diff --git a/CMakeLists.txt b/CMakeLists.txt
index b20fb6d69efe22032e0da05f04dc867356bedfd5..e4d2d6906b29352526f8ef24ba85c80810fd9750 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -301,7 +301,7 @@ if ( ENABLE_CPACK )
set( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},OCE-draw,OCE-foundation,OCE-modeling,OCE-ocaf,OCE-visualization")
set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},poco-crypto,poco-data,poco-mysql,poco-sqlite,poco-odbc,poco-util,poco-xml,poco-zip,poco-net,poco-netssl,poco-foundation,PyQt4" )
set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},sip >= 4.18" )
- set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},python-six,python-ipython >= 1.1.0,python-ipython-notebook,PyYAML" )
+ set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},python-six,python-ipython >= 1.1.0,python-ipython-notebook,PyYAML,python2-psutil" )
# scipy
set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},scipy" )
set ( CPACK_RPM_PACKAGE_REQUIRES "${CPACK_RPM_PACKAGE_REQUIRES},mxml,hdf,hdf5,jsoncpp >= 0.7.0" )
@@ -361,7 +361,8 @@ if ( ENABLE_CPACK )
"libhdf5-cpp-11,"
"python-pycifrw (>= 4.2.1),"
"python-yaml,"
- "python-qtawesome")
+ "python-qtawesome,"
+ "python-psutil")
set ( PERFTOOLS_DEB_PACKAGE "libgoogle-perftools4 (>= 1.7)" )
if( "${UNIX_CODENAME}" STREQUAL "bionic")
list ( APPEND DEPENDS_LIST ",libgsl23,liboce-foundation11,liboce-modeling11,libqscintilla2-qt4-13,jupyter-notebook,libhdf5-cpp-100")
diff --git a/Framework/API/src/ScriptBuilder.cpp b/Framework/API/src/ScriptBuilder.cpp
index d852516ec45cb830b9e4041fa03b3ded94021dad..4b021582bd4b856c4c5294f8b27588fca1042c9e 100644
--- a/Framework/API/src/ScriptBuilder.cpp
+++ b/Framework/API/src/ScriptBuilder.cpp
@@ -12,6 +12,8 @@
#include "MantidKernel/Property.h"
#include "MantidKernel/PropertyHistory.h"
+#include <boost/range/algorithm/remove_if.hpp>
+#include <boost/algorithm/string/classification.hpp>
#include <boost/utility.hpp>
#include <set>
@@ -219,7 +221,10 @@ ScriptBuilder::buildAlgorithmString(const AlgorithmHistory &algHistory) {
propStr.erase(propStr.size() - 1);
}
- return name + "(" + propStr + ")";
+ std::string historyEntry = name + "(" + propStr + ")";
+ historyEntry.erase(boost::remove_if(historyEntry, boost::is_any_of("\n\r")),
+ historyEntry.end());
+ return historyEntry;
}
/**
diff --git a/Framework/API/test/ScriptBuilderTest.h b/Framework/API/test/ScriptBuilderTest.h
index 31e8e8a5bb66a4bc78db0ea85390f7be51c6aa4a..db06f122bdc8bb60bcd8e7e7030bc299ad2260a3 100644
--- a/Framework/API/test/ScriptBuilderTest.h
+++ b/Framework/API/test/ScriptBuilderTest.h
@@ -85,6 +85,38 @@ class ScriptBuilderTest : public CxxTest::TestSuite {
}
};
+ class NewlineAlgorithm : public Algorithm {
+ public:
+ NewlineAlgorithm() : Algorithm() {}
+ ~NewlineAlgorithm() override {}
+ const std::string name() const override { return "Foo\n\rBar"; }
+ const std::string summary() const override { return "Test"; }
+ int version() const override { return 1; }
+ const std::string category() const override { return "Cat;Leopard;Mink"; }
+
+ void afterPropertySet(const std::string &name) override {
+ if (name == "InputWorkspace")
+ declareProperty("DynamicInputProperty", "");
+ }
+
+ void init() override {
+ declareProperty(make_unique<WorkspaceProperty<MatrixWorkspace>>(
+ "InputWorkspace", "", Direction::Input));
+ declareProperty(make_unique<WorkspaceProperty<MatrixWorkspace>>(
+ "OutputWorkspace", "", Direction::Output));
+ declareProperty("PropertyA", "Hello");
+ declareProperty("PropertyB", "World");
+ }
+ void exec() override {
+ declareProperty("DynamicProperty1", "value", Direction::Output);
+ setPropertyValue("DynamicProperty1", "outputValue");
+
+ boost::shared_ptr<MatrixWorkspace> output =
+ boost::make_shared<WorkspaceTester>();
+ setProperty("OutputWorkspace", output);
+ }
+ };
+
// middle layer algorithm executed by a top level algorithm
class NestedAlgorithm : public DataProcessorAlgorithm {
public:
@@ -205,6 +237,7 @@ public:
Mantid::API::AlgorithmFactory::Instance().subscribe<NestedAlgorithm>();
Mantid::API::AlgorithmFactory::Instance().subscribe<BasicAlgorithm>();
Mantid::API::AlgorithmFactory::Instance().subscribe<SubAlgorithm>();
+ Mantid::API::AlgorithmFactory::Instance().subscribe<NewlineAlgorithm>();
Mantid::API::AlgorithmFactory::Instance()
.subscribe<AlgorithmWithDynamicProperty>();
}
@@ -217,6 +250,7 @@ public:
Mantid::API::AlgorithmFactory::Instance().unsubscribe("SubAlgorithm", 1);
Mantid::API::AlgorithmFactory::Instance().unsubscribe(
"AlgorithmWithDynamicProperty", 1);
+ Mantid::API::AlgorithmFactory::Instance().unsubscribe("Foo\n\rBar", 1);
}
void test_Build_Simple() {
@@ -254,6 +288,42 @@ public:
AnalysisDataService::Instance().remove("test_input_workspace");
}
+ void test_newline_chars_removed() {
+ // Check that any newline chars are removed
+ std::string result[] = {"FooBar(InputWorkspace='test_input_workspace',"
+ " OutputWorkspace='test_output_workspace')",
+ ""};
+
+ boost::shared_ptr<WorkspaceTester> input =
+ boost::make_shared<WorkspaceTester>();
+ AnalysisDataService::Instance().addOrReplace("test_input_workspace", input);
+
+ auto alg = AlgorithmFactory::Instance().create("Foo\n\rBar", 1);
+ alg->initialize();
+ alg->setRethrows(true);
+ alg->setProperty("InputWorkspace", input);
+ alg->setPropertyValue("OutputWorkspace", "test_output_workspace");
+ alg->execute();
+
+ auto ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
+ "test_output_workspace");
+ auto wsHist = ws->getHistory();
+
+ ScriptBuilder builder(wsHist.createView());
+ std::string scriptText = builder.build();
+
+ std::vector<std::string> scriptLines;
+ boost::split(scriptLines, scriptText, boost::is_any_of("\n"));
+
+ int i = 0;
+ for (auto it = scriptLines.begin(); it != scriptLines.end(); ++it, ++i) {
+ TS_ASSERT_EQUALS(*it, result[i])
+ }
+
+ AnalysisDataService::Instance().remove("test_output_workspace");
+ AnalysisDataService::Instance().remove("test_input_workspace");
+ }
+
void test_Build_Simple_Timestamped() {
boost::shared_ptr<WorkspaceTester> input =
boost::make_shared<WorkspaceTester>();
diff --git a/Framework/Algorithms/CMakeLists.txt b/Framework/Algorithms/CMakeLists.txt
index d8abd6f6831aba8cff2041d62e64859a05fee2be..81aed1079551058080f4bc89c4c8031e87b1bf94 100644
--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -21,6 +21,7 @@ set ( SRC_FILES
src/CalculateDIFC.cpp
src/CalculateEfficiency.cpp
src/CalculateFlatBackground.cpp
+ src/CalculateIqt.cpp
src/CalculateCarpenterSampleCorrection.cpp
src/CalculatePolynomialBackground.cpp
src/CalculateSlits.cpp
@@ -344,6 +345,7 @@ set ( INC_FILES
inc/MantidAlgorithms/CalculateDIFC.h
inc/MantidAlgorithms/CalculateEfficiency.h
inc/MantidAlgorithms/CalculateFlatBackground.h
+ inc/MantidAlgorithms/CalculateIqt.h
inc/MantidAlgorithms/CalculateCarpenterSampleCorrection.h
inc/MantidAlgorithms/CalculatePolynomialBackground.h
inc/MantidAlgorithms/CalculateSlits.h
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/CalculateIqt.h b/Framework/Algorithms/inc/MantidAlgorithms/CalculateIqt.h
new file mode 100644
index 0000000000000000000000000000000000000000..ff3fbee5bc70b8f33b5a2cfa8070258d511081fc
--- /dev/null
+++ b/Framework/Algorithms/inc/MantidAlgorithms/CalculateIqt.h
@@ -0,0 +1,50 @@
+#ifndef MANTID_ALGORITHMS_CALCULATEIQT_H_
+#define MANTID_ALGORITHMS_CALCULATEIQT_H_
+
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid {
+namespace Algorithms {
+/** Copyright © 2018 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and / or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program.If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at : <https://github.com/mantidproject/mantid>
+ Code Documentation is available at : <http://doxygen.mantidproject.org>
+*/
+
+class DLLExport CalculateIqt : public API::Algorithm {
+public:
+ const std::string name() const override;
+ int version() const override;
+ const std::vector<std::string> seeAlso() 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;
+ std::string rebinParamsAsString();
+ API::MatrixWorkspace_sptr monteCarloErrorCalculation(
+ API::MatrixWorkspace_sptr sample, API::MatrixWorkspace_sptr resolution,
+ const std::string &rebinParams, const int seed, const int nIterations);
+};
+
+} // namespace Algorithms
+} // namespace Mantid
+#endif // MANTID_ALGORITHMS_MONTECARLOABSORPTION_H_
\ No newline at end of file
diff --git a/Framework/Algorithms/src/CalculateIqt.cpp b/Framework/Algorithms/src/CalculateIqt.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f94b61b083b61eb85cf57df8b8433856611b3d55
--- /dev/null
+++ b/Framework/Algorithms/src/CalculateIqt.cpp
@@ -0,0 +1,321 @@
+#include "MantidAlgorithms/CalculateIqt.h"
+#include "MantidAPI/AlgorithmManager.h"
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidHistogramData/HistogramY.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/MersenneTwister.h"
+
+#include <boost/numeric/conversion/cast.hpp>
+#include <cmath>
+#include <functional>
+
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+using namespace Mantid::HistogramData;
+
+namespace {
+constexpr int DEFAULT_ITERATIONS = 100;
+constexpr int DEFAULT_SEED = 89631139;
+
+MatrixWorkspace_sptr rebin(MatrixWorkspace_sptr workspace,
+ const std::string ¶ms) {
+ IAlgorithm_sptr rebinAlgorithm = AlgorithmManager::Instance().create("Rebin");
+ rebinAlgorithm->setChild(true);
+ rebinAlgorithm->initialize();
+ rebinAlgorithm->setProperty("InputWorkspace", workspace);
+ rebinAlgorithm->setProperty("OutputWorkspace", "_");
+ rebinAlgorithm->setProperty("Params", params);
+ rebinAlgorithm->execute();
+ return rebinAlgorithm->getProperty("OutputWorkspace");
+}
+
+MatrixWorkspace_sptr integration(MatrixWorkspace_sptr workspace) {
+ IAlgorithm_sptr integrationAlgorithm =
+ AlgorithmManager::Instance().create("Integration");
+ integrationAlgorithm->setChild(true);
+ integrationAlgorithm->initialize();
+ integrationAlgorithm->setProperty("InputWorkspace", workspace);
+ integrationAlgorithm->setProperty("OutputWorkspace", "_");
+ integrationAlgorithm->execute();
+ return integrationAlgorithm->getProperty("OutputWorkspace");
+}
+
+MatrixWorkspace_sptr convertToPointData(MatrixWorkspace_sptr workspace) {
+ IAlgorithm_sptr pointDataAlgorithm =
+ AlgorithmManager::Instance().create("ConvertToPointData");
+ pointDataAlgorithm->setChild(true);
+ pointDataAlgorithm->initialize();
+ pointDataAlgorithm->setProperty("InputWorkspace", workspace);
+ pointDataAlgorithm->setProperty("OutputWorkspace", "_");
+ pointDataAlgorithm->execute();
+ return pointDataAlgorithm->getProperty("OutputWorkspace");
+}
+
+MatrixWorkspace_sptr extractFFTSpectrum(MatrixWorkspace_sptr workspace) {
+ IAlgorithm_sptr FFTAlgorithm =
+ AlgorithmManager::Instance().create("ExtractFFTSpectrum");
+ FFTAlgorithm->setChild(true);
+ FFTAlgorithm->initialize();
+ FFTAlgorithm->setProperty("InputWorkspace", workspace);
+ FFTAlgorithm->setProperty("OutputWorkspace", "_");
+ FFTAlgorithm->setProperty("FFTPart", 2);
+ FFTAlgorithm->execute();
+ return FFTAlgorithm->getProperty("OutputWorkspace");
+}
+
+MatrixWorkspace_sptr divide(MatrixWorkspace_sptr lhsWorkspace,
+ MatrixWorkspace_sptr rhsWorkspace) {
+ IAlgorithm_sptr divideAlgorithm =
+ AlgorithmManager::Instance().create("Divide");
+ divideAlgorithm->setChild(true);
+ divideAlgorithm->initialize();
+ divideAlgorithm->setProperty("LHSWorkspace", lhsWorkspace);
+ divideAlgorithm->setProperty("RHSWorkspace", rhsWorkspace);
+ divideAlgorithm->setProperty("OutputWorkspace", "_");
+ divideAlgorithm->execute();
+ return divideAlgorithm->getProperty("OutputWorkspace");
+}
+
+MatrixWorkspace_sptr cropWorkspace(MatrixWorkspace_sptr workspace,
+ double xMax) {
+ IAlgorithm_sptr cropAlgorithm =
+ AlgorithmManager::Instance().create("CropWorkspace");
+ cropAlgorithm->setChild(true);
+ cropAlgorithm->initialize();
+ cropAlgorithm->setProperty("InputWorkspace", workspace);
+ cropAlgorithm->setProperty("OutputWorkspace", "_");
+ cropAlgorithm->setProperty("XMax", xMax);
+ cropAlgorithm->execute();
+ return cropAlgorithm->getProperty("OutputWorkspace");
+}
+
+MatrixWorkspace_sptr replaceSpecialValues(MatrixWorkspace_sptr workspace) {
+ IAlgorithm_sptr specialValuesAlgorithm =
+ AlgorithmManager::Instance().create("ReplaceSpecialValues");
+ specialValuesAlgorithm->setChild(true);
+ specialValuesAlgorithm->initialize();
+ specialValuesAlgorithm->setProperty("InputWorkspace", workspace);
+ specialValuesAlgorithm->setProperty("OutputWorkspace", "_");
+ specialValuesAlgorithm->setProperty("InfinityValue", 0.0);
+ specialValuesAlgorithm->setProperty("BigNumberThreshold", 1.0001);
+ specialValuesAlgorithm->setProperty("NaNValue", 0.0);
+ specialValuesAlgorithm->execute();
+ return specialValuesAlgorithm->getProperty("OutputWorkspace");
+}
+
+std::string createRebinString(double minimum, double maximum, double width) {
+ std::stringstream rebinStream;
+ rebinStream.precision(14);
+ rebinStream << minimum << ", " << width << ", " << maximum;
+ return rebinStream.str();
+}
+
+template <typename Generator>
+void randomizeHistogramWithinError(HistogramY &row, const HistogramE &errors,
+ Generator &generator) {
+ for (auto i = 0u; i < row.size(); ++i)
+ row[i] += generator(errors[i]);
+}
+
+MatrixWorkspace_sptr
+randomizeWorkspaceWithinError(MatrixWorkspace_sptr workspace, const int seed) {
+ MersenneTwister mTwister(seed);
+ auto randomNumberGenerator = [&mTwister](const double error) {
+ return mTwister.nextValue(-error, error);
+ };
+ for (auto i = 0u; i < workspace->getNumberHistograms(); ++i)
+ randomizeHistogramWithinError(workspace->mutableY(i), workspace->e(i),
+ randomNumberGenerator);
+ return workspace;
+}
+
+double standardDeviation(const std::vector<double> &inputValues) {
+ const auto inputSize = boost::numeric_cast<double>(inputValues.size());
+ const auto mean =
+ std::accumulate(inputValues.begin(), inputValues.end(), 0.0) / inputSize;
+ double sumOfXMinusMeanSquared = 0;
+ for (auto &&x : inputValues)
+ sumOfXMinusMeanSquared += (x - mean) * (x - mean);
+ return sqrt(sumOfXMinusMeanSquared / (inputSize - 1));
+}
+
+std::vector<double>
+standardDeviationArray(const std::vector<std::vector<double>> &yValues) {
+ std::vector<double> standardDeviations;
+ standardDeviations.reserve(yValues.size());
+ std::transform(yValues.begin(), yValues.end(),
+ std::back_inserter(standardDeviations), standardDeviation);
+ return standardDeviations;
+}
+
+MatrixWorkspace_sptr removeInvalidData(MatrixWorkspace_sptr workspace) {
+ auto binning = (workspace->blocksize() + 1) / 2;
+ auto binV = workspace->x(0)[binning];
+ workspace = cropWorkspace(workspace, binV);
+ return replaceSpecialValues(workspace);
+}
+
+MatrixWorkspace_sptr
+normalizedFourierTransform(MatrixWorkspace_sptr workspace,
+ const std::string &rebinParams) {
+ workspace = rebin(workspace, rebinParams);
+ auto workspace_int = integration(workspace);
+ workspace = convertToPointData(workspace);
+ workspace = extractFFTSpectrum(workspace);
+ return divide(workspace, workspace_int);
+}
+
+MatrixWorkspace_sptr calculateIqt(MatrixWorkspace_sptr workspace,
+ MatrixWorkspace_sptr resolutionWorkspace,
+ const std::string &rebinParams) {
+ workspace = normalizedFourierTransform(workspace, rebinParams);
+ return divide(workspace, resolutionWorkspace);
+}
+
+MatrixWorkspace_sptr doSimulation(MatrixWorkspace_sptr sample,
+ MatrixWorkspace_sptr resolution,
+ const std::string &rebinParams,
+ const int seed) {
+ auto simulatedWorkspace = randomizeWorkspaceWithinError(sample, seed);
+ return calculateIqt(simulatedWorkspace, resolution, rebinParams);
+}
+
+/**
+Get all histograms at a given index from a set of workspaces. Arranges the
+output such that the first vector contains the first value from each workspace,
+the second vector contains all the second values, etc.
+*/
+std::vector<std::vector<double>>
+allYValuesAtIndex(const std::vector<MatrixWorkspace_sptr> &workspaces,
+ const std::size_t index) {
+ std::vector<std::vector<double>> yValues(
+ workspaces[0]->getDimension(0)->getNBins());
+ for (auto &&workspace : workspaces) {
+ const auto values = workspace->y(index).rawData();
+ for (auto j = 0u; j < values.size(); ++j)
+ yValues[j].emplace_back(values[j]);
+ }
+ return yValues;
+}
+
+MatrixWorkspace_sptr setErrorsToStandardDeviation(
+ const std::vector<MatrixWorkspace_sptr> &simulatedWorkspaces) {
+ auto outputWorkspace = simulatedWorkspaces.front();
+ PARALLEL_FOR_IF(Mantid::Kernel::threadSafe(*outputWorkspace))
+ for (int i = 0;
+ i < boost::numeric_cast<int>(outputWorkspace->getNumberHistograms());
+ ++i)
+ outputWorkspace->mutableE(i) =
+ standardDeviationArray(allYValuesAtIndex(simulatedWorkspaces, i));
+ return outputWorkspace;
+}
+
+} // namespace
+
+namespace Mantid {
+namespace Algorithms {
+
+DECLARE_ALGORITHM(CalculateIqt)
+
+const std::string CalculateIqt::name() const { return "CalculateIqt"; }
+
+int CalculateIqt::version() const { return 1; }
+
+const std::vector<std::string> CalculateIqt::seeAlso() const {
+ return {"TransformToIqt"};
+}
+
+const std::string CalculateIqt::category() const {
+ return "Inelastic\\Indirect";
+}
+
+const std::string CalculateIqt::summary() const {
+ return "Calculates I(Q,t) from S(Q,w) and computes the errors using a "
+ "monte-carlo routine.";
+}
+
+void CalculateIqt::init() {
+
+ declareProperty(
+ make_unique<WorkspaceProperty<>>("InputWorkspace", "", Direction::Input),
+ "The name of the sample workspace.");
+ declareProperty(make_unique<WorkspaceProperty<>>("ResolutionWorkspace", "",
+ Direction::Input),
+ "The name of the resolution workspace.");
+
+ declareProperty("EnergyMin", -0.5, "Minimum energy for fit. Default = -0.5.");
+ declareProperty("EnergyMax", 0.5, "Maximum energy for fit. Default = 0.5.");
+ declareProperty("EnergyWidth", 0.1, "Width of energy bins for fit.");
+
+ auto positiveInt = boost::make_shared<Kernel::BoundedValidator<int>>();
+ positiveInt->setLower(1);
+
+ declareProperty("NumberOfIterations", DEFAULT_ITERATIONS, positiveInt,
+ "Number of randomised simulations within error to run.");
+ declareProperty(
+ "SeedValue", DEFAULT_SEED, positiveInt,
+ "Seed the random number generator for monte-carlo error calculation.");
+
+ declareProperty(make_unique<WorkspaceProperty<>>("OutputWorkspace", "",
+ Direction::Output),
+ "The name to use for the output workspace.");
+}
+
+void CalculateIqt::exec() {
+ const auto rebinParams = rebinParamsAsString();
+ const MatrixWorkspace_sptr sampleWorkspace = getProperty("InputWorkspace");
+ MatrixWorkspace_sptr resolution = getProperty("ResolutionWorkspace");
+ const int nIterations = getProperty("NumberOfIterations");
+ const int seed = getProperty("SeedValue");
+ resolution = normalizedFourierTransform(resolution, rebinParams);
+
+ auto outputWorkspace = monteCarloErrorCalculation(
+ sampleWorkspace, resolution, rebinParams, seed, nIterations);
+
+ outputWorkspace = removeInvalidData(outputWorkspace);
+ setProperty("OutputWorkspace", outputWorkspace);
+}
+
+std::string CalculateIqt::rebinParamsAsString() {
+ const double e_min = getProperty("EnergyMin");
+ const double e_max = getProperty("EnergyMax");
+ const double e_width = getProperty("EnergyWidth");
+ return createRebinString(e_min, e_max, e_width);
+}
+
+MatrixWorkspace_sptr CalculateIqt::monteCarloErrorCalculation(
+ MatrixWorkspace_sptr sample, MatrixWorkspace_sptr resolution,
+ const std::string &rebinParams, const int seed, const int nIterations) {
+ auto outputWorkspace = calculateIqt(sample, resolution, rebinParams);
+ std::vector<MatrixWorkspace_sptr> simulatedWorkspaces;
+ simulatedWorkspaces.reserve(nIterations);
+ simulatedWorkspaces.emplace_back(outputWorkspace);
+
+ PARALLEL_FOR_IF(Kernel::threadSafe(*sample, *resolution))
+ for (auto i = 0; i < nIterations - 1; ++i) {
+ PARALLEL_START_INTERUPT_REGION
+ auto simulated =
+ doSimulation(sample->clone(), resolution, rebinParams, seed);
+ PARALLEL_CRITICAL(emplace_back)
+ simulatedWorkspaces.emplace_back(simulated);
+ PARALLEL_END_INTERUPT_REGION
+ }
+ PARALLEL_CHECK_INTERUPT_REGION
+ return setErrorsToStandardDeviation(simulatedWorkspaces);
+}
+
+std::map<std::string, std::string> CalculateIqt::validateInputs() {
+ std::map<std::string, std::string> issues;
+ const double eMin = getProperty("EnergyMin");
+ const double eMax = getProperty("EnergyMax");
+ if (eMin > eMax) {
+ auto energy_swapped = "EnergyMin is greater than EnergyMax";
+ issues["EnergyMin"] = energy_swapped;
+ issues["EnergyMax"] = energy_swapped;
+ }
+ return issues;
+}
+
+} // namespace Algorithms
+} // namespace Mantid
diff --git a/Framework/Algorithms/src/StripPeaks.cpp b/Framework/Algorithms/src/StripPeaks.cpp
index 7b320428b8987b745228b80c871d3317235ad7d7..a5712282c34d3136d9421bc32d092becf699cc98 100644
--- a/Framework/Algorithms/src/StripPeaks.cpp
+++ b/Framework/Algorithms/src/StripPeaks.cpp
@@ -189,7 +189,7 @@ StripPeaks::removePeaks(API::MatrixWorkspace_const_sptr input,
// Get back the gaussian parameters
const double height = peakslist->getRef<double>("Height", i);
const double centre = peakslist->getRef<double>("PeakCentre", i);
- const double width = peakslist->getRef<double>("Sigma", i);
+ const double sigma = peakslist->getRef<double>("Sigma", i);
const double chisq = peakslist->getRef<double>("chi2", i);
// These are some heuristic rules to discard bad fits.
// Hope to be able to remove them when we have better fitting routine
@@ -210,18 +210,25 @@ StripPeaks::removePeaks(API::MatrixWorkspace_const_sptr input,
} else if (chisq < 0.) {
g_log.warning() << "StripPeaks(): Peak Index = " << i
<< " @ X = " << centre
- << ". Error: Peak fit with too wide peak width" << width
+ << ". Error: Peak fit with too wide peak width" << sigma
<< " denoted by chi^2 = " << chisq << " <= 0. \n";
}
{
- auto left = lower_bound(X.begin(), X.end(), centre);
- double delta_d = (*left) - (*(left - 1));
- if ((width / delta_d) < 1.) {
+ // find the bin width at the center of the peak - average of the bins on
+ // either side
+ const auto center_iter = lower_bound(X.begin(), X.end(), centre);
+ const double bin_width = .5 * (*(center_iter + 1) - (*(center_iter - 1)));
+
+ // seek wikipedia if you don't believe the conversion factor
+ const double fwhm = sigma * 2. * std::sqrt(2. * std::log(2.));
+
+ if ((fwhm / bin_width) < 1.5) {
g_log.warning() << "StripPeaks(): Peak Index = " << i
<< " @ X = " << centre
- << " Error: Peak fit with too narrow of peak "
- << "delta_d = " << delta_d
- << " sigma/delta_d = " << (width / delta_d) << "\n";
+ << " Error: Peak fit with too narrow of peak"
+ << " fwhm = " << fwhm << " bin size = " << bin_width
+ << " num bins in peak = " << 2. * (fwhm / bin_width)
+ << " <3\n";
continue;
}
}
@@ -229,7 +236,7 @@ StripPeaks::removePeaks(API::MatrixWorkspace_const_sptr input,
g_log.information() << "Subtracting peak " << i << " from spectrum "
<< peakslist->getRef<int>("spectrum", i)
<< " at x = " << centre << " h = " << height
- << " s = " << width << " chi2 = " << chisq << "\n";
+ << " s = " << sigma << " chi2 = " << chisq << "\n";
{ // log the background function
double a0 = 0.;
@@ -255,12 +262,12 @@ StripPeaks::removePeaks(API::MatrixWorkspace_const_sptr input,
for (int j = 0; j < spectrumLength; ++j) {
double x = binCenters[j];
// Skip if not anywhere near this peak
- if (x < centre - 5.0 * width)
+ if (x < centre - 5.0 * sigma)
continue;
- if (x > centre + 5.0 * width)
+ if (x > centre + 5.0 * sigma)
break;
// Calculate the value of the Gaussian function at this point
- const double funcVal = height * exp(-0.5 * pow((x - centre) / width, 2));
+ const double funcVal = height * exp(-0.5 * pow((x - centre) / sigma, 2));
// Subtract the calculated value from the data
Y[j] -= funcVal;
}
diff --git a/Framework/Algorithms/test/CalculateIqtTest.h b/Framework/Algorithms/test/CalculateIqtTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..fd609cbef8cf4164161c0c4c09398320df54ad2b
--- /dev/null
+++ b/Framework/Algorithms/test/CalculateIqtTest.h
@@ -0,0 +1,148 @@
+#ifndef CALCULATEIQTTEST_H_
+#define CALCULATEIQTTEST_H_
+
+#include "MantidAPI/AlgorithmManager.h"
+#include "MantidAPI/FrameworkManager.h"
+#include "MantidAlgorithms/CalculateIqt.h"
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidTestHelpers/WorkspaceCreationHelper.h"
+
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+
+namespace {
+
+Mantid::API::MatrixWorkspace_sptr setUpSampleWorkspace() {
+ std::vector<double> xData{0.1, 0.2, 0.3, 0.4, 0.5};
+ std::vector<double> yData{0.001, 0.02, 0.4, 0.02, 0.1};
+
+ auto createWorkspace = AlgorithmManager::Instance().create("CreateWorkspace");
+ createWorkspace->setChild(true);
+ createWorkspace->initialize();
+ createWorkspace->setProperty("UnitX", "DeltaE");
+ createWorkspace->setProperty("VerticalAxisUnit", "MomentumTransfer");
+ createWorkspace->setProperty("VerticalAxisValues", "1");
+ createWorkspace->setProperty("DataX", xData);
+ createWorkspace->setProperty("DataY", yData);
+ createWorkspace->setProperty("NSpec", 1);
+ createWorkspace->setPropertyValue("OutputWorkspace", "__calcIqtTest");
+ createWorkspace->execute();
+ return createWorkspace->getProperty("OutputWorkspace");
+}
+
+Mantid::API::MatrixWorkspace_sptr setUpResolutionWorkspace() {
+ std::vector<double> xData{0.1, 0.2, 0.3, 0.4, 0.5};
+ std::vector<double> yData{0.03, 0.22, 0.05, 0.25, 0.3};
+
+ auto createWorkspace = AlgorithmManager::Instance().create("CreateWorkspace");
+ createWorkspace->setChild(true);
+ createWorkspace->initialize();
+ createWorkspace->setProperty("UnitX", "DeltaE");
+ createWorkspace->setProperty("VerticalAxisUnit", "SpectraNumber");
+ createWorkspace->setProperty("DataX", xData);
+ createWorkspace->setProperty("DataY", yData);
+ createWorkspace->setProperty("NSpec", 1);
+ createWorkspace->setPropertyValue("OutputWorkspace", "__calcIqtTest");
+ createWorkspace->execute();
+ return createWorkspace->getProperty("OutputWorkspace");
+}
+
+IAlgorithm_sptr calculateIqtAlgorithm(MatrixWorkspace_sptr sample,
+ MatrixWorkspace_sptr resolution,
+ const double EnergyMin = -0.5,
+ const double EnergyMax = 0.5,
+ const double EnergyWidth = 0.1,
+ const int NumberOfIterations = 10) {
+ auto calculateIqt = AlgorithmManager::Instance().create("CalculateIqt");
+ calculateIqt->setChild(true);
+ calculateIqt->initialize();
+ calculateIqt->setProperty("InputWorkspace", sample);
+ calculateIqt->setProperty("ResolutionWorkspace", resolution);
+ calculateIqt->setProperty("OutputWorkspace", "_");
+ calculateIqt->setProperty("EnergyMin", EnergyMin);
+ calculateIqt->setProperty("EnergyMax", EnergyMax);
+ calculateIqt->setProperty("EnergyWidth", EnergyWidth);
+ calculateIqt->setProperty("NumberOfIterations", NumberOfIterations);
+ return calculateIqt;
+}
+} // namespace
+
+class CalculateIqtTest : public CxxTest::TestSuite {
+public:
+ static CalculateIqtTest *createSuite() { return new CalculateIqtTest(); }
+ static void destroySuite(CalculateIqtTest *suite) { delete suite; }
+ MatrixWorkspace_sptr m_sampleWorkspace;
+ MatrixWorkspace_sptr m_resolutionWorkspace;
+
+ CalculateIqtTest() {
+ m_sampleWorkspace = setUpSampleWorkspace();
+ m_resolutionWorkspace = setUpResolutionWorkspace();
+ }
+
+ void test_algorithm_executes() {
+ auto algorithm =
+ calculateIqtAlgorithm(m_sampleWorkspace, m_resolutionWorkspace);
+ TS_ASSERT_THROWS_NOTHING(algorithm->execute());
+ TS_ASSERT(algorithm->isExecuted());
+ }
+
+ void test_output_dimensions_are_correct() {
+ auto algorithm =
+ calculateIqtAlgorithm(m_sampleWorkspace, m_resolutionWorkspace);
+ algorithm->execute();
+ MatrixWorkspace_sptr outWorkspace =
+ algorithm->getProperty("OutputWorkspace");
+ TS_ASSERT_EQUALS(outWorkspace->getNumberHistograms(), 1);
+ TS_ASSERT_EQUALS(outWorkspace->blocksize(), 6);
+ }
+
+ void test_sample_output_values_are_correct() {
+ auto algorithm =
+ calculateIqtAlgorithm(m_sampleWorkspace, m_resolutionWorkspace);
+ algorithm->execute();
+ MatrixWorkspace_sptr outWorkspace =
+ algorithm->getProperty("OutputWorkspace");
+ auto yValues = outWorkspace->y(0);
+ auto eValues = outWorkspace->e(0);
+ TS_ASSERT_DELTA(yValues[0], 1, 0.0001);
+ TS_ASSERT_DELTA(yValues[1], 0, 0.0001);
+ TS_ASSERT_DELTA(yValues[4], 0.4831171, 0.0001);
+ TS_ASSERT_DELTA(eValues[0], 0, 0.0001);
+ }
+
+ void test_throws_if_energy_bounds_invalid() {
+ auto energyMin = 0.5;
+ auto energyMax = -1; // invalid - less than energyMin
+ auto algorithm = calculateIqtAlgorithm(
+ m_sampleWorkspace, m_resolutionWorkspace, energyMin, energyMax);
+ TS_ASSERT_THROWS(algorithm->execute(), std::runtime_error);
+ TS_ASSERT(!algorithm->isExecuted());
+ }
+
+ void test_throws_if_number_of_iterations_is_negative() {
+ auto nIterations = -1;
+ TS_ASSERT_THROWS(calculateIqtAlgorithm(m_sampleWorkspace,
+ m_resolutionWorkspace, -0.5, 0.5,
+ 0.1, nIterations),
+ std::invalid_argument);
+ }
+
+ void test_throws_if_number_of_iterations_is_zero() {
+ auto nIterations = 0;
+ TS_ASSERT_THROWS(calculateIqtAlgorithm(m_sampleWorkspace,
+ m_resolutionWorkspace, -0.5, 0.5,
+ 0.1, nIterations),
+ std::invalid_argument);
+ }
+
+ // void test_throws_if_number_of_iterations_is_not_an_integer() {
+ // auto nIterations = 0.2;
+ // TS_ASSERT_THROWS(calculateIqtAlgorithm(m_sampleWorkspace,
+ // m_resolutionWorkspace, -0.5, 0.5,
+ // 0.1, nIterations),
+ // std::invalid_argument);
+ //}
+};
+#endif
diff --git a/Framework/Algorithms/test/StripVanadiumPeaks2Test.h b/Framework/Algorithms/test/StripVanadiumPeaks2Test.h
index b4524efc59e0a03b2671aabf56e307952a22cfde..07136fcae541790143b7d5edfaca0a279a7ceb95 100644
--- a/Framework/Algorithms/test/StripVanadiumPeaks2Test.h
+++ b/Framework/Algorithms/test/StripVanadiumPeaks2Test.h
@@ -5,11 +5,14 @@
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
#include "MantidAlgorithms/StripVanadiumPeaks2.h"
#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/Axis.h"
#include "MantidAPI/FrameworkManager.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/VectorHelper.h"
+#include "MantidDataObjects/WorkspaceCreation.h"
using namespace Mantid::API;
+using namespace Mantid::HistogramData;
using namespace Mantid::Kernel::VectorHelper;
using Mantid::Algorithms::StripVanadiumPeaks2;
using Mantid::MantidVec;
@@ -70,7 +73,601 @@ public:
AnalysisDataService::Instance().remove(inputWSName);
}
+ double getYValueAtX(const Histogram &histogram, const double x_value) {
+ const auto &vector_x = histogram.points();
+ const auto pos =
+ std::lower_bound(vector_x.begin(), vector_x.end(), x_value);
+ if (pos == vector_x.end())
+ throw std::runtime_error("failed to find x-value");
+ const auto index = (pos - vector_x.begin());
+ return histogram.y()[index];
+ }
+
+ void testSharpPeaks() {
+ auto PG3_40507 = createPG3_40507();
+
+ // known positions and expected values
+ const std::vector<double> PEAK_X{1.2356, 1.5133,
+ 2.1401}; // peak positions in d-spacing
+ const std::vector<double> PEAK_Y{28.5, 37.8,
+ 12.3}; // low precision results of
+ // stripped peaks
+ // something is wrong with the second peak on windows
+ const std::vector<double> TOL{.1, 10., .1};
+
+ const std::string outputWSName("PG3_40507_stripped");
+ StripVanadiumPeaks2 strip;
+ if (!strip.isInitialized())
+ strip.initialize();
+ strip.setProperty("InputWorkspace", PG3_40507);
+ strip.setPropertyValue("OutputWorkspace", outputWSName);
+ strip.setPropertyValue("BackgroundType", "Quadratic");
+ strip.setProperty("PeakPositionTolerance", 0.05);
+ strip.execute();
+ TS_ASSERT(strip.isExecuted());
+
+ MatrixWorkspace_const_sptr result =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
+ outputWSName);
+ for (size_t i = 0; i < PEAK_X.size(); ++i) {
+ const double newY = getYValueAtX(result->histogram(0), PEAK_X[i]);
+ std::cout << i
+ << ": orig=" << getYValueAtX(PG3_40507->histogram(0), PEAK_X[i])
+ << " exp=" << PEAK_Y[i] << " obs=" << newY << std::endl;
+ TS_ASSERT_DELTA(newY, PEAK_Y[i], TOL[i]);
+ }
+
+ AnalysisDataService::Instance().remove(outputWSName);
+ }
+
private:
+ /**
+ * create a histogram with data hard-coded using data generated with the
+ * following python script
+ *
+ * LoadEventAndCompress(Filename='/SNS/PG3/IPTS-2767/nexus/PG3_40507.nxs.h5',
+ * OutputWorkspace='PG3_40507', MaxChunkSize=0, FilterBadPulses=10)
+ * NormaliseByCurrent(InputWorkspace='PG3_40507', OutputWorkspace='PG3_40507',
