diff --git a/Framework/API/inc/MantidAPI/AlgorithmHistory.h b/Framework/API/inc/MantidAPI/AlgorithmHistory.h
index 7b9208a96c82cabad1c6fcd702a4b77a567ed5c9..583d66e18f70765e89a2d84285eefc4686ee61e5 100644
--- a/Framework/API/inc/MantidAPI/AlgorithmHistory.h
+++ b/Framework/API/inc/MantidAPI/AlgorithmHistory.h
@@ -27,7 +27,7 @@ namespace Detail {
// needing to know the implementation of CompareHistory.
template <class T> struct CompareHistory {
bool operator()(const boost::shared_ptr<T> &lhs,
- const boost::shared_ptr<T> &rhs) {
+ const boost::shared_ptr<T> &rhs) const {
return (*lhs) < (*rhs);
}
};
diff --git a/Framework/API/src/Algorithm.cpp b/Framework/API/src/Algorithm.cpp
index 795addd969ac721041278f3aabd435256340af8d..22239ea2e19b5fbc61d4647d2ff60a2e76503683 100644
--- a/Framework/API/src/Algorithm.cpp
+++ b/Framework/API/src/Algorithm.cpp
@@ -1711,7 +1711,7 @@ void Algorithm::execMasterOnly() {
* non-master ranks in master-only execution. */
void Algorithm::execNonMaster() {
// If there is no output we can simply do nothing.
- if (m_pureOutputWorkspaceProps.size() == 0)
+ if (m_pureOutputWorkspaceProps.empty())
return;
// Does Algorithm have exactly one input and one output workspace property?
if (m_inputWorkspaceProps.size() == 1 &&
diff --git a/Framework/API/src/DetectorSearcher.cpp b/Framework/API/src/DetectorSearcher.cpp
index 76d8f93ebde94c6401f725623b7312ce259264d0..6170612c8930c7bb2f62217ece071b2444bc7cfe 100644
--- a/Framework/API/src/DetectorSearcher.cpp
+++ b/Framework/API/src/DetectorSearcher.cpp
@@ -148,7 +148,7 @@ DetectorSearcher::searchUsingNearestNeighbours(const V3D &q) {
// find where this Q vector should intersect with "extended" space
const auto neighbours =
m_detectorCacheSearch->findNearest(Eigen::Vector3d(q[0], q[1], q[2]), 5);
- if (neighbours.size() == 0)
+ if (neighbours.empty())
return std::make_tuple(false, 0);
const auto result = checkInteceptWithNeighbours(detectorDir, neighbours);
diff --git a/Framework/API/src/IndexTypeProperty.cpp b/Framework/API/src/IndexTypeProperty.cpp
index df454100350d4ab71ce1c45378f118277c757c7d..7a45c4741b78f912e8a8650e3c810070a876abcb 100644
--- a/Framework/API/src/IndexTypeProperty.cpp
+++ b/Framework/API/src/IndexTypeProperty.cpp
@@ -10,7 +10,7 @@ IndexTypeProperty::IndexTypeProperty(const std::string &name,
if (indexType & IndexType::SpectrumNum)
m_allowedValues.push_back("SpectrumNumber");
- if (m_allowedValues.size() == 0)
+ if (m_allowedValues.empty())
throw std::invalid_argument("Argument indexType incorrectly specified");
m_value = m_allowedValues[0];
diff --git a/Framework/API/src/MatrixWorkspace.cpp b/Framework/API/src/MatrixWorkspace.cpp
index 2a1794eb532b86a58fcf5e927b5977f18d57a124..c07904a0494dddf5f2d9e7a94e421caa57f69130 100644
--- a/Framework/API/src/MatrixWorkspace.cpp
+++ b/Framework/API/src/MatrixWorkspace.cpp
@@ -239,7 +239,7 @@ void MatrixWorkspace::initialize(const std::size_t &NVectors,
void MatrixWorkspace::initialize(const std::size_t &NVectors,
const HistogramData::Histogram &histogram) {
// Check validity of arguments
- if (NVectors == 0 || histogram.x().size() == 0) {
+ if (NVectors == 0 || histogram.x().empty()) {
throw std::out_of_range(
"All arguments to init must be positive and non-zero");
}
diff --git a/Framework/Algorithms/CMakeLists.txt b/Framework/Algorithms/CMakeLists.txt
index 94f820fdb7f92358824b5aa92021890ed7421ad9..7ad62267419af2c916cb3a77dcb4d2f88f0cdb80 100644
--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -160,6 +160,7 @@ set ( SRC_FILES
src/IQTransform.cpp
src/IdentifyNoisyDetectors.cpp
src/IntegrateByComponent.cpp
+ src/IntegrateEPP.cpp
src/Integration.cpp
src/InterpolatingRebin.cpp
src/InterpolationOption.cpp
@@ -482,6 +483,7 @@ set ( INC_FILES
inc/MantidAlgorithms/IQTransform.h
inc/MantidAlgorithms/IdentifyNoisyDetectors.h
inc/MantidAlgorithms/IntegrateByComponent.h
+ inc/MantidAlgorithms/IntegrateEPP.h
inc/MantidAlgorithms/Integration.h
inc/MantidAlgorithms/InterpolatingRebin.h
inc/MantidAlgorithms/InterpolationOption.h
@@ -813,6 +815,7 @@ set ( TEST_FILES
IQTransformTest.h
IdentifyNoisyDetectorsTest.h
IntegrateByComponentTest.h
+ IntegrateEPPTest.h
IntegrationTest.h
InterpolatingRebinTest.h
InterpolationOptionTest.h
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCorUser.h b/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCorUser.h
index fc3ea9e400e086797f13c1ebf2a9b2d6e5a0eff9..d37642568e5bcd836788de722336507fc0aa11a9 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCorUser.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCorUser.h
@@ -4,10 +4,17 @@
#include "MantidAPI/Algorithm.h"
#include "MantidKernel/cow_ptr.h"
+// Forward declarations
+namespace mu {
+class Parser;
+} // namespace mu
+
namespace Mantid {
namespace HistogramData {
class Histogram;
+class HistogramE;
+class HistogramY;
class Points;
}
@@ -61,15 +68,14 @@ private:
void init() override;
void exec() override;
void retrieveProperties();
- double calculateFormulaValue(const std::string &formula, double energy);
- MantidVec calculateEfficiency(double eff0, const std::string &formula,
- const HistogramData::Points &xIn);
+ void correctHistogram(const size_t index, const double eff0, double &e,
+ mu::Parser &parser);
+
+ double evaluate(const mu::Parser &parser) const;
- std::string getValFromInstrumentDef(const std::string ¶meterName);
+ mu::Parser generateParser(const std::string &formula, double *e) const;
- HistogramData::Histogram
- applyDetEfficiency(const size_t nChans, const Mantid::MantidVec &effVec,
- const HistogramData::Histogram &histogram);
+ std::string retrieveFormula(const size_t workspaceIndex);
/// The user selected (input) workspace
API::MatrixWorkspace_const_sptr m_inputWS;
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/IntegrateEPP.h b/Framework/Algorithms/inc/MantidAlgorithms/IntegrateEPP.h
new file mode 100644
index 0000000000000000000000000000000000000000..074fa8b52edc3a0455b3a0a8c319dd1fb5fa0d90
--- /dev/null
+++ b/Framework/Algorithms/inc/MantidAlgorithms/IntegrateEPP.h
@@ -0,0 +1,50 @@
+#ifndef MANTID_ALGORITHMS_INTEGRATEEPP_H_
+#define MANTID_ALGORITHMS_INTEGRATEEPP_H_
+
+#include "MantidAlgorithms/DllConfig.h"
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid {
+namespace Algorithms {
+
+/** IntegrateEPP : Integrate a workspace around the elastic peak positions
+ given by a EPP table.
+
+ Copyright © 2017 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_ALGORITHMS_DLL IntegrateEPP : public API::Algorithm {
+public:
+ const std::string name() const override;
+ int version() const override;
+ const std::string category() const override;
+ const std::string summary() const override;
+
+private:
+ void init() override;
+ void exec() override;
+ std::map<std::string, std::string> validateInputs() override;
+};
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif /* MANTID_ALGORITHMS_INTEGRATEEPP_H_ */
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MergeRuns.h b/Framework/Algorithms/inc/MantidAlgorithms/MergeRuns.h
index a90558b4e6bce4972b34c19695d643c44c4f4008..e09a84f57bef8f436e77365ab422fdbe3a36ad66 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MergeRuns.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MergeRuns.h
@@ -141,6 +141,9 @@ private:
API::MatrixWorkspace_sptr
rebinInput(const API::MatrixWorkspace_sptr &workspace,
const std::vector<double> ¶ms);
+ API::MatrixWorkspace_sptr
+ buildScanningOutputWorkspace(const API::MatrixWorkspace_sptr &outWS,
+ const API::MatrixWorkspace_sptr &addee);
/// Progress reporting
std::unique_ptr<API::Progress> m_progress;
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryReductionOne2.h b/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryReductionOne2.h
index 7c9aa809d1604520a24a14c59e89ae1c4966700e..49a8f680da0f60ef7bbbee69bdc303e11b73c018 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryReductionOne2.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryReductionOne2.h
@@ -8,6 +8,9 @@ namespace Mantid {
namespace API {
class SpectrumInfo;
}
+namespace Geometry {
+class ReferenceFrame;
+}
namespace HistogramData {
class HistogramX;
class HistogramY;
@@ -88,6 +91,8 @@ private:
// convert to momentum transfer
Mantid::API::MatrixWorkspace_sptr
convertToQ(Mantid::API::MatrixWorkspace_sptr inputWS);
+ // Get the twoTheta width of a given detector
+ double getDetectorTwoThetaRange(const size_t spectrumIdx);
// Utility function to create name for diagnostic workspaces
std::string createDebugWorkspaceName(const std::string &inputName);
// Utility function to output a diagnostic workspace to the ADS
@@ -152,6 +157,7 @@ private:
API::MatrixWorkspace_sptr m_runWS;
const API::SpectrumInfo *m_spectrumInfo;
+ boost::shared_ptr<const Mantid::Geometry::ReferenceFrame> m_refFrame;
bool m_convertUnits; // convert the input workspace to lambda
bool m_normaliseMonitors; // normalise by monitors and direct beam
bool m_normaliseTransmission; // transmission or algorithmic correction
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/RunCombinationHelpers/RunCombinationHelper.h b/Framework/Algorithms/inc/MantidAlgorithms/RunCombinationHelpers/RunCombinationHelper.h
index 8f961e0ae2a2328e1b326811aec20093d0b8f580..ba4006dc86d0f6c07cde40ebe7d40347ec39a557 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/RunCombinationHelpers/RunCombinationHelper.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/RunCombinationHelpers/RunCombinationHelper.h
@@ -52,11 +52,13 @@ public:
private:
size_t m_numberSpectra;
+ size_t m_numberDetectors;
std::string m_xUnit;
std::string m_yUnit;
std::string m_spectrumAxisUnit;
std::string m_instrumentName;
bool m_isHistogramData;
+ bool m_isScanning;
};
} // namespace Algorithms
diff --git a/Framework/Algorithms/src/AddSampleLog.cpp b/Framework/Algorithms/src/AddSampleLog.cpp
index 5b7be49cd1ec18313fc9cb234d05186019b4b4dd..7abbf956b7f33aed2183fa248bec3a15b7963bee 100644
--- a/Framework/Algorithms/src/AddSampleLog.cpp
+++ b/Framework/Algorithms/src/AddSampleLog.cpp
@@ -228,7 +228,7 @@ void AddSampleLog::addTimeSeriesProperty(Run &run_obj,
is_int_series = true;
} else if (prop_number_type == autoTypeOption) {
// auto type. by default
- if (prop_value.size() == 0)
+ if (prop_value.empty())
g_log.warning("For sample log in TimeSeriesProperty and values are given "
"by MarixWorkspace, the default data type "
"is double.");
@@ -248,8 +248,8 @@ void AddSampleLog::addTimeSeriesProperty(Run &run_obj,
// check using workspace or some specified start value
std::string tsp_ws_name = getPropertyValue("TimeSeriesWorkspace");
- bool use_ws = tsp_ws_name.size() > 0;
- bool use_single_value = prop_value.size() > 0;
+ bool use_ws = !tsp_ws_name.empty();
+ bool use_single_value = !prop_value.empty();
if (use_ws && use_single_value) {
throw std::runtime_error("Both TimeSeries workspace and sing value are "
"specified. It is not allowed.");
diff --git a/Framework/Algorithms/src/ChangeTimeZero.cpp b/Framework/Algorithms/src/ChangeTimeZero.cpp
index 631e7068f154165958d57d7d2dd56897c1dabdad..5494590af12673237310f09444f63aac815b0dfc 100644
--- a/Framework/Algorithms/src/ChangeTimeZero.cpp
+++ b/Framework/Algorithms/src/ChangeTimeZero.cpp
@@ -331,7 +331,7 @@ bool ChangeTimeZero::checkForDateTime(const std::string &val) const {
// Hedge for bad lexical casts in the DateTimeValidator
try {
DateTimeValidator validator = DateTimeValidator();
- isDateTime = validator.isValid(val) == "";
+ isDateTime = validator.isValid(val).empty();
} catch (...) {
isDateTime = false;
}
diff --git a/Framework/Algorithms/src/ConvertAxisByFormula.cpp b/Framework/Algorithms/src/ConvertAxisByFormula.cpp
index ada62fb7d4e67eb951a6db5656442b4f7a2f0481..de1ab2350a84783216df15414e77d9a00103c55e 100644
--- a/Framework/Algorithms/src/ConvertAxisByFormula.cpp
+++ b/Framework/Algorithms/src/ConvertAxisByFormula.cpp
@@ -105,7 +105,7 @@ void ConvertAxisByFormula::exec() {
RefAxis *refAxisPtr = dynamic_cast<RefAxis *>(axisPtr);
if (refAxisPtr != nullptr) {
CommonBinsValidator sameBins;
- if (sameBins.isValid(outputWs) != "") {
+ if (!sameBins.isValid(outputWs).empty()) {
isRaggedBins = true;
}
isRefAxis = true;
@@ -245,14 +245,14 @@ void ConvertAxisByFormula::exec() {
}
// Set the Unit of the Axis
- if ((axisUnits != "") || (axisTitle != "")) {
+ if ((!axisUnits.empty()) || (!axisTitle.empty())) {
try {
axisPtr->unit() = UnitFactory::Instance().create(axisUnits);
} catch (Exception::NotFoundError &) {
- if (axisTitle == "") {
+ if (axisTitle.empty()) {
axisTitle = axisPtr->unit()->caption();
}
- if (axisUnits == "") {
+ if (axisUnits.empty()) {
axisUnits = axisPtr->unit()->label();
}
axisPtr->unit() = boost::make_shared<Units::Label>(axisTitle, axisUnits);
diff --git a/Framework/Algorithms/src/ConvertUnits.cpp b/Framework/Algorithms/src/ConvertUnits.cpp
index 33fa5a87287359031c52e4df80af0856e4246cf9..7f58d71c62d25f033a5ca0ac5004ac5dbd73a63a 100644
--- a/Framework/Algorithms/src/ConvertUnits.cpp
+++ b/Framework/Algorithms/src/ConvertUnits.cpp
@@ -337,7 +337,7 @@ ConvertUnits::convertQuickly(API::MatrixWorkspace_const_sptr inputWS,
// First a quick check using the validator
CommonBinsValidator sameBins;
bool commonBoundaries = false;
- if (sameBins.isValid(inputWS) == "") {
+ if (sameBins.isValid(inputWS).empty()) {
commonBoundaries = WorkspaceHelpers::commonBoundaries(*inputWS);
// Only do the full check if the quick one passes
if (commonBoundaries) {
diff --git a/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp b/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp
index 54475523b3552d23620654bb8315d6bf017366ff..a510174ea8cb0ea4e187237c321c308c37f2aa53 100644
--- a/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp
+++ b/Framework/Algorithms/src/DetectorEfficiencyCorUser.cpp
@@ -2,8 +2,9 @@
#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/Run.h"
-#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidDataObjects/WorkspaceCreation.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/muParser_Silent.h"
#include "MantidKernel/BoundedValidator.h"
@@ -11,6 +12,8 @@
#include "MantidKernel/Strings.h"
using Mantid::HistogramData::Histogram;
+using Mantid::HistogramData::HistogramE;
+using Mantid::HistogramData::HistogramY;
using Mantid::HistogramData::Points;
namespace Mantid {
@@ -62,12 +65,6 @@ void DetectorEfficiencyCorUser::exec() {
// get input properties (WSs, Ei)
retrieveProperties();
- // get Efficiency formula from the IDF
- const std::string effFormula = getValFromInstrumentDef("formula_eff");
-
- // Calculate Efficiency for E = Ei
- const double eff0 = calculateFormulaValue(effFormula, m_Ei);
-
const size_t numberOfChannels = this->m_inputWS->blocksize();
// Calculate the number of spectra in this workspace
const int numberOfSpectra =
@@ -80,12 +77,13 @@ void DetectorEfficiencyCorUser::exec() {
PARALLEL_FOR_IF(Kernel::threadSafe(*m_outputWS, *m_inputWS))
for (int64_t i = 0; i < numberOfSpectra_i; ++i) {
PARALLEL_START_INTERUPT_REGION
-
- const auto effVec =
- calculateEfficiency(eff0, effFormula, m_inputWS->points(i));
- // run this outside to benefit from parallel for (?)
- m_outputWS->setHistogram(i, applyDetEfficiency(numberOfChannels, effVec,
- m_inputWS->histogram(i)));
+ const auto effFormula = retrieveFormula(i);
+ // Calculate Efficiency for E = Ei
+ double e;
+ auto parser = generateParser(effFormula, &e);
+ e = m_Ei;
+ const double eff0 = evaluate(parser);
+ correctHistogram(i, eff0, e, parser);
prog.report("Detector Efficiency correction...");
@@ -97,44 +95,39 @@ void DetectorEfficiencyCorUser::exec() {
}
/**
- * Apply the detector efficiency to a single spectrum
- * @param nChans Number of channels in a spectra (nbins - 1)
- * @param effVec efficiency values (to be divided by the counts)
- * @param histogram uncorrected histogram
-
- * @returns corrected histogram
+ * Apply efficiency corrections to a histogram in the output workspace.
+ * Efficiency = f(Ei-DeltaE) / f(Ei)
+ * @param eff0 :: calculated f(Ei)
+ * @param e :: reference to the parser's energy parameter
+ * @param parser :: muParser used to evalute f(e)
+ * @param index :: the workspace index of the histogram to correct
*/
-Histogram DetectorEfficiencyCorUser::applyDetEfficiency(
- const size_t nChans, const MantidVec &effVec, const Histogram &histogram) {
- Histogram outHist(histogram);
-
- auto &outY = outHist.mutableY();
- auto &outE = outHist.mutableE();
-
- for (unsigned int j = 0; j < nChans; ++j) {
- outY[j] /= effVec[j];
- outE[j] /= effVec[j];
+void DetectorEfficiencyCorUser::correctHistogram(const size_t index,
+ const double eff0, double &e,
+ mu::Parser &parser) {
+ const auto &xIn = m_inputWS->points(index);
+ const auto &yIn = m_inputWS->y(index);
+ const auto &eIn = m_inputWS->e(index);
+ auto &yOut = m_outputWS->mutableY(index);
+ auto &eOut = m_outputWS->mutableE(index);
+ for (size_t i = 0; i < xIn.size(); ++i) {
+ e = m_Ei - xIn[i];
+ const double eff = evaluate(parser);
+ const double corr = eff / eff0;
+ yOut[i] = yIn[i] / corr;
+ eOut[i] = eIn[i] / corr;
}
-
- return outHist;
}
+
/**
- * Calculate the value of a formula
- * @param formula :: Formula
- * @param energy :: value to use in the formula
- * @return value calculated
+ * Calculate the value of a formula parsed by muParser
+ * @param parser :: muParser object
+ * @return calculated value
+ * @throw InstrumentDefinitionError if parser throws during evaluation
*/
-double
-DetectorEfficiencyCorUser::calculateFormulaValue(const std::string &formula,
- double energy) {
+double DetectorEfficiencyCorUser::evaluate(const mu::Parser &parser) const {
try {
- mu::Parser p;
- p.DefineVar("e", &energy);
- p.SetExpr(formula);
- double eff = p.Eval();
- g_log.debug() << "Formula: " << formula << " with: " << energy
- << "evaluated to: " << eff << '\n';
- return eff;
+ return parser.Eval();
} catch (mu::Parser::exception_type &e) {
throw Kernel::Exception::InstrumentDefinitionError(
"Error calculating formula from string. Muparser error message is: " +
@@ -142,58 +135,34 @@ DetectorEfficiencyCorUser::calculateFormulaValue(const std::string &formula,
}
}
-/**
- * Calculate detector efficiency given a formula, the efficiency at the elastic
- * line, and a vector with energies.
- * Efficiency = f(Ei-DeltaE) / f(Ei)
- * @param eff0 :: calculated eff0
- * @param formula :: formula to calculate efficiency (parsed from IDF)
- * @param xIn :: Energy bins vector (X axis)
- * @return a vector with the efficiencies
- */
-MantidVec DetectorEfficiencyCorUser::calculateEfficiency(
- double eff0, const std::string &formula, const Points &xIn) {
- MantidVec effOut(xIn.size());
-
- try {
- double e;
- mu::Parser p;
- p.DefineVar("e", &e);
- p.SetExpr(formula);
-
- for (size_t i = 0; i < effOut.size(); ++i) {
- e = m_Ei - xIn[i];
- double eff = p.Eval();
- effOut[i] = eff / eff0;
- }
- return effOut;
- } catch (mu::Parser::exception_type &e) {
- throw Kernel::Exception::InstrumentDefinitionError(
- "Error calculating formula from string. Muparser error message is: " +
- e.GetMsg());
- }
+mu::Parser DetectorEfficiencyCorUser::generateParser(const std::string &formula,
+ double *e) const {
+ mu::Parser p;
+ p.DefineVar("e", e);
+ p.SetExpr(formula);
+ return p;
}
/**
- * Returns the value associated to a parameter name in the IDF
- * @param parameterName :: parameter name in the IDF
- * @return the value associated to the parameter name
+ * Returns the efficiency correction formula associated to a detector
+ * @param workspaceIndex detector's workspace index
+ * @return the efficiency correction formula
*/
-std::string DetectorEfficiencyCorUser::getValFromInstrumentDef(
- const std::string ¶meterName) {
- const ParameterMap &pmap = m_inputWS->constInstrumentParameters();
- Instrument_const_sptr instrument = m_inputWS->getInstrument();
- Parameter_sptr par =
- pmap.getRecursive(instrument->getChild(0).get(), parameterName);
- if (par) {
- std::string ret = par->asString();
- g_log.debug() << "Parsed parameter " << parameterName << ": " << ret
- << "\n";
- return ret;
- } else {
+std::string
+DetectorEfficiencyCorUser::retrieveFormula(const size_t workspaceIndex) {
+ const std::string formulaParamName("formula_eff");
+ const auto ¶mMap = m_inputWS->constInstrumentParameters();
+ auto det = m_inputWS->getDetector(workspaceIndex);
+ auto param = paramMap.getRecursive(det.get(), formulaParamName, "string");
+ if (!param) {
throw Kernel::Exception::InstrumentDefinitionError(
- "There is no <" + parameterName + "> in the instrument definition!");
+ "No <" + formulaParamName + "> parameter found for component '" +
+ det->getFullName() + "' in the instrument definition.");
}
+ const auto ret = param->asString();
+ g_log.debug() << "Found formula for workspace index " << workspaceIndex
+ << ": " << ret << "\n";
+ return ret;
}
/** Loads and checks the values passed to the algorithm
@@ -210,7 +179,8 @@ void DetectorEfficiencyCorUser::retrieveProperties() {
// If input and output workspaces are not the same, create a new workspace for
// the output
if (m_outputWS != this->m_inputWS) {
- m_outputWS = API::WorkspaceFactory::Instance().create(m_inputWS);
+ m_outputWS.reset(Mantid::DataObjects::create<DataObjects::Workspace2D>(
+ *m_inputWS).release());
}
// these first three properties are fully checked by validators
diff --git a/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp b/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp
index 5136276a2e8c353b52b37d9a0c0f0579530102c0..24381be1b96d7f0ff0d4f7065ef00ae70228f5ad 100644
--- a/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp
+++ b/Framework/Algorithms/src/DiffractionEventCalibrateDetectors.cpp
@@ -299,7 +299,7 @@ void DiffractionEventCalibrateDetectors::exec() {
std::vector<boost::shared_ptr<RectangularDetector>> detList;
// --------- Loading only one bank ----------------------------------
std::string onebank = getProperty("BankName");
- bool doOneBank = (onebank != "");
+ bool doOneBank = (!onebank.empty());
for (int i = 0; i < inst->nelements(); i++) {
boost::shared_ptr<RectangularDetector> det;
boost::shared_ptr<ICompAssembly> assem;
diff --git a/Framework/Algorithms/src/DiffractionFocussing2.cpp b/Framework/Algorithms/src/DiffractionFocussing2.cpp
index 5465caa11d939c648c23b353671c930ae19ecbca..875954fbee9fa68cd2a12920b9a98e9431644b36 100644
--- a/Framework/Algorithms/src/DiffractionFocussing2.cpp
+++ b/Framework/Algorithms/src/DiffractionFocussing2.cpp
@@ -109,7 +109,7 @@ void DiffractionFocussing2::exec() {
throw std::invalid_argument("Workspace Invalid Spacing/UnitID");
}
// --- Do we need to read the grouping workspace? ----
- if (groupingFileName != "") {
+ if (!groupingFileName.empty()) {
progress(0.01, "Reading grouping file");
IAlgorithm_sptr childAlg = createChildAlgorithm("CreateGroupingWorkspace");
childAlg->setProperty(
diff --git a/Framework/Algorithms/src/ExportTimeSeriesLog.cpp b/Framework/Algorithms/src/ExportTimeSeriesLog.cpp
index bdce22f34a065590d40664d9e3b8f1a82431eeda..35c15bc9fa4cbb290bda06618c27f87ce484d0df 100644
--- a/Framework/Algorithms/src/ExportTimeSeriesLog.cpp
+++ b/Framework/Algorithms/src/ExportTimeSeriesLog.cpp
@@ -429,7 +429,7 @@ void ExportTimeSeriesLog::calculateFirstDerivative(bool is_event_ws) {
// error message
std::string errmsg = errmsg_ss.str();
- if (errmsg.size() > 0)
+ if (!errmsg.empty())
g_log.error(errmsg);
return;
diff --git a/Framework/Algorithms/src/FilterByTime.cpp b/Framework/Algorithms/src/FilterByTime.cpp
index dd08a9f46bd68884002419ff6e3d53e8ce330d44..fe151e505ff1fcfcacbe1372c99766a0c8938212 100644
--- a/Framework/Algorithms/src/FilterByTime.cpp
+++ b/Framework/Algorithms/src/FilterByTime.cpp
@@ -77,12 +77,12 @@ void FilterByTime::exec() {
start_str = getPropertyValue("AbsoluteStartTime");
stop_str = getPropertyValue("AbsoluteStopTime");
- if ((start_str != "") && (stop_str != "") && (start_dbl <= 0.0) &&
+ if ((!start_str.empty()) && (!stop_str.empty()) && (start_dbl <= 0.0) &&
(stop_dbl <= 0.0)) {
// Use the absolute string
start = DateAndTime(start_str);
stop = DateAndTime(stop_str);
- } else if ((start_str == "") && (stop_str == "") &&
+ } else if ((start_str.empty()) && (stop_str.empty()) &&
((start_dbl > 0.0) || (stop_dbl > 0.0))) {
// Use the relative times in seconds.
DateAndTime first = inputWS->getFirstPulseTime();
diff --git a/Framework/Algorithms/src/FilterByTime2.cpp b/Framework/Algorithms/src/FilterByTime2.cpp
index 74ab57080842fac8b8418fb0c8327b9b52d0218f..71d70f362807d68d22e2b6c138781d9a8a9e9824 100644
--- a/Framework/Algorithms/src/FilterByTime2.cpp
+++ b/Framework/Algorithms/src/FilterByTime2.cpp
@@ -73,12 +73,12 @@ void FilterByTime2::exec() {
std::string absstoptime = this->getProperty("AbsoluteStopTime");
std::string start, stop;
- if ((absstarttime != "") && (absstoptime != "") && (starttime <= 0.0) &&
+ if ((!absstarttime.empty()) && (!absstoptime.empty()) && (starttime <= 0.0) &&
(stoptime <= 0.0)) {
// Use the absolute string
start = absstarttime;
stop = absstoptime;
- } else if ((absstarttime != "" || absstoptime != "") &&
+ } else if ((!absstarttime.empty() || !absstoptime.empty()) &&
(starttime > 0.0 || stoptime > 0.0)) {
throw std::invalid_argument(
"It is not allowed to provide both absolute time and relative time.");
diff --git a/Framework/Algorithms/src/FilterEvents.cpp b/Framework/Algorithms/src/FilterEvents.cpp
index 9f6b05f04ff7d53d837271dba8553b3b3afe4b43..c4a4cf3116eb8a013bd7e65b0c7f5051326923dc 100644
--- a/Framework/Algorithms/src/FilterEvents.cpp
+++ b/Framework/Algorithms/src/FilterEvents.cpp
@@ -792,7 +792,7 @@ void FilterEvents::convertSplittersWorkspaceToVectors() {
Kernel::SplittingInterval splitter = m_splitters[i_splitter];
int64_t start_time_i64 = splitter.start().totalNanoseconds();
int64_t stop_time_i64 = splitter.stop().totalNanoseconds();
- if (m_vecSplitterTime.size() == 0) {
+ if (m_vecSplitterTime.empty()) {
// first entry: add
m_vecSplitterTime.push_back(start_time_i64);
m_vecSplitterTime.push_back(stop_time_i64);
@@ -949,7 +949,7 @@ void FilterEvents::processTableSplittersWorkspace() {
int64_t stop_64 =
filter_shift_time + static_cast<int64_t>(stop_time * 1.E9);
- if (m_vecSplitterTime.size() == 0) {
+ if (m_vecSplitterTime.empty()) {
// first splitter: push the start time to vector
m_vecSplitterTime.push_back(start_64);
} else if (start_64 - m_vecSplitterTime.back() > TOLERANCE) {
@@ -973,7 +973,7 @@ void FilterEvents::processTableSplittersWorkspace() {
// convert string-target to integer target
bool addnew = false;
int int_target(-1);
- if (m_targetIndexMap.size() == 0) {
+ if (m_targetIndexMap.empty()) {
addnew = true;
} else {
std::map<std::string, int>::iterator mapiter =
diff --git a/Framework/Algorithms/src/GenerateIPythonNotebook.cpp b/Framework/Algorithms/src/GenerateIPythonNotebook.cpp
index 529b33549073a74d25262e8d5c7f7ee6288da4d6..e5e90cd9a25919dd1ca18464b53e17adb9231662 100644
--- a/Framework/Algorithms/src/GenerateIPythonNotebook.cpp
+++ b/Framework/Algorithms/src/GenerateIPythonNotebook.cpp
@@ -80,8 +80,8 @@ void GenerateIPythonNotebook::exec() {
}
// Need at least a start time to do time filter
- if (startTime != "") {
- if (endTime == "") {
+ if (!startTime.empty()) {
+ if (endTime.empty()) {
// If no end time was given then filter up to now
view->filterBetweenExecDate(DateAndTime(startTime));
} else {
diff --git a/Framework/Algorithms/src/GeneratePythonScript.cpp b/Framework/Algorithms/src/GeneratePythonScript.cpp
index 5ee5894becf7f62babb485492b17bdbe834ab4b9..01ee8704fcf951b7ea6119890d47ff0c0de46658 100644
--- a/Framework/Algorithms/src/GeneratePythonScript.cpp
+++ b/Framework/Algorithms/src/GeneratePythonScript.cpp
@@ -79,8 +79,8 @@ void GeneratePythonScript::exec() {
}
// Need at least a start time to do time filter
- if (startTime != "") {
- if (endTime == "") {
+ if (!startTime.empty()) {
+ if (endTime.empty()) {
// If no end time was given then filter up to now
view->filterBetweenExecDate(DateAndTime(startTime));
} else {
diff --git a/Framework/Algorithms/src/IntegrateEPP.cpp b/Framework/Algorithms/src/IntegrateEPP.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..dbaf75c8d0420a766f235b86fd57548100a7cce6
--- /dev/null
+++ b/Framework/Algorithms/src/IntegrateEPP.cpp
@@ -0,0 +1,133 @@
+#include "MantidAlgorithms/IntegrateEPP.h"
+
+#include "MantidAPI/ITableWorkspace.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/CompositeValidator.h"
+#include "MantidKernel/MandatoryValidator.h"
+
+namespace Mantid {
+namespace Algorithms {
+
+using Mantid::Kernel::Direction;
+using Mantid::API::WorkspaceProperty;
+
+namespace {
+/// A private namespace defining property name constants.
+namespace PropertyNames {
+const static std::string EPP_WORKSPACE{"EPPWorkspace"};
+const static std::string INPUT_WORKSPACE{"InputWorkspace"};
+const static std::string OUTPUT_WORKSPACE{"OutputWorkspace"};
+const static std::string WIDTH{"HalfWidthInSigmas"};
+}
+}
+
+// Register the algorithm into the AlgorithmFactory
+DECLARE_ALGORITHM(IntegrateEPP)
+
+//----------------------------------------------------------------------------------------------
+
+/// Algorithms name for identification. @see Algorithm::name
+const std::string IntegrateEPP::name() const { return "IntegrateEPP"; }
+
+/// Algorithm's version for identification. @see Algorithm::version
+int IntegrateEPP::version() const { return 1; }
+
+/// Algorithm's category for identification. @see Algorithm::category
+const std::string IntegrateEPP::category() const {
+ return "Arithmetic;Transforms\\Rebin";
+}
+
+/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
+const std::string IntegrateEPP::summary() const {
+ return "Integrate a workspace around elastic peak positions.";
+}
+
+//----------------------------------------------------------------------------------------------
+/** Initialize the algorithm's properties.
+ */
+void IntegrateEPP::init() {
+ declareProperty(Kernel::make_unique<WorkspaceProperty<API::MatrixWorkspace>>(
+ PropertyNames::INPUT_WORKSPACE, "", Direction::Input),
+ "A workspace to be integrated.");
+ declareProperty(Kernel::make_unique<WorkspaceProperty<API::MatrixWorkspace>>(
+ PropertyNames::OUTPUT_WORKSPACE, "", Direction::Output),
+ "An workspace containing the integrated histograms.");
+ declareProperty(Kernel::make_unique<WorkspaceProperty<API::ITableWorkspace>>(
+ PropertyNames::EPP_WORKSPACE, "", Direction::Input),
+ "Table containing information on the elastic peaks.");
+ const auto mandatoryDouble =
+ boost::make_shared<Kernel::MandatoryValidator<double>>();
+ const auto positiveDouble =
+ boost::make_shared<Kernel::BoundedValidator<double>>();
+ positiveDouble->setLower(0.0);
+ positiveDouble->setLowerExclusive(true);
+ const auto mandatoryPositiveDouble =
+ boost::make_shared<Kernel::CompositeValidator>();
+ mandatoryPositiveDouble->add(mandatoryDouble);
+ mandatoryPositiveDouble->add(positiveDouble);
+ declareProperty(PropertyNames::WIDTH, 5.0, mandatoryPositiveDouble,
+ "Half of the integration width in multiplies of 'Sigma'.");
+}
+
+//----------------------------------------------------------------------------------------------
+/** Execute the algorithm.
+ */
+void IntegrateEPP::exec() {
+ API::MatrixWorkspace_sptr inWS = getProperty(PropertyNames::INPUT_WORKSPACE);
+ API::ITableWorkspace_const_sptr eppWS =
+ getProperty(PropertyNames::EPP_WORKSPACE);
+ const double sigmaMultiplier = getProperty(PropertyNames::WIDTH);
+ const auto indexCol = eppWS->getColumn("WorkspaceIndex");
+ const auto sigmaCol = eppWS->getColumn("Sigma");
+ const auto centreCol = eppWS->getColumn("PeakCentre");
+ const auto statusCol = eppWS->getColumn("FitStatus");
+ std::vector<double> begins(inWS->getNumberHistograms(), 0.0);
+ std::vector<double> ends(begins.size(), 0.0);
+ for (size_t i = 0; i < eppWS->rowCount(); ++i) {
+ const std::string &fitStatus = statusCol->cell<std::string>(i);
+ if (fitStatus != "success") {
+ continue;
+ }
+ const double centre = centreCol->toDouble(i);
+ const double halfWidth = sigmaMultiplier * sigmaCol->toDouble(i);
+ const int index = indexCol->cell<int>(i);
+ if (index < 0 || static_cast<size_t>(index) >= begins.size()) {
+ throw std::runtime_error(
+ "The 'WorkspaceIndex' column contains an invalid value.");
+ }
+ begins[index] = centre - halfWidth;
+ ends[index] = centre + halfWidth;
+ interruption_point();
+ }
+ auto integrate = createChildAlgorithm("Integration", 0.0, 1.0);
+ integrate->setProperty("InputWorkspace", inWS);
+ const std::string outWSName = getProperty(PropertyNames::OUTPUT_WORKSPACE);
+ integrate->setPropertyValue("OutputWorkspace", outWSName);
+ integrate->setProperty("RangeLowerList", begins);
+ integrate->setProperty("RangeUpperList", ends);
+ integrate->setProperty("IncludePartialBins", true);
+ integrate->executeAsChildAlg();
+ API::MatrixWorkspace_sptr outWS = integrate->getProperty("OutputWorkspace");
+ setProperty(PropertyNames::OUTPUT_WORKSPACE, outWS);
+}
+
+/** Validate input properties.
+ *
+ * @return A map mapping input property names to discovered issues.
+ */
+std::map<std::string, std::string> IntegrateEPP::validateInputs() {
+ std::map<std::string, std::string> issues;
+ API::MatrixWorkspace_const_sptr inWS =
+ getProperty(PropertyNames::INPUT_WORKSPACE);
+ API::ITableWorkspace_const_sptr eppWS =
+ getProperty(PropertyNames::EPP_WORKSPACE);
+ if (eppWS->rowCount() > inWS->getNumberHistograms()) {
+ issues[PropertyNames::EPP_WORKSPACE] =
+ "The EPP workspace contains too many rows.";
+ }
+ return issues;
+}
+
+} // namespace Algorithms
+} // namespace Mantid
diff --git a/Framework/Algorithms/src/MergeRuns.cpp b/Framework/Algorithms/src/MergeRuns.cpp
index f6533cadf4591502923bd715f3cbbf5c226421ca..39f3664cefaf3b41c5c6420dc8a7f3b02b9f477f 100644
--- a/Framework/Algorithms/src/MergeRuns.cpp
+++ b/Framework/Algorithms/src/MergeRuns.cpp
@@ -5,14 +5,19 @@
#include "MantidAPI/ADSValidator.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/Axis.h"
+#include "MantidGeometry/Instrument/DetectorInfo.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/WorkspaceGroup.h"
+#include "MantidDataObjects/WorkspaceCreation.h"
+#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument.h"
+#include "MantidIndexing/IndexInfo.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/PropertyWithValue.h"
#include "MantidKernel/Unit.h"
#include "MantidKernel/make_unique.h"
-#include "MantidDataObjects/WorkspaceCreation.h"
+#include "MantidTypes/SpectrumDefinition.h"
using Mantid::HistogramData::HistogramX;
@@ -28,6 +33,42 @@ using namespace Geometry;
using namespace DataObjects;
using namespace RunCombinationOptions;
+namespace {
+/*
+ * Here we build up the correct time indexes for the workspace being added. If
+ *the scan times for the addee workspace and output workspace are the same this
+ *builds the same indexing as the workspace had before. Otherwise, the correct
+ *time indexes are set here.
+ */
+std::vector<SpectrumDefinition>
+buildScanIntervals(const std::vector<SpectrumDefinition> &addeeSpecDefs,
+ const DetectorInfo &addeeDetInfo,
+ const DetectorInfo &outDetInfo,
+ const DetectorInfo &newOutDetInfo) {
+ std::vector<SpectrumDefinition> newAddeeSpecDefs;
+
+ for (auto &specDef : addeeSpecDefs) {
+ for (auto &index : specDef) {
+ SpectrumDefinition newSpecDef;
+ if (addeeDetInfo.scanInterval(index) == outDetInfo.scanInterval(index)) {
+ newSpecDef.add(index.first, index.second);
+ } else {
+ // Find the correct time index for this entry
+ for (size_t i = 0; i < newOutDetInfo.scanCount(index.first); i++) {
+ if (addeeDetInfo.scanInterval(index) ==
+ newOutDetInfo.scanInterval({index.first, i})) {
+ newSpecDef.add(index.first, i);
+ }
+ }
+ }
+ newAddeeSpecDefs.push_back(newSpecDef);
+ }
+ }
+
+ return newAddeeSpecDefs;
+}
+}
+
/// Initialisation method
void MergeRuns::init() {
// declare arbitrary number of input workspaces as a list of strings at the
@@ -119,7 +160,7 @@ void MergeRuns::exec() {
// At least one is not event workspace ----------------
// This gets the list of workspaces
- m_inMatrixWS = this->validateInputs(inputs);
+ m_inMatrixWS = validateInputs(inputs);
// Iterate over the collection of input workspaces
auto it = m_inMatrixWS.begin();
@@ -133,6 +174,8 @@ void MergeRuns::exec() {
sampleLogsWarn, sampleLogsWarnTolerances, sampleLogsFail,
sampleLogsFailTolerances);
+ auto isScanning = outWS->detectorInfo().isScanning();
+
m_progress = Kernel::make_unique<Progress>(this, 0.0, 1.0, numberOfWSs - 1);
// Note that the iterator is incremented before first pass so that 1st
// workspace isn't added to itself
@@ -168,15 +211,18 @@ void MergeRuns::exec() {
try {
sampleLogsBehaviour.mergeSampleLogs(**it, *outWS);
sampleLogsBehaviour.removeSampleLogsFromWorkspace(*addee);
- outWS = outWS + addee;
+ if (isScanning)
+ outWS = buildScanningOutputWorkspace(outWS, addee);
+ else
+ outWS = outWS + addee;
sampleLogsBehaviour.setUpdatedSampleLogs(*outWS);
sampleLogsBehaviour.readdSampleLogToWorkspace(*addee);
} catch (std::invalid_argument &e) {
if (sampleLogsFailBehaviour == SKIP_BEHAVIOUR) {
- g_log.error()
- << "Could not merge run: " << it->get()->getName()
- << ". Reason: \"" << e.what()
- << "\". MergeRuns will continue but this run will be skipped.\n";
+ g_log.error() << "Could not merge run: " << it->get()->getName()
+ << ". Reason: \"" << e.what()
+ << "\". MergeRuns will continue but this run will be "
+ "skipped.\n";
sampleLogsBehaviour.resetSampleLogs(*outWS);
} else {
throw std::invalid_argument(e);
@@ -190,6 +236,58 @@ void MergeRuns::exec() {
}
}
+MatrixWorkspace_sptr
+MergeRuns::buildScanningOutputWorkspace(const MatrixWorkspace_sptr &outWS,
+ const MatrixWorkspace_sptr &addeeWS) {
+ const auto numOutputSpectra =
+ outWS->getNumberHistograms() + addeeWS->getNumberHistograms();
+
+ MatrixWorkspace_sptr newOutWS = DataObjects::create<MatrixWorkspace>(
+ *outWS, numOutputSpectra, outWS->histogram(0).binEdges());
+
+ newOutWS->mutableDetectorInfo().merge(addeeWS->detectorInfo());
+
+ if (newOutWS->detectorInfo().scanSize() == outWS->detectorInfo().scanSize()) {
+ // In this case the detector info objects were identical. We just add the
+ // workspaces as we normally would for MergeRuns.
+ g_log.information()
+ << "Workspaces had identical detector scan information and were "
+ "merged.";
+ return outWS + addeeWS;
+ } else if (newOutWS->detectorInfo().scanSize() != numOutputSpectra) {
+ throw std::runtime_error("Unexpected DetectorInfo size. Merging workspaces "
+ "with some, but not all overlapping scan "
+ "intervals is not currently supported.");
+ }
+
+ g_log.information()
+ << "Workspaces had different, non-overlapping scan intervals "
+ "so spectra will be appended.";
+
+ auto outSpecDefs = *(outWS->indexInfo().spectrumDefinitions());
+ const auto &addeeSpecDefs = *(addeeWS->indexInfo().spectrumDefinitions());
+
+ const auto newAddeeSpecDefs =
+ buildScanIntervals(addeeSpecDefs, addeeWS->detectorInfo(),
+ outWS->detectorInfo(), newOutWS->detectorInfo());
+
+ outSpecDefs.insert(outSpecDefs.end(), newAddeeSpecDefs.begin(),
+ newAddeeSpecDefs.end());
+
+ auto newIndexInfo = Indexing::IndexInfo(numOutputSpectra);
+ newIndexInfo.setSpectrumDefinitions(std::move(outSpecDefs));
+ newOutWS->setIndexInfo(newIndexInfo);
+
+ for (size_t i = 0; i < outWS->getNumberHistograms(); ++i)
+ newOutWS->setHistogram(i, outWS->histogram(i));
+
+ for (size_t i = 0; i < addeeWS->getNumberHistograms(); ++i)
+ newOutWS->setHistogram(i + outWS->getNumberHistograms(),
+ addeeWS->histogram(i));
+
+ return newOutWS;
+}
+
/** Build up addition tables for merging eventlists together.
* Throws an error if there is any incompatibility.
*/
@@ -208,7 +306,8 @@ void MergeRuns::buildAdditionTables() {
try {
lhs_det_to_wi = lhs->getDetectorIDToWorkspaceIndexMap(true);
} catch (std::runtime_error &) {
- // If it fails, then there are some grouped detector IDs, and the map cannot
+ // If it fails, then there are some grouped detector IDs, and the map
+ // cannot
// exist
}
@@ -221,7 +320,8 @@ void MergeRuns::buildAdditionTables() {
// An addition table is a list of pairs:
// First int = workspace index in the EW being added
- // Second int = workspace index to which it will be added in the OUTPUT EW.
+ // Second int = workspace index to which it will be added in the OUTPUT
+ // EW.
// -1 if it should add a new entry at the end.
AdditionTable table;
@@ -234,7 +334,8 @@ void MergeRuns::buildAdditionTables() {
bool done = false;
- // First off, try to match the workspace indices. Most times, this will be
+ // First off, try to match the workspace indices. Most times, this will
+ // be
// ok right away.
int outWI = inWI;
if (outWI < lhs_nhist) // don't go out of bounds
@@ -381,12 +482,12 @@ static bool compare(MatrixWorkspace_sptr first, MatrixWorkspace_sptr second) {
*
* @param inputWorkspaces The names of the input workspaces
* @throw invalid_argument if there is an incompatibility.
- * @return true if all workspaces are event workspaces and valid. False if any
+ * @return true if all workspaces are event workspaces and valid. False if
+ *any
*are not found,
*/
bool MergeRuns::validateInputsForEventWorkspaces(
const std::vector<std::string> &inputWorkspaces) {
-
m_inEventWS.clear();
// TODO: Check that name of instrument matches - think that's the best
@@ -425,14 +526,16 @@ bool MergeRuns::validateInputsForEventWorkspaces(
}
//------------------------------------------------------------------------------------------------
-/** Checks that the input workspace all exist, that they are the same size, have
+/** Checks that the input workspace all exist, that they are the same size,
+ * have
* the same units
* and the same instrument name. Will throw if they don't.
* @param inputWorkspaces The names of the input workspaces
* @return A list of pointers to the input workspace, ordered by increasing
* frame starting point
* @throw Exception::NotFoundError If an input workspace doesn't exist
- * @throw std::invalid_argument If the input workspaces are not compatible
+ * @throw std::invalid_argument If the input workspaces are not
+ * compatible
*/
std::list<API::MatrixWorkspace_sptr>
MergeRuns::validateInputs(const std::vector<std::string> &inputWorkspaces) {
@@ -484,11 +587,13 @@ MergeRuns::validateInputs(const std::vector<std::string> &inputWorkspaces) {
}
//------------------------------------------------------------------------------------------------
-/** Calculates the parameters to hand to the Rebin algorithm. Specifies the new
+/** Calculates the parameters to hand to the Rebin algorithm. Specifies the
+ * new
* binning, bin-by-bin,
* to cover the full range covered by the two input workspaces. In regions of
* overlap, the bins from
- * the workspace having the wider bins are taken. Note that because the list of
+ * the workspace having the wider bins are taken. Note that because the list
+ * of
* input workspaces
* is sorted, ws1 will always start before (or at the same point as) ws2.
* @param ws1 :: The first input workspace. Will start before ws2.
@@ -515,7 +620,8 @@ void MergeRuns::calculateRebinParams(const API::MatrixWorkspace_const_sptr &ws1,
params.push_back(X1[i] - X1[i - 1]);
params.push_back(X1[i]);
}
- // If the range of workspace2 is completely within that of workspace1, then
+ // If the range of workspace2 is completely within that of workspace1,
+ // then
// call the
// 'inclusion' routine. Otherwise call the standard 'intersection' one.
if (end1 < end2) {
@@ -527,7 +633,8 @@ void MergeRuns::calculateRebinParams(const API::MatrixWorkspace_const_sptr &ws1,
}
//------------------------------------------------------------------------------------------------
-/** Calculates the rebin paramters in the case where the two input workspaces do
+/** Calculates the rebin paramters in the case where the two input workspaces
+ * do
* not overlap at all.
* @param X1 :: The bin boundaries from the first workspace
* @param X2 :: The bin boundaries from the second workspace
@@ -619,7 +726,8 @@ void MergeRuns::inclusionParams(const HistogramX &X1, int64_t &i,
//++overlapbins1;
overlapbins2 = X2.size() - 1;
- // In the overlap region, we want to use whichever one has the larger bins (on
+ // In the overlap region, we want to use whichever one has the larger bins
+ // (on
// average)
if (overlapbins1 + 1 <= overlapbins2) {
// In the case where the first workspace has larger bins it's easy
diff --git a/Framework/Algorithms/src/Q1DWeighted.cpp b/Framework/Algorithms/src/Q1DWeighted.cpp
index 36fc5177d2c2f4530407f4927210575af9e9b409..d12104bab2f4c436808e876943745427a871f2ea 100644
--- a/Framework/Algorithms/src/Q1DWeighted.cpp
+++ b/Framework/Algorithms/src/Q1DWeighted.cpp
@@ -213,7 +213,7 @@ void Q1DWeighted::exec() {
// For reference - in the case where we don't use sub-pixels, simply
// use:
// double sinTheta = sin( spectrumInfo.twoTheta(i)/2.0 );
- V3D pos = spectrumInfo.position(i) - V3D(sub_x, sub_y, 0.0);
+ V3D pos = spectrumInfo.position(i) - V3D(sub_x, sub_y, 0.0) - samplePos;
double sinTheta = sin(0.5 * pos.angle(beamLine));
double factor = fmp * sinTheta;
double q = factor * 2.0 / (XIn[j] + XIn[j + 1]);
diff --git a/Framework/Algorithms/src/ReflectometryReductionOne2.cpp b/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
index 181ab0a98afe857255351f6e327cb825fae53810..e6c3288f561814ec1a9a1eb974fd7108c13b003e 100644
--- a/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
+++ b/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
@@ -4,18 +4,22 @@
#include "MantidAPI/SpectrumInfo.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidGeometry/Objects/BoundingBox.h"
#include "MantidHistogramData/LinearGenerator.h"
#include "MantidIndexing/IndexInfo.h"
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/StringTokenizer.h"
#include "MantidKernel/Unit.h"
#include "MantidGeometry/IDetector.h"
+#include "MantidGeometry/Instrument.h"
+#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include <algorithm>
#include <boost/lexical_cast.hpp>
using namespace Mantid::Kernel;
using namespace Mantid::API;
+using namespace Mantid::Geometry;
using namespace Mantid::HistogramData;
using namespace Mantid::Indexing;
@@ -37,27 +41,6 @@ double getDetectorTwoTheta(const SpectrumInfo *spectrumInfo,
return spectrumInfo->signedTwoTheta(spectrumIdx);
}
-/** Get the twoTheta angle range for the top/bottom of the detector associated
-* with the given spectrum
-*
-* @param spectrumInfo : the spectrum info
-* @param spectrumIdx : the workspace index of the spectrum
-* @return : the twoTheta angle in radians
-*/
-double getDetectorTwoThetaRange(const SpectrumInfo *spectrumInfo,
- const size_t spectrumIdx) {
- // Assume the range covered by this pixel is the diff between this
- // pixel's twoTheta and the next/prev pixel)
- double twoTheta = getDetectorTwoTheta(spectrumInfo, spectrumIdx);
- double bTwoTheta = 0;
-
- if (spectrumIdx + 1 < spectrumInfo->size()) {
- bTwoTheta = getDetectorTwoTheta(spectrumInfo, spectrumIdx + 1) - twoTheta;
- }
-
- return bTwoTheta;
-}
-
/** Get the start/end of the lambda range for the detector associated
* with the given spectrum
*
@@ -328,6 +311,34 @@ std::string createProcessingCommandsFromDetectorWS(
return result;
}
+
+/**
+* Get the topbottom extent of a detector for the given axis
+*
+* @param axis [in] : the axis to get the extent for
+* @param top [in] : if true, get the max extent, or min otherwise
+* @return : the max/min extent on the given axis
+*/
+double getBoundingBoxExtent(const BoundingBox &boundingBox,
+ const PointingAlong axis, const bool top) {
+
+ double result = 0.0;
+ switch (axis) {
+ case X:
+ result = top ? boundingBox.xMax() : boundingBox.xMin();
+ break;
+ case Y:
+ result = top ? boundingBox.yMax() : boundingBox.yMin();
+ break;
+ case Z:
+ result = top ? boundingBox.zMax() : boundingBox.zMin();
+ break;
+ default:
+ throw std::runtime_error("Axis is not X/Y/Z");
+ break;
+ }
+ return result;
+}
}
// Register the algorithm into the AlgorithmFactory
@@ -434,7 +445,10 @@ void ReflectometryReductionOne2::exec() {
throw std::invalid_argument(
"InputWorkspace must have units of TOF or Wavelength");
+ // Cache the spectrum info and reference frame
m_spectrumInfo = &m_runWS->spectrumInfo();
+ auto instrument = m_runWS->getInstrument();
+ m_refFrame = instrument->getReferenceFrame();
// Find and cache detector groups and theta0
findDetectorGroups();
@@ -463,6 +477,44 @@ void ReflectometryReductionOne2::exec() {
setProperty("OutputWorkspace", IvsQ);
}
+/** Get the twoTheta angle range for the top/bottom of the detector associated
+* with the given spectrum
+*
+* @param spectrumIdx : the workspace index of the spectrum
+* @return : the twoTheta range in radians
+*/
+double
+ReflectometryReductionOne2::getDetectorTwoThetaRange(const size_t spectrumIdx) {
+
+ double bTwoTheta = 0;
+
+ // Get the sample->detector distance along the beam
+ const V3D detSample =
+ m_spectrumInfo->position(spectrumIdx) - m_spectrumInfo->samplePosition();
+ const double beamOffset =
+ m_refFrame->vecPointingAlongBeam().scalar_prod(detSample);
+ // Get the bounding box for this detector/group
+ BoundingBox boundingBox;
+ auto detector = m_runWS->getDetector(spectrumIdx);
+ detector->getBoundingBox(boundingBox);
+ // Get the top and bottom on the axis pointing up
+ const double top =
+ getBoundingBoxExtent(boundingBox, m_refFrame->pointingUp(), true);
+ const double bottom =
+ getBoundingBoxExtent(boundingBox, m_refFrame->pointingUp(), false);
+ // Calculate the difference in twoTheta between the top and bottom
+ const double twoThetaTop = std::atan(top / beamOffset);
+ const double twoThetaBottom = std::atan(bottom / beamOffset);
+ bTwoTheta = twoThetaTop - twoThetaBottom;
+
+ // We must have non-zero width to project a range
+ if (bTwoTheta < Tolerance) {
+ throw std::runtime_error("Error calculating pixel size.");
+ }
+
+ return bTwoTheta;
+}
+
/**
* Utility function to create a unique workspace name for diagnostic outputs
* based on a given input workspace name
@@ -856,9 +908,19 @@ void ReflectometryReductionOne2::findDetectorGroups() {
return a.front() < b.front();
});
- if (m_detectorGroups.size() == 0) {
+ if (m_detectorGroups.empty()) {
throw std::runtime_error("Invalid processing instructions");
}
+
+ for (const auto &group : m_detectorGroups) {
+ for (const auto &spIdx : group) {
+ if (spIdx > m_spectrumInfo->size() - 1) {
+ throw std::runtime_error(
+ "ProcessingInstructions contains an out-of-range index: " +
+ std::to_string(spIdx));
+ }
+ }
+ }
}
/**
@@ -993,8 +1055,7 @@ void ReflectometryReductionOne2::findIvsLamRange(
const size_t spIdxMin = detectors.front();
const double twoThetaMin = getDetectorTwoTheta(m_spectrumInfo, spIdxMin);
- const double bTwoThetaMin =
- getDetectorTwoThetaRange(m_spectrumInfo, spIdxMin);
+ const double bTwoThetaMin = getDetectorTwoThetaRange(spIdxMin);
// For bLambda, use the average bin size for this spectrum
auto xValues = detectorWS->x(spIdxMin);
double bLambda = (xValues[xValues.size() - 1] - xValues[0]) /
@@ -1004,8 +1065,7 @@ void ReflectometryReductionOne2::findIvsLamRange(
const size_t spIdxMax = detectors.back();
const double twoThetaMax = getDetectorTwoTheta(m_spectrumInfo, spIdxMax);
- const double bTwoThetaMax =
- getDetectorTwoThetaRange(m_spectrumInfo, spIdxMax);
+ const double bTwoThetaMax = getDetectorTwoThetaRange(spIdxMax);
xValues = detectorWS->x(spIdxMax);
bLambda = (xValues[xValues.size() - 1] - xValues[0]) /
static_cast<int>(xValues.size());
@@ -1092,7 +1152,7 @@ ReflectometryReductionOne2::sumInQ(MatrixWorkspace_sptr detectorWS) {
for (auto spIdx : detectors) {
// Get the angle of this detector and its size in twoTheta
const double twoTheta = getDetectorTwoTheta(m_spectrumInfo, spIdx);
- const double bTwoTheta = getDetectorTwoThetaRange(m_spectrumInfo, spIdx);
+ const double bTwoTheta = getDetectorTwoThetaRange(spIdx);
// Check X length is Y length + 1
const auto &inputX = detectorWS->x(spIdx);
@@ -1228,11 +1288,19 @@ void ReflectometryReductionOne2::sumInQShareCounts(
}
// Add a share of the input counts to this bin based on the proportion of
// overlap.
- const double overlapWidth =
- std::min({bLambda, lambdaMax - binStart, binEnd - lambdaMin});
- const double fraction = overlapWidth / totalWidth;
- outputY[outIdx] += inputCounts * fraction;
- outputE[outIdx] += inputErr * fraction;
+ if (totalWidth > Tolerance) {
+ // Share counts out proportionally based on the overlap of this range
+ const double overlapWidth =
+ std::min({bLambda, lambdaMax - binStart, binEnd - lambdaMin});
+ const double fraction = overlapWidth / totalWidth;
+ outputY[outIdx] += inputCounts * fraction;
+ outputE[outIdx] += inputErr * fraction;
+ } else {
+ // Projection to a single value. Put all counts in the overlapping output
+ // bin.
+ outputY[outIdx] += inputCounts;
+ outputE[outIdx] += inputCounts;
+ }
}
}
diff --git a/Framework/Algorithms/src/RenameWorkspaces.cpp b/Framework/Algorithms/src/RenameWorkspaces.cpp
index 9a6855d499bc8585e95af1a14b04ae49ecc1ba51..7af32cd87e4807dc7ad30c1331f03c76c3a6214c 100644
--- a/Framework/Algorithms/src/RenameWorkspaces.cpp
+++ b/Framework/Algorithms/src/RenameWorkspaces.cpp
@@ -61,15 +61,15 @@ std::map<std::string, std::string> RenameWorkspaces::validateInputs() {
std::string suffix = getPropertyValue("Suffix");
// Check properties
- if (newWsName.empty() && prefix == "" && suffix == "") {
+ if (newWsName.empty() && prefix.empty() && suffix.empty()) {
errorList["WorkspaceNames"] =
"No list of Workspace names, prefix or suffix has been supplied.";
}
- if (!newWsName.empty() && (prefix != "" || suffix != "")) {
+ if (!newWsName.empty() && (!prefix.empty() || !suffix.empty())) {
errorList["WorkspaceNames"] = "Both a list of workspace names and a prefix "
"or suffix has been supplied.";
- if (prefix != "") {
+ if (!prefix.empty()) {
errorList["Prefix"] = "Both a list of workspace names and a prefix "
"or suffix has been supplied.";
} else {
diff --git a/Framework/Algorithms/src/ResampleX.cpp b/Framework/Algorithms/src/ResampleX.cpp
index 42d065d13e0cdf07e53ddc75b9197adf743d4260..82c462f4fcd50725b9f2c74e4873f577b573a110 100644
--- a/Framework/Algorithms/src/ResampleX.cpp
+++ b/Framework/Algorithms/src/ResampleX.cpp
@@ -114,8 +114,21 @@ map<string, string> ResampleX::validateInputs() {
*/
string determineXMinMax(MatrixWorkspace_sptr inputWS, vector<double> &xmins,
vector<double> &xmaxs) {
- bool updateXMins = xmins.empty(); // they weren't set
- bool updateXMaxs = xmaxs.empty(); // they weren't set
+ const size_t numSpectra = inputWS->getNumberHistograms();
+
+ // pad out the ranges by copying the first value to the rest that are needed
+ if (xmins.size() == 1 && numSpectra > xmins.size()) {
+ const double value = xmins.front();
+ xmins.insert(xmins.end(), numSpectra - xmins.size(), value);
+ }
+ if (xmaxs.size() == 1 && numSpectra > xmaxs.size()) {
+ const double value = xmaxs.front();
+ xmaxs.insert(xmaxs.end(), numSpectra - xmaxs.size(), value);
+ }
+
+ // should the individiual values be calculated?
+ const bool updateXMins = xmins.empty(); // they weren't set
+ const bool updateXMaxs = xmaxs.empty(); // they weren't set
stringstream msg;
@@ -129,7 +142,6 @@ string determineXMinMax(MatrixWorkspace_sptr inputWS, vector<double> &xmins,
xmax_wksp = inputEventWS->getTofMax();
}
- size_t numSpectra = inputWS->getNumberHistograms();
for (size_t i = 0; i < numSpectra; ++i) {
// determine ranges if necessary
if (updateXMins || updateXMaxs) {
@@ -283,7 +295,7 @@ void ResampleX::exec() {
bool inPlace = (inputWS == outputWS); // Rebinning in-place
m_isDistribution = inputWS->isDistribution();
m_isHistogram = inputWS->isHistogramData();
- int numSpectra = static_cast<int>(inputWS->getNumberHistograms());
+ const int numSpectra = static_cast<int>(inputWS->getNumberHistograms());
// the easy parameters
m_useLogBinning = getProperty("LogBinning");
@@ -335,8 +347,8 @@ void ResampleX::exec() {
if (common_limits) {
// get the delta from the first since they are all the same
BinEdges xValues(0);
- double delta = this->determineBinning(xValues.mutableRawData(),
- xmins[0], xmaxs[0]);
+ const double delta = this->determineBinning(xValues.mutableRawData(),
+ xmins[0], xmaxs[0]);
g_log.debug() << "delta = " << delta << "\n";
outputEventWS->setAllX(xValues);
} else {
@@ -348,7 +360,7 @@ void ResampleX::exec() {
for (int wkspIndex = 0; wkspIndex < numSpectra; ++wkspIndex) {
PARALLEL_START_INTERUPT_REGION
BinEdges xValues(0);
- double delta = this->determineBinning(
+ const double delta = this->determineBinning(
xValues.mutableRawData(), xmins[wkspIndex], xmaxs[wkspIndex]);
g_log.debug() << "delta[wkspindex=" << wkspIndex << "] = " << delta
<< " xmin=" << xmins[wkspIndex]
@@ -378,7 +390,7 @@ void ResampleX::exec() {
// Set the X axis for each output histogram
MantidVec xValues;
- double delta =
+ const double delta =
this->determineBinning(xValues, xmins[wkspIndex], xmaxs[wkspIndex]);
g_log.debug() << "delta[wkspindex=" << wkspIndex << "] = " << delta
<< "\n";
@@ -458,8 +470,8 @@ void ResampleX::exec() {
// create new output X axis
MantidVec XValues_new;
- double delta = this->determineBinning(XValues_new, xmins[wkspIndex],
- xmaxs[wkspIndex]);
+ const double delta = this->determineBinning(XValues_new, xmins[wkspIndex],
+ xmaxs[wkspIndex]);
g_log.debug() << "delta[wkspindex=" << wkspIndex << "] = " << delta
<< "\n";
diff --git a/Framework/Algorithms/src/RunCombinationHelpers/RunCombinationHelper.cpp b/Framework/Algorithms/src/RunCombinationHelpers/RunCombinationHelper.cpp
index 12404cb64efa1fc0e92b5a46a04b3e0b4b4c1bba..c90b3190d76177c5291f7a0e40c9b0bb91b2f661 100644
--- a/Framework/Algorithms/src/RunCombinationHelpers/RunCombinationHelper.cpp
+++ b/Framework/Algorithms/src/RunCombinationHelpers/RunCombinationHelper.cpp
@@ -2,6 +2,7 @@
#include "MantidAPI/AnalysisDataService.h"
#include "MantidAPI/Axis.h"
+#include "MantidGeometry/Instrument/DetectorInfo.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidGeometry/Instrument.h"
@@ -45,10 +46,12 @@ RunCombinationHelper::unWrapGroups(const std::vector<std::string> &inputs) {
*/
void RunCombinationHelper::setReferenceProperties(MatrixWorkspace_sptr ref) {
m_numberSpectra = ref->getNumberHistograms();
+ m_numberDetectors = ref->detectorInfo().size();
m_xUnit = ref->getAxis(0)->unit()->unitID();
m_spectrumAxisUnit = ref->getAxis(1)->unit()->unitID();
m_yUnit = ref->YUnit();
m_isHistogramData = ref->isHistogramData();
+ m_isScanning = ref->detectorInfo().isScanning();
m_instrumentName = ref->getInstrument()->getName();
}
@@ -61,7 +64,7 @@ void RunCombinationHelper::setReferenceProperties(MatrixWorkspace_sptr ref) {
std::string
RunCombinationHelper::checkCompatibility(MatrixWorkspace_sptr ws,
bool checkNumberHistograms) {
- std::string errors;
+ std::string errors = "";
if (ws->getNumberHistograms() != m_numberSpectra && checkNumberHistograms)
errors += "different number of histograms; ";
if (ws->getAxis(0)->unit()->unitID() != m_xUnit)
@@ -72,6 +75,11 @@ RunCombinationHelper::checkCompatibility(MatrixWorkspace_sptr ws,
errors += "different Y units; ";
if (ws->isHistogramData() != m_isHistogramData)
errors += "different distribution or histogram type; ";
+ if (ws->detectorInfo().isScanning() != m_isScanning)
+ errors += "a mix of workspaces with and without detector scans; ";
+ if (m_isScanning && ws->detectorInfo().size() != m_numberDetectors)
+ errors += "workspaces with detectors scans have different number of "
+ "detectors; ";
if (ws->getInstrument()->getName() != m_instrumentName)
errors += "different instrument names; ";
return errors;
diff --git a/Framework/Algorithms/src/Stitch1DMany.cpp b/Framework/Algorithms/src/Stitch1DMany.cpp
index afb9e4feefd4a4d3c78f8e8d38006a298f6218a6..77f76abccba7ac53328b35b749bb6657eac50dda 100644
--- a/Framework/Algorithms/src/Stitch1DMany.cpp
+++ b/Framework/Algorithms/src/Stitch1DMany.cpp
@@ -205,7 +205,7 @@ void Stitch1DMany::validateGroupWorkspacesInputs() {
// Log all errors and throw a runtime error if an error is found
validateCommonInputs(errors);
- if (errors.size() > 0) {
+ if (!errors.empty()) {
auto &warnLog = getLogger().warning();
for (const auto &error : errors) {
warnLog << "Invalid value for " << error.first << ": " << error.second
@@ -241,7 +241,7 @@ void Stitch1DMany::validateCommonInputs(
m_useManualScaleFactors = this->getProperty("UseManualScaleFactors");
m_manualScaleFactors = this->getProperty("ManualScaleFactors");
- if (m_manualScaleFactors.size() > 0) {
+ if (!m_manualScaleFactors.empty()) {
if (m_manualScaleFactors.size() == 1) {
// Single value: fill with list of the same scale factor value
m_manualScaleFactors = std::vector<double>(numStitchableWS - 1,
diff --git a/Framework/Algorithms/test/DetectorEfficiencyCorUserTest.h b/Framework/Algorithms/test/DetectorEfficiencyCorUserTest.h
index f62c03d88b87e8428659669073e61969529aa7fd..840086691fdd23f11d173981be56d4573e2a322c 100644
--- a/Framework/Algorithms/test/DetectorEfficiencyCorUserTest.h
+++ b/Framework/Algorithms/test/DetectorEfficiencyCorUserTest.h
@@ -74,12 +74,15 @@ public:
if (!inWS)
return;
- const auto eff0 = efficiency(m_Ei);
- for (size_t i = 0; i != outWS->getNumberHistograms(); ++i) {
+ const auto nHisto = outWS->getNumberHistograms();
+ for (size_t i = 0; i != nHisto; ++i) {
+ auto eff0 =
+ i < nHisto / 2 ? efficiencyBank1(m_Ei) : efficiencyBank2(m_Ei);
const auto &ys = outWS->counts(i);
const auto &es = outWS->countStandardDeviations(i);
for (size_t j = 0; j != ys.size(); ++j) {
- const auto eff = efficiency(m_Efs[j]);
+ const auto eff = i < nHisto / 2 ? efficiencyBank1(m_Efs[j])
+ : efficiencyBank2(m_Efs[j]);
// By default, input workspace has y = 2, e = sqrt(2).
