value>(), args("self", "newVal"),
+ (arg("self"), arg("newVal")), return_value_policy<return_by_value>(),
"Set distribution flag. If True the workspace has been divided by "
"the bin-width.")
.def("replaceAxis", &MatrixWorkspace::replaceAxis,
- args("self", "axisIndex", "newAxis"))
+ (arg("self"), arg("axisIndex"), arg("newAxis")),
+ "Replaces one of the workspace's axes with the new one provided.")
//--------------------------------------- Read spectrum data
//-------------------------
- .def("readX", &MatrixWorkspace::readX, return_readonly_numpy(),
- args("self", "workspaceIndex"), "Creates a read-only numpy wrapper "
- "around the original X data at the "
- "given index")
+ .def("readX", &MatrixWorkspace::readX,
+ (arg("self"), arg("workspaceIndex")), return_readonly_numpy(),
+ "Creates a read-only numpy wrapper "
+ "around the original X data at the "
+ "given index")
.def("readY", &MatrixWorkspace::readY, return_readonly_numpy(),
args("self", "workspaceIndex"), "Creates a read-only numpy wrapper "
"around the original Y data at the "
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/MultipleExperimentInfos.cpp b/Framework/PythonInterface/mantid/api/src/Exports/MultipleExperimentInfos.cpp
index e1ee933671887581dcfb37ed06065f2045ba4643..1635dd5d4cc22a15a23e6c5c364668734bbd86f4 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/MultipleExperimentInfos.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/MultipleExperimentInfos.cpp
@@ -12,8 +12,9 @@ void export_MultipleExperimentInfos() {
.def("getExperimentInfo",
(ExperimentInfo_sptr (MultipleExperimentInfos::*)(const uint16_t)) &
MultipleExperimentInfos::getExperimentInfo,
+ (arg("self"), arg("run_index")),
"Return the experiment info at the given index.")
.def("getNumExperimentInfo",
- &MultipleExperimentInfos::getNumExperimentInfo,
+ &MultipleExperimentInfos::getNumExperimentInfo, arg("self"),
"Return the number of experiment info objects,");
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Projection.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Projection.cpp
index 080bed5db9c13e75709f93e262432f96f35f05b7..0973bf8190b35b423e6065bea29cadcf4c3531e4 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Projection.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Projection.cpp
@@ -114,21 +114,23 @@ void export_Projection() {
"of u and v.")
.def("__init__", make_constructor(&projCtor3),
"Constructs a 3 dimensional projection")
- .def("getOffset", &Projection::getOffset,
+ .def("getOffset", &Projection::getOffset, (arg("self"), arg("nd")),
"Returns the offset for the given dimension", args("dimension"))
- .def("getAxis", &Projection::getAxis,
+ .def("getAxis", &Projection::getAxis, (arg("self"), arg("nd")),
"Returns the axis for the given dimension", args("dimension"))
- .def("getType", &getUnit, "Returns the unit for the given dimension",
- args("dimension"))
+ .def("getType", &getUnit, (arg("self"), arg("dimension")),
+ "Returns the unit for the given dimension")
.def("setOffset", &Projection::setOffset,
+ (arg("self"), arg("nd"), arg("offset")),
"Sets the offset for the given dimension",
args("dimension", "offset"))
.def("setAxis", &Projection::setAxis,
- "Sets the axis for the given dimension", args("dimension", "axis"))
- .def("setAxis", &projSetAxis, "Sets the axis for the given dimension",
- args("dimension", "axis"))
- .def("setType", &setUnit, "Sets the unit for the given dimension",
- args("dimension", "unit"))
+ (arg("self"), arg("dimension"), arg("axis")),
+ "Sets the axis for the given dimension")
+ .def("setAxis", &projSetAxis, (arg("self"), arg("nd"), arg("data")),
+ "Sets the axis for the given dimension")
+ .def("setType", &setUnit, (arg("self"), arg("dimension"), arg("unit")),
+ "Sets the unit for the given dimension")
.add_property(
"u", make_function(&Projection::U, return_internal_reference<>(),
boost::mpl::vector2<V3D &, Projection &>()),
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Run.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Run.cpp
index 8f8548bbcc57f1bd0fc0ca70815263ec4b454a43..bc950c6e2ff6754c95539fd6a278f394a995040d 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Run.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Run.cpp
@@ -116,67 +116,77 @@ void export_Run() {
// Run class
class_<Run, boost::noncopyable>("Run", no_init)
- .def("getProtonCharge", &Run::getProtonCharge,
+ .def("getProtonCharge", &Run::getProtonCharge, arg("self"),
"Return the total good proton charge for the run")
- .def("integrateProtonCharge", &Run::integrateProtonCharge,
+ .def("integrateProtonCharge", &Run::integrateProtonCharge, arg("self"),
"Return the total good proton charge for the run")
- .def("hasProperty", &Run::hasProperty,
+ .def("hasProperty", &Run::hasProperty, (arg("self"), arg("name")),
"Returns True if the given log value is contained within the run")
- .def("getProperty", &Run::getProperty,
+ .def("getProperty", &Run::getProperty, (arg("self"), arg("name")),
return_value_policy<return_by_value>(), "Returns the named property "
"(log value). Use '.value' "
"to return the value.")
- .def("getProperties", &Run::getProperties, return_internal_reference<>(),
+ .def("getProperties", &Run::getProperties, arg("self"),
+ return_internal_reference<>(),
"Return the list of run properties managed by this object.")
.def("getLogData",
(Property * (Run::*)(const std::string &) const) & Run::getLogData,
- return_value_policy<return_by_value>(),
+ (arg("self"), arg("name")), return_value_policy<return_by_value>(),
"Returns the named log. Use '.value' to return the value. The same "
"as getProperty.")
.def("getLogData",
(const std::vector<Property *> &(Run::*)() const) & Run::getLogData,
- return_internal_reference<>(),
+ arg("self"), return_internal_reference<>(),
"Return the list of logs for this run. The same as getProperties.")
.def("getGoniometer",
(const Mantid::Geometry::Goniometer &(Run::*)() const) &
Run::getGoniometer,
- return_value_policy<reference_existing_object>(),
+ arg("self"), return_value_policy<reference_existing_object>(),
"Get the oriented lattice for this sample")
- .def("addProperty", &addProperty, "Adds a property with the given name "
- "and value. If replace=True then an "
- "existing property is overwritten")
+ .def("addProperty", &addProperty,
+ (arg("self"), arg("name"), arg("value"), arg("replace")),
+ "Adds a property with the given name "
+ "and value. If replace=True then an "
+ "existing property is overwritten")
.def("addProperty", &addPropertyWithUnit,
+ (arg("self"), arg("name"), arg("value"), arg("units"),
+ arg("replace")),
"Adds a property with the given name, value and unit. If "
"replace=True then an existing property is overwritten")
.def("setStartAndEndTime", &Run::setStartAndEndTime,
+ (arg("self"), arg("start"), arg("end")),
"Set the start and end time of the run")
- .def("startTime", &Run::startTime,
+ .def("startTime", &Run::startTime, arg("self"),
"Return the total starting time of the run.")
- .def("endTime", &Run::endTime, "Return the total ending time of the run.")
+ .def("endTime", &Run::endTime, arg("self"),
+ "Return the total ending time of the run.")
//--------------------------- Dictionary
// access----------------------------
- .def("get", &getWithDefault, "Returns the value pointed to by the key or "
- "None if it does not exist")
- .def("get", &get,
+ .def("get", &getWithDefault, (arg("self"), arg("key"), arg("default")),
+ "Returns the value pointed to by the key or "
+ "None if it does not exist")
+ .def("get", &get, (arg("self"), arg("key")),
"Returns the value pointed to by the key or the default value given")
- .def("keys", &keys, "Returns the names of the properties as list")
- .def("__contains__", &Run::hasProperty)
- .def("__getitem__", &Run::getProperty,
+ .def("keys", &keys, arg("self"),
+ "Returns the names of the properties as list")
+ .def("__contains__", &Run::hasProperty, (arg("self"), arg("name")))
+ .def("__getitem__", &Run::getProperty, (arg("self"), arg("name")),
return_value_policy<return_by_value>())
- .def("__setitem__", &addOrReplaceProperty)
+ .def("__setitem__", &addOrReplaceProperty,
+ (arg("self"), arg("name"), arg("value")))
;
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Sample.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Sample.cpp
index cbf45afe13a4c246126189710d15d03a218f85e2..baa9826478dbad9a4c9ee7b2065d468a7cfedf01 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Sample.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Sample.cpp
@@ -16,35 +16,41 @@ void export_Sample() {
class_<Sample, boost::noncopyable>("Sample", no_init)
.def("getName", &Sample::getName,
- return_value_policy<copy_const_reference>(),
+ return_value_policy<copy_const_reference>(), arg("self"),
"Returns the string name of the sample")
.def("getOrientedLattice", (const OrientedLattice &(Sample::*)() const) &
Sample::getOrientedLattice,
- return_value_policy<reference_existing_object>(),
+ arg("self"), return_value_policy<reference_existing_object>(),
"Get the oriented lattice for this sample")
- .def("hasOrientedLattice", &Sample::hasOrientedLattice,
+ .def("hasOrientedLattice", &Sample::hasOrientedLattice, arg("self"),
"Returns True if this sample has an oriented lattice, false "
"otherwise")
- .def("size", &Sample::size,
+ .def("size", &Sample::size, arg("self"),
"Return the number of samples contained within this sample")
// Required for ISIS SANS reduction until the full sample geometry is
// defined on loading
- .def("getGeometryFlag", &Sample::getGeometryFlag,
+ .def("getGeometryFlag", &Sample::getGeometryFlag, arg("self"),
"Return the geometry flag.")
- .def("getThickness", &Sample::getThickness, "Return the thickness in mm")
- .def("getHeight", &Sample::getHeight, "Return the height in mm")
- .def("getWidth", &Sample::getWidth, "Return the width in mm")
+ .def("getThickness", &Sample::getThickness, arg("self"),
+ "Return the thickness in mm")
+ .def("getHeight", &Sample::getHeight, arg("self"),
+ "Return the height in mm")
+ .def("getWidth", &Sample::getWidth, arg("self"), "Return the width in mm")
.def("getMaterial",
(const Material &(Sample::*)() const)(&Sample::getMaterial),
- return_value_policy<reference_existing_object>(),
+ arg("self"), return_value_policy<reference_existing_object>(),
"The material the sample is composed of")
.def("setGeometryFlag", &Sample::setGeometryFlag,
- "Set the geometry flag.")
- .def("setThickness", &Sample::setThickness, "Set the thickness in mm.")
- .def("setHeight", &Sample::setHeight, "Set the height in mm.")
- .def("setWidth", &Sample::setWidth, "Set the width in mm.")
+ (arg("self"), arg("geom_id")), "Set the geometry flag.")
+ .def("setThickness", &Sample::setThickness, (arg("self"), arg("thick")),
+ "Set the thickness in mm.")
+ .def("setHeight", &Sample::setHeight, (arg("self"), arg("height")),
+ "Set the height in mm.")
+ .def("setWidth", &Sample::setWidth, (arg("self"), arg("width")),
+ "Set the width in mm.")
// -------------------------Operators
// -------------------------------------
- .def("__len__", &Sample::size)
+ .def("__len__", &Sample::size, arg("self"),
+ "Gets the number of samples in this collection")
.def("__getitem__", &Sample::operator[], return_internal_reference<>());
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepository.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepository.cpp
index 91979d2a4981d49db39845bc3dc316c1bd95b463..2422b6c7a81b3dace66d938011db87ac2ac29173 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepository.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepository.cpp
@@ -196,11 +196,15 @@ Arguments:\n\
///@todo better description
class_<ScriptRepository, boost::noncopyable>("ScriptRepository", repo_desc,
no_init)
- .def("install", &ScriptRepository::install, install_desc)
- .def("listFiles", &getListFiles, list_files_desc)
- .def("fileInfo", &getInfo, file_info_desc)
- .def("description", &getDescription, file_description_desc)
- .def("fileStatus", &getStatus, file_status_desc)
- .def("download", &ScriptRepository::download, download_desc)
- .def("update", &ScriptRepository::check4Update, update_desc);
+ .def("install", &ScriptRepository::install,
+ (arg("self"), arg("local_path")), install_desc)
+ .def("listFiles", &getListFiles, arg("self"), list_files_desc)
+ .def("fileInfo", &getInfo, (arg("self"), arg("path")), file_info_desc)
+ .def("description", &getDescription, (arg("self"), arg("path")),
+ file_description_desc)
+ .def("fileStatus", &getStatus, (arg("self"), arg("path")),
+ file_status_desc)
+ .def("download", &ScriptRepository::download,
+ (arg("self"), arg("file_path")), download_desc)
+ .def("update", &ScriptRepository::check4Update, arg("self"), update_desc);
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepositoryFactory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepositoryFactory.cpp
index 0f572e8bf639040dd0f7d8e74c9347f270ee083d..91eef3e80418280995943a92161a2537dded62a9 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepositoryFactory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ScriptRepositoryFactory.cpp
@@ -19,6 +19,7 @@ void export_ScriptRepositoryFactory() {
class_<ScriptRepositoryFactoryImpl, boost::noncopyable>(
"ScriptRepositoryFactory", no_init)
.def("create", &ScriptRepositoryFactoryImpl::create,
+ (arg("self"), arg("class_name")),
"Return a pointer to the ScriptRepository object")
.def("Instance", &ScriptRepositoryFactory::Instance,
return_value_policy<reference_existing_object>(),
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp
index 04e52cc2d1278d5a60d6fb28ab6712f6b9f52424..a399b9ca775cb9cdad79cff7a4b904cef7f48692 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp
@@ -14,32 +14,43 @@ using namespace boost::python;
namespace {
///@cond
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(Workspace_isDirtyOverloads,
Workspace::isDirty, 0, 1)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
///@endcond
}
void export_Workspace() {
class_<Workspace, bases<DataItem>, boost::noncopyable>("Workspace", no_init)
.def("getName", &Workspace::getName,
- return_value_policy<copy_const_reference>(), args("self"),
+ return_value_policy<copy_const_reference>(), arg("self"),
"Returns the name of the workspace. This could be an empty string")
- .def("getTitle", &Workspace::getTitle, args("self"),
+ .def("getTitle", &Workspace::getTitle, arg("self"),
"Returns the title of the workspace")
- .def("setTitle", &Workspace::setTitle, args("self", "title"))
- .def("getComment", &Workspace::getComment,
+ .def("setTitle", &Workspace::setTitle, (arg("self"), arg("title")),
+ "Set the title of the workspace")
+ .def("getComment", &Workspace::getComment, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns the comment field on the workspace")
- .def("setComment", &Workspace::setComment, args("self", "comment"))
+ .def("setComment", &Workspace::setComment, (arg("self"), arg("comment")),
+ "Set the comment field of the workspace")
.def("isDirty", &Workspace::isDirty,
- Workspace_isDirtyOverloads(arg("n"), "True if the workspace has run "
- "more than n algorithms "
- "(Default=1)"))
- .def("getMemorySize", &Workspace::getMemorySize, args("self"),
+ Workspace_isDirtyOverloads((arg("self"), arg("n")),
+ "True if the workspace has run "
+ "more than n algorithms "
+ "(Default=1)"))
+ .def("getMemorySize", &Workspace::getMemorySize, arg("self"),
"Returns the memory footprint of the workspace in KB")
.def("getHistory", (const WorkspaceHistory &(Workspace::*)() const) &
Workspace::getHistory,
- return_value_policy<reference_existing_object>(), args("self"),
+ arg("self"), return_value_policy<reference_existing_object>(),
"Return read-only access to the workspace history");
// register pointers
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp
index b77d3cc8a152a36926b9619fbb7cd84fd177162c..94373c2f9d16a87446c5864760cd9c88aa1aeea8 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp
@@ -40,10 +40,18 @@ Workspace_sptr createFromParentPtr(WorkspaceFactoryImpl &self,
}
/// Overload generator for create
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
BOOST_PYTHON_FUNCTION_OVERLOADS(createFromParent_Overload, createFromParentPtr,
2, 5)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(createTable_Overload, createTable, 0, 1)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(createPeaks_Overload, createPeaks, 0, 1)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
}
void export_WorkspaceFactory() {
@@ -62,22 +70,26 @@ void export_WorkspaceFactory() {
class_<WorkspaceFactoryImpl, boost::noncopyable>("WorkspaceFactoryImpl",
no_init)
.def("create", &createFromParentPtr,
- createFromParent_Overload(
- createFromParentDoc, (arg("parent"), arg("NVectors") = -1,
- arg("XLength") = -1, arg("YLength") = -1)))
+ createFromParent_Overload(createFromParentDoc,
+ (arg("self"), arg("parent"),
+ arg("NVectors") = -1, arg("XLength") = -1,
+ arg("YLength") = -1)))
.def("create", (createFromScratchPtr)&WorkspaceFactoryImpl::create,
createFromScratchDoc, return_value_policy<AsType<Workspace_sptr>>(),
- (arg("className"), arg("NVectors"), arg("XLength"), arg("YLength")))
+ (arg("self"), arg("className"), arg("NVectors"), arg("XLength"),
+ arg("YLength")))
.def("createTable", &WorkspaceFactoryImpl::createTable,
- createTable_Overload("Creates an empty TableWorkspace",
- (arg("className") = "TableWorkspace"))
+ createTable_Overload(
+ "Creates an empty TableWorkspace",
+ (arg("self"), arg("className") = "TableWorkspace"))
[return_value_policy<AsType<Workspace_sptr>>()])
.def("createPeaks", &WorkspaceFactoryImpl::createPeaks,
- createPeaks_Overload("Creates an empty PeaksWorkspace",
- (arg("className") = "PeaksWorkspace"))
+ createPeaks_Overload(
+ "Creates an empty PeaksWorkspace",
+ (arg("self"), arg("className") = "PeaksWorkspace"))
[return_value_policy<AsType<Workspace_sptr>>()])
.def("Instance", &WorkspaceFactory::Instance,
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceGroup.cpp b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceGroup.cpp
index 702a7fe490a02376198838b30531fd34f70347cd..8c15d0331d17f326bcc93695ee46b4d083c8f017 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceGroup.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceGroup.cpp
@@ -13,22 +13,26 @@ void export_WorkspaceGroup() {
class_<WorkspaceGroup, bases<Workspace>, boost::noncopyable>("WorkspaceGroup",
no_init)
.def("getNumberOfEntries", &WorkspaceGroup::getNumberOfEntries,
- "Returns the number of entries in the group")
- .def("getNames", &WorkspaceGroup::getNames,
+ arg("self"), "Returns the number of entries in the group")
+ .def("getNames", &WorkspaceGroup::getNames, arg("self"),
"Returns the names of the entries in the group")
.def("contains",
(bool (WorkspaceGroup::*)(const std::string &wsName) const) &
WorkspaceGroup::contains,
+ (arg("self"), arg("workspace")),
"Returns true if the given name is in the group")
- .def("add", &WorkspaceGroup::add, "Add a name to the group")
- .def("size", &WorkspaceGroup::size,
+ .def("add", &WorkspaceGroup::add, (arg("self"), arg("workspace_name")),
+ "Add a name to the group")
+ .def("size", &WorkspaceGroup::size, arg("self"),
"Returns the number of workspaces contained in the group")
- .def("remove", &WorkspaceGroup::remove, "Remove a name from the group")
+ .def("remove", &WorkspaceGroup::remove,
+ (arg("self"), arg("workspace_name")), "Remove a name from the group")
.def("getItem", (Workspace_sptr (WorkspaceGroup::*)(const size_t) const) &
WorkspaceGroup::getItem,
+ (arg("self"), arg("workspace_name")),
return_value_policy<Policies::ToWeakPtr>(),
"Returns the item at the given index")
- .def("isMultiPeriod", &WorkspaceGroup::isMultiperiod,
+ .def("isMultiPeriod", &WorkspaceGroup::isMultiperiod, arg("self"),
"Retuns true if the workspace group is multi-period")
// ------------ Operators --------------------------------
.def("__len__", &WorkspaceGroup::getNumberOfEntries)
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp
index ad3133315cf8f163ccbd0f643d94ee004166d8d1..9a32321b85fe93b711c88e770ae089e673720b86 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp
@@ -38,27 +38,31 @@ void export_WorkspaceHistory() {
class_<WorkspaceHistory, boost::noncopyable>("WorkspaceHistory", no_init)
- .def("getAlgorithmHistories", &getHistoriesAsList,
+ .def("getAlgorithmHistories", &getHistoriesAsList, arg("self"),
"Returns a list of algorithm histories for this workspace history.")
.def("getAlgorithmHistory", &WorkspaceHistory::getAlgorithmHistory,
- arg("index"), return_value_policy<Policies::RemoveConstSharedPtr>(),
+ (arg("self"), arg("index")),
+ return_value_policy<Policies::RemoveConstSharedPtr>(),
"Returns the algorithm history at the given index in the history")
- .def("size", &WorkspaceHistory::size,
+ .def("size", &WorkspaceHistory::size, arg("self"),
"Returns the number of algorithms in the immediate history")
- .def("empty", &WorkspaceHistory::empty,
+ .def("empty", &WorkspaceHistory::empty, arg("self"),
"Returns whether the history has any entries")
- .def("lastAlgorithm", &WorkspaceHistory::lastAlgorithm,
+ .def("lastAlgorithm", &WorkspaceHistory::lastAlgorithm, arg("self"),
"Returns the last algorithm run on this workspace so that its "
"properties can be accessed")
.def("getAlgorithm", &WorkspaceHistory::getAlgorithm,
+ (arg("self"), arg("index")),
"Returns the algorithm at the given index in the history")
// ----------------- Operators --------------------------------------
- .def("__getitem__", &WorkspaceHistory::getAlgorithm)
+ .def("__getitem__", &WorkspaceHistory::getAlgorithm,
+ (arg("self"), arg("index")),
+ "Create an algorithm from a history record at a given index")
.def(self_ns::str(self));
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceValidators.cpp b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceValidators.cpp
index 7bb9257a0765c7c566065d0fc28ab6c5b8c2079d..898b1032bfd0a414f110e83b1296a5cd85837d87 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceValidators.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceValidators.cpp
@@ -1,4 +1,9 @@
-#include "MantidAPI/WorkspaceValidators.h" // They are all defined in one file so export them in one
+#include "MantidAPI/CommonBinsValidator.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/NumericAxisValidator.h"
+#include "MantidAPI/RawCountValidator.h"
+#include "MantidAPI/SpectraAxisValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidPythonInterface/kernel/TypedValidatorExporter.h"
#include <boost/python/class.hpp>
diff --git a/Framework/PythonInterface/mantid/geometry/CMakeLists.txt b/Framework/PythonInterface/mantid/geometry/CMakeLists.txt
index b268c7b2f7b1854ec9b3dcd25e76286f88455ce5..371c0a374891f6ee1601ea94a91f0719f0d49ace 100644
--- a/Framework/PythonInterface/mantid/geometry/CMakeLists.txt
+++ b/Framework/PythonInterface/mantid/geometry/CMakeLists.txt
@@ -35,6 +35,8 @@ set ( EXPORT_FILES
src/Exports/SymmetryElementFactory.cpp
src/Exports/SymmetryOperation.cpp
src/Exports/SymmetryOperationFactory.cpp
+ src/Exports/CrystalStructure.cpp
+ src/Exports/ReflectionGenerator.cpp
)
#############################################################################################
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/BoundingBox.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/BoundingBox.cpp
index 47d718238f0c619778f94be92788e7ba868cf79c..52eb111ecf2762d427a04ebb3d880ff732e19084 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/BoundingBox.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/BoundingBox.cpp
@@ -9,39 +9,40 @@ using namespace boost::python;
void export_BoundingBox() {
class_<BoundingBox>("BoundingBox", "Constructs a zero-sized box")
.def(init<double, double, double, double, double, double>(
- (arg("xmax"), arg("ymax"), arg("zmax"), arg("xmin"), arg("ymin"),
- arg("zmin")),
+ (arg("self"), arg("xmax"), arg("ymax"), arg("zmax"), arg("xmin"),
+ arg("ymin"), arg("zmin")),
"Constructs a box from the six given points"))
- .def("minPoint", &BoundingBox::minPoint,
+ .def("minPoint", &BoundingBox::minPoint, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns a V3D containing the values of the minimum of the box. See "
"mantid.kernel.V3D")
- .def("maxPoint", &BoundingBox::maxPoint,
+ .def("maxPoint", &BoundingBox::maxPoint, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns a V3D containing the values of the minimum of the box. See "
"mantid.kernel.V3D")
- .def("centrePoint", &BoundingBox::centrePoint,
+ .def("centrePoint", &BoundingBox::centrePoint, arg("self"),
"Returns a V3D containing the coordinates of the centre point. See "
"mantid.kernel.V3D")
- .def("width", &BoundingBox::width, "Returns a V3D containing the widths "
- "for each dimension. See "
- "mantid.kernel.V3D")
+ .def("width", &BoundingBox::width, arg("self"),
+ "Returns a V3D containing the widths "
+ "for each dimension. See "
+ "mantid.kernel.V3D")
- .def("isNull", &BoundingBox::isNull,
+ .def("isNull", &BoundingBox::isNull, arg("self"),
"Returns true if the box has no dimensions that have been set")
- .def("isPointInside", &BoundingBox::isPointInside,
+ .def("isPointInside", &BoundingBox::isPointInside, arg("self"),
"Returns true if the given point is inside the object. See "
"mantid.kernel.V3D")
.def("doesLineIntersect",
(bool (BoundingBox::*)(const V3D &, const V3D &) const) &
BoundingBox::doesLineIntersect,
- (arg("startPoint"), arg("lineDir")),
+ (arg("self"), arg("startPoint"), arg("lineDir")),
"Returns true if the line given by the starting point & direction "
"vector passes through the box");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp
index 5ad6c63e6d0715de3c948aa0857a4e78f618ca66..77b295f76a19e855e7abd89b2e65515276e89676 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp
@@ -7,6 +7,11 @@ using Mantid::Geometry::IComponent;
using namespace boost::python;
namespace {
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Default parameter function overloads
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(Component_getParameterNames,
Component::getParameterNames, 0, 1)
@@ -36,45 +41,62 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(Component_getParamShortDescription,
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(Component_getParamDescription,
Component::getParamDescription, 1, 2)
}
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
void export_Component() {
class_<Component, bases<IComponent>, boost::noncopyable>("Component", no_init)
.def("getParameterNames", &Component::getParameterNames,
- Component_getParameterNames())
- .def("hasParameter", &Component::hasParameter, Component_hasParameter())
+ Component_getParameterNames((arg("self"), arg("recursive") = true)))
+ .def("hasParameter", &Component::hasParameter,
+ Component_hasParameter(
+ (arg("self"), arg("name"), arg("recursive") = true)))
.def("getNumberParameter", &Component::getNumberParameter,
- Component_getNumberParameter())
+ Component_getNumberParameter(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
.def("getBoolParameter", &Component::getBoolParameter,
- Component_getBoolParameter())
+ Component_getBoolParameter(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
.def("getPositionParameter", &Component::getPositionParameter,
- Component_getPositionParameter())
+ Component_getPositionParameter(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
.def("getRotationParameter", &Component::getRotationParameter,
- Component_getRotationParameter())
+ Component_getRotationParameter(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
.def("getStringParameter", &Component::getStringParameter,
- Component_getStringParameter())
+ Component_getStringParameter(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
.def("getIntParameter", &Component::getIntParameter,
- Component_getIntParameter())
+ Component_getIntParameter(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
//
- .def("getRotation", &Component::getRotation, Component_getRotation())
+ .def("getRotation", &Component::getRotation,
+ Component_getRotation(arg("self")))
.def("getRelativePos", &Component::getRelativePos,
- Component_getRelativePos())
+ Component_getRelativePos(arg("self")))
//
.def("getParamShortDescription", &Component::getParamShortDescription,
- Component_getParamShortDescription())
+ Component_getParamShortDescription(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
.def("getParamDescription", &Component::getParamDescription,
- Component_getParamDescription())
- .def("getShortDescription", &Component::getShortDescription,
+ Component_getParamDescription(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
+
+ .def("getShortDescription", &Component::getShortDescription, arg("self"),
"Return the short description of current parameterized component")
- .def("getDescription", &Component::getDescription,
+ .def("getDescription", &Component::getDescription, arg("self"),
"Return the description of current parameterized component")
.def("setDescription", &Component::setDescription,
+ (arg("self"), arg("descr")),
"Set component's description, works only if the component is "
"parameterized component")
// HACK -- python should return parameters regardless of type. this is
// untill rows below do not work
.def("getParameterType", &Component::getParameterType,
- Component_getParameterType())
+ Component_getParameterType(
+ (arg("self"), arg("pname"), arg("recursive") = true)))
//// this does not work for some obvious or not obvious reasons
//.def("getParameter", &Component::getNumberParameter,
// Component_getNumberParameter())
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..daf4587a81da370e1ffd0adc07d04f7b625a99c4
--- /dev/null
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp
@@ -0,0 +1,38 @@
+#include "MantidGeometry/Crystal/CrystalStructure.h"
+#include "MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h"
+#include <boost/python/class.hpp>
+#include <boost/python/make_constructor.hpp>
+#include <boost/python/register_ptr_to_python.hpp>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using namespace boost::python;
+
+namespace {
+SpaceGroup_sptr getSpaceGroup(CrystalStructure &self) {
+ return boost::const_pointer_cast<SpaceGroup>(self.spaceGroup());
+}
+
+std::vector<std::string> getScatterers(CrystalStructure &self) {
+ CompositeBraggScatterer_sptr scatterers = self.getScatterers();
+
+ std::vector<std::string> scattererStrings;
+ scattererStrings.reserve(scatterers->nScatterers());
+
+ for (size_t i = 0; i < scatterers->nScatterers(); ++i) {
+ scattererStrings.push_back(
+ getIsotropicAtomBraggScattererString(scatterers->getScatterer(i)));
+ }
+
+ return scattererStrings;
+}
+}
+
+void export_CrystalStructure() {
+ class_<CrystalStructure>("CrystalStructure", no_init)
+ .def(init<const std::string &, const std::string &, const std::string &>(
+ (arg("unitCell"), arg("spaceGroup"), arg("scatterers"))))
+ .def("getUnitCell", &CrystalStructure::cell)
+ .def("getSpaceGroup", &getSpaceGroup)
+ .def("getScatterers", &getScatterers);
+}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/DetectorGroup.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/DetectorGroup.cpp
index fe6107d725d865dd6248c4e34129de1970f47e1d..2a9be545cbb2fc04e75905bdc732db599aa5869b 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/DetectorGroup.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/DetectorGroup.cpp
@@ -8,8 +8,8 @@ using namespace boost::python;
void export_DetectorGroup() {
class_<DetectorGroup, bases<IDetector>, boost::noncopyable>("DetectorGroup",
no_init)
- .def("getDetectorIDs", &DetectorGroup::getDetectorIDs,
+ .def("getDetectorIDs", &DetectorGroup::getDetectorIDs, arg("self"),
"Returns the list of detector IDs within this group")
- .def("getNameSeparator", &DetectorGroup::getNameSeparator,
+ .def("getNameSeparator", &DetectorGroup::getNameSeparator, arg("self"),
"Returns separator for list of names of detectors");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp
index 184ca40caf1c17fbcf4a54d0f95c9972e8dfed47..cf01cad70f650daf90365084fb77c668afc84ed2 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp
@@ -13,9 +13,17 @@ using namespace boost::python;
namespace //<unnamed>
{
///@cond
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// define overloaded functions
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(getEulerAngles_overloads,
Goniometer::getEulerAngles, 0, 1)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
///@endcond
/// Set the U vector via a numpy array
@@ -37,6 +45,6 @@ void export_Goniometer() {
getEulerAngles_overloads(args("self", "convention"),
"Default convention is \'YZX\'. Universal "
"goniometer is \'YZY\'"))
- .def("getR", &Goniometer::getR, return_readonly_numpy())
- .def("setR", &setR);
+ .def("getR", &Goniometer::getR, arg("self"), return_readonly_numpy())
+ .def("setR", &setR, (arg("self"), arg("rot")));
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Group.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Group.cpp
index cc83d3c6c3de24031536b9e297a3b2049257e35e..28565ab5935ed0fbe38202afe72b96b047313d6d 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Group.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Group.cpp
@@ -64,25 +64,35 @@ void export_Group() {
.value("Associativity", Group::Associativity);
class_<Group, boost::noncopyable>("Group", no_init)
- .def("__init__", make_constructor(&constructGroupFromString),
+ .def("__init__",
+ make_constructor(&constructGroupFromString, default_call_policies(),
+ (arg("symmetryOperationString"))),
"Construct a group from the provided initializer string.")
- .def("__init__", make_constructor(&constructGroupFromVector),
+ .def("__init__",
+ make_constructor(&constructGroupFromVector, default_call_policies(),
+ (arg("symmetryOperationVector"))),
"Construct a group from the provided symmetry operation list.")
- .def("__init__", make_constructor(&constructGroupFromPythonList),
+ .def("__init__", make_constructor(&constructGroupFromPythonList,
+ default_call_policies(),
+ (arg("symmetryOperationList"))),
"Construct a group from a python generated symmetry operation list.")
- .def("getOrder", &Group::order, "Returns the order of the group.")
- .def("getCoordinateSystem", &Group::getCoordinateSystem,
+ .def("getOrder", &Group::order, arg("self"),
+ "Returns the order of the group.")
+ .def("getCoordinateSystem", &Group::getCoordinateSystem, arg("self"),
"Returns the type of coordinate system to distinguish groups with "
"hexagonal system definition.")
- .def("getSymmetryOperations", &Group::getSymmetryOperations,
+ .def("getSymmetryOperations", &Group::getSymmetryOperations, arg("self"),
"Returns the symmetry operations contained in the group.")
.def("getSymmetryOperationStrings", &getSymmetryOperationStrings,
+ arg("self"),
"Returns the x,y,z-strings for the contained symmetry operations.")
.def("containsOperation", &Group::containsOperation,
+ (arg("self"), arg("operation")),
"Checks whether a SymmetryOperation is included in Group.")
- .def("isGroup", &Group::isGroup, "Checks whether the contained symmetry "
- "operations fulfill the group axioms.")
- .def("fulfillsAxiom", &Group::fulfillsAxiom,
+ .def("isGroup", &Group::isGroup, arg("self"),
+ "Checks whether the contained symmetry "
+ "operations fulfill the group axioms.")
+ .def("fulfillsAxiom", &Group::fulfillsAxiom, (arg("self"), arg("axiom")),
"Checks if the contained symmetry operations fulfill the specified "
"group axiom.");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/ICompAssembly.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/ICompAssembly.cpp
index bc8d4d2cec5779576dd9e2826a345c1cb12821b7..32e39ed16f535e568e236c64ae2cb23c558f3046 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/ICompAssembly.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/ICompAssembly.cpp
@@ -11,8 +11,9 @@ void export_ICompAssembly() {
class_<ICompAssembly, boost::python::bases<IComponent>, boost::noncopyable>(
"ICompAssembly", no_init)
- .def("nelements", &ICompAssembly::nelements,
+ .def("nelements", &ICompAssembly::nelements, arg("self"),
"Returns the number of elements in the assembly")
- .def("__getitem__", &ICompAssembly::operator[],
+ .def("__getitem__",
+ &ICompAssembly::operator[], (arg("self"), arg("index")),
"Return the component at the given index");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/IComponent.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/IComponent.cpp
index ff0a91941229fe8a31096d5813371858ab8d374f..d6052b1728b8222a660fcca8861641bc14afa51f 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/IComponent.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/IComponent.cpp
@@ -29,16 +29,18 @@ void export_IComponent() {
register_ptr_to_python<boost::shared_ptr<IComponent>>();
class_<IComponent, boost::noncopyable>("IComponent", no_init)
- .def("getPos", &IComponent::getPos,
+ .def("getPos", &IComponent::getPos, arg("self"),
"Returns the absolute position of the component")
- .def("getDistance", &getDistance, "Returns the distance, in metres, "
- "between this and the given component")
- .def("getName", &IComponent::getName, "Returns the name of the component")
- .def("getFullName", &IComponent::getFullName,
+ .def("getDistance", &getDistance, (arg("self"), arg("other")),
+ "Returns the distance, in metres, "
+ "between this and the given component")
+ .def("getName", &IComponent::getName, arg("self"),
+ "Returns the name of the component")
+ .def("getFullName", &IComponent::getFullName, arg("self"),
"Returns full path name of component")
- .def("type", &IComponent::type,
+ .def("type", &IComponent::type, arg("self"),
"Returns the type of the component represented as a string")
- .def("getRelativeRot", &IComponent::getRelativeRot,
+ .def("getRelativeRot", &IComponent::getRelativeRot, arg("self"),
return_value_policy<copy_const_reference>(),
"Returns the relative rotation as a Quat");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/IDetector.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/IDetector.cpp
index 8bb8d0299891a3bd402d20f054313c877b2902c8..669fbd06ccd3263a61b79cddffa4ed6e0f5b5795 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/IDetector.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/IDetector.cpp
@@ -11,18 +11,19 @@ void export_IDetector() {
class_<IDetector, bases<IObjComponent>, boost::noncopyable>("IDetector",
no_init)
- .def("getID", &IDetector::getID, "Returns the detector ID")
- .def("isMasked", &IDetector::isMasked, "Returns the value of the masked "
- "flag. True means ignore this "
- "detector")
- .def("isMonitor", &IDetector::isMonitor,
+ .def("getID", &IDetector::getID, arg("self"), "Returns the detector ID")
+ .def("isMasked", &IDetector::isMasked, arg("self"),
+ "Returns the value of the masked flag. True means ignore this "
+ "detector")
+ .def("isMonitor", &IDetector::isMonitor, arg("self"),
"Returns True if the detector is marked as a monitor in the IDF")
- .def("solidAngle", &IDetector::solidAngle, "Return the solid angle in "
- "steradians between this "
- "detector and an observer")
+ .def("solidAngle", &IDetector::solidAngle, (arg("self"), arg("observer")),
+ "Return the solid angle in steradians between this "
+ "detector and an observer")
.def("getTwoTheta", &IDetector::getTwoTheta,
+ (arg("self"), arg("observer"), arg("axis")),
"Calculate the angle between this detector, another component and "
"an axis")
- .def("getPhi", &IDetector::getPhi,
+ .def("getPhi", &IDetector::getPhi, arg("self"),
"Returns the azimuthal angle of this detector");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/IMDDimension.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/IMDDimension.cpp
index 7f32083e78fdf64734a7f246a1f820ed853d69ee..77f8f1778ea5f7e5b13d3488d92f118368ddae2b 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/IMDDimension.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/IMDDimension.cpp
@@ -39,24 +39,24 @@ void export_IMDDimension() {
register_ptr_to_python<boost::shared_ptr<IMDDimension>>();
class_<IMDDimension, boost::noncopyable>("IMDDimension", no_init)
- .def("getName", &IMDDimension::getName, "Return the name of the "
- "dimension as can be displayed "
- "along the axis")
- .def("getMaximum", &IMDDimension::getMaximum,
+ .def("getName", &IMDDimension::getName, arg("self"),
+ "Return the name of the dimension as can be displayed "
+ "along the axis")
+ .def("getMaximum", &IMDDimension::getMaximum, arg("self"),
"Return the maximum extent of this dimension")
- .def("getMinimum", &IMDDimension::getMinimum,
+ .def("getMinimum", &IMDDimension::getMinimum, arg("self"),
"Return the maximum extent of this dimension")
- .def("getNBins", &IMDDimension::getNBins,
+ .def("getNBins", &IMDDimension::getNBins, arg("self"),
"Return the number of bins dimension have (an integrated has one). "
"A axis directed along dimension would have getNBins+1 axis points.")
- .def("getX", &IMDDimension::getX,
+ .def("getX", &IMDDimension::getX, (arg("self"), arg("ind")),
"Return coordinate of the axis at the given index")
- .def("getDimensionId", &IMDDimension::getDimensionId,
+ .def("getDimensionId", &IMDDimension::getDimensionId, arg("self"),
"Return a short name which identify the dimension among other "
"dimension."
"A dimension can be usually find by its ID and various ")
- .def("getUnits", &getUnitsAsStr,
+ .def("getUnits", &getUnitsAsStr, arg("self"),
"Return the units associated with this dimension.")
- .def("getMDFrame", &getMDFrame,
+ .def("getMDFrame", &getMDFrame, arg("self"),
"Return the multidimensional frame for this dimension.");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/IObjComponent.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/IObjComponent.cpp
index cf9a708a50efb951e0509784e099ca1c7d90a383..fe184670cb1d98c8599a96ee53409e82c426e0ae 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/IObjComponent.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/IObjComponent.cpp
@@ -25,6 +25,7 @@ void export_IObjComponent() {
class_<IObjComponent, boost::python::bases<IComponent>, boost::noncopyable>(
"IObjComponent", no_init)
- .def("shape", &getShape, "Get the object that represents the physical "
- "shape of this component");
+ .def("shape", &getShape, arg("self"), "Get the object that represents "
+ "the physical shape of this "
+ "component");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Instrument.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Instrument.cpp
index d7ba822270890191a23ac0612aea78464ad82b17..d082519344c6fb4c5b6e68d58ed979e01f4ad589 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Instrument.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Instrument.cpp
@@ -15,41 +15,39 @@ void export_Instrument() {
class_<Instrument, bases<CompAssembly>, boost::noncopyable>("Instrument",
no_init)
- .def("getSample", &Instrument::getSample,
+ .def("getSample", &Instrument::getSample, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Return the object that represents the sample")
- .def("getSource", &Instrument::getSource,
+ .def("getSource", &Instrument::getSource, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Return the object that represents the source")
.def("getComponentByName",
(boost::shared_ptr<IComponent>(Instrument::*)(const std::string &)) &
Instrument::getComponentByName,
- "Returns the named component")
+ (arg("self"), arg("cname")), "Returns the named component")
.def("getDetector", (boost::shared_ptr<IDetector>(
Instrument::*)(const detid_t &) const) &
Instrument::getDetector,
+ (arg("self"), arg("detector_id")),
"Returns the detector with the given ID")
.def("getReferenceFrame",
(boost::shared_ptr<const ReferenceFrame>(Instrument::*)()) &
Instrument::getReferenceFrame,
- return_value_policy<RemoveConstSharedPtr>(),
+ arg("self"), return_value_policy<RemoveConstSharedPtr>(),
"Returns the reference frame attached that defines the instrument "
"axes")
- .def("getValidFromDate", &Instrument::getValidFromDate,
+ .def("getValidFromDate", &Instrument::getValidFromDate, arg("self"),
"Return the valid from date of the instrument")
- .def("getValidToDate", &Instrument::getValidToDate,
+ .def("getValidToDate", &Instrument::getValidToDate, arg("self"),
"Return the valid to date of the instrument")
- .def("getBaseInstrument", &Instrument::baseInstrument,
+ .def("getBaseInstrument", &Instrument::baseInstrument, arg("self"),
return_value_policy<RemoveConstSharedPtr>(),
"Return reference to the base instrument");
- ;
-
- ;
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/MDFrame.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/MDFrame.cpp
index 3f6a3e2ed811775b0019107a4cce1f7a29f1114b..af5dad9763b679e40144822ef79e472624536e42 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/MDFrame.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/MDFrame.cpp
@@ -13,6 +13,6 @@ void export_MDFrame() {
register_ptr_to_python<boost::shared_ptr<MDFrame>>();
class_<MDFrame, boost::noncopyable>("MDFrame", no_init)
- .def("getUnitLabel", &MDFrame::getUnitLabel)
- .def("name", &MDFrame::name);
+ .def("getUnitLabel", &MDFrame::getUnitLabel, arg("self"))
+ .def("name", &MDFrame::name, arg("self"));
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Object.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Object.cpp
index 756ed9f2b7d8d8e1a0fed30067fb6c7ca722d43b..33acda45f4d304af7bba24863adb797455708765 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Object.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Object.cpp
@@ -13,9 +13,9 @@ void export_Object() {
class_<Object, boost::noncopyable>("Object", no_init)
.def("getBoundingBox",
(const BoundingBox &(Object::*)() const) & Object::getBoundingBox,
- return_value_policy<copy_const_reference>(),
+ arg("self"), return_value_policy<copy_const_reference>(),
"Return the axis-aligned bounding box for this shape")
- .def("getShapeXML", &Object::getShapeXML,
+ .def("getShapeXML", &Object::getShapeXML, arg("self"),
"Returns the XML that was used to create this shape.");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/OrientedLattice.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/OrientedLattice.cpp
index b392a312a8eefe784c93c74f828db9efda0e334e..14a995b5b9a8a47c38e10f7a23d34f4bd591f057 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/OrientedLattice.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/OrientedLattice.cpp
@@ -55,13 +55,17 @@ void export_OrientedLattice() {
(arg("_a"), arg("_b"), arg("_c"), arg("_alpha"), arg("_beta"),
arg("_gamma"), arg("Unit") = (int)(angDegrees))))
.def(init<UnitCell>(arg("uc")))
- .def("getuVector", (&OrientedLattice::getuVector))
- .def("getvVector", (&OrientedLattice::getvVector))
- .def("getU", &OrientedLattice::getU, return_readonly_numpy())
- .def("setU", &setU)
- .def("getUB", &OrientedLattice::getUB, return_readonly_numpy())
- .def("setUB", &setUB)
- .def("setUFromVectors", &setUFromVectors)
- .def("qFromHKL", &qFromHKL, "Q vector from HKL vector")
- .def("hklFromQ", &hklFromQ, "HKL value from Q vector");
+ .def("getuVector", (&OrientedLattice::getuVector), arg("self"))
+ .def("getvVector", (&OrientedLattice::getvVector), arg("self"))
+ .def("getU", &OrientedLattice::getU, arg("self"), return_readonly_numpy())
+ .def("setU", &setU, (arg("self"), arg("newU")))
+ .def("getUB", &OrientedLattice::getUB, arg("self"),
+ return_readonly_numpy())
+ .def("setUB", &setUB, (arg("self"), arg("newUB")))
+ .def("setUFromVectors", &setUFromVectors,
+ (arg("self"), arg("u"), arg("v")))
+ .def("qFromHKL", &qFromHKL, (arg("self"), arg("vec")),
+ "Q vector from HKL vector")
+ .def("hklFromQ", &hklFromQ, (arg("self"), arg("vec")),
+ "HKL value from Q vector");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/PeakShape.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/PeakShape.cpp
index 420e07c0ea2a4b5fca085a0adb15ba02098b4166..7c8fbf8f63638225abb96f5704d43dbde5b9c84b 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/PeakShape.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/PeakShape.cpp
@@ -9,10 +9,12 @@ void export_PeakShape() {
register_ptr_to_python<Mantid::Geometry::PeakShape_sptr>();
class_<PeakShape, boost::noncopyable>("PeakShape", no_init)
- .def("toJSON", &PeakShape::toJSON, "Serialize object to JSON")
- .def("shapeName", &PeakShape::shapeName, "Shape name for type of shape")
- .def("algorithmVersion", &PeakShape::algorithmVersion,
+ .def("toJSON", &PeakShape::toJSON, arg("self"),
+ "Serialize object to JSON")
+ .def("shapeName", &PeakShape::shapeName, arg("self"),
+ "Shape name for type of shape")
+ .def("algorithmVersion", &PeakShape::algorithmVersion, arg("self"),
"Number of source integration algorithm version")
- .def("algorithmName", &PeakShape::algorithmName,
+ .def("algorithmName", &PeakShape::algorithmName, arg("self"),
"Name of source integration algorithm");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroup.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroup.cpp
index 31d222c1a7f857eb4064efe43111e3034283bbdb..612397d3524a54e1a4bfbd7bcdccc5540e14b3d4 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroup.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroup.cpp
@@ -55,14 +55,16 @@ void export_PointGroup() {
.value("Cubic", PointGroup::Cubic);
class_<PointGroup, boost::noncopyable, bases<Group>>("PointGroup", no_init)
- .def("getName", &PointGroup::getName)
- .def("getHMSymbol", &PointGroup::getSymbol)
- .def("getCrystalSystem", &PointGroup::crystalSystem)
+ .def("getName", &PointGroup::getName, arg("self"))
+ .def("getHMSymbol", &PointGroup::getSymbol, arg("self"))
+ .def("getCrystalSystem", &PointGroup::crystalSystem, arg("self"))
.def("isEquivalent", &isEquivalent,
+ (arg("self"), arg("hkl1"), arg("hkl2")),
"Check whether the two HKLs are symmetrically equivalent.")
- .def("getEquivalents", &getEquivalents, "Returns an array with all "
- "symmetry equivalents of the "
- "supplied HKL.")
+ .def("getEquivalents", &getEquivalents, (arg("self"), arg("hkl")),
+ "Returns an array with all symmetry equivalents of the supplied "
+ "HKL.")
.def("getReflectionFamily", &getReflectionFamily,
+ (arg("self"), arg("hkl")),
"Returns the same HKL for all symmetry equivalents.");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroupFactory.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroupFactory.cpp
index 0ec8f5c51de65da80f1ffe5e224800ae214dc0e9..07ef88cf35da0139bc8344b68d2b0ca4761a4906 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroupFactory.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/PointGroupFactory.cpp
@@ -25,19 +25,23 @@ void export_PointGroupFactory() {
class_<PointGroupFactoryImpl, boost::noncopyable>("PointGroupFactoryImpl",
no_init)
.def("isSubscribed", &PointGroupFactoryImpl::isSubscribed,
+ (arg("self"), arg("hmSymbol")),
"Returns true of the point group with the given symbol is "
"subscribed.")
.def("createPointGroup", &PointGroupFactoryImpl::createPointGroup,
+ (arg("self"), arg("hmSymbol")),
"Creates a point group if registered.")
.def("createPointGroupFromSpaceGroup", &getPointGroupFromSpaceGroup,
+ (arg("self"), arg("group")),
"Creates the point group that corresponds to the given space group.")
.def("createPointGroupFromSpaceGroupSymbol",
- &getPointGroupFromSpaceGroupSymbol,
+ &getPointGroupFromSpaceGroupSymbol, (arg("self"), arg("group")),
"Creates a point group directly from the space group symbol.")
.def("getAllPointGroupSymbols",
- &PointGroupFactoryImpl::getAllPointGroupSymbols,
+ &PointGroupFactoryImpl::getAllPointGroupSymbols, arg("self"),
"Returns all registered point group symbols.")
.def("getPointGroupSymbols", &PointGroupFactoryImpl::getPointGroupSymbols,
+ (arg("self"), arg("crystalsystem")),
"Returns all point groups registered for the given crystal system.")
.def("Instance", &PointGroupFactory::Instance,
return_value_policy<reference_existing_object>(),
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/RectangularDetector.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/RectangularDetector.cpp
index 01cf57f0361b3758262a8f13e8461379ec964353..8738dd36438adefb21edaf65818cf8196e0c93b4 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/RectangularDetector.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/RectangularDetector.cpp
@@ -16,31 +16,33 @@ void export_RectangularDetector() {
class_<RectangularDetector, bases<CompAssembly, IObjComponent>,
boost::noncopyable>("RectangularDetector", no_init)
- .def("xpixels", &RectangularDetector::xpixels,
+ .def("xpixels", &RectangularDetector::xpixels, arg("self"),
"Returns the number of pixels in the X direction")
- .def("ypixels", &RectangularDetector::ypixels,
+ .def("ypixels", &RectangularDetector::ypixels, arg("self"),
"Returns the number of pixels in the Y direction")
- .def("xstep", &RectangularDetector::xstep,
+ .def("xstep", &RectangularDetector::xstep, arg("self"),
"Returns the step size in the X direction")
- .def("ystep", &RectangularDetector::ystep,
+ .def("ystep", &RectangularDetector::ystep, arg("self"),
"Returns the step size in the Y direction")
- .def("xsize", &RectangularDetector::xsize,
+ .def("xsize", &RectangularDetector::xsize, arg("self"),
"Returns the size in the X direction")
- .def("ysize", &RectangularDetector::ysize,
+ .def("ysize", &RectangularDetector::ysize, arg("self"),
"Returns the size in the Y direction")
- .def("xstart", &RectangularDetector::xstart,
+ .def("xstart", &RectangularDetector::xstart, arg("self"),
"Returns the start position in the X direction")
- .def("ystart", &RectangularDetector::ystart,
+ .def("ystart", &RectangularDetector::ystart, arg("self"),
"Returns the start position in the Y direction")
- .def("idstart", &RectangularDetector::idstart, "Returns the idstart")
+ .def("idstart", &RectangularDetector::idstart, arg("self"),
+ "Returns the idstart")
.def("idfillbyfirst_y", &RectangularDetector::idfillbyfirst_y,
- "Returns the idfillbyfirst_y")
- .def("idstepbyrow", &RectangularDetector::idstepbyrow,
+ arg("self"), "Returns the idfillbyfirst_y")
+ .def("idstepbyrow", &RectangularDetector::idstepbyrow, arg("self"),
"Returns the idstepbyrow")
- .def("idstep", &RectangularDetector::idstep, "Returns the idstep")
- .def("minDetectorID", &RectangularDetector::minDetectorID,
+ .def("idstep", &RectangularDetector::idstep, arg("self"),
+ "Returns the idstep")
+ .def("minDetectorID", &RectangularDetector::minDetectorID, arg("self"),
"Returns the minimum detector id")
- .def("maxDetectorID", &RectangularDetector::maxDetectorID,
+ .def("maxDetectorID", &RectangularDetector::maxDetectorID, arg("self"),
"Returns the maximum detector id");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/ReferenceFrame.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/ReferenceFrame.cpp
index be19d8047e4e04829fe7773e7f6ec54823f0f4ab..c8a79ddbbc76e80bf9bf83a2eb08ba863c6b6c7f 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/ReferenceFrame.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/ReferenceFrame.cpp
@@ -21,13 +21,14 @@ void export_ReferenceFrame() {
.export_values();
class_<ReferenceFrame, boost::noncopyable>("ReferenceFrame", no_init)
- .def("pointingAlongBeam", &ReferenceFrame::pointingAlongBeam)
- .def("pointingUp", &ReferenceFrame::pointingUp)
- .def("vecPointingUp", &ReferenceFrame::vecPointingUp)
- .def("vecPointingAlongBeam", &ReferenceFrame::vecPointingAlongBeam)
- .def("pointingAlongBeamAxis", &ReferenceFrame::pointingAlongBeamAxis)
- .def("pointingUpAxis", &ReferenceFrame::pointingUpAxis)
- .def("pointingHorizontalAxis", &ReferenceFrame::pointingHorizontalAxis)
-
- ;
+ .def("pointingAlongBeam", &ReferenceFrame::pointingAlongBeam, arg("self"))
+ .def("pointingUp", &ReferenceFrame::pointingUp, arg("self"))
+ .def("vecPointingUp", &ReferenceFrame::vecPointingUp, arg("self"))
+ .def("vecPointingAlongBeam", &ReferenceFrame::vecPointingAlongBeam,
+ arg("self"))
+ .def("pointingAlongBeamAxis", &ReferenceFrame::pointingAlongBeamAxis,
+ arg("self"))
+ .def("pointingUpAxis", &ReferenceFrame::pointingUpAxis, arg("self"))
+ .def("pointingHorizontalAxis", &ReferenceFrame::pointingHorizontalAxis,
+ arg("self"));
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..83882c117af6c3965b0e7ed3aae8a75d9dab063b
--- /dev/null
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp
@@ -0,0 +1,77 @@
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+#include "MantidPythonInterface/kernel/Converters/PySequenceToVector.h"
+#include <boost/python/class.hpp>
+#include <boost/python/enum.hpp>
+#include <boost/python/list.hpp>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using namespace Mantid::PythonInterface;
+using namespace boost::python;
+
+namespace {
+boost::python::list getListFromV3DVector(const std::vector<V3D> &hkls) {
+ boost::python::list hklList;
+ for (auto it = hkls.begin(); it != hkls.end(); ++it) {
+ hklList.append(*it);
+ }
+ return hklList;
+}
+
+boost::python::list getHKLsDefaultFilter(ReflectionGenerator &self, double dMin,
+ double dMax) {
+ return getListFromV3DVector(self.getHKLs(dMin, dMax));
+}
+
+boost::python::list getHKLsUsingFilter(ReflectionGenerator &self, double dMin,
+ double dMax,
+ ReflectionConditionFilter filter) {
+ return getListFromV3DVector(
+ self.getHKLs(dMin, dMax, self.getReflectionConditionFilter(filter)));
+}
+
+boost::python::list getUniqueHKLsDefaultFilter(ReflectionGenerator &self,
+ double dMin, double dMax) {
+ return getListFromV3DVector(self.getUniqueHKLs(dMin, dMax));
+}
+
+boost::python::list getUniqueHKLsUsingFilter(ReflectionGenerator &self,
+ double dMin, double dMax,
+ ReflectionConditionFilter filter) {
+ return getListFromV3DVector(self.getUniqueHKLs(
+ dMin, dMax, self.getReflectionConditionFilter(filter)));
+}
+
+std::vector<double> getDValues(ReflectionGenerator &self,
+ const boost::python::object &hkls) {
+ Converters::PySequenceToVector<V3D> converter(hkls);
+
+ return self.getDValues(converter());
+}
+
+std::vector<double> getFsSquared(ReflectionGenerator &self,
+ const boost::python::object &hkls) {
+ Converters::PySequenceToVector<V3D> converter(hkls);
+
+ return self.getFsSquared(converter());
+}
+}
+
+void export_ReflectionGenerator() {
+ enum_<ReflectionConditionFilter>("ReflectionConditionFilter")
+ .value("None", ReflectionConditionFilter::None)
+ .value("Centering", ReflectionConditionFilter::Centering)
+ .value("SpaceGroup", ReflectionConditionFilter::SpaceGroup)
+ .value("StructureFactor", ReflectionConditionFilter::StructureFactor)
+ .export_values();
+
+ class_<ReflectionGenerator>("ReflectionGenerator", no_init)
+ .def(init<const CrystalStructure &, optional<ReflectionConditionFilter>>(
+ (arg("crystalStructure"), arg("defaultFilter"))))
+ .def("getHKLs", &getHKLsDefaultFilter)
+ .def("getHKLsUsingFilter", &getHKLsUsingFilter)
+ .def("getUniqueHKLs", &getUniqueHKLsDefaultFilter)
+ .def("getUniqueHKLsUsingFilter", &getUniqueHKLsUsingFilter)
+ .def("getDValues", &getDValues)
+ .def("getFsSquared", &getFsSquared);
+}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroup.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroup.cpp
index 9b83cabe216135b66e9d7a04c8aa141c5c0c5282..919d784341e24fcb868e2eff89e92e5523843112 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroup.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroup.cpp
@@ -53,16 +53,19 @@ void export_SpaceGroup() {
register_ptr_to_python<boost::shared_ptr<SpaceGroup>>();
class_<SpaceGroup, boost::noncopyable, bases<Group>>("SpaceGroup", no_init)
- .def("getNumber", &SpaceGroup::number)
- .def("getHMSymbol", &SpaceGroup::hmSymbol)
+ .def("getNumber", &SpaceGroup::number, arg("self"))
+ .def("getHMSymbol", &SpaceGroup::hmSymbol, arg("self"))
.def("getEquivalentPositions", &getEquivalentPositions,
+ (arg("self"), arg("point")),
"Returns an array with all symmetry equivalents of the supplied "
"HKL.")
.def("isAllowedReflection", &isAllowedReflection,
+ (arg("self"), arg("hkl")),
"Returns True if the supplied reflection is allowed with respect to "
"space group symmetry operations.")
- .def("getPointGroup", &SpaceGroup::getPointGroup,
+ .def("getPointGroup", &SpaceGroup::getPointGroup, arg("self"),
"Returns the point group of the space group.")
.def("getSiteSymmetryGroup", &getSiteSymmetryGroup,
+ (arg("self"), arg("position")),
"Returns the site symmetry group for supplied point coordinates.");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroupFactory.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroupFactory.cpp
index 365d6e02a78ba2b35863b83effebb5d24cca5fe1..2b0a5b54e8302334ba9785e5c532f2d6dd51c2b8 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroupFactory.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/SpaceGroupFactory.cpp
@@ -45,19 +45,24 @@ void export_SpaceGroupFactory() {
class_<SpaceGroupFactoryImpl, boost::noncopyable>("SpaceGroupFactoryImpl",
no_init)
.def("isSubscribedSymbol", &isSubscribedSymbol,
+ (arg("self"), arg("symbol")),
"Returns true if the space group the supplied symbol is subscribed.")
.def("isSubscribedNumber", &isSubscribedNumber,
+ (arg("self"), arg("number")),
"Returns true if a space group with the given number is subscribed.")
- .def("createSpaceGroup", &createSpaceGroup, "Creates a space group.")
- .def("getAllSpaceGroupSymbols", &allSpaceGroupSymbols,
+ .def("createSpaceGroup", &createSpaceGroup, (arg("self"), arg("symbol")),
+ "Creates a space group.")
+ .def("getAllSpaceGroupSymbols", &allSpaceGroupSymbols, arg("self"),
"Returns all subscribed space group symbols.")
.def("getAllSpaceGroupNumbers",
- &SpaceGroupFactoryImpl::subscribedSpaceGroupNumbers,
+ &SpaceGroupFactoryImpl::subscribedSpaceGroupNumbers, arg("self"),
"Returns all subscribed space group numbers.")
.def("subscribedSpaceGroupSymbols", &spaceGroupSymbolsForNumber,
+ (arg("self"), arg("number")),
"Returns all space group symbols that are registered under the "
"given number.")
- .def("getSpaceGroupsForPointGroup", &spaceGroupSymbolsForPointGroup)
+ .def("getSpaceGroupsForPointGroup", &spaceGroupSymbolsForPointGroup,
+ (arg("self"), arg("pointGroup")))
.def("Instance", &SpaceGroupFactory::Instance,
return_value_policy<reference_existing_object>(),
"Returns a reference to the SpaceGroupFactory singleton")
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElement.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElement.cpp
index be79196c0fee3a15bbded1fa0030b42437bef456..f520a92edac03e3880ecc318023e2736efbe506f 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElement.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElement.cpp
@@ -42,12 +42,12 @@ void export_SymmetryElement() {
.value("None", SymmetryElementRotation::None);
class_<SymmetryElement, boost::noncopyable>("SymmetryElement", no_init)
- .def("getHMSymbol", &SymmetryElement::hmSymbol,
+ .def("getHMSymbol", &SymmetryElement::hmSymbol, arg("self"),
"Returns the Hermann-Mauguin symbol for the element.")
- .def("getAxis", &getAxis, "Returns the symmetry axis or [0,0,0] for "
- "identiy, inversion and translations.")
- .def("getRotationSense", &getRotationSense,
- "Returns the rotation sense"
- "of a rotation axis or None"
+ .def("getAxis", &getAxis, arg("self"),
+ "Returns the symmetry axis or [0,0,0] for "
+ "identiy, inversion and translations.")
+ .def("getRotationSense", &getRotationSense, arg("self"),
+ "Returns the rotation sense of a rotation axis or None"
"if the element is not a rotation.");
}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElementFactory.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElementFactory.cpp
index 59db23c9a35c62af611787e2ac2dc1b17e056fde..5804ab01d36d8075314e745c262736fbfa215372 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElementFactory.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryElementFactory.cpp
@@ -9,6 +9,7 @@ void export_SymmetryElementFactory() {
class_<SymmetryElementFactoryImpl, boost::noncopyable>(
"SymmetryElementFactoryImpl", no_init)
.def("createSymElement", &SymmetryElementFactoryImpl::createSymElement,
+ (arg("self"), arg("operation")),
"Creates the symmetry element that corresponds to the supplied "
"symmetry operation.")
.def("Instance", &SymmetryElementFactory::Instance,
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperation.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperation.cpp
index 180a9153aa917276f8037cf9c0e0d1d8943dd0d7..d20617ea9576b16d6affdb008c4cb89aeb5beb1b 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperation.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperation.cpp
@@ -34,19 +34,21 @@ void export_SymmetryOperation() {
register_ptr_to_python<boost::shared_ptr<SymmetryOperation>>();
class_<SymmetryOperation>("SymmetryOperation")
- .def("getOrder", &SymmetryOperation::order,
+ .def("getOrder", &SymmetryOperation::order, arg("self"),
"Returns the order of the symmetry operation, which indicates how "
"often the operation needs to be applied to a point to arrive at "
"identity.")
- .def("getIdentifier", &SymmetryOperation::identifier,
+ .def("getIdentifier", &SymmetryOperation::identifier, arg("self"),
"The identifier of the operation in x,y,z-notation.")
.def("transformCoordinates", &applyToCoordinates,
+ (arg("self"), arg("coordinates")),
"Returns transformed coordinates. For transforming HKLs, use "
"transformHKL.")
- .def("transformHKL", &applyToVector, "Returns transformed HKLs. For "
- "transformation of coordinates use "
- "transformCoordinates.")
- .def("apply", &applyToVector, "An alias for transformHKL.");
+ .def("transformHKL", &applyToVector, (arg("self"), arg("hkl")),
+ "Returns transformed HKLs. For transformation of coordinates use "
+ "transformCoordinates.")
+ .def("apply", &applyToVector, (arg("self"), arg("hkl")),
+ "An alias for transformHKL.");
std_vector_exporter<Mantid::Geometry::SymmetryOperation>::wrap(
"std_vector_symmetryoperation");
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperationFactory.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperationFactory.cpp
index dc78c2bcd5d569943f0c08956a9802974591fb1d..147ff1e85375cdc32b7c96902b8a1d4fb9ab5104 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperationFactory.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/SymmetryOperationFactory.cpp
@@ -25,14 +25,16 @@ void export_SymmetryOperationFactory() {
class_<SymmetryOperationFactoryImpl, boost::noncopyable>(
"SymmetryOperationFactoryImpl", no_init)
.def("exists", &SymmetryOperationFactoryImpl::isSubscribed,
+ (arg("self"), arg("identifier")),
"Returns true if the symmetry operation is supplied.")
.def("createSymOp", &SymmetryOperationFactoryImpl::createSymOp,
+ (arg("self"), arg("identifier")),
"Creates the symmetry operation from the supplied x,y,z-identifier.")
- .def("createSymOps", &createSymOps,
+ .def("createSymOps", &createSymOps, (arg("self"), arg("identifier")),
"Creates a vector of SymmetryOperation objects from a semi-colon "
"separated list of x,y,z-identifiers.")
.def("subscribedSymbols",
- &SymmetryOperationFactoryImpl::subscribedSymbols,
+ &SymmetryOperationFactoryImpl::subscribedSymbols, arg("self"),
"Return all subscribed symbols.")
.def("Instance", &SymmetryOperationFactory::Instance,
return_value_policy<reference_existing_object>(),
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/UnitCell.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/UnitCell.cpp
index 9da36354a38d67012a65986d4586822ff4e7e1a9..326b247bb1c7a501a2711efd64b5728f94ec028a 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/UnitCell.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/UnitCell.cpp
@@ -38,103 +38,129 @@ void export_UnitCell() {
return_readonly_numpy;
class_<UnitCell>("UnitCell", init<>())
- .def(init<UnitCell const &>(arg("other")))
- .def(init<double, double, double>((arg("_a"), arg("_b"), arg("_c"))))
+ .def(init<UnitCell const &>((arg("self"), arg("other"))))
+ .def(init<double, double, double>(
+ (arg("self"), arg("_a"), arg("_b"), arg("_c"))))
.def(init<double, double, double, double, double, double, optional<int>>(
- (arg("_a"), arg("_b"), arg("_c"), arg("_alpha"), arg("_beta"),
- arg("_gamma"), arg("Unit") = (int)(angDegrees))))
- .def("a", (double (UnitCell::*)() const) & UnitCell::a)
- .def("a1", (double (UnitCell::*)() const) & UnitCell::a1)
- .def("a2", (double (UnitCell::*)() const) & UnitCell::a2)
- .def("a3", (double (UnitCell::*)() const) & UnitCell::a3)
- .def("alpha", (double (UnitCell::*)() const) & UnitCell::alpha)
- .def("alpha1", (double (UnitCell::*)() const) & UnitCell::alpha1)
- .def("alpha2", (double (UnitCell::*)() const) & UnitCell::alpha2)
- .def("alpha3", (double (UnitCell::*)() const) & UnitCell::alpha3)
- .def("alphastar", (double (UnitCell::*)() const) & UnitCell::alphastar)
- .def("astar", (double (UnitCell::*)() const) & UnitCell::astar)
- .def("b", (double (UnitCell::*)() const) & UnitCell::b)
- .def("b1", (double (UnitCell::*)() const) & UnitCell::b1)
- .def("b2", (double (UnitCell::*)() const) & UnitCell::b2)
- .def("b3", (double (UnitCell::*)() const) & UnitCell::b3)
- .def("beta", (double (UnitCell::*)() const) & UnitCell::beta)
- .def("beta1", (double (UnitCell::*)() const) & UnitCell::beta1)
- .def("beta2", (double (UnitCell::*)() const) & UnitCell::beta2)
- .def("beta3", (double (UnitCell::*)() const) & UnitCell::beta3)
- .def("betastar", (double (UnitCell::*)() const) & UnitCell::betastar)
- .def("bstar", (double (UnitCell::*)() const) & UnitCell::bstar)
- .def("c", (double (UnitCell::*)() const) & UnitCell::c)
- .def("cstar", (double (UnitCell::*)() const) & UnitCell::cstar)
+ (arg("self"), arg("_a"), arg("_b"), arg("_c"), arg("_alpha"),
+ arg("_beta"), arg("_gamma"), arg("Unit") = (int)(angDegrees))))
+ .def("a", (double (UnitCell::*)() const) & UnitCell::a, arg("self"))
+ .def("a1", (double (UnitCell::*)() const) & UnitCell::a1, arg("self"))
+ .def("a2", (double (UnitCell::*)() const) & UnitCell::a2, arg("self"))
+ .def("a3", (double (UnitCell::*)() const) & UnitCell::a3, arg("self"))
+ .def("alpha", (double (UnitCell::*)() const) & UnitCell::alpha,
+ arg("self"))
+ .def("alpha1", (double (UnitCell::*)() const) & UnitCell::alpha1,
+ arg("self"))
+ .def("alpha2", (double (UnitCell::*)() const) & UnitCell::alpha2,
+ arg("self"))
+ .def("alpha3", (double (UnitCell::*)() const) & UnitCell::alpha3,
+ arg("self"))
+ .def("alphastar", (double (UnitCell::*)() const) & UnitCell::alphastar,
+ arg("self"))
+ .def("astar", (double (UnitCell::*)() const) & UnitCell::astar,
+ arg("self"))
+ .def("b", (double (UnitCell::*)() const) & UnitCell::b, arg("self"))
+ .def("b1", (double (UnitCell::*)() const) & UnitCell::b1, arg("self"))
+ .def("b2", (double (UnitCell::*)() const) & UnitCell::b2, arg("self"))
+ .def("b3", (double (UnitCell::*)() const) & UnitCell::b3, arg("self"))
+ .def("beta", (double (UnitCell::*)() const) & UnitCell::beta, arg("self"))
+ .def("beta1", (double (UnitCell::*)() const) & UnitCell::beta1,
+ arg("self"))
+ .def("beta2", (double (UnitCell::*)() const) & UnitCell::beta2,
+ arg("self"))
+ .def("beta3", (double (UnitCell::*)() const) & UnitCell::beta3,
+ arg("self"))
+ .def("betastar", (double (UnitCell::*)() const) & UnitCell::betastar,
+ arg("self"))
+ .def("bstar", (double (UnitCell::*)() const) & UnitCell::bstar,
+ arg("self"))
+ .def("c", (double (UnitCell::*)() const) & UnitCell::c, arg("self"))
+ .def("cstar", (double (UnitCell::*)() const) & UnitCell::cstar,
+ arg("self"))
.def("d",
(double (UnitCell::*)(double, double, double) const) & UnitCell::d,
- (arg("h"), arg("k"), arg("l")))
+ (arg("self"), arg("h"), arg("k"), arg("l")))
.def("d", (double (UnitCell::*)(const V3D &) const) & UnitCell::d,
- (arg("hkl")))
+ (arg("self"), arg("hkl")))
.def("dstar", (double (UnitCell::*)(double, double, double) const) &
UnitCell::dstar,
- (arg("h"), arg("k"), arg("l")))
- .def("errora", (double (UnitCell::*)() const) & UnitCell::errora)
- .def("errorb", (double (UnitCell::*)() const) & UnitCell::errorb)
- .def("errorc", (double (UnitCell::*)() const) & UnitCell::errorc)
+ (arg("self"), arg("h"), arg("k"), arg("l")))
+ .def("errora", (double (UnitCell::*)() const) & UnitCell::errora,
+ arg("self"))
+ .def("errorb", (double (UnitCell::*)() const) & UnitCell::errorb,
+ arg("self"))
+ .def("errorc", (double (UnitCell::*)() const) & UnitCell::errorc,
+ arg("self"))
.def("erroralpha",
(double (UnitCell::*)(int const) const) & UnitCell::erroralpha,
- (arg("Unit") = (int)(angDegrees)))
+ (arg("self"), arg("Unit") = (int)(angDegrees)))
.def("errorbeta",
(double (UnitCell::*)(int const) const) & UnitCell::errorbeta,
- (arg("Unit") = (int)(angDegrees)))
+ (arg("self"), arg("Unit") = (int)(angDegrees)))
.def("errorgamma",
(double (UnitCell::*)(int const) const) & UnitCell::errorgamma,
- (arg("Unit") = (int)(angDegrees)))
- .def("gamma", (double (UnitCell::*)() const) & UnitCell::gamma)
- .def("gammastar", (double (UnitCell::*)() const) & UnitCell::gammastar)
+ (arg("self"), arg("Unit") = (int)(angDegrees)))
+ .def("gamma", (double (UnitCell::*)() const) & UnitCell::gamma,
+ arg("self"))
+ .def("gammastar", (double (UnitCell::*)() const) & UnitCell::gammastar,
+ arg("self"))
.def("recAngle", (double (UnitCell::*)(double, double, double, double,
double, double, int const) const) &
UnitCell::recAngle,
- (arg("h1"), arg("k1"), arg("l1"), arg("h2"), arg("k2"), arg("l2"),
- arg("Unit") = (int)(angDegrees)))
- .def("recVolume", (double (UnitCell::*)() const) & UnitCell::recVolume)
+ (arg("self"), arg("h1"), arg("k1"), arg("l1"), arg("h2"), arg("k2"),
+ arg("l2"), arg("Unit") = (int)(angDegrees)))
+ .def("recVolume", (double (UnitCell::*)() const) & UnitCell::recVolume,
+ arg("self"))
.def("set", (void (UnitCell::*)(double, double, double, double, double,
double, int const)) &
UnitCell::set,
- (arg("_a"), arg("_b"), arg("_c"), arg("_alpha"), arg("_beta"),
- arg("_gamma"), arg("Unit") = (int)(angDegrees)))
- .def("seta", (void (UnitCell::*)(double))(&UnitCell::seta), (arg("_a")))
+ (arg("self"), arg("_a"), arg("_b"), arg("_c"), arg("_alpha"),
+ arg("_beta"), arg("_gamma"), arg("Unit") = (int)(angDegrees)))
+ .def("seta", (void (UnitCell::*)(double))(&UnitCell::seta),
+ (arg("self"), arg("_a")))
.def("setalpha",
(void (UnitCell::*)(double, int const))(&UnitCell::setalpha),
- (arg("_alpha"), arg("Unit") = (int)(angDegrees)))
- .def("setb", (void (UnitCell::*)(double))(&UnitCell::setb), (arg("_b")))
+ (arg("self"), arg("_alpha"), arg("Unit") = (int)(angDegrees)))
+ .def("setb", (void (UnitCell::*)(double))(&UnitCell::setb),
+ (arg("self"), arg("_b")))
.def("setbeta",
(void (UnitCell::*)(double, int const))(&UnitCell::setbeta),
- (arg("_beta"), arg("Unit") = (int)(angDegrees)))
- .def("setc", (void (UnitCell::*)(double))(&UnitCell::setc), (arg("_c")))
+ (arg("self"), arg("_beta"), arg("Unit") = (int)(angDegrees)))
+ .def("setc", (void (UnitCell::*)(double))(&UnitCell::setc),
+ (arg("self"), arg("_c")))
.def("setgamma",
(void (UnitCell::*)(double, int const))(&UnitCell::setgamma),
- (arg("_gamma"), arg("Unit") = (int)(angDegrees)))
+ (arg("self"), arg("_gamma"), arg("Unit") = (int)(angDegrees)))
.def("setError", (void (UnitCell::*)(double, double, double, double,
double, double, int const)) &
UnitCell::setError,
- (arg("_aerr"), arg("_berr"), arg("_cerr"), arg("_alphaerr"),
- arg("_betaerr"), arg("_gammaerr"), arg("Unit") = (int)(angDegrees)))
+ (arg("self"), arg("_aerr"), arg("_berr"), arg("_cerr"),
+ arg("_alphaerr"), arg("_betaerr"), arg("_gammaerr"),
+ arg("Unit") = (int)(angDegrees)))
.def("setErrora", (void (UnitCell::*)(double))(&UnitCell::setErrora),
- (arg("_aerr")))
+ (arg("self"), arg("_aerr")))
.def("setErroralpha",
(void (UnitCell::*)(double, int const))(&UnitCell::setErroralpha),
- (arg("_alphaerr"), arg("Unit") = (int)(angDegrees)))
+ (arg("self"), arg("_alphaerr"), arg("Unit") = (int)(angDegrees)))
.def("setErrorb", (void (UnitCell::*)(double))(&UnitCell::setErrorb),
- (arg("_berr")))
+ (arg("self"), arg("_berr")))
.def("setErrorbeta",
(void (UnitCell::*)(double, int const))(&UnitCell::setErrorbeta),
- (arg("_betaerr"), arg("Unit") = (int)(angDegrees)))
+ (arg("self"), arg("_betaerr"), arg("Unit") = (int)(angDegrees)))
.def("setErrorc", (void (UnitCell::*)(double))(&UnitCell::setErrorc),
- (arg("_cerr")))
+ (arg("self"), arg("_cerr")))
.def("setErrorgamma",
(void (UnitCell::*)(double, int const))(&UnitCell::setErrorgamma),
- (arg("_gammaerr"), arg("Unit") = (int)(angDegrees)))
- .def("volume", (double (UnitCell::*)() const) & UnitCell::volume)
- .def("getG", &UnitCell::getG, return_readonly_numpy())
- .def("getGstar", &UnitCell::getGstar, return_readonly_numpy())
- .def("getB", &UnitCell::getB, return_readonly_numpy())
- .def("recalculateFromGstar", &recalculateFromGstar);
+ (arg("self"), arg("_gammaerr"), arg("Unit") = (int)(angDegrees)))
+ .def("volume", (double (UnitCell::*)() const) & UnitCell::volume,
+ arg("self"))
+ .def("getG", &UnitCell::getG, arg("self"), return_readonly_numpy())
+ .def("getGstar", &UnitCell::getGstar, arg("self"),
+ return_readonly_numpy())
+ .def("getB", &UnitCell::getB, arg("self"), return_readonly_numpy())
+ .def("recalculateFromGstar", &recalculateFromGstar,
+ (arg("self"), arg("NewGstar")));
scope().attr("deg2rad") = Mantid::Geometry::deg2rad;
scope().attr("rad2deg") = Mantid::Geometry::rad2deg;
diff --git a/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp b/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp
index 61163771c9d2d3e88a73a25de32ab62e32c6cecb..22a6c099010b426e969319b0d978d85180b45722 100644
--- a/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp
+++ b/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp
@@ -28,11 +28,20 @@ std::string getStringUsingCache(ConfigServiceImpl &self,
return self.getString(key, true);
}
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
+
/// Overload generator for getInstrument
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(getInstrument_Overload, getInstrument, 0,
1)
/// Overload generator for getString
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(getString_Overload, getString, 1, 2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
}
void export_ConfigService() {
diff --git a/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp b/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp
index 3cfaf72e9ec1d44d7e3816714d8a8d30c5f98de4..d2f9494ae0059a2f4839abd506fcf8da627f4c0c 100644
--- a/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp
+++ b/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp
@@ -93,10 +93,18 @@ Statistics getStatisticsNumpy(const numeric::array &data,
throw UnknownDataType();
}
}
+
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Define an overload to handle the default argument
BOOST_PYTHON_FUNCTION_OVERLOADS(getStatisticsOverloads, getStatisticsNumpy, 1,
2)
-
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
//============================ Z score
//============================================
@@ -145,9 +153,17 @@ std::vector<double> getModifiedZscoreNumpy(const numeric::array &data,
}
}
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Define an overload to handle the default argument
BOOST_PYTHON_FUNCTION_OVERLOADS(getModifiedZscoreOverloads,
getModifiedZscoreNumpy, 1, 2)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
//============================ getMoments
//============================================
@@ -198,10 +214,17 @@ std::vector<double> getMomentsAboutOriginNumpy(const numeric::array &indep,
return getMomentsNumpyImpl(&getMomentsAboutOrigin, indep, depend, maxMoment);
}
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Define an overload to handle the default argument
BOOST_PYTHON_FUNCTION_OVERLOADS(getMomentsAboutOriginOverloads,
getMomentsAboutOriginNumpy, 2, 3)
-
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
/**
* Proxy for @see Mantid::Kernel::getMomentsAboutMean so that it can accept
* numpy arrays
@@ -213,9 +236,18 @@ std::vector<double> getMomentsAboutMeanNumpy(const numeric::array &indep,
return getMomentsNumpyImpl(&getMomentsAboutMean, indep, depend, maxMoment);
}
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
// Define an overload to handle the default argument
BOOST_PYTHON_FUNCTION_OVERLOADS(getMomentsAboutMeanOverloads,
getMomentsAboutMeanNumpy, 2, 3)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
+
///@endcond
}
diff --git a/Framework/PythonInterface/plugins/algorithms/ComputeCalibrationCoefVan.py b/Framework/PythonInterface/plugins/algorithms/ComputeCalibrationCoefVan.py
new file mode 100644
index 0000000000000000000000000000000000000000..a6964b3768e7acd5a4056f52cbfb721c8c95ef06
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/ComputeCalibrationCoefVan.py
@@ -0,0 +1,168 @@
+from mantid.api import PythonAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty, Progress, InstrumentValidator
+from mantid.kernel import Direction
+import numpy as np
+from scipy import integrate
+import scipy as sp
+import mlzutils
+
+
+class ComputeCalibrationCoefVan(PythonAlgorithm):
+ """ Calculate coefficients to normalize by Vanadium and correct Debye Waller factor
+ """
+ def __init__(self):
+ """
+ Init
+ """
+ PythonAlgorithm.__init__(self)
+ self.vanaws = None
+ self.defaultT = 293.0 # K, default temperature if not given
+ self.Mvan = 50.942 # [g/mol], Vanadium molar mass
+ self.DebyeT = 389.0 # K, Debye temperature for Vanadium
+
+ def category(self):
+ """ Return category
+ """
+ return "PythonAlgorithms;CorrectionFunctions\\EfficiencyCorrections"
+
+ def name(self):
+ """ Return summary
+ """
+ return "ComputeCalibrationCoefVan"
+
+ def summary(self):
+ return "Calculate coefficients for detector efficiency correction using the Vanadium data."
+
+ def PyInit(self):
+ """ Declare properties
+ """
+ self.declareProperty(MatrixWorkspaceProperty("VanadiumWorkspace", "", direction=Direction.Input,
+ validator=InstrumentValidator()),
+ "Input Vanadium workspace")
+ self.declareProperty(MatrixWorkspaceProperty("OutputWorkspace", "", direction=Direction.Output),
+ "Name the workspace that will contain the calibration coefficients")
+ return
+
+ def validateInputs(self):
+ issues = dict()
+ inws = self.getProperty("VanadiumWorkspace").value
+ run = inws.getRun()
+
+ if not run.hasProperty('wavelength'):
+ issues['VanadiumWorkspace'] = "Input workspace must have wavelength sample log."
+ else:
+ try:
+ float(run.getProperty('wavelength').value)
+ except ValueError:
+ issues['VanadiumWorkspace'] = "Invalid value for wavelength sample log. Wavelength must be a number."
+
+ return issues
+
+ def get_temperature(self):
+ """
+ tries to get temperature from the sample logs
+ in the case of fail, default value is returned
+ """
+ run = self.vanaws.getRun()
+ if not run.hasProperty('temperature'):
+ self.log().warning("Temperature sample log is not present in " + self.vanaws.getName() +
+ " T=293K is assumed for Debye-Waller factor.")
+ return self.defaultT
+ try:
+ temperature = float(run.getProperty('temperature').value)
+ except ValueError, err:
+ self.log().warning("Error of getting temperature: " + err +
+ " T=293K is assumed for Debye-Waller factor.")
+ return self.defaultT
+
+ return temperature
+
+ def PyExec(self):
+ """ Main execution body
+ """
+ self.vanaws = self.getProperty("VanadiumWorkspace").value # returns workspace instance
+ outws_name = self.getPropertyValue("OutputWorkspace") # returns workspace name (string)
+ nhist = self.vanaws.getNumberHistograms()
+ prog_reporter = Progress(self, start=0.0, end=1.0, nreports=nhist+1)
+
+ # calculate array of Debye-Waller factors
+ dwf = self.calculate_dwf()
+
+ # for each detector: fit gaussian to get peak_centre and fwhm
+ # sum data in the range [peak_centre - 3*fwhm, peak_centre + 3*fwhm]
+ dataX = self.vanaws.readX(0)
+ coefY = np.zeros(nhist)
+ coefE = np.zeros(nhist)
+ instrument = self.vanaws.getInstrument()
+ detID_offset = self.get_detID_offset()
+ for idx in range(nhist):
+ prog_reporter.report("Setting %dth spectrum" % idx)
+ dataY = self.vanaws.readY(idx)
+ det = instrument.getDetector(idx + detID_offset)
+ if np.max(dataY) == 0 or det.isMasked():
+ coefY[idx] = 0.
+ coefE[idx] = 0.
+ else:
+ dataE = self.vanaws.readE(idx)
+ peak_centre, sigma = mlzutils.do_fit_gaussian(self.vanaws, idx, self.log())
+ fwhm = sigma*2.*np.sqrt(2.*np.log(2.))
+ idxmin = (np.fabs(dataX-peak_centre+3.*fwhm)).argmin()
+ idxmax = (np.fabs(dataX-peak_centre-3.*fwhm)).argmin()
+ coefY[idx] = dwf[idx]*sum(dataY[idxmin:idxmax+1])
+ coefE[idx] = dwf[idx]*sum(dataE[idxmin:idxmax+1])
+
+ # create X array, X data are the same for all detectors, so
+ coefX = np.zeros(nhist)
+ coefX.fill(dataX[0])
+
+ create = self.createChildAlgorithm("CreateWorkspace")
+ create.setPropertyValue('OutputWorkspace', outws_name)
+ create.setProperty('ParentWorkspace', self.vanaws)
+ create.setProperty('DataX', coefX)
+ create.setProperty('DataY', coefY)
+ create.setProperty('DataE', coefE)
+ create.setProperty('NSpec', nhist)
+ create.setProperty('UnitX', 'TOF')
+ create.execute()
+ outws = create.getProperty('OutputWorkspace').value
+
+ self.setProperty("OutputWorkspace", outws)
+
+ def get_detID_offset(self):
+ """
+ returns ID of the first detector
+ """
+ return self.vanaws.getSpectrum(0).getDetectorIDs()[0]
+
+ def calculate_dwf(self):
+ """
+ Calculates Debye-Waller factor according to
+ Sears and Shelley Acta Cryst. A 47, 441 (1991)
+ """
+ run = self.vanaws.getRun()
+ nhist = self.vanaws.getNumberHistograms()
+ thetasort = np.zeros(nhist) # theta in radians, not 2Theta
+
+ instrument = self.vanaws.getInstrument()
+ detID_offset = self.get_detID_offset()
+
+ for i in range(nhist):
+ det = instrument.getDetector(i + detID_offset)
+ thetasort[i] = 0.5*np.sign(np.cos(det.getPhi()))*self.vanaws.detectorTwoTheta(det)
+ # thetasort[i] = 0.5*self.vanaws.detectorSignedTwoTheta(det) # gives opposite sign for detectors 0-24
+
+ temperature = self.get_temperature() # T in K
+ wlength = float(run.getLogData('wavelength').value) # Wavelength, Angstrom
+ mass_vana = 0.001*self.Mvan/sp.constants.N_A # Vanadium mass, kg
+ temp_ratio = temperature/self.DebyeT
+
+ if temp_ratio < 1.e-3:
+ integral = 0.5
+ else:
+ integral = integrate.quad(lambda x: x/sp.tanh(0.5*x/temp_ratio), 0, 1)[0]
+
+ msd = 3.*sp.constants.hbar**2/(2.*mass_vana*sp.constants.k * self.DebyeT)*integral*1.e20
+ return np.exp(-msd*(4.*sp.pi*sp.sin(thetasort)/wlength)**2)
+
+
+# Register algorithm with Mantid.
