DgsReduction.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 "MantidWorkflowAlgorithms/DgsReduction.h"

#include "MantidAPI/FileProperty.h"
#include "MantidAPI/Run.h"
#include "MantidDataObjects/MaskWorkspace.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/FacilityInfo.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/PropertyManager.h"
#include "MantidKernel/PropertyManagerDataService.h"
#include "MantidKernel/PropertyWithValue.h"
#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/System.h"
#include "MantidKernel/VisibleWhenProperty.h"

#include <boost/algorithm/string/erase.hpp>
#include <sstream>

using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::DataObjects;

namespace Mantid::WorkflowAlgorithms {

// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(DgsReduction)

/// Algorithm's name for identification. @see Algorithm::name
const std::string DgsReduction::name() const { return "DgsReduction"; }

/// Algorithm's version for identification. @see Algorithm::version
int DgsReduction::version() const { return 1; }

/// Algorithm's category for identification. @see Algorithm::category
const std::string DgsReduction::category() const { return "Workflow\\Inelastic"; }

/** Initialize the algorithm's properties.
 */
void DgsReduction::init() {
  // Sample setup options
  std::string sampleSetup = "Sample Setup";
  this->declareProperty(std::make_unique<FileProperty>("SampleInputFile", "", FileProperty::OptionalLoad, "_event.nxs"),
                        "File containing the sample data to reduce");
  this->declareProperty(
      std::make_unique<WorkspaceProperty<>>("SampleInputWorkspace", "", Direction::Input, PropertyMode::Optional),
      "Workspace to be reduced");
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("SampleInputMonitorWorkspace", "", Direction::Input,
                                                              PropertyMode::Optional),
                        "A monitor workspace associated with the input sample workspace.");
  this->declareProperty(std::make_unique<FileProperty>("DetCalFilename", "", FileProperty::OptionalLoad),
                        "A detector calibration file.");
  this->declareProperty("RelocateDetectors", false, "Move detectors to position specified in cal file.");
  auto mustBePositive = std::make_shared<BoundedValidator<double>>();
  mustBePositive->setLower(0.0);
  auto mustBePosInt = std::make_shared<BoundedValidator<int>>();
  mustBePosInt->setLower(0);
  this->declareProperty("IncidentEnergyGuess", EMPTY_DBL(), mustBePositive,
                        "Set the value of the incident energy guess in meV.");
  this->declareProperty("UseIncidentEnergyGuess", false,
                        "Use the incident energy guess as the actual value "
                        "(will not be calculated).");
  this->declareProperty("TimeZeroGuess", EMPTY_DBL(), "Set the value of time zero offset in microseconds.");
  this->setPropertySettings("TimeZeroGuess",
                            std::make_unique<VisibleWhenProperty>("UseIncidentEnergyGuess", IS_EQUAL_TO, "1"));
  auto mustBePositiveInt = std::make_shared<BoundedValidator<int>>();
  mustBePositiveInt->setLower(0);
  this->declareProperty("Monitor1SpecId", EMPTY_INT(), mustBePositiveInt,
                        "Spectrum No for the first monitor to use in Ei calculation.");
  this->declareProperty("Monitor2SpecId", EMPTY_INT(), mustBePositiveInt,
                        "Spectrum No for the second monitor to use in Ei calculation.");
  this->declareProperty(
      std::make_unique<ArrayProperty<double>>("EnergyTransferRange", std::make_shared<RebinParamsValidator>(true)),
      "A comma separated list of first bin boundary, width, last bin "
      "boundary.\n"
      "Negative width value indicates logarithmic binning.");
  this->declareProperty("SofPhiEIsDistribution", true, "The final S(Phi, E) data is made to be a distribution.");
  this->declareProperty(std::make_unique<FileProperty>("HardMaskFile", "", FileProperty::OptionalLoad, ".xml"),
                        "A file or workspace containing a hard mask.");
  this->declareProperty(std::make_unique<FileProperty>("GroupingFile", "", FileProperty::OptionalLoad, ".xml"),
                        "A file containing grouping (mapping) information.");
  this->declareProperty("ShowIntermediateWorkspaces", false,
                        "Flag to show the intermediate workspaces (diagnostic "
                        "mask, integrated detector vanadium, "
                        "integrated absolute units) from the reduction.");