TS_ASSERT_DELTA(ys[j], 2 * eff0 / eff, 1e-6);
TS_ASSERT_DELTA(es[j], std::sqrt(2) * eff0 / eff, 1e-6);
@@ -95,17 +98,22 @@ private:
static constexpr double m_Ei = 3.27;
static const int m_numBins = 20;
- static double efficiency(double e) {
+ static double efficiencyBank1(const double e) {
return std::exp(-1.0 / std::sqrt(e)) *
(1.0 - std::exp(-1.0 / std::sqrt(e)));
}
+ static double efficiencyBank2(const double e) {
+ return std::exp(-2.0 / std::sqrt(e)) *
+ (1.0 - std::exp(-2.0 / std::sqrt(e)));
+ }
+
// Final energies.
std::vector<double> m_Efs;
const std::string m_inWSName, m_outWSName;
void createInputWorkSpace() const {
- int numBanks = 1;
+ int numBanks = 2;
int numPixels = 10;
DataObjects::Workspace2D_sptr dataws =
@@ -125,10 +133,13 @@ private:
dataws->getAxis(0)->setUnit("DeltaE");
dataws->mutableRun().addProperty("Ei", double(m_Ei));
// Efficiency formula should be the same as in efficiency().
+ const auto instrument = dataws->getInstrument();
+ auto bank = instrument->getComponentByName("bank1");
dataws->instrumentParameters().addString(
- dataws->getInstrument()->getChild(0).get(), "formula_eff",
- "exp(-1.0/sqrt(e))*(1.0-exp(-1.0/sqrt(e)))");
-
+ bank.get(), "formula_eff", "exp(-1/sqrt(e))*(1-exp(-1/sqrt(e)))");
+ bank = instrument->getComponentByName("bank2");
+ dataws->instrumentParameters().addString(
+ bank.get(), "formula_eff", "exp(-2/sqrt(e))*(1-exp(-2/sqrt(e)))");
API::AnalysisDataService::Instance().addOrReplace(m_inWSName, dataws);
}
};
diff --git a/Framework/Algorithms/test/IntegrateEPPTest.h b/Framework/Algorithms/test/IntegrateEPPTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..c8fc6b68ed0c60ecd4d146e10324994a5c5a887f
--- /dev/null
+++ b/Framework/Algorithms/test/IntegrateEPPTest.h
@@ -0,0 +1,156 @@
+#ifndef MANTID_ALGORITHMS_INTEGRATEEPPTEST_H_
+#define MANTID_ALGORITHMS_INTEGRATEEPPTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAlgorithms/IntegrateEPP.h"
+
+#include "MantidTestHelpers/WorkspaceCreationHelper.h"
+
+using Mantid::Algorithms::IntegrateEPP;
+
+class IntegrateEPPTest : 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 IntegrateEPPTest *createSuite() { return new IntegrateEPPTest(); }
+ static void destroySuite(IntegrateEPPTest *suite) { delete suite; }
+
+ void test_Init() {
+ IntegrateEPP alg;
+ TS_ASSERT_THROWS_NOTHING(alg.initialize())
+ TS_ASSERT(alg.isInitialized())
+ }
+
+ void test_normal_operation() {
+ using namespace Mantid::API;
+ using namespace WorkspaceCreationHelper;
+ const size_t nHist = 3;
+ const size_t nBins = 6;
+ auto inputWS = create2DWorkspaceWhereYIsWorkspaceIndex(nHist, nBins + 1);
+ std::vector<EPPTableRow> eppRows(nHist);
+ for (auto &row : eppRows) {
+ row.peakCentre = static_cast<double>(nBins + 1) / 2.0;
+ row.sigma = 1;
+ }
+ auto eppWS = createEPPTableWorkspace(eppRows);
+ IntegrateEPP alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ TS_ASSERT_THROWS_NOTHING(alg.initialize())
+ TS_ASSERT(alg.isInitialized())
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("InputWorkspace", inputWS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg.setPropertyValue("OutputWorkspace", "_unused_for_child"))
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("EPPWorkspace", eppWS))
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("HalfWidthInSigmas", 1.0))
+ TS_ASSERT_THROWS_NOTHING(alg.execute())
+ TS_ASSERT(alg.isExecuted())
+
+ MatrixWorkspace_sptr outputWS = alg.getProperty("OutputWorkspace");
+ TS_ASSERT(outputWS);
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(), nHist)
+ TS_ASSERT_EQUALS(outputWS->blocksize(), 1)
+ for (size_t i = 0; i < outputWS->getNumberHistograms(); ++i) {
+ const auto ys = outputWS->y(i);
+ const auto xs = outputWS->x(i);
+ TS_ASSERT_EQUALS(ys[0], 2.0 * static_cast<double>(i))
+ TS_ASSERT_EQUALS(xs[0], 2.5)
+ TS_ASSERT_EQUALS(xs[1], 4.5)
+ }
+ }
+
+ void test_WorkspaceIndex_column_is_respected() {
+ using namespace Mantid::API;
+ using namespace WorkspaceCreationHelper;
+ const size_t nHist = 3;
+ const size_t nBins = 6;
+ auto inputWS = create2DWorkspaceWhereYIsWorkspaceIndex(nHist, nBins + 1);
+ std::vector<EPPTableRow> eppRows;
+ const double centre = static_cast<double>(nBins + 1) / 2.0;
+ const double sigma = 1.0;
+ eppRows.emplace_back(2, centre, sigma, 0.0,
+ EPPTableRow::FitStatus::SUCCESS);
+ eppRows.emplace_back(0, centre, sigma, 0.0,
+ EPPTableRow::FitStatus::SUCCESS);
+ auto eppWS = createEPPTableWorkspace(eppRows);
+ IntegrateEPP alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ TS_ASSERT_THROWS_NOTHING(alg.initialize())
+ TS_ASSERT(alg.isInitialized())
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("InputWorkspace", inputWS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg.setPropertyValue("OutputWorkspace", "_unused_for_child"))
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("EPPWorkspace", eppWS))
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("HalfWidthInSigmas", 1.0))
+ TS_ASSERT_THROWS_NOTHING(alg.execute())
+ TS_ASSERT(alg.isExecuted())
+
+ MatrixWorkspace_sptr outputWS = alg.getProperty("OutputWorkspace");
+ TS_ASSERT(outputWS);
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(), nHist)
+ TS_ASSERT_EQUALS(outputWS->blocksize(), 1)
+ TS_ASSERT_EQUALS(outputWS->y(0)[0], 2.0 * 0.0)
+ TS_ASSERT_EQUALS(outputWS->x(0)[0], 2.5)
+ TS_ASSERT_EQUALS(outputWS->x(0)[1], 4.5)
+ TS_ASSERT_EQUALS(outputWS->y(1)[0], 0.0)
+ TS_ASSERT_EQUALS(outputWS->x(1)[0], 0.0)
+ TS_ASSERT_EQUALS(outputWS->x(1)[1], 0.0)
+ TS_ASSERT_EQUALS(outputWS->y(2)[0], 2.0 * 2.0)
+ TS_ASSERT_EQUALS(outputWS->x(2)[0], 2.5)
+ TS_ASSERT_EQUALS(outputWS->x(2)[1], 4.5)
+ }
+
+ void test_failure_too_many_epp_rows() {
+ using namespace Mantid::API;
+ using namespace WorkspaceCreationHelper;
+ const size_t nHist = 3;
+ const size_t nBins = 6;
+ auto inputWS = create2DWorkspaceWhereYIsWorkspaceIndex(nHist, nBins + 1);
+ std::vector<EPPTableRow> eppRows(nHist + 1);
+ for (auto &row : eppRows) {
+ row.peakCentre = static_cast<double>(nBins + 1) / 2.0;
+ row.sigma = 1;
+ }
+ auto eppWS = createEPPTableWorkspace(eppRows);
+ IntegrateEPP alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ TS_ASSERT_THROWS_NOTHING(alg.initialize())
+ TS_ASSERT(alg.isInitialized())
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("InputWorkspace", inputWS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg.setPropertyValue("OutputWorkspace", "_unused_for_child"))
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("EPPWorkspace", eppWS))
+ TS_ASSERT_THROWS_ANYTHING(alg.execute())
+ TS_ASSERT(!alg.isExecuted())
+ }
+
+ void test_failure_invalid_index_in_epp_workspace() {
+ using namespace Mantid::API;
+ using namespace WorkspaceCreationHelper;
+ const size_t nHist = 3;
+ const size_t nBins = 6;
+ auto inputWS = create2DWorkspaceWhereYIsWorkspaceIndex(nHist, nBins + 1);
+ std::vector<EPPTableRow> eppRows;
+ const double centre = static_cast<double>(nBins + 1) / 2.0;
+ const double sigma = 1.0;
+ eppRows.emplace_back(3, centre, sigma, 0.0,
+ EPPTableRow::FitStatus::SUCCESS);
+ auto eppWS = createEPPTableWorkspace(eppRows);
+ IntegrateEPP alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ TS_ASSERT_THROWS_NOTHING(alg.initialize())
+ TS_ASSERT(alg.isInitialized())
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("InputWorkspace", inputWS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg.setPropertyValue("OutputWorkspace", "_unused_for_child"))
+ TS_ASSERT_THROWS_NOTHING(alg.setProperty("EPPWorkspace", eppWS))
+ TS_ASSERT_THROWS_ANYTHING(alg.execute())
+ TS_ASSERT(!alg.isExecuted())
+ }
+};
+
+#endif /* MANTID_ALGORITHMS_INTEGRATEEPPTEST_H_ */
diff --git a/Framework/Algorithms/test/MergeRunsTest.h b/Framework/Algorithms/test/MergeRunsTest.h
index aaee7ce7df95a04e3255327f1e543e1b55d49abe..a9647270255a65af84f118c80ae324b5181dc389 100644
--- a/Framework/Algorithms/test/MergeRunsTest.h
+++ b/Framework/Algorithms/test/MergeRunsTest.h
@@ -7,6 +7,8 @@
#include <stdarg.h>
#include "MantidAPI/AnalysisDataService.h"
+#include "MantidGeometry/Instrument/DetectorInfo.h"
+#include "MantidAPI/SpectrumInfo.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceGroup.h"
@@ -22,6 +24,7 @@
#include <boost/make_shared.hpp>
#include <MantidAlgorithms/RunCombinationHelpers/RunCombinationHelper.h>
#include <MantidAlgorithms/RunCombinationHelpers/SampleLogsBehaviour.h>
+#include "MantidTypes/SpectrumDefinition.h"
using namespace Mantid::API;
using namespace Mantid::Algorithms;
@@ -31,6 +34,8 @@ using namespace Mantid::Kernel;
class MergeRunsTest : public CxxTest::TestSuite {
private:
+ MergeRuns merge;
+
/// Helper method to add an 'nperiods' log value to each workspace in a group.
void add_periods_logs(WorkspaceGroup_sptr ws, bool calculateNPeriods = true,
int nperiods = -1) {
@@ -192,6 +197,43 @@ private:
return group;
}
+ WorkspaceGroup_sptr create_group_detector_scan_workspaces(
+ size_t nTimeIndexes = 2, size_t startTimeForSecondWorkspace = 0) {
+ const int N_HIST = 2;
+ MatrixWorkspace_sptr a = WorkspaceCreationHelper::
+ create2DDetectorScanWorkspaceWithFullInstrument(N_HIST, 1000,
+ nTimeIndexes, 0);
+ MatrixWorkspace_sptr b = WorkspaceCreationHelper::
+ create2DDetectorScanWorkspaceWithFullInstrument(
+ N_HIST, 1000, nTimeIndexes, startTimeForSecondWorkspace);
+
+ // Change the values in the histogram for the workspaces, so we can do
+ // some extra checks
+ for (size_t i = 0; i < a->getNumberHistograms(); ++i) {
+ auto histogram = a->histogram(i);
+ auto &counts = histogram.mutableY();
+ std::transform(counts.begin(), counts.end(), counts.begin(),
+ [](double count) { return count + 1; });
+ a->setHistogram(i, histogram);
+ }
+ for (size_t i = 0; i < b->getNumberHistograms(); ++i) {
+ auto histogram = b->histogram(i);
+ auto &counts = histogram.mutableY();
+ std::transform(counts.begin(), counts.end(), counts.begin(),
+ [](double count) { return count + 2; });
+ b->setHistogram(i, histogram);
+ }
+
+ WorkspaceGroup_sptr group = boost::make_shared<WorkspaceGroup>();
+ group->addWorkspace(a);
+ group->addWorkspace(b);
+
+ AnalysisDataService::Instance().addOrReplace("a1", a);
+ AnalysisDataService::Instance().addOrReplace("b1", b);
+ AnalysisDataService::Instance().addOrReplace("group1", group);
+ return group;
+ }
+
template <typename T>
MatrixWorkspace_sptr create_workspace_with_sample_logs(
const std::string &merge_type, const std::string &merge_list,
@@ -1474,8 +1516,218 @@ public:
do_test_mergeSampleLogs(ws, "prop1", mergeType, "1", 1, true);
}
-private:
- MergeRuns merge;
+ MatrixWorkspace_sptr
+ do_MergeRuns_with_scanning_workspaces(size_t startTime = 0) {
+ auto ws = create_group_detector_scan_workspaces(2, startTime);
+ MatrixWorkspace_sptr outputWS;
+
+ MergeRuns alg;
+ alg.initialize();
+ alg.setPropertyValue("InputWorkspaces", ws->getName());
+ alg.setPropertyValue("OutputWorkspace", "outWS");
+ TS_ASSERT_THROWS_NOTHING(alg.execute();)
+
+ TS_ASSERT_THROWS_NOTHING(
+ outputWS = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
+ "outWS"));
+
+ return outputWS;
+ }
+
+ void assert_scan_intervals_are_correct(const DetectorInfo &detInfo,
+ bool extraTimes = false) {
+ const auto TIME_1 = DateAndTime(0, 0);
+ const auto TIME_2 = DateAndTime(1, 0);
+ const auto TIME_3 = DateAndTime(3, 0);
+
+ const auto PAIR_1 = std::pair<DateAndTime, DateAndTime>(TIME_1, TIME_2);
+ const auto PAIR_2 = std::pair<DateAndTime, DateAndTime>(TIME_2, TIME_3);
+
+ TS_ASSERT_EQUALS(detInfo.scanInterval({0, 0}), PAIR_1)
+ TS_ASSERT_EQUALS(detInfo.scanInterval({1, 0}), PAIR_1)
+ TS_ASSERT_EQUALS(detInfo.scanInterval({0, 1}), PAIR_2)
+ TS_ASSERT_EQUALS(detInfo.scanInterval({1, 1}), PAIR_2)
+
+ if (extraTimes) {
+ const auto TIME_4 = DateAndTime(20, 0);
+ const auto TIME_5 = DateAndTime(21, 0);
+ const auto TIME_6 = DateAndTime(23, 0);
+
+ const auto PAIR_3 = std::pair<DateAndTime, DateAndTime>(TIME_4, TIME_5);
+ const auto PAIR_4 = std::pair<DateAndTime, DateAndTime>(TIME_5, TIME_6);
+
+ TS_ASSERT_EQUALS(detInfo.scanInterval({0, 2}), PAIR_3)
+ TS_ASSERT_EQUALS(detInfo.scanInterval({1, 2}), PAIR_3)
+ TS_ASSERT_EQUALS(detInfo.scanInterval({0, 3}), PAIR_4)
+ TS_ASSERT_EQUALS(detInfo.scanInterval({1, 3}), PAIR_4)
+ }
+ }
+
+ void assert_scanning_indexing_is_correct(const SpectrumInfo &specInfo,
+ bool extraSpectra = false) {
+
+ for (size_t i = 0; i < specInfo.size(); ++i) {
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(i).size(), 1)
+ }
+
+ const auto SPEC_DEF_1 = std::pair<size_t, size_t>(0, 0);
+ const auto SPEC_DEF_2 = std::pair<size_t, size_t>(0, 1);
+ const auto SPEC_DEF_3 = std::pair<size_t, size_t>(1, 0);
+ const auto SPEC_DEF_4 = std::pair<size_t, size_t>(1, 1);
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(0)[0], SPEC_DEF_1)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(1)[0], SPEC_DEF_2)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(2)[0], SPEC_DEF_3)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(3)[0], SPEC_DEF_4)
+
+ if (extraSpectra) {
+ const auto SPEC_DEF_5 = std::pair<size_t, size_t>(0, 2);
+ const auto SPEC_DEF_6 = std::pair<size_t, size_t>(0, 3);
+ const auto SPEC_DEF_7 = std::pair<size_t, size_t>(1, 2);
+ const auto SPEC_DEF_8 = std::pair<size_t, size_t>(1, 3);
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(4)[0], SPEC_DEF_5)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(5)[0], SPEC_DEF_6)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(6)[0], SPEC_DEF_7)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(7)[0], SPEC_DEF_8)
+ } else {
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(4)[0], SPEC_DEF_1)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(5)[0], SPEC_DEF_2)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(6)[0], SPEC_DEF_3)
+ TS_ASSERT_EQUALS(specInfo.spectrumDefinition(7)[0], SPEC_DEF_4)
+ }
+ }
+
+ void
+ assert_scanning_histograms_correctly_set(const MatrixWorkspace_sptr &ws) {
+ TS_ASSERT_EQUALS(ws->histogram(0).y()[0], 1)
+ TS_ASSERT_EQUALS(ws->histogram(1).y()[0], 1)
+ TS_ASSERT_EQUALS(ws->histogram(2).y()[0], 1)
+ TS_ASSERT_EQUALS(ws->histogram(3).y()[0], 1)
+ TS_ASSERT_EQUALS(ws->histogram(4).y()[0], 2)
+ TS_ASSERT_EQUALS(ws->histogram(5).y()[0], 2)
+ TS_ASSERT_EQUALS(ws->histogram(6).y()[0], 2)
+ TS_ASSERT_EQUALS(ws->histogram(7).y()[0], 2)
+ }
+
+ void
+ test_merging_detector_scan_workspaces_with_different_start_times_appends_workspaces() {
+ auto outputWS = do_MergeRuns_with_scanning_workspaces(20);
+
+ const auto &detInfo = outputWS->detectorInfo();
+ TS_ASSERT_EQUALS(detInfo.size(), 2)
+ TS_ASSERT_EQUALS(detInfo.scanCount(0), 4)
+ TS_ASSERT_EQUALS(detInfo.scanCount(1), 4)
+ assert_scan_intervals_are_correct(detInfo, true);
+
+ const auto &specInfo = outputWS->spectrumInfo();
+ TS_ASSERT_EQUALS(specInfo.size(), 8)
+
+ assert_scanning_indexing_is_correct(specInfo, true);
+ assert_scanning_histograms_correctly_set(outputWS);
+ }
+
+ void
+ test_merging_detector_scan_workspaces_with_overlapping_time_intervals_throws() {
+ auto ws = create_group_detector_scan_workspaces(2, 1);
+
+ MergeRuns alg;
+ alg.initialize();
+ alg.setChild(true);
+ alg.setPropertyValue("InputWorkspaces", ws->getName());
+ alg.setPropertyValue("OutputWorkspace", "outWS");
+ TS_ASSERT_THROWS_EQUALS(
+ alg.execute(), const std::runtime_error &e, std::string(e.what()),
+ "Cannot merge DetectorInfo: scan intervals overlap but not identical")
+ }
+
+ void test_merging_detector_scan_workspaces_does_not_append_workspaces() {
+ auto outputWS = do_MergeRuns_with_scanning_workspaces();
+
+ TS_ASSERT_EQUALS(outputWS->detectorInfo().size(), 2)
+ TS_ASSERT_EQUALS(outputWS->detectorInfo().scanCount(0), 2)
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(), 4)
+
+ // Check bins are set correctly
+ TS_ASSERT_EQUALS(outputWS->histogram(0).y()[0], 3)
+ TS_ASSERT_EQUALS(outputWS->histogram(1).y()[0], 3)
+ TS_ASSERT_EQUALS(outputWS->histogram(2).y()[0], 3)
+ TS_ASSERT_EQUALS(outputWS->histogram(3).y()[0], 3)
+ }
+
+ void test_merging_detector_scan_workspaces_with_different_positions_throws() {
+ auto ws = create_group_detector_scan_workspaces(2);
+
+ auto wsA =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>("a1");
+
+ wsA->mutableDetectorInfo().setPosition(std::pair<size_t, size_t>(0, 0),
+ V3D(5, 6, 7));
+ MergeRuns alg;
+ alg.initialize();
+ alg.setChild(true);
+ alg.setPropertyValue("InputWorkspaces", ws->getName());
+ alg.setPropertyValue("OutputWorkspace", "outWS");
+ TS_ASSERT_THROWS_EQUALS(alg.execute(), const std::runtime_error &e,
+ std::string(e.what()), "Cannot merge DetectorInfo: "
+ "matching scan interval but "
+ "positions differ")
+ }
+
+ void test_merging_partially_overlapping_detector_scan_workspaces_throws() {
+ MatrixWorkspace_sptr a = WorkspaceCreationHelper::
+ create2DDetectorScanWorkspaceWithFullInstrument(2, 1000, 2, 0);
+ MatrixWorkspace_sptr b = WorkspaceCreationHelper::
+ create2DDetectorScanWorkspaceWithFullInstrument(2, 1000, 2, 1, 2);
+
+ AnalysisDataService::Instance().addOrReplace("a", a);
+ AnalysisDataService::Instance().addOrReplace("b", b);
+
+ MergeRuns alg;
+ alg.initialize();
+ alg.setChild(true);
+ alg.setPropertyValue("InputWorkspaces", "a, b");
+ alg.setPropertyValue("OutputWorkspace", "outWS");
+ TS_ASSERT_THROWS_EQUALS(
+ alg.execute(), const std::runtime_error &e, std::string(e.what()),
+ "Unexpected DetectorInfo size. Merging workspaces with some, but not "
+ "all overlapping scan intervals is not currently supported.")
+ }
+
+ void test_merging_detector_scan_workspaces_failure_case() {
+ auto ws = create_group_detector_scan_workspaces(2);
+
+ auto wsA =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>("a1");
+ Property *prop1 = new PropertyWithValue<int>("prop1", 1);
+ wsA->mutableRun().addLogData(prop1);
+
+ auto wsB =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>("b1");
+ Property *prop2 = new PropertyWithValue<int>("prop1", 2);
+ wsB->mutableRun().addLogData(prop2);
+
+ MergeRuns alg;
+ alg.initialize();
+ alg.setPropertyValue("InputWorkspaces", ws->getName());
+ alg.setPropertyValue("OutputWorkspace", "outWS");
+ alg.setPropertyValue("SampleLogsFail", "prop1");
+
+ TS_ASSERT_THROWS_NOTHING(alg.execute();)
+
+ MatrixWorkspace_sptr outputWS;
+ TS_ASSERT_THROWS_NOTHING(
+ outputWS = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
+ "outWS"));
+
+ TS_ASSERT_EQUALS(outputWS->detectorInfo().size(), 2)
+ TS_ASSERT_EQUALS(outputWS->detectorInfo().scanCount(0), 2)
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(), 4)
+
+ // Check bins are set correctly
+ TS_ASSERT_EQUALS(outputWS->histogram(0).y()[0], 1)
+ TS_ASSERT_EQUALS(outputWS->histogram(1).y()[0], 1)
+ TS_ASSERT_EQUALS(outputWS->histogram(2).y()[0], 1)
+ TS_ASSERT_EQUALS(outputWS->histogram(3).y()[0], 1)
+ }
};
#endif /*MERGERUNSTEST_H_*/
diff --git a/Framework/Algorithms/test/ReflectometryReductionOne2Test.h b/Framework/Algorithms/test/ReflectometryReductionOne2Test.h
index a81db535a25473585f77dc4c8a3e26cb88f5bd66..66c6b76ee504fe00e961d1d49d8b648e56261ad7 100644
--- a/Framework/Algorithms/test/ReflectometryReductionOne2Test.h
+++ b/Framework/Algorithms/test/ReflectometryReductionOne2Test.h
@@ -18,6 +18,7 @@ using namespace WorkspaceCreationHelper;
class ReflectometryReductionOne2Test : public CxxTest::TestSuite {
private:
+ MatrixWorkspace_sptr m_singleDetectorWS;
MatrixWorkspace_sptr m_multiDetectorWS;
MatrixWorkspace_sptr m_transmissionWS;
@@ -33,6 +34,8 @@ public:
ReflectometryReductionOne2Test() {
FrameworkManager::Instance();
+ // A single detector ws
+ m_singleDetectorWS = create2DWorkspaceWithReflectometryInstrument(0);
// A multi detector ws
m_multiDetectorWS =
create2DWorkspaceWithReflectometryInstrumentMultiDetector(0, 0.1);
@@ -447,12 +450,12 @@ public:
alg.setProperty("ThetaIn", 25.0);
MatrixWorkspace_sptr outLam = runAlgorithmLam(alg, 12);
- TS_ASSERT_DELTA(outLam->x(0)[0], 0.927132, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[3], 5.165740, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[7], 10.817217, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[0], 2.773699, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[3], 2.828460, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[7], 2.816935, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[0], 0.934991, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[3], 5.173599, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[7], 10.825076, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[0], 2.768185, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[3], 2.792649, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[7], 2.787410, 1e-6);
}
void test_sum_in_q_non_flat_sample() {
@@ -469,12 +472,12 @@ public:
alg.setProperty("ReductionType", "NonFlatSample");
MatrixWorkspace_sptr outLam = runAlgorithmLam(alg, 10);
- TS_ASSERT_DELTA(outLam->x(0)[0], 0.822974, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[3], 5.061582, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[7], 10.713059, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[0], 3.140302, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[3], 3.140457, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[7], 3.140644, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[0], 0.825488, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[3], 5.064095, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[7], 10.715573, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[0], 3.141858, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[3], 3.141885, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[7], 3.141920, 1e-6);
}
void test_sum_in_q_direct_beam() {
@@ -492,12 +495,12 @@ public:
alg.setProperty("ThetaIn", 25.0);
MatrixWorkspace_sptr outLam = runAlgorithmLam(alg, 11);
- TS_ASSERT_DELTA(outLam->x(0)[0], 0.913144, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[3], 5.151752, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[7], 10.803229, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[0], 0.447237, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[3], 0.454605, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[7], 0.451946, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[0], 0.920496, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[3], 5.159104, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[7], 10.810581, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[0], 0.446571, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[3], 0.449843, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[7], 0.448591, 1e-6);
}
void test_sum_in_q_monitor_normalization() {
@@ -527,12 +530,12 @@ public:
alg.setProperty("ThetaIn", 25.0);
MatrixWorkspace_sptr outLam = runAlgorithmLam(alg, 13);
- TS_ASSERT_DELTA(outLam->x(0)[0], -0.742692, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[5], 6.321654, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[9], 11.973131, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[0], 5.044175, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[5], 2.118472, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[9], 2.280546, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[0], -0.748671, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[5], 6.315674, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[9], 11.967151, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[0], 5.040302, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[5], 2.193649, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[9], 2.255101, 1e-6);
}
void test_sum_in_q_transmission_correction_run() {
@@ -546,12 +549,12 @@ public:
alg.setProperty("ThetaIn", 25.0);
MatrixWorkspace_sptr outLam = runAlgorithmLam(alg, 12);
- TS_ASSERT_DELTA(outLam->x(0)[0], 0.927132, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[3], 5.165740, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[7], 10.817217, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[0], 0.620714, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[3], 0.899935, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[7], 0.896268, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[0], 0.934991, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[3], 5.173599, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[7], 10.825076, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[0], 0.631775, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[3], 0.888541, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[7], 0.886874, 1e-6);
}
void test_sum_in_q_exponential_correction() {
@@ -567,12 +570,12 @@ public:
alg.setProperty("C1", 0.1);
MatrixWorkspace_sptr outLam = runAlgorithmLam(alg, 11);
- TS_ASSERT_DELTA(outLam->x(0)[0], 0.913144, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[3], 5.151752, 1e-6);
- TS_ASSERT_DELTA(outLam->x(0)[7], 10.803229, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[0], 16.353662, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[3], 24.261270, 1e-6);
- TS_ASSERT_DELTA(outLam->y(0)[7], 39.844321, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[0], 0.920496, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[3], 5.159104, 1e-6);
+ TS_ASSERT_DELTA(outLam->x(0)[7], 10.810581, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[0], 16.351599, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[3], 23.963539, 1e-6);
+ TS_ASSERT_DELTA(outLam->y(0)[7], 39.756738, 1e-6);
}
void test_sum_in_q_IvsQ() {
@@ -590,13 +593,38 @@ public:
MatrixWorkspace_sptr outQ = runAlgorithmQ(alg, 11);
// X range in outQ
- TS_ASSERT_DELTA(outQ->x(0)[0], 0.292253, 1e-6);
- TS_ASSERT_DELTA(outQ->x(0)[3], 0.393656, 1e-6);
- TS_ASSERT_DELTA(outQ->x(0)[7], 0.732554, 1e-6);
+ TS_ASSERT_DELTA(outQ->x(0)[0], 0.292122, 1e-6);
+ TS_ASSERT_DELTA(outQ->x(0)[3], 0.393419, 1e-6);
+ TS_ASSERT_DELTA(outQ->x(0)[7], 0.731734, 1e-6);
// Y counts
- TS_ASSERT_DELTA(outQ->y(0)[0], 2.891639, 1e-6);
- TS_ASSERT_DELTA(outQ->y(0)[3], 2.854571, 1e-6);
- TS_ASSERT_DELTA(outQ->y(0)[7], 2.871364, 1e-6);
+ TS_ASSERT_DELTA(outQ->y(0)[0], 2.852088, 1e-6);
+ TS_ASSERT_DELTA(outQ->y(0)[3], 2.833380, 1e-6);
+ TS_ASSERT_DELTA(outQ->y(0)[7], 2.841288, 1e-6);
+ }
+
+ void test_sum_in_q_IvsQ_point_detector() {
+ // Test IvsQ workspace for a point detector
+ // No monitor normalization
+ // No direct beam normalization
+ // No transmission correction
+ // Processing instructions : 0
+
+ ReflectometryReductionOne2 alg;
+ setupAlgorithm(alg, 1.5, 15.0, "0");
+ alg.setProperty("InputWorkspace", m_singleDetectorWS);
+ alg.setProperty("SummationType", "SumInQ");
+ alg.setProperty("ReductionType", "DivergentBeam");
+ alg.setProperty("ThetaIn", 25.0);
+ MatrixWorkspace_sptr outQ = runAlgorithmQ(alg, 28);
+
+ // X range in outQ
+ TS_ASSERT_DELTA(outQ->x(0)[0], 0.279882, 1e-6);
+ TS_ASSERT_DELTA(outQ->x(0)[3], 0.310524, 1e-6);
+ TS_ASSERT_DELTA(outQ->x(0)[7], 0.363599, 1e-6);
+ // Y counts
+ TS_ASSERT_DELTA(outQ->y(0)[0], 2.900305, 1e-6);
+ TS_ASSERT_DELTA(outQ->y(0)[3], 2.886947, 1e-6);
+ TS_ASSERT_DELTA(outQ->y(0)[7], 2.607359, 1e-6);
}
private:
diff --git a/Framework/Algorithms/test/RunCombinationHelperTest.h b/Framework/Algorithms/test/RunCombinationHelperTest.h
index 009a416f0f8755e77749c9bbe5393db5949e42c4..3545278c02b8566f13f1ef4bde72be731ae3138d 100644
--- a/Framework/Algorithms/test/RunCombinationHelperTest.h
+++ b/Framework/Algorithms/test/RunCombinationHelperTest.h
@@ -4,15 +4,19 @@
#include <cxxtest/TestSuite.h>
#include "MantidAlgorithms/RunCombinationHelpers/RunCombinationHelper.h"
+#include "MantidAPI/FrameworkManager.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidGeometry/Instrument/DetectorInfo.h"
+#include "MantidAlgorithms/CreateSampleWorkspace.h"
#include "MantidAlgorithms/GroupWorkspaces.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
using Mantid::Algorithms::RunCombinationHelper;
using Mantid::Algorithms::GroupWorkspaces;
+using Mantid::Algorithms::CreateSampleWorkspace;
using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace WorkspaceCreationHelper;
@@ -118,6 +122,34 @@ public:
"different X units; different spectrum axis units; ");
}
+ void test_scanning_workspaces_throw_no_error() {
+ const auto scanWS1 = createSampleScanningWorkspace(2);
+ const auto scanWS2 = createSampleScanningWorkspace(2);
+
+ m_testee.setReferenceProperties(scanWS1);
+ TS_ASSERT(m_testee.checkCompatibility(scanWS2).empty());
+ }
+
+ void test_mix_of_scanning_and_non_scanning_workspaces_throws_error() {
+ const auto scanWS = createSampleScanningWorkspace(2);
+ const auto nonScanWS = createSampleScanningWorkspace(1);
+
+ m_testee.setReferenceProperties(scanWS);
+ TS_ASSERT_EQUALS(m_testee.checkCompatibility(nonScanWS),
+ "a mix of workspaces with and without detector scans; ");
+ }
+
+ void
+ test_scanning_workspaces_with_different_numbers_of_detectors_throws_error() {
+ const auto scanWS1 = createSampleScanningWorkspace(2);
+ const auto scanWS2 = createSampleScanningWorkspace(2, 5);
+
+ m_testee.setReferenceProperties(scanWS1);
+ TS_ASSERT_EQUALS(m_testee.checkCompatibility(scanWS2),
+ "workspaces with detectors scans have different number of "
+ "detectors; ");
+ }
+
private:
void setUnits(MatrixWorkspace_sptr ws) {
ws->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
@@ -125,6 +157,12 @@ private:
ws->setYUnit("Counts");
}
+ MatrixWorkspace_sptr createSampleScanningWorkspace(int nTimeIndexes,
+ int nhist = 2) {
+ return create2DDetectorScanWorkspaceWithFullInstrument(
+ nhist, 3, nTimeIndexes, 0, 1, true, false, true, "test");
+ }
+
RunCombinationHelper m_testee;
MatrixWorkspace_sptr m_reference;
};
diff --git a/Framework/Beamline/inc/MantidBeamline/DetectorInfo.h b/Framework/Beamline/inc/MantidBeamline/DetectorInfo.h
index 954a3ed5017f0fda005ed07e33b855143fb8ac39..a64ba14dd840dfeb6f70130fbcf22cdb1963a7a7 100644
--- a/Framework/Beamline/inc/MantidBeamline/DetectorInfo.h
+++ b/Framework/Beamline/inc/MantidBeamline/DetectorInfo.h
@@ -69,6 +69,7 @@ public:
bool isEquivalent(const DetectorInfo &other) const;
size_t size() const;
+ size_t scanSize() const;
bool isScanning() const;
bool isMonitor(const size_t index) const;
diff --git a/Framework/Beamline/src/DetectorInfo.cpp b/Framework/Beamline/src/DetectorInfo.cpp
index f3ce7ccaa36937a4a5fd1043d1fc9ded9f86ace7..8c51b6ceed9e596a941390e41e73cc7aea6205ba 100644
--- a/Framework/Beamline/src/DetectorInfo.cpp
+++ b/Framework/Beamline/src/DetectorInfo.cpp
@@ -91,6 +91,17 @@ bool DetectorInfo::isEquivalent(const DetectorInfo &other) const {
return true;
}
+/** Returns the number of sum of the scan intervals for every detector in the
+ *instrument.
+ *
+ * If a detector is moving, i.e., has more than one associated position, every
+ *position is counted. */
+size_t DetectorInfo::scanSize() const {
+ if (!m_positions)
+ return 0;
+ return m_positions->size();
+}
+
/// Returns true if the detector with given detector index is a monitor.
bool DetectorInfo::isMonitor(const size_t index) const {
// No check for time dependence since monitor flags are not time dependent.
diff --git a/Framework/Beamline/test/DetectorInfoTest.h b/Framework/Beamline/test/DetectorInfoTest.h
index fcb46c74164b9054c2924af3ee79b9ed948427c8..8df5354997fb2a524e660c1e44a4d1dbc251d661 100644
--- a/Framework/Beamline/test/DetectorInfoTest.h
+++ b/Framework/Beamline/test/DetectorInfoTest.h
@@ -23,6 +23,7 @@ public:
std::unique_ptr<DetectorInfo> detInfo;
TS_ASSERT_THROWS_NOTHING(detInfo = Kernel::make_unique<DetectorInfo>());
TS_ASSERT_EQUALS(detInfo->size(), 0);
+ TS_ASSERT_EQUALS(detInfo->scanSize(), 0);
TS_ASSERT(!detInfo->isScanning());
TS_ASSERT(!detInfo->hasComponentInfo());
@@ -39,6 +40,7 @@ public:
TS_ASSERT_THROWS_NOTHING(
info = Kernel::make_unique<DetectorInfo>(PosVec(3), RotVec(3), mons));
TS_ASSERT_EQUALS(info->size(), 3);
+ TS_ASSERT_EQUALS(info->scanSize(), 3);
TS_ASSERT_THROWS_NOTHING(DetectorInfo(PosVec(3), RotVec(3), {}));
TS_ASSERT_THROWS_NOTHING(DetectorInfo(PosVec(3), RotVec(3), {0}));
TS_ASSERT_THROWS_NOTHING(DetectorInfo(PosVec(3), RotVec(3), {0, 1, 2}));
@@ -521,6 +523,7 @@ public:
TS_ASSERT(a.isScanning());
TS_ASSERT(!a.isEquivalent(b));
TS_ASSERT_EQUALS(a.size(), 2);
+ TS_ASSERT_EQUALS(a.scanSize(), 3);
TS_ASSERT_EQUALS(a.scanCount(0), 2);
// Note that the order is not guaranteed, currently these are just in the
// order in which the are merged.
@@ -547,6 +550,7 @@ public:
TS_ASSERT(a.isScanning());
TS_ASSERT(!a.isEquivalent(b));
TS_ASSERT_EQUALS(a.size(), 2);
+ TS_ASSERT_EQUALS(a.scanSize(), 4);
TS_ASSERT_EQUALS(a.scanCount(0), 2);
TS_ASSERT_EQUALS(a.scanCount(1), 2);
// Note that the order is not guaranteed, currently these are just in the
@@ -607,6 +611,7 @@ public:
TS_ASSERT(!a.isEquivalent(b));
TS_ASSERT(!a.isEquivalent(c));
TS_ASSERT_EQUALS(a.size(), 2);
+ TS_ASSERT_EQUALS(a.scanSize(), 4);
TS_ASSERT_EQUALS(a.scanCount(0), 3);
TS_ASSERT_EQUALS(a.scanInterval({0, 0}), interval1);
TS_ASSERT_EQUALS(a.scanInterval({0, 1}), interval2);
@@ -640,6 +645,7 @@ public:
TS_ASSERT(!a.isEquivalent(b));
TS_ASSERT(!a.isEquivalent(c));
TS_ASSERT_EQUALS(a.size(), 2);
+ TS_ASSERT_EQUALS(a.scanSize(), 6);
TS_ASSERT_EQUALS(a.scanCount(0), 3);
TS_ASSERT_EQUALS(a.scanCount(1), 3);
TS_ASSERT_EQUALS(a.scanInterval({0, 0}), interval1);
diff --git a/Framework/Crystal/src/PeakHKLErrors.cpp b/Framework/Crystal/src/PeakHKLErrors.cpp
index cccd488248ddfcb56420e10905411ddbcdb0bdee..08e2cac4993df840ad6fa7b85ff76bd66eaf5d8c 100644
--- a/Framework/Crystal/src/PeakHKLErrors.cpp
+++ b/Framework/Crystal/src/PeakHKLErrors.cpp
@@ -51,7 +51,7 @@ void PeakHKLErrors::init() {
declareParameter("GonRotz", 0.0,
"1st Rotation of Goniometer about the z axis");
initMode = 1;
- if (OptRuns == "")
+ if (OptRuns.empty())
return;
initMode = 2;
diff --git a/Framework/Crystal/src/SCDPanelErrors.cpp b/Framework/Crystal/src/SCDPanelErrors.cpp
index 07fd84a64f618a8b3b05eee9563c8f9cdc1497eb..d6da4f78916bdb4fe7d7a27fe6d3987c7f521a27 100644
--- a/Framework/Crystal/src/SCDPanelErrors.cpp
+++ b/Framework/Crystal/src/SCDPanelErrors.cpp
@@ -263,7 +263,7 @@ void SCDPanelErrors::setAttribute(const std::string &attName,
}
FileValidator fval;
std::string error = fval.isValid(fileName);
- if (error == "") {
+ if (error.empty()) {
storeAttributeValue(attName, Attribute(fileName, true));
storeAttributeValue("Workspace", Attribute(""));
} else {
diff --git a/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp b/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp
index 390821af3be5437760ca7a6fd877039181b7760f..1db18580faec19def2ff5663f27bf94881c73300 100644
--- a/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp
+++ b/Framework/CurveFitting/src/Algorithms/ConvertToYSpace.cpp
@@ -289,7 +289,7 @@ void ConvertToYSpace::createOutputWorkspace() {
m_outputWS->setYUnitLabel("");
// q-Space output workspace
- if (getPropertyValue("QWorkspace") != "") {
+ if (!getPropertyValue("QWorkspace").empty()) {
m_qOutputWS = WorkspaceFactory::Instance().create(m_inputWS);
m_qOutputWS->getAxis(0)->unit() = xLabel;
diff --git a/Framework/CurveFitting/src/Algorithms/Fit.cpp b/Framework/CurveFitting/src/Algorithms/Fit.cpp
index a0d584825b5fc0c7eeeee2d8605d4888f4b7652a..95f0f78800031337e3134444e8b879338c782122 100644
--- a/Framework/CurveFitting/src/Algorithms/Fit.cpp
+++ b/Framework/CurveFitting/src/Algorithms/Fit.cpp
@@ -138,7 +138,7 @@ void Fit::copyMinimizerOutput(const API::IFuncMinimizer &minimizer) {
auto &properties = minimizer.getProperties();
for (auto property : properties) {
if ((*property).direction() == Kernel::Direction::Output &&
- (*property).isValid() == "") {
+ (*property).isValid().empty()) {
auto clonedProperty =
std::unique_ptr<Kernel::Property>((*property).clone());
declareProperty(std::move(clonedProperty));
diff --git a/Framework/CurveFitting/src/Algorithms/PlotPeakByLogValue.cpp b/Framework/CurveFitting/src/Algorithms/PlotPeakByLogValue.cpp
index 97d725beb899d6fe4466f15e30a17dd4bf51e52d..b744e8480cf9bf89d9c9dbd6b8dd10653c4684d3 100644
--- a/Framework/CurveFitting/src/Algorithms/PlotPeakByLogValue.cpp
+++ b/Framework/CurveFitting/src/Algorithms/PlotPeakByLogValue.cpp
@@ -646,7 +646,7 @@ std::string PlotPeakByLogValue::getMinimizerString(const std::string &wsName,
dynamic_cast<Mantid::API::WorkspaceProperty<> *>(minimizerProp);
if (wsProp) {
const std::string &wsPropValue = minimizerProp->value();
- if (wsPropValue != "") {
+ if (!wsPropValue.empty()) {
const std::string &wsPropName = minimizerProp->name();
m_minimizerWorkspaces[wsPropName].push_back(wsPropValue);
}
diff --git a/Framework/CurveFitting/src/Algorithms/SplineInterpolation.cpp b/Framework/CurveFitting/src/Algorithms/SplineInterpolation.cpp
index 9cd6f62a1920daf4dab915a1b389015631baa581..1978323b913878a7139faac8ff1427371338052f 100644
--- a/Framework/CurveFitting/src/Algorithms/SplineInterpolation.cpp
+++ b/Framework/CurveFitting/src/Algorithms/SplineInterpolation.cpp
@@ -223,7 +223,7 @@ void SplineInterpolation::exec() {
}
// Store the output workspaces
std::string derivWsName = getPropertyValue("OutputWorkspaceDeriv");
- if (order > 0 && derivWsName != "") {
+ if (order > 0 && !derivWsName.empty()) {
// Store derivatives in a grouped workspace
WorkspaceGroup_sptr wsg = WorkspaceGroup_sptr(new WorkspaceGroup);
for (size_t i = 0; i < histNo; ++i) {
diff --git a/Framework/CurveFitting/src/Functions/CrystalFieldMultiSpectrum.cpp b/Framework/CurveFitting/src/Functions/CrystalFieldMultiSpectrum.cpp
index 7dec77fd50fe295284bc82eff16b8b33c8432078..a9180754a94ca66c49570cd777d6c7431cab2b73 100644
--- a/Framework/CurveFitting/src/Functions/CrystalFieldMultiSpectrum.cpp
+++ b/Framework/CurveFitting/src/Functions/CrystalFieldMultiSpectrum.cpp
@@ -266,7 +266,7 @@ void CrystalFieldMultiSpectrum::calcExcitations(
// using an index instead of a name for performance reasons
auto &source = dynamic_cast<Peaks &>(*m_source);
double intensityScaling;
- if (source.m_IntensityScalingIdx.size() == 0) {
+ if (source.m_IntensityScalingIdx.empty()) {
intensityScaling = getParameter(m_nOwnParams - nSpec + iSpec);
} else {
intensityScaling = getParameter(source.m_IntensityScalingIdx[iSpec]);
diff --git a/Framework/CurveFitting/src/Functions/TabulatedFunction.cpp b/Framework/CurveFitting/src/Functions/TabulatedFunction.cpp
index a10ed3ab8ab1cd167fe5c6b144c5081ca3fe39e7..a9fe5275204464c18984f565e77659b684cba22e 100644
--- a/Framework/CurveFitting/src/Functions/TabulatedFunction.cpp
+++ b/Framework/CurveFitting/src/Functions/TabulatedFunction.cpp
@@ -174,7 +174,7 @@ void TabulatedFunction::setAttribute(const std::string &attName,
}
FileValidator fval;
std::string error = fval.isValid(fileName);
- if (error == "") {
+ if (error.empty()) {
storeAttributeValue(attName, Attribute(fileName, true));
storeAttributeValue("Workspace", Attribute(""));
} else {
diff --git a/Framework/DataHandling/inc/MantidDataHandling/SaveSESANS.h b/Framework/DataHandling/inc/MantidDataHandling/SaveSESANS.h
index 6a7c461d8c82263b3b2ddf245ac90a1795b06099..185f10b0cbf4ab9b92e1f3756688d0d1b64a7706 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/SaveSESANS.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/SaveSESANS.h
@@ -17,11 +17,12 @@ namespace DataHandling {
<UL>
<LI> InputWorkspace - The name of the workspace to save</LI>
<LI> Filename - The path to save the file</LI>
- <LI> ThetaZMax - TODO : Find a good description for this</LI>
+ <LI> ThetaZMax - The angular acceptance in the encoding direction</LI>
<LI> ThetaZMazUnit - Unit for theta_znmax</LI>
- <LI> ThetaYMax - TODO : Find a good description for this</LI>
+ <LI> ThetaYMax - The angular acceptance in the non-encoding direction</LI>
<LI> ThetaYMazUnit - Unit for theta_ymax</LI>
- <LI> EchoConstant - The echo constant
+ <LI> EchoConstant - The spin echo length, in nanometers,
+ probed by a 1A neutron</LI>
</UL>
@author Joseph Ramsay, ISIS
diff --git a/Framework/DataHandling/src/DataBlockComposite.cpp b/Framework/DataHandling/src/DataBlockComposite.cpp
index 73da894721584cf8180be6ef52c776476cc5b804..50d25d844d1a87d2e834b82e15c32e358dab14d9 100644
--- a/Framework/DataHandling/src/DataBlockComposite.cpp
+++ b/Framework/DataHandling/src/DataBlockComposite.cpp
@@ -412,6 +412,7 @@ void DataBlockComposite::removeSpectra(DataBlockComposite &toRemove) {
// Get intervals for the data blocks which should be removed
auto removeBlocks = toRemove.getDataBlocks();
std::vector<std::pair<int64_t, int64_t>> toRemoveIntervals;
+ toRemoveIntervals.reserve(removeBlocks.size());
for (const auto &dataBlock : removeBlocks) {
toRemoveIntervals.emplace_back(dataBlock.getMinSpectrumID(),
dataBlock.getMaxSpectrumID());
diff --git a/Framework/DataHandling/src/DownloadInstrument.cpp b/Framework/DataHandling/src/DownloadInstrument.cpp
index 5bd0af84487f294cd50e03b5147aa47a95407ef7..1b45d90322b641f2f5e3fa1c6cac454bb072bde9 100644
--- a/Framework/DataHandling/src/DownloadInstrument.cpp
+++ b/Framework/DataHandling/src/DownloadInstrument.cpp
@@ -204,7 +204,7 @@ DownloadInstrument::StringToStringMap DownloadInstrument::processRepository() {
if ((sha != installSha) && (sha != localSha)) {
fileMap.emplace(htmlUrl,
filePath.toString()); // ACTION - DOWNLOAD to localPath
- } else if ((localSha != "") && (sha == installSha) &&
+ } else if ((!localSha.empty()) && (sha == installSha) &&
(sha != localSha)) // matches install, but different local
{
fileMap.emplace(
diff --git a/Framework/DataHandling/src/LoadAscii2.cpp b/Framework/DataHandling/src/LoadAscii2.cpp
index e5ccb44c41b46c8b3b262c1f4f4c205941c92a1e..3ffa5ed3b66a2eeec3fbfd0622c02719f9b90e55 100644
--- a/Framework/DataHandling/src/LoadAscii2.cpp
+++ b/Framework/DataHandling/src/LoadAscii2.cpp
@@ -671,7 +671,7 @@ void LoadAscii2::exec() {
std::string sep;
// If the custom separator property is not empty, then we use that under any
// circumstance.
- if (custom != "") {
+ if (!custom.empty()) {
sep = custom;
}
// Else if the separator drop down choice is not UserDefined then we use that.
diff --git a/Framework/DataHandling/src/LoadFITS.cpp b/Framework/DataHandling/src/LoadFITS.cpp
index 0754635782a1e2666c4d2080767dc144d87ef623..694bbb047437c4c6b578030dab7f6793a178b0b1 100644
--- a/Framework/DataHandling/src/LoadFITS.cpp
+++ b/Framework/DataHandling/src/LoadFITS.cpp
@@ -293,7 +293,7 @@ void LoadFITS::loadHeader(const std::string &filePath, FITSInfo &header) {
}
// scale parameter, header BSCALE in the fits standard
- if ("" == header.headerKeys[m_headerScaleKey]) {
+ if (header.headerKeys[m_headerScaleKey].empty()) {
header.scale = 1;
} else {
try {
@@ -308,7 +308,7 @@ void LoadFITS::loadHeader(const std::string &filePath, FITSInfo &header) {
}
// data offsset parameter, header BZERO in the fits standard
- if ("" == header.headerKeys[m_headerOffsetKey]) {
+ if (header.headerKeys[m_headerOffsetKey].empty()) {
header.offset = 0;
} else {
try {
@@ -361,7 +361,7 @@ void LoadFITS::loadHeader(const std::string &filePath, FITSInfo &header) {
void LoadFITS::headerSanityCheck(const FITSInfo &hdr,
const FITSInfo &hdrFirst) {
bool valid = true;
- if (hdr.extension != "") {
+ if (!hdr.extension.empty()) {
valid = false;
g_log.error() << "File " << hdr.filePath
<< ": extensions found in the header.\n";
@@ -625,7 +625,7 @@ void LoadFITS::parseHeader(FITSInfo &headerInfo) {
if (key == g_END_KEYNAME)
endFound = true;
- if (key != "")
+ if (!key.empty())
headerInfo.headerKeys[key] = value;
}
}
@@ -1141,7 +1141,7 @@ void LoadFITS::setupDefaultKeywordNames() {
* Maps the header keys to specified values
*/
void LoadFITS::mapHeaderKeys() {
- if ("" == getPropertyValue(g_HEADER_MAP_NAME))
+ if (getPropertyValue(g_HEADER_MAP_NAME).empty())
return;
// If a map file is selected, use that.
@@ -1157,19 +1157,19 @@ void LoadFITS::mapHeaderKeys() {
while (getline(fStream, line)) {
boost::split(lineSplit, line, boost::is_any_of("="));
- if (lineSplit[0] == g_ROTATION_NAME && lineSplit[1] != "")
+ if (lineSplit[0] == g_ROTATION_NAME && !lineSplit[1].empty())
m_headerRotationKey = lineSplit[1];
- if (lineSplit[0] == g_BIT_DEPTH_NAME && lineSplit[1] != "")
+ if (lineSplit[0] == g_BIT_DEPTH_NAME && !lineSplit[1].empty())
m_headerBitDepthKey = lineSplit[1];
- if (lineSplit[0] == g_AXIS_NAMES_NAME && lineSplit[1] != "") {
+ if (lineSplit[0] == g_AXIS_NAMES_NAME && !lineSplit[1].empty()) {
m_headerAxisNameKeys.clear();
boost::split(m_headerAxisNameKeys, lineSplit[1],
boost::is_any_of(","));
}
- if (lineSplit[0] == g_IMAGE_KEY_NAME && lineSplit[1] != "") {
+ if (lineSplit[0] == g_IMAGE_KEY_NAME && !lineSplit[1].empty()) {
m_headerImageKeyKey = lineSplit[1];
}
}
diff --git a/Framework/DataHandling/src/LoadFullprofResolution.cpp b/Framework/DataHandling/src/LoadFullprofResolution.cpp
index 32c8bc93506f25537b1ce06e6e4902bd4996d301..cb0e15e01287afd33a56ae11450e397fa30c3717 100644
--- a/Framework/DataHandling/src/LoadFullprofResolution.cpp
+++ b/Framework/DataHandling/src/LoadFullprofResolution.cpp
@@ -189,7 +189,7 @@ void LoadFullprofResolution::exec() {
// Generate output table workspace
API::ITableWorkspace_sptr outTabWs = genTableWorkspace(bankparammap);
- if (getPropertyValue("OutputTableWorkspace") != "") {
+ if (!getPropertyValue("OutputTableWorkspace").empty()) {
// Output the output table workspace
setProperty("OutputTableWorkspace", outTabWs);
}
@@ -225,7 +225,7 @@ void LoadFullprofResolution::exec() {
loadParamAlg->execute();
}
}
- } else if (getPropertyValue("OutputTableWorkspace") == "") {
+ } else if (getPropertyValue("OutputTableWorkspace").empty()) {
// We don't know where to output
throw std::runtime_error(
"Either the OutputTableWorkspace or Workspace property must be set.");
diff --git a/Framework/DataHandling/src/LoadGSASInstrumentFile.cpp b/Framework/DataHandling/src/LoadGSASInstrumentFile.cpp
index 239ea187ff49047152f221f36e53d16d585be4f9..ca4e25413be5a612a4dec884a2942202e9543b29 100644
--- a/Framework/DataHandling/src/LoadGSASInstrumentFile.cpp
+++ b/Framework/DataHandling/src/LoadGSASInstrumentFile.cpp
@@ -151,7 +151,7 @@ void LoadGSASInstrumentFile::exec() {
WorkspaceGroup_sptr wsg = getProperty("Workspace");
// Generate output table workspace
API::ITableWorkspace_sptr outTabWs = genTableWorkspace(bankparammap);
- if (getPropertyValue("OutputTableWorkspace") != "") {
+ if (!getPropertyValue("OutputTableWorkspace").empty()) {
// Output the output table workspace
setProperty("OutputTableWorkspace", outTabWs);
}
diff --git a/Framework/DataHandling/src/LoadIDFFromNexus.cpp b/Framework/DataHandling/src/LoadIDFFromNexus.cpp
index f68ae54eb58d351ee064453a00349d043824e8ed..74305f3eedfbe26a71f97511f9b6c905e52a2abd 100644
--- a/Framework/DataHandling/src/LoadIDFFromNexus.cpp
+++ b/Framework/DataHandling/src/LoadIDFFromNexus.cpp
@@ -88,7 +88,7 @@ void LoadIDFFromNexus::exec() {
// Look for parameter correction file
std::string parameterCorrectionFile =
getPropertyValue("ParameterCorrectionFilePath");
- if (parameterCorrectionFile == "") {
+ if (parameterCorrectionFile.empty()) {
parameterCorrectionFile =
getParameterCorrectionFile(localWorkspace->getInstrument()->getName());
}
@@ -98,7 +98,7 @@ void LoadIDFFromNexus::exec() {
// Read parameter correction file, if found
std::string correctionParameterFile;
bool append = false;
- if (parameterCorrectionFile != "") {
+ if (!parameterCorrectionFile.empty()) {
// Read parameter correction file
// to find out which parameter file to use
// and whether it is appended to default parameters.
@@ -112,7 +112,7 @@ void LoadIDFFromNexus::exec() {
// Load default parameters if either there is no correction parameter file or
// it is to be appended.
- if (correctionParameterFile == "" || append) {
+ if (correctionParameterFile.empty() || append) {
LoadParameters(&nxfile, localWorkspace);
} else { // Else clear the parameters
g_log.notice() << "Parameters to be replaced are cleared.\n";
@@ -120,7 +120,7 @@ void LoadIDFFromNexus::exec() {
}
// Load parameters from correction parameter file, if it exists
- if (correctionParameterFile != "") {
+ if (!correctionParameterFile.empty()) {
Poco::Path corrFilePath(parameterCorrectionFile);
g_log.debug() << "Correction file path: " << corrFilePath.toString()
<< "\n";
@@ -200,7 +200,7 @@ void LoadIDFFromNexus::readParameterCorrectionFile(
append = false;
// Check the date.
- if (date == "") {
+ if (date.empty()) {
g_log.notice() << "No date is supplied for parameter correction file "
<< correction_file << ". Correction file is ignored.\n";
return;
diff --git a/Framework/DataHandling/src/LoadILLDiffraction.cpp b/Framework/DataHandling/src/LoadILLDiffraction.cpp
index 707c1e4661b527c36f25c600b3d8d85ece95de9f..f04af6189a05e10c1f842ad5e917aba0237955e1 100644
--- a/Framework/DataHandling/src/LoadILLDiffraction.cpp
+++ b/Framework/DataHandling/src/LoadILLDiffraction.cpp
@@ -480,7 +480,7 @@ std::vector<double> LoadILLDiffraction::getScannedVaribleByPropertyName(
}
}
- if (scannedVariable.size() == 0)
+ if (scannedVariable.empty())
throw std::runtime_error(
"Can not load file because scanned variable with property name " +
propertyName + " was not found");
diff --git a/Framework/DataHandling/src/LoadILLIndirect2.cpp b/Framework/DataHandling/src/LoadILLIndirect2.cpp
index 4a40a4d3eb8c1a6041b6cf02746190d1be245d6d..9360967a296c627d32fd0d4707f02cd177d87ce5 100644
--- a/Framework/DataHandling/src/LoadILLIndirect2.cpp
+++ b/Framework/DataHandling/src/LoadILLIndirect2.cpp
@@ -130,7 +130,7 @@ void LoadILLIndirect2::exec() {
void LoadILLIndirect2::setInstrumentName(
const NeXus::NXEntry &firstEntry, const std::string &instrumentNamePath) {
- if (instrumentNamePath == "") {
+ if (instrumentNamePath.empty()) {
std::string message("Cannot set the instrument name from the Nexus file!");
g_log.error(message);
throw std::runtime_error(message);
diff --git a/Framework/DataHandling/src/LoadILLReflectometry.cpp b/Framework/DataHandling/src/LoadILLReflectometry.cpp
index 8a5b69d8b49a622c19b667de27f1fe062e352fc3..f5f647ae8293b110d1457b82e47dbcb28641bdf1 100644
--- a/Framework/DataHandling/src/LoadILLReflectometry.cpp
+++ b/Framework/DataHandling/src/LoadILLReflectometry.cpp
@@ -176,7 +176,7 @@ void LoadILLReflectometry::exec() {
void LoadILLReflectometry::setInstrumentName(
const NeXus::NXEntry &firstEntry, const std::string &instrumentNamePath) {
- if (instrumentNamePath == "") {
+ if (instrumentNamePath.empty()) {
std::string message("Cannot set the instrument name from the Nexus file!");
g_log.error(message);
throw std::runtime_error(message);
diff --git a/Framework/DataHandling/src/LoadILLSANS.cpp b/Framework/DataHandling/src/LoadILLSANS.cpp
index 4e04e099d398ab98adc552eb294f460eb6c5f790..b9c0d3667cb8c838b019b135c8574639b6e48914 100644
--- a/Framework/DataHandling/src/LoadILLSANS.cpp
+++ b/Framework/DataHandling/src/LoadILLSANS.cpp
@@ -107,7 +107,7 @@ void LoadILLSANS::exec() {
void LoadILLSANS::setInstrumentName(const NeXus::NXEntry &firstEntry,
const std::string &instrumentNamePath) {
- if (instrumentNamePath == "") {
+ if (instrumentNamePath.empty()) {
std::string message("Cannot set the instrument name from the Nexus file!");
g_log.error(message);
throw std::runtime_error(message);
diff --git a/Framework/DataHandling/src/LoadILLTOF2.cpp b/Framework/DataHandling/src/LoadILLTOF2.cpp
index 50f76c1d0245aa0fb47e150412614312bc4f9e88..9cc3f2e0a7070bf0101ccfd29655e4acf10c3899 100644
--- a/Framework/DataHandling/src/LoadILLTOF2.cpp
+++ b/Framework/DataHandling/src/LoadILLTOF2.cpp
@@ -144,7 +144,7 @@ void LoadILLTOF2::loadInstrumentDetails(NeXus::NXEntry &firstEntry) {
m_instrumentPath = m_loader.findInstrumentNexusPath(firstEntry);
- if (m_instrumentPath == "") {
+ if (m_instrumentPath.empty()) {
throw std::runtime_error(
"Cannot set the instrument name from the Nexus file!");
}
diff --git a/Framework/DataHandling/src/LoadIsawDetCal.cpp b/Framework/DataHandling/src/LoadIsawDetCal.cpp
index f2a479594d1dc83a2400d48665e0a06a681d3210..54638a6518b1b4a2d2dfae8e931dea9cc74fb345 100644
--- a/Framework/DataHandling/src/LoadIsawDetCal.cpp
+++ b/Framework/DataHandling/src/LoadIsawDetCal.cpp
@@ -92,7 +92,7 @@ std::map<std::string, std::string> LoadIsawDetCal::validateInputs() {
// two detcal files is only valid for snap
std::vector<std::string> filenames = getFilenames();
- if (filenames.size() == 0) {
+ if (filenames.empty()) {
result["Filename"] = "Must supply .detcal file";
} else if (filenames.size() == 2) {
Workspace_const_sptr wksp = getProperty("InputWorkspace");
diff --git a/Framework/DataHandling/src/LoadLLB.cpp b/Framework/DataHandling/src/LoadLLB.cpp
index 83f047c87824f9ae25676b5a12dfb0baa1543b7b..6599483496a88d39b8bb412576b4539f2a9a867b 100644
--- a/Framework/DataHandling/src/LoadLLB.cpp
+++ b/Framework/DataHandling/src/LoadLLB.cpp
@@ -104,7 +104,7 @@ void LoadLLB::setInstrumentName(NeXus::NXEntry &entry) {
m_instrumentName =
m_loader.getStringFromNexusPath(entry, m_instrumentPath + "/name");
- if (m_instrumentName == "") {
+ if (m_instrumentName.empty()) {
throw std::runtime_error(
"Cannot read the instrument name from the Nexus file!");
}
diff --git a/Framework/DataHandling/src/LoadMLZ.cpp b/Framework/DataHandling/src/LoadMLZ.cpp
index 1ad5df0508499856145ab39f86435dfc5956a9cf..23159b7e7906fa1d292d109799748df2adcff780 100644
--- a/Framework/DataHandling/src/LoadMLZ.cpp
+++ b/Framework/DataHandling/src/LoadMLZ.cpp
@@ -149,7 +149,7 @@ void LoadMLZ::loadInstrumentDetails(NeXus::NXEntry &firstEntry) {
m_instrumentPath = m_mlzloader.findInstrumentNexusPath(firstEntry);
- if (m_instrumentPath == "") {
+ if (m_instrumentPath.empty()) {
throw std::runtime_error(
"Cannot set the instrument name from the Nexus file!");
}
diff --git a/Framework/DataHandling/src/LoadSINQFocus.cpp b/Framework/DataHandling/src/LoadSINQFocus.cpp
index d7a6a56b7bae9efbc38ec8c7c1bf29f8e529b04b..3494437cfa328e6b800cd8cdf2bdc7615a251e3f 100644
--- a/Framework/DataHandling/src/LoadSINQFocus.cpp
+++ b/Framework/DataHandling/src/LoadSINQFocus.cpp
@@ -112,7 +112,7 @@ void LoadSINQFocus::setInstrumentName(NeXus::NXEntry &entry) {
m_instrumentPath = m_loader.findInstrumentNexusPath(entry);
- if (m_instrumentPath == "") {
+ if (m_instrumentPath.empty()) {
throw std::runtime_error(
"Cannot set the instrument name from the Nexus file!");
}
diff --git a/Framework/DataHandling/src/LoadSassena.cpp b/Framework/DataHandling/src/LoadSassena.cpp
index 3713595548fa142b7461364372b931ab719b8f00..ba2054ea9fd5b72345ba5ad38a7d7abaf6aa8ebc 100644
--- a/Framework/DataHandling/src/LoadSassena.cpp
+++ b/Framework/DataHandling/src/LoadSassena.cpp
@@ -136,6 +136,7 @@ LoadSassena::loadQvectors(const hid_t &h5file, API::WorkspaceGroup_sptr gws,
if (getProperty("SortByQVectors")) {
std::vector<mypair> qvmodpair;
+ qvmodpair.reserve(nq);
for (int iq = 0; iq < nq; iq++)
qvmodpair.emplace_back(qvmod[iq], iq);
std::sort(qvmodpair.begin(), qvmodpair.end(), compare);
diff --git a/Framework/DataHandling/src/LoadSpice2D.cpp b/Framework/DataHandling/src/LoadSpice2D.cpp
index c6a47228130e52fe6c0781238a51dbfcd691786c..04096230e33114217af96c9348b82ed5c73dd46e 100644
--- a/Framework/DataHandling/src/LoadSpice2D.cpp
+++ b/Framework/DataHandling/src/LoadSpice2D.cpp
@@ -468,6 +468,7 @@ void LoadSpice2D::setBeamTrapRunProperty(
// store trap diameters in use
std::vector<double> trapDiametersInUse;
+ trapDiametersInUse.reserve(trapIndexInUse.size());
for (auto index : trapIndexInUse) {
trapDiametersInUse.push_back(trapDiameters[index]);
}
diff --git a/Framework/DataHandling/src/LoadSpiceXML2DDet.cpp b/Framework/DataHandling/src/LoadSpiceXML2DDet.cpp
index eb82237827233b88a0bdd756785990ad0460ec80..f8eda027c8d1960e700628c4e700621d8d0eb0f5 100644
--- a/Framework/DataHandling/src/LoadSpiceXML2DDet.cpp
+++ b/Framework/DataHandling/src/LoadSpiceXML2DDet.cpp
@@ -231,7 +231,7 @@ void LoadSpiceXML2DDet::processInputs() {
if (vec_pixelgeom.size() == 2) {
m_numPixelX = vec_pixelgeom[0];
m_numPixelY = vec_pixelgeom[1];
- } else if (vec_pixelgeom.size() == 0) {
+ } else if (vec_pixelgeom.empty()) {
m_numPixelX = 0;
m_numPixelY = 0;
} else {
@@ -714,7 +714,7 @@ LoadSpiceXML2DDet::parseDetectorNode(const std::string &detvaluestr,
size_t num_empty_line = 0;
size_t num_weird_line = 0;
for (size_t iline = 0; iline < vecLines.size(); ++iline) {
- if (vecLines[iline].size() == 0)
+ if (vecLines[iline].empty())
++num_empty_line;
else if (vecLines[iline].size() < 100)
++num_weird_line;
diff --git a/Framework/DataHandling/src/LoadTBL.cpp b/Framework/DataHandling/src/LoadTBL.cpp
index 1eeaff23a342af8e5aa0729defd686fe1bccbe2f..b5ab7f31e6329b39b45803ba8f5642188566c3ec 100644
--- a/Framework/DataHandling/src/LoadTBL.cpp
+++ b/Framework/DataHandling/src/LoadTBL.cpp
@@ -342,7 +342,7 @@ void LoadTBL::exec() {
std::string line;
int stitchID = 1;
while (Kernel::Strings::extractToEOL(file, line)) {
- if (line == "" || line == ",,,,,,,,,,,,,,,,") {
+ if (line.empty() || line == ",,,,,,,,,,,,,,,,") {
continue;
}
getCells(line, rowVec, 16, isOld);
@@ -351,8 +351,8 @@ void LoadTBL::exec() {
// check if the first run in the row has any data associated with it
// 0 = runs, 1 = theta, 2 = trans, 3 = qmin, 4 = qmax
- if (rowVec[0] != "" || rowVec[1] != "" || rowVec[2] != "" ||
- rowVec[3] != "" || rowVec[4] != "") {
+ if (!rowVec[0].empty() || !rowVec[1].empty() || !rowVec[2].empty() ||
+ !rowVec[3].empty() || !rowVec[4].empty()) {
TableRow row = ws->appendRow();
row << stitchStr;
for (int i = 0; i < 5; ++i) {
@@ -364,8 +364,8 @@ void LoadTBL::exec() {
// check if the second run in the row has any data associated with it
// 5 = runs, 6 = theta, 7 = trans, 8 = qmin, 9 = qmax
- if (rowVec[5] != "" || rowVec[6] != "" || rowVec[7] != "" ||
- rowVec[8] != "" || rowVec[9] != "") {
+ if (!rowVec[5].empty() || !rowVec[6].empty() || !rowVec[7].empty() ||
+ !rowVec[8].empty() || !rowVec[9].empty()) {
TableRow row = ws->appendRow();
row << stitchStr;
for (int i = 5; i < 10; ++i) {
@@ -377,8 +377,8 @@ void LoadTBL::exec() {
// check if the third run in the row has any data associated with it
// 10 = runs, 11 = theta, 12 = trans, 13 = qmin, 14 = qmax
- if (rowVec[10] != "" || rowVec[11] != "" || rowVec[12] != "" ||
- rowVec[13] != "" || rowVec[14] != "") {
+ if (!rowVec[10].empty() || !rowVec[11].empty() || !rowVec[12].empty() ||
+ !rowVec[13].empty() || !rowVec[14].empty()) {
TableRow row = ws->appendRow();
row << stitchStr;
for (int i = 10; i < 17; ++i) {
@@ -413,7 +413,7 @@ void LoadTBL::exec() {
}
size_t expectedCommas = columnHeadings.size() - 1;
while (Kernel::Strings::extractToEOL(file, line)) {
- if (line == "" || line == ",,,,,,,,,,,,,,,,") {
+ if (line.empty() || line == ",,,,,,,,,,,,,,,,") {
// skip over any empty lines
continue;
}
diff --git a/Framework/DataHandling/src/RemoveLogs.cpp b/Framework/DataHandling/src/RemoveLogs.cpp
index e29203f4db23251365da50db228a706f500f2526..78d2a8a53587594478a995694cd0a775f3a8975a 100644
--- a/Framework/DataHandling/src/RemoveLogs.cpp
+++ b/Framework/DataHandling/src/RemoveLogs.cpp
@@ -62,6 +62,7 @@ void RemoveLogs::exec() {
localWorkspace->run().getLogData();
std::vector<std::string> keepLogs = getProperty("KeepLogs");
std::vector<std::string> logNames;
+ logNames.reserve(logData.size());
for (const auto property : logData) {
logNames.push_back(property->name());
}
diff --git a/Framework/DataHandling/src/SaveAscii.cpp b/Framework/DataHandling/src/SaveAscii.cpp
index 090452f80897cbb9e72b013c0da017e7add7fc1b..2b10f7211f0e1cf6208c4e26a2e3855ac0451895 100644
--- a/Framework/DataHandling/src/SaveAscii.cpp
+++ b/Framework/DataHandling/src/SaveAscii.cpp
@@ -111,7 +111,7 @@ void SaveAscii::exec() {
std::string sep;
// If the custom separator property is not empty, then we use that under any
// circumstance.