+ *RecalculatePCharge=True)
+ * PDLoadCharacterizations(Filename='/SNS/PG3/shared/CALIBRATION/2018_2_11A_CAL/PG3_char_2018_06_11-HighRes-PAC.txt,/SNS/PG3/shared/CALIBRATION/2018_2_11A_CAL/PG3_char_2018_05_26.txt',
+ * OutputWorkspace='characterizations', SpectrumIDs='1', L2='3.18',
+ *Polar='90', Azimuthal='0')
+ * PDDetermineCharacterizations(InputWorkspace='PG3_40507',
+ *Characterizations='characterizations',
+ * ReductionProperties='__snspowderreduction')
+ * LoadEventAndCompress(Filename='/SNS/PG3/IPTS-2767/nexus/PG3_40503.nxs.h5',
+ * OutputWorkspace='PG3_40503_loadsum', MaxChunkSize=0, FilterBadPulses=10)
+ * NormaliseByCurrent(InputWorkspace='PG3_40503_loadsum',
+ *OutputWorkspace='PG3_40503_loadsum', RecalculatePCharge=True)
+ * RenameWorkspace(InputWorkspace='PG3_40503_loadsum',
+ *OutputWorkspace='PG3_40503_vanbg')
+ * Minus(LHSWorkspace='PG3_40507', RHSWorkspace='PG3_40503_vanbg',
+ *OutputWorkspace='PG3_40507',
+ * ClearRHSWorkspace=True)
+ * DeleteWorkspace(Workspace='PG3_40503_vanbg')
+ * CompressEvents(InputWorkspace='PG3_40507', OutputWorkspace='PG3_40507',
+ *Tolerance=0.01)
+ * ConvertUnits(InputWorkspace='PG3_40507', OutputWorkspace='PG3_40507',
+ *Target='Wavelength')
+ * SetSampleMaterial(InputWorkspace='PG3_40507', ChemicalFormula='V',
+ *SampleNumberDensity=0.0721)
+ * CarpenterSampleCorrection(InputWorkspace='PG3_40507',
+ *OutputWorkspace='PG3_40507')
+ * ConvertUnits(InputWorkspace='PG3_40507', OutputWorkspace='PG3_40507',
+ *Target='TOF')
+ * AlignAndFocusPowder(InputWorkspace='PG3_40507',
+ *OutputWorkspace='PG3_40507',
+ * CalFileName='/SNS/PG3/shared/CALIBRATION/2018_2_11A_CAL/PG3_PAC_d40481_2018_06_13.h5',
+ *#GroupingWorkspace='PG3_group',
+ * Params='-0.0008', RemovePromptPulseWidth=50, PrimaryFlightPath=60,
+ *SpectrumIDs='1',
+ * L2='3.18', Polar='90', Azimuthal='0',
+ *ReductionProperties='__snspowderreduction', PreserveEvents=False)
+ * ConvertUnits(InputWorkspace='PG3_40507', OutputWorkspace='PG3_40507',
+ *Target='dSpacing')
+ * RemoveLogs(Workspace='PG3_40507')
+ * CropWorkspace(InputWorkspace='PG3_40507', OutputWorkspace='PG3_40507',
+ *XMin=1.15, XMax=2.2)
+ */
+ Mantid::API::MatrixWorkspace_sptr createPG3_40507() {
+ auto space2D = Mantid::DataObjects::create<
+ Mantid::DataObjects::Workspace2D>(
+ 1,
+ Histogram(
+ BinEdges{1.15042999, 1.15135033, 1.15227141, 1.15319323, 1.15411578,
+ 1.15503908, 1.15596311, 1.15688788, 1.15781339, 1.15873964,
+ 1.15966663, 1.16059436, 1.16152284, 1.16245206, 1.16338202,
+ 1.16431272, 1.16524418, 1.16617637, 1.16710931, 1.168043,
+ 1.16897743, 1.16991262, 1.17084855, 1.17178522, 1.17272265,
+ 1.17366083, 1.17459976, 1.17553944, 1.17647987, 1.17742105,
+ 1.17836299, 1.17930568, 1.18024913, 1.18119333, 1.18213828,
+ 1.18308399, 1.18403046, 1.18497768, 1.18592566, 1.1868744,
+ 1.1878239, 1.18877416, 1.18972518, 1.19067696, 1.1916295,
+ 1.19258281, 1.19353687, 1.1944917, 1.1954473, 1.19640366,
+ 1.19736078, 1.19831867, 1.19927732, 1.20023674, 1.20119693,
+ 1.20215789, 1.20311962, 1.20408211, 1.20504538, 1.20600941,
+ 1.20697422, 1.2079398, 1.20890615, 1.20987328, 1.21084118,
+ 1.21180985, 1.2127793, 1.21374952, 1.21472052, 1.2156923,
+ 1.21666485, 1.21763818, 1.21861229, 1.21958718, 1.22056285,
+ 1.2215393, 1.22251653, 1.22349455, 1.22447334, 1.22545292,
+ 1.22643328, 1.22741443, 1.22839636, 1.22937908, 1.23036258,
+ 1.23134687, 1.23233195, 1.23331782, 1.23430447, 1.23529191,
+ 1.23628015, 1.23726917, 1.23825899, 1.23924959, 1.24024099,
+ 1.24123319, 1.24222617, 1.24321995, 1.24421453, 1.2452099,
+ 1.24620607, 1.24720303, 1.2482008, 1.24919936, 1.25019872,
+ 1.25119888, 1.25219984, 1.2532016, 1.25420416, 1.25520752,
+ 1.25621169, 1.25721665, 1.25822243, 1.25922901, 1.26023639,
+ 1.26124458, 1.26225357, 1.26326338, 1.26427399, 1.26528541,
+ 1.26629764, 1.26731067, 1.26832452, 1.26933918, 1.27035465,
+ 1.27137094, 1.27238803, 1.27340594, 1.27442467, 1.27544421,
+ 1.27646456, 1.27748574, 1.27850772, 1.27953053, 1.28055415,
+ 1.2815786, 1.28260386, 1.28362994, 1.28465685, 1.28568457,
+ 1.28671312, 1.28774249, 1.28877269, 1.2898037, 1.29083555,
+ 1.29186821, 1.29290171, 1.29393603, 1.29497118, 1.29600716,
+ 1.29704396, 1.2980816, 1.29912006, 1.30015936, 1.30119949,
+ 1.30224045, 1.30328224, 1.30432486, 1.30536832, 1.30641262,
+ 1.30745775, 1.30850371, 1.30955052, 1.31059816, 1.31164664,
+ 1.31269595, 1.31374611, 1.31479711, 1.31584895, 1.31690162,
+ 1.31795515, 1.31900951, 1.32006472, 1.32112077, 1.32217767,
+ 1.32323541, 1.324294, 1.32535343, 1.32641371, 1.32747485,
+ 1.32853683, 1.32959965, 1.33066333, 1.33172787, 1.33279325,
+ 1.33385948, 1.33492657, 1.33599451, 1.33706331, 1.33813296,
+ 1.33920346, 1.34027483, 1.34134705, 1.34242012, 1.34349406,
+ 1.34456886, 1.34564451, 1.34672103, 1.3477984, 1.34887664,
+ 1.34995574, 1.35103571, 1.35211654, 1.35319823, 1.35428079,
+ 1.35536421, 1.3564485, 1.35753366, 1.35861969, 1.35970659,
+ 1.36079435, 1.36188299, 1.36297249, 1.36406287, 1.36515412,
+ 1.36624624, 1.36733924, 1.36843311, 1.36952786, 1.37062348,
+ 1.37171998, 1.37281736, 1.37391561, 1.37501474, 1.37611475,
+ 1.37721565, 1.37831742, 1.37942007, 1.38052361, 1.38162803,
+ 1.38273333, 1.38383952, 1.38494659, 1.38605455, 1.38716339,
+ 1.38827312, 1.38938374, 1.39049524, 1.39160764, 1.39272093,
+ 1.3938351, 1.39495017, 1.39606613, 1.39718299, 1.39830073,
+ 1.39941937, 1.40053891, 1.40165934, 1.40278067, 1.40390289,
+ 1.40502601, 1.40615003, 1.40727495, 1.40840077, 1.40952749,
+ 1.41065512, 1.41178364, 1.41291307, 1.4140434, 1.41517463,
+ 1.41630677, 1.41743982, 1.41857377, 1.41970863, 1.4208444,
+ 1.42198107, 1.42311866, 1.42425715, 1.42539656, 1.42653687,
+ 1.4276781, 1.42882025, 1.4299633, 1.43110727, 1.43225216,
+ 1.43339796, 1.43454468, 1.43569231, 1.43684087, 1.43799034,
+ 1.43914073, 1.44029205, 1.44144428, 1.44259743, 1.44375151,
+ 1.44490651, 1.44606244, 1.44721929, 1.44837706, 1.44953577,
+ 1.45069539, 1.45185595, 1.45301744, 1.45417985, 1.45534319,
+ 1.45650747, 1.45767267, 1.45883881, 1.46000588, 1.46117389,
+ 1.46234283, 1.4635127, 1.46468351, 1.46585526, 1.46702794,
+ 1.46820157, 1.46937613, 1.47055163, 1.47172807, 1.47290545,
+ 1.47408378, 1.47526304, 1.47644325, 1.47762441, 1.47880651,
+ 1.47998955, 1.48117354, 1.48235848, 1.48354437, 1.4847312,
+ 1.48591899, 1.48710772, 1.48829741, 1.48948805, 1.49067964,
+ 1.49187218, 1.49306568, 1.49426013, 1.49545554, 1.49665191,
+ 1.49784923, 1.49904751, 1.50024674, 1.50144694, 1.5026481,
+ 1.50385022, 1.5050533, 1.50625734, 1.50746235, 1.50866832,
+ 1.50987525, 1.51108315, 1.51229202, 1.51350185, 1.51471265,
+ 1.51592442, 1.51713716, 1.51835087, 1.51956555, 1.52078121,
+ 1.52199783, 1.52321543, 1.524434, 1.52565355, 1.52687407,
+ 1.52809557, 1.52931805, 1.5305415, 1.53176593, 1.53299135,
+ 1.53421774, 1.53544511, 1.53667347, 1.53790281, 1.53913313,
+ 1.54036444, 1.54159673, 1.54283001, 1.54406427, 1.54529952,
+ 1.54653576, 1.54777299, 1.54901121, 1.55025042, 1.55149062,
+ 1.55273181, 1.553974, 1.55521718, 1.55646135, 1.55770652,
+ 1.55895268, 1.56019985, 1.56144801, 1.56269716, 1.56394732,
+ 1.56519848, 1.56645064, 1.5677038, 1.56895796, 1.57021313,
+ 1.5714693, 1.57272647, 1.57398466, 1.57524384, 1.57650404,
+ 1.57776524, 1.57902745, 1.58029068, 1.58155491, 1.58282015,
+ 1.58408641, 1.58535368, 1.58662196, 1.58789126, 1.58916157,
+ 1.5904329, 1.59170525, 1.59297861, 1.59425299, 1.5955284,
+ 1.59680482, 1.59808226, 1.59936073, 1.60064022, 1.60192073,
+ 1.60320227, 1.60448483, 1.60576842, 1.60705303, 1.60833867,
+ 1.60962534, 1.61091304, 1.61220177, 1.61349154, 1.61478233,
+ 1.61607416, 1.61736701, 1.61866091, 1.61995584, 1.6212518,
+ 1.6225488, 1.62384684, 1.62514592, 1.62644604, 1.62774719,
+ 1.62904939, 1.63035263, 1.63165691, 1.63296224, 1.63426861,
+ 1.63557602, 1.63688448, 1.63819399, 1.63950455, 1.64081615,
+ 1.6421288, 1.64344251, 1.64475726, 1.64607307, 1.64738992,
+ 1.64870784, 1.6500268, 1.65134682, 1.6526679, 1.65399004,
+ 1.65531323, 1.65663748, 1.65796279, 1.65928916, 1.66061659,
+ 1.66194508, 1.66327464, 1.66460526, 1.66593694, 1.66726969,
+ 1.66860351, 1.66993839, 1.67127434, 1.67261136, 1.67394945,
+ 1.67528861, 1.67662884, 1.67797014, 1.67931252, 1.68065597,
+ 1.68200049, 1.6833461, 1.68469277, 1.68604053, 1.68738936,
+ 1.68873927, 1.69009026, 1.69144233, 1.69279549, 1.69414972,
+ 1.69550504, 1.69686145, 1.69821894, 1.69957751, 1.70093717,
+ 1.70229792, 1.70365976, 1.70502269, 1.70638671, 1.70775182,
+ 1.70911802, 1.71048531, 1.7118537, 1.71322318, 1.71459376,
+ 1.71596544, 1.71733821, 1.71871208, 1.72008705, 1.72146312,
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+ 0.09810162, 0.09865588, 0.09878608, 0.09882098, 0.09906898,
+ 0.098961, 0.09941916, 0.09937158, 0.09974492, 0.09981188,
+ 0.09983728, 0.1002573, 0.10035837, 0.10052093, 0.10077912,
+ 0.10055007, 0.10111611, 0.10099313, 0.10113983, 0.10152592,
+ 0.10155394, 0.10194169, 0.10199304, 0.10229402, 0.10232422,
+ 0.10218612, 0.10292982, 0.10240724, 0.1026003, 0.10312169,
+ 0.10346476, 0.1033123, 0.10379735, 0.10380127, 0.10398674,
+ 0.10431154, 0.10455596, 0.1052505, 0.10545096, 0.10514618,
+ 0.10611399, 0.10665123, 0.10576578, 0.10584213, 0.10560946,
+ 0.10596352, 0.10580093, 0.10639526, 0.10602661, 0.10661846,
+ 0.10647763, 0.10681167, 0.1068673, 0.10738677, 0.1076679,
+ 0.10763228, 0.10860019, 0.10958406, 0.11618918, 0.1483844,
+ 0.13412824, 0.11691087, 0.11210996, 0.11066458, 0.10979861,
+ 0.10958522, 0.10933175, 0.10949942, 0.10936525, 0.11022655,
+ 0.11057402, 0.1100942, 0.11052932, 0.11069451, 0.11057393,
+ 0.11086957, 0.11116207, 0.11100228, 0.11097875, 0.11133393,
+ 0.11165734, 0.11141227, 0.11168015, 0.11209909, 0.111912,
+ 0.11263736, 0.11225002, 0.11269878, 0.1122586, 0.11278133,
+ 0.11282309, 0.11283156, 0.11285848, 0.11322753, 0.11316201,
+ 0.11337442, 0.11346853, 0.1133641, 0.11362701, 0.1135896,
+ 0.11366064, 0.11400145, 0.11357762, 0.11370818, 0.11389959,
+ 0.11408176, 0.11394538, 0.11377854, 0.11395541, 0.11409542,
+ 0.11391721, 0.1142584, 0.11444837, 0.11416669, 0.11423569,
+ 0.11474726, 0.11454975, 0.11459066, 0.11492783, 0.11483853,
+ 0.11524056, 0.11521504, 0.11503301, 0.11554429, 0.11584337,
+ 0.11556254, 0.11575002, 0.11563652, 0.11542595, 0.11570801,
+ 0.1158586, 0.11600528, 0.11613733, 0.1161795, 0.1163012,
+ 0.11652074, 0.11671698, 0.11649027, 0.11670725, 0.11666918,
+ 0.11704312, 0.1168323, 0.11666211, 0.11713452, 0.11706081,
+ 0.11736878, 0.11781523, 0.11723944, 0.1177871, 0.11786421,
+ 0.11770941, 0.11755727, 0.11779118, 0.11801463, 0.11798372,
+ 0.11835702, 0.11820464, 0.11794876, 0.11833424, 0.11825397,
+ 0.11853825, 0.11868084, 0.11857568, 0.11890506, 0.11834615,
+ 0.11887005, 0.11868061, 0.11900734, 0.11890801, 0.11928773,
+ 0.11933879, 0.11950798, 0.11935514, 0.11928139, 0.11935545,
+ 0.11915067, 0.11939353, 0.11956198, 0.1193625, 0.11961223,
+ 0.11956111, 0.1197357, 0.11963851, 0.11997262, 0.11983564,
+ 0.12003922, 0.11995384, 0.11983126, 0.11978, 0.11990461,
+ 0.11990151, 0.1205824, 0.12024106, 0.12043872, 0.12046799,
+ 0.12051577, 0.12047459, 0.12049854, 0.12087799, 0.12044014,
+ 0.12031675, 0.12044389, 0.12083971, 0.12083157, 0.12082134,
+ 0.12115007, 0.12069022, 0.12083268, 0.12069638, 0.12074078,
+ 0.12092253, 0.12096648, 0.1209408, 0.12083527, 0.12095569,
+ 0.12098025, 0.12076102, 0.12086163, 0.12094667, 0.12139388,
+ 0.12078216, 0.12103414, 0.12126756, 0.12120854, 0.12108292,
+ 0.12100308, 0.12115043, 0.12121332, 0.1206329, 0.12090712,
+ 0.12076863, 0.12074094, 0.12062303, 0.12082079, 0.1209909,
+ 0.12112458, 0.12207246, 0.12218142, 0.12154999, 0.12233238,
+ 0.12345171, 0.12216962, 0.1210342, 0.12071547, 0.12082515,
+ 0.12078011, 0.12059255, 0.12013529, 0.1204411, 0.12030222,
+ 0.12064879, 0.12008365, 0.12085759, 0.12055658, 0.12091152,
+ 0.12039997, 0.12068333, 0.12073999, 0.12102517, 0.12096843,
+ 0.12068165, 0.12119209, 0.12092863, 0.12131486, 0.12109464,
+ 0.1214653, 0.12136762, 0.12149701, 0.12139231, 0.12154187,
+ 0.12189975, 0.12173327, 0.12165145, 0.121803, 0.12168023,
+ 0.12177848, 0.12195502, 0.12209618, 0.12208228, 0.122006,
+ 0.12213498, 0.12195088, 0.12257762, 0.12234055, 0.1221249,
+ 0.12234262, 0.12240725, 0.12253272, 0.12251793, 0.1224379,
+ 0.12299764, 0.12256128, 0.12286631, 0.12255145, 0.1227136,
+ 0.12275076, 0.12261058, 0.12281186, 0.1230996, 0.12306993,
+ 0.12278627, 0.12287486, 0.12310438, 0.12269442, 0.12314675,
+ 0.12307819, 0.12295634, 0.12333423, 0.12371617, 0.12356086,
+ 0.12396455, 0.12659848, 0.14758044, 0.16541888, 0.13957303,
+ 0.12925304, 0.12604731, 0.12459023, 0.12378261, 0.12370793,
+ 0.12335084, 0.12343917, 0.12326433, 0.12357662, 0.12350549,
+ 0.12364156, 0.12359094, 0.12328373, 0.12366544, 0.1234665,
+ 0.12353506, 0.12369789, 0.12331939, 0.12348493, 0.12342986,
+ 0.12325508, 0.12352657, 0.12337392, 0.12310312, 0.12319982,
+ 0.12338479, 0.12319994, 0.1229019, 0.12291918, 0.12285192,
+ 0.12263437, 0.12259662, 0.1223905, 0.1227991, 0.12251541,
+ 0.12171606, 0.12204615, 0.1217534, 0.12143749, 0.12109563,
+ 0.12083896, 0.12050626, 0.12020373, 0.11972535, 0.1196556,
+ 0.11901792, 0.11829378, 0.11842445, 0.11765844, 0.11712006,
+ 0.11653108, 0.11603167, 0.11568374, 0.1150576, 0.11385368,
+ 0.11350685, 0.11312784, 0.11194691, 0.11169322, 0.11102328,
+ 0.11043224, 0.10997193, 0.10913658, 0.10857883, 0.10804441,
+ 0.10736598, 0.10689977, 0.10632894, 0.10583985, 0.10511315,
+ 0.10488256, 0.10440227, 0.10436692, 0.10409351, 0.10326387,
+ 0.10327201, 0.10251131, 0.10227501, 0.10223691, 0.10140431,
+ 0.10134056, 0.10106912, 0.10048082, 0.10015192, 0.10000476,
+ 0.09940061, 0.09911605, 0.09937981, 0.09889048, 0.09833957,
+ 0.09809914, 0.09770799, 0.09799267, 0.09749047, 0.0973443,
+ 0.09721181, 0.09660111, 0.09670059, 0.09632986, 0.09588216,
+ 0.09600354, 0.09579305, 0.09517147, 0.09475963, 0.09434851,
+ 0.09436208, 0.0941166, 0.09412621, 0.09389304, 0.09362614,
+ 0.0934498, 0.09337322, 0.0930348, 0.09255238, 0.09246405,
+ 0.09239633, 0.09228948, 0.09149797, 0.09150998, 0.09091079,
+ 0.09059358, 0.09073656, 0.09044675, 0.09052901, 0.09021704,
+ 0.08983709, 0.08971085, 0.09012132, 0.08936779, 0.08918196,
+ 0.08916877, 0.08892073, 0.08893757, 0.08858692, 0.0881193,
+ 0.08828271, 0.0879663, 0.08785613, 0.08774057, 0.08761425,
+ 0.08746617, 0.08754376, 0.08727514, 0.08697893, 0.08661758,
+ 0.08678746, 0.08670468, 0.08679087, 0.08602114, 0.08557962,
+ 0.08594464, 0.08552812, 0.08579972, 0.08549704, 0.08537773,
+ 0.08484182, 0.08527655, 0.08476341, 0.08501413, 0.08480269,
+ 0.08501053, 0.08471737, 0.08458685, 0.08452883, 0.08437682,
+ 0.08400888, 0.0843093, 0.08404998, 0.08403721, 0.08372893,
+ 0.08403811, 0.08353716, 0.08367217, 0.08358381, 0.08323296,
+ 0.08324134, 0.08313687, 0.0827609, 0.08286916, 0.08265502,
+ 0.08251579, 0.08257177, 0.08254709, 0.08265035, 0.08260576,
+ 0.08239178, 0.08240309, 0.08219041, 0.0817003, 0.08219778,
+ 0.08173714, 0.08195537, 0.0815065, 0.08111007, 0.0816751,
+ 0.08086731, 0.08124781, 0.08148713, 0.08082474, 0.08086508,
+ 0.08082352, 0.08084213, 0.08086525, 0.08057361, 0.08014514,
+ 0.08049376, 0.08034359, 0.07998387, 0.07990817, 0.08010026,
+ 0.08001849, 0.07982477, 0.07970619, 0.07961312, 0.07913916,
+ 0.07960793, 0.07928162, 0.07931951, 0.07911895, 0.07924796,
+ 0.07861915, 0.078851, 0.07869252, 0.07873411, 0.07844709,
+ 0.07851855, 0.07822954, 0.07848927, 0.07842583, 0.07811262,
+ 0.07796776, 0.07790764, 0.07785552, 0.07794405, 0.07750911,
+ 0.07786925, 0.07754503, 0.07765547, 0.07757437, 0.07760141,
+ 0.07724084, 0.07721791, 0.07704123, 0.07685608, 0.0769753,
+ 0.07688559, 0.07670552, 0.07670128, 0.07666367, 0.07615797,
+ 0.0763716, 0.07625804, 0.07633819, 0.0760897, 0.07643624,
+ 0.0760088, 0.07576586, 0.07612283, 0.07564781, 0.07591185,
+ 0.07588707, 0.07589227, 0.07575599, 0.0755274, 0.07583084,
+ 0.07548325, 0.07523937, 0.07541937, 0.07533061, 0.07522039,
+ 0.07464627, 0.0749228, 0.07483709, 0.07499167, 0.07449394,
+ 0.07464648, 0.07453324, 0.07423873, 0.07419753, 0.07467062,
+ 0.07449603, 0.07424625, 0.07415208, 0.07395542, 0.07366103,
+ 0.07372235, 0.07414122, 0.07381445, 0.07341285, 0.07370479,
+ 0.07343342, 0.07317712, 0.07357358, 0.07350074, 0.07323104,
+ 0.07320646, 0.07334826, 0.07278856, 0.07311356, 0.07289351,
+ 0.07258756, 0.07299891, 0.07276867, 0.07213024, 0.07252438,
+ 0.07234726, 0.07247819, 0.07223626, 0.07188469, 0.07236707,
+ 0.07214867, 0.07183589, 0.07216702, 0.07176504, 0.07154792,
+ 0.0714893, 0.07168797, 0.07142927, 0.07117226, 0.07138552,
+ 0.07148576, 0.07125145, 0.07116823, 0.07113642, 0.07089822,
+ 0.07095803, 0.07067905, 0.07122147, 0.07080627, 0.07045241,
+ 0.07064644, 0.07045675, 0.07023966, 0.0702617, 0.07061058,
+ 0.07033734, 0.06987954, 0.07041236, 0.06974364, 0.07027269,
+ 0.07036899, 0.07015203, 0.06978766, 0.06985847, 0.06978652,
+ 0.06992062, 0.06967079, 0.06980092, 0.06984545, 0.06946438,
+ 0.0692113, 0.06947494, 0.06954763, 0.06937168, 0.06917832,
+ 0.06922749, 0.06949966, 0.06966824, 0.06924553, 0.06909893,
+ 0.06914696, 0.06924436, 0.06909882, 0.06917435, 0.06883593,
+ 0.06868457, 0.06879058, 0.06897344, 0.06878056, 0.06893278,
+ 0.06863372, 0.0686559, 0.06896215, 0.0689892, 0.06877229,
+ 0.06850599, 0.06897721, 0.0686959, 0.06878704, 0.06861183,
+ 0.0687965, 0.06880388, 0.06888769, 0.06871961, 0.06868365,
+ 0.06855779, 0.06852955, 0.06859698, 0.06854567, 0.06835265,
+ 0.06848645, 0.06857056, 0.06841071, 0.06798028, 0.06802586,
+ 0.06799168, 0.06815501, 0.06814112, 0.06790047, 0.0678429,
+ 0.06831629, 0.06761858, 0.06764785, 0.06798609, 0.0675935,
+ 0.06775755, 0.06749517, 0.06791124, 0.0673451, 0.06777571,
+ 0.06721334, 0.06713083, 0.06721366, 0.06692459, 0.06728881,
+ 0.06705009, 0.06716039, 0.06658561, 0.06660794, 0.0668228,
+ 0.06639459, 0.06664136, 0.06640293, 0.06659663, 0.06617972,
+ 0.06630982, 0.06628822, 0.06644162, 0.06691039, 0.06988695,
+ 0.07920677, 0.08874079, 0.08334671, 0.07295063, 0.06833664,
+ 0.06653433, 0.06566708, 0.06555435, 0.06527518, 0.06513995,
+ 0.06482874, 0.06460965, 0.06463104, 0.06463471, 0.06481889,
+ 0.06410483, 0.06412912, 0.06425102, 0.06407212, 0.06416003,
+ 0.06395273, 0.06363819, 0.0635063, 0.06364338, 0.06362024,
+ 0.06357006, 0.06292629, 0.06319382, 0.06293484, 0.06333936,
+ 0.06281112, 0.06287284, 0.06251089, 0.06240202, 0.06257857}));
+ space2D->getAxis(0)->unit() =
+ Mantid::Kernel::UnitFactory::Instance().create("dSpacing");
+ return std::move(space2D);
+ }
};
#endif /*STRIPVANADIUMPEAKSTEST_H_*/
diff --git a/Framework/DataHandling/src/LoadLog.cpp b/Framework/DataHandling/src/LoadLog.cpp
index 5c903033ff4fa1986dca0cda30074b3bc8ab5777..b312bf2a83242887d4459f2881815191a81bb30e 100644
--- a/Framework/DataHandling/src/LoadLog.cpp
+++ b/Framework/DataHandling/src/LoadLog.cpp
@@ -39,6 +39,24 @@ using API::WorkspaceProperty;
using DataObjects::Workspace2D_sptr;
using Types::Core::DateAndTime;
+namespace {
+
+template <class MapClass, class LoggerType>
+void addLogDataToRun(Mantid::API::Run &run, MapClass &aMap,
+ LoggerType &logger) {
+ for (auto &itr : aMap) {
+ try {
+ run.addLogData(itr.second.release());
+ } catch (std::invalid_argument &e) {
+ logger.warning() << e.what() << '\n';
+ } catch (Exception::ExistsError &e) {
+ logger.warning() << e.what() << '\n';
+ }
+ }
+}
+
+} // namespace
+
/// Empty default constructor
LoadLog::LoadLog() {}
@@ -288,18 +306,8 @@ void LoadLog::loadThreeColumnLogFile(std::ifstream &logFileStream,
}
}
}
- try {
- for (auto &itr : dMap) {
- run.addLogData(itr.second.release());
- }
- for (auto &sitr : sMap) {
- run.addLogData(sitr.second.release());
- }
- } catch (std::invalid_argument &e) {
- g_log.warning() << e.what();
- } catch (Exception::ExistsError &e) {
- g_log.warning() << e.what();
- }
+ addLogDataToRun(run, dMap, g_log);
+ addLogDataToRun(run, sMap, g_log);
}
/**
diff --git a/Framework/DataHandling/test/LoadLogTest.h b/Framework/DataHandling/test/LoadLogTest.h
index 8238532187042ce3f9dd37c3443e99b759c67572..13212a393045857e284f2268e43149f009083f65 100644
--- a/Framework/DataHandling/test/LoadLogTest.h
+++ b/Framework/DataHandling/test/LoadLogTest.h
@@ -3,23 +3,25 @@
#include <cxxtest/TestSuite.h>
-#include "MantidDataHandling/LoadLog.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidGeometry/Instrument.h"
-#include "MantidDataObjects/Workspace2D.h"
+#include "MantidAPI/Algorithm.h"
#include "MantidAPI/AnalysisDataService.h"
-#include "MantidKernel/Exception.h"
#include "MantidAPI/FrameworkManager.h"
#include "MantidAPI/Workspace.h"
-#include "MantidAPI/Algorithm.h"
+#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidDataHandling/LoadLog.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/Component.h"
+#include "MantidKernel/Exception.h"
#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidTestHelpers/ScopedFileHelper.h"
#include <vector>
using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::DataHandling;
using namespace Mantid::DataObjects;
+using namespace ScopedFileHelper;
using Mantid::Types::Core::DateAndTime;
class LoadLogTest : public CxxTest::TestSuite {
@@ -135,6 +137,37 @@ public:
AnalysisDataService::Instance().remove(outputSpace);
}
+ void test_log_file_has_error() {
+ std::string logFileText("2007-11-16T13:25:48 i1 0 \n"
+ "2007-11-16T13:29:36 str1 a\n"
+ "2007-11-16T13:29:49 i2 1\n"
+ "2007-11-16T13:30:21 str2 b\n"
+ "2007-11-16T13:32:38 num1 3\n"
+ "2007-11-16T13:43:40 nspectra 12\n"
+ "2007-11-16T13:44:33 num2 4\n"
+ "2007-11-16T14:00:21 str3 c\n");
+ ScopedFile file(logFileText, "test_log_file.log");
+ MatrixWorkspace_sptr ws =
+ WorkspaceFactory::Instance().create("Workspace2D", 1, 1, 1);
+ ws->mutableRun().addProperty("nspectra", 1);
+ // "nspectra" is already in the logs when LoadLog runs
+ LoadLog alg;
+ alg.initialize();
+ alg.setPropertyValue("Filename", file.getFileName());
+ alg.setProperty("Workspace", ws);
+ alg.execute();
+ auto props = ws->run().getProperties();
+ TS_ASSERT_EQUALS(props.size(), 8);
+ TS_ASSERT(ws->run().hasProperty("nspectra"));
+ TS_ASSERT(ws->run().hasProperty("i1"));
+ TS_ASSERT(ws->run().hasProperty("i2"));
+ TS_ASSERT(ws->run().hasProperty("num1"));
+ TS_ASSERT(ws->run().hasProperty("num2"));
+ TS_ASSERT(ws->run().hasProperty("str1"));
+ TS_ASSERT(ws->run().hasProperty("str2"));
+ TS_ASSERT(ws->run().hasProperty("str3"));
+ }
+
void do_test_SNSTextFile(std::string names, std::string units, bool willFail,
bool createWorkspace = true,
std::string expectedLastUnit = "Furlongs") {
diff --git a/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventListener.h b/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventListener.h
index e9410dced555084aef336391bd13fb4811574417..bacb2556ca7777c7263abd4ef52e892b80daca21 100644
--- a/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventListener.h
+++ b/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventListener.h
@@ -74,6 +74,8 @@ public:
ILiveListener::RunStatus runStatus() override;
int runNumber() const override;
+ bool dataReset() override;
+
private:
std::unique_ptr<KafkaEventStreamDecoder> m_decoder = nullptr;
std::string m_instrumentName;
diff --git a/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventStreamDecoder.h b/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventStreamDecoder.h
index cb5abb0d20945d56b4743b92c08cbdb06279cb6b..1caa65e8232551c76c587d44f57fa8fe804b9e90 100644
--- a/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventStreamDecoder.h
+++ b/Framework/LiveData/inc/MantidLiveData/Kafka/KafkaEventStreamDecoder.h
@@ -1,5 +1,5 @@
-#ifndef MANTID_LIVEDATA_ISISKAFKAEVENTSTREAMDECODER_H_
-#define MANTID_LIVEDATA_ISISKAFKAEVENTSTREAMDECODER_H_
+#ifndef MANTID_LIVEDATA_KAFKAEVENTSTREAMDECODER_H_
+#define MANTID_LIVEDATA_KAFKAEVENTSTREAMDECODER_H_
#include "MantidAPI/SpectraDetectorTypes.h"
#include "MantidDataObjects/EventWorkspace.h"
@@ -15,7 +15,7 @@ namespace Mantid {
namespace LiveData {
/**
- High-level interface to ISIS Kafka event system. It requires
+ High-level interface to Kafka event system. It requires
3 topic names of the data streams.
A call to capture() starts the process of capturing the stream on a separate
@@ -69,6 +69,7 @@ public:
bool hasData() const noexcept;
int runNumber() const noexcept { return m_runNumber; }
bool hasReachedEndOfRun() noexcept;
+ bool dataReset();
///@}
///@name Callbacks
@@ -92,24 +93,36 @@ private:
size_t nPeriods;
int64_t runStartMsgOffset;
};
+ /// Main loop of listening for data messages and populating the cache
+ /// workspaces
void captureImpl() noexcept;
void captureImplExcept();
- void initLocalCaches();
- DataObjects::EventWorkspace_sptr createBufferWorkspace(const size_t nspectra,
+ /// Create the cache workspaces, LoadLiveData extracts data from these
+ void initLocalCaches(const std::string &rawMsgBuffer,
+ const RunStartStruct &runStartData);
+ DataObjects::EventWorkspace_sptr createBufferWorkspace(size_t nspectra,
const int32_t *spec,
const int32_t *udet,
- const uint32_t length);
+ uint32_t length);
DataObjects::EventWorkspace_sptr
createBufferWorkspace(const DataObjects::EventWorkspace_sptr &parent);
+
+ /// Load a named instrument into a workspace
void loadInstrument(const std::string &name,
DataObjects::EventWorkspace_sptr workspace);
+
+ /// Get an expected message from the run information topic
int64_t getRunInfoMessage(std::string &rawMsgBuffer);
+
+ /// Get an expected RunStart message
RunStartStruct getRunStartMessage(std::string &rawMsgBuffer);
+ /// Populate cache workspaces with data from messages
void eventDataFromMessage(const std::string &buffer);
void sampleDataFromMessage(const std::string &buffer);
+ /// For LoadLiveData to extract the cached data
API::Workspace_sptr extractDataImpl();
/// Broker to use to subscribe to topics
@@ -160,25 +173,37 @@ private:
/// EndRun
bool m_runStatusSeen;
std::atomic<bool> m_extractedEndRunData;
+ /// Indicate if the next data to be extracted should replace LoadLiveData's
+ /// output workspace
+ std::atomic<bool> m_dataReset;
void waitForDataExtraction();
void waitForRunEndObservation();
+ /// Methods for checking if the end of a run was reached
std::unordered_map<std::string, std::vector<int64_t>> getStopOffsets(
std::unordered_map<std::string, std::vector<int64_t>> &stopOffsets,
std::unordered_map<std::string, std::vector<bool>> &reachedEnd,
uint64_t stopTime) const;
-
void checkIfAllStopOffsetsReached(
const std::unordered_map<std::string, std::vector<bool>> &reachedEnd,
bool &checkOffsets);
- // Callbacks
+ /// Callbacks for unit tests
CallbackFn m_cbIterationEnd;
CallbackFn m_cbError;
+
+ /// Waits until a run start message with higher run number is received
+ bool waitForNewRunStartMessage(RunStartStruct &runStartStructOutput);
+ /// Subscribe to event stream at the time specified in a run start message
+ void joinEventStreamAtTime(const RunStartStruct &runStartData);
+ /// Convert a duration in nanoseconds to milliseconds
+ int64_t nanosecondsToMilliseconds(uint64_t timeNanoseconds) const;
+ /// Get a det-spec map message using the time specified in a run start message
+ std::string getDetSpecMapForRun(const RunStartStruct &runStartStruct);
};
} // namespace LiveData
} // namespace Mantid
-#endif /* MANTID_LIVEDATA_ISISKAFKAEVENTSTREAMDECODER_H_ */
+#endif /* MANTID_LIVEDATA_KAFKAEVENTSTREAMDECODER_H_ */
diff --git a/Framework/LiveData/src/Kafka/KafkaEventListener.cpp b/Framework/LiveData/src/Kafka/KafkaEventListener.cpp
index 567a2a883801c81139820eb895db3351835116da..d8bc0a74d163aa3a0543f1e478f0b11d05d06da6 100644
--- a/Framework/LiveData/src/Kafka/KafkaEventListener.cpp
+++ b/Framework/LiveData/src/Kafka/KafkaEventListener.cpp
@@ -97,5 +97,10 @@ API::ILiveListener::RunStatus KafkaEventListener::runStatus() {
int KafkaEventListener::runNumber() const {
return (m_decoder ? m_decoder->runNumber() : -1);
}
+
+/// @copydoc ILiveListener::dataReset
+bool KafkaEventListener::dataReset() {
+ return (m_decoder ? m_decoder->dataReset() : false);
+}
}
}
diff --git a/Framework/LiveData/src/Kafka/KafkaEventStreamDecoder.cpp b/Framework/LiveData/src/Kafka/KafkaEventStreamDecoder.cpp
index 1de3cca7717c31050de637311c035331d08e1dc4..d702caa6db8a3189a43dd6f1ec1a6355926796bf 100644
--- a/Framework/LiveData/src/Kafka/KafkaEventStreamDecoder.cpp
+++ b/Framework/LiveData/src/Kafka/KafkaEventStreamDecoder.cpp
@@ -18,8 +18,8 @@ GCC_DIAG_OFF(conversion)
#include "private/Schema/ba57_run_info_generated.h"
#include "private/Schema/df12_det_spec_map_generated.h"
#include "private/Schema/ev42_events_generated.h"
-#include "private/Schema/is84_isis_events_generated.h"
#include "private/Schema/f142_logdata_generated.h"
+#include "private/Schema/is84_isis_events_generated.h"
GCC_DIAG_ON(conversion)
using namespace Mantid::Types;
@@ -107,14 +107,7 @@ void KafkaEventStreamDecoder::startCapture(bool startNow) {
m_broker->subscribe({m_runInfoTopic}, SubscribeAtOption::LASTTWO);
std::string rawMsgBuffer;
auto runStartData = getRunStartMessage(rawMsgBuffer);
- auto startTimeMilliseconds =
- runStartData.startTime / 1000000; // nanoseconds to milliseconds
- m_eventStream = m_broker->subscribe(
- {m_eventTopic, m_runInfoTopic, m_sampleEnvTopic},
- static_cast<int64_t>(startTimeMilliseconds), SubscribeAtOption::TIME);
- // make sure we listen to the run start topic starting from the run start
- // message we already got the start time from
- m_eventStream->seek(m_runInfoTopic, 0, runStartData.runStartMsgOffset);
+ joinEventStreamAtTime(runStartData);
} else {
m_eventStream =
m_broker->subscribe({m_eventTopic, m_runInfoTopic, m_sampleEnvTopic},
@@ -131,6 +124,33 @@ void KafkaEventStreamDecoder::startCapture(bool startNow) {
m_thread.detach();
}
+/** Indicate if the next data to be extracted should replace LoadLiveData's
+ * output workspace,
+ * for example the first data of a new run
+ */
+bool KafkaEventStreamDecoder::dataReset() {
+ bool result = (m_dataReset == true); // copy from atomic bool
+ m_dataReset = false; // reset to false
+ return result;
+}
+
+void KafkaEventStreamDecoder::joinEventStreamAtTime(
+ const KafkaEventStreamDecoder::RunStartStruct &runStartData) {
+ auto runStartTime = runStartData.startTime;
+ int64_t startTimeMilliseconds = nanosecondsToMilliseconds(runStartTime);
+ m_eventStream =
+ m_broker->subscribe({m_eventTopic, m_runInfoTopic, m_sampleEnvTopic},
+ startTimeMilliseconds, SubscribeAtOption::TIME);
+ // make sure we listen to the run start topic starting from the run start
+ // message we already got the start time from
+ m_eventStream->seek(m_runInfoTopic, 0, runStartData.runStartMsgOffset);
+}
+
+int64_t KafkaEventStreamDecoder::nanosecondsToMilliseconds(
+ uint64_t timeNanoseconds) const {
+ return static_cast<int64_t>(timeNanoseconds / 1000000);
+}
+
/**
* Stop capturing from the stream. This is a blocking call until the capturing
* function has completed
@@ -246,26 +266,35 @@ void KafkaEventStreamDecoder::captureImpl() noexcept {
*/
void KafkaEventStreamDecoder::captureImplExcept() {
g_log.debug("Event capture starting");
- initLocalCaches();
- m_interrupt = false;
- m_endRun = false;
- m_runStatusSeen = false;
- m_extractedEndRunData = true;
+ // Load spectra-detector and runstart struct then initialise the cache
std::string buffer;
+ std::string runBuffer;
int64_t offset;
int32_t partition;
std::string topicName;
+ m_spDetStream->consumeMessage(&buffer, offset, partition, topicName);
+ auto runStartStruct = getRunStartMessage(runBuffer);
+ initLocalCaches(buffer, runStartStruct);
+
+ m_interrupt = false; // Allow MonitorLiveData or user to interrupt
+ m_endRun = false; // Indicates to MonitorLiveData that end of run is reached
+ m_runStatusSeen = false; // Flag to ensure MonitorLiveData observes end of run
+ // Flag to ensure LoadLiveData extracts data before start of next run
+ m_extractedEndRunData = true;
+
+ // Keep track of whether we've reached the end of a run
std::unordered_map<std::string, std::vector<int64_t>> stopOffsets;
std::unordered_map<std::string, std::vector<bool>> reachedEnd;
- // True when should be checking if run stop offsets have been reached
bool checkOffsets = false;
while (!m_interrupt) {
- if (m_endRun)
+ if (m_endRun) {
waitForRunEndObservation();
- else
+ continue;
+ } else {
waitForDataExtraction();
+ }
// Pull in events
m_eventStream->consumeMessage(&buffer, offset, partition, topicName);
// No events, wait for some to come along...
