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IntegratePeaksUsingClusters.cpp
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IntegratePeaksUsingClusters.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidCrystal/IntegratePeaksUsingClusters.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/IMDHistoWorkspace.h"
#include "MantidAPI/IMDIterator.h"
#include "MantidCrystal/ConnectedComponentLabeling.h"
#include "MantidCrystal/HardThresholdBackground.h"
#include "MantidCrystal/ICluster.h"
#include "MantidCrystal/PeakClusterProjection.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/Utils.h"
#include <cmath>
using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::DataObjects;
using namespace Mantid::Crystal::ConnectedComponentMappingTypes;
namespace Mantid::Crystal {
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(IntegratePeaksUsingClusters)
//----------------------------------------------------------------------------------------------
/// Algorithm's name for identification. @see Algorithm::name
const std::string IntegratePeaksUsingClusters::name() const { return "IntegratePeaksUsingClusters"; }
/// Algorithm's version for identification. @see Algorithm::version
int IntegratePeaksUsingClusters::version() const { return 1; }
/// Algorithm's category for identification. @see Algorithm::category
const std::string IntegratePeaksUsingClusters::category() const { return "MDAlgorithms\\Peaks;Crystal\\Integration"; }
//----------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm's properties.
*/
void IntegratePeaksUsingClusters::init() {
declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("InputWorkspace", "", Direction::Input),
"Input md workspace.");
declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("PeaksWorkspace", "", Direction::Input),
"A PeaksWorkspace containing the peaks to integrate.");
auto positiveValidator = std::make_shared<BoundedValidator<double>>();
positiveValidator->setExclusive(true);
positiveValidator->setLower(0);
auto compositeValidator = std::make_shared<CompositeValidator>();
compositeValidator->add(positiveValidator);
compositeValidator->add(std::make_shared<MandatoryValidator<double>>());
declareProperty(std::make_unique<PropertyWithValue<double>>("Threshold", 0, compositeValidator, Direction::Input),
"Threshold signal above which to consider peaks");
std::array<std::string, 3> normalizations = {{"NoNormalization", "VolumeNormalization", "NumEventsNormalization"}};
declareProperty("Normalization", normalizations[1],
Kernel::IValidator_sptr(new Kernel::ListValidator<std::string>(normalizations)),
"Normalization to use with Threshold. Defaults to "
"VolumeNormalization to account for different binning.");
declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("OutputWorkspace", "", Direction::Output),
"An output integrated peaks workspace.");
declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("OutputWorkspaceMD", "", Direction::Output),
"MDHistoWorkspace containing the labeled clusters used by "
"the algorithm.");
}
/**
* Get the normalization. For use with iterators + background strategies.
* @return Chosen normalization
*/
MDNormalization IntegratePeaksUsingClusters::getNormalization() {
std::string normProp = getPropertyValue("Normalization");
Mantid::API::MDNormalization normalization;
if (normProp == "NoNormalization") {
normalization = NoNormalization;
} else if (normProp == "VolumeNormalization") {
normalization = VolumeNormalization;
} else {
normalization = NumEventsNormalization;
}
return normalization;
}
//----------------------------------------------------------------------------------------------
/** Execute the algorithm.
*/
void IntegratePeaksUsingClusters::exec() {
IMDHistoWorkspace_sptr mdWS = getProperty("InputWorkspace");
PeaksWorkspace_sptr inPeakWS = getProperty("PeaksWorkspace");
PeaksWorkspace_sptr peakWS = getProperty("OutputWorkspace");
if (peakWS != inPeakWS) {
peakWS = inPeakWS->clone();
}
{
const SpecialCoordinateSystem mdCoordinates = mdWS->getSpecialCoordinateSystem();
if (mdCoordinates == None) {
throw std::invalid_argument("The coordinate system of the input "
"MDWorkspace cannot be established. Create "
"your workspace with an MDFrame which is "
"not a General Frame or Unknown Frame.");
}
}
const double threshold = getProperty("Threshold");
// Make a background strategy for the CCL analysis to use.
HardThresholdBackground backgroundStrategy(threshold, this->getNormalization());
// CCL. Multi-processor version.
ConnectedComponentLabeling analysis;
Progress progress(this, 0.0, 1.0, 1);
// Perform CCL.
ClusterTuple clusters = analysis.executeAndFetchClusters(mdWS, &backgroundStrategy, progress);
// Extract the clusters
ConnectedComponentMappingTypes::ClusterMap &clusterMap = clusters.get<1>();
// Extract the labeled image
IMDHistoWorkspace_sptr outHistoWS = clusters.get<0>();
// Labels taken by peaks.
std::map<size_t, size_t> labelsTakenByPeaks;
// Make a peak transform so that we can understand a peak in the context of
// the mdworkspace coordinate setup.
PeakClusterProjection projection(outHistoWS); // Projection of PeaksWorkspace
// over labelled cluster
// workspace.
progress.doReport("Performing Peak Integration");
g_log.information("Starting Integration");
progress.resetNumSteps(peakWS->getNumberPeaks(), 0.9, 1);
PARALLEL_FOR_IF(Kernel::threadSafe(*peakWS))
for (int i = 0; i < peakWS->getNumberPeaks(); ++i) {
PARALLEL_START_INTERRUPT_REGION
Geometry::IPeak &peak = peakWS->getPeak(i);
const Mantid::signal_t signalValue =
projection.signalAtPeakCenter(peak); // No normalization when extracting label ids!
if (std::isnan(signalValue)) {
g_log.warning() << "Warning: image for integration is off edge of detector for peak " << i << '\n';
} else if (signalValue < static_cast<Mantid::signal_t>(analysis.getStartLabelId())) {
g_log.information() << "Peak: " << i
<< " Has no corresponding cluster/blob detected on "
"the image. This could be down to your Threshold "
"settings.\n";
} else {
const auto labelIdAtPeak = static_cast<size_t>(signalValue);
ICluster *const cluster = clusterMap[labelIdAtPeak].get();
ICluster::ClusterIntegratedValues integratedValues = cluster->integrate(mdWS);
peak.setIntensity(integratedValues.get<0>());
peak.setSigmaIntensity(std::sqrt(integratedValues.get<1>()));
PARALLEL_CRITICAL(IntegratePeaksUsingClusters) {
auto it = labelsTakenByPeaks.find(labelIdAtPeak);
if (it != labelsTakenByPeaks.end()) {
g_log.warning() << "Overlapping Peaks. Peak: " << i << " overlaps with another Peak: " << it->second
<< " and shares label id: " << it->first << '\n';
}
labelsTakenByPeaks.emplace(labelIdAtPeak, i);
}
progress.report();
}
PARALLEL_END_INTERRUPT_REGION
}
PARALLEL_CHECK_INTERRUPT_REGION
setProperty("OutputWorkspace", peakWS);
setProperty("OutputWorkspaceMD", outHistoWS);
}
} // namespace Mantid::Crystal