- if (custom != "") {
+ if (!custom.empty()) {
sep = custom;
}
// Else if the separator drop down choice is not UserDefined then we use that.
diff --git a/Framework/DataHandling/src/SaveAscii2.cpp b/Framework/DataHandling/src/SaveAscii2.cpp
index e44f640c9e590fbf517dd567532e29532f97a532..55a10b34c34d516607d3aa774885395208c06c75 100644
--- a/Framework/DataHandling/src/SaveAscii2.cpp
+++ b/Framework/DataHandling/src/SaveAscii2.cpp
@@ -166,7 +166,7 @@ void SaveAscii2::exec() {
const std::string custom = getPropertyValue("CustomSeparator");
// If the custom separator property is not empty, then we use that under any
// circumstance.
- if (custom != "") {
+ if (!custom.empty()) {
m_sep = custom;
}
// Else if the separator drop down choice is not UserDefined then we use that.
diff --git a/Framework/DataHandling/src/SaveDiffFittingAscii.cpp b/Framework/DataHandling/src/SaveDiffFittingAscii.cpp
index 1a499698b74dced9a685e490a027347163daa3c8..c7fa62e19a9c75ac305896b0f021f7616fddb983 100644
--- a/Framework/DataHandling/src/SaveDiffFittingAscii.cpp
+++ b/Framework/DataHandling/src/SaveDiffFittingAscii.cpp
@@ -86,6 +86,7 @@ bool SaveDiffFittingAscii::processGroups() {
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(name);
std::vector<API::ITableWorkspace_sptr> input_ws;
+ input_ws.reserve(inputGroup->getNumberOfEntries());
for (int i = 0; i < inputGroup->getNumberOfEntries(); ++i) {
input_ws.push_back(
boost::dynamic_pointer_cast<ITableWorkspace>(inputGroup->getItem(i)));
diff --git a/Framework/DataHandling/src/SaveGSS.cpp b/Framework/DataHandling/src/SaveGSS.cpp
index 14340729bd36bb47b73e3f8f5a8cc31b45e77019..7cc5450a9728fd863c7364ea46e4b4549736ec73 100644
--- a/Framework/DataHandling/src/SaveGSS.cpp
+++ b/Framework/DataHandling/src/SaveGSS.cpp
@@ -9,6 +9,7 @@
#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/VisibleWhenProperty.h"
+#include "MantidKernel/make_unique.h"
#include <Poco/File.h>
#include <Poco/Path.h>
@@ -80,7 +81,7 @@ std::unique_ptr<std::stringstream> makeStringStream() {
// so there are lots of restrictions in place with stream.
// Instead we can work around this by using pointers to streams.
// Tl;dr - This is a workaround for GCC 4.x (RHEL7)
- return std::move(std::unique_ptr<std::stringstream>(new std::stringstream()));
+ return Mantid::Kernel::make_unique<std::stringstream>();
}
void writeBankHeader(std::stringstream &out, const std::string &bintype,
diff --git a/Framework/DataHandling/src/SaveReflCustomAscii.cpp b/Framework/DataHandling/src/SaveReflCustomAscii.cpp
index 6b9a61892c157d851e748b78045e009ac348ee3d..2630e931e3ea1bbdadd0f79fe1f1970db238a00d 100644
--- a/Framework/DataHandling/src/SaveReflCustomAscii.cpp
+++ b/Framework/DataHandling/src/SaveReflCustomAscii.cpp
@@ -34,7 +34,7 @@ void SaveReflCustomAscii::extraHeaders(std::ofstream &file) {
std::string subtitleEntry;
std::string title = getProperty("Title");
- if (title != "") // if is toggled
+ if (!title.empty()) // if is toggled
{
file << "#" << title << '\n';
}
diff --git a/Framework/DataHandling/src/SaveReflThreeColumnAscii.cpp b/Framework/DataHandling/src/SaveReflThreeColumnAscii.cpp
index 29b9218c24ea1de02e57c71e0e2a5321bb4d0467..cf8c9cd7013801a4880ac92aa98f8b7cb27fb5c6 100644
--- a/Framework/DataHandling/src/SaveReflThreeColumnAscii.cpp
+++ b/Framework/DataHandling/src/SaveReflThreeColumnAscii.cpp
@@ -28,7 +28,7 @@ void SaveReflThreeColumnAscii::extraHeaders(std::ofstream &file) {
auto samp = m_ws->run();
std::string title = getProperty("Title");
- if (title != "") // if is toggled
+ if (!title.empty()) // if is toggled
{
file << "#" << title << '\n';
}
diff --git a/Framework/DataHandling/src/SaveSESANS.cpp b/Framework/DataHandling/src/SaveSESANS.cpp
index 3f3a965d8aab223e56643674f6e58a0553752362..de5f3570ccee34ff58bd4e95c2e731de269c8a4c 100644
--- a/Framework/DataHandling/src/SaveSESANS.cpp
+++ b/Framework/DataHandling/src/SaveSESANS.cpp
@@ -66,13 +66,16 @@ void SaveSESANS::init() {
"Filename", "", API::FileProperty::Save, fileExtensions),
"The name to use when saving the file");
- declareProperty("ThetaZMax", EMPTY_DBL(), "Theta_zmax",
+ declareProperty("ThetaZMax", EMPTY_DBL(),
+ "The angular acceptance in the encoding direction",
Kernel::Direction::Input);
declareProperty("ThetaZMaxUnit", "radians", Kernel::Direction::Input);
- declareProperty("ThetaYMax", EMPTY_DBL(), "Theta_ymax",
+ declareProperty("ThetaYMax", EMPTY_DBL(),
+ "The angular acceptance in the non-encoding direction",
Kernel::Direction::Input);
declareProperty("ThetaYMaxUnit", "radians", Kernel::Direction::Input);
- declareProperty("EchoConstant", EMPTY_DBL(), "Echo_constant",
+ declareProperty("EchoConstant", EMPTY_DBL(),
+ "The spin echo length, in nanometers, probed by a 1A neutron",
Kernel::Direction::Input);
declareProperty<std::string>("Sample", "", "Sample name",
diff --git a/Framework/DataHandling/src/SaveToSNSHistogramNexus.cpp b/Framework/DataHandling/src/SaveToSNSHistogramNexus.cpp
index b44854c1b2ffcd7e7b9859d041bca976a5b69bed..38625424c86340cf3b68e44562635a4de5e3b837 100644
--- a/Framework/DataHandling/src/SaveToSNSHistogramNexus.cpp
+++ b/Framework/DataHandling/src/SaveToSNSHistogramNexus.cpp
@@ -560,13 +560,13 @@ int SaveToSNSHistogramNexus::WriteGroup(int is_definition) {
}
//---------------------------------------------------------------------------------------
- if (data_label == "data" && (bank != "")) {
+ if (data_label == "data" && (!bank.empty())) {
if (this->WriteDataGroup(bank, is_definition) != NX_OK)
return NX_ERROR;
;
}
//---------------------------------------------------------------------------------------
- else if (data_label == "time_of_flight" && (bank != "")) {
+ else if (data_label == "time_of_flight" && (!bank.empty())) {
// Get the original info
if (NXgetinfo(inId, &dataRank, dataDimensions, &dataType) != NX_OK)
return NX_ERROR;
diff --git a/Framework/DataObjects/inc/MantidDataObjects/MDEventInserter.h b/Framework/DataObjects/inc/MantidDataObjects/MDEventInserter.h
index f2a20607738abe817bed57b495ff5977e2bf43e3..db2057aa2b565f664b72601e634d287fbf1e4fe9 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/MDEventInserter.h
+++ b/Framework/DataObjects/inc/MantidDataObjects/MDEventInserter.h
@@ -63,15 +63,15 @@ public:
determined internally using type information on the MDEventType.
@param signal : intensity
@param errorSQ : squared value of the error
- @param runno : run number
+ @param runindex : run index (index into the vector of ExperimentInfo)
@param detectno : detector number
@param coords : pointer to coordinates array
*/
- void insertMDEvent(float signal, float errorSQ, uint16_t runno,
+ void insertMDEvent(float signal, float errorSQ, uint16_t runindex,
int32_t detectno, Mantid::coord_t *coords) {
// compile-time overload selection based on nested type information on the
// MDEventType.
- insertMDEvent(signal, errorSQ, runno, detectno, coords,
+ insertMDEvent(signal, errorSQ, runindex, detectno, coords,
IntToType<MDEventType::is_full_mdevent>());
}
@@ -94,14 +94,14 @@ private:
Creates a FULL MDEvent and adds it to the MDEW.
@param signal : intensity
@param errorSQ : squared value of the error
- @param runno : run number
+ @param runindex : run index
@param detectno : detector number
@param coords : pointer to coordinates array
*/
- void insertMDEvent(float signal, float errorSQ, uint16_t runno,
+ void insertMDEvent(float signal, float errorSQ, uint16_t runindex,
int32_t detectno, Mantid::coord_t *coords,
IntToType<true>) {
- m_ws->addEvent(MDEventType(signal, errorSQ, runno, detectno, coords));
+ m_ws->addEvent(MDEventType(signal, errorSQ, runindex, detectno, coords));
}
};
diff --git a/Framework/DataObjects/src/EventList.cpp b/Framework/DataObjects/src/EventList.cpp
index 9471b3bf95b5582ee9268e4a4176cfaad5588f43..64dd418bad5f778f723e338dadd2e63921ec7b79 100644
--- a/Framework/DataObjects/src/EventList.cpp
+++ b/Framework/DataObjects/src/EventList.cpp
@@ -4403,7 +4403,7 @@ void EventList::splitByPulseTimeWithMatrix(
}
// Split
- if (vec_target.size() == 0) {
+ if (vec_target.empty()) {
// No splitter: copy all events to group workspace = -1
(*outputs[-1]) = (*this);
} else {
diff --git a/Framework/DataObjects/src/MDHistoWorkspace.cpp b/Framework/DataObjects/src/MDHistoWorkspace.cpp
index 0b2c563a92242ce5dc0818927df67bcfac233a72..d08c9ffeef6815b3399bc7efbba006dbab01f0c8 100644
--- a/Framework/DataObjects/src/MDHistoWorkspace.cpp
+++ b/Framework/DataObjects/src/MDHistoWorkspace.cpp
@@ -130,6 +130,7 @@ MDHistoWorkspace::~MDHistoWorkspace() {
void MDHistoWorkspace::init(
std::vector<Mantid::Geometry::MDHistoDimension_sptr> &dimensions) {
std::vector<IMDDimension_sptr> dim2;
+ dim2.reserve(dimensions.size());
for (auto &dimension : dimensions)
dim2.push_back(boost::dynamic_pointer_cast<IMDDimension>(dimension));
this->init(dim2);
diff --git a/Framework/DataObjects/src/ScanningWorkspaceBuilder.cpp b/Framework/DataObjects/src/ScanningWorkspaceBuilder.cpp
index 6c34f6d6693141a67e4c541030e04a948867baac..7254f4da513b77841799fc211f4bc97e4fbe7aa7 100644
--- a/Framework/DataObjects/src/ScanningWorkspaceBuilder.cpp
+++ b/Framework/DataObjects/src/ScanningWorkspaceBuilder.cpp
@@ -192,6 +192,8 @@ MatrixWorkspace_sptr ScanningWorkspaceBuilder::buildWorkspace() const {
m_instrument, m_nDetectors * m_nTimeIndexes, m_histogram);
auto &outputDetectorInfo = outputWorkspace->mutableDetectorInfo();
+ for (size_t j = 0; j < m_nDetectors; ++j)
+ outputDetectorInfo.setScanInterval(j, m_timeRanges[0]);
buildOutputDetectorInfo(outputDetectorInfo);
@@ -222,12 +224,13 @@ MatrixWorkspace_sptr ScanningWorkspaceBuilder::buildWorkspace() const {
void ScanningWorkspaceBuilder::buildOutputDetectorInfo(
Geometry::DetectorInfo &outputDetectorInfo) const {
- outputDetectorInfo.setScanInterval(m_timeRanges[0]);
auto mergeWorkspace =
create<Workspace2D>(m_instrument, m_nDetectors, m_histogram.binEdges());
for (size_t i = 1; i < m_nTimeIndexes; ++i) {
auto &mergeDetectorInfo = mergeWorkspace->mutableDetectorInfo();
- mergeDetectorInfo.setScanInterval(m_timeRanges[i]);
+ for (size_t j = 0; j < m_nDetectors; ++j) {
+ mergeDetectorInfo.setScanInterval(j, m_timeRanges[i]);
+ }
outputDetectorInfo.merge(mergeDetectorInfo);
}
}
diff --git a/Framework/DataObjects/test/MDEventInserterTest.h b/Framework/DataObjects/test/MDEventInserterTest.h
index 2fc05b5ecaa53cd4ec5e974c2d1262c2e2adecc3..8caccd71a86fde1c0bd54a3a154eb958862ba019 100644
--- a/Framework/DataObjects/test/MDEventInserterTest.h
+++ b/Framework/DataObjects/test/MDEventInserterTest.h
@@ -69,7 +69,7 @@ public:
Mantid::coord_t coord1[2] = {-1, -1};
float expectedSignal = 1;
float expectedErrorSq = 2;
- inserter.insertMDEvent(expectedSignal, expectedErrorSq, 1, 1, coord1);
+ inserter.insertMDEvent(expectedSignal, expectedErrorSq, 0, 1, coord1);
ws2d->refreshCache();
// Check the mdevent via the parent box.
@@ -78,7 +78,7 @@ public:
TS_ASSERT_EQUALS(expectedErrorSq, ws2d->getBox()->getErrorSquared());
// Add another md event
- inserter.insertMDEvent(expectedSignal, expectedErrorSq, 1, 1, coord1);
+ inserter.insertMDEvent(expectedSignal, expectedErrorSq, 0, 1, coord1);
ws2d->refreshCache();
TS_ASSERT_EQUALS(2, ws2d->getNPoints());
}
@@ -101,7 +101,7 @@ public:
Mantid::coord_t coord1[2] = {-1, -1};
float expectedSignal = 1;
float expectedErrorSq = 2;
- inserter.insertMDEvent(expectedSignal, expectedErrorSq, 1, 1, coord1);
+ inserter.insertMDEvent(expectedSignal, expectedErrorSq, 0, 1, coord1);
ws2d->refreshCache();
// Check the mdevent via the parent box.
@@ -110,7 +110,7 @@ public:
TS_ASSERT_EQUALS(expectedErrorSq, ws2d->getBox()->getErrorSquared());
// Add another md event
- inserter.insertMDEvent(expectedSignal, expectedErrorSq, 1, 1, coord1);
+ inserter.insertMDEvent(expectedSignal, expectedErrorSq, 0, 1, coord1);
ws2d->refreshCache();
TS_ASSERT_EQUALS(2, ws2d->getNPoints());
}
diff --git a/Framework/DataObjects/test/PeakTest.h b/Framework/DataObjects/test/PeakTest.h
index 9f8c9bdca1125e3a55ace9e9b0dada83cf63b89b..02c55fed90de9b19ee8e2c2fde660ed5522e5c1f 100644
--- a/Framework/DataObjects/test/PeakTest.h
+++ b/Framework/DataObjects/test/PeakTest.h
@@ -454,7 +454,6 @@ public:
}
void test_setQSampleFrameVirtualDetectorWithScatteringAngle() {
- constexpr auto radius = 10.;
auto sphereInst =
ComponentCreationHelper::createTestInstrumentRectangular(5, 100);
auto extendedSpaceObj =
@@ -467,7 +466,8 @@ public:
// test with & without extended detector space
// extended space is a sphere, so all points should fall radius*detector
// direction away from the detector direction with extended space
- auto testTheta = [this, &sphereInst, &radius](const double theta) {
+ auto testTheta = [this, &sphereInst](const double theta) {
+ constexpr auto radius = 10.;
const auto expectedDir = V3D(sin(theta), 0., cos(theta));
// test without extended detector space
diff --git a/Framework/Geometry/inc/MantidGeometry/Instrument/DetectorInfo.h b/Framework/Geometry/inc/MantidGeometry/Instrument/DetectorInfo.h
index 8e8ce068830e01298db78331b1c1d8cc9affa1ef..9cfb043aa32bfa15d6b3e6515bb58c7f15e1263f 100644
--- a/Framework/Geometry/inc/MantidGeometry/Instrument/DetectorInfo.h
+++ b/Framework/Geometry/inc/MantidGeometry/Instrument/DetectorInfo.h
@@ -76,6 +76,7 @@ public:
bool isEquivalent(const DetectorInfo &other) const;
size_t size() const;
+ size_t scanSize() const;
bool isScanning() const;
bool isMonitor(const size_t index) const;
diff --git a/Framework/Geometry/src/Crystal/ProductOfCyclicGroups.cpp b/Framework/Geometry/src/Crystal/ProductOfCyclicGroups.cpp
index 3aa2a64504e67418b8aa7b0ffd2f50c4fecea00a..460194a240c20e7c7cc997329f6d9b975859e8dd 100644
--- a/Framework/Geometry/src/Crystal/ProductOfCyclicGroups.cpp
+++ b/Framework/Geometry/src/Crystal/ProductOfCyclicGroups.cpp
@@ -31,7 +31,7 @@ ProductOfCyclicGroups::getGeneratedGroup(const std::string &generators) const {
std::vector<Group_const_sptr> ProductOfCyclicGroups::getFactorGroups(
const std::vector<SymmetryOperation> &symmetryOperations) const {
std::vector<Group_const_sptr> groups;
-
+ groups.reserve(symmetryOperations.size());
for (const auto &symmetryOperation : symmetryOperations) {
groups.push_back(
GroupFactory::create<CyclicGroup>(symmetryOperation.identifier()));
diff --git a/Framework/Geometry/src/Crystal/SymmetryElementFactory.cpp b/Framework/Geometry/src/Crystal/SymmetryElementFactory.cpp
index 09c5dfd1b37e2d2265dc3f2f764ddf5ae6629340..471c225be685c17caa1f65a81234382fe53b5d1b 100644
--- a/Framework/Geometry/src/Crystal/SymmetryElementFactory.cpp
+++ b/Framework/Geometry/src/Crystal/SymmetryElementFactory.cpp
@@ -313,7 +313,7 @@ std::string SymmetryElementMirrorGenerator::determineSymbol(
* proper symbol, so the general symbol "g" is used for these cases.
* Examples can be found in No. 227 (Fd-3m).
*/
- if (symbol == "") {
+ if (symbol.empty()) {
return "g";
}
diff --git a/Framework/Geometry/src/Crystal/SymmetryOperationFactory.cpp b/Framework/Geometry/src/Crystal/SymmetryOperationFactory.cpp
index 35651a9b6bab229e43c57a1090536092dd3c68a0..4630469d7cc882ba38354ce7173a286600812f04 100644
--- a/Framework/Geometry/src/Crystal/SymmetryOperationFactory.cpp
+++ b/Framework/Geometry/src/Crystal/SymmetryOperationFactory.cpp
@@ -32,6 +32,7 @@ SymmetryOperationFactoryImpl::createSymOps(const std::string &identifiers) {
std::vector<SymmetryOperation> SymmetryOperationFactoryImpl::createSymOps(
const std::vector<std::string> &identifiers) {
std::vector<SymmetryOperation> symOps;
+ symOps.reserve(identifiers.size());
for (const auto &identifier : identifiers) {
symOps.push_back(createSymOp(boost::trim_copy(identifier)));
}
diff --git a/Framework/Geometry/src/Instrument/DetectorInfo.cpp b/Framework/Geometry/src/Instrument/DetectorInfo.cpp
index 5979f7d3ada16c0605a6da65f2546c130013d95a..121d7e24b6631478cf13167d56c98da5c2fa63dd 100644
--- a/Framework/Geometry/src/Instrument/DetectorInfo.cpp
+++ b/Framework/Geometry/src/Instrument/DetectorInfo.cpp
@@ -83,6 +83,10 @@ bool DetectorInfo::isEquivalent(const DetectorInfo &other) const {
/// instrument.
size_t DetectorInfo::size() const { return m_detectorIDs->size(); }
+/// Returns the size of DetectorInfo taking into account scanning, i.e., the sum
+/// of the number of scan points for every detector in the instrument.
+size_t DetectorInfo::scanSize() const { return m_detectorInfo->scanSize(); }
+
/// Returns true if the beamline has scanning detectors.
bool DetectorInfo::isScanning() const { return m_detectorInfo->isScanning(); }
diff --git a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
index f079aa5fa59343da650e578f8558d9952af781b0..62e0b6d875c8f4330375bd646fbd4ba9a06d0a87 100644
--- a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
+++ b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
@@ -1282,7 +1282,7 @@ void InstrumentDefinitionParser::createDetectorOrMonitor(
std::stringstream ss1, ss2;
ss1 << idList.vec.size();
ss2 << idList.counted;
- if (idList.idname == "") {
+ if (idList.idname.empty()) {
g_log.error("No list of detector IDs found for location element " + name);
throw Kernel::Exception::InstrumentDefinitionError(
"Detector location element " + name + " has no idlist.", filename);
diff --git a/Framework/Geometry/src/Instrument/InstrumentVisitor.cpp b/Framework/Geometry/src/Instrument/InstrumentVisitor.cpp
index 2f4204d1264234399180b02d13e20b5cfab75ade..a6a070f06c0a9b1fbdc3f4c148984b1d4f5daea3 100644
--- a/Framework/Geometry/src/Instrument/InstrumentVisitor.cpp
+++ b/Framework/Geometry/src/Instrument/InstrumentVisitor.cpp
@@ -56,8 +56,8 @@ void clearLegacyParameters(ParameterMap *pmap, const IComponent &comp) {
*/
InstrumentVisitor::InstrumentVisitor(
boost::shared_ptr<const Instrument> instrument)
- : m_orderedDetectorIds(boost::make_shared<std::vector<detid_t>>(std::move(
- instrument->getDetectorIDs(false /*Do not skip monitors*/)))),
+ : m_orderedDetectorIds(boost::make_shared<std::vector<detid_t>>(
+ instrument->getDetectorIDs(false /*Do not skip monitors*/))),
m_componentIds(boost::make_shared<std::vector<ComponentID>>(
m_orderedDetectorIds->size(), nullptr)),
m_assemblySortedDetectorIndices(
@@ -253,7 +253,7 @@ size_t InstrumentVisitor::registerDetector(const IDetector &detector) {
Kernel::toVector3d(detector.getPos());
(*m_detectorRotations)[detectorIndex] =
Kernel::toQuaterniond(detector.getRotation());
- (*m_shapes)[detectorIndex] = std::move(detector.shape());
+ (*m_shapes)[detectorIndex] = detector.shape();
(*m_scaleFactors)[detectorIndex] =
Kernel::toVector3d(detector.getScaleFactor());
if (m_instrument->isMonitorViaIndex(detectorIndex)) {
diff --git a/Framework/Geometry/src/MDGeometry/MDGeometryXMLParser.cpp b/Framework/Geometry/src/MDGeometry/MDGeometryXMLParser.cpp
index 8cb0b237fa16105e36e04d6084f91a5bc0ba90fc..14f37e578f8364453b0babdd394f66d877a99f6c 100644
--- a/Framework/Geometry/src/MDGeometry/MDGeometryXMLParser.cpp
+++ b/Framework/Geometry/src/MDGeometry/MDGeometryXMLParser.cpp
@@ -93,8 +93,10 @@ void MDGeometryXMLParser::execute() {
throw std::invalid_argument("Cannot determine x-dimension mapping.");
}
m_xDimension = *xDimensionIt;
- vecNonMappedDims.erase(std::remove_if(
- vecNonMappedDims.begin(), vecNonMappedDims.end(), findID(xDimId)));
+ vecNonMappedDims.erase(std::remove_if(vecNonMappedDims.begin(),
+ vecNonMappedDims.end(),
+ findID(xDimId)),
+ vecNonMappedDims.end());
}
Poco::XML::Element *yDimensionElement = geometryXMLElement->getChildElement(
@@ -112,8 +114,10 @@ void MDGeometryXMLParser::execute() {
throw std::invalid_argument("Cannot determine y-dimension mapping.");
}
m_yDimension = *yDimensionIt;
- vecNonMappedDims.erase(std::remove_if(
- vecNonMappedDims.begin(), vecNonMappedDims.end(), findID(yDimId)));
+ vecNonMappedDims.erase(std::remove_if(vecNonMappedDims.begin(),
+ vecNonMappedDims.end(),
+ findID(yDimId)),
+ vecNonMappedDims.end());
}
Poco::XML::Element *zDimensionElement = geometryXMLElement->getChildElement(
@@ -131,8 +135,10 @@ void MDGeometryXMLParser::execute() {
throw std::invalid_argument("Cannot determine z-dimension mapping.");
}
m_zDimension = *zDimensionIt;
- vecNonMappedDims.erase(std::remove_if(
- vecNonMappedDims.begin(), vecNonMappedDims.end(), findID(zDimId)));
+ vecNonMappedDims.erase(std::remove_if(vecNonMappedDims.begin(),
+ vecNonMappedDims.end(),
+ findID(zDimId)),
+ vecNonMappedDims.end());
}
Poco::XML::Element *tDimensionElement = geometryXMLElement->getChildElement(
@@ -150,8 +156,10 @@ void MDGeometryXMLParser::execute() {
}
m_tDimension = *tDimensionIt;
if (!vecNonMappedDims.empty()) {
- vecNonMappedDims.erase(std::remove_if(
- vecNonMappedDims.begin(), vecNonMappedDims.end(), findID(tDimId)));
+ vecNonMappedDims.erase(std::remove_if(vecNonMappedDims.begin(),
+ vecNonMappedDims.end(),
+ findID(tDimId)),
+ vecNonMappedDims.end());
}
}
m_vecNonMappedDims = vecNonMappedDims; // Copy with strong guarantee.
diff --git a/Framework/HistogramData/src/CountStandardDeviations.cpp b/Framework/HistogramData/src/CountStandardDeviations.cpp
index 40fc5823bcd4ea06f3a2525bf358587c0018fb02..439692a50a0fe4ef7d767735a13a146abc643b13 100644
--- a/Framework/HistogramData/src/CountStandardDeviations.cpp
+++ b/Framework/HistogramData/src/CountStandardDeviations.cpp
@@ -24,7 +24,7 @@ CountStandardDeviations::CountStandardDeviations(
throw std::logic_error("CountStandardDeviations: Cannot construct from "
"FrequencyStandardDeviations -- BinEdges are NULL.");
if ((frequencies.size() + 1) != edges.size())
- if (frequencies.size() != 0 || edges.size() != 0)
+ if (!frequencies.empty() || !edges.empty())
throw std::logic_error("CountStandardDeviations: Cannot construct from "
"FrequencyStandardDeviations -- BinEdges size "
"does not "
diff --git a/Framework/HistogramData/src/CountVariances.cpp b/Framework/HistogramData/src/CountVariances.cpp
index 3153e6f540e15c08ab1bd0482191ccf8ffb2bfe7..baf7b9c4c558921a25901aec5e1d4c50c63218bf 100644
--- a/Framework/HistogramData/src/CountVariances.cpp
+++ b/Framework/HistogramData/src/CountVariances.cpp
@@ -23,7 +23,7 @@ CountVariances::CountVariances(FrequencyVariances &&frequencies,
throw std::logic_error("CountVariances: Cannot construct from "
"FrequencyVariances -- BinEdges are NULL.");
if ((frequencies.size() + 1) != edges.size())
- if (frequencies.size() != 0 || edges.size() != 0)
+ if (!frequencies.empty() || !edges.empty())
throw std::logic_error("CountVariances: Cannot construct from "
"FrequencyVariances -- BinEdges size does not "
"match.");
diff --git a/Framework/HistogramData/src/Counts.cpp b/Framework/HistogramData/src/Counts.cpp
index f63e47a0da03f21c57883c07a5ad8f0566e87731..3c5b7e0461fc8daec1982dc5d81b142afa8419bb 100644
--- a/Framework/HistogramData/src/Counts.cpp
+++ b/Framework/HistogramData/src/Counts.cpp
@@ -17,7 +17,7 @@ Counts::Counts(Frequencies &&frequencies, const BinEdges &edges) {
throw std::logic_error(
"Counts: Cannot construct from Frequencies -- BinEdges are NULL.");
if ((frequencies.size() + 1) != edges.size())
- if (frequencies.size() != 0 || edges.size() != 0)
+ if (!frequencies.empty() || !edges.empty())
throw std::logic_error("Counts: Cannot construct from Frequencies -- "
"BinEdges size does not match.");
// Cannot move frequencies private data since it is of different type.
diff --git a/Framework/HistogramData/src/Frequencies.cpp b/Framework/HistogramData/src/Frequencies.cpp
index 21b8836351a4a392a0cb226589b4316ddee4705f..6623ee0b2f8e62e2ebee81bbd310400088d324bf 100644
--- a/Framework/HistogramData/src/Frequencies.cpp
+++ b/Framework/HistogramData/src/Frequencies.cpp
@@ -17,7 +17,7 @@ Frequencies::Frequencies(Counts &&counts, const BinEdges &edges) {
throw std::logic_error(
"Frequencies: Cannot construct from Counts -- BinEdges are NULL.");
if ((counts.size() + 1) != edges.size())
- if (counts.size() != 0 || edges.size() != 0)
+ if (!counts.empty() || !edges.empty())
throw std::logic_error("Frequencies: Cannot construct from Counts -- "
"BinEdges size does not match.");
// Cannot move counts private data since it is of different type.
diff --git a/Framework/HistogramData/src/FrequencyStandardDeviations.cpp b/Framework/HistogramData/src/FrequencyStandardDeviations.cpp
index a4b568727b1d96b0f3a6ef51986ee5143ce0b837..99665e08cf84e9a483d07793f88446a83e571904 100644
--- a/Framework/HistogramData/src/FrequencyStandardDeviations.cpp
+++ b/Framework/HistogramData/src/FrequencyStandardDeviations.cpp
@@ -23,7 +23,7 @@ FrequencyStandardDeviations::FrequencyStandardDeviations(
throw std::logic_error("FrequencyStandardDeviations: Cannot construct from "
"CountStandardDeviations -- BinEdges are NULL.");
if ((counts.size() + 1) != edges.size())
- if (counts.size() != 0 || edges.size() != 0)
+ if (!counts.empty() || !edges.empty())
throw std::logic_error("FrequencyStandardDeviations: Cannot construct "
"from CountStandardDeviations -- BinEdges size "
"does not match.");
diff --git a/Framework/HistogramData/src/FrequencyVariances.cpp b/Framework/HistogramData/src/FrequencyVariances.cpp
index 86c7c47bb61678b0be314e8b1f456c5f0882b02e..a68c1c1ac073dad057b5293b0abe06f031e16d14 100644
--- a/Framework/HistogramData/src/FrequencyVariances.cpp
+++ b/Framework/HistogramData/src/FrequencyVariances.cpp
@@ -23,7 +23,7 @@ FrequencyVariances::FrequencyVariances(CountVariances &&counts,
throw std::logic_error("FrequencyVariances: Cannot construct from "
"CountVariances -- BinEdges are NULL.");
if ((counts.size() + 1) != edges.size())
- if (counts.size() != 0 || edges.size() != 0)
+ if (!counts.empty() || !edges.empty())
throw std::logic_error("FrequencyVariances: Cannot construct from "
"CountVariances -- BinEdges size does not match.");
// Cannot move counts private data since it is of different type.
diff --git a/Framework/HistogramData/src/Histogram.cpp b/Framework/HistogramData/src/Histogram.cpp
index d6367b8cd828eeccdf3530a70ece473b25707cd6..80b28a8e525c9dba994193518abe0547ec73d27b 100644
--- a/Framework/HistogramData/src/Histogram.cpp
+++ b/Framework/HistogramData/src/Histogram.cpp
@@ -1,4 +1,5 @@
#include "MantidHistogramData/Histogram.h"
+#include <sstream>
namespace Mantid {
namespace HistogramData {
@@ -251,8 +252,12 @@ template <> void Histogram::checkSize(const BinEdges &binEdges) const {
// 0 points -> 0 edges, otherwise edges are 1 more than points.
if (xMode() == XMode::Points && target > 0)
target++;
- if (target != binEdges.size())
- throw std::logic_error("Histogram: size mismatch of BinEdges\n");
+ if (target != binEdges.size()) {
+ std::stringstream msg;
+ msg << "Histogram: size mismatch of BinEdges: (" << target
+ << " != " << binEdges.size() << ")";
+ throw std::logic_error(msg.str());
+ }
}
/** Resets the size of the internal x, dx, y, and e data structures
diff --git a/Framework/HistogramData/src/Points.cpp b/Framework/HistogramData/src/Points.cpp
index 78edbfac5fb4bd5c442fe3b325b23a0a62fc9849..a375c2c64f944b47d0760fb3281dfb9c521f1779 100644
--- a/Framework/HistogramData/src/Points.cpp
+++ b/Framework/HistogramData/src/Points.cpp
@@ -10,7 +10,7 @@ Points::Points(const BinEdges &edges) {
return;
if (edges.size() == 1)
throw std::logic_error("Points: Cannot construct from BinEdges of size 1");
- if (edges.size() == 0) {
+ if (edges.empty()) {
m_data = Kernel::make_cow<HistogramX>(0);
return;
}
diff --git a/Framework/Kernel/inc/MantidKernel/MultiFileNameParser.h b/Framework/Kernel/inc/MantidKernel/MultiFileNameParser.h
index d9e1cb55eea705867afddb09ba1f580d91a93ec9..4deb73bcceed16b248e9d60b36fdd9f6a8084356 100644
--- a/Framework/Kernel/inc/MantidKernel/MultiFileNameParser.h
+++ b/Framework/Kernel/inc/MantidKernel/MultiFileNameParser.h
@@ -60,7 +60,7 @@ extern const std::string ANY, LIST;
*/
class MANTID_KERNEL_DLL ReverseCaselessCompare {
public:
- bool operator()(const std::string &a, const std::string &b);
+ bool operator()(const std::string &a, const std::string &b) const;
};
/**
diff --git a/Framework/Kernel/inc/MantidKernel/PropertyWithValue.tcc b/Framework/Kernel/inc/MantidKernel/PropertyWithValue.tcc
index 134f38a8d0c9fc4f11c22beb4fde5d9d4ffa1f55..a4902017dbb7104790d56d09cb1a6fcb93393f37 100644
--- a/Framework/Kernel/inc/MantidKernel/PropertyWithValue.tcc
+++ b/Framework/Kernel/inc/MantidKernel/PropertyWithValue.tcc
@@ -271,7 +271,7 @@ TYPE &PropertyWithValue<TYPE>::operator=(const TYPE &value) {
m_value = value;
}
std::string problem = this->isValid();
- if (problem == "") {
+ if (problem.empty()) {
return m_value;
} else if (problem == "_alias") {
m_value = getValueForAlias(value);
diff --git a/Framework/Kernel/src/CompositeValidator.cpp b/Framework/Kernel/src/CompositeValidator.cpp
index b87ecc4f290104bb1ed23eca042d291e5ac90418..55fd549ab0d6c74c636de5df72cf20184198bb90 100644
--- a/Framework/Kernel/src/CompositeValidator.cpp
+++ b/Framework/Kernel/src/CompositeValidator.cpp
@@ -74,7 +74,7 @@ std::string CompositeValidator::check(const boost::any &value) const {
std::string error = (*itr)->check(value);
// exit on the first error, to avoid passing doing more tests on invalid
// objects that could fail
- if (error != "")
+ if (!error.empty())
return error;
}
// there were no errors
diff --git a/Framework/Kernel/src/ConfigService.cpp b/Framework/Kernel/src/ConfigService.cpp
index 92f5b6b5d4ccb139e745f1f21ee6875600f62774..59ca2639dfb3f5ecfb7605f28ae18f7c238ddf6a 100644
--- a/Framework/Kernel/src/ConfigService.cpp
+++ b/Framework/Kernel/src/ConfigService.cpp
@@ -372,7 +372,7 @@ void ConfigServiceImpl::loadConfig(const std::string &filename,
bool good = readFile(filename, temp);
// check if we have failed to open the file
- if ((!good) || (temp == "")) {
+ if ((!good) || (temp.empty())) {
if (filename == getUserPropertiesDir() + m_user_properties_file_name) {
// write out a fresh file
createUserPropertiesFile();
@@ -382,7 +382,7 @@ void ConfigServiceImpl::loadConfig(const std::string &filename,
}
// store the property string
- if ((append) && (m_PropertyString != "")) {
+ if ((append) && (!m_PropertyString.empty())) {
m_PropertyString = m_PropertyString + "\n" + temp;
} else {
m_PropertyString = temp;
diff --git a/Framework/Kernel/src/DateAndTime.cpp b/Framework/Kernel/src/DateAndTime.cpp
index 904d19ebfdc3e829e4601b7778aa4cfe2163b58d..8d2bd358fc52ca7993fd0aedf0618150192e6413 100644
--- a/Framework/Kernel/src/DateAndTime.cpp
+++ b/Framework/Kernel/src/DateAndTime.cpp
@@ -541,17 +541,23 @@ int DateAndTime::day() const { return to_ptime().date().day(); }
/** Get the hour (0-24) of this time.
* @return the hour
*/
-int DateAndTime::hour() const { return to_ptime().time_of_day().hours(); }
+int DateAndTime::hour() const {
+ return static_cast<int>(to_ptime().time_of_day().hours());
+}
/** Get the minute (0-60) of this time.
* @return the minute
*/
-int DateAndTime::minute() const { return to_ptime().time_of_day().minutes(); }
+int DateAndTime::minute() const {
+ return static_cast<int>(to_ptime().time_of_day().minutes());
+}
/** Get the seconds (0-60) of this time.
* @return the second
*/
-int DateAndTime::second() const { return to_ptime().time_of_day().seconds(); }
+int DateAndTime::second() const {
+ return static_cast<int>(to_ptime().time_of_day().seconds());
+}
/** Get the nanoseconds (remainder, < 1 second) of this time.
* @return the nanoseconds
diff --git a/Framework/Kernel/src/DiskBuffer.cpp b/Framework/Kernel/src/DiskBuffer.cpp
index 28f338f6b3d9fcd7324d6d40387d21ad51666d50..677291daf8ca593f06e7fb9774431f48e0b2abe6 100644
--- a/Framework/Kernel/src/DiskBuffer.cpp
+++ b/Framework/Kernel/src/DiskBuffer.cpp
@@ -367,7 +367,7 @@ void DiskBuffer::setFreeSpaceVector(std::vector<uint64_t> &free) {
throw std::length_error("Free vector size is not a factor of 2.");
for (auto it = free.begin(); it != free.end(); it += 2) {
- auto it_next = boost::next(it);
+ auto it_next = std::next(it);
if (*it == 0 && *it_next == 0) {
continue; // Not really a free space block!
diff --git a/Framework/Kernel/src/MultiFileNameParser.cpp b/Framework/Kernel/src/MultiFileNameParser.cpp
index bb2a7ab4e081b3cae0fb97ecc3d968df4e1e63e0..bed6ddf43b7e8fc73c8b259abaf1b6d3ccdb9c36 100644
--- a/Framework/Kernel/src/MultiFileNameParser.cpp
+++ b/Framework/Kernel/src/MultiFileNameParser.cpp
@@ -176,7 +176,7 @@ std::string suggestWorkspaceName(const std::vector<std::string> &fileNames) {
* overkill.
*/
bool ReverseCaselessCompare::operator()(const std::string &a,
- const std::string &b) {
+ const std::string &b) const {
std::string lowerA(a);
std::string lowerB(b);
diff --git a/Framework/Kernel/src/UsageService.cpp b/Framework/Kernel/src/UsageService.cpp
index 5b77d1be8fa7c5f5b337f7777abcfdfe6d687b6b..54ab2d4a49e74e64a2919b2cc2e6fd49f236f7e6 100644
--- a/Framework/Kernel/src/UsageService.cpp
+++ b/Framework/Kernel/src/UsageService.cpp
@@ -263,7 +263,7 @@ std::string UsageServiceImpl::generateFeatureUsageMessage() {
thisFeature["count"] = featureItem.second;
features.append(thisFeature);
}
- if (features.size() > 0) {
+ if (!features.empty()) {
message["features"] = features;
return writer.write(message);
}
diff --git a/Framework/LiveData/test/KafkaEventStreamDecoderTest.h b/Framework/LiveData/test/KafkaEventStreamDecoderTest.h
index c65715fff17e430d8f2d6bb53d7f2666f8202862..0f18144b7f78637d63c874aaab281f7de6bf3709 100644
--- a/Framework/LiveData/test/KafkaEventStreamDecoderTest.h
+++ b/Framework/LiveData/test/KafkaEventStreamDecoderTest.h
@@ -227,7 +227,7 @@ private:
TS_ASSERT_THROWS_NOTHING(decoder.startCapture());
{
std::unique_lock<std::mutex> lk(m_callbackMutex);
- this->m_callbackCondition.wait(lk, [this, &decoder, maxIterations]() {
+ this->m_callbackCondition.wait(lk, [this, maxIterations]() {
return this->m_niterations == maxIterations;
});
}
diff --git a/Framework/MDAlgorithms/src/CompareMDWorkspaces.cpp b/Framework/MDAlgorithms/src/CompareMDWorkspaces.cpp
index e11d0a2a9c98131cf29363fb787b4066361e7c5d..943900034c059d7d2c7a6042ced52845479c1b8a 100644
--- a/Framework/MDAlgorithms/src/CompareMDWorkspaces.cpp
+++ b/Framework/MDAlgorithms/src/CompareMDWorkspaces.cpp
@@ -341,7 +341,7 @@ void CompareMDWorkspaces::exec() {
this->doComparison();
- if (m_result != "") {
+ if (!m_result.empty()) {
g_log.notice() << "The workspaces did not match: " << m_result << '\n';
this->setProperty("Equals", false);
} else {
diff --git a/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace3.cpp b/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace3.cpp
index 3eb926cae75671c33b69422a520973ab76117c8d..639462ab74555749e74240d3b1a2b3383a94f12f 100644
--- a/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace3.cpp
+++ b/Framework/MDAlgorithms/src/ConvertToDiffractionMDWorkspace3.cpp
@@ -70,7 +70,7 @@ void ConvertToDiffractionMDWorkspace3::convertExtents(
minVal[d] = Extents[2 * d + 0];
maxVal[d] = Extents[2 * d + 1];
}
- } else if (Extents.size() == 0) {
+ } else if (Extents.empty()) {
calculateExtentsFromData(minVal, maxVal);
} else
throw std::invalid_argument(
diff --git a/Framework/MDAlgorithms/src/Integrate3DEvents.cpp b/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
index 60178eb2fed080109d67838e00033f81baed3960..c59cb394f431e2719ac470f1e8a7c23fd3dabeb4 100644
--- a/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
+++ b/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
@@ -98,9 +98,9 @@ Integrate3DEvents::integrateStrongPeak(const IntegrationParameters ¶ms,
std::vector<V3D> eigen_vectors;
getEigenVectors(cov_matrix, eigen_vectors);
- std::vector<double> sigmas;
+ std::vector<double> sigmas(3);
for (int i = 0; i < 3; i++) {
- sigmas.push_back(stdDev(events, eigen_vectors[i], params.regionRadius));
+ sigmas[i] = stdDev(events, eigen_vectors[i], params.regionRadius);
}
bool invalid_peak =
@@ -248,9 +248,9 @@ double Integrate3DEvents::estimateSignalToNoiseRatio(
std::vector<V3D> eigen_vectors;
getEigenVectors(cov_matrix, eigen_vectors);
- std::vector<double> sigmas;
+ std::vector<double> sigmas(3);
for (int i = 0; i < 3; i++) {
- sigmas.push_back(stdDev(events, eigen_vectors[i], params.regionRadius));
+ sigmas[i] = stdDev(events, eigen_vectors[i], params.regionRadius);
}
const auto max_sigma = *std::max_element(sigmas.begin(), sigmas.end());
@@ -404,9 +404,9 @@ Integrate3DEvents::ellipseIntegrateEvents(
std::vector<V3D> eigen_vectors;
getEigenVectors(cov_matrix, eigen_vectors);
- std::vector<double> sigmas;
+ std::vector<double> sigmas(3);
for (int i = 0; i < 3; i++) {
- sigmas.push_back(stdDev(some_events, eigen_vectors[i], m_radius));
+ sigmas[i] = stdDev(some_events, eigen_vectors[i], m_radius);
}
bool invalid_peak =
diff --git a/Framework/Nexus/src/NexusFileIO.cpp b/Framework/Nexus/src/NexusFileIO.cpp
index 502ab8330ec4a90527813dfe3382817c877bc0ea..e373e252dbb4b65913fe202969850358a9c6a311 100644
--- a/Framework/Nexus/src/NexusFileIO.cpp
+++ b/Framework/Nexus/src/NexusFileIO.cpp
@@ -264,7 +264,7 @@ bool NexusFileIO::writeNxNote(const std::string ¬eName,
m_filehandle->makeGroup(noteName, "NXnote", true);
std::vector<std::string> attributes, avalues;
- if (date != "") {
+ if (!date.empty()) {
attributes.emplace_back("date");
avalues.push_back(date);
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
index 889e326b37407529948cd91e19f6da1a88b608af..6115a7a2561c14ec7e23ea0d510e92633f980f0f 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
@@ -93,7 +93,7 @@ struct MandatoryFirst {
/// in the list
bool operator()(const Property *p1, const Property *p2) const {
// this is false, unless p1 is not valid and p2 is valid
- return (p1->isValid() != "") && (p2->isValid() == "");
+ return (!p1->isValid().empty()) && (p2->isValid().empty());
}
};
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShielding.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShielding.py
new file mode 100644
index 0000000000000000000000000000000000000000..9168e0fe7fb0dc5f008062fa7e6ebe9a674be1fc
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShielding.py
@@ -0,0 +1,169 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+import DirectILL_common as common
+from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, InstrumentValidator, MatrixWorkspaceProperty,
+ Progress, PropertyMode, WorkspaceProperty, WorkspaceUnitValidator)
+from mantid.kernel import (CompositeValidator, Direction, FloatBoundedValidator, StringListValidator)
+from mantid.simpleapi import (CreateSingleValuedWorkspace, Divide, Minus, Multiply)
+
+
+def _subtractEC(ws, ecWS, ecScaling, wsNames, wsCleanup, algorithmLogging):
+ """Subtract empty container."""
+ # out = in - ecScaling * EC
+ scalingWSName = wsNames.withSuffix('ecScaling')
+ scalingWS = CreateSingleValuedWorkspace(OutputWorkspace=scalingWSName,
+ DataValue=ecScaling,
+ EnableLogging=algorithmLogging)
+ scaledECWSName = wsNames.withSuffix('scaled_EC')
+ scaledECWS = Multiply(LHSWorkspace=ecWS,
+ RHSWorkspace=scalingWS,
+ OutputWorkspace=scaledECWSName,
+ EnableLogging=algorithmLogging)
+ ecSubtractedWSName = wsNames.withSuffix('EC_subtracted')
+ ecSubtractedWS = Minus(LHSWorkspace=ws,
+ RHSWorkspace=scaledECWS,
+ OutputWorkspace=ecSubtractedWSName,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(scalingWS)
+ wsCleanup.cleanup(scaledECWS)
+ return ecSubtractedWS
+
+
+class DirectILLApplySelfShielding(DataProcessorAlgorithm):
+ """A data reduction workflow algorithm for the direct geometry TOF spectrometers at ILL."""
+
+ def __init__(self):
+ """Initialize an instance of the algorithm."""
+ DataProcessorAlgorithm.__init__(self)
+
+ def category(self):
+ """Return the algorithm's category."""
+ return 'Workflow\\Inelastic'
+
+ def name(self):
+ """Return the algorithm's name."""
+ return 'DirectILLApplySelfShielding'
+
+ def summary(self):
+ """Return a summary of the algorithm."""
+ return 'Applies empty container subtraction and self-shielding corrections.'
+
+ def version(self):
+ """Return the algorithm's version."""
+ return 1
+
+ def PyExec(self):
+ """Executes the data reduction workflow."""
+ progress = Progress(self, 0.0, 1.0, 4)
+ subalgLogging = False
+ if self.getProperty(common.PROP_SUBALG_LOGGING).value == common.SUBALG_LOGGING_ON:
+ subalgLogging = True
+ wsNamePrefix = self.getProperty(common.PROP_OUTPUT_WS).valueAsStr
+ cleanupMode = self.getProperty(common.PROP_CLEANUP_MODE).value
+ wsNames = common.NameSource(wsNamePrefix, cleanupMode)
+ wsCleanup = common.IntermediateWSCleanup(cleanupMode, subalgLogging)
+
+ progress.report('Loading inputs')
+ mainWS = self._inputWS(wsCleanup)
+
+ progress.report('Applying self shielding corrections')
+ mainWS = self._applyCorrections(mainWS, wsNames, wsCleanup, subalgLogging)
+
+ progress.report('Subtracting EC')
+ mainWS = self._subtractEC(mainWS, wsNames, wsCleanup, subalgLogging)
+
+ self._finalize(mainWS, wsCleanup)
+ progress.report('Done')
+
+ def PyInit(self):
+ """Initialize the algorithm's input and output properties."""
+ inputWorkspaceValidator = CompositeValidator()
+ inputWorkspaceValidator.add(InstrumentValidator())
+ inputWorkspaceValidator.add(WorkspaceUnitValidator('TOF'))
+ scalingFactor = FloatBoundedValidator(lower=0, upper=1)
+
+ # Properties.
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INPUT_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ direction=Direction.Input),
+ doc='Input workspace.')
+ self.declareProperty(WorkspaceProperty(name=common.PROP_OUTPUT_WS,
+ defaultValue='',
+ direction=Direction.Output),
+ doc='The output of the algorithm.')
+ self.declareProperty(name=common.PROP_CLEANUP_MODE,
+ defaultValue=common.CLEANUP_ON,
+ validator=StringListValidator([
+ common.CLEANUP_ON,
+ common.CLEANUP_OFF]),
+ direction=Direction.Input,
+ doc='What to do with intermediate workspaces.')
+ self.declareProperty(name=common.PROP_SUBALG_LOGGING,
+ defaultValue=common.SUBALG_LOGGING_OFF,
+ validator=StringListValidator([
+ common.SUBALG_LOGGING_OFF,
+ common.SUBALG_LOGGING_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable subalgorithms to ' +
+ 'print in the logs.')
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_EC_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='Reduced empty container workspace.')
+ self.declareProperty(name=common.PROP_EC_SCALING,
+ defaultValue=1.0,
+ validator=scalingFactor,
+ direction=Direction.Input,
+ doc='Scaling factor (transmission, if no self ' +
+ 'shielding is applied) for empty container.')
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_SELF_SHIELDING_CORRECTION_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='A workspace containing self shielding correction factors.')
+
+ def _applyCorrections(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Applies self shielding corrections to a workspace, if corrections exist."""
+ if self.getProperty(common.PROP_SELF_SHIELDING_CORRECTION_WS).isDefault:
+ return mainWS
+ correctionWS = self.getProperty(common.PROP_SELF_SHIELDING_CORRECTION_WS).value
+ correctedWSName = wsNames.withSuffix('self_shielding_corrected')
+ correctedWS = Divide(LHSWorkspace=mainWS,
+ RHSWorkspace=correctionWS,
+ OutputWorkspace=correctedWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return correctedWS
+
+ def _finalize(self, outWS, wsCleanup):
+ """Do final cleanup and set the output property."""
+ self.setProperty(common.PROP_OUTPUT_WS, outWS)
+ wsCleanup.cleanup(outWS)
+ wsCleanup.finalCleanup()
+
+ def _inputWS(self, wsCleanup):
+ """Return the raw input workspace."""
+ mainWS = self.getProperty(common.PROP_INPUT_WS).value
+ wsCleanup.protect(mainWS)
+ return mainWS
+
+ def _subtractEC(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Subtract the empty container workspace without self-shielding corrections."""
+ if self.getProperty(common.PROP_EC_WS).isDefault:
+ return mainWS
+ ecWS = self.getProperty(common.PROP_EC_WS).value
+ ecScaling = self.getProperty(common.PROP_EC_SCALING).value
+ subtractedWS = _subtractEC(mainWS, ecWS, ecScaling, wsNames, wsCleanup, subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return subtractedWS
+
+
+AlgorithmFactory.subscribe(DirectILLApplySelfShielding)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectData.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectData.py
new file mode 100644
index 0000000000000000000000000000000000000000..4f0041d8a20621f610bbdf46b962340bc582e2a9
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectData.py
@@ -0,0 +1,840 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+import DirectILL_common as common
+from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, FileAction, InstrumentValidator,
+ ITableWorkspaceProperty, MatrixWorkspaceProperty, MultipleFileProperty, Progress, PropertyMode,
+ WorkspaceProperty, WorkspaceUnitValidator)
+from mantid.kernel import (CompositeValidator, Direct, Direction, FloatBoundedValidator, IntBoundedValidator, IntArrayBoundedValidator,
+ IntMandatoryValidator, Property, StringListValidator, UnitConversion)
+from mantid.simpleapi import (AddSampleLog, CalculateFlatBackground, CloneWorkspace, CorrectTOFAxis, CreateEPP, CreateSingleValuedWorkspace,
+ CreateWorkspace, CropWorkspace, Divide, ExtractMonitors, FindEPP, GetEiMonDet, LoadILLTOF, MergeRuns, Minus,
+ NormaliseToMonitor, Scale)
+import numpy
+import os.path
+
+
+def _applyIncidentEnergyCalibration(ws, wsType, eiWS, wsNames, report,
+ algorithmLogging):
+ """Update incident energy and wavelength in the sample logs."""
+ originalEnergy = ws.getRun().getLogData('Ei').value
+ originalWavelength = ws.getRun().getLogData('wavelength').value
+ energy = eiWS.readY(0)[0]
+ wavelength = UnitConversion.run('Energy', 'Wavelength', energy, 0, 0, 0, Direct, 5)
+ if wsType == common.WS_CONTENT_DETS:
+ calibratedWSName = wsNames.withSuffix('incident_energy_calibrated_detectors')
+ elif wsType == common.WS_CONTENT_MONS:
+ calibratedWSName = wsNames.withSuffix('incident_energy_calibrated_monitors')
+ else:
+ raise RuntimeError('Unknown workspace content type')
+ calibratedWS = CloneWorkspace(InputWorkspace=ws,
+ OutputWorkspace=calibratedWSName,
+ EnableLogging=algorithmLogging)
+ AddSampleLog(Workspace=calibratedWS,
+ LogName='Ei',
+ LogText=str(energy),
+ LogType='Number',
+ NumberType='Double',
+ LogUnit='meV',
+ EnableLogging=algorithmLogging)
+ AddSampleLog(Workspace=calibratedWS,
+ Logname='wavelength',
+ LogText=str(wavelength),
+ LogType='Number',
+ NumberType='Double',
+ LogUnit='Ångström',
+ EnableLogging=algorithmLogging)
+ report.notice("Applied Ei calibration to '" + str(ws) + "'.")
+ report.notice('Original Ei: {} new Ei: {}.'.format(originalEnergy, energy))
+ report.notice('Original wavelength: {} new wavelength {}.'.format(originalWavelength, wavelength))
+ return calibratedWS
+
+
+def _calculateEPP(ws, sigma, wsNames, algorithmLogging):
+ eppWSName = wsNames.withSuffix('epp_detectors')
+ eppWS = CreateEPP(InputWorkspace=ws,
+ OutputWorkspace=eppWSName,
+ Sigma=sigma,
+ EnableLogging=algorithmLogging)
+ return eppWS
+
+
+def _calibratedIncidentEnergy(detWorkspace, detEPPWorkspace, monWorkspace, monEPPWorkspace,
+ eiCalibrationMon, wsNames, log, algorithmLogging):
+ """Return the calibrated incident energy."""
+ instrument = detWorkspace.getInstrument().getName()
+ eiWorkspace = None
+ if instrument in ['IN4', 'IN6']:
+ eiCalibrationDets = [i for i in range(detWorkspace.getNumberHistograms())]
+ pulseInterval = detWorkspace.getRun().getLogData('pulse_interval').value
+ energy = GetEiMonDet(DetectorWorkspace=detWorkspace,
+ DetectorEPPTable=detEPPWorkspace,
+ IndexType='Workspace Index',
+ Detectors=eiCalibrationDets,
+ MonitorWorkspace=monWorkspace,
+ MonitorEppTable=monEPPWorkspace,
+ Monitor=eiCalibrationMon,
+ PulseInterval=pulseInterval,
+ EnableLogging=algorithmLogging)
+ eiWSName = wsNames.withSuffix('incident_energy')
+ eiWorkspace = CreateSingleValuedWorkspace(OutputWorkspace=eiWSName,
+ DataValue=energy,
+ EnableLogging=algorithmLogging)
+ else:
+ log.error('Instrument ' + instrument + ' not supported for incident energy calibration')
+ return eiWorkspace
+
+
+def _createFlatBkg(ws, wsType, windowWidth, wsNames, algorithmLogging):
+ """Return a flat background workspace."""
+ if wsType == common.WS_CONTENT_DETS:
+ bkgWSName = wsNames.withSuffix('flat_bkg_for_detectors')
+ else:
+ bkgWSName = wsNames.withSuffix('flat_bkg_for_monitors')
+ bkgWS = CalculateFlatBackground(InputWorkspace=ws,
+ OutputWorkspace=bkgWSName,
+ Mode='Moving Average',
+ OutputMode='Return Background',
+ SkipMonitors=False,
+ NullifyNegativeValues=False,
+ AveragingWindowWidth=windowWidth,
+ EnableLogging=algorithmLogging)
+ firstBinStart = bkgWS.dataX(0)[0]
+ firstBinEnd = bkgWS.dataX(0)[1]
+ bkgWS = CropWorkspace(InputWorkspace=bkgWS,
+ OutputWorkspace=bkgWS,
+ XMin=firstBinStart,
+ XMax=firstBinEnd,
+ EnableLogging=algorithmLogging)
+ return bkgWS
+
+
+def _fitElasticChannel(ys, wsNames, wsCleanup, algorithmLogging):
+ """Return index to the peak position of ys."""
+ xs = numpy.array([i for i in range(len(ys))])
+ l2SumWSName = wsNames.withSuffix('summed_detectors_at_l2')
+ l2SumWS = CreateWorkspace(OutputWorkspace=l2SumWSName,
+ DataX=xs,
+ DataY=ys,
+ EnableLogging=algorithmLogging)
+ fitWSName = wsNames.withSuffix('summed_detectors_at_l2_fit_results')
+ fitWS = FindEPP(InputWorkspace=l2SumWS,
+ OutputWorkspace=fitWSName,
+ EnableLogging=algorithmLogging)
+ peakCentre = float(fitWS.cell('PeakCentre', 0))
+ wsCleanup.cleanup(l2SumWS)
+ wsCleanup.cleanup(fitWS)
+ return int(round(peakCentre))
+
+
+def _fitEPP(ws, wsType, wsNames, algorithmLogging):
+ """Return a fitted EPP table for a workspace."""
+ if wsType == common.WS_CONTENT_DETS:
+ eppWSName = wsNames.withSuffix('epp_detectors')
+ else:
+ eppWSName = wsNames.withSuffix('epp_monitors')
+ eppWS = FindEPP(InputWorkspace=ws,
+ OutputWorkspace=eppWSName,
+ EnableLogging=algorithmLogging)
+ return eppWS
+
+
+def _loadFiles(inputFilenames, wsNames, wsCleanup, algorithmLogging):
+ """Load files specified by inputFilenames, merging them into a single workspace."""
+ filename = inputFilenames.pop(0)
+ runNumber = os.path.basename(filename).split('.')[0]
+ firstWSName = wsNames.withSuffix('raw-' + runNumber)
+ mergedWS = LoadILLTOF(Filename=filename,
+ OutputWorkspace=firstWSName,
+ EnableLogging=algorithmLogging)
+ mergedWSName = wsNames.withSuffix('merged')
+ for i, filename in enumerate(inputFilenames):
+ runNumber = os.path.basename(filename).split('.')[0]
+ rawWSName = wsNames.withSuffix('raw-' + runNumber)
+ rawWS = LoadILLTOF(Filename=filename,
+ OutputWorkspace=rawWSName,
+ EnableLogging=algorithmLogging)
+ mergedWS = MergeRuns(InputWorkspaces=[mergedWS, rawWS],
+ OutputWorkspace=mergedWSName,
+ EnableLogging=algorithmLogging)
+ if i == 0:
+ wsCleanup.cleanup(firstWSName)
+ wsCleanup.cleanup(rawWS)
+ return mergedWS
+
+
+def _normalizeToMonitor(ws, monWS, monIndex, integrationBegin, integrationEnd,
+ wsNames, wsCleanup, algorithmLogging):
+ """Normalize to monitor counts."""
+ normalizedWSName = wsNames.withSuffix('normalized_to_monitor')
+ normalizationFactorWsName = wsNames.withSuffix('normalization_factor_monitor')
+ normalizedWS, normalizationFactorWS = NormaliseToMonitor(InputWorkspace=ws,
+ OutputWorkspace=normalizedWSName,
+ MonitorWorkspace=monWS,
+ MonitorWorkspaceIndex=monIndex,
+ IntegrationRangeMin=integrationBegin,
+ IntegrationRangeMax=integrationEnd,
+ NormFactorWS=normalizationFactorWsName,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(normalizationFactorWS)
+ return normalizedWS
+
+
+def _normalizeToTime(ws, wsNames, wsCleanup, algorithmLogging):
+ """Normalize to the 'actual_time' sample log."""
+ log = ws.run()
+ if not log.hasProperty('duration'):
+ if not log.hasProperty('actual_time'):
+ raise RuntimeError("Cannot normalise to acquisition time: 'duration' missing from sample logs.")
+ time = log.getProperty('actual_time').value
+ else:
+ time = log.getProperty('duration').value
+ if time == 0:
+ raise RuntimeError("Cannot normalise to acquisition time: time is zero.")
+ if time < 0:
+ raise RuntimeError("Cannot normalise to acquisition time: time is negative.")
+ normalizedWSName = wsNames.withSuffix('normalized_to_time')
+ normalizationFactorWsName = wsNames.withSuffix('normalization_factor_time')
+ normalizationFactorWS = CreateSingleValuedWorkspace(OutputWorkspace=normalizationFactorWsName,
+ DataValue=time,
+ EnableLogging=algorithmLogging)
+ normalizedWS = Divide(LHSWorkspace=ws,
+ RHSWorkspace=normalizationFactorWS,
+ OutputWorkspace=normalizedWSName,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(normalizationFactorWS)
+ return normalizedWS
+
+
+def _scaleAfterMonitorNormalization(ws, wsNames, wsCleanup, algorithmLogging):
+ """Scale ws by a factor given in the instrument parameters."""
+ SCALING_PARAM = 'scaling_after_monitor_normalisation'
+ NON_RECURSIVE = False # Prevent recursive calls.
+ instr = ws.getInstrument()
+ if not instr.hasParameter(SCALING_PARAM, NON_RECURSIVE):
+ return ws
+ factor = instr.getNumberParameter(SCALING_PARAM, NON_RECURSIVE)[0]
+ scaledWSName = wsNames.withSuffix('scaled_by_monitor_factor')
+ scaledWS = Scale(InputWorkspace=ws,
+ OutputWorkspace=scaledWSName,
+ Factor=factor,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(ws)
+ return scaledWS
+
+
+def _subtractFlatBkg(ws, wsType, bkgWorkspace, bkgScaling, wsNames,
+ wsCleanup, algorithmLogging):
+ """Subtract a scaled flat background from a workspace."""
+ if wsType == common.WS_CONTENT_DETS:
+ subtractedWSName = wsNames.withSuffix('flat_bkg_subtracted_detectors')
+ scaledBkgWSName = wsNames.withSuffix('flat_bkg_for_detectors_scaled')
+ else:
+ subtractedWSName = wsNames.withSuffix('flat_bkg_subtracted_monitors')
+ scaledBkgWSName = wsNames.withSuffix('flat_bkg_for_monitors_scaled')
+ Scale(InputWorkspace=bkgWorkspace,
+ OutputWorkspace=scaledBkgWSName,
+ Factor=bkgScaling,
+ EnableLogging=algorithmLogging)
+ subtractedWS = Minus(LHSWorkspace=ws,
+ RHSWorkspace=scaledBkgWSName,
+ OutputWorkspace=subtractedWSName,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(scaledBkgWSName)
+ return subtractedWS
+
+
+def _sumDetectorsAtDistance(ws, distance, tolerance):
+ """Return a sum of the Y values of detectors at distance away from the sample."""
+ histogramCount = ws.getNumberHistograms()
+ ySums = numpy.zeros(ws.blocksize())
+ detectorInfo = ws.detectorInfo()
+ sample = ws.getInstrument().getSample()
+ for i in range(histogramCount):
+ det = ws.getDetector(i)
+ sampleToDetector = sample.getDistance(det)
+ if abs(distance - sampleToDetector) < tolerance:
+ if detectorInfo.isMonitor(i) or detectorInfo.isMasked(i):
+ continue
+ ySums += ws.readY(i)
+ return ySums
+
+
+class DirectILLCollectData(DataProcessorAlgorithm):
+ """A workflow algorithm for the initial sample, vanadium and empty container reductions."""
+
+ def __init__(self):
+ """Initialize an instance of the algorithm."""
+ DataProcessorAlgorithm.__init__(self)
+
+ def category(self):
+ """Return the algorithm's category."""
+ return 'Workflow\\Inelastic'
+
+ def name(self):
+ """Return the algorithm's name."""
+ return 'DirectILLCollectData'
+
+ def summary(self):
+ """Return a summary of the algorithm."""
+ return 'An initial step of the reduction workflow for the direct geometry TOF spectrometers at ILL.'
+
+ def version(self):
+ """Return the algorithm's version."""
+ return 1
+
+ def PyExec(self):
+ """Executes the data reduction workflow."""
+ progress = Progress(self, 0.0, 1.0, 9)
+ report = common.Report()
+ subalgLogging = self.getProperty(common.PROP_SUBALG_LOGGING).value == common.SUBALG_LOGGING_ON
+ wsNamePrefix = self.getProperty(common.PROP_OUTPUT_WS).valueAsStr
+ cleanupMode = self.getProperty(common.PROP_CLEANUP_MODE).value
+ wsNames = common.NameSource(wsNamePrefix, cleanupMode)
+ wsCleanup = common.IntermediateWSCleanup(cleanupMode, subalgLogging)
+
+ # The variables 'mainWS' and 'monWS shall hold the current main
+ # data throughout the algorithm.
+
+ # Get input workspace.
+ progress.report('Loading inputs')
+ mainWS = self._inputWS(wsNames, wsCleanup, subalgLogging)
+
+ # Extract monitors to a separate workspace.
+ progress.report('Extracting monitors')
+ mainWS, monWS = self._separateMons(mainWS, wsNames, wsCleanup, subalgLogging)
+
+ # Save the main workspace for later use, if needed.
+ rawWS = None
+ if not self.getProperty(common.PROP_OUTPUT_RAW_WS).isDefault:
+ rawWS = mainWS
+ wsCleanup.protect(rawWS)
+
+ # Normalisation to monitor/time, if requested.
+ progress.report('Normalising to monitor/time')
+ monWS = self._flatBkgMon(monWS, wsNames, wsCleanup, subalgLogging)
+ monEPPWS = self._createEPPWSMon(monWS, wsNames, wsCleanup, subalgLogging)
+ mainWS = self._normalize(mainWS, monWS, monEPPWS, wsNames, wsCleanup, subalgLogging)
+
+ # Time-independent background.
+ progress.report('Calculating backgrounds')
+ mainWS, bkgWS = self._flatBkgDet(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ wsCleanup.cleanupLater(bkgWS)
+
+ # Find elastic peak positions.