  this->setPropertyGroup("SampleInputFile", sampleSetup);
  this->setPropertyGroup("SampleInputWorkspace", sampleSetup);
  this->setPropertyGroup("SampleInputMonitorWorkspace", sampleSetup);
  this->setPropertyGroup("DetCalFilename", sampleSetup);
  this->setPropertyGroup("RelocateDetectors", sampleSetup);
  this->setPropertyGroup("IncidentEnergyGuess", sampleSetup);
  this->setPropertyGroup("UseIncidentEnergyGuess", sampleSetup);
  this->setPropertyGroup("TimeZeroGuess", sampleSetup);
  this->setPropertyGroup("Monitor1SpecId", sampleSetup);
  this->setPropertyGroup("Monitor2SpecId", sampleSetup);
  this->setPropertyGroup("EnergyTransferRange", sampleSetup);
  this->setPropertyGroup("SofPhiEIsDistribution", sampleSetup);
  this->setPropertyGroup("HardMaskFile", sampleSetup);
  this->setPropertyGroup("GroupingFile", sampleSetup);
  this->setPropertyGroup("ShowIntermediateWorkspaces", sampleSetup);

  // Data corrections
  std::string dataCorr = "Data Corrections";
  // this->declareProperty("FilterBadPulses", false, "If true, filter bad pulses
  // from data.");
  std::vector<std::string> incidentBeamNormOptions;
  incidentBeamNormOptions.emplace_back("None");
  incidentBeamNormOptions.emplace_back("ByCurrent");
  incidentBeamNormOptions.emplace_back("ToMonitor");
  this->declareProperty("IncidentBeamNormalisation", "None",
                        std::make_shared<StringListValidator>(incidentBeamNormOptions),
                        "Options for incident beam normalisation on data.");
  this->declareProperty("MonitorIntRangeLow", EMPTY_DBL(), "Set the lower bound for monitor integration.");
  this->setPropertySettings("MonitorIntRangeLow", std::make_unique<VisibleWhenProperty>("IncidentBeamNormalisation",
                                                                                        IS_EQUAL_TO, "ToMonitor"));
  this->declareProperty("MonitorIntRangeHigh", EMPTY_DBL(), "Set the upper bound for monitor integration.");
  this->setPropertySettings("MonitorIntRangeHigh", std::make_unique<VisibleWhenProperty>("IncidentBeamNormalisation",
                                                                                         IS_EQUAL_TO, "ToMonitor"));
  this->declareProperty("TimeIndepBackgroundSub", false,
                        "If true, time-independent background will be calculated and removed.");
  this->declareProperty("TibTofRangeStart", EMPTY_DBL(),
                        "Set the lower TOF bound for time-independent background subtraction.");
  this->setPropertySettings("TibTofRangeStart",
                            std::make_unique<VisibleWhenProperty>("TimeIndepBackgroundSub", IS_EQUAL_TO, "1"));
  this->declareProperty("TibTofRangeEnd", EMPTY_DBL(),
                        "Set the upper TOF bound for time-independent background subtraction.");
  this->setPropertySettings("TibTofRangeEnd",
                            std::make_unique<VisibleWhenProperty>("TimeIndepBackgroundSub", IS_EQUAL_TO, "1"));
  this->declareProperty("CorrectKiKf", true, "Apply the ki/kf correction.");
  this->declareProperty(
      std::make_unique<FileProperty>("DetectorVanadiumInputFile", "", FileProperty::OptionalLoad, "_event.nxs"),
      "File containing the sample detector vanadium data to reduce");
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("DetectorVanadiumInputWorkspace", "", Direction::Input,
                                                              PropertyMode::Optional),
                        "Sample detector vanadium workspace to be reduced");
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("DetectorVanadiumInputMonitorWorkspace", "",
                                                              Direction::Input, PropertyMode::Optional),
                        "A monitor workspace associated with the input sample detector vanadium "
                        "workspace.");
  this->declareProperty("SaveProcessedDetVan", false, "Save the processed detector vanadium workspace");
  this->setPropertySettings("SaveProcessedDetVan",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty(
      std::make_unique<FileProperty>("SaveProcDetVanFilename", "", FileProperty::OptionalSave, ".nxs"),
      "Provide a filename for saving the processed detector vanadium.");
  this->declareProperty("UseProcessedDetVan", false,
                        "If true, treat the detector vanadium as processed.\n"
                        "This includes not running diagnostics on the processed data.");
  this->declareProperty("UseBoundsForDetVan", false, "If true, integrate the detector vanadium over a given range.");
  this->declareProperty("DetVanIntRangeLow", EMPTY_DBL(), "Set the lower bound for integrating the detector vanadium.");
  this->setPropertySettings("DetVanIntRangeLow",
                            std::make_unique<VisibleWhenProperty>("UseBoundsForDetVan", IS_EQUAL_TO, "1"));
  this->declareProperty("DetVanIntRangeHigh", EMPTY_DBL(),
                        "Set the upper bound for integrating the detector vanadium.");
  this->setPropertySettings("DetVanIntRangeHigh",
                            std::make_unique<VisibleWhenProperty>("UseBoundsForDetVan", IS_EQUAL_TO, "1"));
  std::vector<std::string> detvanIntRangeUnits;
  detvanIntRangeUnits.emplace_back("Energy");
  detvanIntRangeUnits.emplace_back("Wavelength");
  detvanIntRangeUnits.emplace_back("TOF");
  this->declareProperty("DetVanIntRangeUnits", "Energy", std::make_shared<StringListValidator>(detvanIntRangeUnits),
                        "Options for the units on the detector vanadium integration.");
  this->setPropertySettings("DetVanIntRangeUnits",
                            std::make_unique<VisibleWhenProperty>("UseBoundsForDetVan", IS_EQUAL_TO, "1"));