+AlgorithmFactory.subscribe(ComputeCalibrationCoefVan)
diff --git a/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py b/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py
index e587a1bfdef0c883ffd6d29d8e7955c34d6b0dfe..477cf69705777a9ce74bfb877129a6023557327e 100644
--- a/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py
+++ b/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py
@@ -132,6 +132,20 @@ class LoadVesuvio(LoadEmptyVesuvio):
else:
self._exec_single_foil_state_mode()
+#----------------------------------------------------------------------------------------
+
+ def validateInputs(self):
+ issues = {}
+
+ # Validtae run number ranges
+ run_str = self.getProperty(RUN_PROP).value
+ if "-" in run_str:
+ lower, upper = run_str.split("-")
+ if upper < lower:
+ issues[RUN_PROP] = "Range must be in format lower-upper"
+
+ return issues
+
#----------------------------------------------------------------------------------------
def _exec_difference_mode(self):
@@ -346,24 +360,42 @@ class LoadVesuvio(LoadEmptyVesuvio):
if index == 0:
out_name, out_mon = SUMMED_WS, SUMMED_MON
else:
- out_name, out_mon = SUMMED_WS+'tmp', SUMMED_MON + 'tmp'
+ out_name, out_mon = SUMMED_WS + 'tmp', SUMMED_MON + 'tmp'
+
# Load data
- ms.LoadRaw(Filename=run, SpectrumList=spectra,
- OutputWorkspace=out_name, LoadMonitors='Exclude',EnableLogging=_LOGGING_)
- ms.LoadRaw(Filename=run,SpectrumList=self._mon_spectra,
- OutputWorkspace=out_mon,EnableLogging=_LOGGING_)
- if index > 0: # sum
- ms.Plus(LHSWorkspace=SUMMED_WS, RHSWorkspace=out_name,
- OutputWorkspace=SUMMED_WS,EnableLogging=_LOGGING_)
- ms.Plus(LHSWorkspace=SUMMED_MON, RHSWorkspace=out_mon,
- OutputWorkspace=SUMMED_MON,EnableLogging=_LOGGING_)
- ms.DeleteWorkspace(out_name,EnableLogging=_LOGGING_)
- ms.DeleteWorkspace(out_mon,EnableLogging=_LOGGING_)
-
- ms.CropWorkspace(Inputworkspace= SUMMED_WS, OutputWorkspace= SUMMED_WS,
- XMax=self._tof_max,EnableLogging=_LOGGING_)
- ms.CropWorkspace(Inputworkspace= SUMMED_MON, OutputWorkspace= SUMMED_MON,
- XMax=self._mon_tof_max, EnableLogging=_LOGGING_)
+ ms.LoadRaw(Filename=run,
+ SpectrumList=spectra,
+ OutputWorkspace=out_name,
+ LoadMonitors='Exclude',
+ EnableLogging=_LOGGING_)
+ ms.LoadRaw(Filename=run,
+ SpectrumList=self._mon_spectra,
+ OutputWorkspace=out_mon,
+ EnableLogging=_LOGGING_)
+
+ # Sum
+ if index > 0:
+ ms.Plus(LHSWorkspace=SUMMED_WS,
+ RHSWorkspace=out_name,
+ OutputWorkspace=SUMMED_WS,
+ EnableLogging=_LOGGING_)
+ ms.Plus(LHSWorkspace=SUMMED_MON,
+ RHSWorkspace=out_mon,
+ OutputWorkspace=SUMMED_MON,
+ EnableLogging=_LOGGING_)
+
+ ms.DeleteWorkspace(out_name, EnableLogging=_LOGGING_)
+ ms.DeleteWorkspace(out_mon, EnableLogging=_LOGGING_)
+
+ ms.CropWorkspace(Inputworkspace= SUMMED_WS,
+ OutputWorkspace=SUMMED_WS,
+ XMax=self._tof_max,
+ EnableLogging=_LOGGING_)
+ ms.CropWorkspace(Inputworkspace= SUMMED_MON,
+ OutputWorkspace=SUMMED_MON,
+ XMax=self._mon_tof_max,
+ EnableLogging=_LOGGING_)
+
return mtd[SUMMED_WS], mtd[SUMMED_MON]
#----------------------------------------------------------------------------------------
@@ -375,9 +407,9 @@ class LoadVesuvio(LoadEmptyVesuvio):
run_str = self.getProperty(RUN_PROP).value
# Load is not doing the right thing when summing. The numbers don't look correct
if "-" in run_str:
- lower,upper = run_str.split("-")
+ lower, upper = run_str.split("-")
# Range goes lower to up-1 but we want to include the last number
- runs = range(int(lower),int(upper)+1)
+ runs = range(int(lower), int(upper)+1)
elif "," in run_str:
runs = run_str.split(",")
diff --git a/Framework/PythonInterface/plugins/algorithms/PDToPDFgetN.py b/Framework/PythonInterface/plugins/algorithms/PDToPDFgetN.py
new file mode 100644
index 0000000000000000000000000000000000000000..db6819bf1d05cb23dc7ed144a29799ca64e6b257
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/PDToPDFgetN.py
@@ -0,0 +1,143 @@
+#pylint: disable=no-init
+from mantid.simpleapi import *
+from mantid.api import *
+from mantid.kernel import Direction, FloatArrayProperty
+import mantid
+
+COMPRESS_TOL_TOF = .01
+
+
+class PDToPDFgetN(DataProcessorAlgorithm):
+ _focusPos = {}
+ _iparmFile = None
+
+ def category(self):
+ return "Workflow\\Diffraction;PythonAlgorithms"
+
+ def name(self):
+ return "PDToPDFgetN"
+
+ def summary(self):
+ return "The algorithm used converting raw data to pdfgetn input files"
+
+ def PyInit(self):
+ group = "Input"
+ self.declareProperty(FileProperty(name="Filename",
+ defaultValue="", action=FileAction.Load,
+ extensions=["_event.nxs", ".nxs.h5"]),
+ "Event file")
+ self.declareProperty("MaxChunkSize", 0.0,
+ "Specify maximum Gbytes of file to read in one chunk. Default is whole file.")
+ self.declareProperty("FilterBadPulses", 95.,
+ doc="Filter out events measured while proton " +
+ "charge is more than 5% below average")
+
+ self.declareProperty(MatrixWorkspaceProperty("InputWorkspace", "",
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc="Handle to reduced workspace")
+ self.setPropertyGroup("Filename", group)
+ self.setPropertyGroup("MaxChunkSize", group)
+ self.setPropertyGroup("FilterBadPulses", group)
+ self.setPropertyGroup("InputWorkspace", group)
+
+ group = "Output"
+ self.declareProperty(MatrixWorkspaceProperty("OutputWorkspace", "",
+ direction=Direction.Output),
+ doc="Handle to reduced workspace")
+ self.declareProperty(FileProperty(name="PDFgetNFile", defaultValue="", action=FileAction.Save,
+ extensions=[".getn"]), "Output filename")
+ self.setPropertyGroup("OutputWorkspace", group)
+ self.setPropertyGroup("PDFgetNFile", group)
+
+ self.declareProperty(FileProperty(name="CalibrationFile",
+ defaultValue="", action=FileAction.OptionalLoad,
+ extensions=[".h5", ".hd5", ".hdf", ".cal"]))
+ self.declareProperty(FileProperty(name="CharacterizationRunsFile", defaultValue="",
+ action=FileAction.OptionalLoad,
+ extensions=["txt"]),
+ "File with characterization runs denoted")
+
+ self.declareProperty("RemovePromptPulseWidth", 0.0,
+ "Width of events (in microseconds) near the prompt pulse to remove. 0 disables")
+ self.declareProperty("CropWavelengthMin", 0.,
+ "Crop the data at this minimum wavelength.")
+ self.declareProperty("CropWavelengthMax", 0.,
+ "Crop the data at this maximum wavelength.")
+
+ self.declareProperty(FloatArrayProperty("Binning", values=[0., 0., 0.],
+ direction=Direction.Input), "Positive is linear bins, negative is logorithmic")
+ self.declareProperty("ResampleX", 0,
+ "Number of bins in x-axis. Non-zero value overrides \"Params\" property. " +
+ "Negative value means logorithmic binning.")
+
+ def _loadCharacterizations(self):
+ self._focusPos = {}
+ self._iparmFile = None
+
+ charFilename = self.getProperty("CharacterizationRunsFile").value
+
+ if charFilename is None or len(charFilename) <= 0:
+ return
+
+ results = PDLoadCharacterizations(Filename=charFilename,
+ OutputWorkspace="characterizations")
+ self._iparmFile = results[1]
+ self._focusPos['PrimaryFlightPath'] = results[2]
+ self._focusPos['SpectrumIDs'] = results[3]
+ self._focusPos['L2'] = results[4]
+ self._focusPos['Polar'] = results[5]
+ self._focusPos['Azimuthal'] = results[6]
+
+ def PyExec(self):
+ self._loadCharacterizations()
+
+ wksp = self.getProperty("InputWorkspace").value
+ if wksp is None:
+ wksp = LoadEventAndCompress(Filename=self.getProperty("Filename").value,
+ OutputWorkspace=self.getPropertyValue("OutputWorkspace"),
+ MaxChunkSize=self.getProperty("MaxChunkSize").value,
+ FilterBadPulses=self.getProperty("FilterBadPulses").value,
+ CompressTOFTolerance=COMPRESS_TOL_TOF)
+ else:
+ self.log().information("Using input workspace. Ignoring properties 'Filename', " +
+ "'OutputWorkspace', 'MaxChunkSize', and 'FilterBadPulses'")
+
+ charac = ""
+ if mtd.doesExist("characterizations"):
+ charac = "characterizations"
+
+ # get the correct row of the table
+ PDDetermineCharacterizations(InputWorkspace=wksp,
+ Characterizations=charac,
+ ReductionProperties="__snspowderreduction")
+
+ wksp = AlignAndFocusPowder(InputWorkspace=wksp, OutputWorkspace=wksp,
+ CalFileName=self.getProperty("CalibrationFile").value,
+ Params=self.getProperty("Binning").value,
+ ResampleX=self.getProperty("ResampleX").value, Dspacing=True,
+ PreserveEvents=False,
+ RemovePromptPulseWidth=self.getProperty("RemovePromptPulseWidth").value,
+ CompressTolerance=COMPRESS_TOL_TOF,
+ CropWavelengthMin=self.getProperty("CropWavelengthMin").value,
+ CropWavelengthMax=self.getProperty("CropWavelengthMax").value,
+ ReductionProperties="__snspowderreduction",
+ **(self._focusPos))
+ wksp = NormaliseByCurrent(InputWorkspace=wksp, OutputWorkspace=wksp)
+ wksp.getRun()['gsas_monitor'] = 1
+ if self._iparmFile is not None:
+ wksp.getRun()['iparm_file'] = self._iparmFile
+
+ wksp = SetUncertainties(InputWorkspace=wksp, OutputWorkspace=wksp,
+ SetError="sqrt")
+ SaveGSS(InputWorkspace=wksp,
+ Filename=self.getProperty("PDFgetNFile").value,
+ SplitFiles=False, Append=False,
+ MultiplyByBinWidth=False,
+ Bank=mantid.pmds["__snspowderreduction"]["bank"].value,
+ Format="SLOG", ExtendedHeader=True)
+
+ self.setProperty("OutputWorkspace", wksp)
+
+# Register algorithm with Mantid.
+AlgorithmFactory.subscribe(PDToPDFgetN)
diff --git a/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py b/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py
index f52fad8cdc115c57000329048628b138798af648..7bc6cc433707c03185ec1ec1402151f124a6de45 100644
--- a/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py
+++ b/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init,unused-variable
+#pylint: disable=no-init,unused-variable,invalid-name,bare-except
from mantid.api import *
from mantid.kernel import *
@@ -76,30 +76,47 @@ class SavePlot1DAsJson(PythonAlgorithm):
return
def _serialize(self, workspace, plotname):
- wname = plotname or workspace.getName()
+ pname = plotname or workspace.getName()
# init dictionary
ishist = workspace.isHistogramData()
plottype = "histogram" if ishist else "point"
- serialized = {"type": plottype}
- # helper
- label = lambda axis: "%s (%s)" % (
- axis.getUnit().caption(),
- axis.getUnit().symbol() or 1,
+ serialized = dict(
+ type = plottype,
+ data = dict(),
)
# loop over spectra
for i in range(workspace.getNumberHistograms()):
- k = "%s%s" % (wname, i)
- value = dict(
- x=list(workspace.readX(i)),
- y=list(workspace.readY(i)),
- e=list(workspace.readE(i)),
- xlabel=label(workspace.getAxis(0)),
- ylabel=label(workspace.getAxis(1)),
- title="long title of %s" % k,
- )
- serialized[k] = value
+ spectrum_no = workspace.getSpectrum(i).getSpectrumNo()
+ # Why do we need label?
+ # label = "%s_spectrum_%d" % (pname, spectrum_no)
+ # labels.append(label)
+ # or title?
+ # title = "%s - spectrum %d" % (workspace.getTitle(), spectrum_no)
+ arr = [
+ list(workspace.readX(i)),
+ list(workspace.readY(i)),
+ list(workspace.readE(i)),
+ ]
+ serialized['data'][spectrum_no] = arr
continue
- return serialized
+ # axes
+ # .. helper
+ label = lambda axis: axis.getUnit().caption()
+ def unit(axis):
+ s = axis.getUnit().symbol()
+ try:
+ return s.latex()
+ except:
+ return '%s' % s
+ axes = dict(
+ xlabel=label(workspace.getAxis(0)),
+ ylabel=label(workspace.getAxis(1)),
+ xunit = unit(workspace.getAxis(0)),
+ # yunit = unit(workspace.getAxis(1)),
+ yunit = workspace.YUnitLabel(),
+ )
+ serialized['axes'] = axes
+ return {pname: serialized}
# Register algorithm with Mantid
diff --git a/Framework/PythonInterface/plugins/algorithms/TOFTOFCropWorkspace.py b/Framework/PythonInterface/plugins/algorithms/TOFTOFCropWorkspace.py
new file mode 100644
index 0000000000000000000000000000000000000000..c7c6f387adb444ff9c0b0ded8ac87c33c0f3bd99
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/TOFTOFCropWorkspace.py
@@ -0,0 +1,70 @@
+from mantid.api import PythonAlgorithm, AlgorithmFactory, WorkspaceProperty # , WorkspaceUnitValidator
+from mantid.kernel import Direction
+import mantid.simpleapi as api
+
+
+class TOFTOFCropWorkspace(PythonAlgorithm):
+ """ Crop empty time channels
+ """
+ def __init__(self):
+ PythonAlgorithm.__init__(self)
+
+ def category(self):
+ """ Return category
+ """
+ return "PythonAlgorithms\\MLZ\\TOFTOF;Utility"
+
+ def name(self):
+ """ Return summary
+ """
+ return "TOFTOFCropWorkspace"
+
+ def summary(self):
+ return "Crop empty time channels."
+
+ def PyInit(self):
+ """ Declare properties
+ """
+ # better would be to use the validator, but it fails if WorkspaceGroup is given as an input
+ # self.declareProperty(WorkspaceProperty("InputWorkspace", "", direction=Direction.Input,
+ # validator=WorkspaceUnitValidator('TOF')),
+ # doc="Input workspace.")
+ self.declareProperty(WorkspaceProperty("InputWorkspace", "", direction=Direction.Input),
+ doc="Input workspace.")
+ self.declareProperty(WorkspaceProperty("OutputWorkspace", "", direction=Direction.Output),
+ doc="Name of the workspace that will contain the results")
+ return
+
+ def validateInputs(self):
+ issues = dict()
+ input_workspace = self.getProperty("InputWorkspace").value
+
+ xunit = input_workspace.getAxis(0).getUnit().unitID()
+ if xunit != 'TOF':
+ issues['InputWorkspace'] = "X axis units must be TOF. "
+
+ # check for required properties
+ run = input_workspace.getRun()
+ if not run.hasProperty('channel_width'):
+ issues['InputWorkspace'] = "Input workpsace must have sample log channel_width."
+ if not run.hasProperty('full_channels'):
+ issues['InputWorkspace'] = "Input workpsace must have sample log full_channels."
+
+ return issues
+
+ def PyExec(self):
+ """ Main execution body
+ """
+ inputws = self.getProperty("InputWorkspace").value
+ outputws = self.getProperty("OutputWorkspace").value
+
+ run = inputws.getRun()
+ channel_width = float(run.getLogData('channel_width').value)
+ full_channels = float(run.getLogData('full_channels').value)
+
+ outputws = api.CropWorkspace(inputws, XMin=0., XMax=full_channels*channel_width, OutputWorkspace=outputws)
+ self.setProperty("OutputWorkspace", outputws)
+
+
+# Register algorithm with Mantid.
+AlgorithmFactory.subscribe(TOFTOFCropWorkspace)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py
index c929a3c23b3afe00c1ed0770e6b38ef0424e4a96..32bb98f27c6a938069e1ccb3c01af95a91ac9472 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py
@@ -1,5 +1,5 @@
from mantid.api import DataProcessorAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty, WorkspaceUnitValidator, \
- Progress
+PropertyMode, Progress
from mantid.kernel import Direction, FloatArrayProperty, FloatArrayBoundedValidator
@@ -22,7 +22,11 @@ class DetectorFloodWeighting(DataProcessorAlgorithm):
self.declareProperty(MatrixWorkspaceProperty('InputWorkspace', '',
direction=Direction.Input, validator=WorkspaceUnitValidator("Wavelength")),
- doc='Flood weighting measurement')
+ doc='Flood weighting measurement')
+ self.declareProperty(MatrixWorkspaceProperty('TransmissionWorkspace', '',
+ direction=Direction.Input, optional=PropertyMode.Optional,
+ validator=WorkspaceUnitValidator("Wavelength")),
+ doc='Flood weighting measurement')
validator = FloatArrayBoundedValidator()
validator.setLower(0.)
@@ -52,9 +56,6 @@ class DetectorFloodWeighting(DataProcessorAlgorithm):
issues['Bands'] = 'Even number of Bands boundaries expected'
return issues # Abort early. Do not continue
- if len(bands) > 2:
- issues['Bands'] = 'Presently this algorithm only supports one pair of bands'
-
all_limits=list()
for i in range(0, len(bands), 2):
lower = bands[i]
@@ -69,6 +70,13 @@ class DetectorFloodWeighting(DataProcessorAlgorithm):
all_limits.append(limits)
if lower >= upper:
issues['Bands'] = 'Bands should form lower, upper pairs'
+ input_ws = self.getProperty('InputWorkspace').value
+ trans_ws = self.getProperty('TransmissionWorkspace').value
+ if trans_ws:
+ if not trans_ws.getNumberHistograms() == input_ws.getNumberHistograms():
+ issues['TransmissionWorkspace'] = 'Transmission should have same number of histograms as flood input workspace'
+ if not trans_ws.blocksize() == input_ws.blocksize():
+ issues['TransmissionWorkspace'] = 'Transmission workspace should be rebinned the same as the flood input workspace'
return issues
@@ -79,53 +87,73 @@ class DetectorFloodWeighting(DataProcessorAlgorithm):
divide.execute()
return divide.getProperty("OutputWorkspace").value
+ def _add(self, lhs, rhs):
+ divide = self.createChildAlgorithm("Plus")
+ divide.setProperty("LHSWorkspace", lhs)
+ divide.setProperty("RHSWorkspace", rhs)
+ divide.execute()
+ return divide.getProperty("OutputWorkspace").value
- def PyExec(self):
-
- progress = Progress(self, 0, 1, 4) # Four coarse steps
-
- in_ws = self.getProperty('InputWorkspace').value
- bands = self.getProperty('Bands').value
-
- # Formulate bands
- params = list()
+ def _integrate_bands(self, bands, in_ws):
+ # Formulate bands, integrate and sum
+ accumulated_output = None
for i in range(0, len(bands), 2):
lower = bands[i]
upper = bands[i+1]
step = upper - lower
- params.append((lower, step, upper))
- progress.report()
+ rebin = self.createChildAlgorithm("Rebin")
+ rebin.setProperty("Params", [lower, step, upper])
+ rebin.setProperty("InputWorkspace", in_ws) # Always integrating the same input workspace
+ rebin.execute()
+ integrated = rebin.getProperty("OutputWorkspace").value
+ if accumulated_output:
+ accumulated_output = self._add(accumulated_output, integrated)
+ else:
+ # First band
+ accumulated_output = integrated
+ return accumulated_output
- accumulated_output = None
- rebin = self.createChildAlgorithm("Rebin")
- rebin.setProperty("Params", params[0])
- rebin.setProperty("InputWorkspace", in_ws)
- rebin.execute()
- accumulated_output = rebin.getProperty("OutputWorkspace").value
- progress.report()
- # Determine the max across all spectra
- y_values = accumulated_output.extractY()
- max_val = np.amax(y_values)
+ def PyExec(self):
- # Create a workspace from the single max value
- create = self.createChildAlgorithm("CreateSingleValuedWorkspace")
- create.setProperty("DataValue", max_val)
- create.execute()
- max_ws = create.getProperty("OutputWorkspace").value
+ progress = Progress(self, 0, 1, 4) # Four coarse steps
- # Divide each entry by max
- normalized = self._divide(accumulated_output, max_ws)
+ in_ws = self.getProperty('InputWorkspace').value
+ trans_ws = self.getProperty('TransmissionWorkspace').value
+ bands = self.getProperty('Bands').value
+
+ accumulated_output = self._integrate_bands(bands, in_ws)
+ if trans_ws:
+ accumulated_trans_output = self._integrate_bands(bands, trans_ws)
progress.report()
# Perform solid angle correction. Calculate solid angle then divide through.
+ normalized=accumulated_output
if self.getProperty("SolidAngleCorrection").value:
solidAngle = self.createChildAlgorithm("SolidAngle")
- solidAngle.setProperty("InputWorkspace", normalized)
+ solidAngle.setProperty("InputWorkspace", accumulated_output)
solidAngle.execute()
solid_angle_weighting = solidAngle.getProperty("OutputWorkspace").value
normalized = self._divide(normalized, solid_angle_weighting)
progress.report()
+ # Divide through by the transmission workspace provided
+ if trans_ws:
+ normalized = self._divide(normalized, accumulated_trans_output)
+ # Determine the max across all spectra
+ y_values = normalized.extractY()
+ mean_val = np.mean(y_values)
+ # Create a workspace from the single max value
+ create = self.createChildAlgorithm("CreateSingleValuedWorkspace")
+ create.setProperty("DataValue", mean_val)
+ create.execute()
+ mean_ws = create.getProperty("OutputWorkspace").value
+ # Divide each entry by mean
+ normalized = self._divide(normalized, mean_ws)
+ progress.report()
+ # Fix-up ranges
+ for i in range(normalized.getNumberHistograms()):
+ normalized.dataX(i)[0] = bands[0]
+ normalized.dataX(i)[1] = bands[-1]
self.setProperty('OutputWorkspace', normalized)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py
new file mode 100644
index 0000000000000000000000000000000000000000..69a0a5485cf1d5ce2e9d537260f2e60f09e913d5
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py
@@ -0,0 +1,209 @@
+#pylint: disable=no-init
+from mantid.simpleapi import *
+from mantid.api import *
+from mantid.kernel import *
+from mantid import config
+
+import os
+
+class EVSDiffractionReduction(DataProcessorAlgorithm):
+
+ _workspace_names = None
+ _chopped_data = None
+ _output_ws = None
+ _data_files = None
+ _instrument_name = None
+ _mode = None
+ _par_filename = None
+ _spectra_range = None
+ _grouping_method = None
+ _rebin_string = None
+ _ipf_filename = None
+ _sum_files = None
+
+
+ def category(self):
+ return 'Diffraction;PythonAlgorithms'
+
+
+ def summary(self):
+ return 'Performs diffraction reduction for VESUVIO'
+
+
+ def PyInit(self):
+ self.declareProperty(StringArrayProperty('InputFiles'),
+ doc='Comma separated list of input files.')
+
+ self.declareProperty(FileProperty('InstrumentParFile', '',
+ action=FileAction.Load,
+ extensions=['.dat', '.par']),
+ doc='PAR file containing instrument definition.')
+
+ self.declareProperty(name='SumFiles', defaultValue=False,
+ doc='Enabled to sum spectra from each input file.')
+
+ self.declareProperty(IntArrayProperty('SpectraRange', [3, 198]),
+ doc='Range of spectra to use.')
+
+ self.declareProperty(name='RebinParam', defaultValue='',
+ doc='Rebin parameters.')
+
+ self.declareProperty(name='GroupingPolicy', defaultValue='All',
+ validator=StringListValidator(['All', 'Individual', 'IPF']),
+ doc='Selects the type of detector grouping to be used.')
+
+ self.declareProperty(WorkspaceGroupProperty('OutputWorkspace', '',
+ direction=Direction.Output),
+ doc='Group name for the result workspaces.')
+
+
+ def validateInputs(self):
+ """
+ Checks for issues with user input.
+ """
+ issues = dict()
+
+ # Validate input files
+ input_files = self.getProperty('InputFiles').value
+ if len(input_files) == 0:
+ issues['InputFiles'] = 'InputFiles must contain at least one filename'
+
+ # Validate detector range
+ detector_range = self.getProperty('SpectraRange').value
+ if len(detector_range) != 2:
+ issues['SpectraRange'] = 'SpectraRange must be an array of 2 values only'
+ else:
+ if detector_range[0] > detector_range[1]:
+ issues['SpectraRange'] = 'SpectraRange must be in format [lower_index,upper_index]'
+
+ return issues
+
+
+ def PyExec(self):
+ from IndirectReductionCommon import (load_files,
+ get_multi_frame_rebin,
+ identify_bad_detectors,
+ unwrap_monitor,
+ process_monitor_efficiency,
+ scale_monitor,
+ scale_detectors,
+ rebin_reduction,
+ group_spectra,
+ fold_chopped,
+ rename_reduction)
+
+ self._setup()
+
+ load_opts = dict()
+ load_opts['Mode'] = 'FoilOut'
+ load_opts['InstrumentParFile'] = self._par_filename
+
+ self._workspace_names, self._chopped_data = load_files(self._data_files,
+ ipf_filename=self._ipf_filename,
+ spec_min=self._spectra_range[0],
+ spec_max=self._spectra_range[1],
+ sum_files=self._sum_files,
+ load_opts=load_opts)
+
+ for c_ws_name in self._workspace_names:
+ is_multi_frame = isinstance(mtd[c_ws_name], WorkspaceGroup)
+
+ # Get list of workspaces
+ if is_multi_frame:
+ workspaces = mtd[c_ws_name].getNames()
+ else:
+ workspaces = [c_ws_name]
+
+ # Process rebinning for framed data
+ rebin_string_2, num_bins = get_multi_frame_rebin(c_ws_name,
+ self._rebin_string)
+
+ masked_detectors = identify_bad_detectors(workspaces[0])
+
+ # Process workspaces
+ for ws_name in workspaces:
+ monitor_ws_name = ws_name + '_mon'
+
+ # Process monitor
+ if not unwrap_monitor(ws_name):
+ ConvertUnits(InputWorkspace=monitor_ws_name,
+ OutputWorkspace=monitor_ws_name,
+ Target='Wavelength',
+ EMode='Elastic')
+
+ process_monitor_efficiency(ws_name)
+ scale_monitor(ws_name)
+
+ # Scale detector data by monitor intensities
+ scale_detectors(ws_name, 'Elastic')
+
+ # Remove the no longer needed monitor workspace
+ DeleteWorkspace(monitor_ws_name)
+
+ # Convert to dSpacing
+ ConvertUnits(InputWorkspace=ws_name,
+ OutputWorkspace=ws_name,
+ Target='dSpacing',
+ EMode='Elastic')
+
+ # Handle rebinning
+ rebin_reduction(ws_name,
+ self._rebin_string,
+ rebin_string_2,
+ num_bins)
+
+ # Group spectra
+ group_spectra(ws_name,
+ masked_detectors,
+ self._grouping_method)
+
+ if is_multi_frame:
+ fold_chopped(c_ws_name)
+
+ # Rename output workspaces
+ output_workspace_names = [rename_reduction(ws_name, self._sum_files) for ws_name in self._workspace_names]
+
+ # Group result workspaces
+ GroupWorkspaces(InputWorkspaces=output_workspace_names,
+ OutputWorkspace=self._output_ws)
+
+ self.setProperty('OutputWorkspace', self._output_ws)
+
+
+ def _setup(self):
+ """
+ Gets algorithm properties.
+ """
+ self._instrument_name = 'VESUVIO'
+ self._mode = 'diffspec'
+
+ self._output_ws = self.getPropertyValue('OutputWorkspace')
+ self._data_files = self.getProperty('InputFiles').value
+ self._par_filename = self.getPropertyValue('InstrumentParFile')
+ self._spectra_range = self.getProperty('SpectraRange').value
+ self._rebin_string = self.getPropertyValue('RebinParam')
+ self._grouping_method = self.getPropertyValue('GroupingPolicy')
+
+ if self._rebin_string == '':
+ self._rebin_string = None
+
+ # Get the IPF filename
+ self._ipf_filename = self._instrument_name + '_diffraction_' + self._mode + '_Parameters.xml'
+ if not os.path.exists(self._ipf_filename):
+ self._ipf_filename = os.path.join(config['instrumentDefinition.directory'], self._ipf_filename)
+ logger.information('IPF filename is: %s' % (self._ipf_filename))
+
+ # Only enable sum files if we actually have more than one file
+ sum_files = self.getProperty('SumFiles').value
+ self._sum_files = False
+
+ if sum_files:
+ num_raw_files = len(self._data_files)
+ if num_raw_files > 1:
+ self._sum_files = True
+ logger.information('Summing files enabled (have %d files)' % num_raw_files)
+ else:
+ logger.information('SumFiles options is ignored when only one file is provided')
+
+
+AlgorithmFactory.subscribe(EVSDiffractionReduction)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py
index 02de852f0963d86fd61d806772c7f34c9e6ceebf..461f44dfac4040837f72c838ae4e1d8c4fd1a4a2 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py
@@ -1,6 +1,7 @@
#pylint: disable=no-init
from mantid.api import (PythonAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty,
- WorkspaceGroup, WorkspaceGroupProperty, Progress)
+ WorkspaceGroup, WorkspaceGroupProperty, ITableWorkspaceProperty,
+ Progress, PropertyMode)
from mantid.kernel import Direction
from mantid.simpleapi import *
@@ -13,6 +14,7 @@ class ResNorm(PythonAlgorithm):
_e_max = None
_create_output = None
_out_ws = None
+ _out_ws_table = None
def category(self):
@@ -53,6 +55,11 @@ class ResNorm(PythonAlgorithm):
direction=Direction.Output),
doc='Fitted parameter output')
+ self.declareProperty(ITableWorkspaceProperty('OutputWorkspaceTable', '',
+ optional=PropertyMode.Optional,
+ direction=Direction.Output),
+ doc='Table workspace of fit parameters')
+
def validateInputs(self):
self._get_properties()
@@ -85,6 +92,8 @@ class ResNorm(PythonAlgorithm):
def PyExec(self):
from IndirectCommon import getWSprefix
+ if self._create_output:
+ self._out_ws_table = self.getPropertyValue('OutputWorkspaceTable')
# Process vanadium workspace
van_ws = ConvertSpectrumAxis(InputWorkspace=self._van_ws,
@@ -103,26 +112,29 @@ class ResNorm(PythonAlgorithm):
input_str = ''
for idx in range(num_hist):
input_str += '%s,i%d;' % (padded_res_ws, idx)
- prog_namer.report()
+ prog_namer.report('Generating PlotPeak input string')
out_name = getWSprefix(self._res_ws) + 'ResNorm_Fit'
function = 'name=TabulatedFunction,Workspace=%s,Scaling=1,Shift=0,XScaling=1,ties=(Shift=0)' % self._van_ws
- fit_params = PlotPeakByLogValue(Input=input_str,
- OutputWorkspace=out_name,
- Function=function,
- FitType='Individual',
- PassWSIndexToFunction=True,
- CreateOutput=self._create_output,
- StartX=self._e_min,
- EndX=self._e_max)
+ plot_peaks = self.createChildAlgorithm(name='PlotPeakByLogValue', startProgress=0.02, endProgress=0.94, enableLogging=True)
+ plot_peaks.setProperty('Input', input_str)
+ plot_peaks.setProperty('OutputWorkspace', out_name)
+ plot_peaks.setProperty('Function', function)
+ plot_peaks.setProperty('FitType', 'Individual')
+ plot_peaks.setProperty('PassWSIndexToFunction', True)
+ plot_peaks.setProperty('CreateOutput', self._create_output)
+ plot_peaks.setProperty('StartX', self._e_min)
+ plot_peaks.setProperty('EndX', self._e_max)
+ plot_peaks.execute()
+ fit_params = plot_peaks.getProperty('OutputWorkspace').value
params = {'XScaling':'Stretch', 'Scaling':'Intensity'}
result_workspaces = []
prog_process = Progress(self, start=0.94, end=1.0, nreports=3)
for param_name, output_name in params.items():
result_workspaces.append(self._process_fit_params(fit_params, param_name, v_values, v_unit, output_name))
- prog_process.report()
+ prog_process.report('Processing Fit data')
GroupWorkspaces(InputWorkspaces=result_workspaces,
OutputWorkspace=self._out_ws)
@@ -130,9 +142,10 @@ class ResNorm(PythonAlgorithm):
DeleteWorkspace(van_ws)
DeleteWorkspace(padded_res_ws)
- prog_process.report()
- if not self._create_output:
- DeleteWorkspace(fit_params)
+ prog_process.report('Deleting workspaces')
+
+ if self._create_output:
+ self.setProperty('OutputWorkspaceTable', fit_params)
def _process_res_ws(self, num_hist):
diff --git a/Framework/PythonInterface/plugins/algorithms/mlzutils.py b/Framework/PythonInterface/plugins/algorithms/mlzutils.py
index 3b69302522b7ef2cd6d2eba41c946e3e548d5673..d0e47dbdc7891c084a714360e66ae6daf3b60f81 100644
--- a/Framework/PythonInterface/plugins/algorithms/mlzutils.py
+++ b/Framework/PythonInterface/plugins/algorithms/mlzutils.py
@@ -1,4 +1,6 @@
import mantid.simpleapi as api
+from mantid.api import AlgorithmManager
+import numpy as np
def cleanup(wslist):
@@ -154,3 +156,69 @@ def compare_mandatory(wslist, plist, logger, tolerance=0.01):
"Workspaces: " + ", ".join(wslist) + "\n Values: " + str(properties)
logger.error(message)
raise RuntimeError(message)
+
+
+def do_fit_gaussian(workspace, index, logger):
+ """
+ Calculates guess values on peak centre, sigma and peak height.
+ Uses them as an input to run a fit algorithm
+ @ param workspace --- input workspace
+ @ param index --- the spectrum with which WorkspaceIndex to fit
+ @ returns peak_centre --- fitted peak centre
+ @ returns sigma --- fitted sigma
+ """
+ nhist = workspace.getNumberHistograms()
+ if index > nhist:
+ message = "Index " + str(index) + " is out of range for the workspace " + workspace.getName()
+ logger.error(message)
+ raise RuntimeError(message)
+
+ x_values = np.array(workspace.readX(index))
+ y_values = np.array(workspace.readY(index))
+
+ # get peak centre position
+ imax = np.argmax(y_values)
+ height = y_values[imax]
+
+ # check for zero or negative signal
+ if height <= 0:
+ logger.warning("Workspace %s, detector %d has maximum <= 0" % (workspace.getName(), index))
+ return [0, 0]
+
+ try_centre = x_values[imax]
+
+ # guess sigma
+ indices = np.argwhere(y_values > 0.5*height)
+ nentries = len(indices)
+ if nentries < 3:
+ message = "Spectrum " + str(index) + " in workspace " + workspace.getName() +\
+ " has too narrow peak. Cannot guess sigma. Check your data."
+ logger.error(message)
+ raise RuntimeError(message)
+ # fwhm = sigma * (2.*np.sqrt(2.*np.log(2.)))
+ fwhm = np.fabs(x_values[indices[nentries - 1, 0]] - x_values[indices[0, 0]])
+ sigma = fwhm/(2.*np.sqrt(2.*np.log(2.)))
+
+ # create and execute Fit algorithm
+ myfunc = 'name=Gaussian, Height='+str(height)+', PeakCentre='+str(try_centre)+', Sigma='+str(sigma)
+ startX = try_centre - 3.0*fwhm
+ endX = try_centre + 3.0*fwhm
+ prefix = "Fit" + workspace.getName() + str(index)
+ fit_alg = AlgorithmManager.createUnmanaged('Fit')
+ fit_alg.initialize()
+ fit_alg.setChild(True)
+ api.set_properties(fit_alg, Function=myfunc, InputWorkspace=workspace, CreateOutput=True, Output=prefix)
+ fit_alg.setProperty('StartX', startX)
+ fit_alg.setProperty('EndX', endX)
+ fit_alg.setProperty('WorkspaceIndex', index)
+ fit_successful = fit_alg.execute()
+ param_table = fit_alg.getProperty('OutputParameters').value
+
+ if not fit_successful:
+ message = "For detector " + str(index) + " in workspace " + workspace.getName() +\
+ "fit was not successful. Input guess parameters are " + str(myfunc)
+ logger.error(message)
+ raise RuntimeError(message)
+
+ # return list: [peak_centre, sigma]
+ return param_table.column(1)[1:3]
diff --git a/Framework/PythonInterface/test/python/mantid/geometry/CMakeLists.txt b/Framework/PythonInterface/test/python/mantid/geometry/CMakeLists.txt
index 0a03316888ee6f52c89b0d38835bcd1b59b56f6a..069ccf32a1663bb22f1e4f7a3bb2fdf6d4376b32 100644
--- a/Framework/PythonInterface/test/python/mantid/geometry/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/mantid/geometry/CMakeLists.txt
@@ -17,6 +17,8 @@ set ( TEST_PY_FILES
SymmetryElementTest.py
SymmetryOperationTest.py
GroupTest.py
+ CrystalStructureTest.py
+ ReflectionGeneratorTest.py
)
check_tests_valid ( ${CMAKE_CURRENT_SOURCE_DIR} ${TEST_PY_FILES} )
diff --git a/Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py b/Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..147d8e1e232adbea44574f5a908e45e4a68614ba
--- /dev/null
+++ b/Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py
@@ -0,0 +1,59 @@
+# pylint: disable=no-init,invalid-name,too-many-public-methods,broad-except
+import unittest
+from mantid.geometry import CrystalStructure
+
+
+class CrystalStructureTest(unittest.TestCase):
+ def test_creation(self):
+ # Some valid constructions
+ self.assertTrue(self.createCrystalStructureOrRaise("5.43 5.43 5.43", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01"))
+ self.assertTrue(self.createCrystalStructureOrRaise("5.43 5.43 5.43", "C m m m", "Al 1/3 0.454 1/12 1.0 0.01;\n"
+ "Si 2/3 0.121 1/8"))
+ self.assertTrue(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43 90 90 120", "R -3 c", "Al 1/3 0.454 1/12 1.0 0.01;\n"
+ "Si 2/3 0.121 1/8"))
+
+ # Invalid unit cell specification
+ self.assertFalse(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43 90.0", "C m m m", "Al 1/3 0.454 1/12 1.0 0.01"))
+
+ # Invalid space group
+ self.assertFalse(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43", "INVALID", "Al 1/3 0.454 1/12 1.0 0.01"))
+
+ # Invalid atom specification
+ self.assertFalse(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43", "C m c e", "Al 1/3 0"))
+
+ def createCrystalStructureOrRaise(self, unitCell, spaceGroup, atomStrings):
+ try:
+ CrystalStructure(unitCell, spaceGroup, atomStrings)
+ return True
+ except Exception:
+ return False
+
+ def test_UnitCell(self):
+ structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01")
+ cell = structure.getUnitCell()
+
+ self.assertEqual(cell.a(), 5.43)
+ self.assertEqual(cell.b(), 5.42)
+ self.assertEqual(cell.c(), 5.41)
+
+ def test_SpaceGroup(self):
+ structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01")
+ spaceGroup = structure.getSpaceGroup()
+
+ self.assertEqual(spaceGroup.getHMSymbol(), "F d -3 m")
+
+ def test_scatterers(self):
+ initialString = "Al 1/3 0.454 1/12 1 0.01;Si 0.1 0.2 0.3 0.99 0.1"
+
+ structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", initialString)
+ scatterers = structure.getScatterers()
+
+ self.assertEqual(';'.join(scatterers), initialString)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py b/Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..4c942f8a7ccd0140d98864097dc3f36f1cfc7ff8
--- /dev/null
+++ b/Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py
@@ -0,0 +1,69 @@
+# pylint: disable=no-init,invalid-name,too-many-public-methods
+import unittest
+from mantid.geometry import CrystalStructure, ReflectionGenerator, ReflectionConditionFilter
+from mantid.kernel import V3D
+import numpy as np
+
+
+class CrystalStructureTest(unittest.TestCase):
+ crystalStructure = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.02")
+
+ def test_create(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ generator = ReflectionGenerator(self.crystalStructure, ReflectionConditionFilter.Centering)
+
+ def test_getHKLs(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getHKLs(1.0, 10.0)
+
+ self.assertEqual(len(hkls), 138)
+
+ # default is filtering by space group reflection condition
+ self.assertTrue(V3D(2, 2, 2) in hkls)
+ self.assertFalse(V3D(1, 0, 0) in hkls)
+
+ def test_getHKLsUsingFilter(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getHKLsUsingFilter(1.0, 10.0, ReflectionConditionFilter.StructureFactor)
+
+ self.assertEqual(len(hkls), 130)
+
+ # The 222 is gone now
+ self.assertFalse(V3D(2, 2, 2) in hkls)
+
+ def test_getUniqueHKLs(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getUniqueHKLs(1.0, 10.0)
+
+ self.assertEqual(len(hkls), 9)
+
+ self.assertTrue(V3D(2, 2, 2) in hkls)
+ self.assertFalse(V3D(1, 0, 0) in hkls)
+
+ def test_getUniqueHKLsUsingFilter(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getUniqueHKLsUsingFilter(1.0, 10.0, ReflectionConditionFilter.StructureFactor)
+
+ self.assertEqual(len(hkls), 8)
+ self.assertFalse(V3D(2, 2, 2) in hkls)
+
+ def test_getDValues(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = [V3D(1, 0, 0), V3D(1, 1, 1)]
+
+ dValues = generator.getDValues(hkls)
+
+ self.assertEqual(len(hkls), len(dValues))
+ self.assertAlmostEqual(dValues[0], 5.431, places=10)
+ self.assertAlmostEqual(dValues[1], 5.431 / np.sqrt(3.), places=10)
+
+ def test_getFsSquared(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getUniqueHKLs(1.0, 10.0)
+
+ fsSquared = generator.getFsSquared(hkls)
+
+ self.assertEqual(len(fsSquared), len(hkls))
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
index c12c040cddbff6f851d86f23bfa144fc0bbeb73f..952bb617bfa603aaaedee0c7393bf6f8a7ad9af5 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
@@ -8,6 +8,7 @@ set ( TEST_PY_FILES
CalculateSampleTransmissionTest.py
CheckForSampleLogsTest.py
ConjoinSpectraTest.py
+ ComputeCalibrationCoefVanTest.py
CorrectLogTimesTest.py
CreateLeBailFitInputTest.py
CreateMDTest.py
@@ -26,6 +27,7 @@ set ( TEST_PY_FILES
EnggFitPeaksTest.py
EnggFocusTest.py
EnggVanadiumCorrectionsTest.py
+ EVSDiffractionReductionTest.py
FilterLogByTimeTest.py
FindReflectometryLinesTest.py
FlatPlatePaalmanPingsCorrectionTest.py
@@ -75,6 +77,7 @@ set ( TEST_PY_FILES
UpdatePeakParameterTableValueTest.py
SANSSubtractTest.py
TimeSliceTest.py
+ TOFTOFCropWorkspaceTest.py
TOFTOFMergeRunsTest.py
TOSCABankCorrectionTest.py
TransformToIqtTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/ComputeCalibrationCoefVanTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/ComputeCalibrationCoefVanTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..aff74c2e324ac2e288cce0a16a55727b9000f691
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/ComputeCalibrationCoefVanTest.py
@@ -0,0 +1,82 @@
+import unittest
+from mantid.simpleapi import DeleteWorkspace, CreateSampleWorkspace, AddSampleLog, EditInstrumentGeometry,\
+ CloneWorkspace, CheckWorkspacesMatch
+from testhelpers import run_algorithm
+from mantid.api import AnalysisDataService
+from scipy.constants import N_A, hbar, k
+import numpy as np
+
+
+class ComputeCalibrationCoefVanTest(unittest.TestCase):
+ def setUp(self):
+ input_ws = CreateSampleWorkspace(Function="User Defined",
+ UserDefinedFunction="name=LinearBackground, A0=0.3;name=Gaussian, \
+ PeakCentre=5, Height=10, Sigma=0.3", NumBanks=2, BankPixelWidth=1,
+ XMin=0, XMax=10, BinWidth=0.1, BankDistanceFromSample=4.0)
+ self._input_ws = input_ws
+ AddSampleLog(self._input_ws, LogName='wavelength', LogText='4.0', LogType='Number', LogUnit='Angstrom')
+
+ def test_output(self):
+ outputWorkspaceName = "output_ws"
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
+
+ # Output = Vanadium ws
+ self.assertEqual(wsoutput.getRun().getLogData('run_title').value,
+ self._input_ws.getRun().getLogData('run_title').value)
+
+ # Size of output workspace
+ self.assertEqual(wsoutput.getNumberHistograms(), self._input_ws.getNumberHistograms())
+
+ DeleteWorkspace(wsoutput)
+ return
+
+ def test_sum(self):
+ outputWorkspaceName = "output_ws"
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
+
+ # check whether sum is calculated correctly, for theta=0, dwf=1
+ y_sum = sum(self._input_ws.readY(0)[27:75])
+ self.assertAlmostEqual(y_sum, wsoutput.readY(0)[0])
+
+ DeleteWorkspace(wsoutput)
+
+ def test_dwf(self):
+ outputWorkspaceName = "output_ws"
+
+ # change theta to make dwf != 1
+ EditInstrumentGeometry(self._input_ws, L2="4,8", Polar="0,15", Azimuthal="0,0", DetectorIDs="1,2")
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
+
+ # check dwf calculation
+ y_sum = sum(self._input_ws.readY(1)[27:75])
+ mvan = 0.001*50.942/N_A
+ Bcoef = 4.736767162094296*1e+20*hbar*hbar/(2.0*mvan*k*389.0)
+ dwf = np.exp(-1.0*Bcoef*(4.0*np.pi*np.sin(0.5*np.radians(15.0))/4.0)**2)
+ self.assertAlmostEqual(y_sum*dwf, wsoutput.readY(1)[0])
+
+ DeleteWorkspace(wsoutput)
+
+ def test_input_not_modified(self):
+ backup = CloneWorkspace(self._input_ws)
+ outputWorkspaceName = "output_ws"
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ self.assertEqual("Success!", CheckWorkspacesMatch(backup, self._input_ws))
+ DeleteWorkspace(backup)
+
+ def tearDown(self):
+ if AnalysisDataService.doesExist(self._input_ws.getName()):
+ DeleteWorkspace(self._input_ws)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/DetectorFloodWeightingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/DetectorFloodWeightingTest.py
index b2ca793e6254f263fb1d48b216104cfcf7f6b3fc..81540f1eda08b040642a558a43169aa48462b1b7 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/DetectorFloodWeightingTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/DetectorFloodWeightingTest.py
@@ -68,8 +68,53 @@ class DetectorFloodWeightingTest(unittest.TestCase):
x_axis = out_ws.readX(0)
self.assertEquals(x_axis[0], bands[0])
self.assertEquals(x_axis[-1], bands[-1])
- print out_ws.readY(0)[0]
self.assertEquals(out_ws.readY(0)[0], 1.0)
+
+ def test_execute_multiple_bands_no_solid_angle(self):
+ alg = AlgorithmManager.create("DetectorFloodWeighting")
+ alg.setChild(True)
+ alg.initialize()
+ alg.setProperty("SolidAngleCorrection", False)
+ signal_value = 2
+ in_ws = self._create_ws(units="Wavelength", signal_value=signal_value, data_x=range(0,10,1))
+ alg.setProperty("InputWorkspace", in_ws)
+ bands = [1,2,3,4]
+ alg.setProperty("Bands", bands) # One band
+ alg.setPropertyValue("OutputWorkspace", "dummy")
+ alg.execute()
+
+ out_ws = alg.getProperty("OutputWorkspace").value
+ self.assertEqual(1, out_ws.blocksize())
+ self.assertEqual("Wavelength", out_ws.getAxis(0).getUnit().unitID())
+ self.assertEqual(in_ws.getNumberHistograms(), out_ws.getNumberHistograms(), msg="Number of histograms should be unchanged.")
+ x_axis = out_ws.readX(0)
+ self.assertEquals(x_axis[0], bands[0])
+ self.assertEquals(x_axis[-1], bands[-1])
+ self.assertEquals(out_ws.readY(0)[0], 1.0)
+
+ def test_execute_multiple_bands_no_solid_angle_with_transmission(self):
+ alg = AlgorithmManager.create("DetectorFloodWeighting")
+ alg.setChild(True)
+ alg.initialize()
+ alg.setProperty("SolidAngleCorrection", False)
+ signal_value = 2
+ in_ws = self._create_ws(units="Wavelength", signal_value=signal_value, data_x=range(0,10,1))
+ alg.setProperty("InputWorkspace", in_ws)
+ alg.setProperty("TransmissionWorkspace", in_ws)
+ bands = [1,2,3,4]
+ alg.setProperty("Bands", bands) # One band
+ alg.setPropertyValue("OutputWorkspace", "dummy")
+ alg.execute()
+
+ out_ws = alg.getProperty("OutputWorkspace").value
+ self.assertEqual(1, out_ws.blocksize())
+ self.assertEqual("Wavelength", out_ws.getAxis(0).getUnit().unitID())
+ self.assertEqual(in_ws.getNumberHistograms(), out_ws.getNumberHistograms(), msg="Number of histograms should be unchanged.")
+ x_axis = out_ws.readX(0)
+ self.assertEquals(x_axis[0], bands[0])
+ self.assertEquals(x_axis[-1], bands[-1])
+ self.assertEquals(out_ws.readY(0)[0], 1.0)
+
def test_execute_single_with_solid_angle(self):
alg = AlgorithmManager.create("DetectorFloodWeighting")
@@ -90,5 +135,6 @@ class DetectorFloodWeightingTest(unittest.TestCase):
self.assertEqual(in_ws.getNumberHistograms(), out_ws.getNumberHistograms(), msg="Number of histograms should be unchanged.")
+
if __name__ == '__main__':
unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/EVSDiffractionReductionTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/EVSDiffractionReductionTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ec89cdaf4051d9055296ecb9f3c04d0239c79d3
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/EVSDiffractionReductionTest.py
@@ -0,0 +1,45 @@
+#pylint: disable=too-many-public-methods,invalid-name
+
+import unittest
+from mantid.simpleapi import *
+from mantid.api import *
+
+
+class EVDDiffractionReductionTest(unittest.TestCase):
+
+ def test_basic_reduction_completes(self):
+ """
+ Sanity test to ensure the most basic reduction actually completes.
+ """
+
+ wks = EVSDiffractionReduction(InputFiles=['EVS15289.raw'],
+ InstrumentParFIle='IP0005.dat')
+
+ self.assertTrue(isinstance(wks, WorkspaceGroup), 'Result workspace should be a workspace group.')
+ self.assertEqual(len(wks), 1)
+ self.assertEqual(wks.getNames()[0], 'EVS15289_diffspec_red')
+
+ red_ws = wks[0]
+ self.assertEqual(red_ws.getAxis(0).getUnit().unitID(), 'dSpacing')
+ self.assertEqual(red_ws.getNumberHistograms(), 1)
+
+
+ def test_grouping_individual(self):
+ """
+ Test setting individual grouping, one spectrum per detector.
+ """
+
+ wks = EVSDiffractionReduction(InputFiles=['EVS15289.raw'],
+ GroupingPolicy='Individual',
+ InstrumentParFIle='IP0005.dat')
+
+ self.assertTrue(isinstance(wks, WorkspaceGroup), 'Result workspace should be a workspace group.')
+ self.assertEqual(len(wks), 1)
+
+ red_ws = wks[0]
+ self.assertEqual(red_ws.getAxis(0).getUnit().unitID(), 'dSpacing')
+ self.assertEqual(red_ws.getNumberHistograms(), 196)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py
index 6e8c6100e3f2d764c4aa5a8b6c5bdb8961b02cbc..62f8c938fa13402e41580886bc0c61f632ad58d6 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name,too-many-public-methods
+#pylint: disable=invalid-name,too-many-public-methods,too-many-arguments
import unittest
import numpy as np
import mantid.simpleapi as api
@@ -9,13 +9,13 @@ from mantid.api import AnalysisDataService
import os, json
-class SaveVulcanGSSTest(unittest.TestCase):
+class SavePlot1DAsJsonTest(unittest.TestCase):
def test_save_one_curve(self):
""" Test to Save one curve
"""
- datawsname = "TestOneCurve"
- E, I, err = self._createOneCurve(datawsname)
+ datawsname = "constant energy cut"
+ E, I, err = self._createOneQCurve(datawsname)
# Execute
out_path = "tempout_curve.json"
@@ -26,11 +26,9 @@ class SaveVulcanGSSTest(unittest.TestCase):
# executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- d0 = d[datawsname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
+ d = json.load(open(out_path))[datawsname]
+ self.assertEqual(d['type'], 'point')
+ self._checkData(d, E, I, err)
# Delete the output file
os.remove(out_path)
return
@@ -51,11 +49,8 @@ class SaveVulcanGSSTest(unittest.TestCase):
# Executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- d0 = d[datawsname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
+ d = json.load(open(out_path))[datawsname]
+ self._checkData(d, E, I, err)
# test overwrite
alg_test = run_algorithm(
"SavePlot1DAsJson",
@@ -80,14 +75,9 @@ class SaveVulcanGSSTest(unittest.TestCase):
# executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- d0 = d[datawsname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
- d1 = d[datawsname+'1'] #
- np.testing.assert_array_equal(d1['y'], I2)
- np.testing.assert_array_equal(d1['e'], err2)
+ d = json.load(open(out_path))[datawsname]
+ self._checkData(d, E, I, err)
+ self._checkData(d, E, I2, err2, ID="2")
# Delete the output file
os.remove(out_path)
return
@@ -97,6 +87,7 @@ class SaveVulcanGSSTest(unittest.TestCase):
""" Test to Save one curve with a name specified by client
"""
datawsname = "TestOneCurve"
+ plotname = "myplot"
E, I, err = self._createOneCurve(datawsname)
# Execute
out_path = "tempout_curve_withname.json"
@@ -104,36 +95,55 @@ class SaveVulcanGSSTest(unittest.TestCase):
"SavePlot1DAsJson",
InputWorkspace = datawsname,
JsonFilename = out_path,
- PlotName = "myplot")
+ PlotName = plotname)
# executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- plotname = "myplot"
- d0 = d[plotname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
+ d = json.load(open(out_path))[plotname]
+ self._checkData(d, E, I, err)
# Delete the output file
os.remove(out_path)
return
+ def _checkData(self, s, E, I, err, ID="1"):
+ d0 = s["data"][ID]
+ np.testing.assert_array_equal(d0[0], E)
+ np.testing.assert_array_equal(d0[1], I)
+ np.testing.assert_array_equal(d0[2], err)
+ return
+
+
def _createOneCurve(self, datawsname):
""" Create data workspace
"""
- E = np.arange(-50, 50, 1.0)
+ E = np.arange(-50, 50, 10.0)
I = 1000 * np.exp(-E**2/10**2)
err = I ** .5
# create workspace
dataws = api.CreateWorkspace(
DataX = E, DataY = I, DataE = err, NSpec = 1,
- UnitX = "Energy(meV)")
+ UnitX = "Energy")
# Add to data service
AnalysisDataService.addOrReplace(datawsname, dataws)
return E, I, err
+ def _createOneQCurve(self, datawsname):
+ """ Create data workspace
+ """
+ Q = np.arange(0, 13, 1.0)
+ I = 1000 * np.exp(-Q**2/10**2)
+ err = I ** .5
+ # create workspace
+ dataws = api.CreateWorkspace(
+ DataX = Q, DataY = I, DataE = err, NSpec = 1,
+ UnitX = "Momentum")
+ # Add to data service
+ AnalysisDataService.addOrReplace(datawsname, dataws)
+ return Q, I, err
+
+
def _createOneHistogram(self, datawsname):
""" Create data workspace
"""
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/TOFTOFCropWorkspaceTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/TOFTOFCropWorkspaceTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..14651813e297fe91d44d8e8006bfc41db7655bbb
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/TOFTOFCropWorkspaceTest.py
@@ -0,0 +1,59 @@
+import unittest
+from mantid.simpleapi import Load, DeleteWorkspace, GroupWorkspaces, TOFTOFCropWorkspace
+from testhelpers import run_algorithm
+from mantid.api import AnalysisDataService
+
+
+class TOFTOFCropWorkspaceTest(unittest.TestCase):
+
+ _input_ws = None
+ _cropped_ws = None
+
+ def setUp(self):
+ input_ws = Load(Filename="TOFTOFTestdata.nxs")
+ self._input_ws = input_ws
+
+ def test_basicrun(self):
+ OutputWorkspaceName = "cropped_ws"
+ alg_test = run_algorithm("TOFTOFCropWorkspace",
+ InputWorkspace=self._input_ws,
+ OutputWorkspace=OutputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ self._cropped_ws = AnalysisDataService.retrieve(OutputWorkspaceName)
+
+ run = self._cropped_ws.getRun()
+ # check existence of required entries in logs
+ self.assertTrue('full_channels' in run.keys())
+ self.assertTrue('channel_width' in run.keys())
+ # check their values
+ full_channels = float(run.getLogData('full_channels').value)
+ channel_width = float(run.getLogData('channel_width').value)
+ self.assertTrue(full_channels > 0.)
+ self.assertTrue(channel_width > 0.)
+ # check unit horizontal axis
+ self.assertEqual(self._cropped_ws.getAxis(0).getUnit().unitID(), 'TOF')
+ # check length of cropped ws
+ self.assertEqual(len(self._cropped_ws.readX(0)), int(full_channels))
+
+ def test_inputgroup(self):
+ group = GroupWorkspaces([self._input_ws])
+ OutputWorkspaceName = "cropped_ws"
+ alg_test = run_algorithm("TOFTOFCropWorkspace",
+ InputWorkspace=group,
+ OutputWorkspace=OutputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+
+ def test_invalid_xunits(self):
+ self._input_ws.getAxis(0).setUnit('Wavelength')
+ OutputWorkspaceName = "cropped_ws"
+ self.assertRaises(RuntimeError, TOFTOFCropWorkspace, InputWorkspace=self._input_ws,
+ OutputWorkspace=OutputWorkspaceName)
+
+ def cleanUp(self):
+ if AnalysisDataService.doesExist(self._input_ws):
+ DeleteWorkspace(self._input_ws)
+ if AnalysisDataService.doesExist(self._cropped_ws):
+ DeleteWorkspace(self._cropped_ws)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp b/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp
index 810d3fe4179fdd9af9c2c3ebafebafcc9e919589..9e6e57799eb3bf45edf789edfa54b8de0d873698 100644
--- a/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp
+++ b/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp
@@ -21,6 +21,11 @@ using namespace Mantid::DataObjects::MDEventsTestHelper;
using namespace Mantid::PythonInterface::Policies;
using namespace WorkspaceCreationHelper;
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
+#pragma clang diagnostic ignored "-Wunused-local-typedef"
+#endif
BOOST_PYTHON_FUNCTION_OVERLOADS(create2DWorkspaceWithFullInstrument_overloads,
create2DWorkspaceWithFullInstrument, 2, 4)
@@ -31,6 +36,10 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(
create2DWorkspaceWithRectangularInstrument_overloads,
create2DWorkspaceWithRectangularInstrument, 3, 3)
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
+
BOOST_PYTHON_MODULE(WorkspaceCreationHelper) {
using namespace boost::python;
diff --git a/Framework/SINQ/inc/MantidSINQ/PoldiCreatePeaksFromCell.h b/Framework/SINQ/inc/MantidSINQ/PoldiCreatePeaksFromCell.h
index b622976ee7e2e3c5f6f2c0689cfe79a0a21b7a39..0e1d54336ca6c9bf1a146f6a4390ea19ff1c6a71 100644
--- a/Framework/SINQ/inc/MantidSINQ/PoldiCreatePeaksFromCell.h
+++ b/Framework/SINQ/inc/MantidSINQ/PoldiCreatePeaksFromCell.h
@@ -57,13 +57,6 @@ protected:
Geometry::SpaceGroup_const_sptr
getSpaceGroup(const std::string &spaceGroupString) const;
- Geometry::CompositeBraggScatterer_sptr
- getScatterers(const std::string &scattererString) const;
- Geometry::BraggScatterer_sptr
- getScatterer(const std::string &singleScatterer) const;
- std::vector<std::string>
- getCleanScattererTokens(const std::vector<std::string> &tokens) const;
-
double getDMaxValue(const Geometry::UnitCell &unitCell) const;
double getLargestDValue(const Geometry::UnitCell &unitCell) const;
diff --git a/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h b/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
index 973c128b27ba685ec33b4abfe7b79f178da2f9a5..1a7c1005d68692eb07359cc90d0ad0731cadf8ed 100644
--- a/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
+++ b/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
@@ -6,6 +6,7 @@
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/IFunction.h"
#include "MantidAPI/IPeakFunction.h"
+#include "MantidGeometry/Crystal/PointGroup.h"
#include "MantidKernel/Matrix.h"
@@ -104,6 +105,9 @@ protected:
getFunctionPawley(std::string profileFunctionName,
const PoldiPeakCollection_sptr &peakCollection);
+ std::string getCrystalSystemFromPointGroup(
+ const Geometry::PointGroup_sptr &pointGroup) const;
+
std::string
getRefinedStartingCell(const std::string &initialCell,
const std::string &crystalSystem,
diff --git a/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiMockInstrumentHelpers.h b/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiMockInstrumentHelpers.h
index 3174172ae4ec2fbf87198add5758e7af44874a4c..717702c21ffc041133aeb9c79238e12b23759e12 100644
--- a/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiMockInstrumentHelpers.h
+++ b/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiMockInstrumentHelpers.h
@@ -532,9 +532,9 @@ public:
CompositeBraggScatterer_sptr atoms = CompositeBraggScatterer::create();
atoms->addScatterer(atomSi);
- CrystalStructure_sptr Si(new CrystalStructure(
+ CrystalStructure Si(
UnitCell(5.43071, 5.43071, 5.43071),
- SpaceGroupFactory::Instance().createSpaceGroup("P m -3 m"), atoms));
+ SpaceGroupFactory::Instance().createSpaceGroup("P m -3 m"), atoms);
return PoldiPeakCollection_sptr(new PoldiPeakCollection(Si, 1.1, 1.95));
}
diff --git a/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiPeakCollection.h b/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiPeakCollection.h
index 041f0be02f56b1197d358fa70149d2a25b0dc909..cbc0d31dd1ea8d87571fcae69723b75e145c169f 100644
--- a/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiPeakCollection.h
+++ b/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiPeakCollection.h
@@ -50,7 +50,7 @@ public:
PoldiPeakCollection(IntensityType intensityType = Maximum);
PoldiPeakCollection(const DataObjects::TableWorkspace_sptr &workspace);
- PoldiPeakCollection(const Geometry::CrystalStructure_sptr &crystalStructure,
+ PoldiPeakCollection(const Geometry::CrystalStructure &crystalStructure,
double dMin, double dMax);
virtual ~PoldiPeakCollection() {}
diff --git a/Framework/SINQ/src/PoldiCreatePeaksFromCell.cpp b/Framework/SINQ/src/PoldiCreatePeaksFromCell.cpp
index 0fd98199d55469039b65d1a46f3706f578313228..94b338277527b5254eac1e4259b9ecb2c2e197dd 100644
--- a/Framework/SINQ/src/PoldiCreatePeaksFromCell.cpp
+++ b/Framework/SINQ/src/PoldiCreatePeaksFromCell.cpp
@@ -6,11 +6,8 @@
#include "MantidSINQ/PoldiUtilities/PoldiPeakCollection.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
-#include "MantidGeometry/Crystal/BraggScattererFactory.h"
-
-#include <boost/tokenizer.hpp>
-#include <boost/algorithm/string.hpp>
-#include <boost/assign.hpp>
+#include "MantidGeometry/Crystal/CompositeBraggScatterer.h"
+#include "MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h"
namespace Mantid {
namespace Poldi {
@@ -75,64 +72,6 @@ SpaceGroup_const_sptr PoldiCreatePeaksFromCell::getSpaceGroup(
return SpaceGroupFactory::Instance().createSpaceGroup(spaceGroupString);
}
-CompositeBraggScatterer_sptr PoldiCreatePeaksFromCell::getScatterers(
- const std::string &scattererString) const {
- boost::char_separator<char> atomSep(";");
- boost::tokenizer<boost::char_separator<char>> tokens(scattererString,
- atomSep);
-
- std::vector<BraggScatterer_sptr> scatterers;
-
- for (auto it = tokens.begin(); it != tokens.end(); ++it) {
- scatterers.push_back(getScatterer(boost::trim_copy(*it)));
- }
-
- return CompositeBraggScatterer::create(scatterers);
-}
-
-BraggScatterer_sptr PoldiCreatePeaksFromCell::getScatterer(
- const std::string &singleScatterer) const {
- std::vector<std::string> tokens;
- boost::split(tokens, singleScatterer, boost::is_any_of(" "));
-
- if (tokens.size() < 4 || tokens.size() > 6) {
- throw std::invalid_argument("Could not parse scatterer string: " +
- singleScatterer);
- }
-
- std::vector<std::string> cleanScattererTokens =
- getCleanScattererTokens(tokens);
- std::vector<std::string> properties =
- boost::assign::list_of("Element")("Position")("Occupancy")("U")
- .convert_to_container<std::vector<std::string>>();
-
- std::string initString;
- for (size_t i = 0; i < cleanScattererTokens.size(); ++i) {
- initString += properties[i] + "=" + cleanScattererTokens[i] + ";";
- }
-
- return BraggScattererFactory::Instance().createScatterer(
- "IsotropicAtomBraggScatterer", initString);
-}
-
-std::vector<std::string> PoldiCreatePeaksFromCell::getCleanScattererTokens(
- const std::vector<std::string> &tokens) const {
- std::vector<std::string> cleanTokens;
-
- // Element
- cleanTokens.push_back(tokens[0]);
-
- // X, Y, Z
- cleanTokens.push_back("[" + tokens[1] + "," + tokens[2] + "," + tokens[3] +
- "]");
-
- for (size_t i = 4; i < tokens.size(); ++i) {
- cleanTokens.push_back(tokens[i]);
- }
-
- return cleanTokens;
-}
-
/** Returns the largest lattice spacing based on the algorithm properties
*
* This method returns the largest allowed lattice spacing for calculations. If
@@ -283,11 +222,11 @@ void PoldiCreatePeaksFromCell::exec() {
g_log.information() << "Constrained unit cell is: " << unitCellToStr(unitCell)
<< std::endl;
- CompositeBraggScatterer_sptr scatterers = getScatterers(getProperty("Atoms"));
+ CompositeBraggScatterer_sptr scatterers = CompositeBraggScatterer::create(
+ IsotropicAtomBraggScattererParser(getProperty("Atoms"))());
// Create a CrystalStructure-object for use with PoldiPeakCollection
- CrystalStructure_sptr crystalStructure =
- boost::make_shared<CrystalStructure>(unitCell, spaceGroup, scatterers);
+ CrystalStructure crystalStructure(unitCell, spaceGroup, scatterers);
double dMin = getProperty("LatticeSpacingMin");
double dMax = getDMaxValue(unitCell);
diff --git a/Framework/SINQ/src/PoldiFitPeaks2D.cpp b/Framework/SINQ/src/PoldiFitPeaks2D.cpp
index 5ace6536c53526aaddd76b1e7faec2a84e5e7b44..dc9755d28fbc0efb9ba8f4463e93b03d0c66e3dc 100644
--- a/Framework/SINQ/src/PoldiFitPeaks2D.cpp
+++ b/Framework/SINQ/src/PoldiFitPeaks2D.cpp
@@ -546,8 +546,7 @@ Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionPawley(
"peaks do not have point group.");
}
- std::string crystalSystem =
- getCrystalSystemAsString(pointGroup->crystalSystem());
+ std::string crystalSystem = getCrystalSystemFromPointGroup(pointGroup);
pawleyFunction->setCrystalSystem(crystalSystem);
UnitCell cell = peakCollection->unitCell();
@@ -575,6 +574,35 @@ Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionPawley(
return mdFunction;
}
+/**
+ * Returns the crystal system for the specified point group
+ *
+ * This function simply uses Geometry::getCrystalSystemAsString(), except when
+ * the crystal system is trigonal but the point group uses hexagonal axes. In
+ * that case this function returns the string for PointGroup::Hexagonal.
+ *
+ * @param pointGroup :: The point group for which to find the crystal system
+ * @return The crystal system for the point group
+ */
+std::string PoldiFitPeaks2D::getCrystalSystemFromPointGroup(
+ const PointGroup_sptr &pointGroup) const {
+ if (!pointGroup) {
+ throw std::invalid_argument(
+ "Cannot return crystal system for null PointGroup.");
+ }
+
+ PointGroup::CrystalSystem crystalSystem = pointGroup->crystalSystem();
+
+ if (crystalSystem == PointGroup::Trigonal) {
+ if (pointGroup->getCoordinateSystem() ==
+ Group::CoordinateSystem::Hexagonal) {
+ return getCrystalSystemAsString(PointGroup::Hexagonal);
+ }
+ }
+
+ return getCrystalSystemAsString(crystalSystem);
+}
+
/**
* Tries to refine the initial cell using the supplied peaks
*
diff --git a/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp b/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
index 4a3ec4167a2bcbb4b2ea8d71ff9529c35d134574..48b5317b0eacdd7fdf4cc32a6cb5af86b2223ca7 100644
--- a/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
+++ b/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
@@ -385,6 +385,18 @@ UncertainValue PoldiAutoCorrelationCore::getCMessAndCSigma(
case 2: {
int middleIndex = cleanIndex((locator.icmin + 1), m_timeBinCount);
+ if (middleIndex < 0) {
+ m_logger.warning() << "Inconsistency foun while calculating correlation "
+ "intensity and error for d-value: "
+ << boost::lexical_cast<std::string>(dValue)
+ << ", with detector index: "
+ << boost::lexical_cast<std::string>(index)
+ << ", got middle index: "
+ << boost::lexical_cast<std::string>(middleIndex)
+ << ", ignoring it." << std::endl;
+ break;
+ }
+
double counts = getCounts(locator.detectorElement, middleIndex);
double normCounts = getNormCounts(locator.detectorElement, middleIndex);
diff --git a/Framework/SINQ/src/PoldiUtilities/PoldiPeakCollection.cpp b/Framework/SINQ/src/PoldiUtilities/PoldiPeakCollection.cpp
index bde86e64c42828a938b3422f1fd4383e408396f7..46ecefa2b6090f3c444b84eb3f9774b7a73c43d8 100644
--- a/Framework/SINQ/src/PoldiUtilities/PoldiPeakCollection.cpp
+++ b/Framework/SINQ/src/PoldiUtilities/PoldiPeakCollection.cpp
@@ -4,6 +4,8 @@
#include "MantidAPI/LogManager.h"
#include "MantidGeometry/Crystal/PointGroupFactory.h"
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+
#include "boost/format.hpp"
#include "boost/algorithm/string/join.hpp"
@@ -33,27 +35,22 @@ PoldiPeakCollection::PoldiPeakCollection(const TableWorkspace_sptr &workspace)
}
PoldiPeakCollection::PoldiPeakCollection(
- const Geometry::CrystalStructure_sptr &crystalStructure, double dMin,
- double dMax)
+ const CrystalStructure &crystalStructure, double dMin, double dMax)
: m_peaks(), m_intensityType(Integral), m_profileFunctionName(),
m_pointGroup() {
- if (!crystalStructure) {
- throw std::invalid_argument(
- "Cannot create PoldiPeakCollection from invalid CrystalStructure.");
- }
-
m_pointGroup = PointGroupFactory::Instance().createPointGroupFromSpaceGroup(
- crystalStructure->spaceGroup());
+ crystalStructure.spaceGroup());
+
+ m_unitCell = crystalStructure.cell();
- m_unitCell = crystalStructure->cell();
+ ReflectionGenerator generator(crystalStructure,
+ ReflectionConditionFilter::StructureFactor);
- std::vector<V3D> uniqueHKL = crystalStructure->getUniqueHKLs(
- dMin, dMax, Geometry::CrystalStructure::UseStructureFactor);
- std::vector<double> dValues = crystalStructure->getDValues(uniqueHKL);
- std::vector<double> structureFactors =
- crystalStructure->getFSquared(uniqueHKL);
+ std::vector<V3D> hkls = generator.getUniqueHKLs(dMin, dMax);
+ std::vector<double> dValues = generator.getDValues(hkls);
+ std::vector<double> structureFactors = generator.getFsSquared(hkls);
- setPeaks(uniqueHKL, dValues, structureFactors);
+ setPeaks(hkls, dValues, structureFactors);
}
PoldiPeakCollection_sptr PoldiPeakCollection::clone() {
diff --git a/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp b/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp
index 02f23178125755897c583659e66ec70e8ca6ed16..665b2f1eefa67af58661bb36d0e4c8d86b5c6904 100644
--- a/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp
+++ b/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp
@@ -99,6 +99,15 @@ void PoldiResidualCorrelationCore::distributeCorrelationCounts(
case 2: {
int middleIndex = cleanIndex((locator.icmin + 1), m_timeBinCount);
+ if (middleIndex < 0) {
+ m_logger.warning()
+ << "Inconsistency foun while calculating distribute "
+ "correlation counts for d-value with index "
+ << boost::lexical_cast<std::string>(k) << ", got middle index: "
+ << boost::lexical_cast<std::string>(middleIndex)
+ << ", ignoring it." << std::endl;
+ break;
+ }
addToCountData(locator.detectorElement, middleIndex, deltaForD);
}
case 1: {
diff --git a/Framework/SINQ/test/PoldiFitPeaks2DTest.h b/Framework/SINQ/test/PoldiFitPeaks2DTest.h
index da95dd9141476a4b1fdef8b7604b044ff0b0f45a..a9f11eb2d9af4e130098bdbf47729f9625cfc4e6 100644
--- a/Framework/SINQ/test/PoldiFitPeaks2DTest.h
+++ b/Framework/SINQ/test/PoldiFitPeaks2DTest.h
@@ -433,6 +433,40 @@ public:
TS_ASSERT_EQUALS(refinedCell, "5 5 5 90 90 90");
}
+ void testGetCrystalSystemFromPointGroup() {
+ TestablePoldiFitPeaks2D alg;
+
+ auto pgCubic = PointGroupFactory::Instance().createPointGroup("m-3m");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgCubic), "Cubic");
+
+ auto pgTetra = PointGroupFactory::Instance().createPointGroup("4/mmm");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTetra), "Tetragonal");
+
+ auto pgOrtho = PointGroupFactory::Instance().createPointGroup("mmm");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgOrtho),
+ "Orthorhombic");
+
+ auto pgMono = PointGroupFactory::Instance().createPointGroup("2/m");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgMono), "Monoclinic");
+
+ auto pgTric = PointGroupFactory::Instance().createPointGroup("-1");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTric), "Triclinic");
+
+ auto pgHex = PointGroupFactory::Instance().createPointGroup("6/mmm");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgHex), "Hexagonal");
+
+ auto pgTrigRh = PointGroupFactory::Instance().createPointGroup("-3m r");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTrigRh), "Trigonal");
+
+ auto pgTrigHex = PointGroupFactory::Instance().createPointGroup("-3m");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTrigHex),
+ "Hexagonal");
+
+ PointGroup_sptr invalid;
+ TS_ASSERT_THROWS(alg.getCrystalSystemFromPointGroup(invalid),
+ std::invalid_argument);
+ }
+
private:
PoldiInstrumentAdapter_sptr m_instrument;
PoldiTimeTransformer_sptr m_timeTransformer;
diff --git a/Framework/SINQ/test/PoldiPeakCollectionTest.h b/Framework/SINQ/test/PoldiPeakCollectionTest.h
index 8f9ec43120a27baaf7fbd5f424f8aacc4fca7fb3..6d75c9df41d49c48e1a5ed0365bb5018ad959b9b 100644
--- a/Framework/SINQ/test/PoldiPeakCollectionTest.h
+++ b/Framework/SINQ/test/PoldiPeakCollectionTest.h
@@ -13,6 +13,7 @@
#include "MantidGeometry/Crystal/PointGroupFactory.h"
#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
#include "MantidGeometry/Crystal/BraggScattererFactory.h"
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
#include <stdexcept>
@@ -323,7 +324,7 @@ public:
}
void testStructureConstructor() {
- CrystalStructure_sptr structure = getCsClStructure();
+ CrystalStructure structure = getCsClStructure();
double dMin = 0.55;
double dMax = 5.0;
@@ -357,18 +358,19 @@ public:
}
void testSetPeaks() {
- CrystalStructure_sptr structure = getCsClStructure();
+ CrystalStructure structure = getCsClStructure();
+ ReflectionGenerator generator(structure);
double dMin = 0.55;
double dMax = 5.0;
- std::vector<V3D> hkls = structure->getUniqueHKLs(dMin, dMax);
- std::vector<double> dValues = structure->getDValues(hkls);
+ std::vector<V3D> hkls = generator.getUniqueHKLs(dMin, dMax);
+ std::vector<double> dValues = generator.getDValues(hkls);
std::vector<double> fSquared(dValues.size(), 0.0);
TestablePoldiPeakCollection p;
- p.setPointGroup(structure->pointGroup());
+ p.setPointGroup(structure.spaceGroup()->getPointGroup());
TS_ASSERT_THROWS_NOTHING(p.setPeaks(hkls, dValues, fSquared));
dValues.pop_back();
@@ -377,7 +379,7 @@ public:
}
private:
- CrystalStructure_sptr getCsClStructure() {
+ CrystalStructure getCsClStructure() {
UnitCell CsCl(4.126, 4.126, 4.126);
SpaceGroup_const_sptr Pm3m =
SpaceGroupFactory::Instance().createSpaceGroup("P m -3 m");
@@ -392,7 +394,7 @@ private:
atoms->addScatterer(cs);
atoms->addScatterer(cl);
- return boost::make_shared<CrystalStructure>(CsCl, Pm3m, atoms);
+ return CrystalStructure(CsCl, Pm3m, atoms);
}
TableWorkspace_sptr m_dummyData;
diff --git a/Framework/TestHelpers/inc/MantidTestHelpers/FakeObjects.h b/Framework/TestHelpers/inc/MantidTestHelpers/FakeObjects.h
index b9c906a2804d32c3049699391f332ba19d3fa9c3..59a51ac705f792a245fb5c3dc9d1ed4f7820f440 100644
--- a/Framework/TestHelpers/inc/MantidTestHelpers/FakeObjects.h
+++ b/Framework/TestHelpers/inc/MantidTestHelpers/FakeObjects.h
@@ -118,7 +118,7 @@ public:
m_axes[1] = new Mantid::API::SpectraAxis(this);
}
size_t size() const { return vec.size() * blocksize(); }
- size_t blocksize() const { return vec[0].dataY().size(); }
+ size_t blocksize() const { return vec.empty() ? 0 : vec[0].dataY().size(); }
ISpectrum *getSpectrum(const size_t index) { return &vec[index]; }
const ISpectrum *getSpectrum(const size_t index) const {
return &vec[index];
diff --git a/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h b/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h
index c5d103d323ea76a43b145d302051846e0c8fcbcf..c2bbf05191f2bacbb0af8f49ad7d46f61e8d42bd 100644
--- a/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h
+++ b/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h
@@ -46,7 +46,7 @@ public:
return out;
}
};
-/** mock algorithn for doing logging/progress reporting*/
+/** mock algorithm for doing logging/progress reporting*/
class MockAlgorithm : public Mantid::API::Algorithm {
public:
MockAlgorithm(size_t nSteps = 100);
@@ -178,8 +178,8 @@ void addNoise(Mantid::API::MatrixWorkspace_sptr ws, double noise,
/**
* Create a test workspace with a fully defined instrument
* Each spectra will have a cylindrical detector defined 2*cylinder_radius away
- * from the centre of the
- * pervious.
+ * from the centre of the previous.