+ progress.report('Calculating EPPs')
+ detEPPWS = self._createEPPWSDet(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ wsCleanup.cleanupLater(detEPPWS, monEPPWS)
+
+ # Calibrate incident energy, if requested.
+ progress.report('Calibrating incident energy')
+ mainWS, monWS = self._calibrateEi(mainWS, detEPPWS, monWS, monEPPWS,
+ wsNames, wsCleanup, report,
+ subalgLogging)
+ wsCleanup.cleanupLater(monWS)
+
+ progress.report('Correcting TOF')
+ mainWS = self._correctTOFAxis(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ self._outputRaw(mainWS, rawWS, subalgLogging)
+
+ # Find elastic peak positions.
+ progress.report('Recalculating EPPs')
+ detEPPWS = self._createEPPWSDet(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ wsCleanup.cleanupLater(detEPPWS, monEPPWS)
+
+ self._finalize(mainWS, wsCleanup, report)
+ progress.report('Done')
+
+ def PyInit(self):
+ """Initialize the algorithm's input and output properties."""
+ PROPGROUP_FLAT_BKG = 'Flat Time-Independent Background'
+ PROPGROUP_INCIDENT_ENERGY_CALIBRATION = 'Indicent Energy Calibration'
+ PROPGROUP_MON_NORMALISATION = 'Neutron Flux Normalisation'
+ # Validators.
+ mandatoryPositiveInt = CompositeValidator()
+ mandatoryPositiveInt.add(IntMandatoryValidator())
+ mandatoryPositiveInt.add(IntBoundedValidator(lower=0))
+ positiveFloat = FloatBoundedValidator(lower=0)
+ positiveInt = IntBoundedValidator(lower=0)
+ positiveIntArray = IntArrayBoundedValidator()
+ positiveIntArray.setLower(0)
+ inputWorkspaceValidator = CompositeValidator()
+ inputWorkspaceValidator.add(InstrumentValidator())
+ inputWorkspaceValidator.add(WorkspaceUnitValidator('TOF'))
+
+ # Properties.
+ self.declareProperty(MultipleFileProperty(name=common.PROP_INPUT_FILE,
+ action=FileAction.OptionalLoad,
+ extensions=['nxs']),
+ doc='An input run number (or a list thereof) or a filename.')
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INPUT_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ optional=PropertyMode.Optional,
+ direction=Direction.Input),
+ doc='Input workspace if no run is given.')
+ self.declareProperty(WorkspaceProperty(name=common.PROP_OUTPUT_WS,
+ defaultValue='',
+ direction=Direction.Output),
+ doc='The output of the algorithm.')
+ self.declareProperty(name=common.PROP_CLEANUP_MODE,
+ defaultValue=common.CLEANUP_ON,
+ validator=StringListValidator([
+ common.CLEANUP_ON,
+ common.CLEANUP_OFF]),
+ direction=Direction.Input,
+ doc='What to do with intermediate workspaces.')
+ self.declareProperty(name=common.PROP_SUBALG_LOGGING,
+ defaultValue=common.SUBALG_LOGGING_OFF,
+ validator=StringListValidator([
+ common.SUBALG_LOGGING_OFF,
+ common.SUBALG_LOGGING_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable subalgorithms to ' +
+ 'print in the logs.')
+ self.declareProperty(ITableWorkspaceProperty(
+ name=common.PROP_EPP_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='Table workspace containing results from the FindEPP ' +
+ 'algorithm.')
+ self.declareProperty(name=common.PROP_EPP_METHOD,
+ defaultValue=common.EPP_METHOD_AUTO,
+ validator=StringListValidator([
+ common.EPP_METHOD_AUTO,
+ common.EPP_METHOD_FIT,
+ common.EPP_METHOD_CALCULATE]),
+ direction=Direction.Input,
+ doc='Method to create the EPP table for detectors (monitor is awlays fitted) if '
+ + common.PROP_EPP_WS + ' is not given.')
+ self.declareProperty(name=common.PROP_EPP_SIGMA,
+ defaultValue=Property.EMPTY_DBL,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc='Nominal sigma for the EPP table when ' + common.PROP_EPP_METHOD +
+ ' is set to ' + common.EPP_METHOD_CALCULATE +
+ ' (default: 10 times the first bin width).')
+ self.declareProperty(name=common.PROP_ELASTIC_CHANNEL_MODE,
+ defaultValue=common.ELASTIC_CHANNEL_AUTO,
+ validator=StringListValidator([
+ common.ELASTIC_CHANNEL_AUTO,
+ common.ELASTIC_CHANNEL_SAMPLE_LOG,
+ common.ELASTIC_CHANNEL_FIT]),
+ direction=Direction.Input,
+ doc='How to acquire the elastic channel.')
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_ELASTIC_CHANNEL_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='A single value workspace containing the elatic channel index. Overrides '
+ + common.PROP_ELASTIC_CHANNEL_MODE + '.')
+ self.declareProperty(name=common.PROP_MON_INDEX,
+ defaultValue=Property.EMPTY_INT,
+ validator=positiveInt,
+ direction=Direction.Input,
+ doc='Index of the incident monitor, if not specified in instrument parameters.')
+ self.declareProperty(name=common.PROP_INCIDENT_ENERGY_CALIBRATION,
+ defaultValue=common.INCIDENT_ENERGY_CALIBRATION_AUTO,
+ validator=StringListValidator([
+ common.INCIDENT_ENERGY_CALIBRATION_AUTO,
+ common.INCIDENT_ENERGY_CALIBRATION_ON,
+ common.INCIDENT_ENERGY_CALIBRATION_OFF]),
+ direction=Direction.Input,
+ doc='Control the incident energy calibration.')
+ self.setPropertyGroup(common.PROP_INCIDENT_ENERGY_CALIBRATION, PROPGROUP_INCIDENT_ENERGY_CALIBRATION)
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INCIDENT_ENERGY_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='A single-valued workspace holding the calibrated ' +
+ 'incident energy.')
+ self.setPropertyGroup(common.PROP_INCIDENT_ENERGY_WS, PROPGROUP_INCIDENT_ENERGY_CALIBRATION)
+ self.declareProperty(name=common.PROP_FLAT_BKG,
+ defaultValue=common.BKG_AUTO,
+ validator=StringListValidator([
+ common.BKG_AUTO,
+ common.BKG_ON,
+ common.BKG_OFF]),
+ direction=Direction.Input,
+ doc='Control flat background subtraction.')
+ self.setPropertyGroup(common.PROP_FLAT_BKG, PROPGROUP_FLAT_BKG)
+ self.declareProperty(name=common.PROP_FLAT_BKG_SCALING,
+ defaultValue=1.0,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc='Flat background scaling constant')
+ self.setPropertyGroup(common.PROP_FLAT_BKG_SCALING, PROPGROUP_FLAT_BKG)
+ self.declareProperty(name=common.PROP_FLAT_BKG_WINDOW,
+ defaultValue=30,
+ validator=mandatoryPositiveInt,
+ direction=Direction.Input,
+ doc='Running average window width (in bins) ' +
+ 'for flat background.')
+ self.setPropertyGroup(common.PROP_FLAT_BKG_WINDOW, PROPGROUP_FLAT_BKG)
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_FLAT_BKG_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='Workspace from which to get flat background data.')
+ self.setPropertyGroup(common.PROP_FLAT_BKG_WS, PROPGROUP_FLAT_BKG)
+ self.declareProperty(name=common.PROP_NORMALISATION,
+ defaultValue=common.NORM_METHOD_MON,
+ validator=StringListValidator([
+ common.NORM_METHOD_MON,
+ common.NORM_METHOD_TIME,
+ common.NORM_METHOD_OFF]),
+ direction=Direction.Input,
+ doc='Normalisation method.')
+ self.setPropertyGroup(common.PROP_NORMALISATION, PROPGROUP_MON_NORMALISATION)
+ self.declareProperty(name=common.PROP_MON_PEAK_SIGMA_MULTIPLIER,
+ defaultValue=3.0,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc="Width of the monitor peak in multiples " +
+ " of 'Sigma' in monitor's EPP table.")
+ self.setPropertyGroup(common.PROP_MON_PEAK_SIGMA_MULTIPLIER, PROPGROUP_MON_NORMALISATION)
+ # Rest of the output properties.
+ self.declareProperty(WorkspaceProperty(
+ name=common.PROP_OUTPUT_RAW_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output the merged runs or ' + common.PROP_INPUT_WS + ' as is.')
+ self.setPropertyGroup(common.PROP_OUTPUT_RAW_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+ self.declareProperty(WorkspaceProperty(
+ name=common.PROP_OUTPUT_ELASTIC_CHANNEL_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output workspace for elastic channel index.')
+ self.setPropertyGroup(common.PROP_OUTPUT_ELASTIC_CHANNEL_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+ self.declareProperty(ITableWorkspaceProperty(
+ name=common.PROP_OUTPUT_DET_EPP_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output workspace for elastic peak positions.')
+ self.setPropertyGroup(common.PROP_OUTPUT_DET_EPP_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+ self.declareProperty(WorkspaceProperty(
+ name=common.PROP_OUTPUT_INCIDENT_ENERGY_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output workspace for calibrated inciden energy.')
+ self.setPropertyGroup(common.PROP_OUTPUT_INCIDENT_ENERGY_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+ self.declareProperty(WorkspaceProperty(
+ name=common.PROP_OUTPUT_FLAT_BKG_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output workspace for flat background.')
+ self.setPropertyGroup(common.PROP_OUTPUT_FLAT_BKG_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+
+ def validateInputs(self):
+ """Check for issues with user input."""
+ issues = dict()
+
+ fileGiven = not self.getProperty(common.PROP_INPUT_FILE).isDefault
+ wsGiven = not self.getProperty(common.PROP_INPUT_WS).isDefault
+ # Validate that an input exists
+ if fileGiven == wsGiven:
+ issues[common.PROP_INPUT_FILE] = \
+ 'Must give either an input file or an input workspace.'
+ if not wsGiven and self.getProperty(common.PROP_INPUT_WS).value:
+ issues[common.PROP_INPUT_WS] = 'Input workspace has to be in the ADS.'
+ return issues
+
+ def _calibrateEi(self, mainWS, detEPPWS, monWS, monEPPWS, wsNames, wsCleanup, report, subalgLogging):
+ """Perform and apply incident energy calibration."""
+ if self._eiCalibrationEnabled(mainWS, report):
+ if self.getProperty(common.PROP_INCIDENT_ENERGY_WS).isDefault:
+ monIndex = self._monitorIndex(monWS)
+ eiCalibrationWS = _calibratedIncidentEnergy(mainWS, detEPPWS, monWS, monEPPWS, monIndex, wsNames,
+ self.log(), subalgLogging)
+ else:
+ eiCalibrationWS = self.getProperty(common.PROP_INCIDENT_ENERGY_WS).value
+ wsCleanup.protect(eiCalibrationWS)
+ if eiCalibrationWS:
+ eiCalibratedDetWS = _applyIncidentEnergyCalibration(mainWS, common.WS_CONTENT_DETS, eiCalibrationWS, wsNames,
+ report, subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ mainWS = eiCalibratedDetWS
+ eiCalibratedMonWS = _applyIncidentEnergyCalibration(monWS, common.WS_CONTENT_MONS, eiCalibrationWS, wsNames, report,
+ subalgLogging)
+ wsCleanup.cleanup(monWS)
+ monWS = eiCalibratedMonWS
+ if not self.getProperty(
+ common.PROP_OUTPUT_INCIDENT_ENERGY_WS).isDefault:
+ self.setProperty(common.PROP_OUTPUT_INCIDENT_ENERGY_WS, eiCalibrationWS)
+ wsCleanup.cleanup(eiCalibrationWS)
+ return mainWS, monWS
+
+ def _chooseElasticChannelMode(self, mainWS, report):
+ """Return suitable elastic channel mode."""
+ mode = self.getProperty(common.PROP_ELASTIC_CHANNEL_MODE).value
+ if mode == common.ELASTIC_CHANNEL_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('enable_elastic_channel_fitting'):
+ if instrument.getBoolParameter('enable_elastic_channel_fitting')[0]:
+ report.notice(common.PROP_ELASTIC_CHANNEL_MODE + ' set to '
+ + common.ELASTIC_CHANNEL_FIT + ' by the IPF.')
+ return common.ELASTIC_CHANNEL_FIT
+ else:
+ report.notice(common.PROP_ELASTIC_CHANNEL_MODE + ' set to '
+ + common.ELASTIC_CHANNEL_SAMPLE_LOG + ' by the IPF.')
+ return common.ELASTIC_CHANNEL_SAMPLE_LOG
+ else:
+ report.notice('Defaulted ' + common.PROP_ELASTIC_CHANNEL_MODE + ' to '
+ + common.ELASTIC_CHANNEL_SAMPLE_LOG + '.')
+ return common.ELASTIC_CHANNEL_SAMPLE_LOG
+ return mode
+
+ def _chooseEPPMethod(self, mainWS, report):
+ """Return a suitable EPP method."""
+ eppMethod = self.getProperty(common.PROP_EPP_METHOD).value
+ if eppMethod == common.EPP_METHOD_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('enable_elastic_peak_fitting'):
+ if instrument.getBoolParameter('enable_elastic_peak_fitting')[0]:
+ report.notice(common.PROP_EPP_METHOD + ' set to '
+ + common.EPP_METHOD_FIT + ' by the IPF.')
+ return common.EPP_METHOD_FIT
+ else:
+ report.notice(common.PROP_EPP_METHOD + ' set to '
+ + common.EPP_METHOD_CALCULATE + ' by the IPF.')
+ return common.EPP_METHOD_CALCULATE
+ else:
+ report.notice('Defaulted ' + common.PROP_EPP_METHOD + ' to '
+ + common.EPP_METHOD_FIT + '.')
+ return common.EPP_METHOD_FIT
+ return eppMethod
+
+ def _correctTOFAxis(self, mainWS, wsNames, wsCleanup, report, subalgLogging):
+ """Adjust the TOF axis to get the elastic channel correct."""
+ try:
+ l2 = float(mainWS.getInstrument().getStringParameter('l2')[0])
+ except IndexError:
+ self.log().warning("No 'l2' instrument parameter defined. TOF axis will not be adjusted")
+ return mainWS
+ if not self.getProperty(common.PROP_ELASTIC_CHANNEL_WS).isDefault:
+ indexWS = self.getProperty(common.PROP_ELASTIC_CHANNEL_WS).value
+ index = int(indexWS.readY(0)[0])
+ else:
+ mode = self._chooseElasticChannelMode(mainWS, report)
+ if mode == common.ELASTIC_CHANNEL_SAMPLE_LOG:
+ if not mainWS.run().hasProperty('Detector.elasticpeak'):
+ self.log().warning('No ' + common.PROP_ELASTIC_CHANNEL_WS +
+ ' given. TOF axis will not be adjusted.')
+ return mainWS
+ index = mainWS.run().getLogData('Detector.elasticpeak').value
+ else:
+ ys = _sumDetectorsAtDistance(mainWS, l2, 1e-5)
+ index = _fitElasticChannel(ys, wsNames, wsCleanup, subalgLogging)
+ correctedWSName = wsNames.withSuffix('tof_axis_corrected')
+ correctedWS = CorrectTOFAxis(InputWorkspace=mainWS,
+ OutputWorkspace=correctedWSName,
+ IndexType='Workspace Index',
+ ElasticBinIndex=index,
+ L2=l2,
+ EnableLogging=subalgLogging)
+ report.notice('Elastic channel index {0} was used for TOF axis adjustment.'.format(index))
+ if not self.getProperty(common.PROP_OUTPUT_ELASTIC_CHANNEL_WS).isDefault:
+ indexOutputWSName = wsNames.withSuffix('elastic_channel_output')
+ indexOutputWS = CreateSingleValuedWorkspace(OutputWorkspace=indexOutputWSName,
+ DataValue=index,
+ EnableLogging=subalgLogging)
+ self.setProperty(common.PROP_OUTPUT_ELASTIC_CHANNEL_WS, indexOutputWS)
+ wsCleanup.cleanup(indexOutputWS)
+ wsCleanup.cleanup(mainWS)
+ return correctedWS
+
+ def _createEPPWSDet(self, mainWS, wsNames, wsCleanup, report, subalgLogging):
+ """Create an EPP table for a detector workspace."""
+ eiCalibration = self.getProperty(common.PROP_INCIDENT_ENERGY_CALIBRATION).value
+ noEiCalibration = eiCalibration == common.INCIDENT_ENERGY_CALIBRATION_OFF
+ yesInputEi = not self.getProperty(common.PROP_INCIDENT_ENERGY_WS).isDefault
+ noOutputEPP = self.getProperty(common.PROP_OUTPUT_DET_EPP_WS).isDefault
+ if (noEiCalibration or yesInputEi) and noOutputEPP:
+ # No epp table needed.
+ return None
+ detEPPInWS = self.getProperty(common.PROP_EPP_WS).value
+ if not detEPPInWS:
+ eppMethod = self._chooseEPPMethod(mainWS, report)
+ if eppMethod == common.EPP_METHOD_FIT:
+ detEPPWS = _fitEPP(mainWS, common.WS_CONTENT_DETS, wsNames, subalgLogging)
+ else:
+ sigma = self.getProperty(common.PROP_EPP_SIGMA).value
+ if sigma == Property.EMPTY_DBL:
+ sigma = 10.0 * (mainWS.readX(0)[1] - mainWS.readX(0)[0])
+ detEPPWS = _calculateEPP(mainWS, sigma, wsNames, subalgLogging)
+ else:
+ detEPPWS = detEPPInWS
+ wsCleanup.protect(detEPPWS)
+ if not self.getProperty(common.PROP_OUTPUT_DET_EPP_WS).isDefault:
+ self.setProperty(common.PROP_OUTPUT_DET_EPP_WS,
+ detEPPWS)
+ return detEPPWS
+
+ def _createEPPWSMon(self, monWS, wsNames, wsCleanup, subalgLogging):
+ """Create an EPP table for a monitor workspace."""
+ monEPPWS = _fitEPP(monWS, common.WS_CONTENT_MONS, wsNames, subalgLogging)
+ return monEPPWS
+
+ def _finalize(self, outWS, wsCleanup, report):
+ """Do final cleanup and set the output property."""
+ self.setProperty(common.PROP_OUTPUT_WS, outWS)
+ wsCleanup.cleanup(outWS)
+ wsCleanup.finalCleanup()
+ report.toLog(self.log())
+
+ def _eiCalibrationEnabled(self, mainWS, report):
+ """Return true if incident energy calibration should be perfomed, false if not."""
+ eppMethod = self.getProperty(common.PROP_INCIDENT_ENERGY_CALIBRATION).value
+ if eppMethod == common.INCIDENT_ENERGY_CALIBRATION_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('enable_incident_energy_calibration'):
+ enabled = instrument.getBoolParameter('enable_incident_energy_calibration')[0]
+ if not enabled:
+ report.notice('Inciden energy calibration disabled by the IPF.')
+ return False
+ report.notice('Incident energy calibration enabled.')
+ return True
+ return eppMethod == common.INCIDENT_ENERGY_CALIBRATION_ON
+
+ def _flatBkgDet(self, mainWS, wsNames, wsCleanup, report, subalgLogging):
+ """Subtract flat background from a detector workspace."""
+ if not self._flatBgkEnabled(mainWS, report):
+ return mainWS, None
+ windowWidth = self.getProperty(common.PROP_FLAT_BKG_WINDOW).value
+ if self.getProperty(common.PROP_FLAT_BKG_WS).isDefault:
+ bkgWS = _createFlatBkg(mainWS, common.WS_CONTENT_DETS, windowWidth, wsNames, subalgLogging)
+ else:
+ bkgWS = self.getProperty(common.PROP_FLAT_BKG_WS).value
+ wsCleanup.protect(bkgWS)
+ if not self.getProperty(common.PROP_OUTPUT_FLAT_BKG_WS).isDefault:
+ self.setProperty(common.PROP_OUTPUT_FLAT_BKG_WS, bkgWS)
+ bkgScaling = self.getProperty(common.PROP_FLAT_BKG_SCALING).value
+ bkgSubtractedWS = _subtractFlatBkg(mainWS, common.WS_CONTENT_DETS, bkgWS, bkgScaling, wsNames,
+ wsCleanup, subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return bkgSubtractedWS, bkgWS
+
+ def _flatBgkEnabled(self, mainWS, report):
+ """Returns true if flat background subtraction is enabled, false otherwise."""
+ flatBkgOption = self.getProperty(common.PROP_FLAT_BKG).value
+ if flatBkgOption == common.BKG_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('enable_flat_background_subtraction'):
+ enabled = instrument.getBoolParameter('enable_flat_background_subtraction')[0]
+ if not enabled:
+ report.notice('Flat background subtraction disabled by the IPF.')
+ return False
+ report.notice('Flat background subtraction enabled.')
+ return True
+ return flatBkgOption == common.BKG_ON
+
+ def _flatBkgMon(self, monWS, wsNames, wsCleanup, subalgLogging):
+ """Subtract flat background from a monitor workspace."""
+ windowWidth = self.getProperty(common.PROP_FLAT_BKG_WINDOW).value
+ monBkgWS = _createFlatBkg(monWS, common.WS_CONTENT_MONS, windowWidth, wsNames, subalgLogging)
+ monBkgScaling = 1
+ bkgSubtractedMonWS = _subtractFlatBkg(monWS, common.WS_CONTENT_MONS, monBkgWS, monBkgScaling, wsNames,
+ wsCleanup, subalgLogging)
+ wsCleanup.cleanup(monBkgWS)
+ wsCleanup.cleanup(monWS)
+ return bkgSubtractedMonWS
+
+ def _inputWS(self, wsNames, wsCleanup, subalgLogging):
+ """Return the raw input workspace."""
+ inputFiles = self.getProperty(common.PROP_INPUT_FILE).value
+ if len(inputFiles) > 0:
+ flattened = list()
+ for i in inputFiles:
+ if isinstance(i, str):
+ flattened.append(i)
+ else:
+ flattened += i
+ mainWS = _loadFiles(flattened, wsNames, wsCleanup, subalgLogging)
+ else:
+ mainWS = self.getProperty(common.PROP_INPUT_WS).value
+ wsCleanup.protect(mainWS)
+ return mainWS
+
+ def _monitorIndex(self, monWS):
+ """Return the workspace index of the main monitor."""
+ if self.getProperty(common.PROP_MON_INDEX).isDefault:
+ NON_RECURSIVE = False # Prevent recursive calls in the following.
+ if not monWS.getInstrument().hasParameter('default-incident-monitor-spectrum', NON_RECURSIVE):
+ raise RuntimeError('default-incident-monitor-spectrum missing in instrument parameters; ' +
+ common.PROP_MON_INDEX + ' must be specified.')
+ monIndex = monWS.getInstrument().getIntParameter('default-incident-monitor-spectrum', NON_RECURSIVE)[0]
+ monIndex = common.convertToWorkspaceIndex(monIndex, monWS, common.INDEX_TYPE_SPECTRUM_NUMBER)
+ else:
+ monIndex = self.getProperty(common.PROP_MON_INDEX).value
+ monIndex = common.convertToWorkspaceIndex(monIndex, monWS)
+ return monIndex
+
+ def _normalize(self, mainWS, monWS, monEPPWS, wsNames, wsCleanup, subalgLogging):
+ """Normalize to monitor or measurement time."""
+ normalisationMethod = self.getProperty(common.PROP_NORMALISATION).value
+ if normalisationMethod != common.NORM_METHOD_OFF:
+ if normalisationMethod == common.NORM_METHOD_MON:
+ sigmaMultiplier = \
+ self.getProperty(common.PROP_MON_PEAK_SIGMA_MULTIPLIER).value
+ monIndex = self._monitorIndex(monWS)
+ eppRow = monEPPWS.row(monIndex)
+ if eppRow['FitStatus'] != 'success':
+ self.log().warning('Fitting to monitor data failed. Integrating the intensity over ' +
+ 'the entire TOF range for normalisation.')
+ begin = monWS.dataX(monIndex)[0]
+ end = monWS.dataX(monIndex)[-1]
+ else:
+ sigma = eppRow['Sigma']
+ centre = eppRow['PeakCentre']
+ begin = centre - sigmaMultiplier * sigma
+ end = centre + sigmaMultiplier * sigma
+ normalizedWS = _normalizeToMonitor(mainWS, monWS, monIndex, begin, end, wsNames, wsCleanup,
+ subalgLogging)
+ normalizedWS = _scaleAfterMonitorNormalization(normalizedWS, wsNames, wsCleanup,
+ subalgLogging)
+ elif normalisationMethod == common.NORM_METHOD_TIME:
+ normalizedWS = _normalizeToTime(mainWS, wsNames, wsCleanup, subalgLogging)
+ else:
+ raise RuntimeError('Unknonwn normalisation method ' + normalisationMethod)
+ wsCleanup.cleanup(mainWS)
+ return normalizedWS
+ return mainWS
+
+ def _outputRaw(self, mainWS, rawWS, subalgLogging):
+ """Optionally sets mainWS as the raw output workspace."""
+ if not self.getProperty(common.PROP_OUTPUT_RAW_WS).isDefault:
+ CorrectTOFAxis(InputWorkspace=rawWS,
+ OutputWorkspace=rawWS,
+ ReferenceWorkspace=mainWS,
+ EnableLogging=subalgLogging)
+ self.setProperty(common.PROP_OUTPUT_RAW_WS, rawWS)
+
+ def _separateMons(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Extract monitors to a separate workspace."""
+ detWSName = wsNames.withSuffix('extracted_detectors')
+ monWSName = wsNames.withSuffix('extracted_monitors')
+ detWS, monWS = ExtractMonitors(InputWorkspace=mainWS,
+ DetectorWorkspace=detWSName,
+ MonitorWorkspace=monWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return detWS, monWS
+
+
+AlgorithmFactory.subscribe(DirectILLCollectData)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py
new file mode 100644
index 0000000000000000000000000000000000000000..e3c3ce10f390f62b3f77829ca148733e99c3f469
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py
@@ -0,0 +1,767 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+import DirectILL_common as common
+import mantid
+from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, InstrumentValidator,
+ ITableWorkspaceProperty, MatrixWorkspaceProperty, mtd, Progress, PropertyMode,
+ WorkspaceProperty, WorkspaceUnitValidator)
+from mantid.kernel import (CompositeValidator, Direction, FloatBoundedValidator, IntArrayBoundedValidator,
+ IntArrayProperty, StringArrayProperty, StringListValidator)
+from mantid.simpleapi import (ClearMaskFlag, CloneWorkspace, CreateEmptyTableWorkspace, Divide,
+ ExtractMask, Integration, LoadMask, MaskDetectors, MedianDetectorTest, Plus, SolidAngle)
+import numpy
+import os.path
+
+_PLOT_TYPE_X = 1
+_PLOT_TYPE_Y = 2
+
+
+class _DiagnosticsSettings:
+ """A class to hold settings for MedianDetectorTest."""
+
+ def __init__(self, lowThreshold, highThreshold, significanceTest):
+ """Initialize an instance of the class."""
+ self.lowThreshold = lowThreshold
+ self.highThreshold = highThreshold
+ self.significanceTest = significanceTest
+
+
+def _beamStopRanges(ws):
+ """Parse beam stop ranges from the instrument parameters of ws."""
+ instrument = ws.getInstrument()
+ definition = instrument.getStringParameter('beam_stop_diagnostics_spectra')[0]
+ ranges = definition.split(',')
+ begins = list()
+ ends = list()
+ for r in ranges:
+ (begin, end) = r.split('-')
+ begin = int(begin)
+ end = int(end)
+ if (begin >= end):
+ raise RuntimeError("While parsing 'beam_stop_diagnostics_spectra' instrument parameter: "
+ + "begin spectrum number greater than the end number.")
+ begin = common.convertToWorkspaceIndex(begin, ws, common.INDEX_TYPE_SPECTRUM_NUMBER)
+ end = common.convertToWorkspaceIndex(end, ws, common.INDEX_TYPE_SPECTRUM_NUMBER)
+ begins.append(begin)
+ ends.append(end)
+ return (begins, ends)
+
+
+def _bkgDiagnostics(bkgWS, noisyBkgSettings, wsNames, algorithmLogging):
+ """Diagnose noisy flat backgrounds and return a mask workspace."""
+ noisyBkgWSName = wsNames.withSuffix('diagnostics_noisy_bkg')
+ noisyBkgDiagnostics, nFailures = \
+ MedianDetectorTest(InputWorkspace=bkgWS,
+ OutputWorkspace=noisyBkgWSName,
+ SignificanceTest=noisyBkgSettings.significanceTest,
+ LowThreshold=noisyBkgSettings.lowThreshold,
+ HighThreshold=noisyBkgSettings.highThreshold,
+ LowOutlier=0.0,
+ EnableLogging=algorithmLogging)
+ ClearMaskFlag(Workspace=noisyBkgDiagnostics,
+ EnableLogging=algorithmLogging)
+ return noisyBkgDiagnostics
+
+
+def _createDiagnosticsReportTable(reportWSName, numberHistograms, algorithmLogging):
+ """Return a table workspace for detector diagnostics reporting."""
+ if mtd.doesExist(reportWSName):
+ reportWS = mtd[reportWSName]
+ else:
+ reportWS = CreateEmptyTableWorkspace(OutputWorkspace=reportWSName,
+ EnableLogging=algorithmLogging)
+ existingColumnNames = reportWS.getColumnNames()
+ if 'WorkspaceIndex' not in existingColumnNames:
+ reportWS.addColumn('int', 'WorkspaceIndex', _PLOT_TYPE_X)
+ reportWS.setRowCount(numberHistograms)
+ for i in range(numberHistograms):
+ reportWS.setCell('WorkspaceIndex', i, i)
+ return reportWS
+
+
+def _createMaskWS(ws, name, algorithmLogging):
+ """Return a single bin workspace with same number of histograms as ws."""
+ maskWS, detList = ExtractMask(InputWorkspace=ws,
+ OutputWorkspace=name,
+ EnableLogging=algorithmLogging)
+ maskWS *= 0.0
+ return maskWS
+
+
+def _elasticPeakDiagnostics(ws, peakSettings, wsNames, algorithmLogging):
+ """Diagnose elastic peaks and return a mask workspace"""
+ elasticPeakDiagnosticsWSName = wsNames.withSuffix('diagnostics_elastic_peak')
+ elasticPeakDiagnostics, nFailures = \
+ MedianDetectorTest(InputWorkspace=ws,
+ OutputWorkspace=elasticPeakDiagnosticsWSName,
+ SignificanceTest=peakSettings.significanceTest,
+ LowThreshold=peakSettings.lowThreshold,
+ HighThreshold=peakSettings.highThreshold,
+ EnableLogging=algorithmLogging)
+ ClearMaskFlag(Workspace=elasticPeakDiagnostics,
+ EnableLogging=algorithmLogging)
+ return elasticPeakDiagnostics
+
+
+def _integrateBkgs(ws, eppWS, sigmaMultiplier, wsNames, wsCleanup, algorithmLogging):
+ """Return a workspace integrated around flat background areas."""
+ histogramCount = ws.getNumberHistograms()
+ binMatrix = ws.extractX()
+ leftBegins = binMatrix[:, 0]
+ leftEnds = numpy.empty(histogramCount)
+ rightBegins = numpy.empty(histogramCount)
+ rightEnds = binMatrix[:, -1]
+ for i in range(histogramCount):
+ eppRow = eppWS.row(i)
+ if eppRow['FitStatus'] != 'success':
+ leftBegins[i] = 0
+ leftEnds[i] = 0
+ rightBegins[i] = 0
+ rightEnds[i] = 0
+ continue
+ peakCentre = eppRow['PeakCentre']
+ sigma = eppRow['Sigma']
+ leftEnds[i] = peakCentre - sigmaMultiplier * sigma
+ if leftBegins[i] > leftEnds[i]:
+ leftBegins[i] = leftEnds[i]
+ rightBegins[i] = peakCentre + sigmaMultiplier * sigma
+ if rightBegins[i] > rightEnds[i]:
+ rightBegins[i] = rightEnds[i]
+ leftWSName = wsNames.withSuffix('integrated_left_bkgs')
+ leftWS = Integration(InputWorkspace=ws,
+ OutputWorkspace=leftWSName,
+ RangeLowerList=leftBegins,
+ RangeUpperList=leftEnds,
+ EnableLogging=algorithmLogging)
+ rightWSName = wsNames.withSuffix('integrated_right_bkgs')
+ rightWS = Integration(InputWorkspace=ws,
+ OutputWorkspace=rightWSName,
+ RangeLowerList=rightBegins,
+ RangeUpperList=rightEnds,
+ EnableLogging=algorithmLogging)
+ sumWSName = wsNames.withSuffix('integrated_bkgs_sum')
+ sumWS = Plus(LHSWorkspace=leftWS,
+ RHSWorkspace=rightWS,
+ OutputWorkspace=sumWSName,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(leftWS)
+ wsCleanup.cleanup(rightWS)
+ return sumWS
+
+
+def _integrateElasticPeaks(ws, eppWS, sigmaMultiplier, wsNames, wsCleanup, algorithmLogging):
+ """Return a workspace integrated around the elastic peak."""
+ histogramCount = ws.getNumberHistograms()
+ integrationBegins = numpy.empty(histogramCount)
+ integrationEnds = numpy.empty(histogramCount)
+ for i in range(histogramCount):
+ eppRow = eppWS.row(i)
+ if eppRow['FitStatus'] != 'success':
+ integrationBegins[i] = 0
+ integrationEnds[i] = 0
+ continue
+ peakCentre = eppRow['PeakCentre']
+ sigma = eppRow['Sigma']
+ integrationBegins[i] = peakCentre - sigmaMultiplier * sigma
+ integrationEnds[i] = peakCentre + sigmaMultiplier * sigma
+ integratedElasticPeaksWSName = \
+ wsNames.withSuffix('integrated_elastic_peak')
+ integratedElasticPeaksWS = \
+ Integration(InputWorkspace=ws,
+ OutputWorkspace=integratedElasticPeaksWSName,
+ IncludePartialBins=True,
+ RangeLowerList=integrationBegins,
+ RangeUpperList=integrationEnds,
+ EnableLogging=algorithmLogging)
+ solidAngleWSName = wsNames.withSuffix('detector_solid_angles')
+ solidAngleWS = SolidAngle(InputWorkspace=ws,
+ OutputWorkspace=solidAngleWSName,
+ EnableLogging=algorithmLogging)
+ solidAngleCorrectedElasticPeaksWSName = \
+ wsNames.withSuffix('solid_angle_corrected_elastic_peak')
+ solidAngleCorrectedElasticPeaksWS = \
+ Divide(LHSWorkspace=integratedElasticPeaksWS,
+ RHSWorkspace=solidAngleWS,
+ OutputWorkspace=solidAngleCorrectedElasticPeaksWSName,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(integratedElasticPeaksWS)
+ wsCleanup.cleanup(solidAngleWS)
+ return solidAngleCorrectedElasticPeaksWS
+
+
+def _maskDiagnosedDetectors(ws, diagnosticsWS, wsNames, algorithmLogging):
+ """Mask detectors according to diagnostics."""
+ maskedWSName = wsNames.withSuffix('diagnostics_applied')
+ maskedWS = CloneWorkspace(InputWorkspace=ws,
+ OutputWorkspace=maskedWSName,
+ EnableLogging=algorithmLogging)
+ MaskDetectors(Workspace=maskedWS,
+ MaskedWorkspace=diagnosticsWS,
+ EnableLogging=algorithmLogging)
+ return maskedWS
+
+
+def _maskedListToStr(masked):
+ """Return a string presentation of a list of spectrum numbers."""
+ if not masked:
+ return 'None'
+
+ def addBlock(string, begin, end):
+ if blockBegin == blockEnd:
+ string += str(blockEnd) + ', '
+ else:
+ string += str(blockBegin) + '-' + str(blockEnd) + ', '
+ return string
+
+ string = str()
+ blockBegin = None
+ blockEnd = None
+ maxMasked = max(masked)
+ for i in sorted(masked):
+ if blockBegin is None:
+ blockBegin = i
+ blockEnd = i
+ if i == maxMasked:
+ if i > blockEnd + 1:
+ string = addBlock(string, blockBegin, blockEnd)
+ string += str(i)
+ else:
+ string += str(blockBegin) + '-' + str(i)
+ break
+ if i > blockEnd + 1:
+ string = addBlock(string, blockBegin, blockEnd)
+ blockBegin = i
+ blockEnd = i
+ return string
+
+
+def _reportBkgDiagnostics(reportWS, bkgWS, diagnosticsWS):
+ """Return masked spectrum numbers and add background diagnostics information to a report workspace."""
+ return _reportDiagnostics(reportWS, bkgWS, diagnosticsWS, 'FlatBkg', 'BkgDiagnosed')
+
+
+def _reportBeamStopMask(reportWS, maskWS):
+ """Return masked spectrum numbers and add default mask information to a report workspace."""
+ return _reportMasking(reportWS, maskWS, 'BeamStopMask')
+
+
+def _reportDefaultMask(reportWS, maskWS):
+ """Return masked spectrum numbers and add default mask information to a report workspace."""
+ return _reportMasking(reportWS, maskWS, 'DefaultMask')
+
+
+def _reportDiagnostics(reportWS, dataWS, diagnosticsWS, dataColumn, diagnosedColumn):
+ """Return masked spectrum numbers and add diagnostics information to a report workspace."""
+ if reportWS is not None:
+ existingColumnNames = reportWS.getColumnNames()
+ if dataColumn not in existingColumnNames:
+ reportWS.addColumn('double', dataColumn, _PLOT_TYPE_Y)
+ if diagnosedColumn not in existingColumnNames:
+ reportWS.addColumn('double', diagnosedColumn, _PLOT_TYPE_Y)
+ maskedSpectra = list()
+ for i in range(dataWS.getNumberHistograms()):
+ diagnosed = int(diagnosticsWS.readY(i)[0])
+ if reportWS is not None:
+ y = dataWS.readY(i)[0]
+ reportWS.setCell(dataColumn, i, y)
+ reportWS.setCell(diagnosedColumn, i, diagnosed)
+ if diagnosed != 0:
+ maskedSpectra.append(dataWS.getSpectrum(i).getSpectrumNo())
+ return maskedSpectra
+
+
+def _reportMasking(reportWS, maskWS, maskedColumn):
+ """Return masked spectrum numbers and add masking information to a report workspace."""
+ if reportWS is not None:
+ existingColumnNames = reportWS.getColumnNames()
+ if maskedColumn not in existingColumnNames:
+ reportWS.addColumn('double', maskedColumn, _PLOT_TYPE_Y)
+ maskedSpectra = list()
+ for i in range(maskWS.getNumberHistograms()):
+ masked = int(maskWS.readY(i)[0])
+ if reportWS is not None:
+ reportWS.setCell(maskedColumn, i, masked)
+ if masked != 0:
+ maskedSpectra.append(maskWS.getSpectrum(i).getSpectrumNo())
+ return maskedSpectra
+
+
+def _reportPeakDiagnostics(reportWS, peakIntensityWS, diagnosticsWS):
+ """Return masked spectrum numbers and add elastic peak diagnostics information to a report workspace."""
+ return _reportDiagnostics(reportWS, peakIntensityWS, diagnosticsWS, 'ElasticIntensity', 'IntensityDiagnosed')
+
+
+def _reportUserMask(reportWS, maskWS):
+ """Return masked spectrum numbers and add user mask information to a report workspace."""
+ return _reportMasking(reportWS, maskWS, 'UserMask')
+
+
+class DirectILLDiagnostics(DataProcessorAlgorithm):
+ """A workflow algorithm for detector diagnostics."""
+
+ def __init__(self):
+ """Initialize an instance of the algorithm."""
+ DataProcessorAlgorithm.__init__(self)
+
+ def category(self):
+ """Return the algorithm's category."""
+ return 'Workflow\\Inelastic'
+
+ def name(self):
+ """Return the algorithm's name."""
+ return 'DirectILLDiagnostics'
+
+ def summary(self):
+ """Return a summary of the algorithm."""
+ return 'Perform detector diagnostics and masking for the direct geometry TOF spectrometers at ILL.'
+
+ def version(self):
+ """Return the algorithm's version."""
+ return 1
+
+ def PyExec(self):
+ """Executes the data reduction workflow."""
+ progress = Progress(self, 0.0, 1.0, 7)
+ report = common.Report()
+ subalgLogging = self.getProperty(common.PROP_SUBALG_LOGGING).value == common.SUBALG_LOGGING_ON
+ wsNamePrefix = self.getProperty(common.PROP_OUTPUT_WS).valueAsStr
+ cleanupMode = self.getProperty(common.PROP_CLEANUP_MODE).value
+ wsNames = common.NameSource(wsNamePrefix, cleanupMode)
+ wsCleanup = common.IntermediateWSCleanup(cleanupMode, subalgLogging)
+
+ progress.report('Loading inputs')
+ mainWS = self._inputWS(wsNames, wsCleanup, subalgLogging)
+
+ maskWSName = wsNames.withSuffix('combined_mask')
+ maskWS = _createMaskWS(mainWS, maskWSName, subalgLogging)
+
+ reportWS = None
+ if not self.getProperty(common.PROP_OUTPUT_DIAGNOSTICS_REPORT_WS).isDefault:
+ reportWSName = self.getProperty(common.PROP_OUTPUT_DIAGNOSTICS_REPORT_WS).valueAsStr
+ reportWS = _createDiagnosticsReportTable(reportWSName, mainWS.getNumberHistograms(), subalgLogging)
+
+ progress.report('Loading default mask')
+ defaultMaskWS = self._defaultMask(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ defaultMaskedSpectra = list()
+ if defaultMaskWS is not None:
+ defaultMaskedSpectra = _reportDefaultMask(reportWS, defaultMaskWS)
+ maskWS = Plus(LHSWorkspace=maskWS,
+ RHSWorkspace=defaultMaskWS,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(defaultMaskWS)
+
+ progress.report('User-defined mask')
+ userMaskWS = self._userMask(mainWS, wsNames, wsCleanup, subalgLogging)
+ userMaskedSpectra = _reportUserMask(reportWS, userMaskWS)
+ maskWS = Plus(LHSWorkspace=maskWS,
+ RHSWorkspace=userMaskWS,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(userMaskWS)
+
+ beamStopMaskedSpectra = list()
+ if self._beamStopDiagnosticsEnabled(mainWS, report):
+ progress.report('Diagnosing beam stop')
+ beamStopMaskWS = self._beamStopDiagnostics(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ beamStopMaskedSpectra = _reportBeamStopMask(reportWS, beamStopMaskWS)
+ maskWS = Plus(LHSWorkspace=maskWS,
+ RHSWorkspace=beamStopMaskWS,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(beamStopMaskWS)
+
+ bkgMaskedSpectra = list()
+ if self._bkgDiagnosticsEnabled(mainWS, report):
+ progress.report('Diagnosing backgrounds')
+ bkgMaskWS, bkgWS = self._bkgDiagnostics(mainWS, maskWS, wsNames, wsCleanup, report, subalgLogging)
+ bkgMaskedSpectra = _reportBkgDiagnostics(reportWS, bkgWS, bkgMaskWS)
+ maskWS = Plus(LHSWorkspace=maskWS,
+ RHSWorkspace=bkgMaskWS,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(bkgMaskWS)
+ wsCleanup.cleanup(bkgWS)
+
+ peakMaskedSpectra = list()
+ if self._peakDiagnosticsEnabled(mainWS, report):
+ progress.report('Diagnosing peaks')
+ peakMaskWS, peakIntensityWS = self._peakDiagnostics(mainWS, maskWS, wsNames, wsCleanup, report, subalgLogging)
+ peakMaskedSpectra = _reportPeakDiagnostics(reportWS, peakIntensityWS, peakMaskWS)
+ maskWS = Plus(LHSWorkspace=maskWS,
+ RHSWorkspace=peakMaskWS,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(peakMaskWS)
+ wsCleanup.cleanup(peakIntensityWS)
+
+ self._outputReports(reportWS, defaultMaskedSpectra, userMaskedSpectra, beamStopMaskedSpectra,
+ peakMaskedSpectra, bkgMaskedSpectra)
+
+ self._finalize(maskWS, wsCleanup, report)
+ progress.report('Done')
+
+ def PyInit(self):
+ """Initialize the algorithm's input and output properties."""
+ PROPGROUP_BEAM_STOP_DIAGNOSTICS = 'Beam Stop Diagnostics'
+ PROPGROUP_BKG_DIAGNOSTICS = 'Background Diagnostics'
+ PROPGROUP_PEAK_DIAGNOSTICS = 'Elastic Peak Diagnostics'
+ PROPGROUP_USER_MASK = 'Additional Masking'
+ greaterThanUnityFloat = FloatBoundedValidator(lower=1)
+ inputWorkspaceValidator = CompositeValidator()
+ inputWorkspaceValidator.add(InstrumentValidator())
+ inputWorkspaceValidator.add(WorkspaceUnitValidator('TOF'))
+ positiveFloat = FloatBoundedValidator(lower=0)
+ positiveIntArray = IntArrayBoundedValidator()
+ positiveIntArray.setLower(0)
+ scalingFactor = FloatBoundedValidator(lower=0, upper=1)
+
+ # Properties.
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INPUT_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ direction=Direction.Input),
+ doc='Raw input workspace.')
+ self.declareProperty(WorkspaceProperty(name=common.PROP_OUTPUT_WS,
+ defaultValue='',
+ direction=Direction.Output),
+ doc='A diagnostics mask workspace.')
+ self.declareProperty(name=common.PROP_CLEANUP_MODE,
+ defaultValue=common.CLEANUP_ON,
+ validator=StringListValidator([
+ common.CLEANUP_ON,
+ common.CLEANUP_OFF]),
+ direction=Direction.Input,
+ doc='What to do with intermediate workspaces.')
+ self.declareProperty(name=common.PROP_SUBALG_LOGGING,
+ defaultValue=common.SUBALG_LOGGING_OFF,
+ validator=StringListValidator([
+ common.SUBALG_LOGGING_OFF,
+ common.SUBALG_LOGGING_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable subalgorithms to ' +
+ 'print in the logs.')
+ self.declareProperty(ITableWorkspaceProperty(
+ name=common.PROP_EPP_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='Table workspace containing results from the FindEPP algorithm.')
+ self.declareProperty(name=common.PROP_ELASTIC_PEAK_DIAGNOSTICS,
+ defaultValue=common.ELASTIC_PEAK_DIAGNOSTICS_AUTO,
+ validator=StringListValidator([
+ common.ELASTIC_PEAK_DIAGNOSTICS_AUTO,
+ common.ELASTIC_PEAK_DIAGNOSTICS_ON,
+ common.ELASTIC_PEAK_DIAGNOSTICS_OFF]),
+ direction=Direction.Input,
+ doc='Enable or disable elastic peak diagnostics.')
+ self.setPropertyGroup(common.PROP_ELASTIC_PEAK_DIAGNOSTICS,
+ PROPGROUP_PEAK_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_ELASTIC_PEAK_SIGMA_MULTIPLIER,
+ defaultValue=3.0,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc="Integration width of the elastic peak in multiples " +
+ " of 'Sigma' in the EPP table.")
+ self.setPropertyGroup(common.PROP_ELASTIC_PEAK_SIGMA_MULTIPLIER,
+ PROPGROUP_PEAK_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_PEAK_DIAGNOSTICS_LOW_THRESHOLD,
+ defaultValue=0.1,
+ validator=scalingFactor,
+ direction=Direction.Input,
+ doc='Multiplier for lower acceptance limit ' +
+ 'used in elastic peak diagnostics.')
+ self.setPropertyGroup(common.PROP_PEAK_DIAGNOSTICS_LOW_THRESHOLD,
+ PROPGROUP_PEAK_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_PEAK_DIAGNOSTICS_HIGH_THRESHOLD,
+ defaultValue=3.0,
+ validator=greaterThanUnityFloat,
+ direction=Direction.Input,
+ doc='Multiplier for higher acceptance limit ' +
+ 'used in elastic peak diagnostics.')
+ self.setPropertyGroup(common.PROP_PEAK_DIAGNOSTICS_HIGH_THRESHOLD,
+ PROPGROUP_PEAK_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_PEAK_DIAGNOSTICS_SIGNIFICANCE_TEST,
+ defaultValue=3.3,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc='Error bar multiplier for significance ' +
+ 'test in the elastic peak diagnostics.')
+ self.setPropertyGroup(common.PROP_PEAK_DIAGNOSTICS_SIGNIFICANCE_TEST,
+ PROPGROUP_PEAK_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BKG_DIAGNOSTICS,
+ defaultValue=common.BKG_DIAGNOSTICS_AUTO,
+ validator=StringListValidator([
+ common.BKG_DIAGNOSTICS_AUTO,
+ common.BKG_DIAGNOSTICS_ON,
+ common.BKG_DIAGNOSTICS_OFF]),
+ direction=Direction.Input,
+ doc='Control the background diagnostics.')
+ self.setPropertyGroup(common.PROP_BKG_DIAGNOSTICS, PROPGROUP_BKG_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BKG_SIGMA_MULTIPLIER,
+ defaultValue=10.0,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc="Width of the range excluded from background integration around " +
+ "the elastic peaks in multiplies of 'Sigma' in the EPP table")
+ self.setPropertyGroup(common.PROP_BKG_SIGMA_MULTIPLIER,
+ PROPGROUP_BKG_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BKG_DIAGNOSTICS_LOW_THRESHOLD,
+ defaultValue=0.1,
+ validator=scalingFactor,
+ direction=Direction.Input,
+ doc='Multiplier for lower acceptance limit ' +
+ 'used in noisy background diagnostics.')
+ self.setPropertyGroup(common.PROP_BKG_DIAGNOSTICS_LOW_THRESHOLD,
+ PROPGROUP_BKG_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BKG_DIAGNOSTICS_HIGH_THRESHOLD,
+ defaultValue=3.3,
+ validator=greaterThanUnityFloat,
+ direction=Direction.Input,
+ doc='Multiplier for higher acceptance limit ' +
+ 'used in noisy background diagnostics.')
+ self.setPropertyGroup(common.PROP_BKG_DIAGNOSTICS_HIGH_THRESHOLD,
+ PROPGROUP_BKG_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BKG_DIAGNOSTICS_SIGNIFICANCE_TEST,
+ defaultValue=3.3,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc='Error bar multiplier for significance ' +
+ 'test in the noisy background diagnostics.')
+ self.setPropertyGroup(common.PROP_BKG_DIAGNOSTICS_SIGNIFICANCE_TEST,
+ PROPGROUP_BKG_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BEAM_STOP_DIAGNOSTICS,
+ defaultValue=common.BEAM_STOP_DIAGNOSTICS_AUTO,
+ validator=StringListValidator([
+ common.BEAM_STOP_DIAGNOSTICS_AUTO,
+ common.BEAM_STOP_DIAGNOSTICS_ON,
+ common.BEAM_STOP_DIAGNOSTICS_OFF]),
+ direction=Direction.Input,
+ doc='Control the beam stop diagnostics.')
+ self.setPropertyGroup(common.PROP_BEAM_STOP_DIAGNOSTICS, PROPGROUP_BEAM_STOP_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_BEAM_STOP_THRESHOLD,
+ defaultValue=0.67,
+ validator=scalingFactor,
+ direction=Direction.Input,
+ doc='Multiplier for the lower acceptance limit for beam stop diagnostics.')
+ self.setPropertyGroup(common.PROP_BEAM_STOP_THRESHOLD, PROPGROUP_BEAM_STOP_DIAGNOSTICS)
+ self.declareProperty(name=common.PROP_DEFAULT_MASK,
+ defaultValue=common.DEFAULT_MASK_ON,
+ validator=StringListValidator([
+ common.DEFAULT_MASK_ON,
+ common.DEFAULT_MASK_OFF]),
+ direction=Direction.Input,
+ doc='Enable or disable instrument specific default mask.')
+ self.declareProperty(IntArrayProperty(name=common.PROP_USER_MASK,
+ values='',
+ validator=positiveIntArray,
+ direction=Direction.Input),
+ doc='List of spectra to mask.')
+ self.setPropertyGroup(common.PROP_USER_MASK, PROPGROUP_USER_MASK)
+ self.declareProperty(
+ StringArrayProperty(name=common.PROP_USER_MASK_COMPONENTS,
+ values='',
+ direction=Direction.Input),
+ doc='List of instrument components to mask.')
+ self.setPropertyGroup(common.PROP_USER_MASK_COMPONENTS, PROPGROUP_USER_MASK)
+ # Rest of the output properties
+ self.declareProperty(ITableWorkspaceProperty(
+ name=common.PROP_OUTPUT_DIAGNOSTICS_REPORT_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output table workspace for detector diagnostics reporting.')
+ self.setPropertyGroup(common.PROP_OUTPUT_DIAGNOSTICS_REPORT_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+ self.declareProperty(name=common.PROP_OUTPUT_DIAGNOSTICS_REPORT,
+ defaultValue='',
+ direction=Direction.Output,
+ doc='Diagnostics report as a string.')
+ self.setPropertyGroup(common.PROP_OUTPUT_DIAGNOSTICS_REPORT,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+
+ def validateInputs(self):
+ """Check for issues with user input."""
+ issues = dict()
+ if self.getProperty(common.PROP_EPP_WS).isDefault:
+ if self.getProperty(common.PROP_ELASTIC_PEAK_DIAGNOSTICS).value == common.ELASTIC_PEAK_DIAGNOSTICS_ON:
+ issues[common.PROP_EPP_WS] = 'An EPP table is needed for elastic peak diagnostics.'
+ if self.getProperty(common.PROP_BKG_DIAGNOSTICS).value == common.BKG_DIAGNOSTICS_ON:
+ issues[common.PROP_EPP_WS] = 'An EPP table is needed for background diagnostics.'
+ return issues
+
+ def _beamStopDiagnostics(self, mainWS, wsNames, wsCleanup, report, algorithmLogging):
+ """Diagnose beam stop and return a mask workspace."""
+ import operator
+
+ def thresholdIndex(ws, begin, end, threshold):
+ """Return an index where the threshold is crossed."""
+ step = -1 if begin < end else 1
+ comp = operator.ge if begin < end else operator.le
+ Ys = numpy.empty(abs(end - begin))
+ i = end + step
+ indexShift = -min(begin, end + 1)
+ while comp(i, begin):
+ index = i + indexShift
+ Ys[index] = numpy.sum(ws.dataY(i))
+ i += step
+ maxIndex = int(numpy.argmax(Ys))
+ thresholdVal = threshold * Ys[maxIndex]
+ i = maxIndex - indexShift + step
+ while comp(i, begin):
+ index = i + indexShift
+ if Ys[index] < thresholdVal:
+ return i
+ i += step
+ return i
+ beamStopDiagnosticsWSName = wsNames.withSuffix('beam_stop_diagnostics')
+ beamStopDiagnosticsWS = _createMaskWS(mainWS, beamStopDiagnosticsWSName, algorithmLogging)
+ threshold = self.getProperty(common.PROP_BEAM_STOP_THRESHOLD).value
+ beginIndices, endIndices = _beamStopRanges(mainWS)
+ for i in range(len(beginIndices)):
+ begin = beginIndices[i]
+ end = endIndices[i]
+ mid = int((end + begin) / 2)
+ lowerIdx = thresholdIndex(mainWS, mid, begin, threshold)
+ upperIdx = thresholdIndex(mainWS, mid, end, threshold)
+ if lowerIdx != upperIdx:
+ for j in range(upperIdx - lowerIdx + 1):
+ ys = beamStopDiagnosticsWS.dataY(lowerIdx + j)
+ ys[0] = 1.0
+ return beamStopDiagnosticsWS
+
+ def _beamStopDiagnosticsEnabled(self, mainWS, report):
+ """Return true if beam stop diagnostics are enabled, false otherwise."""
+ beamStopDiagnostics = self.getProperty(common.PROP_BEAM_STOP_DIAGNOSTICS).value
+ if beamStopDiagnostics == common.BEAM_STOP_DIAGNOSTICS_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('beam_stop_diagnostics_spectra'):
+ return True
+ return False
+ elif beamStopDiagnostics == common.BEAM_STOP_DIAGNOSTICS_ON:
+ instrument = mainWS.getInstrument()
+ if not instrument.hasParameter('beam_stop_diagnostics_spectra'):
+ report.error("'beam_stop_diagnostics_spectra' missing from instrument parameters. "
+ + "Beam stop diagnostics disabled.")
+ return False
+ return True
+ return False
+
+ def _bkgDiagnostics(self, mainWS, maskWS, wsNames, wsCleanup, report, subalgLogging):
+ """Perform background diagnostics."""
+ eppWS = self.getProperty(common.PROP_EPP_WS).value
+ sigmaMultiplier = self.getProperty(common.PROP_BKG_SIGMA_MULTIPLIER).value
+ integratedBkgs = _integrateBkgs(mainWS, eppWS, sigmaMultiplier, wsNames, wsCleanup, subalgLogging)
+ lowThreshold = self.getProperty(common.PROP_BKG_DIAGNOSTICS_LOW_THRESHOLD).value
+ highThreshold = self.getProperty(common.PROP_BKG_DIAGNOSTICS_HIGH_THRESHOLD).value
+ significanceTest = self.getProperty(common.PROP_BKG_DIAGNOSTICS_SIGNIFICANCE_TEST).value
+ settings = _DiagnosticsSettings(lowThreshold, highThreshold, significanceTest)
+ bkgDiagnosticsWS = _bkgDiagnostics(integratedBkgs, settings, wsNames, subalgLogging)
+ return (bkgDiagnosticsWS, integratedBkgs)
+
+ def _bkgDiagnosticsEnabled(self, mainWS, report):
+ """Return true if background diagnostics are enabled, false otherwise."""
+ bkgDiagnostics = self.getProperty(common.PROP_BKG_DIAGNOSTICS).value
+ if bkgDiagnostics == common.BKG_DIAGNOSTICS_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('enable_background_diagnostics'):
+ enabled = instrument.getBoolParameter('enable_background_diagnostics')[0]
+ if not enabled:
+ report.notice('Background diagnostics disable by the IPF.')
+ return False
+ report.notice('Background diagnostics enabled.')
+ return True
+ return bkgDiagnostics == common.BKG_DIAGNOSTICS_ON
+
+ def _defaultMask(self, mainWS, wsNames, wsCleanup, report, algorithmLogging):
+ """Load instrument specific default mask or return None if not available."""
+ option = self.getProperty(common.PROP_DEFAULT_MASK).value
+ if option == common.DEFAULT_MASK_OFF:
+ return None
+ instrument = mainWS.getInstrument()
+ instrumentName = instrument.getName()
+ if not instrument.hasParameter('Workflow.MaskFile'):
+ report.notice('No default mask available for ' + instrumentName + '.')
+ return None
+ maskFilename = instrument.getStringParameter('Workflow.MaskFile')[0]
+ maskFile = os.path.join(mantid.config.getInstrumentDirectory(), 'masks', maskFilename)
+ defaultMaskWSName = wsNames.withSuffix('default_mask')
+ defaultMaskWS = LoadMask(Instrument=instrumentName,
+ InputFile=maskFile,
+ RefWorkspace=mainWS,
+ OutputWorkspace=defaultMaskWSName,
+ EnableLogging=algorithmLogging)
+ report.notice('Default mask loaded from ' + maskFilename)
+ return defaultMaskWS
+
+ def _finalize(self, outWS, wsCleanup, report):
+ """Do final cleanup and set the output property."""
+ self.setProperty(common.PROP_OUTPUT_WS, outWS)
+ wsCleanup.cleanup(outWS)
+ wsCleanup.finalCleanup()
+ report.toLog(self.log())
+
+ def _inputWS(self, wsNames, wsCleanup, subalgLogging):
+ """Return the raw input workspace."""
+ mainWS = self.getProperty(common.PROP_INPUT_WS).value
+ wsCleanup.protect(mainWS)
+ return mainWS
+
+ def _outputReports(self, reportWS, defaultMaskedSpectra, userMaskedSpectra, directBeamMaskedSpectra,
+ peakMaskedSpectra, bkgMaskedSpectra):
+ """Set the optional output report properties."""
+ if reportWS is not None:
+ self.setProperty(common.PROP_OUTPUT_DIAGNOSTICS_REPORT_WS, reportWS)
+ report = 'Spectra masked by default mask file:\n'
+ report += _maskedListToStr(defaultMaskedSpectra)
+ report += '\nSpectra masked by user:\n'
+ report += _maskedListToStr(userMaskedSpectra)
+ report += '\nSpectra masked by beam stop diagnostics:\n'
+ report += _maskedListToStr(directBeamMaskedSpectra)
+ report += '\nSpectra marked as bad by elastic peak diagnostics:\n'
+ report += _maskedListToStr(peakMaskedSpectra)
+ report += '\nSpectra marked as bad by flat background diagnostics:\n'
+ report += _maskedListToStr(bkgMaskedSpectra)
+ self.setProperty(common.PROP_OUTPUT_DIAGNOSTICS_REPORT, report)
+
+ def _peakDiagnostics(self, mainWS, maskWS, wsNames, wsCleanup, report, subalgLogging):
+ """Perform elastic peak diagnostics."""
+ eppWS = self.getProperty(common.PROP_EPP_WS).value
+ sigmaMultiplier = self.getProperty(common.PROP_ELASTIC_PEAK_SIGMA_MULTIPLIER).value
+ integratedPeaksWS = _integrateElasticPeaks(mainWS, eppWS, sigmaMultiplier, wsNames, wsCleanup, subalgLogging)
+ lowThreshold = self.getProperty(common.PROP_PEAK_DIAGNOSTICS_LOW_THRESHOLD).value
+ highThreshold = self.getProperty(common.PROP_PEAK_DIAGNOSTICS_HIGH_THRESHOLD).value
+ significanceTest = self.getProperty(common.PROP_PEAK_DIAGNOSTICS_SIGNIFICANCE_TEST).value
+ settings = _DiagnosticsSettings(lowThreshold, highThreshold, significanceTest)
+ peakDiagnosticsWS = _elasticPeakDiagnostics(integratedPeaksWS, settings, wsNames, subalgLogging)
+ return (peakDiagnosticsWS, integratedPeaksWS)
+
+ def _peakDiagnosticsEnabled(self, mainWS, report):
+ """Return true if elastic peak diagnostics are enabled, false otherwise."""
+ peakDiagnostics = self.getProperty(common.PROP_ELASTIC_PEAK_DIAGNOSTICS).value
+ if peakDiagnostics == common.ELASTIC_PEAK_DIAGNOSTICS_AUTO:
+ instrument = mainWS.getInstrument()
+ if instrument.hasParameter('enable_elastic_peak_diagnostics'):
+ enabled = instrument.getBoolParameter('enable_elastic_peak_diagnostics')[0]
+ if not enabled:
+ report.notice('Elastic peak diagnostics disabled by the IPF.')
+ return False
+ report.notice('Elastic peak diagnostics enabled.')
+ return True
+ return peakDiagnostics == common.ELASTIC_PEAK_DIAGNOSTICS_ON
+
+ def _userMask(self, mainWS, wsNames, wsCleanup, algorithmLogging):
+ """Return combined masked spectra and components."""
+ userMask = self.getProperty(common.PROP_USER_MASK).value
+ maskComponents = self.getProperty(common.PROP_USER_MASK_COMPONENTS).value
+ maskWSName = wsNames.withSuffix('user_mask')
+ maskWS = _createMaskWS(mainWS, maskWSName, algorithmLogging)
+ MaskDetectors(Workspace=maskWS,
+ DetectorList=userMask,
+ ComponentList=maskComponents,
+ EnableLogging=algorithmLogging)
+ maskWS, detectorLsit = ExtractMask(InputWorkspace=maskWS,
+ OutputWorkspace=maskWSName,
+ EnableLogging=algorithmLogging)
+ return maskWS
+
+
+AlgorithmFactory.subscribe(DirectILLDiagnostics)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLIntegrateVanadium.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLIntegrateVanadium.py
new file mode 100644
index 0000000000000000000000000000000000000000..cfb855d68a7edd420b5dafba10579f65ca0de29a
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLIntegrateVanadium.py
@@ -0,0 +1,163 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+import DirectILL_common as common
+from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, InstrumentValidator, ITableWorkspaceProperty,
+ MatrixWorkspaceProperty, Progress, PropertyMode, WorkspaceProperty, WorkspaceUnitValidator)
+from mantid.kernel import (CompositeValidator, Direction, EnabledWhenProperty, FloatBoundedValidator, Property,
+ PropertyCriterion, StringListValidator)
+from mantid.simpleapi import (ComputeCalibrationCoefVan, Integration)
+import numpy
+
+
+class DirectILLIntegrateVanadium(DataProcessorAlgorithm):
+ """A workflow algorithm which integrates the vanadium data."""
+
+ def __init__(self):
+ """Initialize an instance of the algorithm."""
+ DataProcessorAlgorithm.__init__(self)
+
+ def category(self):
+ """Return the algorithm's category."""
+ return 'Workflow\\Inelastic'
+
+ def name(self):
+ """Return the algorithm's name."""
+ return 'DirectILLIntegrateVanadium'
+
+ def summary(self):
+ """Return a summary of the algorithm."""
+ return 'Integrate vanadium workspace. Part of the TOF workflow at ILL.'
+
+ def version(self):
+ """Return the algorithm's version."""
+ return 1
+
+ def PyExec(self):
+ """Executes the data reduction workflow."""
+ progress = Progress(self, 0.0, 1.0, 3)
+ subalgLogging = self.getProperty(common.PROP_SUBALG_LOGGING).value == common.SUBALG_LOGGING_ON
+ cleanupMode = self.getProperty(common.PROP_CLEANUP_MODE).value
+ wsCleanup = common.IntermediateWSCleanup(cleanupMode, subalgLogging)
+
+ progress.report('Loading inputs')
+ mainWS = self._inputWS(wsCleanup)
+
+ progress.report('Integrating')
+ mainWS = self._integrate(mainWS, wsCleanup, subalgLogging)
+
+ self._finalize(mainWS, wsCleanup)
+ progress.report('Done')
+
+ def PyInit(self):
+ inputWorkspaceValidator = CompositeValidator()
+ inputWorkspaceValidator.add(InstrumentValidator())
+ inputWorkspaceValidator.add(WorkspaceUnitValidator('TOF'))
+ positiveFloat = FloatBoundedValidator(lower=0)
+
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INPUT_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ optional=PropertyMode.Mandatory,
+ direction=Direction.Input),
+ doc='Input workspace.')
+ self.declareProperty(WorkspaceProperty(name=common.PROP_OUTPUT_WS,
+ defaultValue='',
+ direction=Direction.Output),
+ doc='The output of the algorithm.')
+ self.declareProperty(name=common.PROP_CLEANUP_MODE,
+ defaultValue=common.CLEANUP_ON,
+ validator=StringListValidator([
+ common.CLEANUP_ON,
+ common.CLEANUP_OFF]),
+ direction=Direction.Input,
+ doc='What to do with intermediate workspaces.')
+ self.declareProperty(name=common.PROP_SUBALG_LOGGING,
+ defaultValue=common.SUBALG_LOGGING_OFF,
+ validator=StringListValidator([
+ common.SUBALG_LOGGING_OFF,
+ common.SUBALG_LOGGING_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable subalgorithms to ' +
+ 'print in the logs.')
+ self.declareProperty(ITableWorkspaceProperty(
+ name=common.PROP_EPP_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Mandatory),
+ doc='Table workspace containing results from the FindEPP algorithm.')
+ self.declareProperty(name=common.PROP_DWF_CORRECTION,
+ defaultValue=common.DWF_ON,
+ validator=StringListValidator([
+ common.DWF_ON,
+ common.DWF_OFF]),
+ direction=Direction.Input,
+ doc='Enable or disable the correction for the Debye-Waller factor for ' + common.PROP_OUTPUT_WS + '.')
+ self.declareProperty(name=common.PROP_TEMPERATURE,
+ defaultValue=Property.EMPTY_DBL,
+ validator=positiveFloat,
+ direction=Direction.Input,
+ doc='Experimental temperature (Vanadium ' +
+ 'reduction type only) for the Debye-Waller correction, in Kelvins.')
+ self.setPropertySettings(common.PROP_TEMPERATURE, EnabledWhenProperty(common.PROP_DWF_CORRECTION,
+ PropertyCriterion.IsDefault))
+
+ def _inputWS(self, wsCleanup):
+ """Return the raw input workspace."""
+ mainWS = self.getProperty(common.PROP_INPUT_WS).value
+ wsCleanup.protect(mainWS)
+ return mainWS
+
+ def _finalize(self, outWS, wsCleanup):
+ """Do final cleanup and set the output property."""
+ self.setProperty(common.PROP_OUTPUT_WS, outWS)
+ wsCleanup.cleanup(outWS)
+ wsCleanup.finalCleanup()
+
+ def _integrate(self, mainWS, wsCleanup, subalgLogging):
+ """Integrate mainWS applying Debye-Waller correction, if requested."""
+ eppWS = self.getProperty(common.PROP_EPP_WS).value
+ calibrationWS = self.getPropertyValue(common.PROP_OUTPUT_WS)
+ if self.getProperty(common.PROP_DWF_CORRECTION).value == common.DWF_ON:
+ if not self.getProperty(common.PROP_TEMPERATURE).isDefault:
+ temperature = self.getProperty(common.PROP_TEMPERATURE).value
+ else:
+ temperature = 293.0
+ ILL_TEMPERATURE_ENTRY = 'sample.temperature'
+ if mainWS.run().hasProperty(ILL_TEMPERATURE_ENTRY):
+ temperatureProperty = mainWS.run().getProperty(ILL_TEMPERATURE_ENTRY)
+ if hasattr(temperatureProperty, 'getStatistics'):
+ temperature = temperatureProperty.getStatistics().mean
+ else:
+ temperature = temperatureProperty.value
+ calibrationWS = ComputeCalibrationCoefVan(VanadiumWorkspace=mainWS,
+ EPPTable=eppWS,
+ OutputWorkspace=calibrationWS,
+ Temperature=temperature,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return calibrationWS
+ # No DWF correction - integrate manually.
+ # TODO revise when ComputeCalibrationCoefVan supports this option.