  // this->setPropertyGroup("FilterBadPulses", dataCorr);
  this->setPropertyGroup("IncidentBeamNormalisation", dataCorr);
  this->setPropertyGroup("MonitorIntRangeLow", dataCorr);
  this->setPropertyGroup("MonitorIntRangeHigh", dataCorr);
  this->setPropertyGroup("TimeIndepBackgroundSub", dataCorr);
  this->setPropertyGroup("TibTofRangeStart", dataCorr);
  this->setPropertyGroup("TibTofRangeEnd", dataCorr);
  this->setPropertyGroup("CorrectKiKf", dataCorr);
  this->setPropertyGroup("DetectorVanadiumInputFile", dataCorr);
  this->setPropertyGroup("DetectorVanadiumInputWorkspace", dataCorr);
  this->setPropertyGroup("DetectorVanadiumInputMonitorWorkspace", dataCorr);
  this->setPropertyGroup("SaveProcessedDetVan", dataCorr);
  this->setPropertyGroup("SaveProcDetVanFilename", dataCorr);
  this->setPropertyGroup("UseProcessedDetVan", dataCorr);
  this->setPropertyGroup("UseBoundsForDetVan", dataCorr);
  this->setPropertyGroup("DetVanIntRangeLow", dataCorr);
  this->setPropertyGroup("DetVanIntRangeHigh", dataCorr);
  this->setPropertyGroup("DetVanIntRangeUnits", dataCorr);

  // Finding bad detectors
  std::string findBadDets = "Finding Bad Detectors";
  this->declareProperty("HighCounts", EMPTY_DBL(), mustBePositive, "Mask detectors above this threshold.");
  this->setPropertySettings("HighCounts",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("LowCounts", EMPTY_DBL(), mustBePositive, "Mask detectors below this threshold.");
  this->setPropertySettings("LowCounts",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("LowOutlier", EMPTY_DBL(), "Lower bound defining outliers as fraction of median value");
  this->setPropertySettings("LowOutlier",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("HighOutlier", EMPTY_DBL(), "Upper bound defining outliers as fraction of median value");
  this->setPropertySettings("HighOutlier",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("MedianTestHigh", EMPTY_DBL(), mustBePositive, "Mask detectors above this threshold.");
  this->setPropertySettings("MedianTestHigh",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("MedianTestLow", EMPTY_DBL(), mustBePositive, "Mask detectors below this threshold.");
  this->setPropertySettings("MedianTestLow",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("MedianTestLevelsUp", 0., mustBePositive, "Mask detectors below this threshold.");
  this->setPropertySettings("MedianTestLevelsUp",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("MedianTestCorrectForSolidAngle", false, "Flag to correct for solid angle efficiency.");
  this->setPropertySettings("MedianTestCorrectForSolidAngle",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty("ErrorBarCriterion", EMPTY_DBL(), mustBePositive,
                        "Some selection criteria for the detector tests.");
  this->setPropertySettings("ErrorBarCriterion",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadiumInputFile", IS_NOT_EQUAL_TO, ""));
  this->declareProperty(
      std::make_unique<FileProperty>("DetectorVanadium2InputFile", "", FileProperty::OptionalLoad, "_event.nxs"),
      "File containing detector vanadium data to compare against");
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("DetectorVanadium2InputWorkspace", "", Direction::Input,
                                                              PropertyMode::Optional),
                        "Detector vanadium workspace to compare against");
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("DetectorVanadium2InputMonitorWorkspace", "",
                                                              Direction::Input, PropertyMode::Optional),
                        "A monitor workspace associated with the input comparison detector "
                        "vanadium workspace.");

