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LoadAndApplyMuonDetectorGrouping.cpp
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LoadAndApplyMuonDetectorGrouping.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 <utility>
#include "MantidMuon/LoadAndApplyMuonDetectorGrouping.h"
#include "MantidMuon/MuonAlgorithmHelper.h"
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/TableRow.h"
#include "MantidAPI/Workspace.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/Strings.h"
#include <algorithm>
namespace {
// Convert the enum PlotType to a string to pass to ApplyMuonDetectorGrouping
std::string plotTypeToString(const Mantid::Muon::PlotType &plotType) {
switch (plotType) {
case Mantid::Muon::PlotType::Asymmetry:
return "Asymmetry";
case Mantid::Muon::PlotType::Counts:
return "Counts";
case Mantid::Muon::PlotType::Logarithm:
return "Counts";
}
// Default to counts
return "Counts";
}
void throwIfGroupNotInPair(const std::string &pairName, const std::string &pairGroup,
const std::vector<std::string> &groupNames) {
bool group1inPair = (std::find(groupNames.begin(), groupNames.end(), pairGroup) != groupNames.end());
if (!group1inPair) {
throw std::invalid_argument("Pairing " + pairName + " : required group " + pairGroup + " is missing");
}
}
void throwIfGroupsNotInPair(const std::string &pairName, const std::string &pairGroup1, const std::string &pairGroup2,
const std::vector<std::string> &groupNames) {
throwIfGroupNotInPair(pairName, pairGroup1, groupNames);
throwIfGroupNotInPair(pairName, pairGroup2, groupNames);
}
} // namespace
using namespace Mantid::API;
using namespace Mantid::DataObjects;
using namespace Mantid::Kernel;
using namespace Mantid::MuonAlgorithmHelper;
namespace Mantid::Muon {
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(LoadAndApplyMuonDetectorGrouping)
void LoadAndApplyMuonDetectorGrouping::init() {
std::string emptyString("");
declareProperty(std::make_unique<FileProperty>("Filename", "", API::FileProperty::Load, ".xml"),
"The XML file containing the grouping and pairing information");
declareProperty(
std::make_unique<WorkspaceProperty<Workspace>>("InputWorkspace", "", Direction::Input, PropertyMode::Mandatory),
"Input workspace containing data from detectors that the "
"grouping/pairing will be applied to.");
declareProperty(std::make_unique<WorkspaceProperty<WorkspaceGroup>>("WorkspaceGroup", "", Direction::InOut,
PropertyMode::Optional),
"The workspaces created by the algorithm will be placed inside this "
"group. If not specified will save to \"MuonAnalysisGroup\" ");
declareProperty("AddGroupingTable", false, "Whether to add a TableWorkspace of the groupings to the ADS.");
// Cropping
declareProperty("CropWorkspaces", false, "Whether to crop the x-axis of the output workspaces.");
declareProperty("TimeMin", 0.0, "Start time for the data in mus.", Direction::Input);
setPropertySettings("TimeMin",
std::make_unique<Kernel::EnabledWhenProperty>("CropWorkspaces", Kernel::IS_EQUAL_TO, "1"));
declareProperty("TimeMax", 32.0, "End time for the data in mus.", Direction::Input);
setPropertySettings("TimeMax",
std::make_unique<Kernel::EnabledWhenProperty>("CropWorkspaces", Kernel::IS_EQUAL_TO, "1"));
// Group asymmetry range
declareProperty("ApplyAsymmetryToGroups", false, "Whether to calculate group asymmetry and store the workspaces.");
declareProperty("AsymmetryTimeMin", EMPTY_DBL(), "Start time for the group asymmetry calculation (micro seconds).",
Direction::Input);
setPropertySettings("AsymmetryTimeMin", std::make_unique<Kernel::EnabledWhenProperty>("ApplyAsymmetryToGroups",
Kernel::IS_EQUAL_TO, "1"));
declareProperty("AsymmetryTimeMax", EMPTY_DBL(), "End time for the group asymmetry calculation (micro seconds).",
Direction::Input);
setPropertySettings("AsymmetryTimeMax", std::make_unique<Kernel::EnabledWhenProperty>("ApplyAsymmetryToGroups",
Kernel::IS_EQUAL_TO, "1"));
// Optional properties
declareProperty("RebinArgs", emptyString, "Rebin arguments. No rebinning if left empty.", Direction::Input);
declareProperty("TimeOffset", 0.0,
"Shift the times of all data by a fixed amount (in micro "
"seconds). The value given corresponds to the bin that will "
"become 0.0 seconds.",
Direction::Input);
declareProperty("SummedPeriods", std::to_string(1), "A list of periods to sum in multiperiod data.",
Direction::Input);
declareProperty("SubtractedPeriods", emptyString, "A list of periods to subtract in multiperiod data.",
Direction::Input);
declareProperty(std::make_unique<WorkspaceProperty<TableWorkspace>>("DeadTimeTable", "", Direction::Input,
PropertyMode::Optional),
"Table with dead time information, used to apply dead time correction.");
// Perform Group Associations.