+ size = eppWS.rowCount()
+ starts = numpy.zeros(size)
+ ends = numpy.zeros(size)
+ for i in range(size):
+ row = eppWS.row(i)
+ if row['FitStatus'] == 'success':
+ fwhm = 2.0 * numpy.sqrt(2.0 * numpy.log(2.0)) * row['Sigma']
+ centre = row['PeakCentre']
+ starts[i] = centre - 3.0 * fwhm
+ ends[i] = centre + 3.0 * fwhm
+ calibrationWS = Integration(InputWorkspace=mainWS,
+ OutputWorkspace=calibrationWS,
+ RangeLowerList=starts,
+ RangeUpperList=ends,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return calibrationWS
+
+
+AlgorithmFactory.subscribe(DirectILLIntegrateVanadium)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py
new file mode 100644
index 0000000000000000000000000000000000000000..05827a29ce0b13b2c051a337ae6993a8f567c3d1
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py
@@ -0,0 +1,487 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+import DirectILL_common as common
+from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, InstrumentValidator,
+ MatrixWorkspaceProperty, Progress, PropertyMode, WorkspaceProperty, WorkspaceUnitValidator)
+from mantid.kernel import (CompositeValidator, Direction, FloatArrayProperty, StringListValidator)
+from mantid.simpleapi import (BinWidthAtX, CloneWorkspace, ConvertSpectrumAxis, ConvertUnits, CorrectKiKf, DetectorEfficiencyCorUser,
+ Divide, GroupDetectors, MaskDetectors, Rebin, Scale, SofQWNormalisedPolygon, Transpose)
+import math
+import numpy
+import roundinghelper
+from scipy import constants
+
+
+def _absoluteUnits(ws, vanaWS, wsNames, wsCleanup, report, algorithmLogging):
+ """Scales ws by an absolute units factor."""
+ sampleMaterial = ws.sample().getMaterial()
+ sampleNumberDensity = sampleMaterial.numberDensity
+ vanaMaterial = vanaWS.sample().getMaterial()
+ vanaNumberDensity = vanaMaterial.numberDensity
+ vanaCrossSection = vanaMaterial.totalScatterXSection()
+ factor = vanaNumberDensity / sampleNumberDensity * vanaCrossSection
+ if factor <= 0 or math.isnan(factor) or math.isinf(factor):
+ raise RuntimeError('Invalid absolute units normalisation factor: {}'.format(factor))
+ report.notice('Absolute units scaling factor: {}'.format(factor))
+ scaledWSName = wsNames.withSuffix('absolute_units')
+ scaledWS = Scale(InputWorkspace=ws,
+ OutputWorkspace=scaledWSName,
+ Factor=factor,
+ EnableLogging=algorithmLogging)
+ wsCleanup.cleanup(ws)
+ return scaledWS
+
+
+def _createDetectorGroups(ws):
+ """Find workspace indices with (almost) same theta and group them. Masked
+ detectors are ignored.
+ """
+ numHistograms = ws.getNumberHistograms()
+ groups = list()
+ detectorGrouped = numHistograms * [False]
+ spectrumInfo = ws.spectrumInfo()
+ twoThetas = numpy.empty(numHistograms)
+ for i in range(numHistograms):
+ det = ws.getDetector(i)
+ twoThetas[i] = ws.detectorTwoTheta(det)
+ for i in range(numHistograms):
+ if spectrumInfo.isMasked(i) or detectorGrouped[i]:
+ continue
+ twoTheta1 = twoThetas[i]
+ currentGroup = [ws.getDetector(i).getID()]
+ twoThetaDiff = numpy.abs(twoThetas[i + 1:] - twoTheta1)
+ equalTwoThetas = numpy.flatnonzero(twoThetaDiff < 0.01 / 180.0 * constants.pi)
+ for j in (i + 1) + equalTwoThetas:
+ if spectrumInfo.isMasked(int(j)):
+ continue
+ currentGroup.append(ws.getDetector(int(j)).getID())
+ detectorGrouped[j] = True
+ groups.append(currentGroup)
+ return groups
+
+
+def _deltaQ(ws):
+ """Estimate a q bin width for a S(theta, w) workspace."""
+ deltaTheta = _medianDeltaTheta(ws)
+ wavelength = ws.run().getProperty('wavelength').value
+ return 2.0 * constants.pi / wavelength * deltaTheta
+
+
+def _detectorGroupsToXml(groups, instrument):
+ """Create grouping pattern XML tree from detector groups."""
+ from xml.etree import ElementTree
+ rootElement = ElementTree.Element('detector-grouping', {'instrument': 'IN5'})
+ for group in groups:
+ name = str(group.pop())
+ groupElement = ElementTree.SubElement(rootElement, 'group', {'name': name})
+ detIds = name
+ for detId in group:
+ detIds += ',' + str(detId)
+ ElementTree.SubElement(groupElement, 'detids', {'val': detIds})
+ return rootElement
+
+
+def _energyBinning(ws, algorithmLogging):
+ """Create common (but nonequidistant) binning for a DeltaE workspace."""
+ xs = ws.extractX()
+ minXIndex = numpy.nanargmin(xs[:, 0])
+ # TODO Fix logging.
+ dx = BinWidthAtX(InputWorkspace=ws,
+ X=0.0,
+ EnableLogging=algorithmLogging)
+ lastX = numpy.max(xs[:, -1])
+ binCount = ws.blocksize()
+ borders = list()
+ templateXs = xs[minXIndex, :]
+ currentX = numpy.nan
+ for i in range(binCount):
+ currentX = templateXs[i]
+ borders.append(currentX)
+ if currentX > 0:
+ break
+ i = 1
+ equalBinStart = borders[-1]
+ while currentX < lastX:
+ currentX = equalBinStart + i * dx
+ borders.append(currentX)
+ i += 1
+ borders[-1] = lastX
+ return numpy.array(borders)
+
+
+def _medianDeltaTheta(ws):
+ """Calculate the median theta spacing for a S(theta, w) workspace."""
+ thetas = list()
+ spectrumInfo = ws.spectrumInfo()
+ for i in range(ws.getNumberHistograms()):
+ if (not spectrumInfo.isMasked(i) and spectrumInfo.hasDetectors(i) and
+ not spectrumInfo.isMonitor(i)):
+ det = ws.getDetector(i)
+ twoTheta = ws.detectorTwoTheta(det)
+ thetas.append(twoTheta)
+ if not thetas:
+ raise RuntimeError('No usable detectors for median DTheta ' +
+ 'calculation.')
+ dThetas = numpy.diff(thetas)
+ return numpy.median(dThetas[dThetas > numpy.radians(0.1)])
+
+
+def _minMaxQ(ws):
+ """Estimate the start and end q bins for a S(theta, w) workspace."""
+ Ei = ws.run().getProperty('Ei').value * 1e-3 * constants.e # in Joules
+ xs = ws.readX(0)
+ minW = xs[0] * 1e-3 * constants.e # in Joules
+ maxEf = Ei - minW
+ # In Ånströms
+ maxQ = numpy.sqrt(2.0 * constants.m_n / constants.hbar**2 *
+ (Ei + maxEf - 2 * numpy.sqrt(Ei * maxEf) * -1.0)) * 1e-10
+ minQ = 0.0
+ return (minQ, maxQ)
+
+
+def _rebin(ws, params, wsNames, algorithmLogging):
+ """Rebin a workspace."""
+ rebinnedWSName = wsNames.withSuffix('rebinned')
+ rebinnedWS = Rebin(InputWorkspace=ws,
+ OutputWorkspace=rebinnedWSName,
+ Params=params,
+ EnableLogging=algorithmLogging)
+ return rebinnedWS
+
+
+def _writeXml(element, filename):
+ """Write XML element to a file."""
+ from xml.etree import ElementTree
+ with open(filename, mode='wb') as outFile:
+ ElementTree.ElementTree(element).write(outFile)
+
+
+class DirectILLReduction(DataProcessorAlgorithm):
+ """A data reduction workflow algorithm for the direct geometry TOF spectrometers at ILL."""
+
+ def __init__(self):
+ """Initialize an instance of the algorithm."""
+ DataProcessorAlgorithm.__init__(self)
+
+ def category(self):
+ """Return the algorithm's category."""
+ return 'Workflow\\Inelastic'
+
+ def name(self):
+ """Return the algorithm's name."""
+ return 'DirectILLReduction'
+
+ def summary(self):
+ """Return a summary of the algorithm."""
+ return 'Data reduction workflow for the direct geometry time-of-flight spectrometers at ILL.'
+
+ def version(self):
+ """Return the algorithm's version."""
+ return 1
+
+ def PyExec(self):
+ """Executes the data reduction workflow."""
+ progress = Progress(self, 0.0, 1.0, 9)
+ report = common.Report()
+ subalgLogging = False
+ if self.getProperty(common.PROP_SUBALG_LOGGING).value == common.SUBALG_LOGGING_ON:
+ subalgLogging = True
+ wsNamePrefix = self.getProperty(common.PROP_OUTPUT_WS).valueAsStr
+ cleanupMode = self.getProperty(common.PROP_CLEANUP_MODE).value
+ wsNames = common.NameSource(wsNamePrefix, cleanupMode)
+ wsCleanup = common.IntermediateWSCleanup(cleanupMode, subalgLogging)
+
+ # The variables 'mainWS' and 'monWS shall hold the current main
+ # data throughout the algorithm.
+
+ # Get input workspace.
+ progress.report('Loading inputs')
+ mainWS = self._inputWS(wsNames, wsCleanup, subalgLogging)
+
+ progress.report('Applying diagnostics')
+ mainWS = self._applyDiagnostics(mainWS, wsNames, wsCleanup, subalgLogging)
+
+ # Vanadium normalization.
+ progress.report('Normalising to vanadium')
+ mainWS = self._normalizeToVana(mainWS, wsNames, wsCleanup, report, subalgLogging)
+
+ # Convert units from TOF to energy.
+ progress.report('Converting to energy')
+ mainWS = self._convertTOFToDeltaE(mainWS, wsNames, wsCleanup,
+ subalgLogging)
+
+ # KiKf conversion.
+ mainWS = self._correctByKiKf(mainWS, wsNames,
+ wsCleanup, subalgLogging)
+
+ # Rebinning.
+ progress.report('Rebinning in energy')
+ mainWS = self._rebinInW(mainWS, wsNames, wsCleanup, report,
+ subalgLogging)
+
+ # Detector efficiency correction.
+ progress.report('Correcting detector efficiency')
+ mainWS = self._correctByDetectorEfficiency(mainWS, wsNames,
+ wsCleanup, subalgLogging)
+
+ progress.report('Grouping detectors')
+ mainWS = self._groupDetectors(mainWS, wsNames, wsCleanup,
+ subalgLogging)
+
+ self._outputWSConvertedToTheta(mainWS, wsNames, wsCleanup,
+ subalgLogging)
+
+ progress.report('Converting to q')
+ mainWS = self._sOfQW(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ mainWS = self._transpose(mainWS, wsNames, wsCleanup, subalgLogging)
+ self._finalize(mainWS, wsCleanup, report)
+ progress.report('Done')
+
+ def PyInit(self):
+ """Initialize the algorithm's input and output properties."""
+ PROPGROUP_REBINNING = 'Rebinning for SofQW'
+ inputWorkspaceValidator = CompositeValidator()
+ inputWorkspaceValidator.add(InstrumentValidator())
+ inputWorkspaceValidator.add(WorkspaceUnitValidator('TOF'))
+
+ # Properties.
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INPUT_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ direction=Direction.Input),
+ doc='Input workspace.')
+ self.declareProperty(WorkspaceProperty(name=common.PROP_OUTPUT_WS,
+ defaultValue='',
+ direction=Direction.Output),
+ doc='The output of the algorithm.')
+ self.declareProperty(name=common.PROP_CLEANUP_MODE,
+ defaultValue=common.CLEANUP_ON,
+ validator=StringListValidator([
+ common.CLEANUP_ON,
+ common.CLEANUP_OFF]),
+ direction=Direction.Input,
+ doc='What to do with intermediate workspaces.')
+ self.declareProperty(name=common.PROP_SUBALG_LOGGING,
+ defaultValue=common.SUBALG_LOGGING_OFF,
+ validator=StringListValidator([
+ common.SUBALG_LOGGING_OFF,
+ common.SUBALG_LOGGING_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable subalgorithms to ' +
+ 'print in the logs.')
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_VANA_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='Reduced vanadium workspace.')
+ self.declareProperty(name=common.PROP_ABSOLUTE_UNITS,
+ defaultValue=common.ABSOLUTE_UNITS_OFF,
+ validator=StringListValidator([
+ common.ABSOLUTE_UNITS_OFF,
+ common.ABSOLUTE_UNITS_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable normalisation to absolute units.')
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_DIAGNOSTICS_WS,
+ defaultValue='',
+ direction=Direction.Input,
+ optional=PropertyMode.Optional),
+ doc='Detector diagnostics workspace obtained from another ' +
+ 'reduction run.')
+ self.declareProperty(FloatArrayProperty(name=common.PROP_REBINNING_PARAMS_W),
+ doc='Manual energy rebinning parameters.')
+ self.setPropertyGroup(common.PROP_REBINNING_PARAMS_W, PROPGROUP_REBINNING)
+ self.declareProperty(FloatArrayProperty(name=common.PROP_BINNING_PARAMS_Q),
+ doc='Manual q rebinning parameters.')
+ self.setPropertyGroup(common.PROP_BINNING_PARAMS_Q, PROPGROUP_REBINNING)
+ self.declareProperty(name=common.PROP_TRANSPOSE_SAMPLE_OUTPUT,
+ defaultValue=common.TRANSPOSING_ON,
+ validator=StringListValidator([
+ common.TRANSPOSING_ON,
+ common.TRANSPOSING_OFF]),
+ direction=Direction.Input,
+ doc='Enable or disable ' + common.PROP_OUTPUT_WS + ' transposing.')
+ self.declareProperty(WorkspaceProperty(
+ name=common.PROP_OUTPUT_THETA_W_WS,
+ defaultValue='',
+ direction=Direction.Output,
+ optional=PropertyMode.Optional),
+ doc='Output workspace for reduced S(theta, DeltaE).')
+ self.setPropertyGroup(common.PROP_OUTPUT_THETA_W_WS,
+ common.PROPGROUP_OPTIONAL_OUTPUT)
+
+ def validateInputs(self):
+ """Check for issues with user input."""
+ # TODO
+ return dict()
+
+ def _applyDiagnostics(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Mask workspace according to diagnostics."""
+ if self.getProperty(common.PROP_DIAGNOSTICS_WS).isDefault:
+ return mainWS
+ diagnosticsWS = self.getProperty(common.PROP_DIAGNOSTICS_WS).value
+ maskedWSName = wsNames.withSuffix('diagnostics_applied')
+ maskedWS = CloneWorkspace(InputWorkspace=mainWS,
+ OutputWorkspace=maskedWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ diagnosticsWS = self.getProperty(common.PROP_DIAGNOSTICS_WS).value
+ MaskDetectors(Workspace=maskedWS,
+ MaskedWorkspace=diagnosticsWS,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return maskedWS
+
+ def _convertTOFToDeltaE(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Convert the X axis units from time-of-flight to energy transfer."""
+ energyConvertedWSName = wsNames.withSuffix('energy_converted')
+ energyConvertedWS = ConvertUnits(InputWorkspace=mainWS,
+ OutputWorkspace=energyConvertedWSName,
+ Target='DeltaE',
+ EMode='Direct',
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return energyConvertedWS
+
+ def _correctByDetectorEfficiency(self, mainWS, wsNames, wsCleanup,
+ subalgLogging):
+ """Apply detector efficiency corrections."""
+ correctedWSName = wsNames.withSuffix('detector_efficiency_corrected')
+ correctedWS = \
+ DetectorEfficiencyCorUser(InputWorkspace=mainWS,
+ OutputWorkspace=correctedWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return correctedWS
+
+ def _correctByKiKf(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Apply the k_i / k_f correction."""
+ correctedWSName = wsNames.withSuffix('kikf')
+ correctedWS = CorrectKiKf(InputWorkspace=mainWS,
+ OutputWorkspace=correctedWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return correctedWS
+
+ def _finalize(self, outWS, wsCleanup, report):
+ """Do final cleanup and set the output property."""
+ self.setProperty(common.PROP_OUTPUT_WS, outWS)
+ wsCleanup.cleanup(outWS)
+ wsCleanup.finalCleanup()
+ report.toLog(self.log())
+
+ def _groupDetectors(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Group detectors with similar thetas."""
+ import os
+ import tempfile
+ groups = _createDetectorGroups(mainWS)
+ instrumentName = mainWS.getInstrument().getName()
+ groupsXml = _detectorGroupsToXml(groups, instrumentName)
+ fileHandle, path = tempfile.mkstemp(suffix='.xml', prefix='grouping-{}-'.format(instrumentName))
+ _writeXml(groupsXml, path)
+ os.close(fileHandle)
+ groupedWSName = wsNames.withSuffix('grouped_detectors')
+ groupedWS = GroupDetectors(InputWorkspace=mainWS,
+ OutputWorkspace=groupedWSName,
+ MapFile=path,
+ KeepUngroupedSpectra=False,
+ Behaviour='Average',
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ os.remove(path)
+ return groupedWS
+
+ def _inputWS(self, wsNames, wsCleanup, subalgLogging):
+ """Return the raw input workspace."""
+ mainWS = self.getProperty(common.PROP_INPUT_WS).value
+ wsCleanup.protect(mainWS)
+ return mainWS
+
+ def _normalizeToVana(self, mainWS, wsNames, wsCleanup, report, subalgLogging):
+ """Normalize to vanadium workspace."""
+ if self.getProperty(common.PROP_VANA_WS).isDefault:
+ return mainWS
+ vanaWS = self.getProperty(common.PROP_VANA_WS).value
+ vanaNormalizedWSName = wsNames.withSuffix('vanadium_normalized')
+ vanaNormalizedWS = Divide(LHSWorkspace=mainWS,
+ RHSWorkspace=vanaWS,
+ OutputWorkspace=vanaNormalizedWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ if self.getProperty(common.PROP_ABSOLUTE_UNITS).value == common.ABSOLUTE_UNITS_ON:
+ vanaNormalizedWS = _absoluteUnits(vanaNormalizedWS, vanaWS, wsNames, wsCleanup, report,
+ subalgLogging)
+ return vanaNormalizedWS
+
+ def _outputWSConvertedToTheta(self, mainWS, wsNames, wsCleanup,
+ subalgLogging):
+ """If requested, convert the spectrum axis to theta and save the result
+ into the proper output property.
+ """
+ thetaWSName = self.getProperty(common.PROP_OUTPUT_THETA_W_WS).valueAsStr
+ if thetaWSName:
+ thetaWSName = self.getProperty(common.PROP_OUTPUT_THETA_W_WS).value
+ thetaWS = ConvertSpectrumAxis(InputWorkspace=mainWS,
+ OutputWorkspace=thetaWSName,
+ Target='Theta',
+ EMode='Direct',
+ EnableLogging=subalgLogging)
+ self.setProperty(common.PROP_OUTPUT_THETA_W_WS, thetaWS)
+
+ def _rebinInW(self, mainWS, wsNames, wsCleanup, report, subalgLogging):
+ """Rebin the horizontal axis of a workspace."""
+ if self.getProperty(common.PROP_REBINNING_PARAMS_W).isDefault:
+ binBorders = _energyBinning(mainWS, subalgLogging)
+ params = list()
+ binWidths = numpy.diff(binBorders)
+ for start, width in zip(binBorders[:-1], binWidths):
+ params.append(start)
+ params.append(width)
+ params.append(binBorders[-1])
+ else:
+ params = self.getProperty(common.PROP_REBINNING_PARAMS_W).value
+ rebinnedWS = _rebin(mainWS, params, wsNames, subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return rebinnedWS
+
+ def _sOfQW(self, mainWS, wsNames, wsCleanup, report, subalgLogging):
+ """Run the SofQWNormalisedPolygon algorithm."""
+ sOfQWWSName = wsNames.withSuffix('sofqw')
+ if self.getProperty(common.PROP_BINNING_PARAMS_Q).isDefault:
+ qMin, qMax = _minMaxQ(mainWS)
+ dq = _deltaQ(mainWS)
+ dq = 10 * roundinghelper.round(dq, roundinghelper.ROUNDING_TEN_TO_INT)
+ params = [qMin, dq, qMax]
+ report.notice('Binned momentum transfer axis to bin width {0}.'.format(dq))
+ else:
+ params = self.getProperty(common.PROP_BINNING_PARAMS_Q).value
+ Ei = mainWS.run().getLogData('Ei').value
+ sOfQWWS = SofQWNormalisedPolygon(InputWorkspace=mainWS,
+ OutputWorkspace=sOfQWWSName,
+ QAxisBinning=params,
+ EMode='Direct',
+ EFixed=Ei,
+ ReplaceNaNs=False,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return sOfQWWS
+
+ def _transpose(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Transpose the final output workspace."""
+ transposing = self.getProperty(common.PROP_TRANSPOSE_SAMPLE_OUTPUT).value
+ if transposing == common.TRANSPOSING_OFF:
+ return mainWS
+ transposedWSName = wsNames.withSuffix('transposed')
+ transposedWS = Transpose(InputWorkspace=mainWS,
+ OutputWorkspace=transposedWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ return transposedWS
+
+
+AlgorithmFactory.subscribe(DirectILLReduction)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShielding.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShielding.py
new file mode 100644
index 0000000000000000000000000000000000000000..9148b8dd70597377b4342ef0f056dc2333e27d29
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShielding.py
@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+import DirectILL_common as common
+from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, InstrumentValidator,
+ MatrixWorkspaceProperty, PropertyMode, WorkspaceUnitValidator)
+from mantid.kernel import (CompositeValidator, Direction, EnabledWhenProperty, IntBoundedValidator,
+ Property, PropertyCriterion, StringListValidator)
+from mantid.simpleapi import (ConvertUnits, MonteCarloAbsorption)
+
+
+class DirectILLSelfShielding(DataProcessorAlgorithm):
+ """A workflow algorithm for self-shielding corrections."""
+
+ def __init__(self):
+ """Initialize an instance of the algorithm."""
+ DataProcessorAlgorithm.__init__(self)
+
+ def category(self):
+ """Return the algorithm's category."""
+ return 'Workflow\\Inelastic'
+
+ def name(self):
+ """Return the algorithm's name."""
+ return 'DirectILLSelfShielding'
+
+ def summary(self):
+ """Return a summary of the algorithm."""
+ return 'Calculates self-shielding correction for the direct geometry TOF spectrometers at ILL.'
+
+ def version(self):
+ """Return the algorithm's version."""
+ return 1
+
+ def PyExec(self):
+ """Execute the algorithm."""
+ subalgLogging = self.getProperty(common.PROP_SUBALG_LOGGING).value == common.SUBALG_LOGGING_ON
+ wsNamePrefix = self.getProperty(common.PROP_OUTPUT_WS).valueAsStr
+ cleanupMode = self.getProperty(common.PROP_CLEANUP_MODE).value
+ wsNames = common.NameSource(wsNamePrefix, cleanupMode)
+ wsCleanup = common.IntermediateWSCleanup(cleanupMode, subalgLogging)
+
+ # Get input workspace.
+ mainWS = self._inputWS(wsNames, wsCleanup, subalgLogging)
+
+ # Self shielding and empty container subtraction, if requested.
+ correctionWS = self._selfShielding(mainWS, wsNames, wsCleanup, subalgLogging)
+
+ self._finalize(correctionWS, wsCleanup)
+
+ def PyInit(self):
+ """Initialize the algorithm's input and output properties."""
+ PROPGROUP_SIMULATION_INSTRUMENT = 'Simulation Instrument Settings'
+ greaterThanOneInt = IntBoundedValidator(lower=2)
+ greaterThanTwoInt = IntBoundedValidator(lower=3)
+ inputWorkspaceValidator = CompositeValidator()
+ inputWorkspaceValidator.add(InstrumentValidator())
+ inputWorkspaceValidator.add(WorkspaceUnitValidator('TOF'))
+
+ # Properties.
+ self.declareProperty(MatrixWorkspaceProperty(
+ name=common.PROP_INPUT_WS,
+ defaultValue='',
+ validator=inputWorkspaceValidator,
+ optional=PropertyMode.Optional,
+ direction=Direction.Input),
+ doc='Input workspace.')
+ self.declareProperty(MatrixWorkspaceProperty(name=common.PROP_OUTPUT_WS,
+ defaultValue='',
+ direction=Direction.Output),
+ doc='The output corrections workspace.')
+ self.declareProperty(name=common.PROP_CLEANUP_MODE,
+ defaultValue=common.CLEANUP_ON,
+ validator=StringListValidator([
+ common.CLEANUP_ON,
+ common.CLEANUP_OFF]),
+ direction=Direction.Input,
+ doc='What to do with intermediate workspaces.')
+ self.declareProperty(name=common.PROP_SUBALG_LOGGING,
+ defaultValue=common.SUBALG_LOGGING_OFF,
+ validator=StringListValidator([
+ common.SUBALG_LOGGING_OFF,
+ common.SUBALG_LOGGING_ON]),
+ direction=Direction.Input,
+ doc='Enable or disable subalgorithms to ' +
+ 'print in the logs.')
+ self.declareProperty(name=common.PROP_SIMULATION_INSTRUMENT,
+ defaultValue=common.SIMULATION_INSTRUMEN_SPARSE,
+ validator=StringListValidator([
+ common.SIMULATION_INSTRUMEN_SPARSE,
+ common.SIMULATION_INSTRUMENT_FULL]),
+ direction=Direction.Input,
+ doc='Select if the simulation should be performed on full or approximated instrument.')
+ self.setPropertyGroup(common.PROP_SIMULATION_INSTRUMENT, PROPGROUP_SIMULATION_INSTRUMENT)
+ self.declareProperty(name=common.PROP_SPARSE_INSTRUMENT_ROWS,
+ defaultValue=5,
+ validator=greaterThanTwoInt,
+ direction=Direction.Input,
+ doc='Number of detector rows in sparse simulation instrument.')
+ self.setPropertyGroup(common.PROP_SPARSE_INSTRUMENT_ROWS, PROPGROUP_SIMULATION_INSTRUMENT)
+ self.setPropertySettings(common.PROP_SPARSE_INSTRUMENT_ROWS, EnabledWhenProperty(common.PROP_SIMULATION_INSTRUMENT,
+ PropertyCriterion.IsEqualTo, common.SIMULATION_INSTRUMEN_SPARSE))
+ self.declareProperty(name=common.PROP_SPARSE_INSTRUMENT_COLUMNS,
+ defaultValue=20,
+ validator=greaterThanOneInt,
+ direction=Direction.Input,
+ doc='Number of detector columns in sparse simulation instrument.')
+ self.setPropertyGroup(common.PROP_SPARSE_INSTRUMENT_COLUMNS, PROPGROUP_SIMULATION_INSTRUMENT)
+ self.setPropertySettings(common.PROP_SPARSE_INSTRUMENT_COLUMNS, EnabledWhenProperty(common.PROP_SIMULATION_INSTRUMENT,
+ PropertyCriterion.IsEqualTo, common.SIMULATION_INSTRUMEN_SPARSE))
+ self.declareProperty(name=common.PROP_NUMBER_OF_SIMULATION_WAVELENGTHS,
+ defaultValue=Property.EMPTY_INT,
+ validator=greaterThanTwoInt,
+ direction=Direction.Input,
+ doc='Number of wavelength points where the simulation is performed (default: all).')
+
+ def validateInputs(self):
+ """Check for issues with user input."""
+ return dict()
+
+ def _finalize(self, outWS, wsCleanup):
+ """Do final cleanup and set the output property."""
+ self.setProperty(common.PROP_OUTPUT_WS, outWS)
+ wsCleanup.cleanup(outWS)
+ wsCleanup.finalCleanup()
+
+ def _inputWS(self, wsNames, wsCleanup, subalgLogging):
+ """Return the raw input workspace."""
+ mainWS = self.getProperty(common.PROP_INPUT_WS).value
+ wsCleanup.protect(mainWS)
+ return mainWS
+
+ def _selfShielding(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Return the self shielding corrections."""
+ wavelengthWSName = wsNames.withSuffix('input_in_wavelength')
+ wavelengthWS = ConvertUnits(InputWorkspace=mainWS,
+ OutputWorkspace=wavelengthWSName,
+ Target='Wavelength',
+ EMode='Direct',
+ EnableLogging=subalgLogging)
+ wavelengthPoints = self.getProperty(common.PROP_NUMBER_OF_SIMULATION_WAVELENGTHS).value
+ correctionWSName = wsNames.withSuffix('correction')
+ useFullInstrument = self.getProperty(common.PROP_SIMULATION_INSTRUMENT).value == common.SIMULATION_INSTRUMENT_FULL
+ if useFullInstrument:
+ correctionWS = MonteCarloAbsorption(InputWorkspace=wavelengthWS,
+ OutputWorkspace=correctionWSName,
+ SparseInstrument=False,
+ NumberOfWavelengthPoints=wavelengthPoints,
+ Interpolation='CSpline',
+ EnableLogging=subalgLogging)
+ else:
+ rows = self.getProperty(common.PROP_SPARSE_INSTRUMENT_ROWS).value
+ columns = self.getProperty(common.PROP_SPARSE_INSTRUMENT_COLUMNS).value
+ correctionWS = MonteCarloAbsorption(InputWorkspace=wavelengthWS,
+ OutputWorkspace=correctionWSName,
+ SparseInstrument=True,
+ NumberOfDetectorRows=rows,
+ NumberOfDetectorColumns=columns,
+ NumberOfWavelengthPoints=wavelengthPoints,
+ Interpolation='CSpline',
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(wavelengthWS)
+ correctionWS = ConvertUnits(InputWorkspace=correctionWS,
+ OutputWorkspace=correctionWSName,
+ Target='TOF',
+ EMode='Direct',
+ EnableLogging=subalgLogging)
+ return correctionWS
+
+
+AlgorithmFactory.subscribe(DirectILLSelfShielding)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILL_common.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILL_common.py
new file mode 100644
index 0000000000000000000000000000000000000000..899657f7afec4fa66911a67f9d684f82685fa30a
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILL_common.py
@@ -0,0 +1,258 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.api import mtd
+from mantid.simpleapi import DeleteWorkspace
+
+
+ABSOLUTE_UNITS_OFF = 'Absolute Units OFF'
+ABSOLUTE_UNITS_ON = 'Absolute Units ON'
+
+BEAM_STOP_DIAGNOSTICS_AUTO = 'Beam Stop Diagnostics AUTO'
+BEAM_STOP_DIAGNOSTICS_OFF = 'Beam Stop Diagnostics OFF'
+BEAM_STOP_DIAGNOSTICS_ON = 'Beam Stop Diagnostics ON'
+
+BKG_AUTO = 'Flat Bkg AUTO'
+BKG_OFF = 'Flat Bkg OFF'
+BKG_ON = 'Flat Bkg ON'
+
+BKG_DIAGNOSTICS_AUTO = 'Bkg Diagnostics AUTO'
+BKG_DIAGNOSTICS_OFF = 'Bkg Diagnostics OFF'
+BKG_DIAGNOSTICS_ON = 'Bkg Diagnostics ON'
+
+CLEANUP_OFF = 'Cleanup OFF'
+CLEANUP_ON = 'Cleanup ON'
+
+DEFAULT_MASK_OFF = 'Default Mask OFF'
+DEFAULT_MASK_ON = 'Default Mask ON'
+
+DWF_OFF = 'Correction OFF'
+DWF_ON = 'Correction ON'
+
+ELASTIC_CHANNEL_AUTO = 'Elastic Channel AUTO'
+ELASTIC_CHANNEL_FIT = 'Fit Elastic Channel'
+ELASTIC_CHANNEL_SAMPLE_LOG = 'Default Elastic Channel'
+
+ELASTIC_PEAK_DIAGNOSTICS_AUTO = 'Peak Diagnostics AUTO'
+ELASTIC_PEAK_DIAGNOSTICS_OFF = 'Peak Diagnostics OFF'
+ELASTIC_PEAK_DIAGNOSTICS_ON = 'Peak Diagnostics ON'
+
+EPP_METHOD_AUTO = 'EPP Method AUTO'
+EPP_METHOD_FIT = 'Fit EPP'
+EPP_METHOD_CALCULATE = 'Calculate EPP'
+
+INCIDENT_ENERGY_CALIBRATION_AUTO = 'Energy Calibration AUTO'
+INCIDENT_ENERGY_CALIBRATION_OFF = 'Energy Calibration OFF'
+INCIDENT_ENERGY_CALIBRATION_ON = 'Energy Calibration ON'
+
+INDEX_TYPE_DET_ID = 'Detector ID'
+INDEX_TYPE_WS_INDEX = 'Workspace Index'
+INDEX_TYPE_SPECTRUM_NUMBER = 'Spectrum Number'
+
+NORM_METHOD_MON = 'Normalisation Monitor'
+NORM_METHOD_OFF = 'Normalisation OFF'
+NORM_METHOD_TIME = 'Normalisation Time'
+
+PROP_ABSOLUTE_UNITS = 'AbsoluteUnitsNormalisation'
+PROP_BEAM_STOP_DIAGNOSTICS = 'BeamStopDiagnostics'
+PROP_BEAM_STOP_THRESHOLD = 'BeamStopThreshold'
+PROP_BINNING_PARAMS_Q = 'QBinningParams'
+PROP_BKG_DIAGNOSTICS = 'BkgDiagnostics'
+PROP_BKG_DIAGNOSTICS_HIGH_THRESHOLD = 'NoisyBkgHighThreshold'
+PROP_BKG_DIAGNOSTICS_LOW_THRESHOLD = 'NoisyBkgLowThreshold'
+PROP_BKG_DIAGNOSTICS_SIGNIFICANCE_TEST = 'NoisyBkgErrorThreshold'
+PROP_BKG_SIGMA_MULTIPLIER = 'NonBkgRegionInSigmas'
+PROP_CLEANUP_MODE = 'Cleanup'
+PROP_DEFAULT_MASK = 'DefaultMask'
+PROP_DIAGNOSTICS_WS = 'DiagnosticsWorkspace'
+PROP_DWF_CORRECTION = 'DebyeWallerCorrection'
+PROP_EC_SCALING = 'EmptyContainerScaling'
+PROP_EC_WS = 'EmptyContainerWorkspace'
+PROP_ELASTIC_PEAK_DIAGNOSTICS = 'ElasticPeakDiagnostics'
+PROP_ELASTIC_CHANNEL_MODE = 'ElasticChannel'
+PROP_ELASTIC_CHANNEL_WS = 'ElasticChannelWorkspace'
+PROP_ELASTIC_PEAK_SIGMA_MULTIPLIER = 'ElasticPeakWidthInSigmas'
+PROP_EPP_METHOD = 'EPPCreationMethod'
+PROP_EPP_SIGMA = 'SigmaForCalculatedEPP'
+PROP_EPP_WS = 'EPPWorkspace'
+PROP_FLAT_BKG = 'FlatBkg'
+PROP_FLAT_BKG_SCALING = 'FlatBkgScaling'
+PROP_FLAT_BKG_WINDOW = 'FlatBkgAveragingWindow'
+PROP_FLAT_BKG_WS = 'FlatBkgWorkspace'
+PROP_INCIDENT_ENERGY_CALIBRATION = 'IncidentEnergyCalibration'
+PROP_INCIDENT_ENERGY_WS = 'IncidentEnergyWorkspace'
+PROP_INPUT_FILE = 'Run'
+PROP_INPUT_WS = 'InputWorkspace'
+PROP_MON_EPP_WS = 'MonitorEPPWorkspace'
+PROP_MON_INDEX = 'Monitor'
+PROP_MON_PEAK_SIGMA_MULTIPLIER = 'MonitorPeakWidthInSigmas'
+PROP_NORMALISATION = 'Normalisation'
+PROP_NUMBER_OF_SIMULATION_WAVELENGTHS = 'NumberOfSimulatedWavelengths'
+PROP_OUTPUT_DET_EPP_WS = 'OutputEPPWorkspace'
+PROP_OUTPUT_DIAGNOSTICS_REPORT = 'OutputReport'
+PROP_OUTPUT_DIAGNOSTICS_REPORT_WS = 'OutputReportWorkspace'
+PROP_OUTPUT_ELASTIC_CHANNEL_WS = 'OutputElasticChannelWorkspace'
+PROP_OUTPUT_FLAT_BKG_WS = 'OutputFlatBkgWorkspace'
+PROP_OUTPUT_INCIDENT_ENERGY_WS = 'OutputIncidentEnergyWorkspace'
+PROP_OUTPUT_MON_EPP_WS = 'OutputMonitorEPPWorkspace'
+PROP_OUTPUT_RAW_WS = 'OutputRawWorkspace'
+PROP_OUTPUT_SELF_SHIELDING_CORRECTION_WS = 'OutputSelfShieldingCorrectionWorkspace'
+PROP_OUTPUT_THETA_W_WS = 'OutputSofThetaEnergyWorkspace'
+PROP_OUTPUT_WS = 'OutputWorkspace'
+PROP_PEAK_DIAGNOSTICS_HIGH_THRESHOLD = 'ElasticPeakHighThreshold'
+PROP_PEAK_DIAGNOSTICS_LOW_THRESHOLD = 'ElasticPeakLowThreshold'
+PROP_PEAK_DIAGNOSTICS_SIGNIFICANCE_TEST = 'ElasticPeakErrorThreshold'
+PROP_REBINNING_PARAMS_W = 'EnergyRebinningParams'
+PROP_SELF_SHIELDING_CORRECTION_WS = 'SelfShieldingCorrectionWorkspace'
+PROP_SIMULATION_INSTRUMENT = 'SimulationInstrument'
+PROP_SPARSE_INSTRUMENT_COLUMNS = 'SparseInstrumentColumns'
+PROP_SPARSE_INSTRUMENT_ROWS = 'SparseInstrumentRows'
+PROP_SUBALG_LOGGING = 'SubalgorithmLogging'
+PROP_TEMPERATURE = 'Temperature'
+PROP_TRANSPOSE_SAMPLE_OUTPUT = 'Transposing'
+PROP_USER_MASK = 'MaskedDetectors'
+PROP_USER_MASK_COMPONENTS = 'MaskedComponents'
+PROP_VANA_WS = 'IntegratedVanadiumWorkspace'
+
+PROPGROUP_OPTIONAL_OUTPUT = 'Optional Output'
+
+SIMULATION_INSTRUMENT_FULL = 'Full Instrument'
+SIMULATION_INSTRUMEN_SPARSE = 'Sparse Instrument'
+
+SUBALG_LOGGING_OFF = 'Logging OFF'
+SUBALG_LOGGING_ON = 'Logging ON'
+
+TRANSPOSING_OFF = 'Transposing OFF'
+TRANSPOSING_ON = 'Transposing ON'
+
+WS_CONTENT_DETS = 0
+WS_CONTENT_MONS = 1
+
+
+class IntermediateWSCleanup:
+ """A class to manage intermediate workspace cleanup."""
+
+ def __init__(self, cleanupMode, deleteAlgorithmLogging):
+ """Initialize an instance of the class."""
+ self._deleteAlgorithmLogging = deleteAlgorithmLogging
+ self._doDelete = cleanupMode == CLEANUP_ON
+ self._protected = set()
+ self._toBeDeleted = set()
+
+ def cleanup(self, *args):
+ """Delete the workspaces listed in *args."""
+ for ws in args:
+ self._delete(ws)
+
+ def cleanupLater(self, *args):
+ """Mark the workspaces listed in *args to be cleaned up later."""
+ for arg in args:
+ self._toBeDeleted.add(str(arg))
+
+ def finalCleanup(self):
+ """Delete all workspaces marked to be cleaned up later."""
+ for ws in self._toBeDeleted:
+ self._delete(ws)
+
+ def protect(self, *args):
+ """Mark the workspaces listed in *args to be never deleted."""
+ for arg in args:
+ self._protected.add(str(arg))
+
+ def _delete(self, ws):
+ """Delete the given workspace in ws if it is not protected, and
+ deletion is actually turned on.
+ """
+ if not self._doDelete:
+ return
+ try:
+ ws = str(ws)
+ except RuntimeError:
+ return
+ if ws not in self._protected and mtd.doesExist(ws):
+ DeleteWorkspace(Workspace=ws, EnableLogging=self._deleteAlgorithmLogging)
+
+
+class NameSource:
+ """A class to provide names for intermediate workspaces."""
+
+ def __init__(self, prefix, cleanupMode):
+ """Initialize an instance of the class."""
+ self._names = set()
+ self._prefix = prefix
+ if cleanupMode == CLEANUP_ON:
+ self._prefix = '__' + prefix
+
+ def withSuffix(self, suffix):
+ """Returns a workspace name with given suffix applied."""
+ return self._prefix + '_' + suffix + '_'
+
+
+class Report:
+ """A logger for final report generation."""
+
+ _LEVEL_NOTICE = 0
+ _LEVEL_WARNING = 1
+ _LEVEL_ERROR = 2
+
+ class _Entry:
+ """A private class for report entries."""
+
+ def __init__(self, text, loggingLevel):
+ """Initialize an entry."""
+ self._text = text
+ self._loggingLevel = loggingLevel
+
+ def contents(self):
+ """Return the contents of this entry."""
+ return self._text
+
+ def level(self):
+ """Return the logging level of this entry."""
+ return self._loggingLevel
+
+ def __init__(self):
+ """Initialize a report."""
+ self._entries = list()
+
+ def error(self, text):
+ """Add an error entry to this report."""
+ self._entries.append(Report._Entry(text, Report._LEVEL_ERROR))
+
+ def notice(self, text):
+ """Add an information entry to this report."""
+ self._entries.append(Report._Entry(text, Report._LEVEL_NOTICE))
+
+ def warning(self, text):
+ """Add a warning entry to this report."""
+ self._entries.append(Report._Entry(text, Report._LEVEL_WARNING))
+
+ def toLog(self, log):
+ """Write this report to a log."""
+ for entry in self._entries:
+ loggingLevel = entry.level()
+ if loggingLevel == Report._LEVEL_NOTICE:
+ log.notice(entry.contents())
+ elif loggingLevel == Report._LEVEL_WARNING:
+ log.warning(entry.contents())
+ elif loggingLevel == Report._LEVEL_ERROR:
+ log.error(entry.contents())
+
+
+def convertToWorkspaceIndex(i, ws, indexType=INDEX_TYPE_DET_ID):
+ """Convert given number to workspace index."""
+ if indexType == INDEX_TYPE_WS_INDEX:
+ return i
+ elif indexType == INDEX_TYPE_SPECTRUM_NUMBER:
+ return ws.getIndexFromSpectrumNumber(i)
+ else: # INDEX_TYPE_DET_ID
+ for j in range(ws.getNumberHistograms()):
+ if ws.getSpectrum(j).hasDetectorID(i):
+ return j
+ raise RuntimeError('No workspace index found for detector id {0}'.format(i))
+
+
+def convertListToWorkspaceIndices(indices, ws, indexType=INDEX_TYPE_DET_ID):
+ """Convert a list of spectrum nubmers/detector IDs to workspace indices."""
+ return [convertToWorkspaceIndex(i, ws, indexType) for i in indices]
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
index d775bcef76a39eaa6ac5bc636dcbd8f1b0d45cf6..99e0747dda996a610c3db8d7841f80bef0700118 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
@@ -8,6 +8,12 @@ set ( TEST_PY_FILES
BayesQuasiTest.py
BayesStretchTest.py
DetectorFloodWeightingTest.py
+ DirectILLApplySelfShieldingTest.py
+ DirectILLCollectDataTest.py
+ DirectILLDiagnosticsTest.py
+ DirectILLIntegrateVanadiumTest.py
+ DirectILLReductionTest.py
+ DirectILLSelfShieldingTest.py
EnergyWindowScanTest.py
FlatPlatePaalmanPingsCorrectionTest.py
IndirectAnnulusAbsorptionTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..8c029f33935473a4b2503e468bfaea58dace09c9
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py
@@ -0,0 +1,78 @@
+# -*- coding: utf-8 -*-
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.api import (mtd)
+from mantid.simpleapi import (CloneWorkspace)
+import numpy.testing
+from testhelpers import illhelpers, run_algorithm
+import unittest
+
+
+class DirectILLApplySelfShieldingTest(unittest.TestCase):
+ _BKG_LEVEL = 0.0
+ _TEST_WS_NAME = 'testWS_'
+
+ def __init__(self, methodName='runTest'):
+ unittest.TestCase.__init__(self, methodName)
+ self._testIN5WS = illhelpers.create_poor_mans_in5_workspace(self._BKG_LEVEL, illhelpers.default_test_detectors)
+
+ def tearDown(self):
+ mtd.clear()
+
+ def testEmptyContainerSubtraction(self):
+ ws = self._cloneTestWorkspace()
+ ecWSName = 'testECWS_'
+ ecWS = self._cloneTestWorkspace(ecWSName)
+ ecFactor = 0.13
+ ecWS *= ecFactor
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'EmptyContainerWorkspace': ecWSName,
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLApplySelfShielding', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), ws.getNumberHistograms())
+ ys = outWS.extractY()
+ originalYs = ws.extractY()
+ numpy.testing.assert_almost_equal(ys, (1.0 - ecFactor) *originalYs)
+
+ def testEmptyContainerSubtractionWithScaling(self):
+ ws = self._cloneTestWorkspace()
+ ecWSName = 'testECWS_'
+ ecWS = self._cloneTestWorkspace(ecWSName)
+ ecFactor = 0.13
+ ecWS *= ecFactor
+ outWSName = 'outWS'
+ ecScaling = 0.876
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'EmptyContainerWorkspace': ecWSName,
+ 'EmptyContainerScaling': ecScaling,
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLApplySelfShielding', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), ws.getNumberHistograms())
+ ys = outWS.extractY()
+ originalYs = ws.extractY()
+ numpy.testing.assert_almost_equal(ys, (1.0 - ecScaling * ecFactor) *originalYs)
+
+ def _cloneTestWorkspace(self, wsName=None):
+ if not wsName:
+ # Cannot use as default parameter as 'self' is not know in argument list.
+ wsName = self._TEST_WS_NAME
+ tempName = 'temp_testWS_'
+ mtd.addOrReplace(tempName, self._testIN5WS)
+ ws = CloneWorkspace(InputWorkspace=tempName,
+ OutputWorkspace=wsName)
+ mtd.remove(tempName)
+ return ws
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..8d9dbc66932e8b5ce918800c37cad53d185e9217
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py
@@ -0,0 +1,147 @@
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.api import mtd
+import numpy.testing
+from testhelpers import illhelpers, run_algorithm
+import unittest
+
+
+class DirectILLCollectDataTest(unittest.TestCase):
+ _BKG_LEVEL = 2.3
+ _TEST_WS_NAME = 'testWS_'
+ _TEST_WS = None
+
+ def __init__(self, methodName='runTest'):
+ unittest.TestCase.__init__(self, methodName)
+
+ def setUp(self):
+ if not DirectILLCollectDataTest._TEST_WS:
+ DirectILLCollectDataTest._TEST_WS = illhelpers.create_poor_mans_in5_workspace(self._BKG_LEVEL,
+ illhelpers.default_test_detectors)
+ mtd.addOrReplace(self._TEST_WS_NAME, DirectILLCollectDataTest._TEST_WS)
+
+ def tearDown(self):
+ mtd.clear()
+
+ def testBackgroundSubtraction(self):
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'FlatBkg': 'Flat Bkg ON',
+ 'FlatBkgScaling': 1.0,
+ 'IncidentEnergyCalibration': 'Energy Calibration OFF',
+ 'Normalisation': 'Normalisation OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLCollectData', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ inWS = mtd[self._TEST_WS_NAME]
+ self.assertEquals(outWS.getNumberHistograms(), inWS.getNumberHistograms() - 1)
+ ys = outWS.extractY()
+ originalYs = inWS.extractY()
+ numpy.testing.assert_almost_equal(ys, originalYs[1:, :] - self._BKG_LEVEL)
+
+ def testBackgroundOutput(self):
+ outWSName = 'outWS'
+ outBkgWSName = 'outBkg'
+ bkgScaling = 0.33 # Output should not be scaled, actually.
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'FlatBkg': 'Flat Bkg ON',
+ 'FlatBkgScaling': bkgScaling,
+ 'IncidentEnergyCalibration': 'Energy Calibration OFF',
+ 'Normalisation': 'Normalisation OFF',
+ 'OutputFlatBkgWorkspace': outBkgWSName,
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLCollectData', **algProperties)
+ self.assertTrue(mtd.doesExist(outBkgWSName))
+ outBkgWS = mtd[outBkgWSName]
+ numpy.testing.assert_almost_equal(outBkgWS.extractY(), self._BKG_LEVEL)
+
+ def testNormalisationToTime(self):
+ outWSName = 'outWS'
+ duration = 3612.3
+ mtd[self._TEST_WS_NAME].mutableRun().addProperty('duration', duration, True)
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'FlatBkg': 'Flat Bkg OFF',
+ 'IncidentEnergyCalibration': 'Energy Calibration OFF',
+ 'Normalisation': 'Normalisation Time',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLCollectData', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ inWS = mtd[self._TEST_WS_NAME]
+ ys = outWS.extractY()
+ originalYs = inWS.extractY()
+ numpy.testing.assert_almost_equal(ys, originalYs[1:, :] / duration)
+ es = outWS.extractE()
+ originalEs = inWS.extractE()
+ numpy.testing.assert_almost_equal(es, originalEs[1:, :] / duration)
+
+ def testRawWorkspaceOutput(self):
+ outWSName = 'outWS'
+ rawWSName = 'rawWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'OutputRawWorkspace': rawWSName,
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLCollectData', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ inWS = mtd[self._TEST_WS_NAME]
+ self.assertTrue(mtd.doesExist(rawWSName))
+ rawWS = mtd[rawWSName]
+ ys = rawWS.extractY()
+ originalYS = inWS.extractY()
+ numpy.testing.assert_almost_equal(ys, originalYS[1:, :])
+ es = rawWS.extractE()
+ originalES = inWS.extractE()
+ numpy.testing.assert_almost_equal(es, originalES[1:, :])
+ xs = rawWS.extractX()
+ outXS = outWS.extractX()
+ numpy.testing.assert_almost_equal(xs, outXS)
+ Ei = rawWS.getRun().getProperty('Ei').value
+ outEi = outWS.getRun().getProperty('Ei').value
+ self.assertEqual(Ei, outEi)
+ wavelength = outWS.getRun().getProperty('wavelength').value
+ outWavelength = outWS.getRun().getProperty('wavelength').value
+ self.assertEqual(wavelength, outWavelength)
+
+ def testSuccessWhenEverythingDisabled(self):
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'FlatBkg': 'Flat Bkg OFF',
+ 'IncidentEnergyCalibration': 'Energy Calibration OFF',
+ 'Normalisation': 'Normalisation OFF',
+ 'ElasticChannel': 'Default Elastic Channel',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLCollectData', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ inWS = mtd[self._TEST_WS_NAME]
+ self.assertEquals(outWS.getNumberHistograms(), inWS.getNumberHistograms() - 1)
+ xs = outWS.extractX()
+ originalXs = inWS.extractX()
+ numpy.testing.assert_almost_equal(xs, originalXs[1:, :])
+ ys = outWS.extractY()
+ originalYs = inWS.extractY()
+ numpy.testing.assert_almost_equal(ys, originalYs[1:, :])
+ es = outWS.extractE()
+ originalEs = inWS.extractE()
+ numpy.testing.assert_almost_equal(es, originalEs[1:, :])
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnosticsTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnosticsTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..f96d3820519481349700b23bfebfbf3133cc77ad
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnosticsTest.py
@@ -0,0 +1,225 @@
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.api import mtd
+from testhelpers import illhelpers, run_algorithm
+import unittest
+
+
+class DirectILLDiagnosticsTest(unittest.TestCase):
+ _BKG_LEVEL = 1.42
+ _EPP_WS_NAME = 'eppWS_'
+ _RAW_WS_NAME = 'rawWS_'
+ _TEST_WS = None
+ _TEST_WS_NAME = 'testWS_'
+
+ def __init__(self, methodName='runTest'):
+ unittest.TestCase.__init__(self, methodName)
+
+ def setUp(self):
+ if DirectILLDiagnosticsTest._TEST_WS is None:
+ DirectILLDiagnosticsTest._TEST_WS = illhelpers.create_poor_mans_in5_workspace(self._BKG_LEVEL,
+ illhelpers.default_test_detectors)
+ inWSName = 'inputWS'
+ mtd.addOrReplace(inWSName, DirectILLDiagnosticsTest._TEST_WS)
+ kwargs = {
+ 'InputWorkspace': DirectILLDiagnosticsTest._TEST_WS,
+ 'OutputWorkspace': self._TEST_WS_NAME,
+ 'EPPCreationMethod': 'Fit EPP',
+ 'FlatBkg': 'Flat Bkg ON',
+ 'OutputEPPWorkspace': self._EPP_WS_NAME,
+ 'OutputRawWorkspace': self._RAW_WS_NAME
+ }
+ run_algorithm('DirectILLCollectData', **kwargs)
+ mtd.remove(inWSName)
+
+ def tearDown(self):
+ mtd.clear()
+
+ def testAllDetectorsPass(self):
+ outWSName = 'diagnosticsWS'
+ kwargs = {
+ 'InputWorkspace': self._RAW_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'EPPWorkspace': self._EPP_WS_NAME,
+ 'BeamStopDiagnostics': 'Beam Stop Diagnostics OFF',
+ 'DefaultMask': 'Default Mask OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLDiagnostics', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ inWS = mtd[self._RAW_WS_NAME]
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), inWS.getNumberHistograms())
+ self.assertEquals(outWS.blocksize(), 1)
+ spectrumInfo = outWS.spectrumInfo()
+ for i in range(outWS.getNumberHistograms()):
+ self.assertEquals(outWS.readY(i)[0], 0)
+ self.assertFalse(spectrumInfo.isMasked(i))
+
+ def testBackgroundDiagnostics(self):
+ rawWS = mtd[self._RAW_WS_NAME]
+ spectraCount = rawWS.getNumberHistograms()
+ highBkgIndices = [0, int(spectraCount / 3), spectraCount - 1]
+ for i in highBkgIndices:
+ ys = rawWS.dataY(i)
+ ys += 10.0 * self._BKG_LEVEL
+ lowBkgIndices = [int(spectraCount / 4), int(2 * spectraCount / 3)]
+ for i in lowBkgIndices:
+ ys = rawWS.dataY(i)
+ ys -= self._BKG_LEVEL
+ outWSName = 'diagnosticsWS'
+ kwargs = {
+ 'InputWorkspace': self._RAW_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'ElasticPeakDiagnostics': 'Peak Diagnostics OFF',
+ 'EPPWorkspace': self._EPP_WS_NAME,
+ 'BkgDiagnostics': 'Bkg Diagnostics ON',
+ 'NoisyBkgLowThreshold': 0.01,
+ 'NoisyBkgHighThreshold': 9.99,
+ 'BeamStopDiagnostics': 'Beam Stop Diagnostics OFF',
+ 'DefaultMask': 'Default Mask OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLDiagnostics', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), spectraCount)
+ self.assertEquals(outWS.blocksize(), 1)
+ spectrumInfo = outWS.spectrumInfo()
+ for i in range(spectraCount):
+ self.assertFalse(spectrumInfo.isMasked(i))
+ ys = outWS.readY(i)
+ if i in highBkgIndices + lowBkgIndices:
+ self.assertEquals(ys[0], 1)
+ else:
+ self.assertEquals(ys[0], 0)
+
+ def testDirectBeamMasking(self):
+ beamWSName = 'beam_masking_ws'
+ kwargs = {
+ 'OutputWorkspace': beamWSName,
+ 'Function': 'One Peak',
+ 'rethrow': True
+ }
+ run_algorithm('CreateSampleWorkspace', **kwargs)
+ kwargs = {
+ 'Workspace': beamWSName,
+ 'ParameterName': 'beam_stop_diagnostics_spectra',
+ 'ParameterType': 'String',
+ 'Value': '43-57, 90-110, 145-155', # Spectrum numbers.
+ 'rethrow': True
+ }
+ run_algorithm('SetInstrumentParameter', **kwargs)
+ beamWS = mtd[beamWSName]
+ # From now on, we work on workspace indices.
+ # First range is fully covered by the beam stop.
+ for i in range(42, 57):
+ ys = beamWS.dataY(i)
+ ys *= 0.0
+ # Second range is partially covered by the beam stop.
+ # Actually, only this range will be recongnized as beam stop's shadow.
+ for i in range(92, 105):
+ ys = beamWS.dataY(i)
+ ys *= 0.0
+ # The third range is not covered by the beam stop at all.
+ outWSName = 'diagnosticsWS'
+ kwargs = {
+ 'InputWorkspace': beamWSName,
+ 'OutputWorkspace': outWSName,
+ 'ElasticPeakDiagnostics': 'Peak Diagnostics OFF',
+ 'BkgDiagnostics': 'Bkg Diagnostics OFF',
+ 'DefaultMask': 'Default Mask OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLDiagnostics', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), beamWS.getNumberHistograms())
+ self.assertEquals(outWS.blocksize(), 1)
+ for i in range(outWS.getNumberHistograms()):
+ ys = outWS.readY(i)
+ if i >= 92 and i < 105:
+ self.assertEquals(ys[0], 1)
+ else:
+ self.assertEquals(ys[0], 0)
+
+ def testElasticPeakDiagnostics(self):
+ inWS = mtd[self._RAW_WS_NAME]
+ spectraCount = inWS.getNumberHistograms()
+ highPeakIndices = [0, int(spectraCount / 3), spectraCount - 1]
+ for i in highPeakIndices:
+ ys = inWS.dataY(i)
+ ys *= 10.0
+ lowPeakIndices = [int(spectraCount / 4), int(2 * spectraCount / 3)]
+ for i in lowPeakIndices:
+ ys = inWS.dataY(i)
+ ys *= 0.1
+ outWSName = 'diagnosticsWS'
+ kwargs = {
+ 'InputWorkspace': self._RAW_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'EPPWorkspace': self._EPP_WS_NAME,
+ 'ElasticPeakDiagnostics': 'Peak Diagnostics ON',
+ 'ElasticPeakLowThreshold': 0.2,
+ 'ElasticPeakHighThreshold': 9.7,
+ 'BkgDiagnostics': 'Bkg Diagnostics OFF',
+ 'BeamStopDiagnostics': 'Beam Stop Diagnostics OFF',
+ 'DefaultMask': 'Default Mask OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLDiagnostics', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), spectraCount)
+ self.assertEquals(outWS.blocksize(), 1)
+ spectrumInfo = outWS.spectrumInfo()
+ for i in range(spectraCount):
+ self.assertFalse(spectrumInfo.isMasked(i))
+ ys = outWS.readY(i)
+ if i in highPeakIndices + lowPeakIndices:
+ self.assertEquals(ys[0], 1)
+ else:
+ self.assertEquals(ys[0], 0)
+
+ def testOutputIsUsable(self):
+ inWS = mtd[self._RAW_WS_NAME]
+ spectraCount = inWS.getNumberHistograms()
+ maskedIndices = [0, int(spectraCount / 3), spectraCount - 1]
+ for i in maskedIndices:
+ ys = inWS.dataY(i)
+ ys *= 10.0
+ outWSName = 'diagnosticsWS'
+ kwargs = {
+ 'InputWorkspace': self._RAW_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'EPPWorkspace': self._EPP_WS_NAME,
+ 'ElasticPeakDiagnostics': 'Peak Diagnostics ON',
+ 'ElasticPeakLowThreshold': 0.2,
+ 'ElasticPeakHighThreshold': 9.7,
+ 'BkgDiagnostics': 'Bkg Diagnostics OFF',
+ 'BeamStopDiagnostics': 'Beam Stop Diagnostics OFF',
+ 'DefaultMask': 'Default Mask OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLDiagnostics', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), spectraCount)
+ self.assertEquals(outWS.blocksize(), 1)
+ kwargs = {
+ 'Workspace': self._RAW_WS_NAME,
+ 'MaskedWorkspace': outWSName,
+ 'rethrow': True
+ }
+ run_algorithm('MaskDetectors', **kwargs)
+ maskedWS = mtd[self._RAW_WS_NAME]
+ spectrumInfo = maskedWS.spectrumInfo()
+ for i in range(spectraCount):
+ if i in maskedIndices:
+ self.assertTrue(spectrumInfo.isMasked(i))
+ else:
+ self.assertFalse(spectrumInfo.isMasked(i))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLIntegrateVanadiumTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLIntegrateVanadiumTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..75224719eb2dc124cdabb081289cfb8b2e81e77e
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLIntegrateVanadiumTest.py
@@ -0,0 +1,59 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import (absolute_import, division, print_function)
+
+from mantid import mtd
+from mantid.simpleapi import (CloneWorkspace, FindEPP)
+from testhelpers import illhelpers, run_algorithm
+import unittest
+
+
+class DirectILLIntegrateVanadiumTest(unittest.TestCase):
+ _BKG_LEVEL = 0.0
+ _TEST_WS_NAME = 'testWS_'
+
+ def __init__(self, methodName='runTest'):
+ unittest.TestCase.__init__(self, methodName)
+ self._testIN5WS = illhelpers.create_poor_mans_in5_workspace(self._BKG_LEVEL, illhelpers.default_test_detectors)
+
+ def tearDown(self):
+ mtd.clear()
+
+ def testIntegration(self):
+ ws = self._cloneTestWorkspace()
+ eppWSName = 'eppWS'
+ self._EPPTable(ws, eppWSName)
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'EPPWorkspace': eppWSName,
+ 'DebyeWallerCorrection': 'Correction OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLIntegrateVanadium', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), ws.getNumberHistograms())
+ self.assertEquals(outWS.blocksize(), 1)
+
+ def _cloneTestWorkspace(self, wsName=None):
+ if not wsName:
+ # Cannot use as default parameter as 'self' is not know in argument list.
+ wsName = self._TEST_WS_NAME
+ tempName = 'temp_testWS_'
+ mtd.addOrReplace(tempName, self._testIN5WS)
+ ws = CloneWorkspace(InputWorkspace=tempName,
+ OutputWorkspace=wsName)
+ mtd.remove(tempName)
+ return ws
+
+ def _EPPTable(self, ws, eppWSName):
+ eppWS = FindEPP(InputWorkspace=ws,
+ OutputWorkspace=eppWSName,
+ EnableLogging=False)
+ return eppWS
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..98aedfce8148d40eed5cab7e4a0b3f68a3f0a4ab
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
@@ -0,0 +1,128 @@
+from __future__ import (absolute_import, division, print_function)
+
+import collections
+from mantid.api import mtd
+from scipy import constants
+from testhelpers import illhelpers, run_algorithm
+import unittest
+
+
+class DirectILLReductionTest(unittest.TestCase):
+ _BKG_LEVEL = 0.0
+ _EPP_WS_NAME = 'eppWS_'
+ _TEST_WS_NAME = 'testWS_'
+ _VANADIUM_WS_NAME = 'vanadiumWS_'
+
+ def __init__(self, methodName='runTest'):
+ unittest.TestCase.__init__(self, methodName)
+ self._testIN5WS = None
+
+ def setUp(self):
+ if not self._testIN5WS:
+ self._testIN5WS = illhelpers.create_poor_mans_in5_workspace(self._BKG_LEVEL,
+ illhelpers.default_test_detectors)
+ inWSName = 'inputWS'
+ mtd.addOrReplace(inWSName, self._testIN5WS)
+ kwargs = {
+ 'InputWorkspace': self._testIN5WS,
+ 'OutputWorkspace': self._TEST_WS_NAME,
+ 'OutputEPPWorkspace': self._EPP_WS_NAME
+ }
+ run_algorithm('DirectILLCollectData', **kwargs)
+ kwargs = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': self._VANADIUM_WS_NAME,
+ 'EPPWorkspace': self._EPP_WS_NAME
+ }
+ run_algorithm('DirectILLIntegrateVanadium', **kwargs)
+ vanadiumWS = mtd[self._VANADIUM_WS_NAME]
+ for i in range(vanadiumWS.getNumberHistograms()):
+ vanadiumYs = vanadiumWS.dataY(i)
+ vanadiumYs.fill(1.0)
+ mtd.remove(inWSName)
+
+ def tearDown(self):
+ mtd.clear()
+
+ def testSuccessfulRun(self):
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'SubalgorithmLogging': 'Logging ON',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLReduction', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+
+ def testDetectorGrouping(self):
+ ws = illhelpers.create_poor_mans_in5_workspace(0.0, _groupingTestDetectors)
+ originalNDetectors = ws.getNumberHistograms()
+ detectorIds = list()
+ for i in range(originalNDetectors):
+ detectorIds.append(ws.getDetector(i).getID())
+ mtd.addOrReplace('inWS', ws)
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': ws,
+ 'OutputWorkspace': outWSName,
+ 'Cleanup': 'Cleanup OFF',
+ 'Transposing': 'Transposing OFF',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLReduction', **algProperties)
+ groupedWSName = outWSName + '_grouped_detectors_'
+ self.assertTrue(groupedWSName in mtd)
+ groupedWS = mtd[groupedWSName]
+ self.assertEqual(groupedWS.getNumberHistograms(), 1)
+ groupIds = groupedWS.getDetector(0).getDetectorIDs()
+ self.assertEqual(collections.Counter(detectorIds), collections.Counter(groupIds))
+
+ def _checkAlgorithmsInHistory(self, ws, *args):
+ """Return true if algorithm names listed in *args are found in the
+ workspace's history.
+ """
+ # This method is currently unused and kept here for nostalgic reasons.
+ # However, it might be interesting to start using it again in tests.
+ history = ws.getHistory()
+ reductionHistory = history.getAlgorithmHistory(history.size() - 1)
+ algHistories = reductionHistory.getChildHistories()
+ algNames = [alg.name() for alg in algHistories]
+ for algName in args:
+ return algName in algNames
+
+
+def _groupingTestDetectors(ws):
+ """Mask detectors for detector grouping tests."""
+ indexBegin = 63106 # Detector at L2 and at 2theta = 40.6.
+ kwargs = {
+ 'Workspace': ws,
+ 'StartWorkspaceIndex': 0,
+ 'EndWorkspaceIndex': indexBegin - 1,
+ 'child': True
+ }
+ run_algorithm('MaskDetectors', **kwargs)
+ referenceDetector = ws.getDetector(indexBegin)
+ reference2Theta = ws.detectorTwoTheta(referenceDetector)
+ mask = list()
+ for i in range(indexBegin + 1, indexBegin + 10000):
+ det = ws.getDetector(i)
+ twoTheta = ws.detectorTwoTheta(det)
+ if abs(reference2Theta - twoTheta) >= 0.01 / 180 * constants.pi:
+ mask.append(i)
+ kwargs = {
+ 'Workspace': ws,
+ 'DetectorList': mask,
+ 'child': True
+ }
+ run_algorithm('MaskDetectors', **kwargs)
+ kwargs = {
+ 'Workspace': ws,
+ 'StartWorkspaceIndex': indexBegin + 10000,
+ 'child': True
+ }
+ run_algorithm('MaskDetectors', **kwargs)
+ return ws
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..5ba4ae974eb1b7ef4cfea8b38e7f3f2e507a25c6
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py
@@ -0,0 +1,94 @@
+from __future__ import (absolute_import, division, print_function)
+
+from testhelpers import illhelpers, run_algorithm
+from mantid.api import mtd
+import numpy.testing
+import unittest
+
+
+class DirectILLSelfShieldingTest(unittest.TestCase):
+ _TEST_WS = None
+
+ def __init__(self, methodName='runTest'):
+ unittest.TestCase.__init__(self, methodName)
+ self._TEST_WS_NAME = '_testWS_'
+
+ def setUp(self):
+ if DirectILLSelfShieldingTest._TEST_WS is None:
+ bkgLevel = 0.0
+ DirectILLSelfShieldingTest._TEST_WS = illhelpers.create_poor_mans_in5_workspace(bkgLevel,
+ illhelpers.default_test_detectors)
+ tempMonitorWSName = 'monitors'
+ kwargs = {
+ 'InputWorkspace': DirectILLSelfShieldingTest._TEST_WS,
+ 'DetectorWorkspace': self._TEST_WS_NAME,
+ 'MonitorWorkspace': tempMonitorWSName
+ }
+ run_algorithm('ExtractMonitors', **kwargs)
+ kwargs = {
+ 'Workspace': tempMonitorWSName
+ }
+ run_algorithm('DeleteWorkspace', **kwargs)
+
+ def tearDown(self):
+ mtd.clear()
+
+ def testExecSparseInstrument(self):
+ self._setDefaultSample(self._TEST_WS_NAME)
+ outWSName = 'correctionWS'
+ kwargs = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'SimulationInstrument': 'Sparse Instrument',
+ 'SparseInstrumentRows': 3,
+ 'SparseInstrumentColumns': 2,
+ 'NumberOfSimulatedWavelengths': 3,
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLSelfShielding', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ inWS = mtd[self._TEST_WS_NAME]
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), inWS.getNumberHistograms())
+ xs = outWS.extractX()
+ originalXs = inWS.extractX()
+ numpy.testing.assert_almost_equal(xs, originalXs[:, :])
+
+ def testOutputHasCommonBinningWithInput(self):
+ self._setDefaultSample(self._TEST_WS_NAME)
+ outWSName = 'correctionWS'
+ kwargs = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLSelfShielding', **kwargs)
+ self.assertTrue(mtd.doesExist(outWSName))
+ inWS = mtd[self._TEST_WS_NAME]
+ outWS = mtd[outWSName]
+ self.assertEquals(outWS.getNumberHistograms(), inWS.getNumberHistograms())
+ xs = outWS.extractX()
+ originalXs = inWS.extractX()
+ numpy.testing.assert_almost_equal(xs, originalXs[:, :])
+
+ def _setDefaultSample(self, wsName):
+ geometry = {
+ 'Shape': 'Cylinder',
+ 'Height': 8.0,
+ 'Radius': 2.0,
+ 'Center': [0.0, 0.0, 0.0]
+ }
+ material = {
+ 'ChemicalFormula': 'V',
+ 'SampleNumberDensity': 0.1
+ }
+ kwargs = {
+ 'InputWorkspace': wsName,
+ 'Geometry': geometry,
+ 'Material': material
+ }
+ run_algorithm('SetSample', **kwargs)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/testhelpers/CMakeLists.txt b/Framework/PythonInterface/test/testhelpers/CMakeLists.txt
index 1f3f44d2d4b9f58caca1da014167fc61de55119c..9b4bbb3997011c639e06e7aaf600138085e15deb 100644
--- a/Framework/PythonInterface/test/testhelpers/CMakeLists.txt
+++ b/Framework/PythonInterface/test/testhelpers/CMakeLists.txt
@@ -5,6 +5,7 @@
set ( PY_FILES
__init__.py
algorithm_decorator.py
+ illhelpers.py
tempfile_wrapper.py
testrunner.py
mlzhelpers.py
diff --git a/Framework/PythonInterface/test/testhelpers/illhelpers.py b/Framework/PythonInterface/test/testhelpers/illhelpers.py
new file mode 100644
index 0000000000000000000000000000000000000000..20d86b73d3e9446c624ad1b2a10277f90a1d07de
--- /dev/null
+++ b/Framework/PythonInterface/test/testhelpers/illhelpers.py
@@ -0,0 +1,153 @@
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.kernel import DeltaEModeType, UnitConversion
+import numpy
+from testhelpers import run_algorithm
+
+
+def _gaussian(x, height, x0, sigma):
+ """Return a point in the gaussian curve."""