  this->declareProperty("DetVanRatioVariation", EMPTY_DBL(), mustBePositive,
                        "Mask detectors if the time variation is above this threshold.");
  this->setPropertySettings("DetVanRatioVariation",
                            std::make_unique<VisibleWhenProperty>("DetectorVanadium2InputFile", IS_NOT_EQUAL_TO, ""));

  this->declareProperty("BackgroundCheck", false, "If true, run a background check on detector vanadium.");
  this->declareProperty("SamBkgMedianTestHigh", EMPTY_DBL(), mustBePositive, "Mask detectors above this threshold.");
  this->setPropertySettings("SamBkgMedianTestHigh",
                            std::make_unique<VisibleWhenProperty>("BackgroundCheck", IS_EQUAL_TO, "1"));
  this->declareProperty("SamBkgMedianTestLow", EMPTY_DBL(), mustBePositive, "Mask detectors below this threshold.");
  this->setPropertySettings("SamBkgMedianTestLow",
                            std::make_unique<VisibleWhenProperty>("BackgroundCheck", IS_EQUAL_TO, "1"));
  this->declareProperty("SamBkgErrorBarCriterion", EMPTY_DBL(), mustBePositive,
                        "Some selection criteria for the detector tests.");
  this->setPropertySettings("SamBkgErrorBarCriterion",
                            std::make_unique<VisibleWhenProperty>("BackgroundCheck", IS_EQUAL_TO, "1"));
  this->declareProperty("BackgroundTofStart", EMPTY_DBL(), mustBePositive, "Start TOF for the background check.");
  this->setPropertySettings("BackgroundTofStart",
                            std::make_unique<VisibleWhenProperty>("BackgroundCheck", IS_EQUAL_TO, "1"));
  this->declareProperty("BackgroundTofEnd", EMPTY_DBL(), mustBePositive, "End TOF for the background check.");
  this->setPropertySettings("BackgroundTofEnd",
                            std::make_unique<VisibleWhenProperty>("BackgroundCheck", IS_EQUAL_TO, "1"));
  this->declareProperty("RejectZeroBackground", false, "If true, check the background region for anomolies.");
  this->declareProperty("PsdBleed", false, "If true, perform a PSD bleed test.");
  this->declareProperty("MaxFramerate", EMPTY_DBL(), "The maximum framerate to check.");
  this->setPropertySettings("MaxFramerate", std::make_unique<VisibleWhenProperty>("PsdBleed", IS_EQUAL_TO, "1"));
  this->declareProperty("IgnoredPixels", EMPTY_DBL(), "A list of pixels to ignore in the calculations.");
  this->setPropertySettings("IgnoredPixels", std::make_unique<VisibleWhenProperty>("PsdBleed", IS_EQUAL_TO, "1"));

  this->setPropertyGroup("HighCounts", findBadDets);
  this->setPropertyGroup("LowCounts", findBadDets);
  this->setPropertyGroup("LowOutlier", findBadDets);
  this->setPropertyGroup("HighOutlier", findBadDets);
  this->setPropertyGroup("MedianTestHigh", findBadDets);
  this->setPropertyGroup("MedianTestLow", findBadDets);
  this->setPropertyGroup("MedianTestLevelsUp", findBadDets);
  this->setPropertyGroup("MedianTestCorrectForSolidAngle", findBadDets);
  this->setPropertyGroup("ErrorBarCriterion", findBadDets);
  this->setPropertyGroup("DetectorVanadium2InputFile", findBadDets);
  this->setPropertyGroup("DetectorVanadium2InputWorkspace", findBadDets);
  this->setPropertyGroup("DetectorVanadium2InputMonitorWorkspace", findBadDets);
  this->setPropertyGroup("DetVanRatioVariation", findBadDets);
  this->setPropertyGroup("BackgroundCheck", findBadDets);
  this->setPropertyGroup("SamBkgMedianTestHigh", findBadDets);
  this->setPropertyGroup("SamBkgMedianTestLow", findBadDets);
  this->setPropertyGroup("SamBkgErrorBarCriterion", findBadDets);
  this->setPropertyGroup("BackgroundTofStart", findBadDets);
  this->setPropertyGroup("BackgroundTofEnd", findBadDets);
  this->setPropertyGroup("RejectZeroBackground", findBadDets);
  this->setPropertyGroup("PsdBleed", findBadDets);
  this->setPropertyGroup("MaxFramerate", findBadDets);
  this->setPropertyGroup("IgnoredPixels", findBadDets);