std::string analysisGrp("Analysis Options");
setPropertyGroup("RebinArgs", analysisGrp);
setPropertyGroup("TimeOffset", analysisGrp);
setPropertyGroup("SummedPeriods", analysisGrp);
setPropertyGroup("SubtractedPeriods", analysisGrp);
setPropertyGroup("DeadTimeTable", analysisGrp);
std::string croppingGrp("Cropping");
setPropertyGroup("TimeMin", croppingGrp);
setPropertyGroup("TimeMax", croppingGrp);
setPropertyGroup("CropWorkspaces", croppingGrp);
std::string groupAsymmetryGrp("Asymmetry");
setPropertyGroup("AsymmetryTimeMin", groupAsymmetryGrp);
setPropertyGroup("AsymmetryTimeMax", groupAsymmetryGrp);
setPropertyGroup("ApplyAsymmetryToGroups", groupAsymmetryGrp);
}
/**
* Performs validation of inputs to the algorithm.
* - Check the input workspace and WorkspaceGroup are not the same
*/
std::map<std::string, std::string> LoadAndApplyMuonDetectorGrouping::validateInputs() {
std::map<std::string, std::string> errors;
if (!this->isDefault("WorkspaceGroup")) {
WorkspaceGroup_sptr groupedWS = getProperty("WorkspaceGroup");
Workspace_sptr inputWS = getProperty("InputWorkspace");
if (groupedWS && groupedWS->getName() == inputWS->getName()) {
errors["WorkspaceGroup"] = "The WorkspaceGroup should not have "
"the same name as InputWorkspace.";
}
}
return errors;
}
void LoadAndApplyMuonDetectorGrouping::getTimeLimitsFromInputWorkspace(const Workspace_sptr &inputWS,
AnalysisOptions &options) {
MatrixWorkspace_sptr inputMatrixWS = std::dynamic_pointer_cast<MatrixWorkspace>(inputWS);
WorkspaceGroup_sptr inputGroupWS = std::dynamic_pointer_cast<WorkspaceGroup>(inputWS);
if (inputMatrixWS) {
if (inputMatrixWS->getNumberHistograms() > 0) {
double timeMin = inputMatrixWS->mutableX(0)[0];
auto sizex = inputMatrixWS->mutableX(0).size();
double timeMax = inputMatrixWS->mutableX(0)[sizex - 1];
options.timeLimits = std::make_pair(timeMin, timeMax);
}
} else if (inputGroupWS) {
MatrixWorkspace_sptr ws1 = std::dynamic_pointer_cast<MatrixWorkspace>(inputGroupWS->getItem(0));
double timeMin = ws1->mutableX(0)[0];
auto sizex = ws1->mutableX(0).size();
double timeMax = ws1->mutableX(0)[sizex - 1];
options.timeLimits = std::make_pair(timeMin, timeMax);
} else {
// Use sensible defaults
options.timeLimits = std::make_pair(0.1, 32.0);
}
}
void LoadAndApplyMuonDetectorGrouping::getTimeLimitsFromInputs(AnalysisOptions &options) {
auto timeMin = getProperty("TimeMin");
auto timeMax = getProperty("TimeMax");
options.timeLimits = std::make_pair(timeMin, timeMax);
}
void LoadAndApplyMuonDetectorGrouping::exec() {
this->setRethrows(true);
AnalysisOptions options = setDefaultOptions();
options.grouping = loadGroupsAndPairs();
Workspace_sptr inputWS = getProperty("InputWorkspace");
if (!getProperty("CropWorkspaces")) {
getTimeLimitsFromInputWorkspace(inputWS, options);
} else {
getTimeLimitsFromInputs(options);
}
checkDetectorIDsInWorkspace(options.grouping, inputWS);
WorkspaceGroup_sptr groupedWS = getProperty("WorkspaceGroup");
if (!groupedWS) {
groupedWS = addGroupedWSWithDefaultName(inputWS);
}
// Perform the analysis specified in options
addGroupingToADS(options, inputWS, groupedWS);
addPairingToADS(options, inputWS, groupedWS);
if (getProperty("ApplyAsymmetryToGroups")) {
options.plotType = PlotType::Asymmetry;
addGroupingToADS(options, inputWS, groupedWS);
}
if (getProperty("AddGroupingTable")) {
addGroupingInformationToADS(options.grouping);
}
}
// Checks that the detector IDs in grouping are in the workspace
void LoadAndApplyMuonDetectorGrouping::checkDetectorIDsInWorkspace(API::Grouping &grouping,
const Workspace_sptr &workspace) {
bool check = MuonAlgorithmHelper::checkGroupDetectorsInWorkspace(grouping, workspace);
if (!check) {
g_log.error("One or more detector IDs specified in the groups is not "
"contained in the InputWorkspace");
throw std::runtime_error("One or more detector IDs specified in the groups is not "
"contained in the InputWorkspace");
}
}
/**
* Adds an empty WorkspaceGroup to the ADS with a name
* that it would have if created by the MuonAnalysis GUI.