@@ -327,12 +356,6 @@ void KafkaEventStreamDecoder::captureImplExcept() {
stopOffsets = getStopOffsets(stopOffsets, reachedEnd, stopTime);
checkOffsets = true;
checkIfAllStopOffsetsReached(reachedEnd, checkOffsets);
- } else if (runMsg->info_type_type() == InfoTypes_RunStart) {
- auto runStartMsg = static_cast<const RunStart *>(runMsg->info_type());
- m_runNumber = runStartMsg->run_number();
- auto runStartTime =
- static_cast<time_t>(runStartMsg->start_time() / 1000000000);
- m_runStart.set_from_time_t(runStartTime);
}
}
m_cbIterationEnd();
@@ -401,9 +424,6 @@ KafkaEventStreamDecoder::getStopOffsets(
auto &partitionOffsets = topicOffsets.second;
for (uint32_t partitionNumber = 0;
partitionNumber < partitionOffsets.size(); partitionNumber++) {
- // -1 to get last offset _before_ the stop time
- partitionOffsets[partitionNumber] =
- partitionOffsets[partitionNumber] - 1;
auto offset = partitionOffsets[partitionNumber];
// If the stop offset is negative then there are no messages for us
// to collect on this topic, so mark reachedEnd as true already
@@ -444,10 +464,94 @@ void KafkaEventStreamDecoder::waitForRunEndObservation() {
m_endRun = false;
m_runStatusSeen = false;
runStatusLock.unlock();
+
+ // Set to zero until we have the new run number, MonitorLiveData will
+ // queries before each time it extracts data until it gets non-zero
+ m_runNumber = 0;
+
+ // Get new run message now so that new run number is available for
+ // MonitorLiveData as early as possible
+ RunStartStruct runStartStruct;
+ if (waitForNewRunStartMessage(runStartStruct))
+ return;
+
// Give time for MonitorLiveData to act on runStatus information
// and trigger m_interrupt for next loop iteration if user requested
// LiveData algorithm to stop at the end of the run
std::this_thread::sleep_for(std::chrono::milliseconds(100));
+ if (m_interrupt)
+ return;
+
+ // Rejoin event stream at start of new run
+ joinEventStreamAtTime(runStartStruct);
+ std::string detSpecMapMsgBuffer = getDetSpecMapForRun(runStartStruct);
+ initLocalCaches(detSpecMapMsgBuffer, runStartStruct);
+}
+
+/**
+ * Try to find a detector-spectrum map message published after the
+ * current run start time
+ *
+ * @param runStartStruct details of the current run
+ * @return received detector-spectrum map message buffer
+ */
+std::string KafkaEventStreamDecoder::getDetSpecMapForRun(
+ const KafkaEventStreamDecoder::RunStartStruct &runStartStruct) {
+ std::string rawMsgBuffer;
+ int64_t offset;
+ int32_t partition;
+ std::string topicName;
+ m_spDetStream = m_broker->subscribe(
+ {m_spDetTopic}, nanosecondsToMilliseconds(runStartStruct.startTime),
+ SubscribeAtOption::TIME);
+ m_spDetStream->consumeMessage(&rawMsgBuffer, offset, partition, topicName);
+ if (rawMsgBuffer.empty()) {
+ std::runtime_error(
+ "No detector-spectrum map message found for run number " +
+ std::to_string(runStartStruct.runNumber));
+ }
+ return rawMsgBuffer;
+}
+
+/**
+ * Wait for a run start message until we get one with a higher run number
+ * than the current run or the algorithm is interrupted
+ *
+ * @param runStartStructOutput details of the new run
+ * @return true if interrupted, false if got a new run start message
+ */
+bool KafkaEventStreamDecoder::waitForNewRunStartMessage(
+ RunStartStruct &runStartStructOutput) {
+ while (!m_interrupt) {
+ std::string runMsgBuffer;
+
+ int64_t offset;
+ int32_t partition;
+ std::string topicName;
+ m_runStream->consumeMessage(&runMsgBuffer, offset, partition, topicName);
+ if (runMsgBuffer.empty()) {
+ continue; // no message available, try again
+ } else {
+ auto runMsg =
+ GetRunInfo(reinterpret_cast<const uint8_t *>(runMsgBuffer.c_str()));
+ if (runMsg->info_type_type() == InfoTypes_RunStart) {
+ // We got a run start message, deserialise it
+ auto runStartData = static_cast<const RunStart *>(runMsg->info_type());
+ KafkaEventStreamDecoder::RunStartStruct runStartStruct = {
+ runStartData->instrument_name()->str(), runStartData->run_number(),
+ runStartData->start_time(),
+ static_cast<size_t>(runStartData->n_periods()), offset};
+ if (runStartStruct.runNumber > m_runNumber) {
+ runStartStructOutput = runStartStruct;
+ m_runNumber = runStartStruct.runNumber;
+ return false; // not interrupted
+ }
+ } else {
+ continue; // received message wasn't a RunStart message, try again
+ }
+ }
+ }
+ return true; // interrupted
}
/**
@@ -461,7 +565,7 @@ void KafkaEventStreamDecoder::waitForRunEndObservation() {
void KafkaEventStreamDecoder::sampleDataFromMessage(const std::string &buffer) {
std::lock_guard<std::mutex> lock(m_mutex);
- // Add sample log values to every the workspace for every period
+ // Add sample log values to every workspace for every period
for (const auto &periodBuffer : m_localEvents) {
auto &mutableRunInfo = periodBuffer->mutableRun();
@@ -559,14 +663,9 @@ KafkaEventStreamDecoder::getRunStartMessage(std::string &rawMsgBuffer) {
* By the end of this method the local event buffer is ready to accept
* events
*/
-void KafkaEventStreamDecoder::initLocalCaches() {
- std::string rawMsgBuffer;
+void KafkaEventStreamDecoder::initLocalCaches(
+ const std::string &rawMsgBuffer, const RunStartStruct &runStartData) {
- // Load spectra-detector mapping from stream
- int64_t offset;
- int32_t partition;
- std::string topicName;
- m_spDetStream->consumeMessage(&rawMsgBuffer, offset, partition, topicName);
if (rawMsgBuffer.empty()) {
throw std::runtime_error("KafkaEventStreamDecoder::initLocalCaches() - "
"Empty message received from spectrum-detector "
@@ -583,13 +682,14 @@ void KafkaEventStreamDecoder::initLocalCaches() {
"found nspec=" << nspec << ", ndet=" << nudet;
throw std::runtime_error(os.str());
}
+
+ m_runNumber = runStartData.runNumber;
+
// Create buffer
auto eventBuffer = createBufferWorkspace(
static_cast<size_t>(spDetMsg->n_spectra()), spDetMsg->spectrum()->data(),
spDetMsg->detector_id()->data(), nudet);
- // Load run metadata
- auto runStartData = getRunStartMessage(rawMsgBuffer);
// Load the instrument if possible but continue if we can't
auto instName = runStartData.instrumentName;
if (!instName.empty())
@@ -606,8 +706,8 @@ void KafkaEventStreamDecoder::initLocalCaches() {
auto timeString = m_runStart.toISO8601String();
// Run number
mutableRun.addProperty(RUN_START_PROPERTY, std::string(timeString));
- m_runNumber = runStartData.runNumber;
- mutableRun.addProperty(RUN_NUMBER_PROPERTY, std::to_string(m_runNumber));
+ mutableRun.addProperty(RUN_NUMBER_PROPERTY,
+ std::to_string(runStartData.runNumber));
// Create the proton charge property
mutableRun.addProperty(
new Kernel::TimeSeriesProperty<double>(PROTON_CHARGE_PROPERTY));
@@ -622,13 +722,18 @@ void KafkaEventStreamDecoder::initLocalCaches() {
"KafkaEventStreamDecoder - Message has n_periods==0. This is "
"an error by the data producer");
}
- std::lock_guard<std::mutex> lock(m_mutex);
- m_localEvents.resize(nperiods);
- m_localEvents[0] = eventBuffer;
- for (size_t i = 1; i < nperiods; ++i) {
- // A clone should be cheap here as there are no events yet
- m_localEvents[i] = eventBuffer->clone();
+ {
+ std::lock_guard<std::mutex> lock(m_mutex);
+ m_localEvents.resize(nperiods);
+ m_localEvents[0] = eventBuffer;
+ for (size_t i = 1; i < nperiods; ++i) {
+ // A clone should be cheap here as there are no events yet
+ m_localEvents[i] = eventBuffer->clone();
+ }
}
+
+ // New caches so LoadLiveData's output workspace needs to be replaced
+ m_dataReset = true;
}
/**
diff --git a/Framework/LiveData/src/Kafka/KafkaTopicSubscriber.cpp b/Framework/LiveData/src/Kafka/KafkaTopicSubscriber.cpp
index af2e75c343f750650f2d66cb67019d62f643b2f6..0aa79a2a999ab437e819b23f815eccde01d266ea 100644
--- a/Framework/LiveData/src/Kafka/KafkaTopicSubscriber.cpp
+++ b/Framework/LiveData/src/Kafka/KafkaTopicSubscriber.cpp
@@ -157,6 +157,11 @@ KafkaTopicSubscriber::getCurrentOffsets() {
throw std::runtime_error("In KafkaTopicSubscriber failed to lookup "
"current partition assignment.");
}
+ error = m_consumer->position(partitions);
+ if (error != RdKafka::ERR_NO_ERROR) {
+ throw std::runtime_error("In KafkaTopicSubscriber failed to lookup "
+ "current partition positions.");
+ }
for (auto topicPartition : partitions) {
std::vector<int64_t> offsetList = {topicPartition->offset()};
auto result = currentOffsets.emplace(
diff --git a/Framework/LiveData/test/KafkaEventStreamDecoderTest.h b/Framework/LiveData/test/KafkaEventStreamDecoderTest.h
index 6a83ccdd50fcf8815e054f1efd6ba00631a2533f..a8e9621d918a92c814e18e286518213c816aa1f6 100644
--- a/Framework/LiveData/test/KafkaEventStreamDecoderTest.h
+++ b/Framework/LiveData/test/KafkaEventStreamDecoderTest.h
@@ -85,7 +85,6 @@ public:
TSM_ASSERT(
"Expected an EventWorkspace from extractData(). Found something else",
eventWksp);
-
checkWorkspaceMetadata(*eventWksp);
checkWorkspaceEventData(*eventWksp);
}
@@ -106,6 +105,8 @@ public:
.WillOnce(Return(new FakeISISSpDetStreamSubscriber));
auto decoder = createTestDecoder(mockBroker);
// Need 2 full loops to get both periods
+ // Note: Only 2 iterations required as FakeISISEventSubscriber does not send
+ // start/stop messages
startCapturing(*decoder, 2);
Workspace_sptr workspace;
@@ -132,6 +133,67 @@ public:
}
}
+ void test_Varying_Period_Event_Stream() {
+ /**
+ * Test that period number is correctly updated between runs
+ * e.g If the first run has 1 period and the next has 2 periods
+ */
+ using namespace ::testing;
+ using namespace KafkaTesting;
+ using Mantid::API::Workspace_sptr;
+ using Mantid::API::WorkspaceGroup;
+ using Mantid::DataObjects::EventWorkspace;
+ using namespace Mantid::LiveData;
+
+ auto mockBroker = std::make_shared<MockKafkaBroker>();
+ EXPECT_CALL(*mockBroker, subscribe_(_, _))
+ .Times(Exactly(3))
+ .WillOnce(Return(new FakeVariablePeriodSubscriber(0))) // 1st run
+ .WillOnce(Return(new FakeRunInfoStreamSubscriberVaryingNPeriods))
+ .WillOnce(Return(new FakeISISSpDetStreamSubscriber));
+ EXPECT_CALL(*mockBroker, subscribe_(_, _, _))
+ .Times(Exactly(2))
+ .WillOnce(Return(new FakeVariablePeriodSubscriber(4))) // 2nd run
+ .WillOnce(
+ Return(new FakeISISSpDetStreamSubscriber)); // det-spec for 2nd run
+
+ auto decoder = createTestDecoder(mockBroker);
+ TSM_ASSERT("Decoder should not have create data buffers yet",
+ !decoder->hasData());
+ // Run start, Event, Run stop, Run start (2 period)
+ startCapturing(*decoder, 4);
+ Workspace_sptr workspace;
+ // Extract the data from single period and inform the decoder
+ TS_ASSERT_THROWS_NOTHING(workspace = decoder->extractData());
+ TS_ASSERT(decoder->hasReachedEndOfRun());
+ // Continue to capture multi period data
+ // (one extra iteration to ensure stop signal is acted on before data
+ // extraction)
+ continueCapturing(*decoder, 7);
+ TS_ASSERT_THROWS_NOTHING(workspace = decoder->extractData());
+ TS_ASSERT(decoder->hasReachedEndOfRun());
+ TS_ASSERT_THROWS_NOTHING(decoder->stopCapture());
+ TS_ASSERT(!decoder->isCapturing());
+
+ // --- Workspace checks ---
+ TSM_ASSERT("Expected non-null workspace pointer from extractData()",
+ workspace);
+ auto group = boost::dynamic_pointer_cast<WorkspaceGroup>(workspace);
+ TSM_ASSERT(
+ "Expected a WorkspaceGroup from extractData(). Found something else.",
+ group);
+
+ TS_ASSERT_EQUALS(2, group->size());
+ for (size_t i = 0; i < 2; ++i) {
+ auto eventWksp =
+ boost::dynamic_pointer_cast<EventWorkspace>(group->getItem(i));
+ TSM_ASSERT("Expected an EventWorkspace for each member of the group",
+ eventWksp);
+ checkWorkspaceMetadata(*eventWksp);
+ checkWorkspaceEventData(*eventWksp);
+ }
+ }
+
void test_End_Of_Run_Reported_After_Run_Stop_Reached() {
using namespace ::testing;
using namespace KafkaTesting;
@@ -354,19 +416,30 @@ private:
uint8_t maxIterations) {
// Register callback to know when a whole loop as been iterated through
m_niterations = 0;
- auto callback = [this, maxIterations]() {
- {
- std::unique_lock<std::mutex> lock(this->m_callbackMutex);
- this->m_niterations++;
- if (this->m_niterations == maxIterations) {
- lock.unlock();
- this->m_callbackCondition.notify_one();
- }
- }
- };
+ auto callback =
+ [this, maxIterations]() { this->iterationCallback(maxIterations); };
decoder.registerIterationEndCb(callback);
decoder.registerErrorCb(callback);
TS_ASSERT_THROWS_NOTHING(decoder.startCapture());
+ continueCapturing(decoder, maxIterations);
+ }
+
+ void iterationCallback(uint8_t maxIterations) {
+ std::unique_lock<std::mutex> lock(this->m_callbackMutex);
+ this->m_niterations++;
+ if (this->m_niterations == maxIterations) {
+ lock.unlock();
+ this->m_callbackCondition.notify_one();
+ }
+ }
+
+ void continueCapturing(Mantid::LiveData::KafkaEventStreamDecoder &decoder,
+ uint8_t maxIterations) {
+ // Re-register callback with the (potentially) new value of maxIterations
+ auto callback =
+ [this, maxIterations]() { this->iterationCallback(maxIterations); };
+ decoder.registerIterationEndCb(callback);
+ decoder.registerErrorCb(callback);
{
std::unique_lock<std::mutex> lk(m_callbackMutex);
this->m_callbackCondition.wait(lk, [this, maxIterations]() {
diff --git a/Framework/LiveData/test/KafkaTesting.h b/Framework/LiveData/test/KafkaTesting.h
index 01e1d6b342b66878188c23b973e0220b54a98af9..10fccde3adf19a3f535466174d5fb3d24ea7cb5e 100644
--- a/Framework/LiveData/test/KafkaTesting.h
+++ b/Framework/LiveData/test/KafkaTesting.h
@@ -12,8 +12,8 @@ GCC_DIAG_OFF(conversion)
#include "Kafka/private/Schema/ba57_run_info_generated.h"
#include "Kafka/private/Schema/df12_det_spec_map_generated.h"
#include "Kafka/private/Schema/ev42_events_generated.h"
-#include "Kafka/private/Schema/is84_isis_events_generated.h"
#include "Kafka/private/Schema/f142_logdata_generated.h"
+#include "Kafka/private/Schema/is84_isis_events_generated.h"
GCC_DIAG_ON(conversion)
#include <ctime>
@@ -69,17 +69,20 @@ public:
UNUSED_ARG(topic);
throw std::runtime_error("FakeExceptionThrowingStreamSubscriber");
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {
std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return offsets;
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -103,17 +106,20 @@ public:
UNUSED_ARG(partition);
UNUSED_ARG(topic);
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {
std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return offsets;
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -229,17 +235,20 @@ public:
UNUSED_ARG(partition);
UNUSED_ARG(topic);
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {
std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return offsets;
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -281,16 +290,19 @@ public:
UNUSED_ARG(partition);
UNUSED_ARG(topic);
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {std::pair<std::string, std::vector<int64_t>>(m_topicName, {1})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return {std::pair<std::string, std::vector<int64_t>>(m_topicName, {1})};
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -322,17 +334,20 @@ public:
UNUSED_ARG(partition);
UNUSED_ARG(topic);
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {
std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return offsets;
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -358,21 +373,74 @@ public:
fakeReceiveARunStartMessage(buffer, m_runNumber, m_startTime, m_instName,
m_nperiods);
+ m_runNumber++;
+ UNUSED_ARG(offset);
+ UNUSED_ARG(partition);
+ UNUSED_ARG(topic);
+ }
+
+ std::unordered_map<std::string, std::vector<int64_t>>
+ getOffsetsForTimestamp(int64_t timestamp) override {
+ UNUSED_ARG(timestamp);
+ return {
+ std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
+ }
+
+ std::unordered_map<std::string, std::vector<int64_t>>
+ getCurrentOffsets() override {
+ std::unordered_map<std::string, std::vector<int64_t>> offsets;
+ return offsets;
+ }
+
+ void seek(const std::string &topic, uint32_t partition,
+ int64_t offset) override {
+ UNUSED_ARG(topic);
+ UNUSED_ARG(partition);
+ UNUSED_ARG(offset);
+ }
+
+private:
+ std::string m_startTime = "2016-08-31T12:07:42";
+ int32_t m_runNumber = 1000;
+ std::string m_instName = "HRPDTEST";
+ int32_t m_nperiods = 1;
+};
+
+// -----------------------------------------------------------------------------
+// Fake run data stream with incrementing number of periods
+// -----------------------------------------------------------------------------
+class FakeRunInfoStreamSubscriberVaryingNPeriods
+ : public Mantid::LiveData::IKafkaStreamSubscriber {
+public:
+ void subscribe() override {}
+ void subscribe(int64_t offset) override { UNUSED_ARG(offset) }
+ void consumeMessage(std::string *buffer, int64_t &offset, int32_t &partition,
+ std::string &topic) override {
+ assert(buffer);
+
+ fakeReceiveARunStartMessage(buffer, m_runNumber, m_startTime, m_instName,
+ m_nperiods);
+
+ m_nperiods++;
+ m_runNumber++;
UNUSED_ARG(offset);
UNUSED_ARG(partition);
UNUSED_ARG(topic);
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {
std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return offsets;
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -387,6 +455,82 @@ private:
int32_t m_nperiods = 1;
};
+// -----------------------------------------------------------------------------
+// Varing period data stream with run and event messages
+// -----------------------------------------------------------------------------
+class FakeVariablePeriodSubscriber
+ : public Mantid::LiveData::IKafkaStreamSubscriber {
+public:
+ explicit FakeVariablePeriodSubscriber(uint32_t startOffset)
+ : m_nextOffset(startOffset) {}
+ void subscribe() override {}
+ void subscribe(int64_t offset) override { UNUSED_ARG(offset) }
+ void consumeMessage(std::string *buffer, int64_t &offset, int32_t &partition,
+ std::string &topic) override {
+ assert(buffer);
+
+ // Return messages in this order:
+ // Run start (with 1 period)
+ // Event data
+ // Run start (with 2 periods)
+ // Run stop
+ // Event data
+ // Event data (data for 2nd period)
+ // Run stop
+
+ switch (m_nextOffset) {
+ case 0:
+ fakeReceiveARunStartMessage(buffer, 1000, m_startTime, m_instName,
+ m_nperiods);
+ break;
+ case 2:
+ fakeReceiveARunStartMessage(buffer, 1001, m_startTime, m_instName, 2);
+ break;
+ case 3:
+ fakeReceiveARunStopMessage(buffer, m_stopTime);
+ break;
+ case 5:
+ fakeReceiveAnISISEventMessage(buffer, 1);
+ break;
+ case 6:
+ fakeReceiveARunStopMessage(buffer, m_stopTime);
+ break;
+ default:
+ fakeReceiveAnISISEventMessage(buffer, 0);
+ }
+ topic = "topic_name";
+ offset = m_nextOffset;
+ partition = 0;
+ m_nextOffset++;
+ }
+
+ std::unordered_map<std::string, std::vector<int64_t>>
+ getOffsetsForTimestamp(int64_t timestamp) override {
+ UNUSED_ARG(timestamp);
+ return {std::pair<std::string, std::vector<int64_t>>(m_topicName, {2})};
+ }
+
+ std::unordered_map<std::string, std::vector<int64_t>>
+ getCurrentOffsets() override {
+ return {std::pair<std::string, std::vector<int64_t>>(m_topicName, {2})};
+ }
+
+ void seek(const std::string &topic, uint32_t partition,
+ int64_t offset) override {
+ UNUSED_ARG(topic);
+ UNUSED_ARG(partition);
+ UNUSED_ARG(offset);
+ }
+
+private:
+ const std::string m_topicName = "topic_name";
+ uint32_t m_nextOffset;
+ std::string m_startTime = "2016-08-31T12:07:42";
+ std::string m_stopTime = "2016-08-31T12:07:52";
+ const std::string m_instName = "HRPDTEST";
+ int32_t m_nperiods = 1;
+};
+
// -----------------------------------------------------------------------------
// Fake data stream with run and event messages
// -----------------------------------------------------------------------------
@@ -429,19 +573,20 @@ public:
partition = 0;
m_nextOffset++;
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
- // + 1 because rdkafka::offsetsForTimes returns the first offset _after_ the
- // given timestamp
return {std::pair<std::string, std::vector<int64_t>>(m_topicName,
- {m_stopOffset + 1})};
+ {m_stopOffset})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
return {std::pair<std::string, std::vector<int64_t>>(m_topicName,
{m_nextOffset - 1})};
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
@@ -486,17 +631,20 @@ public:
UNUSED_ARG(partition);
UNUSED_ARG(topic);
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getOffsetsForTimestamp(int64_t timestamp) override {
UNUSED_ARG(timestamp);
return {
std::pair<std::string, std::vector<int64_t>>("topic_name", {1, 2, 3})};
}
+
std::unordered_map<std::string, std::vector<int64_t>>
getCurrentOffsets() override {
std::unordered_map<std::string, std::vector<int64_t>> offsets;
return offsets;
}
+
void seek(const std::string &topic, uint32_t partition,
int64_t offset) override {
UNUSED_ARG(topic);
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/BinaryOperations.cpp b/Framework/PythonInterface/mantid/api/src/Exports/BinaryOperations.cpp
index 2b17e22dd61246cdda5b989c54b92d9d9cc6b6d3..e35e23bf6a8c8b794fdf4e1199a047cabf622dbe 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/BinaryOperations.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/BinaryOperations.cpp
@@ -156,31 +156,50 @@ ResultType performBinaryOpWithDouble(const LHSType inputWS, const double value,
const std::string &op,
const std::string &name, bool inplace,
bool reverse) {
- const std::string &algoName = op;
-
- // Create the single valued workspace first so that it is run as a top-level
- // algorithm
- // such that it's history can be recreated
- API::Algorithm_sptr alg = API::AlgorithmManager::Instance().createUnmanaged(
+ // RAII struct to add/remove workspace from ADS
+ struct ScopedADSEntry {
+ ScopedADSEntry(const std::string &entryName,
+ const MatrixWorkspace_sptr &value)
+ : name(entryName) {
+ ads.addOrReplace(entryName, value);
+ }
+ ~ScopedADSEntry() { ads.remove(name); }
+
+ const std::string &name;
+ API::AnalysisDataServiceImpl &ads = API::AnalysisDataService::Instance();
+ };
+
+ // In order to recreate a history record of the final binary operation
+ // there must be a record of the creation of the single value workspace used
+ // on the RHS here. This is achieved by running CreateSingleValuedWorkspace
+ // algorithm and adding the output workspace to the ADS. Adding the output
+ // to the ADS is critical so that workspace.name() is updated, by the ADS, to
+ // return the same string. WorkspaceProperty<TYPE>::createHistory() then
+ // records the correct workspace name for input into the final binary
+ // operation rather than creating a temporary name.
+ auto alg = API::AlgorithmManager::Instance().createUnmanaged(
"CreateSingleValuedWorkspace");
alg->setChild(false);
+ // we manually store the workspace as it's easier to retrieve the correct
+ // type from alg->getProperty rather than calling the ADS again and casting
alg->setAlwaysStoreInADS(false);
alg->initialize();
alg->setProperty<double>("DataValue", value);
- const std::string tmp_name("not_applicable");
- alg->setPropertyValue("OutputWorkspace", tmp_name);
+ const std::string tmpName("__python_binary_op_single_value");
+ alg->setPropertyValue("OutputWorkspace", tmpName);
alg->execute();
+
MatrixWorkspace_sptr singleValue;
if (alg->isExecuted()) {
singleValue = alg->getProperty("OutputWorkspace");
} else {
- throw std::runtime_error(
- "performBinaryOp: Error in execution of CreateSingleValuedWorkspace");
+ throw std::runtime_error("performBinaryOp: Error in execution of "
+ "CreateSingleValuedWorkspace");
}
- // Call the function above with the signle-value workspace
+ ScopedADSEntry removeOnExit(tmpName, singleValue);
ResultType result =
performBinaryOp<LHSType, MatrixWorkspace_sptr, ResultType>(
- inputWS, singleValue, algoName, name, inplace, reverse);
+ inputWS, singleValue, op, name, inplace, reverse);
return result;
}
diff --git a/Framework/PythonInterface/plugins/algorithms/RefineSatellitePeaks.py b/Framework/PythonInterface/plugins/algorithms/FindSatellitePeaks.py
similarity index 64%
rename from Framework/PythonInterface/plugins/algorithms/RefineSatellitePeaks.py
rename to Framework/PythonInterface/plugins/algorithms/FindSatellitePeaks.py
index 5ac6f4baa15865596b8a50d6ef673978019a8278..8fe13342dd650925b80b5fc0f884e736a8f84437 100644
--- a/Framework/PythonInterface/plugins/algorithms/RefineSatellitePeaks.py
+++ b/Framework/PythonInterface/plugins/algorithms/FindSatellitePeaks.py
@@ -2,18 +2,23 @@ from mantid.kernel import *
from mantid.dataobjects import PeaksWorkspaceProperty
from mantid.api import *
from mantid.simpleapi import *
+import fractional_indexing as indexing
-import numpy as np
-from scipy.spatial import KDTree
-from scipy.cluster.vq import kmeans2
-import scipy.cluster.hierarchy as hcluster
-
-class RefineSatellitePeaks(DataProcessorAlgorithm):
+class FindSatellitePeaks(DataProcessorAlgorithm):
def category(self):
return 'Crystal\\Peaks'
+ def seeAlso(self):
+ return [ "IndexSatellitePeaks" ]
+
+ def name(self):
+ return "FindSatellitePeaks"
+
+ def summary(self):
+ return "Algorithm for finding satellite peaks in an MDWorkspace in the HKL frame."
+
def PyInit(self):
self.declareProperty(PeaksWorkspaceProperty(name="NuclearPeaks",
defaultValue="",
@@ -71,12 +76,12 @@ class RefineSatellitePeaks(DataProcessorAlgorithm):
nuclear = self.getProperty("NuclearPeaks").value
sats = self.getProperty("SatellitePeaks").value
- nuclear_hkls = self.get_hkls(nuclear)
- sats_hkls = self.get_hkls(sats)
+ nuclear_hkls = indexing.get_hkls(nuclear)
+ sats_hkls = indexing.get_hkls(sats)
- qs = self.find_q_vectors(nuclear_hkls, sats_hkls)
- clusters, k = self.cluster_qs(qs, threshold=cluster_threshold)
- qs = self.average_clusters(qs, clusters)
+ qs = indexing.find_q_vectors(nuclear_hkls, sats_hkls)
+ clusters, k = indexing.cluster_qs(qs, threshold=cluster_threshold, k=k)
+ qs = indexing.average_clusters(qs, clusters)
predicted_satellites = self.create_fractional_peaks_workspace(qs, nuclear)
centroid_satellites = CentroidPeaksMD(InputWorkspace=md, PeaksWorkspace=predicted_satellites,
@@ -92,73 +97,6 @@ class RefineSatellitePeaks(DataProcessorAlgorithm):
self.log().notice("Q vectors are: \n{}".format(qs))
self.setProperty("OutputWorkspace", satellites_int_spherical)
- def get_hkls(self, peaks_workspace):
- """Return a 2D numpy array from a peaks workspace.
-
- :param peaks_workpace: the PeaksWorkspace to extract HKL values from
- :returns: np.ndarry -- 2D array of HKL values
- """
- return np.array([np.array([peak['h'], peak['k'], peak['l']]) for peak in peaks_workspace])
-
- def cluster_qs(self, qs, k=None, threshold=1.5):
- """Cluster q vectors into discrete groups.
-
- Classifies each of the q vectors into a number of clusters. The number of clusters used is decided by the parameters passed:
- * If the k parameter is supplied then the q vectors are grouped into k clusters using kmeans.
- * If the threshold parameter is supplied then the q vectors a split into groups based on cophenetic distance.
-
- :param qs: list of q vectors to cluster. Each element should be a numpy array of length three.
- :param k: number of clusters to use (optional).
- :param threshold: cophenetic distance cut off point for new clusters (optional)
- :returns: tuple (clusters, k)
- Where:
- list -- clusters is a list of cluster indicies which each q belongs to
- int -- k is the number of clusters used
- """
- if k is not None:
- centroid, clusters = kmeans2(qs, k)
- else:
- clusters = hcluster.fclusterdata(qs, threshold, criterion="distance")
- return clusters, len(set(clusters))
-
- def average_clusters(self, qs, clusters):
- """Find the centroid of the clusters.
-
- For each q vector, group them by their designated cluster and then compute
- the average of the group.
-
- :param qs: list of q vectors. Each element should be a numpy array.
- :param clusters: the indicies of the cluster that each q belongs to.
- :returns: np.ndarry -- the list of centroids for each cluster.
- """
-
- averaged_qs = []
- for cluster_index in set(clusters):
- averaged_qs.append(np.mean(qs[clusters==cluster_index], axis=0))
- return np.array(averaged_qs)
-
- def find_q_vectors(self, nuclear_hkls, sats_hkls):
- """Find the q vector between the nuclear HKLs and the satellite peaks
-
- Given a list of HKL positions and a list of fractional HKL positions of
- satellite peaks, find the difference between each satellite and its nearest
- integer HKL.
-
- :param nuclear_hkls: the positions of integer HKL peaks.
- :param sats_hkl: the positions of fractional "satellite" HKL peaks.
- :returns: np.ndarray -- array of q vectors.
- """
- peak_map = KDTree(nuclear_hkls)
- qs = []
- for sat in sats_hkls:
- distance, index = peak_map.query(sat, k=1)
- if distance > 2:
- #peak to far away from satellite ignore
- continue
- nearest_peak = nuclear_hkls[index]
- qs.append(sat - nearest_peak)
- return np.array(qs)
-
def create_fractional_peaks_workspace(self, qs, nuclear):
"""Generate a peaks workspace of possible satellite peaks from a list of q vectors.
@@ -179,4 +117,4 @@ class RefineSatellitePeaks(DataProcessorAlgorithm):
return predicted_satellites
-AlgorithmFactory.subscribe(RefineSatellitePeaks)
+AlgorithmFactory.subscribe(FindSatellitePeaks)
diff --git a/Framework/PythonInterface/plugins/algorithms/IndexSatellitePeaks.py b/Framework/PythonInterface/plugins/algorithms/IndexSatellitePeaks.py
new file mode 100644
index 0000000000000000000000000000000000000000..375a12114f8e5b128eba618b8310cf42db2b763d
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/IndexSatellitePeaks.py
@@ -0,0 +1,151 @@
+import numpy as np
+from scipy.spatial import KDTree
+import fractional_indexing as indexing
+
+from mantid.kernel import Direction
+from mantid.api import (IPeaksWorkspaceProperty,
+ ITableWorkspaceProperty, PythonAlgorithm, AlgorithmFactory)
+import mantid.simpleapi as api
+
+
+class IndexSatellitePeaks(PythonAlgorithm):
+
+ def category(self):
+ return 'Crystal\\Peaks'
+
+ def seeAlso(self):
+ return [ "FindSatellitePeaks" ]
+
+ def name(self):
+ return "IndexSatellitePeaks"
+
+ def summary(self):
+ return "Algorithm for indexing satellite peaks in superspace"
+
+ def PyInit(self):
+ self.declareProperty(IPeaksWorkspaceProperty(name="NuclearPeaks",
+ defaultValue="",
+ direction=Direction.Input),
+ doc="Main integer HKL peaks. Q vectors will be calculated relative to these peaks.")
+
+ self.declareProperty(IPeaksWorkspaceProperty(name="SatellitePeaks",
+ defaultValue="",
+ direction=Direction.Input),
+ doc="Positions of satellite peaks with fractional \
+ HKL coordinates")
+
+ self.declareProperty(ITableWorkspaceProperty(name="OutputWorkspace",
+ defaultValue="",
+ direction=Direction.Output),
+ doc="The indexed satellite peaks. This will be a \
+ table workspace with miller indicies h, k, l, m1, \
+ m2, ..., mn.")
+
+ self.declareProperty('Tolerance', 0.3, direction=Direction.Input,
+ doc="Tolerance on the noise of the q vectors")
+
+ self.declareProperty('NumOfQs', 1, direction=Direction.Input,
+ doc="Number of independant q vectors")
+
+ self.declareProperty('ClusterThreshold', 1.5, direction=Direction.Input,
+ doc="Threshold for automaticallty deciding on the number of q vectors to use. If NumOfQs found is set then this \
+ is property is ignored.")
+
+ def PyExec(self):
+ tolerance = self.getProperty("Tolerance").value
+ k = int(self.getProperty("NumOfQs").value)
+ nuclear = self.getProperty("NuclearPeaks").value
+ satellites = self.getProperty("SatellitePeaks").value
+ cluster_threshold = self.getProperty("ClusterThreshold").value
+ n_trunc_decimals = int(np.ceil(abs(np.log10(tolerance))))
+
+ if nuclear.getNumberPeaks() == 0:
+ raise RuntimeError("The NuclearPeaks parameter must have at least one peak")
+
+ if satellites.getNumberPeaks() == 0:
+ raise RuntimeError("The SatellitePeaks parameter must have at least one peak")
+
+ nuclear_hkls = indexing.get_hkls(nuclear)
+ sats_hkls = indexing.get_hkls(satellites)
+
+ qs = indexing.find_q_vectors(nuclear_hkls, sats_hkls)
+ self.log().notice("K value is {}".format(k))
+
+ k = None if k == -1 else k
+ clusters, k = indexing.cluster_qs(qs, k=k, threshold=cluster_threshold)
+
+ qs = indexing.average_clusters(qs, clusters)
+ qs = indexing.trunc_decimals(qs, n_trunc_decimals)
+ qs = indexing.sort_vectors_by_norm(qs)
+
+ self.log().notice("Q vectors are: \n{}".format(qs))
+
+ indices = indexing.index_q_vectors(qs, tolerance)
+ ndim = indices.shape[1] + 3
+
+ hkls = indexing.find_nearest_integer_peaks(nuclear_hkls, sats_hkls)
+
+ hklm = np.zeros((hkls.shape[0], ndim))
+ hklm[:, :3] = np.round(hkls)
+
+ raw_qs = hkls - sats_hkls
+ peak_map = KDTree(qs)
+ for i, q in enumerate(raw_qs):
+ distance, index = peak_map.query(q, k=1)
+ hklm[i, 3:] = indices[index]
+
+ indexed = self.create_indexed_workspace(satellites, ndim, hklm)
+ self.setProperty("OutputWorkspace", indexed)
+
+ def create_indexed_workspace(self, fractional_peaks, ndim, hklm):
+ """Create a TableWorkepace that contains indexed peak data.
+
+ This produces a TableWorkepace that looks like a PeaksWorkspace but
+ with the additional index columns included. In future releases support
+ for indexing should be added to the PeaksWorkspace data type itself.
+
+ :param fractional_peaks: the peaks workspace containing peaks with
+ fractional HKL values.
+ :param ndim: the number of additional indexing columns to add.
+ :param hklm: the new higher dimensional miller indicies to add.
+ :returns: a table workspace with the indexed peak data
+ """
+ # Create table with the number of columns we need
+ types = ['int', 'long64', 'double', 'double', 'double', 'double', 'double', 'double',
+ 'double', 'double', 'double', 'float', 'str', 'float', 'float', 'V3D', 'V3D']
+ name = self.getPropertyValue("OutputWorkspace")
+ indexed = api.CreateEmptyTableWorkspace(name)
+ names = fractional_peaks.getColumnNames()
+
+ # Insert the extra columns for the addtional indicies
+ for i in range(ndim - 3):
+ names.insert(5 + i, 'm{}'.format(i + 1))
+ types.insert(5 + i, 'double')
+
+ names = np.array(names)
+ types = np.array(types)
+
+ # Create columns in the table workspace
+ for name, column_type in zip(names, types):
+ indexed.addColumn(column_type, name)
+
+ # Copy all columns from original workspace, ignoring HKLs
+ column_data = []
+ idx = np.arange(0, names.size)
+ hkl_mask = (idx < 2) | (idx > 4 + (ndim - 3))
+ for name in names[hkl_mask]:
+ column_data.append(fractional_peaks.column(name))
+
+ # Insert the addtional HKL columns into the data
+ for i, col in enumerate(hklm.T.tolist()):
+ column_data.insert(i + 2, col)
+
+ # Insert the columns into the table workspace
+ for i in range(fractional_peaks.rowCount()):
+ row = [column_data[j][i] for j in range(indexed.columnCount())]
+ indexed.addRow(row)
+
+ return indexed
+
+
+AlgorithmFactory.subscribe(IndexSatellitePeaks)
diff --git a/Framework/PythonInterface/plugins/algorithms/SaveGEMMAUDParamFile.py b/Framework/PythonInterface/plugins/algorithms/SaveGEMMAUDParamFile.py
index 87e24f224fdaecc696dc66e83d31e95a360e4f6d..dc56f6cc7ee83aa15b9044d4c6bbf2d41a010bfc 100644
--- a/Framework/PythonInterface/plugins/algorithms/SaveGEMMAUDParamFile.py
+++ b/Framework/PythonInterface/plugins/algorithms/SaveGEMMAUDParamFile.py
@@ -85,7 +85,12 @@ class SaveGEMMAUDParamFile(PythonAlgorithm):
def create_empty_param_list(default_value="0"):
return "\n".join(default_value for _ in range(num_banks))
- with open(self.getProperty(self.PROP_TEMPLATE_FILE).value) as template_file:
+ template_file_path = self.getProperty(self.PROP_TEMPLATE_FILE).value
+ if len(template_file_path) == 0:
+ logger.error("Could not find default diffraction directory for .maud template file: "
+ "you'll have to find it yourself")
+
+ with open(template_file_path) as template_file:
template = template_file.read()
output_params["function_types"] = create_empty_param_list("1")
@@ -136,8 +141,6 @@ class SaveGEMMAUDParamFile(PythonAlgorithm):
if os.path.exists(path_to_test):
return path_to_test
- logger.warning("Could not find default diffraction directory for .maud template file: "
- "you'll have to find it yourself")
return ""
def _format_param_list(self, param_list):
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ISISIndirectEnergyTransfer.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ISISIndirectEnergyTransfer.py
index 0264b539e70ba35a53f60c52c73b4bae8561bed3..cfac6af11333b81e12211ea16bac8584b24b9430 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ISISIndirectEnergyTransfer.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ISISIndirectEnergyTransfer.py
@@ -360,9 +360,6 @@ class ISISIndirectEnergyTransfer(DataProcessorAlgorithm):
self._output_ws = self.getPropertyValue('OutputWorkspace')
- if self._grouping_string is not None:
- self._grouping_string = self._grouping_string.replace('-', ':')
-
# Disable sum files if there is only one file
if len(self._data_files) == 1:
if self._sum_files:
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLReductionQENS.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLReductionQENS.py
index 85b1ab7b4ddb5498a991341eb50b0f4ad0b4fccd..75a0e432b648f8dd11f3a71275f0271ef1e1a772 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLReductionQENS.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLReductionQENS.py
@@ -271,7 +271,7 @@ class IndirectILLReductionQENS(PythonAlgorithm):
for item in mtd[tmp_int]:
for index in range(item.getNumberHistograms()):
if item.readY(index)[0] <= 0:
- raise RuntimeError('Negative or 0 integral in spectrum #{0} {1}'.format(index,message))
+ self.log().warning('Negative or 0 integral in spectrum #{0} {1}'.format(index,message))
DeleteWorkspace(tmp_int)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSBeamCentreFinder.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSBeamCentreFinder.py
index 75a461497d5d538c539c58b07ec6148960644b90..7780bcf3ccb1c6a90d96491d9be5b68759ae940a 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSBeamCentreFinder.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSBeamCentreFinder.py
@@ -187,8 +187,8 @@ class SANSBeamCentreFinder(DataProcessorAlgorithm):
residueTB.append(self._calculate_residuals(sample_quartiles[MaskingQuadrant.Top],
sample_quartiles[MaskingQuadrant.Bottom]))
if(j == 0):
- logger.notice("Itr " + str(j) + ": (" + str(self.scale_1 * centre1) + ", " + str(self.scale_2 * centre2) + ") SX="
- + str(residueLR[j]) + " SY=" + str(residueTB[j]))
+ logger.notice("Itr {0}: ( {1}, {2} ) SX={3:.5g} SY={4:.5g}".
+ format(j, self.scale_1 * centre1, self.scale_2 * centre2, residueLR[j], residueTB[j]))
if mantidplot:
self._plot_quartiles(output_workspaces, state.data.sample_scatter)
@@ -200,8 +200,8 @@ class SANSBeamCentreFinder(DataProcessorAlgorithm):
if residueTB[j] > residueTB[j-1]:
position_2_step = - position_2_step / 2
- logger.notice("Itr " + str(j) + ": (" + str(self.scale_1 * centre1) + ", " + str(self.scale_2 * centre2) + ") SX="
- + str(residueLR[j]) + " SY=" + str(residueTB[j]))
+ logger.notice("Itr {0}: ( {1}, {2} ) SX={3:.5g} SY={4:.5g}".