  // Absolute units correction
  std::string absUnitsCorr = "Absolute Units Correction";
  this->declareProperty("DoAbsoluteUnits", false, "If true, perform an absolute units normalisation.");
  this->declareProperty(std::make_unique<FileProperty>("AbsUnitsSampleInputFile", "", FileProperty::OptionalLoad),
                        "The sample (vanadium) file used in the absolute units normalisation.");
  this->setPropertySettings("AbsUnitsSampleInputFile",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("AbsUnitsSampleInputWorkspace", "", Direction::Input,
                                                              PropertyMode::Optional),
                        "The sample (vanadium) workspace for absolute units normalisation.");
  this->setPropertySettings("AbsUnitsSampleInputWorkspace",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("AbsUnitsSampleInputMonitorWorkspace", "",
                                                              Direction::Input, PropertyMode::Optional),
                        "A monitor workspace associated with the input absolute units sample "
                        "workspace.");
  this->setPropertySettings("AbsUnitsSampleInputMonitorWorkspace",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsGroupingFile", "", "Grouping file for absolute units normalisation.");
  this->setPropertySettings("AbsUnitsGroupingFile",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty(
      std::make_unique<FileProperty>("AbsUnitsDetectorVanadiumInputFile", "", FileProperty::OptionalLoad),
      "The detector vanadium file used in the absolute units normalisation.");
  this->setPropertySettings("AbsUnitsDetectorVanadiumInputFile",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("AbsUnitsDetectorVanadiumInputWorkspace", "",
                                                              Direction::Input, PropertyMode::Optional),
                        "The detector vanadium workspace for absolute units normalisation.");
  this->setPropertySettings("AbsUnitsDetectorVanadiumInputWorkspace",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty(std::make_unique<WorkspaceProperty<>>("AbsUnitsDetectorVanadiumInputMonitorWorkspace", "",
                                                              Direction::Input, PropertyMode::Optional),
                        "A monitor workspace associated with the input absolute units sample "
                        "detector vanadium workspace.");
  this->setPropertySettings("AbsUnitsDetectorVanadiumInputMonitorWorkspace",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsIncidentEnergy", EMPTY_DBL(), mustBePositive,
                        "The incident energy for the vanadium sample.");
  this->setPropertySettings("AbsUnitsIncidentEnergy",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsMinimumEnergy", EMPTY_DBL(), "The minimum energy for the integration range.");
  this->setPropertySettings("AbsUnitsMinimumEnergy",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsMaximumEnergy", EMPTY_DBL(), "The maximum energy for the integration range.");
  this->setPropertySettings("AbsUnitsMaximumEnergy",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("VanadiumMass", EMPTY_DBL(), "The mass of vanadium.");
  this->setPropertySettings("VanadiumMass", std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("SampleMass", 1.0, "The mass of sample.");
  this->setPropertySettings("SampleMass", std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("SampleRmm", 1.0, "The rmm of sample.");
  this->setPropertySettings("SampleRmm", std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsLowOutlier", EMPTY_DBL(), "Lower bound defining outliers as fraction of median value");
  this->setPropertySettings("AbsUnitsLowOutlier",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsHighOutlier", EMPTY_DBL(),
                        "Upper bound defining outliers as fraction of median value");
  this->setPropertySettings("AbsUnitsHighOutlier",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsMedianTestHigh", EMPTY_DBL(), mustBePositive, "Mask detectors above this threshold.");
  this->setPropertySettings("AbsUnitsMedianTestHigh",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsMedianTestLow", EMPTY_DBL(), mustBePositive, "Mask detectors below this threshold.");
  this->setPropertySettings("AbsUnitsMedianTestLow",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));
  this->declareProperty("AbsUnitsErrorBarCriterion", EMPTY_DBL(), mustBePositive,
                        "Some selection criteria for the detector tests.");
  this->setPropertySettings("AbsUnitsErrorBarCriterion",
                            std::make_unique<VisibleWhenProperty>("DoAbsoluteUnits", IS_EQUAL_TO, "1"));

  this->setPropertyGroup("DoAbsoluteUnits", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsSampleInputFile", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsSampleInputWorkspace", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsSampleInputMonitorWorkspace", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsGroupingFile", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsDetectorVanadiumInputFile", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsDetectorVanadiumInputWorkspace", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsDetectorVanadiumInputMonitorWorkspace", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsIncidentEnergy", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsMinimumEnergy", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsMaximumEnergy", absUnitsCorr);
  this->setPropertyGroup("VanadiumMass", absUnitsCorr);
  this->setPropertyGroup("SampleMass", absUnitsCorr);
  this->setPropertyGroup("SampleRmm", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsLowOutlier", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsHighOutlier", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsMedianTestHigh", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsMedianTestLow", absUnitsCorr);
  this->setPropertyGroup("AbsUnitsErrorBarCriterion", absUnitsCorr);