* e.g. MUSR0001234
*/
WorkspaceGroup_sptr LoadAndApplyMuonDetectorGrouping::addGroupedWSWithDefaultName(Workspace_sptr workspace) {
auto &ads = AnalysisDataService::Instance();
std::string groupedWSName = MuonAlgorithmHelper::getRunLabel(std::move(workspace));
WorkspaceGroup_sptr groupedWS;
if (ads.doesExist(groupedWSName)) {
if ((groupedWS = std::dynamic_pointer_cast<WorkspaceGroup>(ads.retrieve(groupedWSName)))) {
return groupedWS;
}
}
groupedWS = std::make_shared<WorkspaceGroup>();
AnalysisDataService::Instance().addOrReplace(groupedWSName, groupedWS);
return groupedWS;
}
// Set the parameters in options to sensible defaults for this algorithm
AnalysisOptions LoadAndApplyMuonDetectorGrouping::setDefaultOptions() {
AnalysisOptions options;
options.summedPeriods = this->getPropertyValue("SummedPeriods");
options.subtractedPeriods = this->getPropertyValue("SubtractedPeriods");
options.timeZero = 0.0;
options.loadedTimeZero = this->getProperty("TimeOffset");
options.rebinArgs = this->getPropertyValue("RebinArgs");
options.plotType = Muon::PlotType::Counts;
return options;
}
/**
* Adds the group names and corresponding detector IDs to
* a TableWorkspace in the ADS named "MuonGroupings"
*/
void LoadAndApplyMuonDetectorGrouping::addGroupingInformationToADS(const Mantid::API::Grouping &grouping) {
auto groupingTable =
std::dynamic_pointer_cast<ITableWorkspace>(WorkspaceFactory::Instance().createTable("TableWorkspace"));
groupingTable->addColumn("str", "GroupName");
groupingTable->addColumn("vector_int", "Detectors");
size_t numGroups = grouping.groups.size();
for (size_t i = 0; i < numGroups; i++) {
TableRow newRow = groupingTable->appendRow();
newRow << grouping.groupNames[i];
std::vector<int> detectorIDs = Kernel::Strings::parseRange(grouping.groups[i]);
std::sort(detectorIDs.begin(), detectorIDs.end());
newRow << detectorIDs;
}
AnalysisDataServiceImpl &ads = AnalysisDataService::Instance();
ads.addOrReplace("MuonGroupings", groupingTable);
}
/**
* Load the grouping and pairing information from the input file
* into the Grouping struct, after performing some checks.
*/
API::Grouping LoadAndApplyMuonDetectorGrouping::loadGroupsAndPairs() {
Grouping grouping;
std::string filename = getProperty("Filename");
GroupingLoader::loadGroupingFromXML(filename, grouping);
CheckValidGroupsAndPairs(grouping);
return grouping;
}
/**
* Check if the group/pair names are valid, and if all the groups which
* are paired are also included as groups.