+ format(j, self.scale_1 * centre1, self.scale_2 * centre2, residueLR[j], residueTB[j]))
if (residueLR[j]+residueTB[j]) < (residueLR[j-1]+residueTB[j-1]) or state.compatibility.use_compatibility_mode:
centre_1_hold = centre1
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSSave.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSSave.py
index a3fa9121a8378898af8d6d15dbcab46395797783..8b1691134d19d728101a872bc411b2983c78b81d 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSSave.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSSave.py
@@ -127,7 +127,7 @@ class SANSSave(DataProcessorAlgorithm):
# SaveNXcanSAS clashes with SaveNexusProcessed
self.add_file_format_with_appended_name_requirement(file_formats, SaveType.NXcanSAS, file_types,
- [SaveType.Nexus])
+ [])
# SaveNISTDAT clashes with SaveRKH, both can save to .dat
self.add_file_format_with_appended_name_requirement(file_formats, SaveType.NistQxy, file_types, [SaveType.RKH])
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransformToIqt.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransformToIqt.py
index 4dc32f79920b617f299ec6d76c3137225b6a24a1..e660256e1f83c7501c64db3d0ae9984881f710c9 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransformToIqt.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransformToIqt.py
@@ -3,8 +3,10 @@ from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
from mantid.api import (PythonAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty,
ITableWorkspaceProperty, PropertyMode, Progress)
-from mantid.kernel import Direction, logger
-import math
+from mantid.kernel import Direction, logger, IntBoundedValidator
+
+DEFAULT_ITERATIONS = 50
+DEFAULT_SEED = 89631139
class TransformToIqt(PythonAlgorithm):
@@ -17,6 +19,8 @@ class TransformToIqt(PythonAlgorithm):
_parameter_table = None
_output_workspace = None
_dry_run = None
+ _number_of_iterations = None
+ _seed = None
def category(self):
return "Workflow\\Inelastic;Workflow\\MIDAS"
@@ -43,6 +47,12 @@ class TransformToIqt(PythonAlgorithm):
doc='Decrease total number of spectrum points by this ratio through merging of '
'intensities from neighbouring bins. Default=1')
+ self.declareProperty('NumberOfIterations', DEFAULT_ITERATIONS, IntBoundedValidator(lower=1),
+ doc="Number of randomised simulations for monte-carlo error calculation.")
+
+ self.declareProperty('SeedValue', DEFAULT_SEED, IntBoundedValidator(lower=1),
+ doc="Seed for pseudo-random number generator in monte-carlo error calculation.")
+
self.declareProperty(ITableWorkspaceProperty('ParameterWorkspace', '',
direction=Direction.Output,
optional=PropertyMode.Optional),
@@ -62,7 +72,7 @@ class TransformToIqt(PythonAlgorithm):
self._calculate_parameters()
if not self._dry_run:
- self._transform()
+ self._output_workspace = self._transform()
self._add_logs()
@@ -93,6 +103,9 @@ class TransformToIqt(PythonAlgorithm):
if self._parameter_table == '':
self._parameter_table = getWSprefix(self._sample) + 'TransformToIqtParameters'
+ self._number_of_iterations = self.getProperty("NumberOfIterations").value
+ self._seed = self.getProperty("SeedValue").value
+
self._output_workspace = self.getPropertyValue('OutputWorkspace')
if self._output_workspace == '':
self._output_workspace = getWSprefix(self._sample) + 'iqt'
@@ -200,7 +213,6 @@ class TransformToIqt(PythonAlgorithm):
Run TransformToIqt.
"""
from IndirectCommon import CheckHistZero, CheckHistSame, CheckAnalysers
- trans_prog = Progress(self, start=0.3, end=0.8, nreports=15)
try:
CheckAnalysers(self._sample, self._resolution)
except ValueError:
@@ -215,92 +227,15 @@ class TransformToIqt(PythonAlgorithm):
if num_res_hist > 1:
CheckHistSame(self._sample, 'Sample', self._resolution, 'Resolution')
- # Float conversion to str differs in precision between python 2 and 3, this gives consistent results
- rebin_param = '{:.14f},{:.14f},{:.14f}'.format(self._e_min, self._e_width, self._e_max)
- trans_prog.report('Rebinning Workspace')
- Rebin(InputWorkspace=self._sample,
- OutputWorkspace='__sam_data',
- Params=rebin_param,
- FullBinsOnly=True)
-
- # Sample
- trans_prog.report('Rebinning sample')
- Rebin(InputWorkspace='__sam_data',
- OutputWorkspace='__sam_data',
- Params=rebin_param)
- trans_prog.report('Integrating Sample')
- Integration(InputWorkspace='__sam_data',
- OutputWorkspace='__sam_int')
- trans_prog.report('Converting Sample to data points')
- ConvertToPointData(InputWorkspace='__sam_data',
- OutputWorkspace='__sam_data')
- trans_prog.report('Extracting FFT spectrum for Sample')
- ExtractFFTSpectrum(InputWorkspace='__sam_data',
- OutputWorkspace='__sam_fft',
- FFTPart=2)
- trans_prog.report('Dividing Sample')
- Divide(LHSWorkspace='__sam_fft',
- RHSWorkspace='__sam_int',
- OutputWorkspace='__sam')
-
- # Resolution
- trans_prog.report('Rebinnig Resolution')
- Rebin(InputWorkspace=self._resolution,
- OutputWorkspace='__res_data',
- Params=rebin_param)
- trans_prog.report('Integrating Resolution')
- Integration(InputWorkspace='__res_data',
- OutputWorkspace='__res_int')
- trans_prog.report('Converting Resolution to data points')
- ConvertToPointData(InputWorkspace='__res_data',
- OutputWorkspace='__res_data')
- trans_prog.report('Extractig FFT Resolution spectrum')
- ExtractFFTSpectrum(InputWorkspace='__res_data',
- OutputWorkspace='__res_fft',
- FFTPart=2)
- trans_prog.report('Dividing Resolution')
- Divide(LHSWorkspace='__res_fft',
- RHSWorkspace='__res_int',
- OutputWorkspace='__res')
-
- trans_prog.report('Diving Workspaces')
- Divide(LHSWorkspace='__sam',
- RHSWorkspace='__res',
- OutputWorkspace=self._output_workspace)
-
- # Cleanup sample workspaces
- trans_prog.report('Deleting Sample temp')
- DeleteWorkspace('__sam_data')
- DeleteWorkspace('__sam_int')
- DeleteWorkspace('__sam_fft')
- DeleteWorkspace('__sam')
-
- # Crop nonsense values off workspace
- binning = int(math.ceil(mtd[self._output_workspace].blocksize() / 2.0))
- bin_v = mtd[self._output_workspace].dataX(0)[binning]
- trans_prog.report('Cropping output')
- CropWorkspace(InputWorkspace=self._output_workspace,
- OutputWorkspace=self._output_workspace,
- XMax=bin_v)
-
- # Replace NaN values in last bin, with zeroes
- ReplaceSpecialValues(InputWorkspace=self._output_workspace,
- OutputWorkspace=self._output_workspace,
- InfinityValue=0.0,
- BigNumberThreshold=1.0001,
- NaNValue=0.0)
+ iqt = CalculateIqt(InputWorkspace=self._sample, ResolutionWorkspace=self._resolution, EnergyMin=self._e_min,
+ EnergyMax=self._e_max, EnergyWidth=self._e_width,
+ NumberOfIterations=self._number_of_iterations, SeedValue=self._seed,
+ StoreInADS=False, OutputWorkspace="__ciqt")
# Set Y axis unit and label
- mtd[self._output_workspace].setYUnit('')
- mtd[self._output_workspace].setYUnitLabel('Intensity')
-
- trans_prog.report('Deleting Resolution temp')
- # Clean up resolution workspaces
- DeleteWorkspace('__res_data')
- DeleteWorkspace('__res_int')
- DeleteWorkspace('__res_fft')
- DeleteWorkspace('__res')
-
+ iqt.setYUnit('')
+ iqt.setYUnitLabel('Intensity')
+ return iqt
# Register algorithm with Mantid
AlgorithmFactory.subscribe(TransformToIqt)
diff --git a/Framework/PythonInterface/plugins/algorithms/fractional_indexing.py b/Framework/PythonInterface/plugins/algorithms/fractional_indexing.py
new file mode 100644
index 0000000000000000000000000000000000000000..a6f5ba568d6867d7a97f40dc9d68fab20caa7ce7
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/fractional_indexing.py
@@ -0,0 +1,302 @@
+import itertools
+import numpy as np
+import scipy.cluster.hierarchy as hcluster
+from scipy.cluster.vq import kmeans2
+from scipy.spatial import KDTree
+
+_MAX_REFLECTIONS = 10
+
+
+def find_bases(qs, tolerance):
+ """Find bases for the higher dimensional indexing scheme
+
+ This will attempt to find a set of basis vectors for the
+ higher dimensional indexing scheme.
+
+ :param qs: list of q vectors in HKL space defining satellite peak offsets
+ :param tolerance: the tolerance how close each vector must be to be indexed
+ using the generated scheme
+ :return: tuple of (number of dimensions, nx3 matrix of basis vectors)
+ """
+ qs = list(sort_vectors_by_norm(qs))
+ final_qs = [qs.pop(0)]
+ refs, hkls = generate_hkl_grid(np.array(final_qs), _MAX_REFLECTIONS)
+
+ for q in qs:
+ regenerate_grid = not is_indexed(q, refs, tolerance)
+
+ if regenerate_grid:
+ final_qs.append(q)
+ refs, hkls = generate_hkl_grid(np.array(final_qs), _MAX_REFLECTIONS)
+
+ return len(final_qs), np.vstack(final_qs)
+
+
+def generate_hkl_grid(bases, upper_bound):
+ """Generate a grid of reflections and hkl values
+
+ :param bases: the set of bases to generate the reflections and HKL grid.
+ :param upper_bound: the upper bound HKL index to generate
+ :return tuple of (nx3 matrix of reflections, nx3 matrix of HKL indices)
+ """
+ search_range = np.arange(-upper_bound, upper_bound)
+ ndim = len(bases)
+ hkls = np.array(list(itertools.product(*[search_range] * ndim)))
+ reflections = np.array([np.dot(bases.T, hkl) for hkl in hkls])
+ return reflections, hkls
+
+
+def find_nearest_hkl(qs, reflections, hkls, tolerance):
+ """Find the nearest HKL value that indexes each of the q vectors
+
+ :param qs: the q vectors for satellite peaks to index
+ :param reflections: the list of reflections to search
+ :param hkls: the list of hkl values mapping to each reflection
+ :param tolerance: the tolerance on the difference between a given q and
+ the nearest reflection
+ :return: MxN matrix of integers indexing the q vectors. Unindexed vectors
+ will be returned as all zeros.
+ """
+ kdtree = KDTree(reflections)
+
+ final_indexing = []
+ for i, q in enumerate(qs):
+ result = kdtree.query_ball_point(q, r=tolerance)
+ if len(result) > 0:
+ smallest = sort_vectors_by_norm(hkls[result])
+ final_indexing.append(smallest[0])
+ else:
+ final_indexing.append(np.zeros_like(hkls.shape[1]))
+
+ return np.vstack(final_indexing)
+
+
+def is_indexed(q, reflections, tolerance):
+ """Check if a q vector is indexed by a set of reflections
+
+ :param q: the q vector to check
+ :param reflections: the list of reflections to find if this matches
+ :param tolerance: the tolerance on the difference between q and the nearest
+ reflection.
+ :return: whether this q is indexed by this list of reflections
+ """
+ kdtree = KDTree(reflections)
+ result = kdtree.query_ball_point(q, r=tolerance)
+ return len(result) > 0
+
+
+def unique_rows(a):
+ """Return the unique rows of a numpy array
+
+ In numpy >= 1.13 np.unique(x, axis=0) can be user instead. But for versions of
+ numpy before 1.13 this function can be used to achieve the same result.
+
+ :param a: the array to find unique rows for.
+ :returns: the unique rows of a
+ """
+ a = np.ascontiguousarray(a)
+ unique_a = np.unique(a.view([('', a.dtype)] * a.shape[1]))
+ return unique_a.view(a.dtype).reshape((unique_a.shape[0], a.shape[1]))
+
+
+def index_q_vectors(qs, tolerance=.03):
+ """Find the n-dimensional index of a collection of q vectors
+
+ This function will automatically attempt infer the correct number of
+ additional dimensions required to index the given list of q vectors.
+
+ :param qs: the q vectors to find indicies for
+ :param tolerance: the tolerance on whether two equivilent or multiple qs
+ should be classifed as the same.
+ :return: ndarray of indicies for each q vector
+ """
+
+ ndim, bases = find_bases(qs, tolerance)
+ refs, hkls = generate_hkl_grid(bases, _MAX_REFLECTIONS)
+ return find_nearest_hkl(qs, refs, hkls, tolerance)
+
+
+def cluster_qs(qs, k=None, threshold=1.5):
+ """Cluster q vectors into discrete groups.
+
+ Classifies each of the q vectors into a number of clusters. The number of clusters used is decided by the parameters passed:
+ * If the k parameter is supplied then the q vectors are grouped into k clusters using kmeans.
+ * If the threshold parameter is supplied then the q vectors a split into groups based on cophenetic distance.
+
+ :param qs: list of q vectors to cluster. Each element should be a numpy array of length three.
+ :param k: number of clusters to use (optional).
+ :param threshold: cophenetic distance cut off point for new clusters (optional)
+ :returns: tuple (clusters, k)
+ Where:
+ list -- clusters is a list of cluster indicies which each q belongs to
+ int -- k is the number of clusters used
+ """
+ if k is not None:
+ centroids = kmeans_plus_plus(qs, k)
+ _, clusters = kmeans2(qs, centroids, minit='matrix')
+ if len(set(clusters)) != k:
+ raise ValueError("Could not group the satellite reflections "
+ "into {} clusters. Please check that you have "
+ "at least {} satellites.".format(k,k))
+ else:
+ clusters = hcluster.fclusterdata(qs, threshold, criterion="distance")
+ return clusters, len(set(clusters))
+
+
+def find_q_vectors(nuclear_hkls, sats_hkls):
+ """Find the q vector between the nuclear HKLs and the satellite peaks
+
+ Given a list of HKL positions and a list of fractional HKL positions of
+ satellite peaks, find the difference between each satellite and its nearest
+ integer HKL.
+
+ :param nuclear_hkls: the positions of integer HKL peaks.
+ :param sats_hkls: the positions of fractional "satellite" HKL peaks.
+ :returns: np.ndarray -- array of q vectors.
+ """
+ peak_map = KDTree(nuclear_hkls)
+ qs = []
+ for sat in sats_hkls:
+ distance, index = peak_map.query(sat, k=1)
+ if distance > 2:
+ # peak too far away from satellite ignore
+ continue
+ nearest_peak = nuclear_hkls[index]
+ qs.append(sat - nearest_peak)
+ return np.array(qs)
+
+
+def find_nearest_integer_peaks(nuclear_hkls, sat_hkls):
+ """Find the nearest integer peak for each fractional peak
+
+ This will perform a spatial search to find the intger peak which is nearest the fractional satellite peak.
+
+ :param nuclear_hkls: the hkl poistions of each of the nuclear peaks.
+ :param sat_hkls: the fractional hkl position of the satellite peaks.
+ :returns: np.ndarray -- 2D array of HKL integer values for each fractional peak
+ """
+ peak_map = KDTree(nuclear_hkls)
+ hkls = []
+ for sat in sat_hkls:
+ distance, index = peak_map.query(sat, k=1)
+ nearest_peak = nuclear_hkls[index]
+ hkls.append(nearest_peak)
+ return np.array(hkls)
+
+
+def average_clusters(qs, clusters):
+ """Compute the centroid of each cluster of vectors
+
+ :param qs: the q vectors to find the centroids of
+ :param clusters: the cluster index that each q belongs to
+ :return: an ndarray of cluster centroids
+ """
+ averaged_qs = []
+ for cluster_index in set(clusters):
+ averaged_qs.append(np.mean(qs[clusters == cluster_index], axis=0))
+ return np.array(averaged_qs)
+
+
+def get_hkls(peaks_workspace):
+ """Get the H, K, and L columns from a PeaksWorkspace.
+
+ :param peaks_workspace: the peaks workspace to extract HKL values from
+ :return: 2D numpy array of HKL values.
+ """
+ return np.array([np.array([peak['h'], peak['k'], peak['l']])
+ for peak in peaks_workspace])
+
+
+def remove_noninteger(matrix):
+ """Remove any non integer values from a matrix
+
+ :param matrix: the matrix to remove non integer values from
+ :return: matrix with non integer elements set to zero
+ """
+ matrix[np.absolute(np.mod(matrix, 1)) > 1e-14] = 0
+ return matrix
+
+
+def trunc_decimals(vec, n_decimals=2):
+ """Truncate the elements of a vector below n decimals places
+
+ :param vec: the vector to truncate the elements of
+ :param n_decimals: the number of decimal places to truncate from
+ :return: the vector with truncated elements
+ """
+ decade = 10**n_decimals
+ return np.trunc(vec*decade)/decade
+
+
+def sort_vectors_by_norm(vecs):
+ """Sort a list of row vectors by the Euclidean norm
+ :param vecs: vectors to sort according to their norms
+ :returns: ndarray of sorted row vectors
+ """
+ idx = np.argsort(norm_along_axis(np.abs(vecs)))
+ vecs = vecs[idx]
+ return vecs
+
+
+def norm_along_axis(vecs, axis=-1):
+ """Compute the euclidean norm along the rows of a matrix
+
+ :param vecs: vectors to compute the Euclidean norm for
+ :param axis: the axis to compute the norm along
+ :return: a ndarray with the norms along the chosen axis
+ """
+ return np.sum(vecs**2, axis=axis)**(1./2)
+
+
+def kmeans_plus_plus(points, k):
+ """Generate centroids for kmeans using the kmeans++ algorithm
+
+ Select a good set of starting values for kmeans by weighting the choice of
+ the next centroid by the distance to the existing centroids.
+
+ This algorithm roughly works as follows:
+ 1) The first centroid is selected uniformly from the data.
+ 2) The squared euclidean distance between all points to all centroids is calculated.
+ 3) Take the minimum computed distance for each point over all centroids.
+ 4) Normalise the list of distances
+ 5) Choose a new centroid weighted by the computed distances
+
+ :param points: the points to select centroids from
+ :param k: the desired number of centroids
+ :return: Kx3 matrix of centroids
+ """
+ if points.shape[0] < k:
+ raise RuntimeError("k is greater than the number of points! Please choose a smaller k value")
+
+ centroid_indices = []
+ centroids = []
+
+ # pick the first point uniformly at random from the data
+ indices = np.indices(points.shape)[0][:, 0]
+ centroid_index = np.random.choice(indices)
+ centroid = points[centroid_index]
+
+ centroid_indices.append(centroid_index)
+ centroids.append(centroid)
+
+ for i in range(k-1):
+ # choose all points that are not already centroids
+ mask = np.array([x for x in indices if x not in centroid_indices])
+ pts = points[mask]
+
+ # calculate probability distribution for being picked based on squared
+ # distance from each centroid
+ distance_squared = np.array([norm_along_axis(pts - c, axis=1)**2 for c in centroids])
+ distance_squared = np.min(distance_squared, axis=0)
+ distance_squared /= np.sum(distance_squared)
+
+ # choose a new random centroid weighted by how far it is from the other
+ # centroids
+ centroid_index = np.random.choice(mask, p=distance_squared)
+ centroid_index = indices[centroid_index]
+ centroid = points[centroid_index]
+
+ centroid_indices.append(centroid_index)
+ centroids.append(centroid)
+
+ return np.array(centroids)
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
index 1031a6a8e4d6c52e78c8ca3e87fb7f16b0031f32..2aa190d32ad242014581c093468d62cef0510403 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
@@ -45,9 +45,11 @@ set ( TEST_PY_FILES
FindEPPTest.py
FindReflectometryLinesTest.py
FitGaussianTest.py
+ FractionalIndexingTest.py
GetEiT0atSNSTest.py
GetNegMuMuonicXRDTest.py
IndirectTransmissionTest.py
+ IndexSatellitePeaksTest.py
LoadAndMergeTest.py
LoadDNSLegacyTest.py
LoadEmptyVesuvioTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f1c5982ca115d88a71e2919498d34dac745e5a4
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py
@@ -0,0 +1,246 @@
+import unittest
+import numpy as np
+import numpy.testing as npt
+import fractional_indexing as indexing
+
+from mantid.geometry import UnitCell
+from mantid.simpleapi import CreatePeaksWorkspace, CreateSimulationWorkspace
+
+
+class FractionIndexingTests(unittest.TestCase):
+
+ def setUp(self):
+ # Need to set the random seed because the scipy kmeans algorithm
+ # randomly initilizes the starting centroids. This can lead to a
+ # different but equivilent indexing.
+ np.random.seed(10)
+
+ def test_find_bases_with_1d_modulation(self):
+ qs = np.array([
+ [0, 0, .13],
+ ])
+
+ ndim, bases = indexing.find_bases(qs, tolerance=.02)
+
+ self.assertEqual(ndim, 1)
+ npt.assert_array_equal(bases[0], qs[0])
+
+ def test_find_bases_with_2d_modulation(self):
+ qs = np.array([
+ [0, 0, .1],
+ [0, .1, 0],
+ ])
+
+ ndim, bases = indexing.find_bases(qs, tolerance=.02)
+
+ self.assertEqual(ndim, 2)
+ npt.assert_array_equal(bases[0], qs[0])
+ npt.assert_array_equal(bases[1], qs[1])
+
+ def test_find_bases_with_3d_modulation(self):
+ qs = np.array([
+ [0, 0, .1],
+ [0, .1, 0],
+ [.1, 0, 0],
+ ])
+
+ ndim, bases = indexing.find_bases(qs, tolerance=.02)
+
+ self.assertEqual(ndim, 3)
+ npt.assert_array_equal(bases[0], qs[0])
+ npt.assert_array_equal(bases[1], qs[1])
+ npt.assert_array_equal(bases[2], qs[2])
+
+ def test_find_bases_with_4d_modulation(self):
+ qs = np.array([
+ [0, 0, .1],
+ [0, .1, 0],
+ [.1, 0, 0],
+ [.15, 0, 0],
+ ])
+
+ ndim, bases = indexing.find_bases(qs, tolerance=.02)
+
+ self.assertEqual(ndim, 4)
+ npt.assert_array_equal(bases[0], qs[0])
+ npt.assert_array_equal(bases[1], qs[1])
+ npt.assert_array_equal(bases[2], qs[2])
+
+ def test_find_bases_with_2d_modulation_with_linear_combination(self):
+ qs = np.array([
+ [0, .1, .1],
+ [0, 0, .1],
+ [0, .1, 0],
+ [0, 0, .15],
+ [0, .1, .2],
+ ])
+
+ ndim, bases = indexing.find_bases(qs, tolerance=.02)
+
+ self.assertEqual(ndim, 3)
+ npt.assert_array_equal(bases[0], np.array([0, 0, .1]))
+ npt.assert_array_equal(bases[1], np.array([0, .1, 0]))
+ npt.assert_array_equal(bases[2], np.array([0, 0, .15]))
+
+ def test_find_bases_with_non_orthogonal_cell(self):
+ cell = UnitCell(1, 1, 1, 90, 95, 103)
+ cart_cell = cell.getB()
+ qs = np.array([
+ [.5, 0, 0],
+ [0, .5, 0],
+ [0, 0, .5],
+ [0, 0, .25],
+ ])
+
+ qs = np.dot(qs, cart_cell)
+
+ ndim, bases = indexing.find_bases(qs, 1e-5)
+ self.assertEqual(ndim, 3, "Number of dimensions must be 3")
+
+ expected_bases = np.array([
+ [0., 0., 0.25],
+ [0., .5, 0.],
+ [0.51521732, 0.11589868, 0.04490415]
+ ])
+
+ npt.assert_almost_equal(bases, expected_bases, err_msg="Basis vectors do not match")
+
+ def test_find_indexing_with_non_orthogonal_cell(self):
+ cell = UnitCell(1, 1, 1, 90, 95, 103)
+ cart_cell = cell.getB()
+ qs = np.array([
+ [.5, 0, 0],
+ [0, .5, 0],
+ [0, 0, .5],
+ [0, 0, .25],
+ ])
+
+ qs = np.dot(qs, cart_cell)
+
+ indices = indexing.index_q_vectors(qs)
+
+ expected_indexing = np.array([
+ [0, 0, 1],
+ [0, 1, 0],
+ [2, 0, 0],
+ [1, 0, 0]
+ ])
+
+ npt.assert_equal(indices, expected_indexing, err_msg="Indexing does not match expected.")
+
+ def test_index_with_modulation(self):
+ qs = np.array([
+ [0, .1, .1],
+ [0, -.1, 0],
+ [0, 0, .1],
+ [0, 0, -.1],
+ [0, .1, .2],
+ [0, 0, .45],
+ ])
+
+ expected_indexing = np.array([
+ [-1, 1, 0],
+ [ 1, 0, 0],
+ [ 0, 1, 0],
+ [ 0, -1, 0],
+ [-1, 2, 0],
+ [ 0, 0, 1]
+ ])
+
+ actual_indexing = indexing.index_q_vectors(qs, tolerance=.03)
+ npt.assert_array_equal(actual_indexing, expected_indexing)
+
+ def test_norm_along_axis(self):
+ vecs = np.array([
+ [0, 0, 3],
+ [0, 2, 0],
+ [1, 0, 0],
+ [0, 5, 5],
+ [0, 4, 4],
+ ])
+
+ expected_output = np.array([3, 2, 1, 7.071068, 5.656854])
+ norms = indexing.norm_along_axis(vecs)
+ npt.assert_allclose(norms, expected_output)
+
+ def test_sort_vectors_by_norm(self):
+ vecs = np.array([
+ [0, 0, 3],
+ [0, 2, 0],
+ [1, 0, 0],
+ [0, 5, 5],
+ [0, 4, 4],
+ ])
+
+ expected_output = np.array([
+ [1, 0, 0],
+ [0, 2, 0],
+ [0, 0, 3],
+ [0, 4, 4],
+ [0, 5, 5],
+ ])
+
+ vecs_sorted = indexing.sort_vectors_by_norm(vecs)
+ npt.assert_allclose(vecs_sorted, expected_output)
+
+ def test_trunc_decimals(self):
+ reference = np.array([0, 0, 0.1])
+ test_input = reference + np.random.random(3) * 0.1
+ result = indexing.trunc_decimals(test_input, 1)
+ npt.assert_array_equal(result, reference)
+
+ def test_remove_noninteger(self):
+ test_input = np.array([1, 2, 3, 1.1, 3.4, -10, -1.8])
+ reference = np.array([1, 2, 3, 0, 0, -10, 0])
+ result = indexing.remove_noninteger(test_input)
+ npt.assert_array_equal(result, reference)
+
+ def test_get_hkls(self):
+ ws = CreateSimulationWorkspace("IRIS", BinParams="1,5,10")
+ peaks = CreatePeaksWorkspace(ws, 2)
+ reference = np.array([
+ [1, 1, 2],
+ [2, 1, 4],
+ ])
+
+ peak = peaks.getPeak(0)
+ peak.setHKL(1, 1, 2)
+ peak = peaks.getPeak(1)
+ peak.setHKL(2, 1, 4)
+
+ hkl = indexing.get_hkls(peaks)
+ npt.assert_array_equal(hkl, reference)
+
+ def test_cluster_qs_with_fixed_k(self):
+ qs = np.array([
+ [0, .1, .1],
+ [0, .1, .1],
+ [0, .0, .1],
+ [0, .0, .1],
+ [0, .1, .1],
+ ])
+
+ qs += np.random.random(qs.shape) * 0.01
+
+ k = 2
+ clusters, k = indexing.cluster_qs(qs, k)
+ self.assertEqual(k, 2)
+ npt.assert_array_equal(clusters, np.array([0, 0, 1, 1, 0]))
+
+ def test_cluster_qs_with_auto_k(self):
+ qs = np.array([
+ [0, .1, .1],
+ [0, .1, .1],
+ [0, .0, .1],
+ [0, .0, .1],
+ [0, .1, .1],
+ ])
+
+ qs += np.random.random(qs.shape) * 0.01
+
+ clusters, k = indexing.cluster_qs(qs, threshold=0.01)
+ self.assertEqual(k, 2)
+ npt.assert_array_equal(clusters, np.array([2, 2, 1, 1, 2]))
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/IndexSatellitePeaksTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/IndexSatellitePeaksTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..550c85419677cb53a12de4328eab29272850ce8d
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/IndexSatellitePeaksTest.py
@@ -0,0 +1,42 @@
+from mantid.simpleapi import mtd, Load, IndexSatellitePeaks
+import unittest
+import numpy as np
+import numpy.testing as npt
+
+
+class IndexSatellitePeaksTest(unittest.TestCase):
+
+ def setUp(self):
+ # Need to set the random seed because the scipy kmeans algorithm
+ # randomly initilizes the starting centroids.
+ np.random.seed(100)
+ self._nuclear_peaks = Load(
+ "WISH_peak_hkl_small.nxs", OutputWorkspace="nuclear_peaks")
+ self._peaks = Load(
+ "refine_satellites_fixed_q_test.nxs", OutputWorkspace="peaks")
+
+ def tearDown(self):
+ mtd.clear()
+
+ def test_exec_with_cluster_threshold(self):
+ expected_values = np.array([-1, -1, 1, 1])
+ indexed_peaks = IndexSatellitePeaks(self._nuclear_peaks, self._peaks,
+ Tolerance=0.1,
+ ClusterThreshold=1.5, NumOfQs=-1)
+ index_values = np.array(indexed_peaks.column("m1"))
+
+ npt.assert_array_equal(index_values, expected_values)
+ self.assertRaises(RuntimeError, indexed_peaks.column, "m2")
+
+ def test_exec_with_number_of_qs(self):
+ expected_values = np.array([-1, -1, 1, 1])
+ indexed_peaks = IndexSatellitePeaks(self._nuclear_peaks, self._peaks,
+ Tolerance=0.1, NumOfQs=2)
+ index_values = np.array(indexed_peaks.column("m1"))
+
+ npt.assert_array_equal(index_values, expected_values)
+ self.assertRaises(RuntimeError, indexed_peaks.column, "m2")
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp b/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp
index efa41473f509565a852bcf62a7487e1084159090..457f9f169d640d558b06c7b9083fcdbae0f4a7c7 100644
--- a/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp
+++ b/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp
@@ -256,26 +256,35 @@ void AlignAndFocusPowder::exec() {
dspace = false;
}
if (dspace) {
- if (m_params.size() == 1 && dmax > 0) {
- double step = m_params[0];
- m_params.clear();
- if (step > 0 || dmin > 0) {
+ if (m_params.size() == 1 && (!isEmpty(dmin)) && (!isEmpty(dmax))) {
+ if (dmin > 0. && dmax > dmin) {
+ double step = m_params[0];
+ m_params.clear();
m_params.push_back(dmin);
m_params.push_back(step);
m_params.push_back(dmax);
- g_log.information() << "d-Spacing Binning: " << m_params[0] << " "
- << m_params[1] << " " << m_params[2] << "\n";
+ g_log.information() << "d-Spacing binning updated: " << m_params[0]
+ << " " << m_params[1] << " " << m_params[2]
+ << "\n";
+ } else {
+ g_log.warning() << "something is wrong with dmin (" << dmin
+ << ") and dmax (" << dmax
+ << "). They are being ignored.\n";
}
}
} else {
- if (m_params.size() == 1 && tmax > 0) {
- double step = m_params[0];
- if (step > 0 || tmin > 0) {
+ if (m_params.size() == 1 && (!isEmpty(tmin)) && (!isEmpty(tmax))) {
+ if (tmin > 0. && tmax > tmin) {
+ double step = m_params[0];
m_params[0] = tmin;
m_params.push_back(step);
m_params.push_back(tmax);
- g_log.information() << "TOF Binning: " << m_params[0] << " "
+ g_log.information() << "TOF binning updated: " << m_params[0] << " "
<< m_params[1] << " " << m_params[2] << "\n";
+ } else {
+ g_log.warning() << "something is wrong with tmin (" << tmin
+ << ") and tmax (" << tmax
+ << "). They are being ignored.\n";
}
}
}
@@ -776,6 +785,10 @@ AlignAndFocusPowder::rebin(API::MatrixWorkspace_sptr matrixws) {
g_log.information() << param << " ";
g_log.information() << ") started at "
<< Types::Core::DateAndTime::getCurrentTime() << "\n";
+ for (double param : m_params)
+ if (isEmpty(param))
+ g_log.warning("encountered empty binning parameter");
+
API::IAlgorithm_sptr rebin3Alg = createChildAlgorithm("Rebin");
rebin3Alg->setProperty("InputWorkspace", matrixws);
rebin3Alg->setProperty("OutputWorkspace", matrixws);
diff --git a/MantidPlot/CMakeLists.txt b/MantidPlot/CMakeLists.txt
index 7ea2943c40f2bdb611a5224926459f37bba02b51..b5b9670e1c502cfef2537ab1deba3d5c29ab58ef 100644
--- a/MantidPlot/CMakeLists.txt
+++ b/MantidPlot/CMakeLists.txt
@@ -91,6 +91,7 @@ set ( QTIPLOT_SRCS src/ApplicationWindow.cpp
src/PluginFit.cpp
src/PolynomFitDialog.cpp
src/PolynomialFit.cpp
+ src/Process.cpp
src/ProjectRecovery.cpp
src/ProjectSaveView.cpp
src/ProjectSerialiser.cpp
@@ -291,6 +292,7 @@ set ( QTIPLOT_HDRS src/ApplicationWindow.h
src/PluginFit.h
src/PolynomFitDialog.h
src/PolynomialFit.h
+ src/Process.h
src/ProjectRecovery.h
src/ProjectSerialiser.h
src/ProjectSaveView.h
diff --git a/MantidPlot/src/ApplicationWindow.cpp b/MantidPlot/src/ApplicationWindow.cpp
index f75919758dfb3b38fc21f20275d6f031743ce383..44d7eae1edbf1091bdcc14113d3b4bb56f0568bc 100644
--- a/MantidPlot/src/ApplicationWindow.cpp
+++ b/MantidPlot/src/ApplicationWindow.cpp
@@ -91,6 +91,7 @@
#include "PlotWizard.h"
#include "PolynomFitDialog.h"
#include "PolynomialFit.h"
+#include "Process.h"
#include "ProjectRecovery.h"
#include "ProjectSerialiser.h"
#include "QwtErrorPlotCurve.h"
@@ -9771,10 +9772,12 @@ void ApplicationWindow::closeEvent(QCloseEvent *ce) {
}
}
- // Stop background saving thread, so it doesn't try to use a destroyed
- // resource
- m_projectRecovery.stopProjectSaving();
- m_projectRecovery.clearAllCheckpoints();
+ if (m_projectRecoveryRunOnStart) {
+ // Stop background saving thread, so it doesn't try to use a destroyed
+ // resource
+ m_projectRecovery.stopProjectSaving();
+ m_projectRecovery.clearAllCheckpoints();
+ }
// Close the remaining MDI windows. The Python API is required to be active
// when the MDI window destructor is called so that those references can be
@@ -16637,8 +16640,20 @@ void ApplicationWindow::onAboutToStart() {
// Make sure we see all of the startup messages
resultsLog->scrollToTop();
- // Kick off project recovery
- checkForProjectRecovery();
+ // Kick off project recovery iff we are able to determine if we are the only
+ // instance currently running
+ try {
+ if (!Process::isAnotherInstanceRunning()) {
+ checkForProjectRecovery();
+ } else {
+ g_log.debug("Another MantidPlot process is running. Project recovery is "
+ "disabled.");
+ }
+ } catch (std::runtime_error &exc) {
+ g_log.warning("Unable to determine if other MantidPlot processes are "
+ "running. Project recovery is disabled. Error msg: " +
+ std::string(exc.what()));
+ }
}
/**
@@ -16768,12 +16783,33 @@ bool ApplicationWindow::saveProjectRecovery(std::string destination) {
return projectWriter.save(QString::fromStdString(destination));
}
+/**
+ * Checks for any recovery checkpoint and starts project
+ * saving if one doesn't exist. If one does, it prompts
+ * the user whether they would like to recover
+ */
void ApplicationWindow::checkForProjectRecovery() {
+ m_projectRecoveryRunOnStart = true;
if (!m_projectRecovery.checkForRecovery()) {
m_projectRecovery.startProjectSaving();
return;
}
// Recovery file present
- m_projectRecovery.attemptRecovery();
+ try {
+ m_projectRecovery.attemptRecovery();
+ } catch (std::exception &e) {
+ std::string err{
+ "Project Recovery failed to recover this checkpoint. Details: "};
+ err.append(e.what());
+ g_log.error(err);
+ QMessageBox::information(this, "Could Not Recover",
+ "We could not fully recover your work.\nMantid "
+ "will continue to run normally now.",
+ "OK");
+
+ // Restart project recovery manually
+ m_projectRecovery.clearAllCheckpoints();
+ m_projectRecovery.startProjectSaving();
+ }
}
diff --git a/MantidPlot/src/ApplicationWindow.h b/MantidPlot/src/ApplicationWindow.h
index ba7830dd663b9b52535dd1cd3b8c111d830922f8..1e0122798c3b7846121c284c68e50acb3d48b8fc 100644
--- a/MantidPlot/src/ApplicationWindow.h
+++ b/MantidPlot/src/ApplicationWindow.h
@@ -1642,6 +1642,8 @@ private:
/// Owns a thread which automatically triggers project recovery for the GUI
MantidQt::ProjectRecovery m_projectRecovery;
+ /// True if project recovery was started when MantidPlot started
+ bool m_projectRecoveryRunOnStart{false};
#ifdef SHARED_MENUBAR
QMenuBar *m_sharedMenuBar; ///< Pointer to the shared menubar
diff --git a/MantidPlot/src/MultiTabScriptInterpreter.cpp b/MantidPlot/src/MultiTabScriptInterpreter.cpp
index 29f7982f3497e5c8dcfc4b1a952bc47027bc817f..49c5834910a319f2a1a825902efe8d6af969d97c 100644
--- a/MantidPlot/src/MultiTabScriptInterpreter.cpp
+++ b/MantidPlot/src/MultiTabScriptInterpreter.cpp
@@ -272,8 +272,8 @@ void MultiTabScriptInterpreter::uncomment() { m_current->uncomment(); }
* Execute the highlighted code from the current tab
* *@param mode :: The mode used to execute
*/
-void MultiTabScriptInterpreter::executeAll(const Script::ExecutionMode mode) {
- m_current->executeAll(mode);
+bool MultiTabScriptInterpreter::executeAll(const Script::ExecutionMode mode) {
+ return m_current->executeAll(mode);
}
/** Execute the highlighted code from the current tab using the
diff --git a/MantidPlot/src/MultiTabScriptInterpreter.h b/MantidPlot/src/MultiTabScriptInterpreter.h
index c96aa5b7fec9c370c15dfe24c6476e585ca0f3d2..d0dbc4f1bc15d71d0bd4d9a5db95b1421fcd0ff6 100644
--- a/MantidPlot/src/MultiTabScriptInterpreter.h
+++ b/MantidPlot/src/MultiTabScriptInterpreter.h
@@ -149,7 +149,7 @@ public slots:
/** @name Execute members.*/
//@{
/// Execute all using the given mode
- void executeAll(const Script::ExecutionMode mode);
+ bool executeAll(const Script::ExecutionMode mode);
/// Execute selection using the given mode
void executeSelection(const Script::ExecutionMode mode);
/// Abort the current script
diff --git a/MantidPlot/src/Process.cpp b/MantidPlot/src/Process.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..20fc6d3ead9885a397efa48c784093a72ef7f3b9
--- /dev/null
+++ b/MantidPlot/src/Process.cpp
@@ -0,0 +1,125 @@
+// clang-format off
+#include "MantidQtWidgets/Common/PythonThreading.h"
+// clang-format on
+
+#include "Process.h"
+
+#include <iostream>
+#include <stdexcept>
+#include <QCoreApplication>
+
+namespace {
+
+class PyObjectNewReference {
+public:
+ explicit PyObjectNewReference(PyObject *object) : m_object(object) {}
+ ~PyObjectNewReference() { Py_XDECREF(m_object); }
+
+ PyObjectNewReference(const PyObjectNewReference &) = delete;
+ PyObjectNewReference &operator=(const PyObjectNewReference &) = delete;
+
+ PyObjectNewReference(PyObjectNewReference &&o) { *this = std::move(o); }
+
+ PyObjectNewReference &operator=(PyObjectNewReference &&other) {
+ this->m_object = other.m_object;
+ other.m_object = nullptr;
+ return *this;
+ }
+
+ inline PyObject *ptr() const { return m_object; }
+
+private:
+ PyObject *m_object;
+};
+
+/**
+ * @brief Retrieve a named attribute
+ * @param source The source object
+ * @param name The name of the attribute
+ * @return The attribute
+ * @throws std::runtime_error if an error occurs retrieving the attribute
+ */
+PyObjectNewReference attr(PyObject *source, const char *name) {
+ PyObjectNewReference attr(PyObject_GetAttrString(source, name));
+ if (attr.ptr()) {
+ return attr;
+ } else {
+ PyErr_Print();
+ throw std::runtime_error(std::string("Process: No attribute ") + name +
+ " found");
+ }
+}
+
+/**
+ * @brief Call a named function with an check for errors
+ * @param source The source object
+ * @param name The name of the attribute to call
+ * @return The return value of the function
+ * @throws std::runtime_error if an error occurs retrieving the attribute
+ */
+PyObjectNewReference call(PyObject *source, const char *name) {
+ auto returnedAttr = attr(source, name);
+ auto result = PyObject_CallFunction(returnedAttr.ptr(), nullptr);
+ if (result)
+ return PyObjectNewReference(result);
+ else {
+ PyErr_Print();
+ throw std::runtime_error(std::string("Process: Error calling function ") +
+ name);
+ }
+}
+
+/**
+ * @return Return a pointer to the psutil module. A new reference is returned.