  // Powder data conversion
  std::string powder = "Powder Data Conversion";
  this->declareProperty("DoPowderDataConversion", false, "Flag to switch on converting DeltaE to SQW.");
  this->declareProperty(
      std::make_unique<ArrayProperty<double>>("PowderMomTransferRange", std::make_shared<RebinParamsValidator>(true)),
      "A comma separated list of first bin boundary, width, last bin "
      "boundary.\n"
      "Negative width value indicates logarithmic binning.");
  this->setPropertySettings("PowderMomTransferRange",
                            std::make_unique<VisibleWhenProperty>("DoPowderDataConversion", IS_EQUAL_TO, "1"));
  this->declareProperty("SavePowderNexusFile", true, "Flag to use to save a processed NeXus file for powder data.");
  this->setPropertySettings("SavePowderNexusFile",
                            std::make_unique<VisibleWhenProperty>("DoPowderDataConversion", IS_EQUAL_TO, "1"));
  this->declareProperty(
      std::make_unique<FileProperty>("SavePowderNexusFilename", "", FileProperty::OptionalSave, ".nxs"),
      "Provide a filename for saving the processed powder data.");
  this->setPropertySettings("SavePowderNexusFilename",
                            std::make_unique<VisibleWhenProperty>("DoPowderDataConversion", IS_EQUAL_TO, "1"));

  this->setPropertyGroup("DoPowderDataConversion", powder);
  this->setPropertyGroup("PowderMomTransferRange", powder);
  this->setPropertyGroup("SavePowderNexusFile", powder);
  this->setPropertyGroup("SavePowderNexusFilename", powder);

  // Common to PD and SC

  this->declareProperty(std::make_unique<WorkspaceProperty<>>("OutputWorkspace", "", Direction::Output),
                        "Provide a name for the output workspace.");
  this->declareProperty("ReductionProperties", "__dgs_reduction_properties", Direction::Output);
}

/**
 * Create a workspace by either loading a file or using an existing
 * workspace.
 */
Workspace_sptr DgsReduction::loadInputData(const std::string &prop, const bool mustLoad) {
  g_log.debug() << "MustLoad = " << mustLoad << '\n';
  Workspace_sptr inputWS;

  const std::string inFileProp = prop + "InputFile";
  const std::string inWsProp = prop + "InputWorkspace";

  std::string inputData = this->getPropertyValue(inFileProp);
  const std::string inputWSName = this->getPropertyValue(inWsProp);
  if (!inputWSName.empty() && !inputData.empty()) {
    if (mustLoad) {
      std::ostringstream mess;
      mess << "DgsReduction: Either the " << inFileProp << " property or ";
      mess << inWsProp << " property must be provided, NOT BOTH!";
      throw std::runtime_error(mess.str());
    } else {
      return std::shared_ptr<Workspace>();
    }
  } else if (!inputWSName.empty()) {
    inputWS = this->load(inputWSName);
  } else if (!inputData.empty()) {
    const std::string facility = ConfigService::Instance().getFacility().name();
    this->setLoadAlg("Load");
    if ("ISIS" == facility) {
      std::string detCalFileFromAlg = this->getProperty("DetCalFilename");
      std::string detCalFileProperty = prop + "DetCalFilename";
      if (!detCalFileFromAlg.empty()) {
        this->reductionManager->declareProperty(
            std::make_unique<PropertyWithValue<std::string>>(detCalFileProperty, detCalFileFromAlg));
      }
    }

    inputWS = this->load(inputData, true);

    auto smlog = createChildAlgorithm("AddSampleLog");
    smlog->setProperty("Workspace", inputWS);
    smlog->setProperty("LogName", "Filename");
    smlog->setProperty("LogText", inputData);
    smlog->executeAsChildAlg();
  } else {
    if (mustLoad) {
      std::ostringstream mess;
      mess << "DgsReduction: Either the " << inFileProp << " property or ";
      mess << inWsProp << " property must be provided!";
      throw std::runtime_error(mess.str());
    } else {
      return std::shared_ptr<Workspace>();
    }
  }