+ x = x - x0
+ sigma2 = 2 * sigma * sigma
+ return height * numpy.exp(- x * x / sigma2)
+
+
+def _fillTemplateWorkspace(templateWS, bkgLevel):
+ """Fill a workspace with somewhat sane data."""
+ nHistograms = templateWS.getNumberHistograms()
+ E_i = 23.0
+ nBins = 128
+ binWidth = 2.63
+ elasticIndex = int(nBins / 3)
+ monitorElasticIndex = int(nBins / 2)
+ xs = numpy.empty(nHistograms*(nBins+1))
+ ys = numpy.empty(nHistograms*nBins)
+ es = numpy.empty(nHistograms*nBins)
+ instrument = templateWS.getInstrument()
+ sample = instrument.getSample()
+ l1 = sample.getDistance(instrument.getSource())
+ l2 = float(instrument.getStringParameter('l2')[0])
+ tofElastic = UnitConversion.run('Energy', 'TOF', E_i, l1, l2, 0.0, DeltaEModeType.Direct, 0.0)
+ tofBegin = tofElastic - elasticIndex * binWidth
+ monitor = instrument.getDetector(0)
+ monitorSampleDistance = sample.getDistance(monitor)
+ tofElasticMonitor = tofBegin + monitorElasticIndex * binWidth
+ tofMonitorDetector = UnitConversion.run('Energy', 'TOF', E_i, monitorSampleDistance, l2, 0.0,
+ DeltaEModeType.Direct, 0.0)
+ elasticPeakSigma = nBins * binWidth * 0.03
+ elasticPeakHeight = 1723.0
+ bkgMonitor = 1
+
+ def fillBins(histogramIndex, elasticTOF, elasticPeakHeight, bkgLevel):
+ xIndexOffset = histogramIndex*(nBins+1)
+ yIndexOffset = histogramIndex*nBins
+ xs[xIndexOffset] = tofBegin - binWidth / 2
+ for binIndex in range(nBins):
+ x = tofBegin + binIndex * binWidth
+ xs[xIndexOffset+binIndex+1] = x + binWidth / 2
+ y = round(_gaussian(x, elasticPeakHeight, elasticTOF,
+ elasticPeakSigma)) + bkgLevel
+ ys[yIndexOffset+binIndex] = y
+ es[yIndexOffset+binIndex] = numpy.sqrt(y)
+
+ fillBins(0, tofElasticMonitor, 1623 * elasticPeakHeight, bkgMonitor)
+ for histogramIndex in range(1, nHistograms):
+ trueL2 = sample.getDistance(templateWS.getDetector(histogramIndex))
+ trueTOF = UnitConversion.run('Energy', 'TOF', E_i, l1, trueL2, 0.0, DeltaEModeType.Direct, 0.0)
+ fillBins(histogramIndex, trueTOF, elasticPeakHeight, bkgLevel)
+ kwargs = {
+ 'DataX': xs,
+ 'DataY': ys,
+ 'DataE': es,
+ 'NSpec': nHistograms,
+ 'ParentWorkspace': templateWS,
+ 'child': True
+ }
+ alg = run_algorithm('CreateWorkspace', **kwargs)
+ ws = alg.getProperty('OutputWorkspace').value
+ ws.getAxis(0).setUnit('TOF')
+ kwargs = {
+ 'Workspace': ws,
+ 'LogName': 'Ei',
+ 'LogText': str(E_i),
+ 'LogType': 'Number',
+ 'NumberType': 'Double',
+ 'child': True
+ }
+ run_algorithm('AddSampleLog', **kwargs)
+ wavelength = UnitConversion.run('Energy', 'Wavelength', E_i, l1, l2, 0.0, DeltaEModeType.Direct, 0.0)
+ kwargs = {
+ 'Workspace': ws,
+ 'LogName': 'wavelength',
+ 'LogText': str(float(wavelength)),
+ 'LogType': 'Number',
+ 'NumberType': 'Double',
+ 'child': True
+ }
+ run_algorithm('AddSampleLog', **kwargs)
+ pulseInterval = \
+ tofMonitorDetector + (monitorElasticIndex - elasticIndex) * binWidth
+ kwargs = {
+ 'Workspace': ws,
+ 'LogName': 'pulse_interval',
+ 'LogText': str(float(pulseInterval * 1e-6)),
+ 'LogType': 'Number',
+ 'NumberType': 'Double',
+ 'child': True
+ }
+ run_algorithm('AddSampleLog', **kwargs)
+ kwargs = {
+ 'Workspace': ws,
+ 'LogName': 'Detector.elasticpeak',
+ 'LogText': str(elasticIndex),
+ 'LogType': 'Number',
+ 'NumberType': 'Int',
+ 'child': True
+ }
+ run_algorithm('AddSampleLog', **kwargs)
+ kwargs = {
+ 'Workspace': ws,
+ 'ParameterName': 'default-incident-monitor-spectrum',
+ 'ParameterType': 'Number',
+ 'Value': '1',
+ 'child': True
+ }
+ run_algorithm('SetInstrumentParameter', **kwargs)
+ return ws
+
+
+def create_poor_mans_in5_workspace(bkgLevel, removeDetectors):
+ kwargs = {
+ 'InstrumentName': 'IN5',
+ 'child': True
+ }
+ alg = run_algorithm('LoadEmptyInstrument', **kwargs)
+ ws = removeDetectors(alg.getProperty('OutputWorkspace').value)
+ kwargs = {
+ 'InputWorkspace': ws,
+ 'child': True
+ }
+ alg = run_algorithm('RemoveMaskedSpectra', **kwargs)
+ ws = alg.getProperty('OutputWorkspace').value
+ ws = _fillTemplateWorkspace(ws, bkgLevel)
+ return ws
+
+
+def default_test_detectors(ws):
+ mask = list()
+ for i in range(513):
+ if i % 10 != 0:
+ mask.append(i)
+ kwargs = {
+ 'Workspace': ws,
+ 'DetectorList': mask,
+ 'child': True
+ }
+ run_algorithm('MaskDetectors', **kwargs)
+ kwargs = {
+ 'Workspace': ws,
+ 'StartWorkspaceIndex': 512,
+ 'child': True
+ }
+ run_algorithm('MaskDetectors', **kwargs)
+ return ws
diff --git a/Framework/SINQ/src/PoldiPeakSearch.cpp b/Framework/SINQ/src/PoldiPeakSearch.cpp
index f6091db34bbda36f2cffc36a54bbcce16d7fb2ca..2b502b516b603112695686036ad0ccf2fc074b6f 100644
--- a/Framework/SINQ/src/PoldiPeakSearch.cpp
+++ b/Framework/SINQ/src/PoldiPeakSearch.cpp
@@ -564,7 +564,7 @@ void PoldiPeakSearch::exec() {
Unit_sptr xUnit = correlationWorkspace->getAxis(0)->unit();
- if (xUnit->caption() == "") {
+ if (xUnit->caption().empty()) {
g_log.information()
<< " Workspace does not have unit, defaulting to MomentumTransfer.\n";
diff --git a/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h b/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h
index 6d3702ea0ad593196bff5d80d9f2bdd58ef4c7f5..9fb43aa103d15b9ac493121080938ee10445ff46 100644
--- a/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h
+++ b/Framework/TestHelpers/inc/MantidTestHelpers/WorkspaceCreationHelper.h
@@ -89,9 +89,13 @@ struct EPPTableRow {
/// Construct a row with the default values.
EPPTableRow() = default;
- /// Construct a row with errors set to zero.
+ /// Construct a row with default workspace index and errors set to zero.
EPPTableRow(const double peakCentre, const double sigma, const double height,
const FitStatus fitStatus);
+ /// Construct a row with errors set to zero.
+ EPPTableRow(const int index, const double peakCentre, const double sigma,
+ const double height, const FitStatus fitStatus);
+ int workspaceIndex = -1;
double peakCentre = 0;
double peakCentreError = 0;
double sigma = 0;
@@ -226,6 +230,20 @@ Mantid::DataObjects::Workspace2D_sptr create2DWorkspaceWithFullInstrument(
bool startYNegative = false, bool isHistogram = true,
const std::string &instrumentName = std::string("testInst"));
+/**
+ * Create a workspace as for create2DWorkspaceWithFullInstrument, but including
+ *time indexing, i.e. detector scans. Note that no positions or rotations are
+ *currently changed for the detector scan workspaces.
+ *
+ * Data filled with: Y: 2.0, E: sqrt(2.0), X: nbins of width 1 starting at 0
+ */
+Mantid::API::MatrixWorkspace_sptr
+create2DDetectorScanWorkspaceWithFullInstrument(
+ int nhist, int nbins, size_t nTimeIndexes, size_t startTime = 0,
+ size_t firstInterval = 1, bool includeMonitors = false,
+ bool startYNegative = false, bool isHistogram = true,
+ const std::string &instrumentName = std::string("testInst"));
+
/**
* Create a test workspace with a Theta numeric axis instead of a spectrum axis
* the values run from 1 to nhist
diff --git a/Framework/TestHelpers/src/FileComparisonHelper.cpp b/Framework/TestHelpers/src/FileComparisonHelper.cpp
index 5da64ccbeec582d9a8877421d18e9b54c03481c2..ccf783e80f24838877556223c3d75f81d45e8f30 100644
--- a/Framework/TestHelpers/src/FileComparisonHelper.cpp
+++ b/Framework/TestHelpers/src/FileComparisonHelper.cpp
@@ -112,7 +112,7 @@ bool areIteratorsEqual(streamCharIter refStream, streamCharIter testStream,
Mantid::Kernel::Logger g_log("FileComparisonHelper");
g_log.error("Length of both files were not identical");
areStreamsEqual = false;
- } else if (numNewLines == 0 && seenChars.size() == 0) {
+ } else if (numNewLines == 0 && seenChars.empty()) {
Mantid::Kernel::Logger g_log("FileComparisonHelper");
g_log.error("No characters checked in FileComparisonHelper");
areStreamsEqual = false;
@@ -190,7 +190,7 @@ bool isEqualToReferenceFile(const std::string &referenceFileName,
const std::string referenceFilePath =
Mantid::API::FileFinder::Instance().getFullPath(referenceFileName);
- if (referenceFilePath == "") {
+ if (referenceFilePath.empty()) {
throw std::invalid_argument("No reference file with the name: " +
referenceFileName +
" could be found by FileComparisonHelper");
diff --git a/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp b/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp
index a1fbbcfba6b236346be0cf62c310b319995d015e..a71f823efa7b946f74d5ae885e34695ada2ae87f 100644
--- a/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp
+++ b/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp
@@ -22,6 +22,7 @@
#include "MantidAPI/SpectrumInfo.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidDataObjects/PeaksWorkspace.h"
+#include "MantidDataObjects/ScanningWorkspaceBuilder.h"
#include "MantidDataObjects/WorkspaceCreation.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/Component.h"
@@ -57,8 +58,14 @@ MockAlgorithm::MockAlgorithm(size_t nSteps)
EPPTableRow::EPPTableRow(const double peakCentre_, const double sigma_,
const double height_, const FitStatus fitStatus_)
- : peakCentre(peakCentre_), peakCentreError(0), sigma(sigma_), sigmaError(0),
- height(height_), heightError(0), chiSq(0), fitStatus(fitStatus_) {}
+ : peakCentre(peakCentre_), sigma(sigma_), height(height_),
+ fitStatus(fitStatus_) {}
+
+EPPTableRow::EPPTableRow(const int index, const double peakCentre_,
+ const double sigma_, const double height_,
+ const FitStatus fitStatus_)
+ : workspaceIndex(index), peakCentre(peakCentre_), sigma(sigma_),
+ height(height_), fitStatus(fitStatus_) {}
/**
* @param name :: The name of the workspace
@@ -372,6 +379,33 @@ create2DWorkspaceWithFullInstrument(int nhist, int nbins, bool includeMonitors,
return space;
}
+//================================================================================================================
+/*
+ * startTime is in seconds
+ */
+MatrixWorkspace_sptr create2DDetectorScanWorkspaceWithFullInstrument(
+ int nhist, int nbins, size_t nTimeIndexes, size_t startTime,
+ size_t firstInterval, bool includeMonitors, bool startYNegative,
+ bool isHistogram, const std::string &instrumentName) {
+
+ auto baseWS = create2DWorkspaceWithFullInstrument(
+ nhist, nbins, includeMonitors, startYNegative, isHistogram,
+ instrumentName);
+
+ auto builder =
+ ScanningWorkspaceBuilder(baseWS->getInstrument(), nTimeIndexes, nbins);
+
+ std::vector<double> timeRanges;
+ for (size_t i = 0; i < nTimeIndexes; ++i) {
+ timeRanges.push_back(double(i + firstInterval));
+ }
+
+ builder.setTimeRanges(Mantid::Kernel::DateAndTime(int(startTime), 0),
+ timeRanges);
+
+ return builder.buildWorkspace();
+}
+
//================================================================================================================
/** Create an Workspace2D with an instrument that contains
*RectangularDetector's.
@@ -1409,7 +1443,11 @@ createEPPTableWorkspace(const std::vector<EPPTableRow> &rows) {
auto statusColumn = ws->addColumn("str", "FitStatus");
for (size_t i = 0; i != rows.size(); ++i) {
const auto &row = rows[i];
- wsIndexColumn->cell<int>(i) = static_cast<int>(i);
+ if (row.workspaceIndex < 0) {
+ wsIndexColumn->cell<int>(i) = static_cast<int>(i);
+ } else {
+ wsIndexColumn->cell<int>(i) = row.workspaceIndex;
+ }
centreColumn->cell<double>(i) = row.peakCentre;
centreErrorColumn->cell<double>(i) = row.peakCentreError;
sigmaColumn->cell<double>(i) = row.sigma;
diff --git a/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp b/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp
index c5536b678ce7ba80ca84eae5e8d21f99c5ce6294..ca1966529fef5d90e05ca6d0897d5e8365f43bbb 100644
--- a/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp
+++ b/Framework/WorkflowAlgorithms/src/EQSANSLoad.cpp
@@ -579,24 +579,44 @@ void EQSANSLoad::exec() {
throw std::runtime_error("Could not cast (interpret) the property " +
dzName + " as a time series property value.");
sfdd = dp->getStatistics().mean;
- s2d = sfdd;
// Modify SDD according to the DetectorDistance offset if given
const double sampleflange_det_offset = getProperty("DetectorOffset");
if (!isEmpty(sampleflange_det_offset))
sfdd += sampleflange_det_offset;
- // Modify S2D according to the SampleDistance offset if given
- // This assumes that a positive offset moves the sample toward the detector
- const double sampleflange_sample_offset = getProperty("SampleOffset");
- if (!isEmpty(sampleflange_sample_offset))
- s2d = s2d - sampleflange_sample_offset + sampleflange_det_offset;
-
- // Modify SDD according to SampleDetectorDistanceOffset offset if given
+ // Modify SDD according to SampleDetectorDistanceOffset offset if given.
+ // This is here for backward compatibility.
const double sample_det_offset =
getProperty("SampleDetectorDistanceOffset");
if (!isEmpty(sample_det_offset))
- s2d += sample_det_offset;
+ sfdd += sample_det_offset;
+ if (!isEmpty(sample_det_offset) && !isEmpty(sampleflange_det_offset))
+ g_log.error() << "Both DetectorOffset and SampleDetectorDistanceOffset "
+ "are set. Only one should be used.\n";
+
+ s2d = sfdd;
+ // Modify S2D according to the SampleDistance offset if given
+ // This assumes that a positive offset moves the sample toward the detector
+ const double sampleflange_sample_offset = getProperty("SampleOffset");
+ if (!isEmpty(sampleflange_sample_offset)) {
+ s2d -= sampleflange_sample_offset;
+
+ // Move the sample to its correct position
+ IAlgorithm_sptr mvAlg =
+ createChildAlgorithm("MoveInstrumentComponent", 0.2, 0.4);
+ mvAlg->setProperty<MatrixWorkspace_sptr>("Workspace", dataWS);
+ mvAlg->setProperty("ComponentName", "sample-position");
+ mvAlg->setProperty("Z", sampleflange_sample_offset / 1000.0);
+ mvAlg->setProperty("RelativePosition", false);
+ mvAlg->executeAsChildAlg();
+ g_log.information() << "Moving sample to "
+ << sampleflange_sample_offset / 1000.0 << " meters\n";
+ m_output_message += " Sample position: " +
+ Poco::NumberFormatter::format(
+ sampleflange_sample_offset / 1000.0, 3) +
+ " m\n";
+ }
}
dataWS->mutableRun().addProperty("sampleflange_detector_distance", sfdd, "mm",
true);
@@ -812,7 +832,6 @@ void EQSANSLoad::exec() {
getPropertyValue("OutputWorkspace"), true);
setProperty<MatrixWorkspace_sptr>(
"OutputWorkspace", boost::dynamic_pointer_cast<MatrixWorkspace>(dataWS));
- // m_output_message = "Loaded " + fileName + '\n' + m_output_message;
setPropertyValue("OutputMessage", m_output_message);
}
diff --git a/MantidPlot/src/ApplicationWindow.cpp b/MantidPlot/src/ApplicationWindow.cpp
index 20d5eac82f2721f6289e0839770dc286c59fa4b7..fc9010bc2a65aef1d17f09b351baf7f7b5f2719d 100644
--- a/MantidPlot/src/ApplicationWindow.cpp
+++ b/MantidPlot/src/ApplicationWindow.cpp
@@ -15064,7 +15064,7 @@ bool ApplicationWindow::runPythonScript(const QString &code, bool async,
}
bool success(false);
if (async) {
- m_iface_script->recursiveAsyncSetup();
+ const bool locked = m_iface_script->recursiveAsyncSetup();
auto job = m_iface_script->executeAsync(ScriptCode(code));
// Start a local event loop to keep processing events
// while we are running the script. Inspired by the IPython
@@ -15077,7 +15077,7 @@ bool ApplicationWindow::runPythonScript(const QString &code, bool async,
eventLoop.exec();
timer.stop();
}
- m_iface_script->recursiveAsyncTeardown();
+ m_iface_script->recursiveAsyncTeardown(locked);
success = job.result();
} else {
success = m_iface_script->execute(ScriptCode(code));
diff --git a/MantidPlot/src/PythonScript.cpp b/MantidPlot/src/PythonScript.cpp
index c0b617a2e0a032e52eca356395f62094874a7b7e..4059ba6fef91d3688c2cc8c4e84a1616b24c612a 100644
--- a/MantidPlot/src/PythonScript.cpp
+++ b/MantidPlot/src/PythonScript.cpp
@@ -457,19 +457,24 @@ void PythonScript::endStdoutRedirect() {
/**
* To be called from the main thread before an async call that is
* recursive. See ApplicationWindow::runPythonScript
+ * @return True if the lock was released by this call, false otherwise
*/
-void PythonScript::recursiveAsyncSetup() {
+bool PythonScript::recursiveAsyncSetup() {
if (gil().locked()) {
gil().release();
+ return true;
}
+ return false;
}
/**
* To be called from the main thread immediately after an async call
* that is recursive. See ApplicationWindow::runPythonScript
+ * @param relock If true then relock the GIL on this thread. This should use the
+ * value returned by recursiveAsyncSetup.
*/
-void PythonScript::recursiveAsyncTeardown() {
- if (!gil().locked()) {
+void PythonScript::recursiveAsyncTeardown(bool relock) {
+ if (relock) {
gil().acquire();
}
}
diff --git a/MantidPlot/src/PythonScript.h b/MantidPlot/src/PythonScript.h
index 33d23551d1aa22643df2ffdebce2dc25c4d03911..39ea07d97986365364521a67357c22fb852be465 100644
--- a/MantidPlot/src/PythonScript.h
+++ b/MantidPlot/src/PythonScript.h
@@ -172,8 +172,8 @@ private:
// are used for this purpose and are NOT used by the general executeAsync
// methods where the GILState API functions can cope and there is no
// recursion.
- virtual void recursiveAsyncSetup() override;
- virtual void recursiveAsyncTeardown() override;
+ virtual bool recursiveAsyncSetup() override;
+ virtual void recursiveAsyncTeardown(bool relock) override;
/// Compile the code, returning true if it was successful, false otherwise
bool compileImpl() override;
diff --git a/MantidPlot/src/PythonScripting.cpp b/MantidPlot/src/PythonScripting.cpp
index d6ea4bb74be6ccd0becf9bbc68a03bdf56f58379..e57095be4a676a3fd1638d783ea14223e6ad6390 100644
--- a/MantidPlot/src/PythonScripting.cpp
+++ b/MantidPlot/src/PythonScripting.cpp
@@ -137,9 +137,8 @@ bool PythonScripting::start() {
#else
PyImport_AppendInittab("_qti", &init_qti);
#endif
- Py_Initialize();
- // Assume this is called at startup by the the main thread so no GIL
- // required...yet
+ PythonInterpreter::initialize();
+ ScopedPythonGIL lock(gil());
// Keep a hold of the globals, math and sys dictionary objects
PyObject *mainmod = PyImport_AddModule("__main__");
@@ -189,20 +188,6 @@ bool PythonScripting::start() {
} else {
d_initialized = false;
}
- if (d_initialized) {
- // We will be using C threads created outside of the Python threading module
- // so we need the GIL. This creates and acquires the lock for this thread
- PyEval_InitThreads();
- // We immediately release the lock and threadstate so that other points in
- // the code can simply use the PyGILstate_Ensure/PyGILstate_Release()
- // mechanism (through the ScopedPythonGIL class) and they don't
- // need to worry about swapping out the threadstate before hand.
- // It would be better if the ScopedPythonGIL handled this but
- // PyEval_SaveThread() needs to be called in the thread that spawns the
- // new C thread meaning that ScopedPythonGIL could no longer
- // be used as a simple RAII class on the stack from within the new thread.
- m_mainThreadState = PyEval_SaveThread();
- }
return d_initialized;
}
@@ -210,9 +195,12 @@ bool PythonScripting::start() {
* Shutdown the interpreter
*/
void PythonScripting::shutdown() {
- PyEval_RestoreThread(m_mainThreadState);
+ // The scoped lock cannot be used here as after the
+ // finalize call no Python code can execute.
+ PythonGIL gil;
+ gil.acquire();
Py_XDECREF(m_math);
- Py_Finalize();
+ PythonInterpreter::finalize();
}
void PythonScripting::setupPythonPath() {
diff --git a/MantidPlot/src/Script.h b/MantidPlot/src/Script.h
index 0baf7eebeccc14fb6174b48cc8f7374017a1fc7d..b1f6c0aed7c6af624073585d26e6a7bd9427bcc3 100644
--- a/MantidPlot/src/Script.h
+++ b/MantidPlot/src/Script.h
@@ -91,8 +91,8 @@ public:
bool redirectStdOut() const { return m_redirectOutput; }
void redirectStdOut(bool on) { m_redirectOutput = on; }
- virtual void recursiveAsyncSetup() {}
- virtual void recursiveAsyncTeardown() {}
+ virtual bool recursiveAsyncSetup() { return false; }
+ virtual void recursiveAsyncTeardown(bool) {}
/// Create a list of keywords for the code completion API
virtual void generateAutoCompleteList() {}
diff --git a/Testing/SystemTests/tests/analysis/EnggCalibrationTest.py b/Testing/SystemTests/tests/analysis/EnggCalibrationTest.py
index 51971cb36097c9111a61cadc9a91c40848e79b0b..3adc980142a5e1b65dd653d5599f40b916ab4b57 100644
--- a/Testing/SystemTests/tests/analysis/EnggCalibrationTest.py
+++ b/Testing/SystemTests/tests/analysis/EnggCalibrationTest.py
@@ -1,6 +1,7 @@
#pylint: disable=no-init
import stresstesting
from mantid.simpleapi import *
+from six import PY2
def rel_err_less_delta(val, ref, epsilon):
@@ -234,7 +235,8 @@ class EnginXCalibrateFullThenCalibrateTest(stresstesting.MantidStressTest):
for idx in [0, 12, 516, 789, 891, 1112]:
cell_val = self.peaks_info.cell(idx,1)
self.assertTrue(isinstance(cell_val, str))
- self.assertEquals(cell_val[0:11], '{"1": {"A":')
+ if PY2: # This test depends on consistent ordering of a dict which is not guaranteed for python 3
+ self.assertEquals(cell_val[0:11], '{"1": {"A":')
self.assertEquals(cell_val[-2:], '}}')
self.assertEquals(self.difa, 0)
diff --git a/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py b/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
index e9faa5b9a02dc3d199b3c7fc5f69fd29a572301d..542abbf0f7add7821efb4f9802f403983405d37a 100644
--- a/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
+++ b/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
@@ -106,7 +106,8 @@ BANNED_FILES = ['80_tubes_Top_and_Bottom_April_2015.xml',
'TolueneLargerOrderAbins.out',
'TolueneScale.out',
'TolueneScratchAbins.out',
- 'SingleCrystalDiffuseReduction_UB.mat'
+ 'SingleCrystalDiffuseReduction_UB.mat',
+ 'Na2SiF6_DMOL3.outmol'
]
EXPECTED_EXT = '.expected'
diff --git a/buildconfig/CMake/DarwinSetup.cmake b/buildconfig/CMake/DarwinSetup.cmake
index 3599de27c11070389f5fdf40fdaf3871c018baea..33f09b2c68ee640ec3a6fbdb0b72b8dc539ac07f 100644
--- a/buildconfig/CMake/DarwinSetup.cmake
+++ b/buildconfig/CMake/DarwinSetup.cmake
@@ -51,25 +51,12 @@ else ()
set ( PY_VER 2.7 )
endif ()
-execute_process(COMMAND python${PY_VER}-config --prefix OUTPUT_VARIABLE PYTHON_PREFIX OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-if(${PYTHON_VERSION_MAJOR} GREATER 2)
- execute_process(COMMAND python${PY_VER}-config --abiflags OUTPUT_VARIABLE PY_ABI OUTPUT_STRIP_TRAILING_WHITESPACE)
-else()
- # --abiflags option not available in python 2
- set(PY_ABI "")
-endif()
-
-set( PYTHON_LIBRARY "${PYTHON_PREFIX}/lib/libpython${PY_VER}${PY_ABI}.dylib" CACHE FILEPATH "PYTHON_LIBRARY" FORCE )
-set( PYTHON_INCLUDE_DIR "${PYTHON_PREFIX}/include/python${PY_VER}${PY_ABI}" CACHE PATH "PYTHON_INCLUDE_DIR" FORCE )
-
find_package ( PythonLibs REQUIRED )
# If found, need to add debug library into libraries variable
if ( PYTHON_DEBUG_LIBRARIES )
set ( PYTHON_LIBRARIES optimized ${PYTHON_LIBRARIES} debug ${PYTHON_DEBUG_LIBRARIES} )
endif ()
-
# Generate a target to put a mantidpython wrapper in the appropriate directory
if ( NOT TARGET mantidpython )
if(MAKE_VATES)
diff --git a/docs/source/algorithms/AbsorptionCorrection-v1.rst b/docs/source/algorithms/AbsorptionCorrection-v1.rst
index 471c597be764b4007cc817d67d41e605c2371cc5..8a79dfef66b416f82e30cc1a3fd39f3b31f784fe 100644
--- a/docs/source/algorithms/AbsorptionCorrection-v1.rst
+++ b/docs/source/algorithms/AbsorptionCorrection-v1.rst
@@ -21,6 +21,9 @@ calculated for the centre-point of each element, and a numerical
integration is carried out using these path lengths over the volume
elements.
+The output workspace will contain the attenuation factors. To apply
+the correction you must divide your data set by the resulting factors.
+
Note that the duration of this algorithm is strongly dependent on the
element size chosen, and that too small an element size can cause the
algorithm to fail because of insufficient memory.
@@ -75,12 +78,12 @@ Usage
**Example: A simple spherical sample**
.. testcode:: ExSimpleSpere
-
+
#setup the sample shape
sphere = '''<sphere id="sample-sphere">
- <centre x="0" y="0" z="0"/>
- <radius val="0.1" />
- </sphere>'''
+ <centre x="0" y="0" z="0"/>
+ <radius val="0.1" />
+ </sphere>'''
ws = CreateSampleWorkspace("Histogram",NumBanks=1,BankPixelWidth=1)
ws = ConvertUnits(ws,"Wavelength")
@@ -90,14 +93,21 @@ Usage
#restrict the number of wavelength points to speed up the example
wsOut = AbsorptionCorrection(ws, NumberOfWavelengthPoints=5, ElementSize=3)
+ wsCorrected = ws / wsOut
print "The created workspace has one entry for each spectra: %i" % wsOut.getNumberHistograms()
+ print "Original y values: ", ws.readY(0)
+ print "Corrected y values: ", wsCorrected.readY(0)
Output:
.. testoutput:: ExSimpleSpere
The created workspace has one entry for each spectra: 1
+ Original y values: [ 5.68751434 5.68751434 15.68751434 5.68751434 5.68751434
+ 1.56242829]
+ Corrected y values: [ 818.30188422 2375.96165593 14211.52238463 9472.21381511
+ 15718.79220638 5747.16759791]
.. categories::
diff --git a/docs/source/algorithms/DetectorEfficiencyCorUser-v1.rst b/docs/source/algorithms/DetectorEfficiencyCorUser-v1.rst
index c28ba24ddebd75a3af6860801faff47a71ca08da..38da80b091eaa98c6adb57b803aa71b7d04edeb4 100644
--- a/docs/source/algorithms/DetectorEfficiencyCorUser-v1.rst
+++ b/docs/source/algorithms/DetectorEfficiencyCorUser-v1.rst
@@ -13,7 +13,13 @@ This algorithm will correct detector efficiency according to the ILL INX
program for time-of-flight data reduction.
A formula named "formula\_eff" must be defined in the instrument
-parameters file. The input workspace must be in DeltaE units.
+parameters file and linked to all detectors in the input workspace. Different
+components can have different formulas. The formula for each detector is
+searched recursively. Thus, there can be, for example, a global formula for the
+entire instrument and a specific formula for a bank or tube overriding the
+global one.
+
+The input workspace must be in DeltaE units.
The output data will be corrected as:
@@ -33,10 +39,9 @@ the formula used by this algorithm
is provided by instrument scientist and is adjusted for the instrument,
accounting for a number of additional instrument specific factors.
-
As example, for `TOFTOF <http://www.mlz-garching.de/toftof>`_ instrument, the energy-dependent intensity
loss factor accounts also for absorption of neutrons by the Ar gas in the flight chamber, Al windows
-of sample environment etc..
+of sample environment etc.
The formula used by DetectorEfficiencyCorUser algorithm is derived for TOFTOF in paper of
T. Unruh, 2007, doi:10.1016/j.nima.2007.07.015 and is set up in the TOFTOF instrument parameters file.
diff --git a/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst b/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2db0d942e6fbdc95d0986a0a76492c6468014536
--- /dev/null
+++ b/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst
@@ -0,0 +1,133 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm subtracts empty container data and applies self-shielding corrections to *InputWorkspace*. Both operations are optional: what is actually done depends on the input properties.
+
+This algorithm is part of :ref:`ILL's direct geometry data reduction algorithms <DirectILL>`.
+
+*SelfShieldingCorrectionWorkspace* can be obtained from the :ref:`DirectILLSelfShielding <algm-DirectILLSelfShielding>` algorithm.
+
+Usage
+-----
+
+**Example - Absorption corrections and empty container subtraction**
+
+.. testcode:: FakeIN4Example
+
+ import numpy
+ import scipy.stats
+
+ # Create a fake IN4 workspace.
+ # We need an instrument and a template first.
+ empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
+ nHist = empty_IN4.getNumberHistograms()
+ # Make TOF bin edges.
+ xs = numpy.arange(530.0, 2420.0, 4.0)
+ # Make some Gaussian spectra.
+ ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
+ # Repeat data for each histogram.
+ xs = numpy.tile(xs, nHist)
+ ys = numpy.tile(ys, nHist)
+ ws = CreateWorkspace(
+ DataX=xs,
+ DataY=ys,
+ NSpec=nHist,
+ UnitX='TOF',
+ ParentWorkspace=empty_IN4
+ )
+ # Manually correct monitor spectrum number as LoadEmptyInstrument does
+ # not know about such details.
+ SetInstrumentParameter(
+ Workspace=ws,
+ ParameterName='default-incident-monitor-spectrum',
+ ParameterType='Number',
+ Value=str(1)
+ )
+ # Add incident energy information to sample logs.
+ AddSampleLog(
+ Workspace=ws,
+ LogName='Ei',
+ LogText=str(57),
+ LogType='Number',
+ LogUnit='meV',
+ NumberType='Double'
+ )
+ # Elastic channel information is missing in the sample logs.
+ # It can be given as single valued workspace, as well.
+ elasticChannelWS = CreateSingleValuedWorkspace(107)
+
+ # Create a fake 'empty container' workspace for background subtraction.
+ ecws = Scale(
+ InputWorkspace=ws,
+ Factor=0.1
+ )
+
+ DirectILLCollectData(
+ InputWorkspace=ws,
+ OutputWorkspace='preprocessed',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
+ )
+
+ DirectILLCollectData(
+ InputWorkspace=ecws,
+ OutputWorkspace='preprocessed_ecws',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF'
+ )
+
+ sampleGeometry = {
+ 'Shape': 'Cylinder',
+ 'Height': 8.0,
+ 'Radius': 1.5,
+ 'Center': [0.0, 0.0, 0.0]
+ }
+ sampleMaterial = {
+ 'ChemicalFormula': 'V',
+ 'SampleNumberDensity': 0.05
+ }
+ SetSample(
+ InputWorkspace='preprocessed',
+ Geometry=sampleGeometry,
+ Material=sampleMaterial
+ )
+
+ DirectILLSelfShielding(
+ InputWorkspace='preprocessed',
+ OutputWorkspace='absorption_corrections',
+ SimulationInstrument='Full Instrument', # IN4 is small enough.
+ NumberOfSimulatedWavelengths=10
+ )
+
+ DirectILLApplySelfShielding(
+ InputWorkspace='preprocessed',
+ OutputWorkspace='absorptionCorrected',
+ EmptyContainerWorkspace='preprocessed_ecws',
+ SelfShieldingCorrectionWorkspace='absorption_corrections'
+ )
+
+ preprocessed = mtd['preprocessed']
+ maxY = numpy.amax(preprocessed.readY(0))
+ print('Elastic peak maximum before corrections: {:.3}'.format(maxY))
+ corrected = mtd['absorptionCorrected']
+ maxY = numpy.amax(corrected.readY(0))
+ print('After empty container subtraction and absorption corrections: {:.3}'.format(maxY))
+
+Output:
+
+.. testoutput:: FakeIN4Example
+
+ Elastic peak maximum before corrections: 26.7
+ After empty container subtraction and absorption corrections: 48.0
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/DirectILLCollectData-v1.rst b/docs/source/algorithms/DirectILLCollectData-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..34673867bd7ca7f3b4573bbc4b92afe0b2339ccf
--- /dev/null
+++ b/docs/source/algorithms/DirectILLCollectData-v1.rst
@@ -0,0 +1,164 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm preprocesses data for the other algorithms in :ref:`ILL's time-of-flight data reduction suite <DirectILL>`. Thus, it is usually the first algorithm to call in the reduction process. The algorithm (optionally) loads data from disk, performs some common basic data reduction steps to the raw data, and provides other workspaces, such as flat background information, which can be used in subsequent reduction steps. The workflow of the algorithm is shown in the diagram below:
+
+.. diagram:: DirectILLCollectData-v1_wkflw.dot
+
+Input data
+##########
+
+Either *Run* or *InputWorkspace* has to be specified. *Run* can take multiple run numbers. In this case the files will be merged using the :ref:`MergeRuns <algm-MergeRuns>` algorihtm. For example, `'/data/0100:0103,0200:0202'` would merge runs 100, 101, 102, 103, 200, 201 and 202 from directory `/data/`.
+
+Basic reduction steps
+#####################
+
+Some basic reduction steps are done to the input data.
+
+#. Separate monitor and detector spectra to different workspaces.
+#. Optionally normalise the detector specta to monitor counts or acquisition time.
+#. Subtract time-independent background from the detector spectra.
+#. Optionally find the elastic peak positions.
+#. Optionally calibrate the incident energy.
+#. Adjust the TOF axis so that the elastic time-of-flight corresponds to the L1+L2 distances.
+#. Find elastic peak positions again, if *OutputEPPWorkspace* is requested.
+
+More detailed description of some of these steps is given below.
+
+.. note::
+ The initial time-of-flight axis of ILL's spectrometers has an arbitrary starting point. Therefore, the TOF values in the intermediate workspaces do not correspond to any physical flight distances until they are corrected at step 6.
+
+Normalisation to monitor
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+If *Normalisation* is set to 'Normalisation Monitor', the monitor spectrum specified by the 'default-incident-monitor-spectrum' instrument parameter is used for normalisation. If the parameter is not present, the *Monitor* property is used. A flat background is subtracted from the spectrum (no scaling applied), and it is integrated over the range specified by *ElasticPeakWidthInSigmas*. The monitor peak is found using :ref:`FindEPP <algm-FindEPP>`. If :ref:`FindEPP <algm-FindEPP>` fails to find a peak in the monitor spectrum, the entire monitor range is integrated.
+
+Afterwards, the counts are scaled by a factor defined by the 'scaling_after_monitor_normalisation' entry in instrument parameters, if present.
+
+Flat background subtraction
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A flat time-independent background for subtraction can be given by *FlatBkgWorkspace*. If this input property is not specified, flat background will be calculated from the detector spectra by (:ref:`CalculateFlatBackground <algm-CalculateFlatBackground>`) using the 'Moving Average' mode. The *FlatBkgAveragingWindow* property is passed directly to (:ref:`CalculateFlatBackground <algm-CalculateFlatBackground>`) as *AveragingWindowWidth*.
+
+Before subtraction, the background workspace is multiplied by *FlatBkgScaling*.
+
+The background used for the subtraction can be retrieved using the *OutputFlatBkgWorkspace* property. This property holds either the same workspace as *FlatBkgWorkspace*, or a workspace created by :ref:`CalculateFlatBackground <algm-CalculateFlatBackground>`. Note that no *FlatBkgScaling* is applied to this workspace.
+
+Elastic peak positions (EPP)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Information on the elastic peaks (position, peak width) is needed for incident energy calibration, as well as for the :ref:`DirectILLDiagnostics <algm-DirectILLDiagnostics>` and :ref:`DirectILLIntegrateVanadium <algm-DirectILLIntegrateVanadium>` algorithms. This data comes in the form of a EPP workspace which is a TableWorkspace containing columns specified by the :ref:`FindEPP <algm-FindEPP>` algorithm.
+
+If no external EPP table is given by the *EPPWorkspace* property, the algorithm either fits the elastic peaks using :ref:`FindEPP <algm-FindEPP>`, or calculates their nominal positions using :ref:`CreateEPP <algm-CreateEPP>`. This behavior can be controlled by the *EPPCreationMode* property. The default ('EPP Method AUTO') is to calculate the positions for the IN5 instrument, and to fit for any other instrument.
+
+In the calculation case, a nominal peak width can be given using the *Sigma* property. The peak width is needed for some integration operations. If *Sigma* is not specified, ten times the first bin width in the workspace will be used.
+
+Incident energy calibration
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This step applies to IN4 and IN6 only. Incident energy calibration is disabled for IN5 by default.
+
+Incident energy is calibrated either by giving a new energy as a single-value workspace in *IncidentEnergyWorkspace* or calculating it from the elastic peak positions. The elastic peak position can be given by *EPPWorkspace*. If this parameter not specified, :ref:`FindEPP <algm-FindEPP>` is used.
+
+The calibrated energy can be retrieved as a single-value workspace using the *OutputIncidentEnergyWorkspace* property.
+
+TOF axis adjustment
+^^^^^^^^^^^^^^^^^^^
+
+The TOF axis is adjusted according to the elastic channel number found in the 'Detector.elasticpeak' sample log.
+
+Optional inputs and outputs
+###########################
+
+The algorithm has some optional input and output workspaces. Their purpose is to extract some common information from a single data set and use it as input for other algorithms or data sets. An example would be backgrounds extracted from a low temperature measurement which can be used when reducing data taken at higher temperatures.
+
+The optional input and output workspaces come in pairs. If the input workspace is specified, it will be used in the reduction and returned as the corresponding output workspace. If the input workspace is not specified, the needed information is calculated from the current spectra, and returned in the output workspace.
+
+* *EPPWorkspace* --- *OutputEPPWorkspace*: elastic peak position table, used for incident energy calibration, but also in :ref:`DirectILLDiagnostics <algm-DirectILLDiagnostics>` and :ref:`DirectILLIntegrateVanadium <algm-DirectILLIntegrateVanadium>`.
+* *IncidentEnergyWorkspace* --- *OutputIncidentEnergyWorkspace*: single-valued workspace containing calibrated incident energy, used for incident energy calibration.
+* *FlatBkgWorkspace* --- *OutputFlatBkgWorkspace*: a MatrixWorkspace containing the flat backgrounds. Used for flat background subtraction. Note that *FlatBkgScaling* is not applied to *OutputFlatBkgWorkspace*.
+
+Raw output workspace
+^^^^^^^^^^^^^^^^^^^^
+
+The *OutputRawWorkspace* property provides an access to a 'raw' data workspace in the sense that no normalisation or background subtraction is applied to this workspace. The raw workspace is useful as an input workspace for the :ref:`DirectILLDiagnostics <algm-DirectILLDiagnostics>` algorithm.
+
+Usage
+-----
+
+**Example - Fake IN4 workspace as input**
+
+.. testcode:: FakeIN4Example
+
+ import numpy
+ import scipy.stats
+
+ # Create a fake IN4 workspace.
+ # We need an instrument and a template first.
+ empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
+ nHist = empty_IN4.getNumberHistograms()
+ # Make TOF bin edges.
+ xs = numpy.arange(530.0, 2420.0, 4.0)
+ # Make some Gaussian spectra.
+ ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
+ # Repeat data for each histogram.
+ xs = numpy.tile(xs, nHist)
+ ys = numpy.tile(ys, nHist)
+ ws = CreateWorkspace(
+ DataX=xs,
+ DataY=ys,
+ NSpec=nHist,
+ UnitX='TOF',
+ ParentWorkspace=empty_IN4
+ )
+ # Manually correct monitor spectrum number as LoadEmptyInstrument does
+ # not know about such details.
+ SetInstrumentParameter(
+ Workspace=ws,
+ ParameterName='default-incident-monitor-spectrum',
+ ParameterType='Number',
+ Value=str(1)
+ )
+ # Add incident energy information to sample logs.
+ AddSampleLog(
+ Workspace=ws,
+ LogName='Ei',
+ LogText=str(57),
+ LogType='Number',
+ LogUnit='meV',
+ NumberType='Double'
+ )
+ # Elastic channel information is missing in the sample logs.
+ # It can be given as single valued workspace, as well.
+ elasticChannelWS = CreateSingleValuedWorkspace(107)
+
+ DirectILLCollectData(
+ InputWorkspace=ws,
+ OutputWorkspace='preprocessed',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would enable this for IN4.
+ )
+
+ # Notably, the TOF axis got adjusted in DirectILLCollectData
+ preprocessedWS = mtd['preprocessed']
+ print('TOF offset without corrections: {:.4} microseconds'.format(ws.readX(0)[0]))
+ print('Corrected TOF offset: {:.4} microseconds'.format(preprocessedWS.readX(0)[0]))
+
+Output:
+
+.. testoutput:: FakeIN4Example
+
+ TOF offset without corrections: 530.0 microseconds
+ Corrected TOF offset: 380.1 microseconds
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/DirectILLDiagnostics-v1.rst b/docs/source/algorithms/DirectILLDiagnostics-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a1c73dfcd34c5bb96a9e7a02827078fcce7898c5
--- /dev/null
+++ b/docs/source/algorithms/DirectILLDiagnostics-v1.rst
@@ -0,0 +1,170 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm performs detector diagnostics and masking. It is part of :ref:`ILL's direct geometry data reduction suite <DirectILL>`. The diagnostics are calculated using the counts from *InputWorkspace* which is preferably the raw workspace provided by the *OutputRawWorkspace* property of :ref:`DirectILLCollectData <algm-DirectILLCollectData>`. The output is a special mask workspace which can be further fed to :ref:`DirectILLReduction <algm-DirectILLReduction>` to mask the detectors diagnosed as bad. Optionally, an instrument specific default mask, a beam stop mask and/or a user specified hard mask given by *MaskedDetectors* or *MaskedComponents* can be added to the diagnostics mask.
+
+A workflow diagram for the diagnostics is shown below:
+
+.. diagram:: DirectILLDiagnostics-v1_wkflw.dot
+
+Diagnostics performed
+#####################
+
+The algorithm performs two tests for each spectrum in *InputWorkspace*: elastic peak diagnostics and flat background diagnostics. Basically both tests calculate the median of the test values over all spectra, then compare the individual values to the median. For more detailed information, see :ref:`MedianDetectorTest <algm-MedianDetectorTest>`.
+
+Elastic peak diagnostics
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The EPP table given in *EPPWorkspace* and the value of *ElasticPeakWidthInSigmas* are used to integrate the spectra around the elastic peaks, giving the elastic intensities. The intensities are further normalised by the opening solid angles of the detectors, given by :ref:`SolidAngle <algm-SolidAngle>` before the actual diagnostics.
+
+Flat background diagnostics
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Similarly to elastic peak diagnostics, *EPPWorkspace* and *NonBgkRegionInSigmas* are used to integrate the time-independent background regions of *InputWorkspace*. *NonBkgRegionInSigmas* is a factor applied to the 'Sigma' column in *EPPWorkspace* and this interval around the elastic peak positions is excluded from the integration. No opening angle corrections are applied to the background diagnostics.
+
+Beam stop
+#########
+
+The shadow cast on the detectors by a beam stop can be masked by the diagnostics, as well. This functionality is automatically enabled when 'beam_stop_diagnostics_spectra' instrument parameter is defined and can be disabled by *BeamStopDiagnostics*. The algorithm tries to mask a continuous region within the spectra listed in 'beam_stop_diagnostics_spectra'. The *BeamStopThreshold* property can be used to fine-tune the operation.
+
+The 'beam_stop_diagnostics_spectra' instrument parameter lists ranges of spectrum numbers. Each range should cover a region of a physical detector tube, part of which is behind the beam stop.
+
+The masking procedure proceeds as follows:
+
+#. Pick a range from 'beam_stop_diagnostics_spectra'.
+#. Integrate the spectra within the range.
+#. Divide the range into two halves from the middle.
+#. Pick one of the halves, take the maximum integrated value.
+#. Starting from the spectrum containing the maximum value, and stepping towards the center of the range, find the first spectrum where the integrated intensity is less than the maximum intensity multiplied by *BeamStopThreshold*. Lets call this the threshold spectrum.
+#. Mark all spectra from the middle of the range to the threshold spectrum as masked.
+#. Repeat for the other half.
+
+Defaul mask
+###########
+
+The default mask file is defined by the 'Workflow.MaskFile' instrument parameter.
+
+Diagnostics reporting
+#####################
+
+The optional *OutputReportWorkspace* property returns a table workspace summarizing the diagnostics. The table has six columns:
+
+#. 'WorkspaceIndex'
+#. 'UserMask': Holds non-zero values for spectra masked by the default mask, *MaskedDetectors* and *MaskedComponents*.
+#. 'ElasticIntensity': Holds the value of integrated elastic peaks used for the diagnostics.
+#. 'IntensityDiagnosed': Holds non-zero values for spectra diagnosed as 'bad' in elastic peak diagnostics.
+#. 'FlagBkg': Holds the value of the flat backgrounds used for the diagnostics.
+#. 'FlatBkgDiagnosed': Non-zero values in this column indicate that the spectrum did not pass the background diagnostics.
+
+The columns can be plotted to get an overview of the diagnostics.
+
+Additionally, a string listing the masked and diagnosed detectors can be accessed via the *OutputReport* property.
+
+Usage
+-----
+
+**Example - Diagnostics on fake IN4 workspace**
+
+.. testcode:: FakeIN4Example
+
+ import numpy
+ import scipy.stats
+
+ # Create a fake IN4 workspace.
+ # We need an instrument and a template first.
+ empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
+ nHist = empty_IN4.getNumberHistograms()
+ # Make TOF bin edges.
+ xs = numpy.arange(530.0, 2420.0, 4.0)
+ # Make some Gaussian spectra.
+ ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
+ # Repeat data for each histogram.
+ xs = numpy.tile(xs, nHist)
+ ys = numpy.tile(ys, nHist)
+ ws = CreateWorkspace(
+ DataX=xs,
+ DataY=ys,
+ NSpec=nHist,
+ UnitX='TOF',
+ ParentWorkspace=empty_IN4
+ )
+ # Set some histograms to zero to see if the diagnostics can catch them.
+ ys = ws.dataY(13)
+ ys *= 0.0
+ ys = ws.dataY(101)
+ ys *= 0.0
+
+ # Manually correct monitor spectrum number as LoadEmptyInstrument does
+ # not know about such details.
+ SetInstrumentParameter(
+ Workspace=ws,
+ ParameterName='default-incident-monitor-spectrum',
+ ParameterType='Number',
+ Value=str(1)
+ )
+ # Add incident energy information to sample logs.
+ AddSampleLog(
+ Workspace=ws,
+ LogName='Ei',
+ LogText=str(57),
+ LogType='Number',
+ LogUnit='meV',
+ NumberType='Double'
+ )
+ # Elastic channel information is missing in the sample logs.
+ # It can be given as single valued workspace, as well.
+ elasticChannelWS = CreateSingleValuedWorkspace(107)
+
+ DirectILLCollectData(
+ InputWorkspace=ws,
+ OutputWorkspace='preprocessed',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
+ OutputEPPWorkspace='epps' # Needed for the diagnostics.
+ )
+
+ diagnostics = DirectILLDiagnostics(
+ InputWorkspace='preprocessed',
+ OutputWorkspace='diagnosed',
+ EPPWorkspace='epps',
+ NoisyBkgLowThreshold=0.01,
+ OutputReportWorkspace='diagnostics_report'
+ )
+
+ print(diagnostics.OutputReport)
+ print('Some small-angle detectors got diagnosed as bad due to detector solid angle corrections.')
+ report = mtd['diagnostics_report']
+ I0 = report.cell('ElasticIntensity', 0)
+ I304 = report.cell('ElasticIntensity', 303)
+ print('Solid-angle corrected elastic intensity of spectrum 1: {:.8}'.format(I0))
+ print('vs. corrected intensity of spectrum 304: {:.8}'.format(I304))
+
+Output:
+
+.. testoutput:: FakeIN4Example
+
+ Spectra masked by default mask file:
+ None
+ Spectra masked by user:
+ None
+ Spectra masked by beam stop diagnostics:
+ None
+ Spectra marked as bad by elastic peak diagnostics:
+ 14, 102, 302-305, 314-317, 326-329, 338-341, 350-353, 362-365, 374-377, 386-389
+ Spectra marked as bad by flat background diagnostics:
+ 14, 102
+ Some small-angle detectors got diagnosed as bad due to detector solid angle corrections.
+ Solid-angle corrected elastic intensity of spectrum 1: 555524.7
+ vs. corrected intensity of spectrum 304: 1795774.9
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst b/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b96cba3937ddf1acc3c88ca473fd1f018d3d014a
--- /dev/null
+++ b/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst
@@ -0,0 +1,106 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm integrates the workspace given in *InputWorkspace* using the :ref:`ComputeCalibrationCoefVan <algm-ComputeCalibrationCoefVan>` algorithm. It is part of :ref:`ILL's direct geometry reduction algorithms <DirectILL>`.
+
+.. note::
+ At the moment, the integration range is fixed to :math:`\pm` 3 * FWHM (:math:`2\sqrt{2 \ln 2}`) times the 'Sigma' column in *EPPWorkspace*).
+
+Input workspaces
+################
+
+The *InputWorkspace* should be loaded using the :ref:`DirectILLCollectData <algm-DirectILLCollectData>` algorithm. It will also give the EPP workspace needed for *EPPWorkspace*.
+
+Vanadium temperature
+####################
+
+A correction for the Debye-Waller factor is applied to the integrated vanadium, as explained in the documentation of :ref:`ComputeCalibrationCoefVan <algm-ComputeCalibrationCoefVan>`. The temperature for the DWF calculation is taken from the 'Sample.temperature' sample log of the *InputWorkspace*. This value can be overriden by the *Temperature* property, if needed.
+
+Usage
+-----
+
+**Example - Integrating fake IN4 workspace**
+
+.. testcode:: FakeIN4Example
+
+ import numpy
+ import scipy.stats
+
+ # Create a fake IN4 workspace.
+ # We need an instrument and a template first.
+ empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
+ nHist = empty_IN4.getNumberHistograms()
+ # Make TOF bin edges.
+ xs = numpy.arange(530.0, 2420.0, 4.0)
+ # Make some Gaussian spectra.
+ ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
+ # Repeat data for each histogram.
+ xs = numpy.tile(xs, nHist)
+ ys = numpy.tile(ys, nHist)
+ ws = CreateWorkspace(
+ DataX=xs,
+ DataY=ys,
+ NSpec=nHist,
+ UnitX='TOF',
+ ParentWorkspace=empty_IN4
+ )
+ # Manually correct monitor spectrum number as LoadEmptyInstrument does
+ # not know about such details.
+ SetInstrumentParameter(
+ Workspace=ws,
+ ParameterName='default-incident-monitor-spectrum',
+ ParameterType='Number',
+ Value=str(1)
+ )
+ # Add incident energy information to sample logs.
+ AddSampleLog(
+ Workspace=ws,
+ LogName='Ei',
+ LogText=str(57),
+ LogType='Number',
+ LogUnit='meV',
+ NumberType='Double'
+ )
+ # Elastic channel information is missing in the sample logs.
+ # It can be given as single valued workspace, as well.
+ elasticChannelWS = CreateSingleValuedWorkspace(107)
+
+ # Prepare the workspace for integration.
+ # We also need the elastic peak position table (EPP).
+ DirectILLCollectData(
+ InputWorkspace=ws,
+ OutputWorkspace='preprocessed',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF', # Normally enabled for IN4.
+ OutputEPPWorkspace='epps'
+ )
+
+ DirectILLIntegrateVanadium(
+ InputWorkspace='preprocessed',
+ OutputWorkspace='norm-factors',
+ EPPWorkspace='epps',
+ DebyeWallerCorrection='Correction OFF',
+ Temperature=293
+ )
+
+ norms = mtd['norm-factors']
+ print('Integrated vanadium contains {} bin in each of {} histograms.'
+ .format(norms.blocksize(), norms.getNumberHistograms()))
+
+Output:
+
+.. testoutput:: FakeIN4Example
+
+ Integrated vanadium contains 1 bin in each of 396 histograms.
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/DirectILLReduction-v1.rst b/docs/source/algorithms/DirectILLReduction-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..fbb2ea4d6be244cf5b39a375d6e913a4f67ce5c8
--- /dev/null
+++ b/docs/source/algorithms/DirectILLReduction-v1.rst
@@ -0,0 +1,178 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This is the main data reduction algorithm in :ref:`ILL's time-of-flight reduction suite <DirectILL>`. It performs the last steps of the reduction workflow, namely vanadium normalisation and transformation to :math:`S(q,\omega)` space (optionally :math:`S(2\theta,\omega)`). The algorithm's workflow diagram is shown below:
+
+.. diagram:: DirectILLReduction-v1_wkflw.dot
+
+Input workspaces
+################
+
+*InputWorkspace* should contain data treated by :ref:`DirectILLCollectData <algm-DirectILLCollectData>` and, optionally, by :ref:`DirectILLApplySelfShielding <algm-DirectILLApplySelfShielding>`.
+
+The mandatory *IntegratedVanadiumWorkspace* should have gone through :ref:`DirectILLIntegrateVanadium <algm-DirectILLIntegrateVanadium>`. This workspace is used for the vanadium normalisation.
+
+*DiagnosticsWorkspace* should be a product of :ref:`DirectILLDiagnostics <algm-DirectILLDiagnostics>`. It is used to mask the spectra of *InputWorkspace*.
+
+Outputs
+#######
+
+The algorithm will transform the time-of-flight and spectrum numbers of *InputWorkspace* into :math:`S(q,\omega)` at its output. For :math:`2\theta` to :math:`q` transformation, :ref:`SofQWNormalisedPolygon <algm-SofQWNormalisedPolygon>` is used. By default, the output is transposed by :ref:`Transpose <algm-Transpose>`. This behavior can be turned off by the *Transpose* property.
+
+The optional :math:`S(2\theta,\omega)` output can be enabled by the *OutputSofThetaEnergyWorkspace*.
+
+Normalisation to absolute units
+###############################
+
+Normalisation to absolute units can be enabled by setting *AbsoluteUnitsNormalisation* to 'Absolute Units ON'. In this case the data is scaled by a factor
+
+ :math:`f = \frac{N_V \sigma_V}{N_S}`
+
+after normalisation to vanadium. In the above, :math:`N_V` stands for the vanadium number density, :math:`\sigma_V` for vanadium total scattering cross section and :math:`N_S` sample number density.
+
+The material properties should be set for *InputWorkspace* and *IntegratedVanadiumWorkspace* by :ref:`SetSample <algm-SetSample>` before running this algorithm .
+
+(Re)binning in energy and momentum transfer
+###########################################
+
+After conversion from time-of-flight to energy transfer, the binning may differ from spectrum to spectrum if the sample to detector distances are unequal. The :ref:`SofQWNormalisedPolygon <algm-SofQWNormalisedPolygon>` algorithm cannot work with such ragged workspaces and thus rebinning is necessary. The rebinning can be specified by the *EnergyRebinningParams* property. This is directly passed to :ref:`Rebin <algm-Rebin>` as the *Params* property. If *EnergyRebinningParams* is not specified, an automatic rebinning scheme is used:
+- Find the spectrum with smallest bin border. Copy binning from this spectrum for negative energy transfers.
+- For positive energy transfers, use the median bin width at zero energy transfer.
+
+*QBinningParams* are passed to :ref:`SofQWNormalisedPolygon <algm-SofQWNormalisedPolygon>` and have the same format as *EnergyRebinningParamas*. If the property is not specified, :math:`q` is binned to ten times the median :math:`2\theta` steps between the spectra.
+
+Usage
+-----
+
+**Example - Fake IN4 workspace reduction**
+
+.. testcode:: FakeIN4Example
+
+ from mantid.kernel import DeltaEModeType, UnitConversion
+ import numpy
+ import scipy.stats
+
+ # Create a fake IN4 workspace.
+ # We need an instrument and a template first.
+ empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
+ nHist = empty_IN4.getNumberHistograms()
+ # Make TOF bin edges.
+ xs = numpy.arange(530.0, 2420.0, 4.0)
+ # Make some Gaussian spectra.
+ ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
+ # Repeat data for each histogram.
+ xs = numpy.tile(xs, nHist)
+ ys = numpy.tile(ys, nHist)
+ ws = CreateWorkspace(
+ DataX=xs,
+ DataY=ys,
+ NSpec=nHist,
+ UnitX='TOF',
+ ParentWorkspace=empty_IN4
+ )
+ # Set some histograms to zero for detector diagnostics.
+ ys = ws.dataY(13)
+ ys *= 0.0
+ ys = ws.dataY(101)
+ ys *= 0.0
+
+ # Manually correct monitor spectrum number as LoadEmptyInstrument does
+ # not know about such details.
+ SetInstrumentParameter(
+ Workspace=ws,
+ ParameterName='default-incident-monitor-spectrum',
+ ParameterType='Number',
+ Value=str(1)
+ )
+ # Add incident energy information to sample logs.
+ AddSampleLog(
+ Workspace=ws,
+ LogName='Ei',
+ LogText=str(57),
+ LogType='Number',
+ LogUnit='meV',
+ NumberType='Double'
+ )
+ # Add wavelength to sample logs
+ wl = UnitConversion.run('Energy', 'Wavelength', 57.0, 0.0, 0.0, 0.0, DeltaEModeType.Direct, 0.0)
+ AddSampleLog(
+ Workspace=ws,
+ LogName='wavelength',
+ LogText=str(wl),
+ LogType='Number',
+ LogUnit='Angstrom',
+ NumberType='Double'
+ )
+ # Elastic channel information is missing in the sample logs.
+ # It can be given as single valued workspace, as well.
+ elasticChannelWS = CreateSingleValuedWorkspace(107)
+
+ # Create a fake 'vanadium' reference workspace.
+ V_ws = Scale(
+ InputWorkspace=ws,
+ Factor=1.3
+ )
+
+ # Process vanadium.
+ DirectILLCollectData(
+ InputWorkspace=V_ws,
+ OutputWorkspace='vanadium',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
+ OutputEPPWorkspace='epps' # Needed for diagnostics and integration.
+ )
+
+ DirectILLDiagnostics(
+ InputWorkspace='vanadium',
+ OutputWorkspace='diagnostics_mask',
+ EPPWorkspace='epps',
+ MaskedComponents='rosace', #Exclude small-angle detectors.
+ )
+
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium',
+ OutputWorkspace='vanadium_factors',
+ SubalgorithmLogging='Logging ON',
+ EPPWorkspace='epps',
+ Temperature=273.0
+ )
+
+ # Process sample.
+ DirectILLCollectData(
+ InputWorkspace=ws,
+ OutputWorkspace='preprocessed',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF'
+ )
+
+ # Absorption corrections and empty container subtractions could be added here.
+
+ DirectILLReduction(
+ InputWorkspace='preprocessed',
+ OutputWorkspace='SofQW',
+ IntegratedVanadiumWorkspace='vanadium_factors',
+ DiagnosticsWorkspace='diagnostics_mask'
+ )
+
+ sofqw = mtd['SofQW']
+ nHist = sofqw.getNumberHistograms()
+ nBin = sofqw.blocksize()
+ print('Size of the final S(q,w) workspace: {} histograms, {} bins'.format(nHist, nBin))
+
+Output:
+
+.. testoutput:: FakeIN4Example
+
+ Size of the final S(q,w) workspace: 177 histograms, 234 bins
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/DirectILLSelfShielding-v1.rst b/docs/source/algorithms/DirectILLSelfShielding-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6fe5566b416aa1b8434e5a72c1e2c16c1e147721
--- /dev/null
+++ b/docs/source/algorithms/DirectILLSelfShielding-v1.rst
@@ -0,0 +1,116 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm calculates self shielding correction factors for the input workspace. It is part of :ref:`ILL's direct geometry reduction suite <DirectILL>`. *InputWorkspace* should have a sample defined using :ref:`SetSample <algm-SetSample>`. Beam profile can be optionally set using :ref:`SetBeam <algm-SetBeam>`. The algorithm uses :ref:`MonteCarloAbsorption <algm-MonteCarloAbsorption>` as its backend.
+
+To speed up the simulation, the sparse instrument option of :ref:`MonteCarloAbsorption <algm-MonteCarloAbsorption>` is used by default. The number of detectors to simulate can be given by *SparseInstrumentRows* and *SparseInstrumentColumns*.
+
+By default the correction factors are calculated for each bin. By specifying *NumberOfSimulatedWavelengths*, one can restrict the number of points at which the calculation is done thus reducing the execution time. In this case CSplines are used to interpolate the correction factor over all bins.
+
+The correction factor contained within the *OutputWorkspace* can be further fed to :ref:`DirectILLApplySelfShielding <algm-DirectILLApplySelfShielding>`.
+
+Usage
+-----
+
+**Example - Absorption corrections of fake IN4 workspace**
+
+.. testcode:: FakeIN4Example
+
+ import numpy
+ import scipy.stats
+
+ # Create a fake IN4 workspace.
+ # We need an instrument and a template first.
+ empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
+ nHist = empty_IN4.getNumberHistograms()
+ # Make TOF bin edges.
+ xs = numpy.arange(530.0, 2420.0, 4.0)
+ # Make some Gaussian spectra.
+ ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
+ # Repeat data for each histogram.
+ xs = numpy.tile(xs, nHist)
+ ys = numpy.tile(ys, nHist)
+ ws = CreateWorkspace(
+ DataX=xs,
+ DataY=ys,
+ NSpec=nHist,
+ UnitX='TOF',
+ ParentWorkspace=empty_IN4
+ )
+ # Manually correct monitor spectrum number as LoadEmptyInstrument does
+ # not know about such details.
+ SetInstrumentParameter(
+ Workspace=ws,
+ ParameterName='default-incident-monitor-spectrum',
+ ParameterType='Number',
+ Value=str(1)
+ )
+ # Add incident energy information to sample logs.
+ AddSampleLog(
+ Workspace=ws,
+ LogName='Ei',
+ LogText=str(57),
+ LogType='Number',
+ LogUnit='meV',
+ NumberType='Double'
+ )
+ # Elastic channel information is missing in the sample logs.
+ # It can be given as single valued workspace, as well.
+ elasticChannelWS = CreateSingleValuedWorkspace(107)
+
+ DirectILLCollectData(
+ InputWorkspace=ws,
+ OutputWorkspace='preprocessed',
+ ElasticChannelWorkspace=elasticChannelWS,
+ IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
+ )
+
+ sampleGeometry = {
+ 'Shape': 'Cylinder',
+ 'Height': 8.0,
+ 'Radius': 1.5,
+ 'Center': [0.0, 0.0, 0.0]
+ }
+ sampleMaterial = {
+ 'ChemicalFormula': 'V',
+ 'SampleNumberDensity': 0.05
+ }
+ SetSample(
+ InputWorkspace='preprocessed',
+ Geometry=sampleGeometry,
+ Material=sampleMaterial
+ )
+
+ DirectILLSelfShielding(
+ InputWorkspace='preprocessed',
+ OutputWorkspace='absorption_corrections',
+ SimulationInstrument='Full Instrument', # IN4 is small enough.
+ NumberOfSimulatedWavelengths=10
+ )
+ # The correction factors should be applied using DirectILLApplySelfShielding.
+ corrections = mtd['absorption_corrections']
+ f_short = corrections.readY(0)[0]
+ f_long = corrections.readY(0)[-1]
+ print('Absoprtion corrections factors for detector 1')
+ print('Short final wavelengths: {:.4f}'.format(f_short))
+ print('Long final wavelengths: {:.4f}'.format(f_long))
+
+Output:
+
+.. testoutput:: FakeIN4Example
+
+ Absoprtion corrections factors for detector 1
+ Short final wavelengths: 0.4047
+ Long final wavelengths: 0.2267
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/IntegrateEPP-v1.rst b/docs/source/algorithms/IntegrateEPP-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ec821f4b43c482a0d386f6e19dc1bef21a6170c9
--- /dev/null
+++ b/docs/source/algorithms/IntegrateEPP-v1.rst
@@ -0,0 +1,47 @@
+
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm integrates a workspace around the peak positions given in an elastic peak position (EPP) table. The integration is done using the :ref:`algm-Integration` algorithm. *EPPWorkspace* should be a table workspace in the format returned by :ref:`algm-FindEPP`. The integration limits for workspace index :math:`i` in *InputWorkspace* are given by
+
+ :math:`d_i = c_i \pm w \sigma_i`,
+
+where :math:`-` is for the lower and :math:`+` for the upper limit, :math:`c_i` the value from the 'PeakCentre' column, :math:`w` the *HalfWidthInSigmas* property and :math:`\sigma_i` the value from the 'Sigma' column.
+
+If a workspace index is missing from *EPPWorkspace*, the integration limits will be set to zero.
+
+Usage
+-----
+**Example - IntegrateEPP**
+
+.. testcode:: IntegrateEPPExample
+
+ gaussian = 'name=Gaussian, PeakCentre=7000, Height=230, Sigma=680'
+ ws = CreateSampleWorkspace('Histogram', 'User Defined', gaussian)
+
+ epps = FindEPP(ws)
+
+ integrated = IntegrateEPP(ws, epps, 3)
+
+ xs = integrated.readX(0)
+ ys = integrated.readY(0)
+ print('Integral from {} to {} yields {:.5}'.format(xs[0], xs[1], ys[0]))
+
+Output:
+
+.. testoutput:: IntegrateEPPExample
+
+ Integral from 5060.0 to 9140.0 yields 1954.6
+
+.. categories::
+
+.. sourcelink::
+
diff --git a/docs/source/algorithms/LoadSESANS-v1.rst b/docs/source/algorithms/LoadSESANS-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..757143e7bd64a1f02271bb3af2b7da27c9713b5c
--- /dev/null
+++ b/docs/source/algorithms/LoadSESANS-v1.rst
@@ -0,0 +1,57 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Loads the given file in the SESANS text format. The file begins with a
+number of compulsory headers, the first of which must be
+'FileFormatVersion'. There are four compulsory data columns -
+SpinEchoLength, Depolarisation, Depolarisation_error and
+Wavelength. The output workspace has X values of SpinEchoLength and Y
+values of depolarisation.