+ */
+PyObjectNewReference psutil() {
+ if (auto process = PyImport_ImportModule("psutil")) {
+ return PyObjectNewReference(process);
+ } else {
+ PyErr_Clear();
+ throw std::runtime_error("Python module psutil cannot be imported.");
+ }
+}
+} // namespace
+
+namespace Process {
+
+/**
+ * Returns true is another instance of Mantid is running
+ * on this machine
+ * @return True if another instance is running
+ * @throws std::runtime_error if the PID list cannot be determined
+ */
+bool isAnotherInstanceRunning() { return !otherInstancePIDs().empty(); }
+
+/**
+ * @brief Return a list of process IDs for other instances of this process.
+ * @return A list of other processes running. The PID for this process is
+ * removed from the list. An empty list is returned
+ * if no other processes are running.
+ * @throws std::runtime_error if the PID list cannot be determined
+ */
+std::vector<int64_t> otherInstancePIDs() {
+ ScopedPythonGIL lock;
+ const int64_t ourPID(QCoreApplication::applicationPid());
+ const PyObjectNewReference ourName(
+ FROM_CSTRING(QCoreApplication::applicationName().toLatin1().data()));
+ auto psutilModule(psutil());
+ auto processIter(call(psutilModule.ptr(), "process_iter"));
+
+ std::vector<int64_t> otherPIDs;
+ PyObject *item(nullptr);
+ while ((item = PyIter_Next(processIter.ptr()))) {
+ auto name = call(item, "name");
+ if (PyObject_RichCompareBool(name.ptr(), ourName.ptr(), Py_EQ)) {
+ auto pid = PyLong_AsLong(attr(item, "pid").ptr());
+ if (pid != ourPID) {
+ otherPIDs.emplace_back(pid);
+ }
+ }
+ Py_DECREF(item);
+ }
+ return otherPIDs;
+}
+
+} // namespace Process
diff --git a/MantidPlot/src/Process.h b/MantidPlot/src/Process.h
new file mode 100644
index 0000000000000000000000000000000000000000..e7a467a8cd4258741bfc8a94ea1480e0f66ef530
--- /dev/null
+++ b/MantidPlot/src/Process.h
@@ -0,0 +1,39 @@
+#ifndef PROCESS_H_
+#define PROCESS_H_
+/*
+Copyright © 2008-18 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+National Laboratory & European Spallation Source
+
+This file is part of Mantid.
+
+Mantid is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or
+(at your option) any later version.
+
+Mantid is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+File change history is stored at: <https://github.com/mantidproject/mantid>
+Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+#include <cstdint>
+#include <vector>
+
+/*
+ * A minimal wrapper around Python's psutil package to gather information
+ * about processes
+ */
+
+namespace Process {
+
+bool isAnotherInstanceRunning();
+
+std::vector<int64_t> otherInstancePIDs();
+}
+#endif // PROCESS_H_
diff --git a/MantidPlot/src/ProjectRecovery.cpp b/MantidPlot/src/ProjectRecovery.cpp
index cc10f27086cf6d3237927ebb264f942ed810068b..3e8fb692394adf3f8d699fb49a2d89b5e8c7f4d9 100644
--- a/MantidPlot/src/ProjectRecovery.cpp
+++ b/MantidPlot/src/ProjectRecovery.cpp
@@ -16,8 +16,10 @@
#include "boost/range/algorithm_ext/erase.hpp"
#include "Poco/DirectoryIterator.h"
+#include "Poco/Environment.h"
#include "Poco/NObserver.h"
#include "Poco/Path.h"
+#include "Poco/Process.h"
#include <QMessageBox>
#include <QMetaObject>
@@ -62,8 +64,11 @@ boost::optional<bool> getConfigBool(const std::string &key) {
/// Returns a string to the current top level recovery folder
std::string getRecoveryFolder() {
- static std::string recoverFolder =
- Mantid::Kernel::ConfigService::Instance().getAppDataDir() + "/recovery/";
+ static std::string appData =
+ Mantid::Kernel::ConfigService::Instance().getAppDataDir();
+ static std::string hostname = Poco::Environment::nodeName();
+
+ static std::string recoverFolder = appData + "/recovery/" + hostname + '/';
return recoverFolder;
}
@@ -341,7 +346,6 @@ void ProjectRecovery::stopProjectSaving() {
* to recreate all Qt objects / widgets
*
* @param recoveryFolder : The checkpoint folder
- * @throws : If Qt binding fails to main GUI thread
*/
void ProjectRecovery::loadRecoveryCheckpoint(const Poco::Path &recoveryFolder) {
ScriptingWindow *scriptWindow = m_windowPtr->getScriptWindowHandle();
@@ -351,6 +355,17 @@ void ProjectRecovery::loadRecoveryCheckpoint(const Poco::Path &recoveryFolder) {
// Ensure the window repaints so it doesn't appear frozen before exec
scriptWindow->executeCurrentTab(Script::ExecutionMode::Serialised);
+ if (scriptWindow->getSynchronousErrorFlag()) {
+ // We failed to run the whole script
+ // Note: We must NOT throw from the method for excepted failures,
+ // since doing so will cause the application to terminate from a uncaught
+ // exception
+ g_log.error("Project recovery script did not finish. Your work has been "
+ "partially recovered.");
+ this->clearAllCheckpoints();
+ this->startProjectSaving();
+ return;
+ }
g_log.notice("Re-opening GUIs");
auto projectFile = Poco::Path(recoveryFolder).append(OUTPUT_PROJ_NAME);
diff --git a/MantidPlot/src/ScriptFileInterpreter.cpp b/MantidPlot/src/ScriptFileInterpreter.cpp
index d96c4098a28fa1b8f5753ec85f3070de44e6c9ba..58a703d5732e65f2b8f23a7e21c6ca1ede50807c 100644
--- a/MantidPlot/src/ScriptFileInterpreter.cpp
+++ b/MantidPlot/src/ScriptFileInterpreter.cpp
@@ -350,9 +350,9 @@ void ScriptFileInterpreter::showFindReplaceDialog() {
* Execute the whole script in the editor. Always clears the contents of the
* local variable dictionary first.
*/
-void ScriptFileInterpreter::executeAll(const Script::ExecutionMode mode) {
+bool ScriptFileInterpreter::executeAll(const Script::ExecutionMode mode) {
m_runner->clearLocals();
- executeCode(ScriptCode(m_editor->text()), mode);
+ return executeCode(ScriptCode(m_editor->text()), mode);
}
/**
@@ -511,20 +511,25 @@ bool ScriptFileInterpreter::readFileIntoEditor(const QString &filename) {
* Use the current Script object to execute the code asynchronously
* @param code :: The code string to run
*/
-void ScriptFileInterpreter::executeCode(const ScriptCode &code,
+bool ScriptFileInterpreter::executeCode(const ScriptCode &code,
const Script::ExecutionMode mode) {
if (code.isEmpty())
- return;
+ // This cannot fail
+ return true;
if (mode == Script::Asynchronous) {
try {
m_runner->executeAsync(code);
+ // Best attempt at returning a status
+ return true;
} catch (std::runtime_error &exc) {
QMessageBox::critical(this, "MantidPlot", exc.what());
+ return false; // To silence the compiler despite being useless
}
} else if (mode == Script::Serialised) {
- m_runner->execute(code);
+ return m_runner->execute(code);
} else {
QMessageBox::warning(this, "MantidPlot", "Unknown script execution mode");
+ return false;
}
}
diff --git a/MantidPlot/src/ScriptFileInterpreter.h b/MantidPlot/src/ScriptFileInterpreter.h
index e318afadb44eb029366ce470631d6a11786fa79a..7cf7f4e9c68fda6d6833b530fc20900706d004df 100644
--- a/MantidPlot/src/ScriptFileInterpreter.h
+++ b/MantidPlot/src/ScriptFileInterpreter.h
@@ -87,7 +87,7 @@ public slots:
virtual void spacesToTabs();
/// Execute the whole script.
- virtual void
+ virtual bool
executeAll(const Script::ExecutionMode mode = Script::Asynchronous);
/// Execute the current selection
virtual void
@@ -152,7 +152,7 @@ private:
void setupScriptRunner(const ScriptingEnv &env, const QString &identifier);
bool readFileIntoEditor(const QString &filename);
- void executeCode(const ScriptCode &code, const Script::ExecutionMode mode);
+ bool executeCode(const ScriptCode &code, const Script::ExecutionMode mode);
void toggleComment(bool addComment);
@@ -200,7 +200,7 @@ private slots:
void showFindReplaceDialog() override {}
/// Does nothing
- void executeAll(const Script::ExecutionMode) override {}
+ bool executeAll(const Script::ExecutionMode) override { return true; }
/// Does nothing
void executeSelection(const Script::ExecutionMode) override {}
/// Does nothing
diff --git a/MantidPlot/src/ScriptingWindow.cpp b/MantidPlot/src/ScriptingWindow.cpp
index 893a4b54e62f13de2bffc98d9adcfbba022aa51f..c6ccd9822854ebab7c16ab98c539b625e0877c5c 100644
--- a/MantidPlot/src/ScriptingWindow.cpp
+++ b/MantidPlot/src/ScriptingWindow.cpp
@@ -199,7 +199,8 @@ void ScriptingWindow::open(const QString &filename, bool newtab) {
* @param mode :: The execution type
* */
void ScriptingWindow::executeCurrentTab(const Script::ExecutionMode mode) {
- m_manager->executeAll(mode);
+ // Async will always return true before executing
+ m_failureFlag = !m_manager->executeAll(mode);
}
//-------------------------------------------
diff --git a/MantidPlot/src/ScriptingWindow.h b/MantidPlot/src/ScriptingWindow.h
index 09c9cb306881ed64e6b8a19ccf2a9cde4c2f5820..c405b90d3d9dc88ae746e11dc4cd703fbcb1abf0 100644
--- a/MantidPlot/src/ScriptingWindow.h
+++ b/MantidPlot/src/ScriptingWindow.h
@@ -6,6 +6,8 @@
//----------------------------------
#include "MantidQtWidgets/Common/IProjectSerialisable.h"
#include "Script.h"
+
+#include <boost/optional.hpp>
#include <QMainWindow>
//----------------------------------------------------------
@@ -63,6 +65,11 @@ public:
const int fileVersion);
// Loads the scripts from a list of filenames
void loadFromFileList(const QStringList &files);
+
+ /// Sets a flag which is set to true if synchronous execution fails
+ // We set a flag on failure to avoid problems with Async not returning success
+ bool getSynchronousErrorFlag() { return m_failureFlag; }
+
signals:
/// Show the scripting language dialog
void chooseScriptingLanguage();
@@ -184,6 +191,8 @@ private:
QAction *m_scripting_lang;
/// Flag to define whether we should accept a close event
bool m_acceptClose;
+
+ bool m_failureFlag{false};
};
#endif // SCRIPTINGWINDOW_H_
diff --git a/Testing/Data/SystemTest/BSS_13387_event.nxs.expected.md5 b/Testing/Data/SystemTest/BSS_13387_event.nxs.expected.md5
deleted file mode 100644
index 5c36defee038e167e2c1749881d74e58422e3f1f..0000000000000000000000000000000000000000
--- a/Testing/Data/SystemTest/BSS_13387_event.nxs.expected.md5
+++ /dev/null
@@ -1 +0,0 @@
-8be1b5ef4ac6834d48e481afcf865033
\ No newline at end of file
diff --git a/Testing/Data/SystemTest/BSS_13387_event.nxs.md5 b/Testing/Data/SystemTest/BSS_13387_event.nxs.md5
deleted file mode 100644
index 3aa4405f7e336e689014d4d9cbf2fb9df5456288..0000000000000000000000000000000000000000
--- a/Testing/Data/SystemTest/BSS_13387_event.nxs.md5
+++ /dev/null
@@ -1 +0,0 @@
-6357b83d42c4604120cce423273e8557
\ No newline at end of file
diff --git a/Testing/Data/SystemTest/II.IRISFury.nxs.md5 b/Testing/Data/SystemTest/II.IRISFury.nxs.md5
index d286dfb3a5e81878db4f0f0a857d64b1b00db52a..66e968b5588f83183156fc823bd7d1c3c4aba1f8 100644
--- a/Testing/Data/SystemTest/II.IRISFury.nxs.md5
+++ b/Testing/Data/SystemTest/II.IRISFury.nxs.md5
@@ -1 +1 @@
-e50ce6433cf07f6cb7e42755d486a473
+71e13e46035efb3926454423a7265b54
diff --git a/Testing/Data/SystemTest/II.OSIRISFury.nxs.md5 b/Testing/Data/SystemTest/II.OSIRISFury.nxs.md5
index f94cb0eab5bc073418ff6e10cd1a6f642e120349..eb262bc62507ba570c3b4ffc84ce1f90bfd88332 100644
--- a/Testing/Data/SystemTest/II.OSIRISFury.nxs.md5
+++ b/Testing/Data/SystemTest/II.OSIRISFury.nxs.md5
@@ -1 +1 @@
-608eb58252e275e528a61d1be084a794
+5b56a5d3aeaf25da5e67bca3cd16421f
diff --git a/Testing/Data/SystemTest/II.OSIRISIqt.nxs.md5 b/Testing/Data/SystemTest/II.OSIRISIqt.nxs.md5
index 9d86d0b7090804c2e1438efb37b44519cbbfd703..59c4c9e86355ffa619b9e0918ad0f73889b89583 100644
--- a/Testing/Data/SystemTest/II.OSIRISIqt.nxs.md5
+++ b/Testing/Data/SystemTest/II.OSIRISIqt.nxs.md5
@@ -1 +1 @@
-cff1d7adcc73a34e9468eaaca731ced7
+9798e5cee12a0f1af99c8b8132449543
diff --git a/Testing/Data/UnitTest/LARMOR00013065-add.nxs.md5 b/Testing/Data/UnitTest/LARMOR00013065-add.nxs.md5
deleted file mode 100644
index 3724fe80717f5576a57bb7c9f6aeb103cd4afb28..0000000000000000000000000000000000000000
--- a/Testing/Data/UnitTest/LARMOR00013065-add.nxs.md5
+++ /dev/null
@@ -1 +0,0 @@
-0ad830e195879c54ff64583338d0e80a
diff --git a/Testing/Data/SystemTest/refine_satellites_fixed_q_test.nxs.md5 b/Testing/Data/UnitTest/refine_satellites_fixed_q_test.nxs.md5
similarity index 100%
rename from Testing/Data/SystemTest/refine_satellites_fixed_q_test.nxs.md5
rename to Testing/Data/UnitTest/refine_satellites_fixed_q_test.nxs.md5
diff --git a/Testing/SystemTests/scripts/CMakeLists.txt b/Testing/SystemTests/scripts/CMakeLists.txt
index d24c6d34d1151828fa8eeb087de05ed0180d0ee1..2e3853686a2db7f23b083ffd3f4b2b3b142cdf9c 100644
--- a/Testing/SystemTests/scripts/CMakeLists.txt
+++ b/Testing/SystemTests/scripts/CMakeLists.txt
@@ -17,6 +17,8 @@ list(APPEND DATA_DIRS ${SYSTEM_TEST_DATA_DIR}/LARMOR)
list(APPEND DATA_DIRS ${SYSTEM_TEST_DATA_DIR}/INTER)
# Reference results
list(APPEND DATA_DIRS ${ExternalData_BINARY_ROOT}/Testing/SystemTests/tests/analysis/reference)
+# Unit tests
+list(APPEND DATA_DIRS ${ExternalData_BINARY_ROOT}/Testing/Data/UnitTest)
# Doc tests
list(APPEND DATA_DIRS ${ExternalData_BINARY_ROOT}/Testing/Data/DocTest)
diff --git a/Testing/SystemTests/tests/analysis/BASISAutoReduction.py b/Testing/SystemTests/tests/analysis/BASISAutoReduction.py
deleted file mode 100644
index 516d1ac06e4467c11f1ab3a25bf3a9d36ac34115..0000000000000000000000000000000000000000
--- a/Testing/SystemTests/tests/analysis/BASISAutoReduction.py
+++ /dev/null
@@ -1,79 +0,0 @@
-#pylint: disable=no-init,attribute-defined-outside-init
-"""
-System Test for BASIS autoreduction
-"""
-import stresstesting
-import os
-
-from mantid.simpleapi import *
-
-
-class BASISAutoReductionTest(stresstesting.MantidStressTest):
-
- def skipTests(self):
- return True
-
- def requiredFiles(self):
- return ['BSS_13387_event.nxs']
-
- def cleanup(self):
- return True
-
- def runTest(self):
- idfdir = config['instrumentDefinition.directory']
- autows = 'data_ws'
- autows_monitor = 'monitor_ws'
- Load(Filename='BSS_13387_event.nxs', OutputWorkspace=autows)
- LoadMask(Instrument='BASIS', OutputWorkspace='BASIS_MASK', InputFile='BASIS_AutoReduction_Mask.xml')
- MaskDetectors(Workspace=autows, DetectorList="5,49,69,113,133,177,197,241,261,305,325,369,389,433,453,497,517,"
- "561,581,625,645,689,709,753,773,817,837,881,901,945,965,1009,"
- "1029,1073,1093,1137,1157,1201,1221,1265,1285,1329,1349,"
- "1393,1413,1457,1477,1521,1541,1585,1605,1649,1669,1713,"
- "1733,1777,1797,1841,1861,1905,1925,1969,1989,2033,2053,"
- "2097,2117,2161,2181,2225,2245,2289,2309,2353,2373,2417,"
- "2437,2481,2501,2545,2565,2609,2629,2673,2693,2737,2757,"
- "2801,2821,2865,2885,2929,2949,2993,3013,3057,3077,"
- "3121,3141,3185,3205,3249,3269,3313,3333,3377,3397,3441,"
- "3461,3505,3525,3569,3589-3633,3653-3697,3717-3761,"
- "3781-3825,3845-3889,3909-3953,3973-4017,4037-4081,4110,"
- "4154,4174,4218,4238,4282,4302,4346,4366,4410,4430,4474,4494,"
- "4538,4558,4602,4622,4666,4686,4730,4750,4794,4814,4858,"
- "4878,4922,4942,4986,5006,5050,5070,5114,5134,5178,5198,"
- "5242,5262,5306,5326,5370,5390,5434,5454,5498,5518,5562,5582,5626,5646,"
- "5690,5710,5754,5774,5818,5838,5882,5902,5946,5966,6010,"
- "6030,6074,6094,6138,6158,6202,6222,6266,6286,6330,6350,"
- "6394,6414,6458,6478,6522,6542,6586,6606,6650,6670,"
- "6714,6734,6778,6798,6842,6862,6906,6926,6970,6990,"
- "7034,7054,7098,7118,7162,7182,7226,7246,7290,7310,7354,"
- "7374,7418,7438,7482,7502,7546,7566,7610,7630,7674,"
- "7694-7738,7758-7802,7822-7866,7886-7930,7950-7994,"
- "8014-8058,8078-8122,8142-8186,8192-15871") #MaskedWorkspace='BASIS_MASK')
- ModeratorTzeroLinear(InputWorkspace=autows,OutputWorkspace=autows)
- LoadParameterFile(Workspace=autows, Filename=os.path.join(idfdir,'BASIS_silicon_111_Parameters.xml'))
- LoadNexusMonitors(Filename='BSS_13387_event.nxs', OutputWorkspace=autows_monitor)
- Rebin(InputWorkspace=autows_monitor,OutputWorkspace=autows_monitor,Params='10')
- ConvertUnits(InputWorkspace=autows_monitor, OutputWorkspace=autows_monitor, Target='Wavelength')
- OneMinusExponentialCor(InputWorkspace=autows_monitor, OutputWorkspace=autows_monitor, C='0.20749999999999999', C1='0.001276')
- Scale(InputWorkspace=autows_monitor, OutputWorkspace=autows_monitor, Factor='9.9999999999999995e-07')
- ConvertUnits(InputWorkspace=autows, OutputWorkspace=autows, Target='Wavelength', EMode='Indirect')
- RebinToWorkspace(WorkspaceToRebin=autows, WorkspaceToMatch=autows_monitor, OutputWorkspace=autows)
- Divide(LHSWorkspace=autows, RHSWorkspace=autows_monitor, OutputWorkspace=autows)
- ConvertUnits(InputWorkspace=autows, OutputWorkspace=autows, Target='DeltaE', EMode='Indirect')
- CorrectKiKf(InputWorkspace=autows, OutputWorkspace=autows,EMode='Indirect')
-
- Rebin(InputWorkspace=autows, OutputWorkspace=autows, Params='-0.12,0.0004,0.12')
- #GroupDetectors(InputWorkspace=autows, OutputWorkspace=autows, MapFile='/SNS/BSS/shared/autoreduce/BASIS_Grouping.xml',
- #Behaviour='Sum')
- SofQW3(InputWorkspace=autows, OutputWorkspace=autows+'_sqw', QAxisBinning='0.2,0.2,2.0', EMode='Indirect', EFixed='2.082')
- #SaveDaveGrp(Filename=dave_grp_filename, InputWorkspace=autows+'_sqw', ToMicroEV=True)
- #SaveNexus(Filename="basis_auto_sqw.nxs", InputWorkspace=autows+'_sqw')
-
- def validate(self):
- # Need to disable checking of the Spectra-Detector map because it isn't
- # fully saved out to the nexus file; some masked detectors should be picked
- # up with by the mask values in the spectra
- self.tolerance = 1e-7
- self.disableChecking.append('Axes')
- self.disableChecking.append('SpectraMap')
- self.disableChecking.append('Instrument')
- return 'data_ws_sqw','BASISAutoReductionReference.nxs'
diff --git a/Testing/SystemTests/tests/analysis/RefineSatellitePeaksTest.py b/Testing/SystemTests/tests/analysis/FindSatellitePeaksTest.py
similarity index 58%
rename from Testing/SystemTests/tests/analysis/RefineSatellitePeaksTest.py
rename to Testing/SystemTests/tests/analysis/FindSatellitePeaksTest.py
index 407d0f23c14f24a2ba1cb4a6d88f754c7dfda208..660e754f810d27978bb76ba1f5751aa711ad86e5 100644
--- a/Testing/SystemTests/tests/analysis/RefineSatellitePeaksTest.py
+++ b/Testing/SystemTests/tests/analysis/FindSatellitePeaksTest.py
@@ -1,10 +1,11 @@
-from mantid.simpleapi import RefineSatellitePeaks, Load
+from mantid.simpleapi import FindSatellitePeaks, Load
import unittest
import stresstesting
def load_files():
- md_workspace = Load(Filename="WISH_md_small.nxs", OutputWorkspace='md_workspace')
+ md_workspace = Load(Filename="WISH_md_small.nxs",
+ OutputWorkspace='md_workspace')
main_peaks = Load(Filename="WISH_peak_hkl_small.nxs",
OutputWorkspace='main_peaks')
satellite_peaks = Load(Filename="WISH_peak_hkl_frac_small.nxs",
@@ -12,7 +13,7 @@ def load_files():
return md_workspace, main_peaks, satellite_peaks
-class RefineSatellitePeaksTestFixedNumQ(stresstesting.MantidStressTest):
+class FindSatellitePeaksTestFixedNumQ(stresstesting.MantidStressTest):
def requiredFiles(self):
return ["WISH_md_small.nxs", "WISH_peak_hkl_small.nxs", "WISH_peak_hkl_frac_small.nxs"]
@@ -29,14 +30,14 @@ class RefineSatellitePeaksTestFixedNumQ(stresstesting.MantidStressTest):
k = 2
- self._satellites_refined = RefineSatellitePeaks(NuclearPeaks=main_peaks, SatellitePeaks=satellite_peaks, MDWorkspace=md_workspace,
- NumOfQs=k, **fixed_params)
+ self._satellites_refined = FindSatellitePeaks(NuclearPeaks=main_peaks, SatellitePeaks=satellite_peaks, MDWorkspace=md_workspace,
+ NumOfQs=k, **fixed_params)
def validate(self):
- return self._satellites_refined.name(),'refine_satellites_fixed_q_test.nxs'
+ return self._satellites_refined.name(), 'refine_satellites_fixed_q_test.nxs'
-class RefineSatellitePeaksTestAutoFindQ(stresstesting.MantidStressTest):
+class FindSatellitePeaksTestAutoFindQ(stresstesting.MantidStressTest):
def requiredFiles(self):
return ["WISH_md_small.nxs", "WISH_peak_hkl_small.nxs", "WISH_peak_hkl_frac_small.nxs"]
@@ -52,11 +53,11 @@ class RefineSatellitePeaksTestAutoFindQ(stresstesting.MantidStressTest):
}
threshold = 1.0
- self._satellites_refined = RefineSatellitePeaks(NuclearPeaks=main_peaks, SatellitePeaks=satellite_peaks, MDWorkspace=md_workspace,
- ClusterThreshold=threshold, **fixed_params)
+ self._satellites_refined = FindSatellitePeaks(NuclearPeaks=main_peaks, SatellitePeaks=satellite_peaks, MDWorkspace=md_workspace,
+ ClusterThreshold=threshold, **fixed_params)
def validate(self):
- return self._satellites_refined.name(),'refine_satellites_auto_q_test.nxs'
+ return self._satellites_refined.name(), 'refine_satellites_auto_q_test.nxs'
if __name__ == "__main__":
diff --git a/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py b/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
index c57e39910cbbd25966e3a1500aaeb3169b2d5a82..e7b828dfe5835d6ac248f162103e6fd9e19be490 100644
--- a/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
+++ b/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
@@ -69,13 +69,13 @@ stresstesting.MantidStressTest
from __future__ import (absolute_import, division, print_function)
import stresstesting
-import os
from abc import ABCMeta, abstractmethod
from mantid.simpleapi import *
# For debugging only.
from mantid.api import FileFinder
+import platform
from six import with_metaclass
@@ -744,7 +744,7 @@ class ISISIndirectInelasticIqtAndIqtFit(with_metaclass(ABCMeta, ISISIndirectInel
def _run(self):
'''Defines the workflow for the test'''
- self.tolerance = 1e-7
+ self.tolerance = 1e-3
self.samples = [sample[:-4] for sample in self.samples]
# Load files into Mantid
@@ -757,7 +757,8 @@ class ISISIndirectInelasticIqtAndIqtFit(with_metaclass(ABCMeta, ISISIndirectInel
EnergyMin=self.e_min,
EnergyMax=self.e_max,
BinReductionFactor=self.num_bins,
- DryRun=False)
+ DryRun=False,
+ NumberOfIterations=200)
# Test IqtFit Sequential
iqtfitSeq_ws, params, fit_group = IqtFitSequential(InputWorkspace=iqt_ws, Function=self.func,
@@ -818,7 +819,7 @@ class OSIRISIqtAndIqtFit(ISISIndirectInelasticIqtAndIqtFit):
self.endx = 0.118877
def get_reference_files(self):
- self.tolerance = 1e-4
+ self.tolerance = 1e-3
return ['II.OSIRISFury.nxs',
'II.OSIRISFuryFitSeq.nxs']
@@ -846,9 +847,13 @@ class IRISIqtAndIqtFit(ISISIndirectInelasticIqtAndIqtFit):
self.endx = 0.169171
def get_reference_files(self):
- self.tolerance = 1e-4
- return ['II.IRISFury.nxs',
- 'II.IRISFuryFitSeq.nxs']
+ self.tolerance = 1e-3
+ ref_files = ['II.IRISFury.nxs']
+ if platform.system() == "Darwin" or platform.linux_distribution()[0] == "Ubuntu":
+ ref_files += ['II.IRISFuryFitSeq.nxs']
+ else:
+ ref_files += ['II.IRISFuryFitSeq_win.nxs']
+ return ref_files
#==============================================================================
@@ -862,7 +867,7 @@ class ISISIndirectInelasticIqtAndIqtFitMulti(with_metaclass(ABCMeta, ISISIndirec
def _run(self):
'''Defines the workflow for the test'''
- self.tolerance = 1e-6
+ self.tolerance = 1e-2
self.samples = [sample[:-4] for sample in self.samples]
#load files into mantid
@@ -875,7 +880,8 @@ class ISISIndirectInelasticIqtAndIqtFitMulti(with_metaclass(ABCMeta, ISISIndirec
EnergyMin=self.e_min,
EnergyMax=self.e_max,
BinReductionFactor=self.num_bins,
- DryRun=False)
+ DryRun=False,
+ NumberOfIterations=200)
# Test IqtFitMultiple
iqtfitSeq_ws, params, fit_group = IqtFitMultiple(iqt_ws.name(),
@@ -944,7 +950,7 @@ class OSIRISIqtAndIqtFitMulti(ISISIndirectInelasticIqtAndIqtFitMulti):
self.spec_max = 41
def get_reference_files(self):
- self.tolerance = 1e-3
+ self.tolerance = 1e-2
return ['II.OSIRISIqt.nxs',
'II.OSIRISIqtFitMulti.nxs']
@@ -973,7 +979,7 @@ class IRISIqtAndIqtFitMulti(ISISIndirectInelasticIqtAndIqtFitMulti):
self.endx = 0.156250
def get_reference_files(self):
- self.tolerance = 1e-4
+ self.tolerance = 1e-3
return ['II.IRISFury.nxs',
'II.IRISFuryFitMulti.nxs']
diff --git a/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py b/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
index 6bed93409417cb9025a3e71e1ea320dab602ac3f..c7e1637fa9fa4e35e8f405c4b64f14eda79880d3 100644
--- a/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
+++ b/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
@@ -114,7 +114,6 @@ BANNED_FILES = ['80_tubes_Top_and_Bottom_April_2015.xml',
'Fe-alpha.cif',
'Sm2O3.cif',
'template_ENGINX_241391_236516_North_bank.prm',
- 'BSS_13387_event.nxs' # bad event_index
]
EXPECTED_EXT = '.expected'
@@ -133,7 +132,7 @@ BANNED_REGEXP = [r'SANS2D\d+.log$',
r'.*_pulseid\.dat',
r'.*\.phonon']
-BANNED_DIRS = ["DocTest", "reference"]
+BANNED_DIRS = ["DocTest", "UnitTest", "reference"]
# This list stores files that will be loaded first.
# Implemented as simple solution to avoid failures on
diff --git a/Testing/SystemTests/tests/analysis/SANSSaveTest.py b/Testing/SystemTests/tests/analysis/SANSSaveTest.py
index 8cfa862cac4ebd044997706f38a4a9491f404307..e553c244b8b06d9f3a8b6bec1d3be9c990fcb2f0 100644
--- a/Testing/SystemTests/tests/analysis/SANSSaveTest.py
+++ b/Testing/SystemTests/tests/analysis/SANSSaveTest.py
@@ -80,7 +80,7 @@ class SANSSaveTest(unittest.TestCase):
# Assert
expected_files = ["sample_sans_save_file.xml", "sample_sans_save_file.txt", "sample_sans_save_file_nistqxy.dat",
- "sample_sans_save_file_nxcansas.nxs", "sample_sans_save_file.nxs",
+ "sample_sans_save_file.h5", "sample_sans_save_file.nxs",
"sample_sans_save_file.csv"]
expected_full_file_names = [os.path.join(mantid.config.getString('defaultsave.directory'), elem)
for elem in expected_files]
diff --git a/Testing/SystemTests/tests/analysis/reference/II.IRISFury.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.IRISFury.nxs.md5
index d3db92bc4d79f44d399bb3696b31e2ca35e12dbb..66e968b5588f83183156fc823bd7d1c3c4aba1f8 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.IRISFury.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.IRISFury.nxs.md5
@@ -1 +1 @@
-589e60ec316d1082e54de36a08b92788
+71e13e46035efb3926454423a7265b54
diff --git a/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitMulti.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitMulti.nxs.md5
index edb4373c11ff9675e179b95ced5af3985da7ee8b..9d190e2983d7acce1d631209794472f4e5f80c7e 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitMulti.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitMulti.nxs.md5
@@ -1 +1 @@
-d3c125646057bc0d1291c3286ddfab82
+2527ccdd4907cfa04fe11b227e035245
diff --git a/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq.nxs.md5
index fe215d074cdcf5e657d0479060929cfd83f35168..738da79a31b6e60de025786b5f905c6b4a629045 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq.nxs.md5
@@ -1 +1 @@
-67073e555a16dc10647139a039d25f67
+6eac4e677742306141278a91de3d6f2a
diff --git a/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq_win.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq_win.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..6e02012474a4f94972e2ad91d65d657a40dfe7df
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/II.IRISFuryFitSeq_win.nxs.md5
@@ -0,0 +1 @@
+243fa6f6224393377d695a895822b6cb
diff --git a/Testing/SystemTests/tests/analysis/reference/II.OSIRISFury.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.OSIRISFury.nxs.md5
index 56ef9130054fb70ffbd1472e3216421faa288154..eb262bc62507ba570c3b4ffc84ce1f90bfd88332 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.OSIRISFury.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.OSIRISFury.nxs.md5
@@ -1 +1 @@
-844ffeedb95ed346b289c22acf56cec3
+5b56a5d3aeaf25da5e67bca3cd16421f
diff --git a/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitMulti.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitMulti.nxs.md5
index 98153cb5b1cd215f5d15b19ffd68e59219ceffdb..66f74d9fe34e4a18c76ade933175f60635514d88 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitMulti.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitMulti.nxs.md5
@@ -1 +1 @@
-4c21ab6a0a21e619c9260d43de060e58
+9b093756c218852b66f6ab1a998dda58
diff --git a/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitSeq.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitSeq.nxs.md5
index b3c30c2539d686a8a0a389185aed43b1c6af1fe5..a6b12ef28591e3bfef345aa90e406e0506f20973 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitSeq.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.OSIRISFuryFitSeq.nxs.md5
@@ -1 +1 @@
-d86b302c2850c630c1e6598004224d9e
+099bcc9a5ef978f7245aa502fd65133e
diff --git a/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqt.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqt.nxs.md5
index 78b1c07ef1232835a5656c2465efb4d384582dfc..59c4c9e86355ffa619b9e0918ad0f73889b89583 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqt.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqt.nxs.md5
@@ -1 +1 @@
-6d182db6499e4b9648c3487c4cb23ad2
+9798e5cee12a0f1af99c8b8132449543
diff --git a/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqtFitMulti.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqtFitMulti.nxs.md5
index 31e9dcf91184192e2203f4d9ff7d0c7df0483fae..792910a8508ea1056f325b5e26a0728a107a7fc5 100644
--- a/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqtFitMulti.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/II.OSIRISIqtFitMulti.nxs.md5
@@ -1 +1 @@
-e69721879e1f40059beb3061459203c6
+9ca2a951f4650802964faba254bad533
diff --git a/buildconfig/Jenkins/buildscript b/buildconfig/Jenkins/buildscript
index 814eca620ec6dab2214bae1d686912c19132efc1..8fa2a4c145719e21ed9ca1297afe0aab5b071e86 100755
--- a/buildconfig/Jenkins/buildscript
+++ b/buildconfig/Jenkins/buildscript
@@ -257,7 +257,7 @@ cd $BUILD_DIR
# Clean up any artifacts from last build so that if it fails
# they don't get archived again
###############################################################################
-rm -f -- *.dmg *.rpm *.deb *.tar.gz
+rm -f -- *.dmg *.rpm *.deb *.tar.gz *.tar.xz
###############################################################################
# CMake configuration
diff --git a/docs/source/algorithms/CalculateIqt-v1.rst b/docs/source/algorithms/CalculateIqt-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..843cc8cfb4389bbb45ab22efeda62502e5a41040
--- /dev/null
+++ b/docs/source/algorithms/CalculateIqt-v1.rst
@@ -0,0 +1,18 @@
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm calculates an I(Q, t) workspace from either a reduced (*_red*) or S(Q, w) (*_sqw*)
+workspace, using a Monte Carlo method for the error calculation.
+
+
+.. categories::
+
+.. sourcelink::
\ No newline at end of file
diff --git a/docs/source/algorithms/RefineSatellitePeaks-v1.rst b/docs/source/algorithms/FindSatellitePeaks-v1.rst
similarity index 84%
rename from docs/source/algorithms/RefineSatellitePeaks-v1.rst
rename to docs/source/algorithms/FindSatellitePeaks-v1.rst
index f6b8287b388c58a48f86027d5c2358827ea42b66..0919add7283f98eb3ff70e002e07d3ee396b762e 100644
--- a/docs/source/algorithms/RefineSatellitePeaks-v1.rst
+++ b/docs/source/algorithms/FindSatellitePeaks-v1.rst
@@ -7,17 +7,17 @@
Description
-----------
-RefineSatellitePeaks can be used to refine the locations of "satellite" peaks
-occurring at fractional HKL locations in reciprocal space. RefineSatellitePeaks
+FindSatellitePeaks can be used to refine the locations of "satellite" peaks
+occurring at fractional HKL locations in reciprocal space. FindSatellitePeaks
takes a :ref:`MDWorkspace <MDWorkspace>` of experimental data, a
:ref:`PeaksWorkspace <PeaksWorkspace>` containing the locations of peaks with
integer HKL, and another PeaksWorkspace containing a subset of peaks found at
fractional HKL.
-.. figure:: /images/RefineSatellitePeaks-satellites.png
+.. figure:: ../images/FindSatellitePeaks-satellites.png
:align: center
:width: 600px
- :alt: RefineSatellitePeaks-satellites.png
+ :alt: FindSatellitePeaks-satellites.png
Satellite peaks exist at fractional HKL coordinates. The vector `q` is the
Euclidean distance from the nearest integer HKL peak to the satellite. A
@@ -33,10 +33,10 @@ this threshold. The centroid of each cluster calculated for each group and is
used as the offset to predict the location of fractional peaks everywhere in
the :ref:`MDWorkspace <MDWorkspace>`.
-.. figure:: /images/RefineSatellitePeaks-clustering.png
+.. figure:: ../images/FindSatellitePeaks-clustering.png
:align: center
:width: 700px
- :alt: RefineSatellitePeaks-clustering.png
+ :alt: FindSatellitePeaks-clustering.png
Due to noise in the experimental data the `q` vector for every satellite may
vary slightly. This algorithm calculates the `q` vectors for all peaks passed
@@ -54,10 +54,10 @@ Finally the found satellite peaks are integerated using the
`BackgroundInnerRadius`, and `BackgroundOuterRadius`. Satellite peaks are
discarded if there I/sigma value is less than the parameter `IOverSigma`.
-.. figure:: /images/RefineSatellitePeaks-centroids.png
+.. figure:: ../images/FindSatellitePeaks-centroids.png
:align: center
:width: 700px
- :alt: RefineSatellitePeaks-centroid.png
+ :alt: FindSatellitePeaks-centroid.png
Finally, using the predicted satellite peak positions (green) the local
centroid is found and this is used as the true position of the experimental
@@ -102,15 +102,19 @@ Related Algorithms
- :ref:`FilterPeaks <algm-FilterPeaks-v1>` is used to remove peaks with zero
intensity or a I/sigma below the desired threshold.
+- :ref:`IndexSatellitePeaks <algm-IndexSatellitePeaks-v1>` can be used to
+ obtain a superspace indexing of the peaks workspace output from this
+ algorithm.
+
Usage
-----
.. include:: ../usagedata-note.txt
-**Example - calling RefineSatellitePeaks:**
+**Example - calling FindSatellitePeaks:**
-.. testcode:: RefineSatellitePeaks
+.. testcode:: FindSatellitePeaks
md_workspace = Load(Filename='WISH_md_small.nxs', OutputWorkspace='WISH_md_small')
satellite_peaks = Load(Filename='WISH_peak_hkl_frac_small.nxs', OutputWorkspace='WISH_peak_hkl_frac_small')
@@ -125,11 +129,11 @@ Usage
}
- satellites_refined = RefineSatellitePeaks(NuclearPeaks=main_peaks, SatellitePeaks=satellite_peaks, MDWorkspace=md_workspace, **params)
+ satellites_refined = FindSatellitePeaks(NuclearPeaks=main_peaks, SatellitePeaks=satellite_peaks, MDWorkspace=md_workspace, **params)
print (len(satellites_refined))
-.. testcleanup:: RefineSatellitePeaks
+.. testcleanup:: FindSatellitePeaks
DeleteWorkspace('WISH_md_small')
DeleteWorkspace('WISH_peak_hkl_small')
@@ -138,7 +142,7 @@ Usage
Output:
-.. testoutput:: RefineSatellitePeaks
+.. testoutput:: FindSatellitePeaks
4
diff --git a/docs/source/algorithms/IndexSatellitePeaks-v1.rst b/docs/source/algorithms/IndexSatellitePeaks-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4d7a644b49983da502e88a75b6cc22dd18f99b25
--- /dev/null
+++ b/docs/source/algorithms/IndexSatellitePeaks-v1.rst
@@ -0,0 +1,94 @@
+.. algorithm::
+
+.. summary::
+
+.. properties::
+
+Description
+-----------
+
+IndexSatellitePeaks is used to find the higher dimensional miller indices that
+index a collection of "satellite" fractional single crystal peaks. This
+algorithm takes a PeaksWorkspace, output from the algorithm
+FindSatellitePeaks, and returns a new table with integer indices for each
+peak.