+ *
* Data filled with: Y: 2.0, E: sqrt(2.0), X: nbins of width 1 starting at 0
*/
Mantid::DataObjects::Workspace2D_sptr create2DWorkspaceWithFullInstrument(
@@ -262,7 +262,7 @@ CreateRandomEventWorkspace(size_t numbins, size_t numpixels,
Mantid::API::MatrixWorkspace_sptr
CreateGroupedWorkspace2D(size_t numHist, int numBins, double binDelta);
-// grouped workpsace with detectors arranges in rings in centre and into boxes
+// grouped workspace with detectors arranges in rings in center and into boxes
// outside
Mantid::API::MatrixWorkspace_sptr CreateGroupedWorkspace2DWithRingsAndBoxes(
size_t RootOfNumHist = 10, int numBins = 10, double binDelta = 1.0);
diff --git a/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp b/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp
index 88c67d797f42b4ec54f1238219a455cb436b9bf2..3d601ae49bc433f40bfb0c82aa8d02d8b936706c 100644
--- a/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp
+++ b/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp
@@ -23,6 +23,7 @@
#include "MantidGeometry/Instrument/Detector.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
+#include "MantidGeometry/Instrument/Component.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidKernel/MersenneTwister.h"
@@ -403,6 +404,10 @@ create2DWorkspaceWithFullInstrument(int nhist, int nbins, bool includeMonitors,
testInst->setPos(0.0, 0.0, 0.0);
testInst->add(sample);
testInst->markAsSamplePos(sample);
+ // chopper position
+ Component *chop_pos =
+ new Component("chopper-position", Kernel::V3D(-10, 0, 0), testInst.get());
+ testInst->add(chop_pos);
return space;
}
diff --git a/Framework/WorkflowAlgorithms/src/DgsProcessDetectorVanadium.cpp b/Framework/WorkflowAlgorithms/src/DgsProcessDetectorVanadium.cpp
index 1c4871d97d7b8db3862fe870e3319b4933f3ce3a..408d66a7a4c11e6f9f6d21de3cbacd75d833a6c2 100644
--- a/Framework/WorkflowAlgorithms/src/DgsProcessDetectorVanadium.cpp
+++ b/Framework/WorkflowAlgorithms/src/DgsProcessDetectorVanadium.cpp
@@ -1,6 +1,5 @@
#include "MantidWorkflowAlgorithms/DgsProcessDetectorVanadium.h"
#include "MantidAPI/PropertyManagerDataService.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/FacilityInfo.h"
#include "MantidWorkflowAlgorithms/WorkflowAlgorithmHelpers.h"
diff --git a/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction.cpp b/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction.cpp
index 399c082990d5ae1903aa0881595a2839e27aac15..5871e64724186557a97628ef0d2ed1f37ccd3fdb 100644
--- a/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction.cpp
+++ b/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction.cpp
@@ -3,7 +3,7 @@
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/EQSANSDarkCurrentSubtraction.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidAPI/FileProperty.h"
#include "Poco/Path.h"
@@ -24,8 +24,7 @@ using namespace Geometry;
using namespace DataObjects;
void EQSANSDarkCurrentSubtraction::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("Wavelength");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("Wavelength");
declareProperty(new WorkspaceProperty<>("InputWorkspace", "",
Direction::Input, wsValidator));
diff --git a/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction2.cpp b/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction2.cpp
index a87fa664cd67a50b5f24dde3a289d0b123619f0e..6497a24bf70fb8e393d2cf3f648b21a4ec9b47ef 100644
--- a/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction2.cpp
+++ b/Framework/WorkflowAlgorithms/src/EQSANSDarkCurrentSubtraction2.cpp
@@ -3,7 +3,7 @@
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/EQSANSDarkCurrentSubtraction2.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidAPI/FileProperty.h"
#include "Poco/Path.h"
@@ -24,8 +24,7 @@ using namespace Geometry;
using namespace DataObjects;
void EQSANSDarkCurrentSubtraction2::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("Wavelength");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("Wavelength");
declareProperty(new WorkspaceProperty<>("InputWorkspace", "",
Direction::Input, wsValidator));
diff --git a/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp b/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp
index bf6eea1e2cc6be9404ce09046a013733cbaeaf5c..e93f43068f858c373d6eaa75efbd6a9deb7a1ba9 100644
--- a/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp
+++ b/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/EQSANSLoad.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/AnalysisDataService.h"
#include <MantidAPI/FileFinder.h>
#include <MantidAPI/FileProperty.h>
@@ -40,8 +40,7 @@ void EQSANSLoad::init() {
"_event.nxs"),
"The name of the input event Nexus file to load");
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("TOF");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("TOF");
declareProperty(new WorkspaceProperty<EventWorkspace>(
"InputWorkspace", "", Direction::Input,
PropertyMode::Optional, wsValidator),
diff --git a/Framework/WorkflowAlgorithms/src/EQSANSMonitorTOF.cpp b/Framework/WorkflowAlgorithms/src/EQSANSMonitorTOF.cpp
index 6b9de1045cc2608430b59656950347fc00f24447..5298328007ab8970b5696008b4288eebc426d944 100644
--- a/Framework/WorkflowAlgorithms/src/EQSANSMonitorTOF.cpp
+++ b/Framework/WorkflowAlgorithms/src/EQSANSMonitorTOF.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/EQSANSMonitorTOF.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidGeometry/Instrument.h"
#include "Poco/NumberFormatter.h"
diff --git a/Framework/WorkflowAlgorithms/src/EQSANSQ2D.cpp b/Framework/WorkflowAlgorithms/src/EQSANSQ2D.cpp
index fdedcf9074f68177be3891380e98ae05df6525d8..cf1207541d0d89ec0358253783a97be6969730ee 100644
--- a/Framework/WorkflowAlgorithms/src/EQSANSQ2D.cpp
+++ b/Framework/WorkflowAlgorithms/src/EQSANSQ2D.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/EQSANSQ2D.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "Poco/NumberFormatter.h"
#include "MantidWorkflowAlgorithms/EQSANSInstrument.h"
@@ -17,8 +17,7 @@ using namespace API;
using namespace Geometry;
void EQSANSQ2D::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("Wavelength");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("Wavelength");
declareProperty(new WorkspaceProperty<>("InputWorkspace", "",
Direction::Input, wsValidator),
"Workspace to calculate I(qx,qy) from");
diff --git a/Framework/WorkflowAlgorithms/src/HFIRDarkCurrentSubtraction.cpp b/Framework/WorkflowAlgorithms/src/HFIRDarkCurrentSubtraction.cpp
index cbcbc6da35a9aba7d385f2f1896cf4ecfec50a29..14e681d1d3c88a6d79afb6dc0abd10da664591ba 100644
--- a/Framework/WorkflowAlgorithms/src/HFIRDarkCurrentSubtraction.cpp
+++ b/Framework/WorkflowAlgorithms/src/HFIRDarkCurrentSubtraction.cpp
@@ -3,7 +3,7 @@
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/HFIRDarkCurrentSubtraction.h"
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidAPI/FileProperty.h"
#include "Poco/Path.h"
#include "Poco/String.h"
@@ -22,8 +22,7 @@ using namespace API;
using namespace Geometry;
void HFIRDarkCurrentSubtraction::init() {
- auto wsValidator = boost::make_shared<CompositeValidator>();
- wsValidator->add<WorkspaceUnitValidator>("Wavelength");
+ auto wsValidator = boost::make_shared<WorkspaceUnitValidator>("Wavelength");
declareProperty(new WorkspaceProperty<>("InputWorkspace", "",
Direction::Input, wsValidator));
diff --git a/Framework/WorkflowAlgorithms/src/HFIRLoad.cpp b/Framework/WorkflowAlgorithms/src/HFIRLoad.cpp
index 986917a278f4ed47309b0d49c1a70fb07ee7873e..e0bf04db46e939d9bd85ae7d691fd70dbbdecc94 100644
--- a/Framework/WorkflowAlgorithms/src/HFIRLoad.cpp
+++ b/Framework/WorkflowAlgorithms/src/HFIRLoad.cpp
@@ -3,7 +3,6 @@
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/HFIRLoad.h"
#include "MantidWorkflowAlgorithms/HFIRInstrument.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include <MantidAPI/FileProperty.h>
#include "Poco/NumberFormatter.h"
#include "MantidKernel/BoundedValidator.h"
diff --git a/Framework/WorkflowAlgorithms/src/RefReduction.cpp b/Framework/WorkflowAlgorithms/src/RefReduction.cpp
index 4ece40c1ee5a6b08b584bceb6cc4eb34b8aee91b..9cc5678a2d2df87113a607c4a9ac52bc0976f26b 100644
--- a/Framework/WorkflowAlgorithms/src/RefReduction.cpp
+++ b/Framework/WorkflowAlgorithms/src/RefReduction.cpp
@@ -2,7 +2,6 @@
// Includes
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/RefReduction.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/UnitFactory.h"
@@ -629,6 +628,8 @@ double RefReduction::calculateAngleREFM(MatrixWorkspace_sptr workspace) {
Mantid::Kernel::Property *prop = workspace->run().getProperty("SampleDetDis");
Mantid::Kernel::TimeSeriesProperty<double> *dp =
dynamic_cast<Mantid::Kernel::TimeSeriesProperty<double> *>(prop);
+ if (!dp)
+ throw std::runtime_error("SampleDetDis was not a TimeSeriesProperty");
const double det_distance = dp->getStatistics().mean / 1000.0;
double direct_beam_pix = getProperty("DirectPixel");
diff --git a/Framework/WorkflowAlgorithms/src/RefRoi.cpp b/Framework/WorkflowAlgorithms/src/RefRoi.cpp
index 749b6985016a59cbf9128175a128c9e37e2e2720..075e69641f0e62ad3b877b1b5e9376c7470270fd 100644
--- a/Framework/WorkflowAlgorithms/src/RefRoi.cpp
+++ b/Framework/WorkflowAlgorithms/src/RefRoi.cpp
@@ -2,7 +2,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/RefRoi.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidKernel/UnitFactory.h"
#include "Poco/String.h"
diff --git a/Framework/WorkflowAlgorithms/src/SANSBeamFinder.cpp b/Framework/WorkflowAlgorithms/src/SANSBeamFinder.cpp
index b6d6835037646809ff3be516f62d22e18b7bf203..71df22fd7c07a21f80d56c4705e0e33911690513 100644
--- a/Framework/WorkflowAlgorithms/src/SANSBeamFinder.cpp
+++ b/Framework/WorkflowAlgorithms/src/SANSBeamFinder.cpp
@@ -3,7 +3,6 @@
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/SANSBeamFinder.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "Poco/Path.h"
#include "Poco/String.h"
#include "Poco/NumberFormatter.h"
diff --git a/Framework/WorkflowAlgorithms/src/SANSSensitivityCorrection.cpp b/Framework/WorkflowAlgorithms/src/SANSSensitivityCorrection.cpp
index 807806137409e9139a123f46a2b2b0be75f3d0c5..0cd3944adc2b6d71b3f434d5d675019aee8dd2c9 100644
--- a/Framework/WorkflowAlgorithms/src/SANSSensitivityCorrection.cpp
+++ b/Framework/WorkflowAlgorithms/src/SANSSensitivityCorrection.cpp
@@ -3,7 +3,6 @@
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/SANSSensitivityCorrection.h"
#include "MantidDataObjects/EventWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
#include "MantidAPI/AnalysisDataService.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidKernel/TimeSeriesProperty.h"
diff --git a/Framework/WorkflowAlgorithms/src/SANSSolidAngleCorrection.cpp b/Framework/WorkflowAlgorithms/src/SANSSolidAngleCorrection.cpp
index d100a795e047dc7c6213ca3f1bbd635c89a0577a..dbceb9892670dabce847ec333ae46dabdd3b2606 100644
--- a/Framework/WorkflowAlgorithms/src/SANSSolidAngleCorrection.cpp
+++ b/Framework/WorkflowAlgorithms/src/SANSSolidAngleCorrection.cpp
@@ -2,13 +2,15 @@
// Includes
//----------------------------------------------------------------------
#include "MantidWorkflowAlgorithms/SANSSolidAngleCorrection.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/HistogramValidator.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidGeometry/IDetector.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidAPI/AlgorithmProperty.h"
#include "MantidAPI/PropertyManagerDataService.h"
+#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/PropertyManager.h"
namespace Mantid {
diff --git a/Framework/WorkflowAlgorithms/src/StepScan.cpp b/Framework/WorkflowAlgorithms/src/StepScan.cpp
index 4541b25d6eae0ecaea86cc41b15ff4131c4a5bb3..c3a9522b10e3faf1b0a7e525668ee38d568cb1aa 100644
--- a/Framework/WorkflowAlgorithms/src/StepScan.cpp
+++ b/Framework/WorkflowAlgorithms/src/StepScan.cpp
@@ -1,6 +1,6 @@
#include "MantidWorkflowAlgorithms/StepScan.h"
#include "MantidAPI/ITableWorkspace.h"
-#include "MantidAPI/WorkspaceValidators.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitFactory.h"
diff --git a/MantidPlot/pymantidplot/__init__.py b/MantidPlot/pymantidplot/__init__.py
index f77ce7c983d7da2f2fb6446947c212e40fcbedd5..3ea6a0189f54e0505309f7f71b712aba68fe14c9 100644
--- a/MantidPlot/pymantidplot/__init__.py
+++ b/MantidPlot/pymantidplot/__init__.py
@@ -300,7 +300,9 @@ def plotMD(source, plot_axis=-2, normalization=DEFAULT_MD_NORMALIZATION, error_b
Args:
source: Workspace(s) to plot
plot_axis: Index of the plot axis (defaults to auto-select)
- normalization: Type of normalization required (defaults to volume)
+ normalization: Type of normalization required (defaults to volume, options available:
+ MDNormalization.NoNormalization, MDNormalization.NumEventsNormalization, and
+ MDNormalization.VolumeNormalization).
error_bars: Flag for error bar plotting.
window: window used for plotting. If None a new one will be created
clearWindow: if is True, the window specified will be cleared before adding new curve
diff --git a/MantidPlot/src/ApplicationWindow.cpp b/MantidPlot/src/ApplicationWindow.cpp
index d9455438c81ff03c2f0516cc79f00b0934b5c201..3fa69dd633f1932060d53fc279973fe2ed4731c0 100644
--- a/MantidPlot/src/ApplicationWindow.cpp
+++ b/MantidPlot/src/ApplicationWindow.cpp
@@ -10153,6 +10153,7 @@ void ApplicationWindow::showGraphContextMenu() {
QMenu axes(this);
QMenu colour(this);
QMenu normalization(this);
+ QMenu normMD(this);
QMenu exports(this);
QMenu copy(this);
QMenu prints(this);
@@ -10218,6 +10219,27 @@ void ApplicationWindow::showGraphContextMenu() {
noNorm->setChecked(!ag->isDistribution());
binNorm->setChecked(ag->isDistribution());
cm.insertItem(tr("&Normalization"), &normalization);
+ } else if (ag->normalizableMD()) {
+ QAction *noNormMD = new QAction(tr("N&one"), &normMD);
+ noNormMD->setCheckable(true);
+ connect(noNormMD, SIGNAL(activated()), ag, SLOT(noNormalizationMD()));
+ normMD.addAction(noNormMD);
+
+ QAction *volNormMD = new QAction(tr("&Volume"), &normMD);
+ volNormMD->setCheckable(true);
+ connect(volNormMD, SIGNAL(activated()), ag, SLOT(volumeNormalizationMD()));
+ normMD.addAction(volNormMD);
+
+ QAction *eventsNormMD = new QAction(tr("&Events"), &normMD);
+ eventsNormMD->setCheckable(true);
+ connect(eventsNormMD, SIGNAL(activated()), ag, SLOT(numEventsNormalizationMD()));
+ normMD.addAction(eventsNormMD);
+
+ int normalization = ag->normalizationMD();
+ noNormMD->setChecked(0 == normalization);
+ volNormMD->setChecked(1 == normalization);
+ eventsNormMD->setChecked(2 == normalization);
+ cm.insertItem("MD &Normalization", &normMD);
}
QMenu plotType(this);
diff --git a/MantidPlot/src/ConfigDialog.cpp b/MantidPlot/src/ConfigDialog.cpp
index 6344d67d31cb6107058a72196d4b9b7feec1ac5a..87e74e4ea83cab6eb72537345019aeadb92dc4f3 100644
--- a/MantidPlot/src/ConfigDialog.cpp
+++ b/MantidPlot/src/ConfigDialog.cpp
@@ -2341,8 +2341,11 @@ void ConfigDialog::apply()
QList<MdiSubWindow*> windows = app->windowsList();
foreach(MdiSubWindow *w, windows){
if (w->isA("MultiLayer")){
- (dynamic_cast<MultiLayer*>(w))->setScaleLayersOnPrint(boxScaleLayersOnPrint->isChecked());
- (dynamic_cast<MultiLayer*>(w))->printCropmarks(boxPrintCropmarks->isChecked());
+ MultiLayer* multiLayer = dynamic_cast<MultiLayer*>(w);
+ if (multiLayer) {
+ multiLayer->setScaleLayersOnPrint(boxScaleLayersOnPrint->isChecked());
+ multiLayer->printCropmarks(boxPrintCropmarks->isChecked());
+ }
}
}
// general page: application tab
diff --git a/MantidPlot/src/ContourLinesEditor.cpp b/MantidPlot/src/ContourLinesEditor.cpp
index 19ff48b3bf2c9a39d2da9d592d99f953a1315e9b..144b2c7f245cd9c0bbb736cbee787ba77a733413 100644
--- a/MantidPlot/src/ContourLinesEditor.cpp
+++ b/MantidPlot/src/ContourLinesEditor.cpp
@@ -108,10 +108,14 @@ void ContourLinesEditor::updateContourLevels()
int rows = table->rowCount();
QwtValueList levels;
- for (int i = 0; i < rows; i++)
- levels << dynamic_cast<DoubleSpinBox*>(table->cellWidget(i, 0))->value();
+ for (int i = 0; i < rows; i++) {
+ DoubleSpinBox *spinBox =
+ dynamic_cast<DoubleSpinBox *>(table->cellWidget(i, 0));
+ if (spinBox)
+ levels << spinBox->value();
+ }
- d_spectrogram->setContourLevels(levels);
+ d_spectrogram->setContourLevels(levels);
}
void ContourLinesEditor::updateContourPens()
diff --git a/MantidPlot/src/CustomActionDialog.cpp b/MantidPlot/src/CustomActionDialog.cpp
index 0ffe792247682d974fbf3c6af8338c200fa32c61..8b779deb8ec2a2fb4978b0b5a1439b5d8ba7b504 100644
--- a/MantidPlot/src/CustomActionDialog.cpp
+++ b/MantidPlot/src/CustomActionDialog.cpp
@@ -514,7 +514,10 @@ void CustomActionDialog::chooseFolder()
QAction * CustomActionDialog::actionAt(int row)
{
ApplicationWindow *app = dynamic_cast<ApplicationWindow *>(parent());
- QList<QAction *>actions = app->customActionsList();
+ if (!app)
+ throw std::runtime_error(
+ "The parent of this dialog was not the Application Window");
+ QList<QAction *>actions = app->customActionsList();
if (actions.isEmpty() || row < 0 || row >= actions.count())
return 0;
diff --git a/MantidPlot/src/Graph.cpp b/MantidPlot/src/Graph.cpp
index db3b3e6fcd290c43819c2df94f5f38d021aee8a4..b90d59c0c2ba39d003eb0589957f4663b3ab805e 100644
--- a/MantidPlot/src/Graph.cpp
+++ b/MantidPlot/src/Graph.cpp
@@ -60,6 +60,7 @@
#include "MantidAPI/AnalysisDataService.h"
#include "Mantid/MantidMatrixCurve.h"
+#include "Mantid/MantidMDCurve.h"
#include "MantidQtAPI/PlotAxis.h"
#include "MantidQtAPI/QwtRasterDataMD.h"
#include "MantidQtAPI/QwtWorkspaceSpectrumData.h"
@@ -209,6 +210,9 @@ Graph::Graph(int x, int y, int width, int height, QWidget* parent, Qt::WFlags f)
m_isDistribution = false;
m_normalizable = false;
+
+ m_normalizableMD = false;
+ m_normalizationMD = 0;
}
void Graph::notifyChanges()
@@ -1436,7 +1440,8 @@ void Graph::setAxisScale(int axis, double start, double end, int type, double st
QwtScaleWidget *rightAxis = d_plot->axisWidget(QwtPlot::yRight);
if(rightAxis)
{
- if (type == ScaleTransformation::Log10 && (start <= 0 || start == DBL_MAX))
+ //if (type == ScaleTransformation::Log10 && (start <= 0 || start == DBL_MAX))
+ if (type == GraphOptions::Log10 && (start <= 0 || start == DBL_MAX))
{
start = sp->getMinPositiveValue();
}
@@ -3411,12 +3416,15 @@ QString Graph::yAxisTitleFromFirstCurve()
using namespace Mantid::API;
QString wsName = firstCurve->workspaceName();
auto ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(wsName.toStdString());
- return MantidQt::API::PlotAxis(m_isDistribution, *ws).title();
- }
- else
- {
- return axisTitle(0);
+ if (ws)
+ return MantidQt::API::PlotAxis(m_isDistribution, *ws).title();
+ } else if (auto *firstCurve = dynamic_cast<MantidMDCurve*>(curve(0))) {
+ MantidQwtIMDWorkspaceData* data = firstCurve->mantidData();
+ if (data)
+ return data->getYAxisLabel();
}
+
+ return axisTitle(0);
}
void Graph::contextMenuEvent(QContextMenuEvent *e)
@@ -5519,9 +5527,9 @@ void Graph::noNormalization()
if(!m_isDistribution) return; // Nothing to do
m_isDistribution = false;
- updateDataCurves();
- d_plot->updateAxes();
- setYAxisTitle(yAxisTitleFromFirstCurve());
+
+ updateCurvesAndAxes();
+
notifyChanges();
}
@@ -5533,11 +5541,65 @@ void Graph::binWidthNormalization()
if(m_isDistribution) return; // Nothing to do
m_isDistribution = true;
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Set 'None' normalization for MD plots
+ */
+void Graph::noNormalizationMD()
+{
+ if (!normalizableMD())
+ return;
+
+ setNormalizationMD(0);
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Set volume normalization for MD plots
+ */
+void Graph::volumeNormalizationMD()
+{
+ if (!normalizableMD())
+ return;
+
+ setNormalizationMD(1);
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Set number of events normalization for MD plots
+ */
+void Graph::numEventsNormalizationMD()
+{
+ if (!normalizableMD())
+ return;
+
+ setNormalizationMD(2);
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Convenience method to use when updating the normalization types
+ * (whether Matrix or MD data normalizatio).
+ */
+void Graph::updateCurvesAndAxes() {
updateDataCurves();
d_plot->updateAxes();
setYAxisTitle(yAxisTitleFromFirstCurve());
-
- notifyChanges();
}
void Graph::setWaterfallXOffset(int offset)
@@ -5653,6 +5715,15 @@ void Graph::updateDataCurves()
mc->invalidateBoundingRect();
mc->loadData();
}
+ else if (MantidMDCurve *mdc = dynamic_cast<MantidMDCurve*>(pc))
+ {
+ //mdc->setDrawAsDistribution(m_isDistribution);
+ // yes, using int in Graph and ApplicationWindow instead of the proper enum, just so that
+ // IMDWorkspace.h does not need to be included in more places in MantidPlot
+ mdc->mantidData()->setNormalization(static_cast<Mantid::API::MDNormalization>(m_normalizationMD));
+ mdc->invalidateBoundingRect();
+ }
+
}
QApplication::restoreOverrideCursor();
}
diff --git a/MantidPlot/src/Graph.h b/MantidPlot/src/Graph.h
index 9512139404943318a36ffc5dc9fa343d9fc82d7d..34ae08f03ca7eacf89224cf0b37a0bffcc81b19d 100644
--- a/MantidPlot/src/Graph.h
+++ b/MantidPlot/src/Graph.h
@@ -209,6 +209,20 @@ public slots:
bool isDistribution() const { return m_isDistribution; }
void setDistribution(const bool on) { m_isDistribution = on; }
+ void noNormalizationMD();
+ void numEventsNormalizationMD();
+ void volumeNormalizationMD();
+
+ /// normalizable in the MD sense, don't confuse with (bin width) normalizable(),
+ /// True if this is a plot MD
+ bool normalizableMD() const { return m_normalizableMD; }
+ void setNormalizableMD(const bool on) { m_normalizableMD = on; }
+
+ /// when using MD curves (true == normalizbleMD()), what type of normalization
+ int normalizationMD() const { return m_normalizationMD; }
+ void setNormalizationMD(const int normalization) { m_normalizationMD = normalization; }
+
+
//! Accessor method for #d_plot.
Plot* plotWidget(){return d_plot;};
@@ -813,6 +827,8 @@ private:
QString yAxisTitleFromFirstCurve();
+ void updateCurvesAndAxes();
+
Plot *d_plot;
QwtPlotZoomer *d_zoomer[2];
TitlePicker *titlePicker;
@@ -877,6 +893,12 @@ private:
bool m_isDistribution;
// True, if the graph can be plotted as distribution
bool m_normalizable;
+
+ // True if the graph is an MD plot and can be normalized (none, volume, events)
+ bool m_normalizableMD;
+ /// type of normalization for MD curves
+ int m_normalizationMD;
+
// x and y units of MantidCurves
boost::shared_ptr<Mantid::Kernel::Unit> m_xUnits;
boost::shared_ptr<Mantid::Kernel::Unit> m_yUnits;
diff --git a/MantidPlot/src/ImportASCIIDialog.cpp b/MantidPlot/src/ImportASCIIDialog.cpp
index 44c2ff0105b2c0636fe4a8fcebce9f9dbdcb0dcd..075910ef35fb89d929af75626a20ae8a6845b781 100644
--- a/MantidPlot/src/ImportASCIIDialog.cpp
+++ b/MantidPlot/src/ImportASCIIDialog.cpp
@@ -450,62 +450,67 @@ void ImportASCIIDialog::preview()
void ImportASCIIDialog::previewTable()
{
- if (!d_preview_table)
- return;
+ if (!d_preview_table)
+ return;
- if (!d_preview_table->isVisible())
- d_preview_table->show();
+ if (!d_preview_table->isVisible())
+ d_preview_table->show();
- if (d_current_path.trimmed().isEmpty()){
- d_preview_table->clear();
- d_preview_table->resetHeader();
- return;
- }
+ if (d_current_path.trimmed().isEmpty()){
+ d_preview_table->clear();
+ d_preview_table->resetHeader();
+ return;
+ }
- int importMode = d_import_mode->currentIndex();
- if (importMode == NewTables)
- importMode = Table::Overwrite;
- else
- importMode -= 2;
-
- d_preview_table->resetHeader();
- d_preview_table->importASCII(d_current_path, columnSeparator(), d_ignored_lines->value(),
- d_rename_columns->isChecked(), d_strip_spaces->isChecked(),
- d_simplify_spaces->isChecked(), d_import_comments->isChecked(),
- d_comment_string->text(), (Table::ImportMode)importMode,
- boxEndLine->currentIndex(), d_preview_lines_box->value());
-
- if (d_import_dec_separators->isChecked())
- d_preview_table->updateDecimalSeparators(decimalSeparators());
- if (!d_preview_table->isVisible())
- d_preview_table->show();
+ int importMode = d_import_mode->currentIndex();
+ if (importMode == NewTables) {
+ importMode = (ImportASCIIDialog::ImportMode)Table::Overwrite;
+ } else {
+ importMode -= 2;
+ }
+
+ d_preview_table->resetHeader();
+ d_preview_table->importASCII(d_current_path, columnSeparator(), d_ignored_lines->value(),
+ d_rename_columns->isChecked(), d_strip_spaces->isChecked(),
+ d_simplify_spaces->isChecked(), d_import_comments->isChecked(),
+ d_comment_string->text(), (Table::ImportMode)importMode,
+ boxEndLine->currentIndex(), d_preview_lines_box->value());
+
+ if (d_import_dec_separators->isChecked())
+ d_preview_table->updateDecimalSeparators(decimalSeparators());
+
+ if (!d_preview_table->isVisible())
+ d_preview_table->show();
}
-void ImportASCIIDialog::previewMatrix()
-{
- if (!d_preview_matrix)
- return;
+void ImportASCIIDialog::previewMatrix() {
+ if (!d_preview_matrix)
+ return;
- if (d_current_path.trimmed().isEmpty()){
- d_preview_matrix->clear();
- return;
- }
+ if (d_current_path.trimmed().isEmpty()) {
+ d_preview_matrix->clear();
+ return;
+ }
- int importMode = d_import_mode->currentIndex();
- if (importMode == NewMatrices)
- importMode = Matrix::Overwrite;
- else
- importMode -= 2;
+ int importMode = d_import_mode->currentIndex();
+ if (importMode == NewMatrices) {
+ importMode = (ImportASCIIDialog::ImportMode)Matrix::Overwrite;
+ } else {
+ // Overwrite-2 => NewColumns (in both Matrix::importMode and
+ // ImportASCIIDialog::importMode)
+ importMode -= 2;
+ }
- QLocale locale = d_preview_matrix->locale();
- if(d_import_dec_separators->isChecked())
- locale = decimalSeparators();
+ QLocale locale = d_preview_matrix->locale();
+ if (d_import_dec_separators->isChecked())
+ locale = decimalSeparators();
- d_preview_matrix->importASCII(d_current_path, columnSeparator(), d_ignored_lines->value(),
- d_strip_spaces->isChecked(), d_simplify_spaces->isChecked(),
- d_comment_string->text(), importMode, locale,
- boxEndLine->currentIndex(), d_preview_lines_box->value());
- d_preview_matrix->resizeColumnsToContents();
+ d_preview_matrix->importASCII(
+ d_current_path, columnSeparator(), d_ignored_lines->value(),
+ d_strip_spaces->isChecked(), d_simplify_spaces->isChecked(),
+ d_comment_string->text(), importMode, locale, boxEndLine->currentIndex(),
+ d_preview_lines_box->value());
+ d_preview_matrix->resizeColumnsToContents();
}
void ImportASCIIDialog::changePreviewFile(const QString& path)
@@ -542,8 +547,8 @@ void ImportASCIIDialog::setNewWindowsOnly(bool on)
if (on){
d_import_mode->clear();
d_import_mode->addItem(tr("New Table"));
- d_import_mode->addItem(tr("New Matrice"));
- d_import_mode->addItem(tr("New Workspace"));
+ d_import_mode->addItem(tr("New Matrix"));
+ d_import_mode->addItem(tr("New Workspace"));
}
d_preview_button->setChecked(false);
diff --git a/MantidPlot/src/Mantid/InstrumentWidget/InstrumentActor.cpp b/MantidPlot/src/Mantid/InstrumentWidget/InstrumentActor.cpp
index 5e35f163b3589f562ab5ea69a329485be9cd5c8e..5c0e4b60da7f2cdbfbfe322332e9c4b39058df5e 100644
--- a/MantidPlot/src/Mantid/InstrumentWidget/InstrumentActor.cpp
+++ b/MantidPlot/src/Mantid/InstrumentWidget/InstrumentActor.cpp
@@ -1,35 +1,37 @@
#include "InstrumentActor.h"
#include "CompAssemblyActor.h"
-#include "ObjComponentActor.h"
-#include "SampleActor.h"
#include "ComponentActor.h"
+#include "GLActorVisitor.h"
#include "ObjCompAssemblyActor.h"
+#include "ObjComponentActor.h"
#include "RectangularDetectorActor.h"
-#include "GLActorVisitor.h"
+#include "SampleActor.h"
-#include "MantidKernel/Exception.h"
-#include "MantidKernel/V3D.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidGeometry/Objects/Object.h"
-#include "MantidGeometry/ICompAssembly.h"
-#include "MantidGeometry/IObjComponent.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/IMaskWorkspace.h"
#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/CommonBinsValidator.h"
#include "MantidAPI/FrameworkManager.h"
#include "MantidAPI/IAlgorithm.h"
+#include "MantidAPI/IMaskWorkspace.h"
+#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidAPI/WorkspaceValidators.h"
-#include <boost/math/special_functions/fpclassify.hpp>
+#include "MantidGeometry/Objects/Object.h"
+#include "MantidGeometry/ICompAssembly.h"
+#include "MantidGeometry/IDTypes.h"
+#include "MantidGeometry/IObjComponent.h"
+
+#include "MantidKernel/ConfigService.h"
+#include "MantidKernel/Exception.h"
+#include "MantidKernel/ReadLock.h"
+#include "MantidKernel/V3D.h"
+
#include <boost/algorithm/string.hpp>
+#include <boost/math/special_functions/fpclassify.hpp>
-#include <QSettings>
#include <QMessageBox>
+#include <QSettings>
#include <numeric>
-#include "MantidGeometry/IDTypes.h"
-#include "MantidKernel/ReadLock.h"
using namespace Mantid::Kernel::Exception;
using namespace Mantid::Geometry;
diff --git a/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.cpp b/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.cpp
index 8da241a02ea906a903b8742b08ca3c812e99e00f..afa7126f7499db695f9a5f731a0b5a23eb26f4bc 100644
--- a/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.cpp
+++ b/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.cpp
@@ -33,3 +33,8 @@ std::ostream& OpenGLError::log()
{
return g_log.error();
}
+
+std::ostream& OpenGLError::logDebug()
+{
+ return g_log.debug();
+}
diff --git a/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.h b/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.h
index cdeb10d98f2ca333a20654e82d640597988998f8..c5e63188a828b6325d5725d70a9a11ba5006b648 100644
--- a/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.h
+++ b/MantidPlot/src/Mantid/InstrumentWidget/OpenGLError.h
@@ -16,6 +16,8 @@ public:
static bool check(const std::string& funName);
static bool hasError(const std::string& funName){return check(funName);}
static std::ostream& log();
+ static std::ostream& logDebug();
+
private:
std::string m_msg;
};
diff --git a/MantidPlot/src/Mantid/InstrumentWidget/ProjectionSurface.cpp b/MantidPlot/src/Mantid/InstrumentWidget/ProjectionSurface.cpp
index 1c6a0052da5fb529510990d2b153790c8ae3dee3..37a85ee1cfdd7f02149a70bff5c8a43c632989ad 100644
--- a/MantidPlot/src/Mantid/InstrumentWidget/ProjectionSurface.cpp
+++ b/MantidPlot/src/Mantid/InstrumentWidget/ProjectionSurface.cpp
@@ -220,7 +220,8 @@ void ProjectionSurface::draw(MantidGLWidget *widget,bool picking)const
getController()->onPaint( painter );
painter.end();
// Discard any error generated here
- glGetError();
+ GLuint ecode = glGetError();
+ OpenGLError::logDebug() << "Discarding OpenGL error: " << gluErrorString(ecode);
}
}
diff --git a/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp b/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp
index d83662b41b3b486ee0e4da6bce7f7fb13c2a5f1c..77766f8eff2801fa872fa1d9c612ba5122370e61 100644
--- a/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp
+++ b/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp
@@ -581,8 +581,8 @@ void UnwrappedSurface::drawSimpleToImage(QImage* image,bool picking)const
if ( iw < 4 ) iw = 4;
if ( ih < 4 ) ih = 4;
- double w = (iw == 0)? dw : udet.width/2;
- double h = (ih == 0)? dh : udet.height/2;
+ double w = udet.width/2;
+ double h = udet.height/2;
if (!(m_viewRect.contains(udet.u-w, udet.v-h) || m_viewRect.contains(udet.u+w, udet.v+h))) continue;
diff --git a/MantidPlot/src/Mantid/MantidUI.cpp b/MantidPlot/src/Mantid/MantidUI.cpp
index d076bdf157480feeeb4f10b4ff922a8c1a7c90e4..f6ddf9efda70d0a46db18176e62f79426ebffe43 100644
--- a/MantidPlot/src/Mantid/MantidUI.cpp
+++ b/MantidPlot/src/Mantid/MantidUI.cpp
@@ -617,6 +617,9 @@ MultiLayer* MantidUI::plotMDList(const QStringList& wsNames, const int plotAxis,
data->setPlotAxisChoice(plotAxis);
data->setNormalization(normalization);
+ g->setNormalizableMD(true);
+ g->setNormalizationMD(normalization);
+
// Using information from the first graph
if( i == 0 && isGraphNew )
g->setAutoScale();
diff --git a/MantidPlot/src/ScaleDetails.cpp b/MantidPlot/src/ScaleDetails.cpp
index 71190376094ff0093f8972b303d2eba67214edcd..e6ef88b10316eb1eaf83abc126038653d8a710d5 100644
--- a/MantidPlot/src/ScaleDetails.cpp
+++ b/MantidPlot/src/ScaleDetails.cpp
@@ -272,6 +272,10 @@ void ScaleDetails::initWidgets()
if (type == ScaleDraw::Date)
{
ScaleDraw *sclDraw = dynamic_cast<ScaleDraw *>(d_plot->axisScaleDraw(m_mappedaxis));
+ if (!sclDraw) {
+ throw std::runtime_error("Could not convert the axis Scale Draw object "
+ "to a ScaleDraw object");
+ }
QDateTime origin = sclDraw->dateTimeOrigin();
m_dspnStart->hide();
diff --git a/MantidPlot/src/importOPJ.cpp b/MantidPlot/src/importOPJ.cpp
index f5d393e96b4239a28a8c3f23f98e9eabfeca5a7d..458e67fe47debd7431cdd9268e58cb0edb4594b5 100644
--- a/MantidPlot/src/importOPJ.cpp
+++ b/MantidPlot/src/importOPJ.cpp
@@ -702,6 +702,8 @@ bool ImportOPJ::importGraphs(const OPJFile& opj)
break;
case 'F':
s=opj.functionIndex(data.right(data.length()-2).toStdString().c_str());
+ if (s<0)
+ break;
int type;
if(opj.functionType(s)==1)//Polar
{
diff --git a/MantidPlot/src/origin/OPJFile.cpp b/MantidPlot/src/origin/OPJFile.cpp
index c0eaf257564f31fb9b64b0ffd2f0ac8fb75696b6..73c397f65f2b0677228b8845a3ee1219b7708505 100644
--- a/MantidPlot/src/origin/OPJFile.cpp
+++ b/MantidPlot/src/origin/OPJFile.cpp
@@ -52,6 +52,7 @@
#include <stdio.h>
#include <stdlib.h>
+#include <limits.h>
#include <math.h>
#include <cstring>
#include <algorithm> //required for std::swap
@@ -1327,6 +1328,12 @@ void OPJFile::readSpreadInfo(FILE *f, FILE *debug)
fread(&sec_size,4,1,f);
if(IsBigEndian()) SwapBytes(sec_size);
+ if (INT_MAX == sec_size) {
+ // this would end in an overflow and it's obviously wrong
+ fprintf(debug, "Error: while reading spread info, found section size: %d\n", sec_size);
+ fflush(debug);
+ }
+
//section_body_1
LAYER+=0x5;
fseek(f,LAYER,SEEK_SET);
@@ -1335,6 +1342,9 @@ void OPJFile::readSpreadInfo(FILE *f, FILE *debug)
if(col_index!=-1)
{
char *stmp=new char[sec_size+1];
+ if (!stmp)
+ break;
+
stmp[sec_size]='\0';
fread(stmp,sec_size,1,f);
SPREADSHEET[spread].column[col_index].command=stmp;
@@ -1552,6 +1562,12 @@ void OPJFile::readExcelInfo(FILE *f, FILE *debug)
fread(&sec_size,4,1,f);
if(IsBigEndian()) SwapBytes(sec_size);
+ if (INT_MAX == sec_size) {
+ // this would end in an overflow for new[] below and it's obviously wrong
+ fprintf(debug, "Error: while reading Excel info, found section size: %d\n", sec_size);
+ fflush(debug);
+ }
+
//section_body_1
LAYER+=0x5;
fseek(f,LAYER,SEEK_SET);
@@ -1802,6 +1818,12 @@ void OPJFile::readMatrixInfo(FILE *f, FILE *debug)
fread(&sec_size,4,1,f);
if(IsBigEndian()) SwapBytes(sec_size);
+ if (INT_MAX == sec_size) {
+ // this would end in an overflow for new[] below and it's obviously wrong
+ fprintf(debug, "Error: while reading matrix info, found section size: %d\n", sec_size);
+ fflush(debug);
+ }
+
//section_body_1
LAYER+=0x5;
//check if it is a formula
@@ -2933,11 +2955,17 @@ void OPJFile::readProjectTreeFolder(FILE *f, FILE *debug, tree<projectNode>::ite
fread(&namesize,4,1,f);
if(IsBigEndian()) SwapBytes(namesize);
- POS+=5;
+ if (INT_MAX == namesize) {
+ // this would cause an overflow and it's anyway obviously wrong
+ fprintf(debug, "Error: while reading project tree folder, found project/folder name size: %d\n", namesize);
+ fflush(debug);
+ }
// read folder name
char* name=new char[namesize+1];
name[namesize]='\0';
+
+ POS+=5;
fseek(f,POS,SEEK_SET);
fread(name,namesize,1,f);
tree<projectNode>::iterator current_folder=projectTree.append_child(parent, projectNode(name, 1, creation_date, modification_date));
diff --git a/MantidPlot/src/zlib123/minigzip.c b/MantidPlot/src/zlib123/minigzip.c
index 6f12762c8ecedb7a71ddf33c3f7f848178ba3075..5263508908db17952ab8df54cbd0d1bfc0575657 100644
--- a/MantidPlot/src/zlib123/minigzip.c
+++ b/MantidPlot/src/zlib123/minigzip.c
@@ -209,8 +209,9 @@ void file_compress(file, mode)
FILE *in;
gzFile out;
- strcpy(outfile, file);
- strcat(outfile, GZ_SUFFIX);
+ strncpy(outfile, file, MAX_NAME_LEN-1);
+ outfile[MAX_NAME_LEN-1] = '\0';
+ strncat(outfile, GZ_SUFFIX, MAX_NAME_LEN - strlen(outfile) - 1);
in = fopen(file, "rb");
if (in == NULL) {
diff --git a/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h b/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h
index 85fa109a4511bb3ef96de179827dc54d33baab32..4d375e8cdc124c9d04bf0274f849ee4f597b7a13 100644
--- a/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h
+++ b/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h
@@ -36,19 +36,20 @@ namespace CustomDialogs {
class GetNegMuMuonicXRDDialog : public API::AlgorithmDialog {
Q_OBJECT
- public:
+public:
/// Constructor
GetNegMuMuonicXRDDialog(QWidget *parent = 0);
- private:
+private:
/// Periodic Table widget used for selection of elements property
- PeriodicTableWidget *periodicTable;
+ PeriodicTableWidget *m_periodicTable;
/// QLineEdit used for input of y-position property
- QLineEdit *yPosition;
+ QLineEdit *m_yPosition;
/// QLineEdit used for input of GroupWorkspaceSpace
- QLineEdit *groupWorkspaceNameInput;
- //Check box for showing or hiding the Legend for PeriodicTableWidget
- QCheckBox *showLegendCheck;
+ QLineEdit *m_groupWorkspaceNameInput;
+ // Check box for showing or hiding the Legend for PeriodicTableWidget
+ QCheckBox *m_showLegendCheck;
+
/// Validate that the input is not empty before running algorithm
bool validateDialogInput(QString input);
/** Enables a the buttons corresponding to the elements
@@ -56,15 +57,15 @@ class GetNegMuMuonicXRDDialog : public API::AlgorithmDialog {
*/
void enableElementsForGetNegMuMuonicXRD();
- private slots:
+private slots:
/// When the "Run" button is clicked, the algorithm is executed with inputs
void runClicked();
void showLegend();
- protected:
+protected:
// create the initial layout
void initLayout();
- signals:
+signals:
/// signal emitted when validateDialogInput passes
void validInput();
};
diff --git a/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp b/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp
index 963da0325e8764e67562bd8801154cbca51c2648..463fae15e31cc0b36834b70bb1dfbef1ecd0c5a8 100644
--- a/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp
+++ b/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp
@@ -7,7 +7,6 @@
#include <QValidator>
#include <QFormLayout>
-
namespace MantidQt {
namespace CustomDialogs {
DECLARE_DIALOG(GetNegMuMuonicXRDDialog)
@@ -18,7 +17,8 @@ DECLARE_DIALOG(GetNegMuMuonicXRDDialog)
*/
GetNegMuMuonicXRDDialog::GetNegMuMuonicXRDDialog(QWidget *parent)
- : API::AlgorithmDialog(parent) {}
+ : API::AlgorithmDialog(parent), m_periodicTable(NULL), m_yPosition(NULL),
+ m_groupWorkspaceNameInput(NULL), m_showLegendCheck(NULL) {}
/// Initialise the layout
void GetNegMuMuonicXRDDialog::initLayout() {
@@ -26,18 +26,18 @@ void GetNegMuMuonicXRDDialog::initLayout() {
this->setMaximumHeight(400);
this->setMaximumWidth(675);
// assign periodicTable member to a new periodicTable
- periodicTable = new PeriodicTableWidget();
+ m_periodicTable = new PeriodicTableWidget();
- // assign yPosition member to a new QLineEdit
- yPosition = new QLineEdit();
- //assign GroupWorkspaceName member to a new QLineEdit
- groupWorkspaceNameInput = new QLineEdit();
+ // assign m_yPosition member to a new QLineEdit
+ m_yPosition = new QLineEdit();
+ // assign GroupWorkspaceName member to a new QLineEdit
+ m_groupWorkspaceNameInput = new QLineEdit();
auto *groupWsInputLabel = new QLabel("OutputWorkspace");
- groupWorkspaceNameInput->setMaximumWidth(250);
+ m_groupWorkspaceNameInput->setMaximumWidth(250);
// Disable all buttons on the periodicTable
// as we only have a select few that need to be
// enabled.
- periodicTable->disableAllElementButtons();
+ m_periodicTable->disableAllElementButtons();
/*Elements Enabled Correspond to those for which we
* have data for in the dictionary found in
@@ -51,44 +51,44 @@ void GetNegMuMuonicXRDDialog::initLayout() {
// run button for executing the algorithm
auto *runButton = new QPushButton("Run");
- // label for the QLineEdit for yPosition property
- auto *yPositionLabel = new QLabel("Y Position");
+ // label for the QLineEdit for m_yPosition property
+ auto *m_yPositionLabel = new QLabel("Y Position");
- /*validator allows only numeric input for yPosition
+ /*validator allows only numeric input for m_yPosition
*this helps with validating the input.
*Does not detect empty string as invalid input.
*/
- auto yPositionNumericValidator = new QDoubleValidator();
+ auto m_yPositionNumericValidator = new QDoubleValidator();
// YPosition LineEdit Attributes
- yPosition->setMaximumWidth(250);
- yPosition->setPlaceholderText("-0.01");
- yPosition->setValidator(yPositionNumericValidator);
+ m_yPosition->setMaximumWidth(250);
+ m_yPosition->setPlaceholderText("-0.01");
+ m_yPosition->setValidator(m_yPositionNumericValidator);
// Run Button Attributes and signal/slot assignment
runButton->setMaximumWidth(100);
connect(runButton, SIGNAL(clicked()), this, SLOT(runClicked()));
connect(this, SIGNAL(validInput()), this, SLOT(accept()));
- //Show Legend button attributes and signal/slot asssignment
- showLegendCheck = new QCheckBox("Show Legend");
- connect(showLegendCheck, SIGNAL(clicked()), this, SLOT(showLegend()));
+ // Show Legend button attributes and signal/slot asssignment
+ m_showLegendCheck = new QCheckBox("Show Legend");
+ connect(m_showLegendCheck, SIGNAL(clicked()), this, SLOT(showLegend()));
// Adding Widgets to Layout
- main_layout->addWidget(periodicTable);
- main_layout->addWidget(showLegendCheck);
- main_layout->addWidget(yPositionLabel);
- main_layout->addWidget(yPosition);
+ main_layout->addWidget(m_periodicTable);
+ main_layout->addWidget(m_showLegendCheck);
+ main_layout->addWidget(m_yPositionLabel);
+ main_layout->addWidget(m_yPosition);
main_layout->addWidget(groupWsInputLabel);
- main_layout->addWidget(groupWorkspaceNameInput);
+ main_layout->addWidget(m_groupWorkspaceNameInput);
main_layout->addWidget(runButton);
}
/**
*
*/
-void GetNegMuMuonicXRDDialog::showLegend(){
- bool checked = showLegendCheck->isChecked();
- periodicTable->showGroupLegend(checked);
+void GetNegMuMuonicXRDDialog::showLegend() {
+ bool checked = m_showLegendCheck->isChecked();
+ m_periodicTable->showGroupLegend(checked);
}
/**
@@ -102,13 +102,13 @@ void GetNegMuMuonicXRDDialog::enableElementsForGetNegMuMuonicXRD() {
* for the algorithm, and the button for that element can be enabled
* the same as the elements are below.
*/
- periodicTable->enableButtonByName("Au");
- periodicTable->enableButtonByName("Ag");
- periodicTable->enableButtonByName("Cu");
- periodicTable->enableButtonByName("Zn");
- periodicTable->enableButtonByName("Pb");
- periodicTable->enableButtonByName("As");
- periodicTable->enableButtonByName("Sn");
+ m_periodicTable->enableButtonByName("Au");
+ m_periodicTable->enableButtonByName("Ag");
+ m_periodicTable->enableButtonByName("Cu");
+ m_periodicTable->enableButtonByName("Zn");
+ m_periodicTable->enableButtonByName("Pb");
+ m_periodicTable->enableButtonByName("As");
+ m_periodicTable->enableButtonByName("Sn");
}
/**
@@ -128,7 +128,7 @@ bool GetNegMuMuonicXRDDialog::validateDialogInput(QString input) {
*/
void GetNegMuMuonicXRDDialog::runClicked() {
// getting a list of strings of elements selected from periodicTableWidget
- QString elementsSelectedStr = periodicTable->getAllCheckedElementsStr();
+ QString elementsSelectedStr = m_periodicTable->getAllCheckedElementsStr();
// if no elements are selected from the PeriodicTableWidget, a pop-up appears
// to the user.
if (!validateDialogInput(elementsSelectedStr)) {
@@ -141,15 +141,16 @@ void GetNegMuMuonicXRDDialog::runClicked() {
// signal.
if (validateDialogInput(elementsSelectedStr)) {
storePropertyValue("Elements", elementsSelectedStr);
- if (validateDialogInput(yPosition->text())) {
- storePropertyValue("YAxisPosition", yPosition->text());
+ if (validateDialogInput(m_yPosition->text())) {
+ storePropertyValue("YAxisPosition", m_yPosition->text());
} else {
- // used as default value for yPosition property if the user does not input
+ // used as default value for m_yPosition property if the user does not
+ // input
// one.
- storePropertyValue("YAxisPosition", yPosition->placeholderText());
+ storePropertyValue("YAxisPosition", m_yPosition->placeholderText());
}
- if (validateDialogInput(groupWorkspaceNameInput->text())){
- storePropertyValue("OutputWorkspace", groupWorkspaceNameInput->text());
+ if (validateDialogInput(m_groupWorkspaceNameInput->text())) {
+ storePropertyValue("OutputWorkspace", m_groupWorkspaceNameInput->text());
}
emit validInput();
}
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionPresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionPresenter.h
index ab2cb4672c86bae2b479c406c6ba8a9076e5fe9b..5c4f2dba65bcd8cfe98cfdd5f0f267ba89a52a9b 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionPresenter.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionPresenter.h
@@ -11,6 +11,8 @@
#include <boost/scoped_ptr.hpp>
+#include <Poco/Path.h>
+
#include <QObject>
class QThread;
@@ -176,6 +178,23 @@ private:
Mantid::API::ITableWorkspace_sptr &vanIntegWS,
Mantid::API::MatrixWorkspace_sptr &vanCurvesWS);
+ // plots workspace according to the user selection
+ void plotFocusedWorkspace(std::string outWSName, std::string bank);
+
+ // algorithms to save the generated workspace
+ void saveGSS(std::string inputWorkspace, std::string bank, std::string runNo);
+ void saveFocusedXYE(std::string inputWorkspace, std::string bank,
+ std::string runNo);
+ void saveOpenGenie(std::string inputWorkspace, std::string specNums,
+ std::string bank, std::string runNo);
+
+ // generates the required file name of the output files
+ std::string outFileNameFactory(std::string inputWorkspace, std::string runNo,
+ std::string bank, std::string format);
+
+ // generates a directory if not found and handles the path
+ Poco::Path outFilesDir(std::string runNo);
+
/// string to use for ENGINX file names (as a prefix, etc.)
const static std::string g_enginxStr;
@@ -192,6 +211,9 @@ private:
/// true if the last focusing completed successfully
bool m_focusFinishedOK;
+ /// Counter for the cropped output files
+ static int g_croppedCounter;
+
/// Associated view for this presenter (MVP pattern)
IEnggDiffractionView *const m_view;
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabCalib.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabCalib.ui
index cfd09d9f143835bce84f95d414ecd3e64cd86f96..6381604907d9e6602362cb87b8b9f8afccd1f7bc 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabCalib.ui
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabCalib.ui
@@ -168,32 +168,30 @@
<bool>false</bool>
</property>
<layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="label_new_vanadium_num">
- <property name="text">
- <string>Vanadium #:</string>
- </property>
- </widget>
- </item>
<item row="0" column="1" colspan="2">
- <widget class="QLineEdit" name="lineEdit_new_vanadium_num">
- <property name="text">
+ <widget class="MantidQt::MantidWidgets::MWRunFiles" name="lineEdit_new_vanadium_num" native="true">
+ <property name="text" stdset="0">
<string>236516</string>
</property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_new_ceria_num">
- <property name="text">
- <string>Calibration sample #:</string>
+ <property name="label" stdset="0">
+ <string>Vanadium #:</string>
+ </property>
+ <property name="multipleFiles" stdset="0">
+ <bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="1" colspan="2">
- <widget class="QLineEdit" name="lineEdit_new_ceria_num">
- <property name="text">
+ <widget class="MantidQt::MantidWidgets::MWRunFiles" name="lineEdit_new_ceria_num" native="true">
+ <property name="text" stdset="0">
<string>241391</string>
</property>
+ <property name="label" stdset="0">
+ <string>Calibration sample #:</string>
+ </property>
+ <property name="multipleFiles" stdset="0">
+ <bool>true</bool>
+ </property>
</widget>
</item>
<item row="2" column="0" colspan="2">
@@ -216,6 +214,20 @@
</property>
</widget>
</item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_new_ceria_num">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_new_vanadium_num">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
</layout>
</widget>
</item>
@@ -236,6 +248,13 @@
</item>
</layout>
</widget>
+ <customwidgets>
+ <customwidget>
+ <class>MantidQt::MantidWidgets::MWRunFiles</class>
+ <extends>QWidget</extends>
+ <header>MantidQtMantidWidgets/MWRunFiles.h</header>
+ </customwidget>
+ </customwidgets>
<resources/>
<connections/>
</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabFocus.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabFocus.ui
index da4954af8627faf0c93a9d1c3268b22d655fb790..b6f46a4ab6b44f102950099e87f1ce59e34e8819 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabFocus.ui
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionQtTabFocus.ui
@@ -7,30 +7,123 @@
<x>0</x>
<y>0</y>
<width>614</width>
- <height>533</height>
+ <height>551</height>
</rect>
</property>
<property name="windowTitle">
<string>Form</string>
</property>
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="6" column="0">
- <widget class="QGroupBox" name="groupBox_focus_2">
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QGroupBox" name="groupBox_focus">
<property name="title">
- <string>Output</string>
+ <string>Focus run</string>
</property>
- <layout class="QGridLayout" name="gridLayout_2">
+ <layout class="QGridLayout" name="gridLayout">
+ <item row="1" column="0">
+ <layout class="QHBoxLayout" name="horizontalLayout_5">
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_4">
+ <item>
+ <widget class="QLabel" name="label_banks_sel">
+ <property name="text">
+ <string>Banks:</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>298</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>18</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_4">
+ <item>
+ <widget class="QCheckBox" name="checkBox_focus_bank1">
+ <property name="text">
+ <string>1</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_focus_bank2">
+ <property name="text">
+ <string>2</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item row="2" column="0">
+ <layout class="QHBoxLayout" name="horizontalLayout_3">
+ <item>
+ <spacer name="horizontalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>238</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_focus">
+ <property name="text">
+ <string>Focus</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
<item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_6">
+ <layout class="QHBoxLayout" name="horizontalLayout">
<item>
- <widget class="QCheckBox" name="checkBox_FocusedWS">
+ <widget class="QLabel" name="label_run_num">
<property name="text">
- <string>Plot Focused Workspace</string>
+ <string/>
</property>
</widget>
</item>
<item>
- <spacer name="horizontalSpacer_4">
+ <spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
@@ -42,12 +135,28 @@
</property>
</spacer>
</item>
+ <item>
+ <widget class="MantidQt::MantidWidgets::MWRunFiles" name="lineEdit_run_num" native="true">
+ <property name="text" stdset="0">
+ <string/>
+ </property>
+ <property name="readOnly" stdset="0">
+ <bool>false</bool>
+ </property>
+ <property name="label" stdset="0">
+ <string>Run #:</string>
+ </property>
+ <property name="multipleFiles" stdset="0">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
</layout>
</item>
</layout>
</widget>
</item>
- <item row="2" column="0">
+ <item>
<widget class="QGroupBox" name="groupBox">
<property name="title">
<string>Focus Cropped</string>
@@ -58,7 +167,7 @@
<item>
<widget class="QLabel" name="label_cropped_run_num">
<property name="text">
- <string>Run #:</string>
+ <string/>
</property>
</widget>
</item>
@@ -76,13 +185,19 @@
</spacer>
</item>
<item>
- <widget class="QLineEdit" name="lineEdit_cropped_run_num">
- <property name="text">
+ <widget class="MantidQt::MantidWidgets::MWRunFiles" name="lineEdit_cropped_run_num" native="true">
+ <property name="text" stdset="0">
<string/>
</property>
- <property name="readOnly">
+ <property name="readOnly" stdset="0">
<bool>false</bool>
</property>
+ <property name="label" stdset="0">
+ <string>Run #:</string>
+ </property>
+ <property name="multipleFiles" stdset="0">
+ <bool>true</bool>
+ </property>
</widget>
</item>
</layout>
@@ -148,147 +263,102 @@
</layout>
</widget>
</item>
- <item row="4" column="0">
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>388</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="0" column="0">
- <widget class="QGroupBox" name="groupBox_focus">
+ <item>
+ <widget class="QGroupBox" name="groupBox_2">
<property name="title">
- <string>Focus run</string>
+ <string>Focus Texture</string>
</property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="2" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_3">
+ <layout class="QGridLayout" name="gridLayout_4">
+ <item row="0" column="0">
+ <layout class="QHBoxLayout" name="horizontalLayout_7">
<item>
- <spacer name="horizontalSpacer_3">
+ <widget class="QLabel" name="label_texture_run_num">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_6">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
- <width>238</width>
+ <width>98</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item>
- <widget class="QPushButton" name="pushButton_focus">
- <property name="text">
- <string>Focus</string>
+ <widget class="MantidQt::MantidWidgets::MWRunFiles" name="lineEdit_texture_run_num" native="true">
+ <property name="text" stdset="0">
+ <string/>
+ </property>
+ <property name="readOnly" stdset="0">
+ <bool>false</bool>
+ </property>
+ <property name="label" stdset="0">
+ <string>Run #:</string>
+ </property>
+ <property name="multipleFiles" stdset="0">
+ <bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_5">
+ <layout class="QHBoxLayout" name="horizontalLayout_8">
<item>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QLabel" name="label_banks_sel">
- <property name="text">
- <string>Banks:</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>298</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>18</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
+ <widget class="QLabel" name="label_2">
+ <property name="text">
+ <string>Detector Grouping File:</string>
+ </property>
+ </widget>
</item>
<item>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QCheckBox" name="checkBox_focus_bank1">
- <property name="text">
- <string>1</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_focus_bank2">
- <property name="text">
- <string>2</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
+ <widget class="QLineEdit" name="lineEdit_texture_grouping_file">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>1</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="readOnly">
+ <bool>true</bool>
+ </property>
+ </widget>
</item>
- </layout>
- </item>
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout">
<item>
- <widget class="QLabel" name="label_run_num">
+ <widget class="QPushButton" name="pushButton_texture_browse_grouping_file">
<property name="text">
- <string>Run #:</string>
+ <string>Browse</string>
</property>
</widget>
</item>
+ </layout>
+ </item>
+ <item row="2" column="0">
+ <layout class="QHBoxLayout" name="horizontalLayout_11">
<item>
- <spacer name="horizontalSpacer">
+ <spacer name="horizontalSpacer_9">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
- <width>98</width>
+ <width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item>
- <widget class="QLineEdit" name="lineEdit_run_num">
+ <widget class="QPushButton" name="pushButton_focus_texture">
<property name="text">
- <string/>
- </property>
- <property name="readOnly">
- <bool>false</bool>
+ <string>Focus</string>
</property>
</widget>
</item>
@@ -297,23 +367,42 @@
</layout>
</widget>
</item>
- <item row="3" column="0">
- <widget class="QGroupBox" name="groupBox_2">
+ <item>
+ <spacer name="verticalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_focus_3">
+ <property name="minimumSize">
+ <size>
+ <width>596</width>
+ <height>111</height>
+ </size>
+ </property>
<property name="title">
- <string>Focus Texture</string>
+ <string>Output</string>
</property>
- <layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_7">
+ <layout class="QVBoxLayout" name="verticalLayout_6">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_20">
<item>
- <widget class="QLabel" name="label_texture_run_num">
+ <widget class="QCheckBox" name="checkBox_FocusedWS">
<property name="text">
- <string>Run #:</string>
+ <string>Plot Focused Workspace</string>
</property>
</widget>
</item>
<item>
- <spacer name="horizontalSpacer_6">
+ <spacer name="horizontalSpacer_18">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
@@ -325,77 +414,106 @@
</property>
</spacer>
</item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_21">
<item>
- <widget class="QLineEdit" name="lineEdit_texture_run_num">
- <property name="text">
- <string/>
+ <spacer name="horizontalSpacer_19">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
</property>
- <property name="readOnly">
- <bool>false</bool>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>98</width>
+ <height>20</height>
+ </size>
</property>
- </widget>
+ </spacer>
</item>
- </layout>
- </item>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_8">
<item>
- <widget class="QLabel" name="label_2">
+ <widget class="QLabel" name="label_4">
<property name="text">
- <string>Detector Grouping File:</string>
+ <string>Plot Data Representation:</string>
</property>
</widget>
</item>
<item>
- <widget class="QLineEdit" name="lineEdit_texture_grouping_file">
+ <widget class="QComboBox" name="comboBox_PlotData">
<property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>1</horstretch>
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
- <property name="readOnly">
- <bool>true</bool>
+ <property name="minimumSize">
+ <size>
+ <width>175</width>
+ <height>10</height>
+ </size>
+ </property>
+ <property name="sizeIncrement">
+ <size>
+ <width>0</width>
+ <height>0</height>
+ </size>
</property>
+ <property name="baseSize">
+ <size>
+ <width>0</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="layoutDirection">
+ <enum>Qt::LeftToRight</enum>
+ </property>
+ <item>
+ <property name="text">
+ <string>One Window - Replacing Plots</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>One Window - Waterfall</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Multiple Windows</string>
+ </property>
+ </item>
</widget>
</item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_22">
<item>
- <widget class="QPushButton" name="pushButton_texture_browse_grouping_file">
+ <widget class="QCheckBox" name="checkBox_SaveOutputFiles">
<property name="text">
- <string>Browse</string>
+ <string>Output Files</string>
</property>
</widget>
</item>
- </layout>
- </item>
- <item row="2" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_11">
<item>
- <spacer name="horizontalSpacer_9">
+ <spacer name="horizontalSpacer_20">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
- <width>40</width>
+ <width>98</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
- <item>
- <widget class="QPushButton" name="pushButton_focus_texture">
- <property name="text">
- <string>Focus</string>
- </property>
- </widget>
- </item>
</layout>
</item>
</layout>
</widget>
</item>
- <item row="5" column="0">
+ <item>
<layout class="QHBoxLayout" name="horizontalLayout_13">
<item>
<spacer name="horizontalSpacer_11">
@@ -421,6 +539,13 @@
</item>
</layout>
</widget>
+ <customwidgets>
+ <customwidget>
+ <class>MantidQt::MantidWidgets::MWRunFiles</class>
+ <extends>QWidget</extends>
+ <header>MantidQtMantidWidgets/MWRunFiles.h</header>
+ </customwidget>
+ </customwidgets>
<resources/>
<connections/>
</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h
index baed981c8f15aa12f32c87aa18132004d4e24ec8..f813d2b37cb5782b6d39ef2ed7e7ac013d330350 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h
@@ -121,6 +121,14 @@ public:
virtual void plotFocusedSpectrum(const std::string &wsName);
+ virtual void plotWaterfallSpectrum(const std::string &wsName);
+
+ virtual void plotReplacingWindow(const std::string &wsName);
+
+ virtual bool saveOutputFiles() const;
+
+ int currentPlotType() const { return m_currentType; }
+
private slots:
/// for buttons, do calibrate, focus and similar
void loadCalibrationClicked();
@@ -145,6 +153,12 @@ private slots:
// slots of the general part of the interface
void instrumentChanged(int idx);
+ // slots of the focus part of the interface
+ void plotRepChanged(int idx);
+
+ // slots of plot spectrum check box status
+ void plotFocusStatus();
+
// show the standard Mantid help window with this interface's help
void openHelpWin();
@@ -183,6 +197,10 @@ private:
/// instrument selected (ENGIN-X, etc.)
std::string m_currentInst;
+
+ // plot data representation type selected
+ int static m_currentType;
+
/// current calibration produced in the 'Calibration' tab
std::string m_currentCalibFilename;
/// calibration settings - from/to the 'settings' tab
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionPresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionPresenter.h
index a2c0240d4cefb1d2befa48388c9bb25ab47bfc01..01fcbcaa76dce48d4ff93578b350e60faef98845 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionPresenter.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionPresenter.h
@@ -38,16 +38,16 @@ public:
/// These are user actions, triggered from the (passive) view, that need
/// handling by the presenter
enum Notification {
- Start, ///< Start and setup interface
- LoadExistingCalib, ///< Load a calibration already availble on disk
- CalcCalib, ///< Calculate a (new) calibration
- FocusRun, ///< Focus one or more run files
- FocusCropped, ///< Focus one or more run files, cropped variant
- FocusTexture, ///< Focus one or more run files, texture variant
- ResetFocus, ///< Re-set / clear all focus inputs and options
- LogMsg, ///< need to send a message to the Mantid log system
- InstrumentChange, ///< Instrument selection updated
- ShutDown ///< closing the interface
+ Start, ///< Start and setup interface
+ LoadExistingCalib, ///< Load a calibration already availble on disk
+ CalcCalib, ///< Calculate a (new) calibration
+ FocusRun, ///< Focus one or more run files
+ FocusCropped, ///< Focus one or more run files, cropped variant
+ FocusTexture, ///< Focus one or more run files, texture variant
+ ResetFocus, ///< Re-set / clear all focus inputs and options
+ LogMsg, ///< need to send a message to the Mantid log system
+ InstrumentChange, ///< Instrument selection updated
+ ShutDown ///< closing the interface
};
/**
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionView.h
index e701764dac3f0d11fa716a65cde8b98fd4ea1e00..91cd94e0835b6f9da52f9896e98843f7d6f469d2 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/EnggDiffraction/IEnggDiffractionView.h
@@ -115,6 +115,14 @@ public:
*/
virtual std::string currentInstrument() const = 0;
+ /**
+ * Selected plot data representation will be applied, which will
+ * ran through python script
+ *
+ * @return which format should to applied for plotting data
+ */
+ virtual int currentPlotType() const = 0;
+
/**
* The Vanadium run number used in the current calibration
*
@@ -262,6 +270,14 @@ public:
*/
virtual void saveSettings() const = 0;
+ /**
+ * Saves the ouput files which are generated, this can be done
+ * via Output Files checkbox on the focus tab
+ *
+ * @return bool
+ */
+ virtual bool saveOutputFiles() const = 0;
+
/**
* Produces a single spectrum graph for focused output. Runs
* plotSpectrum function via python.
@@ -269,6 +285,22 @@ public:
* @param wsName name of the workspace to plot (must be in the ADS)
*/
virtual void plotFocusedSpectrum(const std::string &wsName) = 0;
+
+ /**
+ * Produces a waterfall spectrum graph for focused output. Runs
+ * plotSpectrum function via python.
+ *
+ * @param wsName name of the workspace to plot (must be in the ADS)
+ */
+ virtual void plotWaterfallSpectrum(const std::string &wsName) = 0;
+
+ /**
+ * Produces a replaceable spectrum graph for focused output. Runs
+ * plotSpectrum function via python.
+ *
+ * @param wsName name of the workspace to plot (must be in the ADS)
+ */
+ virtual void plotReplacingWindow(const std::string &wsName) = 0;
};
} // namespace CustomInterfaces
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
index ed25cc6eed04b5788c3f2a4eb7fad4e11b2c3eeb..6ec99813345874f90ebcfe5d3f91ee85d5af963e 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
@@ -77,6 +77,9 @@ private:
QStringList m_fitStrings;
QString m_previousFit;
QString m_baseName;
+ int m_runMin;
+ int m_runMax;
+
};
} // namespace IDA
} // namespace CustomInterfaces
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h
index d164fa8aa6aae3a65e4c873d541e6d5527df0039..49090162ee653bd896774ab56d46edfcee8606f6 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h
@@ -6,68 +6,66 @@
#include "MantidKernel/System.h"
#include "MantidQtCustomInterfaces/Background.h"
-namespace MantidQt
-{
-namespace CustomInterfaces
-{
- /** ISISEnergyTransfer
- Handles an energy transfer reduction for ISIS instruments.
-
- @author Dan Nixon
- @date 23/07/2014
-
- Copyright © 2013 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- File change history is stored at: <https://github.com/mantidproject/mantid>
- Code Documentation is available at: <http://doxygen.mantidproject.org>
- */
- class DLLExport ISISEnergyTransfer : public IndirectDataReductionTab
- {
- Q_OBJECT
-
- public:
- ISISEnergyTransfer(IndirectDataReduction * idrUI, QWidget * parent = 0);
- virtual ~ISISEnergyTransfer();
-
- virtual void setup();
- virtual void run();
-
- public slots:
- virtual bool validate();
-
- private slots:
- void algorithmComplete(bool error);
- void setInstrumentDefault(); ///< Sets default parameters for current instrument
- void mappingOptionSelected(const QString& groupType); ///< change ui to display appropriate options
- void plotRaw(); ///< plot raw data from instrument
- void pbRunEditing(); //< Called when a user starts to type / edit the runs to load.
- void pbRunFinding(); //< Called when the FileFinder starts finding the files.
- void pbRunFinished(); //< Called when the FileFinder has finished finding the files.
- void plotRawComplete(bool error); //< Called when the Plot Raw algorithmm chain completes
-
- private:
- Ui::ISISEnergyTransfer m_uiForm;
-
- QPair<QString, QString> createMapFile(const QString& groupType); ///< create the mapping file with which to group results
- std::vector<std::string> getSaveFormats(); ///< get a vector of save formats
-
- };
+namespace MantidQt {
+namespace CustomInterfaces {
+/** ISISEnergyTransfer
+ Handles an energy transfer reduction for ISIS instruments.
+
+ @author Dan Nixon
+ @date 23/07/2014
+
+ Copyright © 2013 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class DLLExport ISISEnergyTransfer : public IndirectDataReductionTab {
+ Q_OBJECT
+
+public:
+ ISISEnergyTransfer(IndirectDataReduction *idrUI, QWidget *parent = 0);
+ virtual ~ISISEnergyTransfer();
+
+ virtual void setup();
+ virtual void run();
+
+public slots:
+ virtual bool validate();
+
+private slots:
+ void algorithmComplete(bool error);
+ void
+ setInstrumentDefault(); ///< Sets default parameters for current instrument
+ void mappingOptionSelected(const QString &groupType); ///< change ui to display appropriate options
+ void plotRaw(); ///< plot raw data from instrument
+ void pbRunEditing(); //< Called when a user starts to type / edit the runs to load.
+ void pbRunFinding(); //< Called when the FileFinder starts finding the files.
+ void pbRunFinished(); //< Called when the FileFinder has finished finding the files.
+ void plotRawComplete(bool error); //< Called when the Plot Raw algorithmm chain completes
+
+private:
+ Ui::ISISEnergyTransfer m_uiForm;
+
+ QPair<QString, QString> createMapFile(const QString &groupType); ///< create the mapping file with which to group results
+ std::vector<std::string> getSaveFormats(); ///< get a vector of save formats
+};
} // namespace CustomInterfaces
} // namespace Mantid
-#endif //MANTIDQTCUSTOMINTERFACES_ISISENERGYTRANSFER_H_
+#endif // MANTIDQTCUSTOMINTERFACES_ISISENERGYTRANSFER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
index 5423d7311d73d879001d488f2bdcd02e9b6ef5dc..9afef697eac851d26f37c65428ed899de1968700 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
@@ -62,6 +62,11 @@ namespace MantidQt
virtual void giveUserWarning(std::string prompt, std::string title);
virtual void giveUserCritical(std::string prompt, std::string title);
virtual void showAlgorithmDialog(const std::string& algorithm);
+ virtual std::string requestNotebookPath();
+
+ //Settings
+ virtual void saveSettings(const std::map<std::string,QVariant>& options);
+ virtual void loadSettings(std::map<std::string,QVariant>& options);
//Plotting
virtual void plotWorkspaces(const std::set<std::string>& workspaces);
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
index ba7cfe632c3682ec2472b1778fbfee8efb29998f..a60b2df5525e7d4ef0a35effba9220db034e6313 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
@@ -57,6 +57,11 @@ namespace MantidQt
virtual void giveUserWarning(std::string prompt, std::string title) = 0;
virtual void giveUserCritical(std::string prompt, std::string title) = 0;
virtual void showAlgorithmDialog(const std::string& algorithm) = 0;
+ virtual std::string requestNotebookPath() = 0;
+
+ //Settings
+ virtual void saveSettings(const std::map<std::string,QVariant>& options) = 0;
+ virtual void loadSettings(std::map<std::string,QVariant>& options) = 0;
//Plotting
virtual void plotWorkspaces(const std::set<std::string>& workspaces) = 0;
diff --git a/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionPresenter.cpp b/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionPresenter.cpp
index 0b0be67c9f4055f395f0eedcd8b963851a9b1b64..c2c32c4e2a7eb2f60de3a3a222bdf21b9fed3695 100644
--- a/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionPresenter.cpp
+++ b/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionPresenter.cpp
@@ -13,7 +13,6 @@
#include <boost/lexical_cast.hpp>
#include <Poco/File.h>
-#include <Poco/Path.h>
#include <QThread>
@@ -32,6 +31,7 @@ const std::string EnggDiffractionPresenter::g_enginxStr = "ENGINX";
const bool EnggDiffractionPresenter::g_askUserCalibFilename = false;
const std::string EnggDiffractionPresenter::g_vanIntegrationWSName =
"engggui_vanadium_integration_ws";
+int EnggDiffractionPresenter::g_croppedCounter = 0;
EnggDiffractionPresenter::EnggDiffractionPresenter(IEnggDiffractionView *view)
: m_workerThread(NULL), m_calibFinishedOK(false), m_focusFinishedOK(false),
@@ -57,7 +57,8 @@ void EnggDiffractionPresenter::cleanup() {
if (m_workerThread) {
if (m_workerThread->isRunning()) {
g_log.notice() << "A calibration process is currently running, shutting "
- "it down immediately..." << std::endl;
+ "it down immediately..."
+ << std::endl;
m_workerThread->wait(10);
}
delete m_workerThread;
@@ -146,7 +147,8 @@ void EnggDiffractionPresenter::processCalcCalib() {
return;
}
g_log.notice() << "EnggDiffraction GUI: starting new calibration. This may "
- "take a few seconds... " << std::endl;
+ "take a few seconds... "
+ << std::endl;
const std::string outFilename = outputCalibFilename(vanNo, ceriaNo);
@@ -414,10 +416,9 @@ void EnggDiffractionPresenter::parseCalibrateFilename(const std::string &path,
* @param vanNo vanadium run number
* @param ceriaNo ceria run number
*/
-void
-EnggDiffractionPresenter::startAsyncCalibWorker(const std::string &outFilename,
- const std::string &vanNo,
- const std::string &ceriaNo) {
+void EnggDiffractionPresenter::startAsyncCalibWorker(
+ const std::string &outFilename, const std::string &vanNo,
+ const std::string &ceriaNo) {
delete m_workerThread;
m_workerThread = new QThread(this);
EnggDiffWorker *worker =
@@ -466,11 +467,13 @@ void EnggDiffractionPresenter::doNewCalibration(const std::string &outFilename,
} catch (std::runtime_error &) {
g_log.error() << "The calibration calculations failed. One of the "
"algorithms did not execute correctly. See log messages "
- "for details. " << std::endl;
+ "for details. "
+ << std::endl;
} catch (std::invalid_argument &) {
g_log.error()
<< "The calibration calculations failed. Some input properties "
- "were not valid. See log messages for details. " << std::endl;
+ "were not valid. See log messages for details. "
+ << std::endl;
}
// restore normal data search paths
conf.setDataSearchDirs(tmpDirs);
@@ -710,8 +713,8 @@ void EnggDiffractionPresenter::inputChecksBeforeFocusTexture(
inputChecksBeforeFocus();
}
-void
-EnggDiffractionPresenter::inputChecksBanks(const std::vector<bool> &banks) {
+void EnggDiffractionPresenter::inputChecksBanks(
+ const std::vector<bool> &banks) {
if (0 == banks.size()) {
const std::string msg =
"Error in specification of banks found when starting the "
@@ -848,7 +851,8 @@ void EnggDiffractionPresenter::doFocusRun(
const std::string &specNos, const std::string &dgFile) {
g_log.notice() << "Generating new focusing workspace(s) and file(s) into "
- "this directory: " << dir << std::endl;
+ "this directory: "
+ << dir << std::endl;
// TODO: this is almost 100% common with doNewCalibrate() - refactor
EnggDiffCalibSettings cs = m_view->currentCalibSettings();
@@ -887,7 +891,8 @@ void EnggDiffractionPresenter::doFocusRun(
loadDetectorGroupingCSV(dgFile, bankIDs, specs);
} catch (std::runtime_error &re) {
g_log.error() << "Error loading detector grouping file: " + dgFile +
- ". Detailed error: " + re.what() << std::endl;
+ ". Detailed error: " + re.what()
+ << std::endl;
bankIDs.clear();
specs.clear();
}
@@ -903,8 +908,8 @@ void EnggDiffractionPresenter::doFocusRun(
fpath.append(effectiveFilenames[idx]).toString();
g_log.notice() << "Generating new focused file (bank " +
boost::lexical_cast<std::string>(bankIDs[idx]) +
- ") for run " + runNo +
- " into: " << effectiveFilenames[idx] << std::endl;
+ ") for run " + runNo + " into: "
+ << effectiveFilenames[idx] << std::endl;
try {
doFocusing(cs, fullFilename, runNo, bankIDs[idx], specs[idx], dgFile);
m_focusFinishedOK = true;
@@ -916,7 +921,8 @@ void EnggDiffractionPresenter::doFocusRun(
} catch (std::invalid_argument &ia) {
g_log.error()
<< "The focusing failed. Some input properties were not valid. "
- "See log messages for details. Error: " << ia.what() << std::endl;
+ "See log messages for details. Error: "
+ << ia.what() << std::endl;
}
}
@@ -1015,8 +1021,8 @@ void EnggDiffractionPresenter::focusingFinished() {
*
* @param bank instrument bank number to focus
*
- * @param specNos string specifying a list of spectra (for cropped
- * focusing), only considered if not empty
+ * @param specNos string specifying a list of spectra (for "cropped"
+ * focusing or "texture" focusing), only considered if not empty
*
* @param dgFile detector grouping file name. If not empty implies
* texture focusing
@@ -1056,16 +1062,29 @@ void EnggDiffractionPresenter::doFocusing(const EnggDiffCalibSettings &cs,
}
std::string outWSName;
+ std::string specNumsOpenGenie;
if (!dgFile.empty()) {
+ // doing focus "texture"
outWSName = "engggui_focusing_output_ws_texture_bank_" +
boost::lexical_cast<std::string>(bank);
+ specNumsOpenGenie = specNos;
} else if (specNos.empty()) {
+ // doing focus "normal" / by banks
outWSName = "engggui_focusing_output_ws_bank_" +
boost::lexical_cast<std::string>(bank);
+
+ // specnum for opengenie according to bank number
+ if (boost::lexical_cast<std::string>(bank) == "1") {
+ specNumsOpenGenie = "1 - 1200";
+ } else if (boost::lexical_cast<std::string>(bank) == "2") {
+ specNumsOpenGenie = "1201 - 1400";
+ }
+
} else {
+ // doing focus "cropped"
outWSName = "engggui_focusing_output_ws_cropped";
+ specNumsOpenGenie = specNos;
}
-
try {
auto alg = Algorithm::fromString("EnggFocus");
alg->initialize();
@@ -1082,12 +1101,8 @@ void EnggDiffractionPresenter::doFocusing(const EnggDiffCalibSettings &cs,
// TODO: use detector positions (from calibrate full) when available
// alg->setProperty(DetectorPositions, TableWorkspace)
alg->execute();
-
- const bool plotFocusedWS = m_view->focusedOutWorkspace();
- if (plotFocusedWS == true) {
- m_view->plotFocusedSpectrum(outWSName);
- }
-
+ // plot Focused workspace according to the data type selected
+ plotFocusedWorkspace(outWSName, boost::lexical_cast<std::string>(bank));
} catch (std::runtime_error &re) {
g_log.error() << "Error in calibration. ",
"Could not run the algorithm EnggCalibrate succesfully for bank " +
@@ -1095,8 +1110,8 @@ void EnggDiffractionPresenter::doFocusing(const EnggDiffCalibSettings &cs,
re.what() + " Please check also the log messages for details.";
throw;
}
-
g_log.notice() << "Produced focused workspace: " << outWSName << std::endl;
+
try {
g_log.debug() << "Going to save focused output into nexus file: "
<< fullFilename << std::endl;
@@ -1114,6 +1129,14 @@ void EnggDiffractionPresenter::doFocusing(const EnggDiffCalibSettings &cs,
}
g_log.notice() << "Saved focused workspace as file: " << fullFilename
<< std::endl;
+
+ bool saveOutputFiles = m_view->saveOutputFiles();
+ if (saveOutputFiles) {
+ saveFocusedXYE(outWSName, boost::lexical_cast<std::string>(bank), runNo);
+ saveGSS(outWSName, boost::lexical_cast<std::string>(bank), runNo);
+ saveOpenGenie(outWSName, specNumsOpenGenie,
+ boost::lexical_cast<std::string>(bank), runNo);
+ }
}
/**
@@ -1160,7 +1183,8 @@ void EnggDiffractionPresenter::loadOrCalcVanadiumWorkspaces(
"This is possibly because some of the settings are not "
"consistent. Please check the log messages for "
"details. Details: " +
- std::string(ia.what()) << std::endl;
+ std::string(ia.what())
+ << std::endl;
throw;
} catch (std::runtime_error &re) {
g_log.error() << "Failed to calculate Vanadium corrections. "
@@ -1169,7 +1193,8 @@ void EnggDiffractionPresenter::loadOrCalcVanadiumWorkspaces(
"There was no obvious error in the input properties "
"but the algorithm failed. Please check the log "
"messages for details." +
- std::string(re.what()) << std::endl;
+ std::string(re.what())
+ << std::endl;
throw;
}
} else {
@@ -1325,5 +1350,226 @@ void EnggDiffractionPresenter::calcVanadiumWorkspaces(
vanCurvesWS = ADS.retrieveWS<MatrixWorkspace>(curvesName);
}
+/**
+ * Checks the plot type selected and applies the appropriate
+ * python function to apply during first bank and second bank
+ *
+ * @param outWSName title of the focused workspace
+ * @param bank the number of bank
+ */
+void EnggDiffractionPresenter::plotFocusedWorkspace(std::string outWSName,
+ std::string bank) {
+ const bool plotFocusedWS = m_view->focusedOutWorkspace();
+ int plotType = m_view->currentPlotType();
+ if (plotFocusedWS) {
+ if (plotType == 0) {
+ if (bank == "1")
+ m_view->plotFocusedSpectrum(outWSName);
+ if (bank == "2")
+ m_view->plotReplacingWindow(outWSName);
+ } else if (1 == plotType) {
+ if (bank == "1")
+ m_view->plotFocusedSpectrum(outWSName);
+ if (bank == "2")
+ m_view->plotWaterfallSpectrum(outWSName);
+ } else if (2 == plotType) {
+ m_view->plotFocusedSpectrum(outWSName);
+ }
+ }
+}
+
+/**
+ * Convert the generated output files and saves them in
+ * FocusedXYE format
+ *
+ * @param inputWorkspace title of the focused workspace
+ * @param bank the number of the bank as a string
+ * @param runNo the run number as a string
+ */
+void EnggDiffractionPresenter::saveFocusedXYE(const std::string inputWorkspace,
+ std::string bank,
+ std::string runNo) {
+
+ // Generates the file name in the appropriate format
+ std::string fullFilename =
+ outFileNameFactory(inputWorkspace, runNo, bank, ".dat");
+
+ // Creates appropriate directory
+ Poco::Path saveDir = outFilesDir(runNo);
+
+ // append the full file name in the end
+ saveDir.append(fullFilename);
+
+ try {
+ g_log.debug() << "Going to save focused output into OpenGenie file: "
+ << fullFilename << std::endl;
+ auto alg = Algorithm::fromString("SaveFocusedXYE");
+ alg->initialize();
+ alg->setProperty("InputWorkspace", inputWorkspace);
+ std::string filename(saveDir.toString());
+ alg->setPropertyValue("Filename", filename);
+ alg->setProperty("SplitFiles", false);
+ alg->setPropertyValue("StartAtBankNumber", bank);
+ alg->execute();
+ } catch (std::runtime_error &re) {
+ g_log.error() << "Error in saving FocusedXYE format file. ",
+ "Could not run the algorithm SaveFocusXYE succesfully for "
+ "workspace " +
+ inputWorkspace + ". Error description: " + re.what() +
+ " Please check also the log messages for details.";
+ throw;
+ }
+ g_log.notice() << "Saved focused workspace as file: " << saveDir.toString()
+ << std::endl;
+}
+
+/**
+ * Convert the generated output files and saves them in
+ * GSS format
+ *
+ * @param inputWorkspace title of the focused workspace
+ * @param bank the number of the bank as a string
+ * @param runNo the run number as a string
+ */
+void EnggDiffractionPresenter::saveGSS(const std::string inputWorkspace,
+ std::string bank, std::string runNo) {
+
+ // Generates the file name in the appropriate format
+ std::string fullFilename =
+ outFileNameFactory(inputWorkspace, runNo, bank, ".gss");
+
+ // Creates appropriate directory
+ Poco::Path saveDir = outFilesDir(runNo);
+
+ // append the full file name in the end
+ saveDir.append(fullFilename);
+
+ try {
+ g_log.debug() << "Going to save focused output into OpenGenie file: "
+ << fullFilename << std::endl;
+ auto alg = Algorithm::fromString("SaveGSS");
+ alg->initialize();
+ alg->setProperty("InputWorkspace", inputWorkspace);
+ std::string filename(saveDir.toString());
+ alg->setPropertyValue("Filename", filename);
+ alg->setProperty("SplitFiles", false);
+ alg->setPropertyValue("Bank", bank);
+ alg->execute();
+ } catch (std::runtime_error &re) {
+ g_log.error() << "Error in saving GSS format file. ",
+ "Could not run the algorithm saveGSS succesfully for "
+ "workspace " +
+ inputWorkspace + ". Error description: " + re.what() +
+ " Please check also the log messages for details.";
+ throw;
+ }
+ g_log.notice() << "Saved focused workspace as file: " << saveDir.toString()
+ << std::endl;
+}
+
+/**
+ * Convert the generated output files and saves them in
+ * OpenGenie format
+ *
+ * @param inputWorkspace title of the focused workspace
+ * @param specNums number of spectrum to display
+ * @param bank the number of the bank as a string
+ * @param runNo the run number as a string
+ */
+void EnggDiffractionPresenter::saveOpenGenie(const std::string inputWorkspace,
+ std::string specNums,
+ std::string bank,
+ std::string runNo) {
+
+ // Generates the file name in the appropriate format
+ std::string fullFilename =
+ outFileNameFactory(inputWorkspace, runNo, bank, ".his");
+
+ // Creates appropriate directory
+ Poco::Path saveDir = outFilesDir(runNo);
+
+ // append the full file name in the end
+ saveDir.append(fullFilename);
+
+ try {
+ g_log.debug() << "Going to save focused output into OpenGenie file: "
+ << fullFilename << std::endl;
+ auto alg = Algorithm::fromString("SaveOpenGenieAscii");
+ alg->initialize();
+ alg->setProperty("InputWorkspace", inputWorkspace);
+ std::string filename(saveDir.toString());
+ alg->setPropertyValue("Filename", filename);
+ alg->setPropertyValue("SpecNumberField", specNums);
+ alg->execute();
+ } catch (std::runtime_error &re) {
+ g_log.error() << "Error in saving OpenGenie format file. ",
+ "Could not run the algorithm SaveOpenGenieAscii succesfully for "
+ "workspace " +
+ inputWorkspace + ". Error description: " + re.what() +
+ " Please check also the log messages for details.";
+ throw;
+ }
+ g_log.notice() << "Saved focused workspace as file: " << saveDir.toString()
+ << std::endl;
+}
+
+/**
+ * Generates the required file name of the output files
+ *
+ * @param inputWorkspace title of the focused workspace
+ * @param runNo the run number as a string
+ * @param bank the number of the bank as a string
+ * @param format the format of the file to be saved as
+ */
+std::string EnggDiffractionPresenter::outFileNameFactory(
+ std::string inputWorkspace, std::string runNo, std::string bank,
+ std::string format) {
+ std::string fullFilename;
+ if (inputWorkspace.std::string::find("texture") != std::string::npos) {
+ fullFilename = "ENGINX_" + runNo + "_texture_" + bank + format;
+ }
+ if (inputWorkspace.std::string::find("cropped") != std::string::npos) {
+ fullFilename = "ENGINX_" + runNo + "_cropped_" +
+ boost::lexical_cast<std::string>(g_croppedCounter) + format;
+ g_croppedCounter++;
+ } else {
+ fullFilename = "ENGINX_" + runNo + "_bank_" + bank + format;
+ }
+ return fullFilename;
+}
+
+/**
+ * Generates a directory if not found and handles the path
+ *
+ * @param runNo the run number as a string
+ */
+Poco::Path EnggDiffractionPresenter::outFilesDir(std::string runNo) {
+ Poco::Path saveDir;
+ try {
+
+// takes to the root of directory according to the platform
+// and appends the following string provided
+#ifdef __unix__
+ saveDir = Poco::Path().home();
+ saveDir.append("EnginX_Mantid");
+ saveDir.append("User");
+ saveDir.append(runNo);
+ saveDir.append("Focus");
+#else
+ // else or for windows run this
+ saveDir = (saveDir).expand("C:/EnginX_Mantid/User/" + runNo + "/Focus/");
+#endif
+
+ if (!Poco::File(saveDir.toString()).exists()) {
+ Poco::File(saveDir.toString()).createDirectories();
+ }
+ } catch (Poco::FileAccessDeniedException &e) {
+ g_log.error() << "error caused by file access/permission: " << e.what();
+ } catch (std::runtime_error &re) {
+ g_log.error() << "Error while find/creating a path: " << re.what();
+ }
+ return saveDir;
+}
+
} // namespace CustomInterfaces
} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionViewQtGUI.cpp b/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionViewQtGUI.cpp
index c594b5b2732fcbf545042214fcd30a80cc6dc117..ccd98974eb014d04e86557d598cd852ebdcbe4a4 100644
--- a/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionViewQtGUI.cpp
+++ b/MantidQt/CustomInterfaces/src/EnggDiffraction/EnggDiffractionViewQtGUI.cpp
@@ -25,6 +25,7 @@ namespace CustomInterfaces {
DECLARE_SUBWINDOW(EnggDiffractionViewQtGUI)
const double EnggDiffractionViewQtGUI::g_defaultRebinWidth = -0.0005;
+int EnggDiffractionViewQtGUI::m_currentType = 0;
const std::string EnggDiffractionViewQtGUI::g_iparmExtStr =
"GSAS instrument parameters, IPARM file: PRM, PAR, IPAR, IPARAM "
@@ -149,6 +150,7 @@ void EnggDiffractionViewQtGUI::doSetupTabSettings() {
}
void EnggDiffractionViewQtGUI::doSetupTabFocus() {
+
connect(m_uiTabFocus.pushButton_focus, SIGNAL(released()), this,
SLOT(focusClicked()));
@@ -163,6 +165,12 @@ void EnggDiffractionViewQtGUI::doSetupTabFocus() {
connect(m_uiTabFocus.pushButton_reset, SIGNAL(released()), this,
SLOT(focusResetClicked()));
+
+ connect(m_uiTabFocus.comboBox_PlotData, SIGNAL(currentIndexChanged(int)),
+ this, SLOT(plotRepChanged(int)));
+
+ connect(m_uiTabFocus.checkBox_FocusedWS, SIGNAL(clicked()), this,
+ SLOT(plotFocusStatus()));
}
void EnggDiffractionViewQtGUI::doSetupGeneralWidgets() {
@@ -209,9 +217,11 @@ void EnggDiffractionViewQtGUI::readSettings() {
qs.beginReadArray("user-params-focus-bank_i");
qs.setArrayIndex(0);
- m_uiTabFocus.checkBox_focus_bank1->setChecked(qs.value("value", true).toBool());
+ m_uiTabFocus.checkBox_focus_bank1->setChecked(
+ qs.value("value", true).toBool());
qs.setArrayIndex(1);
- m_uiTabFocus.checkBox_focus_bank2->setChecked(qs.value("value", true).toBool());
+ m_uiTabFocus.checkBox_focus_bank2->setChecked(
+ qs.value("value", true).toBool());
qs.endArray();
m_uiTabFocus.lineEdit_cropped_run_num->setText(
@@ -230,6 +240,8 @@ void EnggDiffractionViewQtGUI::readSettings() {
m_uiTabFocus.checkBox_FocusedWS->setChecked(
qs.value("user-params-focus-plot-ws", true).toBool());
+ m_uiTabFocus.comboBox_PlotData->setCurrentIndex(0);
+
QString lastPath =
MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
// TODO: this should become << >> operators on
@@ -272,12 +284,13 @@ void EnggDiffractionViewQtGUI::saveSettings() const {
m_uiTabCalib.lineEdit_current_calib_filename->text());
qs.setValue("user-params-new-vanadium-num",
- m_uiTabCalib.lineEdit_new_vanadium_num->text());
+ m_uiTabCalib.lineEdit_new_vanadium_num->getText());
qs.setValue("user-params-new-ceria-num",
- m_uiTabCalib.lineEdit_new_ceria_num->text());
+ m_uiTabCalib.lineEdit_new_ceria_num->getText());
// user params - focusing
- qs.setValue("user-params-focus-runno", m_uiTabFocus.lineEdit_run_num->text());
+ qs.setValue("user-params-focus-runno",
+ m_uiTabFocus.lineEdit_run_num->getText());
qs.beginWriteArray("user-params-focus-bank_i");
qs.setArrayIndex(0);
@@ -287,17 +300,16 @@ void EnggDiffractionViewQtGUI::saveSettings() const {
qs.endArray();
qs.setValue("user-params-focus-cropped-runno",
- m_uiTabFocus.lineEdit_cropped_run_num->text());
+ m_uiTabFocus.lineEdit_cropped_run_num->getText());
qs.setValue("user-params-focus-cropped-spectrum-nos",
m_uiTabFocus.lineEdit_cropped_spec_ids->text());
qs.setValue("user-params-focus-texture-runno",
- m_uiTabFocus.lineEdit_texture_run_num->text());
+ m_uiTabFocus.lineEdit_texture_run_num->getText());
qs.setValue("user-params-focus-texture-detector-grouping-file",
m_uiTabFocus.lineEdit_texture_grouping_file->text());
- qs.setValue("user-params-focus-plot-ws",
- m_uiTabFocus.checkBox_FocusedWS->checkState());
+ qs.setValue("value", m_uiTabFocus.checkBox_FocusedWS->isChecked());
// TODO: this should become << >> operators on EnggDiffCalibSettings
qs.setValue("input-dir-calib-files",
@@ -374,11 +386,11 @@ std::string EnggDiffractionViewQtGUI::currentCeriaNo() const {
}
std::string EnggDiffractionViewQtGUI::newVanadiumNo() const {
- return m_uiTabCalib.lineEdit_new_vanadium_num->text().toStdString();
+ return m_uiTabCalib.lineEdit_new_vanadium_num->getText().toStdString();
}
std::string EnggDiffractionViewQtGUI::newCeriaNo() const {
- return m_uiTabCalib.lineEdit_new_ceria_num->text().toStdString();
+ return m_uiTabCalib.lineEdit_new_ceria_num->getText().toStdString();
}
std::string EnggDiffractionViewQtGUI::currentCalibFile() const {
@@ -414,6 +426,7 @@ void EnggDiffractionViewQtGUI::enableCalibrateAndFocusActions(bool enable) {
m_uiTabFocus.lineEdit_run_num->setEnabled(enable);
m_uiTabFocus.pushButton_focus->setEnabled(enable);
m_uiTabFocus.checkBox_FocusedWS->setEnabled(enable);
+ m_uiTabFocus.checkBox_SaveOutputFiles->setEnabled(enable);
m_uiTabFocus.pushButton_focus->setEnabled(enable);
m_uiTabFocus.pushButton_focus_cropped->setEnabled(enable);
@@ -421,10 +434,33 @@ void EnggDiffractionViewQtGUI::enableCalibrateAndFocusActions(bool enable) {
}
void EnggDiffractionViewQtGUI::plotFocusedSpectrum(const std::string &wsName) {
- std::string pyCode = "plotSpectrum('" + wsName + "', 0)";
+ std::string pyCode = "win = plotSpectrum('" + wsName + "', 0)";
+
+ std::string status =
+ runPythonCode(QString::fromStdString(pyCode), false).toStdString();
+ m_logMsgs.push_back("Plotted output focused data, with status string " +
+ status);
+ m_presenter->notify(IEnggDiffractionPresenter::LogMsg);
+}
+
+void EnggDiffractionViewQtGUI::plotWaterfallSpectrum(
+ const std::string &wsName) {
+ // parameter of list ?