+
+Usage
+-----
+
+**Example - Loading a file**
+
+.. testcode:: LoadSESANSRoundTrip
+
+ import os
+
+ # Create dummy workspace
+ dataX = [1,2,3,4,5]
+ dataY = [6,1,9,14]
+ dataE = [1,1,4,5]
+ out_ws = CreateWorkspace(dataX, dataY, dataE)
+ out_ws.setTitle("Dummy workspace")
+
+ file_path = os.path.join(config["defaultsave.directory"], "example.ses")
+
+ # Do a 'roundtrip' of the data
+ SaveSESANS(InputWorkspace=out_ws, Filename=file_path, ThetaZMax=1,ThetaYMax=1, EchoConstant=1, Sample="Sample")
+ LoadSESANS(Filename=file_path, OutputWorkspace="in_ws")
+
+ # Retrieve loaded workspace from ADS
+ in_ws = mtd["in_ws"]
+ print("Y values of loaded workspace = " + str(in_ws.readY(0)))
+
+.. testcleanup:: LoadSESANSRoundTrip
+
+ os.remove(file_path)
+
+Output:
+
+.. testoutput:: LoadSESANSRoundTrip
+
+ Y values of loaded workspace = [ 0.796338 0. 0.179365 0.130324]
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/MergeRuns-v1.rst b/docs/source/algorithms/MergeRuns-v1.rst
index dfc8f240bc7bcf7fb1b9f0071eb987c61d1cfd8e..0dc8a4786c767205ca91cf502d25de20c1e9cb21 100644
--- a/docs/source/algorithms/MergeRuns-v1.rst
+++ b/docs/source/algorithms/MergeRuns-v1.rst
@@ -104,6 +104,24 @@ for a given sample log.
<value val="0, 0.1, 2" />
</parameter>
+Merging Workspaces with Detector Scans
+######################################
+
+If the workspaces being merged contain detector scans then there are currently two options:
+
+1. The workspaces have identical scan intervals
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In this case the workspaces will be merged as they normally would be by MergeRuns,
+that is the counts in the two workspaces are summed. The detectors must have the same
+positions, rotations etc. for all time intervals, else the algorithm will throw.
+
+2. The workspaces have different scan intervals
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For this case the scan intervals must not overlap. The merged workspace histograms are
+appended to the end of the first workspace.
+
ChildAlgorithms used
####################
diff --git a/docs/source/algorithms/SaveSESANS-v1.rst b/docs/source/algorithms/SaveSESANS-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1d53164654ea5f9149407877b87f9f877eee6d8e
--- /dev/null
+++ b/docs/source/algorithms/SaveSESANS-v1.rst
@@ -0,0 +1,54 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Saves the given workspace to a file which will be formatted in the
+SESANS data format. A workspace with a single spectrum is expected,
+where the X values are wavelength and the Y values are polarisation
+
+Usage
+-----
+
+**Example - Loading a file**
+
+.. testcode:: LoadSESANSRoundTrip
+
+ import os
+
+ # Create dummy workspace
+ dataX = [1,2,3,4,5]
+ dataY = [6,1,9,14]
+ dataE = [1,1,4,5]
+ out_ws = CreateWorkspace(dataX, dataY, dataE)
+ out_ws.setTitle("Dummy workspace")
+
+ file_path = os.path.join(config["defaultsave.directory"], "example.ses")
+
+ # Do a 'roundtrip' of the data
+ SaveSESANS(InputWorkspace=out_ws, Filename=file_path, ThetaZMax=1,ThetaYMax=1, EchoConstant=1, Sample="Sample")
+ LoadSESANS(Filename=file_path, OutputWorkspace="in_ws")
+
+ # Retrieve loaded workspace from ADS
+ in_ws = mtd["in_ws"]
+ print("Y values of loaded workspace = " + str(in_ws.readY(0)))
+
+.. testcleanup:: LoadSESANSRoundTrip
+
+ os.remove(file_path)
+
+Output:
+
+.. testoutput:: LoadSESANSRoundTrip
+
+ Y values of loaded workspace = [ 0.796338 0. 0.179365 0.130324]
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/diagrams/DirectILLCollectData-v1_wkflw.dot b/docs/source/diagrams/DirectILLCollectData-v1_wkflw.dot
new file mode 100644
index 0000000000000000000000000000000000000000..064d008b8ae34db018b191156b1c942da9d6b4d3
--- /dev/null
+++ b/docs/source/diagrams/DirectILLCollectData-v1_wkflw.dot
@@ -0,0 +1,92 @@
+digraph DirectILLCollectData {
+ label = "DirectILLCollectData workflow diagram"
+ $global_style
+
+ subgraph params {
+ $param_style
+ bkgScaling [label="FlatBkgScaling"]
+ inputFile [label="Run"]
+ inputWS [label="InputWorkspace"]
+ inputEPP [label="EPPWorkspace"]
+ inputBkg [label="FlatBkgWorkspace"]
+ inputEi [label="IncidentEnergyWorkspace"]
+ outputBkg [label="OutputFlatBkgWorkspace"]
+ outputEi [label="OutputIncidentEnergyWorkspace"]
+ outputEPP [label="OutputEPPWorkspace"]
+ outputRaw [label="OutputRawWorkspace"]
+ outputWS [label="OutputWorkspace"]
+ }
+
+ subgraph algorithms {
+ $algorithm_style
+ CalculateFlatBackground [label="CalculateFlatBackground"]
+ CalibrateEi [label="Calibrate incident energy"]
+ CorrectTOFAxis [label="CorrectTOFAxis"]
+ CorrectTOFAxisRaw [label="CorrectTOFAxis"]
+ ExtractMonitors [label="ExtractMonitors"]
+ FindEPP [label="FindEPP \n or \n CreateEPP"]
+ FindEPPAgain [label="FindEPP \n or \n CreateEPP"]
+ IntegrateMonitor [label="Integrate monitor"]
+ LoadILLTOF [label="LoadILLTOF"]
+ MergeRuns [label="MergeRuns"]
+ Normalize [label="Normalise to monitor/time"]
+ ScaleAfterNormalization [label="Scale"]
+ ScaleBkg [label="Scale"]
+ SubtractBkgDetector [label="Subtract flat background"]
+ SubtractBkgMonitor [label="Subtract flat background"]
+ }
+
+ subgraph values {
+ $value_style
+ detectors [label="Detector workspace"]
+ monitors [label="Monitor workspace"]
+ }
+
+ subgraph decisions {
+ $decision_style
+ inputBkgGiven [label="FlatBkgWorkspace given?"]
+ inputEiGiven [label="IncidentEnergyWorkspace given?"]
+ inputEPPGiven [label="EPPWorkspace given?"]
+ inputFileGiven [label="Run given?"]
+ }
+
+ inputFileGiven -> inputFile [label="yes"]
+ inputFile -> LoadILLTOF
+ LoadILLTOF -> MergeRuns
+ MergeRuns -> ExtractMonitors
+ inputFileGiven -> inputWS [label="no"]
+ inputWS -> ExtractMonitors
+ ExtractMonitors -> monitors
+ monitors -> SubtractBkgMonitor
+ SubtractBkgMonitor -> IntegrateMonitor
+ IntegrateMonitor -> Normalize
+ ExtractMonitors -> detectors
+ detectors -> Normalize
+ detectors -> CorrectTOFAxisRaw
+ Normalize -> ScaleAfterNormalization
+ ScaleAfterNormalization -> inputBkgGiven
+ inputBkgGiven -> CalculateFlatBackground [label="no"]
+ CalculateFlatBackground -> outputBkg
+ CalculateFlatBackground -> ScaleBkg
+ inputBkgGiven -> inputBkg [label="yes"]
+ inputBkg -> ScaleBkg
+ bkgScaling -> ScaleBkg
+ ScaleBkg -> SubtractBkgDetector
+ ScaleAfterNormalization -> SubtractBkgDetector
+ inputEPPGiven -> FindEPP [label="no"]
+ SubtractBkgDetector -> FindEPP
+ FindEPP -> CalibrateEi
+ inputEPPGiven -> inputEPP [label="yes"]
+ inputEPP -> CalibrateEi
+ SubtractBkgDetector -> CalibrateEi
+ inputEiGiven -> inputEPPGiven [label="no"]
+ CalibrateEi -> outputEi
+ inputEiGiven -> inputEi [label="yes"]
+ inputEi -> CalibrateEi
+ CalibrateEi -> CorrectTOFAxis
+ CalibrateEi -> CorrectTOFAxisRaw [label="as reference workspace"]
+ CorrectTOFAxisRaw -> outputRaw
+ CorrectTOFAxis -> FindEPPAgain
+ CorrectTOFAxis ->outputWS
+ FindEPPAgain -> outputEPP
+}
diff --git a/docs/source/diagrams/DirectILLDiagnostics-v1_wkflw.dot b/docs/source/diagrams/DirectILLDiagnostics-v1_wkflw.dot
new file mode 100644
index 0000000000000000000000000000000000000000..c3198993cf1a1d4cc4e4d74067ef5098c35f73a4
--- /dev/null
+++ b/docs/source/diagrams/DirectILLDiagnostics-v1_wkflw.dot
@@ -0,0 +1,67 @@
+digraph DirectILLDiagnostics {
+ label = "DirectILLDiagnostics workflow diagram"
+ $global_style
+
+ subgraph params {
+ $param_style
+ beamStopThreshold [label="BeamStopThreshold"]
+ bkgExcludeWidth [label="NonBkgRegionInSigmas"]
+ bkgThresholds [label="Bkg thresholds"]
+ elasticPeakWidth [label="ElasticPeakWidthInSigmas"]
+ inputEPP [label="EPPWorkspace"]
+ inputWS [label="InputWorkspace"]
+ maskIndices [label="MaskedDetectors"]
+ maskComponents [label="MaskedComponents"]
+ outputDiagnostics [label="OutputWorkspace"]
+ peakThresholds [label="Peak thresholds"]
+ }
+
+ subgraph algorithms {
+ $algorithm_style
+ DiagnoseBkg [label="Diagnose flat backgrounds"]
+ DiagnosePeaks [label="Diagnose elastic peaks"]
+ DefineBeamStop [label="Define beam\nstop shadow"]
+ IntegrateBkg [label="Integrate\nbackgrounds"]
+ IntegrateIntensities [label="Integrate"]
+ IntegratePeaks [label="Integrate\nelastic peak"]
+ Plus [label="Plus"]
+ }
+
+ subgraph values {
+ $value_style
+ beamStopMask [label="Beam stop\nmask"]
+ beamStopSpectra [label="Beam stop spectra"]
+ bkgDiagnostics [label="Background diagnostics\nworkspace"]
+ defaultMask [label="Default mask\nfrom file"]
+ peakDiagnostics [label="Peak diagnostics\nworkspace"]
+ }
+
+ subgraph decisions {
+ $decision_style
+ }
+
+ inputWS -> IntegratePeaks
+ inputEPP -> IntegratePeaks
+ elasticPeakWidth -> IntegratePeaks
+ inputWS -> IntegrateBkg
+ inputEPP -> IntegrateBkg
+ bkgExcludeWidth -> IntegrateBkg
+ IntegratePeaks -> DiagnosePeaks
+ peakThresholds -> DiagnosePeaks
+ DiagnosePeaks -> peakDiagnostics
+ IntegrateBkg -> DiagnoseBkg
+ bkgThresholds -> DiagnoseBkg
+ DiagnoseBkg -> bkgDiagnostics
+ peakDiagnostics -> Plus
+ bkgDiagnostics -> Plus
+ beamStopSpectra -> IntegrateIntensities
+ inputWS -> IntegrateIntensities
+ IntegrateIntensities -> DefineBeamStop
+ beamStopThreshold -> DefineBeamStop
+ DefineBeamStop -> beamStopMask
+ beamStopMask -> Plus
+ maskIndices -> Plus
+ maskComponents -> Plus
+ defaultMask -> Plus
+ Plus -> outputDiagnostics
+}
diff --git a/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot b/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot
new file mode 100644
index 0000000000000000000000000000000000000000..6a91ffb61d548a16f3c732297b58f17718a10d7e
--- /dev/null
+++ b/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot
@@ -0,0 +1,58 @@
+digraph DirectILLReduction {
+ label = "DirectILLReduction workflow diagram"
+ $global_style
+
+ subgraph params {
+ $param_style
+ inputDiagnostics [label="DiagnosticsWorkspace"]
+ inputVana [label="IntegratedVanadiumWorkspace"]
+ inputWS [label="InputWorkspace"]
+ outputWS [label="OutputWorkspace"]
+ outputOptionalWS [label="OutputSofThetaEnergyWorkspace"]
+ qBinParams [label="q rebinning settings"]
+ wRebinParams [label="Energy rebinning settings"]
+ }
+
+ subgraph decisions {
+ $decision_style
+ absoluteUnitsEnabled [label="Normalise to absolute units?"]
+ inputDiagnosticsGiven [label="DiagnosticsWorkspace given?"]
+ }
+
+ subgraph algorithms {
+ $algorithm_style
+ AbsoluteUnits [label="Scale to absolute units"]
+ ApplyDiagnostics [label="Mask spectra"]
+ ConvertToEnergy [label="Convert TOF to energy transfer"]
+ CorrectKiKf [label="CorrectKiKf"]
+ DetectorEfficiency [label="DetectorEfficiencyCorUser"]
+ GroupDetectors [label="GroupDetectors"]
+ Normalize [label="Divide"]
+ Rebin [label="Rebin in energy"]
+ SofQW [label="SofQWNormalisedPolygon"]
+ }
+
+ subgraph values {
+ $value_style
+ }
+
+ inputWS -> inputDiagnosticsGiven
+ inputDiagnosticsGiven -> Normalize [label="no"]
+ inputDiagnosticsGiven -> ApplyDiagnostics [label="yes"]
+ inputDiagnostics -> ApplyDiagnostics
+ ApplyDiagnostics -> Normalize
+ inputVana -> Normalize
+ Normalize -> absoluteUnitsEnabled
+ absoluteUnitsEnabled -> ConvertToEnergy [label="no"]
+ absoluteUnitsEnabled -> AbsoluteUnits [label="yes"]
+ AbsoluteUnits -> ConvertToEnergy
+ ConvertToEnergy -> CorrectKiKf
+ CorrectKiKf -> Rebin
+ wRebinParams -> Rebin
+ Rebin -> DetectorEfficiency
+ DetectorEfficiency -> GroupDetectors
+ GroupDetectors -> outputOptionalWS
+ GroupDetectors -> SofQW
+ qBinParams -> SofQW
+ SofQW -> outputWS
+}
diff --git a/docs/source/release/v3.11.0/diffraction.rst b/docs/source/release/v3.11.0/diffraction.rst
index 3bd30339ef17998c433e9410ed1cb45a874d428f..88951c92c9d55378872e66dc3591b6cc701da4b1 100644
--- a/docs/source/release/v3.11.0/diffraction.rst
+++ b/docs/source/release/v3.11.0/diffraction.rst
@@ -22,9 +22,9 @@ Powder Diffraction
- :ref:`LoadILLDiffraction <algm-LoadILLDiffraction>` now supports loading D2B data with detector scans. The D2B IDF has been updated, as previously it contained some errors in the positions of the tubes and size of the pixels.
- :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder>` now correctly supports overloading the grouping file in the presence of a masking workspace.
- :ref:`PDCalibration <algm-PDCalibration>` has changed how it calculates constants from peak positions to use a simplex optimization rather than Gauss-Markov method.
+- :ref:`ResampleX <algm-ResampleX>` has a bug fix in how it automatically determines the data range for a workspace with multiple spectra.
- The powder diffraction GUI has had numerous bugfixes and now has an option to override the detector grouping.
-
Single Crystal Diffraction
--------------------------
diff --git a/docs/source/release/v3.11.0/direct_inelastic.rst b/docs/source/release/v3.11.0/direct_inelastic.rst
index 280318585a6f3e8e6c87fa81e3bef50d876fb08d..ab2bcc4e611edd3ec0abcac2e8762c66e42b9a69 100644
--- a/docs/source/release/v3.11.0/direct_inelastic.rst
+++ b/docs/source/release/v3.11.0/direct_inelastic.rst
@@ -5,6 +5,15 @@ Direct Inelastic Changes
.. contents:: Table of Contents
:local:
+New features
+------------
+
+Algorithms
+##########
+
+- Data reduction workflow algorithms for ILL's TOF spectrometers IN4, IN5 and IN6 have been added to Mantid. A guide to the six new algorithms is provided :ref:`here <DirectILL>`.
+- :ref:`algm-DetectorEfficiencyCorUser` now accepts component-specific efficiency correction formulas.
+
`Full list of changes on GitHub <http://github.com/mantidproject/mantid/pulls?q=is%3Apr+milestone%3A%22Release+3.11%22+is%3Amerged+label%3A%22Component%3A+Direct+Inelastic%22>`_
Algorithms
diff --git a/docs/source/release/v3.11.0/framework.rst b/docs/source/release/v3.11.0/framework.rst
index 41a8ebd545b2cbf46b786c21ef8458e5b289f01e..b7ccaa7ce66ea33e3106c85fc0827d188607da41 100644
--- a/docs/source/release/v3.11.0/framework.rst
+++ b/docs/source/release/v3.11.0/framework.rst
@@ -23,7 +23,8 @@ New
- :ref:`ConjoinXRuns <algm-ConjoinXRuns>` performs concatenation of the workspaces into a single one by handling the sample logs merging as in :ref:`MergeRuns <algm-MergeRuns>`.
- :ref:`LoadSESANS <algm-LoadSESANS>` Loading SESANS data to a MatrixWorkspace is now supported.
- :ref:`SaveSESANS <algm-SaveSESANS>` Saving a workspace using the SESANS format is now supported.
-- :ref:`PaddingAndApodization <algm-PaddingAndApodization-v1>` a new algorithm for padding data and adding an apodization function.
+- :ref:`PaddingAndApodization <algm-PaddingAndApodization-v1>` a new algorithm for padding data and adding an apodization function.
+- :ref:`algm-IntegrateEPP` integrates a workspace around the elastic peak positions given in an EPP table.
Improved
@@ -44,6 +45,7 @@ Improved
- :ref:`algm-MonteCarloAbsorption` now supports approximating the input instrument with a sparse grid of detectors enabling quick simulation of huge pixel arrays. Also, the NumberOfWavelengthPoints input property is now validated more rigorously.
- :ref:`SaveGSS <algm-SaveGSS-v1>` now supports saving in the legacy GSAS ALT format. This is useful for older tools however the default format FXYE should be used whenever possible.
- :ref:`SaveMDWorkspaceToVTK <algm-SaveMDWorkspaceToVTK-v1>` and :ref:`LoadVTK <algm-LoadVTK-v1>` algorithms are now accessible from python.
+- :ref:`MergeRuns <algm-MergeRuns-v1>` will now merge workspaces with detector scans.
- :ref:`SetUncertainties <algm-SetUncertainties-v1>` now provides a "custom" mode, which lets the user specify both an arbitrary error value whose occurences are to be replaced in the input workspace, as well as the value to replace it with.
- :ref:`SimpleShapeMonteCarloAbsorption <algm-SimpleShapeMonteCarloAbsorption>` has been added to simplify sample environment inputs for MonteCarloAbsorption
- :ref:`SumSpectra <algm-SumSpectra-v1>`: Fixed a bug where a wrong fallback value would be used in case of invalid values being set for min/max worspace index, and improved input validation for those properties.
diff --git a/docs/source/release/v3.11.0/reflectometry.rst b/docs/source/release/v3.11.0/reflectometry.rst
index 709724662d82a02a4c0ec5b541ecb9df2a852a49..57ba862cb5cf3cdd8e5653f7a02701f249274a0d 100644
--- a/docs/source/release/v3.11.0/reflectometry.rst
+++ b/docs/source/release/v3.11.0/reflectometry.rst
@@ -11,6 +11,7 @@ Algorithms
- The following bugs have been fixed in the summation in Q functionality in :ref:`algm-ReflectometryReductionOne`:
- the incorrect angle was being used in the final conversion to Q in the divergent beam case
- the input was being cropped, causing loss of counts
+ - summation in Q was giving incorrect results for a point detector
- A new property, ``Diagnostics``, has been added to :ref:`algm-ReflectometryReductionOne` to allow the output of additional interim workspaces for debug purposes.
Reflectometry Reduction Interface
diff --git a/docs/source/release/v3.11.0/sans.rst b/docs/source/release/v3.11.0/sans.rst
index cdcd6e4947a919860b66b08a427bca65a05aaafd..8b75217d5b181bbfae9442a2004f7e52485d5a15 100644
--- a/docs/source/release/v3.11.0/sans.rst
+++ b/docs/source/release/v3.11.0/sans.rst
@@ -16,6 +16,9 @@ Bug Fixes
- Displaying the masked workspace in the mask tab now makes sure that the masks are displayed in a grey color.
-|
+EQSANS
+------
+
+- Following hardware changes in the instrument, sample and detector offsets were added as parameters of the reduction.
`Full list of changes on github <http://github.com/mantidproject/mantid/pulls?q=is%3Apr+milestone%3A%22Release+3.11%22+is%3Amerged+label%3A%22Component%3A+SANS%22>`__
diff --git a/docs/source/techniques/DirectILL.rst b/docs/source/techniques/DirectILL.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e518fbde52abc29f5f344501714749de94ed8b4b
--- /dev/null
+++ b/docs/source/techniques/DirectILL.rst
@@ -0,0 +1,700 @@
+.. _DirectILL:
+
+====================================================
+Data reduction for ILL's direct geometry instruments
+====================================================
+
+.. contents:: Table of contents
+ :local:
+
+There are six workflow algorithms supporting data reduction at ILL's time-of-flight instruments. These algorithms are:
+
+:ref:`algm-DirectILLCollectData`
+ Loads data from disk and applies some simple reduction steps. The starting point of all reductions, as most of the other DirectILL algorithms expect their input data to originate from here.
+
+:ref:`algm-DirectILLReduction`
+ Does the actual reduction and produces the final :math:`S(q,\omega)`.
+
+:ref:`algm-DirectILLIntegrateVanadium`
+ Integrates a calibration workspace.
+
+:ref:`algm-DirectILLDiagnostics`
+ Provides a masking workspace to remove detectors (faulty or otherwise) from the reduction.
+
+:ref:`algm-DirectILLSelfShielding`
+ Calculates absorption corrections for usage with :ref:`algm-DirectILLApplySelfShielding`.
+
+:ref:`algm-DirectILLApplySelfShielding`
+ Applies absorption corrections and subtracts an empty container measurement.
+
+The algorithms can be used as flexible building blocks in Python scripts. Not all of them need to be necessarily used in a reduction: the simplest script could call :ref:`algm-DirectILLCollectData` and :ref:`algm-DirectILLReduction` only.
+
+Together with the other algorithms and services provided by the Mantid framework, the reduction algorithms can handle a great number of reduction scenarios. If this proves insufficient, however, the algorithms can be accessed using Python. Before making modifications it is recommended to copy the source files and rename the algorithms as not to break the original behavior.
+
+This document tries to give an overview on how the algorithms work together via Python examples. Please refer to the algorithm documentation for details of each individual algorithm.
+
+Reduction basics
+================
+
+A very basic reduction would include a vanadium reference and a sample and follow the steps:
+
+#. Load vanadium data.
+
+#. Integrate vanadium.
+
+#. Run diagnostics.
+
+ * Generally, this step should not be skipped even if no actual diagnostics were performed, as :ref:`algm-DirectILLDiagnostics` may create a default mask for the instrument. This is the case of IN5, for example, where the pixels at the detector tube ends are masked.
+
+#. Load sample data.
+
+#. Reduce the data applying vanadium calibration coefficients and diagnostics mask.
+
+These steps would translate to something like the following simple Python script:
+
+.. code-block:: python
+
+ # Add a temporary data search directory.
+ mantid.config.appendDataSearchDir('/data/')
+
+ # Vanadium
+ DirectILLCollectData(
+ Run='0100:0109',
+ OutputWorkspace='vanadium',
+ OutputEPPWorkspace='vanadium-epps', # Elastic peak positions.
+ OutputRawWorkspace='vanadium-raw' # 'Raw' data for diagnostics.
+ )
+
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium',
+ OutputWorkspace='integrated',
+ EPPWorkspace='vanadium-epps'
+ )
+
+ DirectILLDiagnostics(
+ InputWorkspace='vanadium-raw',
+ OutputWorkspace='diagnostics',
+ EPPWorkspace='vanadium-epps',
+ RawWorkspace='vanadium-raw'
+ )
+
+ # Sample
+ DirectILLCollectData(
+ Run='0201, 0205, 0209-0210',
+ OutputWorkspace='sample'
+ )
+
+ DirectILLReduction(
+ InputWorkspace='sample',
+ OutputWorkspace='SofQW',
+ IntegratedVanadiumWorkspace='integrated'
+ DiagnosticsWorkspace='diagnostics'
+ )
+
+Connecting inputs and outputs
+=============================
+
+Every ``DirectILL`` algorithm has an *OutputWorkspace* property which provides the main output workspace. Additionally, the algorithms may provide optional output workspaces to be used with other algorithms or for reporting/debugging purposes. The linking of outputs to inputs is an important feature of the ``DirectILL`` algorithms and allows for great flexibility in the reduction. An example of the usage of these optional output workspaces is the *OutputEPPWorkspace* which in the vanadium case above is needed in the integration and diagnostics steps:
+
+.. code-block:: python
+
+ ...
+ # Vanadium
+ DirectILLCollectData(
+ ...
+ OutputEPPWorkspace='vanadium-epps' # This workspace...
+ )
+ DirectILLIntegrateVanadium(
+ ...
+ EPPWorkspace='vanadium-epps' # ...is needed here...
+ )
+ DirectILLDiagnostics(
+ ...
+ EPPWorkspace='vanadium-epps' # ...and here.
+ )
+ ...
+
+As shown above, these optional outputs are sometimes named similarly the corresponding inputs giving a hint were they are supposed to be used.
+
+Self-shielding corrections
+==========================
+
+A more complete reduction example would include corrections for self-shielding:
+
+#. Load vanadium data.
+
+#. Integrate vanadium.
+
+#. Run diagnostics.
+
+#. Load sample data.
+
+#. Calculate absorption corrections for the sample.
+
+ * This may be a time consuming step. Fortunately, the resulting correction factors can be reused as many times as needed.
+
+ * Sample and beam parameters can be set using :ref:`algm-SetSample` and :ref:`algm-SetBeam`.
+
+#. Apply the corrections.
+
+#. Reduce the data applying vanadium calibration coefficients and diagnostics mask.
+
+The above workflow would translate to this kind of Python script:
+
+.. code-block:: python
+
+ # Add a temporary data search directory.
+ mantid.config.appendDataSearchDir('/data/')
+
+ # Vanadium
+ DirectILLCollectData(
+ Run='0100:0109',
+ OutputWorkspace='vanadium',
+ OutputEPPWorkspace='vanadium-epps', # Elastic peak positions.
+ OutputRawWorkspace='vanadium-raw' # 'Raw' data for diagnostics.
+ )
+
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium',
+ OutputWorkspace='integrated',
+ EPPWorkspace='vanadium-epps'
+ )
+
+ DirectILLDiagnostics(
+ InputWorkspace='vanadium-raw',
+ OutputWorkspace='diagnostics',
+ EPPWorkspace='vanadium-epps',
+ RawWorkspace='vanadium-raw'
+ )
+
+ # Sample
+ DirectILLCollectData(
+ Run='0201, 0205, 0209-0210',
+ OutputWorkspace='sample',
+ )
+
+ geometry = {
+ 'Shape': 'FlatPlate',
+ 'Width': 4.0,
+ 'Height': 5.0,
+ 'Thick': 0.1,
+ 'Center': [0.0, 0.0, 0.0],
+ 'Angle': 45.0
+ }
+ material = {
+ 'ChemicalFormula': 'Ni Cr Fe',
+ 'SampleNumberDensity': 0.09
+ }
+ SetSample(
+ InputWorkspace='sample',
+ Geometry=geometry,
+ Material=material
+ )
+ DirectILLSelfShielding(
+ InputWorkspace='sample',
+ OutputWorkspace='corrections'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='sample',
+ OutputWorkspace='sample-corrected',
+ SelfShieldingCorrectionWorkspace='corrections',
+ )
+
+ DirectILLReduction(
+ InputWorkspace='sample-corrected',
+ OutputWorkspace='SofQW',
+ IntegratedVanadiumWorkspace='integrated'
+ DiagnosticsWorkspace='diagnostics'
+ )
+
+Workspace compatibility
+=======================
+
+Mantid can be picky with binning when doing arithmetics between workspaces. This is an issue for the time-of-flight instruments at ILL as the time axis needs to be corrected to correspond to a physical flight distance. Even thought data is recorded with the same nominal wavelength, the actual value written in the NeXus files may differ between runs. Incident energy calibration further complicates matters. As the correction to the time-of-flight axis depends on the wavelength, two datasets loaded into Mantid with :ref:`algm-DirectILLCollectData` may have slightly different time-of-flight axis. This prevents arithmetics between the workspaces. The situation is most often encountered between sample and the corresponding empty container.
+
+To alleviate the situation, the output workspaces of :ref:`algm-DirectILLCollectData` can be forced to use the same wavelength. The following Python script shows how to propagate the calibrated incident energy from the first loaded workspace into the rest:
+
+.. code-block:: python
+
+ DirectILLCollectData(
+ Run='0100:0109',
+ OutputWorkspace='sample1',
+ OutputIncidentEnergyWorkspace='Ei' # Get a common incident energy.
+ )
+
+ # Empty container.
+ DirectILLCollectData(
+ Run='0201:0205',
+ OutputWorkspace='container',
+ IncidentEnergyWorkspace='Ei' # Empty container should have same TOF binning.
+ )
+
+ # More samples with same nominal wavelength and container as 'sample1'.
+ runs = ['0110:0119,', '0253:0260']
+ index = 1
+ for run in runs:
+ DirectILLCollectData(
+ Run=run,
+ OutputWorkspace='sample{}'.format(index),
+ IncidentEnergyWorkspace='Ei'
+ )
+ index += 1
+
+ # The empty container is now compatible with all the samples.
+
+Container background subtraction
+================================
+
+The container background subtraction is done perhaps a bit counterintuitively in :ref:`algm-DirectILLApplySelfShielding`. At the moment the self-shielding corrections and the empty container data do not have much to do with each other but this may change in the future if the so called Paalman-Pings corrections are used.
+
+With empty container data, the steps to reduce the experimental data might look like this:
+
+#. Load vanadium data.
+
+#. Integrate vanadium.
+
+#. Run diagnostics.
+
+#. Load sample data.
+
+#. Load container data.
+
+ * Propagate the incident energy from the sample, see `Workspace compatibility`_.
+
+#. Calculate and apply absorption corrections for the container.
+
+#. Calculate the absorption corrections for the sample.
+
+#. Apply the absoprtion corrections and subtract the container.
+
+#. Reduce the data applying vanadium calibration coefficients and diagnostics mask.
+
+A corresponding Python script follows.
+
+.. code-block:: python
+
+ mantid.config.appendDataSearchDir('/data/')
+
+ # Vanadium
+ DirectILLCollectData(
+ Run='0100:0109',
+ OutputWorkspace='vanadium',
+ OutputEPPWorkspace='vanadium-epps',
+ OutputRawWorkspace='vanadium-raw'
+ )
+
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium',
+ OutputWorkspace='integrated',
+ EPPWorkspace='vanadium-epps'
+ )
+
+ DirectILLDiagnostics(
+ InputWorkspace='vanadium-raw',
+ OutputWorkspace='diagnostics',
+ EPPWorkspace='vanadium-epps',
+ RawWorkspace='vanadium-raw'
+ )
+
+ # Sample
+ DirectILLCollectData(
+ Run='0201, 0205, 0209-0210',
+ OutputWorkspace='sample',
+ OutputIncidentEnergyWorkspace='Ei'
+ )
+
+ # Container
+ DirectILLCollectData(
+ Run='0333:0335',
+ OutputWorkspace='container',
+ IncidentEnergyWorkspace='Ei'
+ )
+
+ # Container self-shielding.
+ # Geometry XML allows for very complex geometries.
+ containerShape = """
+ <hollow-cylinder id="inner-ring">
+ <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <inner-radius val="0.017" />
+ <outer-radius val="0.018" />
+ <height val="0.08" />
+ </hollow-cylinder>
+ <hollow-cylinder id="outer-ring">
+ <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <inner-radius val="0.02" />
+ <outer-radius val="0.021" />
+ <height val="0.08" />
+ </hollow-cylinder>
+ <algebra val="inner-ring : outer-ring" />
+ """
+ geometry = {
+ 'Shape': 'CSG',
+ 'Value': containerShape
+ }
+ material = {
+ 'ChemicalFormula': 'Al',
+ 'SampleNumberDensity': 0.09
+ }
+ SetSample(
+ InputWorkspace='container',
+ Geometry=geometry,
+ Material=material
+ )
+ DirectILLSelfShielding(
+ InputWorkspace='container',
+ OutputWorkspace='container-corrections'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='container',
+ OutputWorkspace='container-corrected',
+ SelfShieldingCorrectionWorkspace='container-corrections',
+ )
+
+ # Sample self-shielding and container subtraction.
+ geometry = {
+ 'Shape': 'HollowCylinder',
+ 'Height': 8.0,
+ 'InnerRadius': 1.8,
+ 'OuterRadium': 2.0,
+ 'Center': [0.0, 0.0, 0.0]
+ }
+ material = {
+ 'ChemicalFormula': 'C2 O D6',
+ 'SampleNumberDensity': 0.1
+ }
+ SetSample('sample', geometry, material)
+ DirectILLSelfShielding(
+ InputWorkspace='sample',
+ OutputWorkspace='sample-corrections'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='sample',
+ OutputWorkspace='sample-corrected',
+ SelfShieldingCorrectionWorkspace='sample-corrections',
+ EmptyContainerWorkspace='container-corrected'
+ )
+
+ DirectILLReduction(
+ InputWorkspace='sample-corrected',
+ OutputWorkspace='SofQW',
+ IntegratedVanadiumWorkspace='integrated'
+ DiagnosticsWorkspace='diagnostics'
+ )
+
+Interpolation of container data to different temperatures
+---------------------------------------------------------
+
+Sometimes the empty container is not measured at all the experiment's temperature points. One can use Mantid's workspace arithmetics to perform simple linear interpolation in temperature:
+
+.. code-block:: python
+
+ # Container measurement temperatures.
+ T0 = 3.0
+ T1 = 250.0
+ DT = T1 - T0
+ # Target sample temperature.
+ Ts = 190.0
+ # Linear interpolation.
+ container_190 = (T1 - Ts) / DT * mtd['container_3'] + (Ts - T0) / DT * mtd['container_250']
+
+ DirectILLApplySelfShielding(
+ InputWorkspace='sample',
+ EmptyContainerWorkspace=container_190
+ )
+
+As usual, care should be taken when extrapolating the container data outside the measured range.
+
+Finding out what went wrong
+===========================
+
+The reduction algorithms do not produce much output to Mantid logs by default. Also, none of the intermediate workspaces generated during the run of the ``DirectILL`` algorithms will show up in the analysis data service. Both behaviors can be controlled by the *SubalgorithmLogging* and *Cleanup* properties. Enabling *SubalgorithmLogging* will log all messages from child algorithms to Mantid's logs. Disabling *Cleanup* will unhide the intermediate workspaces created during the algorithm run and disable their deletion.
+
+Note, that disabling *Cleanup* might produce a large number of workspaces and cause the computer to run out of memory.
+
+Instrument specific defaults and recommendations
+================================================
+
+Elastic peak positions
+----------------------
+
+The intensities of individual pixels on IN5 are very low. This makes the fitting procedure employed by :ref:`algm-FindEPP` to work unreliably or fail altogether. Because of this, :ref:`algm-DirectILLCollectData` will use :ref:`algm-CreateEPP` instead by default for IN5. :ref:`algm-CreateEPP` produces an artificial EPP workspace based on the instrument geometry. This should be accurate enough for vanadium integration and diagnostics.
+
+Diagnostics
+-----------
+
+The elastic peak diagnostics might be usable to mask the beam stop of IN5. The background diagnostics, on the other hand, are turned off by default as it makes no sense to mask individual pixels based on them.
+
+Memory management
+-----------------
+
+When working on memory constrained systems, it is recommended to manually delete the workspaces which are not needed anymore in the reduction script. The :ref:`algm-SaveNexus` can be used to save the data to disk.
+
+Full example
+============
+
+Lets put it all together into a complex Python script. The script below reduces the following dataset:
+
+* Vanadium reference.
+
+* An empty vanadium container.
+
+ * Same shape as the sample container.
+ * Complex shape: has to be given as XML.
+
+* Sample measured at wavelength 1 at 50, 100 and 150K.
+
+ * Share time-independent backgrounds from the measurement at 50K.
+
+* Empty container measured at wavelength 1 at 50 and 150K.
+
+ * Need to interpolate to 150K.
+
+* Sample measured at wavelength 2 at 50, 100 and 150K.
+
+ * Share time-independent backgrounds from the measurement at 50K.
+
+* Empty container measured at wavelength 2.
+
+
+
+.. code-block:: python
+
+ mantid.config.appendDataSearchDir('/data/')
+
+ # Gather dataset information.
+ containerRuns = '96,97'
+ vanadiumRuns = '100-103'
+ # Samples at 50K, 100K and 150K.
+ # Wavelength 1
+ containerRuns1 = {
+ 50: '131-137',
+ 150: '138-143'
+ }
+ runs1 = {
+ 50: '105, 107-110',
+ 100: '112-117',
+ 150: '119-123, 125'
+ }
+ # Wavelength 2
+ containerRun2 = '166-170'
+ runs2 = {
+ 50: '146, 148, 150',
+ 100: '151-156',
+ 150: '160-165'
+ }
+
+ # Vanadium & vanadium container.
+
+ DirectILLCollectData(
+ Run=vanadiumRuns,
+ OutputWorkspace='vanadium',
+ OutputEPPWorkspace='vanadium-epp',
+ OutputRawWorkspace='vanadium-raw',
+ OutputIncidentEnergyWorkspace='vanadium-Ei' # Use for container
+ )
+
+ DirectILLCollectData(
+ Run=containerRuns,
+ OutputWorkspace='vanadium-container',
+ IncidentEnergyWorkspace='vanadium-Ei'
+ )
+
+ containerShape = """
+ <hollow-cylinder id="inner-ring">
+ <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <inner-radius val="0.017" />
+ <outer-radius val="0.018" />
+ <height val="0.08" />
+ </hollow-cylinder>
+ <hollow-cylinder id="outer-ring">
+ <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <inner-radius val="0.02" />
+ <outer-radius val="0.021" />
+ <height val="0.08" />
+ </hollow-cylinder>
+ <algebra val="inner-ring : outer-ring" />
+ """
+ containerGeometry = {
+ 'CSG': containerShape
+ }
+ containerMaterial = {
+ 'ChemicalFormula': 'Al',
+ 'SampleNumberDensity': 0.1
+ }
+ SetSample('vanadium-container', containerGeometry, containerMaterial)
+ DirectILLSelfShielding(
+ InputWorkspace='vanadium-container',
+ OutputWorkspace='vanadium-container-self-shielding'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='vanadium-container',
+ OutputWorkspace='vanadium-container-corrected'
+ SelfShieldingCorrectionWorkspace='vanadium-container-self-shielding'
+ )
+
+ sampleGeometry = {
+ 'Shape': 'HollowCylinder',
+ 'Height': 8.0,
+ 'InnerRadius': 1.8,
+ 'OuterRadium': 2.0,
+ 'Center': [0.0, 0.0, 0.0]
+ }
+ vanadiumMaterial = {
+ 'ChemicalFormula': 'V',
+ 'SampleNumberDensity': 0.15
+ }
+ SetSample('vanadium', sampleGeometry, vanadiumMaterial)
+ DirectILLSelfShielding(
+ InputWorkspace='vanadium',
+ OutputWorkspace='vanadium-self-shielding'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='vanadium',
+ OutputWorkspace='vanadium-corrected',
+ SelfShieldingCorrectionWorkspace='vanadium-self-shielding',
+ EmptyContainerWorkspace='vanadium-container-corrected'
+ )
+
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium-corrected',
+ OutputWorkspace='vanadium-calibration',
+ EPPWorkspace='vanadium-epp'
+ )
+
+ diagnosticsResult = DirectILLDiagnoseDetectors(
+ InputWorkspace='vanadium-raw',
+ OutputWorkspace='mask',
+ EPPWorkspace='vanadium-epp',
+ OutputReportWorkspace='diagnostics-report'
+ )
+
+ # Sample and container at wavelength 1.
+
+ DirectILLCollectData(
+ Run=runs1[50],
+ OutputWorkspace='run1-50K',
+ OutputIncidentEnergyWorkspace='Ei1',
+ OutputFlatBkgWorkspace='bkg1-50K'
+ )
+
+ DirectILLCollectData(
+ Run=containerRuns1[50],
+ OutputWorkspace='container1-50K',
+ IncidentEnergyWorkspace='Ei1'
+ )
+
+ SetSample('container1-50K', containerGeometry, containerMaterial)
+ DirectILLSelfShielding(
+ InputWorkspace='container1-50K',
+ OutputWorkspace='container1-self-shielding'
+ )
+
+ DirectILLCollectData(
+ Run=containerRuns1[150],
+ OutputWorkspace='container1-150K',
+ IncidentEnergyWorkspace='Ei1'
+ )
+
+ interpolated = 0.5 * (mtd['container1-50K'] + mtd['container1-150K'])
+ RenameWorkspace(interpolated, 'container1-100K')
+
+ for T in [50, 100, 150]:
+ DirectILLApplySelfShielding(
+ InputWorkspace='container1-{}K'.format(T),
+ OutputWorkspace='container1-{}K-corrected'.format(T),
+ SelfShieldingCorrectionWorkspace='container1-self-shielding'
+ )
+
+ sampleMaterial = {
+ 'ChemicalFormula': 'Fe 2 O 3',
+ 'SampleNumberDensity': 0.23
+ }
+ SetSample('run1-50K', sampleGeometry, sampleMaterial)
+ DirectILLSelfShielding(
+ InputWorkspace='run1-50K',
+ OutputWorkspace='run1-self-shielding',
+ )
+
+ for T in runs1:
+ if T != 50:
+ # 50K data has been loaded already.
+ DirectILLCollectData(
+ Run=runs1[T],
+ OutputWorkspace='run1-{}K'.format(T),
+ IncidentEnergyWorkspace='Ei1',
+ FlatBkgWorkspace='bkg1-50K'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='run1-{}K'.format(T),
+ OutputWorkspace='run1-{}K-corrected'.format(T),
+ SelfShieldingCorrectionWorkspace='run1-self-shielding',
+ EmptyContainerWorkspace='container1-{}K-corrected'.format(T)
+ )
+ DirectILLReduction(
+ InputWorkspace='run1-{}K-corrected'.format(T),
+ OutputWorkspace='SofQW1-{}K'.format(T),
+ IntegratedVanadiumWorkspace='vanadium-calibration',
+ DiagnosticsWorkspace='mask'
+ )
+ SaveNexus('SofQW1-{}K'.format(T), '/data/output2-{}.nxs'.format(T))
+
+ # Sample and container at wavelength 2.
+
+ DirectILLCollectData(
+ Run=runs2[50],
+ OutputWorkspace='run2-50K',
+ OutputIncidentEnergyWorkspace=Ei2',
+ OutputFlatBkgWorkspace='bgk2-50K'
+ )
+
+ DirectILLCollectData(
+ Run=containerRun2,
+ OutputWorkspace='container2',
+ IncidentEnergyWorkspace='Ei2'
+ )
+
+ SetSample('container2', containerGeometry, containerMaterial)
+ DirectILLSelfShielding(
+ InputWorkspace='container2',
+ OutputWorkspace='container2-self-shielding'
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='container2',
+ OutputWorkspace='container2-corrected',
+ SelfShieldingCorrectionWorkspace='container2-self-shielding'
+ )
+
+ SetSample('run2-50K', sampleGeometry, sampleMaterial)
+ DirectILLSelfShielding(
+ InputWorkspace='run2-50K',
+ OutputWorkspace='run2-self-shielding'
+ )
+
+ for T in runs2:
+ if T != 50:
+ # 50K data has been loaded already.
+ DirectILLCollectData(
+ Run=runs2[T]
+ OuputWorkspace='run2-{}K'.format(T),
+ IncidentEnergyWorkspace='Ei2',
+ FlatBkgWorkspace='bkg2-50K
+ )
+ DirectILLApplySelfShielding(
+ InputWorkspace='run2-{}K'.format(T),
+ OutputWorkspace='run2-{}K-corrected'.format(T),
+ SelfShieldingCorrectionWorkspace='run2-self-shielding',
+ EmptyContainerWorkspace='container2'
+ )
+ DirectILLReduction(
+ InputWorkspace='run2-{}K-corrected'.format(T),
+ OutputWorkspace='SofQW2-{}K'.format(T),
+ IntegratedVanadiumWorkspace='vanadium-calibration',
+ DiagnosticsWorkspace='mask'
+ )
+ SaveNexus('SofQW2-{}K'.format(T), '/data/output2-{}.nxs'.format(T))
+
+.. categories:: Techniques
diff --git a/instrument/Facilities.xml b/instrument/Facilities.xml
index 626db9ec6ac762edfe5ea0aa9eba2ce7b40ff876..b93d57ccac249cfa797b48394b5a54b08f05c866 100644
--- a/instrument/Facilities.xml
+++ b/instrument/Facilities.xml
@@ -492,6 +492,9 @@
<instrument name="VULCAN" beamline="7">
<technique>Neutron Diffraction</technique>
+ <livedata>
+ <connection name="event" address="bl7-daq1.sns.gov:31415" listener="SNSLiveEventDataListener" />
+ </livedata>
</instrument>
<instrument name="CORELLI" beamline="9">
diff --git a/instrument/IN4_Parameters.xml b/instrument/IN4_Parameters.xml
index bf6592e161e90a68226eda4b97dfe3fd6d1b1a45..0e8ef605772c9241cde72665584bf35d4c23e7f5 100644
--- a/instrument/IN4_Parameters.xml
+++ b/instrument/IN4_Parameters.xml
@@ -17,7 +17,34 @@
See http://muparser.sourceforge.net/mup_features.html#idDef2 for available
operators -->
<parameter name="formula_eff" type="string">
- <value val="0.951*exp(-0.0887/sqrt(e))*(1.0-exp(-5.597/sqrt(e)))" />
+ <value val="0.951*exp(-0.0887/sqrt(e))*(1-exp(-5.597/sqrt(e)))" />
+ </parameter>
+ <!-- Default monitor spectrum number for monitor normalisation. -->
+ <parameter name="default-incident-monitor-spectrum" type="int">
+ <value val="397" />
+ </parameter>
+ <!-- Preferred scaling after normalisation to monitor counts. -->
+ <parameter name="scaling_after_monitor_normalisation">
+ <value val="1000" />
+ </parameter>
+ <!-- MergeRuns behavior when merging sample logs. -->
+ <parameter name="sample_logs_sum" type="string">
+ <value val="actual_time, Detector.detsum, Detector_Rosace.detsum, duration, monitor.monsum" />
+ </parameter>
+ <parameter name="sample_logs_time_series" type="string">
+ <value val="sample.temperature" />
+ </parameter>
+ <parameter name="sample_logs_warn" type="string">
+ <value val="sample.temperature" />
+ </parameter>
+ <parameter name="sample_logs_warn_tolerances" type="string">
+ <value val="1.0" />
+ </parameter>
+ <parameter name="sample_logs_fail" type="string">
+ <value val="monitor.time_of_flight_0, monitor.time_of_flight_1, monitor.time_of_flight_2" />
+ </parameter>
+ <parameter name="sample_logs_fail_tolerances" type="string">
+ <value val="0, 0, 0" />
</parameter>
</component-link>
diff --git a/instrument/IN5_Parameters.xml b/instrument/IN5_Parameters.xml
index c1565b88d52a490bdc08dd2761a858eab887c71a..d6772afac080980786962206230acd3b581bd1ea 100644
--- a/instrument/IN5_Parameters.xml
+++ b/instrument/IN5_Parameters.xml
@@ -17,7 +17,59 @@
See http://muparser.sourceforge.net/mup_features.html#idDef2 for available
operators -->
<parameter name="formula_eff" type="string">
- <value val="exp(-0.0565/sqrt(e))*(1.0-exp(-3.284/sqrt(e)))" />
+ <value val="1-exp(-5.6/sqrt(e))" />
+ </parameter>
+
+ <!-- Default monitor spectrum number for monitor normalisation. -->
+ <parameter name="default-incident-monitor-spectrum" type="int">
+ <value val="98305" />
+ </parameter>
+ <!-- Preferred scaling after normalisation to monitor counts. -->
+ <parameter name="scaling_after_monitor_normalisation">
+ <value val="100000" />
+ </parameter>
+ <parameter name="enable_flat_background_subtraction" type="bool">
+ <value val="false" />
+ </parameter>
+ <parameter name="enable_background_diagnostics" type="bool">
+ <value val="false" />
+ </parameter>
+ <parameter name="enable_elastic_peak_diagnostics" type="bool">
+ <value val="false" />
+ </parameter>
+ <parameter name="beam_stop_diagnostics_spectra" type="string">
+ <value val="84861-84870, 85114-85129, 85367-85388, 85620-85647, 85873-85906, 86126-86165, 86379-86424, 86632-86683, 86885-86942, 87138-87201, 87391-87460, 87644-87719, 87897-87978, 88150-88237, 88403-88496, 88656-88755, 88909-89014, 89162-89273, 89415-89532, 89668-89791, 89921-90050, 90177-90306, 90436-90559, 90695-90812, 90954-91065, 91213-91318, 91472-91571, 91731-91824, 91990-92077, 92249-92330, 92508-92583, 92767-92836, 93026-93089, 93285-93342, 93544-93595, 93803-93848, 94062-94101, 94321-94354, 94580-94607, 94839-94860, 95098-95113, 95357-95366"/>
+ </parameter>
+ <parameter name="enable_incident_energy_calibration" type="bool">
+ <value val="false" />
+ </parameter>
+ <parameter name="enable_elastic_peak_fitting" type="bool">
+ <value val="false" />
+ </parameter>
+ <parameter name="enable_elastic_channel_fitting" type="bool">
+ <value val="true" />
+ </parameter>
+ <parameter name="Workflow.MaskFile" type="string">
+ <value val="IN5_Mask.xml" />
+ </parameter>
+ <!-- MergeRuns behavior when merging sample logs. -->
+ <parameter name="sample_logs_sum" type="string">
+ <value val="Detector.detsum, duration, monitor.monsum" />
+ </parameter>
+ <parameter name="sample_logs_time_series" type="string">
+ <value val="sample.temperature" />
+ </parameter>
+ <parameter name="sample_logs_warn" type="string">
+ <value val="sample.temperature" />
+ </parameter>
+ <parameter name="sample_logs_warn_tolerances" type="string">
+ <value val="1.0" />
+ </parameter>
+ <parameter name="sample_logs_fail" type="string">
+ <value val="monitor.time_of_flight_0, monitor.time_of_flight_1, monitor.time_of_flight_2" />
+ </parameter>
+ <parameter name="sample_logs_fail_tolerances" type="string">
+ <value val="0, 0, 0" />
</parameter>
</component-link>
diff --git a/instrument/IN6_Parameters.xml b/instrument/IN6_Parameters.xml
index 6395558d05c47cff743bd401e1c0ace62cc110fc..a08765e7ded044f47544fbebf497a61bca0e2443 100644
--- a/instrument/IN6_Parameters.xml
+++ b/instrument/IN6_Parameters.xml
@@ -17,7 +17,36 @@
See http://muparser.sourceforge.net/mup_features.html#idDef2 for available
operators -->
<parameter name="formula_eff" type="string">
- <value val="exp(-0.0565/sqrt(e))*(1.0-exp(-3.284/sqrt(e)))" />
+ <!-- The xml escape sequence > below means 'greater than' -->
+ <value val="e > 5.113 ? 0.94*(1-exp(-3.284/sqrt(e))) : exp(-0.0565/sqrt(e))*(1-exp(-3.284/sqrt(e)))" />
+ </parameter>
+
+ <!-- Default monitor spectrum number for monitor normalisation. -->
+ <parameter name="default-incident-monitor-spectrum" type="int">
+ <value val="338" />
+ </parameter>
+ <!-- Preferred scaling after normalisation to monitor counts. -->
+ <parameter name="scaling_after_monitor_normalisation">
+ <value val="1000" />
+ </parameter>
+ <!-- MergeRuns behavior when merging sample logs. -->
+ <parameter name="sample_logs_sum" type="string">
+ <value val="Detector.detsum, duration, monitor1.monsum" />
+ </parameter>
+ <parameter name="sample_logs_time_series" type="string">
+ <value val="sample.temperature" />
+ </parameter>
+ <parameter name="sample_logs_warn" type="string">
+ <value val="sample.temperature" />
+ </parameter>
+ <parameter name="sample_logs_warn_tolerances" type="string">
+ <value val="1.0" />
+ </parameter>
+ <parameter name="sample_logs_fail" type="string">
+ <value val="monitor1.time_of_flight_0, monitor1.time_of_flight_1, monitor1.time_of_flight_2" />
+ </parameter>
+ <parameter name="sample_logs_fail_tolerances" type="string">
+ <value val="0, 0, 0" />
</parameter>
</component-link>
diff --git a/instrument/MERLIN_Definition_2017_02.xml b/instrument/MERLIN_Definition_2017_02.xml
new file mode 100644
index 0000000000000000000000000000000000000000..062b2d9b1923f5805d38768d5ba07af50ff5e7da
--- /dev/null
+++ b/instrument/MERLIN_Definition_2017_02.xml
@@ -0,0 +1,881 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- For help on the notation used to specify an Instrument Definition File
+ see http://www.mantidproject.org/IDF -->
+<instrument xmlns="http://www.mantidproject.org/IDF/1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd"
+ name="MERLIN" valid-from ="2017-09-12 11:00:01"
+ valid-to ="2100-01-31 23:59:59"
+ last-modified="2017-09-11 14:00:05">
+
+ <defaults>
+ <length unit="meter"/>
+ <angle unit="degree"/>
+ <reference-frame>
+ <!-- The z-axis is set parallel to and in the direction of the beam. the
+ y-axis points up and the coordinate system is right handed. -->
+ <along-beam axis="z"/>
+ <pointing-up axis="y"/>
+ <handedness val="right"/>
+ </reference-frame>
+ <default-view view="cylindrical_y"/>
+ </defaults>
+
+
+ <!-- DESCRIPTION OF INSTRUMENT IN WORDS:
+
+ The data for Merlin was obtained from Robert Bewley.
+
+ 2012-05-17 - added names to tubes
+ 2013-11-14 - use locations tag in tube definitions
+ 2017-09-11 - change to 512 detectors per tube
+ -->
+
+
+ <!-- SOURCE AND SAMPLE POSITION -->
+
+ <component type="undulator">
+ <location z="-11.8" />
+ </component>
+ <type name="undulator" is="Source"> </type>
+
+ <component type="sample-position">
+ <location />
+ </component>
+ <type name="sample-position" is="SamplePos"></type>
+
+ <!-- Aperture -->
+ <component type="aperture" name="aperture">
+ <location z="-10.1"/>
+ </component>
+
+ <type name="aperture">
+ <cuboid id="aperture0">
+ <left-front-bottom-point x="0.047" y="-0.047" z="-0.0001" />
+ <left-front-top-point x="0.047" y="-0.047" z="0.0001" />
+ <left-back-bottom-point x="-0.047" y="-0.047" z="-0.0001" />
+ <right-front-bottom-point x="0.047" y="0.047" z="-0.0001" />
+ </cuboid>
+ <algebra val="aperture0" />
+ </type>
+
+ <!-- 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>
+
+
+ <!-- DETECTORS -->
+
+ <component type="door1" idlist="door1">
+ <location />
+ </component>
+
+ <!-- Uncomment to include door 6. If this is done you MUST also
+ uncomment the <idlist name="door6"> at the bottom of this file
+ -->
+ <component type="door2" idlist="door2">
+ <location />
+ </component>
+
+ <component type="door3" idlist="door3">
+ <location />
+ </component>
+
+ <component type="door4" idlist="door4">
+ <location />
+ </component>
+
+ <component type="door5" idlist="door5">
+ <location />
+ </component>
+
+ <component type="door6" idlist="door6">
+ <location />
+ </component>
+
+ <component type="door7" idlist="door7">
+ <location />
+ </component>
+
+ <component type="door8" idlist="door8">
+ <location />
+ </component>
+
+ <component type="door9" idlist="door9">
+ <location />
+ </component>
+
+ <component type="monitors" idlist="monitors">
+ <location />
+ </component>
+
+ <type name="monitors">
+ <component type="monitor">
+ <location r="3.25800" t="180.0" p="0.0" />
+ <location r="1.50400" t="180.0" p="0.0" />
+ <location r="1.50400" t="180.0" p="0.0" />
+ <location r="1.50400" t="180.0" p="0.0" />
+ <location r="1.50400" t="180.0" p="0.0" />
+ <location r="4.24700" t="0.000" p="0.0" />
+ <location r="4.24700" t="0.000" p="0.0" />
+ <location r="4.24700" t="0.000" p="0.0" />
+ <location r="4.24700" t="0.000" p="0.0" />
+ </component>
+ </type>
+
+ <type name="door1">
+ <component type="standard-tube">
+ <location r="2.5" t="-45.01000" name="tube_1_1" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-44.37977" name="tube_1_2" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-43.74954" name="tube_1_3" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-43.11931" name="tube_1_4" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-42.48908" name="tube_1_5" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-41.85885" name="tube_1_6" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-41.22862" name="tube_1_7" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-40.59839" name="tube_1_8" > <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="-39.97000" name="tube_2_1" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-39.33977" name="tube_2_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-38.70954" name="tube_2_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-38.07931" name="tube_2_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-37.44908" name="tube_2_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-36.81885" name="tube_2_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-36.18862" name="tube_2_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-35.55839" name="tube_2_8"> <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="-34.93000" name="tube_3_1"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-34.29977" name="tube_3_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-33.66954" name="tube_3_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-33.03931" name="tube_3_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-32.40908" name="tube_3_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-31.77885" name="tube_3_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-31.14863" name="tube_3_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-30.51840" name="tube_3_8"> <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="-29.89001" name="tube_4_1"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-29.25978" name="tube_4_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-28.62955" name="tube_4_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-27.99932" name="tube_4_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-27.36909" name="tube_4_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-26.73886" name="tube_4_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-26.10863" name="tube_4_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-25.47840" name="tube_4_8"> <facing x="0" y="0" z="0"/> </location>
+ </component>
+ </type>
+
+ <type name="door2">
+ <component type="standard-tube">
+ <location r="2.5" t="-23.57801" name="tube_1_1" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-22.94778" name="tube_1_2" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-22.31755" name="tube_1_3" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-21.68732" name="tube_1_4" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-21.05709" name="tube_1_5" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-20.42686" name="tube_1_6" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-19.79664" name="tube_1_7" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-19.16641" name="tube_1_8" > <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="-18.53802" name="tube_2_1" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-17.90779" name="tube_2_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-17.27756" name="tube_2_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-16.64733" name="tube_2_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-16.01710" name="tube_2_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-15.38687" name="tube_2_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-14.75664" name="tube_2_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-14.12642" name="tube_2_8"> <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="-13.49803" name="tube_3_1"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-12.86780" name="tube_3_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-12.23757" name="tube_3_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-11.60734" name="tube_3_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-10.97712" name="tube_3_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-10.34689" name="tube_3_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-9.716660" name="tube_3_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-9.086440" name="tube_3_8"> <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="-8.458050" name="tube_4_1"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-7.827830" name="tube_4_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-7.197600" name="tube_4_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-6.567380" name="tube_4_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-5.937160" name="tube_4_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-5.306940" name="tube_4_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="-4.676720" name="tube_4_7"> <facing x="0" y="0" z="0"/> </location>
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+ <location r="2.5" t="111.64368" name="tube_2_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="112.27391" name="tube_2_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="112.90414" name="tube_2_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="113.53437" name="tube_2_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="114.16460" name="tube_2_8"> <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="114.79499" name="tube_3_1"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="115.42522" name="tube_3_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="116.05545" name="tube_3_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="116.68568" name="tube_3_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="117.31591" name="tube_3_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="117.94614" name="tube_3_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="118.57636" name="tube_3_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="119.20659" name="tube_3_8"> <facing x="0" y="0" z="0"/> </location>
+ </component>
+ </type>
+
+ <type name="door9">
+ <component type="standard-tube">
+ <location r="2.5" t="121.19498" name="tube_1_1" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="121.82521" name="tube_1_2" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="122.45544" name="tube_1_3" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="123.08567" name="tube_1_4" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="123.71590" name="tube_1_5" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="124.34613" name="tube_1_6" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="124.97636" name="tube_1_7" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="125.60659" name="tube_1_8" > <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="126.23698" name="tube_2_1" > <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="126.86721" name="tube_2_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="127.49744" name="tube_2_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="128.12767" name="tube_2_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="128.75790" name="tube_2_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="129.38813" name="tube_2_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="130.01836" name="tube_2_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="130.64859" name="tube_2_8"> <facing x="0" y="0" z="0"/> </location>
+
+ <location r="2.5" t="131.27898" name="tube_3_1"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="131.90921" name="tube_3_2"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="132.53944" name="tube_3_3"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="133.16967" name="tube_3_4"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="133.79990" name="tube_3_5"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="134.43013" name="tube_3_6"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="135.06036" name="tube_3_7"> <facing x="0" y="0" z="0"/> </location>
+ <location r="2.5" t="135.69059" name="tube_3_8"> <facing x="0" y="0" z="0"/> </location>
+ </component>
+ </type>
+
+
+ <type name="standard-tube" outline="yes">
+ <component type="standard-pixel">
+ <locations y="-1.4635693359375" y-end="1.46356933593751" n-elements="512"/>
+ </component>
+ </type>
+
+ <type name="straight-through-beam-tube" outline="yes">
+ <component type="straight-through-beam-pixel">
+ <locations y="0" y-end="1.22879882812501" n-elements="512" />
+ </component>
+ </type>
+
+
+ <type name="standard-pixel" is="detector">
+ <cylinder id="shape">
+ <centre-of-bottom-base x="0.0" y="-0.0028614" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <radius val="0.0127" />
+ <height val="0.00572" />
+ </cylinder>
+ <algebra val="shape" />
+ </type>
+
+ <type name="straight-through-beam-pixel" is="detector">
+ <cylinder id="shape">
+ <centre-of-bottom-base x="0.0" y="-0.001201172" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <radius val="0.0127" />
+ <height val="0.0024024" />
+ </cylinder>
+ <algebra val="shape" />
+ </type>
+
+ <type name="monitor" is="monitor">
+ <cylinder id="some-shape">
+ <centre-of-bottom-base r="0.0" t="0.0" p="0.0" />
+ <axis x="0.0" y="0.0" z="1.0" />
+ <radius val="0.01" />
+ <height val="0.03" />
+ </cylinder>
+ <algebra val="some-shape" />
+ </type>
+
+
+ <!-- DETECTOR ID LISTS -->
+
+ <idlist idname="monitors">
+ <id val="11" />
+ <id start="21" end="24" />
+ <id start="31" end="34" />
+ </idlist>
+
+ <idlist idname="door1">
+ <id start="1110001" end="1110512" />
+ <id start="1120001" end="1120512" />
+ <id start="1130001" end="1130512" />
+ <id start="1140001" end="1140512" />
+ <id start="1150001" end="1150512" />
+ <id start="1160001" end="1160512" />
+ <id start="1170001" end="1170512" />
+ <id start="1180001" end="1180512" />
+ <id start="1210001" end="1210512" />
+ <id start="1220001" end="1220512" />
+ <id start="1230001" end="1230512" />
+ <id start="1240001" end="1240512" />
+ <id start="1250001" end="1250512" />
+ <id start="1260001" end="1260512" />
+ <id start="1270001" end="1270512" />
+ <id start="1280001" end="1280512" />
+ <id start="1310001" end="1310512" />
+ <id start="1320001" end="1320512" />
+ <id start="1330001" end="1330512" />
+ <id start="1340001" end="1340512" />
+ <id start="1350001" end="1350512" />
+ <id start="1360001" end="1360512" />
+ <id start="1370001" end="1370512" />
+ <id start="1380001" end="1380512" />
+ <id start="1410001" end="1410512" />
+ <id start="1420001" end="1420512" />
+ <id start="1430001" end="1430512" />
+ <id start="1440001" end="1440512" />
+ <id start="1450001" end="1450512" />
+ <id start="1460001" end="1460512" />
+ <id start="1470001" end="1470512" />
+ <id start="1480001" end="1480512" />
+ </idlist>
+
+ <idlist idname="door2">
+ <id start="2110001" end="2110512" />
+ <id start="2120001" end="2120512" />
+ <id start="2130001" end="2130512" />
+ <id start="2140001" end="2140512" />
+ <id start="2150001" end="2150512" />
+ <id start="2160001" end="2160512" />
+ <id start="2170001" end="2170512" />
+ <id start="2180001" end="2180512" />
+ <id start="2210001" end="2210512" />
+ <id start="2220001" end="2220512" />
+ <id start="2230001" end="2230512" />
+ <id start="2240001" end="2240512" />
+ <id start="2250001" end="2250512" />
+ <id start="2260001" end="2260512" />
+ <id start="2270001" end="2270512" />
+ <id start="2280001" end="2280512" />
+ <id start="2310001" end="2310512" />
+ <id start="2320001" end="2320512" />
+ <id start="2330001" end="2330512" />
+ <id start="2340001" end="2340512" />
+ <id start="2350001" end="2350512" />
+ <id start="2360001" end="2360512" />
+ <id start="2370001" end="2370512" />
+ <id start="2380001" end="2380512" />
+ <id start="2410001" end="2410512" />
+ <id start="2420001" end="2420512" />
+ <id start="2430001" end="2430512" />
+ <id start="2440001" end="2440512" />
+ <id start="2450001" end="2450512" />
+ <id start="2460001" end="2460512" />
+ <id start="2470001" end="2470512" />
+ <id start="2480001" end="2480512" />
+ </idlist>
+
+ <idlist idname="door3">
+ <id start="3110001" end="3110512" />
+ <id start="3120001" end="3120512" />
+ <id start="3130001" end="3130512" />
+ <id start="3140001" end="3140512" />
+ <id start="3150001" end="3150512" />
+ <id start="3160001" end="3160512" />
+ <id start="3170001" end="3170512" />
+ <id start="3180001" end="3180512" />
+ <id start="3210001" end="3210512" />
+ <id start="3220001" end="3220512" />
+ <id start="3230001" end="3230512" />
+ <id start="3240001" end="3240512" />
+ <id start="3250001" end="3250512" />
+ <id start="3260001" end="3260512" />
+ <id start="3270001" end="3270512" />
+ <id start="3280001" end="3280512" />
+ <id start="3310001" end="3310512" />
+ <id start="3320001" end="3320512" />
+ <id start="3330001" end="3330512" />
+ <id start="3340001" end="3340512" />
+ <id start="3350001" end="3350512" />
+ <id start="3360001" end="3360512" />
+ <id start="3370001" end="3370512" />
+ <id start="3380001" end="3380512" />
+ <id start="3410001" end="3410512" />
+ <id start="3420001" end="3420512" />
+ <id start="3430001" end="3430512" />
+ <id start="3440001" end="3440512" />
+ <id start="3450001" end="3450512" />
+ <id start="3460001" end="3460512" />
+ <id start="3470001" end="3470512" />
+ <id start="3480001" end="3480512" />
+ <id start="3510001" end="3510512" />
+ <id start="3520001" end="3520512" />
+ <id start="3530001" end="3530512" />
+ <id start="3540001" end="3540512" />
+ <id start="3550001" end="3550512" />
+ <id start="3560001" end="3560512" />
+ <id start="3570001" end="3570512" />
+ <id start="3580001" end="3580512" />
+ </idlist>
+
+ <idlist idname="door4">
+ <id start="4110001" end="4110512" />
+ <id start="4120001" end="4120512" />
+ <id start="4130001" end="4130512" />
+ <id start="4140001" end="4140512" />
+ <id start="4150001" end="4150512" />
+ <id start="4160001" end="4160512" />
+ <id start="4170001" end="4170512" />
+ <id start="4180001" end="4180512" />
+ <id start="4210001" end="4210512" />
+ <id start="4220001" end="4220512" />
+ <id start="4230001" end="4230512" />
+ <id start="4240001" end="4240512" />
+ <id start="4250001" end="4250512" />
+ <id start="4260001" end="4260512" />
+ <id start="4270001" end="4270512" />
+ <id start="4280001" end="4280512" />
+ <id start="4310001" end="4310512" />
+ <id start="4320001" end="4320512" />
+ <id start="4330001" end="4330512" />
+ <id start="4340001" end="4340512" />
+ <id start="4350001" end="4350512" />
+ <id start="4360001" end="4360512" />
+ <id start="4370001" end="4370512" />
+ <id start="4380001" end="4380512" />
+ <id start="4410001" end="4410512" />
+ <id start="4420001" end="4420512" />
+ <id start="4430001" end="4430512" />
+ <id start="4440001" end="4440512" />
+ <id start="4450001" end="4450512" />
+ <id start="4460001" end="4460512" />
+ <id start="4470001" end="4470512" />
+ <id start="4480001" end="4480512" />
+ </idlist>
+
+ <idlist idname="door5">
+ <id start="5110001" end="5110512" />
+ <id start="5120001" end="5120512" />
+ <id start="5130001" end="5130512" />
+ <id start="5140001" end="5140512" />
+ <id start="5150001" end="5150512" />
+ <id start="5160001" end="5160512" />
+ <id start="5170001" end="5170512" />
+ <id start="5180001" end="5180512" />
+ <id start="5210001" end="5210512" />
+ <id start="5220001" end="5220512" />
+ <id start="5230001" end="5230512" />
+ <id start="5240001" end="5240512" />
+ <id start="5250001" end="5250512" />
+ <id start="5260001" end="5260512" />
+ <id start="5270001" end="5270512" />
+ <id start="5280001" end="5280512" />
+ <id start="5310001" end="5310512" />
+ <id start="5320001" end="5320512" />
+ <id start="5330001" end="5330512" />
+ <id start="5340001" end="5340512" />
+ <id start="5350001" end="5350512" />
+ <id start="5360001" end="5360512" />
+ <id start="5370001" end="5370512" />
+ <id start="5380001" end="5380512" />
+ <id start="5410001" end="5410512" />
+ <id start="5420001" end="5420512" />
+ <id start="5430001" end="5430512" />
+ <id start="5440001" end="5440512" />
+ <id start="5450001" end="5450512" />
+ <id start="5460001" end="5460512" />
+ <id start="5470001" end="5470512" />
+ <id start="5480001" end="5480512" />
+ </idlist>
+
+ <idlist idname="door6">
+ <id start="6110001" end="6110512" />
+ <id start="6120001" end="6120512" />
+ <id start="6130001" end="6130512" />
+ <id start="6140001" end="6140512" />
+ <id start="6150001" end="6150512" />
+ <id start="6160001" end="6160512" />
+ <id start="6170001" end="6170512" />
+ <id start="6180001" end="6180512" />
+ <id start="6210001" end="6210512" />
+ <id start="6220001" end="6220512" />
+ <id start="6230001" end="6230512" />
+ <id start="6240001" end="6240512" />
+ <id start="6250001" end="6250512" />
+ <id start="6260001" end="6260512" />
+ <id start="6270001" end="6270512" />
+ <id start="6280001" end="6280512" />
+ <id start="6310001" end="6310512" />
+ <id start="6320001" end="6320512" />
+ <id start="6330001" end="6330512" />
+ <id start="6340001" end="6340512" />
+ <id start="6350001" end="6350512" />
+ <id start="6360001" end="6360512" />
+ <id start="6370001" end="6370512" />
+ <id start="6380001" end="6380512" />
+ <id start="6410001" end="6410512" />
+ <id start="6420001" end="6420512" />
+ <id start="6430001" end="6430512" />
+ <id start="6440001" end="6440512" />
+ <id start="6450001" end="6450512" />
+ <id start="6460001" end="6460512" />
+ <id start="6470001" end="6470512" />
+ <id start="6480001" end="6480512" />
+ </idlist>
+
+ <idlist idname="door7">
+ <id start="7110001" end="7110512" />
+ <id start="7120001" end="7120512" />
+ <id start="7130001" end="7130512" />
+ <id start="7140001" end="7140512" />
+ <id start="7150001" end="7150512" />
+ <id start="7160001" end="7160512" />
+ <id start="7170001" end="7170512" />
+ <id start="7180001" end="7180512" />
+ <id start="7210001" end="7210512" />
+ <id start="7220001" end="7220512" />
+ <id start="7230001" end="7230512" />
+ <id start="7240001" end="7240512" />
+ <id start="7250001" end="7250512" />
+ <id start="7260001" end="7260512" />
+ <id start="7270001" end="7270512" />
+ <id start="7280001" end="7280512" />
+ <id start="7310001" end="7310512" />
+ <id start="7320001" end="7320512" />
+ <id start="7330001" end="7330512" />
+ <id start="7340001" end="7340512" />
+ <id start="7350001" end="7350512" />
+ <id start="7360001" end="7360512" />
+ <id start="7370001" end="7370512" />
+ <id start="7380001" end="7380512" />
+ <id start="7410001" end="7410512" />
+ <id start="7420001" end="7420512" />
+ <id start="7430001" end="7430512" />
+ <id start="7440001" end="7440512" />
+ <id start="7450001" end="7450512" />
+ <id start="7460001" end="7460512" />
+ <id start="7470001" end="7470512" />
+ <id start="7480001" end="7480512" />
+ </idlist>
+
+ <idlist idname="door8">
+ <id start="8110001" end="8110512" />
+ <id start="8120001" end="8120512" />
+ <id start="8130001" end="8130512" />
+ <id start="8140001" end="8140512" />
+ <id start="8150001" end="8150512" />
+ <id start="8160001" end="8160512" />
+ <id start="8170001" end="8170512" />
+ <id start="8180001" end="8180512" />
+ <id start="8210001" end="8210512" />
+ <id start="8220001" end="8220512" />
+ <id start="8230001" end="8230512" />
+ <id start="8240001" end="8240512" />
+ <id start="8250001" end="8250512" />
+ <id start="8260001" end="8260512" />
+ <id start="8270001" end="8270512" />
+ <id start="8280001" end="8280512" />
+ <id start="8310001" end="8310512" />
+ <id start="8320001" end="8320512" />
+ <id start="8330001" end="8330512" />
+ <id start="8340001" end="8340512" />
+ <id start="8350001" end="8350512" />
+ <id start="8360001" end="8360512" />
+ <id start="8370001" end="8370512" />
+ <id start="8380001" end="8380512" />
+ </idlist>
+
+ <idlist idname="door9">
+ <id start="9110001" end="9110512" />
+ <id start="9120001" end="9120512" />
+ <id start="9130001" end="9130512" />
+ <id start="9140001" end="9140512" />
+ <id start="9150001" end="9150512" />
+ <id start="9160001" end="9160512" />
+ <id start="9170001" end="9170512" />
+ <id start="9180001" end="9180512" />
+ <id start="9210001" end="9210512" />
+ <id start="9220001" end="9220512" />
+ <id start="9230001" end="9230512" />
+ <id start="9240001" end="9240512" />
+ <id start="9250001" end="9250512" />
+ <id start="9260001" end="9260512" />
+ <id start="9270001" end="9270512" />
+ <id start="9280001" end="9280512" />
+ <id start="9310001" end="9310512" />
+ <id start="9320001" end="9320512" />
+ <id start="9330001" end="9330512" />
+ <id start="9340001" end="9340512" />
+ <id start="9350001" end="9350512" />
+ <id start="9360001" end="9360512" />
+ <id start="9370001" end="9370512" />
+ <id start="9380001" end="9380512" />
+ </idlist>
+
+ <!-- DETECTOR PARAMETERS -->
+ <component-link name="monitors">
+ <parameter name="DelayTime">
+ <value units="microseconds" val="0"/>
+ </parameter>
+ </component-link>
+
+ <!-- Set the same across the reset of the instrument -->
+ <component-link name = "MERLIN">
+ <parameter name="TubePressure">
+ <value units="atm" val="10.0"/>
+ </parameter>
+ <parameter name="TubeThickness">
+ <value units="metre" val="0.0008"/>
+ </parameter>
+ <parameter name="DelayTime">
+ <value units="microseconds" val="-5.3"/>
+ </parameter>
+ </component-link>
+
+
+</instrument>
diff --git a/instrument/MERLIN_Definition_after2013_4.xml b/instrument/MERLIN_Definition_after2013_4.xml
index 4bb893e054a38bf4804f602fffac62d6dc918b69..be7883a7525425a6ffe594d089b0d9ce5889592d 100644
--- a/instrument/MERLIN_Definition_after2013_4.xml
+++ b/instrument/MERLIN_Definition_after2013_4.xml
@@ -5,8 +5,8 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd"
name="MERLIN" valid-from ="2014-02-10 00:00:01"
- valid-to ="2100-01-31 23:59:59"
- last-modified="2015-03-01 12:00:05">
+ valid-to ="2017-09-12 11:00:00"
+ last-modified="2017-09-11 14:00:05">
<defaults>
<length unit="meter"/>
diff --git a/instrument/MERLIN_Parameters_2017_02.xml b/instrument/MERLIN_Parameters_2017_02.xml
new file mode 100644
index 0000000000000000000000000000000000000000..018e2af2443b53119523e43835d3757b57c859dc
--- /dev/null
+++ b/instrument/MERLIN_Parameters_2017_02.xml
@@ -0,0 +1,478 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<parameter-file instrument = "MERLIN" valid-from = "2017-09-12T11:00:01">
+
+<component-link name = "MERLIN">
+
+<!-- files properties : -->
+
+<!-- Specify that the detector positions should be taken from the data file (Not used ) -->
+<parameter name="det-pos-source" type="string">
+ <value val="datafile"/>
+</parameter>
+<!-- The file which defines proper (calibrated) detector positions
+ if None - it is undefined -->
+<parameter name="det_cal_file" type="string">
+ <value val="det_corr_172.dat"/>
+ <description is = "The file which defines proper (calibrated) detector positions.