+
+This algorithm works by first attempting to finding the minimum number of
+distinct modulation (`q`) vectors that are required to fully index the
+collection of peaks. The full list of q vectors is found using the same method
+described in the :ref:`FindSatellitePeaks <algm-FindSatellitePeaks-v1>`
+algorithm. The basis set is then chosen from this list. If there are multiple
+choices of vectors the algorithm will always choose the smallest one. This
+defines the number of additional dimensions required to index the crystal with
+integer indices.
+
+Once a basis of `q` vectors has been chosen for indexing the system all integer
+multiples of the basis set are generated. Each `q` vector is then compared with
+the set of all possible integer reflections and is assigned to the closest one
+found within the radius of the `Tolerance` parameter (measured by Euclidean
+distance in HKL space). Reflections which cannot be indexed within the
+tolerance are set to (0,0,0).
+
+.. warning:: The current version of the algorithm returns a
+ :ref:`TableWorkspace <Table Workspaces>` and not a :ref:`PeaksWorkspace
+ <PeaksWorkspace>`. This means that the workspace cannot be overlaid on the
+ slice viewer or the instrument view.
+
+.. seealso:: As well as being able to export the data to the nexus file format,
+ saving the data to the Jana format is supported via the :ref:`SaveReflections
+ <algm-SaveReflections-v1>` algorithm.
+
+For more information on superspace crystallography see:
+
+- Van Smaalen, Sander. "An elementary introduction to superspace
+ crystallography." Zeitschrift für Kristallographie-Crystalline Materials
+ 219, no. 11 (2004): 681-691.
+
+- Van Smaalen, Sander. "Incommensurate crystal structures." Crystallography
+ Reviews 4, no. 2 (1995): 79-202.
+
+Related Algorithms
+------------------
+
+- :ref:`FindSatellitePeaks <algm-FindSatellitePeaks-v1>` can be used to
+ obtain a workspace of satellite peak positions in fractional HKL that is
+ required for input to this algorithm.
+
+- :ref:`SaveReflections <algm-SaveReflections-v1>` algorithm can be used to save
+ the table workspace output from this algorithm to the Jana text file format.
+
+Usage
+-----
+
+.. include:: ../usagedata-note.txt
+
+
+**Example - calling IndexSatellitePeaks:**
+
+.. testcode:: IndexSatellitePeaks
+
+ import numpy as np
+ np.random.seed(1)
+
+ nuclear_peaks = Load('WISH_peak_hkl_small.nxs')
+ satellite_peaks = Load("refine_satellites_fixed_q_test.nxs")
+ indexed_peaks = IndexSatellitePeaks(nuclear_peaks, satellite_peaks, tolerance=0.1, NumOfQs=2)
+ index_values = np.array(indexed_peaks.column("m1"))
+
+ for peak in indexed_peaks:
+ print("H: {h:>5} K: {k:>5} L: {l:>5} M1: {m1:>5}".format(**peak))
+
+Output:
+
+.. testoutput:: IndexSatellitePeaks
+
+ H: 2.0 K: -1.0 L: -3.0 M1: -1.0
+ H: 2.0 K: -1.0 L: 0.0 M1: -1.0
+ H: 2.0 K: -1.0 L: -3.0 M1: 1.0
+ H: 2.0 K: -1.0 L: 0.0 M1: 1.0
+
+.. categories::
+
+.. sourcelink::
+ :cpp: None
+ :h: None
diff --git a/docs/source/concepts/ProjectRecovery.rst b/docs/source/concepts/ProjectRecovery.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0c31c3ad0795cc56b26081b0ac01ab19e659696f
--- /dev/null
+++ b/docs/source/concepts/ProjectRecovery.rst
@@ -0,0 +1,71 @@
+.. _Project Recovery:
+
+Project Recovery
+================
+
+What is it?
+-----------
+
+If Mantid crashes for some reason, we have introduced the functionality to attempt to recover the state that Mantid was in prior to the crash.
+
+Project recovery is a key part of our efforts to make Mantid as stable and reliable as possible.
+
+How it works
+------------
+
+Project recovery works in two parts:
+
+* History writer: This writes the history of the workspaces in your workspace dialog, periodically saving the files. It is not likely that you will ever notice the history writer process.
+* Project recovery: This rebuilds the last saved state of Mantid after a crash, it uses the files produced by the history writer
+
+If Mantid has crashed, then on the subsequent reboot you will be presented with the project recovery dialog (see image)
+
+.. image:: ../images/ProjectRecoveryDialog.png
+ :width: 400px
+ :align: center
+ :alt: alternate text
+
+You can choose to attempt a full recovery, to open a recovery script or not to attempt a recovery. Full recovery will attempt to recover all workspaces present at the time of the crash as well as additional dialogs like plots or data windows. Script mode will attempt to construct a script that contains the history of all workspaces at the time of the crash.
+
+If full project recovery runs succesfully the scripting window will remain open in MantidPlot. It is safe to close this after a recovery.
+
+**NB** This is an early version of project recovery. We think that it is a lot better than nothing, but we know it won't always work. Known caveats are listed below. Moreover, we would sincerely appreciate feedback and input from users. Contact us at `mantid-help@mantidproject.org`
+
+The settings for project recovery, including switiching the feature on/off, and how to set them, are listed at the bottom of this page.
+
+Caveats
+-------
+
+* Multiple instances of Mantid
+ * Please allow first instance to start history writer before starting the next instance, otherwise it will not start for either. This usually means leaving Mantid until the GUI has opened fully.
+ * Only the first instance will have history writer enabled. There will be no project recovery for subsequent instances.
+ * All running instances of Mantid must be closed for project recovery to work after a crash.
+
+* Interfaces
+ * Muon - project recovery does not work at all with the existing Muon interfaces.
+ * Indirect analysis - project recovery does not work when performing fitting routines within the indirect analysis interface.
+ * SANS - project recovery does not currently work with the SANS interface.
+
+* Multi-line commands
+ * Currently if a workspace history contains any multi-line commands then the recovery script builder will fail.
+
+* If full project recovery does not work:
+ * If the project recovery process has managed to create a script of the ordered workspace histories, this will appear in MantidPlot, it will have a red arrow beside the line where the process failed. In many cases it is possible to edit the script by hand to get it to run.
+ * If project recovery did not manage to generate the ordered history script then it will return to MantidPlot as normal, with an error message.
+
+
+Settings
+--------
+
+* Project recovery behaviour can be edited by editing the `Mantid.user.properties` file
+ * Windows: `$MantidInstallDirectory\bin\Mantid.user.properties`
+ * OSX: `$HOME/.mantid/Mantid.user.properties`
+ * Linux:`$HOME/.mantid/Mantid.user.properties`
+
+
+* Three settings you can add to this file:
+ * **On/off:** `projectRecovery.enabled=true`
+ * **Regularity:** `projectRecovery.secondsBetween = 60`
+ * **Number of backups to keep:** `projectRecovery.numberOfCheckpoints = 5`
+
+.. categories:: Concepts
\ No newline at end of file
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 205bbf43ceabb698cb3a63d9cd77c7c1d40c9e76..34096bd1c63377235fade1069c361f94b0b09dbb 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -96,8 +96,11 @@ except TypeError:
# Run this after each test group has executed
doctest_global_cleanup = """
+import time
from mantid.api import FrameworkManager
FrameworkManager.Instance().clear()
+# sleep for short period to allow memory to be freed
+time.sleep(2)
"""
# -- Options for pngmath --------------------------------------------------
diff --git a/docs/source/images/RefineSatellitePeaks-centroids.png b/docs/source/images/FindSatellitePeaks-centroids.png
similarity index 100%
rename from docs/source/images/RefineSatellitePeaks-centroids.png
rename to docs/source/images/FindSatellitePeaks-centroids.png
diff --git a/docs/source/images/RefineSatellitePeaks-clustering.png b/docs/source/images/FindSatellitePeaks-clustering.png
similarity index 100%
rename from docs/source/images/RefineSatellitePeaks-clustering.png
rename to docs/source/images/FindSatellitePeaks-clustering.png
diff --git a/docs/source/images/RefineSatellitePeaks-satellites.png b/docs/source/images/FindSatellitePeaks-satellites.png
similarity index 100%
rename from docs/source/images/RefineSatellitePeaks-satellites.png
rename to docs/source/images/FindSatellitePeaks-satellites.png
diff --git a/docs/source/images/ISIS_SANS_release313.png b/docs/source/images/ISIS_SANS_release313.png
new file mode 100644
index 0000000000000000000000000000000000000000..542be77c3200cbbe8fb46eba3461788fca8a4cce
Binary files /dev/null and b/docs/source/images/ISIS_SANS_release313.png differ
diff --git a/docs/source/images/ISIS_reflectometry_release313.png b/docs/source/images/ISIS_reflectometry_release313.png
new file mode 100644
index 0000000000000000000000000000000000000000..a3b84b685d3707ea1ad87353e5fea7262dbb4b7e
Binary files /dev/null and b/docs/source/images/ISIS_reflectometry_release313.png differ
diff --git a/docs/source/images/ProjectRecoveryDialog.png b/docs/source/images/ProjectRecoveryDialog.png
new file mode 100644
index 0000000000000000000000000000000000000000..f21af61f7e938786301e92de7e97f516987efddb
Binary files /dev/null and b/docs/source/images/ProjectRecoveryDialog.png differ
diff --git a/docs/source/images/WorkspaceWidgetSortSize.png b/docs/source/images/WorkspaceWidgetSortSize.png
index 91127401ba4d7156a24a4c6d4fd57aa0392beeaa..f34977d4088e4bbf9a3017e479c53f7bd3f4bbe1 100644
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diff --git a/docs/source/images/indirect-data-analysis-multiple-input.png b/docs/source/images/indirect-data-analysis-multiple-input.png
new file mode 100644
index 0000000000000000000000000000000000000000..3aa328796e7d2f9c8fb758268cc49ccba70d472b
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diff --git a/docs/source/images/instrument-view.png b/docs/source/images/instrument-view.png
new file mode 100644
index 0000000000000000000000000000000000000000..2f205b60834112800effddd1cfb0ada32399fa50
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diff --git a/docs/source/images/multidataset-fitting/multidataset-add-workspace.png b/docs/source/images/multidataset-fitting/multidataset-add-workspace.png
new file mode 100644
index 0000000000000000000000000000000000000000..ccdd0256b0fefcb5433a3d9e5fb789c5f42a4293
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diff --git a/docs/source/images/multidataset-fitting/multidataset-edit-local-params.png b/docs/source/images/multidataset-fitting/multidataset-edit-local-params.png
new file mode 100644
index 0000000000000000000000000000000000000000..fea1760a63d650b19bc9b5b5be899be784f8b144
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diff --git a/docs/source/images/multidataset-fitting/multidataset-fit-prop-dialog.png b/docs/source/images/multidataset-fitting/multidataset-fit-prop-dialog.png
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diff --git a/docs/source/images/multidataset-fitting/multidataset-tie-added.png b/docs/source/images/multidataset-fitting/multidataset-tie-added.png
new file mode 100644
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diff --git a/docs/source/interfaces/Indirect Data Reduction.rst b/docs/source/interfaces/Indirect Data Reduction.rst
index 2bde134bbc16e73aed23796b97fa604b3c94297e..11a42b5c4a58ed078b854c3ad1655fe4d4bcb7e8 100644
--- a/docs/source/interfaces/Indirect Data Reduction.rst
+++ b/docs/source/interfaces/Indirect Data Reduction.rst
@@ -136,7 +136,11 @@ Grouping
The following options are available for grouping output data:
Custom
- A comma separated list can be entered to specify the groups, e.g. 1, 3-5, 6-8, 10.
+ Follows the same grouping patterns used in the :ref:`GroupDetectors <algm-GroupDetectors>` algorithm.
+ An example of the syntax is 1,2+3,4-6,7-10
+
+ This would produce spectra for: spectra 1, the sum of spectra 2 and 3, the sum of spectra 4-6 (4+5+6)
+ and individual spectra from 7 to 10 (7,8,9,10)
Individual
All detectors will remain on individual spectra.
diff --git a/docs/source/interfaces/Multi-dataset Fitting.rst b/docs/source/interfaces/Multi-dataset Fitting.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ee282c362704018cabdd63453cea08f158888f71
--- /dev/null
+++ b/docs/source/interfaces/Multi-dataset Fitting.rst
@@ -0,0 +1,203 @@
+.. _Multi-dataset-Fitting-Interface:
+
+Multi-dataset Fitting Interface
+===============================
+
+.. contents:: Table of Contents
+ :local:
+
+Interface Overview
+------------------
+
+The Multi-dataset fitting interface can be used to fit multiple spectra using
+the same model and starting parameters for each spectrum. This interface can be
+accessed from the main menu of MantidPlot, in *Interfaces → General →
+Multi-dataset Fitting*. The interface consists of three major parts: The fit
+property window, the spectrum & fit viewer, and the list of spectra to operate
+on.
+
+.. figure:: ../images/multidataset-fitting/multidataset-fitting-labelled.png
+ :align: center
+ :width: 1000px
+
+ A high level overview of the various sections of the multidataset fitting
+ interface.
+
+List of Spectra
+---------------
+
+To start fitting data with this interface some data of interest first needs to
+be loaded into the view. Using the "Add workspace" button you can choose a
+workspace to add spectra from. This will let you choose from a list of loaded
+workspaces and optionally select which workspace indices to include for
+fitting. Spectra can be removed by highlighting a corresponding row (or rows)
+and clicking "Remove". To remove all spectra click the "workspace" column name
+and then click the "Remove" button.
+
+.. figure:: ../images/multidataset-fitting/multidataset-add-workspace.png
+ :align: center
+ :width: 800px
+
+ The dialog box shown after clicking "Add workspace".
+
+
+After a list of spectra have been imported from a workspace the table of
+spectra will be populated with one entry for each spectrum. Here you can see
+which workspace the spectrum came from, what the workspace index was, and what
+the start and end `x` values are for this particular spectrum for each fit. The
+start and end values are editable and can be changed by the user by double
+clicking on an entry.
+
+.. figure:: ../images/multidataset-fitting/multidataset-spectra.png
+ :align: center
+ :width: 800px
+
+ The list of spectra after loading a workspace.
+
+Fit Property Browser
+--------------------
+
+The fit property browser is located on the left of the interface. The operation
+of the fit property browser is very similar to the `general fitting view
+<https://www.mantidproject.org/MBC_Setup_And_Execute_First_Fit>`_ available in
+Mantid but with slightly reduced functionality. The fit property browser is
+split into two major parts. The top panel allows the user to define the
+specifics of the model they wish to fit to the dataset. The bottom panel
+contains the parameters for the minimizer and general parameters not associated
+with the model (e.g. the number of iterations). The bottom panel also allows
+the user to choose between simultaneous and sequential fitting mode:
+
+* **Simultaneous Fitting**: Fit all spectra at the same time as a multi-domain
+ function.
+
+* **Sequential Fitting**: Has two different modes of operation specified by the
+ "Fit Type" property:
+
+ * *Sequential*: in which the fitted parameters of the previous spectrum are
+ used as the starting values for the next one.
+ * *Individual*: when all spectra have the same starting values.
+
+Another import general option in the bottom panel is the *CreateOutput* option
+(available in sequential mode). With this checked, as well as the output
+parameters, the fit will also output a workspace with the normalised covariance
+matrices and workspace with parameters for each spectrum. It will also output
+one workspace for each spectrum containing the data, fitted model, and
+difference between model and data.
+
+.. figure:: ../images/multidataset-fitting/multidataset-fit-prop.png
+ :align: center
+ :width: 300px
+
+ The fit property browser. The top panel contains the specifics of the model
+ to fit. The bottom panel contains general parameters not associated with
+ the model.
+
+
+A model can be created by right clicking and choosing "Add function" in the top
+panel of the fit property window. This will produce a dialog box containing a
+large number of different fit functions which can be added to the model.
+
+.. figure:: ../images/multidataset-fitting/multidataset-fit-prop-dialog.png
+ :align: center
+ :width: 400px
+
+ The dialog containing the list of fit functions that can be added to the
+ model.
+
+After adding a function a new entry will appear in the top left panel with the
+name of the fit function and a list of fitting parameters. The user can enter
+appropriate guesses at starting values for the model parameters. Once a model
+has been created the "Plot Guess" checkbox can be used to show a plot of the
+model in the spectrum viewer using the starting parameter. To fit the model
+click the "Fit" button.
+
+
+.. figure:: ../images/multidataset-fitting/multidataset-fit-prop-with-model.png
+ :align: center
+ :width: 300px
+
+ The fit property browser with a model added. The browser shows the current
+ starting values for each of the parameters of the model.
+
+Global Parameters & Ties
+^^^^^^^^^^^^^^^^^^^^^^^^
+In the simultaneous fitting model parameters can be set as global. This means
+the same parameter will be shared across all spectra. To set a parameter as
+global click the checkbox in the "Global" column of the fit property browser
+next to the name and value of the model parameter.
+
+.. figure:: ../images/multidataset-fitting/multidataset-global-param.png
+ :align: center
+ :width: 300px
+
+ Setting a model parameter to be global.
+
+Model parameters can also be tied together or fixed to a given value. This can
+be done by right clicking on the parameter and choosing either "Tie" or "Fix".
+A fixed parameter's value will not change during a fit. A tied parameter can be
+used to either bound a parameter to a range or to tie the values of two
+parameters together.
+
+.. figure:: ../images/multidataset-fitting/multidataset-fit-prop-right-click.png
+ :align: center
+ :width: 300px
+
+ Right clicking on a parameter shows the context menu with the fix, tie, and
+ contraint options
+
+.. figure:: ../images/multidataset-fitting/multidataset-set-tie.png
+ :align: center
+ :width: 300px
+
+ Tieing the height parameter to the sigma parameter. More complex expressions
+ are allowed. See the documentation in the :ref:`Fit <algm-Fit-v1>`
+ algorithm.
+
+.. figure:: ../images/multidataset-fitting/multidataset-tie-added.png
+ :align: center
+ :width: 300px
+
+ The fit property browser after the tie has been added to the parameter.
+
+Local Parameters
+^^^^^^^^^^^^^^^^
+As well as setting the starting values for global parameters, the local
+parameter values of the model used for each spectrum can be set individually.
+The local parameter values can be edited by clicking on the value you wish to
+modify, then clicking on the "..." button next to the value. This will open a
+dialog of values for every spectrum. Here individual values can be set, fixed,
+and tied as with the global parameters.
+
+.. figure:: ../images/multidataset-fitting/multidataset-edit-local-params.png
+ :align: center
+ :width: 400px
+
+ Button to open the window to edit local parameter values.
+
+.. figure:: ../images/multidataset-fitting/multidataset-local-params.png
+ :align: center
+ :width: 800px
+
+ Editing local parameter values for each spectrum.
+
+Spectrum Viewer
+---------------
+
+The spectrum viewer is shown in the bottom panel of the interface. This shows a
+plot of a single spectrum from the loaded list. It also shows a plot of the
+model with the current parameters overlaid on the spectrum. Using the buttons
+shown in the screenshot below the user can select which spectrum they wish to
+view. The plot is interactive and can be panned and zoomed.
+
+The user can also interactively select `x` bounds either for a single spectrum
+or for all spectra by selecting the "Apply to all spectra option. To select
+`x` bounds click and drag the blue dashed vertical lines to move define the
+fitting window.
+
+.. figure:: ../images/multidataset-fitting/multidataset-spectrum-view.png
+ :align: center
+ :width: 800px
+
+ The spectrum view in the multidataset fitting interface.
+
+.. categories:: Interfaces Fitting
diff --git a/docs/source/release/v3.13.0/diffraction.rst b/docs/source/release/v3.13.0/diffraction.rst
index 2aa2024a226bc3082bcb2a861b5c9e7a38bf0cc6..eb98c4eab28fc5a74b2b0d4d279a35e93e63771a 100644
--- a/docs/source/release/v3.13.0/diffraction.rst
+++ b/docs/source/release/v3.13.0/diffraction.rst
@@ -5,9 +5,7 @@ Diffraction Changes
.. contents:: Table of Contents
:local:
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
+:ref:`Release 3.13.0 <v3.13.0>`
Powder Diffraction
------------------
@@ -15,6 +13,13 @@ Powder Diffraction
New
###
+.. figure:: ../../images/D2B_calib.png
+ :align: center
+
+ D2B calibration constants generated from PowderDiffILLDetEffCorr
+ :ref:`PowderDiffILLDetEffCorr <algm-PowderDiffILLDetEffCorr-v1>`
+
+
- :ref:`LoadILLDiffraction <algm-LoadILLDiffraction>` is extended to apply vertical and horizontal tube alignment for D2B, based on the IPF.
- :ref:`LoadILLDiffraction <algm-LoadILLDiffraction>` is modified to comply with the U-shape convention for tube numbering for D2B.
- :ref:`PowderDiffILLDetEffCorr <algm-PowderDiffILLDetEffCorr>` is extended to compute the detector efficiencies also for the 2-dimensional scanning diffractometer D2B at the ILL.
@@ -40,6 +45,9 @@ Improvements
- The ``.maud`` calibration file format, for conversion to d-spacing (uses a new algorithm
:ref:`SaveGEMMAUDParamFile <algm-SaveGEMMAUDParamFile>`
- :ref:`PDCalibration <algm-PDCalibration>` has major upgrades including making use of :ref:`FitPeaks <algm-FitPeaks>` for the individual peak fitting
+- :ref:`StripPeaks <algm-StripPeaks>` has been adjusted to allow for removing peaks that have only 3 bins across them (decreased from 5 bins)
+- :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder>` had a bug when binning in time-of-flight without using a property manager to specify the time-of-flight range. In other words: characterization files are no longer necessary.
+
Engineering Diffraction
-----------------------
@@ -70,31 +78,38 @@ Improvements
- The ``.nxs`` file from the Focus tab is now saved in the Focus directory with all the other focus output
-:ref:`Release 3.13.0 <v3.13.0>`
-
Single Crystal Diffraction
--------------------------
New
###
-- New algorithm :ref:`LoadDNSSCD <algm-LoadDNSSCD>` to load multiple single crystal diffraction data files from the DNS instrument into MDEventWorkspace.
+.. figure:: ../../images/LoadWANDSCD.png
+ :align: center
-- :ref:`SaveLauenorm <algm-SaveLauenorm>` now has input options for crystal system and reflection condition for lscale output instead of trying to determine from lattice parameters.
+ Integrated output from LoadWANDSCD :ref:`LoadDNSSCD <algm-LoadWANDSCD-v1>`
-- :ref:`CreatePeaksWorkspace <algm-CreatePeaksWorkspace>` now accepts MD workspaces as input.
+- New algorithm :ref:`LoadDNSSCD <algm-LoadDNSSCD>` to load multiple single crystal diffraction data files from the DNS instrument into MDEventWorkspace.
- New algorithms :ref:`LoadWANDSCD <algm-LoadWANDSCD>` and :ref:`ConvertWANDSCDtoQ <algm-ConvertWANDSCDtoQ>` to load single crystal HB2C data and convert it to either Q-sample or HKL space.
- New algorithm :ref:`IntegratePeaksProfileFitting <algm-IntegratePeaksProfileFitting>` to integrate peaks using 3D profile fitting in reciprocal space.
-- New algorithm :ref:`RefineSatellitePeaks <algm-RefineSatellitePeaks>` to predict the location of fractional satellite peaks using a set of nuclear peaks and a set of seed satellite peaks.
+- New algorithm :ref:`FindSatellitePeaks <algm-FindSatellitePeaks>` to predict the location of fractional satellite peaks using a set of nuclear peaks and a set of seed satellite peaks.
+
+- New algorithm :ref:`IndexSatellitePeaks <algm-IndexSatellitePeaks>` to index satellite peaks found using the :ref:`FindSatellitePeaks <algm-FindSatellitePeaks>` algorithm.
+
+- :ref:`SaveLauenorm <algm-SaveLauenorm>` now has input options for crystal system and reflection condition for lscale output instead of trying to determine from lattice parameters.
- New TOPAZ instrument geometry for 2018 run cycle
Improvements
############
+- :ref:`CreatePeaksWorkspace <algm-CreatePeaksWorkspace>` now accepts MD workspaces as input.
+
- PeaksWorkspace has column added for the unique peak number so peaks can be found after sorting or filtering.
- :ref:`StatisticsOfPeaksWorkspace <algm-StatisticsOfPeaksWorkspace>` has option to use a weighted Z score for determining which peaks are outliers and has a new output workspace for plotting intensities of equivalent peaks.
+
+
diff --git a/docs/source/release/v3.13.0/direct_inelastic.rst b/docs/source/release/v3.13.0/direct_inelastic.rst
index 305e47d358629adbb85a8f90a2df5d10ac3773ba..51ad9e074354592f98b3c2e8c8d382bc095b7f86 100644
--- a/docs/source/release/v3.13.0/direct_inelastic.rst
+++ b/docs/source/release/v3.13.0/direct_inelastic.rst
@@ -5,25 +5,20 @@ Direct Inelastic Changes
.. contents:: Table of Contents
:local:
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
-
Interfaces
----------
-
New
###
- Added the ability to manually specify a temperature for a set of runs in the TOFTOF reduction dialog.
-
Improvements
############
- :ref:`PyChop <PyChop>` has been updated to calculate rep-rate multiplication for MAPS and MARI. In addition, it now supports loading instrument parameters from a YAML file, and also plots the Q-E coverage.
-
+- Workspaces used in MSlice are no longer added to the MantidPlot window automatically, and can be added using the ``Save To MantidPlot`` button.
+- Improved default limits for 2D plots of large datasets in MSlice.
Algorithms
----------
@@ -59,7 +54,6 @@ Deprecated
Instrument Definitions
----------------------
-
- The source component of ILL's IN5 has been moved from :math:`z = -2` to :math:`z = -2.10945` meters and renamed to ``frame-overlap_chopper``.
- The source component of ILL's IN6 has been moved from :math:`z = -0.395` to :math:`z = -0.595` meters and renamed to ``suppressor_chopper``.
- ILL's IN4 and IN6 now validate the wavelengths and chopper speeds in :ref:`MergeRuns <algm-MergeRuns>`.
diff --git a/docs/source/release/v3.13.0/framework.rst b/docs/source/release/v3.13.0/framework.rst
index 1b7b638a15f698727a5e7fd79ecf89df2d56eaf1..dc5e9719f56eeb2e1839f63ed112ae9b71cd343c 100644
--- a/docs/source/release/v3.13.0/framework.rst
+++ b/docs/source/release/v3.13.0/framework.rst
@@ -5,25 +5,24 @@ Framework Changes
.. contents:: Table of Contents
:local:
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
-
Instrument Definition Updates
-----------------------------
- The ALF IDF has been updated following a detector array alteration.
- The LARMOR IDF has been updated following the addition of a new detector to the instrument.
+- Instrument definition for IN4, 5, and 6 at the ILL have been updated
+- REF_L and CNCS has update instrument files and EQSANS, REF_M, ARCS and CNCS are now configured for loading live data.
Stability
---------
+- We have introduced a Project Recovery mechanism for Mantidplot in order to be able to recover the lost state of the interface in the event of a crash or unexpected shutdown. There are more details in the UI section of the release notes.
+- The error reporter can now catches hard crashes to desktop, allowing us to get more information on causes of hangs or crashes in Mantid. Since the last release error reports sent to us led directly to the identification of and fixes for 3 seperate bugs in Mantid.
- Mantid now handles poor network stability better when reading live data from the ISIS DAE. Mantid will now timeout after a couple of minutes of loss of network connectivity and remains responsive during this time. You can alter the duration of this timeout by adding a line to the mantid.user.properties file like:
```
ISISDAE.Timeout = 100 #seconds
```
-- The error reporter now catches hard crashes to desktop.
Algorithms
@@ -32,10 +31,7 @@ Algorithms
New
###
-New Features
-************
-
-- A list of Related Algorithms has been added to each algorithm, and is displayed in the documentation page of each algorithm as part of it's summary.
+- Sometimes the algorithm you are looking at is close to what you want, but not quite, to help you find the right one a list of related algorithms has been added to each algorithm, and is displayed in the documentation page of each algorithm as part of it's summary.
New Algorithms
**************
diff --git a/docs/source/release/v3.13.0/index.rst b/docs/source/release/v3.13.0/index.rst
index 0e6f8aba5dbf1b8093a94ffd257aa20045775aa7..d2ce930b2e3c1f95203fc5c08030da0c250ded67 100644
--- a/docs/source/release/v3.13.0/index.rst
+++ b/docs/source/release/v3.13.0/index.rst
@@ -7,6 +7,8 @@ Mantid 3.13.0 Release Notes
.. figure:: ../../images/Release3-13.png
:class: screenshot
:align: right
+
+ Mantid introduces project recovery for Mantidplot.
.. contents:: Table of Contents
:local:
@@ -14,7 +16,14 @@ Mantid 3.13.0 Release Notes
We are proud to announce version 3.13.0 of Mantid.
-Here is a load of stuff we have done.
+This release includes a first implementation of Project Recovery for Mantidplot, Mantid maintains a recovery script while running, in the event of a crash or unexpected shutdown of Mantidplot Mantid will attempt to recover to it's most recent recovery checkpoint. This feature may not fully recover in all situations, but we will continue to improve it in future releases. There have also been some significant performance enhancements in the instrument view, improvements in error reporting, and the peaks view within the slice viewer now handles non-orthogonal axes.
+
+These are just some of the many improvements in this release, so please take a
+look at the release notes, which are filled with details of the
+important changes and improvements in many areas. The development team
+has put a great effort into making all of these improvements within
+Mantid, and we would like to thank all of our beta testers for their
+time and effort helping us to make this another reliable version of Mantid.
Citation
--------
@@ -40,7 +49,6 @@ Changes
SANS <sans>
Direct Inelastic <direct_inelastic>
Indirect Inelastic <indirect_inelastic>
- Instrument Visualization <instrument_view>
Full Change Listings
--------------------
diff --git a/docs/source/release/v3.13.0/indirect_inelastic.rst b/docs/source/release/v3.13.0/indirect_inelastic.rst
index 53d685a0b16f2d51843a9d975a5d67aae12cfa8b..48c2b20df70321ab93f87b5da547b854059d3329 100644
--- a/docs/source/release/v3.13.0/indirect_inelastic.rst
+++ b/docs/source/release/v3.13.0/indirect_inelastic.rst
@@ -5,10 +5,6 @@ Indirect Inelastic Changes
.. contents:: Table of Contents
:local:
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
-
:ref:`Release 3.13.0 <v3.13.0>`
Data Reduction Interfaces
@@ -42,10 +38,17 @@ Improvements
- :ref:`algm-ConvolutionFitSequential` and :ref:`algm-IqtFitSequential` can now accept multiple datasets as input, in
the same format as that of :ref:`algm-PlotPeakByLogValue`.
- :ref:`algm-IndirectILLEnergyTransfer` was fixed to have the correct sign for the energy transfer.
+- :ref:`algm-TransformToIqt` now calculates errors using a monte carlo method, and can take a number of iterations as input.
Data Analysis Interfaces
------------------------
+.. figure:: ../../images/indirect-data-analysis-multiple-input.png
+ :align: center
+ :width: 700px
+
+ The ConvFit interface with the new multiple input section.
+
New
###
@@ -55,6 +58,11 @@ New
- The QENS Fitting interfaces can now be provided multiple data-sets as input -- these data-sets can be viewed
individually within the interface (plot, fit result, etc.)
+Improved
+########
+
+- A number of iterations for the new monte carlo error calculation can be specified in the I(Q,t) interface.
+
Bugfixes
########
diff --git a/docs/source/release/v3.13.0/instrument_view.rst b/docs/source/release/v3.13.0/instrument_view.rst
deleted file mode 100644
index fc6de74b9c44411a4807b5b139eed42da75d7634..0000000000000000000000000000000000000000
--- a/docs/source/release/v3.13.0/instrument_view.rst
+++ /dev/null
@@ -1,39 +0,0 @@
-========================
-Instrument Visualization
-========================
-
-.. contents:: Table of Contents
- :local:
-
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
-
-Instrument View
----------------
-
-Improvements
-############
-
-The `Instrument View <https://www.mantidproject.org/MantidPlot:_Instrument_View>`__ visualization tool in Mantid has undergone some major changes under-the-hood which has resulted in a smoother, more responsive interface.
-Instruments generally load faster as well. Below are a few noteworthy improvements to load times:
-
-+------------+-----------+
-| Instrument | Speedup |
-+============+===========+
-| WISH | 5x |
-+------------+-----------+
-| BASIS | 5x |
-+------------+-----------+
-| GEM | 4x |
-+------------+-----------+
-| SANS2D | 3x |
-+------------+-----------+
-| POLARIS | 3x |
-+------------+-----------+
-| CNCS | 2x |
-+------------+-----------+
-
-Tested on Windows 10.
-
-:ref:`Release 3.13.0 <v3.13.0>`
diff --git a/docs/source/release/v3.13.0/reflectometry.rst b/docs/source/release/v3.13.0/reflectometry.rst
index ef27f595abdafb3c371c26f72747532880457cdf..2b2b15d358d68bf9a7121eeaac06c4bde29e8df0 100644
--- a/docs/source/release/v3.13.0/reflectometry.rst
+++ b/docs/source/release/v3.13.0/reflectometry.rst
@@ -5,12 +5,11 @@ Reflectometry Changes
.. contents:: Table of Contents
:local:
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
-
ISIS Reflectometry Interface
----------------------------
+.. image:: ../../images/ISIS_reflectometry_release313.png
+ :align: right
+ :width: 800px
New
###
@@ -19,62 +18,54 @@ New
- A new option has been added to the Settings tab to control whether partial bins should be included when summing in Q.
- ``ReflectometryReductionOneAuto`` takes the polarization correction properties from the instrument parameter file when ``PolarizationAnalysis`` is set to ``ParameterFile``. The instrument parameter file can store the efficiencies as vectors of doubles.
-Improvements
-############
-
-Bugfixes
-########
-
Features Removed
################
-* Added deprecation notice to ISIS Reflectometry (Old) due to be removed in March 2019.
+* Added a deprecation notice to the ISIS Reflectometry (Old) interface, this is due to be removed in March 2019. It will be present in releases up until that date, but new features will only be added to the new interface.
Algorithms
----------
-* Removed version 1 of ``ReflectometryReductionOne`` and ``ReflectometryReductionOneAuto``.
-* Renamed algorithms ``PolarizationCorrection`` to ``PolarizationCorrectionFredrikze`` and ``PolarizationEfficiencyCor`` to ``PolarizationCorrectionWildes``.
+- Removed version 1 of ``ReflectometryReductionOne`` and ``ReflectometryReductionOneAuto``.
+- Renamed algorithms ``PolarizationCorrection`` to ``PolarizationCorrectionFredrikze`` and ``PolarizationEfficiencyCor`` to ``PolarizationCorrectionWildes``.
New
###
-* Added algorithm ``PolarizationEfficiencyCor`` which calls ``PolarizationCorrectionFredrikze`` or ``PolarizationCorrectionWildes`` depending on chosen ``Method`` property.
-* Added algorithms that help create a matrix workspace with polarization efficiencies ready to be used with ``PolarizationEfficiencyCor``
+- Added algorithm ``PolarizationEfficiencyCor`` which calls ``PolarizationCorrectionFredrikze`` or ``PolarizationCorrectionWildes`` depending on chosen ``Method`` property.
+- Added algorithms that help create a matrix workspace with polarization efficiencies ready to be used with ``PolarizationEfficiencyCor``
- ``CreatePolarizationEfficiencies`` creates efficiencies from polynomial coefficients
- ``JoinISISPolarizationEfficiencies`` joins individual efficiencies into one matrix workspace
- ``LoadISISPolarizationEfficiencies`` loads efficiencies form files
-* The ILL reflectometry loader :ref:`algm-LoadILLReflectometry` implements the NeXus file changes of January 2018 and can load again all valid Nexus files for D17 and FIGARO which are available since 2013 and 2017, respectively.
-* Algorithms for reflectometry reduction at ILL have been added. These handle the basic polarized/unpolarized reduction in SumInLambda or SumInQ modes. Included algorithms:
- - :ref:`algm-ReflectometryILLPreprocess`
- - :ref:`algm-ReflectometryILLSumForeground`
- - :ref:`algm-ReflectometryILLPolarizationCor`
- - :ref:`algm-ReflectometryILLConvertToQ`
-* A new algorithm :ref:`algm-ReflectometryMomentumTransfer` provides conversion to momentum transfer and :math:`Q_{z}` resolution calculation for reflectivity workspaces.
-* A new algorithm :ref:`ReflectometrySumInQ <algm-ReflectometrySumInQ>` is available for coherent summation of the reflected beam.
+- The ILL reflectometry loader :ref:`algm-LoadILLReflectometry` implements the NeXus file changes of January 2018 and can load again all valid Nexus files for D17 and FIGARO which are available since 2013 and 2017, respectively.
+- Algorithms for reflectometry reduction at ILL have been added. These handle the basic polarized/unpolarized reduction in SumInLambda or SumInQ modes. Included algorithms:
-- :ref:`algm-ReflectometryReductionOne` and :ref:`algm-ReflectometryReductionOneAuto` no longer include partial bins by default when summing in Q. A new property, `IncludePartialBins`, has been added to re-enable partial bins.
+ - :ref:`algm-ReflectometryILLPreprocess`
+ - :ref:`algm-ReflectometryILLSumForeground`
+ - :ref:`algm-ReflectometryILLPolarizationCor`
+ - :ref:`algm-ReflectometryILLConvertToQ`
+- A new algorithm :ref:`algm-ReflectometryMomentumTransfer` provides conversion to momentum transfer and :math:`Q_{z}` resolution calculation for reflectivity workspaces.
+- A new algorithm :ref:`ReflectometrySumInQ <algm-ReflectometrySumInQ>` is available for coherent summation of the reflected beam.
-Improvements
-############
+- :ref:`algm-ReflectometryReductionOne` and :ref:`algm-ReflectometryReductionOneAuto` no longer include partial bins by default when summing in Q. A new property, `IncludePartialBins`, has been added to re-enable partial bins.
- Added a boolean property ``Debug`` to the reflectometry algorithms that controls output of additional and/or intermediate workspaces.
Bug fixes
#########
-* Correct the angle to the value of ``ThetaIn`` property if summing in lambda in ``ReflectometryReductionOne-v2``.
-* Fixed an incorrectly calculated detector angle when loading FIGARO files using :ref:`algm-LoadILLReflectometry`.
+- Correct the angle to the value of ``ThetaIn`` property if summing in lambda in ``ReflectometryReductionOne-v2``.
+- Fixed an incorrectly calculated detector angle when loading FIGARO files using :ref:`algm-LoadILLReflectometry`.
Liquids Reflectometer
---------------------
-* New REF_L instrument geometry for 2018 run cycle.
+- New REF_L instrument geometry for 2018 run cycle.
Magnetism Reflectometer
-----------------------
-* Added live data information to Facilities.xml
-* Allow for the use of workspace groups as input to the reduction.
-* Added algorithm to compute scattering angle from a workspace.
+- Added live data information to Facilities.xml
+- Allow for the use of workspace groups as input to the reduction.
+- Added algorithm to compute scattering angle from a workspace.
:ref:`Release 3.13.0 <v3.13.0>`
diff --git a/docs/source/release/v3.13.0/sans.rst b/docs/source/release/v3.13.0/sans.rst
index 351fe2e48ef14842d2829f643ecaa39735a5d289..b5f40975a0053fbfe36cd116896193e23913850d 100644
--- a/docs/source/release/v3.13.0/sans.rst
+++ b/docs/source/release/v3.13.0/sans.rst
@@ -5,16 +5,26 @@ SANS Changes
.. contents:: Table of Contents
:local:
+ILL
+---
+
* :ref:`LoadILLSANS <algm-LoadILLSANS>` is upgraded to load the modern nexus files from instruments D11, D22 and D33 at the ILL.
+* :ref:`SANSMask <algm-SANSMask>` is extended to have a `MaskedWorkspace` property, to copy the mask from.
+
+SNS
+---
+
* EQSANS is configured for live data
ISIS SANS Interface
-----------------------------
+-------------------
+.. image:: ../../images/ISIS_SANS_release313.png
+ :align: right
+ :width: 800px
New
###
* A string of wavelength ranges can now be specified. A reduction is then done for each wavelength range.
-* :ref:`SANSMask <algm-SANSMask>` is extended to have a `MaskedWorkspace` property, to copy the mask from.
Improvements
############
@@ -27,6 +37,7 @@ Improvements
* Improved error messages in the new GUI to be more obvious and clearer.
* Updated the naming of workspace groups in a sliced reduction.
* Updated old backend to mask by detector ID rather than spectrum number, improving reliability.
+* NXcanSAS is now saved out with a .h5 extension so it can be read into SASView.
Bugfixes
########
@@ -37,10 +48,12 @@ Bugfixes
* Fixed a bug where save_format was not being specified if a user file was entered for a row.
* Use gravity now defaulting to false.
* MASK/TIME and TIME/MASK now both work in new backend.
+* SET Centre/HAB command is now correctly parsed into a seperate variable to SET Centre.
Features Removed
################
* Removed SaveNist as an option from both GUI's
+* The Q range option on the beam centre tab was producing erroneous results so has been removed until it can be improved and fixed.