*/
void LoadAndApplyMuonDetectorGrouping::CheckValidGroupsAndPairs(const Grouping &grouping) {
const auto it = std::find_if_not(grouping.groupNames.cbegin(), grouping.groupNames.cend(), [](auto &&groupName) {
return MuonAlgorithmHelper::checkValidGroupPairName(groupName);
});
if (it != grouping.groupNames.cend())
throw std::invalid_argument("Some group names are invalid : " + *it);
for (auto p = 0u; p < grouping.pairs.size(); ++p) {
std::string pairName = grouping.pairNames[p];
if (!MuonAlgorithmHelper::checkValidGroupPairName(pairName)) {
throw std::invalid_argument("Some pair names are invalid" + pairName);
}
std::string pairGroup1 = grouping.groupNames[grouping.pairs[p].first];
std::string pairGroup2 = grouping.groupNames[grouping.pairs[p].second];
throwIfGroupsNotInPair(pairName, pairGroup1, pairGroup2, grouping.groupNames);
}
}
/**
* Add all the supplied groups to the ADS, inside wsGrouped, by
* executing the ApplyMuonDetectorGrouping algorithm
*/
void LoadAndApplyMuonDetectorGrouping::addGroupingToADS(const Mantid::Muon::AnalysisOptions &options,
const Mantid::API::Workspace_sptr &ws,
const Mantid::API::WorkspaceGroup_sptr &wsGrouped) {
size_t numGroups = options.grouping.groups.size();
for (auto i = 0u; i < numGroups; ++i) {
auto alg = createChildAlgorithm("ApplyMuonDetectorGrouping");
if (!this->isLogging())
alg->setLogging(false);
alg->setProperty("InputWorkspace", ws->getName());
alg->setProperty("InputWorkspaceGroup", wsGrouped->getName());
alg->setProperty("GroupName", options.grouping.groupNames[i]);
alg->setProperty("Grouping", options.grouping.groups[i]);
alg->setProperty("AnalysisType", plotTypeToString(options.plotType));
alg->setProperty("TimeMin", options.timeLimits.first);
alg->setProperty("TimeMax", options.timeLimits.second);
// Analysis options
alg->setProperty("RebinArgs", options.rebinArgs);
alg->setProperty("TimeOffset", options.loadedTimeZero - options.timeZero);
alg->setProperty("SummedPeriods", options.summedPeriods);
alg->setProperty("SubtractedPeriods", options.subtractedPeriods);
TableWorkspace_sptr DTT = getProperty("DeadTimeTable");
if (DTT) {
alg->setProperty("ApplyDeadTimeCorrection", true);
alg->setProperty("DeadTimeTable", DTT);
}
alg->execute();
}
}
/**
* Add all the supplied pairs to the ADS, inside wsGrouped, by
* executing the ApplyMuonDetectorGroupPairing algorithm
*/
void LoadAndApplyMuonDetectorGrouping::addPairingToADS(const Mantid::Muon::AnalysisOptions &options,
const Mantid::API::Workspace_sptr &ws,
const Mantid::API::WorkspaceGroup_sptr &wsGrouped) {
size_t numPairs = options.grouping.pairs.size();
for (size_t i = 0; i < numPairs; i++) {
auto alg = createChildAlgorithm("ApplyMuonDetectorGroupPairing");
if (!this->isLogging())
alg->setLogging(false);
alg->setProperty("SpecifyGroupsManually", true);
alg->setProperty("InputWorkspace", ws->getName());
alg->setProperty("InputWorkspaceGroup", wsGrouped->getName());
alg->setProperty("PairName", options.grouping.pairNames[i]);
alg->setProperty("Alpha", options.grouping.pairAlphas[i]);
alg->setProperty("TimeMin", options.timeLimits.first);
alg->setProperty("TimeMax", options.timeLimits.second);
std::string group1 = options.grouping.groups[options.grouping.pairs[i].first];
std::string group2 = options.grouping.groups[options.grouping.pairs[i].second];
alg->setProperty("Group1", group1);
alg->setProperty("Group2", group2);
// Analysis options
alg->setProperty("RebinArgs", options.rebinArgs);
alg->setProperty("TimeOffset", options.loadedTimeZero - options.timeZero);
alg->setProperty("SummedPeriods", options.summedPeriods);
alg->setProperty("SubtractedPeriods", options.subtractedPeriods);
TableWorkspace_sptr DTT = getProperty("DeadTimeTable");
if (DTT) {
alg->setProperty("ApplyDeadTimeCorrection", true);
alg->setProperty("DeadTimeTable", DTT);
}
alg->execute();
};
}
// Allow WorkspaceGroup property to function correctly.
bool LoadAndApplyMuonDetectorGrouping::checkGroups() { return false; }
} // namespace Mantid::Muon