+ std::string pyCode =
+ "plotSpectrum('" + wsName + "', 0, waterfall = True, window = win)";
+ std::string status =
+ runPythonCode(QString::fromStdString(pyCode), false).toStdString();
+ m_logMsgs.push_back("Plotted output focused data, with status string " +
+ status);
+ m_presenter->notify(IEnggDiffractionPresenter::LogMsg);
+}
+void EnggDiffractionViewQtGUI::plotReplacingWindow(const std::string &wsName) {
+ std::string pyCode =
+ "plotSpectrum('" + wsName + "', 0, window = win, clearWindow = True)";
std::string status =
runPythonCode(QString::fromStdString(pyCode), false).toStdString();
+
m_logMsgs.push_back("Plotted output focused data, with status string " +
status);
m_presenter->notify(IEnggDiffractionPresenter::LogMsg);
@@ -442,10 +478,9 @@ void EnggDiffractionViewQtGUI::resetFocus() {
m_uiTabFocus.lineEdit_texture_grouping_file->setText("");
}
-void
-EnggDiffractionViewQtGUI::writeOutCalibFile(const std::string &outFilename,
- const std::vector<double> &difc,
- const std::vector<double> &tzero) {
+void EnggDiffractionViewQtGUI::writeOutCalibFile(
+ const std::string &outFilename, const std::vector<double> &difc,
+ const std::vector<double> &tzero) {
// TODO: this is horrible and should not last much here.
// Avoid running Python code
// Update this as soon as we have a more stable way of generating IPARM
@@ -643,15 +678,15 @@ void EnggDiffractionViewQtGUI::browseTextureDetGroupingFile() {
}
std::string EnggDiffractionViewQtGUI::focusingRunNo() const {
- return m_uiTabFocus.lineEdit_run_num->text().toStdString();
+ return m_uiTabFocus.lineEdit_run_num->getText().toStdString();
}
std::string EnggDiffractionViewQtGUI::focusingCroppedRunNo() const {
- return m_uiTabFocus.lineEdit_cropped_run_num->text().toStdString();
+ return m_uiTabFocus.lineEdit_cropped_run_num->getText().toStdString();
}
std::string EnggDiffractionViewQtGUI::focusingTextureRunNo() const {
- return m_uiTabFocus.lineEdit_texture_run_num->text().toStdString();
+ return m_uiTabFocus.lineEdit_texture_run_num->getText().toStdString();
}
std::string EnggDiffractionViewQtGUI::focusingDir() const {
@@ -677,6 +712,25 @@ bool EnggDiffractionViewQtGUI::focusedOutWorkspace() const {
return m_uiTabFocus.checkBox_FocusedWS->checkState();
}
+bool EnggDiffractionViewQtGUI::saveOutputFiles() const {
+ return m_uiTabFocus.checkBox_SaveOutputFiles->checkState();
+}
+
+void EnggDiffractionViewQtGUI::plotFocusStatus() {
+ if (focusedOutWorkspace()) {
+ m_uiTabFocus.comboBox_PlotData->setEnabled(true);
+ } else {
+ m_uiTabFocus.comboBox_PlotData->setEnabled(false);
+ }
+}
+
+void EnggDiffractionViewQtGUI::plotRepChanged(int /*idx*/) {
+ QComboBox *plotType = m_uiTabFocus.comboBox_PlotData;
+ if (!plotType)
+ return;
+ m_currentType = plotType->currentIndex();
+}
+
void EnggDiffractionViewQtGUI::instrumentChanged(int /*idx*/) {
QComboBox *inst = m_ui.comboBox_instrument;
if (!inst)
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp b/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp
index 42270faab779a63de3226cd5b3b3cc4ebd2c2de6..e4e9d4484706608f74596258ca4846cf1bc906b7 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp
@@ -145,6 +145,7 @@ void ApplyPaalmanPings::run() {
switch (result) {
case QMessageBox::YesToAll:
interpolateAll = true;
+ //fall through
case QMessageBox::Yes:
addInterpolationStep(factorWs, absCorProps["SampleWorkspace"]);
break;
@@ -175,9 +176,18 @@ void ApplyPaalmanPings::run() {
correctionType = "cyl";
break;
}
- const QString outputWsName =
+ QString outputWsName =
sampleWsName.left(nameCutIndex) + +"_" + correctionType + "_Corrected";
+ if (useCan) {
+ auto containerWsName = m_uiForm.dsContainer->getCurrentDataName();
+ int cutIndex = containerWsName.indexOf("_");
+ if (cutIndex == -1) {
+ cutIndex = containerWsName.length();
+ }
+ outputWsName += "_Subtract_" + containerWsName.left(cutIndex);
+ }
+
applyCorrAlg->setProperty("OutputWorkspace", outputWsName.toStdString());
// Add corrections algorithm to queue
diff --git a/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp b/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp
index 81277fad6d9919ec6d2057026a52be6716bff9c2..49584757883539d7ef1a4332893875067f9017e1 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp
@@ -122,8 +122,17 @@ void CalculatePaalmanPings::run() {
break;
}
- const QString outputWsName =
+ QString outputWsName =
sampleWsName.left(nameCutIndex) + "_" + correctionType + "_abs";
+ if (useCan) {
+ auto containerWsName = m_uiForm.dsContainer->getCurrentDataName();
+ int cutIndex = containerWsName.indexOf("_");
+ if (cutIndex == -1) {
+ cutIndex = containerWsName.length();
+ }
+ outputWsName += "_Subtract_" + containerWsName.left(cutIndex);
+ }
+
absCorAlgo->setProperty("OutputWorkspace", outputWsName.toStdString());
// Add corrections algorithm to queue
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp b/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
index c4e727187fc8084c0e25ba20eab0bc8384a87a9a..07fef6447c8a24678b514740f03f64a9664d855f 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
@@ -35,6 +35,8 @@ ConvFit::ConvFit(QWidget *parent)
void ConvFit::setup() {
// Create Property Managers
m_stringManager = new QtStringPropertyManager();
+ m_runMin = 0;
+ m_runMax = 0;
// Initialise fitTypeStrings
m_fitStrings = QStringList() << ""
@@ -237,6 +239,8 @@ void ConvFit::run() {
std::string function = std::string(func->asString());
std::string stX = m_properties["StartX"]->valueText().toStdString();
std::string enX = m_properties["EndX"]->valueText().toStdString();
+ m_runMin = m_uiForm.spSpectraMin->value();
+ m_runMax = m_uiForm.spSpectraMax->value();
std::string specMin = m_uiForm.spSpectraMin->text().toStdString();
std::string specMax = m_uiForm.spSpectraMax->text().toStdString();
int maxIterations =
@@ -984,17 +988,24 @@ void ConvFit::updatePlot() {
}
// If there is a result plot then plot it
- std::string groupName = m_baseName.toStdString() + "_Workspaces";
+ std::string groupName = m_baseName.toStdString() + "_Workspaces";
if (AnalysisDataService::Instance().doesExist(groupName)) {
WorkspaceGroup_sptr outputGroup =
- AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
- groupName);
- if (specNo >= static_cast<int>(outputGroup->size()))
+ AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(groupName);
+ if (specNo - m_runMin >= static_cast<int>(outputGroup->size()))
return;
- MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
- outputGroup->getItem(specNo));
- if (ws)
- m_uiForm.ppPlot->addSpectrum("Fit", ws, 1, Qt::red);
+ if ((specNo - m_runMin) >= 0) {
+ MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
+ outputGroup->getItem(specNo- m_runMin));
+ if (ws) {
+ m_uiForm.ppPlot->addSpectrum("Fit", ws, 1, Qt::red);
+ m_uiForm.ppPlot->addSpectrum("Diff", ws, 2, Qt::blue);
+ if (m_uiForm.ckPlotGuess->isChecked()) {
+ m_uiForm.ppPlot->removeSpectrum("Guess");
+ m_uiForm.ckPlotGuess->setChecked(false);
+ }
+ }
+ }
}
}
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp b/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp
index ae32ddc36c2e30d07b9ff6dd2d5de8769a48a24a..684a600758ee1da57dd55c4810ab16df27c780fe 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp
@@ -69,19 +69,19 @@ bool ISISEnergyTransfer::validate() {
UserInputValidator uiv;
// Run files input
- if (!m_uiForm.dsRunFiles->isValid()){
+ if (!m_uiForm.dsRunFiles->isValid()) {
uiv.addErrorMessage("Run file range is invalid.");
}
// Calibration file input
if (m_uiForm.ckUseCalib->isChecked() &&
- !m_uiForm.dsCalibrationFile->isValid()){
+ !m_uiForm.dsCalibrationFile->isValid()) {
uiv.addErrorMessage("Calibration file/workspace is invalid.");
}
// Mapping file
if ((m_uiForm.cbGroupingOptions->currentText() == "File") &&
- (!m_uiForm.dsMapFile->isValid())){
+ (!m_uiForm.dsMapFile->isValid())) {
uiv.addErrorMessage("Mapping file is invalid.");
}
@@ -115,17 +115,63 @@ bool ISISEnergyTransfer::validate() {
// Spectra Number check
const int specMin = m_uiForm.spSpectraMin->value();
const int specMax = m_uiForm.spSpectraMax->value();
- if(specMin > specMax){
- uiv.addErrorMessage("Spectra Min must be less than Spectra Max");
+ if (specMin > specMax) {
+ uiv.addErrorMessage("Spectra Min must be less than Spectra Max");
}
// Background Removal (TOF)
- if(m_uiForm.ckBackgroundRemoval->isChecked()){
- const int start = m_uiForm.spBackgroundStart->value();
- const int end = m_uiForm.spBackgroundEnd->value();
- if(start > end){
- uiv.addErrorMessage("Background Start must be less than Background End");
- }
+ if (m_uiForm.ckBackgroundRemoval->isChecked()) {
+ const int start = m_uiForm.spBackgroundStart->value();
+ const int end = m_uiForm.spBackgroundEnd->value();
+ if (start > end) {
+ uiv.addErrorMessage("Background Start must be less than Background End");
+ }
+ }
+
+ if (m_uiForm.dsRunFiles->isValid()) {
+ int detectorMin = m_uiForm.spPlotTimeSpecMin->value();
+ int detectorMax = m_uiForm.spPlotTimeSpecMax->value();
+
+ QString rawFile = m_uiForm.dsRunFiles->getFirstFilename();
+ auto pos = rawFile.lastIndexOf(".");
+ auto extension = rawFile.right(rawFile.length() - pos);
+ QFileInfo rawFileInfo(rawFile);
+ std::string name = rawFileInfo.baseName().toStdString();
+
+ IAlgorithm_sptr loadAlg = AlgorithmManager::Instance().create("Load");
+ loadAlg->initialize();
+ loadAlg->setProperty("Filename", rawFile.toStdString());
+ loadAlg->setProperty("OutputWorkspace", name);
+ if (extension.compare(".nxs") == 0) {
+ int64_t detectorMin =
+ static_cast<int64_t>(m_uiForm.spPlotTimeSpecMin->value());
+ int64_t detectorMax =
+ static_cast<int64_t>(m_uiForm.spPlotTimeSpecMax->value());
+ loadAlg->setProperty("SpectrumMin", detectorMin);
+ loadAlg->setProperty("SpectrumMax", detectorMax);
+ } else {
+ loadAlg->setProperty("SpectrumMin", detectorMin);
+ loadAlg->setProperty("SpectrumMax", detectorMax);
+ }
+
+ loadAlg->execute();
+
+ if (m_uiForm.ckBackgroundRemoval->isChecked()) {
+ MatrixWorkspace_sptr tempWs =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(name);
+ const double minBack = tempWs->readX(0)[0];
+ const double maxBack = tempWs->readX(0)[tempWs->blocksize()];
+
+ if (m_uiForm.spBackgroundStart->value() < minBack) {
+ uiv.addErrorMessage("The Start of Background Removal is less than the "
+ "minimum of the data range");
+ }
+
+ if (m_uiForm.spBackgroundEnd->value() > maxBack) {
+ uiv.addErrorMessage("The End of Background Removal is more than the "
+ "maximum of the data range");
+ }
+ }
}
QString error = uiv.generateErrorMessage();
@@ -446,6 +492,15 @@ void ISISEnergyTransfer::plotRaw() {
"Minimum spectra must be less than or equal to maximum spectra.");
return;
}
+ const int startBack = m_uiForm.spBackgroundStart->value();
+ const int endBack = m_uiForm.spBackgroundEnd->value();
+
+ if (m_uiForm.ckBackgroundRemoval->isChecked() == true) {
+ if (startBack > endBack) {
+ emit showMessageBox("Background Start must be less than Background End");
+ return;
+ }
+ }
QString rawFile = m_uiForm.dsRunFiles->getFirstFilename();
auto pos = rawFile.lastIndexOf(".");
@@ -453,7 +508,7 @@ void ISISEnergyTransfer::plotRaw() {
QFileInfo rawFileInfo(rawFile);
std::string name = rawFileInfo.baseName().toStdString();
- IAlgorithm_sptr loadAlg = AlgorithmManager::Instance().create("Load");
+ IAlgorithm_sptr loadAlg = AlgorithmManager::Instance().create("Load");
loadAlg->initialize();
loadAlg->setProperty("Filename", rawFile.toStdString());
loadAlg->setProperty("OutputWorkspace", name);
@@ -468,7 +523,27 @@ void ISISEnergyTransfer::plotRaw() {
loadAlg->setProperty("SpectrumMin", detectorMin);
loadAlg->setProperty("SpectrumMax", detectorMax);
}
- m_batchAlgoRunner->addAlgorithm(loadAlg);
+
+ loadAlg->execute();
+
+ if (m_uiForm.ckBackgroundRemoval->isChecked()) {
+ MatrixWorkspace_sptr tempWs =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(name);
+ const double minBack = tempWs->readX(0)[0];
+ const double maxBack = tempWs->readX(0)[tempWs->blocksize()];
+
+ if (startBack < minBack) {
+ emit showMessageBox("The Start of Background Removal is less than the "
+ "minimum of the data range");
+ return;
+ }
+
+ if (endBack > maxBack) {
+ emit showMessageBox("The End of Background Removal is more than the "
+ "maximum of the data range");
+ return;
+ }
+ }
// Rebin the workspace to its self to ensure constant binning
BatchAlgorithmRunner::AlgorithmRuntimeProps inputToRebin;
diff --git a/MantidQt/CustomInterfaces/src/Indirect/IqtFit.cpp b/MantidQt/CustomInterfaces/src/Indirect/IqtFit.cpp
index 73551bd016c94b0fe116358e3a8051c4b20dd6a6..50a15e9f3e337ede61b2cec93184f7237eafe548 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/IqtFit.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/IqtFit.cpp
@@ -17,881 +17,902 @@
using namespace Mantid::API;
-namespace
-{
- Mantid::Kernel::Logger g_log("IqtFit");
+namespace {
+Mantid::Kernel::Logger g_log("IqtFit");
}
-namespace MantidQt
-{
-namespace CustomInterfaces
-{
-namespace IDA
-{
- IqtFit::IqtFit(QWidget * parent) :
- IndirectDataAnalysisTab(parent),
- m_stringManager(NULL), m_ffTree(NULL),
- m_ffRangeManager(NULL),
- m_fixedProps(),
- m_ffInputWS(), m_ffOutputWS(),
- m_ffInputWSName(),
- m_ties()
- {
- m_uiForm.setupUi(parent);
- }
-
- void IqtFit::setup()
- {
- m_stringManager = new QtStringPropertyManager(m_parentWidget);
-
- m_ffTree = new QtTreePropertyBrowser(m_parentWidget);
- m_uiForm.properties->addWidget(m_ffTree);
-
- auto fitRangeSelector = m_uiForm.ppPlot->addRangeSelector("FuryFitRange");
- connect(fitRangeSelector, SIGNAL(minValueChanged(double)), this, SLOT(xMinSelected(double)));
- connect(fitRangeSelector, SIGNAL(maxValueChanged(double)), this, SLOT(xMaxSelected(double)));
+namespace MantidQt {
+namespace CustomInterfaces {
+namespace IDA {
+IqtFit::IqtFit(QWidget *parent)
+ : IndirectDataAnalysisTab(parent), m_stringManager(NULL), m_ffTree(NULL),
+ m_ffRangeManager(NULL), m_fixedProps(), m_ffInputWS(), m_ffOutputWS(),
+ m_ffInputWSName(), m_ties() {
+ m_uiForm.setupUi(parent);
+}
- auto backgroundRangeSelector = m_uiForm.ppPlot->addRangeSelector("FuryFitBackground",
- MantidWidgets::RangeSelector::YSINGLE);
- backgroundRangeSelector->setRange(0.0,1.0);
- backgroundRangeSelector->setColour(Qt::darkGreen);
- connect(backgroundRangeSelector, SIGNAL(minValueChanged(double)), this, SLOT(backgroundSelected(double)));
+void IqtFit::setup() {
+ m_stringManager = new QtStringPropertyManager(m_parentWidget);
+
+ m_ffTree = new QtTreePropertyBrowser(m_parentWidget);
+ m_uiForm.properties->addWidget(m_ffTree);
+
+ auto fitRangeSelector = m_uiForm.ppPlot->addRangeSelector("FuryFitRange");
+ connect(fitRangeSelector, SIGNAL(minValueChanged(double)), this,
+ SLOT(xMinSelected(double)));
+ connect(fitRangeSelector, SIGNAL(maxValueChanged(double)), this,
+ SLOT(xMaxSelected(double)));
+
+ auto backgroundRangeSelector = m_uiForm.ppPlot->addRangeSelector(
+ "FuryFitBackground", MantidWidgets::RangeSelector::YSINGLE);
+ backgroundRangeSelector->setRange(0.0, 1.0);
+ backgroundRangeSelector->setColour(Qt::darkGreen);
+ connect(backgroundRangeSelector, SIGNAL(minValueChanged(double)), this,
+ SLOT(backgroundSelected(double)));
+
+ // setupTreePropertyBrowser
+ m_ffRangeManager = new QtDoublePropertyManager(m_parentWidget);
+
+ m_ffTree->setFactoryForManager(m_blnManager, m_blnEdFac);
+ m_ffTree->setFactoryForManager(m_dblManager, m_dblEdFac);
+ m_ffTree->setFactoryForManager(m_ffRangeManager, m_dblEdFac);
+
+ m_properties["StartX"] = m_ffRangeManager->addProperty("StartX");
+ m_ffRangeManager->setDecimals(m_properties["StartX"], NUM_DECIMALS);
+ m_properties["EndX"] = m_ffRangeManager->addProperty("EndX");
+ m_dblManager->setDecimals(m_properties["EndX"], NUM_DECIMALS);
+ m_properties["MaxIterations"] = m_dblManager->addProperty("Max Iterations");
+ m_dblManager->setDecimals(m_properties["MaxIterations"], 0);
+ m_dblManager->setValue(m_properties["MaxIterations"], 500);
+
+ // FABADA
+ m_properties["FABADA"] = m_grpManager->addProperty("Bayesian");
+ m_properties["UseFABADA"] = m_blnManager->addProperty("Use FABADA");
+ m_properties["FABADA"]->addSubProperty(m_properties["UseFABADA"]);
+ m_properties["OutputFABADAChain"] = m_blnManager->addProperty("Output Chain");
+ m_properties["FABADAChainLength"] = m_dblManager->addProperty("Chain Length");
+ m_dblManager->setDecimals(m_properties["FABADAChainLength"], 0);
+ m_dblManager->setValue(m_properties["FABADAChainLength"], 10000);
+ m_properties["FABADAConvergenceCriteria"] =
+ m_dblManager->addProperty("Convergence Criteria");
+ m_dblManager->setValue(m_properties["FABADAConvergenceCriteria"], 0.1);
+ m_properties["FABADAJumpAcceptanceRate"] =
+ m_dblManager->addProperty("Acceptance Rate");
+ m_dblManager->setValue(m_properties["FABADAJumpAcceptanceRate"], 0.25);
+ m_ffTree->addProperty(m_properties["FABADA"]);
+
+ connect(m_ffRangeManager, SIGNAL(valueChanged(QtProperty *, double)), this,
+ SLOT(propertyChanged(QtProperty *, double)));
+ connect(m_dblManager, SIGNAL(valueChanged(QtProperty *, double)), this,
+ SLOT(propertyChanged(QtProperty *, double)));
+
+ m_properties["LinearBackground"] =
+ m_grpManager->addProperty("LinearBackground");
+ m_properties["BackgroundA0"] = m_ffRangeManager->addProperty("A0");
+ m_ffRangeManager->setDecimals(m_properties["BackgroundA0"], NUM_DECIMALS);
+ m_properties["LinearBackground"]->addSubProperty(
+ m_properties["BackgroundA0"]);
+
+ m_properties["Exponential1"] = createExponential("Exponential1");
+ m_properties["Exponential2"] = createExponential("Exponential2");
+
+ m_properties["StretchedExp"] = createStretchedExp("StretchedExp");
+
+ m_ffRangeManager->setMinimum(m_properties["BackgroundA0"], 0);
+ m_ffRangeManager->setMaximum(m_properties["BackgroundA0"], 1);
+
+ m_dblManager->setMinimum(m_properties["Exponential1.Intensity"], 0);
+ m_dblManager->setMaximum(m_properties["Exponential1.Intensity"], 1);
+
+ m_dblManager->setMinimum(m_properties["Exponential2.Intensity"], 0);
+ m_dblManager->setMaximum(m_properties["Exponential2.Intensity"], 1);
+
+ m_dblManager->setMinimum(m_properties["StretchedExp.Intensity"], 0);
+ m_dblManager->setMaximum(m_properties["StretchedExp.Intensity"], 1);
+
+ typeSelection(m_uiForm.cbFitType->currentIndex());
+
+ // Update guess curve on property change
+ connect(m_dblManager, SIGNAL(propertyChanged(QtProperty *)), this,
+ SLOT(plotGuess(QtProperty *)));
+
+ // Signal/slot ui connections
+ connect(m_uiForm.dsSampleInput, SIGNAL(dataReady(const QString &)), this,
+ SLOT(newDataLoaded(const QString &)));
+ connect(m_uiForm.cbFitType, SIGNAL(currentIndexChanged(int)), this,
+ SLOT(typeSelection(int)));
+ connect(m_uiForm.pbSingle, SIGNAL(clicked()), this, SLOT(singleFit()));
+
+ connect(m_uiForm.dsSampleInput, SIGNAL(filesFound()), this,
+ SLOT(updatePlot()));
+
+ connect(m_uiForm.spPlotSpectrum, SIGNAL(valueChanged(int)), this,
+ SLOT(updatePlot()));
+
+ connect(m_uiForm.spSpectraMin, SIGNAL(valueChanged(int)), this,
+ SLOT(specMinChanged(int)));
+ connect(m_uiForm.spSpectraMax, SIGNAL(valueChanged(int)), this,
+ SLOT(specMaxChanged(int)));
+
+ // Set a custom handler for the QTreePropertyBrowser's ContextMenu event
+ m_ffTree->setContextMenuPolicy(Qt::CustomContextMenu);
+ connect(m_ffTree, SIGNAL(customContextMenuRequested(const QPoint &)), this,
+ SLOT(fitContextMenu(const QPoint &)));
+
+ connect(m_blnManager, SIGNAL(valueChanged(QtProperty *, bool)), this,
+ SLOT(checkBoxUpdate(QtProperty *, bool)));
+}
- // setupTreePropertyBrowser
- m_ffRangeManager = new QtDoublePropertyManager(m_parentWidget);
+void IqtFit::run() {
+ if (m_ffInputWS == NULL) {
+ return;
+ }
- m_ffTree->setFactoryForManager(m_blnManager, m_blnEdFac);
- m_ffTree->setFactoryForManager(m_dblManager, m_dblEdFac);
- m_ffTree->setFactoryForManager(m_ffRangeManager, m_dblEdFac);
+ const bool constrainBeta = m_uiForm.ckConstrainBeta->isChecked();
+ const bool constrainIntens = m_uiForm.ckConstrainIntensities->isChecked();
+ CompositeFunction_sptr func = createFunction();
+ func->tie("f0.A1", "0");
- m_properties["StartX"] = m_ffRangeManager->addProperty("StartX");
- m_ffRangeManager->setDecimals(m_properties["StartX"], NUM_DECIMALS);
- m_properties["EndX"] = m_ffRangeManager->addProperty("EndX");
- m_dblManager->setDecimals(m_properties["EndX"], NUM_DECIMALS);
- m_properties["MaxIterations"] = m_dblManager->addProperty("Max Iterations");
- m_dblManager->setDecimals(m_properties["MaxIterations"], 0);
- m_dblManager->setValue(m_properties["MaxIterations"], 500);
+ if (constrainIntens) {
+ constrainIntensities(func);
+ }
- // FABADA
- m_properties["FABADA"] = m_grpManager->addProperty("Bayesian");
- m_properties["UseFABADA"] = m_blnManager->addProperty("Use FABADA");
- m_properties["FABADA"]->addSubProperty(m_properties["UseFABADA"]);
- m_properties["OutputFABADAChain"] = m_blnManager->addProperty("Output Chain");
- m_properties["FABADAChainLength"] = m_dblManager->addProperty("Chain Length");
- m_dblManager->setDecimals(m_properties["FABADAChainLength"], 0);
- m_dblManager->setValue(m_properties["FABADAChainLength"], 10000);
- m_properties["FABADAConvergenceCriteria"] = m_dblManager->addProperty("Convergence Criteria");
- m_dblManager->setValue(m_properties["FABADAConvergenceCriteria"], 0.1);
- m_properties["FABADAJumpAcceptanceRate"] = m_dblManager->addProperty("Acceptance Rate");
- m_dblManager->setValue(m_properties["FABADAJumpAcceptanceRate"], 0.25);
- m_ffTree->addProperty(m_properties["FABADA"]);
+ func->applyTies();
+
+ std::string function = std::string(func->asString());
+ QString fitType = fitTypeString();
+ QString specMin = m_uiForm.spSpectraMin->text();
+ QString specMax = m_uiForm.spSpectraMax->text();
+
+ QString pyInput =
+ "from IndirectDataAnalysis import furyfitSeq, furyfitMult\n"
+ "input = '" +
+ m_ffInputWSName + "'\n"
+ "func = r'" +
+ QString::fromStdString(function) + "'\n"
+ "ftype = '" +
+ fitTypeString() + "'\n"
+ "startx = " +
+ m_properties["StartX"]->valueText() + "\n"
+ "endx = " +
+ m_properties["EndX"]->valueText() + "\n"
+ "plot = '" +
+ m_uiForm.cbPlotType->currentText() + "'\n"
+ "spec_min = " +
+ specMin + "\n"
+ "spec_max = " +
+ specMax + "\n"
+ "spec_max = None\n"
+ "minimizer = '" +
+ minimizerString("$outputname_$wsindex") + "'\n"
+ "max_iterations = " +
+ QString::number(m_dblManager->value(m_properties["MaxIterations"])) +
+ "\n";
+
+ if (constrainIntens)
+ pyInput += "constrain_intens = True \n";
+ else
+ pyInput += "constrain_intens = False \n";
+
+ if (m_uiForm.ckSave->isChecked())
+ pyInput += "save = True\n";
+ else
+ pyInput += "save = False\n";
+
+ if (!constrainBeta) {
+ pyInput += "furyfitSeq(input, func, ftype, startx, endx, "
+ "spec_min=spec_min, spec_max=spec_max, "
+ "intensities_constrained=constrain_intens, Save=save, "
+ "Plot=plot, minimizer=minimizer, "
+ "max_iterations=max_iterations)\n";
+ } else {
+ pyInput += "furyfitMult(input, func, ftype, startx, endx, "
+ "spec_min=spec_min, spec_max=spec_max, "
+ "intensities_constrained=constrain_intens, Save=save, "
+ "Plot=plot, minimizer=minimizer, "
+ "max_iterations=max_iterations)\n";
+ }
- connect(m_ffRangeManager, SIGNAL(valueChanged(QtProperty*, double)), this, SLOT(propertyChanged(QtProperty*, double)));
- connect(m_dblManager, SIGNAL(valueChanged(QtProperty*, double)), this, SLOT(propertyChanged(QtProperty*, double)));
+ QString pyOutput = runPythonCode(pyInput);
- m_properties["LinearBackground"] = m_grpManager->addProperty("LinearBackground");
- m_properties["BackgroundA0"] = m_ffRangeManager->addProperty("A0");
- m_ffRangeManager->setDecimals(m_properties["BackgroundA0"], NUM_DECIMALS);
- m_properties["LinearBackground"]->addSubProperty(m_properties["BackgroundA0"]);
+ // Set the result workspace for Python script export
+ QString inputWsName = QString::fromStdString(m_ffInputWS->getName());
+ QString resultWsName = inputWsName.left(inputWsName.lastIndexOf("_")) +
+ "_fury_" + fitType + specMin + "_to_" + specMax +
+ "_Workspaces";
+ m_pythonExportWsName = resultWsName.toStdString();
- m_properties["Exponential1"] = createExponential("Exponential1");
- m_properties["Exponential2"] = createExponential("Exponential2");
+ updatePlot();
+}
- m_properties["StretchedExp"] = createStretchedExp("StretchedExp");
+bool IqtFit::validate() {
+ UserInputValidator uiv;
- m_ffRangeManager->setMinimum(m_properties["BackgroundA0"], 0);
- m_ffRangeManager->setMaximum(m_properties["BackgroundA0"], 1);
+ uiv.checkDataSelectorIsValid("Sample", m_uiForm.dsSampleInput);
- m_dblManager->setMinimum(m_properties["Exponential1.Intensity"], 0);
- m_dblManager->setMaximum(m_properties["Exponential1.Intensity"], 1);
+ auto range = std::make_pair(m_ffRangeManager->value(m_properties["StartX"]),
+ m_ffRangeManager->value(m_properties["EndX"]));
+ uiv.checkValidRange("Ranges", range);
- m_dblManager->setMinimum(m_properties["Exponential2.Intensity"], 0);
- m_dblManager->setMaximum(m_properties["Exponential2.Intensity"], 1);
+ QString error = uiv.generateErrorMessage();
+ showMessageBox(error);
- m_dblManager->setMinimum(m_properties["StretchedExp.Intensity"], 0);
- m_dblManager->setMaximum(m_properties["StretchedExp.Intensity"], 1);
+ return error.isEmpty();
+}
- typeSelection(m_uiForm.cbFitType->currentIndex());
+void IqtFit::loadSettings(const QSettings &settings) {
+ m_uiForm.dsSampleInput->readSettings(settings.group());
+}
- // Update guess curve on property change
- connect(m_dblManager, SIGNAL(propertyChanged(QtProperty*)), this, SLOT(plotGuess(QtProperty*)));
+/**
+ * Called when new data has been loaded by the data selector.
+ *
+ * Configures ranges for spin boxes before raw plot is done.
+ *
+ * @param wsName Name of new workspace loaded
+ */
+void IqtFit::newDataLoaded(const QString wsName) {
+ m_ffInputWSName = wsName;
+ m_ffInputWS = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
+ m_ffInputWSName.toStdString());
- // Signal/slot ui connections
- connect(m_uiForm.dsSampleInput, SIGNAL(dataReady(const QString&)), this, SLOT(newDataLoaded(const QString&)));
- connect(m_uiForm.cbFitType, SIGNAL(currentIndexChanged(int)), this, SLOT(typeSelection(int)));
- connect(m_uiForm.pbSingle, SIGNAL(clicked()), this, SLOT(singleFit()));
+ int maxSpecIndex = static_cast<int>(m_ffInputWS->getNumberHistograms()) - 1;
- connect(m_uiForm.dsSampleInput, SIGNAL(filesFound()), this, SLOT(updatePlot()));
+ m_uiForm.spPlotSpectrum->setMaximum(maxSpecIndex);
+ m_uiForm.spPlotSpectrum->setMinimum(0);
+ m_uiForm.spPlotSpectrum->setValue(0);
- connect(m_uiForm.spPlotSpectrum, SIGNAL(valueChanged(int)), this, SLOT(updatePlot()));
+ m_uiForm.spSpectraMin->setMaximum(maxSpecIndex);
+ m_uiForm.spSpectraMin->setMinimum(0);
- connect(m_uiForm.spSpectraMin, SIGNAL(valueChanged(int)), this, SLOT(specMinChanged(int)));
- connect(m_uiForm.spSpectraMax, SIGNAL(valueChanged(int)), this, SLOT(specMaxChanged(int)));
+ m_uiForm.spSpectraMax->setMaximum(maxSpecIndex);
+ m_uiForm.spSpectraMax->setMinimum(0);
+ m_uiForm.spSpectraMax->setValue(maxSpecIndex);
- // Set a custom handler for the QTreePropertyBrowser's ContextMenu event
- m_ffTree->setContextMenuPolicy(Qt::CustomContextMenu);
- connect(m_ffTree, SIGNAL(customContextMenuRequested(const QPoint &)), this, SLOT(fitContextMenu(const QPoint &)));
+ updatePlot();
+}
- connect(m_blnManager, SIGNAL(valueChanged(QtProperty *, bool)), this, SLOT(checkBoxUpdate(QtProperty *, bool)));
+CompositeFunction_sptr IqtFit::createFunction(bool tie) {
+ CompositeFunction_sptr result(new CompositeFunction);
+ QString fname;
+ const int fitType = m_uiForm.cbFitType->currentIndex();
+
+ IFunction_sptr func =
+ FunctionFactory::Instance().createFunction("LinearBackground");
+ func->setParameter("A0",
+ m_ffRangeManager->value(m_properties["BackgroundA0"]));
+ result->addFunction(func);
+ result->tie("f0.A1", "0");
+ if (tie) {
+ result->tie("f0.A0",
+ m_properties["BackgroundA0"]->valueText().toStdString());
}
- void IqtFit::run()
- {
- if ( m_ffInputWS == NULL )
- {
- return;
- }
-
- const bool constrainBeta = m_uiForm.ckConstrainBeta->isChecked();
- const bool constrainIntens = m_uiForm.ckConstrainIntensities->isChecked();
- CompositeFunction_sptr func = createFunction();
- func->tie("f0.A1", "0");
+ if (fitType == 2) {
+ fname = "StretchedExp";
+ } else {
+ fname = "Exponential1";
+ }
- if ( constrainIntens )
- {
- constrainIntensities(func);
- }
+ result->addFunction(createUserFunction(fname, tie));
- func->applyTies();
-
- std::string function = std::string(func->asString());
- QString fitType = fitTypeString();
- QString specMin = m_uiForm.spSpectraMin->text();
- QString specMax = m_uiForm.spSpectraMax->text();
-
- QString pyInput = "from IndirectDataAnalysis import furyfitSeq, furyfitMult\n"
- "input = '" + m_ffInputWSName + "'\n"
- "func = r'" + QString::fromStdString(function) + "'\n"
- "ftype = '" + fitTypeString() + "'\n"
- "startx = " + m_properties["StartX"]->valueText() + "\n"
- "endx = " + m_properties["EndX"]->valueText() + "\n"
- "plot = '" + m_uiForm.cbPlotType->currentText() + "'\n"
- "spec_min = " + specMin + "\n"
- "spec_max = " + specMax + "\n"
- "spec_max = None\n"
- "minimizer = '" + minimizerString("$outputname_$wsindex") + "'\n"
- "max_iterations = " + QString::number(m_dblManager->value(m_properties["MaxIterations"])) + "\n";
-
- if (constrainIntens) pyInput += "constrain_intens = True \n";
- else pyInput += "constrain_intens = False \n";
-
- if ( m_uiForm.ckSave->isChecked() ) pyInput += "save = True\n";
- else pyInput += "save = False\n";
-
- if( !constrainBeta )
- {
- pyInput += "furyfitSeq(input, func, ftype, startx, endx, spec_min=spec_min, spec_max=spec_max, intensities_constrained=constrain_intens, Save=save, Plot=plot, minimizer=minimizer, max_iterations=max_iterations)\n";
- }
- else
- {
- pyInput += "furyfitMult(input, func, ftype, startx, endx, spec_min=spec_min, spec_max=spec_max, intensities_constrained=constrain_intens, Save=save, Plot=plot, minimizer=minimizer, max_iterations=max_iterations)\n";
+ if (fitType == 1 || fitType == 3) {
+ if (fitType == 1) {
+ fname = "Exponential2";
+ } else {
+ fname = "StretchedExp";
}
+ result->addFunction(createUserFunction(fname, tie));
+ }
- QString pyOutput = runPythonCode(pyInput);
+ // Return CompositeFunction object to caller.
+ result->applyTies();
+ return result;
+}
- // Set the result workspace for Python script export
- QString inputWsName = QString::fromStdString(m_ffInputWS->getName());
- QString resultWsName = inputWsName.left(inputWsName.lastIndexOf("_")) + "_fury_" + fitType + specMin + "_to_" + specMax + "_Workspaces";
- m_pythonExportWsName = resultWsName.toStdString();
+IFunction_sptr IqtFit::createUserFunction(const QString &name, bool tie) {
+ IFunction_sptr result =
+ FunctionFactory::Instance().createFunction("UserFunction");
+ std::string formula;
- updatePlot();
+ if (name.startsWith("Exp")) {
+ formula = "Intensity*exp(-(x/Tau))";
+ } else {
+ formula = "Intensity*exp(-(x/Tau)^Beta)";
}
- bool IqtFit::validate()
- {
- UserInputValidator uiv;
+ IFunction::Attribute att(formula);
+ result->setAttribute("Formula", att);
- uiv.checkDataSelectorIsValid("Sample", m_uiForm.dsSampleInput);
+ QList<QtProperty *> props = m_properties[name]->subProperties();
+ for (int i = 0; i < props.size(); i++) {
+ std::string name = props[i]->propertyName().toStdString();
+ result->setParameter(name, m_dblManager->value(props[i]));
- auto range = std::make_pair(m_ffRangeManager->value(m_properties["StartX"]), m_ffRangeManager->value(m_properties["EndX"]));
- uiv.checkValidRange("Ranges", range);
-
- QString error = uiv.generateErrorMessage();
- showMessageBox(error);
-
- return error.isEmpty();
+ // add tie if parameter is fixed
+ if (tie || !props[i]->subProperties().isEmpty()) {
+ std::string value = props[i]->valueText().toStdString();
+ result->tie(name, value);
+ }
}
- void IqtFit::loadSettings(const QSettings & settings)
- {
- m_uiForm.dsSampleInput->readSettings(settings.group());
- }
+ result->applyTies();
+ return result;
+}
- /**
- * Called when new data has been loaded by the data selector.
- *
- * Configures ranges for spin boxes before raw plot is done.
- *
- * @param wsName Name of new workspace loaded
- */
- void IqtFit::newDataLoaded(const QString wsName)
- {
- m_ffInputWSName = wsName;
- m_ffInputWS = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(m_ffInputWSName.toStdString());
+QtProperty *IqtFit::createExponential(const QString &name) {
+ QtProperty *expGroup = m_grpManager->addProperty(name);
+ m_properties[name + ".Intensity"] = m_dblManager->addProperty("Intensity");
+ m_dblManager->setDecimals(m_properties[name + ".Intensity"], NUM_DECIMALS);
+ m_properties[name + ".Tau"] = m_dblManager->addProperty("Tau");
+ m_dblManager->setDecimals(m_properties[name + ".Tau"], NUM_DECIMALS);
+ expGroup->addSubProperty(m_properties[name + ".Intensity"]);
+ expGroup->addSubProperty(m_properties[name + ".Tau"]);
+ return expGroup;
+}
- int maxSpecIndex = static_cast<int>(m_ffInputWS->getNumberHistograms()) - 1;
+QtProperty *IqtFit::createStretchedExp(const QString &name) {
+ QtProperty *prop = m_grpManager->addProperty(name);
+ m_properties[name + ".Intensity"] = m_dblManager->addProperty("Intensity");
+ m_properties[name + ".Tau"] = m_dblManager->addProperty("Tau");
+ m_properties[name + ".Beta"] = m_dblManager->addProperty("Beta");
+ m_dblManager->setRange(m_properties[name + ".Beta"], 0, 1);
+ m_dblManager->setDecimals(m_properties[name + ".Intensity"], NUM_DECIMALS);
+ m_dblManager->setDecimals(m_properties[name + ".Tau"], NUM_DECIMALS);
+ m_dblManager->setDecimals(m_properties[name + ".Beta"], NUM_DECIMALS);
+ prop->addSubProperty(m_properties[name + ".Intensity"]);
+ prop->addSubProperty(m_properties[name + ".Tau"]);
+ prop->addSubProperty(m_properties[name + ".Beta"]);
+ return prop;
+}
- m_uiForm.spPlotSpectrum->setMaximum(maxSpecIndex);
- m_uiForm.spPlotSpectrum->setMinimum(0);
- m_uiForm.spPlotSpectrum->setValue(0);
+QString IqtFit::fitTypeString() const {
+ switch (m_uiForm.cbFitType->currentIndex()) {
+ case 0:
+ return "1E_s";
+ case 1:
+ return "2E_s";
+ case 2:
+ return "1S_s";
+ case 3:
+ return "1E1S_s";
+ default:
+ return "s";
+ };
+}
- m_uiForm.spSpectraMin->setMaximum(maxSpecIndex);
- m_uiForm.spSpectraMin->setMinimum(0);
+void IqtFit::typeSelection(int index) {
+ m_ffTree->clear();
- m_uiForm.spSpectraMax->setMaximum(maxSpecIndex);
- m_uiForm.spSpectraMax->setMinimum(0);
- m_uiForm.spSpectraMax->setValue(maxSpecIndex);
+ m_ffTree->addProperty(m_properties["StartX"]);
+ m_ffTree->addProperty(m_properties["EndX"]);
+ m_ffTree->addProperty(m_properties["MaxIterations"]);
+ m_ffTree->addProperty(m_properties["LinearBackground"]);
+ m_ffTree->addProperty(m_properties["FABADA"]);
- updatePlot();
+ // option should only be available with a single stretched exponential
+ m_uiForm.ckConstrainBeta->setEnabled((index == 2));
+ if (!m_uiForm.ckConstrainBeta->isEnabled()) {
+ m_uiForm.ckConstrainBeta->setChecked(false);
}
- CompositeFunction_sptr IqtFit::createFunction(bool tie)
- {
- CompositeFunction_sptr result( new CompositeFunction );
- QString fname;
- const int fitType = m_uiForm.cbFitType->currentIndex();
-
- IFunction_sptr func = FunctionFactory::Instance().createFunction("LinearBackground");
- func->setParameter("A0", m_ffRangeManager->value(m_properties["BackgroundA0"]));
- result->addFunction(func);
- result->tie("f0.A1", "0");
- if ( tie ) { result->tie("f0.A0", m_properties["BackgroundA0"]->valueText().toStdString()); }
-
- if ( fitType == 2 ) { fname = "StretchedExp"; }
- else { fname = "Exponential1"; }
+ switch (index) {
+ case 0:
+ m_ffTree->addProperty(m_properties["Exponential1"]);
+
+ // remove option to plot beta
+ m_uiForm.cbPlotType->removeItem(4);
+ break;
+ case 1:
+ m_ffTree->addProperty(m_properties["Exponential1"]);
+ m_ffTree->addProperty(m_properties["Exponential2"]);
+
+ // remove option to plot beta
+ m_uiForm.cbPlotType->removeItem(4);
+ break;
+ case 2:
+ m_ffTree->addProperty(m_properties["StretchedExp"]);
+
+ // add option to plot beta
+ if (m_uiForm.cbPlotType->count() == 4) {
+ m_uiForm.cbPlotType->addItem("Beta");
+ }
- result->addFunction(createUserFunction(fname, tie));
+ break;
+ case 3:
+ m_ffTree->addProperty(m_properties["Exponential1"]);
+ m_ffTree->addProperty(m_properties["StretchedExp"]);
- if ( fitType == 1 || fitType == 3 )
- {
- if ( fitType == 1 ) { fname = "Exponential2"; }
- else { fname = "StretchedExp"; }
- result->addFunction(createUserFunction(fname, tie));
+ // add option to plot beta
+ if (m_uiForm.cbPlotType->count() == 4) {
+ m_uiForm.cbPlotType->addItem("Beta");
}
- // Return CompositeFunction object to caller.
- result->applyTies();
- return result;
+ break;
}
- IFunction_sptr IqtFit::createUserFunction(const QString & name, bool tie)
- {
- IFunction_sptr result = FunctionFactory::Instance().createFunction("UserFunction");
- std::string formula;
-
- if ( name.startsWith("Exp") ) { formula = "Intensity*exp(-(x/Tau))"; }
- else { formula = "Intensity*exp(-(x/Tau)^Beta)"; }
+ plotGuess(NULL);
+}
- IFunction::Attribute att(formula);
- result->setAttribute("Formula", att);
+void IqtFit::updatePlot() {
+ if (!m_ffInputWS) {
+ g_log.error("No workspace loaded, cannot create preview plot.");
+ return;
+ }
- QList<QtProperty*> props = m_properties[name]->subProperties();
- for ( int i = 0; i < props.size(); i++ )
- {
- std::string name = props[i]->propertyName().toStdString();
- result->setParameter(name, m_dblManager->value(props[i]));
+ int specNo = m_uiForm.spPlotSpectrum->value();
+
+ m_uiForm.ppPlot->clear();
+ m_uiForm.ppPlot->addSpectrum("Sample", m_ffInputWS, specNo);
+
+ try {
+ const QPair<double, double> curveRange =
+ m_uiForm.ppPlot->getCurveRange("Sample");
+ const std::pair<double, double> range(curveRange.first, curveRange.second);
+ m_uiForm.ppPlot->getRangeSelector("FuryFitRange")
+ ->setRange(range.first, range.second);
+ m_ffRangeManager->setRange(m_properties["StartX"], range.first,
+ range.second);
+ m_ffRangeManager->setRange(m_properties["EndX"], range.first, range.second);
+
+ setDefaultParameters("Exponential1");
+ setDefaultParameters("Exponential2");
+ setDefaultParameters("StretchedExp");
+
+ m_uiForm.ppPlot->resizeX();
+ m_uiForm.ppPlot->setAxisRange(qMakePair(0.0, 1.0), QwtPlot::yLeft);
+ } catch (std::invalid_argument &exc) {
+ showMessageBox(exc.what());
+ }
- //add tie if parameter is fixed
- if ( tie || ! props[i]->subProperties().isEmpty() )
- {
- std::string value = props[i]->valueText().toStdString();
- result->tie(name, value);
+ // If there is a result plot then plot it
+ if (AnalysisDataService::Instance().doesExist(m_pythonExportWsName)) {
+ WorkspaceGroup_sptr outputGroup =
+ AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
+ m_pythonExportWsName);
+ if (specNo >= static_cast<int>(outputGroup->size()))
+ return;
+ MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
+ outputGroup->getItem(specNo));
+ if (ws) {
+ if (m_uiForm.ckPlotGuess->isChecked()) {
+ m_uiForm.ppPlot->removeSpectrum("Guess");
}
+ m_uiForm.ppPlot->addSpectrum("Fit", ws, 1, Qt::red);
+ m_uiForm.ppPlot->addSpectrum("Diff", ws, 2, Qt::blue);
}
-
- result->applyTies();
- return result;
- }
-
- QtProperty* IqtFit::createExponential(const QString & name)
- {
- QtProperty* expGroup = m_grpManager->addProperty(name);
- m_properties[name+".Intensity"] = m_dblManager->addProperty("Intensity");
- m_dblManager->setDecimals(m_properties[name+".Intensity"], NUM_DECIMALS);
- m_properties[name+".Tau"] = m_dblManager->addProperty("Tau");
- m_dblManager->setDecimals(m_properties[name+".Tau"], NUM_DECIMALS);
- expGroup->addSubProperty(m_properties[name+".Intensity"]);
- expGroup->addSubProperty(m_properties[name+".Tau"]);
- return expGroup;
}
+}
- QtProperty* IqtFit::createStretchedExp(const QString & name)
- {
- QtProperty* prop = m_grpManager->addProperty(name);
- m_properties[name+".Intensity"] = m_dblManager->addProperty("Intensity");
- m_properties[name+".Tau"] = m_dblManager->addProperty("Tau");
- m_properties[name+".Beta"] = m_dblManager->addProperty("Beta");
- m_dblManager->setRange(m_properties[name+".Beta"], 0, 1);
- m_dblManager->setDecimals(m_properties[name+".Intensity"], NUM_DECIMALS);
- m_dblManager->setDecimals(m_properties[name+".Tau"], NUM_DECIMALS);
- m_dblManager->setDecimals(m_properties[name+".Beta"], NUM_DECIMALS);
- prop->addSubProperty(m_properties[name+".Intensity"]);
- prop->addSubProperty(m_properties[name+".Tau"]);
- prop->addSubProperty(m_properties[name+".Beta"]);
- return prop;
- }
+void IqtFit::setDefaultParameters(const QString &name) {
+ double background = m_dblManager->value(m_properties["BackgroundA0"]);
+ // intensity is always 1-background
+ m_dblManager->setValue(m_properties[name + ".Intensity"], 1.0 - background);
+ auto x = m_ffInputWS->readX(0);
+ auto y = m_ffInputWS->readY(0);
+ double tau = 0;
- QString IqtFit::fitTypeString() const
- {
- switch ( m_uiForm.cbFitType->currentIndex() )
- {
- case 0:
- return "1E_s";
- case 1:
- return "2E_s";
- case 2:
- return "1S_s";
- case 3:
- return "1E1S_s";
- default:
- return "s";
- };
+ if (x.size() > 4) {
+ tau = -x[4] / log(y[4]);
}
- void IqtFit::typeSelection(int index)
- {
- m_ffTree->clear();
-
- m_ffTree->addProperty(m_properties["StartX"]);
- m_ffTree->addProperty(m_properties["EndX"]);
- m_ffTree->addProperty(m_properties["MaxIterations"]);
- m_ffTree->addProperty(m_properties["LinearBackground"]);
- m_ffTree->addProperty(m_properties["FABADA"]);
-
- //option should only be available with a single stretched exponential
- m_uiForm.ckConstrainBeta->setEnabled((index == 2));
- if (!m_uiForm.ckConstrainBeta->isEnabled())
- {
- m_uiForm.ckConstrainBeta->setChecked(false);
- }
-
- switch ( index )
- {
- case 0:
- m_ffTree->addProperty(m_properties["Exponential1"]);
+ m_dblManager->setValue(m_properties[name + ".Tau"], tau);
+ m_dblManager->setValue(m_properties[name + ".Beta"], 1.0);
+}
- //remove option to plot beta
- m_uiForm.cbPlotType->removeItem(4);
- break;
- case 1:
- m_ffTree->addProperty(m_properties["Exponential1"]);
- m_ffTree->addProperty(m_properties["Exponential2"]);
+/**
+ * Handles the user entering a new minimum spectrum index.
+ *
+ * Prevents the user entering an overlapping spectra range.
+ *
+ * @param value Minimum spectrum index
+ */
+void IqtFit::specMinChanged(int value) {
+ m_uiForm.spSpectraMax->setMinimum(value);
+}
- //remove option to plot beta
- m_uiForm.cbPlotType->removeItem(4);
- break;
- case 2:
- m_ffTree->addProperty(m_properties["StretchedExp"]);
+/**
+ * Handles the user entering a new maximum spectrum index.
+ *
+ * Prevents the user entering an overlapping spectra range.
+ *
+ * @param value Maximum spectrum index
+ */
+void IqtFit::specMaxChanged(int value) {
+ m_uiForm.spSpectraMin->setMaximum(value);
+}
- //add option to plot beta
- if(m_uiForm.cbPlotType->count() == 4)
- {
- m_uiForm.cbPlotType->addItem("Beta");
- }
+void IqtFit::xMinSelected(double val) {
+ m_ffRangeManager->setValue(m_properties["StartX"], val);
+}
- break;
- case 3:
- m_ffTree->addProperty(m_properties["Exponential1"]);
- m_ffTree->addProperty(m_properties["StretchedExp"]);
-
- //add option to plot beta
- if(m_uiForm.cbPlotType->count() == 4)
- {
- m_uiForm.cbPlotType->addItem("Beta");
- }
+void IqtFit::xMaxSelected(double val) {
+ m_ffRangeManager->setValue(m_properties["EndX"], val);
+}
- break;
- }
+void IqtFit::backgroundSelected(double val) {
+ m_ffRangeManager->setValue(m_properties["BackgroundA0"], val);
+ m_dblManager->setValue(m_properties["Exponential1.Intensity"], 1.0 - val);
+ m_dblManager->setValue(m_properties["Exponential2.Intensity"], 1.0 - val);
+ m_dblManager->setValue(m_properties["StretchedExp.Intensity"], 1.0 - val);
+}
- plotGuess(NULL);
+void IqtFit::propertyChanged(QtProperty *prop, double val) {
+ auto fitRangeSelector = m_uiForm.ppPlot->getRangeSelector("FuryFitRange");
+ auto backgroundRangeSelector =
+ m_uiForm.ppPlot->getRangeSelector("FuryFitBackground");
+
+ if (prop == m_properties["StartX"]) {
+ fitRangeSelector->setMinimum(val);
+ } else if (prop == m_properties["EndX"]) {
+ fitRangeSelector->setMaximum(val);
+ } else if (prop == m_properties["BackgroundA0"]) {
+ backgroundRangeSelector->setMinimum(val);
+ m_dblManager->setValue(m_properties["Exponential1.Intensity"], 1.0 - val);
+ m_dblManager->setValue(m_properties["Exponential2.Intensity"], 1.0 - val);
+ m_dblManager->setValue(m_properties["StretchedExp.Intensity"], 1.0 - val);
+ } else if (prop == m_properties["Exponential1.Intensity"] ||
+ prop == m_properties["Exponential2.Intensity"] ||
+ prop == m_properties["StretchedExp.Intensity"]) {
+ backgroundRangeSelector->setMinimum(1.0 - val);
+ m_dblManager->setValue(m_properties["Exponential1.Intensity"], val);
+ m_dblManager->setValue(m_properties["Exponential2.Intensity"], val);
+ m_dblManager->setValue(m_properties["StretchedExp.Intensity"], val);
}
+}
- void IqtFit::updatePlot()
- {
- if(!m_ffInputWS)
- {
- g_log.error("No workspace loaded, cannot create preview plot.");
- return;
+void IqtFit::checkBoxUpdate(QtProperty *prop, bool checked) {
+ if (prop == m_properties["UseFABADA"]) {
+ if (checked) {
+ m_dblManager->setValue(m_properties["MaxIterations"], 20000);
+
+ m_properties["FABADA"]->addSubProperty(m_properties["OutputFABADAChain"]);
+ m_properties["FABADA"]->addSubProperty(m_properties["FABADAChainLength"]);
+ m_properties["FABADA"]->addSubProperty(
+ m_properties["FABADAConvergenceCriteria"]);
+ m_properties["FABADA"]->addSubProperty(
+ m_properties["FABADAJumpAcceptanceRate"]);
+ } else {
+ m_dblManager->setValue(m_properties["MaxIterations"], 500);
+
+ m_properties["FABADA"]->removeSubProperty(
+ m_properties["OutputFABADAChain"]);
+ m_properties["FABADA"]->removeSubProperty(
+ m_properties["FABADAChainLength"]);
+ m_properties["FABADA"]->removeSubProperty(
+ m_properties["FABADAConvergenceCriteria"]);
+ m_properties["FABADA"]->removeSubProperty(
+ m_properties["FABADAJumpAcceptanceRate"]);
}
+ }
+}
- int specNo = m_uiForm.spPlotSpectrum->value();
-
- m_uiForm.ppPlot->clear();
- m_uiForm.ppPlot->addSpectrum("Sample", m_ffInputWS, specNo);
-
- try
- {
- const QPair<double, double> curveRange = m_uiForm.ppPlot->getCurveRange("Sample");
- const std::pair<double, double> range(curveRange.first, curveRange.second);
- m_uiForm.ppPlot->getRangeSelector("FuryFitRange")->setRange(range.first, range.second);
- m_ffRangeManager->setRange(m_properties["StartX"], range.first, range.second);
- m_ffRangeManager->setRange(m_properties["EndX"], range.first, range.second);
-
- setDefaultParameters("Exponential1");
- setDefaultParameters("Exponential2");
- setDefaultParameters("StretchedExp");
-
- m_uiForm.ppPlot->resizeX();
- m_uiForm.ppPlot->setAxisRange(qMakePair(0.0, 1.0), QwtPlot::yLeft);
- }
- catch(std::invalid_argument & exc)
- {
- showMessageBox(exc.what());
+void IqtFit::constrainIntensities(CompositeFunction_sptr func) {
+ std::string paramName = "f1.Intensity";
+ size_t index = func->parameterIndex(paramName);
+
+ switch (m_uiForm.cbFitType->currentIndex()) {
+ case 0: // 1 Exp
+ case 2: // 1 Str
+ if (!func->isFixed(index)) {
+ func->tie(paramName, "1-f0.A0");
+ } else {
+ std::string paramValue =
+ boost::lexical_cast<std::string>(func->getParameter(paramName));
+ func->tie(paramName, paramValue);
+ func->tie("f0.A0", "1-" + paramName);
}
-
- // If there is a result plot then plot it
- if(AnalysisDataService::Instance().doesExist(m_pythonExportWsName))
- {
- WorkspaceGroup_sptr outputGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(m_pythonExportWsName);
- if(specNo >= static_cast<int>(outputGroup->size()))
- return;
- MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(outputGroup->getItem(specNo));
- if(ws)
- m_uiForm.ppPlot->addSpectrum("Fit", ws, 1, Qt::red);
+ break;
+ case 1: // 2 Exp
+ case 3: // 1 Exp & 1 Str
+ if (!func->isFixed(index)) {
+ func->tie(paramName, "1-f2.Intensity-f0.A0");
+ } else {
+ std::string paramValue =
+ boost::lexical_cast<std::string>(func->getParameter(paramName));
+ func->tie(paramName, "1-f2.Intensity-f0.A0");
+ func->tie(paramName, paramValue);
}
+ break;
}
+}
- void IqtFit::setDefaultParameters(const QString& name)
- {
- double background = m_dblManager->value(m_properties["BackgroundA0"]);
- //intensity is always 1-background
- m_dblManager->setValue(m_properties[name+".Intensity"], 1.0-background);
- auto x = m_ffInputWS->readX(0);
- auto y = m_ffInputWS->readY(0);
- double tau = 0;
-
- if (x.size() > 4)
- {
- tau = -x[4] / log(y[4]);
- }
+/**
+ * Generates a string that defines the fitting minimizer based on the user
+ * options.
+ *
+ * @return Minimizer as a string
+ */
+QString IqtFit::minimizerString(QString outputName) const {
+ QString minimizer = "Levenberg-Marquardt";
- m_dblManager->setValue(m_properties[name+".Tau"], tau);
- m_dblManager->setValue(m_properties[name+".Beta"], 1.0);
- }
+ if (m_blnManager->value(m_properties["UseFABADA"])) {
+ minimizer = "FABADA";
- /**
- * Handles the user entering a new minimum spectrum index.
- *
- * Prevents the user entering an overlapping spectra range.
- *
- * @param value Minimum spectrum index
- */
- void IqtFit::specMinChanged(int value)
- {
- m_uiForm.spSpectraMax->setMinimum(value);
- }
+ int chainLength = static_cast<int>(
+ m_dblManager->value(m_properties["FABADAChainLength"]));
+ minimizer += ",ChainLength=" + QString::number(chainLength);
- /**
- * Handles the user entering a new maximum spectrum index.
- *
- * Prevents the user entering an overlapping spectra range.
- *
- * @param value Maximum spectrum index
- */
- void IqtFit::specMaxChanged(int value)
- {
- m_uiForm.spSpectraMin->setMaximum(value);
- }
+ double convergenceCriteria =
+ m_dblManager->value(m_properties["FABADAConvergenceCriteria"]);
+ minimizer += ",ConvergenceCriteria=" + QString::number(convergenceCriteria);
- void IqtFit::xMinSelected(double val)
- {
- m_ffRangeManager->setValue(m_properties["StartX"], val);
- }
+ double jumpAcceptanceRate =
+ m_dblManager->value(m_properties["FABADAJumpAcceptanceRate"]);
+ minimizer += ",JumpAcceptanceRate=" + QString::number(jumpAcceptanceRate);
- void IqtFit::xMaxSelected(double val)
- {
- m_ffRangeManager->setValue(m_properties["EndX"], val);
- }
+ minimizer += ",PDF=" + outputName + "_PDF";
- void IqtFit::backgroundSelected(double val)
- {
- m_ffRangeManager->setValue(m_properties["BackgroundA0"], val);
- m_dblManager->setValue(m_properties["Exponential1.Intensity"], 1.0-val);
- m_dblManager->setValue(m_properties["Exponential2.Intensity"], 1.0-val);
- m_dblManager->setValue(m_properties["StretchedExp.Intensity"], 1.0-val);
+ if (m_blnManager->value(m_properties["OutputFABADAChain"]))
+ minimizer += ",Chains=" + outputName + "_Chain";
}
- void IqtFit::propertyChanged(QtProperty* prop, double val)
- {
- auto fitRangeSelector = m_uiForm.ppPlot->getRangeSelector("FuryFitRange");
- auto backgroundRangeSelector = m_uiForm.ppPlot->getRangeSelector("FuryFitBackground");
+ return minimizer;
+}
- if ( prop == m_properties["StartX"] )
- {
- fitRangeSelector->setMinimum(val);
- }
- else if ( prop == m_properties["EndX"] )
- {
- fitRangeSelector->setMaximum(val);
- }
- else if ( prop == m_properties["BackgroundA0"])
- {
- backgroundRangeSelector->setMinimum(val);
- m_dblManager->setValue(m_properties["Exponential1.Intensity"], 1.0-val);
- m_dblManager->setValue(m_properties["Exponential2.Intensity"], 1.0-val);
- m_dblManager->setValue(m_properties["StretchedExp.Intensity"], 1.0-val);
- }
- else if( prop == m_properties["Exponential1.Intensity"]
- || prop == m_properties["Exponential2.Intensity"]
- || prop == m_properties["StretchedExp.Intensity"])
- {
- backgroundRangeSelector->setMinimum(1.0-val);
- m_dblManager->setValue(m_properties["Exponential1.Intensity"], val);
- m_dblManager->setValue(m_properties["Exponential2.Intensity"], val);
- m_dblManager->setValue(m_properties["StretchedExp.Intensity"], val);
- }
- }
+void IqtFit::singleFit() {
+ if (!validate())
+ return;
- void IqtFit::checkBoxUpdate(QtProperty * prop, bool checked)
- {
- if(prop == m_properties["UseFABADA"])
- {
- if(checked)
- {
- m_dblManager->setValue(m_properties["MaxIterations"], 20000);
-
- m_properties["FABADA"]->addSubProperty(m_properties["OutputFABADAChain"]);
- m_properties["FABADA"]->addSubProperty(m_properties["FABADAChainLength"]);
- m_properties["FABADA"]->addSubProperty(m_properties["FABADAConvergenceCriteria"]);
- m_properties["FABADA"]->addSubProperty(m_properties["FABADAJumpAcceptanceRate"]);
- }
- else
- {
- m_dblManager->setValue(m_properties["MaxIterations"], 500);
-
- m_properties["FABADA"]->removeSubProperty(m_properties["OutputFABADAChain"]);
- m_properties["FABADA"]->removeSubProperty(m_properties["FABADAChainLength"]);
- m_properties["FABADA"]->removeSubProperty(m_properties["FABADAConvergenceCriteria"]);
- m_properties["FABADA"]->removeSubProperty(m_properties["FABADAJumpAcceptanceRate"]);
- }
- }
- }
+ // Don't plot a new guess curve until there is a fit
+ disconnect(m_dblManager, SIGNAL(propertyChanged(QtProperty *)), this,
+ SLOT(plotGuess(QtProperty *)));
- void IqtFit::constrainIntensities(CompositeFunction_sptr func)
- {
- std::string paramName = "f1.Intensity";
- size_t index = func->parameterIndex(paramName);
+ // First create the function
+ auto function = createFunction();
- switch ( m_uiForm.cbFitType->currentIndex() )
- {
+ const int fitType = m_uiForm.cbFitType->currentIndex();
+ if (m_uiForm.ckConstrainIntensities->isChecked()) {
+ switch (fitType) {
case 0: // 1 Exp
case 2: // 1 Str
- if(!func->isFixed(index))
- {
- func->tie(paramName, "1-f0.A0");
- }
- else
- {
- std::string paramValue = boost::lexical_cast<std::string>(func->getParameter(paramName));
- func->tie(paramName, paramValue);
- func->tie("f0.A0", "1-"+paramName);
- }
+ m_ties = "f1.Intensity = 1-f0.A0";
break;
case 1: // 2 Exp
case 3: // 1 Exp & 1 Str
- if(!func->isFixed(index))
- {
- func->tie(paramName,"1-f2.Intensity-f0.A0");
- }
- else
- {
- std::string paramValue = boost::lexical_cast<std::string>(func->getParameter(paramName));
- func->tie(paramName,"1-f2.Intensity-f0.A0");
- func->tie(paramName, paramValue);
- }
+ m_ties = "f1.Intensity=1-f2.Intensity-f0.A0";
+ break;
+ default:
break;
}
}
+ QString ftype = fitTypeString();
- /**
- * Generates a string that defines the fitting minimizer based on the user
- * options.
- *
- * @return Minimizer as a string
- */
- QString IqtFit::minimizerString(QString outputName) const
- {
- QString minimizer = "Levenberg-Marquardt";
-
- if(m_blnManager->value(m_properties["UseFABADA"]))
- {
- minimizer = "FABADA";
-
- int chainLength = static_cast<int>(m_dblManager->value(m_properties["FABADAChainLength"]));
- minimizer += ",ChainLength=" + QString::number(chainLength);
-
- double convergenceCriteria = m_dblManager->value(m_properties["FABADAConvergenceCriteria"]);
- minimizer += ",ConvergenceCriteria=" + QString::number(convergenceCriteria);
-
- double jumpAcceptanceRate = m_dblManager->value(m_properties["FABADAJumpAcceptanceRate"]);
- minimizer += ",JumpAcceptanceRate=" + QString::number(jumpAcceptanceRate);
-
- minimizer += ",PDF=" + outputName + "_PDF";
-
- if(m_blnManager->value(m_properties["OutputFABADAChain"]))
- minimizer += ",Chains=" + outputName + "_Chain";
- }
-
- return minimizer;
+ updatePlot();
+ if (m_ffInputWS == NULL) {
+ return;
}
- void IqtFit::singleFit()
- {
- if(!validate())
- return;
-
- // Don't plot a new guess curve until there is a fit
- disconnect(m_dblManager, SIGNAL(propertyChanged(QtProperty*)), this, SLOT(plotGuess(QtProperty*)));
-
- // First create the function
- auto function = createFunction();
-
- const int fitType = m_uiForm.cbFitType->currentIndex();
- if ( m_uiForm.ckConstrainIntensities->isChecked() )
- {
- switch ( fitType )
- {
- case 0: // 1 Exp
- case 2: // 1 Str
- m_ties = "f1.Intensity = 1-f0.A0";
- break;
- case 1: // 2 Exp
- case 3: // 1 Exp & 1 Str
- m_ties = "f1.Intensity=1-f2.Intensity-f0.A0";
- break;
- default:
- break;
- }
- }
- QString ftype = fitTypeString();
-
- updatePlot();
- if ( m_ffInputWS == NULL )
- {
- return;
- }
-
- QString pyInput = "from IndirectCommon import getWSprefix\nprint getWSprefix('%1')\n";
- pyInput = pyInput.arg(m_ffInputWSName);
- m_singleFitOutputName = runPythonCode(pyInput).trimmed() +
- QString("fury_") +
- ftype +
- m_uiForm.spPlotSpectrum->text();
-
- // Create the Fit Algorithm
- m_singleFitAlg = AlgorithmManager::Instance().create("Fit");
- m_singleFitAlg->initialize();
- m_singleFitAlg->setPropertyValue("Function", function->asString());
- m_singleFitAlg->setPropertyValue("InputWorkspace", m_ffInputWSName.toStdString());
- m_singleFitAlg->setProperty("WorkspaceIndex", m_uiForm.spPlotSpectrum->text().toInt());
- m_singleFitAlg->setProperty("StartX", m_ffRangeManager->value(m_properties["StartX"]));
- m_singleFitAlg->setProperty("EndX", m_ffRangeManager->value(m_properties["EndX"]));
- m_singleFitAlg->setProperty("MaxIterations", static_cast<int>(m_dblManager->value(m_properties["MaxIterations"])));
- m_singleFitAlg->setProperty("Minimizer", minimizerString(m_singleFitOutputName).toStdString());
- m_singleFitAlg->setProperty("Ties", m_ties.toStdString());
- m_singleFitAlg->setPropertyValue("Output", m_singleFitOutputName.toStdString());
-
- connect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)),
- this, SLOT(singleFitComplete(bool)));
-
- m_batchAlgoRunner->addAlgorithm(m_singleFitAlg);
- m_batchAlgoRunner->executeBatchAsync();
- }
+ QString pyInput =
+ "from IndirectCommon import getWSprefix\nprint getWSprefix('%1')\n";
+ pyInput = pyInput.arg(m_ffInputWSName);
+ m_singleFitOutputName = runPythonCode(pyInput).trimmed() + QString("fury_") +
+ ftype + m_uiForm.spPlotSpectrum->text();
+
+ // Create the Fit Algorithm
+ m_singleFitAlg = AlgorithmManager::Instance().create("Fit");
+ m_singleFitAlg->initialize();
+ m_singleFitAlg->setPropertyValue("Function", function->asString());
+ m_singleFitAlg->setPropertyValue("InputWorkspace",
+ m_ffInputWSName.toStdString());
+ m_singleFitAlg->setProperty("WorkspaceIndex",
+ m_uiForm.spPlotSpectrum->text().toInt());
+ m_singleFitAlg->setProperty("StartX",
+ m_ffRangeManager->value(m_properties["StartX"]));
+ m_singleFitAlg->setProperty("EndX",
+ m_ffRangeManager->value(m_properties["EndX"]));
+ m_singleFitAlg->setProperty(
+ "MaxIterations",
+ static_cast<int>(m_dblManager->value(m_properties["MaxIterations"])));
+ m_singleFitAlg->setProperty(
+ "Minimizer", minimizerString(m_singleFitOutputName).toStdString());
+ m_singleFitAlg->setProperty("Ties", m_ties.toStdString());
+ m_singleFitAlg->setPropertyValue("Output",
+ m_singleFitOutputName.toStdString());
+
+ connect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
+ SLOT(singleFitComplete(bool)));
+
+ m_batchAlgoRunner->addAlgorithm(m_singleFitAlg);
+ m_batchAlgoRunner->executeBatchAsync();
+}
- void IqtFit::singleFitComplete(bool error)
- {
- disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)),
- this, SLOT(singleFitComplete(bool)));
+void IqtFit::singleFitComplete(bool error) {
+ disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
+ SLOT(singleFitComplete(bool)));
- if(error)
- {
- QString msg = "There was an error executing the fitting algorithm. Please see the "
+ if (error) {
+ QString msg =
+ "There was an error executing the fitting algorithm. Please see the "
"Results Log pane for more details.";
- showMessageBox(msg);
- return;
- }
+ showMessageBox(msg);
+ return;
+ }
- IFunction_sptr outputFunc = m_singleFitAlg->getProperty("Function");
+ IFunction_sptr outputFunc = m_singleFitAlg->getProperty("Function");
- // Get params.
- QMap<QString,double> parameters;
- std::vector<std::string> parNames = outputFunc->getParameterNames();
- std::vector<double> parVals;
+ // Get params.
+ QMap<QString, double> parameters;
+ std::vector<std::string> parNames = outputFunc->getParameterNames();
+ std::vector<double> parVals;
- for( size_t i = 0; i < parNames.size(); ++i )
- parVals.push_back(outputFunc->getParameter(parNames[i]));
+ for (size_t i = 0; i < parNames.size(); ++i)
+ parVals.push_back(outputFunc->getParameter(parNames[i]));
- for ( size_t i = 0; i < parNames.size(); ++i )
- parameters[QString(parNames[i].c_str())] = parVals[i];
+ for (size_t i = 0; i < parNames.size(); ++i)
+ parameters[QString(parNames[i].c_str())] = parVals[i];
- m_ffRangeManager->setValue(m_properties["BackgroundA0"], parameters["f0.A0"]);
+ m_ffRangeManager->setValue(m_properties["BackgroundA0"], parameters["f0.A0"]);
- const int fitType = m_uiForm.cbFitType->currentIndex();
- if ( fitType != 2 )
- {
- // Exp 1
- m_dblManager->setValue(m_properties["Exponential1.Intensity"], parameters["f1.Intensity"]);
- m_dblManager->setValue(m_properties["Exponential1.Tau"], parameters["f1.Tau"]);
+ const int fitType = m_uiForm.cbFitType->currentIndex();
+ if (fitType != 2) {
+ // Exp 1
+ m_dblManager->setValue(m_properties["Exponential1.Intensity"],
+ parameters["f1.Intensity"]);
+ m_dblManager->setValue(m_properties["Exponential1.Tau"],
+ parameters["f1.Tau"]);
- if ( fitType == 1 )
- {
- // Exp 2
- m_dblManager->setValue(m_properties["Exponential2.Intensity"], parameters["f2.Intensity"]);
- m_dblManager->setValue(m_properties["Exponential2.Tau"], parameters["f2.Tau"]);
- }
+ if (fitType == 1) {
+ // Exp 2
+ m_dblManager->setValue(m_properties["Exponential2.Intensity"],
+ parameters["f2.Intensity"]);
+ m_dblManager->setValue(m_properties["Exponential2.Tau"],
+ parameters["f2.Tau"]);
}
+ }
- if ( fitType > 1 )
- {
- // Str
- QString fval;
- if ( fitType == 2 ) { fval = "f1."; }
- else { fval = "f2."; }
-
- m_dblManager->setValue(m_properties["StretchedExp.Intensity"], parameters[fval+"Intensity"]);
- m_dblManager->setValue(m_properties["StretchedExp.Tau"], parameters[fval+"Tau"]);
- m_dblManager->setValue(m_properties["StretchedExp.Beta"], parameters[fval+"Beta"]);
+ if (fitType > 1) {
+ // Str
+ QString fval;
+ if (fitType == 2) {
+ fval = "f1.";
+ } else {
+ fval = "f2.";
}
- // Can start upddating the guess curve again
- connect(m_dblManager, SIGNAL(propertyChanged(QtProperty*)), this, SLOT(plotGuess(QtProperty*)));
-
- // Plot the guess first so that it is under the fit
- plotGuess(NULL);
- // Now show the fitted curve of the mini plot
- m_uiForm.ppPlot->addSpectrum("Fit", m_singleFitOutputName + "_Workspace", 1, Qt::red);
-
- m_pythonExportWsName = "";
+ m_dblManager->setValue(m_properties["StretchedExp.Intensity"],
+ parameters[fval + "Intensity"]);
+ m_dblManager->setValue(m_properties["StretchedExp.Tau"],
+ parameters[fval + "Tau"]);
+ m_dblManager->setValue(m_properties["StretchedExp.Beta"],
+ parameters[fval + "Beta"]);
}
- void IqtFit::plotGuess(QtProperty*)
- {
- // Do nothing if there is no sample data curve
- if(!m_uiForm.ppPlot->hasCurve("Sample"))
- return;
+ // Can start upddating the guess curve again
+ connect(m_dblManager, SIGNAL(propertyChanged(QtProperty *)), this,
+ SLOT(plotGuess(QtProperty *)));
- CompositeFunction_sptr function = createFunction(true);
+ // Plot the guess first so that it is under the fit
+ plotGuess(NULL);
+ // Now show the fitted curve of the mini plot
+ m_uiForm.ppPlot->addSpectrum("Fit", m_singleFitOutputName + "_Workspace", 1,
+ Qt::red);
- // Create the double* array from the input workspace
- const size_t binIndxLow = m_ffInputWS->binIndexOf(m_ffRangeManager->value(m_properties["StartX"]));
- const size_t binIndxHigh = m_ffInputWS->binIndexOf(m_ffRangeManager->value(m_properties["EndX"]));
- const size_t nData = binIndxHigh - binIndxLow;
+ m_pythonExportWsName = "";
+}
- std::vector<double> inputXData(nData);
+void IqtFit::plotGuess(QtProperty *) {
+ // Do nothing if there is no sample data curve
+ if (!m_uiForm.ppPlot->hasCurve("Sample"))
+ return;
- const Mantid::MantidVec& XValues = m_ffInputWS->readX(0);
+ CompositeFunction_sptr function = createFunction(true);
- const bool isHistogram = m_ffInputWS->isHistogramData();
+ // Create the double* array from the input workspace
+ const size_t binIndxLow =
+ m_ffInputWS->binIndexOf(m_ffRangeManager->value(m_properties["StartX"]));
+ const size_t binIndxHigh =
+ m_ffInputWS->binIndexOf(m_ffRangeManager->value(m_properties["EndX"]));
+ const size_t nData = binIndxHigh - binIndxLow;
- for ( size_t i = 0; i < nData ; i++ )
- {
- if ( isHistogram )
- inputXData[i] = 0.5*(XValues[binIndxLow+i]+XValues[binIndxLow+i+1]);
- else
- inputXData[i] = XValues[binIndxLow+i];
- }
+ std::vector<double> inputXData(nData);
- FunctionDomain1DVector domain(inputXData);
- FunctionValues outputData(domain);
- function->function(domain, outputData);
+ const Mantid::MantidVec &XValues = m_ffInputWS->readX(0);
- QVector<double> dataX;
- QVector<double> dataY;
+ const bool isHistogram = m_ffInputWS->isHistogramData();
- for ( size_t i = 0; i < nData; i++ )
- {
- dataX.append(inputXData[i]);
- dataY.append(outputData.getCalculated(i));
- }
- IAlgorithm_sptr createWsAlg = AlgorithmManager::Instance().create("CreateWorkspace");
- createWsAlg->initialize();
- createWsAlg->setChild(true);
- createWsAlg->setLogging(false);
- createWsAlg->setProperty("OutputWorkspace", "__GuessAnon");
- createWsAlg->setProperty("NSpec", 1);
- createWsAlg->setProperty("DataX", dataX.toStdVector());
- createWsAlg->setProperty("DataY", dataY.toStdVector());
- createWsAlg->execute();
- MatrixWorkspace_sptr guessWs = createWsAlg->getProperty("OutputWorkspace");
-
- m_uiForm.ppPlot->addSpectrum("Guess", guessWs, 0, Qt::green);
+ for (size_t i = 0; i < nData; i++) {
+ if (isHistogram)
+ inputXData[i] =
+ 0.5 * (XValues[binIndxLow + i] + XValues[binIndxLow + i + 1]);
+ else
+ inputXData[i] = XValues[binIndxLow + i];
}
- void IqtFit::fitContextMenu(const QPoint &)
- {
- QtBrowserItem* item(NULL);
+ FunctionDomain1DVector domain(inputXData);
+ FunctionValues outputData(domain);
+ function->function(domain, outputData);
- item = m_ffTree->currentItem();
+ QVector<double> dataX;
+ QVector<double> dataY;
- if ( ! item )
- return;
+ for (size_t i = 0; i < nData; i++) {
+ dataX.append(inputXData[i]);
+ dataY.append(outputData.getCalculated(i));
+ }
+ IAlgorithm_sptr createWsAlg =
+ AlgorithmManager::Instance().create("CreateWorkspace");
+ createWsAlg->initialize();
+ createWsAlg->setChild(true);
+ createWsAlg->setLogging(false);
+ createWsAlg->setProperty("OutputWorkspace", "__GuessAnon");
+ createWsAlg->setProperty("NSpec", 1);
+ createWsAlg->setProperty("DataX", dataX.toStdVector());
+ createWsAlg->setProperty("DataY", dataY.toStdVector());
+ createWsAlg->execute();
+ MatrixWorkspace_sptr guessWs = createWsAlg->getProperty("OutputWorkspace");
+
+ m_uiForm.ppPlot->addSpectrum("Guess", guessWs, 0, Qt::green);
+}
- // is it a fit property ?
- QtProperty* prop = item->property();
+void IqtFit::fitContextMenu(const QPoint &) {
+ QtBrowserItem *item(NULL);
- // is it already fixed?
- bool fixed = prop->propertyManager() != m_dblManager;
+ item = m_ffTree->currentItem();
- if ( fixed && prop->propertyManager() != m_stringManager )
- return;
+ if (!item)
+ return;
- // Create the menu
- QMenu* menu = new QMenu("IqtFit", m_ffTree);
- QAction* action;
+ // is it a fit property ?
+ QtProperty *prop = item->property();
- if ( ! fixed )
- {
- action = new QAction("Fix", m_parentWidget);
- connect(action, SIGNAL(triggered()), this, SLOT(fixItem()));
- }
- else
- {
- action = new QAction("Remove Fix", m_parentWidget);
- connect(action, SIGNAL(triggered()), this, SLOT(unFixItem()));
- }
+ // is it already fixed?
+ bool fixed = prop->propertyManager() != m_dblManager;
- menu->addAction(action);
+ if (fixed && prop->propertyManager() != m_stringManager)
+ return;
- // Show the menu
- menu->popup(QCursor::pos());
+ // Create the menu
+ QMenu *menu = new QMenu("IqtFit", m_ffTree);
+ QAction *action;
+
+ if (!fixed) {
+ action = new QAction("Fix", m_parentWidget);
+ connect(action, SIGNAL(triggered()), this, SLOT(fixItem()));
+ } else {
+ action = new QAction("Remove Fix", m_parentWidget);
+ connect(action, SIGNAL(triggered()), this, SLOT(unFixItem()));
}
- void IqtFit::fixItem()
- {
- QtBrowserItem* item = m_ffTree->currentItem();
+ menu->addAction(action);
- // Determine what the property is.
- QtProperty* prop = item->property();
+ // Show the menu
+ menu->popup(QCursor::pos());
+}
- QtProperty* fixedProp = m_stringManager->addProperty( prop->propertyName() );
- QtProperty* fprlbl = m_stringManager->addProperty("Fixed");
- fixedProp->addSubProperty(fprlbl);
- m_stringManager->setValue(fixedProp, prop->valueText());
+void IqtFit::fixItem() {
+ QtBrowserItem *item = m_ffTree->currentItem();
- item->parent()->property()->addSubProperty(fixedProp);
- m_fixedProps[fixedProp] = prop;
- item->parent()->property()->removeSubProperty(prop);
- }
+ // Determine what the property is.