  return inputWS;
}

MatrixWorkspace_sptr DgsReduction::loadHardMask() {
  const std::string hardMask = this->getProperty("HardMaskFile");
  if (hardMask.empty()) {
    return std::shared_ptr<MatrixWorkspace>();
  } else {
    IAlgorithm_sptr loadMask;
    bool castWorkspace = false;
    if (boost::ends_with(hardMask, ".nxs")) {
      loadMask = this->createChildAlgorithm("Load");
      loadMask->setProperty("Filename", hardMask);
    } else {
      const std::string instName = this->reductionManager->getProperty("InstrumentName");
      loadMask = this->createChildAlgorithm("LoadMask");
      loadMask->setProperty("Instrument", instName);
      loadMask->setProperty("InputFile", hardMask);
      castWorkspace = true;
    }
    loadMask->execute();
    if (castWorkspace) {
      MaskWorkspace_sptr tmp = loadMask->getProperty("OutputWorkspace");
      return std::dynamic_pointer_cast<MatrixWorkspace>(tmp);
    }
    return loadMask->getProperty("OutputWorkspace");
  }
}

MatrixWorkspace_sptr DgsReduction::loadGroupingFile(const std::string &prop) {
  const std::string propName = prop + "GroupingFile";
  const std::string groupFile = this->getProperty(propName);
  if (groupFile.empty()) {
    return std::shared_ptr<MatrixWorkspace>();
  } else {
    try {
      auto loadGrpFile = createChildAlgorithm("LoadDetectorsGroupingFile");
      loadGrpFile->setProperty("InputFile", groupFile);
      loadGrpFile->execute();
      return loadGrpFile->getProperty("OutputWorkspace");
    } catch (...) {
      // This must be an old format grouping file.
      // Set a property to use later.
      g_log.warning() << "Old format grouping file in use.\n";
      this->reductionManager->declareProperty(
          std::make_unique<PropertyWithValue<std::string>>(prop + "OldGroupingFilename", groupFile));
      return std::shared_ptr<MatrixWorkspace>();
    }
  }
}

double DgsReduction::getParameter(const std::string &algParam, const MatrixWorkspace_sptr &ws,
                                  const std::string &altParam) {
  double param = this->getProperty(algParam);
  if (EMPTY_DBL() == param) {
    param = ws->getInstrument()->getNumberParameter(altParam)[0];
  }
  return param;
}

//----------------------------------------------------------------------------------------------
/** Execute the algorithm.
 */
void DgsReduction::exec() {
  // Reduction property manager - don't call getProcessProperties as
  // it will reuse. This needs to create a fresh one every time
  const std::string reductionManagerName = this->getProperty("ReductionProperties");
  if (reductionManagerName.empty()) {
    g_log.error() << "ERROR: Reduction Property Manager name is empty\n";
    return;
  }
  this->reductionManager = std::make_shared<PropertyManager>();
  PropertyManagerDataService::Instance().addOrReplace(reductionManagerName, this->reductionManager);

  // Put all properties except input files/workspaces into property manager.
  const std::vector<Property *> props = this->getProperties();
  for (auto prop : props) {
    if (!boost::contains(prop->name(), "Input")) {
      this->reductionManager->declareProperty(std::unique_ptr<Property>(prop->clone()));
    }
  }

  Progress progress(this, 0.0, 1.0, 7);

  progress.report();

  // Determine the default facility
  const FacilityInfo defaultFacility = ConfigService::Instance().getFacility();

  // Need to load data to get certain bits of information.
  Workspace_sptr sampleWS = this->loadInputData("Sample");
  MatrixWorkspace_sptr WS = std::dynamic_pointer_cast<MatrixWorkspace>(sampleWS);
  this->reductionManager->declareProperty(
      std::make_unique<PropertyWithValue<std::string>>("InstrumentName", WS->getInstrument()->getName()));

  // Check the facility for the loaded file and make sure it's the
  // same as the default.
  const InstrumentInfo info = ConfigService::Instance().getInstrument(WS->getInstrument()->getName());
  if (defaultFacility.name() != info.facility().name()) {
    std::ostringstream mess;
    mess << "Default facility must be set to " << info.facility().name();
    mess << " in order for reduction to work!";
    throw std::runtime_error(mess.str());
  }

  MatrixWorkspace_sptr sampleMonWS = this->getProperty("SampleInputMonitorWorkspace");

  const bool showIntermedWS = this->getProperty("ShowIntermediateWorkspaces");

  std::string outputWsName = this->getPropertyValue("OutputWorkspace");
  if (boost::ends_with(outputWsName, "_spe")) {
    boost::erase_all(outputWsName, "_spe");
  }

  progress.report("Loading hard mask...");