:ref:`Release 3.13.0 <v3.13.0>`
diff --git a/docs/source/release/v3.13.0/ui.rst b/docs/source/release/v3.13.0/ui.rst
index da6ff22d23b502ed2b951eddf622b349e02b36a4..6dd5dbad52f737b4d3732de3bb3f1e465e3c64dc 100644
--- a/docs/source/release/v3.13.0/ui.rst
+++ b/docs/source/release/v3.13.0/ui.rst
@@ -5,28 +5,23 @@ UI & Usability Changes
.. contents:: Table of Contents
:local:
-.. warning:: **Developers:** Sort changes under appropriate heading
- putting new features at the top of the section, followed by
- improvements, followed by bug fixes.
-
-:ref:`Release 3.13.0 <v3.13.0>`
MantidPlot
----------
- MantidPlot's pyplot API has been removed.
+-
+.. figure:: ../../images/WorkspaceWidgetSortSize.png
+ :class: screenshot
+ :align: right
+ :figwidth: 70%
Improvements
############
- Added functionality to sort based on Memory Size of the workspace
-.. figure:: ../../images/WorkspaceWidgetSortSize.png
- :class: screenshot
- :align: center
- :figwidth: 70%
-
Bugfixes
########
@@ -54,3 +49,40 @@ New
###
- DGSPlanner has an option to load the UB matrix from the Nexus file metadata
+
+Instrument View
+---------------
+
+Improvements
+############
+
+.. figure:: ../../images/instrument-view.png
+ :align: right
+ :width: 700px
+
+ The instrument view showing data from WISH.
+
+The `Instrument View
+<https://www.mantidproject.org/MantidPlot:_Instrument_View>`__ visualization
+tool in Mantid has undergone some major changes under-the-hood which has
+resulted in a smoother, more responsive interface. Instruments generally load
+faster as well. Below are a few noteworthy improvements to load times (as tested on Windows 10):
+
++------------+-----------+
+| Instrument | Speedup |
++============+===========+
+| WISH | 5x |
++------------+-----------+
+| BASIS | 5x |
++------------+-----------+
+| GEM | 4x |
++------------+-----------+
+| SANS2D | 3x |
++------------+-----------+
+| POLARIS | 3x |
++------------+-----------+
+| CNCS | 2x |
++------------+-----------+
+
+
+:ref:`Release 3.13.0 <v3.13.0>`
\ No newline at end of file
diff --git a/instrument/D2B_Definition_2018-05-01.xml b/instrument/D2B_Definition_2018-05-01.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e18e8e72b48c23e458a24b07b39dc2a4b2d0fa5b
--- /dev/null
+++ b/instrument/D2B_Definition_2018-05-01.xml
@@ -0,0 +1,325 @@
+<?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 Schema/IDFSchema.xsd" name="D2B" valid-from="2018-05-01 23:59:59"
+valid-to="2100-01-31 23:59:59" last-modified="2018-03-20 14:05:02">
+ <!-- Author: bush@ill.fr -->
+ <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" />
+ <theta-sign axis="x" />
+ </reference-frame>
+ </defaults>
+ <!-- Source position -->
+ <component type="monochromator">
+ <location z="-2.997" />
+ </component>
+ <type name="monochromator" is="Source" />
+ <!-- Monitor position -->
+ <component type="monitor" idlist="monitors">
+ <location z="-1.594" name="monitor" />
+ </component>
+ <type name="monitor" is="monitor">
+ <cuboid id="shape">
+ <left-front-bottom-point x="-0.005" y="-0.005" z="-0.005" />
+ <left-front-top-point x="-0.005" y="0.005" z="-0.005" />
+ <left-back-bottom-point x="-0.005" y="-0.005" z="0.005" />
+ <right-front-bottom-point x="0.005" y="-0.005" z="-0.005" />
+ </cuboid>
+ <algebra val="shape" />
+ </type>
+ <idlist idname="monitors">
+ <id val="0" />
+ </idlist>
+ <!-- Sample position -->
+ <component type="sample-position">
+ <location x="0.0" y="0.0" z="0.0" />
+ </component>
+ <type name="sample-position" is="SamplePos" />
+ <!-- Detector IDs -->
+ <idlist idname="detectors">
+ <id start="1" end="16384" />
+ </idlist>
+ <!-- Detector list def -->
+ <component type="detectors" idlist="detectors">
+ <location x="0.0" y="0.0" z="0.0" />
+ </component>
+ <type name="detectors">
+ <component type="standard_tube">
+ <location r="1.296" t="-6.25" name="tube_1" />
+ <location r="1.296" t="-7.5" name="tube_2" />
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+ <location y="-0.051236328125" />
+ <location y="-0.048466796875" />
+ <location y="-0.045697265625" />
+ <location y="-0.042927734375" />
+ <location y="-0.040158203125" />
+ <location y="-0.037388671875" />
+ <location y="-0.034619140625" />
+ <location y="-0.031849609375" />
+ <location y="-0.029080078125" />
+ <location y="-0.026310546875" />
+ <location y="-0.023541015625" />
+ <location y="-0.020771484375" />
+ <location y="-0.018001953125" />
+ <location y="-0.015232421875" />
+ <location y="-0.012462890625" />
+ <location y="-0.009693359375" />
+ <location y="-0.006923828125" />
+ <location y="-0.004154296875" />
+ <location y="-0.001384765625" />
+ <location y="0.001384765625" />
+ <location y="0.004154296875" />
+ <location y="0.006923828125" />
+ <location y="0.009693359375" />
+ <location y="0.012462890625" />
+ <location y="0.015232421875" />
+ <location y="0.018001953125" />
+ <location y="0.020771484375" />
+ <location y="0.023541015625" />
+ <location y="0.026310546875" />
+ <location y="0.029080078125" />
+ <location y="0.031849609375" />
+ <location y="0.034619140625" />
+ <location y="0.037388671875" />
+ <location y="0.040158203125" />
+ <location y="0.042927734375" />
+ <location y="0.045697265625" />
+ <location y="0.048466796875" />
+ <location y="0.051236328125" />
+ <location y="0.054005859375" />
+ <location y="0.056775390625" />
+ <location y="0.059544921875" />
+ <location y="0.062314453125" />
+ <location y="0.065083984375" />
+ <location y="0.067853515625" />
+ <location y="0.070623046875" />
+ <location y="0.073392578125" />
+ <location y="0.076162109375" />
+ <location y="0.078931640625" />
+ <location y="0.081701171875" />
+ <location y="0.084470703125" />
+ <location y="0.087240234375" />
+ <location y="0.090009765625" />
+ <location y="0.092779296875" />
+ <location y="0.095548828125" />
+ <location y="0.098318359375" />
+ <location y="0.101087890625" />
+ <location y="0.103857421875" />
+ <location y="0.106626953125" />
+ <location y="0.109396484375" />
+ <location y="0.112166015625" />
+ <location y="0.114935546875" />
+ <location y="0.117705078125" />
+ <location y="0.120474609375" />
+ <location y="0.123244140625" />
+ <location y="0.126013671875" />
+ <location y="0.128783203125" />
+ <location y="0.131552734375" />
+ <location y="0.134322265625" />
+ <location y="0.137091796875" />
+ <location y="0.139861328125" />
+ <location y="0.142630859375" />
+ <location y="0.145400390625" />
+ <location y="0.148169921875" />
+ <location y="0.150939453125" />
+ <location y="0.153708984375" />
+ <location y="0.156478515625" />
+ <location y="0.159248046875" />
+ <location y="0.162017578125" />
+ <location y="0.164787109375" />
+ <location y="0.167556640625" />
+ <location y="0.170326171875" />
+ <location y="0.173095703125" />
+ <location y="0.175865234375" />
+ </component>
+ </type>
+ <type name="standard_pixel" is="detector">
+ <cylinder id="shape">
+ <centre-of-bottom-base x="0.0" y="-0.001384765625" z="0.0" />
+ <axis x="0.0" y="1.0" z="0.0" />
+ <radius val="0.000565486605872" />
+ <height val="0.00276953125" />
+ </cylinder>
+ <algebra val="shape" />
+ </type>
+</instrument>
diff --git a/instrument/D2B_Parameters_2018-05-01.xml b/instrument/D2B_Parameters_2018-05-01.xml
new file mode 100644
index 0000000000000000000000000000000000000000..60cb21e252886b3817b7a8d54bb60486bdfdb598
--- /dev/null
+++ b/instrument/D2B_Parameters_2018-05-01.xml
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<parameter-file instrument="D2B" valid-from="2018-05-01 23:59:59">
+ <component-link name="D2B">
+
+ <!-- The detector name for the height axis used in SumOverlappingTubes -->
+ <parameter name="detector_for_height_axis" type="string">
+ <value val="tube_1" />
+ </parameter>
+
+ <!-- The flag for mirroring the angles in SumOverlappingTubes -->
+ <parameter name="mirror_scattering_angles" type="bool">
+ <value val="True" />
+ </parameter>
+
+ <!-- Number of pixels to trim from the top and the bottom of the tubes when
+ calculating the chiˆ2 in the detector efficiencies in case of autoiterations -->
+ <parameter name="pixels_to_trim" type="int">
+ <value val="28" />
+ </parameter>
+
+ <!-- The chiˆ2/NdoF threshold for termination of autoiterations
+ in detector efficiency calculation -->
+ <parameter name="chi2_ndof" type="float">
+ <value val="0.01" />
+ </parameter>
+
+ <!-- The central pixel indices of the tubes; these must be rounded!-->
+ <parameter name="tube_centers" type="string">
+ <value val="71,64,66,69,68,68,67,70,66,71,69,66,71,68,67,71,
+ 68,69,66,70,67,70,68,68,67,69,68,67,68,68,69,69,
+ 65,67,66,68,67,68,67,67,67,70,68,69,66,67,67,66,
+ 67,67,67,67,66,66,66,69,66,68,72,64,66,68,63,68,
+ 68,68,69,68,67,70,68,71,64,70,67,70,69,70,69,68,
+ 66,70,70,66,66,69,66,68,67,69,67,66,69,66,66,70,
+ 70,68,68,71,66,69,67,68,72,68,68,70,68,69,68,70,
+ 67,70,69,68,64,69,68,68,69,70,71,68,68,69,70,67"/>
+ </parameter>
+
+ <!-- Relative 2theta positions of the tubes wrt the last tube -->
+ <parameter name="tube_angles" type="string">
+ <value val="-158.750,-157.500,-156.250,-155.000,-153.750,-152.500,
+ -151.250,-150.000,-148.750,-147.500,-146.250,-145.000,
+ -143.750,-142.500,-141.250,-140.000,-138.750,-137.500,
+ -136.250,-135.000,-133.750,-132.500,-131.262,-130.027,
+ -128.764,-127.501,-126.262,-124.986,-123.744,-122.488,
+ -121.250,-119.996,-118.749,-117.503,-116.240,-115.000,
+ -113.760,-112.510,-111.225,-110.011,-108.726,-107.537,
+ -106.240,-104.974,-103.739,-102.491,-101.254,-99.9934,
+ -98.7551,-97.5007,-96.2569,-94.9937,-93.7413,-92.5081,
+ -91.2396,-89.9824,-88.7602,-87.5170,-86.2329,-84.9932,
+ -83.7641,-82.5050,-81.2662,-79.9966,-78.7527,-77.5035,
+ -76.2564,-74.9872,-73.7477,-72.5086,-71.2457,-70.0003,
+ -68.7467,-67.4861,-66.2499,-65.0244,-63.7557,-62.5025,
+ -61.2484,-59.9862,-58.7416,-57.4992,-56.2372,-54.9913,
+ -53.7547,-52.4989,-51.2399,-50.0088,-48.7492,-47.4948,
+ -46.2517,-45.0034,-43.7366,-42.4932,-41.2465,-39.9866,
+ -38.7377,-37.5183,-36.2678,-35.0202,-33.7731,-32.4958,
+ -31.2734,-30.0018,-28.7291,-27.4887,-26.2319,-24.9728,
+ -23.7554,-22.4771,-21.2376,-20.0052,-18.7470,-17.5007,
+ -16.2531,-14.9891,-13.7492,-12.5056,-11.2798,-10.0067,
+ -8.73692,-7.50000,-6.25000,-5.00000,-3.75000,-2.50000,
+ -1.25000,0.000000"/>
+ </parameter>
+ </component-link>
+</parameter-file>
diff --git a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/MdViewerWidget.cpp b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/MdViewerWidget.cpp
index 5123d319ff97f97dae1b588d0a447ad0a0ca2c38..001c03fc090a22278c84351825636e2534d27b4e 100644
--- a/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/MdViewerWidget.cpp
+++ b/qt/paraview_ext/VatesSimpleGui/ViewWidgets/src/MdViewerWidget.cpp
@@ -1054,6 +1054,10 @@ void MdViewerWidget::setActiveObjects(pqView *view, pqPipelineSource *source) {
*/
std::string MdViewerWidget::saveToProject(ApplicationWindow *app) {
UNUSED_ARG(app);
+ // Early exit if there are no sources
+ auto &activeObjects = pqActiveObjects::instance();
+ if (!activeObjects.activeSource())
+ return "";
TSVSerialiser tsv, contents;
// save window position & size
@@ -1064,7 +1068,7 @@ std::string MdViewerWidget::saveToProject(ApplicationWindow *app) {
auto fileName = workingDir.toStdString() + "/VSI.xml";
// Dump the state of VSI to a XML file
- auto session = pqActiveObjects::instance().activeServer()->proxyManager();
+ auto session = activeObjects.activeServer()->proxyManager();
session->SaveXMLState(fileName.c_str());
contents.writeLine("FileName") << fileName;
@@ -1072,7 +1076,6 @@ std::string MdViewerWidget::saveToProject(ApplicationWindow *app) {
auto vtype = currentView->getViewType();
contents.writeLine("ViewType") << static_cast<int>(vtype);
- auto &activeObjects = pqActiveObjects::instance();
auto proxyManager = activeObjects.activeServer()->proxyManager();
auto view = activeObjects.activeView()->getProxy();
auto source = activeObjects.activeSource()->getProxy();
diff --git a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp
index 7a48c3b849527844d75cf79bd1202f949df1065d..10f1d75a203a5505c378e4337e15cf17f197ba32 100644
--- a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp
+++ b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp
@@ -48,7 +48,7 @@ ISISEnergyTransfer::ISISEnergyTransfer(IndirectDataReduction *idrUI,
mappingOptionSelected(m_uiForm.cbGroupingOptions->currentText());
// Add validation to custom detector grouping
- QRegExp re("([0-9]+[-]?[0-9]*,[ ]?)*[0-9]+[-]?[0-9]*");
+ QRegExp re("([0-9]+[-:+]?[0-9]*,[ ]?)*[0-9]+[-:+]?[0-9]*");
m_uiForm.leCustomGroups->setValidator(new QRegExpValidator(re, this));
// Validate to remove invalid markers
diff --git a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.ui b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.ui
index 09dbd67a51858b8dff66a090ca56671eb441771d..1585025f02389920ccca2f28dac35263e3588dc2 100644
--- a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.ui
+++ b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.ui
@@ -313,6 +313,13 @@
<property name="enabled">
<bool>true</bool>
</property>
+ <property name="toolTip">
+ <string>, allows you to specify additional indices. 1,2,4 will keep indices 1, 2 and 4 only.
+: indicates a continuous range of indices. For example, 1:5 is the same as 1,2,3,4,5.
++ sums two spectra together. 7+9 will produce a single spectra listing the sum of 7 and 9, ignoring any others.
+- sums a range of spectra together. For example, 3-8 is the same as 3+4+5+6+7+8.
+ </string>
+ </property>
<property name="maximumSize">
<size>
<width>16777215</width>
diff --git a/qt/scientific_interfaces/Indirect/Iqt.cpp b/qt/scientific_interfaces/Indirect/Iqt.cpp
index ac9810dae9cee4b2c3104b77fd377bf24da307f3..cd1f72acf96cfce9e603e2af7703de554bdec30a 100644
--- a/qt/scientific_interfaces/Indirect/Iqt.cpp
+++ b/qt/scientific_interfaces/Indirect/Iqt.cpp
@@ -142,6 +142,7 @@ void Iqt::run() {
QString wsName = m_uiForm.dsInput->getCurrentDataName();
QString resName = m_uiForm.dsResolution->getCurrentDataName();
+ QString nIterations = m_uiForm.spIterations->cleanText();
double energyMin = m_dblManager->value(m_properties["ELow"]);
double energyMax = m_dblManager->value(m_properties["EHigh"]);
@@ -153,6 +154,7 @@ void Iqt::run() {
IqtAlg->setProperty("SampleWorkspace", wsName.toStdString());
IqtAlg->setProperty("ResolutionWorkspace", resName.toStdString());
+ IqtAlg->setProperty("NumberOfIterations", nIterations.toStdString());
IqtAlg->setProperty("EnergyMin", energyMin);
IqtAlg->setProperty("EnergyMax", energyMax);
diff --git a/qt/scientific_interfaces/Indirect/Iqt.ui b/qt/scientific_interfaces/Indirect/Iqt.ui
index d63cb92889fb4149912ccf9edf59b1e5f45868fc..0bf9f8fddecc3a044080100543be56ee86473ca6 100644
--- a/qt/scientific_interfaces/Indirect/Iqt.ui
+++ b/qt/scientific_interfaces/Indirect/Iqt.ui
@@ -187,6 +187,53 @@
</item>
</layout>
</item>
+ <item>
+ <widget class="QGroupBox" name="ErrorCalc">
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>65</height>
+ </size>
+ </property>
+ <property name="title">
+ <string>Monte Carlo Error Calculation</string>
+ </property>
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QLabel" name="label">
+ <property name="maximumSize">
+ <size>
+ <width>130</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Number of Iterations:</string>
+ </property>
+ </widget>
+ </item>
+ <item alignment="Qt::AlignLeft">
+ <widget class="QSpinBox" name="spIterations">
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>26</height>
+ </size>
+ </property>
+ <property name="minimum">
+ <number>3</number>
+ </property>
+ <property name="maximum">
+ <number>10000</number>
+ </property>
+ <property name="value">
+ <number>50</number>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
<item>
<widget class="QGroupBox" name="gbOutput">
<property name="title">
diff --git a/qt/widgets/common/src/FitPropertyBrowser.cpp b/qt/widgets/common/src/FitPropertyBrowser.cpp
index 90d34b8fc01609da0ffdaece0f32135962a29430..60ed90ca9ad07006894f371dca1a30478a41b278 100644
--- a/qt/widgets/common/src/FitPropertyBrowser.cpp
+++ b/qt/widgets/common/src/FitPropertyBrowser.cpp
@@ -1361,6 +1361,7 @@ void FitPropertyBrowser::doubleChanged(QtProperty *prop) {
if (prop == m_startX) {
// call setWorkspace to change maxX in functions
setWorkspace(m_compositeFunction);
+ m_doubleManager->setMinimum(m_endX, value);
getHandler()->setAttribute("StartX", value);
emit startXChanged(startX());
emit xRangeChanged(startX(), endX());
@@ -1368,6 +1369,7 @@ void FitPropertyBrowser::doubleChanged(QtProperty *prop) {
} else if (prop == m_endX) {
// call setWorkspace to change minX in functions
setWorkspace(m_compositeFunction);
+ m_doubleManager->setMaximum(m_startX, value);
getHandler()->setAttribute("EndX", value);
emit endXChanged(endX());
emit xRangeChanged(startX(), endX());
diff --git a/qt/widgets/common/src/MWRunFiles.cpp b/qt/widgets/common/src/MWRunFiles.cpp
index a9b1975c9b40fbfca26c431d323dbb69068f8c1c..d53e222aa9806d8b2a147d224e4f8647e3eaa0ac 100644
--- a/qt/widgets/common/src/MWRunFiles.cpp
+++ b/qt/widgets/common/src/MWRunFiles.cpp
@@ -586,13 +586,11 @@ const QString MWRunFiles::findFilesGetSearchText(QString &searchText) {
* @param searchText :: text to create search parameters from
*/
void MWRunFiles::runFindFiles(const QString &searchText) {
- if (!searchText.isEmpty()) {
- emit findingFiles();
+ emit findingFiles();
- const auto parameters =
- createFindFilesSearchParameters(searchText.toStdString());
- m_pool.createWorker(this, parameters);
- }
+ const auto parameters =
+ createFindFilesSearchParameters(searchText.toStdString());
+ m_pool.createWorker(this, parameters);
}
/** Calls cancel on a running instance of MonitorLiveData.
diff --git a/scripts/ExternalInterfaces/CMakeLists.txt b/scripts/ExternalInterfaces/CMakeLists.txt
index 9f8cee956a296afe9b5841a474804783bd1e4e5c..029a93077806bc5d2c5a1b57e81f1a5839364660 100644
--- a/scripts/ExternalInterfaces/CMakeLists.txt
+++ b/scripts/ExternalInterfaces/CMakeLists.txt
@@ -6,7 +6,7 @@ set ( _mslice_external_root ${CMAKE_CURRENT_BINARY_DIR}/mslice )
ExternalProject_Add ( mslice
PREFIX ${_mslice_external_root}
GIT_REPOSITORY "https://github.com/mantidproject/mslice.git"
- GIT_TAG 01292c88ccc508acb16735aa5f96450e076161bb
+ GIT_TAG 82c4fae1356f770d5f8ad59edea4bd5f58206190
EXCLUDE_FROM_ALL 1
CONFIGURE_COMMAND ""
diff --git a/scripts/Interface/compile_sans_ui.py b/scripts/Interface/compile_sans_ui.py
index 557c84c86f659f8a156fdbc9e7b9b25921f80ced..45b09da88a0b5a7bded37fb1ce8e241997cf3bf7 100644
--- a/scripts/Interface/compile_sans_ui.py
+++ b/scripts/Interface/compile_sans_ui.py
@@ -19,7 +19,6 @@ try:
os.system("pyuic4 -o ui/sans/ui_eqsans_info.py ui/sans/eqsans_info.ui")
os.system("pyuic4 -o ui/ui_cluster_status.py ui/cluster_status.ui")
- os.system("pyuic4 -o ui/ui_cluster_details_dialog.py ui/cluster_details_dialog.ui")
os.system("pyuic4 -o ui/ui_reduction_main.py ui/reduction_main.ui")
os.system("pyuic4 -o ui/ui_hfir_output.py ui/hfir_output.ui")
os.system("pyuic4 -o ui/ui_trans_direct_beam.py ui/trans_direct_beam.ui")
diff --git a/scripts/Interface/reduction_application.py b/scripts/Interface/reduction_application.py
index ed5b8c44be8dcb1b90c5934f9e2bda75517a4945..e6d7041da7f6711b9b9fcd31d19efebc16499010 100644
--- a/scripts/Interface/reduction_application.py
+++ b/scripts/Interface/reduction_application.py
@@ -14,8 +14,6 @@ try:
import mantidplot # noqa
IS_IN_MANTIDPLOT = True
from mantid.kernel import ConfigService
- from mantid.api import AlgorithmFactory
- CLUSTER_ENABLED = "SubmitRemoteJob" in AlgorithmFactory.getRegisteredAlgorithms(True)
except:
import sip
sip.setapi('QString',2)
@@ -45,11 +43,10 @@ if IS_IN_MANTIDPLOT:
WARNING_MESSAGE = "Please contact the Mantid team with the following message:\n\n\n"
WARNING_MESSAGE += unicode(traceback.format_exc())
-from reduction_gui.instruments.instrument_factory import instrument_factory, INSTRUMENT_DICT # noqa
-from reduction_gui.settings.application_settings import GeneralSettings # noqa
-import ui.ui_reduction_main # noqa
-import ui.ui_instrument_dialog # noqa
-import ui.ui_cluster_details_dialog # noqa
+from reduction_gui.instruments.instrument_factory import instrument_factory, INSTRUMENT_DICT # noqa
+from reduction_gui.settings.application_settings import GeneralSettings # noqa
+import ui.ui_reduction_main # noqa
+import ui.ui_instrument_dialog # noqa
class ReductionGUI(QtGui.QMainWindow, ui.ui_reduction_main.Ui_SANSReduction):
@@ -111,7 +108,6 @@ class ReductionGUI(QtGui.QMainWindow, ui.ui_reduction_main.Ui_SANSReduction):
# Event connections
if not IS_IN_MANTIDPLOT:
self.reduce_button.hide()
- self.cluster_button.hide()
self.connect(self.export_button, QtCore.SIGNAL("clicked()"), self._export)
self.connect(self.reduce_button, QtCore.SIGNAL("clicked()"), self.reduce_clicked)
self.connect(self.save_button, QtCore.SIGNAL("clicked()"), self._save)
@@ -182,17 +178,6 @@ class ReductionGUI(QtGui.QMainWindow, ui.ui_reduction_main.Ui_SANSReduction):
else:
self.interface_chk.hide()
- # Show the parallel reduction button if enabled
- if self._interface.is_cluster_enabled() and IS_IN_MANTIDPLOT \
- and CLUSTER_ENABLED:
- config = ConfigService.Instance()
- if config.hasProperty("cluster.submission") \
- and config.getString("cluster.submission").lower()=='on':
- self.cluster_button.show()
- self.connect(self.cluster_button, QtCore.SIGNAL("clicked()"), self.cluster_clicked)
- else:
- self.cluster_button.hide()
-
if load_last:
self._interface.load_last_reduction()
else:
@@ -267,14 +252,6 @@ class ReductionGUI(QtGui.QMainWindow, ui.ui_reduction_main.Ui_SANSReduction):
self.tools_menu.addAction(instrAction)
self.tools_menu.addAction(debugAction)
- # Cluster submission details
- if IS_IN_MANTIDPLOT and CLUSTER_ENABLED:
- jobAction = QtGui.QAction("Remote submission details", self)
- jobAction.setShortcut("Ctrl+R")
- jobAction.setStatusTip("Set the cluster information for remote job submission")
- self.connect(jobAction, QtCore.SIGNAL("triggered()"), self._cluster_details_dialog)
- self.tools_menu.addAction(jobAction)
-
recent_files = []
for fname in self._recent_files:
if fname != self._filename and QtCore.QFile.exists(fname) and fname not in recent_files:
@@ -347,40 +324,6 @@ class ReductionGUI(QtGui.QMainWindow, ui.ui_reduction_main.Ui_SANSReduction):
self.close()
return False
- def _cluster_details_dialog(self):
- """
- Show dialog to get cluster submission details
- """
- class ClusterDialog(QtGui.QDialog, ui.ui_cluster_details_dialog.Ui_Dialog):
- def __init__(self, compute_resources=None):
- QtGui.QDialog.__init__(self)
- self.setupUi(self)
- self.resource_combo.clear()
- for res in compute_resources:
- self.resource_combo.addItem(QtGui.QApplication.translate("Dialog", res, None, QtGui.QApplication.UnicodeUTF8))
-
- # Fill out the defaults
- dialog = ClusterDialog(self._compute_resources)
- if self.general_settings.cluster_user is not None:
- dialog.username_edit.setText(str(self.general_settings.cluster_user))
- dialog.pass_edit.setText(str(self.general_settings.cluster_pass))
-
- dialog.nodes_box.setValue(int(self._number_of_nodes))
- dialog.cores_box.setValue(int(self._cores_per_node))
- for i in range(dialog.resource_combo.count()):
- if dialog.resource_combo.itemText(i)==self.general_settings.compute_resource:
- dialog.resource_combo.setCurrentIndex(i)
- break
-
- dialog.exec_()
- if dialog.result()==1:
- self.general_settings.cluster_user = str(dialog.username_edit.text())
- self.general_settings.cluster_pass = str(dialog.pass_edit.text())
- self._cluster_details_set = True
- self._number_of_nodes = int(dialog.nodes_box.value())
- self._cores_per_node = int(dialog.cores_box.value())
- self.general_settings.compute_resource = dialog.resource_combo.currentText()
-
def _clear_and_close(self):
"""
Clear all QSettings parameters
diff --git a/scripts/Interface/reduction_gui/instruments/dgs_interface_dev.py b/scripts/Interface/reduction_gui/instruments/dgs_interface_dev.py
index 6ae1574ab49567d634bf18881bcacda304713788..40bb05a93cfeb5d7dc7c198e23d289686705ba0b 100644
--- a/scripts/Interface/reduction_gui/instruments/dgs_interface_dev.py
+++ b/scripts/Interface/reduction_gui/instruments/dgs_interface_dev.py
@@ -4,7 +4,6 @@ from reduction_gui.widgets.inelastic.dgs_sample_setup import SampleSetupWidget
from reduction_gui.widgets.inelastic.dgs_data_corrections import DataCorrectionsWidget
from reduction_gui.widgets.inelastic.dgs_diagnose_detectors import DiagnoseDetectorsWidget
from reduction_gui.widgets.inelastic.dgs_absolute_units import AbsoluteUnitsWidget
-from reduction_gui.widgets.cluster_status import RemoteJobsWidget
from reduction_gui.reduction.inelastic.dgs_reduction_script import DgsReductionScripter
@@ -39,16 +38,4 @@ class DgsInterface(InstrumentInterface):
self.attach(AbsoluteUnitsWidget(settings = self._settings,
data_type = self.data_type))
- # Powder and Single Crystal conversion
- #self.attach(PdAndScConversionWidget(settings = self._settings,
- # data_type = self.data_type))
-
- # Remote jobs status
- if self.remote_resources_available():
- self.attach(RemoteJobsWidget(settings = self._settings))
-
- def is_cluster_enabled(self):
- """
- Returns true if the instrument is compatible with remote submission
- """
- return True
+ return
diff --git a/scripts/Interface/reduction_gui/instruments/diffraction_interface_dev.py b/scripts/Interface/reduction_gui/instruments/diffraction_interface_dev.py
index 221d2373c7a3f8382514c26c9b76ab00174365a3..7494f87eabac1899ba6fbf2311f4c9d129a7a94c 100644
--- a/scripts/Interface/reduction_gui/instruments/diffraction_interface_dev.py
+++ b/scripts/Interface/reduction_gui/instruments/diffraction_interface_dev.py
@@ -3,7 +3,6 @@ from reduction_gui.instruments.interface import InstrumentInterface
from reduction_gui.widgets.diffraction.diffraction_run_setup import RunSetupWidget
from reduction_gui.widgets.diffraction.diffraction_adv_setup import AdvancedSetupWidget
from reduction_gui.widgets.diffraction.diffraction_filter_setup import FilterSetupWidget
-from reduction_gui.widgets.cluster_status import RemoteJobsWidget
from reduction_gui.reduction.diffraction.diffraction_reduction_script import DiffractionReductionScripter
@@ -34,13 +33,4 @@ class DiffractionInterface(InstrumentInterface):
# Tab 3: Event filters setup
self.attach(FilterSetupWidget(settings = self._settings, data_type = self.data_type))
- # Remote jobs status
- if self.remote_resources_available():
- self.attach(RemoteJobsWidget(settings = self._settings))
return
-
- def is_cluster_enabled(self):
- """
- Returns true if the instrument is compatible with remote submission
- """
- return True
diff --git a/scripts/Interface/reduction_gui/instruments/eqsans_interface_dev.py b/scripts/Interface/reduction_gui/instruments/eqsans_interface_dev.py
index 60464d94335032a2b78adc08b0d5496e75c68ce0..a903265f71161fdc6f250dfcc00c0faf4e383058 100644
--- a/scripts/Interface/reduction_gui/instruments/eqsans_interface_dev.py
+++ b/scripts/Interface/reduction_gui/instruments/eqsans_interface_dev.py
@@ -16,7 +16,6 @@ from reduction_gui.widgets.sans.sans_catalog import SANSCatalogWidget
from reduction_gui.reduction.sans.eqsans_catalog import DataCatalog
from reduction_gui.reduction.sans.eqsans_data_proxy import DataProxy
-from reduction_gui.widgets.cluster_status import RemoteJobsWidget
IS_IN_MANTIDPLOT = False
try:
@@ -31,7 +30,7 @@ class EQSANSInterface(InstrumentInterface):
"""
Defines the widgets for EQSANS reduction
"""
- data_type = "Data files *.nxs *.dat (*.nxs *.dat)"
+ data_type = "Data files *.nxs *.dat *.h5 (*.nxs *.dat *.h5)"
def __init__(self, name, settings):
super(EQSANSInterface, self).__init__(name, settings)
@@ -64,20 +63,10 @@ class EQSANSInterface(InstrumentInterface):
# Reduction output
self.attach(OutputWidget(settings = self._settings))
- # Tabs that only make sense within MantidPlot
- if IS_IN_MANTIDPLOT:
- # Remote jobs status
- if self.remote_resources_available():
- self.attach(RemoteJobsWidget(settings = self._settings))
+ return
def has_advanced_version(self):
"""
Returns true if the instrument has simple and advanced views
"""
return False
-
- def is_cluster_enabled(self):
- """
- Returns true if the instrument is compatible with remote submission
- """
- return True
diff --git a/scripts/Interface/reduction_gui/instruments/interface.py b/scripts/Interface/reduction_gui/instruments/interface.py
index aed97587986a091fdec3f2f062d52055d79a1e0b..f8137fa5652e4f2c56ca77e3da7c7b25b2e8a144 100644
--- a/scripts/Interface/reduction_gui/instruments/interface.py
+++ b/scripts/Interface/reduction_gui/instruments/interface.py
@@ -271,12 +271,6 @@ class InstrumentInterface(object):
"""
return False
- def is_cluster_enabled(self):
- """
- Returns true if the instrument is compatible with remote submission
- """
- return False
-
def is_live_enabled(self):
"""
Returns true if the instrument interface includes a live data button
diff --git a/scripts/Interface/reduction_gui/widgets/cluster_status.py b/scripts/Interface/reduction_gui/widgets/cluster_status.py
deleted file mode 100644
index bd0777c0ba425b63332c5dd42c2bddaf9a3603f2..0000000000000000000000000000000000000000
--- a/scripts/Interface/reduction_gui/widgets/cluster_status.py
+++ /dev/null
@@ -1,273 +0,0 @@
-#pylint: disable=invalid-name
-from __future__ import (absolute_import, division, print_function)
-from PyQt4 import QtGui, QtCore
-import sys
-from functools import partial
-from reduction_gui.settings.application_settings import GeneralSettings
-from reduction_gui.widgets.base_widget import BaseWidget
-from reduction_gui.widgets import util
-import ui.ui_cluster_status
-
-from mantid.kernel import ConfigService, DateAndTime, Logger
-from mantid.api import AlgorithmManager
-
-from reduction_gui.reduction.scripter import BaseScriptElement
-
-
-class RemoteJobs(BaseScriptElement):
- def __init__(self):
- pass
-
-
-class RemoteJobsWidget(BaseWidget):
- """
- Widget that presents a list of remote jobs for the user
- """
- ## Widget name
- name = "Remote Jobs"
-
- copyAction = None
-
- def __init__(self, parent=None, state=None, settings=None):
- super(RemoteJobsWidget, self).__init__(parent, state, settings)
-
- class DataFrame(QtGui.QFrame, ui.ui_cluster_status.Ui_Frame):
- def __init__(self, parent=None):
- QtGui.QFrame.__init__(self, parent)
- self.setupUi(self)
-
- self._content = DataFrame(self)
- self.initialize_content()
- self._layout.addWidget(self._content)
-
- # General GUI settings
- if settings is None:
- settings = GeneralSettings()
- self._settings = settings
-
- def initialize_content(self):
- # Add functionality to copy and paste
- self.copyAction = QtGui.QAction("Copy", self)
- self.copyAction.setShortcut("Ctrl+C")
- self.addAction(self.copyAction)
- self.connect(self.copyAction, QtCore.SIGNAL("triggered()"), self.copyCells)
- self._content.job_table.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
- self.connect(self._content.job_table, QtCore.SIGNAL("customContextMenuRequested(QPoint)"), self.tableWidgetContext)
-
- self.connect(self._content.refresh_button, QtCore.SIGNAL("clicked()"), self._update_content)
-
- # Set the time of the oldest displayed job to 2 days ago
- self._content.date_time_edit.setDateTime(QtCore.QDateTime().currentDateTime().addDays(-2))
-
- compute_resources = ConfigService.Instance().getFacility().computeResources()
- self._content.resource_combo.clear()
- for res in compute_resources:
- self._content.resource_combo.addItem(QtGui.QApplication.translate("Dialog", res, None, QtGui.QApplication.UnicodeUTF8))
-
- self._clear_table()
-
- def tableWidgetContext(self, point):
- '''Create a menu for the tableWidget and associated actions'''
- tw_menu = QtGui.QMenu("Menu", self)
- tw_menu.addAction(self.copyAction)
- tw_menu.exec_(self.mapToGlobal(point))
-
- def copyCells(self):
- indices = self._content.job_table.selectedIndexes()
- if len(indices)==0:
- return
-
- col_count = self._content.job_table.columnCount()
- rows = []
- for r in indices:
- if r.row() not in rows:
- rows.append(r.row())
-
- selected_text = ""
- for row in rows:
- for i in range(col_count):
- data = self._content.job_table.item(row,i)
- if data is not None:
- selected_text += str(data.text())
- if i<col_count-1:
- selected_text += '\t'
- selected_text += '\n'
-
- QtGui.QApplication.clipboard().setText(selected_text)
-
- def paintEvent(self, event):
- """
- Catch the paint events and update the credential info.
- """
- super(RemoteJobsWidget, self).paintEvent(event)
- self._fill_in_defaults()
-
- def _fill_in_defaults(self):
- """
- Fill in the credentials boxes if we have the information
- """
- if self._settings.compute_resource is not None:
- for i in range(self._content.resource_combo.count()):
- if self._content.resource_combo.itemText(i)==self._settings.compute_resource:
- self._content.resource_combo.setCurrentIndex(i)
- break
-
- if self._settings.cluster_user is not None \
- and self._settings.cluster_pass is not None:
- self._content.username_edit.setText(self._settings.cluster_user)
- self._content.password_edit.setText(self._settings.cluster_pass)
-
- def _clear_table(self):
- """
- Clear the job table and set the headers
- """
- self._content.job_table.clear()
- headers = ["Job ID", "Title", "Status", "Start", "End", "Action"]
- self._content.job_table.setColumnCount(len(headers))
- self._content.job_table.setHorizontalHeaderLabels(headers)
- # Stretch the columns evenly
- h = self._content.job_table.horizontalHeader()
- h.setStretchLastSection(True)
- h.setResizeMode(1)
-
- def _update_content(self):
- """
- Get the job status from the compute resource and
- update the job table content.
- """
- self._fill_in_defaults()
-
- user = str(self._content.username_edit.text())
- pwd = str(self._content.password_edit.text())
- if len(user)==0 or len(pwd)==0:
- util.set_valid(self._content.username_edit, False)
- util.set_valid(self._content.password_edit, False)
- return
- else:
- self._settings.cluster_user = user
- self._settings.cluster_pass = pwd
- util.set_valid(self._content.username_edit, True)
- util.set_valid(self._content.password_edit, True)
- # Note: here and in the following create() calls. Version 1 of
- # the remote algorithms is guaranteed to work at SNS. Version
- # 2 generalizes the remote algorithms (see tickets #9277 and
- # #11126). While the v2 implementation for the remote job
- # submission API has been refactored without changes, it would
- # need to be tested before upgrading v1->v2 in this script.