+ QtProperty *prop = item->property();
- void IqtFit::unFixItem()
- {
- QtBrowserItem* item = m_ffTree->currentItem();
+ QtProperty *fixedProp = m_stringManager->addProperty(prop->propertyName());
+ QtProperty *fprlbl = m_stringManager->addProperty("Fixed");
+ fixedProp->addSubProperty(fprlbl);
+ m_stringManager->setValue(fixedProp, prop->valueText());
- QtProperty* prop = item->property();
- if ( prop->subProperties().empty() )
- {
- item = item->parent();
- prop = item->property();
- }
+ item->parent()->property()->addSubProperty(fixedProp);
+ m_fixedProps[fixedProp] = prop;
+ item->parent()->property()->removeSubProperty(prop);
+}
+
+void IqtFit::unFixItem() {
+ QtBrowserItem *item = m_ffTree->currentItem();
- item->parent()->property()->addSubProperty(m_fixedProps[prop]);
- item->parent()->property()->removeSubProperty(prop);
- m_fixedProps.remove(prop);
- QtProperty* proplbl = prop->subProperties()[0];
- delete proplbl;
- delete prop;
+ QtProperty *prop = item->property();
+ if (prop->subProperties().empty()) {
+ item = item->parent();
+ prop = item->property();
}
+ item->parent()->property()->addSubProperty(m_fixedProps[prop]);
+ item->parent()->property()->removeSubProperty(prop);
+ m_fixedProps.remove(prop);
+ QtProperty *proplbl = prop->subProperties()[0];
+ delete proplbl;
+ delete prop;
+}
+
} // namespace IDA
} // namespace CustomInterfaces
} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp b/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp
index db18d7446223cff9a200a74af6b1c3b7d576843c..8df7976a765664a6cc7bd659a8c9cd7924592c82 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp
@@ -112,6 +112,7 @@ void ResNorm::run() {
resNorm->setProperty("EnergyMax", eMax);
resNorm->setProperty("CreateOutput", true);
resNorm->setProperty("OutputWorkspace", outputWsName.toStdString());
+ resNorm->setProperty("OutputWorkspaceTable", (outputWsName + "_Fit").toStdString());
m_batchAlgoRunner->addAlgorithm(resNorm);
// Handle saving
diff --git a/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp b/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp
index a52e8a9ea46656ce5503523ea3af0e8a01bf2846..f70fe204e98fc0c6d7dd30b80c2caff417715d33 100644
--- a/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp
+++ b/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp
@@ -31,6 +31,7 @@ namespace CustomInterfaces
ALCInterface::ALCInterface(QWidget* parent)
: UserSubWindow(parent), m_ui(),
+ m_baselineModellingView(NULL), m_peakFittingView(NULL),
m_dataLoading(NULL), m_baselineModelling(NULL), m_peakFitting(NULL),
m_baselineModellingModel(new ALCBaselineModellingModel()),
m_peakFittingModel(new ALCPeakFittingModel())
diff --git a/MantidQt/CustomInterfaces/src/QtReflMainView.cpp b/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
index a2c94562df9b0f759051ea6d4a835b49f4ab67b0..7e2e98744f4fd4d7bac53712c2f43c88f9bd4a91 100644
--- a/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
+++ b/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
@@ -8,6 +8,12 @@
#include <qinputdialog.h>
#include <qmessagebox.h>
+
+namespace
+{
+ const QString ReflSettingsGroup = "Mantid/CustomInterfaces/ISISReflectometry";
+}
+
namespace MantidQt
{
namespace CustomInterfaces
@@ -434,6 +440,44 @@ namespace MantidQt
runPythonCode(QString::fromStdString(pythonSrc.str()));
}
+ /**
+ Show the user file dialog to choose save location of notebook
+ */
+ std::string QtReflMainView::requestNotebookPath()
+ {
+ QString qfilename = QFileDialog::getSaveFileName(0, "Save notebook file", QDir::currentPath(),
+ "IPython Notebook files (*.ipynb);;All files (*.*)",
+ new QString("IPython Notebook files (*.ipynb)"));
+ return qfilename.toStdString();
+ }
+
+ /**
+ Save settings
+ @param options : map of user options to save
+ */
+ void QtReflMainView::saveSettings(const std::map<std::string,QVariant>& options)
+ {
+ QSettings settings;
+ settings.beginGroup(ReflSettingsGroup);
+ for(auto it = options.begin(); it != options.end(); ++it)
+ settings.setValue(QString::fromStdString(it->first), it->second);
+ settings.endGroup();
+ }
+
+ /**
+ Load settings
+ @param options : map of user options to load into
+ */
+ void QtReflMainView::loadSettings(std::map<std::string,QVariant>& options)
+ {
+ QSettings settings;
+ settings.beginGroup(ReflSettingsGroup);
+ QStringList keys = settings.childKeys();
+ for(auto it = keys.begin(); it != keys.end(); ++it)
+ options[it->toStdString()] = settings.value(*it);
+ settings.endGroup();
+ }
+
/**
Plot a workspace
*/
diff --git a/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
index 8b813d6392f361ddceaef1748a5cf1a5cec4e2eb..9323fb9b10cc1e91839a520a0f17ac3b65a302f9 100644
--- a/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
+++ b/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
@@ -24,9 +24,6 @@
#include <fstream>
#include <sstream>
-#include <QSettings>
-#include <QFileDialog>
-
using namespace Mantid::API;
using namespace Mantid::Geometry;
@@ -36,7 +33,6 @@ using namespace MantidQt::MantidWidgets;
namespace
{
- const QString ReflSettingsGroup = "Mantid/CustomInterfaces/ISISReflectometry";
void validateModel(ITableWorkspace_sptr model)
{
@@ -295,16 +291,15 @@ namespace MantidQt
*/
void ReflMainViewPresenter::saveNotebook(std::map<int,std::set<int>> groups, std::set<int> rows)
{
- std::unique_ptr<ReflGenerateNotebook> notebook(new ReflGenerateNotebook(
- m_wsName, m_model, m_view->getProcessInstrument(), COL_RUNS, COL_TRANSMISSION, COL_OPTIONS, COL_ANGLE,
- COL_QMIN, COL_QMAX, COL_DQQ, COL_SCALE, COL_GROUP));
- QString qfilename = QFileDialog::getSaveFileName(0, "Save notebook file", QDir::currentPath(),
- "IPython Notebook files (*.ipynb);;All files (*.*)",
- new QString("IPython Notebook files (*.ipynb)"));
- std::string filename = qfilename.toStdString();
+
+ std::string filename = m_view->requestNotebookPath();
if (filename == "") {
return;
}
+
+ std::unique_ptr<ReflGenerateNotebook> notebook(new ReflGenerateNotebook(
+ m_wsName, m_model, m_view->getProcessInstrument(), COL_RUNS, COL_TRANSMISSION, COL_OPTIONS, COL_ANGLE,
+ COL_QMIN, COL_QMAX, COL_DQQ, COL_SCALE, COL_GROUP));
std::string generatedNotebook = notebook->generateNotebook(groups, rows);
std::ofstream file(filename.c_str(), std::ofstream::trunc);
@@ -1512,11 +1507,7 @@ namespace MantidQt
m_options[it->first] = it->second;
//Save any changes to disk
- QSettings settings;
- settings.beginGroup(ReflSettingsGroup);
- for(auto it = m_options.begin(); it != m_options.end(); ++it)
- settings.setValue(QString::fromStdString(it->first), it->second);
- settings.endGroup();
+ m_view->saveSettings(m_options);
}
/** Load options from disk if possible, or set to defaults */
@@ -1538,12 +1529,7 @@ namespace MantidQt
m_options["RoundDQQPrecision"] = 3;
//Load saved values from disk
- QSettings settings;
- settings.beginGroup(ReflSettingsGroup);
- QStringList keys = settings.childKeys();
- for(auto it = keys.begin(); it != keys.end(); ++it)
- m_options[it->toStdString()] = settings.value(*it);
- settings.endGroup();
+ m_view->loadSettings(m_options);
}
}
}
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp b/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
index 60d8a1e2bd0dbc8a26e01cb9dcae0898e0a27395..b343d7c20876fa95bda014ff49ed75407ab2daaf 100644
--- a/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
+++ b/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
@@ -5,9 +5,7 @@ using namespace MantidQt::CustomInterfaces;
namespace MantidQt {
namespace CustomInterfaces {
-ImageStackPreParams::ImageStackPreParams()
-{
+ImageStackPreParams::ImageStackPreParams() : medianFilter(false) {}
-}
} // namespace CustomInterfaces
} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
index 15c9f4550e6d57228cd464e6c3cb350e47c23449..5aaaaccde66a10647182a685e42fefe0ca5570aa 100644
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
+++ b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
@@ -582,7 +582,6 @@ TomographyIfaceModel::loadFITSImage(const std::string &path) {
"Failed to load image. Could not load this file as a "
"FITS image: " +
std::string(e.what()));
- return WorkspaceGroup_sptr();
}
if (!alg->isExecuted()) {
throw std::runtime_error(
diff --git a/MantidQt/CustomInterfaces/test/EnggDiffractionPresenterTest.h b/MantidQt/CustomInterfaces/test/EnggDiffractionPresenterTest.h
index 043aba68ed970e70f14f1dd292e947a3ddcf03a6..6a83147a7069e733967abf8766e7cce520a39664 100644
--- a/MantidQt/CustomInterfaces/test/EnggDiffractionPresenterTest.h
+++ b/MantidQt/CustomInterfaces/test/EnggDiffractionPresenterTest.h
@@ -385,6 +385,8 @@ public:
// check automatic plotting
EXPECT_CALL(mockView, focusedOutWorkspace()).Times(1).WillOnce(Return(true));
EXPECT_CALL(mockView, plotFocusedSpectrum(testing::_)).Times(1);
+ // There are two/three other tests that have the disabled_ prefix so they
+ // normally run
// Should not try to use options for other types of focusing
EXPECT_CALL(mockView, focusingCroppedRunNo()).Times(0);
diff --git a/MantidQt/CustomInterfaces/test/EnggDiffractionViewMock.h b/MantidQt/CustomInterfaces/test/EnggDiffractionViewMock.h
index 36c5bdd0a65a6a4d027c6a2f19146fc64ec9bf73..3f099eb845d1bcddcc1e9ca3c33c41e3eece692e 100644
--- a/MantidQt/CustomInterfaces/test/EnggDiffractionViewMock.h
+++ b/MantidQt/CustomInterfaces/test/EnggDiffractionViewMock.h
@@ -50,6 +50,9 @@ public:
// virtual std::string currentCalibFile() const;
MOCK_CONST_METHOD0(currentCalibFile, std::string());
+ // std::string currentPlotType
+ MOCK_CONST_METHOD0(currentPlotType, int());
+
// virtual std::string newVanadiumNo() const;
MOCK_CONST_METHOD0(newVanadiumNo, std::string());
@@ -104,8 +107,25 @@ public:
// void saveSettings() const;
MOCK_CONST_METHOD0(saveSettings, void());
+ // std::string saveOutputFiles
+ MOCK_CONST_METHOD0(saveOutputFiles, bool());
+
// virtual void plotFocusedSpectrum();
- MOCK_METHOD1(plotFocusedSpectrum, void(const std::string&));
+ MOCK_METHOD1(plotFocusedSpectrum, void(const std::string &));
+
+ // void plotFocusStatus();
+ MOCK_METHOD0(plotFocusStatus, void());
+
+ // void plotRepChanged();
+ MOCK_METHOD1(plotRepChanged, void(int idx));
+
+ // virtual void plotWaterfallSpectrum
+ MOCK_METHOD1(plotWaterfallSpectrum, void(const std::string &wsName));
+
+ // virtual void plotReplacingWindow
+ MOCK_METHOD1(plotReplacingWindow, void(const std::string &wsName));
+
+
};
#endif // MANTID_CUSTOMINTERFACES_ENGGDIFFRACTIONVIEWMOCK_H
diff --git a/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h b/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
index 2d7f91d24a4c10c40bf3b3b3eb28cd15585c7b90..e42a5a70d0bc573e435fb47faf22d0f7b0a6a2b6 100644
--- a/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
+++ b/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
@@ -33,6 +33,7 @@ public:
MOCK_METHOD2(giveUserCritical, void(std::string, std::string));
MOCK_METHOD2(giveUserInfo, void(std::string, std::string));
MOCK_METHOD2(giveUserWarning, void(std::string, std::string));
+ MOCK_METHOD0(requestNotebookPath, std::string());
MOCK_METHOD1(showAlgorithmDialog, void(const std::string&));
MOCK_METHOD1(plotWorkspaces, void(const std::set<std::string>&));
@@ -46,6 +47,7 @@ public:
MOCK_CONST_METHOD0(getClipboard, std::string());
MOCK_CONST_METHOD0(getSearchString, std::string());
MOCK_CONST_METHOD0(getSearchInstrument, std::string());
+ MOCK_METHOD0(getEnableNotebook, bool());
//Calls we don't care about
virtual void showTable(QReflTableModel_sptr) {};
@@ -53,9 +55,10 @@ public:
virtual void setOptionsHintStrategy(MantidQt::MantidWidgets::HintStrategy*) {};
virtual void setProgressRange(int,int) {};
virtual void setProgress(int) {};
- virtual bool getEnableNotebook() {return false;};
virtual void setTableList(const std::set<std::string>&) {};
virtual void setInstrumentList(const std::vector<std::string>&, const std::string&) {};
+ virtual void saveSettings(const std::map<std::string,QVariant>&) {};
+ virtual void loadSettings(std::map<std::string,QVariant>&) {};
virtual std::string getProcessInstrument() const {return "FAKE";}
virtual boost::shared_ptr<IReflPresenter> getPresenter() const {return boost::shared_ptr<IReflPresenter>();}
};
diff --git a/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h b/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h
index 4c53fb56bf68c8693e9933f650f7aa5440c18545..36d043f921e47425dc4ed88c241c0207f61cee26 100644
--- a/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h
+++ b/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h
@@ -13,6 +13,7 @@
#include "MantidQtCustomInterfaces/ReflMainViewPresenter.h"
#include "ReflMainViewMockObjects.h"
+#include "../inc/MantidQtCustomInterfaces/IReflPresenter.h"
using namespace MantidQt::CustomInterfaces;
using namespace Mantid::API;
@@ -136,6 +137,8 @@ public:
TS_ASSERT(AnalysisDataService::Instance().doesExist("TestWorkspace"));
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testSaveExisting() {
@@ -152,6 +155,8 @@ public:
presenter.notify(IReflPresenter::SaveFlag);
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testSaveAs() {
@@ -180,6 +185,8 @@ public:
AnalysisDataService::Instance().remove("TestWorkspace");
AnalysisDataService::Instance().remove("Workspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testAppendRow() {
@@ -220,6 +227,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testAppendRowSpecify() {
@@ -263,6 +272,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testAppendRowSpecifyPlural() {
@@ -305,6 +316,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPrependRow() {
@@ -344,6 +357,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPrependRowSpecify() {
@@ -386,6 +401,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPrependRowSpecifyPlural() {
@@ -429,6 +446,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testDeleteRowNone() {
@@ -460,6 +479,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testDeleteRowSingle() {
@@ -495,6 +516,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testDeleteRowPlural() {
@@ -533,6 +556,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testProcess() {
@@ -559,6 +584,11 @@ public:
EXPECT_CALL(mockView, getSelectedRows())
.Times(1)
.WillRepeatedly(Return(rowlist));
+ EXPECT_CALL(mockView, getEnableNotebook())
+ .Times(1)
+ .WillRepeatedly(Return(false));
+ EXPECT_CALL(mockView, requestNotebookPath())
+ .Times(0);
presenter.notify(IReflPresenter::ProcessFlag);
// Check output workspaces were created as expected
@@ -579,6 +609,52 @@ public:
AnalysisDataService::Instance().remove("IvsLam_12346");
AnalysisDataService::Instance().remove("TOF_12346");
AnalysisDataService::Instance().remove("IvsQ_12345_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
+ }
+
+ void testProcessWithNotebook() {
+ MockView mockView;
+ ReflMainViewPresenter presenter(&mockView);
+
+ createPrefilledWorkspace("TestWorkspace");
+ EXPECT_CALL(mockView, getWorkspaceToOpen())
+ .Times(1)
+ .WillRepeatedly(Return("TestWorkspace"));
+ presenter.notify(IReflPresenter::OpenTableFlag);
+
+ std::set<int> rowlist;
+ rowlist.insert(0);
+ rowlist.insert(1);
+
+ createTOFWorkspace("TOF_12345", "12345");
+ createTOFWorkspace("TOF_12346", "12346");
+
+ // We should not receive any errors
+ EXPECT_CALL(mockView, giveUserCritical(_, _)).Times(0);
+
+ // The user hits the "process" button with the first two rows selected
+ EXPECT_CALL(mockView, getSelectedRows())
+ .Times(1)
+ .WillRepeatedly(Return(rowlist));
+ EXPECT_CALL(mockView, getEnableNotebook())
+ .Times(1)
+ .WillRepeatedly(Return(true));
+ EXPECT_CALL(mockView, requestNotebookPath())
+ .Times(1);
+ presenter.notify(IReflPresenter::ProcessFlag);
+
+ // Tidy up
+ AnalysisDataService::Instance().remove("TestWorkspace");
+ AnalysisDataService::Instance().remove("IvsQ_12345");
+ AnalysisDataService::Instance().remove("IvsLam_12345");
+ AnalysisDataService::Instance().remove("TOF_12345");
+ AnalysisDataService::Instance().remove("IvsQ_12346");
+ AnalysisDataService::Instance().remove("IvsLam_12346");
+ AnalysisDataService::Instance().remove("TOF_12346");
+ AnalysisDataService::Instance().remove("IvsQ_12345_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
/*
@@ -641,6 +717,8 @@ public:
AnalysisDataService::Instance().remove("IvsQ_12346");
AnalysisDataService::Instance().remove("IvsLam_12346");
AnalysisDataService::Instance().remove("IvsQ_dataA_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testBadWorkspaceType() {
@@ -671,6 +749,8 @@ public:
presenter.notify(IReflPresenter::OpenTableFlag);
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testBadWorkspaceLength() {
@@ -705,6 +785,8 @@ public:
presenter.notify(IReflPresenter::OpenTableFlag);
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveAfterAppendRow() {
@@ -732,6 +814,8 @@ public:
// The user tries to create a new table again, and does not get bothered
EXPECT_CALL(mockView, askUserYesNo(_, _)).Times(0);
presenter.notify(IReflPresenter::NewTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveAfterDeleteRow() {
@@ -771,6 +855,8 @@ public:
// The user tries to create a new table again, and does not get bothered
EXPECT_CALL(mockView, askUserYesNo(_, _)).Times(0);
presenter.notify(IReflPresenter::NewTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveAndDiscard() {
@@ -791,6 +877,8 @@ public:
// These next two times they don't get prompted - they have a new table
presenter.notify(IReflPresenter::NewTableFlag);
presenter.notify(IReflPresenter::NewTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveOnOpen() {
@@ -823,6 +911,8 @@ public:
.WillRepeatedly(Return("TestWorkspace"));
EXPECT_CALL(mockView, askUserYesNo(_, _)).Times(0);
presenter.notify(IReflPresenter::OpenTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testExpandSelection() {
@@ -984,6 +1074,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testClearRows() {
@@ -1043,6 +1135,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCopyRow() {
@@ -1066,6 +1160,8 @@ public:
.Times(1)
.WillRepeatedly(Return(rowlist));
presenter.notify(IReflPresenter::CopySelectedFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCopyRows() {
@@ -1095,6 +1191,8 @@ public:
.Times(1)
.WillRepeatedly(Return(rowlist));
presenter.notify(IReflPresenter::CopySelectedFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCutRow() {
@@ -1129,6 +1227,8 @@ public:
TS_ASSERT_EQUALS(ws->String(0, RunCol), "12345");
TS_ASSERT_EQUALS(ws->String(1, RunCol), "24681");
TS_ASSERT_EQUALS(ws->String(2, RunCol), "24682");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCutRows() {
@@ -1165,6 +1265,8 @@ public:
TS_ASSERT_EQUALS(ws->rowCount(), 1);
// Check the only unselected row is left behind
TS_ASSERT_EQUALS(ws->String(0, RunCol), "24682");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteRow() {
@@ -1212,6 +1314,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(1, ScaleCol), 5.0);
TS_ASSERT_EQUALS(ws->Int(1, GroupCol), 6);
TS_ASSERT_EQUALS(ws->String(1, OptionsCol), "abc");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteNewRow() {
@@ -1257,6 +1361,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(4, ScaleCol), 5.0);
TS_ASSERT_EQUALS(ws->Int(4, GroupCol), 6);
TS_ASSERT_EQUALS(ws->String(4, OptionsCol), "abc");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteRows() {
@@ -1315,6 +1421,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(2, ScaleCol), 3.0);
TS_ASSERT_EQUALS(ws->Int(2, GroupCol), 2);
TS_ASSERT_EQUALS(ws->String(2, OptionsCol), "def");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteNewRows() {
@@ -1371,6 +1479,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(5, ScaleCol), 3.0);
TS_ASSERT_EQUALS(ws->Int(5, GroupCol), 2);
TS_ASSERT_EQUALS(ws->String(5, OptionsCol), "def");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testImportTable() {
@@ -1378,6 +1488,8 @@ public:
ReflMainViewPresenter presenter(&mockView);
EXPECT_CALL(mockView, showAlgorithmDialog("LoadReflTBL"));
presenter.notify(IReflPresenter::ImportTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testExportTable() {
@@ -1385,6 +1497,8 @@ public:
ReflMainViewPresenter presenter(&mockView);
EXPECT_CALL(mockView, showAlgorithmDialog("SaveReflTBL"));
presenter.notify(IReflPresenter::ExportTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPlotRowWarn() {
@@ -1416,6 +1530,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
AnalysisDataService::Instance().remove("TOF_12345");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPlotGroupWarn() {
@@ -1447,6 +1563,8 @@ public:
AnalysisDataService::Instance().remove("TestWorkspace");
AnalysisDataService::Instance().remove("TOF_12345");
AnalysisDataService::Instance().remove("TOF_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
};
diff --git a/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h b/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h
index 87c698152d416147984d697f1388586bcfcbb8c6..c9ed1e70dcc5161d9133979b1a95a8ff6dcd466e 100644
--- a/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h
+++ b/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h
@@ -296,6 +296,8 @@ protected slots:
void parameterChanged(QtProperty*);
void parameterButtonClicked(QtProperty*);
void globalChanged(QtProperty*, const QString&, bool);
+ /// Set value of an attribute (as a property) to a function
+ void setAttributeToFunction(Mantid::API::IFunction& fun, QtProperty* prop);
protected:
/// Manager for function group properties
diff --git a/MantidQt/MantidWidgets/src/FunctionBrowser.cpp b/MantidQt/MantidWidgets/src/FunctionBrowser.cpp
index edd8806fe5a7c6193b98df76b252a8d114346712..4184cc459586d37d77b198d246ceac180de1eab4 100644
--- a/MantidQt/MantidWidgets/src/FunctionBrowser.cpp
+++ b/MantidQt/MantidWidgets/src/FunctionBrowser.cpp
@@ -1348,6 +1348,28 @@ void FunctionBrowser::addFunction()
emit functionStructureChanged();
}
+/**
+ * Set value of an attribute (as a property) to a function.
+ * @param fun :: Function to which attribute is set.
+ * @param prop :: A property with the name and value of the attribute.
+ */
+void FunctionBrowser::setAttributeToFunction(Mantid::API::IFunction& fun, QtProperty* prop)
+{
+ std::string attName = prop->propertyName().toStdString();
+ SetAttributeFromProperty setter(this,prop);
+ Mantid::API::IFunction::Attribute attr = fun.getAttribute(attName);
+ attr.apply(setter);
+ try
+ {
+ fun.setAttribute(attName,attr);
+ }
+ catch(std::exception& expt)
+ {
+ QMessageBox::critical(this,"MantidPlot - Error", "Cannot set attribute " + QString::fromStdString(attName) +
+ " of function " + prop->propertyName() + ":\n\n" + QString::fromStdString(expt.what()));
+ }
+}
+
/**
* Return the function
* @param prop :: Function property
@@ -1380,6 +1402,10 @@ Mantid::API::IFunction_sptr FunctionBrowser::getFunction(QtProperty* prop, bool
cf->addFunction(f);
}
}
+ else if (isAttribute(child))
+ {
+ setAttributeToFunction(*fun, child);
+ }
}
}
else
@@ -1390,19 +1416,7 @@ Mantid::API::IFunction_sptr FunctionBrowser::getFunction(QtProperty* prop, bool
{
if (isAttribute(child))
{
- std::string attName = child->propertyName().toStdString();
- SetAttributeFromProperty setter(this,child);
- Mantid::API::IFunction::Attribute attr = fun->getAttribute(attName);
- attr.apply(setter);
- try
- {
- fun->setAttribute(attName,attr);
- }
- catch(std::exception& expt)
- {
- QMessageBox::critical(this,"MantidPlot - Error", "Cannot set attribute " + QString::fromStdString(attName) +
- " of function " + prop->propertyName() + ":\n\n" + QString::fromStdString(expt.what()));
- }
+ setAttributeToFunction(*fun, child);
}
else if (!attributesOnly && isParameter(child))
{
diff --git a/MantidQt/Python/mantidqt.sip b/MantidQt/Python/mantidqt.sip
index 47824677bf3e1bcd8e3a02a951fbbfa38afd5ad5..8278d788941a600a84f1dd6cc448d1fde138bc8f 100644
--- a/MantidQt/Python/mantidqt.sip
+++ b/MantidQt/Python/mantidqt.sip
@@ -1171,9 +1171,9 @@ void SliceViewer::setRebinNumBins(int xBins, int yBins)
%End
- void setRebinMode(bool mode, bool locked) throw (std::runtime_error);
+ void setRebinMode(bool mode) throw (std::runtime_error);
%Docstring
-void SliceViewer::setRebinMode(bool mode, bool locked)
+void SliceViewer::setRebinMode(bool mode)
------------------------------------------------------
Sets the SliceViewer in dynamic rebin mode.
In this mode, the current view area (see setXYLimits()) is used as the
@@ -1183,8 +1183,6 @@ void SliceViewer::setRebinMode(bool mode, bool locked)
Args:
mode :: true for rebinning mode
- locked :: if true, then the rebinned area is only refreshed manually
- or when changing rebinning parameters.
%End
diff --git a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h
index f2eded1e2fa66061992d0583adf13527708f6afc..75014b4c584c09308350b1e6a85956cc64fa9d8a 100644
--- a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h
+++ b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h
@@ -117,7 +117,7 @@ public:
/// Dynamic Rebinning-related Python bindings
void setRebinThickness(int dim, double thickness);
void setRebinNumBins(int xBins, int yBins);
- void setRebinMode(bool mode, bool locked);
+ void setRebinMode(bool mode);
void refreshRebin();
/// Methods relating to peaks overlays.
@@ -188,7 +188,6 @@ public slots:
void LineMode_toggled(bool);
void SnapToGrid_toggled(bool);
void RebinMode_toggled(bool);
- void RebinLock_toggled(bool);
void autoRebin_toggled(bool);
// Dynamic rebinning
@@ -333,7 +332,7 @@ private:
/// Synced menu/buttons
MantidQt::API::SyncedCheckboxes *m_syncLineMode, *m_syncSnapToGrid,
- *m_syncRebinMode, *m_syncRebinLock, *m_syncAutoRebin;
+ *m_syncRebinMode, *m_syncAutoRebin;
/// Cached double for infinity
double m_inf;
diff --git a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui
index 9414476bc32f0f92da829ed186475e2fdcb485cb..d3b64c0df10eab853bd8fcc3abe0e5fe74e5c353 100644
--- a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui
+++ b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui
@@ -489,47 +489,6 @@
</property>
</widget>
</item>
- <item>
- <widget class="QToolButton" name="btnRebinLock">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimumSize">
- <size>
- <width>45</width>
- <height>45</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>45</width>
- <height>45</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Lock the rebinned workspace in place (use the refresh button to refresh)</string>
- </property>
- <property name="text">
- <string>...</string>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>:/SliceViewer/icons/stock-lock.png</normaloff>:/SliceViewer/icons/stock-lock.png</iconset>
- </property>
- <property name="iconSize">
- <size>
- <width>32</width>
- <height>32</height>
- </size>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
<item>
<spacer name="horizontalSpacer_5">
<property name="orientation">
diff --git a/MantidQt/SliceViewer/src/PeaksViewer.cpp b/MantidQt/SliceViewer/src/PeaksViewer.cpp
index 8034a80c7909877c78b2e430082b98b8e5b4776a..ac8fb544ccfb0608c79fc78374bcc485ece737eb 100644
--- a/MantidQt/SliceViewer/src/PeaksViewer.cpp
+++ b/MantidQt/SliceViewer/src/PeaksViewer.cpp
@@ -122,9 +122,9 @@ PeaksViewer::~PeaksViewer() {}
*/
bool PeaksViewer::hasThingsToShow() const { return m_presenter->size() >= 1; }
-void PeaksViewer:: clearPeaksModeRequest(
+void PeaksViewer::clearPeaksModeRequest(
const PeaksWorkspaceWidget *const originWidget, const bool on) {
- EditMode mode;
+ EditMode mode = None;
if (on) {
QList<PeaksWorkspaceWidget *> children =
qFindChildren<PeaksWorkspaceWidget *>(this);
@@ -149,7 +149,7 @@ void PeaksViewer:: clearPeaksModeRequest(
void PeaksViewer::addPeaksModeRequest(const PeaksWorkspaceWidget * const originWidget, const bool on)
{
- EditMode mode;
+ EditMode mode = None;
if(on) {
QList<PeaksWorkspaceWidget *> children =
qFindChildren<PeaksWorkspaceWidget *>(this);
diff --git a/MantidQt/SliceViewer/src/SliceViewer.cpp b/MantidQt/SliceViewer/src/SliceViewer.cpp
index f251baaf4445e9f32142a3d54ea3d16ef6fe62a6..34bba3a13bc370f18250ec802dc46ad8a141908e 100644
--- a/MantidQt/SliceViewer/src/SliceViewer.cpp
+++ b/MantidQt/SliceViewer/src/SliceViewer.cpp
@@ -122,8 +122,6 @@ SliceViewer::SliceViewer(QWidget *parent)
// hide unused buttons
ui.btnZoom->hide(); // hidden for a long time
- ui.btnRebinLock->hide(); // now replaced by auto rebin mode
- // ui.btnClearLine->hide(); // turning off line mode now removes line
// ----------- Toolbar button signals ----------------
QObject::connect(ui.btnResetZoom, SIGNAL(clicked()), this, SLOT(resetZoom()));
@@ -379,13 +377,6 @@ void SliceViewer::initMenus() {
SLOT(RebinMode_toggled(bool)));
m_menuView->addAction(action);
- action = new QAction(QPixmap(), "&Lock Rebinned WS", this);
- m_syncRebinLock = new SyncedCheckboxes(action, ui.btnRebinLock, true);
- connect(m_syncRebinLock, SIGNAL(toggled(bool)), this,
- SLOT(RebinLock_toggled(bool)));
- action->setVisible(false); // hide this action
- m_menuView->addAction(action);
-
action = new QAction(QPixmap(), "Rebin Current View", this);
action->setShortcut(Qt::Key_R + Qt::ControlModifier);
action->setEnabled(false);
@@ -691,7 +682,6 @@ void SliceViewer::setWorkspace(Mantid::API::IMDWorkspace_sptr ws) {
// Can't use dynamic rebin mode with a MatrixWorkspace
m_syncRebinMode->setEnabled(!matrix);
- m_syncRebinLock->setEnabled(!matrix);
// Go to no normalization by default for MatrixWorkspaces
if (matrix)
@@ -1008,13 +998,10 @@ void SliceViewer::setRebinNumBins(int xBins, int yBins) {
* See setRebinThickness() to adjust the thickness in other dimensions.
*
* @param mode :: true for rebinning mode
- * @param locked :: if true, then the rebinned area is only refreshed manually
- * or when changing rebinning parameters.
*/
-void SliceViewer::setRebinMode(bool mode, bool locked) {
+void SliceViewer::setRebinMode(bool mode) {
// The events associated with these controls will trigger a re-draw
m_syncRebinMode->toggle(mode);
- m_syncRebinLock->toggle(locked);
}
//------------------------------------------------------------------------------
@@ -1098,7 +1085,6 @@ void SliceViewer::RebinMode_toggled(bool checked) {
for (size_t d = 0; d < m_dimWidgets.size(); d++)
m_dimWidgets[d]->showRebinControls(checked);
ui.btnRebinRefresh->setEnabled(checked);
- ui.btnRebinLock->setEnabled(checked);
m_syncAutoRebin->setEnabled(checked);
m_actionRefreshRebin->setEnabled(checked);
m_rebinMode = checked;
@@ -1118,17 +1104,6 @@ void SliceViewer::RebinMode_toggled(bool checked) {
}
}
-//------------------------------------------------------------------------------
-/** Slot called when locking/unlocking the dynamically rebinned
- * overlaid workspace
- * @param checked :: DO lock the workspace in place
- */
-void SliceViewer::RebinLock_toggled(bool checked) {
- m_rebinLocked = checked;
- // Rebin immediately
- if (!m_rebinLocked && m_rebinMode)
- this->rebinParamsChanged();
-}
//------------------------------------------------------------------------------
/// Slot for zooming into
diff --git a/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py b/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py
index f7ac61b15e55516acb33bf420257de185ef081dc..cff5c28c1d8bc20a66cc35ae89fff4f6f0cb077d 100644
--- a/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py
+++ b/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py
@@ -449,7 +449,7 @@ class SliceViewerPythonInterfaceTest(unittest.TestCase):
sv.setRebinThickness(2, 1.0)
sv.setRebinNumBins(50, 200)
sv.refreshRebin()
- sv.setRebinMode(True, True)
+ sv.setRebinMode(True)
time.sleep(1)
self.assertTrue(mtd.doesExist('uniform_rebinned'), 'Dynamically rebinned workspace was created.')
ws = mtd['uniform_rebinned']
diff --git a/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h b/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h
index b3cd39f36e9a261ea1cfe2f29978d28b1efbb2c1..a7cdd630803f9bf82ed17fe8141e2dfad3eaac94 100644
--- a/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h
+++ b/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h
@@ -96,7 +96,7 @@ class EXPORT_OPT_MANTIDQT_SPECTRUMVIEWER GraphDisplay
double m_minY;
double m_maxY;
- static QColor g_curveColors[];
+ static std::vector<QColor> g_curveColors;
};
diff --git a/MantidQt/SpectrumViewer/src/GraphDisplay.cpp b/MantidQt/SpectrumViewer/src/GraphDisplay.cpp
index fb458c40088478e07a1b3a7bc941514268b022d4..3b3f3f25de46e91737a218ce8c00db2f5d172919 100644
--- a/MantidQt/SpectrumViewer/src/GraphDisplay.cpp
+++ b/MantidQt/SpectrumViewer/src/GraphDisplay.cpp
@@ -12,7 +12,7 @@ namespace MantidQt
namespace SpectrumView
{
-QColor GraphDisplay::g_curveColors[] = {Qt::black, Qt::red, Qt::green, Qt::blue};
+std::vector<QColor> GraphDisplay::g_curveColors;
/**
* Construct a GraphDisplay to display selected graph on the specifed plot
@@ -40,6 +40,11 @@ GraphDisplay::GraphDisplay( QwtPlot* graphPlot,
{
if(isVertical)
graphPlot->setAxisMaxMajor( QwtPlot::xBottom, 3 );
+
+ g_curveColors.push_back(Qt::black);
+ g_curveColors.push_back(Qt::red);
+ g_curveColors.push_back(Qt::green);
+ g_curveColors.push_back(Qt::blue);
}
@@ -130,7 +135,7 @@ void GraphDisplay::setData(const QVector<double> & xData,
auto curve = new QwtPlotCurve;
curve->setData( xData, yData );
curve->attach( m_graphPlot );
- auto colorIndex = m_curves.size() % sizeof(g_curveColors);
+ auto colorIndex = m_curves.size() % g_curveColors.size();
curve->setPen(QPen(g_curveColors[colorIndex]));
m_curves.append(curve);
diff --git a/Testing/Data/DocTest/EVS15289.raw.md5 b/Testing/Data/DocTest/EVS15289.raw.md5
new file mode 100644
index 0000000000000000000000000000000000000000..dc2506b23352680b70b700899227c9fd2fc8a379
--- /dev/null
+++ b/Testing/Data/DocTest/EVS15289.raw.md5
@@ -0,0 +1 @@
+ea1cb1b0d1daa9579fbeb4acf3716162
\ No newline at end of file
diff --git a/Testing/Data/UnitTest/EVS15289.raw.md5 b/Testing/Data/UnitTest/EVS15289.raw.md5
new file mode 100644
index 0000000000000000000000000000000000000000..dc2506b23352680b70b700899227c9fd2fc8a379
--- /dev/null
+++ b/Testing/Data/UnitTest/EVS15289.raw.md5
@@ -0,0 +1 @@
+ea1cb1b0d1daa9579fbeb4acf3716162
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/ISISDirectReductionComponents.py b/Testing/SystemTests/tests/analysis/ISISDirectReductionComponents.py
index 214f517a7cc9a5b79b8f123ede6d7174597f4e39..437c4668bf1496371331dfb39d53947f1a15ef43 100644
--- a/Testing/SystemTests/tests/analysis/ISISDirectReductionComponents.py
+++ b/Testing/SystemTests/tests/analysis/ISISDirectReductionComponents.py
@@ -53,6 +53,7 @@ class ISIS_ReductionWebLike(stresstesting.MantidStressTest):
if 'outWS' in mtd:
return 'outWS'
saveFileName = self.rd.reducer.save_file_name
+#pylint: disable=unused-variable
outWS = Load(Filename=saveFileName+'.nxs')
outWS *= 0.997979227566217
fullRezPath =FileFinder.getFullPath(saveFileName+'.nxs')
@@ -63,7 +64,11 @@ class ISIS_ReductionWebLike(stresstesting.MantidStressTest):
def validate(self):
"""Returns the name of the workspace & file to compare"""
+ # tolerance defined outside of init
+#pylint: disable=W0201
self.tolerance = 1e-6
+ # tolerance_is_reller defined outside of init
+#pylint: disable=W0201
self.tolerance_is_reller=True
self.disableChecking.append('SpectraMap')
self.disableChecking.append('Instrument')
@@ -97,6 +102,8 @@ class ISIS_ReductionWrapperValidate(stresstesting.MantidStressTest):
# this is correct workflow for the ref file
#rd.reducer.prop_man.save_file_name = ref_file
# temporary workflow, until we fix workspace adjustment
+ # disable pylint -- access to protected member
+#pylint: disable=W0212
rd._tolerr =3.e-3
rd.reducer.prop_man.save_file_name = 'MARIReduction.nxs'
rd.validate_run_number=11001
@@ -239,6 +246,13 @@ class ISISLoadFilesMER(stresstesting.MantidStressTest):
det = mon_ws.getDetector(0)
self.assertTrue(det.isMonitor())
+ ei_ws = GetAllEi(mon_ws,69634,69638,IgnoreSecondMonitor=False)
+ self.assertTrue(isinstance(ei_ws,Workspace))
+
+ en_peaks = ei_ws.readX(0)
+ self.assertAlmostEquals(len(en_peaks),1)
+ self.assertAlmostEqual(en_peaks[0],108.94,2)
+
self.valid = True
@@ -283,12 +297,16 @@ class ISISLoadFilesLET(stresstesting.MantidStressTest):
#
self.assertEqual(mon_ws.getNumberHistograms(),27)
+ ei_ws = GetAllEi(mon_ws,40966,40967,IgnoreSecondMonitor=True)
+ self.assertTrue(isinstance(ei_ws,Workspace))
self.valid = True
+
def validate(self):
return self.valid
if __name__=="__main__":
- ISISLoadFilesMER.runTest()
+ tester = ISISLoadFilesLET()
+ tester.runTest()
diff --git a/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py b/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py
index d0fbaa674ef409534fa863367f3485c382d0a7c4..11fa3b62ea0893150faf633ee78992f4c4117bdd 100644
--- a/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py
+++ b/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py
@@ -238,6 +238,10 @@ class VesuvioTests(unittest.TestCase):
#================== Failure cases ================================
+ def test_run_range_bad_order_raises_error(self):
+ self.assertRaises(RuntimeError, ms.LoadVesuvio, Filename="14188-14187",
+ OutputWorkspace=self.ws_name)
+
def test_missing_spectra_property_raises_error(self):
self.assertRaises(RuntimeError, ms.LoadVesuvio, Filename="14188",
OutputWorkspace=self.ws_name)
diff --git a/Testing/SystemTests/tests/analysis/SNSPowderRedux.py b/Testing/SystemTests/tests/analysis/SNSPowderRedux.py
index 7db8091f619f1dcf2c0250cc97f6dbacadb17943..2f6331ed6f310ef032875a9aa46700b0c3b4093a 100644
--- a/Testing/SystemTests/tests/analysis/SNSPowderRedux.py
+++ b/Testing/SystemTests/tests/analysis/SNSPowderRedux.py
@@ -17,7 +17,8 @@ def getSaveDir():
return os.path.abspath(os.path.curdir)
def do_cleanup():
- Files = ["PG3_9829.gsa",
+ Files = ["PG3_9829.getn",
+ "PG3_9829.gsa",
"PG3_9829.py",
"PG3_9830.gsa",
"PG3_9830.py",
@@ -249,3 +250,38 @@ class SeriesAndConjoinFilesTest(stresstesting.MantidStressTest):
self.tolerance = 1.0e-2
return ('PG3_9829','PG3_9829_golden')
#return ('PG3_9830','PG3_9830_golden') # can only validate one workspace
+
+class ToPDFgetNTest(stresstesting.MantidStressTest):
+ cal_file = "PG3_FERNS_d4832_2011_08_24.cal"
+ char_file = "PG3_characterization_2012_02_23-HR-ILL.txt"
+ data_file = "PG3_9829_event.nxs"
+ getn_file = "PG3_9829.getn"
+
+ def cleanup(self):
+ do_cleanup()
+ return True
+
+ def requiredMemoryMB(self):
+ """Requires 3Gb"""
+ return 3000
+
+ def requiredFiles(self):
+ files = [self.cal_file, self.char_file, self.data_file]
+ return files
+
+ def runTest(self):
+ savedir = getSaveDir()
+ PDToPDFgetN(Filename=self.data_file,
+ FilterBadPulses=25,
+ OutputWorkspace=self.data_file,
+ PDFgetNFile=os.path.join(savedir, self.getn_file),
+ CalibrationFile=self.cal_file,
+ CharacterizationRunsFile=self.char_file,
+ RemovePromptPulseWidth=50,
+ Binning=-.0004)
+
+ def validateMethod(self):
+ return None # it running is all that we need
+
+ def validate(self):
+ pass
diff --git a/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py b/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
index f4df6a0b791a56ac268dde824c99b4884f2bf9e0..299d6d5dc17f3a001ae3e1cb7aa485ce5db73da2 100644
--- a/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
+++ b/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#pylint: disable=no-init
from mantid import config
import os
@@ -10,6 +11,8 @@ EXPECTED_EXT = '.expected'
class ValidateInstrumentDefinitionFiles(stresstesting.MantidStressTest):
xsdFile=''
+ # Explicitly specify single file to test. If None, test all.
+ theFileToTest=None #"MARI_Definition.xml"
def skipTests(self):
try:
@@ -66,7 +69,10 @@ class ValidateInstrumentDefinitionFiles(stresstesting.MantidStressTest):
direc = config['instrumentDefinition.directory']
self.xsdFile = os.path.join(direc,'Schema/IDF/1.0/','IDFSchema.xsd')
- files = self.__getDataFileList__()
+ if self.theFileToTest is None:
+ files = self.__getDataFileList__()
+ else:
+ files = [os.path.join(direc,self.theFileToTest)]
# run the tests
failed = []
@@ -94,5 +100,7 @@ class ValidateInstrumentDefinitionFiles(stresstesting.MantidStressTest):
if __name__ == '__main__':
valid = ValidateInstrumentDefinitionFiles()
+ # validate specific file
+ #valid.theFileToTest = "MARI_Definition.xml"
valid.runTest()
diff --git a/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp b/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp
index 748722813c5ac3a15ecafcdd812c525e03cee2c2..5413e173b246519bac7a43cb2f923107b971d8ea 100644
--- a/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp
+++ b/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp
@@ -92,6 +92,12 @@ namespace Mantid
coord_t incrementX = (maxX - minX) / static_cast<coord_t>(nBinsX);
coord_t incrementY = (maxY - minY) / static_cast<coord_t>(nBinsY);
+ boost::scoped_ptr<MDHistoWorkspaceIterator> iterator(dynamic_cast<MDHistoWorkspaceIterator*>(createIteratorWithNormalization(m_normalizationOption, m_workspace.get())));
+ if (!iterator) {
+ throw std::runtime_error(
+ "Could not convert IMDIterator to a MDHistoWorkspaceIterator");
+ }
+
const int imageSize = (nBinsX ) * (nBinsY );
vtkPoints *points = vtkPoints::New();
points->Allocate(static_cast<int>(imageSize));
@@ -119,8 +125,7 @@ namespace Mantid
double progressFactor = 0.5/double(nBinsX);
double progressOffset = 0.5;
- boost::scoped_ptr<MDHistoWorkspaceIterator> iterator(dynamic_cast<MDHistoWorkspaceIterator*>(createIteratorWithNormalization(m_normalizationOption, m_workspace.get())));
-
+
size_t index = 0;
for (int i = 0; i < nBinsX; i++)
{
diff --git a/buildconfig/CMake/PylintSetup.cmake b/buildconfig/CMake/PylintSetup.cmake
index cb29dd4f648ff8e008c3a66f99566ecf1395c589..fda959056926555585a1e69bf8dd59578befa888 100644
--- a/buildconfig/CMake/PylintSetup.cmake
+++ b/buildconfig/CMake/PylintSetup.cmake
@@ -33,6 +33,8 @@ if ( PYLINT_FOUND )
Framework/PythonInterface/plugins
scripts
Testing/SystemTests/tests/analysis
+ tools
+ docs/sphinxext/mantiddoc
)
set ( PYLINT_EXCLUDES
scripts/lib1to2
diff --git a/docs/source/algorithms/CompactMD-v1.rst b/docs/source/algorithms/CompactMD-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..388f9ca7a084c437305608994667507b9665158f
--- /dev/null
+++ b/docs/source/algorithms/CompactMD-v1.rst
@@ -0,0 +1,62 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+Used to crop an n-dimensional :ref:`MDHistoWorkspace <MDHistoWorkspace>` to the first non-zero signal values found in all dimensions.
+
+Cropping
+--------
+The cropping is done by supplying `IntegrateMDHistoWorkspace <http://docs.mantidproject.org/nightly/algorithms/IntegrateMDHistoWorkspace-v1.html>`__ with the minimum and maximum extents associated with the first non-zero
+signal values in the workspace.
+
+
+Usage
+-----
+
+
+**Example - CompactMD on MDHistoWorkspace**
+
+.. testcode:: CompactMDOnMDHistoWorkspace
+
+ import math
+ #create an MDEventWorkspace for Rebinning
+ mdws = CreateMDWorkspace(Dimensions=3, Extents='-10,10,-10,10,-10,10', Names='A,B,C', Units='U,U,U')
+ FakeMDEventData(InputWorkspace=mdws, PeakParams='100000,-5,-5,0,1')
+ FakeMDEventData(InputWorkspace=mdws, PeakParams='100000,0,0,0,1')
+ FakeMDEventData(InputWorkspace=mdws, PeakParams='100000,5,5,0,1')
+ #Rebin mdws to create an MDHistoWorkspace
+ binned_ws = BinMD(InputWorkspace=mdws, AxisAligned=False, BasisVector0='a,unit,1,1,0',BasisVector1='b,unit,-1,1,0',BasisVector2='c,unit,0,0,1',NormalizeBasisVectors=True,Translation=[-10,-10,0], OutputExtents=[0,math.sqrt(2*20*20),-2,2,-10,10], OutputBins=[100, 100, 1] )
+
+ #A visualisation of the rebinned_ws can be found in the 'Input' section below.
+
+ #run CompactMD on the rebinned workspace
+ compact_output = CompactMD(binned_ws)
+
+ #A visualisation of the compacted workspace can be found in the 'Output' section below.
+
+Input:
+
+.. figure:: /images/RebbinedWorkspaceNoCompactMDApplied.jpg
+ :alt: RebbinedWorkspaceNoCompactMDApplied.jpg
+ :width: 400px
+ :align: center
+
+
+Output:
+
+.. figure:: /images/RebbinedWorkspaceWithCompactMDApplied.jpg
+ :alt: RebbinedWorkspaceWithCompactMDApplied.jpg
+ :width: 400px
+ :align: center
+
+
+
+.. categories::
+
+.. sourcelink::
\ No newline at end of file
diff --git a/docs/source/algorithms/ComputeCalibrationCoefVan-v1.rst b/docs/source/algorithms/ComputeCalibrationCoefVan-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..47661c2ffe102b08e1a498d0c60dc5ee66232113
--- /dev/null
+++ b/docs/source/algorithms/ComputeCalibrationCoefVan-v1.rst
@@ -0,0 +1,83 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Algorithm creates a workspace with detector sensitivity correction coefficients using the given Vanadium workspace. The correction coefficients are calculated as follows.
+
+1. Calculate the Debye-Waller factor according to Sears and Shelley *Acta Cryst. A* **47**, 441 (1991):
+
+ :math:`D_i = \exp\left(-B_i\cdot\frac{4\pi\sin\theta_i}{\lambda^2}\right)`
+
+ :math:`B_i = \frac{3\hbar^2\cdot 10^{20}}{2m_VkT_m}\cdot J(y)`
+
+ where :math:`J(y) = 0.5` if :math:`y < 10^{-3}`, otherwise
+
+ :math:`J(y) = \int_0^1 x\cdot\mathrm{coth}\left(\frac{x}{2y}\right)\,\mathrm{d}x`
+
+ where :math:`y=T/T_m` is the ratio of the temperature during the experiment :math:`T` to the Debye temperature :math:`T_m = 389K`, :math:`m_V` is the Vanadium atomic mass (in kg) and :math:`\theta_i` is the polar angle of the i-th detector.
+
+.. warning::
+
+ If sample log *temperature* is not present in the given Vanadium workspace or temperature is set to an invalid value, T=293K will be taken for the Debye-Waller factor calculation. Algorithm will produce warning in this case.
+
+2. Perform Gaussian fit of the data to find out the position of the peak centre and FWHM. These values are used to calculate sum :math:`S_i` as
+
+ :math:`S_i = \sum_{x = x_C - 3\,\mathrm{fwhm}}^{x_C + 3\,\mathrm{fwhm}} Y_i(x)`
+
+ where :math:`x_C` is the peak centre position and :math:`Y_i(x)` is the coresponding to :math:`x` :math:`Y` value for i-th detector.
+
+3. Finally, the correction coefficients :math:`K_i` are calculated as
+
+ :math:`K_i = D_i\times S_i`
+
+Workspace containing these correction coefficients is created as an output and can be used as a RHS workspace in :ref:`algm-Divide` to apply correction to the LHS workspace.
+
+.. note::
+
+ If gaussian fit fails, algorithm terminates with an error message. The error message contains name of the workspace and detector number.
+
+Restrictions on the input workspace
+###################################
+
+The valid input workspace:
+
+- must have an instrument set
+- must have a *wavelength* sample log
+
+
+Usage
+-----
+
+**Example**
+
+.. testcode:: ExComputeCalibrationCoefVan
+
+ # load Vanadium data
+ wsVana = LoadMLZ(Filename='TOFTOFTestdata.nxs')
+ # calculate correction coefficients
+ wsCoefs = ComputeCalibrationCoefVan(wsVana)
+ print 'Spectrum 4 of the output workspace is filled with: ', round(wsCoefs.readY(999)[0])
+
+ # wsCoefs can be used as rhs with Divide algorithm to apply correction to the data
+ wsCorr = wsVana/wsCoefs
+ print 'Spectrum 4 of the input workspace is filled with: ', round(wsVana.readY(999)[0], 1)
+ print 'Spectrum 4 of the corrected workspace is filled with: ', round(wsCorr.readY(999)[0], 5)
+
+Output:
+
+.. testoutput:: ExComputeCalibrationCoefVan
+
+ Spectrum 4 of the output workspace is filled with: 6596.0
+ Spectrum 4 of the input workspace is filled with: 1.0
+ Spectrum 4 of the corrected workspace is filled with: 0.00015
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst b/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst
index 904b8dd2a5ccd21368da10509b6c936c4aa5fe42..1d88cdd45e69e58036d500ee26a3af2f5b079de6 100644
--- a/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst
+++ b/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst
@@ -19,18 +19,22 @@ In this algorithm's name, ConvertCWSDToMomentum, *CW* stands for constant wave
This algorithm takes ??? as inputs.
Futhermore, the unit of the output matrix workspace can be converted to
-momentum transfer (:math:`Q`).
+momentum transfer (Q).
Outline of algorithm
####################
-1. Create output workspace.
+1. Create output workspace
+
* Build a virtual instrument, requiring
+
- position of source
- position of sample
- detector ID, position, detector size of pixels
+
2. Read in data via table workspace
+
* From each row, (1) file name and (2) starting detector ID are read in.
* Detector position in (virtual) instrument of MDEventWorkspace is compared with the position in MatrixWorkspace
* Momentum is calcualted by goniometry values
@@ -75,8 +79,6 @@ Each MDEvent in output MDEventWorkspace contain
* Detector ID
* Run Number
-
-
Combine Experiment Into One MDEventWorkspace
--------------------------------------------
@@ -90,7 +92,7 @@ In order to integrate them into an organized data structure, i.e., *MDEventWorks
a virtual instrument is built in the algorithm.
Virtual instrument
-==================
+##################
A virtual instrument is built in the algorithm.
In this virtual instrument, the number of detectors and their position are determined
@@ -98,13 +100,13 @@ by the number of individual detector's positions in the *experiment*.
MDEventWorkspace
-================
+################
There is only one *virtual* instrument and *N* ExperimentInfo.
*N* is the total number of experiment points in the *experiment*.
Inconsistency between using virtual instrument and copying instrument
-=====================================================================
+#####################################################################
It is found that the results, i.e., the peak's position in sample-momentum
space, by FindPeaksMD, are different betweent the MDEventWorkspaces
@@ -145,7 +147,7 @@ with 2D angular detector.
Usage
-----
-**Example - convert an HB3A's experiment to MDWorkspace in sample momentum workspae and creating virtual instrument.:**
+**Example - convert an HB3A's experiment to MDWorkspace in sample momentum workspae and creating virtual instrument**
.. testcode:: ExConvertHB3AToMDVirtualInstrument
diff --git a/docs/source/algorithms/DetectorFloodWeighting-v1.rst b/docs/source/algorithms/DetectorFloodWeighting-v1.rst
index b248c4b9d900d79aff5dd5ec4825d7438e445d8b..68f78e13e9da56d2e6ce28321e11fa362144bfc2 100644
--- a/docs/source/algorithms/DetectorFloodWeighting-v1.rst
+++ b/docs/source/algorithms/DetectorFloodWeighting-v1.rst
@@ -10,8 +10,7 @@ Description
-----------
This algorithm is used to calculate the detector flood weighting workspace use for pixel flood corrections. It was originally developed for the ANSTO Bilby instrument.
-This algorithm crops the data over the specified wavelength region, then normalizes each spectrum to the workspace spectrum maxima. The algorithm will then
-perform a solid angle correction on each spectra via :ref:`algm-SolidAngle`.
+This algorithm crops the data over the specified wavelength region, and sums it. The algorithm will then perform a solid angle correction on each spectra via :ref:`algm-SolidAngle` if specified, and divides through by the provided transmission workspace if provided. The result is divided by the mean spectrum value in the previous result.
Usage
-----
@@ -30,8 +29,6 @@ Usage
print 'Number Histograms',out_ws.getNumberHistograms()
print 'Min X:', out_ws.readX(0)[0], 'Max X:', out_ws.readX(0)[1]
- y_data = out_ws.extractY()
- print 'Min Y:', np.amin(y_data), 'Max Y:', np.amax(y_data)
Output:
@@ -39,7 +36,6 @@ Output:
Number Histograms 2
Min X: 0.0 Max X: 10.0
- Min Y: 0.5 Max Y: 1.0
**Example - With Solid Angle Correction **
diff --git a/docs/source/algorithms/EVSDiffractionReduction-v1.rst b/docs/source/algorithms/EVSDiffractionReduction-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c6fd73dc8b257b04e86d4a71bb6d984f9da39d6e
--- /dev/null
+++ b/docs/source/algorithms/EVSDiffractionReduction-v1.rst
@@ -0,0 +1,44 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+A version of :ref:`ISISIndirectDiffractionReduction
+<algm-ISISIndirectDiffractionReduction>` specific to use with VESUVIO (EVS)
+data, the reduction is performed in the same way however there is the additional
+option to load a PAR file.
+
+Usage
+-----
+
+**Example - Running EVSDiffractionReduction.**
+
+.. testcode:: ExEVSDiffractionReductionSimple
+
+ EVSDiffractionReduction(InputFiles='EVS15289.raw',
+ OutputWorkspace='DiffractionReductions',
+ InstrumentParFile='IP0005.dat')
+
+ ws = mtd['DiffractionReductions'].getItem(0)
+
+ print 'Workspace name: %s' % ws.getName()
+ print 'Number of spectra: %d' % ws.getNumberHistograms()
+ print 'Number of bins: %s' % ws.blocksize()
+
+Output:
+
+.. testoutput:: ExEVSDiffractionReductionSimple
+
+ Workspace name: EVS15289_diffspec_red
+ Number of spectra: 1
+ Number of bins: 3875
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/GetAllEi-v1.rst b/docs/source/algorithms/GetAllEi-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c0e46da75eb0b368df50457ff64c7b2b4f1fb2e5
--- /dev/null
+++ b/docs/source/algorithms/GetAllEi-v1.rst
@@ -0,0 +1,95 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Algorithm finds the estimate for all incident energies allowed by chopper system of an inelastic instrument and returns a workspace,
+with the estimates for positions, heights and width of incident energies provided by the choppers and registered on monitors.
+These estimates can be used as guess value for :ref:`algm-GetEi` algorithm or as inputs for a peak fitting procedure.
+
+Algorithm performs number of steps to identify the values requested:
+
+#. It takes appropriate log names from instrument definition file (IDF), namely chopper-position component and calculates last chopper speed and delay as average
+ of the filtered log values. Guess chopper opening times are calculated from chopper speed and delay time. The "chopper-position" component with appropriate properties
+ has to be present in IDF for this algorithm to work. See ISIS MARI or MAPS instrument definition files for example of "chopper-position" component.
+
+#. Algorithm uses estimate for the minimal energy resolution of an instrument and searches for real peaks around guess values obtained
+ earlier within 4 sigma of this resolution interval.
+
+#. If peaks are found, the algorithm performs running averages over signal in the appropriate time interval until first derivative
+ of the signal has only one zero. The position of this zero is returned as the guess energy and the distance between closest to
+ the guess energy zeros of the second derivative are returned as the guess values for the peak width. The peak amplitude
+ is estimated from the total intensity of the signal within the search interval, assuming that the peak shape is Gaussian.
+
+#. Similar procedure is performed for second monitor. The peak is accepted only if the peak width lies between the minimal and maximal instrument resolution values
+ and the distance between peaks positions on two monitors (on energy scale) is smaller then two sigma.
+
+Algorithm returns matrix workspace containing single spectrum, with x-values representing peak positions, y-values: peak heights and the error: peak width. X-values are
+sorted according to energy in peaks (peaks with maximal energy are returned first).
+
+Used Subalgorithms
+------------------
+The algorithm uses :ref:`Unit Factory <Unit Factory>` and :ref:`algm-ConvertUnits` algorithm
+to convert units from TOF to energy.
+
+
+**Example: Find all incident energies for test workspace**
+
+.. testcode:: foundAllEi
+
+ # BUILD SAMPLE WORKSPACE
+ # Build sample workspace with chopper and in energy units to
+ # have defined peaks in defined energy positions
+ wsEn=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=1, BankPixelWidth=2, NumEvents=10000, XUnit='Energy', XMin=10, XMax=200, BinWidth=0.1)
+ # convert units to TOF to simulate real workspace obtained from experiment
+ ws = ConvertUnits(InputWorkspace=wsEn, Target='TOF')
+ # find chopper log values would be present in real workspace
+ l_chop = 7.5 # chopper position build into test workspace
+ l_mon1 = 15. # monitor 1 position (detector 1), build into test workspace
+ t_mon1 = 3100. # the time of flight defined by incident energy of the peak generated by CreateSampelpWorkspace algorithm.
+ t_chop = (l_chop/l_mon1)*t_mon1
+ # Add these log values to simulated workspace to represent real sample logs
+ AddTimeSeriesLog(ws, Name="fermi_delay", Time="2010-01-01T00:00:00", Value=t_chop ,DeleteExisting=True)
+ AddTimeSeriesLog(ws, Name="fermi_delay", Time="2010-01-01T00:30:00", Value=t_chop )
+ AddTimeSeriesLog(ws, Name="fermi_speed", Time="2010-01-01T00:00:00", Value=900 ,DeleteExisting=True)
+ AddTimeSeriesLog(ws, Name="fermi_speed", Time="2010-01-01T00:30:00", Value=900)
+ #-------------------------------------------------------------
+
+ # FIND GUESS PEAKS
+ allEiWs=GetAllEi(ws,Monitor1SpecID=1,Monitor2SpecID=2)
+ # Analyze results
+ allEi = allEiWs.readX(0);
+ peakHeight = allEiWs.readY(0);
+ peakWidth = allEiWs.readE(0);
+
+ # Check if peaks positions are indeed correct:
+ #-------------------------------------------------------------
+ resEi=[]
+ for ei_guess in allEi:
+ nop,t_peak,monIndex,tZero=GetEi(InputWorkspace=ws, Monitor1Spec=1, Monitor2Spec=2, EnergyEstimate=ei_guess)
+ resEi.append((nop,t_peak));
+ print "! Guess Ei ! peak TOF ! peak height ! peak width !"
+ for ind,val in enumerate(resEi):
+ print "! {0: >6.1f} ! {1: >6.2f} ! {2: >6.2f} ! {3: >6.2f} !".format(allEi[ind],val[1],peakHeight[ind],peakWidth[ind])
+ #
+ # NOTE: incident energy of GetEi is calculated from distance between monitor 1 and 2, and this distance is not correct in
+ # the test workspace. The tested point is that getEi can find energies from guess values and TOF for peaks is correct.
+
+Output:
+
+.. testoutput:: foundAllEi
+ :options: +NORMALIZE_WHITESPACE
+
+ ! Guess Ei ! peak TOF ! peak height ! peak width !
+ ! 67.0 ! 4188.03 ! 34.68 ! 2.35 !
+ ! 124.1 ! 3079.09 ! 14.01 ! 4.35 !
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/LoadEventAndCompress-v1.rst b/docs/source/algorithms/LoadEventAndCompress-v1.rst
index 904f90502164953738e1a6948991f082077e233c..62a3f3d65ff40e21572ce2ba45219dfb24bfb24a 100644
--- a/docs/source/algorithms/LoadEventAndCompress-v1.rst
+++ b/docs/source/algorithms/LoadEventAndCompress-v1.rst
@@ -41,6 +41,44 @@ download due to their size. They can however be downloaded using these links:
PG3_9830_event = LoadEventAndCompress(Filename='PG3_9830_event.nxs',
MaxChunkSize=1.)
+**Example - Usage with MPI**
+
+Create a python driver script called test_mpi.py
+
+.. code-block:: python
+
+ from mantid.simpleapi import *
+ import mantid
+ if AlgorithmFactory.exists('GatherWorkspaces'):
+ HAVE_MPI = True
+ from mpi4py import MPI
+ mpiRank = MPI.COMM_WORLD.Get_rank()
+ mpiSize = MPI.COMM_WORLD.Get_size()
+ else:
+ HAVE_MPI = False
+ mpiRank = 0 # simplify if clauses
+ mpiSize = 1 # simplify if clauses
+
+ wksp = LoadEventAndCompress(Filename="PG3_2538_event.nxs")
+ print "Rank = ", mpiRank, "Number of Events = ", wksp.getNumberEvents()
+ if mpiRank == 0:
+ reduce = AlignAndFocusPowder(InputWorkspace=wksp, CalFileName='PG3_calibrate_d2538_2014_05_13.cal', Params='0.5,0.01,2')
+ SaveNexus(reduce,Filename=str(mpiSize)+"tasks.nxs")
+
+And run it using the following commands
+
+.. code-block::
+
+ $ module load mpi/openmpi-x86_64
+ $ export LD_PRELOAD=/usr/lib64/openmpi/lib/libmpi.so
+ $ mpirun -np 8 mantidpython test_mpi.py
+
+to run without mpi is simply
+
+.. code-block::
+
+ $ mantidpython test_mpi.py
+
.. categories::
.. sourcelink::
diff --git a/docs/source/algorithms/LoadMuonNexus-v1.rst b/docs/source/algorithms/LoadMuonNexus-v1.rst
index acd6e582bb31550062f1022df13e320769f1b1b6..5f8aaf88a3c54b19f06667b7430512ea550aefdc 100644
--- a/docs/source/algorithms/LoadMuonNexus-v1.rst
+++ b/docs/source/algorithms/LoadMuonNexus-v1.rst
@@ -79,77 +79,6 @@ The ChildAlgorithms used by LoadMuonNexus are:
LoadInstrument fails. As the Nexus file has limited instrument data,
this only populates a few fields.
-Usage
------
-
-.. include:: ../usagedata-note.txt
-
-**Example - Load ISIS muon MUSR dataset:**
-
-.. testcode:: LoadMuonNexusOnePeriod
-
- # Load MUSR dataset
- ws = LoadMuonNexus(Filename="MUSR00015189.nxs",EntryNumber=1)
- print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
-
-Output:
-
-.. testoutput:: LoadMuonNexusOnePeriod
-
- Workspace has 64 spectra
-
-**Example - Load event nexus file with time filtering:**
-
-.. testcode:: ExLoadMuonNexusSomeSpectra
-
- # Load some spectra
- ws = LoadMuonNexus(Filename="MUSR00015189.nxs",SpectrumMin=5,SpectrumMax=10,EntryNumber=1)
- print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
-
-Output:
-
-.. testoutput:: ExLoadMuonNexusSomeSpectra
-
- Workspace has 6 spectra
-
-**Example - Load dead times into table:**
-
-.. testcode:: ExLoadDeadTimeTable
-
- # Load some spectra
- ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumMin=5,SpectrumMax=10,DeadTimeTable="deadTimeTable")
- tab = mtd['deadTimeTable']
- for i in range(0,tab.rowCount()):
- print tab.cell(i,0), tab.cell(i,1)
-
-Output:
-
-.. testoutput:: ExLoadDeadTimeTable
-
- 5 0.00161112251226
- 6 0.00215016817674
- 7 0.0102171599865
- 8 0.00431686220691
- 9 0.00743605662137
- 10 0.00421147653833
-
-**Example - Load detector grouping into table:**
-
-.. testcode:: ExLoadDetectorGrouping
-
- # Load some spectra
- ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumList="1,16,17,32",DetectorGroupingTable="detectorTable")
- tab = mtd['detectorTable']
- for i in range(0,tab.rowCount()):
- print tab.cell(i,0)
-
-Output:
-
-.. testoutput:: ExLoadDetectorGrouping
-
- [ 1 16]
- [17 32]
-
.. categories::
.. sourcelink::
diff --git a/docs/source/algorithms/LoadMuonNexus-v2.rst b/docs/source/algorithms/LoadMuonNexus-v2.rst
index 0ca954061e4aad8e1f7858f51b8fbd86d6ad6d88..2e0732e98a485b22bc128fe43e25cb757d49a566 100644
--- a/docs/source/algorithms/LoadMuonNexus-v2.rst
+++ b/docs/source/algorithms/LoadMuonNexus-v2.rst
@@ -80,6 +80,77 @@ detects that it has been asked to load a previous version muon nexus
file it will call the previous version of the algorithm to perform the
task.
+Usage
+-----
+
+.. include:: ../usagedata-note.txt
+
+**Example - Load ISIS muon MUSR dataset:**
+
+.. testcode:: LoadMuonNexusOnePeriod
+
+ # Load MUSR dataset
+ ws = LoadMuonNexus(Filename="MUSR00015189.nxs",EntryNumber=1)
+ print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
+
+Output:
+
+.. testoutput:: LoadMuonNexusOnePeriod
+
+ Workspace has 64 spectra
+
+**Example - Load event nexus file with time filtering:**
+
+.. testcode:: ExLoadMuonNexusSomeSpectra
+
+ # Load some spectra
+ ws = LoadMuonNexus(Filename="MUSR00015189.nxs",SpectrumMin=5,SpectrumMax=10,EntryNumber=1)
+ print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
+
+Output:
+
+.. testoutput:: ExLoadMuonNexusSomeSpectra
+
+ Workspace has 6 spectra
+
+**Example - Load dead times into table:**
+
+.. testcode:: ExLoadDeadTimeTable
+
+ # Load some spectra
+ ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumMin=5,SpectrumMax=10,DeadTimeTable="deadTimeTable")
+ tab = mtd['deadTimeTable']
+ for i in range(0,tab.rowCount()):
+ print tab.cell(i,0), tab.cell(i,1)
+
+Output:
+
+.. testoutput:: ExLoadDeadTimeTable
+
+ 5 0.00161112251226
+ 6 0.00215016817674
+ 7 0.0102171599865
+ 8 0.00431686220691
+ 9 0.00743605662137
+ 10 0.00421147653833
+
+**Example - Load detector grouping into table:**
+
+.. testcode:: ExLoadDetectorGrouping
+
+ # Load some spectra
+ ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumList="1,16,17,32",DetectorGroupingTable="detectorTable")
+ tab = mtd['detectorTable']
+ for i in range(0,tab.rowCount()):
+ print tab.cell(i,0)
+
+Output:
+
+.. testoutput:: ExLoadDetectorGrouping
+
+ [ 1 16]
+ [17 32]
+
.. categories::
.. sourcelink::
diff --git a/docs/source/algorithms/PDToPDFgetN-v1.rst b/docs/source/algorithms/PDToPDFgetN-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f37aae644e29dee983a0c7e1ab829a772546b5a4
--- /dev/null
+++ b/docs/source/algorithms/PDToPDFgetN-v1.rst
@@ -0,0 +1,32 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This is a workflow algorithm that creates files suitable as input
+into `PDFgetN <http://pdfgetn.sourceforge.net/>`_.
+
+#. :ref:`algm-PDLoadCharacterizations`
+#. :ref:`algm-LoadEventAndCompress` if ``InputWorkspace`` is not
+ provided
+#. :ref:`algm-PDDetermineCharacterizations` to determine information
+ from the characterization file
+#. :ref:`algm-AlignAndFocusPowder`
+#. :ref:`algm-NormaliseByCurrent`
+#. :ref:`algm-SetUncertainties` (``SetError="sqrt"``)
+#. :ref:`algm-SaveGSS`
+
+Workflow
+########
+
+.. diagram:: PDToPDFgetN-v1_wkflw.dot
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/ReflectometryReductionOneAuto-v1.rst b/docs/source/algorithms/ReflectometryReductionOneAuto-v1.rst
index 0cce65d4d5d91397826b2e8058ac0d1287e328ac..487796977b1aeaf78bd6e31e7ecdc875b6bd4277 100644
--- a/docs/source/algorithms/ReflectometryReductionOneAuto-v1.rst
+++ b/docs/source/algorithms/ReflectometryReductionOneAuto-v1.rst
@@ -13,13 +13,19 @@ Facade over :ref:`algm-ReflectometryReductionOne`.
Pulls numeric parameters out of the instrument parameters where possible. You can override any of these automatically applied defaults by providing your own value for the input.
+See :ref:`algm-ReflectometryReductionOne` for more information on the wrapped algorithm.
+
+ProcessingInstructions
+######################
+
If ProcessingInstructions is not set its value is inferred from other properties:
* If AnalysisMode = PointDetectorAnalaysis and PointDetectorStart = PointDetectorStop then the spectrum specified by PointDetectorStart is used.
* If AnalysisMode = PointDetectorAnalaysis and PointDetectorStart ≠PointDetectorStop then the sum of the spectra from PointDetectorStart to PointDetectorStop is used.
* If AnalysisMode = MultiDetectorAnalaysis then all of the spectra from MultiDetectorStart onwards are used.
-See :ref:`algm-ReflectometryReductionOne` for more information on the wrapped algorithm.
+Note, the ProcessingInstructions are workspace indicies, not detector IDs. The first few workspaces may correspond to monitors, rather than detectors of interest.
+For the syntax of this property, see :ref:`algm-GroupDetectors`.
Workflow for WorkspaceGroups
############################
diff --git a/docs/source/algorithms/RemoveExpDecay-v1.rst b/docs/source/algorithms/RemoveExpDecay-v1.rst
index 7307a59b69f6df06cd07ce3e4b48d5faa0791848..099f5988544139bcfb50a2bec4e27a834ad1fb42 100644
--- a/docs/source/algorithms/RemoveExpDecay-v1.rst
+++ b/docs/source/algorithms/RemoveExpDecay-v1.rst
@@ -9,8 +9,9 @@
Description
-----------
-This algorithm removes the exponential time decay from a specified muon
-spectra. By default, all the spectra in a workspace will be corrected.
+This algorithm removes the exponential time decay from the specified muon
+spectra, leaving the rest unchanged. By default, all the spectra
+in a workspace will be corrected.
The formula for removing the exponential decay is given by:
diff --git a/docs/source/algorithms/SavePlot1DAsJson-v1.rst b/docs/source/algorithms/SavePlot1DAsJson-v1.rst
index 86cbeeefd4e066d2a6f835388fa7cd9269f02e8e..85bb7a8d062628aad864fac2e7a84bdde2c6c871 100644
--- a/docs/source/algorithms/SavePlot1DAsJson-v1.rst
+++ b/docs/source/algorithms/SavePlot1DAsJson-v1.rst
@@ -26,12 +26,12 @@ Usage
import os, numpy as np
# prepare input
- E = np.arange(-50, 50, 1.0)
+ E = np.arange(-50, 50, 10.0)
I = 1000 * np.exp(-E**2/10**2)
err = I ** .5
dataws = CreateWorkspace(
DataX = E, DataY = I, DataE = err, NSpec = 1,
- UnitX = "Energy(meV)")
+ UnitX = "Energy")
# output path
out_json = "myplot.json"
# run algorithm
diff --git a/docs/source/algorithms/TOFTOFCropWorkspace-v1.rst b/docs/source/algorithms/TOFTOFCropWorkspace-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2a390bc98a778ae33750d5aaaa43175e39501f3b
--- /dev/null
+++ b/docs/source/algorithms/TOFTOFCropWorkspace-v1.rst
@@ -0,0 +1,59 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Applies algorithm :ref:`algm-Cropworkspace` to an input workspace or a group of workspaces to crop the empty time channels. Boundaries are calculated as follows:
+
+ :math:`X_{min} = 0`
+
+ :math:`X_{max} = N_{fc}\times\Delta t`
+
+where :math:`N_{fc}` is the number of full time channels defined in the *full_channels* sample log and :math:`\Delta t` is the channel width defined in the *channel_width* sample log.
+
+
+Restrictions on the input workspace
+###################################
+
+- The unit of the X-axis must be **Time-of-flight**.
+- Workspace must contain *channel_width* and *full_channels* sample logs.
+
+
+Usage
+-----
+
+**Example**
+
+.. testcode:: ExTOFTOFCropWorkspace
+
+ # Load data
+ ws=Load(Filename='TOFTOFTestdata.nxs')
+
+ print "Input workspace"
+ print "Total number of time channels: ", len(ws.readX(0))
+ print "Number of filled time channels: ", ws.getRun().getLogData('full_channels').value
+
+ wscropped = TOFTOFCropWorkspace(ws)
+
+ print "Output workspace"
+ print "Total number of time channels: ", len(wscropped.readX(0))
+
+Output:
+
+.. testoutput:: ExTOFTOFCropWorkspace
+
+ Input workspace
+ Total number of time channels: 1025
+ Number of filled time channels: 1020.0
+ Output workspace
+ Total number of time channels: 1020
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/concepts/CrystalStructureAndReflections.rst b/docs/source/concepts/CrystalStructureAndReflections.rst
new file mode 100644
index 0000000000000000000000000000000000000000..443dd594566083f6cdd9d048bc7a2e6e3d1b698d
--- /dev/null
+++ b/docs/source/concepts/CrystalStructureAndReflections.rst
@@ -0,0 +1,293 @@
+.. _Crystal structure and reflections:
+
+Crystal structure and reflections
+=================================
+
+This document describes how crystal structure data can be processed and used in Mantid. For the understanding of the
+concepts of :ref:`symmetry <Symmetry groups>` and :ref:`space groups <Point and space groups>` in Mantid it may be
+useful to read those introductory articles before proceeding with this document. While there is a short introduction
+into theoretical aspects this page is not a replacement for proper introductory text books on the subject where all
+these principles are explained in great detail and on a much more general basis.
+
+Theoretical aspects
+~~~~~~~~~~~~~~~~~~~
+
+Crystal structures
+------------------
+
+A crystal is modelled as an infinitely repeating three-dimensional arrangement of scatterers, usually atoms. Due to
+the periodic nature of crystals, the entire object can be described by specifying the repeated unit and how
+it is repeated. These information are called "crystal structure" and comprise three components:
+
+ 1. Lattice (describes the periodicity of the structure)
+ 2. Basis (distribution of scatterers in the unit cell)
+ 3. Space group (describes the symmetry of the arrangement of scatterers)
+
+The description of the basis depends on the model's level of detail. In the simplest case it could be a list of
+point scatterers that are fully characterized by three coordinates (x, y and z in terms of the lattice vectors) and
+a scattering length. In reality however, the scatterers are usually atoms that fluctuate about their average position
+due to thermal agitation. A basic way to model this motion is to assume it to be an isotropic phenomenon, allowing the
+description with one single parameter that quantifies the radius of a sphere in which the scatterer oscillates
+harmonically. This so called Debye-Waller-factor will be introduced later on.
+
+Another important parameter for a basic description of the basis is the so called occupancy. It describes the fraction
+of the total number of scatterer-positions that is actually occupied. A common example where this is required are
+unordered binary metal mixtures where the same position in the crystal structure is partly filled with two different
+atoms in a randomly distributed manner.
+
+To summarize, a very basic model of the basis comprises a list of scatterers that are in turn characterized by
+six parameters:
+
+ 1. Scattering length (known for each element)
+ 2. Fractional coordinate x
+ 3. Fractional coordinate y
+ 4. Fractional coordinate z
+ 5. Occupancy of the site
+ 6. Isotropic thermal displacement parameter
+
+Knowledge of the space group makes it possible to derive all scatterers in the entire unit cell. The symmetry operations
+of the space group map each scatterer-position onto a set of equivalent positions that are consequently occupied by the
+same type of scatterer as well. Since the unit cell is repeated infinitely in all three directions of space, it is
+enough to describe one unit cell. Finally, the lattice is described by six parameters as well, the lengths of the three
+lattice vectors (usually given in :math:`\mathrm{\AA{}}`) and the three angles (in degree) between these vectors.
+
+Reflections and structure factors
+---------------------------------
+
+In a diffraction experiment the periodic arrangement of atoms is probed using radiation, in this case in the form of
+neutrons, of an appropriate wavelength (on the same scale of interatomic distances, typically between 0.5 and
+5 :math:`\mathrm{\AA{}}`). The incident beam interacts with the scatterers and in certain orientations the beam is
+"reflected" by a flock of lattice planes, a phenomenon which is described by Bragg's law:
+
+.. math::
+ 2d\sin\theta = \lambda
+
+In this equation :math: `d` is the spacing between the lattice planes, :math:`\theta` is the angle of the incoming beam
+and the lattice plane normal and lambda is the wavelength of the radiation. In an experiment theta and lambda are
+usually limited, thus they are limiting the range of interplanar spacings that can be probed. In Bragg's law the lattice
+plane families are only described by one parameter, the interplanar distance. But each lattice plane family also has an
+orientation in space which can be described by the plane's normal vector. Usually the vector is given in terms of the
+reciprocal lattice of the structure, where it is reduced to three integers H, K, L, the so called Miller indices. With
+knowledge of the :ref:`unit cell <Lattice>` (and thus the :math:`\mathbf{B}`-matrix), the interplanar spacing can also
+be computed like this:
+
+.. math::
+ d = \frac{1}{\left|\mathbf{B}\cdot\mathbf{h}\right|}
+
+The parameters taken into account so far determine the geometric characteristics of Bragg-reflections, i.e. their
+position on a detector and their time of flight. But besides these, each reflection also has an intensity. The
+intensity is proportional to the squared structure factor, which depends on the kind and arrangement of scatterers in
+the unit cell. The structure factor is a complex number and can be calculated for a certain HKL by summing the
+contributions of all N atoms j in the unit cell:
+
+.. math::
+ F_{\mathbf{h}} = \sum\limits_{j}^{N}b_j\exp\left(2\pi i \mathbf{h} \cdot \mathbf{x}_j\right)
+
+In the above equation :math:`b` is the scattering length, :math:`\mathbf{h}` is the Miller index triplet HKL and
+:math:`\mathbf{x}` contains the fractional coordinates of the j-th atom. To take into account isotropic thermal
+motion of atoms, the term is multiplied with the Debye-Waller factor:
+
+.. math::
+ F_{\mathbf{h}} = \sum\limits_{j}^{N}b_j\exp\left(2\pi i \mathbf{h} \cdot \mathbf{x}_j\right)
+ \exp\left(-2\pi^2 U/d_{\mathbf{h}}^2\right)
+
+Here, :math:`U` is the isotropic atomic displacement parameter, usually given in :math:`\mathrm{\AA{}}^2` and
+:math:`d` is the lattice spacing discussed above. There are other, more complex models to describe the movement of
+atoms, taking into account anisotropic movement and also anharmonic effects.
+
+Implementation in Mantid
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The concepts described above are available through the Python interface of Mantid. Crystal structures are represented
+by a class that stores the three necessary pieces of information. Objects of that class can be created by supplying
+string representations of those three arguments.
+
+.. testcode:: ExCrystalStructureConstruction
+
+ from mantid.geometry import CrystalStructure
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+
+ unitCell = silicon.getUnitCell()
+ print 'Crystal structure of silicon:'
+ print ' Unit cell:', unitCell.a(), unitCell.b(), unitCell.c(), unitCell.alpha(), unitCell.beta(), unitCell.gamma()
+
+ spaceGroup = silicon.getSpaceGroup()
+ print ' Space group:', spaceGroup.getHMSymbol()
+ print ' Point group:', spaceGroup.getPointGroup().getHMSymbol()
+
+ scatterers = silicon.getScatterers()
+ print ' Total number of scatterers:', len(scatterers)
+
+ for i, scatterer in enumerate(scatterers):
+ print ' ' + str(i) + ':', scatterer
+
+The above script produces the following output:
+
+.. testoutput:: ExCrystalStructureConstruction
+
+ Crystal structure of silicon:
+ Unit cell: 5.431 5.431 5.431 90.0 90.0 90.0
+ Space group: F d -3 m
+ Point group: m-3m
+ Total number of scatterers: 1
+ 0: Si 0 0 0 1 0.05
+
+In general, the unit cell must be specified using either 3 or 6 space-separated floating point numbers, representing
+the three axis lengths and the three angles between them. The list of scatterers is required to be a semi-colon
+separated list of strings which contain the following information: Element symbol, x, y, z (fractional coordinates),
+occupancy (between 0 and 1) and isotropic atomic displacement parameter. The fractional coordinates can also be given
+as fractions (for example :math:`1/2` or :math:`1/3`) and for giving the coordinates in hexagonal or trigonal structures
+this is highly recommended as there may be precision problems with decimal numbers.
+
+While the CrystalStructure class is storing information, there is another class that makes use of these information to
+generate reflections and calculate structure factors. This class is called ReflectionGenerator and can be constructed
+from a CrystalStructure-object:
+
+.. testcode:: ExReflectionGeneratorConstruction
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator
+ from mantid.kernel import V3D
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom
+ hkls = generator.getUniqueHKLs(0.7, 3.0)
+
+ print 'There are', len(hkls), 'unique reflections for Si in the specified resolution range.'
+ print 'The reflection [222] is' + (' not' if not V3D(2, 2, 2) in hkls else '') + ' contained in the list.'
+
+.. testoutput:: ExReflectionGeneratorConstruction
+
+ There are 20 unique reflections for Si in the specified resolution range.
+ The reflection [222] is contained in the list.
+
+Checking the reflection conditions of space group :math:`Fd\bar{3}m` (origin choice 1) in the International Tables for
+Crystallography shows that if an atom is on the 8a position, additional conditions apply (:math:`h=2n+1` or
+:math:`h+k+l=4n` for general reflections). Using these additional conditions, the 222 reflection should in fact
+not be in the list. This can be verified by calculating structure factors for the list of reflections and check if
+there are very small values present.
+
+.. testcode:: ExReflectionGeneratorViolations
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator
+ import numpy as np
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom
+ hkls = generator.getUniqueHKLs(0.7, 3.0)
+
+ # Calculate structure factors for those HKLs
+ fSquared = generator.getFsSquared(hkls)
+
+ # Find HKLs with very small structure factors:
+ zeroFSquared = [(hkl, sf) for hkl, sf in zip(hkls, fSquared) if sf < 1e-9]
+
+ print 'HKL F^2'
+ for hkl, sf in zeroFSquared:
+ print hkl, ' ', np.round(sf, 2)
+
+The output of the above script should show three reflections with very small values for :math:`F^2`. Their indices
+violate the special conditions mentioned in the previous paragraph, so the reflections are actually extinct:
+
+.. testoutput:: ExReflectionGeneratorViolations
+
+ HKL F^2
+ [2,2,2] 0.0
+ [4,4,2] 0.0
+ [6,2,2] 0.0
+
+Those three reflections are included in the list of unique HKLs, because the standard method to determine whether a
+reflection is allowed or not uses the space group symmetry which only reflects the general conditions listed in ITA.
+It is however possible to exclude those reflections at the cost of more computations by making use of the structure
+factor calculation. This can either be done by passing an additional enum-value of the type ReflectionConditionFilter
+to the constructor of ReflectionGenerator or by passing it to the actual generator function:
+
+.. testcode:: ExReflectionGeneratorSF
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator, ReflectionConditionFilter
+ from mantid.kernel import V3D
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom, use structure factors for filtering
+ hkls = generator.getUniqueHKLsUsingFilter(0.7, 3.0, ReflectionConditionFilter.StructureFactor)
+
+ print 'There are', len(hkls), 'unique reflections for Si in the specified resolution range.'
+ print 'The reflection [222] is' + (' not' if not V3D(2, 2, 2) in hkls else '') + ' contained in the list.'
+
+With this option, the three reflections from the example above are missing and as an indicator, the [222] reflection
+is actually checked:
+
+.. testoutput:: ExReflectionGeneratorSF
+
+ There are 17 unique reflections for Si in the specified resolution range.
+ The reflection [222] is not contained in the list.
+
+Other options for filtering are Centering and None. If the latter one is used the reflections are only filtered
+according to their :math:`d`-value to fit the specified range.
+
+Another capability of ReflectionGenerator is the calculation of :math:`d`-values for a list of HKLs, very similar
+to the process for :math:`F^2`:
+
+.. testcode:: ExReflectionGeneratorCalculateD
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator, ReflectionConditionFilter
+ import numpy as np
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom
+ hkls = generator.getUniqueHKLsUsingFilter(0.7, 3.0, ReflectionConditionFilter.StructureFactor)
+
+ # Calculate d and F^2
+ dValues = generator.getDValues(hkls)
+ fSquared = generator.getFsSquared(hkls)
+
+ pg = silicon.getSpaceGroup().getPointGroup()
+
+ # Make list of tuples and sort by d-values, descending, include point group for multiplicity.
+ reflections = sorted([(hkl, d, fsq, len(pg.getEquivalents(hkl))) for hkl, d, fsq in zip(hkls, dValues, fSquared)],
+ key=lambda x: x[1], reverse=True)
+
+ print '{0:<8}{1:>8}{2:>8}{3:>4}'.format('HKL', 'd', 'F^2', 'M')
+ for reflection in reflections:
+ print '{0!s:<8}{1:>8.5f}{2:>8.2f}{3:>4}'.format(*reflection)
+
+This script will print a table with the reflections including their :math:`d`-value, :math:`F^2` and multiplicity due to point group
+symmetry:
+
+.. testoutput:: ExReflectionGeneratorCalculateD
+
+ HKL d F^2 M
+ [2,2,0] 1.92015 645.02 12
+ [3,1,1] 1.63751 263.85 24
+ [4,0,0] 1.35775 377.63 6
+ [3,3,1] 1.24596 154.47 24
+ [4,2,2] 1.10860 221.08 24
+ [3,3,3] 1.04520 90.43 8
+ [5,1,1] 1.04520 90.43 24
+ [4,4,0] 0.96007 129.43 12
+ [5,3,1] 0.91801 52.94 48
+ [6,2,0] 0.85872 75.78 24
+ [5,3,3] 0.82822 31.00 24
+ [4,4,4] 0.78390 44.36 8
+ [5,5,1] 0.76049 18.15 24
+ [7,1,1] 0.76049 18.15 24
+ [6,4,2] 0.72575 25.97 48
+ [5,5,3] 0.70706 10.62 24
+ [7,3,1] 0.70706 10.62 48
+
+Further reading
+~~~~~~~~~~~~~~~
+
+This concept page explains what's available in the Python interface. Some underlying parts may be interesting for C++
+developers, as the concepts of generating and filtering HKLs are pretty much hidden behind the ReflectionGenerator class
+in the Python interface. More detail is available in the generated C++ documentation.
+
+.. categories:: Concepts
diff --git a/docs/source/concepts/DiffractionCalibrationWorkspace.rst b/docs/source/concepts/DiffractionCalibrationWorkspace.rst
index 58ee3f066f1239d1014fabe0b5b590fe423205f9..105e6e31562877adb9521585cdb43bf2205a28ff 100644
--- a/docs/source/concepts/DiffractionCalibrationWorkspace.rst
+++ b/docs/source/concepts/DiffractionCalibrationWorkspace.rst
@@ -57,3 +57,5 @@ various parameters on an instrument view.
* ``offset`` (double array) not used. Value of the legacy calibration file.
The `group` information will still be extracted into separate `GroupingWorkspace` and `MaskWorkspace`.
+
+.. categories:: Concepts
diff --git a/docs/source/concepts/MDNorm.rst b/docs/source/concepts/MDNorm.rst
index 1a1fdf7a1e8cda9fd304ef831f7c0537bcf981d6..8f2d64ba4430c6a34de7cd74f4a404caf449b819 100644
--- a/docs/source/concepts/MDNorm.rst
+++ b/docs/source/concepts/MDNorm.rst
@@ -158,4 +158,6 @@ Current implementation
As of release 3.3, the normalization can be calculated for single crystal
diffraction (:ref:`MDNormSCD <algm-MDNormSCD>`)
and single crystal direct geometry inelastic scattering
-(:ref:`MDNormDirectSC <algm-MDNormDirectSC>`).
+(:ref:`MDNormDirectSC <algm-MDNormDirectSC>`).
+
+.. categories:: Concepts
diff --git a/docs/source/diagrams/PDToPDFgetN-v1_wkflw.dot b/docs/source/diagrams/PDToPDFgetN-v1_wkflw.dot
new file mode 100644
index 0000000000000000000000000000000000000000..23d7d3128f5710701b37233d9e12463bd670748e
--- /dev/null
+++ b/docs/source/diagrams/PDToPDFgetN-v1_wkflw.dot
@@ -0,0 +1,34 @@
+digraph AlignAndFocusPowder {
+ label="AlignAndFocusPowder Flowchart"
+ $global_style
+
+ subgraph params {
+ $param_style
+ InputWorkspace
+ }
+
+ subgraph algoritms {
+ $algorithm_style
+ loadChar [label="PDLoadCharacterizations v1"]
+ loadEvent [label="LoadEventAndCompress v1"]
+ determineChar [label="PDDetermineCharacterizations v1"]
+ alignAndFocus [label="AlignAndFocusPowder v1"]
+ norm [label="NormaliseByCurrent v1"]
+ setUncert [label="SetUncertainties v1"]
+ saveGSS [label="SaveGSS v1"]
+ }
+
+ subgraph decisions {
+ $decision_style
+ }
+
+
+ loadChar -> determineChar
+ loadEvent -> InputWorkspace
+ InputWorkspace -> determineChar
+ InputWorkspace -> alignAndFocus
+ determineChar -> alignAndFocus
+ alignAndFocus -> norm
+ norm -> setUncert
+ setUncert -> saveGSS
+}
diff --git a/docs/source/images/RebbinedWorkspaceNoCompactMDApplied.JPG b/docs/source/images/RebbinedWorkspaceNoCompactMDApplied.JPG
new file mode 100644
index 0000000000000000000000000000000000000000..977b23d832c1c10900d09d518dd9e1745776aa92
Binary files /dev/null and b/docs/source/images/RebbinedWorkspaceNoCompactMDApplied.JPG differ
diff --git a/docs/source/images/RebbinedWorkspaceWithCompactMDApplied.JPG b/docs/source/images/RebbinedWorkspaceWithCompactMDApplied.JPG
new file mode 100644
index 0000000000000000000000000000000000000000..36a4fbc0a412fce0fbb71bd17b3e0c75414ebce4
Binary files /dev/null and b/docs/source/images/RebbinedWorkspaceWithCompactMDApplied.JPG differ
diff --git a/docs/source/interfaces/Engineering_Diffraction.rst b/docs/source/interfaces/Engineering_Diffraction.rst
index fa92627075643a5f5df84bfa47f8633c0877e737..10c7cd263bfae9de07007325f2efb5606b076898 100644
--- a/docs/source/interfaces/Engineering_Diffraction.rst
+++ b/docs/source/interfaces/Engineering_Diffraction.rst
@@ -99,6 +99,24 @@ numbers. For example:
2, 100, 102, 107
3, 300, 310, 320-329, 350-370
+Output
+^^^^^^
+
+Under the output section, the user is provided with an option of
+plotting data in three different formats. One Window - Replacing
+Plots: will replace the previous graph and plot a new graph on top.
