LoadAndApplyMuonDetectorGrouping.cpp

// 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"

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 {
namespace 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, Workspace_sptr workspace) {
  bool check = MuonAlgorithmHelper::checkGroupDetectorsInWorkspace(grouping, std::move(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) {
  for (auto &&groupName : grouping.groupNames) {
    if (!MuonAlgorithmHelper::checkValidGroupPairName(groupName)) {
      throw std::invalid_argument("Some group names are invalid : " + groupName);
    }
  }

  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 Muon
} // namespace Mantid