- alg = AlgorithmManager.create("Authenticate", 1)
- alg.initialize()
- alg.setProperty("ComputeResource", str(self._settings.compute_resource))
- alg.setProperty("UserName", str(self._settings.cluster_user))
- alg.setProperty("Password", str(self._settings.cluster_pass))
- alg.execute()
-
- alg = AlgorithmManager.create("QueryAllRemoteJobs", 1)
- alg.initialize()
- alg.setProperty("ComputeResource", str(self._settings.compute_resource))
- alg.execute()
- job_id = alg.getProperty("JobId").value
- job_status = alg.getProperty("JobStatusString").value
- job_name = alg.getProperty("JobName").value
- job_trans_id = alg.getProperty("TransID").value
-
- job_start = alg.getProperty("StartDate").value
- job_end = alg.getProperty("CompletionDate").value
-
- job_list = zip(*(job_id, job_status, job_name, job_start, job_end, job_trans_id))
-
- self._clear_table()
- self._content.job_table.setSortingEnabled(False)
- self._content.job_table.setRowCount(len(job_list))
- unavailable = DateAndTime(0)
- unavailable.setToMinimum()
-
- for i in range(len(job_list)):
- # Make sure that only recent jobs are displayed
- oldest = DateAndTime(str(self._content.date_time_edit.dateTime().toString(QtCore.Qt.ISODate)))
- end_time = job_list[i][4]
- if end_time == '':
- job_end = unavailable
- else:
- job_end = DateAndTime(end_time)
- if job_end>unavailable and job_end<oldest:
- self._content.job_table.setRowHidden(i, True)
- continue
- self._content.job_table.setRowHidden(i, False)
-
- # Job ID
- item = QtGui.QTableWidgetItem(str(job_list[i][0]))
- item.setFlags(QtCore.Qt.ItemIsSelectable |QtCore.Qt.ItemIsEnabled )
- self._content.job_table.setItem(i, 0, item)
- job_id = str(job_list[i][0])
-
- # Title
- item = QtGui.QTableWidgetItem(str(job_list[i][2]))
- item.setFlags(QtCore.Qt.ItemIsSelectable |QtCore.Qt.ItemIsEnabled )
- self._content.job_table.setItem(i, 1, item)
-
- # Status
- item = QtGui.QTableWidgetItem(str(job_list[i][1]))
- item.setFlags(QtCore.Qt.ItemIsSelectable |QtCore.Qt.ItemIsEnabled )
- self._content.job_table.setItem(i, 2, item)
- is_running = str(job_list[i][1]).lower()=='running'
-
- # Start time
- time_displayed = str(job_list[i][3]).replace('T', ' ')
- if DateAndTime(job_list[i][3]) == unavailable:
- time_displayed = ''
- item = QtGui.QTableWidgetItem(time_displayed)
- item.setFlags(QtCore.Qt.ItemIsSelectable |QtCore.Qt.ItemIsEnabled )
- self._content.job_table.setItem(i, 3, item)
-
- # Completion time
- time_displayed = end_time.replace('T', ' ')
- if job_end == unavailable:
- time_displayed = ''
- item = QtGui.QTableWidgetItem(time_displayed)
- item.setFlags(QtCore.Qt.ItemIsSelectable |QtCore.Qt.ItemIsEnabled )
- self._content.job_table.setItem(i, 4, item)
-
- # create an cell widget
- btn = QtGui.QPushButton(self._content.job_table)
- if is_running:
- btn.setText('Abort')
- btn.setToolTip('Cleanly abort this job')
- else:
- btn.setText('Remove')
- btn.setToolTip('Remove this job and its temporary files')
- call_back = partial(self._remove_job, is_running=is_running, job_id=job_id, trans_id=job_list[i][5])
- self.connect(btn, QtCore.SIGNAL("clicked()"), call_back)
- self._content.job_table.setCellWidget(i, 5, btn)
-
- self._content.job_table.setSortingEnabled(True)
- self._content.job_table.sortItems(3, 1)
-
- def _remove_job(self, trans_id, job_id=None, is_running=False):
- """
- Abort job and/or stop transaction
- @param trans_id: remote transaction ID
- @param job_id: remote job ID
- @param is_running: True if the job is currently running
- """
- if is_running:
- try:
- # At this point we are authenticated so just purge
- alg = AlgorithmManager.create("AbortRemoteJob", 1)
- alg.initialize()
- alg.setProperty("ComputeResource", str(self._settings.compute_resource))
- alg.setProperty("JobID", job_id)
- alg.execute()
- except:
- Logger("cluster_status").error("Problem aborting job: %s" % sys.exc_info()[1])
- try:
- alg = AlgorithmManager.create("StopRemoteTransaction", 1)
- alg.initialize()
- alg.setProperty("ComputeResource", str(self._settings.compute_resource))
- alg.setProperty("TransactionID", trans_id)
- alg.execute()
- except:
- Logger("cluster_status").error("Project stopping remote transaction: %s" % sys.exc_info()[1])
- self._update_content()
-
- def get_state(self):
- return RemoteJobs()
diff --git a/scripts/Interface/ui/CMakeLists.txt b/scripts/Interface/ui/CMakeLists.txt
index 3b08fd2c6d3d6f00f94fcbe806bcc356e078a60a..bf4ef3c4c1c13192e082312b0d5fac6c621d985a 100644
--- a/scripts/Interface/ui/CMakeLists.txt
+++ b/scripts/Interface/ui/CMakeLists.txt
@@ -9,8 +9,6 @@ add_subdirectory(batchwidget)
add_subdirectory(poldi)
SET(UI_FILES
-cluster_details_dialog.ui
-cluster_status.ui
data_catalog.ui
hfir_output.ui
instrument_dialog.ui
diff --git a/scripts/Interface/ui/cluster_details_dialog.ui b/scripts/Interface/ui/cluster_details_dialog.ui
deleted file mode 100644
index 01a74247d1ce8c8b9c4bd407a7bab547eef600a3..0000000000000000000000000000000000000000
--- a/scripts/Interface/ui/cluster_details_dialog.ui
+++ /dev/null
@@ -1,219 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Dialog</class>
- <widget class="QDialog" name="Dialog">
- <property name="windowModality">
- <enum>Qt::ApplicationModal</enum>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>439</width>
- <height>433</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="windowTitle">
- <string>Dialog</string>
- </property>
- <property name="sizeGripEnabled">
- <bool>false</bool>
- </property>
- <property name="modal">
- <bool>true</bool>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QLabel" name="label_3">
- <property name="minimumSize">
- <size>
- <width>160</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>160</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Compute resource:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="resource_combo"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QLabel" name="label_4">
- <property name="minimumSize">
- <size>
- <width>160</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>160</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Number of nodes:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="nodes_box"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QLabel" name="label_5">
- <property name="minimumSize">
- <size>
- <width>160</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>160</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Number of cores:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="cores_box"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label_2">
- <property name="minimumSize">
- <size>
- <width>160</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>160</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Username:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="username_edit"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>160</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>160</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Password:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="pass_edit">
- <property name="echoMode">
- <enum>QLineEdit::Password</enum>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QDialogButtonBox" name="buttonBox">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="standardButtons">
- <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections>
- <connection>
- <sender>buttonBox</sender>
- <signal>accepted()</signal>
- <receiver>Dialog</receiver>
- <slot>accept()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>248</x>
- <y>254</y>
- </hint>
- <hint type="destinationlabel">
- <x>157</x>
- <y>274</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>buttonBox</sender>
- <signal>rejected()</signal>
- <receiver>Dialog</receiver>
- <slot>reject()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>316</x>
- <y>260</y>
- </hint>
- <hint type="destinationlabel">
- <x>286</x>
- <y>274</y>
- </hint>
- </hints>
- </connection>
- </connections>
-</ui>
diff --git a/scripts/Interface/ui/cluster_status.ui b/scripts/Interface/ui/cluster_status.ui
deleted file mode 100644
index 4396b771405f1a825f9b87de63d4f379efdcd1b8..0000000000000000000000000000000000000000
--- a/scripts/Interface/ui/cluster_status.ui
+++ /dev/null
@@ -1,170 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Frame</class>
- <widget class="QFrame" name="Frame">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>753</width>
- <height>563</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Frame</string>
- </property>
- <property name="frameShape">
- <enum>QFrame::StyledPanel</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QLabel" name="label_3">
- <property name="minimumSize">
- <size>
- <width>160</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>160</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Compute resource:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="resource_combo"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QTableWidget" name="job_table">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Username:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="username_edit">
- <property name="toolTip">
- <string>Enter compute resource username</string>
- </property>
- <property name="inputMask">
- <string/>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Password:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="password_edit">
- <property name="toolTip">
- <string>Enter compute resource password</string>
- </property>
- <property name="inputMask">
- <string/>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="echoMode">
- <enum>QLineEdit::Password</enum>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Show items after:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDateTimeEdit" name="date_time_edit"/>
- </item>
- <item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="refresh_button">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Click to refresh the job list</string>
- </property>
- <property name="text">
- <string>Refresh</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/scripts/Interface/ui/reduction_main.ui b/scripts/Interface/ui/reduction_main.ui
index dd626115f467eb5cb3b93ebd0ac9f77ba2d92148..049229aa6663fe06f2c4d27f728ad1500a7672d2 100644
--- a/scripts/Interface/ui/reduction_main.ui
+++ b/scripts/Interface/ui/reduction_main.ui
@@ -125,22 +125,6 @@ p, li { white-space: pre-wrap; }
</property>
</widget>
</item>
- <item>
- <widget class="QPushButton" name="cluster_button">
- <property name="minimumSize">
- <size>
- <width>95</width>
- <height>0</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Click to send the reduction job to a remote compute resource</string>
- </property>
- <property name="text">
- <string>Send cluster</string>
- </property>
- </widget>
- </item>
<item>
<widget class="QPushButton" name="save_button">
<property name="enabled">
@@ -189,7 +173,7 @@ p, li { white-space: pre-wrap; }
<x>0</x>
<y>0</y>
<width>1062</width>
- <height>23</height>
+ <height>22</height>
</rect>
</property>
<widget class="QMenu" name="file_menu">
diff --git a/scripts/Interface/ui/sans_isis/beam_centre.py b/scripts/Interface/ui/sans_isis/beam_centre.py
index b2cbaaebc11c1e5f758687731755bebb2635370d..4ca38ece1ad97fe99e806d8827f195c6282c7f44 100644
--- a/scripts/Interface/ui/sans_isis/beam_centre.py
+++ b/scripts/Interface/ui/sans_isis/beam_centre.py
@@ -38,6 +38,13 @@ class BeamCentre(QtGui.QWidget, ui_beam_centre.Ui_BeamCentre):
# Attach validators
self._attach_validators()
+ # This feature is currently broken and not strictly needed so I am hiding this part of the GUI.
+ self.Q_limits.hide()
+ self.Q_from.hide()
+ self.q_min_line_edit.hide()
+ self.q_max_line_edit.hide()
+ self.Q_to.hide()
+
def _setup_log_widget(self):
self.log_widget = MantidQt.MantidWidgets.MessageDisplay(self.groupBox_2)
self.log_widget.setMinimumSize(QtCore.QSize(491, 371))
diff --git a/scripts/Interface/ui/sans_isis/beam_centre.ui b/scripts/Interface/ui/sans_isis/beam_centre.ui
index c38ae4ba5be4b5d1d3e677973bff66d9605d943d..bf6f24652d62053605200b8da688ed02e68206a3 100644
--- a/scripts/Interface/ui/sans_isis/beam_centre.ui
+++ b/scripts/Interface/ui/sans_isis/beam_centre.ui
@@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>1015</width>
- <height>649</height>
+ <height>709</height>
</rect>
</property>
<property name="windowTitle">
@@ -130,7 +130,7 @@
</widget>
</item>
<item row="5" column="3">
- <widget class="QLabel" name="label">
+ <widget class="QLabel" name="Q_to">
<property name="text">
<string>to</string>
</property>
@@ -151,7 +151,7 @@
</widget>
</item>
<item row="5" column="0">
- <widget class="QLabel" name="label_3">
+ <widget class="QLabel" name="Q_from">
<property name="text">
<string>from</string>
</property>
@@ -161,7 +161,7 @@
<widget class="QLineEdit" name="r_max_line_edit"/>
</item>
<item row="3" column="2">
- <widget class="QLabel" name="label_2">
+ <widget class="QLabel" name="Q_limits">
<property name="toolTip">
<string><html><head/><body><p>The Q range which will be considered when finding the beam centre.</p></body></html></string>
</property>
@@ -310,6 +310,26 @@
</item>
</layout>
</widget>
+ <tabstops>
+ <tabstop>lab_pos_1_line_edit</tabstop>
+ <tabstop>lab_pos_2_line_edit</tabstop>
+ <tabstop>hab_pos_1_line_edit</tabstop>
+ <tabstop>hab_pos_2_line_edit</tabstop>
+ <tabstop>component_combo_box</tabstop>
+ <tabstop>update_lab_check_box</tabstop>
+ <tabstop>update_hab_check_box</tabstop>
+ <tabstop>r_min_line_edit</tabstop>
+ <tabstop>r_max_line_edit</tabstop>
+ <tabstop>q_min_line_edit</tabstop>
+ <tabstop>q_max_line_edit</tabstop>
+ <tabstop>max_iterations_line_edit</tabstop>
+ <tabstop>tolerance_line_edit</tabstop>
+ <tabstop>verbose_check_box</tabstop>
+ <tabstop>COM_check_box</tabstop>
+ <tabstop>left_right_check_box</tabstop>
+ <tabstop>up_down_check_box</tabstop>
+ <tabstop>run_button</tabstop>
+ </tabstops>
<resources/>
<connections/>
</ui>
diff --git a/scripts/Interface/ui/sans_isis/diagnostics_page.ui b/scripts/Interface/ui/sans_isis/diagnostics_page.ui
index 4dac19dd279a70d916152ff52eaef463e52fca5e..d99f39cab1d5e92bc71f014b0730f464eb115341 100644
--- a/scripts/Interface/ui/sans_isis/diagnostics_page.ui
+++ b/scripts/Interface/ui/sans_isis/diagnostics_page.ui
@@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>695</width>
- <height>252</height>
+ <height>297</height>
</rect>
</property>
<property name="windowTitle">
@@ -58,6 +58,9 @@
</item>
<item row="0" column="2">
<widget class="QPushButton" name="browse_button">
+ <property name="focusPolicy">
+ <enum>Qt::StrongFocus</enum>
+ </property>
<property name="text">
<string>Browse</string>
</property>
@@ -133,6 +136,9 @@
</item>
<item row="2" column="0">
<widget class="QPushButton" name="time_button">
+ <property name="focusPolicy">
+ <enum>Qt::StrongFocus</enum>
+ </property>
<property name="text">
<string>Time Integral</string>
</property>
@@ -146,6 +152,9 @@
</item>
<item row="0" column="0">
<widget class="QPushButton" name="horizontal_button">
+ <property name="focusPolicy">
+ <enum>Qt::StrongFocus</enum>
+ </property>
<property name="text">
<string>Horizontal Integral</string>
</property>
@@ -160,6 +169,9 @@
</item>
<item row="1" column="0">
<widget class="QPushButton" name="vertical_button">
+ <property name="focusPolicy">
+ <enum>Qt::StrongFocus</enum>
+ </property>
<property name="text">
<string>Vertical Integral</string>
</property>
@@ -239,6 +251,21 @@
</item>
</layout>
</widget>
+ <tabstops>
+ <tabstop>run_input_line_edit</tabstop>
+ <tabstop>browse_button</tabstop>
+ <tabstop>detector_combo_box</tabstop>
+ <tabstop>period_line_edit</tabstop>
+ <tabstop>horizontal_button</tabstop>
+ <tabstop>horizontal_range_line_edit</tabstop>
+ <tabstop>horizontal_mask_check_box</tabstop>
+ <tabstop>vertical_button</tabstop>
+ <tabstop>vertical_range_line_edit</tabstop>
+ <tabstop>vertical_mask_check_box</tabstop>
+ <tabstop>time_button</tabstop>
+ <tabstop>time_range_line_edit</tabstop>
+ <tabstop>time_mask_checkbox</tabstop>
+ </tabstops>
<resources/>
<connections/>
</ui>
diff --git a/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui b/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui
index cf23f0c13b51d3afdfd115cc463fa649135f7f6f..39d87d57b2e467e80af34b80b926f5428086092d 100644
--- a/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui
+++ b/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui
@@ -95,7 +95,7 @@ QGroupBox::title {
<item>
<widget class="QStackedWidget" name="main_stacked_widget">
<property name="currentIndex">
- <number>0</number>
+ <number>1</number>
</property>
<widget class="QWidget" name="run_page">
<layout class="QVBoxLayout" name="verticalLayout_3">
@@ -291,7 +291,7 @@ QGroupBox::title {
<string>Memor&y</string>
</property>
<property name="checked">
- <bool>true</bool>
+ <bool>false</bool>
</property>
</widget>
</item>
@@ -313,6 +313,9 @@ QGroupBox::title {
<property name="text">
<string>Both</string>
</property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
</widget>
</item>
</layout>
@@ -626,7 +629,7 @@ QGroupBox::title {
<item>
<widget class="QGroupBox" name="slice_event_group_box">
<property name="toolTip">
- <string><html><head/><body><p>In the case of data which was measured in event-mode, it is possible to perform time-of-flight slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies time slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a time slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slcie from teh start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications useing comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p></body></html></string>
+ <string><html><head/><body><p>In the case of data which was measured in event-mode, it is possible to perform time-of-flight slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies time slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a time slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slice from the start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications useing comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p></body></html></string>
</property>
<property name="title">
<string>Event Slice</string>
@@ -912,7 +915,7 @@ QGroupBox::title {
<string><html><head/><body><p>Spectrum number of the incident monitor which is used for monitor normalization.</p></body></html></string>
</property>
<property name="text">
- <string>Incidient monitor</string>
+ <string>Incident monitor</string>
</property>
</widget>
</item>
@@ -1054,7 +1057,7 @@ QGroupBox::title {
<item row="4" column="2">
<widget class="QLineEdit" name="transmission_mn_shift_line_edit">
<property name="toolTip">
- <string><html><head/><body><p>An option shift of the M4 monitor.</p></body></html></string>
+ <string><html><head/><body><p>Distance between beamstop monitor and detector.</p></body></html></string>
</property>
</widget>
</item>
@@ -1568,7 +1571,7 @@ QGroupBox::title {
</sizepolicy>
</property>
<property name="toolTip">
- <string><html><head/><body><p>Settings concerning the wavelength binning when dat a is transformed from time-of-flight to wavlength units.</p></body></html></string>
+ <string><html><head/><body><p>Settings concerning the wavelength binning when data is transformed from time-of-flight to wavelength units.</p></body></html></string>
</property>
<property name="title">
<string>Wavelength</string>
@@ -1626,7 +1629,7 @@ QGroupBox::title {
<item row="1" column="0">
<widget class="QLabel" name="label_7">
<property name="toolTip">
- <string><html><head/><body><p>It is possible to perform wavelength slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies time slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a time slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slcie from teh start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications useing comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p><p>A reduction will always be done between the maximum and minimum wavelengths of a given set.</p></body></html></string>
+ <string><html><head/><body><p>It is possible to perform wavelength slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies wavelength slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a wavelength slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slice from the start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications useing comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p><p>A reduction will always be done between the maximum and minimum wavelengths of a given set.</p></body></html></string>
</property>
<property name="text">
<string>Ranges [Ã…]</string>
@@ -1879,12 +1882,12 @@ QGroupBox::title {
</property>
<item>
<property name="text">
- <string>Circular</string>
+ <string>Pinhole</string>
</property>
</item>
<item>
<property name="text">
- <string>Rectangular</string>
+ <string>Slit</string>
</property>
</item>
</widget>
@@ -1899,7 +1902,7 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="3" column="4">
+ <item row="3" column="2">
<widget class="QLabel" name="q_resolution_sample_a_label">
<property name="toolTip">
<string><html><head/><body><p>Diameter of a circular sample aperature.</p></body></html></string>
@@ -1916,7 +1919,7 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="2" column="4">
+ <item row="2" column="2">
<widget class="QLabel" name="q_resolution_sample_w_label">
<property name="toolTip">
<string><html><head/><body><p>Width of a rectangular sample aperature.</p></body></html></string>
@@ -1926,14 +1929,14 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="2" column="5">
+ <item row="2" column="3">
<widget class="QLineEdit" name="q_resolution_sample_w_line_edit">
<property name="toolTip">
<string><html><head/><body><p>Width of a rectangular sample aperature.</p></body></html></string>
</property>
</widget>
</item>
- <item row="6" column="0">
+ <item row="5" column="0">
<widget class="QLabel" name="q_resolution_collimation_length_label">
<property name="toolTip">
<string><html><head/><body><p>The collimation length.</p></body></html></string>
@@ -1943,7 +1946,7 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="6" column="4">
+ <item row="5" column="2">
<widget class="QLabel" name="q_resolution_delta_r_label">
<property name="toolTip">
<string><html><head/><body><p>Delta r.</p></body></html></string>
@@ -1953,21 +1956,21 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="7" column="1" colspan="4">
+ <item row="6" column="1" colspan="2">
<widget class="QLineEdit" name="q_resolution_moderator_file_line_edit">
<property name="toolTip">
<string><html><head/><body><p>Path to the moderator file.</p></body></html></string>
</property>
</widget>
</item>
- <item row="7" column="5">
+ <item row="6" column="3">
<widget class="QPushButton" name="q_resolution_moderator_file_push_button">
<property name="text">
<string>Browse</string>
</property>
</widget>
</item>
- <item row="7" column="0">
+ <item row="6" column="0">
<widget class="QLabel" name="q_resolution_moderator_file_label">
<property name="toolTip">
<string><html><head/><body><p>Path to the moderator file.</p></body></html></string>
@@ -1977,24 +1980,24 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="6" column="1">
+ <item row="5" column="1">
<widget class="QLineEdit" name="q_resolution_collimation_length_line_edit">
<property name="toolTip">
<string><html><head/><body><p>The collimation length.</p></body></html></string>
</property>
</widget>
</item>
- <item row="6" column="5">
+ <item row="5" column="3">
<widget class="QLineEdit" name="q_resolution_delta_r_line_edit">
<property name="toolTip">
<string><html><head/><body><p>Delta r.</p></body></html></string>
</property>
</widget>
</item>
- <item row="5" column="0" colspan="6">
- <widget class="Line" name="line_6">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
+ <item row="3" column="3">
+ <widget class="QLineEdit" name="q_resolution_sample_a_line_edit">
+ <property name="toolTip">
+ <string><html><head/><body><p>Diameter of a circular sample aperature.</p></body></html></string>
</property>
</widget>
</item>
@@ -2005,10 +2008,10 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="3" column="5">
- <widget class="QLineEdit" name="q_resolution_sample_a_line_edit">
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="q_resolution_source_w_line_edit">
<property name="toolTip">
- <string><html><head/><body><p>Diameter of a circular sample aperature.</p></body></html></string>
+ <string><html><head/><body><p>Width of a rectangular source aperature.</p></body></html></string>
</property>
</widget>
</item>
@@ -2022,10 +2025,10 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="2" column="1">
- <widget class="QLineEdit" name="q_resolution_source_w_line_edit">
+ <item row="1" column="3">
+ <widget class="QLineEdit" name="q_resolution_sample_h_line_edit">
<property name="toolTip">
- <string><html><head/><body><p>Width of a rectangular source aperature.</p></body></html></string>
+ <string><html><head/><body><p>Height of a rectangular sample aperature.</p></body></html></string>
</property>
</widget>
</item>
@@ -2039,14 +2042,7 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="1" column="5">
- <widget class="QLineEdit" name="q_resolution_sample_h_line_edit">
- <property name="toolTip">
- <string><html><head/><body><p>Height of a rectangular sample aperature.</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="1" column="4">
+ <item row="1" column="2">
<widget class="QLabel" name="q_resolution_sample_h_label">
<property name="toolTip">
<string><html><head/><body><p>Height of a rectangular sample aperature.</p></body></html></string>
@@ -2056,13 +2052,6 @@ QGroupBox::title {
</property>
</widget>
</item>
- <item row="1" column="2" rowspan="3">
- <widget class="Line" name="line_7">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- </widget>
- </item>
</layout>
</widget>
</item>
@@ -2158,11 +2147,12 @@ QGroupBox::title {
</customwidget>
</customwidgets>
<tabstops>
- <tabstop>tab_choice_list</tabstop>
- <tabstop>batch_button</tabstop>
+ <tabstop>instrument_combo_box</tabstop>
+ <tabstop>manage_directories_button</tabstop>
<tabstop>user_file_button</tabstop>
- <tabstop>batch_line_edit</tabstop>
- <tabstop>user_file_line_edit</tabstop>
+ <tabstop>batch_button</tabstop>
+ <tabstop>process_button</tabstop>
+ <tabstop>multi_period_check_box</tabstop>
<tabstop>reduction_dimensionality_1D</tabstop>
<tabstop>reduction_dimensionality_2D</tabstop>
<tabstop>output_mode_memory_radio_button</tabstop>
@@ -2173,7 +2163,8 @@ QGroupBox::title {
<tabstop>rkh_checkbox</tabstop>
<tabstop>save_zero_error_free</tabstop>
<tabstop>use_optimizations_checkbox</tabstop>
- <tabstop>settings_tab_widget</tabstop>
+ <tabstop>plot_results_checkbox</tabstop>
+ <tabstop>help_button</tabstop>
<tabstop>reduction_mode_combo_box</tabstop>
<tabstop>merged_scale_line_edit</tabstop>
<tabstop>merged_shift_line_edit</tabstop>
@@ -2187,19 +2178,12 @@ QGroupBox::title {
<tabstop>slice_event_line_edit</tabstop>
<tabstop>event_binning_group_box</tabstop>
<tabstop>event_binning_line_edit</tabstop>
- <tabstop>wavelength_min_line_edit</tabstop>
- <tabstop>wavelength_max_line_edit</tabstop>
<tabstop>absolute_scale_line_edit</tabstop>
<tabstop>geometry_combo_box</tabstop>
<tabstop>height_line_edit</tabstop>
<tabstop>width_line_edit</tabstop>
<tabstop>thickness_line_edit</tabstop>
<tabstop>z_offset_line_edit</tabstop>
- <tabstop>phi_limit_min_line_edit</tabstop>
- <tabstop>phi_limit_max_line_edit</tabstop>
- <tabstop>phi_limit_use_mirror_check_box</tabstop>
- <tabstop>radius_limit_min_line_edit</tabstop>
- <tabstop>radius_limit_max_line_edit</tabstop>
<tabstop>mask_file_input_line_edit</tabstop>
<tabstop>mask_file_browse_push_button</tabstop>
<tabstop>mask_file_add_push_button</tabstop>
@@ -2222,6 +2206,7 @@ QGroupBox::title {
<tabstop>fit_sample_wavelength_combo_box</tabstop>
<tabstop>fit_sample_wavelength_min_line_edit</tabstop>
<tabstop>fit_sample_wavelength_max_line_edit</tabstop>
+ <tabstop>show_transmission_view</tabstop>
<tabstop>fit_can_use_fit_check_box</tabstop>
<tabstop>fit_can_fit_type_combo_box</tabstop>
<tabstop>fit_can_polynomial_order_spin_box</tabstop>
@@ -2229,13 +2214,25 @@ QGroupBox::title {
<tabstop>fit_can_wavelength_min_line_edit</tabstop>
<tabstop>fit_can_wavelength_max_line_edit</tabstop>
<tabstop>pixel_adjustment_det_1_line_edit</tabstop>
- <tabstop>pixel_adjustment_det_2_line_edit</tabstop>
<tabstop>pixel_adjustment_det_1_push_button</tabstop>
+ <tabstop>pixel_adjustment_det_2_line_edit</tabstop>
<tabstop>pixel_adjustment_det_2_push_button</tabstop>
<tabstop>wavelength_adjustment_det_1_line_edit</tabstop>
- <tabstop>wavelength_adjustment_det_2_line_edit</tabstop>
<tabstop>wavelength_adjustment_det_1_push_button</tabstop>
+ <tabstop>wavelength_adjustment_det_2_line_edit</tabstop>
<tabstop>wavelength_adjustment_det_2_push_button</tabstop>
+ <tabstop>radius_limit_min_line_edit</tabstop>
+ <tabstop>radius_limit_max_line_edit</tabstop>
+ <tabstop>phi_limit_min_line_edit</tabstop>
+ <tabstop>phi_limit_max_line_edit</tabstop>
+ <tabstop>phi_limit_use_mirror_check_box</tabstop>
+ <tabstop>wavelength_min_line_edit</tabstop>
+ <tabstop>wavelength_max_line_edit</tabstop>
+ <tabstop>wavelength_slices_line_edit</tabstop>
+ <tabstop>wavelength_step_line_edit</tabstop>
+ <tabstop>wavelength_step_type_combo_box</tabstop>
+ <tabstop>r_cut_line_edit</tabstop>
+ <tabstop>w_cut_line_edit</tabstop>
<tabstop>q_1d_min_line_edit</tabstop>
<tabstop>q_1d_max_line_edit</tabstop>
<tabstop>q_1d_step_line_edit</tabstop>
@@ -2245,8 +2242,8 @@ QGroupBox::title {
<tabstop>q_xy_step_type_combo_box</tabstop>
<tabstop>gravity_group_box</tabstop>
<tabstop>gravity_extra_length_line_edit</tabstop>
- <tabstop>q_resolution_shape_combo_box</tabstop>
<tabstop>q_resolution_group_box</tabstop>
+ <tabstop>q_resolution_shape_combo_box</tabstop>
<tabstop>q_resolution_source_h_line_edit</tabstop>
<tabstop>q_resolution_source_w_line_edit</tabstop>
<tabstop>q_resolution_source_a_line_edit</tabstop>
@@ -2257,6 +2254,10 @@ QGroupBox::title {
<tabstop>q_resolution_delta_r_line_edit</tabstop>
<tabstop>q_resolution_moderator_file_line_edit</tabstop>
<tabstop>q_resolution_moderator_file_push_button</tabstop>
+ <tabstop>settings_tab_widget</tabstop>
+ <tabstop>user_file_line_edit</tabstop>
+ <tabstop>tab_choice_list</tabstop>
+ <tabstop>batch_line_edit</tabstop>
</tabstops>
<resources/>
<connections/>
diff --git a/scripts/SANS/sans/algorithm_detail/save_workspace.py b/scripts/SANS/sans/algorithm_detail/save_workspace.py
index 121df937ea1356df9c9a4d60ca5ad208e1930477..530462b3478776a1c03f84b8489213c6f666a455 100644
--- a/scripts/SANS/sans/algorithm_detail/save_workspace.py
+++ b/scripts/SANS/sans/algorithm_detail/save_workspace.py
@@ -43,7 +43,7 @@ def get_save_strategy(file_format_bundle, file_name, save_options):
file_name = get_file_name(file_format_bundle, file_name, "", ".xml")
save_name = "SaveCanSAS1D"
elif file_format is SaveType.NXcanSAS:
- file_name = get_file_name(file_format_bundle, file_name, "_nxcansas", ".nxs")
+ file_name = get_file_name(file_format_bundle, file_name, "_nxcansas", ".h5")
save_name = "SaveNXcanSAS"
elif file_format is SaveType.NistQxy:
file_name = get_file_name(file_format_bundle, file_name, "_nistqxy", ".dat")
diff --git a/scripts/SANS/sans/gui_logic/models/beam_centre_model.py b/scripts/SANS/sans/gui_logic/models/beam_centre_model.py
index 1c42eec1f3639ea1825d551a0bbb31ae108c12e7..e885c80ad5ad502cbc4cbbefd8e7510f701cca33 100644
--- a/scripts/SANS/sans/gui_logic/models/beam_centre_model.py
+++ b/scripts/SANS/sans/gui_logic/models/beam_centre_model.py
@@ -28,7 +28,7 @@ class BeamCentreModel(object):
self._r_max = r_range["beam_centre_radius_max"] if "beam_centre_radius_max" in r_range else 280
self._left_right = True
self._up_down = True
- self._tolerance = 0.000125
+ self._tolerance = 0.0001251
self._lab_pos_1 = ''
self._lab_pos_2 = ''
self._hab_pos_2 = ''
@@ -73,11 +73,6 @@ class BeamCentreModel(object):
logger.notice("Have chosen no find direction exiting early")
return {"pos1": self.lab_pos_1, "pos2": self.lab_pos_2}
- if self.q_min:
- state.convert_to_q.q_min = self.q_min
- if self.q_max:
- state.convert_to_q.q_max = self.q_max
-
if self.COM:
centre = centre_finder(state, r_min=self.r_min, r_max=self.r_max,
max_iter=self.max_iterations,
diff --git a/scripts/SANS/sans/gui_logic/models/state_gui_model.py b/scripts/SANS/sans/gui_logic/models/state_gui_model.py
index 3d631702dd9b6b850c821dfa71e9f6f6b2d12913..aa760cbe58ad3e1de8202ee1e54bb47a63767039 100644
--- a/scripts/SANS/sans/gui_logic/models/state_gui_model.py
+++ b/scripts/SANS/sans/gui_logic/models/state_gui_model.py
@@ -110,7 +110,7 @@ class StateGuiModel(object):
@property
def hab_pos_1(self):
- return self.get_simple_element_with_attribute(element_id=SetId.centre, default_value='', attribute="pos1")
+ return self.get_simple_element_with_attribute(element_id=SetId.centre_HAB, default_value='', attribute="pos1")
@hab_pos_1.setter
def hab_pos_1(self, value):
@@ -118,7 +118,7 @@ class StateGuiModel(object):
@property
def hab_pos_2(self):
- return self.get_simple_element_with_attribute(element_id=SetId.centre, default_value='', attribute="pos2")
+ return self.get_simple_element_with_attribute(element_id=SetId.centre_HAB, default_value='', attribute="pos2")
@hab_pos_2.setter
def hab_pos_2(self, value):
diff --git a/scripts/SANS/sans/gui_logic/presenter/beam_centre_presenter.py b/scripts/SANS/sans/gui_logic/presenter/beam_centre_presenter.py
index 75ab0491dd792d4e92fe4fc9d4c55686cd0586d6..62a210c6f4ec5a625c2ac7b7cbc970626663ff8f 100644
--- a/scripts/SANS/sans/gui_logic/presenter/beam_centre_presenter.py
+++ b/scripts/SANS/sans/gui_logic/presenter/beam_centre_presenter.py
@@ -117,6 +117,19 @@ class BeamCentrePresenter(object):
self._beam_centre_model.update_hab = self._view.update_hab
self._beam_centre_model.update_lab = self._view.update_lab
+ def update_centre_positions(self, state_model):
+ lab_pos_1 = getattr(state_model, 'lab_pos_1')
+ lab_pos_2 = getattr(state_model, 'lab_pos_2')
+
+ hab_pos_1 = getattr(state_model, 'hab_pos_1') if getattr(state_model, 'hab_pos_1') else lab_pos_1
+ hab_pos_2 = getattr(state_model, 'hab_pos_2') if getattr(state_model, 'hab_pos_2') else lab_pos_2
+
+ self._view.lab_pos_1 = lab_pos_1
+ self._view.lab_pos_2 = lab_pos_2
+
+ self._view.hab_pos_1 = hab_pos_1
+ self._view.hab_pos_2 = hab_pos_2
+
def set_on_state_model(self, attribute_name, state_model):
attribute = getattr(self._view, attribute_name)
if attribute or isinstance(attribute, bool):
diff --git a/scripts/SANS/sans/gui_logic/presenter/run_tab_presenter.py b/scripts/SANS/sans/gui_logic/presenter/run_tab_presenter.py
index 4348ccb345233ea6aeecc88a667b50ef1af790bd..db7891cdb74e1bebaf38bcf296456f0312bce587 100644
--- a/scripts/SANS/sans/gui_logic/presenter/run_tab_presenter.py
+++ b/scripts/SANS/sans/gui_logic/presenter/run_tab_presenter.py
@@ -215,6 +215,7 @@ class RunTabPresenter(object):
self._state_model = StateGuiModel(user_file_items)
# 5. Update the views.
self._update_view_from_state_model()
+ self._beam_centre_presenter.update_centre_positions(self._state_model)
# 6. Perform calls on child presenters
self._masking_table_presenter.on_update_rows()
@@ -588,12 +589,6 @@ class RunTabPresenter(object):
self._set_on_view("radius_limit_min")
self._set_on_view("radius_limit_max")
- # Beam Centre
- self._beam_centre_presenter.set_on_view('lab_pos_1', self._state_model)
- self._beam_centre_presenter.set_on_view('lab_pos_2', self._state_model)
- self._beam_centre_presenter.set_on_view('hab_pos_1', self._state_model)
- self._beam_centre_presenter.set_on_view('hab_pos_2', self._state_model)
-
def _set_on_view_transmission_fit_sample_settings(self):
# Set transmission_sample_use_fit
fit_type = self._state_model.transmission_sample_fit_type
diff --git a/scripts/SANS/sans/user_file/settings_tags.py b/scripts/SANS/sans/user_file/settings_tags.py
index 1341b2efb5d61db33be532f71f475f2565e191a4..445caf2c8b4b24703fad3e875c57f67bd58178ea 100644
--- a/scripts/SANS/sans/user_file/settings_tags.py
+++ b/scripts/SANS/sans/user_file/settings_tags.py
@@ -80,7 +80,7 @@ class SampleId(object):
# --- SET
-@serializable_enum("scales", "centre")
+@serializable_enum("scales", "centre", "centre_HAB")
class SetId(object):
pass
diff --git a/scripts/SANS/sans/user_file/user_file_parser.py b/scripts/SANS/sans/user_file/user_file_parser.py
index 7365bc41db2cb07b7541ac9bcb8c701f10cba861..3d3ea0523185cb988ebc770ab72ac13f6ac31bed 100644
--- a/scripts/SANS/sans/user_file/user_file_parser.py
+++ b/scripts/SANS/sans/user_file/user_file_parser.py
@@ -1145,10 +1145,14 @@ class SetParser(UserFileComponentParser):
self._hab = "\\s*(HAB|FRONT)\\s*"
self._lab = "\\s*(LAB|REAR|MAIN)\\s*"
self._hab_or_lab = "\\s*(/" + self._hab + "|/" + self._lab + ")\\s*"
- self._centre_pattern = re.compile(start_string + self._centre + "\\s*(" + self._hab_or_lab + space_string +
+ self._centre_pattern = re.compile(start_string + self._centre + "\\s*(/" + self._lab + space_string +
")?\\s*" + float_number + space_string + float_number +
"\\s*(" + space_string + float_number + space_string + float_number +
")?\\s*" + end_string)
+ self._centre_pattern_HAB = re.compile(start_string + self._centre + "\\s*(/" + self._hab + space_string +
+ ")?\\s*" + float_number + space_string + float_number +
+ "\\s*(" + space_string + float_number + space_string + float_number +
+ ")?\\s*" + end_string)
def parse_line(self, line):
# Get the settings, ie remove command
@@ -1159,6 +1163,8 @@ class SetParser(UserFileComponentParser):
output = self._extract_scales(setting)
elif self._is_centre(setting):
output = self._extract_centre(setting)
+ elif self._is_centre_HAB(setting):
+ output = self._extract_centre_HAB(setting)
else:
raise RuntimeError("SetParser: Unknown command for SET: {0}".format(line))
return output
@@ -1169,6 +1175,9 @@ class SetParser(UserFileComponentParser):
def _is_centre(self, line):
return does_pattern_match(self._centre_pattern, line)
+ def _is_centre_HAB(self, line):
+ return does_pattern_match(self._centre_pattern_HAB, line)
+
def _extract_scales(self, line):
scales_string = re.sub(self._scales, "", line)
scales = extract_float_list(scales_string, separator=" ")
@@ -1179,11 +1188,19 @@ class SetParser(UserFileComponentParser):
def _extract_centre(self, line):
detector_type = DetectorType.HAB if re.search(self._hab, line) is not None else DetectorType.LAB
centre_string = re.sub(self._centre, "", line)
- centre_string = re.sub(self._hab_or_lab, "", centre_string)
+ centre_string = re.sub("/" + self._lab, "", centre_string)
centre_string = ' '.join(centre_string.split())
centre = extract_float_list(centre_string, separator=" ")
return {SetId.centre: position_entry(pos1=centre[0], pos2=centre[1], detector_type=detector_type)}
+ def _extract_centre_HAB(self, line):
+ detector_type = DetectorType.HAB if re.search(self._hab, line) is not None else DetectorType.LAB
+ centre_string = re.sub(self._centre, "", line)
+ centre_string = re.sub("/" + self._hab, "", centre_string)
+ centre_string = ' '.join(centre_string.split())
+ centre = extract_float_list(centre_string, separator=" ")
+ return {SetId.centre_HAB: position_entry(pos1=centre[0], pos2=centre[1], detector_type=detector_type)}
+
@staticmethod
def get_type():
return SetParser.Type
diff --git a/scripts/test/SANS/gui_logic/beam_centre_model_test.py b/scripts/test/SANS/gui_logic/beam_centre_model_test.py
index 558a2127fa31cd897d8d12e6ffb1270c2bace9ce..0c4bceb9a26b8737cae1d0ee8cfb6b1727da8a1e 100644
--- a/scripts/test/SANS/gui_logic/beam_centre_model_test.py
+++ b/scripts/test/SANS/gui_logic/beam_centre_model_test.py
@@ -29,7 +29,7 @@ class BeamCentreModelTest(unittest.TestCase):
self.assertEqual(self.beam_centre_model.r_max, 280)
self.assertEqual(self.beam_centre_model.left_right, True)
self.assertEqual(self.beam_centre_model.up_down, True)
- self.assertEqual(self.beam_centre_model.tolerance, 0.000125)
+ self.assertEqual(self.beam_centre_model.tolerance, 0.0001251)
self.assertEqual(self.beam_centre_model.lab_pos_1, '')
self.assertEqual(self.beam_centre_model.lab_pos_2, '')
self.assertEqual(self.beam_centre_model.hab_pos_2, '')
@@ -88,9 +88,6 @@ class BeamCentreModelTest(unittest.TestCase):
reduction_method=True,
verbose=False, component=DetectorType.LAB)
- self.assertEqual(state.convert_to_q.q_min, self.beam_centre_model.q_min)
- self.assertEqual(state.convert_to_q.q_max, self.beam_centre_model.q_max)
-
def test_that_find_beam_centre_calls_centre_finder_twice_when_COM_is_TRUE(self):
state = mock.MagicMock()
self.beam_centre_model.COM = True
diff --git a/scripts/test/SANS/user_file/user_file_parser_test.py b/scripts/test/SANS/user_file/user_file_parser_test.py
index 18d8ec015d110cb7f3eea8028401afa35f7ed917..fe0c381717cdd84c609e740cecfb1b2c646f8a44 100644
--- a/scripts/test/SANS/user_file/user_file_parser_test.py
+++ b/scripts/test/SANS/user_file/user_file_parser_test.py
@@ -514,11 +514,11 @@ class SetParserTest(unittest.TestCase):
detector_type=DetectorType.LAB)},
"SET centre / lAb 23 45": {SetId.centre: position_entry(pos1=23, pos2=45,
detector_type=DetectorType.LAB)},
- "SET centre / hAb 23 45": {SetId.centre: position_entry(pos1=23, pos2=45,
+ "SET centre / hAb 23 45": {SetId.centre_HAB: position_entry(pos1=23, pos2=45,
detector_type=DetectorType.HAB)},
- "SET centre /FRONT 23 45": {SetId.centre: position_entry(pos1=23, pos2=45,
+ "SET centre /FRONT 23 45": {SetId.centre_HAB: position_entry(pos1=23, pos2=45,
detector_type=DetectorType.HAB)},
- "SET centre /FRONT 23 45 55 67": {SetId.centre: position_entry(pos1=23, pos2=45,
+ "SET centre /FRONT 23 45 55 67": {SetId.centre_HAB: position_entry(pos1=23, pos2=45,
detector_type=DetectorType.HAB)},
}