+One Window - Waterfall: will plot all the generated focused
+workspace graphs in one window which can be useful while comparing
+various graphs. The Multiple Windows: will plot graph in
+separate windows.
+
+The user also has an option of generated GSS, XYE and OpenGenie
+formatted file by clicking the Output Files checkbox. This will
+generated three different files for each focused output workspace
+in Mantid. These files can be found with appropriate name at location:
+C:\EnginX_Mantid\User\236516\Focus on Windows, the
+EnginX_Mantid folder can be found on Desktop/Home on other platforms.
+
Settings
--------
diff --git a/docs/source/interfaces/HFIR_4Circle_Reduction.rst b/docs/source/interfaces/HFIR_4Circle_Reduction.rst
new file mode 100644
index 0000000000000000000000000000000000000000..01c42636b87472ebfb13e637f5a3ceb0597b8c99
--- /dev/null
+++ b/docs/source/interfaces/HFIR_4Circle_Reduction.rst
@@ -0,0 +1,116 @@
+HFIR Single Crystal Reduction Interface
+=======================================
+
+.. contents:: Table of Contents
+ :local:
+
+Overview
+--------
+
+HFIR single crystalreduction interface is a GUI to download, view and reduce data from
+HFIR's four-circle single crystal diffractometer in SPICE format.
+
+
+Introduction of Tabs
+--------------------
+
+ 1. **Setup and Data Access**: Configure the instrument name, data server URL and directories.
+
+ - Configure the instrument name;
+ - Set up and test HB3A data server's URL;
+ - Configure the directory to save raw data;
+ - Configure the directory to save working result;
+ - Download data from server;
+
+ 2. **View Raw Data**: View 2D image of counts on detector of one measurement.
+
+ - Plot the counts of the 256 by 256 2D detector;
+
+ 3. **Calculate UB**: Calculate UB matrix.
+
+ - Find peak in one measurement;
+ - Option to load Miller index directly from SPICE file;
+ - Calculate UB matrix;
+ - Re-index the peaks;
+
+ 4. **Merge Scan**: Merge all the measurements in a scan.
+
+ - Merge all measuring points in a scan to an MDEventWorkspace in HKL-frame or Q-sample-frame;
+ - Allow various ways to set up UB matrix
+
+ 5. **Refine UB**: Refine UB matrix
+
+ - Disabled becaues it is in development still;
+
+ 6. **Peak Integration**: Integrate peaks
+
+ - Disabled because it is still in development.
+
+Use Cases
+---------
+
+Here are some use cases that can be used as examples.
+
+
+Workflow to calculate UB matrix
++++++++++++++++++++++++++++++++
+
+Here is a typical use case to calculate UB matrix
+
+ 1. User specifies *Experiment* and pushes button *Set*
+
+ 2. User enters tab *View Raw Data*
+
+ 3. User inputs scan number and list all the measuring points
+
+ 4. User views all the measurements
+
+ 5. User finds out the measurement with the strongest reflection and push button use
+
+ 6. GUI shifts to tab *Calculate UB* automatically
+
+ 7. User pushes button *Find Peak* with checking *Load HKL from file*
+
+ 8. GUI finds the peak center and load HKL
+
+ 9. User pushes button *Add peak* to add the peak to table
+
+ 10. User repeats step 2 to 9 to add other peaks
+
+ 11. User select the peaks that are linearly independent and pushes *Calcualte UB*
+
+ 12. GUI calculates UB matrix and show the result
+
+ 13. User may push *Index peak* to use the calculated UB matrix to index peaks in the table to check UB matrix.
+
+
+Workflow to merge measurements in scan
+++++++++++++++++++++++++++++++++++++++
+
+Here is a typical use case to merge all the measuring points (Pt.) in a scan.
+
+ 1. User specifies *Experiment* and pushes button *Set*
+
+ 2. User enters tab *Merge Scan*
+
+ 3. User specifies the UB matrix either by *From tab Calculate UB* or by entering the values to text editor
+
+ 4. User pushes button *Set*.
+
+ 5. User specifies the frame in which the merged data will be in. If the target frame is Q-Sample-Sapce, then there is
+ no need to specify UB matrix;
+
+ 6. User specifies the scan numbers and push button *Add*;
+
+ 7. User specifies the base name for the output MDEventWorkspaces;
+
+ 8. User pushes button *Process*;
+
+ 9. User goes to MantidPlot to view the merged scan by SliceView or Vates.
+
+
+
+Limitation
+----------
+
+- HFIR single crystal reduction GUI supports for instrument HB3A only from release 3.5.0 and nightly.
diff --git a/docs/sphinxext/mantiddoc/autodoc.py b/docs/sphinxext/mantiddoc/autodoc.py
index 7817b508f97653e2d5eb9815fe7730779ad70056..bd4837657e339d297da7d8e938dd67ef301de427 100644
--- a/docs/sphinxext/mantiddoc/autodoc.py
+++ b/docs/sphinxext/mantiddoc/autodoc.py
@@ -21,4 +21,4 @@ def skip(app, what, name, obj, skip, options):
def setup(app):
# Define which methods are skipped when running autodoc
# on a member
- app.connect("autodoc-skip-member", skip)
\ No newline at end of file
+ app.connect("autodoc-skip-member", skip)
diff --git a/docs/sphinxext/mantiddoc/directives/__init__.py b/docs/sphinxext/mantiddoc/directives/__init__.py
index aea156091ece2b95afd69e828c186a76bc2469b3..f6e7c496ec600f27ad1f1ae1b1f68f7995899d6d 100644
--- a/docs/sphinxext/mantiddoc/directives/__init__.py
+++ b/docs/sphinxext/mantiddoc/directives/__init__.py
@@ -7,7 +7,15 @@
'mantiddoc.directives' to be added to the Sphinx extensions configuration.
"""
-import algorithm, alias, attributes, categories, diagram, interface, properties, sourcelink, summary
+import mantiddoc.directives.algorithm
+import mantiddoc.directives.alias
+import mantiddoc.directives.attributes
+import mantiddoc.directives.categories
+import mantiddoc.directives.diagram
+import mantiddoc.directives.interface
+import mantiddoc.directives.properties
+import mantiddoc.directives.sourcelink
+import mantiddoc.directives.summary
def setup(app):
"""
diff --git a/docs/sphinxext/mantiddoc/directives/algorithm.py b/docs/sphinxext/mantiddoc/directives/algorithm.py
index 92afaa96abf20ab2192d2837ac53b722f614fcc4..9333d680eea9274d2bf3de4d7f6ed1b82a5d56f6 100644
--- a/docs/sphinxext/mantiddoc/directives/algorithm.py
+++ b/docs/sphinxext/mantiddoc/directives/algorithm.py
@@ -1,7 +1,4 @@
-from base import AlgorithmBaseDirective
-from docutils import nodes
-from sphinx.locale import _
-from sphinx.util.compat import make_admonition
+from mantiddoc.directives.base import AlgorithmBaseDirective
import os
import re
@@ -205,7 +202,7 @@ class AlgorithmDirective(AlgorithmBaseDirective):
#------------------------------------------------------------------------------------------------------------
-def html_collect_pages(app):
+def html_collect_pages(dummy_app):
"""
Write out unversioned algorithm pages that redirect to the highest version of the algorithm
"""
diff --git a/docs/sphinxext/mantiddoc/directives/alias.py b/docs/sphinxext/mantiddoc/directives/alias.py
index 14000548f1ad1cd5fa59c4c3bf19537dab22a25c..b567306969544d6f79d66e5272eaef34ffc163b6 100644
--- a/docs/sphinxext/mantiddoc/directives/alias.py
+++ b/docs/sphinxext/mantiddoc/directives/alias.py
@@ -1,4 +1,4 @@
-from base import AlgorithmBaseDirective
+from mantiddoc.directives.base import AlgorithmBaseDirective
class AliasDirective(AlgorithmBaseDirective):
diff --git a/docs/sphinxext/mantiddoc/directives/attributes.py b/docs/sphinxext/mantiddoc/directives/attributes.py
index 2c224b2d79852b628654509419dc9e1e5c48efc3..3f45b202129a686f71c19b224fbe38a4c3a3da49 100644
--- a/docs/sphinxext/mantiddoc/directives/attributes.py
+++ b/docs/sphinxext/mantiddoc/directives/attributes.py
@@ -1,6 +1,4 @@
-from properties import PropertiesDirective
-import string
-
+from mantiddoc.directives.properties import PropertiesDirective
class AttributesDirective(PropertiesDirective):
diff --git a/docs/sphinxext/mantiddoc/directives/categories.py b/docs/sphinxext/mantiddoc/directives/categories.py
index 178c05b633724ba16044b6ad1e95e7e7edcb5b13..c651f0b4a13b3445e5967eed588a0daaba1e2bae 100644
--- a/docs/sphinxext/mantiddoc/directives/categories.py
+++ b/docs/sphinxext/mantiddoc/directives/categories.py
@@ -6,7 +6,7 @@
creates "index" pages that lists the contents of each category. The display of each
"index" page is controlled by a jinja2 template.
"""
-from base import AlgorithmBaseDirective, algorithm_name_and_version
+from mantiddoc.directives.base import AlgorithmBaseDirective, algorithm_name_and_version
from sphinx.util.osutil import relative_uri
import os
@@ -299,8 +299,6 @@ def create_category_pages(app):
Arguments:
app: A Sphinx application object
"""
- import os.path
-
env = app.builder.env
# jinja2 html template
template = CATEGORY_PAGE_TEMPLATE
diff --git a/docs/sphinxext/mantiddoc/directives/diagram.py b/docs/sphinxext/mantiddoc/directives/diagram.py
index e9fd957acb915fbaef50a8af7fbd0dac8d43d6df..863d8256ad46a40680288bd5b884f44ea71d6808 100644
--- a/docs/sphinxext/mantiddoc/directives/diagram.py
+++ b/docs/sphinxext/mantiddoc/directives/diagram.py
@@ -1,4 +1,4 @@
-from base import BaseDirective
+from mantiddoc.directives.base import BaseDirective
from sphinx.locale import _
import os, string, subprocess
@@ -63,7 +63,7 @@ class DiagramDirective(BaseDirective):
dot_executable = os.environ["DOT_EXECUTABLE"]
except:
self.add_rst(".. figure:: /images/ImageNotFound.png\n\n" +
- " graphviz not found - diagram could not be rendered.")
+ " graphviz not found - diagram could not be rendered.")
return []
#Make sure we have an output directory
diff --git a/docs/sphinxext/mantiddoc/directives/interface.py b/docs/sphinxext/mantiddoc/directives/interface.py
index 531e6297162a747d64b7dea005e2099b69dd85d7..42dbbaef231993cf19b5f83fb1fcad2809f6e6c7 100644
--- a/docs/sphinxext/mantiddoc/directives/interface.py
+++ b/docs/sphinxext/mantiddoc/directives/interface.py
@@ -1,5 +1,4 @@
-from base import BaseDirective
-from sphinx.locale import _
+from mantiddoc.directives.base import BaseDirective
import os
class InterfaceDirective(BaseDirective):
diff --git a/docs/sphinxext/mantiddoc/directives/properties.py b/docs/sphinxext/mantiddoc/directives/properties.py
index 3fdf7c0d4837eeb32668294db801a2cb4405c9c4..2e14a854077bea111e82ccfd43608175a5733b77 100644
--- a/docs/sphinxext/mantiddoc/directives/properties.py
+++ b/docs/sphinxext/mantiddoc/directives/properties.py
@@ -1,7 +1,7 @@
-from base import AlgorithmBaseDirective
+#pylint: disable=invalid-name
+from mantiddoc.directives.base import AlgorithmBaseDirective
import string
-
class PropertiesDirective(AlgorithmBaseDirective):
"""
@@ -33,14 +33,14 @@ class PropertiesDirective(AlgorithmBaseDirective):
header = ('Name', 'Default', 'Description')
for i in xrange(ifunc.numParams()):
- properties.append((
- ifunc.parameterName(i),
- str(ifunc.getParameterValue(i)),
- ifunc.paramDescription(i)
- ))
+ properties.append((ifunc.parameterName(i),
+ str(ifunc.getParameterValue(i)),
+ ifunc.paramDescription(i)
+ ))
self.add_rst(self.make_header("Properties (fitting parameters)"))
else: # this is an Algorithm
- alg = self.create_mantid_algorithm(self.algorithm_name(), self.algorithm_version())
+ alg = self.create_mantid_algorithm(self.algorithm_name(),
+ self.algorithm_version())
alg_properties = alg.getProperties()
if len(alg_properties) == 0:
return False
@@ -100,7 +100,7 @@ class PropertiesDirective(AlgorithmBaseDirective):
# Added 10 to the length to ensure if table_content is 0 that
# the table is still displayed.
col_sizes = [max( (len(row[i] * 10) + 10) for row in table_content)
- for i in range(len(header_content))]
+ for i in range(len(header_content))]
# Use the column widths as a means to formatting columns.
formatter = ' '.join('{%d:<%d}' % (index,col) for index, col in enumerate(col_sizes))
@@ -138,7 +138,7 @@ class PropertiesDirective(AlgorithmBaseDirective):
if (direction_string[prop.direction] == "Output") and \
(not isinstance(prop, IWorkspaceProperty)):
default_prop = ""
- elif (prop.isValid == ""):
+ elif prop.isValid == "":
default_prop = self._create_property_default_string(prop)
else:
default_prop = "*Mandatory*"
@@ -161,14 +161,14 @@ class PropertiesDirective(AlgorithmBaseDirective):
# Convert to int, then float, then any string
try:
val = int(default)
- if (val >= 2147483647):
+ if val >= 2147483647:
defaultstr = "*Optional*"
else:
defaultstr = str(val)
except:
try:
val = float(default)
- if (val >= 1e+307):
+ if val >= 1e+307:
defaultstr = "*Optional*"
else:
defaultstr = str(val)
@@ -214,7 +214,7 @@ class PropertiesDirective(AlgorithmBaseDirective):
allowedValueString = str(prop.allowedValues)
# 4 allows for ['']
- if len(allowedValueString) > 4:
+ if len(allowedValueString) > 4:
##make sure the last sentence ended with a full stop (or equivalent)
if (not desc.rstrip().endswith(".")) \
and (not desc.rstrip().endswith("!")) \
@@ -227,7 +227,7 @@ class PropertiesDirective(AlgorithmBaseDirective):
if (not item.startswith(".")) and (not item[-4:].startswith(".")):
isFileExts = False
break
-
+
prefixString = " Allowed values: "
if isFileExts:
prefixString = " Allowed extensions: "
diff --git a/docs/sphinxext/mantiddoc/directives/sourcelink.py b/docs/sphinxext/mantiddoc/directives/sourcelink.py
index 8ff7598f5290b338d98fd45c75198c6f80274f1d..1e436b1f71b441e1c1e965677e7e8391578d7249 100644
--- a/docs/sphinxext/mantiddoc/directives/sourcelink.py
+++ b/docs/sphinxext/mantiddoc/directives/sourcelink.py
@@ -87,7 +87,7 @@ class SourceLinkDirective(AlgorithmBaseDirective):
raise SourceLinkError(error_string)
try:
- self.output_to_page(file_paths,file_name,sanity_checks);
+ self.output_to_page(file_paths,file_name,sanity_checks)
except SourceLinkError as err:
error_string += str(err) + "\n"
@@ -112,12 +112,15 @@ class SourceLinkDirective(AlgorithmBaseDirective):
suggested_path = "os_agnostic_path_to_file_from_source_root"
if len(path_list) > 1:
suggested_path = path_list[0].replace(self.source_root, "")
- raise SourceLinkError("Found multiple possibilities for " + file_name + "." + extension + "\n" +
- "Possible matches" + str(path_list) + "\n" +
- "Specify one using the " + extension + " option\n" +
- "e.g. \n" +
- ".. sourcelink:\n" +
- " :" + extension + ": " + suggested_path)
+ raise SourceLinkError("Found multiple possibilities for " +
+ file_name + "." + extension + "\n" +
+ "Possible matches" + str(path_list) +
+ "\n" +
+ "Specify one using the " + extension +
+ " option\n" +
+ "e.g. \n" +
+ ".. sourcelink:\n" +
+ " :" + extension + ": " + suggested_path)
return self.file_lookup[file_name][extension]
except KeyError:
@@ -147,7 +150,7 @@ class SourceLinkDirective(AlgorithmBaseDirective):
builddir = os.path.join(builddir, "..", "..")
builddir = os.path.abspath(builddir)
- for dirName, subdirList, fileList in os.walk(self.source_root):
+ for dirName, dummy_subdirList, fileList in os.walk(self.source_root):
if dirName.startswith(builddir):
continue # don't check or add to the cache
for fname in fileList:
@@ -183,29 +186,31 @@ class SourceLinkDirective(AlgorithmBaseDirective):
suggested_path = "os_agnostic_path_to_file_from_Code/Mantid"
if len(valid_ext_list) == 0:
raise SourceLinkError("No file possibilities for " + file_name + " have been found\n" +
- "Please specify a better one using the :filename: opiton or use the " + str(self.file_types.keys()) + " options\n" +
- "e.g. \n" +
- ".. sourcelink:\n" +
- " :" + self.file_types.keys()[0] + ": " + suggested_path + "\n "+
- "or \n" +
- ".. sourcelink:\n" +
- " :filename: " + file_name)
+ "Please specify a better one using the :filename: opiton or use the " +
+ str(self.file_types.keys()) + " options\n" +
+ "e.g. \n" +
+ ".. sourcelink:\n" +
+ " :" + self.file_types.keys()[0] + ": " + suggested_path + "\n "+
+ "or \n" +
+ ".. sourcelink:\n" +
+ " :filename: " + file_name)
#if the have a cpp we should also have a h
if ("cpp" in valid_ext_list) or ("h" in valid_ext_list):
if ("cpp" not in valid_ext_list) or ("h" not in valid_ext_list):
raise SourceLinkError("Only one of .h and .cpp found for " + file_name + "\n" +
- "valid files found for " + str(valid_ext_list) + "\n" +
- "Please specify the missing one using an " + str(self.file_types.keys()) + " option\n" +
- "e.g. \n" +
- ".. sourcelink:\n" +
- " :" + self.file_types.keys()[0] + ": " + suggested_path)
+ "valid files found for " + str(valid_ext_list) + "\n" +
+ "Please specify the missing one using an " +
+ str(self.file_types.keys()) + " option\n" +
+ "e.g. \n" +
+ ".. sourcelink:\n" +
+ " :" + self.file_types.keys()[0] + ": " + suggested_path)
return
def output_path_to_page(self, filepath, extension):
"""
Outputs the source link for a file to the rst page
"""
- dirName,fName = os.path.split(filepath)
+ dummy_dirName,fName = os.path.split(filepath)
self.add_rst(self.file_types[extension] + ": `" + fName + " <" + self.convert_path_to_github_url(filepath) + ">`_\n\n")
return
diff --git a/docs/sphinxext/mantiddoc/directives/summary.py b/docs/sphinxext/mantiddoc/directives/summary.py
index cb0403e75fe1f092343fbfb26867452cd0b95583..71870dc64b418cfa06419eadf0eccb074e92664e 100644
--- a/docs/sphinxext/mantiddoc/directives/summary.py
+++ b/docs/sphinxext/mantiddoc/directives/summary.py
@@ -1,4 +1,4 @@
-from base import AlgorithmBaseDirective
+from mantiddoc.directives.base import AlgorithmBaseDirective
class SummaryDirective(AlgorithmBaseDirective):
diff --git a/docs/sphinxext/mantiddoc/doctest.py b/docs/sphinxext/mantiddoc/doctest.py
index 3bd4bea3581dcdcfd5a281f716c43a475eca4ae0..d6d176e0159c852380fc41e67e5d3993c89f0b7d 100644
--- a/docs/sphinxext/mantiddoc/doctest.py
+++ b/docs/sphinxext/mantiddoc/doctest.py
@@ -172,8 +172,10 @@ class TestSuiteReport(object):
@property
def nfailed(self):
def sum_failure(fails, case):
- if case.failed: return fails + 1
- else: return fails
+ if case.failed:
+ return fails + 1
+ else:
+ return fails
return reduce(sum_failure, self.testcases, 0)
@property
@@ -196,7 +198,7 @@ class TestCaseReport(object):
@property
def passed(self):
- return (self.failure_descr == "")
+ return self.failure_descr == ""
@property
def failed(self):
@@ -307,7 +309,7 @@ class DocTestOutputParser(object):
% text[1])
results = results[2:] # trim off top two lines of header information
maintests, cleanup = self.__split_on_cleanup(results)
- overall_success = not (maintests[0] == FAILURE_MARKER)
+ overall_success = not maintests[0] == FAILURE_MARKER
if overall_success:
testcases = self.__parse_success(fullname, maintests)
diff --git a/docs/sphinxext/mantiddoc/tools/screenshot.py b/docs/sphinxext/mantiddoc/tools/screenshot.py
index e6e5eea328b0e1d2affaefb49dd89ebcffb17b99..ae3fcc38ef56cdf21781dd35b73886696dd37095 100644
--- a/docs/sphinxext/mantiddoc/tools/screenshot.py
+++ b/docs/sphinxext/mantiddoc/tools/screenshot.py
@@ -86,14 +86,14 @@ def custominterface_screenshot(name, directory, ext = ".png", widget_name = None
dlg = threadsafe_call(iface_mgr.createSubWindow, name, None)
if dlg is None:
- raise RuntimeError("Interface '%s' could not be created" % name)
+ raise RuntimeError("Interface '%s' could not be created" % name)
if widget_name:
- widget = dlg.findChild(QWidget, widget_name)
- if widget is None:
- raise RuntimeError("Widget '%s' does not exist in interface '%s'" % (widget_name, name))
- picture = Screenshot(widget, name.replace(' ','_') + "_" + widget_name + "_widget" + ext, directory)
+ widget = dlg.findChild(QWidget, widget_name)
+ if widget is None:
+ raise RuntimeError("Widget '%s' does not exist in interface '%s'" % (widget_name, name))
+ picture = Screenshot(widget, name.replace(' ','_') + "_" + widget_name + "_widget" + ext, directory)
else:
- picture = Screenshot(dlg, name.replace(' ','_') + "_interface" + ext, directory)
+ picture = Screenshot(dlg, name.replace(' ','_') + "_interface" + ext, directory)
threadsafe_call(dlg.close)
return picture
diff --git a/instrument/Bilby_Definition.xml b/instrument/Bilby_Definition.xml
index 81029ac258ae427777382b1c5f79f82a6478b94b..baa7b5eabc3295fd9b5a62f63f452d9a2aff8810 100644
--- a/instrument/Bilby_Definition.xml
+++ b/instrument/Bilby_Definition.xml
@@ -26,7 +26,7 @@
<component name="Source" type="source">
<location x="0.0" y="0.0" />
<parameter name="z">
- <logfile id="L1_chopper_value" eq="1*value"/>
+ <logfile id="L1_chopper_value" eq="-1*value"/>
</parameter>
</component>
<type name="source" is="Source" />
@@ -503,4 +503,4 @@
</instrument>
-
\ No newline at end of file
+
diff --git a/instrument/LET_Definition.xml b/instrument/LET_Definition.xml
index a79bb314a74bb19549a4f00e59d65464e242a800..7080cc17821f2160e36408f35283559141c0a7f8 100644
--- a/instrument/LET_Definition.xml
+++ b/instrument/LET_Definition.xml
@@ -6,7 +6,7 @@
xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd"
name="LET" valid-from ="1900-01-31 23:59:59"
valid-to ="2014-02-10 23:59:59"
- last-modified="2015-03-09 00:00:00">
+ last-modified="2015-03-09 00:00:00">
<defaults>
<length unit="meter"/>
@@ -672,6 +672,32 @@
<value units="microseconds" val="0"/>
</parameter>
</component-link>
+<!-- Chopper position -->
+ <component type="chopper-position">
+ <location z="-1.5"/>
+ <!--description is="The component provides sample-choper distance, used
+ to estimate chopper delay time and Tobyfit resolution calculations."/-->
+ <parameter name="initial_phase">
+ <value val="-0."/>
+ <description is="The initial rotation phase of the disk used to caluclate the time
+ for neutrons arriving at the chopper according to the formula time = delay + initial_phase/Speed"/>
+ </parameter>
+ <parameter name="ChopperDelayLog" type="string">
+ <value val="Chopper5_Disk2_phase"/>
+ </parameter>
+ <parameter name="ChopperSpeedLog" type="string">
+ <value val="Chopper5_Disk2_speed"/>
+ </parameter>
+ <parameter name="FilterBaseLog" type="string">
+ <value val="good_uah_log"/>
+ </parameter>
+ <!-- if the log above should be used as it is or
+ one should calculate its derivative -->
+ <parameter name="filter_with_derivative" type="bool">
+ <value val="True"/>
+ </parameter>
+ </component>
+ <type name="chopper-position" is="ChopperPos"></type>
<!-- Set the same across the rest of the instrument -->
<component-link name = "LET">
diff --git a/instrument/LET_Definition_dr2to12.xml b/instrument/LET_Definition_dr2to12.xml
index b3aaebc9f94ba4bf49a735c4af897b356ee0477a..063d32140eec5dc1f503d07252fb7045d2f94b1c 100644
--- a/instrument/LET_Definition_dr2to12.xml
+++ b/instrument/LET_Definition_dr2to12.xml
@@ -25,6 +25,7 @@
components defined in this file to face a position by default -->
<components-are-facing x="0.0" y="0.0" z="0.0" />
</defaults>
+
<!-- LIST OF PHYSICAL COMPONENTS (which the instrument consists of) -->
<!-- detector components -->
<properties>
@@ -89,6 +90,7 @@
</cylinder>
<algebra val="some-shape" />
</type>
+
<!-- Sample-position types -->
<type name="nickel-holder" is="SamplePos">
@@ -666,6 +668,35 @@
<id start="12470001" end="12471024" />
<id start="12480001" end="12481024" />
</idlist>
+<!-- Chopper position -->
+ <component type="chopper-position">
+ <location z="-1.5"/>
+ <!--description is="The component provides sample-choper distance, used
+ to estimate chopper delay time and Tobyfit resolution calculations."/-->
+ <parameter name="initial_phase">
+ <value val="-0."/>
+ <description is="The initial rotation phase of the disk used to caluclate the time
+ for neutrons arriving at the chopper according to the formula time = delay + initial_phase/Speed"/>
+ </parameter>
+ <parameter name="ChopperDelayLog" type="string">
+ <value val="Chopper5_Disk2_phase"/>
+ </parameter>
+ <parameter name="ChopperSpeedLog" type="string">
+ <value val="Chopper5_Disk2_speed"/>
+ </parameter>
+ <parameter name="FilterBaseLog" type="string">
+ <value val="good_uah_log"/>
+ </parameter>
+ <!-- if the log above should be used as it is or
+ one should calculate its derivative -->
+ <parameter name="filter_with_derivative" type="bool">
+ <value val="True"/>
+ </parameter>
+
+ </component>
+ <type name="chopper-position" is="ChopperPos"></type>
+
+
<!-- DETECTOR PARAMETERS -->
<component-link name="monitors">
<parameter name="DelayTime">
diff --git a/instrument/MAPS_Definition.xml b/instrument/MAPS_Definition.xml
index 5945f1ff1bdb314b8188dd48326e052f114087e9..ac7e3e16db7e15e5001ef00ef8a6f2cdbefc77c4 100644
--- a/instrument/MAPS_Definition.xml
+++ b/instrument/MAPS_Definition.xml
@@ -40,6 +40,36 @@
<location />
</component>
<type name="sample-position" is="SamplePos"></type>
+
+<!-- Chopper position -->
+ <component type="chopper-position">
+ <location z="-1.895"/>
+ <!--description is="The component provides sample-choper distance, used
+ to estimate chopper delay time and Tobyfit resolution calculations."/-->
+ <parameter name="initial_phase">
+ <value val="130000."/>
+ <description is="The initial rotation phase of the disk used to caluclate the time
+ for neutrons arriving at the chopper according to the formula time = delay + initial_phase/Speed"/>
+ </parameter>
+ <parameter name="ChopperDelayLog" type="string">
+ <value val="Chopper_delay"/>
+ </parameter>
+ <parameter name="ChopperSpeedLog" type="string">
+ <value val="Chopper_Speed"/>
+ </parameter>
+ <parameter name="FilterBaseLog" type="string">
+ <value val="good_uah_log"/>
+ </parameter>
+ <!-- if the log above should be used as it is or
+ one should calculate its derivative -->
+ <parameter name="filter_with_derivative" type="bool">
+ <value val="True"/>
+ </parameter>
+
+ </component>
+ <type name="chopper-position" is="ChopperPos"></type>
+
+
<component type="monitors" idlist="monitors">
diff --git a/instrument/MARI_Definition.xml b/instrument/MARI_Definition.xml
index 41a9900ffe0290b5c789aa22b3bd8cc6bd0e2d95..5ef895cb7b30160d062f8001a44364d251267eb1 100644
--- a/instrument/MARI_Definition.xml
+++ b/instrument/MARI_Definition.xml
@@ -42,6 +42,38 @@
<!-- CHOPPERS -->
+ <!-- Chopper position -->
+ <component type="chopper-position">
+ <location z="-1.689"/>
+ <!--description is="The component provides sample-choper distance, used
+ to estimate chopper delay time and Tobyfit resolution calculations."/ -->
+ <!-- if chopper "a": t_offset = -3281.8/SPEED + 16.2;
+ if chopper "g": t_offset = -2822.5/SPEED + 9.7
+ if chopper "s": t_offset = -3326.8/SPEED + 7.7
+ -->
+ <parameter name="initial_phase">
+ <value val="-3000."/>
+ <description is="The initial rotation phase of the disk used to caluclate the time
+ for neutrons arriving at the chopper according to the formula time = delay + initial_phase/Speed"/>
+ </parameter>
+ <parameter name="ChopperDelayLog" type="string">
+ <value val="fermi_delay"/>
+ </parameter>
+ <parameter name="ChopperSpeedLog" type="string">
+ <value val="fermi_speed"/>
+ </parameter>
+ <parameter name="FilterBaseLog" type="string">
+ <value val="good_uah_log"/>
+ </parameter>
+ <!-- if the log above should be used as it is or
+ one should calculate its derivative -->
+ <parameter name="filter_with_derivative" type="bool">
+ <value val="True"/>
+ </parameter>
+
+ </component>
+ <type name="chopper-position" is="ChopperPos"></type>
+
<component type="fermi-chopper">
<location y="-0.1" z="-1.689" />
@@ -50,9 +82,11 @@
</parameter>
<parameter name="Delay (us)">
<logfile id="fermi_delay" extract-single-value-as="last_value" />
- <description is="Delay is the time chopper waits for...? (test description)"/>
+ <description is="Delay is the time between the moment when beam hits moderator and the moment,
+ when neutron passes through chopper for the first time."/>
</parameter>
- </component>
+
+ </component>
<type name="fermi-chopper" is="chopper">
<cylinder id="body">
<centre-of-bottom-base x="0.0" y="0.0" z="0.0" />
diff --git a/instrument/MERLIN_Definition_after2013_4.xml b/instrument/MERLIN_Definition_after2013_4.xml
index fd69107e5c7fdd2600996cd426f5dfb5fb84af57..4bb893e054a38bf4804f602fffac62d6dc918b69 100644
--- a/instrument/MERLIN_Definition_after2013_4.xml
+++ b/instrument/MERLIN_Definition_after2013_4.xml
@@ -62,8 +62,31 @@
<!-- Chopper position -->
<component type="chopper-position">
<location z="-1.8"/>
+ <!--description is="The component provides sample-choper distance, used
+ to estimate chopper delay time and Tobyfit resolution calculations."/-->
+ <parameter name="initial_phase">
+ <value val="-490000."/>
+ <description is="The initial rotation phase of the disk used to caluclate the time
+ for neutrons arriving at the chopper according to the formula time = delay + initial_phase/Speed"/>
+ </parameter>
+ <parameter name="ChopperDelayLog" type="string">
+ <value val="Chopper_delay"/>
+ </parameter>
+ <parameter name="ChopperSpeedLog" type="string">
+ <value val="Chopper_Speed"/>
+ </parameter>
+ <parameter name="FilterBaseLog" type="string">
+ <value val="good_uah_log"/>
+ </parameter>
+ <!-- if the log above should be used as it is or
+ one should calculate its derivative -->
+ <parameter name="filter_with_derivative" type="bool">
+ <value val="True"/>
+ </parameter>
+
</component>
- <type name="chopper-position" is="ChopperPos"></type>
+ <type name="chopper-position" is="ChopperPos"></type>
+
<!-- DETECTORS -->
diff --git a/instrument/Schema/IDF/1.0/IDFSchema.xsd b/instrument/Schema/IDF/1.0/IDFSchema.xsd
index 4b2ea38bf59fbf02f4d836c6ae2b28c8e0c6e0f5..d2a3c79d955145c7a7aeef77f51e1ef3634fff75 100644
--- a/instrument/Schema/IDF/1.0/IDFSchema.xsd
+++ b/instrument/Schema/IDF/1.0/IDFSchema.xsd
@@ -289,9 +289,11 @@
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:anyAttribute/>
+
</xs:extension>
</xs:simpleContent>
</xs:complexType>
+
</xs:element>
<xs:element name="properties">
<xs:complexType>
diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 7c00c508283118881ab92f0d7c8e6b079bc1f0f3..7cd45300f74869139a60cf613343c6613fe322d6 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -6,6 +6,7 @@ add_subdirectory(Interface/ui)
add_subdirectory(lib1to2/gui)
add_subdirectory(PyChop)
add_subdirectory(TofConverter)
+add_subdirectory(HFIR_4Circle_Reduction)
# Chain all required interface custom targets into CompilePyUI
add_custom_target(CompilePyUI DEPENDS
@@ -15,6 +16,7 @@ add_custom_target(CompilePyUI DEPENDS
CompileUITofConverter
CompileUIUI
CompileUILib1To2
+ CompileUIHFIR_4Circle_Reduction
)
set ( TEST_PY_FILES
diff --git a/scripts/HFIR_4Circle_Reduction.py b/scripts/HFIR_4Circle_Reduction.py
new file mode 100644
index 0000000000000000000000000000000000000000..89742c6bfa9f75bb50d994cf3148f7d9e1c84476
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction.py
@@ -0,0 +1,17 @@
+#pylint: disable=invalid-name
+from HFIR_4Circle_Reduction import reduce4circleGUI
+from PyQt4 import QtGui
+import sys
+
+def qapp():
+ if QtGui.QApplication.instance():
+ _app = QtGui.QApplication.instance()
+ else:
+ _app = QtGui.QApplication(sys.argv)
+ return _app
+
+app = qapp()
+
+reducer = reduce4circleGUI.MainWindow() #the main ui class in this file is called MainWindow
+reducer.show()
+app.exec_()
diff --git a/scripts/HFIR_4Circle_Reduction/CMakeLists.txt b/scripts/HFIR_4Circle_Reduction/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67fe46df205d951ff83380c933f71c88d5325604
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/CMakeLists.txt
@@ -0,0 +1,8 @@
+include(UiToPy)
+
+# List of UIs to Auto convert
+set( UI_FILES
+ MainWindow.ui
+)
+
+UiToPy( UI_FILES CompileUIHFIR_4Circle_Reduction)
diff --git a/scripts/HFIR_4Circle_Reduction/MainWindow.ui b/scripts/HFIR_4Circle_Reduction/MainWindow.ui
new file mode 100644
index 0000000000000000000000000000000000000000..4f7fa462e7008c7cf9e167e822ad5b0b47996aca
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/MainWindow.ui
@@ -0,0 +1,2312 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>1292</width>
+ <height>783</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>4-Circle Reduction</string>
+ </property>
+ <widget class="QWidget" name="centralwidget">
+ <layout class="QHBoxLayout" name="horizontalLayout_11">
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_General">
+ <item>
+ <widget class="QLabel" name="label_exp">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Experiment</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_exp">
+ <property name="minimumSize">
+ <size>
+ <width>40</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_setExp">
+ <property name="text">
+ <string>Set</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_11">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_15">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Unit Cell</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_16">
+ <property name="text">
+ <string>a</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_a">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_23">
+ <property name="text">
+ <string>b</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_b">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_24">
+ <property name="text">
+ <string>c</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_c">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_25">
+ <property name="text">
+ <string>alpha</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_alpha">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_26">
+ <property name="text">
+ <string>beta</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_beta">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_27">
+ <property name="text">
+ <string>gamma</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_gamma">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_Tab">
+ <item>
+ <widget class="QTabWidget" name="tabWidget">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="currentIndex">
+ <number>0</number>
+ </property>
+ <widget class="QWidget" name="tab">
+ <attribute name="title">
+ <string>Setup && Data Access</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_5">
+ <item row="1" column="0">
+ <widget class="QTextEdit" name="textEdit">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="readOnly">
+ <bool>true</bool>
+ </property>
+ <property name="html">
+ <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;">
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-weight:600;">1. Configure the data reduction</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(a) Do not modify ServerURL unless necessary;</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(b) Click 'Apply' to check internet connection and directories;</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(c) If 'Time out' is popped out, try to click 'Apply' again. Server may not be able to respond promptly.</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:10pt; font-style:italic;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-weight:600;">2. Start to reduce data</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(a) Set</span><span style=" font-size:10pt;"> Experiment</span></p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="0">
+ <spacer name="verticalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="0">
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>Configuration</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_11">
+ <item row="1" column="2">
+ <widget class="QPushButton" name="pushButton_testURLs">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>200</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Test</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QPushButton" name="pushButton_browseLocalDataDir">
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="3">
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="lineEdit_localSpiceDir">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory for local data storage</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_instrument">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Instrument</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_dir">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory for local data storage</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Data Directory</string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QComboBox" name="comboBox_instrument">
+ <item>
+ <property name="text">
+ <string>HB3A</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QPushButton" name="pushButton_useDefaultDir">
+ <property name="font">
+ <font>
+ <pointsize>10</pointsize>
+ </font>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Use default set up</p><p><br/></p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Load Default</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="1">
+ <widget class="QLineEdit" name="lineEdit_workDir">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory to save outcome of the data reduction</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="lineEdit_url">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_url">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>URL of the http server to download HB3A data</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Server URL</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QPushButton" name="pushButton_browseWorkDir">
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QLabel" name="label_2">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>140</width>
+ <height>1</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>140</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory to save outcome of the data reduction</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Working Direcotry</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="2">
+ <widget class="QPushButton" name="pushButton_applySetup">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Apply</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QGroupBox" name="groupBox_2">
+ <property name="title">
+ <string>Data Download</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_12">
+ <item row="0" column="2">
+ <widget class="QPushButton" name="pushButton_browseLocalCache">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Scans List</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QComboBox" name="comboBox_mode">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Mode &quot;download&quot;: download data to local disk;</p><p>Mode &quot;http server only&quot;: download data to cache, process and delete cached data upon returning</p></body></html></string>
+ </property>
+ <item>
+ <property name="text">
+ <string>Download Complete Experiment</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Download Selected Scans</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_localSrcDir">
+ <property name="toolTip">
+ <string><html><head/><body><p>Cache on local disk. The dowloaded data will be saved to here. </p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_datamode">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Download Mode</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_4">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>140</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>140</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Destination</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="6">
+ <spacer name="horizontalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Minimum</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="1" column="2">
+ <widget class="QPushButton" name="pushButton_downloadExpData">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p><span style=" font-weight:400;">Download scans specified by 'Scans List'; </span></p><p><span style=" font-weight:400;">If 'Scans List' is empty, then the complete experiment data will be downloaded</span></p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Download</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="lineEdit_downloadScans"/>
+ </item>
+ <item row="2" column="2">
+ <widget class="QPushButton" name="pushButton_ListScans">
+ <property name="text">
+ <string>List Scans</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <spacer name="verticalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_4">
+ <attribute name="title">
+ <string>View Raw Data</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_9">
+ <item row="0" column="0">
+ <layout class="QGridLayout" name="gridLayout_3">
+ <item row="0" column="3">
+ <layout class="QVBoxLayout" name="verticalLayout_5">
+ <item>
+ <layout class="QGridLayout" name="gridLayout"/>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_3">
+ <property name="title">
+ <string>Scan</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QLineEdit" name="lineEdit_run">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>10</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>10000</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_setScanInfo">
+ <property name="text">
+ <string>Set</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_showPtList">
+ <property name="text">
+ <string>List Pt.</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="Line" name="line">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_4">
+ <property name="title">
+ <string> Pt</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <widget class="QLineEdit" name="lineEdit_rawDataPtNo">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>1000</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_plotRawPt">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Plot</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_usePt4UB">
+ <property name="toolTip">
+ <string><html><head/><body><p>Use this peak to calcualate UB matrix</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Use</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Minimum</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_8">
+ <item>
+ <widget class="QPushButton" name="pushButton_prevPtNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>30</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>40</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Previous Pt. No</p></body></html></string>
+ </property>
+ <property name="text">
+ <string><---|</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_7">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>5</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_nextPtNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>30</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>40</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>|--></string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_6">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item row="0" column="0">
+ <widget class="MplGraphicsView" name="graphicsView">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_2">
+ <attribute name="title">
+ <string>Calculate UB</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_6">
+ <item row="0" column="0">
+ <layout class="QVBoxLayout" name="verticalLayout_4">
+ <item>
+ <widget class="QGroupBox" name="groupBox_7">
+ <property name="title">
+ <string>Add Peak</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_2">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_scanNo">
+ <property name="text">
+ <string>Scan Number</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="8">
+ <widget class="QLineEdit" name="lineEdit_H">
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>40</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_PtNo">
+ <property name="text">
+ <string>Pt Number</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="12">
+ <widget class="QLineEdit" name="lineEdit_sampleQy">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="11">
+ <widget class="QLabel" name="label_11">
+ <property name="text">
+ <string>K</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="13">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string>L</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="8">
+ <widget class="QLineEdit" name="lineEdit_sampleQx">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="6">
+ <widget class="QLabel" name="label_7">
+ <property name="text">
+ <string> Q-Sample </string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLineEdit" name="lineEdit_ptNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="11">
+ <widget class="QLabel" name="label_9">
+ <property name="text">
+ <string>Y</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="14">
+ <widget class="QLineEdit" name="lineEdit_sampleQz">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="7">
+ <widget class="QLabel" name="label_8">
+ <property name="text">
+ <string>X</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_scanNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="12">
+ <widget class="QLineEdit" name="lineEdit_K">
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="14">
+ <widget class="QLineEdit" name="lineEdit_L">
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="7">
+ <widget class="QLabel" name="label_12">
+ <property name="text">
+ <string>H</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="13">
+ <widget class="QLabel" name="label_10">
+ <property name="text">
+ <string>Z</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <spacer name="horizontalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="6">
+ <widget class="QLabel" name="label_31">
+ <property name="text">
+ <string>Miller Index</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4">
+ <widget class="QPushButton" name="pushButton_findPeak">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Find Peak</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="4">
+ <widget class="QCheckBox" name="checkBox_loadHKLfromFile">
+ <property name="font">
+ <font>
+ <pointsize>9</pointsize>
+ </font>
+ </property>
+ <property name="text">
+ <string>Load HKL from file</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_7">
+ <item>
+ <widget class="UBMatrixPeakTable" name="tableWidget_peaksCalUB"/>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_8">
+ <item>
+ <widget class="QPushButton" name="pushButton_addPeakToCalUB">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Add Peak</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_roundHKLInt">
+ <property name="font">
+ <font>
+ <pointsize>9</pointsize>
+ </font>
+ </property>
+ <property name="text">
+ <string>RoundHKL to int</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_11">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_deleteUBPeak">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>200</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Delete</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_clearUBPeakTable">
+ <property name="text">
+ <string>Clear</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_7">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_13">
+ <item>
+ <widget class="QLabel" name="label_32">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="font">
+ <font>
+ <pointsize>14</pointsize>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>UB Matrix</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_6">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="UBMatrixTable" name="tableWidget_ubMatrix">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>360</width>
+ <height>0</height>
+ </size>
+ </property>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_12">
+ <item>
+ <widget class="QPushButton" name="pushButton_calUB">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Calculate UB</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_8">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_acceptUB">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Accept</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_9">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_8">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_9">
+ <item>
+ <widget class="QPushButton" name="pushButton_indexUBPeaks">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Index Peak</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_12">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_resetPeakHKLs">
+ <property name="text">
+ <string>Reset HKL</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_advsetup">
+ <attribute name="title">
+ <string>Merge Scan</string>
+ </attribute>
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QGroupBox" name="groupBox_5">
+ <property name="title">
+ <string>UB Matrix</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_13">
+ <item>
+ <widget class="UBMatrixTable" name="tableWidget_ubSiceView">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>16777215</width>
+ <height>150</height>
+ </size>
+ </property>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <item row="0" column="0">
+ <property name="text">
+ <string>1</string>
+ </property>
+ </item>
+ <item row="1" column="1">
+ <property name="text">
+ <string>1</string>
+ </property>
+ </item>
+ <item row="2" column="2">
+ <property name="text">
+ <string>1</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_13">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QGridLayout" name="gridLayout_4">
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_3">
+ <property name="text">
+ <string>From tab 'Caclulate UB'</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QRadioButton" name="radioButton_ubFromTab1">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <spacer name="horizontalSpacer_9">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="0">
+ <widget class="QRadioButton" name="radioButton_ubFromTab3">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLabel" name="label_28">
+ <property name="text">
+ <string>From tab 'Refine UB'</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QPlainTextEdit" name="plainTextEdit_ubInput">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <layout class="QVBoxLayout" name="verticalLayout_15">
+ <item>
+ <widget class="QRadioButton" name="radioButton_ubFromList">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_15">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_14">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_setUBSliceView">
+ <property name="text">
+ <string>Set</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_10">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_6">
+ <property name="title">
+ <string>Process Data</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_14">
+ <item>
+ <layout class="QGridLayout" name="gridLayout_10">
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_29">
+ <property name="toolTip">
+ <string><html><head/><body><p>For MDEventsWorkspace with merged runs</p><p><br/></p><p>For example:</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Base Workspace Name</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_30">
+ <property name="text">
+ <string>Scans List</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_listScansSliceView"/>
+ </item>
+ <item row="0" column="2">
+ <widget class="QPushButton" name="pushButton_addScanSliceView">
+ <property name="text">
+ <string>Add</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QLineEdit" name="lineEdit_baseMergeMDName">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QComboBox" name="comboBox_mergeScanFrame">
+ <property name="minimumSize">
+ <size>
+ <width>140</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Type of frame that the final merged scan will be in.</p></body></html></string>
+ </property>
+ <item>
+ <property name="text">
+ <string>HKL-Space</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Q-Sample-Space</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_10">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Expanding</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="2">
+ <widget class="QPushButton" name="pushButton_process4SliceView">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Process</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="ProcessTableWidget" name="tableWidget_sliceViewProgress">
+ <property name="toolTip">
+ <string><html><head/><body><p>? columns: </p><p><br/></p><p>1. Scan number</p><p>2. Number of Pts.</p><p>3. Status: </p><p>(a) done</p><p>(b) error with error message</p><p>(c) on-going</p><p>(d) empty as not yet</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_3">
+ <attribute name="title">
+ <string>Refine UB</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_8">
+ <item row="0" column="0">
+ <layout class="QVBoxLayout" name="verticalLayout_6">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_14">
+ <item>
+ <widget class="QLabel" name="label_14">
+ <property name="text">
+ <string>Scan</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_scanRefineUB">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Maximum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_13">
+ <property name="text">
+ <string>Pt.</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_ptRefineUB">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_addToRefine">
+ <property name="toolTip">
+ <string><html><head/><body><p>Add a data point or data points (defined by scan number and pt number) to the list to refine UB matrix; </p><p><br/></p><p>Scan number can be a list of integers;</p><p><br/></p><p>Pt number can be empty such that all Pt. of that scan will be searched for peak and then used to refine UB matrix</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Add</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_addAllRefineUB">
+ <property name="text">
+ <string>Add All</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_15">
+ <item>
+ <widget class="UBMatrixTable" name="tableWidget_refinedUB">
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ </widget>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_7"/>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_10">
+ <item>
+ <widget class="QPushButton" name="pushButton_acceptRefinedUB">
+ <property name="text">
+ <string>Accept</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_resetRefinedUB">
+ <property name="text">
+ <string>Reset</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QGridLayout" name="gridLayout_7">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_17">
+ <property name="text">
+ <string>a</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_19">
+ <property name="text">
+ <string>c</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4">
+ <widget class="QLabel" name="label_21">
+ <property name="text">
+ <string>beta</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="label_18">
+ <property name="text">
+ <string>b</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLabel" name="label_20">
+ <property name="text">
+ <string>alpha</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <widget class="QLabel" name="label_22">
+ <property name="text">
+ <string>gamma</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="lineEdit_bUnitCell"/>
+ </item>
+ <item row="1" column="2">
+ <widget class="QLineEdit" name="lineEdit_cUnitCell"/>
+ </item>
+ <item row="1" column="3">
+ <widget class="QLineEdit" name="lineEdit_alphaUnitCell"/>
+ </item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="lineEdit_bError"/>
+ </item>
+ <item row="1" column="4">
+ <widget class="QLineEdit" name="lineEdit_betaUnitCell"/>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLineEdit" name="lineEdit_aUnitCell"/>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLineEdit" name="lineEdit_cError"/>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLineEdit" name="lineEdit_aError"/>
+ </item>
+ <item row="2" column="3">
+ <widget class="QLineEdit" name="lineEdit_alphaError"/>
+ </item>
+ <item row="2" column="4">
+ <widget class="QLineEdit" name="lineEdit_betaError"/>
+ </item>
+ <item row="1" column="5">
+ <widget class="QLineEdit" name="lineEdit_gammaUnitCell"/>
+ </item>
+ <item row="2" column="5">
+ <widget class="QLineEdit" name="lineEdit_gammaError"/>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="0">
+ <spacer name="verticalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_indexPeak">
+ <attribute name="title">
+ <string>Peak Integration</string>
+ </attribute>
+ <layout class="QVBoxLayout" name="verticalLayout_11">
+ <item>
+ <layout class="QGridLayout" name="gridLayout_13">
+ <item row="1" column="6">
+ <widget class="QCheckBox" name="checkBox_adaptQBkgd">
+ <property name="text">
+ <string>Adaptive Q Background</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_scanIntegratePeak">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QCheckBox" name="checkBox_cylinder">
+ <property name="text">
+ <string>Cylinder</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="3">
+ <widget class="QLineEdit" name="lineEdit_bkgdInnerR"/>
+ </item>
+ <item row="1" column="5">
+ <widget class="QLineEdit" name="lineEdit_bkgdOuterR"/>
+ </item>
+ <item row="2" column="4">
+ <widget class="QLabel" name="label_36">
+ <property name="text">
+ <string>Percent Background</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="7">
+ <widget class="QCheckBox" name="checkBox_integrateOnEdge">
+ <property name="text">
+ <string>Integrate on Edge</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_5">
+ <property name="text">
+ <string>Scan Number</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_34">
+ <property name="text">
+ <string>Peak Radius</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLineEdit" name="lineEdit_ptNumListIntPeak"/>
+ </item>
+ <item row="2" column="7">
+ <widget class="QComboBox" name="comboBox_cylinderIntOption"/>
+ </item>
+ <item row="0" column="7">
+ <widget class="QPushButton" name="pushButton_integratePeak">
+ <property name="text">
+ <string>Integrate Peaks</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="5">
+ <widget class="QLineEdit" name="lineEdit_cylinderBkgdPercent"/>
+ </item>
+ <item row="1" column="4">
+ <widget class="QLabel" name="label_35">
+ <property name="text">
+ <string>Background Outer Radius</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <widget class="QComboBox" name="comboBox_3">
+ <property name="toolTip">
+ <string><html><head/><body><p>Choose the name of the tab, in which the UB matrix is used to convert signals to HKL frame.</p></body></html></string>
+ </property>
+ <item>
+ <property name="text">
+ <string>Calculate UB</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Merge Scan</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Refine UB</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="2" column="6">
+ <widget class="QComboBox" name="comboBox_cylinderProfile">
+ <item>
+ <property name="text">
+ <string>Gaussian</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLabel" name="label_39">
+ <property name="text">
+ <string>Cylinder Length</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <widget class="QLabel" name="label_37">
+ <property name="text">
+ <string>Background Inner Radius</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="3">
+ <widget class="QLineEdit" name="lineEdit_cylinderLength"/>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_33">
+ <property name="text">
+ <string>Pt Numbers</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="lineEdit_peakRadius"/>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="IntegratePeaksTableWidget" name="tableWidget_peakIndex"/>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QMenuBar" name="menubar">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>1292</width>
+ <height>25</height>
+ </rect>
+ </property>
+ <widget class="QMenu" name="menuFile">
+ <property name="title">
+ <string>File</string>
+ </property>
+ <addaction name="separator"/>
+ <addaction name="actionExit"/>
+ <addaction name="separator"/>
+ </widget>
+ <widget class="QMenu" name="menuTools">
+ <property name="title">
+ <string>Tools</string>
+ </property>
+ <addaction name="actionSave_Session"/>
+ <addaction name="actionLoad_Session"/>
+ <addaction name="separator"/>
+ </widget>
+ <addaction name="menuFile"/>
+ <addaction name="menuTools"/>
+ </widget>
+ <widget class="QStatusBar" name="statusbar"/>
+ <action name="actionNew">
+ <property name="text">
+ <string>New</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+N</string>
+ </property>
+ </action>
+ <action name="actionOpen">
+ <property name="text">
+ <string>Open</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+O</string>
+ </property>
+ </action>
+ <action name="actionSave">
+ <property name="text">
+ <string>Save</string>
+ </property>
+ </action>
+ <action name="actionLog">
+ <property name="text">
+ <string>Log</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+L</string>
+ </property>
+ </action>
+ <action name="actionSave_Session">
+ <property name="text">
+ <string>Save Session</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+Shift+S</string>
+ </property>
+ </action>
+ <action name="actionExit">
+ <property name="text">
+ <string>Exit</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+Q</string>
+ </property>
+ </action>
+ <action name="actionLoad_Session">
+ <property name="text">
+ <string>Load Session</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+Shift+L</string>
+ </property>
+ </action>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>MplGraphicsView</class>
+ <extends>QGraphicsView</extends>
+ <header>mplgraphicsview.h</header>
+ </customwidget>
+ <customwidget>
+ <class>UBMatrixPeakTable</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ <customwidget>
+ <class>UBMatrixTable</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ <customwidget>
+ <class>ProcessTableWidget</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ <customwidget>
+ <class>IntegratePeaksTableWidget</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/scripts/HFIR_4Circle_Reduction/NTableWidget.py b/scripts/HFIR_4Circle_Reduction/NTableWidget.py
new file mode 100644
index 0000000000000000000000000000000000000000..198725f41ef1492b822dfddb572ecb7c75b0a3aa
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/NTableWidget.py
@@ -0,0 +1,268 @@
+#pylint: disable=C0103,R0904
+# N(DAV)TableWidget
+#
+
+from PyQt4 import QtGui, QtCore
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ _fromUtf8 = lambda s: s
+
+
+class NTableWidget(QtGui.QTableWidget):
+ """
+ NdavTableWidget inherits from QTableWidget by extending the features
+ for easy application.
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ QtGui.QTableWidget.__init__(self, parent)
+
+ self._myParent = parent
+
+ self._myHeaderList = None
+ self._myColumnTypeList = None
+
+ return
+
+ def append_row(self, row_value_list, type_list=None):
+ """
+
+ :param row_value_list:
+ :return:
+ """
+ # Check input
+ assert isinstance(row_value_list, list)
+ if type_list is not None:
+ assert isinstance(type_list, list)
+ assert len(row_value_list) == len(type_list)
+ else:
+ type_list = self._myColumnTypeList
+ if len(row_value_list) != self.columnCount():
+ ret_msg = 'Input number of values (%d) is different from ' \
+ 'column number (%d).' % (len(row_value_list), self.columnCount())
+ return False, ret_msg
+ else:
+ ret_msg = ''
+
+ # Insert new row
+ row_number = self.rowCount()
+ self.insertRow(row_number)
+
+ # Set values
+ for i_col in xrange(min(len(row_value_list), self.columnCount())):
+ item = QtGui.QTableWidgetItem()
+ item.setText(_fromUtf8(str(row_value_list[i_col])))
+ item.setFlags(item.flags() & ~QtCore.Qt.ItemIsEditable)
+ if type_list[i_col] == 'checkbox':
+ self.set_check_box(row_number, i_col, False)
+ else:
+ self.setItem(row_number, i_col, item)
+ # END-FOR(i_col)
+
+ return True, ret_msg
+
+ def delete_rows(self, row_number_list):
+ """ Delete rows
+ :param row_number_list:
+ :return:
+ """
+ # Check and re-order row numbers
+ assert isinstance(row_number_list, list)
+ row_number_list.sort(reverse=True)
+
+ for row_number in row_number_list:
+ self.removeRow(row_number)
+
+ return
+
+ def get_selected_rows(self):
+ """
+
+ :return: list of row numbers that are selected
+ """
+ rows_list = list()
+ index_status = self._myColumnTypeList.index('checkbox')
+ for i_row in xrange(self.rowCount()):
+ is_checked = self.get_row_value(i_row)[index_status]
+ if is_checked:
+ rows_list.append(i_row)
+
+ return rows_list
+
+ def get_cell_value(self, row_index, col_index):
+ """
+
+ :param row_index:
+ :param col_index:
+ :return:
+ """
+ c_type = self._myColumnTypeList[col_index]
+
+ return_value = None
+ if c_type == 'checkbox':
+ # Check box
+ cell_i_j = self.cellWidget(row_index, col_index)
+ assert isinstance(cell_i_j, QtGui.QCheckBox)
+ return_value = cell_i_j.isChecked()
+ else:
+ # Regular cell
+ item_i_j = self.item(row_index, col_index)
+ assert isinstance(item_i_j, QtGui.QTableWidgetItem)
+ value = str(item_i_j.text())
+ if c_type == 'int':
+ return_value = int(value)
+ elif c_type == 'float':
+ return_value = float(value)
+
+ return return_value
+
+ def get_row_value(self, row_index):
+ """
+ :param row_index:
+ :return: list of objects
+ """
+ if row_index < 0 or row_index >= self.rowCount():
+ raise IndexError('Index of row (%d) is out of range.' % row_index)
+
+ ret_list = list()
+ for i_col in xrange(len(self._myColumnTypeList)):
+ c_type = self._myColumnTypeList[i_col]
+
+ if c_type == 'checkbox':
+ # Check box
+ cell_i_j = self.cellWidget(row_index, i_col)
+ assert isinstance(cell_i_j, QtGui.QCheckBox)
+ is_checked = cell_i_j.isChecked()
+ ret_list.append(is_checked)
+ else:
+ # Regular cell
+ item_i_j = self.item(row_index, i_col)
+ assert isinstance(item_i_j, QtGui.QTableWidgetItem)
+ value = str(item_i_j.text()).strip()
+ if len(value) > 0:
+ if c_type == 'int':
+ value = int(value)
+ elif c_type == 'float':
+ value = float(value)
+ else:
+ value = None
+
+ ret_list.append(value)
+ # END-IF-ELSE
+ # END-FOR
+
+ return ret_list
+
+ def init_setup(self, column_tup_list):
+ """ Initial setup
+ :param column_tup_list: list of 2-tuple as string (column name) and string (data type)
+ :return:
+ """
+ # Define column headings
+ num_cols = len(column_tup_list)
+
+ # Class variables
+ self._myHeaderList = list()
+ self._myColumnTypeList = list()
+
+ for c_tup in column_tup_list:
+ c_name = c_tup[0]
+ c_type = c_tup[1]
+ self._myHeaderList.append(c_name)
+ self._myColumnTypeList.append(c_type)
+
+ self.setColumnCount(num_cols)
+ self.setHorizontalHeaderLabels(self._myHeaderList)
+
+ return
+
+ def init_size(self, num_rows, num_cols):
+ """
+
+ :return:
+ """
+ self.setColumnCount(num_cols)
+ self.setRowCount(num_rows)
+
+ return
+
+ def set_check_box(self, row, col, state):
+ """ function to add a new select checkbox to a cell in a table row
+ won't add a new checkbox if one already exists
+ """
+ # Check input
+ assert isinstance(state, bool)
+
+ # Check if cellWidget exists
+ if self.cellWidget(row,col):
+ # existing: just set the value
+ self.cellWidget(row, col).setChecked(state)
+ else:
+ # case to add checkbox
+ checkbox = QtGui.QCheckBox()
+ checkbox.setText('')
+ checkbox.setChecked(state)
+
+ # Adding a widget which will be inserted into the table cell
+ # then centering the checkbox within this widget which in turn,
+ # centers it within the table column :-)
+ self.setCellWidget(row, col, checkbox)
+ # END-IF-ELSE
+
+ return
+
+ def set_value_cell(self, row, col, value=''):
+ """
+ Set value to a cell with integer, float or string
+ :param row:
+ :param col:
+ :param value:
+ :return:
+ """
+ # Check
+ if row < 0 or row >= self.rowCount() or col < 0 or col >= self.columnCount():
+ raise IndexError('Input row number or column number is out of range.')
+
+ # Init cell
+ cell_item = QtGui.QTableWidgetItem()
+ cell_item.setText(_fromUtf8(str(value)))
+ cell_item.setFlags(cell_item.flags() & ~QtCore.Qt.ItemIsEditable)
+
+ self.setItem(row, col, cell_item)
+
+ return
+
+ def update_cell_value(self, row, col, value):
+ """
+
+ :param row:
+ :param col:
+ :param value:
+ :return:
+ """
+ cell_item = self.item(row, col)
+ cell_widget = self.cellWidget(row, col)
+
+ if cell_item is not None and cell_widget is None:
+ # TableWidgetItem
+ assert isinstance(cell_item, QtGui.QTableWidgetItem)
+ if isinstance(value, float):
+ cell_item.setText(_fromUtf8('%.7f' % value))
+ else:
+ cell_item.setText(_fromUtf8(str(value)))
+ elif cell_item is None and cell_widget is not None:
+ # TableCellWidget
+ if isinstance(cell_item, QtGui.QCheckBox) is True:
+ cell_item.setChecked(value)
+ else:
+ raise TypeError('Cell of type %s is not supported.' % str(type(cell_item)))
+ else:
+ raise TypeError('Table cell (%d, %d) is in an unsupported situation!' % (row, col))
+
+ return
diff --git a/scripts/HFIR_4Circle_Reduction/__init__.py b/scripts/HFIR_4Circle_Reduction/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..04a95e8315757618d54dc05da33da722b0774d94
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/__init__.py
@@ -0,0 +1,2 @@
+#pylint: disable=invalid-name
+#pylint: disable=invalid-name
diff --git a/scripts/HFIR_4Circle_Reduction/fourcircle_utility.py b/scripts/HFIR_4Circle_Reduction/fourcircle_utility.py
new file mode 100644
index 0000000000000000000000000000000000000000..35dc1fe387e6bd1597eed0a9eb6c52f8c08811f8
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/fourcircle_utility.py
@@ -0,0 +1,188 @@
+#pylint: disable=W0633,too-many-branches
+__author__ = 'wzz'
+
+import os
+import urllib2
+import socket
+
+
+def check_url(url, read_lines=False):
+ """ Check whether a URL is valid
+ :param url:
+ :return: boolean, error message
+ """
+ lines = None
+ try:
+ # Access URL
+ url_stream = urllib2.urlopen(url, timeout=2)
+
+ # Read lines
+ if read_lines is True:
+ lines = url_stream.readlines()
+ except urllib2.URLError as url_error:
+ url_stream = url_error
+ except socket.timeout:
+ return False, 'Time out. Try again!'
+
+ # Return result
+ if url_stream.code in (200, 401):
+ url_good = True
+ else:
+ url_good = False
+
+ # Close connect
+ url_stream.close()
+
+ # Return
+ if read_lines is True:
+ return url_good, lines
+ if url_good is False:
+ error_message = 'Unable to access %s. Check internet access. Code %d' % (url, url_stream.code)
+ else:
+ error_message = ''
+
+ return url_good, error_message
+
+
+def get_scans_list(server_url, exp_no, return_list=False):
+ """ Get list of scans under one experiment
+ :param server_url:
+ :param exp_no:
+ :return: message
+ """
+ if server_url.endswith('/') is False:
+ server_url = '%s/' % server_url
+ data_dir_url = '%sexp%d/Datafiles' % (server_url, exp_no)
+
+ does_exist, raw_lines = check_url(data_dir_url, read_lines=True)
+ if does_exist is False:
+ return "Experiment %d's URL %s cannot be found." % (exp_no, data_dir_url)
+
+ # Scan through the index page
+ scan_list = []
+ header = 'HB3A_exp%04d_scan' % exp_no
+ for line in raw_lines:
+ if line.count(header) > 0:
+ # try to find file HB3A_exp0123_scan6789.dat
+ term = line.split(header)[1].split('.dat')[0]
+ scan = int(term)
+ # check
+ if '%04d' % scan == term:
+ scan_list.append(scan)
+ # END_FOR
+ scan_list = sorted(scan_list)
+ if return_list is True:
+ return scan_list
+
+ message = 'Experiment %d: Scan from %d to %d' % (exp_no, scan_list[0], scan_list[-1])
+
+ return message
+
+
+def get_scans_list_local_disk(local_dir, exp_no):
+ """ Get scans from a specified directory on local disk
+ :param local_dir:
+ :param exp_no:
+ :return:
+ """
+ scan_list = []
+
+ file_names = os.listdir(local_dir)
+ header = 'HB3A_exp%04d_scan' % exp_no
+ for name in file_names:
+ if name.count(header) > 0:
+ scan = int(name.split(header)[1].split('.dat')[0])
+ scan_list.append(scan)
+
+ scan_list = sorted(scan_list)
+
+ if len(scan_list) == 0:
+ message = 'Experiment %d: No scan can be found.' % exp_no
+ else:
+ message = 'Experiment %d: Scan from %d to %d ' % (exp_no, scan_list[0], scan_list[-1])
+ num_skip_scans = scan_list[-1] - scan_list[0] + 1 - len(scan_list)
+ if num_skip_scans > 0:
+ message += 'with %d ' % num_skip_scans
+ else:
+ message += 'without '
+ message += 'missing scans.'
+
+ return message
+
+
+def parse_int_array(int_array_str):
+ """ Validate whether the string can be divided into integer strings.
+ Allowed: a, b, c-d, e, f
+ :param int_array_str:
+ :return:
+ """
+ int_array_str = str(int_array_str)
+ if int_array_str == "":
+ return True, []
+
+ # Split by ","
+ term_level_0 = int_array_str.split(",")
+ integer_list = []
+
+ # For each term
+ err_msg = ""
+ ret_status = True
+
+ for level0_term in term_level_0:
+ level0_term = level0_term.strip()
+
+ # split upon dash -
+ num_dashes = level0_term.count("-")
+ if num_dashes == 0:
+ # one integer
+ value_str = level0_term
+ try:
+ int_value = int(value_str)
+ if str(int_value) != value_str:
+ ret_status = False
+ err_msg = "Contains non-integer string %s." % value_str
+ except ValueError:
+ ret_status = False
+ err_msg = "String %s is not an integer." % (value_str)
+ else:
+ integer_list.append(int_value)
+
+ elif num_dashes == 1:
+ # Integer range
+ two_terms = level0_term.split("-")
+ temp_list = []
+ for i in xrange(2):
+ value_str = two_terms[i]
+ try:
+ int_value = int(value_str)
+ if str(int_value) != value_str:
+ ret_status = False
+ err_msg = "Contains non-integer string %s." % (value_str)
+ except ValueError:
+ ret_status = False
+ err_msg = "String %s is not an integer." % (value_str)
+ else:
+ temp_list.append(int_value)
+
+ # break loop
+ if ret_status is False:
+ break
+ # END_FOR(i)
+ integer_list.extend(range(temp_list[0], temp_list[1]+1))
+
+ else:
+ # Undefined situation
+ ret_status = False
+ err_msg = "Term %s contains more than 1 dash." % level0_term
+ # END-IF-ELSE
+
+ # break loop if something is wrong
+ if ret_status is False:
+ break
+ # END-FOR(level0_term)
+
+ # Return with false
+ if ret_status is False:
+ return False, err_msg
+
+ return True, integer_list
diff --git a/scripts/HFIR_4Circle_Reduction/guiutility.py b/scripts/HFIR_4Circle_Reduction/guiutility.py
new file mode 100644
index 0000000000000000000000000000000000000000..79237a5729470b372017478b24a0564159d67fb1
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/guiutility.py
@@ -0,0 +1,164 @@
+#
+# GUI Utility Methods
+#
+from PyQt4 import QtGui
+
+
+def parse_float_array(array_str):
+ """ Parse a string to an array of float
+ :param array_str:
+ :return: boolean, list of floats/error message
+ """
+ print array_str
+ assert isinstance(array_str, str)
+ array_str = array_str.replace(',', ' ')
+ array_str = array_str.replace('\n', ' ')
+ array_str = array_str.replace('\t ', ' ')
+ array_str = array_str.strip()
+ print '[DB] After processing: ', array_str
+
+ float_str_list = array_str.split()
+ float_list = list()
+ for float_str in float_str_list:
+ try:
+ value = float(float_str)
+ except ValueError as value_error:
+ return False, 'Unable to parse %s due to %s.' % (float_str, str(value_error))
+ else:
+ float_list.append(value)
+ # END-FOR
+
+ return True, float_list
+
+
+def parse_integer_list(array_str):
+ """ Parse a string to an array of integer separated by ','
+ also, the format as 'a-b' is supported too
+ :param array_str:
+ :return: boolean, list of floats/error message
+ """
+ assert isinstance(array_str, str)
+ array_str = array_str.replace(' ', '')
+ array_str = array_str.replace('\n', '')
+ array_str = array_str.replace('\t ', '')
+
+ int_str_list = array_str.split(',')
+ integer_list = list()
+ for int_str in int_str_list:
+
+ try:
+ int_value = int(int_str)
+ integer_list.append(int_value)
+ except ValueError:
+ num_dash = int_str.count('-')
+ if num_dash == 1:
+ terms = int_str.split('-')
+ try:
+ start_value = int(terms[0])
+ end_value = int(terms[1])
+ except ValueError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ elif num_dash == 2 and int_str.startswith('-'):
+ terms = int_str[1:].split('-')
+ try:
+ start_value = int(terms[0])*-1
+ end_value = int(terms[1])
+ except ValueError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ elif num_dash == 3:
+ terms = int_str.split('-')
+ try:
+ start_value = -1*int(terms[1])
+ end_value = -1*int(terms[3])
+ except ValueError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ except IndexError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ else:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+
+ integer_list.extend(xrange(start_value, end_value+1))
+ # END-FOR
+
+ return integer_list
+
+
+def parse_float_editors(line_edits):
+ """
+ :param line_edits:
+ :return: (True, list of floats); (False, error message)
+ """
+ # Set flag
+ return_single_value = False
+
+ if isinstance(line_edits, QtGui.QLineEdit) is True:
+ line_edit_list = [line_edits]
+ return_single_value = True
+ elif isinstance(line_edits, list) is True:
+ line_edit_list = line_edits
+ else:
+ raise RuntimeError('Input is not LineEdit or list of LineEdit.')
+
+ error_message = ''
+ float_list = []
+
+ for line_edit in line_edit_list:
+ assert isinstance(line_edit, QtGui.QLineEdit)
+ try:
+ str_value = str(line_edit.text()).strip()
+ float_value = float(str_value)
+ except ValueError as value_err:
+ error_message += 'Unable to parse to integer. %s\n' % (str(value_err))
+ else:
+ float_list.append(float_value)
+ # END-TRY
+ # END-FOR
+
+ if len(error_message) > 0:
+ return False, error_message
+ elif return_single_value is True:
+ return True, float_list[0]
+
+ return True, float_list
+
+
+def parse_integers_editors(line_edits):
+ """
+ :param line_edits:
+ :return: (True, list of integers); (False, error message)
+ """
+ # Set flag
+ return_single_value = False
+
+ if isinstance(line_edits, QtGui.QLineEdit) is True:
+ line_edit_list = [line_edits]
+ return_single_value = True
+ elif isinstance(line_edits, list) is True:
+ line_edit_list = line_edits
+ else:
+ raise RuntimeError('Input is not LineEdit or list of LineEdit.')
+
+ error_message = ''
+ integer_list = []
+
+ for line_edit in line_edit_list:
+ assert isinstance(line_edit, QtGui.QLineEdit)
+ try:
+ str_value = str(line_edit.text()).strip()
+ int_value = int(str_value)
+ except ValueError as value_err:
+ error_message += 'Unable to parse to integer. %s\n' % (str(value_err))
+ else:
+ if str_value != '%d' % int_value:
+ error_message += 'Value %s is not a proper integer.\n' % str_value
+ else:
+ integer_list.append(int_value)
+ # END-TRY
+ # END-FOR
+
+ if len(error_message) > 0:
+ return False, error_message
+ elif return_single_value is True:
+ return True, integer_list[0]
+
+ return True, integer_list
diff --git a/scripts/HFIR_4Circle_Reduction/hfctables.py b/scripts/HFIR_4Circle_Reduction/hfctables.py
new file mode 100644
index 0000000000000000000000000000000000000000..dba8cb64a3aefb4adff82b540655251d9fe41311
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/hfctables.py
@@ -0,0 +1,385 @@
+#pylint: disable=W0403,C0103,R0901,R0904
+import numpy
+import NTableWidget as tableBase
+
+# UB peak information table
+Peak_Integration_Table_Setup = [('Scan', 'int'),
+ ('Pt', 'int'),
+ ('H', 'float'),
+ ('K', 'float'),
+ ('L', 'float'),
+ ('Q_x', 'float'),
+ ('Q_y', 'float'),
+ ('Q_z', 'float'),
+ ('Intensity', 'float')]
+
+
+class IntegratePeaksTableWidget(tableBase.NTableWidget):
+ """
+ Extended table widget for peak integration
+ """
+ def __init__(self, parent):
+ """
+ :param parent:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ return
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ self.init_setup(Peak_Integration_Table_Setup)
+
+ return
+
+
+class UBMatrixTable(tableBase.NTableWidget):
+ """
+ Extended table for UB matrix
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ # Matrix
+ self._matrix = numpy.ndarray((3, 3), float)
+ for i in xrange(3):
+ for j in xrange(3):
+ self._matrix[i][j] = 0.
+
+ return
+
+ def _set_to_table(self):
+ """
+ Set values in holder '_matrix' to TableWidget
+ :return:
+ """
+ for i_row in xrange(3):
+ for j_col in xrange(3):
+ self.update_cell_value(i_row, j_col, self._matrix[i_row][j_col])
+
+ return
+
+ def get_matrix(self):
+ """
+ Get the copy of the matrix
+ :return:
+ """
+ # print '[DB] MatrixTable: _Matrix = ', self._matrix
+ return self._matrix.copy()
+
+ def set_from_list(self, element_array):
+ """
+ Set table value including holder and QTable from a 1D numpy array
+ :param element_array:
+ :return:
+ """
+ # Check
+ assert isinstance(element_array, list)
+ assert len(element_array) == 9
+
+ # Set value
+ i_array = 0
+ for i in xrange(3):
+ for j in xrange(3):
+ self._matrix[i][j] = element_array[i_array]
+ i_array += 1
+
+ # Set to table
+ self._set_to_table()
+
+ return
+
+ def set_from_matrix(self, matrix):
+ """
+ Set value to both holder and QTable from a numpy 3 x 3 matrix
+ :param matrix:
+ :return:
+ """
+ # Check
+ assert isinstance(matrix, numpy.ndarray)
+ assert matrix.shape == (3, 3)
+
+ for i in xrange(3):
+ for j in xrange(3):
+ self._matrix[i][j] = matrix[i][j]
+
+ self._set_to_table()
+
+ return
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ # self.init_size(3, 3)
+
+ for i in xrange(3):
+ for j in xrange(3):
+ self.set_value_cell(i, j)
+
+ self._set_to_table()
+
+ return
+
+
+# UB peak information table
+UB_Peak_Table_Setup = [('Scan', 'int'),
+ ('Pt', 'int'),
+ ('H', 'float'),
+ ('K', 'float'),
+ ('L', 'float'),
+ ('Q_x', 'float'),
+ ('Q_y', 'float'),
+ ('Q_z', 'float'),
+ ('Selected', 'checkbox'),
+ ('m1', 'float'),
+ ('Error', 'float')]
+
+
+class UBMatrixPeakTable(tableBase.NTableWidget):
+ """
+ Extended table for peaks used to calculate UB matrix
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ return
+
+ def get_exp_info(self, row_index):
+ """
+ Get experiment information from a row
+ :return: scan number, pt number
+ """
+ assert isinstance(row_index, int)
+
+ scan_number = self.get_cell_value(row_index, 0)
+ assert isinstance(scan_number, int)
+ pt_number = self.get_cell_value(row_index, 1)
+ assert isinstance(pt_number, int)
+
+ return scan_number, pt_number
+
+ def get_hkl(self, row_index):
+ """
+ Get reflection's miller index
+ :param row_index:
+ :return:
+ """
+ assert isinstance(row_index, int)
+
+ m_h = self.get_cell_value(row_index, 2)
+ m_k = self.get_cell_value(row_index, 3)
+ m_l = self.get_cell_value(row_index, 4)
+
+ assert isinstance(m_h, float)
+ assert isinstance(m_k, float)
+ assert isinstance(m_l, float)
+
+ return m_h, m_k, m_l
+
+ def get_scan_pt(self, row_number):
+ """
+ Get Scan and Pt from a row
+ :param row_number:
+ :return:
+ """
+ scan_number = self.get_cell_value(row_number, 0)
+ pt_number = self.get_cell_value(row_number, 1)
+
+ return scan_number, pt_number
+
+ def is_selected(self, row_index):
+ """
+
+ :return:
+ """
+ if row_index < 0 or row_index >= self.rowCount():
+ raise IndexError('Input row number %d is out of range [0, %d)' % (row_index, self.rowCount()))
+
+ col_index = UB_Peak_Table_Setup.index(('Selected', 'checkbox'))
+
+ return self.get_cell_value(row_index, col_index)
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ self.init_setup(UB_Peak_Table_Setup)
+
+ return
+
+ def set_hkl(self, i_row, hkl, error=None):
+ """
+ Set HKL to table
+ :param irow:
+ :param hkl:
+ """
+ # Check
+ assert isinstance(i_row, int)
+ assert isinstance(hkl, list)
+
+ i_col_h = UB_Peak_Table_Setup.index(('H', 'float'))
+ i_col_k = UB_Peak_Table_Setup.index(('K', 'float'))
+ i_col_l = UB_Peak_Table_Setup.index(('L', 'float'))
+
+ self.update_cell_value(i_row, i_col_h, hkl[0])
+ self.update_cell_value(i_row, i_col_k, hkl[1])
+ self.update_cell_value(i_row, i_col_l, hkl[2])
+
+ if error is not None:
+ i_col_error = UB_Peak_Table_Setup.index(('Error', 'float'))
+ self.update_cell_value(i_row, i_col_error, error)
+
+ return
+
+ def update_hkl(self, i_row, h, k, l):
+ """ Update HKL value
+ """
+ self.update_cell_value(i_row, 2, h)
+ self.update_cell_value(i_row, 3, k)
+ self.update_cell_value(i_row, 4, l)
+
+ return
+
+
+# Processing status table
+Process_Table_Setup = [('Scan', 'int'),
+ ('Number Pt', 'int'),
+ ('Status', 'str'),
+ ('Merged Workspace', 'str'),
+ ('Group Name', 'str'),
+ ('Select', 'checkbox')]
+
+
+class ProcessTableWidget(tableBase.NTableWidget):
+ """
+ Extended table for peaks used to calculate UB matrix
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ return
+
+ def append_scans(self, scans):
+ """ Append rows
+ :param scans:
+ :return:
+ """
+ # Check
+ assert isinstance(scans, list)
+
+ # Append rows
+ for scan in scans:
+ row_value_list = [scan, 0, 'In Queue', '', '', False]
+ status, err = self.append_row(row_value_list)
+ if status is False:
+ raise RuntimeError(err)
+
+ return
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ self.init_setup(Process_Table_Setup)
+
+ return
+
+ def set_scan_pt(self, scan_no, pt_list):
+ """
+ :param scan_no:
+ :param pt_list:
+ :return:
+ """
+ # Check
+ assert isinstance(scan_no, int)
+
+ num_rows = self.rowCount()
+ set_done = False
+ for i_row in xrange(num_rows):
+ tmp_scan_no = self.get_cell_value(i_row, 0)
+ if scan_no == tmp_scan_no:
+ self.update_cell_value(i_row, 1, len(pt_list))
+ set_done = True
+ break
+ # END-FOR
+
+ if set_done is False:
+ return 'Unable to find scan %d in table.' % scan_no
+
+ return ''
+
+ def set_status(self, scan_no, status):
+ """
+ Set the status for merging scan to QTable
+ :param status:
+ :return:
+ """
+ # Check
+ assert isinstance(scan_no, int)
+
+ num_rows = self.rowCount()
+ set_done = False
+ for i_row in xrange(num_rows):
+ tmp_scan_no = self.get_cell_value(i_row, 0)
+ if scan_no == tmp_scan_no:
+ self.update_cell_value(i_row, 2, status)
+ set_done = True
+ break
+ # END-FOR
+
+ if set_done is False:
+ return 'Unable to find scan %d in table.' % scan_no
+
+ return ''
+
+ def set_ws_names(self, scan_num, merged_md_name, ws_group_name):
+ """
+ Set the output workspace and workspace group's names to QTable
+ :param merged_md_name:
+ :param ws_group_name:
+ :return:
+ """
+ # Check
+ assert isinstance(scan_num, int)
+ assert isinstance(merged_md_name, str) or merged_md_name is None
+ assert isinstance(ws_group_name, str) or ws_group_name is None
+
+ num_rows = self.rowCount()
+ set_done = False
+ for i_row in xrange(num_rows):
+ tmp_scan_no = self.get_cell_value(i_row, 0)
+ if scan_num == tmp_scan_no:
+ if merged_md_name is not None:
+ self.update_cell_value(i_row, 3, merged_md_name)
+ if ws_group_name is not None:
+ self.update_cell_value(i_row, 4, ws_group_name)
+ set_done = True
+ break
+ # END-FOR
+
+ if set_done is False:
+ return 'Unable to find scan %d in table.' % scan_num
+
+ return
diff --git a/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py b/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
new file mode 100644
index 0000000000000000000000000000000000000000..152ffc29c4775c6f98b8b67befe0554a36d66032
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
@@ -0,0 +1,1255 @@
+#pylint: disable=invalid-name,too-many-public-methods,too-many-arguments,non-parent-init-called,R0902,too-many-branches,C0302
+import os
+import numpy as np
+
+from PyQt4 import QtGui
+
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar2
+from matplotlib.figure import Figure
+import matplotlib.image
+
+MplLineStyles = ['-' , '--' , '-.' , ':' , 'None' , ' ' , '']
+MplLineMarkers = [
+ ". (point )",
+ "* (star )",
+ "x (x )",
+ "o (circle )",
+ "s (square )",
+ "D (diamond )",
+ ", (pixel )",
+ "v (triangle_down )",
+ "^ (triangle_up )",
+ "< (triangle_left )",
+ "> (triangle_right)",
+ "1 (tri_down )",
+ "2 (tri_up )",
+ "3 (tri_left )",
+ "4 (tri_right )",
+ "8 (octagon )",
+ "p (pentagon )",
+ "h (hexagon1 )",
+ "H (hexagon2 )",
+ "+ (plus )",
+ "d (thin_diamond )",
+ "| (vline )",
+ "_ (hline )",
+ "None (nothing )"]
+
+# Note: in colors, "white" is removed
+MplBasicColors = [
+ "black",
+ "red",
+ "blue",
+ "green",
+ "cyan",
+ "magenta",
+ "yellow"]
+
+
+class IndicatorManager(object):
+ """ Manager for all indicator lines
+ """
+ def __init__(self):
+ """
+
+ :return:
+ """
+ # Auto color index
+ self._colorIndex = 0
+ # Auto line ID
+ self._autoLineID = 1
+
+ self._lineManager = dict()
+ self._canvasLineKeyDict = dict()
+ self._indicatorTypeDict = dict() # value: 0 (horizontal), 1 (vertical), 2 (2-way)
+
+ return
+
+ def add_2way_indicator(self, x, x_min, x_max, y, y_min, y_max, color):
+ """
+
+ :param x:
+ :param x_min:
+ :param x_max:
+ :param y:
+ :param y_min:
+ :param y_max:
+ :param color:
+ :return:
+ """
+ # Set up indicator ID
+ this_id = str(self._autoLineID)
+ self._autoLineID += 1
+
+ # Set up vectors
+ vec_x_horizontal = np.array([x_min, x_max])
+ vec_y_horizontal = np.array([y, y])
+
+ vec_x_vertical = np.array([x, x])
+ vec_y_vertical = np.array([y_min, y_max])
+
+ #
+ self._lineManager[this_id] = [vec_x_horizontal, vec_y_horizontal, vec_x_vertical, vec_y_vertical, color]
+ self._indicatorTypeDict[this_id] = 2
+
+ return this_id
+
+ def add_horizontal_indicator(self, y, x_min, x_max, color):
+ """
+ Add a horizontal indicator
+ :param y:
+ :param x_min:
+ :param x_max:
+ :param color:
+ :return:
+ """
+ # Get ID
+ this_id = str(self._autoLineID)
+ self._autoLineID += 1
+
+ #
+ vec_x = np.array([x_min, x_max])
+ vec_y = np.array([y, y])
+
+ #
+ self._lineManager[this_id] = [vec_x, vec_y, color]
+ self._indicatorTypeDict[this_id] = 0
+
+ return this_id
+
+ def add_vertical_indicator(self, x, y_min, y_max, color):
+ """
+ Add a vertical indicator to data structure
+ :return: indicator ID
+ """
+ # Get ID
+ this_id = str(self._autoLineID)
+ self._autoLineID += 1
+
+ #
+ vec_x = np.array([x, x])
+ vec_y = np.array([y_min, y_max])
+
+ #
+ self._lineManager[this_id] = [vec_x, vec_y, color]
+ self._indicatorTypeDict[this_id] = 1
+
+ return this_id
+
+ def get_canvas_line_index(self, my_id):
+ """
+
+ :param my_id:
+ :return:
+ """
+ assert isinstance(my_id, str)
+
+ if my_id not in self._canvasLineKeyDict:
+ raise RuntimeError('Indicator ID %s cannot be found. Current keys are %s.' % (
+ my_id, str(sorted(self._canvasLineKeyDict.keys()))
+ ))
+ return self._canvasLineKeyDict[my_id]
+
+ def get_line_type(self, my_id):
+ """
+
+ :param my_id:
+ :return:
+ """
+ return self._indicatorTypeDict[my_id]
+
+ def get_2way_data(self, line_id):
+ """
+
+ :param line_id:
+ :return:
+ """
+ assert self._indicatorTypeDict.has_key(line_id)
+ assert self._indicatorTypeDict[line_id] == 2
+
+ vec_set = [self._lineManager[line_id][0:2], self._lineManager[line_id][2:4]]
+
+ return vec_set
+
+ def get_data(self, line_id):
+ """
+ Get line's vector x and vector y
+ :param line_id:
+ :return:
+ """
+ return self._lineManager[line_id][0], self._lineManager[line_id][1]
+
+ def get_line_style(self, line_id=None):
+ """
+
+ :param line_id:
+ :return:
+ """
+ assert isinstance(line_id, None)
+ return '--'
+
+ def get_live_indicator_ids(self):
+ """
+
+ :return:
+ """
+ return sorted(self._lineManager.keys())
+
+ def get_marker(self):
+ """
+ Get the marker a line
+ :param line_id:
+ :return:
+ """
+ return 'o'
+
+ def get_next_color(self):
+ """
+ Get next color by auto color index
+ :return: string as color
+ """
+ next_color = MplBasicColors[self._colorIndex]
+
+ # Advance and possibly reset color scheme
+ self._colorIndex += 1
+ if self._colorIndex == len(MplBasicColors):
+ self._colorIndex = 0
+
+ return next_color
+
+ def set_canvas_line_index(self, my_id, canvas_line_index):
+ """
+
+ :param my_id:
+ :param canvas_line_index:
+ :return:
+ """
+ self._canvasLineKeyDict[my_id] = canvas_line_index
+
+ def shift(self, my_id, dx, dy):
+ """
+
+ :param my_id:
+ :param dx:
+ :param dy:
+ :return:
+ """
+ print self._lineManager[my_id][0]
+
+ if self._indicatorTypeDict[my_id] == 0:
+ # horizontal
+ self._lineManager[my_id][1] += dy
+
+ elif self._indicatorTypeDict[my_id] == 1:
+ # vertical
+ self._lineManager[my_id][0] += dx
+
+ elif self._indicatorTypeDict[my_id] == 2:
+ # 2-way
+ self._lineManager[my_id][2] += dx
+ self._lineManager[my_id][1] += dy
+
+ else:
+ raise RuntimeError('Unsupported indicator of type %d' % self._indicatorTypeDict[my_id])
+
+ return
+
+ def update_indicators_range(self, x_range, y_range):
+ """
+ Update indicator's range
+ :param x_range:
+ :param y_range:
+ :return:
+ """
+ for i_id in self._lineManager.keys():
+ # NEXT - Need a new flag for direction of the indicating line, vertical or horizontal
+ if True:
+ self._lineManager[i_id][1][0] = y_range[0]
+ self._lineManager[i_id][1][-1] = y_range[1]
+ else:
+ self._lineManager[i_id][0][0] = x_range[0]
+ self._lineManager[i_id][0][-1] = x_range[1]
+
+ return
+
+
+class MplGraphicsView(QtGui.QWidget):
+ """ A combined graphics view including matplotlib canvas and
+ a navigation tool bar
+
+ Note: Merged with HFIR_Powder_Reduction.MplFigureCAnvas
+ """
+ def __init__(self, parent):
+ """ Initialization
+ """
+ # Initialize parent
+ QtGui.QWidget.__init__(self, parent)
+
+ # set up canvas
+ self._myCanvas = Qt4MplCanvas(self)
+ self._myToolBar = MyNavigationToolbar(self, self._myCanvas)
+
+ # set up layout
+ self._vBox = QtGui.QVBoxLayout(self)
+ self._vBox.addWidget(self._myCanvas)
+ self._vBox.addWidget(self._myToolBar)
+
+ # auto line's maker+color list
+ self._myLineMarkerColorList = []
+ self._myLineMarkerColorIndex = 0
+ self.setAutoLineMarkerColorCombo()
+
+ # Declaration of class variables
+ self._indicatorKey = None
+
+ # Indicator manager
+ self._myIndicatorsManager = IndicatorManager()
+
+ return
+
+ def add_line_set(self, vec_set, color, marker, line_style, line_width):
+ """ Add a set of line and manage together
+ :param vec_set:
+ :param color:
+ :param marker:
+ :param line_style:
+ :param line_width:
+ :return:
+ """
+ key_list = list()
+ for vec_x, vec_y in vec_set:
+ temp_key = self._myCanvas.add_plot_1d(vec_x, vec_y, color=color, marker=marker,
+ line_style=line_style, line_width=line_width)
+ assert isinstance(temp_key, int)
+ assert temp_key >= 0
+ key_list.append(temp_key)
+
+ return key_list
+
+ def add_plot_1d(self, vec_x, vec_y, y_err=None, color=None, label="", x_label=None, y_label=None,
+ marker=None, line_style=None, line_width=1):
+ """ Add a new plot
+ """
+ line_key = self._myCanvas.add_plot_1d(vec_x, vec_y, y_err, color, label, x_label, y_label, marker, line_style,
+ line_width)
+
+ return line_key
+
+ def add_plot_1d_right(self, vec_x, vec_y, color=None, label='', marker=None, line_style=None, line_width=1):
+ """
+ Add 1 line (1-d plot) to right axis
+ :param vec_x:
+ :param vec_y:
+ :param color:
+ :param label:
+ :param marker:
+ :param line_style:
+ :param line_width:
+ :return:
+ """
+ line_key = self._myCanvas.add_1d_plot_right(vec_x, vec_y, label=label,
+ color=color, marker=marker,
+ linestyle=line_style, linewidth=line_width)
+
+ return line_key
+
+ def add_2way_indicator(self, x=None, y=None, color=None, master_line=None):
+ """ Add a 2-way indicator following an existing line?