+ If property set to None - this file is undefined."/>
+</parameter>
+<!-- The file which defines detectors to spectra mapping; File extension has to be specified here but filepath not
+ if None - one2one map is used -->
+<parameter name="map_file" type="string">
+ <value val="None"/>
+</parameter>
+
+<!-- Preferred extension of the data files obtained from DAE, e.g. what to prefer if two
+ files with the same name and different extension are found
+ -->
+<parameter name="data_file_ext" type="string">
+ <value val=".nxs"/>
+</parameter>
+<!-- The name of the hard mask file to use together with diag masking 4to1_124mod.msk-->
+<parameter name="hard_mask_file" type="string">
+ <value val="None"/>
+</parameter>
+
+<!-- The map file used when calculating absolute units conversion integrals
+ This map usually groups together large areas of detectors to obtain proper vanadium statistics -->
+<parameter name="monovan_mapfile" type="string">
+ <value val="mono_van_map.map"/>
+</parameter>
+
+
+
+
+<!-- RunNumber to use for diag instead of the input run number if none - use input run
+ if yes, will probably change from command line-->
+<parameter name="mask_run" type="string">
+ <value val="None"/>
+</parameter>
+
+<!-- Energy conversion mode direct/indirect/elastic (the one the reducer understands) -->
+<parameter name="deltaE-mode" type="string">
+ <value val="direct"/>
+</parameter>
+
+<!-- normalise_method normalization. To compare different runs with different length one uses normalization by some flux-dependent parameter
+ Available values are: none (-largely meaningless), monitor-1,monitor-2, current
+ the acceptable values are defined in DirectEnergyConversion initialization routine as recognized by direct energy conversion normalize method
+ these three are currently disabled/unknown: uamph peak-->
+<parameter name="normalise_method" type="string">
+ <value val="monitor-1"/>
+</parameter>
+
+<!-- Monitor used to estimate total current on the sample while normalizing by monitor 1. -->
+<parameter name="norm-mon1-spec" >
+ <value val="69633"/>
+</parameter>
+
+<!-- Time interval used for integration to estimate current on the sample
+ This interval is usually taken around the monitor peak-->
+<parameter name="norm-mon1-min">
+ <value val="1000"/>
+</parameter>
+<parameter name="norm-mon1-max">
+ <value val="2000"/>
+</parameter>
+<parameter name="norm_mon_integration_range" type="string">
+ <value val="norm-mon1-min:norm-mon1-max"/>
+</parameter>
+
+<!-- Monitor after chopper used to estimate total current on the sample, if normalization is done on monitor 2 -->
+<parameter name="norm-mon2-spec" type="int">
+ <value val="69634"/>
+</parameter>
+<!-- Relative energy range (wrt. to the incident energy) in which monitor 2 signal is present and the integration to
+ calculate monitor-2 current occurs -->
+<parameter name="mon2_norm_energy_range" type = "string">
+ <value val="0.8,1.2"/>
+</parameter>
+
+<!-- Usually one wants to avoid loading monitors together with data except in special cases. One of this cases is
+ MARI which monitors numbers are in the beginning of the spectra. If one loads them separately,
+ spectra numbers change and ISIS hard masks (msk) prepared for workspace with monitors become invalid.
+ This parameter is actual until Mantid Masking change.
+ -->
+<parameter name="load_monitors_with_workspace" type="bool">
+<value val="False"/>
+</parameter>
+
+<!-- -->
+<parameter name="ei-mon1-spec" type="string">
+ <value val="69634,69635,69636,69637"/>
+ <description is="First spectra number (monitor's spectra number) to use when measuring incident energy,
+ or comma separated list of such numbers.
+ Should be spectra with well defined energy peak or monitor's spectra.
+ If list of numbers is provided, the final spectrum is the sum of the spectra with the numbers provided.
+ It is important to have the detectors for these spectra to be located at the same distance from the source,
+ as the position of the combined detector will be defined by the position of the first spectra's detector."/>
+</parameter>
+<!-- -->
+<parameter name="ei-mon2-spec" type="string">
+ <value val="69638,69639,69640,69641"/>
+ <description is="Second spectra number (monitor's spectra number) to use when measuring incident energy,
+ or comma separated list of such numbers.
+ Should be spectra with well defined energy peak or monitor's spectra.
+ If list of numbers is provided, the final spectrum is the sum of the spectra with the numbers provided.
+ It is important to have the detectors for these spectra to be located at the same distance from the source,
+ as the position of the combined detector will be defined by the position of the first spectra's detector."/>
+</parameter>
+<!-- -->
+<parameter name="ei_mon_spectra" type="string">
+ <value val="ei-mon1-spec:ei-mon2-spec"/>
+ <description is="List of spectra, used to calculate incident energy of beam in inelastic experiments by GetEi algorithm.
+ It is complex property, dependent on two other properties, namely ei-mon1-spec and ei-mon2-spec, which define spectrum or
+ spectra lists for each of two monitors, used in GetEi calculations"/>
+</parameter>
+<!-- -->
+<parameter name="spectra_to_monitors_list" type="string">
+ <value val="None"/>
+ <description is="If you use some detectors as monitors and work in event mode,
+ one needs to specify the comma separated list of these detectors as the value of this property
+ to copy detectors spectra to monitors spectra collected in histogram mode.
+ If no such monitors are used, None (or text string 'None' in IDF) has to be specified as the value.
+ This is also necessary in Histogram mode if you want to use some detectors as monitors and
+ load_monitors_with_workspace is set to False necessary if monitors are measured with different time channels"/>
+</parameter>
+
+<!-- -->
+<parameter name="multirep_tof_specta_list" type="string">
+ <value val="382,68353"/>
+ <description is="List of two spectra corresponding to the detectors which are closest and furthest from the sample.
+ These detectors locations are used to identify TOF range, contributing into each energy range
+ in multirep mode"/>
+</parameter>
+
+
+<!-- by default getEi looks for peaks within (1+-0.1)*TOF_GUES range where TOF_GUES is evaluated on the basis of ei guess.
+ If the peaks are very narrow, or there are a lot of them very close to each other,
+ this value can be reduced. For example, such situation happens on MARI for very high incident energies Ei=1800.
+ -->
+<parameter name="ei_mon_peak_search_range">
+ <value val="0.1"/>
+</parameter>
+
+
+<parameter name="scale-factor">
+ <value val="1.7016e8"/>
+</parameter>
+
+<parameter name="wb-scale-factor">
+ <value val="1000"/>
+</parameter>
+
+<!-- Remove the count rate seen in the regions of the histograms defined as the background regions -->
+<parameter name="check_background" type="bool">
+ <value val="False"/>
+ <description is="If True, remove the count rate seen in the regions of the
+ histograms defined as the background regions.
+ The background region is defined by background_range property."/>
+</parameter>
+<parameter name="nullify_negative_signal" type="bool">
+ <value val="True"/>
+ <description is="If True and background removed, nullify the negative signal, which
+ may occur at some detectors at some moments of time due to flat background removal and modify errors accordingly.
+ If False, leave signals and errors unchanged. "/>
+</parameter>
+
+
+<!-- detector_van_range- integratin in E(mev) for detector(white beam) vanadium data [20,100] -->
+<parameter name="wb-integr-min">
+ <value val="20"/>
+</parameter>
+<parameter name="wb-integr-max">
+ <value val="55"/>
+</parameter>
+<parameter name="wb_integr_range" type="string">
+ <value val="wb-integr-min:wb-integr-max"/>
+</parameter>
+
+
+<!-- integration range for background tests (in TOF) - composite property
+ Used in test to reject high backgound (FlatBackground) and in High Background tests integration in Diagnostics
+ if diag_background_test_range is not set -->
+<parameter name="bkgd-range-min">
+ <value val="12000"/>
+</parameter>
+<parameter name="bkgd-range-max">
+ <value val="18000"/>
+</parameter>
+<parameter name="background_range" type="string">
+ <value val="bkgd-range-min:bkgd-range-max"/>
+</parameter>
+
+<!-- ******************************** DIAGNOSTICS DEFAILTS **************************************** -->
+
+<!-- Perform diag by bank. These are the spectrum numbers -->
+<parameter name="diag_spectra" type="string">
+ <value val="None"/>
+</parameter>
+
+<!-- Absolute lo threshold for vanadium diag (tiny) -->
+<parameter name="diag_tiny">
+ <value val="1e-10"/>
+</parameter>
+
+<!-- Absolute hi threshold for vanadium diag (large) -->
+<parameter name="diag_huge">
+ <value val="1e10"/>
+</parameter>
+
+<!-- Setting diag to reject zero backgrounds; If true then zeroes in (vanadium) data are masked as fail -->
+<parameter name="diag_samp_zero" type="bool">
+ <value val="False"/>
+</parameter>
+
+<!-- Fraction of median to consider counting low for the white beam diag (diag_van_median_rate_limit_hi sv_lo)-->
+<parameter name="diag_samp_lo">
+ <value val="0.0"/>
+</parameter>
+<!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+<parameter name="diag_samp_hi">
+ <value val="1.5"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (sv_sig)
+ i.e. to fail the test, the magnitude of the
+ difference with respect to the median value must also exceed this number of error bars (default=3.3)
+-->
+<parameter name="diag_samp_sig">
+ <value val="3.3"/>
+</parameter>
+
+<!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+<parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+</parameter>
+
+<!-- Upper bound defining outliers as fraction of median value (v_out_hi) -->
+<parameter name="diag_van_out_hi">
+ <value val="100."/>
+</parameter>
+
+<!-- Fraction of median to consider counting low for the white beam diag (vv_lo) vanlo=0.1 -->
+<parameter name="diag_van_lo">
+ <value val="0.1"/>
+</parameter>
+
+<!-- Fraction of median to consider counting high for the white beam diag (vv_hi) vanhi=1.5 -->
+<parameter name="diag_van_hi">
+ <value val="1.5"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar van_sig "
+ i.e. to fail the test, the magnitude of the difference with respect to the median value must also exceed this number of error bars (default=0.0)
+-->
+<parameter name="diag_van_sig">
+ <value val="0.0"/>
+</parameter>
+
+<!-- Variation for ratio test with second white beam -->
+<parameter name="diag_variation">
+ <value val="1.1"/>
+</parameter>
+<!-- The range used in diagnostics and rejecting high background.
+ If none, the diag background range uses background ranges from background_range. Has to be directly set otherwise -->
+<parameter name="diag_background_test_range" type="string" >
+ <value val="None"/>
+</parameter>
+
+<!-- -->
+<!-- Bleeding corrections -->
+
+<!-- the number of pixels ignored within the bleed test diagnostic -->
+<parameter name="bleed_pixels">
+ <value val="80"/>
+</parameter>
+<!-- the maximum framerate allowed in a tube -->
+<parameter name="bleed_maxrate">
+ <value val="0.01"/>
+</parameter>
+<!-- True if the bleed tests should be run use_bleeding-->
+<parameter name="diag_bleed_test" type="bool">
+ <value val="False"/>
+</parameter>
+
+<!-- **************************************** DIAGNOSTICS DEFAILTS END **************************************** -->
+
+
+<!-- **************************************** ABSOLUTE UNITS CORRECTION DEFAULTS ******************************** -->
+<!-- Absolute units conversion average -->
+<parameter name="monovan_lo_bound">
+ <value val="0.01"/>
+</parameter>
+
+<parameter name="monovan_hi_bound">
+ <value val="100"/>
+</parameter>
+
+<!-- This property is the part of the composite definition for abs_units_van_range:
+ It specifies the relative to incident energy lower integration limit for monochromatic vanadium in the mono-vanadium integration -->
+<parameter name="monovan_lo_frac">
+ <value val="-0.6"/>
+</parameter>
+
+<!-- This property is the part of the composite definition for abs_units_van_range:
+ It specifies the the lower limit of energy range in the monochromatic-vanadium integration
+ Used only if abs_units_van_range is set to val="monovan_lo_value,monovan_hi_value"-->
+<parameter name="monovan_lo_value">
+ <value val="-40."/>
+</parameter>
+
+<!-- This property is the part of the composite definition for abs_units_van_range
+ It specifies the relative to incident energy higher integration limit for monochromatic vanadium in the mono-vanadium integration -->
+<parameter name="monovan_hi_frac">
+ <value val="0.6"/>
+</parameter>
+<!-- This property is the part of the composite definition for abs_units_van_range
+ It specifies the the higher limit of energy range in the monochromatic-vanadium integration
+ Used only if abs_units_van_range is set to val="monovan_lo_value,monovan_hi_value"-->
+<parameter name="monovan_hi_value">
+ <value val="40."/>
+</parameter>
+
+<!-- energy range for integration calculating absolute units correction vanadium data.
+ if None, range is calculated from monovan_hi_frac/monovan_lo_frac
+ - providing the fractions of the incident energy
+ if one wants to specify the energy values here it has to be defined in the form:
+ <value val="monovan_lo_value,monovan_hi_value"/> -->
+<parameter name="abs_units_van_range" type="string">
+ <value val="None"/>
+</parameter>
+<!-- Sample mass used in absolute units normalization and should usually be changed by user-->
+<parameter name="sample_mass">
+ <value val="1"/>
+</parameter>
+<!-- Sample rmm used in absolute units normalization should usually be changed by user -->
+<parameter name="sample_rmm">
+ <value val="1"/>
+</parameter>
+<!-- Vanaduim mass used in absolute units normalization and is usually instrument specific (changes rarely) -->
+<parameter name="vanadium-mass">
+ <value val="7.85"/>
+</parameter>
+<!-- if this value set to true, modo-vanadium run is not analyzed and masks obtained for arbitrary units are used for mono-vanadium -->
+<parameter name="use_sam_msk_on_monovan" type = "bool">
+ <value val="False"/>
+</parameter>
+
+<!-- if this value is provided (not None) it is string reperesentation of the number used instead of calculating mono-vanadium based normalization factor
+ one does not need to provide mono-vanadium run if this value is provided as it will be used instead
+ -->
+<parameter name="mono_correction_factor" type="string">
+ <value val="None"/>
+</parameter>
+
+<!-- **************************************** ABSOLUTE UNITS CORRECTION DEFAULTS END **************************** -->
+
+<!-- if defined to true, fix incident energy to this value and do not calculate the energy from the run -->
+<parameter name="fixei" type="bool">
+ <value val="False"/>
+</parameter>
+
+<!-- **************************************** Workflow control **************************** -->
+
+<!-- This parameter controls the format of output data written by reducer.
+ Three values are currently supported, namely .spe, .nxspe, and nexus (mantid workspace) (.nxs)
+ Three possible values for this are defined inin DirectEnergyConversion init routine as recognized by save method
+ If None is there, no internal script saving occurs and one needs to use external save operations -->
+<parameter name="save_format" type="string">
+ <value val="None"/>
+</parameter>
+
+<!-- If one wants to sum runs. By default no, as in addition to the key word one has to provide list of input run-numbers
+ but presence of this key here allows to propagate this key-word to the reducer -->
+<parameter name="sum_runs" type="bool">
+ <value val="False"/>
+</parameter>
+
+<!-- # Run Detector Efficiency Correction -->
+<parameter name="apply_detector_eff" type="bool">
+ <value val="True"/>
+</parameter>
+<!-- # Multiply result by ki/kf value -->
+<parameter name="apply_kikf_correction" type="bool">
+ <value val="True"/>
+</parameter>
+
+<!-- The if true, use only hard mask file specified above and do not run diagnostics procedures -->
+<parameter name="use_hard_mask_only" type="bool">
+ <value val="False"/>
+</parameter>
+
+<!-- Parameter specifies if one wants to run diagnostics (which include applying hard mask file) or not-->
+<parameter name="run_diagnostics" type="bool">
+ <value val="True"/>
+</parameter>
+
+
+<!-- If this parameter is set to true, dgreduce will try to load mask from the mask file
+ correspondent to the run if finds it and uses this mask as hard mask only (does not run diagnostics).
+ If such file has not been found, it will run diagnostics and save the masks into mask file for reuse
+ Hard Mask file, provided separately or as additional hard mask file is ignored in this case -->
+<parameter name="save_and_reuse_masks" type="bool">
+ <value val="False"/>
+</parameter>
+
+<!-- The semicolon separated list of possible log names, containing information on crystl rotation.
+ First found log will be used togethere with motor_offset to identify crystal rotation
+ (psi in Horace) -->
+<parameter name="motor_log_names" type="string">
+ <value val="CCR_ROT;wccr"/>
+</parameter>
+<!-- Initial value used to identify crytsal rotation angle psi=motor_offset+wccr.timeAverageValue() -->
+<parameter name="motor_offset">
+ <value val="None"/>
+</parameter>
+
+
+<!-- List of the words which can be used as a command line arguments to define reducer keywords
+ the form is reducer_keword1=synonim1=synonim2=synonim3;reducer_keword1=synonim1a, so,
+ the reducer keywords are the leftmost values of the keyword assignments below
+ Each keyword met in command line or file above are converted into reducer keyword as below
+-->
+<parameter name="synonims" type="string">
+ <value val="normalise_method=norm_method;
+ fix_ei=fixei;
+ sum_runs=sum;
+ wb_integr_range=detector_van_range;
+ motor_log_names = motor_name;
+ van_mass=vanadium-mass;
+ check_background = background;
+
+ mon1_norm_spec=norm-mon1-spec;
+ mon2_norm_spec=norm-mon2-spec;
+ scale_factor=scale-factor;
+ wb_scale_factor=wb-scale-factor;
+ monovan_integr_range=abs_units_van_range;
+ monovan_lo_value = monovan-integr-min;
+ monovan_hi_value = monovan-integr-max;
+ bkgd_range = background_range;
+ background_test_range = diag_background_test_range;
+ hard_mask_file=hard_mask;
+ van_out_lo = diag_van_median_rate_limit_lo=diag_van_out_lo;
+ van_out_hi = diag_van_median_rate_limit_hi=diag_van_out_hi;
+ van_lo = diag_van_median_sigma_lo=diag_van_lo;
+ van_hi = diag_van_median_sigma_hi=diag_van_hi;
+ van_sig = diag_van_median_sigma=diag_van_sig;
+ tiny = diag_tiny;
+ huge = diag_huge=large;
+ samp_zero = diag_remove_zero=diag_samp_zero;
+ samp_lo = diag_samp_median_sigma_lo=diag_samp_lo;
+ samp_hi = diag_samp_median_sigma_hi=diag_samp_hi;
+ samp_sig = diag_samp_median_sigma=diag_samp_sig;
+ variation = diag_variation;
+ bleed_test = bleed = diag_bleed_test;
+ bleed_maxrate= diag_bleed_maxrate;
+ bleed_pixels = diag_bleed_pixels;
+ deltaE_mode = deltaE-mode;
+ ei-mon1-spec=ei_mon1_spec;
+ ei-mon2-spec = test_ei2_mon_spectra=ei_mon2_spec;
+ ei_mon_spectra=test_mon_spectra_composite"
+ />
+</parameter>
+
+ <!-- -->
+</component-link>
+
+</parameter-file>
diff --git a/instrument/masks/IN5_Mask.xml b/instrument/masks/IN5_Mask.xml
index 3e369afee704e8405d1e683a2916aa053d4f523a..8975f7c29cacb352b40cc56e68ddacac80a6949d 100644
--- a/instrument/masks/IN5_Mask.xml
+++ b/instrument/masks/IN5_Mask.xml
@@ -1,7 +1,6 @@
<?xml version="1.0"?>
<detector-masking>
<group>
- 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diff --git a/instrument/masks/IN5_Mask_bs_top_bottom.xml b/instrument/masks/IN5_Mask_bs_top_bottom.xml
deleted file mode 100644
index 3b412c3e304d04dc807148fbb572ddad08d2579c..0000000000000000000000000000000000000000
--- a/instrument/masks/IN5_Mask_bs_top_bottom.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<detector-masking>
- <group>
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- </detids>
- </group>
-
-</detector-masking>
diff --git a/instrument/masks/IN5_Mask_bs_top_bottom_lastPannel.xml b/instrument/masks/IN5_Mask_bs_top_bottom_lastPannel.xml
deleted file mode 100644
index 3725b3376d802ccdb2a13f70b9bbd7221d8012c3..0000000000000000000000000000000000000000
--- a/instrument/masks/IN5_Mask_bs_top_bottom_lastPannel.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<detector-masking>
- <group>
- 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- </detids>
- </group>
-
-</detector-masking>
diff --git a/instrument/masks/IN5_Mask_bs_top_bottom_positive_panels.xml b/instrument/masks/IN5_Mask_bs_top_bottom_positive_panels.xml
deleted file mode 100644
index 0df020e71023ca8ab22f97abbc667fb290062422..0000000000000000000000000000000000000000
--- a/instrument/masks/IN5_Mask_bs_top_bottom_positive_panels.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<detector-masking>
- <group>
- 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055,92056,92057,92058,92059,92060,92061,92062,92063,92064,92065,92066,92067,92068,92069,92070,92071,92154,92155,92156,92157,92158,92159,92160,92161,92162,92163,92164,92165,92166,92167,92168,92253,92254,92255,92256,92257,92258,92259,92260,92261,92262,92263,92264,92265,92266,92267,92268,92269,92270,92271,92272,92273,92274,92275,92276,92277,92278,92279,92280,92281,92282,92283,92284,92285,92286,92287,92288,92289,92290,92291,92292,92293,92294,92295,92296,92297,92298,92299,92300,92301,92302,92303,92304,92305,92306,92307,92308,92309,92310,92311,92312,92313,92314,92315,92316,92317,92318,92319,92320,92321,92322,92323,92324,92410,92411,92412,92413,92414,92415,92416,92417,92418,92419,92420,92421,92422,92423,92424,92512,92513,92514,92515,92516,92517,92518,92519,92520,92521,92522,92523,92524,92525,92526,92527,92528,92529,92530,92531,92532,92533,92534,92535,92536,92537,92538,92539,92540,92541,92542,92543,92544,92545,92546,92547,92548,92549,92550,92551,92552,92553,92554,92555,92556,92557,92558,92559,92560,92561,92562,92563,92564,92565,92566,92567,92568,92569,92570,92571,92572,92573,92574,92575,92576,92577,92578,92666,92667,92668,92669,92670,92671,92672,92673,92674,92675,92676,92677,92678,92679,92680,92771,92772,92773,92774,92775,92776,92777,92778,92779,92780,92781,92782,92783,92784,92785,92786,92787,92788,92789,92790,92791,92792,92793,92794,92795,92796,92797,92798,92799,92800,92801,92802,92803,92804,92805,92806,92807,92808,92809,92810,92811,92812,92813,92814,92815,92816,92817,92818,92819,92820,92821,92822,92823,92824,92825,92826,92827,92828,92829,92830,92922,92923,92924,92925,92926,92927,92928,92929,92930,92931,92932,92933,92934,92935,92936,93029,93030,93031,93032,93033,93034,93035,93036,93037,93038,93039,93040,93041,93042,93043,93044,93045,93046,93047,93048,93049,93050,93051,93052,93053,93054,93055,93056,93057,93058,93059,93060,93061,93062,93063,93064,93065,93066,93067,93068,93069,93070,93071,93072,93073,93074,93075,93076,93077,93078,93079,93080,93081,93178,93179,93180,93181,93182,93183,93184,93185,93186,93187,93188,93189,93190,93191,93192,93289,93290,93291,93292,93293,93294,93295,93296,93297,93298,93299,93300,93301,93302,93303,93304,93305,93306,93307,93308,93309,93310,93311,93312,93313,93314,93315,93316,93317,93318,93319,93320,93321,93322,93323,93324,93325,93326,93327,93328,93329,93330,93331,93332,93333,93334,93335,93434,93435,93436,93437,93438,93439,93440,93441,93442,93443,93444,93445,93446,93447,93448,93547,93548,93549,93550,93551,93552,93553,93554,93555,93556,93557,93558,93559,93560,93561,93562,93563,93564,93565,93566,93567,93568,93569,93570,93571,93572,93573,93574,93575,93576,93577,93578,93579,93580,93581,93582,93583,93584,93585,93586,93587,93588,93690,93691,93692,93693,93694,93695,93696,93697,93698,93699,93700,93701,93702,93703,93704,93808,93809,93810,93811,93812,93813,93814,93815,93816,93817,93818,93819,93820,93821,93822,93823,93824,93825,93826,93827,93828,93829,93830,93831,93832,93833,93834,93835,93836,93837,93838,93839,93840,93841,93946,93947,93948,93949,93950,93951,93952,93953,93954,93955,93956,93957,93958,93959,93960,94067,94068,94069,94070,94071,94072,94073,94074,94075,94076,94077,94078,94079,94080,94081,94082,94083,94084,94085,94086,94087,94088,94089,94090,94091,94092,94093,94094,94202,94203,94204,94205,94206,94207,94208,94209,94210,94211,94212,94213,94214,94215,94216,94325,94326,94327,94328,94329,94330,94331,94332,94333,94334,94335,94336,94337,94338,94339,94340,94341,94342,94343,94344,94345,94346,94458,94459,94460,94461,94462,94463,94464,94465,94466,94467,94468,94469,94470,94471,94472,94584,94585,94586,94587,94588,94589,94590,94591,94592,94593,94594,94595,94596,94597,94598,94599,94600,94714,94715,94716,94717,94718,94719,94720,94721,94722,94723,94724,94725,94726,94727,94728,94845,94846,94847,94848,94849,94850,94851,94852,94853,94970,94971,94972,94973,94974,94975,94976,94977,94978,94979,94980,94981,94982,94983,94984,95226,95227,95228,95229,95230,95231,95232,95233,95234,95235,95236,95237,95238,95239,95240,95482,95483,95484,95485,95486,95487,95488,95489,95490,95491,95492,95493,95494,95495,95496,95738,95739,95740,95741,95742,95743,95744,95745,95746,95747,95748,95749,95750,95751,95752,95994,95995,95996,95997,95998,95999,96000,96001,96002,96003,96004,96005,96006,96007,96008,96250,96251,96252,96253,96254,96255,96256,96257,96258,96259,96260,96261,96262,96263,96264,96506,96507,96508,96509,96510,96511,96512,96513,96514,96515,96516,96517,96518,96519,96520,96762,96763,96764,96765,96766,96767,96768,96769,96770,96771,96772,96773,96774,96775,96776,97018,97019,97020,97021,97022,97023,97024,97025,97026,97027,97028,97029,97030,97031,97032,97274,97275,97276,97277,97278,97279,97280,97281,97282,97283,97284,97285,97286,97287,97288,97530,97531,97532,97533,97534,97535,97536,97537,97538,97539,97540,97541,97542,97543,97544,97786,97787,97788,97789,97790,97791,97792,97793,97794,97795,97796,97797,97798,97799,97800,98042,98043,98044,98045,98046,98047,98048,98049,98050,98051,98052,98053,98054,98055,98056,98298,98299,98300,98301,98302,98303,98304
- </detids>
- </group>
-
-</detector-masking>
diff --git a/qt/paraview_ext/PVPlugins/Representations/AlignedThreeSliceFilter.cxx b/qt/paraview_ext/PVPlugins/Representations/AlignedThreeSliceFilter.cxx
index 703d923eb41335d1a6186c91f2352388cdbf7182..ef1b8714bffbed5105fe993e3aca4b218a501481 100644
--- a/qt/paraview_ext/PVPlugins/Representations/AlignedThreeSliceFilter.cxx
+++ b/qt/paraview_ext/PVPlugins/Representations/AlignedThreeSliceFilter.cxx
@@ -18,7 +18,7 @@
#include "vtkAppendPolyData.h"
#include "vtkPlane.h"
-#include <math.h>
+#include <cmath>
vtkStandardNewMacro(AlignedThreeSliceFilter);
diff --git a/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.cxx b/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.cxx
index 5edce31a5ca28f8bd51dd5e665328918a6ae98b2..f7230cb6108e7c2ed40086ca3adf9b895b1c9ec6 100644
--- a/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.cxx
+++ b/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.cxx
@@ -85,7 +85,7 @@ public:
return true;
}
static bool ExtractCachedBounds(vtkDataObject *dataObject, double bounds[6]) {
- if (dataObject == NULL || dataObject->GetFieldData() == NULL) {
+ if (dataObject == nullptr || dataObject->GetFieldData() == nullptr) {
return false;
}
vtkFieldData *fd = dataObject->GetFieldData();
@@ -108,9 +108,8 @@ public:
static vtkGSRGeometryFilter *New();
vtkTypeMacro(vtkGSRGeometryFilter, vtkPVGeometryFilter);
- virtual int RequestData(vtkInformation *req,
- vtkInformationVector **inputVector,
- vtkInformationVector *outputVector) VTK_OVERRIDE {
+ int RequestData(vtkInformation *req, vtkInformationVector **inputVector,
+ vtkInformationVector *outputVector) VTK_OVERRIDE {
vtkSmartPointer<vtkDataObject> inputDO =
vtkDataObject::GetData(inputVector[0]);
vtkSmartPointer<vtkMatrix4x4> changeOfBasisMatrix =
@@ -165,7 +164,7 @@ public:
protected:
vtkGSRGeometryFilter() {}
- virtual ~vtkGSRGeometryFilter() {}
+ ~vtkGSRGeometryFilter() override {}
private:
vtkGSRGeometryFilter(const vtkGSRGeometryFilter &);
@@ -214,7 +213,7 @@ void vtkAlignedGeometrySliceRepresentation::SetupDefaults() {
this->Internals->OutlineSource->GetOutputPort());
this->Internals->OutlineActor->SetMapper(
this->Internals->OutlineMapper.GetPointer());
- this->Internals->OutlineActor->SetUseBounds(0);
+ this->Internals->OutlineActor->SetUseBounds(false);
this->Internals->OutlineActor->SetVisibility(0);
}
diff --git a/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.h b/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.h
index 1e24e767c3bd85c30b843c992bfb12c348d4e559..9bfad8b3434ab0b91ab862237de9435cfb4765f2 100644
--- a/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.h
+++ b/qt/paraview_ext/PVPlugins/Representations/vtkAlignedGeometrySliceRepresentation.h
@@ -35,9 +35,9 @@ public:
vtkGeometryRepresentation);
void PrintSelf(ostream &os, vtkIndent indent) VTK_OVERRIDE;
- virtual int ProcessViewRequest(vtkInformationRequestKey *request_type,
- vtkInformation *inInfo,
- vtkInformation *outInfo) VTK_OVERRIDE;
+ int ProcessViewRequest(vtkInformationRequestKey *request_type,
+ vtkInformation *inInfo,
+ vtkInformation *outInfo) VTK_OVERRIDE;
enum { X_SLICE_ONLY, Y_SLICE_ONLY, Z_SLICE_ONLY, ALL_SLICES };
vtkSetClampMacro(Mode, int, X_SLICE_ONLY, ALL_SLICES);
@@ -53,15 +53,14 @@ public:
protected:
vtkAlignedGeometrySliceRepresentation();
- ~vtkAlignedGeometrySliceRepresentation();
+ ~vtkAlignedGeometrySliceRepresentation() override;
- virtual void SetupDefaults() VTK_OVERRIDE;
- virtual int RequestData(vtkInformation *request,
- vtkInformationVector **inputVector,
- vtkInformationVector *outputVector) VTK_OVERRIDE;
+ void SetupDefaults() VTK_OVERRIDE;
+ int RequestData(vtkInformation *request, vtkInformationVector **inputVector,
+ vtkInformationVector *outputVector) VTK_OVERRIDE;
- virtual bool AddToView(vtkView *view) VTK_OVERRIDE;
- virtual bool RemoveFromView(vtkView *view) VTK_OVERRIDE;
+ bool AddToView(vtkView *view) VTK_OVERRIDE;
+ bool RemoveFromView(vtkView *view) VTK_OVERRIDE;
private:
vtkAlignedGeometrySliceRepresentation(
diff --git a/qt/paraview_ext/VatesAPI/src/EventNexusLoadingPresenter.cpp b/qt/paraview_ext/VatesAPI/src/EventNexusLoadingPresenter.cpp
index 72f9f932108be9198b967126a34b4757b1d3aa21..301e885bcd6d0fed8a3ddfa8f77a8a91eb3ccf92 100644
--- a/qt/paraview_ext/VatesAPI/src/EventNexusLoadingPresenter.cpp
+++ b/qt/paraview_ext/VatesAPI/src/EventNexusLoadingPresenter.cpp
@@ -44,7 +44,7 @@ EventNexusLoadingPresenter::EventNexusLoadingPresenter(
*/
bool EventNexusLoadingPresenter::canReadFile() const {
if (!canLoadFileBasedOnExtension(m_filename, ".nxs")) {
- return 0;
+ return false;
}
std::unique_ptr<NeXus::File> file;
@@ -55,7 +55,7 @@ bool EventNexusLoadingPresenter::canReadFile() const {
file->openGroup("entry", "NXentry");
} catch (::NeXus::Exception &) {
file->close();
- return 0;
+ return false;
}
// But only eventNexus files have bank123_events as a group name
std::map<std::string, std::string> entries = file->getEntries();
@@ -74,7 +74,7 @@ bool EventNexusLoadingPresenter::canReadFile() const {
if (file)
file->close();
}
- return 0;
+ return false;
}
/*
diff --git a/qt/paraview_ext/VatesAPI/src/MDEWEventNexusLoadingPresenter.cpp b/qt/paraview_ext/VatesAPI/src/MDEWEventNexusLoadingPresenter.cpp
index 81cc8b7afd0a2764e51dec715f01108be679c5ea..02d1db6ebf552f3778e264aca8b201e7429a107d 100644
--- a/qt/paraview_ext/VatesAPI/src/MDEWEventNexusLoadingPresenter.cpp
+++ b/qt/paraview_ext/VatesAPI/src/MDEWEventNexusLoadingPresenter.cpp
@@ -43,19 +43,19 @@ is attempted to be loaded.
bool MDEWEventNexusLoadingPresenter::canReadFile() const {
// Quick check based on extension.
if (!canLoadFileBasedOnExtension(m_filename, ".nxs")) {
- return 0;
+ return false;
}
auto file = Kernel::make_unique<::NeXus::File>(this->m_filename);
// MDEventWorkspace file has a different name for the entry
try {
file->openGroup("MDEventWorkspace", "NXentry");
- return 1;
+ return true;
} catch (::NeXus::Exception &) {
// If the entry name does not match, then it can't read the file.
- return 0;
+ return false;
}
- return 0;
+ return false;
}
/*
diff --git a/qt/paraview_ext/VatesAPI/src/MDHWNexusLoadingPresenter.cpp b/qt/paraview_ext/VatesAPI/src/MDHWNexusLoadingPresenter.cpp
index e8654c3c990a163327961a2d90c1ba6170b48bfa..92eaa9ad25f37c84016930f9d38dceac933a4f5e 100644
--- a/qt/paraview_ext/VatesAPI/src/MDHWNexusLoadingPresenter.cpp
+++ b/qt/paraview_ext/VatesAPI/src/MDHWNexusLoadingPresenter.cpp
@@ -43,18 +43,18 @@ MDHWNexusLoadingPresenter::MDHWNexusLoadingPresenter(
bool MDHWNexusLoadingPresenter::canReadFile() const {
// Quick check based on extension.
if (!canLoadFileBasedOnExtension(m_filename, ".nxs")) {
- return 0;
+ return false;
}
auto file = Kernel::make_unique<::NeXus::File>(this->m_filename);
// MDHistoWorkspace file has a different name for the entry
try {
file->openGroup("MDHistoWorkspace", "NXentry");
- return 1;
+ return true;
} catch (::NeXus::Exception &) {
// If the entry name does not match, then it can't read the file.
- return 0;
+ return false;
}
- return 0;
+ return false;
}
/**
diff --git a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/pqCameraToolbarNonOrthogonalAxes.ui b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/pqCameraToolbarNonOrthogonalAxes.ui
index 47b7da8e99a439e29e7d02800b7fbabbd553ab7e..caebcfff948f4be1869707e1eaa0891502e3d932 100644
--- a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/pqCameraToolbarNonOrthogonalAxes.ui
+++ b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/pqCameraToolbarNonOrthogonalAxes.ui
@@ -21,8 +21,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqResetCamera.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqResetCamera.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqResetCamera.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqResetCamera.png</iconset>
</property>
<property name="text">
<string>&Reset</string>
@@ -39,8 +39,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqXPlus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqXPlus.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqXPlus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqXPlus.png</iconset>
</property>
<property name="text">
<string>+U</string>
@@ -60,8 +60,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqXMinus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqXMinus.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqXMinus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqXMinus.png</iconset>
</property>
<property name="text">
<string>-U</string>
@@ -81,8 +81,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqYPlus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqYPlus.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqYPlus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqYPlus.png</iconset>
</property>
<property name="text">
<string>+V</string>
@@ -102,8 +102,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqYMinus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqYMinus.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqYMinus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqYMinus.png</iconset>
</property>
<property name="text">
<string>-V</string>
@@ -123,8 +123,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZPlus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZPlus.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZPlus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZPlus.png</iconset>
</property>
<property name="text">
<string>+W</string>
@@ -144,8 +144,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZMinus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZMinus.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZMinus.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZMinus.png</iconset>
</property>
<property name="text">
<string>-W</string>
@@ -165,8 +165,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqRotateCameraCW.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqRotateCameraCW.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqRotateCameraCW.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqRotateCameraCW.png</iconset>
</property>
<property name="text">
<string/>
@@ -186,8 +186,8 @@
<bool>false</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqRotateCameraCCW.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqRotateCameraCCW.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqRotateCameraCCW.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqRotateCameraCCW.png</iconset>
</property>
<property name="text">
<string/>
@@ -207,8 +207,8 @@
<bool>true</bool>
</property>
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZoomToSelection.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZoomToSelection.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZoomToSelection.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZoomToSelection.png</iconset>
</property>
<property name="text">
<string>Zoom to Box</string>
@@ -219,8 +219,8 @@
</action>
<action name="actionZoomToData">
<property name="icon">
- <iconset resource="../../icons/ViewWidgetsIcons.qrc">
- <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZoomToData.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqWidgets/Icons/pqZoomToData.png</iconset>
+ <iconset resource="../../../../../resources/icons/ViewWidgetsIcons.qrc">
+ <normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZoomToData.png</normaloff>:/VatesSimpleGuiViewWidgets/icons/pqZoomToData.png</iconset>
</property>
<property name="text">
<string>ZTD</string>
@@ -242,7 +242,7 @@
<addaction name="actionRotate90degCCW"/>
</widget>
<resources>
- <include location="../../icons/ViewWidgetsIcons.qrc"/>
+ <include location="../../../../../resources/icons/ViewWidgetsIcons.qrc"/>
</resources>
<connections/>
</ui>
diff --git a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraReactionNonOrthogonalAxes.cpp b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraReactionNonOrthogonalAxes.cpp
index 75b67ee37970f2714b40fca42a7e3e9bb41fe101..bf37322877cfa255ab623cbd0e0521b1f17d7ac0 100644
--- a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraReactionNonOrthogonalAxes.cpp
+++ b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraReactionNonOrthogonalAxes.cpp
@@ -93,7 +93,7 @@ void pqCameraReactionNonOrthogonalAxes::updateEnableState() {
this->parentAction()->setEnabled(true);
} else if (rview) {
if (this->ReactionMode == ZOOM_TO_DATA) {
- this->parentAction()->setEnabled(source != 0);
+ this->parentAction()->setEnabled(source != nullptr);
} else {
// Check hints to see if actions should be disabled
bool cameraResetButtonsEnabled = true;
diff --git a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraToolbarNonOrthogonalAxes.cpp b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraToolbarNonOrthogonalAxes.cpp
index 1b9410c7dffefc0e3974689cbfe763d803092a61..9482ec1aa71da8e20962e34b1ae989c0bf39f188 100644
--- a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraToolbarNonOrthogonalAxes.cpp
+++ b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/pqCameraToolbarNonOrthogonalAxes.cpp
@@ -68,7 +68,7 @@ void pqCameraToolbarNonOrthogonalAxes::constructor() {
this->ZoomToDataAction = ui.actionZoomToData;
this->ZoomToDataAction->setEnabled(
- pqActiveObjects::instance().activeSource() != 0);
+ pqActiveObjects::instance().activeSource() != nullptr);
QObject::connect(&pqActiveObjects::instance(), SIGNAL(viewChanged(pqView *)),
this, SLOT(updateEnabledState()));
diff --git a/qt/scientific_interfaces/Indirect/ConvFit.cpp b/qt/scientific_interfaces/Indirect/ConvFit.cpp
index 2d2d75f432fa5485feffb6fc5857a27e3384fdae..f1cd772b7255fdee13a4fb8e87f39cf6a8ca4677 100644
--- a/qt/scientific_interfaces/Indirect/ConvFit.cpp
+++ b/qt/scientific_interfaces/Indirect/ConvFit.cpp
@@ -7,6 +7,8 @@
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/FunctionDomain1D.h"
#include "MantidAPI/FunctionFactory.h"
+#include "MantidAPI/ITableWorkspace.h"
+#include "MantidAPI/TableRow.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidGeometry/Instrument.h"
@@ -171,7 +173,7 @@ void ConvFit::setup() {
// Replot input automatically when file / spec no changes
connect(m_uiForm.spPlotSpectrum, SIGNAL(valueChanged(int)), this,
- SLOT(updatePlot()));
+ SLOT(plotSpecChanged(int)));
connect(m_uiForm.dsSampleInput, SIGNAL(dataReady(const QString &)), this,
SLOT(newDataLoaded(const QString &)));
@@ -207,7 +209,9 @@ void ConvFit::setup() {
connect(m_uiForm.pbPlotPreview, SIGNAL(clicked()), this,
SLOT(plotCurrentPreview()));
+ m_uiForm.ckTieCentres->setChecked(true);
m_previousFit = m_uiForm.cbFitType->currentText();
+ m_fittedIndex = -1;
updatePlotOptions();
}
@@ -315,6 +319,7 @@ IAlgorithm_sptr ConvFit::sequentialFit(const std::string &specMin,
// Add fit specific suffix
const auto bgType = backgroundString();
const auto fitType = fitTypeString();
+ m_fittedIndex = m_uiForm.cbFitType->currentIndex();
outputWSName += "conv_";
outputWSName += fitType;
outputWSName += bgType;
@@ -442,15 +447,19 @@ void ConvFit::plotCurrentPreview() {
*/
void ConvFit::algorithmComplete(bool error, const QString &outputWSName) {
- if (error)
+ if (error) {
+ m_fittedIndex = -1;
return;
+ }
+
+ std::string outputPrefix = outputWSName.toStdString();
- const auto resultName = outputWSName.toStdString() + "_Result";
+ const auto resultName = outputPrefix + "_Result";
MatrixWorkspace_sptr resultWs =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(resultName);
// Name for GroupWorkspace
- const auto groupName = outputWSName.toStdString() + "_Workspaces";
+ const auto groupName = outputPrefix + "_Workspaces";
// Add Sample logs for ResolutionFiles
const auto resFile = m_uiForm.dsResInput->getCurrentDataName().toStdString();
addSampleLogsToWorkspace(resultName, "resolution_filename", resFile,
@@ -481,6 +490,15 @@ void ConvFit::algorithmComplete(bool error, const QString &outputWSName) {
}
m_batchAlgoRunner->executeBatchAsync();
updatePlot();
+
+ std::string paramWsName = outputPrefix + "_Parameters";
+
+ if (AnalysisDataService::Instance().doesExist(paramWsName)) {
+ m_paramWs = AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(
+ paramWsName);
+ updateParameters(m_uiForm.spPlotSpectrum->value());
+ }
+
m_uiForm.pbSave->setEnabled(true);
m_uiForm.pbPlot->setEnabled(true);
}
@@ -1174,29 +1192,170 @@ void ConvFit::updatePlot() {
}
// If there is a result workspace plot then plot it
- const auto groupName = m_baseName.toStdString() + "_Workspaces";
-
- if (AnalysisDataService::Instance().doesExist(groupName)) {
- WorkspaceGroup_sptr outputGroup =
- AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(groupName);
- if (specNo - m_runMin >= static_cast<int>(outputGroup->size()))
- return;
- if ((specNo - m_runMin) >= 0) {
- MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
- outputGroup->getItem(specNo - m_runMin));
- if (ws) {
- m_previewPlotData = 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);
- }
+ const auto baseGroupName = m_baseName.toStdString() + "_Workspaces";
+ const auto singleGroupName =
+ m_singleFitOutputName.toStdString() + "_Workspaces";
+
+ if (AnalysisDataService::Instance().doesExist(baseGroupName)) {
+ plotOutput(baseGroupName, specNo);
+ } else if (AnalysisDataService::Instance().doesExist(singleGroupName)) {
+ plotOutput(singleGroupName, specNo);
+ }
+}
+
+/*
+ * Plots the specified spectrum of the output group workspace witht the
+ *specified name;
+ * created from Convolution Fitting.
+ *
+ * @param outputWsName The name of the output workspace whose data to plot.
+ * @param specNo The spectrum number to plot from the output workspace.
+ */
+void ConvFit::plotOutput(std::string const &outputWsName, int specNo) {
+ WorkspaceGroup_sptr outputGroup =
+ AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputWsName);
+ if (specNo - m_runMin >= static_cast<int>(outputGroup->size()))
+ return;
+ if ((specNo - m_runMin) >= 0) {
+ MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
+ outputGroup->getItem(specNo - m_runMin));
+ if (ws) {
+ m_previewPlotData = 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);
}
}
}
}
+void ConvFit::updateParameters(int specNo) {
+ // Check parameter table workspace has been created
+ if (!m_paramWs)
+ return;
+
+ size_t row = boost::numeric_cast<size_t>(specNo - m_runMin);
+
+ std::vector<std::string> columnNames = m_paramWs->getColumnNames();
+ QMap<QString, double> parameters;
+
+ for (size_t column = 0; column < columnNames.size(); ++column) {
+ double value = m_paramWs->Double(row, column);
+ parameters.insert(QString::fromStdString(columnNames[column]), value);
+ }
+
+ QString functionName = m_uiForm.cbFitType->currentText();
+
+ QStringList params = getFunctionParameters(functionName);
+ params.reserve(static_cast<int>(parameters.size()));
+
+ // Populate Tree widget with values
+ // Background should always be f0
+ m_dblManager->setValue(m_properties["BGA0"], parameters["f0.A0"]);
+ m_dblManager->setValue(m_properties["BGA1"], parameters["f0.A1"]);
+
+ const int fitTypeIndex = m_uiForm.cbFitType->currentIndex();
+
+ int funcIndex = 0;
+ int subIndex = 0;
+
+ // check if we're using a temperature correction
+ if (m_uiForm.ckTempCorrection->isChecked() &&
+ !m_uiForm.leTempCorrection->text().isEmpty()) {
+ subIndex++;
+ }
+
+ const bool usingDeltaFunc = m_blnManager->value(m_properties["UseDeltaFunc"]);
+
+ // If using a delta function with any fit type or using two Lorentzians
+ const bool usingCompositeFunc =
+ ((usingDeltaFunc && m_fittedIndex > 0) || m_fittedIndex == 2);
+
+ const QString prefBase = "f1.f1.";
+
+ if (usingDeltaFunc) {
+ QString key = prefBase;
+ if (usingCompositeFunc) {
+ key += "f0.";
+ }
+
+ m_dblManager->setValue(m_properties["DeltaHeight"],
+ parameters[key + "Height"]);
+ m_dblManager->setValue(m_properties["DeltaCentre"],
+ parameters[key + "Centre"]);
+ funcIndex++;
+ }
+
+ QString pref = prefBase;
+
+ if (usingCompositeFunc) {
+ pref += "f" + QString::number(funcIndex) + ".f" +
+ QString::number(subIndex) + ".";
+ } else {
+ pref += "f" + QString::number(subIndex) + ".";
+ }
+
+ if (fitTypeIndex == 2 && m_fittedIndex == 2) {
+ functionName = "Lorentzian 1";
+ updateParameters(functionName, pref, params, parameters, 0, 3);
+
+ funcIndex++;
+ pref = prefBase;
+ pref += "f" + QString::number(funcIndex) + ".f" +
+ QString::number(subIndex) + ".";
+
+ functionName = "Lorentzian 2";
+ updateParameters(functionName, pref, params, parameters, 3, 0);
+ } else {
+
+ if (fitTypeIndex == 2 && m_fittedIndex == 1) {
+ functionName = "Lorentzian 1";
+ }
+
+ updateParameters(functionName, pref, params, parameters);
+ }
+}
+
+/*
+ * Updates the values of the function parameters for the function with the
+ *specified name,
+ * in the parameters table.
+ *
+ * @param functionName The name of the function whose parameters to update in
+ *the parameters
+ * table.
+ *
+ * @param prefix The prefixes of the names of the parameters, to be used
+ *to find the
+ * correct parameter in the specified parameter values map.
+ * @param paramNames The names of the function parameters to update.
+ * @param paramValues The updated parameter values stored in a map from the
+ *name of the
+ * function parameter (preceded by prefix) to the updated
+ *value of that
+ * parameter.
+ * @param startOffset The start offset, if set to N, the first N parameters
+ *won't be updated.
+ * @param endOffset The end offset, if set to N, the last N parameters won't
+ *be updated.
+ */
+void ConvFit::updateParameters(const QString &functionName,
+ const QString &prefix,
+ const QStringList ¶mNames,
+ const QMap<QString, double> ¶mValues,
+ int startOffset, int endOffset) {
+
+ for (auto it = paramNames.begin() + startOffset;
+ it != paramNames.end() - endOffset; ++it) {
+ const QString functionParam = functionName + "." + *it;
+ const QString paramValue = prefix + *it;
+ double value = paramValues[paramValue];
+ m_dblManager->setValue(m_properties[functionParam], value);
+ }
+}
+
/**
* Updates the guess for the plot
*/
@@ -1269,12 +1428,15 @@ void ConvFit::singleFit() {
SLOT(singleFit(bool)));
// ensure algorithm was successful
m_uiForm.ckPlotGuess->setChecked(false);
- std::string specNo = m_uiForm.spPlotSpectrum->text().toStdString();
+ int specNo = m_uiForm.spPlotSpectrum->value();
+ m_runMin = specNo;
+ m_runMax = specNo;
+ std::string specNoStr = m_uiForm.spPlotSpectrum->text().toStdString();
- m_singleFitAlg = sequentialFit(specNo, specNo, m_singleFitOutputName);
+ auto cfs = sequentialFit(specNoStr, specNoStr, m_singleFitOutputName);
// Connection to singleFitComplete SLOT (post algorithm completion)
- m_batchAlgoRunner->addAlgorithm(m_singleFitAlg);
+ m_batchAlgoRunner->addAlgorithm(cfs);
connect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(singleFitComplete(bool)));
m_batchAlgoRunner->executeBatchAsync();
@@ -1292,6 +1454,16 @@ void ConvFit::singleFitComplete(bool error) {
algorithmComplete(error, m_singleFitOutputName);
}
+void ConvFit::plotSpecChanged(int value) {
+ updatePlot();
+
+ if (value < m_runMin || value > m_runMax) {
+ fitFunctionSelected(m_uiForm.cbFitType->currentText());
+ } else {
+ updateParameters(value);
+ }
+}
+
/**
* Handles the user entering a new minimum spectrum index.
*
@@ -1601,19 +1773,26 @@ void ConvFit::fitFunctionSelected(const QString &functionName) {
m_defaultParams["FWHM"] = res;
m_defaultParams["default_FWHM"] = res;
}
+
// If the previous fit was One Lorentzian and the new fit is Two Lorentzian
// preserve the values of One Lorentzian Fit
const QString currentFitFunction = m_uiForm.cbFitType->currentText();
- if (m_previousFit.compare("One Lorentzian") == 0 &&
- currentFitFunction.compare("Two Lorentzians") == 0) {
- const double amplitude =
- m_dblManager->value(m_properties["Lorentzian 1.Amplitude"]);
- const double peakCentre =
- m_dblManager->value(m_properties["Lorentzian 1.PeakCentre"]);
- const double fwhm = m_dblManager->value(m_properties["Lorentzian 1.FWHM"]);
- m_defaultParams.insert("PeakCentre", peakCentre);
- m_defaultParams.insert("FWHM", fwhm);
- m_defaultParams.insert("Amplitude", amplitude);
+ if (currentFitFunction.compare("Two Lorentzians") == 0) {
+ m_uiForm.ckTieCentres->setChecked(true);
+
+ if (m_previousFit.compare("One Lorentzian") == 0) {
+ const double amplitude =
+ m_dblManager->value(m_properties["One Lorentzian.Amplitude"]);
+ const double peakCentre =
+ m_dblManager->value(m_properties["One Lorentzian.PeakCentre"]);
+ const double fwhm =
+ m_dblManager->value(m_properties["One Lorentzian.FWHM"]);
+ m_defaultParams.insert("PeakCentre", peakCentre);
+ m_defaultParams.insert("FWHM", fwhm);
+ m_defaultParams.insert("Amplitude", amplitude);
+ }
+ } else {
+ m_uiForm.ckTieCentres->setChecked(false);
}
// Remove previous parameters from tree
@@ -1621,7 +1800,6 @@ void ConvFit::fitFunctionSelected(const QString &functionName) {
m_cfTree->removeProperty(m_properties["FitFunction2"]);
m_uiForm.ckPlotGuess->setChecked(false);
- m_uiForm.ckTieCentres->setChecked(false);
updatePlotOptions();
@@ -1690,17 +1868,18 @@ void ConvFit::updatePlotOptions() {
plotOptions << "Height";
}
- QStringList params;
-
- if (fitFunctionType != 2) {
- params = getFunctionParameters(m_uiForm.cbFitType->currentText());
- } else {
- params = getFunctionParameters(QString("One Lorentzian"));
- }
- if (fitFunctionType < 3 && fitFunctionType != 0) {
- params.removeAll("PeakCentre");
- }
if (fitFunctionType != 0) {
+ QStringList params;
+
+ if (fitFunctionType != 2) {
+ params = getFunctionParameters(m_uiForm.cbFitType->currentText());
+ } else {
+ params = getFunctionParameters(QString("One Lorentzian"));
+ }
+ if (fitFunctionType < 3) {
+ params.removeAll("PeakCentre");
+ }
+
plotOptions.append(params);
}
diff --git a/qt/scientific_interfaces/Indirect/ConvFit.h b/qt/scientific_interfaces/Indirect/ConvFit.h
index 57bf31a68ac91b4738ffb20da0dba594d4f56b67..95d798c89dce57fe8e010a17c6ccfe608e4e2489 100644
--- a/qt/scientific_interfaces/Indirect/ConvFit.h
+++ b/qt/scientific_interfaces/Indirect/ConvFit.h
@@ -29,6 +29,7 @@ private slots:
void updatePlot();
void plotGuess();
void singleFit();
+ void plotSpecChanged(int value);
void specMinChanged(int value);
void specMaxChanged(int value);
void minChanged(double);
@@ -63,7 +64,13 @@ private:
QString backgroundString() const;
QString minimizerString(QString outputName) const;
QStringList getFunctionParameters(QString);
+ void updateParameters(int specNo);
+ void updateParameters(const QString &functionName, const QString &prefix,
+ const QStringList ¶mNames,
+ const QMap<QString, double> ¶mValues,
+ int startOffset = 0, int endOffset = 0);
void updatePlotOptions();
+ void plotOutput(std::string const &outputWs, int specNo);
void addParametersToTree(const QStringList ¶meters,
const QString ¤tFitFunction);
void addSampleLogsToWorkspace(const std::string &workspaceName,
@@ -85,9 +92,10 @@ private:
// Pointer to sample workspace object
Mantid::API::MatrixWorkspace_sptr m_cfInputWS;
Mantid::API::MatrixWorkspace_sptr m_previewPlotData;
+ Mantid::API::ITableWorkspace_sptr m_paramWs;
QString m_cfInputWSName;
+ int m_fittedIndex;
bool m_confitResFileType;
- Mantid::API::IAlgorithm_sptr m_singleFitAlg;
QString m_singleFitOutputName;
QString m_previousFit;
QString m_baseName;
diff --git a/qt/widgets/common/inc/MantidQtWidgets/Common/PythonSystemHeader.h b/qt/widgets/common/inc/MantidQtWidgets/Common/PythonSystemHeader.h
index 155a2b1a675692f8561470ddb46d4f8e21f99806..f12bd91a498bd53510ab275d75761b71a7fb33fa 100644
--- a/qt/widgets/common/inc/MantidQtWidgets/Common/PythonSystemHeader.h
+++ b/qt/widgets/common/inc/MantidQtWidgets/Common/PythonSystemHeader.h
@@ -22,6 +22,7 @@
#define TO_CSTRING _PyUnicode_AsString
#define FROM_CSTRING PyUnicode_FromString
#define CODE_OBJECT(x) x
+#define GET_CURRENT_THREADSTATE _PyThreadState_UncheckedGet()
#else
#define INT_CHECK PyInt_Check
#define TO_LONG PyInt_AsLong
@@ -29,6 +30,7 @@
#define TO_CSTRING PyString_AsString
#define FROM_CSTRING PyString_FromString
#define CODE_OBJECT(x) (PyCodeObject *) x
+#define GET_CURRENT_THREADSTATE _PyThreadState_Current
#endif
#endif // PYTHONSYSTEMHEADER_H_
diff --git a/qt/widgets/common/inc/MantidQtWidgets/Common/PythonThreading.h b/qt/widgets/common/inc/MantidQtWidgets/Common/PythonThreading.h
index 2b33468c29e1630382a803019529e11b63287473..bbe1cd475981d24e6fbdeb2bb421e1f7afa8bdf0 100644
--- a/qt/widgets/common/inc/MantidQtWidgets/Common/PythonThreading.h
+++ b/qt/widgets/common/inc/MantidQtWidgets/Common/PythonThreading.h
@@ -4,6 +4,15 @@
#include "MantidQtWidgets/Common/PythonSystemHeader.h" // this needs to go first
#include "MantidQtWidgets/Common/DllOption.h"
+//------------------------------------------------------------------------------
+// Python Interpreter
+//------------------------------------------------------------------------------
+class EXPORT_OPT_MANTIDQT_COMMON PythonInterpreter {
+public:
+ static void initialize();
+ static void finalize();
+};
+
//------------------------------------------------------------------------------
// PythonGIL
//------------------------------------------------------------------------------
@@ -13,18 +22,20 @@
*
*/
class EXPORT_OPT_MANTIDQT_COMMON PythonGIL {
+
+public:
+ static bool locked();
+
public:
PythonGIL();
+ PythonGIL(const PythonGIL &) = delete;
+ PythonGIL &operator=(const PythonGIL &) = delete;
- inline bool locked() const { return m_acquired; }
void acquire();
void release();
private:
- PythonGIL(const PythonGIL &);
- /// Current GIL state
PyGILState_STATE m_state;
- bool m_acquired;
};
//------------------------------------------------------------------------------
diff --git a/qt/widgets/common/src/PythonThreading.cpp b/qt/widgets/common/src/PythonThreading.cpp
index cbe5dd54c54240a5471605a0015394491d1c7c2a..e7931684660ecc489d344b188c4ddbb9904e99cf 100644
--- a/qt/widgets/common/src/PythonThreading.cpp
+++ b/qt/widgets/common/src/PythonThreading.cpp
@@ -2,36 +2,55 @@
// Includes
//------------------------------------------------------------------------------
#include "MantidQtWidgets/Common/PythonThreading.h"
-#include <iostream>
-#include <QThread>
+namespace {
+PyThreadState *INITIAL_TS = nullptr;
+}
+
+//------------------------------------------------------------------------------
+// PythonInterpreter Public members
+//------------------------------------------------------------------------------
+void PythonInterpreter::initialize() {
+ Py_Initialize();
+ PyEval_InitThreads();
+ // Release GIL
+ INITIAL_TS = PyEval_SaveThread();
+}
+
+// Finalize the Python process. The GIL must be held to
+// call this function but after it completes calling
+// any python functions is undefined behaviour
+void PythonInterpreter::finalize() { Py_Finalize(); }
//------------------------------------------------------------------------------
// PythonGIL Public members
//------------------------------------------------------------------------------
+/**
+ * Check if the current thread has the lock
+ * @return True if the current thread holds the GIL, false otherwise
+ */
+bool PythonGIL::locked() {
+ PyThreadState *ts = GET_CURRENT_THREADSTATE;
+ return (ts && ts == PyGILState_GetThisThreadState());
+}
+
/**
* Leaves the lock unlocked. You are strongly encouraged to use
* the ScopedInterpreterLock class to control this
*/
-PythonGIL::PythonGIL() : m_state(PyGILState_UNLOCKED), m_acquired(false) {}
+PythonGIL::PythonGIL() : m_state(PyGILState_UNLOCKED) {}
/**
* Calls PyGILState_Ensure. A call to this must be matched by a call to release
* on the same thread.
*/
-void PythonGIL::acquire() {
- m_state = PyGILState_Ensure();
- m_acquired = true;
-}
+void PythonGIL::acquire() { m_state = PyGILState_Ensure(); }
/**
* Calls PyGILState_Release
*/
-void PythonGIL::release() {
- PyGILState_Release(m_state);
- m_acquired = false;
-}
+void PythonGIL::release() { PyGILState_Release(m_state); }
//------------------------------------------------------------------------------
// RecursivePythonGIL public members
diff --git a/scripts/reduction_workflow/instruments/sans/sns_command_interface.py b/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
index 5af57ec224172740e5d2d05781241ba7f22123b1..8c8ba289f485695cc12f9ae6adec877430fc7f90 100644
--- a/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
+++ b/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
@@ -125,3 +125,11 @@ def Resolution(sample_aperture_diameter=10.0):
def IndependentBinning(independent_binning=True):
ReductionSingleton().reduction_properties["IQIndependentBinning"]=independent_binning
+
+
+def SetDetectorOffset(distance):
+ ReductionSingleton().reduction_properties["DetectorOffset"] = distance
+
+
+def SetSampleOffset(distance):
+ ReductionSingleton().reduction_properties["SampleOffset"] = distance