+ :param x:
+ :param y:
+ :param color:
+ :return:
+ """
+ if master_line is not None:
+ raise RuntimeError('Implement how to use master_line ASAP.')
+
+ x_min, x_max = self._myCanvas.getXLimit()
+ if x is None:
+ x = (x_min + x_max) * 0.5
+ else:
+ assert isinstance(x, float)
+
+ y_min, y_max = self._myCanvas.getYLimit()
+ if y is None:
+ y = (y_min + y_max) * 0.5
+ else:
+ assert isinstance(y, float)
+
+ if color is None:
+ color = self._myIndicatorsManager.get_next_color()
+ else:
+ assert isinstance(color, str)
+
+ my_id = self._myIndicatorsManager.add_2way_indicator(x, x_min, x_max,
+ y, y_min, y_max,
+ color)
+ vec_set = self._myIndicatorsManager.get_2way_data(my_id)
+
+ canvas_line_index = self.add_line_set(vec_set, color=color,
+ marker=self._myIndicatorsManager.get_marker(),
+ line_style=self._myIndicatorsManager.get_line_style(),
+ line_width=1)
+ self._myIndicatorsManager.set_canvas_line_index(my_id, canvas_line_index)
+
+ return my_id
+
+ def add_horizontal_indicator(self, y=None, color=None):
+ """ Add an indicator line
+ """
+ # Default
+ if y is None:
+ y_min, y_max = self._myCanvas.getYLimit()
+ y = (y_min + y_max) * 0.5
+ else:
+ assert isinstance(y, float)
+
+ x_min, x_max = self._myCanvas.getXLimit()
+
+ # For color
+ if color is None:
+ color = self._myIndicatorsManager.get_next_color()
+ else:
+ assert isinstance(color, str)
+
+ # Form
+ my_id = self._myIndicatorsManager.add_horizontal_indicator(y, x_min, x_max, color)
+ vec_x, vec_y = self._myIndicatorsManager.get_data(my_id)
+
+ canvas_line_index = self._myCanvas.add_plot_1d(vec_x=vec_x, vec_y=vec_y,
+ color=color, marker=self._myIndicatorsManager.get_marker(),
+ line_style=self._myIndicatorsManager.get_line_style(),
+ line_width=1)
+
+ self._myIndicatorsManager.set_canvas_line_index(my_id, canvas_line_index)
+
+ return my_id
+
+ def add_vertical_indicator(self, x=None, color=None):
+ """
+ Add a vertical indicator line
+ :param x: None as the automatic mode using default from middle of canvas
+ :param color: None as the automatic mode using default
+ :return: indicator ID
+ """
+ # For indicator line's position
+ if x is None:
+ x_min, x_max = self._myCanvas.getXLimit()
+ x = (x_min + x_max) * 0.5
+ else:
+ assert isinstance(x, float)
+
+ y_min, y_max = self._myCanvas.getYLimit()
+
+ # For color
+ if color is None:
+ color = self._myIndicatorsManager.get_next_color()
+ else:
+ assert isinstance(color, str)
+
+ # Form
+ my_id = self._myIndicatorsManager.add_vertical_indicator(x, y_min, y_max, color)
+ vec_x, vec_y = self._myIndicatorsManager.get_data(my_id)
+
+ canvas_line_index = self._myCanvas.add_plot_1d(vec_x=vec_x, vec_y=vec_y,
+ color=color, marker=self._myIndicatorsManager.get_marker(),
+ line_style=self._myIndicatorsManager.get_line_style(),
+ line_width=1)
+
+ self._myIndicatorsManager.set_canvas_line_index(my_id, canvas_line_index)
+
+ return my_id
+
+ def add_plot_2d(self, array2d, x_min, x_max, y_min, y_max, hold_prev_image=True, y_tick_label=None):
+ """
+ Add a 2D image to canvas
+ :param array2d: numpy 2D array
+ :param x_min:
+ :param x_max:
+ :param y_min:
+ :param y_max:
+ :param hold_prev_image:
+ :param y_tick_label:
+ :return:
+ """
+ self._myCanvas.addPlot2D(array2d, x_min, x_max, y_min, y_max, hold_prev_image, y_tick_label)
+
+ return
+
+
+ def addImage(self, imagefilename):
+ """ Add an image by file
+ """
+ # check
+ if os.path.exists(imagefilename) is False:
+ raise NotImplementedError("Image file %s does not exist." % (imagefilename))
+
+ self._myCanvas.addImage(imagefilename)
+
+ return
+
+ def clear_all_lines(self):
+ """
+ """
+ self._myCanvas.clear_all_1d_plots()
+
+ def clear_canvas(self):
+ """ Clear canvas
+ """
+ return self._myCanvas.clear_canvas()
+
+ def draw(self):
+ """ Draw to commit the change
+ """
+ return self._myCanvas.draw()
+
+ def evt_view_updated(self):
+ """ Event handling as canvas size updated
+ :return:
+ """
+ # update the indicator
+ new_x_range = self.getXLimit()
+ new_y_range = self.getYLimit()
+
+ self._myIndicatorsManager.update_indicators_range(new_x_range, new_y_range)
+ for indicator_key in self._myIndicatorsManager.get_live_indicator_ids():
+ canvas_line_id = self._myIndicatorsManager.get_canvas_line_index(indicator_key)
+ data_x, data_y = self._myIndicatorsManager.get_data(indicator_key)
+ self.updateLine(canvas_line_id, data_x, data_y)
+ # END-FOR
+
+ return
+
+ def getPlot(self):
+ """
+ """
+ return self._myCanvas.getPlot()
+
+ def getLastPlotIndexKey(self):
+ """ Get ...
+ """
+ return self._myCanvas.getLastPlotIndexKey()
+
+ def getXLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self._myCanvas.getXLimit()
+
+ def getYLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self._myCanvas.getYLimit()
+
+ def move_indicator(self, line_id, dx, dy):
+ """
+ Move the indicator line in horizontal
+ :param line_id:
+ :param dx:
+ :return:
+ """
+ # Shift value
+ self._myIndicatorsManager.shift(line_id, dx=dx, dy=dy)
+
+ # apply to plot on canvas
+ if self._myIndicatorsManager.get_line_type(line_id) < 2:
+ # horizontal or vertical
+ canvas_line_index = self._myIndicatorsManager.get_canvas_line_index(line_id)
+ vec_x, vec_y = self._myIndicatorsManager.get_data(line_id)
+ self._myCanvas.updateLine(ikey=canvas_line_index, vecx=vec_x, vecy=vec_y)
+ else:
+ # 2-way
+ canvas_line_index_h, canvas_line_index_v = self._myIndicatorsManager.get_canvas_line_index(line_id)
+ h_vec_set, v_vec_set = self._myIndicatorsManager.get_2way_data(line_id)
+
+ self._myCanvas.updateLine(ikey=canvas_line_index_h, vecx=h_vec_set[0], vecy=h_vec_set[1])
+ self._myCanvas.updateLine(ikey=canvas_line_index_v, vecx=v_vec_set[0], vecy=v_vec_set[1])
+
+ return
+
+ def remove_indicator(self, indicator_key):
+ """ Remove indicator line
+ :param indicator_key:
+ :return:
+ """
+ #
+ plot_id = self._myIndicatorsManager.get_canvas_line_index(indicator_key)
+ self._myCanvas.remove_plot_1d(plot_id)
+
+ return
+
+ def removePlot(self, ikey):
+ """
+ """
+ return self._myCanvas.remove_plot_1d(ikey)
+
+ def updateLine(self, ikey, vecx, vecy, linestyle=None, linecolor=None, marker=None, markercolor=None):
+ """
+ """
+ return self._myCanvas.updateLine(ikey, vecx, vecy, linestyle, linecolor, marker, markercolor)
+
+ def update_indicator(self, i_key, color):
+ """
+ Update indicator with new color
+ :param i_key:
+ :param vec_x:
+ :param vec_y:
+ :param color:
+ :return:
+ """
+ if self._myIndicatorsManager.get_line_type(i_key) < 2:
+ # horizontal or vertical
+ canvas_line_index = self._myIndicatorsManager.get_canvas_line_index(i_key)
+ self._myCanvas.updateLine(ikey=canvas_line_index, vecx=None, vecy=None, linecolor=color)
+ else:
+ # 2-way
+ canvas_line_index_h, canvas_line_index_v = self._myIndicatorsManager.get_canvas_line_index(i_key)
+ # h_vec_set, v_vec_set = self._myIndicatorsManager.get_2way_data(i_key)
+
+ self._myCanvas.updateLine(ikey=canvas_line_index_h, vecx=None, vecy=None, linecolor=color)
+ self._myCanvas.updateLine(ikey=canvas_line_index_v, vecx=None, vecy=None, linecolor=color)
+
+ return
+
+ def get_indicator_position(self, indicator_key):
+ """ Get position (x or y) of the indicator
+ :return:
+ """
+ # NEXT - Consider a better and more consistent return
+ vec_x, vec_y = self._myIndicatorsManager.get_data(indicator_key)
+ if vec_x[0] == vec_x[1]:
+ return vec_x[0]
+
+ return vec_y[0]
+
+ def getLineStyleList(self):
+ """
+ """
+ return MplLineStyles
+
+ def getLineMarkerList(self):
+ """
+ """
+ return MplLineMarkers
+
+ def getLineBasicColorList(self):
+ """
+ """
+ return MplBasicColors
+
+ def getDefaultColorMarkerComboList(self):
+ """ Get a list of line/marker color and marker style combination
+ as default to add more and more line to plot
+ """
+ return self._myCanvas.getDefaultColorMarkerComboList()
+
+ def getNextLineMarkerColorCombo(self):
+ """ As auto line's marker and color combo list is used,
+ get the NEXT marker/color combo
+ """
+ # get from list
+ marker, color = self._myLineMarkerColorList[self._myLineMarkerColorIndex]
+ # process marker if it has information
+ if marker.count(' (') > 0:
+ marker = marker.split(' (')[0]
+ print "[DB] Print line %d: marker = %s, color = %s" % (self._myLineMarkerColorIndex, marker, color)
+
+ # update the index
+ self._myLineMarkerColorIndex += 1
+ if self._myLineMarkerColorIndex == len(self._myLineMarkerColorList):
+ self._myLineMarkerColorIndex = 0
+
+ return marker, color
+
+ def resetLineColorStyle(self):
+ """ Reset the auto index for line's color and style
+ """
+ self._myLineMarkerColorIndex = 0
+ return
+
+ # NEXT-Urgent! - Find out difference between setXYLimit() and setXYLimits()
+ def setXYLimit(self, xmin, xmax, ymin, ymax):
+ """ Set X-Y limit automatically
+ """
+ self._myCanvas.axes.set_xlim([xmin, xmax])
+ self._myCanvas.axes.set_ylim([ymin, ymax])
+
+ self._myCanvas.draw()
+
+ return
+
+ def setXYLimits(self, xmin=None, xmax=None, ymin=None, ymax=None):
+ """
+ """
+ return self._myCanvas.setXYLimit(xmin, xmax, ymin, ymax)
+
+ def setAutoLineMarkerColorCombo(self):
+ """
+ """
+ self._myLineMarkerColorList = []
+ for marker in MplLineMarkers:
+ for color in MplBasicColors:
+ self._myLineMarkerColorList.append( (marker, color) )
+
+ return
+
+ def setLineMarkerColorIndex(self, newindex):
+ """
+ """
+ self._myLineMarkerColorIndex = newindex
+
+ return
+
+
+class Qt4MplCanvas(FigureCanvas):
+ """ A customized Qt widget for matplotlib figure.
+ It can be used to replace GraphicsView of QtGui
+ """
+ def __init__(self, parent):
+ """ Initialization
+ """
+ # from mpl_toolkits.axes_grid1 import host_subplot
+ # import mpl_toolkits.axisartist as AA
+ # import matplotlib.pyplot as plt
+
+ # Instantiating matplotlib Figure
+ self.fig = Figure()
+ self.fig.patch.set_facecolor('white')
+
+ if True:
+ self.axes = self.fig.add_subplot(111) # return: matplotlib.axes.AxesSubplot
+ self.axes2 = None
+ else:
+ self.axes = self.fig.add_host_subplot(111)
+
+ # Initialize parent class and set parent
+ FigureCanvas.__init__(self, self.fig)
+ self.setParent(parent)
+
+ # Set size policy to be able to expanding and resizable with frame
+ FigureCanvas.setSizePolicy(self, QtGui.QSizePolicy.Expanding,QtGui.QSizePolicy.Expanding)
+ FigureCanvas.updateGeometry(self)
+
+ # Variables to manage all lines/subplot
+ self._lineDict = {}
+ self._lineIndex = 0
+
+ # legend and color bar
+ self._colorBar = None
+
+ return
+
+ def add_plot_1d(self, vec_x, vec_y, y_err=None, color=None, label="", x_label=None, y_label=None,
+ marker=None, line_style=None, line_width=1):
+ """
+
+ :param vec_x: numpy array X
+ :param vec_y: numpy array Y
+ :param y_err:
+ :param color:
+ :param label:
+ :param x_label:
+ :param y_label:
+ :param marker:
+ :param line_style:
+ :param line_width:
+ :return: new key
+ """
+ # Check input
+ if isinstance(vec_x, np.ndarray) is False or isinstance(vec_y, np.ndarray) is False:
+ raise NotImplementedError('Input vec_x or vec_y for addPlot() must be numpy.array.')
+ plot_error = y_err is not None
+ if plot_error is True:
+ if isinstance(y_err, np.ndarray) is False:
+ raise NotImplementedError('Input y_err must be either None or numpy.array.')
+
+ if len(vec_x) != len(vec_y):
+ raise NotImplementedError('Input vec_x and vec_y must have same size.')
+ if plot_error is True and len(y_err) != len(vec_x):
+ raise NotImplementedError('Input vec_x, vec_y and y_error must have same size.')
+
+ # Hold previous data
+ self.axes.hold(True)
+
+ # process inputs and defaults
+ if color is None:
+ color = (0,1,0,1)
+ if marker is None:
+ marker = 'o'
+ if line_style is None:
+ line_style = '-'
+
+ # color must be RGBA (4-tuple)
+ if plot_error is False:
+ print "[DB] line_style = ", line_style, "line_width = ", line_width, "marker = ", marker, "color = ", color
+ r = self.axes.plot(vec_x, vec_y, color=color, marker=marker, linestyle=line_style,
+ label=label, linewidth=line_width)
+ # return: list of matplotlib.lines.Line2D object
+ else:
+ r = self.axes.errorbar(vec_x, vec_y, yerr=y_err, color=color, marker=marker, linestyle=line_style,
+ label=label, linewidth=line_width)
+
+ self.axes.set_aspect('auto')
+
+ # set x-axis and y-axis label
+ if x_label is not None:
+ self.axes.set_xlabel(x_label, fontsize=20)
+ if y_label is not None:
+ self.axes.set_ylabel(y_label, fontsize=20)
+
+ # set/update legend
+ self._setupLegend()
+
+ # Register
+ line_key = self._lineIndex
+ if len(r) == 1:
+ self._lineDict[line_key] = r[0]
+ self._lineIndex += 1
+ else:
+ print "Impoooooooooooooooosible! Return from plot is a %d-tuple. " % (len(r))
+
+ # Flush/commit
+ self.draw()
+
+ return line_key
+
+ def add_1d_plot_right(self, x, y, color=None, label="", x_label=None, ylabel=None, marker=None, linestyle=None,
+ linewidth=1):
+ """ Add a line (1-d plot) at right axis
+ """
+ if self.axes2 is None:
+ self.axes2 = self.axes.twinx()
+ # print self.par1, type(self.par1)
+
+ # Hold previous data
+ self.axes2.hold(True)
+
+ # Default
+ if color is None:
+ color = (0, 1, 0, 1)
+ if marker is None:
+ marker = 'o'
+ if linestyle is None:
+ linestyle = '-'
+
+ # Special default
+ if len(label) == 0:
+ label = 'right'
+ color = 'red'
+
+ # color must be RGBA (4-tuple)
+ r = self.axes2.plot(x, y, color=color, marker=marker, linestyle=linestyle,
+ label=label, linewidth=linewidth)
+ # return: list of matplotlib.lines.Line2D object
+
+ self.axes2.set_aspect('auto')
+
+ # set x-axis and y-axis label
+ if x_label is not None:
+ self.axes2.set_xlabel(x_label, fontsize=20)
+ if ylabel is not None:
+ self.axes2.set_ylabel(ylabel, fontsize=20)
+
+ # set/update legend
+ self._setupLegend()
+
+ # Register
+ line_key = -1
+ if len(r) == 1:
+ line_key = self._lineIndex
+ self._lineDict[line_key] = r[0]
+ self._lineIndex += 1
+ else:
+ print "Impoooooooooooooooosible!"
+
+ # Flush/commit
+ self.draw()
+
+ return line_key
+
+
+ def addPlot2D(self, array2d, xmin, xmax, ymin, ymax, holdprev, yticklabels=None):
+ """ Add a 2D plot
+
+ Arguments:
+ - yticklabels :: list of string for y ticks
+ """
+ # Release the current image
+ self.axes.hold(holdprev)
+
+ # Do plot
+ # y ticks will be shown on line 1, 4, 23, 24 and 30
+ # yticks = [1, 4, 23, 24, 30]
+ # self.axes.set_yticks(yticks)
+
+ # show image
+ imgplot = self.axes.imshow(array2d, extent=[xmin,xmax,ymin,ymax], interpolation='none')
+ # set y ticks as an option:
+ if yticklabels is not None:
+ # it will always label the first N ticks even image is zoomed in
+ print "--------> [FixMe]: Set up the Y-axis ticks is erroreous"
+ #self.axes.set_yticklabels(yticklabels)
+
+ # explicitly set aspect ratio of the image
+ self.axes.set_aspect('auto')
+
+ # Set color bar. plt.colorbar() does not work!
+ if self._colorBar is None:
+ # set color map type
+ imgplot.set_cmap('spectral')
+ self._colorBar = self.fig.colorbar(imgplot)
+ else:
+ self._colorBar.update_bruteforce(imgplot)
+
+ # Flush...
+ self._flush()
+
+ return
+
+ def addImage(self, imagefilename):
+ """ Add an image by file
+ """
+ #import matplotlib.image as mpimg
+
+ # set aspect to auto mode
+ self.axes.set_aspect('auto')
+
+ img = matplotlib.image.imread(str(imagefilename))
+ # lum_img = img[:,:,0]
+ # FUTURE : refactor for image size, interpolation and origin
+ imgplot = self.axes.imshow(img, extent=[0, 1000, 800, 0], interpolation='none', origin='lower')
+
+ # Set color bar. plt.colorbar() does not work!
+ if self._colorBar is None:
+ # set color map type
+ imgplot.set_cmap('spectral')
+ self._colorBar = self.fig.colorbar(imgplot)
+ else:
+ self._colorBar.update_bruteforce(imgplot)
+
+ self._flush()
+
+ return
+
+ def clear_all_1d_plots(self):
+ """ Remove all lines from the canvas
+ """
+ for ikey in self._lineDict.keys():
+ plot = self._lineDict[ikey]
+ if plot is None:
+ continue
+ if isinstance(plot, tuple) is False:
+ try:
+ self.axes.lines.remove(plot)
+ except ValueError as e:
+ print "[Error] Plot %s is not in axes.lines which has %d lines. Error mesage: %s" % (
+ str(plot), len(self.axes.lines), str(e))
+ self._lineDict[ikey] = None
+ else:
+ # error bar
+ plot[0].remove()
+ for line in plot[1]:
+ line.remove()
+ for line in plot[2]:
+ line.remove()
+ self._lineDict[ikey] = None
+ # ENDIF(plot)
+ # ENDFOR
+
+ self._setupLegend()
+
+ self.draw()
+
+ return
+
+ def clear_canvas(self):
+ """ Clear data including lines and image from canvas
+ """
+ # clear the image for next operation
+ self.axes.hold(False)
+
+ # Clear all lines
+ self.clear_all_1d_plots()
+
+ # clear image
+ self.axes.cla()
+ # Try to clear the color bar
+ if len(self.fig.axes) > 1:
+ self.fig.delaxes(self.fig.axes[1])
+ self._colorBar = None
+ # This clears the space claimed by color bar but destroys sub_plot too.
+ self.fig.clear()
+ # Re-create subplot
+ self.axes = self.fig.add_subplot(111)
+
+ # flush/commit
+ self._flush()
+
+ return
+
+
+ def getLastPlotIndexKey(self):
+ """ Get the index/key of the last added line
+ """
+ return self._lineIndex-1
+
+
+ def getPlot(self):
+ """ reture figure's axes to expose the matplotlib figure to PyQt client
+ """
+ return self.axes
+
+ def getXLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self.axes.get_xlim()
+
+ def getYLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self.axes.get_ylim()
+
+ def setXYLimit(self, xmin, xmax, ymin, ymax):
+ """
+ """
+ # for X
+ xlims = self.axes.get_xlim()
+ xlims = list(xlims)
+ if xmin is not None:
+ xlims[0] = xmin
+ if xmax is not None:
+ xlims[1] = xmax
+ self.axes.set_xlim(xlims)
+
+ # for Y
+ ylims = self.axes.get_ylim()
+ ylims = list(ylims)
+ if ymin is not None:
+ ylims[0] = ymin
+ if ymax is not None:
+ ylims[1] = ymax
+ self.axes.set_ylim(ylims)
+
+ # try draw
+ self.draw()
+
+ return
+
+ def remove_plot_1d(self, plot_key):
+ """ Remove the line with its index as key
+ :param plot_key:
+ :return:
+ """
+ # self._lineDict[ikey].remove()
+ print 'Remove line... ',
+
+ # Get all lines in list
+ lines = self.axes.lines
+ assert isinstance(lines, list)
+
+ print 'Number of lines = %d, List: %s' % (len(lines), str(lines))
+ print 'Line to remove: key = %s, Line Dict has key = %s' % (str(plot_key), str(self._lineDict.has_key(plot_key)))
+
+ if plot_key in self._lineDict:
+ self.axes.lines.remove(self._lineDict[plot_key])
+ self._lineDict[plot_key] = None
+ else:
+ raise RuntimeError('Line with ID %s is not recorded.' % plot_key)
+
+ # Draw
+ self.draw()
+
+ return
+
+ def updateLine(self, ikey, vecx, vecy, linestyle=None, linecolor=None, marker=None, markercolor=None):
+ """
+ """
+ line = self._lineDict[ikey]
+
+ if vecx is not None and vecy is not None:
+ line.set_xdata(vecx)
+ line.set_ydata(vecy)
+
+ if linecolor is not None:
+ line.set_color(linecolor)
+
+ if linestyle is not None:
+ line.set_linestyle(linestyle)
+
+ if marker is not None:
+ line.set_marker(marker)
+
+ if markercolor is not None:
+ line.set_markerfacecolor(markercolor)
+
+ oldlabel = line.get_label()
+ line.set_label(oldlabel)
+
+ self.axes.legend()
+
+ # commit
+ self.draw()
+
+ return
+
+ def getLineStyleList(self):
+ """
+ """
+ return MplLineStyles
+
+
+ def getLineMarkerList(self):
+ """
+ """
+ return MplLineMarkers
+
+ def getLineBasicColorList(self):
+ """
+ """
+ return MplBasicColors
+
+ def getDefaultColorMarkerComboList(self):
+ """ Get a list of line/marker color and marker style combination
+ as default to add more and more line to plot
+ """
+ combolist = []
+ nummarkers = len(MplLineMarkers)
+ numcolors = len(MplBasicColors)
+
+ for i in xrange(nummarkers):
+ marker = MplLineMarkers[i]
+ for j in xrange(numcolors):
+ color = MplBasicColors[j]
+ combolist.append( (marker, color) )
+ # ENDFOR (j)
+ # ENDFOR(i)
+
+ return combolist
+
+ def _flush(self):
+ """ A dirty hack to flush the image
+ """
+ w, h = self.get_width_height()
+ self.resize(w+1,h)
+ self.resize(w,h)
+
+ return
+
+ def _setupLegend(self, location='best'):
+ """ Set up legend
+ self.axes.legend()
+ Handler is a Line2D object. Lable maps to the line object
+ """
+ loclist = [
+ "best",
+ "upper right",
+ "upper left",
+ "lower left",
+ "lower right",
+ "right",
+ "center left",
+ "center right",
+ "lower center",
+ "upper center",
+ "center"]
+
+ # Check legend location valid or not
+ if location not in loclist:
+ location = 'best'
+
+ handles, labels = self.axes.get_legend_handles_labels()
+ self.axes.legend(handles, labels, loc=location)
+ # print handles
+ # print labels
+ #self.axes.legend(self._myLegendHandlers, self._myLegentLabels)
+
+ return
+
+# END-OF-CLASS (MplGraphicsView)
+
+
+class MyNavigationToolbar(NavigationToolbar2):
+ """ A customized navigation tool bar attached to canvas
+ Note:
+ * home, left, right: will not disable zoom/pan mode
+ * zoom and pan: will turn on/off both's mode
+
+ Other methods
+ * drag_pan(self, event): event handling method for dragging canvas in pan-mode
+ """
+ NAVIGATION_MODE_NONE = 0
+ NAVIGATION_MODE_PAN = 1
+ NAVIGATION_MODE_ZOOM = 2
+
+ def __init__(self, parent, canvas):
+ """ Initialization
+ """
+ NavigationToolbar2.__init__(self, canvas, canvas)
+
+ self._myParent = parent
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_NONE
+
+ return
+
+ def get_mode(self):
+ """
+ :return: integer as none/pan/zoom mode
+ """
+ return self._navigationMode
+
+ # Overriding base's methods
+ def draw(self):
+ """
+ Canvas is drawn called by pan(), zoom()
+ :return:
+ """
+ NavigationToolbar2.draw(self)
+
+ self._myParent.evt_view_updated()
+
+ return
+
+ def pan(self, *args):
+ """
+
+ :param args:
+ :return:
+ """
+ NavigationToolbar2.pan(self, args)
+
+ if self._navigationMode == MyNavigationToolbar.NAVIGATION_MODE_PAN:
+ # out of pan mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_NONE
+ else:
+ # into pan mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_PAN
+
+ return
+
+ def zoom(self, *args):
+ """
+ Turn on/off zoom (zoom button)
+ :param args:
+ :return:
+ """
+ NavigationToolbar2.zoom(self, args)
+
+ if self._navigationMode == MyNavigationToolbar.NAVIGATION_MODE_ZOOM:
+ # out of zoom mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_NONE
+ else:
+ # into zoom mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_ZOOM
+
+ return
+
+ def _update_view(self):
+ """
+ view update called by home(), back() and forward()
+ :return:
+ """
+ NavigationToolbar2._update_view(self)
+
+ self._myParent.evt_view_updated()
+
+ return
+
diff --git a/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py b/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
new file mode 100644
index 0000000000000000000000000000000000000000..bb11355d3c1b09e8e5b011cd8b698d64614939aa
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
@@ -0,0 +1,1263 @@
+#pylint: disable=C0302,C0103,R0902,R0904,R0913,W0212,W0621,R0912
+################################################################################
+#
+# Controlling class
+#
+# == Data download and storage ==
+# - Local data storage (local-mode)
+# - Download from internet to cache (download-mode)
+#
+################################################################################
+import os
+import urllib2
+
+import numpy
+
+import mantid
+import mantid.simpleapi as api
+from mantid.api import AnalysisDataService
+
+DebugMode = True
+
+DET_X_SIZE = 256
+DET_Y_SIZE = 256
+
+
+class PeakInfo(object):
+ """ Class containing a peak's information for GUI
+ In order to manage some operations for a peak
+ It does not contain peak workspace but will hold
+ """
+ def __init__(self, parent):
+ """ Init
+ """
+ assert isinstance(parent, CWSCDReductionControl)
+
+ # Define class variable
+ self._myParent = parent
+ self._userHKL = [0, 0, 0]
+
+ self._myExpNumber = None
+ self._myScanNumber = None
+ self._myPtNumber = None
+
+ self._myPeakWSKey = (None, None, None)
+ self._myPeakIndex = None
+ # IPeak instance
+ self._myPeak = None
+
+ self._myLastPeakUB = None
+
+ return
+
+ def get_peak_workspace(self):
+ """
+ Get peak workspace related
+ :return:
+ """
+ assert isinstance(self._myPeakWSKey, tuple)
+ exp_number, scan_number, pt_number = self._myPeakWSKey
+
+ return self._myParent.get_ub_peak_ws(exp_number, scan_number, pt_number)[1]
+
+ def get_peak_ws_hkl(self):
+ """ Get HKL from PeakWorkspace
+ :return:
+ """
+ hkl = self._myPeak.getHKL()
+
+ return hkl.getX(), hkl.getY(), hkl.getZ()
+
+ def get_user_hkl(self):
+ """
+ Get HKL set to this object by client
+ :return: 3-tuple of float as (H, K, L)
+ """
+ hkl = self._userHKL
+
+ return hkl[0], hkl[1], hkl[2]
+
+ def set_from_run_info(self, exp_number, scan_number, pt_number):
+ """ Set from run information with parent
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ status, peak_ws = self._myParent.get_ub_peak_ws(exp_number, scan_number, pt_number)
+ if status is True:
+ self._myPeakWSKey = (exp_number, scan_number, pt_number)
+ self._myPeakIndex = 0
+ self._myPeak = peak_ws.getPeak(0)
+ else:
+ error_message = peak_ws
+ return False, error_message
+
+ self._myExpNumber = exp_number
+ self._myScanNumber = scan_number
+ self._myPtNumber = pt_number
+
+ return True, ''
+
+ def set_from_peak_ws(self, peak_ws, peak_index):
+ """
+ Set from peak workspace
+ :param peak_ws:
+ :return:
+ """
+ # Check
+ assert isinstance(peak_ws, mantid.dataobjects.PeaksWorkspace)
+
+ # Get peak
+ try:
+ peak = peak_ws.getPeak(peak_index)
+ except RuntimeError as run_err:
+ raise RuntimeError(run_err)
+
+ self._myPeak = peak
+
+ return
+
+ def set_peak_ws_hkl_from_user(self):
+ """
+
+ :return:
+ """
+ # Check
+ if isinstance(self._myPeak, mantid.api.IPeak) is False:
+ raise RuntimeError('self._myPeakWS should be an instance of mantid.api.IPeak. '
+ 'But it is of instance of %s now.' % str(type(self._myPeak)))
+
+ # Get hkl
+ h, k, l = self._userHKL
+ print '[DB] PeakInfo Get User HKL = (%f, %f, %f) to IPeak ' % (h, k, l)
+
+ self._myPeak.setHKL(h, k, l)
+
+ return
+
+ def set_user_hkl(self, h, k, l):
+ """
+ Set HKL to this peak Info
+ :return:
+ """
+ assert isinstance(h, float)
+ assert isinstance(k, float)
+ assert isinstance(l, float)
+
+ self._userHKL[0] = h
+ self._userHKL[1] = k
+ self._userHKL[2] = l
+
+ print '[DB] PeakInfo Set User HKL to (%f, %f, %f) ' % (self._userHKL[0], self._userHKL[1], self._userHKL[2])
+
+ return
+
+ def getExpInfo(self):
+ """
+
+ :return: 3-tuple of integer as experiment number, scan number and Pt number
+ """
+ return self._myExpNumber, self._myScanNumber, self._myPtNumber
+
+ def getQSample(self):
+ """
+
+ :return: 3-tuple of floats as Qx, Qy, Qz
+ """
+ q_sample = self._myPeak.getQSampleFrame()
+ return q_sample.getX(), q_sample.getY(), q_sample.getZ()
+
+
+class CWSCDReductionControl(object):
+ """ Controlling class for reactor-based single crystal diffraction reduction
+ """
+ def __init__(self, instrument_name=None):
+ """ init
+ """
+ if isinstance(instrument_name, str):
+ self._instrumentName = instrument_name
+ elif instrument_name is None:
+ self._instrumentName = ''
+ else:
+ raise RuntimeError('Instrument name %s of type %s is not allowed.' % (str(instrument_name),
+ str(type(instrument_name))))
+
+ # Experiment number, data storage
+ # No Use/Confusing: self._expNumber = 0
+
+ self._dataDir = None
+ self._workDir = '/tmp'
+
+ self._myServerURL = ''
+
+ # Some set up
+ self._expNumber = None
+
+ # Container for MDEventWorkspace for each Pt.
+ self._myPtMDDict = dict()
+ # Container for loaded workspaces
+ self._mySpiceTableDict = {}
+ # Container for loaded raw pt workspace
+ self._myRawDataWSDict = dict()
+ # Container for PeakWorkspaces for calculating UB matrix
+ self._myUBPeakWSDict = dict()
+ # Container for UB matrix
+ self._myUBMatrixDict = dict()
+
+ # Peak Info
+ self._myPeakInfoDict = dict()
+ # Last UB matrix calculated
+ self._myLastPeakUB = None
+ # Flag for data storage
+ self._cacheDataOnly = False
+
+ # A dictionary to manage all loaded and processed MDEventWorkspaces
+ # self._expDataDict = {}
+
+ return
+
+ def add_peak_info(self, exp_number, scan_number, pt_number):
+ """ Add a peak info for calculating UB matrix
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return: (boolean, PeakInfo/string)
+ """
+ has_peak_ws, peak_ws = self.get_ub_peak_ws(exp_number, scan_number, pt_number)
+ if has_peak_ws is False:
+ err_msg = 'No peak workspace found for Exp %s Scan %s Pt %s' % (
+ exp_number, scan_number, pt_number)
+ print '\n[DB] Fail to add peak info due to %s\n' % err_msg
+ return False, err_msg
+
+ if peak_ws.rowCount() > 1:
+ err_msg = 'There are more than 1 peak in PeaksWorkspace.'
+ print '\n[DB] Fail to add peak info due to %s\n' % err_msg
+ return False, err_msg
+
+ peak_info = PeakInfo(self)
+ peak_info.set_from_run_info(exp_number, scan_number, pt_number)
+
+ # Add to data management
+ self._myPeakInfoDict[(exp_number, scan_number, pt_number)] = peak_info
+
+ return True, peak_info
+
+ def calculate_ub_matrix(self, peak_info_list, a, b, c, alpha, beta, gamma):
+ """
+ Calculate UB matrix
+
+ Set Miller index from raw data in Workspace2D.
+ :param peakws:
+ :param a:
+ :param b:
+ :param c:
+ :param alpha:
+ :param beta:
+ :param gamma:
+ :return:
+ """
+ # Check
+ assert isinstance(peak_info_list, list)
+ for peak_info in peak_info_list:
+ if isinstance(peak_info, PeakInfo) is False:
+ raise NotImplementedError('Input PeakList is of type %s.' % str(type(peak_info_list[0])))
+ assert isinstance(peak_info, PeakInfo)
+
+ if len(peak_info_list) < 2:
+ return False, 'Too few peaks are input to calculate UB matrix. Must be >= 2.'
+
+ # Construct a new peak workspace by combining all single peak
+ ub_peak_ws_name = 'Temp_UB_Peak'
+ ub_peak_ws = api.CloneWorkspace(InputWorkspace=peak_info_list[0].get_peak_workspace(),
+ OutputWorkspace=ub_peak_ws_name)
+
+ for i_peak_info in xrange(1, len(peak_info_list)):
+ # Set HKL as optional
+ peak_ws = peak_info_list[i_peak_info].get_peak_workspace()
+
+ # Combine peak workspace
+ ub_peak_ws = api.CombinePeaksWorkspaces(LHSWorkspace=ub_peak_ws,
+ RHSWorkspace=peak_ws,
+ CombineMatchingPeaks=False,
+ OutputWorkspace=ub_peak_ws_name)
+ # END-FOR(i_peak_info)
+
+ # Calculate UB matrix
+ try:
+ api.CalculateUMatrix(PeaksWorkspace=ub_peak_ws_name,
+ a=a, b=b, c=c, alpha=alpha, beta=beta, gamma=gamma)
+ except ValueError as val_err:
+ return False, str(val_err)
+
+ ub_matrix = ub_peak_ws.sample().getOrientedLattice().getUB()
+
+ self._myLastPeakUB = ub_peak_ws
+
+ return True, ub_matrix
+
+ def does_raw_loaded(self, exp_no, scan_no, pt_no):
+ """
+ Check whether the raw Workspace2D for a Pt. exists
+ :param exp_no:
+ :param scan_no:
+ :param pt_no:
+ :return:
+ """
+ return (exp_no, scan_no, pt_no) in self._myRawDataWSDict
+
+ def does_spice_loaded(self, exp_no, scan_no):
+ """ Check whether a SPICE file has been loaded
+ :param exp_no:
+ :param scan_no:
+ :return:
+ """
+ return (exp_no, scan_no) in self._mySpiceTableDict
+
+ def download_spice_file(self, exp_number, scan_number, over_write):
+ """
+ Download a scan/pt data from internet
+ :param exp_number: experiment number
+ :param scan_number:
+ :return:
+ """
+ # Check
+ if exp_number is None:
+ exp_number = self._expNumber
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+
+ # Generate the URL for SPICE data file
+ file_url = '%sexp%d/Datafiles/HB3A_exp%04d_scan%04d.dat' % (self._myServerURL, exp_number,
+ exp_number, scan_number)
+ file_name = '%s_exp%04d_scan%04d.dat' % (self._instrumentName, exp_number, scan_number)
+ file_name = os.path.join(self._dataDir, file_name)
+ if os.path.exists(file_name) is True and over_write is False:
+ return True, file_name
+
+ # Download
+ try:
+ api.DownloadFile(Address=file_url, Filename=file_name)
+ except RuntimeError as run_err:
+ return False, str(run_err)
+
+ # Check file exist?
+ if os.path.exists(file_name) is False:
+ return False, "Unable to locate downloaded file %s." % file_name
+
+ return True, file_name
+
+ def download_spice_xml_file(self, scan_no, pt_no, exp_no=None, overwrite=False):
+ """ Download a SPICE XML file for one measurement in a scan
+ :param scan_no:
+ :param pt_no:
+ :param exp_no:
+ :param overwrite:
+ :return: tuple (boolean, local file name/error message)
+ """
+ # Experiment number
+ if exp_no is None:
+ exp_no = self._expNumber
+
+ # Form the target file name and path
+ xml_file_name = '%s_exp%d_scan%04d_%04d.xml' % (self._instrumentName, exp_no, scan_no, pt_no)
+ local_xml_file_name = os.path.join(self._dataDir, xml_file_name)
+ if os.path.exists(local_xml_file_name) is True and overwrite is False:
+ return True, local_xml_file_name
+
+ # Generate the URL for XML file
+ xml_file_url = '%sexp%d/Datafiles/%s' % (self._myServerURL, exp_no, xml_file_name)
+
+ # Download
+ try:
+ api.DownloadFile(Address=xml_file_url,
+ Filename=local_xml_file_name)
+ except RuntimeError as run_err:
+ return False, 'Unable to download Detector XML file %s dur to %s.' % (xml_file_name, str(run_err))
+
+ # Check file exist?
+ if os.path.exists(local_xml_file_name) is False:
+ return False, "Unable to locate downloaded file %s."%(local_xml_file_name)
+
+ return True, local_xml_file_name
+
+ def download_data_set(self, scan_list, overwrite=False):
+ """
+ Download data set including (1) spice file for a scan and (2) XML files for measurements
+ :param scan_list:
+ :return:
+ """
+ # Check
+ if self._expNumber is None:
+ raise RuntimeError('Experiment number is not set up for controller.')
+
+ error_message = ''
+
+ for scan_no in scan_list:
+ # Download single spice file for a run
+ status, ret_obj = self.download_spice_file(exp_number=self._expNumber,
+ scan_number=scan_no,
+ over_write=overwrite)
+
+ # Reject if SPICE file cannot download
+ if status is False:
+ error_message += '%s\n' % ret_obj
+ continue
+
+ # Load SPICE file to Mantid
+ spice_file_name = ret_obj
+ status, ret_obj = self.load_spice_scan_file(self._expNumber, scan_no, spice_file_name)
+ if status is False:
+ error_message = ret_obj
+ return False, error_message
+ else:
+ spice_table = self._mySpiceTableDict[(self._expNumber, scan_no)]
+ assert spice_table
+ pt_no_list = self._get_pt_list_from_spice_table(spice_table)
+
+ # Download all single-measurement file
+ for pt_no in pt_no_list:
+ status, ret_obj = self.download_spice_xml_file(scan_no, pt_no, overwrite=overwrite)
+ if status is False:
+ error_message += '%s\n' % ret_obj
+ # END-FOR
+ # END-FOR (scan_no)
+
+ return True, error_message
+
+ def existDataFile(self, scanno, ptno):
+ """
+ Check whether data file for a scan or pt number exists
+ :param scanno:
+ :param ptno:
+ :return:
+ """
+ # Check spice file
+ spice_file_name = '%s_exp%04d_scan%04d.dat'%(self._instrumentName,
+ self._expNumber, scanno)
+ spice_file_name = os.path.join(self._dataDir, spice_file_name)
+ if os.path.exists(spice_file_name) is False:
+ return False, 'Spice data file %s cannot be found.'% spice_file_name
+
+ # Check xml file
+ xmlfilename = '%s_exp%d_scan%04d_%04d.xml'%(self._instrumentName, self._expNumber,
+ scanno, ptno)
+ xmlfilename = os.path.join(self._dataDir, xmlfilename)
+ if os.path.exists(xmlfilename) is False:
+ return (False, "Pt. XML file %s cannot be found."%(xmlfilename))
+
+ return True, ""
+
+ def find_peak(self, exp_number, scan_number, pt_number):
+ """ Find 1 peak in sample Q space for UB matrix
+ :param scan_number:
+ :param pt_number:
+ :return:tuple as (boolean, object) such as (false, error message) and (true, PeakInfo object)
+
+ This part will be redo as 11847_Load_HB3A_Experiment
+ """
+ # Check
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Download or make sure data are there
+ status_sp, err_msg_sp = self.download_spice_file(exp_number, scan_number, over_write=False)
+ status_det, err_msg_det = self.download_spice_xml_file(scan_number, pt_number, exp_number,
+ overwrite=False)
+ if status_sp is False or status_det is False:
+ return False, 'Unable to access data (1) %s (2) %s' % (err_msg_sp, err_msg_det)
+
+ # Collect reduction information: example
+ exp_info_ws_name = get_pt_info_ws_name(exp_number, scan_number)
+ virtual_instrument_info_table_name = get_virtual_instrument_table_name(exp_number, scan_number, pt_number)
+ api.CollectHB3AExperimentInfo(
+ ExperimentNumber=exp_number,
+ GenerateVirtualInstrument=False,
+ ScanList=[scan_number],
+ PtLists=[-1, pt_number],
+ DataDirectory=self._dataDir,
+ GetFileFromServer=False,
+ Detector2ThetaTolerance=0.01,
+ OutputWorkspace=exp_info_ws_name,
+ DetectorTableWorkspace=virtual_instrument_info_table_name)
+
+ # Load XML file to MD
+ pt_md_ws_name = get_single_pt_md_name(exp_number, scan_number, pt_number)
+ api.ConvertCWSDExpToMomentum(InputWorkspace=exp_info_ws_name,
+ CreateVirtualInstrument=False,
+ OutputWorkspace=pt_md_ws_name,
+ Directory=self._dataDir)
+
+ # Find peak in Q-space
+ pt_peak_ws_name = get_single_pt_peak_ws_name(exp_number, scan_number, pt_number)
+ api.FindPeaksMD(InputWorkspace=pt_md_ws_name, MaxPeaks=10,
+ DensityThresholdFactor=0.01, OutputWorkspace=pt_peak_ws_name)
+ peak_ws = AnalysisDataService.retrieve(pt_peak_ws_name)
+ pt_md_ws = AnalysisDataService.retrieve(pt_md_ws_name)
+ self._myPtMDDict[(exp_number, scan_number, pt_number)] = pt_md_ws
+
+ num_peaks = peak_ws.getNumberPeaks()
+ if num_peaks != 1:
+ err_msg = 'Find %d peak from scan %d pt %d. ' \
+ 'For UB matrix calculation, 1 and only 1 peak is allowed' % (num_peaks, scan_number, pt_number)
+ return False, err_msg
+ else:
+ self._add_ub_peak_ws(exp_number, scan_number, pt_number, peak_ws)
+ status, ret_obj = self.add_peak_info(exp_number, scan_number, pt_number)
+ if status is True:
+ pass
+ # peak_info = ret_obj
+ # peak_info.set_md_ws(pt_md_ws)
+ else:
+ err_msg = ret_obj
+ return False, err_msg
+
+ return True, ''
+
+ def get_experiment(self):
+ """
+ Get experiment number
+ :return:
+ """
+ return self._expNumber
+
+ def get_pt_numbers(self, exp_no, scan_no, load_spice_scan=False):
+ """ Get Pt numbers (as a list) for a scan in an experiment
+ :param exp_no:
+ :param scan_no:
+ :param load_spice_scan:
+ :return: (Boolean, Object) as (status, pt number list/error message)
+ """
+ # Check
+ if exp_no is None:
+ exp_no = self._expNumber
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+
+ # Get workspace
+ table_ws = self._get_spice_workspace(exp_no, scan_no)
+ if table_ws is None:
+ if load_spice_scan is False:
+ return False, 'Spice file for Exp %d Scan %d is not loaded.' % (exp_no, scan_no)
+ else:
+ status, error_message = self.load_spice_scan_file(exp_no, scan_no)
+ if status is True:
+ table_ws = self._get_spice_workspace(exp_no, scan_no)
+ if table_ws is None:
+ raise NotImplementedError('Logic error! Cannot happen!')
+ else:
+ return False, 'Unable to load Spice file for Exp %d Scan %d due to %s.' % (
+ exp_no, scan_no, error_message)
+
+ col_name_list = table_ws.getColumnNames()
+ i_pt = col_name_list.index('Pt.')
+ if i_pt < 0 or i_pt >= len(col_name_list):
+ return False, 'No column with name Pt. can be found in SPICE table.'
+
+ pt_number_list = []
+ num_rows = table_ws.rowCount()
+ for i in xrange(num_rows):
+ pt_number = table_ws.cell(i, i_pt)
+ pt_number_list.append(pt_number)
+
+ return True, pt_number_list
+
+ def get_raw_detector_counts(self, exp_no, scan_no, pt_no):
+ """
+ Get counts on raw detector
+ :param scan_no:
+ :param pt_no:
+ :return: boolean, 2D numpy data
+ """
+ # Get workspace (in memory or loading)
+ raw_ws = self.get_raw_data_workspace(exp_no, scan_no, pt_no)
+ if raw_ws is None:
+ return False, 'Raw data for Exp %d Scan %d Pt %d is not loaded.' % (exp_no, scan_no, pt_no)
+
+ # Convert to numpy array
+ array2d = numpy.ndarray(shape=(DET_X_SIZE, DET_Y_SIZE), dtype='float')
+ for i in xrange(DET_X_SIZE):
+ for j in xrange(DET_Y_SIZE):
+ array2d[i][j] = raw_ws.readY(i * DET_X_SIZE + j)[0]
+
+ return array2d
+
+ def get_sample_log_value(self, exp_number, scan_number, pt_number, log_name):
+ """
+ Get sample log's value
+ :param exp_number:
+ :param scan_number:167
+ :param pt_number:
+ :param log_name:
+ :return: float
+ """
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+ assert isinstance(log_name, str)
+ try:
+ md_ws = self._myPtMDDict[(exp_number, scan_number, pt_number)]
+ except KeyError as ke:
+ return 'Unable to find log value %s due to %s.' % (log_name, str(ke))
+
+ return md_ws.getExperimentInfo(0).run().getProperty(log_name).value
+
+ def get_peak_info(self, exp_number, scan_number, pt_number):
+ """
+ get peak information instance
+ :param exp_number: experiment number. if it is None, then use the current exp number
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ # Check for type
+ if exp_number is None:
+ exp_number = self._expNumber
+
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Check for existence
+ if (exp_number, scan_number, pt_number) not in self._myUBPeakWSDict: # self._myPeakInfoDict:
+ err_msg = 'Unable to find PeakInfo for Exp %d Scan %d Pt %d. ' \
+ 'Existing keys are %s' % (exp_number, scan_number, pt_number,
+ str(self._myUBPeakWSDict.keys()))
+ return False, err_msg
+
+ print '[DB] PeakInfoDictionary Keys = %s' % str(self._myPeakInfoDict.keys())
+
+ return True, self._myPeakInfoDict[(exp_number, scan_number, pt_number)]
+
+ def get_ub_peak_ws(self, exp_number, scan_number, pt_number):
+ """
+ Get peak workspace for the peak picked to calculate UB matrix
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ if (exp_number, scan_number, pt_number) not in self._myUBPeakWSDict:
+ return False, 'Exp %d Scan %d Pt %d has no peak workspace.' % (exp_number,
+ scan_number,
+ pt_number)
+
+ return True, self._myUBPeakWSDict[(exp_number, scan_number, pt_number)]
+
+ def index_peak(self, ub_matrix, scan_number, pt_number):
+ """ Index peaks in a Pt.
+ :param ub_matrix: numpy.ndarray (3, 3)
+ :param scan_number:
+ :param pt_number:
+ :return: boolean, object (list of HKL or error message)
+ """
+ # Check
+ assert isinstance(ub_matrix, numpy.ndarray)
+ assert ub_matrix.shape == (3, 3)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Find out the peak workspace
+ exp_num = self._expNumber
+ if (exp_num, scan_number, pt_number) in self._myUBPeakWSDict is False:
+ err_msg = 'No PeakWorkspace is found for exp %d scan %d pt %d' % (
+ exp_num, scan_number, pt_number)
+ return False, err_msg
+
+ peak_ws = self._myUBPeakWSDict[(exp_num, scan_number, pt_number)]
+ ub_1d = ub_matrix.reshape(9,)
+ print '[DB] UB matrix = ', ub_1d
+
+ # Set UB
+ api.SetUB(Workspace=peak_ws, UB=ub_1d)
+
+ # Note: IndexPeaks and CalcualtePeaksHKL do the same job
+ # while IndexPeaks has more control on the output
+ num_peak_index, error = api.IndexPeaks(PeaksWorkspace=peak_ws,
+ Tolerance=0.4,
+ RoundHKLs=False)
+
+ if num_peak_index == 0:
+ return False, 'No peak can be indexed.'
+ elif num_peak_index > 1:
+ raise RuntimeError('Case for PeaksWorkspace containing more than 1 peak is not '
+ 'considered. Contact developer for this issue.')
+ else:
+ hkl_v3d = peak_ws.getPeak(0).getHKL()
+ hkl = [hkl_v3d.X(), hkl_v3d.Y(), hkl_v3d.Z()]
+
+ return True, (hkl, error)
+
+ def load_spice_scan_file(self, exp_no, scan_no, spice_file_name=None):
+ """
+ Load a SPICE scan file to table workspace and run information matrix workspace.
+ :param scan_no:
+ :param spice_file_name:
+ :return: status (boolean), error message (string)
+ """
+ # Default for exp_no
+ if exp_no is None:
+ exp_no = self._expNumber
+
+ # Check whether the workspace has been loaded
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ out_ws_name = get_spice_table_name(exp_no, scan_no)
+ if (exp_no, scan_no) in self._mySpiceTableDict:
+ return True, out_ws_name
+
+ # Form standard name for a SPICE file if name is not given
+ if spice_file_name is None:
+ spice_file_name = os.path.join(self._dataDir, get_spice_file_name(exp_no, scan_no))
+
+ # Download SPICE file if necessary
+ if os.path.exists(spice_file_name) is False:
+ self.download_spice_file(exp_no, scan_no, over_write=True)
+
+ try:
+ spice_table_ws, info_matrix_ws = api.LoadSpiceAscii(Filename=spice_file_name,
+ OutputWorkspace=out_ws_name,
+ RunInfoWorkspace='TempInfo')
+ api.DeleteWorkspace(Workspace=info_matrix_ws)
+ except RuntimeError as run_err:
+ return False, 'Unable to load SPICE data %s due to %s' % (spice_file_name, str(run_err))
+
+ # Store
+ self._add_spice_workspace(exp_no, scan_no, spice_table_ws)
+
+ return True, out_ws_name
+
+ def load_spice_xml_file(self, exp_no, scan_no, pt_no, xml_file_name=None):
+ """
+ Load SPICE's XML file to
+ :param scan_no:
+ :param pt_no:
+ :return:
+ """
+ # Form XMIL file as ~/../HB3A_exp355_scan%04d_%04d.xml'%(scan_no, pt)
+ if xml_file_name is None:
+ xml_file_name = os.path.join(self._dataDir,
+ 'HB3A_exp%d_scan%04d_%04d.xml' % (exp_no, scan_no, pt_no))
+
+ # Get spice table
+ spice_table_ws = self._get_spice_workspace(exp_no, scan_no)
+ assert isinstance(spice_table_ws, mantid.dataobjects.TableWorkspace)
+ spice_table_name = spice_table_ws.name()
+
+ # Load SPICE Pt. file
+ # spice_table_name = 'Table_Exp%d_Scan%04d' % (exp_no, scan_no)
+ pt_ws_name = get_raw_data_workspace_name(exp_no, scan_no, pt_no)
+ try:
+ ret_obj = api.LoadSpiceXML2DDet(Filename=xml_file_name,
+ OutputWorkspace=pt_ws_name,
+ DetectorGeometry='256,256',
+ SpiceTableWorkspace=spice_table_name,
+ PtNumber=pt_no)
+ except RuntimeError as run_err:
+ return False, str(run_err)
+
+ pt_ws = ret_obj
+
+ # Add data storage
+ self._add_raw_workspace(exp_no, scan_no, pt_no, pt_ws)
+
+ return True, pt_ws_name
+
+ def group_workspaces(self, exp_number, group_name):
+ """
+
+ :return:
+ """
+ # Find out the input workspace name
+ ws_names_str = ''
+ for key in self._myRawDataWSDict.keys():
+ if key[0] == exp_number:
+ ws_names_str += '%s,' % self._myRawDataWSDict[key].name()
+
+ for key in self._mySpiceTableDict.keys():
+ if key[0] == exp_number:
+ ws_names_str += '%s,' % self._mySpiceTableDict[key].name()
+
+ # Check
+ if len(ws_names_str) == 0:
+ return False, 'No workspace is found for experiment %d.' % exp_number
+
+ # Remove last ','
+ ws_names_str = ws_names_str[:-1]
+
+ # Group
+ api.GroupWorkspaces(InputWorkspaces=ws_names_str,
+ OutputWorkspace=group_name)
+
+ return
+
+ def merge_pts_in_scan(self, exp_no, scan_no, target_ws_name, target_frame):
+ """
+ Merge Pts in Scan
+ All the workspaces generated as internal results will be grouped
+ :param exp_no:
+ :param scan_no:
+ :param target_ws_name:
+ :param target_frame:
+ :return: (merged workspace name, workspace group name)
+ """
+ # Check
+ if exp_no is None:
+ exp_no = self._expNumber
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(target_frame, str)
+ assert isinstance(target_ws_name, str)
+
+ ub_matrix_1d = None
+
+ # Target frame
+ if target_frame.lower().startswith('hkl'):
+ target_frame = 'hkl'
+ ub_matrix_1d = self._myUBMatrixDict[self._expNumber].reshape(9,)
+ elif target_frame.lower().startswith('q-sample'):
+ target_frame = 'qsample'
+
+ else:
+ raise RuntimeError('Target frame %s is not supported.' % target_frame)
+
+ # Process data and save
+ status, pt_num_list = self.get_pt_numbers(exp_no, scan_no, True)
+ if status is False:
+ err_msg = pt_num_list
+ return False, err_msg
+ else:
+ print '[DB] Number of Pts for Scan %d is %d' % (scan_no, len(pt_num_list))
+ print '[DB] Data directory: %s' % self._dataDir
+ max_pts = 0
+ ws_names_str = ''
+ ws_names_to_group = ''
+
+ for pt in pt_num_list:
+ try:
+ self.download_spice_xml_file(scan_no, pt, overwrite=False)
+ api.CollectHB3AExperimentInfo(ExperimentNumber=exp_no, ScanList='%d' % scan_no, PtLists='-1,%d' % pt,
+ DataDirectory=self._dataDir,
+ GenerateVirtualInstrument=False,
+ OutputWorkspace='ScanPtInfo_Exp%d_Scan%d' % (exp_no, scan_no),
+ DetectorTableWorkspace='MockDetTable')
+
+ out_q_name = 'HB3A_Exp%d_Scan%d_Pt%d_MD' % (exp_no, scan_no, pt)
+ api.ConvertCWSDExpToMomentum(InputWorkspace='ScanPtInfo_Exp406_Scan%d' % scan_no,
+ CreateVirtualInstrument=False,
+ OutputWorkspace=out_q_name,
+ Directory=self._dataDir)
+
+ ws_names_to_group += out_q_name + ','
+ if target_frame == 'hkl':
+ out_hkl_name = 'HKL_Scan%d_Pt%d' % (scan_no, pt)
+ api.ConvertCWSDMDtoHKL(InputWorkspace=out_q_name,
+ UBMatrix=ub_matrix_1d,
+ OutputWorkspace=out_hkl_name)
+ ws_names_str += out_hkl_name + ','
+ ws_names_to_group += out_hkl_name + ','
+ else:
+ ws_names_str += out_q_name + ','
+
+ except RuntimeError as e:
+ print '[Error] Reducing scan %d pt %d due to %s' % (scan_no, pt, str(e))
+ continue
+
+ else:
+ max_pts = pt
+ # END-FOR
+
+ # Merge
+ if target_frame == 'qsample':
+ out_ws_name = target_ws_name + '_QSample'
+ elif target_frame == 'hkl':
+ out_ws_name = target_ws_name + '_HKL'
+ else:
+ raise RuntimeError('Impossible to have target frame %s' % target_frame)
+
+ ws_names_str = ws_names_str[:-1]
+ api.MergeMD(InputWorkspaces=ws_names_str, OutputWorkspace=out_ws_name, SplitInto=max_pts)
+
+ # Group workspaces
+ group_name = 'Group_Exp406_Scan%d' % scan_no
+ api.GroupWorkspaces(InputWorkspaces=ws_names_to_group, OutputWorkspace=group_name)
+ spice_table_name = get_spice_table_name(exp_no, scan_no)
+ api.GroupWorkspaces(InputWorkspaces='%s,%s' % (group_name, spice_table_name), OutputWorkspace=group_name)
+
+ ret_tup = out_ws_name, group_name
+
+ return ret_tup
+
+ def set_server_url(self, server_url):
+ """
+ Set URL for server to download the data
+ :param server_url:
+ :return:
+ """
+ # Server URL must end with '/'
+ self._myServerURL = str(server_url)
+ if self._myServerURL.endswith('/') is False:
+ self._myServerURL += '/'
+
+ # Test URL valid or not
+ is_url_good = False
+ error_message = None
+ try:
+ result = urllib2.urlopen(self._myServerURL)
+ except urllib2.HTTPError, err:
+ error_message = str(err.code)
+ except urllib2.URLError, err:
+ error_message = str(err.args)
+ else:
+ is_url_good = True
+ result.close()
+
+ if error_message is None:
+ error_message = ''
+ else:
+ error_message = 'Unable to open data server URL: %s due to %s.' % (server_url, error_message)
+
+ return is_url_good, error_message
+
+ def setWebAccessMode(self, mode):
+ """
+ Set data access mode form server
+ :param mode:
+ :return:
+ """
+ if isinstance(mode, str) is False:
+ raise RuntimeError('Input mode is not string')
+
+ if mode == 'cache':
+ self._cacheDataOnly = True
+ elif mode == 'download':
+ self._cacheDataOnly = False
+
+ return
+
+ def set_local_data_dir(self, local_dir):
+ """
+ Set local data storage
+ :param local_dir:
+ :return:
+ """
+ # Get absolute path
+ if os.path.isabs(local_dir) is False:
+ # Input is relative path to current working directory
+ cwd = os.getcwd()
+ local_dir = os.path.join(cwd, local_dir)
+
+ # Create cache directory if necessary
+ if os.path.exists(local_dir) is False:
+ try:
+ os.mkdir(local_dir)
+ except OSError as os_err:
+ return False, str(os_err)
+
+ # Check whether the target is writable
+ if os.access(local_dir, os.W_OK) is False:
+ return False, 'Specified local data directory %s is not writable.' % local_dir
+
+ # Successful
+ self._dataDir = local_dir
+
+ return True, ''
+
+ def set_ub_matrix(self, exp_number, ub_matrix):
+ """
+ Set up UB matrix to _UBMatrix dictionary
+ :param exp_number:
+ :param ub_matrix:
+ :return:
+ """
+ # Check
+ if exp_number is None:
+ exp_number = self._expNumber
+
+ assert isinstance(exp_number, int)
+ assert isinstance(ub_matrix, numpy.ndarray)
+ assert ub_matrix.shape == (3, 3)
+
+ # Set up
+ self._myUBMatrixDict[exp_number] = ub_matrix
+
+ def set_working_directory(self, work_dir):
+ """
+ Set up the directory for working result
+ :return: (boolean, string)
+ """
+ if os.path.exists(work_dir) is False:
+ try:
+ os.mkdir(work_dir)
+ except OSError as os_err:
+ return False, 'Unable to create working directory %s due to %s.' % (work_dir, str(os_err))
+ elif os.access(work_dir, os.W_OK) is False:
+ return False, 'User specified working directory %s is not writable.' % work_dir
+
+ self._workDir = work_dir
+
+ return True, ''
+
+ def set_instrument_name(self, instrument_name):
+ """
+ Set instrument name
+ :param instrument_name:
+ :return:
+ """
+ # Check
+ if isinstance(instrument_name, str) is False:
+ return False, 'Input instrument name is not a string but of type %s.' % str(type(instrument_name))
+ if len(instrument_name) == 0:
+ return False, 'Input instrument name is an empty string.'
+
+ self._instrumentName = instrument_name
+
+ return True, ''
+
+ def set_exp_number(self, exp_number):
+ """ Add experiment number
+ :param exp_number:
+ :return:
+ """
+ assert isinstance(exp_number, int)
+ self._expNumber = exp_number
+
+ return True
+
+ def set_hkl_to_peak(self, exp_number, scan_number, pt_number):
+ """
+ Get HKL as _h, _k, _l from MDEventWorkspace. It is for HB3A only
+ :return:
+ """
+ status, peak_info = self.get_peak_info(exp_number, scan_number, pt_number)
+ if status is False:
+ err_msg = peak_info
+ return False, err_msg
+
+ md_ws = self._myPtMDDict[(exp_number, scan_number, pt_number)]
+ assert md_ws.getNumExperimentInfo() == 1
+ exp_info = md_ws.getExperimentInfo(0)
+
+ try:
+ m_h = float(exp_info.run().getProperty('_h').value)
+ m_k = float(exp_info.run().getProperty('_k').value)
+ m_l = float(exp_info.run().getProperty('_l').value)
+ except RuntimeError as error:
+ return False, 'Unable to retrieve HKL due to %s.' % (str(error))
+
+ peak_ws = peak_info.get_peak_workspace()
+ peak = peak_ws.getPeak(0)
+ peak.setHKL(m_h, m_k, m_l)
+
+ return True, (m_h, m_k, m_l)
+
+ def _add_raw_workspace(self, exp_no, scan_no, pt_no, raw_ws):
+ """ Add raw Pt.'s workspace
+ :param exp_no:
+ :param scan_no:
+ :param pt_no:
+ :param raw_ws: workspace or name of the workspace
+ :return: None
+ """
+ # Check
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(pt_no, int)
+
+ if isinstance(raw_ws, str):
+ # Given by name
+ matrix_ws = AnalysisDataService.retrieve(raw_ws)
+ else:
+ matrix_ws = raw_ws
+ assert isinstance(matrix_ws, mantid.dataobjects.Workspace2D)
+
+ self._myRawDataWSDict[(exp_no, scan_no, pt_no)] = matrix_ws
+
+ return
+
+ def _add_md_workspace(self, exp_no, scan_no, pt_no, md_ws):
+ """
+ Add MD workspace to storage
+ :param exp_no:
+ :param scan_no:
+ :param pt_no:
+ :param md_ws:
+ :return:
+ """
+ # Check input
+ print '[DB] Type of md_ws is %s.' % str(type(md_ws))
+ assert isinstance(md_ws, mantid.dataobjects.MDEventWorkspace)
+
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(pt_no)
+
+ self._myPtMDDict[(exp_no, scan_no, pt_no)] = md_ws
+
+ return
+
+ def _add_ub_peak_ws(self, exp_number, scan_number, pt_number, peak_ws):
+ """
+ Add peak workspace for UB matrix
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :param peak_ws:
+ :return:
+ """
+ # Check
+ assert isinstance(peak_ws, mantid.dataobjects.PeaksWorkspace)
+
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Add
+ self._myUBPeakWSDict[(exp_number, scan_number, pt_number)] = peak_ws
+
+ return
+
+ def _add_spice_workspace(self, exp_no, scan_no, spice_table_ws):
+ """
+ """
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(spice_table_ws, mantid.dataobjects.TableWorkspace)
+ self._mySpiceTableDict[(exp_no, scan_no)] = spice_table_ws
+
+ return
+
+ def _get_spice_workspace(self, exp_no, scan_no):
+ """ Get SPICE's scan table workspace
+ :param exp_no:
+ :param scan_no:
+ :return: Table workspace or None
+ """
+ try:
+ ws = self._mySpiceTableDict[(exp_no, scan_no)]
+ except KeyError:
+ print '[DB] Keys to SPICE TABLE: %s' % str(self._mySpiceTableDict.keys())
+ return None
+
+ return ws
+
+ def get_raw_data_workspace(self, exp_no, scan_no, pt_no):
+ """ Get raw workspace
+ """
+ try:
+ ws = self._myRawDataWSDict[(exp_no, scan_no, pt_no)]
+ assert isinstance(ws, mantid.dataobjects.Workspace2D)
+ except KeyError:
+ return None
+
+ return ws
+
+ def _get_pt_list_from_spice_table(self, spice_table_ws):
+ """
+ Get list of Pt. from a SPICE table workspace
+ :param spice_table_ws: SPICE table workspace
+ :return: list of Pt.
+ """
+ numrows = spice_table_ws.rowCount()
+ ptlist = []
+ for irow in xrange(numrows):
+ ptno = int(spice_table_ws.cell(irow, 0))
+ ptlist.append(ptno)
+
+ return ptlist
+
+
+def get_spice_file_name(exp_number, scan_number):
+ """
+ Get standard HB3A SPICE file name from experiment number and scan number
+ :param exp_number:
+ :param scan_num:
+ :return:
+ """
+ file_name = 'HB3A_exp%04d_scan%04d.dat' % (exp_number, scan_number)
+
+ return file_name
+
+
+def get_spice_table_name(exp_number, scan_number):
+ """ Form the name of the table workspace for SPICE
+ :param exp_number:
+ :param scan_number:
+ :return:
+ """
+ table_name = 'HB3A_%03d_%04d_SpiceTable' % (exp_number, scan_number)
+
+ return table_name
+
+
+def get_raw_data_workspace_name(exp_number, scan_number, pt_number):
+ """ Form the name of the matrix workspace to which raw pt. XML file is loaded
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'HB3A_exp%d_scan%04d_%04d' % (exp_number, scan_number, pt_number)
+
+ return ws_name
+
+
+def get_pt_info_ws_name(exp_number, scan_number):
+ """
+ Information table workspace'name from CollectHB3AInfo
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'ScanPtInfo_Exp%d_Scan%d' % (exp_number, scan_number)
+
+ return ws_name
+
+
+def get_single_pt_peak_ws_name(exp_number, scan_number, pt_number):
+ """
+ Form the name of the peak workspace
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'Peak_Exp%d_Scan%d_Pt%d' % (exp_number, scan_number, pt_number)
+
+ return ws_name
+
+
+def get_single_pt_md_name(exp_number, scan_number, pt_number):
+ """ Form the name of the MDEvnetWorkspace for a single Pt. measurement
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'HB3A_Exp%d_Scan%d_Pt%d_MD' % (exp_number, scan_number, pt_number)
+
+ return ws_name
+
+
+def get_virtual_instrument_table_name(exp_number, scan_number, pt_number):
+ """
+ Generate the name of the table workspace containing the virtual instrument information
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'VirtualInstrument_Exp%d_Scan%d_Pt%d_Table' % (exp_number, scan_number, pt_number)
+
+ return ws_name
diff --git a/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py b/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
new file mode 100644
index 0000000000000000000000000000000000000000..7009c1e8b8ec763ec515120f212242332cf5e2b9
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
@@ -0,0 +1,1092 @@
+#pylint: disable=invalid-name,relative-import,W0611,R0921,R0902,R0904,R0921,C0302
+################################################################################
+#
+# MainWindow application for reducing HFIR 4-circle
+#
+################################################################################
+import os
+import math
+import csv
+import time
+
+from PyQt4 import QtCore, QtGui
+
+import reduce4circleControl as r4c
+import guiutility as gutil
+import fourcircle_utility as fcutil
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ def _fromUtf8(s):
+ return s
+
+# import line for the UI python class
+from ui_MainWindow import Ui_MainWindow
+
+
+class MainWindow(QtGui.QMainWindow):
+ """ Class of Main Window (top)
+ """
+ def __init__(self, parent=None):
+ """ Initialization and set up
+ """
+ # Base class
+ QtGui.QMainWindow.__init__(self,parent)
+
+ # UI Window (from Qt Designer)
+ self.ui = Ui_MainWindow()
+ self.ui.setupUi(self)
+
+ # Mantid configuration
+ self._instrument = str(self.ui.comboBox_instrument.currentText())
+ # config = ConfigService.Instance()
+ # self._instrument = config["default.instrument"]
+
+ # Event handling definitions
+ # Top
+ self.connect(self.ui.pushButton_setExp, QtCore.SIGNAL('clicked()'),
+ self.do_set_experiment)
+
+ # Tab 'Data Access'
+ self.connect(self.ui.pushButton_applySetup, QtCore.SIGNAL('clicked()'),
+ self.do_apply_setup)
+ self.connect(self.ui.pushButton_browseLocalDataDir, QtCore.SIGNAL('clicked()'),
+ self.do_browse_local_spice_data)
+ self.connect(self.ui.pushButton_testURLs, QtCore.SIGNAL('clicked()'),
+ self.do_test_url)
+ self.connect(self.ui.pushButton_ListScans, QtCore.SIGNAL('clicked()'),
+ self.do_list_scans)
+ self.connect(self.ui.pushButton_downloadExpData, QtCore.SIGNAL('clicked()'),
+ self.do_download_spice_data)
+ self.connect(self.ui.comboBox_mode, QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.change_data_access_mode)
+
+ # Tab 'View Raw Data'
+ self.connect(self.ui.pushButton_setScanInfo, QtCore.SIGNAL('clicked()'),
+ self.do_load_scan_info)
+ self.connect(self.ui.pushButton_plotRawPt, QtCore.SIGNAL('clicked()'),
+ self.do_plot_pt_raw)
+ self.connect(self.ui.pushButton_prevPtNumber, QtCore.SIGNAL('clicked()'),
+ self.do_plot_prev_pt_raw)
+ self.connect(self.ui.pushButton_nextPtNumber, QtCore.SIGNAL('clicked()'),
+ self.do_plot_next_pt_raw)
+ self.connect(self.ui.pushButton_showPtList, QtCore.SIGNAL('clicked()'),
+ self.show_scan_pt_list)
+ self.connect(self.ui.pushButton_usePt4UB, QtCore.SIGNAL('clicked()'),
+ self.do_add_peak_to_find)
+
+ # Tab 'calculate ub matrix'
+ self.connect(self.ui.pushButton_findPeak, QtCore.SIGNAL('clicked()'),
+ self.do_find_peak)
+ self.connect(self.ui.pushButton_addPeakToCalUB, QtCore.SIGNAL('clicked()'),
+ self.do_add_ub_peak)
+ self.connect(self.ui.pushButton_calUB, QtCore.SIGNAL('clicked()'),
+ self.do_cal_ub_matrix)
+ self.connect(self.ui.pushButton_acceptUB, QtCore.SIGNAL('clicked()'),
+ self.doAcceptCalUB)
+ self.connect(self.ui.pushButton_indexUBPeaks, QtCore.SIGNAL('clicked()'),
+ self.do_index_ub_peaks)
+ self.connect(self.ui.pushButton_deleteUBPeak, QtCore.SIGNAL('clicked()'),
+ self.do_del_ub_peaks)
+ self.connect(self.ui.pushButton_clearUBPeakTable, QtCore.SIGNAL('clicked()'),
+ self.do_clear_ub_peaks)
+ self.connect(self.ui.pushButton_resetPeakHKLs, QtCore.SIGNAL('clicked()'),
+ self.do_reset_ub_peaks_hkl)
+
+ # Tab 'Slice View'
+ self.connect(self.ui.pushButton_setUBSliceView, QtCore.SIGNAL('clicked()'),
+ self.do_set_ub_sv)
+ self.connect(self.ui.pushButton_process4SliceView, QtCore.SIGNAL('clicked()'),
+ self.do_merge_scans)
+
+ # Tab 'Advanced'
+ self.connect(self.ui.pushButton_useDefaultDir, QtCore.SIGNAL('clicked()'),
+ self.do_setup_dir_default)
+ self.connect(self.ui.pushButton_browseLocalCache, QtCore.SIGNAL('clicked()'),
+ self.do_browse_local_cache_dir)
+ self.connect(self.ui.pushButton_browseWorkDir, QtCore.SIGNAL('clicked()'),
+ self.do_browse_working_dir)
+ self.connect(self.ui.comboBox_instrument, QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.change_instrument_name)
+
+ # Refine UB matrix
+ self.connect(self.ui.pushButton_addToRefine, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+ self.connect(self.ui.pushButton_addAllRefineUB, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+ self.connect(self.ui.pushButton_acceptRefinedUB, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+ self.connect(self.ui.pushButton_resetRefinedUB, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+
+ # Tab 'Integrate Peaks'
+ self.connect(self.ui.pushButton_integratePeak, QtCore.SIGNAL('clicked()'),
+ self.do_integrate_peaks)
+
+ # Menu
+ self.connect(self.ui.actionExit, QtCore.SIGNAL('triggered()'),
+ self.menu_quit)
+
+ self.connect(self.ui.actionSave_Session, QtCore.SIGNAL('triggered()'),
+ self.save_current_session)
+ self.connect(self.ui.actionLoad_Session, QtCore.SIGNAL('triggered()'),
+ self.load_session)
+
+ # Event handling for tab 'refine ub matrix'
+ self.connect(self.ui.pushButton_addToRefine, QtCore.SIGNAL('clicked()'),
+ self.doAddScanPtToRefineUB)
+
+ # Validator ... (NEXT)
+
+ # Declaration of class variable
+ # some configuration
+ self._homeSrcDir = os.getcwd()
+ self._homeDir = os.getcwd()
+
+ # Control
+ self._myControl = r4c.CWSCDReductionControl(self._instrument)
+ self._allowDownload = True
+ self._dataAccessMode = 'Download'
+
+ # Initial setup
+ self.ui.tabWidget.setCurrentIndex(0)
+ self.ui.tabWidget.setTabEnabled(4, False)
+ self.ui.tabWidget.setTabEnabled(5, False)
+ self._init_ub_table()
+ self.ui.radioButton_ubFromTab1.setChecked(True)
+
+ # Tab 'Access'
+ self.ui.lineEdit_url.setText('http://neutron.ornl.gov/user_data/hb3a/')
+ self.ui.comboBox_mode.setCurrentIndex(0)
+ self.ui.lineEdit_localSpiceDir.setEnabled(True)
+ self.ui.pushButton_browseLocalDataDir.setEnabled(True)
+
+ return
+
+ def do_integrate_peaks(self):
+ """
+
+ :return:
+ """
+ raise RuntimeError('ASAP')
+
+ def do_refine_ub(self):
+ """
+
+ :return:
+ """
+ raise RuntimeError('Next Release')
+
+ def _init_ub_table(self):
+ """ DOC
+ :return:
+ """
+ # UB-peak table
+ # NOTE: have to call this because pyqt set column and row to 0 after __init__
+ # thus a 2-step initialization has to been adopted
+ self.ui.tableWidget_peaksCalUB.setup()
+
+ self.ui.tableWidget_ubMatrix.setup()
+ self.ui.tableWidget_ubSiceView.setup()
+ self.ui.tableWidget_refinedUB.setup()
+
+ self.ui.tableWidget_sliceViewProgress.setup()
+
+ return
+
+ def change_data_access_mode(self):
+ """ Change data access mode between downloading from server and local
+ Event handling methods
+ :return:
+ """
+ new_mode = str(self.ui.comboBox_mode.currentText())
+ self._dataAccessMode = new_mode
+
+ if new_mode.startswith('Local') is True:
+ self.ui.lineEdit_localSpiceDir.setEnabled(True)
+ self.ui.pushButton_browseLocalDataDir.setEnabled(True)
+ self.ui.lineEdit_url.setEnabled(False)
+ self.ui.lineEdit_localSrcDir.setEnabled(False)
+ self.ui.pushButton_browseLocalCache.setEnabled(False)
+ self._allowDownload = False
+ else:
+ self.ui.lineEdit_localSpiceDir.setEnabled(False)
+ self.ui.pushButton_browseLocalDataDir.setEnabled(False)
+ self.ui.lineEdit_url.setEnabled(True)
+ self.ui.lineEdit_localSrcDir.setEnabled(True)
+ self.ui.pushButton_browseLocalCache.setEnabled(True)
+ self._allowDownload = True
+
+ return
+
+ def change_instrument_name(self):
+ """ Handing the event as the instrument name is changed
+ :return:
+ """
+ new_instrument = str(self.ui.comboBox_instrument.currentText())
+ self.pop_one_button_dialog('Change of instrument during data processing is dangerous.')
+ status, error_message = self._myControl.set_instrument_name(new_instrument)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+
+ return
+
+ def do_add_ub_peak(self):
+ """ Add current to ub peaks
+ :return:
+ """
+ # Add peak
+ status, int_list = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_scanNumber,
+ self.ui.lineEdit_ptNumber])
+ if status is False:
+ self.pop_one_button_dialog(int_list)
+ exp_no, scan_no, pt_no = int_list
+
+ # Get HKL from GUI
+ status, float_list = gutil.parse_float_editors([self.ui.lineEdit_H,
+ self.ui.lineEdit_K,
+ self.ui.lineEdit_L])
+ if status is False:
+ err_msg = float_list
+ self.pop_one_button_dialog(err_msg)
+ return
+ h, k, l = float_list
+
+ status, peak_info_obj = self._myControl.get_peak_info(exp_no, scan_no, pt_no)
+ if status is False:
+ error_message = peak_info_obj
+ self.pop_one_button_dialog(error_message)
+ return
+ assert isinstance(peak_info_obj, r4c.PeakInfo)
+
+ if self.ui.checkBox_roundHKLInt.isChecked():
+ h = math.copysign(1, h)*int(abs(h)+0.5)
+ k = math.copysign(1, k)*int(abs(k)+0.5)
+ l = math.copysign(1, l)*int(abs(l)+0.5)
+ peak_info_obj.set_user_hkl(h, k, l)
+ self.set_ub_peak_table(peak_info_obj)
+
+ # Clear
+ self.ui.lineEdit_scanNumber.setText('')
+ self.ui.lineEdit_ptNumber.setText('')
+
+ self.ui.lineEdit_sampleQx.setText('')
+ self.ui.lineEdit_sampleQy.setText('')
+ self.ui.lineEdit_sampleQz.setText('')
+
+ self.ui.lineEdit_H.setText('')
+ self.ui.lineEdit_K.setText('')
+ self.ui.lineEdit_L.setText('')
+
+ return
+
+ def doAcceptCalUB(self):
+ """ Accept the calculated UB matrix
+ """
+ raise RuntimeError('ASAP')
+ return
+
+ def doAddScanPtToRefineUB(self):
+ """ Add scan/pt numbers to the list of data points for refining ub matrix
+
+ And the added scan number and pt numbers will be reflected in the (left sidebar)
+
+ """
+ raise RuntimeError("ASAP")
+
+ def do_add_peak_to_find(self):
+ """
+ Add the scan/pt to the next
+ :return:
+ """
+ scan_no = self.ui.lineEdit_run.text()
+ pt_no = self.ui.lineEdit_rawDataPtNo.text()
+
+ self.ui.lineEdit_scanNumber.setText(scan_no)
+ self.ui.lineEdit_ptNumber.setText(pt_no)
+
+ self.ui.tabWidget.setCurrentIndex(2)
+
+ def do_browse_local_cache_dir(self):
+ """ Browse local cache directory
+ :return:
+ """
+ local_cache_dir = str(QtGui.QFileDialog.getExistingDirectory(self,
+ 'Get Local Cache Directory',
+ self._homeSrcDir))
+
+ # Set local directory to control
+ status, error_message = self._myControl.set_local_data_dir(local_cache_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ # Synchronize to local data/spice directory and local cache directory
+ if str(self.ui.lineEdit_localSpiceDir.text()) != '':
+ prev_dir = str(self.ui.lineEdit_localSrcDir.text())
+ self.pop_one_button_dialog('Local data directory was set up as %s' %
+ prev_dir)
+ self.ui.lineEdit_localSrcDir.setText(local_cache_dir)
+ self.ui.lineEdit_localSpiceDir.setText(local_cache_dir)
+
+ return
+
+ def do_browse_local_spice_data(self):
+ """ Browse local source SPICE data directory
+ """
+ src_spice_dir = str(QtGui.QFileDialog.getExistingDirectory(self, 'Get Directory',
+ self._homeSrcDir))
+ # Set local data directory to controller
+ status, error_message = self._myControl.set_local_data_dir(src_spice_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ self._homeSrcDir = src_spice_dir
+ self.ui.lineEdit_localSpiceDir.setText(src_spice_dir)
+
+ return
+
+ def do_browse_working_dir(self):
+ """
+ Browse and set up working directory
+ :return:
+ """
+ work_dir = str(QtGui.QFileDialog.getExistingDirectory(self, 'Get Working Directory', self._homeDir))
+ status, error_message = self._myControl.set_working_directory(work_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ else:
+ self.ui.lineEdit_workDir.setText(work_dir)
+
+ return
+
+ def do_cal_ub_matrix(self):
+ """ Calculate UB matrix by 2 or 3 reflections
+ """
+ # Get reflections
+ num_rows = self.ui.tableWidget_peaksCalUB.rowCount()
+ peak_info_list = list()
+ status, exp_number = gutil.parse_integers_editors(self.ui.lineEdit_exp)
+ for i_row in xrange(num_rows):
+ if self.ui.tableWidget_peaksCalUB.is_selected(i_row) is True:
+ scan_num, pt_num = self.ui.tableWidget_peaksCalUB.get_exp_info(i_row)
+ status, peak_info = self._myControl.get_peak_info(exp_number, scan_num, pt_num)
+ peak_info.set_peak_ws_hkl_from_user()
+ if status is False:
+ self.pop_one_button_dialog(peak_info)
+ return
+ assert isinstance(peak_info, r4c.PeakInfo)
+ peak_info_list.append(peak_info)
+ # END-FOR
+
+ # Get lattice
+ status, ret_obj = self._get_lattice_parameters()
+ if status is True:
+ a, b, c, alpha, beta, gamma = ret_obj
+ else:
+ err_msg = ret_obj
+ self.pop_one_button_dialog(err_msg)
+ return
+
+ # Calculate UB matrix
+ status, ub_matrix = self._myControl.calculate_ub_matrix(peak_info_list, a, b, c,
+ alpha, beta, gamma)
+
+ # Deal with result
+ if status is True:
+ self._show_ub_matrix(ub_matrix)
+ else:
+ err_msg = ub_matrix
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def do_clear_ub_peaks(self):
+ """
+ Clear all peaks in UB-Peak table
+ :return:
+ """
+ self.ui.tableWidget_peaksCalUB.clear()
+
+ return
+
+ def do_del_ub_peaks(self):
+ """
+ Delete a peak in UB-Peak table
+ :return:
+ """
+ # Find out the lines to get deleted
+ row_num_list = self.ui.tableWidget_peaksCalUB.get_selected_rows()
+ print '[DB] Row %s are selected' % str(row_num_list)
+
+ # Delete
+ self.ui.tableWidget_peaksCalUB.delete_rows(row_num_list)
+
+ return
+
+ def do_download_spice_data(self):
+ """ Download SPICE data
+ :return:
+ """
+ # Check scans to download
+ scan_list_str = str(self.ui.lineEdit_downloadScans.text())
+ if len(scan_list_str) > 0:
+ # user specifies scans to download
+ valid, scan_list = fcutil.parse_int_array(scan_list_str)
+ if valid is False:
+ error_message = scan_list
+ self.pop_one_button_dialog(error_message)
+ else:
+ # Get all scans
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp])
+ if status is False:
+ self.pop_one_button_dialog(ret_obj)
+ return
+ exp_no = ret_obj
+ assert isinstance(exp_no, int)
+ server_url = str(self.ui.lineEdit_url.text())
+ scan_list = fcutil.get_scans_list(server_url, exp_no, return_list=True)
+ self.pop_one_button_dialog('Going to download scans %s.' % str(scan_list))
+
+ # Check location
+ destination_dir = str(self.ui.lineEdit_localSrcDir.text())
+ status, error_message = self._myControl.set_local_data_dir(destination_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ else:
+ self.pop_one_button_dialog('Spice files will be downloaded to %s.' % destination_dir)
+
+ # Set up myControl for downloading data
+ exp_no = int(self.ui.lineEdit_exp.text())
+ self._myControl.set_exp_number(exp_no)
+
+ server_url = str(self.ui.lineEdit_url.text())
+ status, error_message = self._myControl.set_server_url(server_url)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ # Download
+ self._myControl.download_data_set(scan_list)
+
+ return
+
+ def do_find_peak(self):
+ """ Find peak in a given scan/pt and record it
+ """
+ # Get experiment, scan and pt
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_scanNumber,
+ self.ui.lineEdit_ptNumber])
+ if status is True:
+ exp_no, scan_no, pt_no = ret_obj
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Find peak
+ status, err_msg = self._myControl.find_peak(exp_no, scan_no, pt_no)
+ if status is False:
+ self.pop_one_button_dialog(ret_obj)
+ return
+ if self.ui.checkBox_loadHKLfromFile.isChecked() is True:
+ # This is the first time that in the workflow to get HKL from MD workspace
+ status, err_msg = self._myControl.set_hkl_to_peak(exp_no, scan_no, pt_no)
+ if status is False:
+ self.pop_one_button_dialog('Unable to locate peak info due to %s.' % err_msg)
+
+ # Set up correct values to table tableWidget_peaksCalUB
+ self._myControl.add_peak_info(exp_no, scan_no, pt_no)
+ status, peak_info = self._myControl.get_peak_info(exp_no, scan_no, pt_no)
+ if status is False:
+ err_msg = peak_info
+ raise KeyError(err_msg)
+ assert isinstance(peak_info, r4c.PeakInfo)
+
+ # Set the HKL value from PeakInfo directly
+ # BAD PROGRAMMING! THERE ARE TOO MANY WAYS TO ACCESS STORED HKL
+ h, k, l = peak_info.get_peak_ws_hkl()
+ self.ui.lineEdit_H.setText('%.2f' % h)
+ self.ui.lineEdit_K.setText('%.2f' % k)
+ self.ui.lineEdit_L.setText('%.2f' % l)
+
+ q_sample = peak_info.getQSample()
+ self.ui.lineEdit_sampleQx.setText('%.5E' % q_sample[0])
+ self.ui.lineEdit_sampleQy.setText('%.5E' % q_sample[1])
+ self.ui.lineEdit_sampleQz.setText('%.5E' % q_sample[2])
+
+ # self.set_ub_peak_table(peak_info)
+
+ return
+
+ def do_index_ub_peaks(self):
+ """ Index the peaks in the UB matrix peak table
+ :return:
+ """
+ # Get UB matrix
+ ub_matrix = self.ui.tableWidget_ubMatrix.get_matrix()
+ print '[DB] Get UB matrix ', ub_matrix
+
+ # Do it for each peak
+ num_peaks = self.ui.tableWidget_peaksCalUB.rowCount()
+ err_msg = ''
+ for i_peak in xrange(num_peaks):
+ scan_no, pt_no = self.ui.tableWidget_peaksCalUB.get_exp_info(i_peak)
+ status, ret_obj = self._myControl.index_peak(ub_matrix, scan_number=scan_no,
+ pt_number=pt_no)
+ if status is True:
+ new_hkl = ret_obj[0]
+ error = ret_obj[1]
+ self.ui.tableWidget_peaksCalUB.set_hkl(i_peak, new_hkl, error)
+ else:
+ err_msg += ret_obj + '\n'
+ # END-FOR
+
+ if len(err_msg) > 0:
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def do_list_scans(self):
+ """ List all scans available
+ :return:
+ """
+ # Experiment number
+ exp_no = int(self.ui.lineEdit_exp.text())
+
+ access_mode = str(self.ui.comboBox_mode.currentText())
+ if access_mode == 'Local':
+ spice_dir = str(self.ui.lineEdit_localSpiceDir.text())
+ message = fcutil.get_scans_list_local_disk(spice_dir, exp_no)
+ else:
+ url = str(self.ui.lineEdit_url.text())
+ message = fcutil.get_scans_list(url, exp_no)
+
+ self.pop_one_button_dialog(message)
+
+ return
+
+ def do_load_scan_info(self):
+ """ Load SIICE's scan file
+ :return:
+ """
+ # Get scan number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_run])
+ if status is True:
+ scan_no = ret_obj[0]
+ else:
+ err_msg = ret_obj
+ self.pop_one_button_dialog('Unable to get scan number in raw data tab due to %s.' % err_msg)
+ return
+
+ status, err_msg = self._myControl.load_spice_scan_file(exp_no=None, scan_no=scan_no)
+ if status is False:
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def do_plot_pt_raw(self):
+ """ Plot the Pt.
+ """
+ # Get measurement pt and the file number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_run,
+ self.ui.lineEdit_rawDataPtNo])
+ if status is True:
+ exp_no = ret_obj[0]
+ scan_no = ret_obj[1]
+ pt_no = ret_obj[2]
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Call to plot 2D
+ self._plot_raw_xml_2d(exp_no, scan_no, pt_no)
+
+ return
+
+ def do_plot_prev_pt_raw(self):
+ """ Plot the Pt.
+ """
+ # Get measurement pt and the file number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_run,
+ self.ui.lineEdit_rawDataPtNo])
+ if status is True:
+ exp_no = ret_obj[0]
+ scan_no = ret_obj[1]
+ pt_no = ret_obj[2]
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Previous one
+ pt_no -= 1
+ if pt_no <= 0:
+ self.pop_one_button_dialog('Pt. = 1 is the first one.')
+ return
+ else:
+ self.ui.lineEdit_rawDataPtNo.setText('%d' % pt_no)
+
+ # Plot
+ self._plot_raw_xml_2d(exp_no, scan_no, pt_no)
+
+ return
+
+ def do_plot_next_pt_raw(self):
+ """ Plot the Pt.
+ """
+ # Get measurement pt and the file number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_run,
+ self.ui.lineEdit_rawDataPtNo])
+ if status is True:
+ exp_no = ret_obj[0]
+ scan_no = ret_obj[1]
+ pt_no = ret_obj[2]
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Previous one
+ pt_no += 1
+ # get last Pt. number
+ status, last_pt_no = self._myControl.get_pt_numbers(exp_no, scan_no)
+ if status is False:
+ error_message = last_pt_no
+ self.pop_one_button_dialog('Unable to access Spice table for scan %d. Reason" %s.' % (
+ scan_no, error_message))
+ if pt_no > last_pt_no:
+ self.pop_one_button_dialog('Pt. = %d is the last one of scan %d.' % (pt_no, scan_no))
+ return
+ else:
+ self.ui.lineEdit_rawDataPtNo.setText('%d' % pt_no)
+
+ # Plot
+ self._plot_raw_xml_2d(exp_no, scan_no, pt_no)
+
+ return
+
+ def do_merge_scans(self):
+ """ Process data for slicing view
+ :return:
+ """
+ # Get UB matrix
+ ub_matrix = self.ui.tableWidget_ubSiceView.get_matrix()
+ self._myControl.set_ub_matrix(exp_number=None, ub_matrix=ub_matrix)
+
+ # Get list of scans
+ scan_list = gutil.parse_integer_list(str(self.ui.lineEdit_listScansSliceView.text()))
+ if len(scan_list) == 0:
+ self.pop_one_button_dialog('Scan list is empty.')
+
+ # Set table
+ self.ui.tableWidget_sliceViewProgress.append_scans(scans=scan_list)
+
+ # Warning
+ self.pop_one_button_dialog('Data processing is long. Be patient!')
+
+ # Process
+ base_name = str(self.ui.lineEdit_baseMergeMDName.text())
+ scan_list.sort()
+ frame = str(self.ui.comboBox_mergeScanFrame.currentText())
+ for scan_no in scan_list:
+ # Download/check SPICE file
+ self._myControl.download_spice_file(None, scan_no, over_write=False)
+
+ # Get some information
+ status, pt_list = self._myControl.get_pt_numbers(None, scan_no, load_spice_scan=True)
+ if status is False:
+ err_msg = pt_list
+ self.pop_one_button_dialog('Failed to get Pt. number: %s' % err_msg)
+ return
+ else:
+ # Set information to table
+ err_msg = self.ui.tableWidget_sliceViewProgress.set_scan_pt(scan_no, pt_list)
+ if len(err_msg) > 0:
+ self.pop_one_button_dialog(err_msg)
+
+ out_ws_name = base_name + '%04d' % scan_no
+ self.ui.tableWidget_sliceViewProgress.set_scan_pt(scan_no, 'In Processing')
+ try:
+ ret_tup = self._myControl.merge_pts_in_scan(exp_no=None, scan_no=scan_no,
+ target_ws_name=out_ws_name,
+ target_frame=frame)
+ merge_status = 'Done'
+ merged_name = ret_tup[0]
+ group_name = ret_tup[1]
+ except RuntimeError as e:
+ merge_status = 'Failed. Reason: %s' % str(e)
+ merged_name = ''
+ group_name = ''
+ finally:
+ self.ui.tableWidget_sliceViewProgress.set_status(scan_no, merge_status)
+ self.ui.tableWidget_sliceViewProgress.set_ws_names(scan_no, merged_name, group_name)
+
+ # Sleep for a while
+ time.sleep(0.1)
+ # END-FOR
+
+ return
+
+ def do_reset_ub_peaks_hkl(self):
+ """
+ Reset user specified HKL value to peak table
+ :return:
+ """
+ num_rows = self.ui.tableWidget_peaksCalUB.rowCount()
+ for i_row in xrange(num_rows):
+ print '[DB] Update row %d' % (i_row)
+ scan, pt = self.ui.tableWidget_peaksCalUB.get_scan_pt(i_row)
+ status, peak_info = self._myControl.get_peak_info(None, scan, pt)
+ if status is False:
+ error_message = peak_info
+ raise RuntimeError(error_message)
+ h, k, l = peak_info.get_user_hkl()
+ self.ui.tableWidget_peaksCalUB.update_hkl(i_row, h, k, l)
+ # END-FOR
+
+ return
+
+ def do_set_experiment(self):
+ """ Set experiment
+ :return:
+ """
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp])
+ if status is True:
+ exp_number = ret_obj[0]
+ curr_exp_number = self._myControl.get_experiment()
+ if curr_exp_number is not None and exp_number != curr_exp_number:
+ self.pop_one_button_dialog('Changing experiment to %d. Clean previous experiment %d\'s result'
+ ' in Mantid manually.' % (exp_number, curr_exp_number))
+ self._myControl.set_exp_number(exp_number)
+ self.ui.lineEdit_exp.setStyleSheet('color: black')
+ else:
+ err_msg = ret_obj
+ self.pop_one_button_dialog('Unable to set experiment as %s' % err_msg)
+ self.ui.lineEdit_exp.setStyleSheet('color: red')
+
+ self.ui.tabWidget.setCurrentIndex(0)
+
+ return
+
+ def do_set_ub_sv(self):
+ """ Set UB matrix in Slice view
+ :return:
+ """
+ if self.ui.radioButton_ubFromTab1.isChecked():
+ self.ui.tableWidget_ubSiceView.set_from_matrix(self.ui.tableWidget_ubMatrix.get_matrix())
+ elif self.ui.radioButton_ubFromTab3.isChecked():
+ self.ui.tableWidget_ubSiceView.set_from_matrix(self.ui.tableWidget_refinedUB.get_matrix())
+ elif self.ui.radioButton_ubFromList.isChecked():
+ status, ret_obj = gutil.parse_float_array(str(self.ui.plainTextEdit_ubInput.toPlainText()))
+ if status is False:
+ self.pop_one_button_dialog(ret_obj)
+ elif len(ret_obj) != 9:
+ self.pop_one_button_dialog('Requiring 9 floats for UB matrix. Only %d are given.' % len(ret_obj))
+ else:
+ self.ui.tableWidget_ubSiceView.set_from_list(ret_obj)
+ else:
+ self.pop_one_button_dialog('None is selected to set UB matrix.')
+
+ return
+
+ def do_setup_dir_default(self):
+ """
+ Set up default directory for storing data and working
+ :return:
+ """
+ home_dir = os.path.expanduser('~')
+
+ # Data cache directory
+ data_cache_dir = os.path.join(home_dir, 'Temp/HB3ATest')
+ self.ui.lineEdit_localSpiceDir.setText(data_cache_dir)
+ self.ui.lineEdit_localSrcDir.setText(data_cache_dir)
+
+ work_dir = os.path.join(data_cache_dir, 'Workspace')
+ self.ui.lineEdit_workDir.setText(work_dir)
+
+ return
+
+ def do_apply_setup(self):
+ """
+ Apply set up ...
+ :return:
+ """
+ # Local data directory
+ local_data_dir = str(self.ui.lineEdit_localSpiceDir.text())
+ if os.path.exists(local_data_dir) is False:
+ try:
+ os.mkdir(local_data_dir)
+ except OSError as os_error:
+ self.pop_one_button_dialog('Unable to create local data directory %s due to %s.' % (
+ local_data_dir, str(os_error)))
+ self.ui.lineEdit_localSpiceDir.setStyleSheet("color: red;")
+ return
+ else:
+ self.ui.lineEdit_localSpiceDir.setStyleSheet("color: black;")
+ # END-IF
+
+ # Working directory
+ working_dir = str(self.ui.lineEdit_workDir.text())
+ if os.path.exists(working_dir) is False:
+ try:
+ os.mkdir(working_dir)
+ except OSError as os_error:
+ self.pop_one_button_dialog('Unable to create working directory %s due to %s.' % (
+ working_dir, str(os_error)))
+ self.ui.lineEdit_workDir.setStyleSheet("color: red;")
+ return
+ else:
+ self.ui.lineEdit_workDir.setStyleSheet("color: black;")
+ # END-IF
+
+ # Server URL
+ data_server = str(self.ui.lineEdit_url.text())
+ url_is_good = self.do_test_url()
+ if url_is_good is False:
+ self.ui.lineEdit_url.setStyleSheet("color: red;")
+ return
+ else:
+ self.ui.lineEdit_url.setStyleSheet("color: black;")
+
+ # Set to control
+ self._myControl.set_local_data_dir(local_data_dir)
+ self._myControl.set_working_directory(working_dir)
+ self._myControl.set_server_url(data_server)
+
+ return
+
+ def do_test_url(self):
+ """ Test whether the root URL provided specified is good
+ """
+ url = str(self.ui.lineEdit_url.text())
+
+ url_is_good, err_msg = fcutil.check_url(url)
+ if url_is_good is True:
+ self.pop_one_button_dialog("URL %s is valid." % url)
+ else:
+ self.pop_one_button_dialog(err_msg)
+
+ return url_is_good
+
+ def pop_one_button_dialog(self, message):
+ """ Pop up a one-button dialog
+ :param message:
+ :return:
+ """
+ assert isinstance(message, str)
+ QtGui.QMessageBox.information(self, '4-circle Data Reduction', message)
+
+ return
+
+ def save_current_session(self, filename=None):
+ """ Save current session/value setup to
+ :return:
+ """
+ # Set up dictionary
+ save_dict = dict()
+
+ # Setup
+ save_dict['lineEdit_localSpiceDir'] = str(self.ui.lineEdit_localSpiceDir.text())
+ save_dict['lineEdit_url'] = str(self.ui.lineEdit_url.text())
+ save_dict['lineEdit_workDir']= str(self.ui.lineEdit_workDir.text())
+
+ # Experiment
+ save_dict['lineEdit_exp'] = str(self.ui.lineEdit_exp.text())
+ save_dict['lineEdit_scanNumber'] = self.ui.lineEdit_scanNumber.text()
+ save_dict['lineEdit_ptNumber'] = str(self.ui.lineEdit_ptNumber.text())
+
+ # Lattice
+ save_dict['lineEdit_a'] = str(self.ui.lineEdit_a.text())
+ save_dict['lineEdit_b'] = str(self.ui.lineEdit_b.text())
+ save_dict['lineEdit_c'] = str(self.ui.lineEdit_c.text())
+ save_dict['lineEdit_alpha'] = str(self.ui.lineEdit_alpha.text())
+ save_dict['lineEdit_beta'] = str(self.ui.lineEdit_beta.text())
+ save_dict['lineEdit_gamma'] = str(self.ui.lineEdit_gamma.text())
+
+ # Merge scan
+ save_dict['plainTextEdit_ubInput'] = str(self.ui.plainTextEdit_ubInput.toPlainText())
+ save_dict['lineEdit_listScansSliceView'] = str(self.ui.lineEdit_listScansSliceView.text())
+ save_dict['lineEdit_baseMergeMDName'] = str(self.ui.lineEdit_baseMergeMDName.text())
+
+ # Save to csv file
+ if filename is None:
+ filename = 'session_backup.csv'
+ ofile = open(filename, 'w')
+ writer = csv.writer(ofile)
+ for key, value in save_dict.items():
+ writer.writerow([key, value])
+ ofile.close()
+
+ return
+
+ def load_session(self, filename=None):
+ """
+ To load a session, i.e., read it back:
+ :param filename:
+ :return:
+ """
+ if filename is None:
+ filename = 'session_backup.csv'
+
+ in_file = open(filename, 'r')
+ reader = csv.reader(in_file)
+ my_dict = dict(x for x in reader)
+
+ # ...
+ for key, value in my_dict.items():
+ if key.startswith('lineEdit') is True:
+ self.ui.__getattribute__(key).setText(value)
+ elif key.startswith('plainText') is True:
+ self.ui.__getattribute__(key).setPlainText(value)
+ elif key.startswith('comboBox') is True:
+ self.ui.__getattribute__(key).setCurrentIndex(int(value))
+ else:
+ self.pop_one_button_dialog('Error! Widget name %s is not supported' % key)
+ # END-FOR
+
+ # ...
+ self._myControl.set_local_data_dir(str(self.ui.lineEdit_localSpiceDir.text()))
+
+ return
+
+ def menu_quit(self):
+ """
+
+ :return:
+ """
+ self.close()
+
+ def show_scan_pt_list(self):
+ """ Show the range of Pt. in a scan
+ :return:
+ """
+ # Get parameters
+ status, inp_list = gutil.parse_integers_editors([self.ui.lineEdit_exp, self.ui.lineEdit_run])
+ if status is False:
+ self.pop_one_button_dialog(inp_list)
+ return
+ else:
+ exp_no = inp_list[0]
+ scan_no = inp_list[1]
+
+ status, ret_obj = self._myControl.get_pt_numbers(exp_no, scan_no)
+
+ # Form message
+ if status is False:
+ # Failed to get Pt. list
+ error_message = ret_obj
+ self.pop_one_button_dialog(error_message)
+ else:
+ # Form message
+ pt_list = sorted(ret_obj)
+ num_pts = len(pt_list)
+ info = 'Exp %d Scan %d has %d Pt. ranging from %d to %d.\n' % (exp_no, scan_no, num_pts,
+ pt_list[0], pt_list[-1])
+ num_miss_pt = pt_list[-1] - pt_list[0] + 1 - num_pts
+ if num_miss_pt > 0:
+ info += 'There are %d Pt. skipped.\n' % num_miss_pt
+
+ self.pop_one_button_dialog(info)
+
+ return
+
+ def set_ub_peak_table(self, peakinfo):
+ """
+ DOC
+ :param peak_info:
+ :return:
+ """
+ assert isinstance(peakinfo, r4c.PeakInfo)
+
+ # Get data
+ exp_number, scan_number, pt_number = peakinfo.getExpInfo()
+ h, k, l = peakinfo.get_user_hkl()
+ q_sample = peakinfo.getQSample()
+ m1 = self._myControl.get_sample_log_value(exp_number, scan_number, pt_number, '_m1')
+
+ # Set to table
+ status, err_msg = self.ui.tableWidget_peaksCalUB.append_row(
+ [scan_number, pt_number, h, k, l, q_sample[0], q_sample[1], q_sample[2], False, m1, ''])
+ if status is False:
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def _get_lattice_parameters(self):
+ """
+ Get lattice parameters from GUI
+ :return: (Boolean, Object). True, 6-tuple as a, b, c, alpha, beta, gamm
+ False: error message
+ """
+ status, ret_list = gutil.parse_float_editors([self.ui.lineEdit_a,
+ self.ui.lineEdit_b,
+ self.ui.lineEdit_c,
+ self.ui.lineEdit_alpha,
+ self.ui.lineEdit_beta,
+ self.ui.lineEdit_gamma])
+ if status is False:
+ err_msg = ret_list
+ err_msg = 'Unable to parse unit cell due to %s' % err_msg
+ return False, err_msg
+
+ a, b, c, alpha, beta, gamma = ret_list
+
+ return True, (a, b, c, alpha, beta, gamma)
+
+ def _plot_raw_xml_2d(self, exp_no, scan_no, pt_no):
+ """ Plot raw workspace from XML file for a measurement/pt.
+ """
+ # Check and load SPICE table file
+ does_exist = self._myControl.does_spice_loaded(exp_no, scan_no)
+ if does_exist is False:
+ # Download data
+ status, error_message = self._myControl.download_spice_file(exp_no, scan_no, over_write=False)
+ if status is True:
+ status, error_message = self._myControl.load_spice_scan_file(exp_no, scan_no)
+ if status is False and self._allowDownload is False:
+ self.pop_one_button_dialog(error_message)
+ return
+ else:
+ self.pop_one_button_dialog(error_message)
+ return
+ # END-IF(does_exist)
+
+ # Load Data for Pt's xml file
+ does_exist = self._myControl.does_raw_loaded(exp_no, scan_no, pt_no)
+
+ if does_exist is False:
+ # Check whether needs to download
+ status, error_message = self._myControl.download_spice_xml_file(scan_no, pt_no, exp_no=exp_no)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+ # Load SPICE xml file
+ status, error_message = self._myControl.load_spice_xml_file(exp_no, scan_no, pt_no)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ # Convert a list of vector to 2D numpy array for imshow()
+ # Get data and plot
+ raw_det_data = self._myControl.get_raw_detector_counts(exp_no, scan_no, pt_no)
+ self.ui.graphicsView.clear_canvas()
+ self.ui.graphicsView.add_plot_2d(raw_det_data, x_min=0, x_max=256, y_min=0, y_max=256,
+ hold_prev_image=False)
+
+ return
+
+ def _show_ub_matrix(self, ubmatrix):
+ """ Show UB matrix
+ :param ubmatrix:
+ :return:
+ """
+ assert ubmatrix.shape == (3, 3)
+
+ self.ui.tableWidget_ubMatrix.set_from_matrix(ubmatrix)
+
+ return
diff --git a/scripts/Inelastic/Direct/DirectEnergyConversion.py b/scripts/Inelastic/Direct/DirectEnergyConversion.py
index 56043ad5aeed4096c76b402026bf270c95982230..74394d53c59d56718d782f4b99e3b56634f1a1f9 100644
--- a/scripts/Inelastic/Direct/DirectEnergyConversion.py
+++ b/scripts/Inelastic/Direct/DirectEnergyConversion.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from mantid.simpleapi import *
from mantid.kernel import funcreturns
diff --git a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
index 624f599ba04d0e2848de1d7eae90cd134bcf83b3..f3c816ecbac11ce60b67842eb3f6dfbf1c4caad9 100644
--- a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
+++ b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
@@ -484,12 +484,12 @@ class MantidConfigDirectInelastic(object):
#
def init_user(self,fedIDorUser,theUser=None):
"""Define settings, specific to a user
- Supports two interfaces -- old and the new one
+ Supports two interfaces -- old and the new one
where
- OldInterface: requested two input parameters
+ OldInterface: requested two input parameters
fedID -- users federal id
theUser -- class defining all other user property
- NewInterface: requested single parameter:
+ NewInterface: requested single parameter:
theUser -- class defining all user's properties including fedID
"""
if not theUser:
diff --git a/scripts/Inelastic/Direct/PropertiesDescriptors.py b/scripts/Inelastic/Direct/PropertiesDescriptors.py
index f05779e6e22cb3be785e93284470526939658be8..aec0169cd240da45e7d63e5218902c7578eb579e 100644
--- a/scripts/Inelastic/Direct/PropertiesDescriptors.py
+++ b/scripts/Inelastic/Direct/PropertiesDescriptors.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
""" File contains collection of Descriptors used to define complex
properties in NonIDF_Properties and PropertyManager classes
diff --git a/scripts/Inelastic/Direct/RunDescriptor.py b/scripts/Inelastic/Direct/RunDescriptor.py
index 9fda6508d6224a370358ac200b8968be3aeca2c5..b5e959ff885084e6a088e0647532fa21445b65ca 100644
--- a/scripts/Inelastic/Direct/RunDescriptor.py
+++ b/scripts/Inelastic/Direct/RunDescriptor.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
""" File contains Descriptors used describe run for direct inelastic reduction """
@@ -995,8 +996,8 @@ class RunDescriptor(PropDescriptor):
Load(Filename=data_file, OutputWorkspace=ws_name,LoadMonitors = '1',MonitorsAsEvents='0')
#HACK >>> , necessary until #11565 is fixed
if nxs_file :
- instr_name = RunDescriptor._holder.instr_name
- if instr_name == 'LET' and self._run_number>14151 and self._run_number<14382:
+ instr_name = RunDescriptor._holder.instr_name
+ if instr_name == 'LET' and self._run_number>14151 and self._run_number<14382:
FrameworkManager.clearInstruments()
idf_file = api.ExperimentInfo.getInstrumentFilename(instr_name)
idf_path,tile = os.path.split(idf_file)
diff --git a/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py b/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py
index 7140a4df5633e57ccaaca3b9719cc32474b3539f..abbd2f4eee91d7db012641d90db791d3ecdec1b6 100644
--- a/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py
+++ b/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py
@@ -84,7 +84,7 @@ class DiffractionReductionScripter(BaseReductionScripter):
file_name, autosavexmlfname)
wbuf += script
wbuf += "\n========== End of Script ==========="
- print (wbuf)
+ print wbuf
return script
diff --git a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
index ea324c63828a6e03190b8b2c5fc99b90bdf2fd80..72cfb428315fa574ee295ed307c2e1e696f1eb99 100644
--- a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
+++ b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name,unused-import
from PyQt4 import QtGui, QtCore
import reduction_gui.widgets.util as util
diff --git a/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py b/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py
index bfb043368ad53ccaeb13b243a916cea1f8f5e615..8816e2f91ded5277314a7b6e267a8a72f8c424ac 100644
--- a/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py
+++ b/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from PyQt4 import QtGui, uic, QtCore
import reduction_gui.widgets.util as util
diff --git a/scripts/Interface/ui/reflectometer/refl_gui.py b/scripts/Interface/ui/reflectometer/refl_gui.py
index 3bb3aed9b003789fd1786e1f1ecfa46f82878888..8f1a384733c2e605fd61b22f192b30ccc26b3b90 100644
--- a/scripts/Interface/ui/reflectometer/refl_gui.py
+++ b/scripts/Interface/ui/reflectometer/refl_gui.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
import ui_refl_window
import refl_save
diff --git a/scripts/Interface/ui/reflectometer/refl_save.py b/scripts/Interface/ui/reflectometer/refl_save.py
index 6dabce7fe2a500d16899e687dde973628f1c98de..52f4c8dc61f64444d7263953e7a70dcf40d99a0a 100644
--- a/scripts/Interface/ui/reflectometer/refl_save.py
+++ b/scripts/Interface/ui/reflectometer/refl_save.py
@@ -1,8 +1,8 @@
-#pylint: disable=invalid-name
+#pylint: disable-all
from PyQt4 import QtCore, QtGui
import os
from mantid.simpleapi import *
-from mantid.api import WorkspaceGroup
+from mantid.api import WorkspaceGroup, AnalysisDataService
import xml.etree.ElementTree as xml
from isis_reflectometry.quick import *
from isis_reflectometry.procedures import *
@@ -32,10 +32,12 @@ class Ui_SaveWindow(object):
def setupUi(self, SaveWindow):
self.SavePath=""
SaveWindow.setObjectName(_fromUtf8("SaveWindow"))
- SaveWindow.resize(700, 450)
+ SaveWindow.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding))
SaveWindow.setAcceptDrops(True)
-
+ main_layout = QtGui.QHBoxLayout()
+ SaveWindow.setLayout(main_layout)
self.centralWidget = QtGui.QWidget(SaveWindow)
+ main_layout.addWidget(self.centralWidget)
self.centralWidget.setObjectName(_fromUtf8("centralWidget"))
self.gridLayout_2 = QtGui.QGridLayout(self.centralWidget)
self.gridLayout_2.setObjectName(_fromUtf8("gridLayout_2"))
@@ -236,12 +238,18 @@ class Ui_SaveWindow(object):
def retranslateUi(self, SaveWindow):
SaveWindow.setWindowTitle(QtGui.QApplication.translate("SaveWindow", "SaveWindow", None, QtGui.QApplication.UnicodeUTF8))
- self.pushButton.setText(QtGui.QApplication.translate("SaveWindow", "SAVE", None, QtGui.QApplication.UnicodeUTF8))
+ self.pushButton.setText(QtGui.QApplication.translate("SaveWindow", "Save", None, QtGui.QApplication.UnicodeUTF8))
self.pushButton_2.setText(QtGui.QApplication.translate("SaveWindow", "Refresh", None, QtGui.QApplication.UnicodeUTF8))
+ def _get_saveable_workspace_names(self):
+ names = mtd.getObjectNames()
+ # Exclude WorkspaceGroups from our list. We cannot save them to ASCII.
+ names = [i for i in names if not isinstance(AnalysisDataService.retrieve(i), WorkspaceGroup)]
+ return names
+
def filterWksp(self):
self.listWidget.clear()
- names = mtd.getObjectNames()
+ names = self._get_saveable_workspace_names()
if self.regExCheckBox.isChecked():
regex=re.compile(self.filterEdit.text())
filtered = list()
@@ -268,7 +276,7 @@ class Ui_SaveWindow(object):
def populateList(self):
self.listWidget.clear()
- names = mtd.getObjectNames()
+ names = self._get_saveable_workspace_names()
if len(names):
RB_Number=groupGet(names[0],'samp','rb_proposal')
for ws in names:
diff --git a/scripts/Reflectometry/isis_reflectometry/procedures.py b/scripts/Reflectometry/isis_reflectometry/procedures.py
index 999dd0a65df4c3c69b2b8d82f085be1fa5d886ab..11d1a52448ec5749956eca3315db82a7a2537801 100644
--- a/scripts/Reflectometry/isis_reflectometry/procedures.py
+++ b/scripts/Reflectometry/isis_reflectometry/procedures.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from math import *
diff --git a/scripts/SANS/ISISCommandInterface.py b/scripts/SANS/ISISCommandInterface.py
index 0ed8fd805b698e6a5c35ffdf68ae9425299ed478..3f06b3229bf67e2a871806a1a62459c5db70707b 100644
--- a/scripts/SANS/ISISCommandInterface.py
+++ b/scripts/SANS/ISISCommandInterface.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
"""
Enables the SANS commands (listed at http://www.mantidproject.org/SANS) to
@@ -574,7 +575,7 @@ def _fitRescaleAndShift(rAnds, frontData, rearData):
# We need to make sure at this point that the workspaces are 1D. We
# don't really know how to match the workspaces for the 2D case.
- if (not su.is_1D_workspace(mtd[frontData]) or not su.is_1D_workspace(mtd[rearData])):
+ if not su.is_1D_workspace(mtd[frontData]) or not su.is_1D_workspace(mtd[rearData]):
sanslog.warning("Request to perform a fit to find the shift and scale values for"
"a non-1D workspace is not possible. Default values are provided.")
scale = rAnds.scale
diff --git a/scripts/SANS/SANSBatchMode.py b/scripts/SANS/SANSBatchMode.py
index 3419a9c6cd16d07aede08f6ca2a48e6918fb1d9b..38f01016a7b8b7744b9bdd942883cb8c133268b4 100644
--- a/scripts/SANS/SANSBatchMode.py
+++ b/scripts/SANS/SANSBatchMode.py
@@ -178,7 +178,8 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
original_settings = settings,
original_prop_man_settings = prop_man_settings)
except (RunTimeError, ValueError) as e:
- sanslog.warning("Error in Batchmode user files: Could not reset the specified user file %s. More info: %s" %(str(run['user_file']),str(e)))
+ sanslog.warning("Error in Batchmode user files: Could not reset the specified user file %s. More info: %s" %(
+ str(run['user_file']),str(e)))
local_settings = copy.deepcopy(ReductionSingleton().reference())
local_prop_man_settings = ReductionSingleton().settings.clone("TEMP_SETTINGS")
diff --git a/scripts/SANS/SANSUtility.py b/scripts/SANS/SANSUtility.py
index b22d9e8c19ad5d785f2d99beb9479be8769d5258..c594e7548e3d319888d9136a2b8c14c6831b8221 100644
--- a/scripts/SANS/SANSUtility.py
+++ b/scripts/SANS/SANSUtility.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
#########################################################
# This module contains utility functions common to the
diff --git a/scripts/SANS/isis_instrument.py b/scripts/SANS/isis_instrument.py
index b4c0a9a507d3bbcb0a063ac2c540d05a12eeb1ce..821b956195403a29bfb2b308d0a83d29286235c9 100644
--- a/scripts/SANS/isis_instrument.py
+++ b/scripts/SANS/isis_instrument.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
import math
import os
diff --git a/scripts/SANS/isis_reduction_steps.py b/scripts/SANS/isis_reduction_steps.py
index ebb89992488267b445b04ba4d1b5f16f99c55a98..f98175cf90062335d14d3cf0894e08d7e117e840 100644
--- a/scripts/SANS/isis_reduction_steps.py
+++ b/scripts/SANS/isis_reduction_steps.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
"""
This file defines what happens in each step in the data reduction, it's
diff --git a/scripts/reduction/instruments/reflectometer/wks_utility.py b/scripts/reduction/instruments/reflectometer/wks_utility.py
index b9dec721553ac63bdbeb835d613fe0b306a45bb4..7544a27a51147a23863c1579e17d2db0afac45d3 100644
--- a/scripts/reduction/instruments/reflectometer/wks_utility.py
+++ b/scripts/reduction/instruments/reflectometer/wks_utility.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from numpy import zeros, arctan2, arange, shape, sqrt, fliplr, asfarray, mean, sum, NAN
from mantid.simpleapi import *
diff --git a/tools/DOI/authors.py b/tools/DOI/authors.py
index aefa191509e7cae27eb14df35dfc91e564189b23..2d35b45b4aec8710fb2a8a7cff85ed3b137977e2 100644
--- a/tools/DOI/authors.py
+++ b/tools/DOI/authors.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from itertools import chain, ifilterfalse
import string, os, re
diff --git a/tools/DOI/doi.py b/tools/DOI/doi.py
index 523d8c6399e989ea5f51f3fd05bb997df28031fd..56c4a8782a92cef962d8e76cd0750eac47717d4d 100644
--- a/tools/DOI/doi.py
+++ b/tools/DOI/doi.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
"""A script for generating DataCite DOI's for Mantid releases, to be called by
a Jenkins job during the release process. When given a major, minor and patch
release number along with username and password credentials, it will build a
@@ -60,7 +61,6 @@ import xml.etree.ElementTree as ET
import subprocess
import re
-import os
from datetime import date
import authors
@@ -69,7 +69,7 @@ import authors
# two forms:
# - 'OK'
# - 'OK ([DOI])'
-SUCCESS_RESPONSE = '^OK( \((.+)\))?$'
+SUCCESS_RESPONSE = r'^OK( \((.+)\))?$'
# Point all "deleted" DOIs to here:
INVALID_URL = 'http://www.datacite.org/invalidDOI'
@@ -210,8 +210,10 @@ def _http_request(body, method, url, options):
]
# Set how loud cURL should be while running.
- if options.debug: args.append('--verbose')
- else: args.append('--silent')
+ if options.debug:
+ args.append('--verbose')
+ else:
+ args.append('--silent')
args.append(url)
@@ -529,4 +531,4 @@ if __name__ == "__main__":
'details. Note that this does NOT delete the DOI.'
)
- run(parser.parse_args())
\ No newline at end of file
+ run(parser.parse_args())
diff --git a/tools/DefaultConfigFiles/configToCpp.py b/tools/DefaultConfigFiles/configToCpp.py
index 6cd03a271650bc81ed2e03fcdc93110c0f563604..bb924e92af41df65efb48cf20fa26230099a49f7 100644
--- a/tools/DefaultConfigFiles/configToCpp.py
+++ b/tools/DefaultConfigFiles/configToCpp.py
@@ -7,8 +7,8 @@ import sys
with open(sys.argv[2]) as f:
for line in f:
- line = line.rstrip('\n')
- if line == "":
- print sys.argv[1] + " << std::endl;"
- else:
- print sys.argv[1] + " << \"" + line + "\" << std::endl;"
+ line = line.rstrip('\n')
+ if line == "":
+ print sys.argv[1] + " << std::endl;"
+ else:
+ print sys.argv[1] + " << \"" + line + "\" << std::endl;"
diff --git a/tools/PeriodicTable/generate_atom_code.py b/tools/PeriodicTable/generate_atom_code.py
index 030cb3c39b70b79c292f827b48865e6eaa833d73..3e2be400a0091c7ae44503bf0c060233302194e2 100755
--- a/tools/PeriodicTable/generate_atom_code.py
+++ b/tools/PeriodicTable/generate_atom_code.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#!/usr/bin/env python
VERSION = "1.0"
@@ -30,13 +31,13 @@ def writeMiddle(handle, abundance, atom):
if density is None:
density = "NAN"
else:
- desnity = str(density)
+ density = str(density)
except TypeError:
density = "NAN"
handle.write("%f, %f, %s" % (abundance, mass, density))
def writeEnd(handle):
- handle.write(");\n");
+ handle.write(");\n")
def writeIsotope(handle, element, atomicnumber):
isotope = element._isotopes[atomicnumber]
diff --git a/tools/Pylint/fixPylint.py b/tools/Pylint/fixPylint.py
new file mode 100644
index 0000000000000000000000000000000000000000..5f3cf1d6990bde995780868418b7132eef3e4060
--- /dev/null
+++ b/tools/Pylint/fixPylint.py
@@ -0,0 +1,173 @@
+#pylint: disable=invalid-name,anomalous-backslash-in-string
+import os
+import re
+import argparse
+
+def fixBadIndent(toModify,indent):
+ err_string=indent.replace(' Bad indentation. Found ','').replace('(bad-indentation)','').split('spaces, expected')
+ bad=int(err_string[0])
+ good=int(err_string[1])
+ return toModify.replace(' '*bad,' '*good)
+
+def fixParens(fname,errorlist,errlines):
+ tofixf=open(fname,'r')
+ file_content=tofixf.readlines()
+ tofixf.close()
+ newcontent=file_content
+ for i,error in zip(errlines,errorlist):
+ if error.find('(superfluous-parens)')!=-1:
+ kwd=error.split("'")[1]
+ pattern=re.compile(kwd+'(?P<spaces>\ *)\((?P<file_content>.*)\)')
+ match=pattern.search(file_content[i])
+ d=match.groupdict()
+ newcontent[i]=file_content[i].replace(kwd+d['spaces']+'('+d['file_content']+')',kwd+' '+d['file_content'])
+ tofixf=open(fname,'w')
+ tofixf.write(''.join(newcontent))
+ tofixf.close()
+
+def fixSeveralErrors(fname,errorlist,errlines):
+ tofixf=open(fname,'r')
+ file_content=tofixf.readlines()
+ tofixf.close()
+ newcontent=file_content
+ for i,error in zip(errlines,errorlist):
+ if error.find('Bad indentation')!=-1:
+ newcontent[i]=fixBadIndent(file_content[i],error)
+ if error.find('missing-final-newline')!=-1:
+ newcontent[-1]+='\n'
+ if error.find('mixed-indentation')!=-1:
+ newcontent[i]=file_content[i].replace('\t', ' ')
+ if error.find('trailing-whitespace')!=-1:
+ newcontent[i]=file_content[i].rstrip()+'\n'
+ if error.find('Unnecessary semicolon')!=-1:
+ newcontent[i]=file_content[i].replace(';','')
+ tofixf=open(fname,'w')
+ tofixf.write(''.join(newcontent))
+ tofixf.close()
+
+def addIgnoreStatement(fname,errorlist):
+ tofixf=open(fname,'r')
+ file_content=tofixf.readlines()
+ tofixf.close()
+ ignore=[]
+ for error in errorlist:
+ if error.find('(invalid-name)')!=-1 and 'invalid-name' not in ignore:
+ ignore.append('invalid-name')
+ if error.find('(no-init)')!=-1 and 'no-init' not in ignore:
+ ignore.append('no-init')
+ if error.find('(too-many-lines)')!=-1 and 'too-many-lines' not in ignore:
+ ignore.append('too-many-lines')
+ if len(ignore)!=0:
+ tofixf=open(fname,'w')
+ tofixf.write("#pylint: disable="+','.join(ignore)+'\n')
+ tofixf.write(''.join(file_content))
+ tofixf.close()
+
+def generate_choices():
+ ch=['simple','parentheses','add_ignores']
+ ch_help=['simple - fixes the following warning: bad-indentation, missing-final-newline, '+\
+ 'mixed_indentation, trailing-whitespace, unnecesary-semicolon',
+ 'parentheses - fixes superfluous-parens warning',
+ 'add_ignores - adds ignore statemets at the beginning of each file to ignore invalid-name, no-init, too-many-lines']
+ chhelp="The possible choices supported are:\n\t"+'\n\t'.join(ch_help)
+ return (ch,chhelp)
+
+if __name__=='__main__':
+ choices,choices_help=generate_choices()
+ parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
+ epilog=choices_help,
+ description='Fix some pylint warnings. It is STRONGLY RECOMMENDED to '+\
+ 'rerun the pylintcheck between fixes')
+ parser.add_argument('-fix','--fix', default='simple',
+ choices=choices,
+ help='Select things to fix (default: simple). \nSee the choices options below.')
+ parser.add_argument('Filename', type=file, help='The output from "make pylint"')
+ parser.add_argument('-v','--version', action='version', version='%(prog)s 1.0')
+
+ #read pylint.log
+ args = parser.parse_args()
+ oneline=args.Filename.read()
+ args.Filename.close()
+ #ignore everything up to the first error
+ oneline=oneline[oneline.find('****'):]
+ content=oneline.split('\n')
+
+ fileindex=content.index('Checks of the following modules FAILED:')
+ files=[f.strip() for f in content[fileindex+1:-1]]
+ filenumber=0
+ linenumber=0
+ prevFile=True
+
+
+ while linenumber<fileindex:
+ filename=files[filenumber]
+ line=content[linenumber]
+ #find a file
+ if line.find('****')==0 and line.find('PyChop')==-1:
+ modname=line.split('************* Module ')[1]
+ if prevFile:
+ if os.path.isfile(filename):
+ correct_filename=filename
+ filenumber+=1
+ prevFile=True
+ else:
+ prevFile=False
+ modname=modname.replace('.','/')
+ firstslash=modname.find('/')
+ if firstslash==-1:
+ correct_filename=filename+'/__init__.py'
+ else:
+ correct_filename=filename+modname[firstslash:]+'.py'
+ else:
+ lastmodulename=os.path.split(filename)[1]
+ modbase=modname.split('.')[0]
+ if lastmodulename==modbase: #still in the same module
+ modname=modname.replace('.','/')
+ firstslash=modname.find('/')
+ if firstslash==-1:
+ correct_filename=filename+'/__init__.py'
+ else:
+ correct_filename=filename+modname[firstslash:]+'.py'
+ else: #go to the next file or module
+ filenumber+=1
+ filename=files[filenumber]
+ prevFile=True
+ if os.path.isfile(filename):
+ correct_filename=filename
+ filenumber+=1
+ prevFile=True
+ else:
+ prevFile=False
+ modname=modname.replace('.','/')
+ firstslash=modname.find('/')
+ if firstslash==-1:
+ correct_filename=filename+'/__init__.py'
+ else:
+ correct_filename=filename+modname[firstslash:]+'.py'
+ #process it
+ j=1
+ errors=[]
+ errorlines=[]
+ while linenumber+j<fileindex and content[linenumber+j].find('****')==-1:
+ err=content[linenumber+j]
+ if len(err)>0 and err[0] in ['C','W','E'] and err[1]==':':
+ lineNumber=int(err.split(':')[1].split(',')[0])-1
+ errors.append(err.split(':')[2])
+ errorlines.append(lineNumber)
+ j+=1
+ if args.fix=='simple':
+ fixSeveralErrors(correct_filename,errors,errorlines)
+ elif args.fix=='add_ignores':
+ addIgnoreStatement(correct_filename,errors)
+ elif args.fix=='parentheses':
+ fixParens(correct_filename,errors,errorlines)
+ linenumber+=j-1
+ else:
+ linenumber+=1
+
+
+
+
+
+
+
diff --git a/tools/Pylint/pylint.cfg b/tools/Pylint/pylint.cfg
index eec53d4f7b22bdfd67bc5e8f1c30b956fa6be060..cbf3bb4a69987805eca098774a89baba10598196 100644
--- a/tools/Pylint/pylint.cfg
+++ b/tools/Pylint/pylint.cfg
@@ -57,7 +57,7 @@ disable=W0142,I0011,F0401,W0614,E0602,C0111,C0326,W0401,R0201,R0801
output-format=colorized
# Include message's id in output
-include-ids=yes
+#include-ids=yes
# Put messages in a separate file for each module / package specified on the
# command line instead of printing them on stdout. Reports (if any) will be
diff --git a/tools/Pylint/run_pylint.py b/tools/Pylint/run_pylint.py
index 4af4d89a1555aac11bb0ebba05fbc09d58ae5f6d..8368854c1fcafe1db6c7f464b3fe0a61a6f7922b 100644
--- a/tools/Pylint/run_pylint.py
+++ b/tools/Pylint/run_pylint.py
@@ -57,7 +57,7 @@ class Results(object):
"""
Return true if all files were clean
"""
- return (len(self.failures) == 0)
+ return len(self.failures) == 0
def add(self, modulename, status):
"""
@@ -172,8 +172,8 @@ def parse_arguments(argv):
help="If provided, store the output in the given file.")
parser.add_option("-x", "--exclude", dest="exclude", metavar="EXCLUDES",
help="If provided, a space-separated list of "
- "files/directories to exclude. Relative paths are "
- "taken as relative to --basedir")
+ "files/directories to exclude. Relative paths are "
+ "taken as relative to --basedir")
parser.set_defaults(format=DEFAULT_PYLINT_FORMAT, exe=DEFAULT_PYLINT_EXE, nofail=False,
basedir=os.getcwd(), rcfile=DEFAULT_RCFILE, exclude="")
@@ -242,6 +242,7 @@ def check_module_imports():
str: String indicating success/failure
"""
msg = ""
+ #pylint: disable=unused-variable
try:
import mantid
except ImportError, exc:
@@ -292,7 +293,7 @@ def run_checks(targets, serializer, options):
targetpath = os.path.join(options.basedir, target)
pkg_init = os.path.join(targetpath, "__init__.py")
if os.path.isfile(targetpath) or os.path.isfile(pkg_init):
- overall_stats.add(exec_pylint_on_importable(targetpath, serializer, options))
+ overall_stats.add(targetpath, exec_pylint_on_importable(targetpath, serializer, options))
else:
overall_stats.update(exec_pylint_on_all(targetpath, serializer, options, excludes))
##
@@ -352,7 +353,7 @@ def find_importable_targets(dirpath):
pkg_init = os.path.join(abspath, "__init__.py")
if (os.path.isfile(abspath) and item.endswith(".py")) or \
os.path.isfile(pkg_init):
- importables.append(abspath)
+ importables.append(abspath)
elif os.path.isdir(abspath):
importables.extend(package_walk(abspath))
return importables
@@ -386,7 +387,7 @@ def exec_pylint_on_importable(srcpath, serializer, options):
with temp_dir_change(os.path.dirname(srcpath)):
status = subp.call(cmd, stdout=serializer)
- return (status == 0)
+ return status == 0
#------------------------------------------------------------------------------
diff --git a/tools/TestViewer/TestViewer.py b/tools/TestViewer/TestViewer.py
index 428762ca8577534af6bc5449a80c9e08df2360d4..987819601d5c954e4bb51b9a0ce43707c03fdf91 100755
--- a/tools/TestViewer/TestViewer.py
+++ b/tools/TestViewer/TestViewer.py
@@ -4,4 +4,4 @@
""" Launch the GUI Test Viewer """
import main_window
-main_window.start()
\ No newline at end of file
+main_window.start()
diff --git a/tools/TestViewer/main_window.py b/tools/TestViewer/main_window.py
index 06bbb4291e5da4fc4a11f68830377229835f6d0a..48975b55710a5871b9c86f8211cbe22a839e7ebc 100644
--- a/tools/TestViewer/main_window.py
+++ b/tools/TestViewer/main_window.py
@@ -1,12 +1,12 @@
+#pylint: disable=invalid-name
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import time
-import optparse
import os
-from PyQt4 import QtGui, uic, QtCore
+from PyQt4 import QtGui, QtCore
import PyQt4.QtCore
from PyQt4.QtCore import *
import PyQt4.QtGui
@@ -14,10 +14,9 @@ from PyQt4.QtGui import *
import ui_main_window
import test_info
-from test_info import TestSuite, TestSingle, TestProject, MultipleProjects
+from test_info import TestSuite, TestSingle, TestProject
-import test_tree
-from test_tree import TestTreeModel, TreeItemSuite, TreeItemProject, TreeFilterProxyModel
+from test_tree import TestTreeModel, TreeFilterProxyModel
#==================================================================================================
@@ -285,11 +284,11 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
# --- Text settings ---
memory = s.value("memory_limit_MB", 8000).toInt()[0]
- test_info.memory_limit_kb = memory*1024;
+ test_info.memory_limit_kb = memory*1024
self.textMemory.setPlainText("%d" % memory)
timeout = s.value("process_timeout_sec", 30).toInt()[0]
- test_info.process_timeout_sec = timeout;
+ test_info.process_timeout_sec = timeout
self.textTimeout.setPlainText("%d" % timeout)
self.select_by_string_lastValue = str(s.value("select_by_string_lastValue", "-Performance").toString())
@@ -313,10 +312,10 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
try:
s = plainTextBox.toPlainText()
value = int(s)
- plainTextBox.setStyleSheet("QPlainTextEdit { background-color: white; }");
+ plainTextBox.setStyleSheet("QPlainTextEdit { background-color: white; }")
return value
except:
- plainTextBox.setStyleSheet("QPlainTextEdit { background-color: tomato; }");
+ plainTextBox.setStyleSheet("QPlainTextEdit { background-color: tomato; }")
return None
@@ -326,14 +325,14 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
""" called when one of the text boxes changes """
s = self.settings
- memory = self.get_int_from_text(self.textMemory);
+ memory = self.get_int_from_text(self.textMemory)
if not memory is None:
- test_info.memory_limit_kb = memory*1024;
+ test_info.memory_limit_kb = memory*1024
s.setValue("memory_limit_MB", memory)
- timeout = self.get_int_from_text(self.textTimeout);
+ timeout = self.get_int_from_text(self.textTimeout)
if not timeout is None:
- test_info.process_timeout_sec = timeout;
+ test_info.process_timeout_sec = timeout
s.setValue("process_timeout_sec", timeout)
@@ -460,8 +459,8 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
if (time.time() - self.last_console_update) > 1.5: # Dont update more often than this:
self.textConsole.setText( u'<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n' +
self.stdout )
- sb = self.textConsole.verticalScrollBar();
- sb.setValue(sb.maximum());
+ sb = self.textConsole.verticalScrollBar()
+ sb.setValue(sb.maximum())
self.last_console_update = time.time()
@@ -540,7 +539,7 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
elif isinstance(res, TestSingle):
self.labelTestType.setText("Single Test Results:")
else:
- raise "Incorrect object passed to show_results; should be TestProject, TestSuite, or TestSingle."
+ raise RuntimeError("Incorrect object passed to show_results; should be TestProject, TestSuite, or TestSingle.")
self.labelTestName.setText( res.get_fullname() )
self.labelTestName.hide()
self.textResults.setText( u'<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n'
@@ -574,7 +573,8 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
parallel = self.checkInParallel.isChecked()
# Do some setup of the worker and GUI
num_steps = self.worker.set_parameters(self, selected_only=selected_only, make_tests=True, parallel=parallel)
- if num_steps < 1: num_steps = 1
+ if num_steps < 1:
+ num_steps = 1
self.progTest.setValue(0)
self.progTest.setMaximum( num_steps )
self.set_running(True)
@@ -631,15 +631,17 @@ class TestViewerMainWindow(QtGui.QMainWindow, ui_main_window.Ui_MainWindow):
def start():
# Start the settings object.
# TODO: Change the company name here and in MantidPlot
- settings = QSettings("ISIS", "MantidTestViewer");
+ settings = QSettings("ISIS", "MantidTestViewer")
settings_bin_folder = str(settings.value("bin_folder", "../../Mantid/bin").toString())
settings_source_folder = str(settings.value("source_folder", "../../Mantid/Framework").toString())
bin_folder = ""
- if len(sys.argv) > 1: bin_folder = sys.argv[1]
+ if len(sys.argv) > 1:
+ bin_folder = sys.argv[1]
source_folder = ""
- if len(sys.argv) > 2: source_folder = sys.argv[2]
+ if len(sys.argv) > 2:
+ source_folder = sys.argv[2]
if bin_folder == "--help":
print """TestViewer.py [BINFOLDER] [SOURCEFOLDER]
@@ -690,4 +692,3 @@ def start():
if __name__ == '__main__':
start()
-
diff --git a/tools/TestViewer/test_info.py b/tools/TestViewer/test_info.py
index c43fb05c0cf7a6b8ba340dea515ec46d1c5643cf..e93f07021bebedf3cb17b4ab1e53fe6281c46a4f 100644
--- a/tools/TestViewer/test_info.py
+++ b/tools/TestViewer/test_info.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines,invalid-name
# -*- coding: utf-8 -*-
""" Classes describing test projects,
how they are run,
@@ -77,7 +78,7 @@ class TestResult:
def __eq__(self, other):
""" Equality comparison """
if isinstance(other, TestResult):
- return ((self.value == other.value) and (self.old == other.old))
+ return (self.value == other.value) and (self.old == other.old)
else:
return self.value == other
@@ -372,7 +373,7 @@ class TestSuite(object):
self.contents_changed = True
else:
for i in xrange(len(self.tests)):
- if (self.tests[i].name != other.tests[i].name):
+ if self.tests[i].name != other.tests[i].name:
self.contents_changed = True
self.tests[i].replace_contents( other.tests[i] )
# Copy local values
@@ -402,7 +403,7 @@ class TestSuite(object):
oldtime = self.source_file_mtime
if os.path.exists(self.source_file):
self.source_file_mtime = os.path.getmtime(self.source_file)
- return (self.source_file_mtime != oldtime)
+ return self.source_file_mtime != oldtime
def get_selected(self):
return self.selected
@@ -587,7 +588,7 @@ class TestSuite(object):
return
elif len(suites) > 1:
for xmlSuite in suites:
- if (suites[0].getAttribute("name") == self.name):
+ if suites[0].getAttribute("name") == self.name:
break
else:
xmlSuite = suites[0]
@@ -596,7 +597,7 @@ class TestSuite(object):
xmlCases = xmlSuite.getElementsByTagName("testcase")
for case in xmlCases:
classname = case.getAttribute("classname")
- if (classname == self.classname):
+ if classname == self.classname:
# This is the single test name
test_name = case.getAttribute("name")
test = self.find_test(test_name)
@@ -752,7 +753,7 @@ class TestProject(object):
# This will run while calling the stdout callback.
(status, output) = run_command_with_callback(full_command, callback_func)
- if (status != 0):
+ if status != 0:
msg = "-------- BUILD FAILED! ---------"
if not callback_func is None: callback_func("%s" % msg)
self.build_succeeded = False
@@ -1055,7 +1056,7 @@ class MultipleProjects(object):
word = val[1:]
for pj in self.projects:
for suite in pj.suites:
- suite.selected = not (word in suite.name)
+ suite.selected = not word in suite.name
if suite.selected: num += 1
else:
word = val
@@ -1486,14 +1487,14 @@ def test_results_compiling():
def test_age():
a = TestSingle("my_test_test", None)
- assert (a.state == TestResult.NOT_RUN)
+ assert a.state == TestResult.NOT_RUN
a.age()
- assert (a.state == TestResult.NOT_RUN)
- assert (a.state.old)
+ assert a.state == TestResult.NOT_RUN
+ assert a.state.old
a = TestSingle("my_test_test", None)
a.state = TestResult(TestResult.ALL_PASSED)
a.age()
- assert (a.state.old)
+ assert a.state.old
test_results_compiling()
test_age()
diff --git a/tools/TestViewer/test_tree.py b/tools/TestViewer/test_tree.py
index ac53c73d42d7350dcb87faf20c225b5e7e2bc71c..9c233db03d27a2f1b4e6569cd9ba148cf84dbf37 100644
--- a/tools/TestViewer/test_tree.py
+++ b/tools/TestViewer/test_tree.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name,no-init
""" An AbstractTreeItem implementation for a QTreeView
that uses the results from test runners. """
@@ -8,8 +9,7 @@ import PyQt4.QtGui
from PyQt4.QtGui import *
import test_info
-from test_info import TestSuite, TestSingle, TestProject, MultipleProjects
-import random
+from test_info import TestSuite, TestProject
import datetime
HORIZONTAL_HEADERS = ("Test", "Status", "Time (sec)", "Last Run")
@@ -81,16 +81,19 @@ def get_background_color(state):
elif state == test_info.TestResult.ALL_PASSED:
col = MyColors.lightGreen
- if state.old: col = MyColors.darkishGreen
+ if state.old:
+ col = MyColors.darkishGreen
elif state == test_info.TestResult.ALL_FAILED or (state == test_info.TestResult.SOME_FAILED) \
or state == test_info.TestResult.ABORTED:
col = QColor(Qt.red)
- if state.old: col = QColor( 200, 50, 50 )
+ if state.old:
+ col = QColor( 200, 50, 50 )
elif state == test_info.TestResult.BUILD_ERROR:
col = QColor(Qt.magenta)
- if state.old: col = desaturate(col, 0.5)
+ if state.old:
+ col = desaturate(col, 0.5)
# elif state == test_info.TestResult.SOME_FAILED:
# col = MyColors.lightRed
@@ -293,7 +296,7 @@ class TestTreeModel(QtCore.QAbstractItemModel):
# What background color?
if role == Qt.BackgroundRole:
- return item.background_color();
+ return item.background_color()
#User role is used when directly querying the contents of the item
if role == Qt.UserRole:
@@ -488,7 +491,7 @@ class TestTreeModel(QtCore.QAbstractItemModel):
for k in xrange(num_tests):
test_indx = self.index(k, 0, suite_indx)
# Sets it as checked.
- self.setData(test_indx, QtCore.Qt.Checked, QtCore.Qt.CheckStateRole);
+ self.setData(test_indx, QtCore.Qt.Checked, QtCore.Qt.CheckStateRole)
def mouseDoubleClickEvent(self):
print "mouseDoubleClickEvent"
@@ -534,7 +537,7 @@ class TreeFilterProxyModel(QSortFilterProxyModel):
return False
if self.selected_only:
if isinstance(item, TestProject) or isinstance(item, TestSuite) :
- return (item.get_selected() > 0)
+ return item.get_selected() > 0
else:
# Don't filter out TestSingles based on selection (since they're all selected)
return True
diff --git a/tools/TestViewer/ui_main_window.py b/tools/TestViewer/ui_main_window.py
index 415f4cf3f0b9fc2ffc51ce79f3bb345c6d99e958..d33d69c8a7d567dd0f6e2337f7b286e84a9f8ab6 100644
--- a/tools/TestViewer/ui_main_window.py
+++ b/tools/TestViewer/ui_main_window.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'main_window.ui'
diff --git a/tools/VTKConverter/VTKConvert.py b/tools/VTKConverter/VTKConvert.py
index 161b2fe69d72aad166bbf001c659f96c95df070d..3048c2c46f2f3071bb0b9f104c26f61ca1d7706f 100644
--- a/tools/VTKConverter/VTKConvert.py
+++ b/tools/VTKConverter/VTKConvert.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#! /usr/bin/python
# Convert an acor file into VTK format (specifically a vtp file)
from xml.dom import minidom
@@ -10,19 +11,19 @@ def convertToVTU(infile, outpath):
planelist=[]
npoints = 0
for line in datafile:
- numbers = line.split();
- if( len(numbers) != 4 ):
+ numbers = line.split()
+ if len(numbers) != 4 :
continue
- if( npoints == 0 ):
+ if npoints == 0 :
curz = numbers[2]
- if( numbers[2] != curz ):
+ if numbers[2] != curz :
datalist.append(planelist)
curz = numbers[2]
planelist=[]
planelist.append(numbers)
npoints += 1
-# Append last set
+ # Append last set
datalist.append(planelist)
datafile.close()
@@ -43,7 +44,7 @@ def convertToVTU(infile, outpath):
piece.setAttribute( "NumberOfPoints", str(npoints))
piece.setAttribute( "NumberOfCells", str(ncells))
-# First the PointData element
+ # First the PointData element
point_data = doc.createElement("PointData")
piece.appendChild(point_data)
point_data.setAttribute("Scalars", "Intensity")
@@ -59,7 +60,7 @@ def convertToVTU(infile, outpath):
txt = doc.createTextNode(str(point[3]))
data_array.appendChild(txt)
-# Now the Points element
+ # Now the Points element
points = doc.createElement("Points")
piece.appendChild(points)
@@ -111,12 +112,12 @@ def convertToVTU(infile, outpath):
txt = doc.createTextNode("4")
data_array.appendChild(txt)
-# #print doc.toprettyxml(newl="\n")
+ #print doc.toprettyxml(newl="\n")
shortname = infile.split('/')
name = outpath + shortname[len(shortname)-1] + ".vtu"
- file = open(name,'w')
- doc.writexml(file, newl="\n")
- file.close()
+ handle = open(name,'w')
+ doc.writexml(handle, newl="\n")
+ handle.close()
del datalist
del planelist
@@ -160,6 +161,6 @@ def writeParallelVTU(files, prefix):
# print doc.toprettyxml(newl="\n")
filename = prefix + files[0].split('.')[0] + ".pvtu"
# print filename
- file = open(filename,'w')
- doc.writexml(file, newl="\n")
- file.close()
+ handle = open(filename,'w')
+ doc.writexml(handle, newl="\n")
+ handle.close()
diff --git a/tools/VTKConverter/processISISData.py b/tools/VTKConverter/processISISData.py
index 7d00849ca3f3d570c99e3dc54354b7cbac107ff3..7a988d0adbbaab4180538af8c941ed45a67dca34 100644
--- a/tools/VTKConverter/processISISData.py
+++ b/tools/VTKConverter/processISISData.py
@@ -1,24 +1,25 @@
+#pylint: disable=invalid-name
#!/usr/bin/python
import os
import sys
import VTKConvert
-if( len(sys.argv) == 1 ):
+if len(sys.argv) == 1 :
print "Usage: processISISData file-name1 file-name2 ...\n processISISDATA dir-name"
exit(1)
names=[]
is_dir = os.path.isdir(sys.argv[1])
-if( is_dir ):
+if is_dir :
names = os.listdir(sys.argv[1])
else:
for i in range(1,len(sys.argv)):
names.append(sys.argv[i])
prefix=""
-if( is_dir ):
+if is_dir :
prefix = sys.argv[1].split('/')[0] + "-VTU/"
- if( os.path.isdir(prefix) ):
+ if os.path.isdir(prefix) :
print "Directory " + prefix + " already exists, please move\n"
exit(1)
else:
@@ -27,7 +28,7 @@ else:
prefix = "./"
for file in names:
- if( is_dir ):
+ if is_dir :
filename = sys.argv[1] + file
VTKConvert.convertToVTU(filename, prefix)
diff --git a/tools/reports/facility-code-changes.py b/tools/reports/facility-code-changes.py
index 9233650ef8185ed9ed41966af314de8365b1dde4..f8f1e906cde51814c8d5fd820b323dceb9f08b5a 100644
--- a/tools/reports/facility-code-changes.py
+++ b/tools/reports/facility-code-changes.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function, unicode_literals)
__author__ = 'Stuart Campbell'
@@ -176,14 +177,14 @@ if __name__ == '__main__':
print("Getting stats for {0}-{1:02d}".format(str(year), month))
since = "--since='{0}-{1}-1'".format(str(year), str(month))
until = "--before='{0}-{1}-{2}'".format(str(year), str(month), str(days_in_month[month-1]))
-
+
date_key = str(year)+'-{0:02d}'.format(month)
facility_commits[date_key] = {}
facility_changed[date_key] = {}
facility_added[date_key] = {}
facility_removed[date_key] = {}
-
+
freading = open('facility-file-changes-{0}.stdout'.format(date_key),'r',buffering=0)
# initialize facility counters
@@ -197,7 +198,7 @@ if __name__ == '__main__':
changed = 0
added = 0
removed = 0
-
+
# Is the line blank (or None)
if line is None or len(line) is 0:
# print("BLANK:'{0}'".format(str(line)))
diff --git a/tools/reports/release-list.py b/tools/reports/release-list.py
index f6a48764d64dbeade4b1df4a4ed9dfb7e7a93045..a74995bfa317d57197b2f7726be302e138e8ff08 100644
--- a/tools/reports/release-list.py
+++ b/tools/reports/release-list.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function, unicode_literals)
import csv
diff --git a/tools/scripts/AddAlgorithmWikiLinksToText.py b/tools/scripts/AddAlgorithmWikiLinksToText.py
deleted file mode 100644
index e372fe01a3384d8b37ac4b5f1dbb15028a8f6810..0000000000000000000000000000000000000000
--- a/tools/scripts/AddAlgorithmWikiLinksToText.py
+++ /dev/null
@@ -1,17 +0,0 @@
-text = """
-===Algorithms===
-* PlotPeakByLogValue now optionally outputs calculated spectra like the Fit algorithm.
-* StartLiveData now checks whether the instrument listener supports the provision of historic values.
-* LiveData processing now handles the transition between runs much better at facilities that support this functionality (at present only the SNS).
-* LoadEventNexus reads the Pause log and discards any events found during Paused time spans.
-* GenerateEventsFilter has been improved to make it easier to use and allowing split sections to be added together into workplaces on a cyclic basis.
-* LoadPreNexus is now more forgiving if it encounters bad event indexes in pulse ID file .
-
-"""
-
-import re
-
-algs = AlgorithmFactory.getRegisteredAlgorithms(True)
-for alg in algs:
- text = re.sub(r'\b' + alg+ r'\b',r'[http://docs.mantidproject.org/algorithms/' + alg + '.html ' + alg + '] ',text)
-print text
\ No newline at end of file
diff --git a/tools/scripts/ConvertBadAlgmLinks.py b/tools/scripts/ConvertBadAlgmLinks.py
index 4d7d71e86989bbaa469f1535c5510afdd5ce52ee..6759d9d23b3b5bdf2004bd2afeb048e9b6edd5c4 100644
--- a/tools/scripts/ConvertBadAlgmLinks.py
+++ b/tools/scripts/ConvertBadAlgmLinks.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
import re, glob, os
def grep(patt,lines):
@@ -30,13 +31,13 @@ for filename in files:
#print os.path.basename(filename)[:-4]
with open(filename) as file:
- lines = file.readlines()
- for alg in algs:
- expr = regexs[alg]
- results = grep(expr, lines)
- if results:
- print filename
- print results
+ lines = file.readlines()
+ for alg in algs:
+ expr = regexs[alg]
+ results = grep(expr, lines)
+ if results:
+ print filename
+ print results
diff --git a/tools/scripts/ConvertToRST/ConvertWikiPage.py b/tools/scripts/ConvertToRST/ConvertWikiPage.py
deleted file mode 100644
index 696cb94f8c0c04968d309297b3ee10bea224d892..0000000000000000000000000000000000000000
--- a/tools/scripts/ConvertToRST/ConvertWikiPage.py
+++ /dev/null
@@ -1,284 +0,0 @@
-###########################################################################################
-# Converts mediawiki pages to rst pages for sphinx.
-# run with -h for command line arguments
-#
-# sample command C:\MantidInstall\bin\python.exe C:/Mantid/tools/scripts/ConvertToRST/ConvertWikiPage.py
-# -o C:/Mantid/Code/Mantid/docs/source/training/MBC_Displaying_data_Formatting.rst
-#
-# pandoc must be installed an in the path
-#
-# extends pandoc by downloading and correcting image links, and adding links for algorithms,
-# fit functions and common concepts (workspace types)
-#
-# Limitations:
-# 1. in adding text to links or images in tables the table formatting will be disrupted
-# 2. pandoc creates some images in an inline format, these cannot have the align tags added
-# back on, this is marked with a comment, the solution is probably to move the image from
-# the inline to normal format.
-# 3. Image links cannot have spaces in the filename in rst.
-# The spaces are removed in the downloaded file names, but not the links in the rst files.
-#
-##########################################################################################
-import os
-import re
-import sys
-import urllib2
-import urlparse
-import argparse
-import subprocess
-import mantid
-
-def readWebPage(url):
- # set your environment HTTP_PROXY to be your proxy
- # for ral HTTP_PROXY=http://wwwcache.rl.ac.uk:8080
- aResp = urllib2.urlopen(url)
- web_pg = aResp.read()
- return web_pg
-
-def downloadImage(imgUrl, filePath):
- downloadedImage = file(filePath, "wb")
-
- imageOnWeb = urllib2.urlopen(imgUrl)
- while True:
- buf = imageOnWeb.read(65536)
- if len(buf) == 0:
- break
- downloadedImage.write(buf)
- downloadedImage.close()
- imageOnWeb.close()
-
- return filePath
-
-def convertURLToRaw(url):
- return url + "?action=raw"
-
-def covertMediaWikiToRST(url):
- cmd = 'pandoc -f mediawiki -t rst "' + url + '"'
- print cmd
-
- return runProcess(cmd)
-
-def runProcess(cmd):
- # instantiate a startupinfo obj:
- startupinfo = subprocess.STARTUPINFO()
- # set the use show window flag, might make conditional on being in Windows:
- startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
-
- p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
- startupinfo=startupinfo)
- output, error = p.communicate()
- output = output.replace("\r\n","\n")
- print error
- return output
-
-def processImageLinks(mediawikiText,rstText, imagePath, relImagePath):
- retRstText = rstText
- mwImagePattern = re.compile(r'\[\[(Image|File):(.+?)(\|.*?)?(\|.*?)?(\|.*?)?(\|.*?)?(\|.*?)?(\|.*?)?\]\]',
- re.IGNORECASE)
- rstImagePattern = re.compile(r'figure:: (([\w\-\_\\\/]+)\.(\w{2,5}))(.{0,50}\3){2}',
- re.DOTALL)
- rstSubstitutionImagePattern = re.compile(r'(figure|image):: (([\w\-\_\\\/]+)\.(\w{2,5}))')
-
-
- imgLinkDict ={}
- #for all of the mediawiki links
- for m in re.finditer(mwImagePattern, mediawikiText):
- print ("processing image link",m.group(0))
- rstLink = generateRstImageLink(m,relImagePath)
- imgLinkDict[m.group(2)] = rstLink
- print (rstLink)
-
- #for all of the rst figure links
- replacements = []
- for m in re.finditer(rstImagePattern, retRstText):
- rstLink = imgLinkDict[m.group(1)]
- replacements.append((m.start(), m.end(), m.group(1), rstLink))
-
- #perform replacements in reverse order
- for (start,end,imagefile,rstLink) in reversed(replacements):
- retRstText = retRstText[0:start] + rstLink + retRstText[end:]
-
- replacements = []
- for m in re.finditer(rstSubstitutionImagePattern, retRstText):
- rstLink = imgLinkDict[m.group(2)]
- rstLink = cleanInlineImagesDefinition(rstLink)
- replacements.append((m.start(), m.end(), m.group(2), rstLink))
-
- #perform replacements in reverse order
- for (start,end,imagefile,rstLink) in reversed(replacements):
- retRstText = retRstText[0:start] + rstLink + retRstText[end:]
-
- #get all of the image files
- for imageName in imgLinkDict.keys():
- saveImageFromMW(imageName,imagePath)
-
-
- return retRstText
-
-def saveImageFromMW(imageName,path):
- url = "http://www.mantidproject.org/File:"+imageName.replace(" ","_")
- print "Downloading image: ", url
- imagePage = readWebPage(url)
- mwImagePattern = re.compile(r'<div class="fullImageLink" id="file"><a href="([\/\w\.\-]+)">')
-
- imagePath = path + "/" + imageName.replace(" ","")
-
- match = re.search(mwImagePattern,imagePage)
- if match is not None:
- imageURL = match.group(1)
- imageURL = "http://www.mantidproject.org" + imageURL
- if not os.path.exists(imagePath):
- print "saving ", imageName, "to", imagePath
- downloadImage(imageURL,imagePath)
-
-def generateRstImageLink(match,relImagePath):
- link = "image:: " + relImagePath+ "/" + match.group(2) + "\n"
- for i in range(3,len(match.groups())):
- if match.group(i) is None:
- break
- #strip off the first character as it is the | pipe
- imageOption = addImageOption(match.group(i)[1:])
- if imageOption is not None:
- link += "\t\t\t" + imageOption + "\n"
- return link
-
-def addImageOption(mwImageOption):
- imageOption = mwImageOption.strip()
- if len(imageOption)>0:
- if imageOption.endswith("px"):
- return ":width: " + imageOption
- elif imageOption in ["right","left","middle","centre"]:
- return ":align: " + imageOption
- else:
- return ":alt: " + imageOption
-
-def cleanInlineImagesDefinition(rstLink):
- match = re.search(r'^\s+:align:\s+\w+\s*$',rstLink,re.MULTILINE)
- if match is not None:
- #take the align out
- rstLink = rstLink[0:match.start()] + rstLink[match.end()+1:]
- #then add it at the end as a comment
- rstLink += ".. FIXME (inline definition does not allow align)" + match.group(0)
- return rstLink
-
-def ensureDirectoriesExist(path):
- try:
- os.makedirs(path)
- except OSError:
- pass
-
-def addLocalLinks(rstText,list,prefix):
- retRstText = rstText
- #build regex string for simple words
- regex = r"[^`<]((\*{0,2})(\b" + r"\b|\b".join(list) + r"\b)\2)[^`_]"
- pattern = re.compile(regex)
-
- replacements = []
- for m in re.finditer(pattern, retRstText):
- rstLink = ":ref:`" + m.group(3) + " <" + prefix + m.group(3) + ">`"
- print ("processing new link",m.group(1), rstLink)
- replacements.append((m.start(1), m.end(1), m.group(1), rstLink))
-
- #perform replacements in reverse order
- for (start,end,item,rstLink) in reversed(replacements):
- retRstText = retRstText[0:start] + rstLink + retRstText[end:]
-
- #build regex string for links
- regexLink = r"`(.+?)<(\b" + r"\b|\b".join(list) + r"\b)>`__"
- patternLink = re.compile(regexLink)
- replacements = []
- for m in re.finditer(patternLink, retRstText):
- rstLink = ":ref:`" + m.group(1) + " <" + prefix + m.group(2) + ">`"
- print ("processing existing link",m.group(0), rstLink)
- replacements.append((m.start(), m.end(), m.group(0), rstLink))
-
- #perform replacements in reverse order
- for (start,end,item,rstLink) in reversed(replacements):
- retRstText = retRstText[0:start] + rstLink + retRstText[end:]
-
- return retRstText
-
-def fixUnderscoresInRefLinks(rstText):
- retRstText = rstText
- retRstText = re.sub(r"\b\\\_","_",retRstText)
-
- return retRstText
-
-################################################################################################################
-
-parser = argparse.ArgumentParser(description='Converts mediawiki pages to rst pages for sphinx.')
-parser.add_argument('inputURL', help='the url of a mediawiki page')
-parser.add_argument('-o', '--o',
- help='Provide a path to output to a file')
-parser.add_argument('-i', '--i',
- help='Provide a relative path from the file to the images directory')
-parser.add_argument('-rp', '--rp',
- help='Provide a reference link prefix')
-parser.add_argument('-r', '--r',
- help='Provide a reference link')
-
-args = parser.parse_args()
-print args.inputURL
-print args.o
-
-urlSegments = urlparse.urlparse(args.inputURL)
-pageName = urlSegments.path[1:]
-print "Parsing ", pageName
-
-#run pandoc and get the output in rst
-mediawikiText = readWebPage(convertURLToRaw(args.inputURL))
-
-#run pandoc and get the output in rst
-rstText = covertMediaWikiToRST(convertURLToRaw(args.inputURL))
-
-#print "*****************"
-#print rstText
-#print "*****************"
-
-relPath = "../images"
-if args.i is not None:
- relPath = os.path.dirname(args.i)
-outDir = os.curdir
-if args.o is not None:
- outDir = os.path.dirname(args.o)
-
-imagePath = os.path.join(outDir,relPath)
-imagePath = os.path.abspath(imagePath)
-print imagePath, outDir
-
-ensureDirectoriesExist(imagePath)
-ensureDirectoriesExist(outDir)
-
-#perform any processing beyond pandoc
-rstText = fixUnderscoresInRefLinks(rstText)
-
-rstText = processImageLinks(mediawikiText,rstText, imagePath, relPath)
-
-wsList = ['EventWorkspace','MatrixWorkspace','PeaksWorkspace','MDWorkspace','Table Workspaces','WorkspaceGroup',
- 'RectangularDetector','RAW File','Facilities File','FitConstraint','Framework Manager',
- 'Instrument Data Service','InstrumentDefinitionFile','InstrumentParameterFile','Properties File',
- 'MDHistoWorkspace','MDNorm','Nexus file','PeaksWorkspace','Point and space groups','RAW File'
- 'Shared Pointer','Symmetry groups','Unit Factory','UserAlgorithms','Workflow Algorithm',
- 'Workspace','Workspace2D','WorkspaceGroup']
-rstText = addLocalLinks(rstText,wsList,"")
-
-algList = mantid.AlgorithmFactory.getRegisteredAlgorithms(False).keys()
-rstText = addLocalLinks(rstText,algList,"algm-")
-
-funcList = mantid.FunctionFactory.getFunctionNames()
-rstText = addLocalLinks(rstText,funcList,"func-")
-
-#add reference name
-refPrefix = "train-"
-if args.rp is not None:
- refPrefix = args.rp
-refName = pageName
-if args.r is not None:
- refName = args.r
-rstText = ".. _" + refPrefix + refName + ":\n\n" + rstText
-
-#save output
-if args.o is not None:
- sys.stdout = open(args.o, 'w')
-print rstText
-
diff --git a/tools/scripts/CorrectConceptLinksinAlgPages.py b/tools/scripts/CorrectConceptLinksinAlgPages.py
index 700472f0529451dd752ec48008bf364e34f51806..7dcd787a465a2a84151c64ec152e6b0f2ba720c7 100644
--- a/tools/scripts/CorrectConceptLinksinAlgPages.py
+++ b/tools/scripts/CorrectConceptLinksinAlgPages.py
@@ -1,51 +1,52 @@
+#pylint: disable=invalid-name
import os, re
import urllib2
concepts = ['Algorithm',
-'Analysis_Data_Service',
-'categories',
-'Create_an_IDF',
-'Data_Service',
-'Dynamic_Factory',
-'Error_Propagation',
-'EventWorkspace',
-'Facilities_File',
-'FitConstraint',
-'Framework_Manager',
-'Geometry',
-'Geometry_of_Position',
-'Geometry_of_Shape',
-'HowToDefineGeometricShape',
-'index',
-'Instrument',
-'InstrumentDefinitionFile',
-'InstrumentParameterFile',
-'Instrument_Data_Service',
-'Lattice',
-'LET_Sample_IDF',
-'MatrixWorkspace',
-'MDHistoWorkspace',
-'MDWorkspace',
-'Nexus_file',
-'Plugin',
-'Project',
-'Properties',
-'Properties_File',
-'RAW_File',
-'Run',
-'SANS2D_Sample_IDF',
-'Shared_Pointer',
-'Table_Workspaces',
-'Unit_Factory',
-'UserAlgorithms',
-'Workflow_Algorithm',
-'Workspace',
-'Workspace2D',
-'WorkspaceGroup']
+ 'Analysis_Data_Service',
+ 'categories',
+ 'Create_an_IDF',
+ 'Data_Service',
+ 'Dynamic_Factory',
+ 'Error_Propagation',
+ 'EventWorkspace',
+ 'Facilities_File',
+ 'FitConstraint',
+ 'Framework_Manager',
+ 'Geometry',
+ 'Geometry_of_Position',
+ 'Geometry_of_Shape',
+ 'HowToDefineGeometricShape',
+ 'index',
+ 'Instrument',
+ 'InstrumentDefinitionFile',
+ 'InstrumentParameterFile',
+ 'Instrument_Data_Service',
+ 'Lattice',
+ 'LET_Sample_IDF',
+ 'MatrixWorkspace',
+ 'MDHistoWorkspace',
+ 'MDWorkspace',
+ 'Nexus_file',
+ 'Plugin',
+ 'Project',
+ 'Properties',
+ 'Properties_File',
+ 'RAW_File',
+ 'Run',
+ 'SANS2D_Sample_IDF',
+ 'Shared_Pointer',
+ 'Table_Workspaces',
+ 'Unit_Factory',
+ 'UserAlgorithms',
+ 'Workflow_Algorithm',
+ 'Workspace',
+ 'Workspace2D',
+ 'WorkspaceGroup']
def outputError(alg, algVersion, description, notes=""):
- print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
+ print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
rstdir = r"C:\Mantid\Code\Mantid\docs\source\algorithms"
conceptsPattern = {}
@@ -61,17 +62,17 @@ for alg in algs:
fileFound = False
filename = os.path.join(rstdir,alg + "-v" + str(algVersion) + ".rst")
if os.path.exists(filename):
- algText = ""
- with open (filename, "r") as algRst:
- fileFound = True
- algText = algRst.read()
- for concept in concepts:
- regex = conceptsPattern[concept]
- while (regex.search(algText) != None):
- outputError(alg, algVersion, "found", concept)
- algText = regex.sub(r":ref:`\1 <\2>`",algText)
+ algText = ""
+ with open (filename, "r") as algRst:
+ fileFound = True
+ algText = algRst.read()
+ for concept in concepts:
+ regex = conceptsPattern[concept]
+ while regex.search(algText) != None:
+ outputError(alg, algVersion, "found", concept)
+ algText = regex.sub(r":ref:`\1 <\2>`",algText)
with open (filename, "w") as algRst:
- algRst.write(algText)
+ algRst.write(algText)
if fileFound==False:
outputError(alg, algVersion, "File not found")
diff --git a/tools/scripts/FindIncompleteAlgRSTPages.py b/tools/scripts/FindIncompleteAlgRSTPages.py
index 27cd76c148f5d5c5450578f75e745419e65fe5b5..f4d05d10629102eab5eb160a5ed24eb1b0ff7749 100644
--- a/tools/scripts/FindIncompleteAlgRSTPages.py
+++ b/tools/scripts/FindIncompleteAlgRSTPages.py
@@ -1,26 +1,27 @@
+#pylint: disable=invalid-name
import os, re
import urllib2
def readWebPage(url):
- proxy = urllib2.ProxyHandler({'http': 'wwwcache.rl.ac.uk:8080'})
- opener = urllib2.build_opener(proxy)
- urllib2.install_opener(opener)
- aResp =urllib2.urlopen(url)
- web_pg = aResp.read();
- return web_pg
+ proxy = urllib2.ProxyHandler({'http': 'wwwcache.rl.ac.uk:8080'})
+ opener = urllib2.build_opener(proxy)
+ urllib2.install_opener(opener)
+ aResp =urllib2.urlopen(url)
+ web_pg = aResp.read()
+ return web_pg
def ticketExists(alg, ticketHash):
- retVal = ""
- algPattern = re.compile(alg, re.IGNORECASE)
- for ticket in ticketHash:
- ticketText = ticketHash[ticket]
- if algPattern.search(ticketText):
- retVal = str(ticket)
- break
- return retVal
+ retVal = ""
+ algPattern = re.compile(alg, re.IGNORECASE)
+ for ticket in ticketHash:
+ ticketText = ticketHash[ticket]
+ if algPattern.search(ticketText):
+ retVal = str(ticket)
+ break
+ return retVal
def outputError(alg, algVersion, description, notes=""):
- print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
+ print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
rstdir = r"C:\Mantid\Code\Mantid\docs\source\algorithms"
ticketList = [9582,9586,9607,9610,9704,9804,9726]
@@ -39,13 +40,12 @@ for alg in algs:
fileFound = False
filename = os.path.join(rstdir,alg + "-v" + str(algVersion) + ".rst")
if os.path.exists(filename):
- with open (filename, "r") as algRst:
- fileFound = True
- algText = algRst.read()
- if (usagePattern.search(algText) == None) and (excusesPattern.search(algText) == None):
- #check if already in a ticket
- usageTicket = ticketExists(alg,ticketHash)
- outputError(alg, algVersion, "No usage section", usageTicket)
+ with open (filename, "r") as algRst:
+ fileFound = True
+ algText = algRst.read()
+ if (usagePattern.search(algText) == None) and (excusesPattern.search(algText) == None):
+ #check if already in a ticket
+ usageTicket = ticketExists(alg,ticketHash)
+ outputError(alg, algVersion, "No usage section", usageTicket)
if fileFound==False:
- outputError(alg, algVersion, "File not found")
-
+ outputError(alg, algVersion, "File not found")
diff --git a/tools/scripts/TestWikiPython.py b/tools/scripts/TestWikiPython.py
index ff44eabe84669c17f9de58bd14b2ee19f5153da7..63d0e4b367106c17a36bebcbf2cdb8caec1f337b 100644
--- a/tools/scripts/TestWikiPython.py
+++ b/tools/scripts/TestWikiPython.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
###########################################################################################
# Extracts code blocks marked as python from mediawiki pages and checks they run
# run with -h for command line arguments
@@ -7,7 +8,6 @@ import os
import re
import sys
import urllib2
-import urlparse
import argparse
import json
@@ -31,6 +31,7 @@ def getTestablePages(url):
def convertURLToRaw(url):
return url.replace(" ","%20") + "?action=raw"
+
def writeTestRst(filepath,mediawikiText,pageName):
'''
for a block of wiki text, writes out all tests found to an rst page
@@ -133,7 +134,7 @@ parser.add_argument('-o', '--o',
help='Provide a path to output to an output directory')
args = parser.parse_args()
-urlList = [];
+urlList = []
baseUrl = "http://www.mantidproject.org/"
if args.s is not None:
baseUrl = args.s
@@ -164,6 +165,3 @@ for url in urlList:
#run pandoc and get the output in rst
mediawikiText = readWebPage(convertURLToRaw(baseUrl + url))
writeTestRst(outputFile,mediawikiText,pageName)
-
-
-
diff --git a/tools/scripts/extractAlgorithmNames.py b/tools/scripts/extractAlgorithmNames.py
index 05120ece167861601920362aa08ca0105a6bda7e..8945b898c9e698c5c3d261c1d0ba9d35ad42635e 100644
--- a/tools/scripts/extractAlgorithmNames.py
+++ b/tools/scripts/extractAlgorithmNames.py
@@ -1,17 +1,14 @@
+#pylint: disable=invalid-name
# simply just print out all algorithm names in a directory which can be piped
# to a file
-import string, os, re
-
import glob
-import mmap
-
os.chdir("PythonInterface/plugins/algorithms/WorkflowAlgorithms")
-for file in glob.glob("*.py"):
+for filename in glob.glob("*.py"):
#print file
- if 'PythonAlgorithm' in open(file).read():
- print file
+ if 'PythonAlgorithm' in open(filename).read():
+ print filename
#os.chdir("LiveData/src")
@@ -19,4 +16,3 @@ for file in glob.glob("*.py"):
# #print file
# if 'DECLARE_ALGORITHM' in open(file).read():
# print file
-
diff --git a/tools/scripts/extractAuthorNamesFromGit.py b/tools/scripts/extractAuthorNamesFromGit.py
index ee6bf1e2eceb5ff853dc9c5baa93a86814ee91d0..728ac36dadd8f2cc94f81df3cf512a7f4f4b93bb 100644
--- a/tools/scripts/extractAuthorNamesFromGit.py
+++ b/tools/scripts/extractAuthorNamesFromGit.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
# This python script is run after running extractAlgorithmNames.py, where
# the output of that script is saved to a *.txt
#
@@ -18,7 +19,7 @@ allAlgs = [line.strip() for line in open(algorithmList)]
os.chdir('PythonInterface/plugins/algorithms/WorkflowAlgorithms')
for line in allAlgs:
#print line
- fullline = line
+ fullline = line
args = [
'git', 'log',
'--pretty=short',
@@ -30,11 +31,11 @@ for line in allAlgs:
authors = subprocess.check_output(args).replace('"', '').split('\n')
authors = set(authors)
authors = authors - set([''])
-
+
for author in authors:
#print author
fullline = fullline + ", " + author
-
+
print fullline
#line = 'GroupWorkspaces.cpp'
@@ -54,5 +55,5 @@ for line in allAlgs:
#for author in authors:
#print author
# fullline = fullline + ", " + author
-
+
#print fullline
diff --git a/tools/skipped_systemtests.py b/tools/skipped_systemtests.py
index c13d3e140d18102f3e4e847377f2ebcaacca1c8b..3ffdb9fb5837d1c055e93e8f019d11e31384d56e 100755
--- a/tools/skipped_systemtests.py
+++ b/tools/skipped_systemtests.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#!/usr/bin/env python
import ast
@@ -33,7 +34,7 @@ def addTestResult(results, case, label):
def printResultCell(mark, length):
- if (mark):
+ if mark:
left = int(length/2)
right = length-left-1
print "%sx%s" % (' '*left, ' '*right),