  // Load the hard mask if available
  MatrixWorkspace_sptr hardMaskWS = this->loadHardMask();
  if (hardMaskWS && showIntermedWS) {
    std::string hardMaskName = outputWsName + "_hardmask";
    this->declareProperty(std::make_unique<WorkspaceProperty<>>("ReductionHardMask", hardMaskName, Direction::Output));
    this->setProperty("ReductionHardMask", hardMaskWS);
  }

  progress.report("Loading grouping file...");
  // Load the grouping file if available
  MatrixWorkspace_sptr groupingWS = this->loadGroupingFile("");
  if (groupingWS && showIntermedWS) {
    std::string groupName = outputWsName + "_grouping";
    this->declareProperty(std::make_unique<WorkspaceProperty<>>("ReductionGrouping", groupName, Direction::Output));
    this->setProperty("ReductionGrouping", groupingWS);
  }

  // This will be diagnostic mask if DgsDiagnose is run and hard mask if not.
  MatrixWorkspace_sptr maskWS;

  // Process the sample detector vanadium if present
  Workspace_sptr detVanWS = this->loadInputData("DetectorVanadium", false);
  MatrixWorkspace_sptr detVanMonWS = this->getProperty("DetectorVanadiumInputMonitorWorkspace");
  bool isProcessedDetVan = this->getProperty("UseProcessedDetVan");
  // Process a comparison detector vanadium if present
  Workspace_sptr detVan2WS = this->loadInputData("DetectorVanadium2", false);
  MatrixWorkspace_sptr detVan2MonWS = this->getProperty("DetectorVanadium2InputMonitorWorkspace");
  IAlgorithm_sptr detVan;
  Workspace_sptr idetVanWS;
  if (detVanWS && !isProcessedDetVan) {
    std::string detVanMaskName = outputWsName + "_diagmask";

    auto diag = createChildAlgorithm("DgsDiagnose");
    diag->setProperty("DetVanWorkspace", detVanWS);
    diag->setProperty("DetVanMonitorWorkspace", detVanMonWS);
    diag->setProperty("DetVanCompWorkspace", detVan2WS);
    diag->setProperty("DetVanCompMonitorWorkspace", detVan2MonWS);
    diag->setProperty("SampleWorkspace", sampleWS);
    diag->setProperty("SampleMonitorWorkspace", sampleMonWS);
    diag->setProperty("HardMaskWorkspace", hardMaskWS);
    diag->setProperty("ReductionProperties", getPropertyValue("ReductionProperties"));
    diag->executeAsChildAlg();
    maskWS = diag->getProperty("OutputWorkspace");

    if (showIntermedWS) {
      this->declareProperty(
          std::make_unique<WorkspaceProperty<>>("SampleDetVanDiagMask", detVanMaskName, Direction::Output));
      this->setProperty("SampleDetVanDiagMask", maskWS);
    }

    detVan = this->createChildAlgorithm("DgsProcessDetectorVanadium");
    detVan->setProperty("InputWorkspace", detVanWS);
    detVan->setProperty("InputMonitorWorkspace", detVanMonWS);
    detVan->setProperty("MaskWorkspace", maskWS);
    std::string idetVanName = outputWsName + "_idetvan";
    detVan->setProperty("ReductionProperties", getPropertyValue("ReductionProperties"));
    detVan->executeAsChildAlg();
    MatrixWorkspace_sptr oWS = detVan->getProperty("OutputWorkspace");
    idetVanWS = std::dynamic_pointer_cast<Workspace>(oWS);

    if (showIntermedWS) {
      this->declareProperty(
          std::make_unique<WorkspaceProperty<>>("IntegratedNormWorkspace", idetVanName, Direction::Output));
      this->setProperty("IntegratedNormWorkspace", idetVanWS);
    }
  } else {
    idetVanWS = detVanWS;
    maskWS = std::dynamic_pointer_cast<MatrixWorkspace>(idetVanWS);
    detVanWS.reset();
  }

  progress.report("Converting to energy transfer...");
  auto etConv = createChildAlgorithm("DgsConvertToEnergyTransfer");
  etConv->setProperty("InputWorkspace", sampleWS);
  etConv->setProperty("InputMonitorWorkspace", sampleMonWS);
  etConv->setProperty("IntegratedDetectorVanadium", idetVanWS);
  const double ei = this->getProperty("IncidentEnergyGuess");
  etConv->setProperty("IncidentEnergyGuess", ei);
  if (!maskWS && hardMaskWS) {
    maskWS = hardMaskWS;
  }
  etConv->setProperty("MaskWorkspace", maskWS);
  if (groupingWS) {
    etConv->setProperty("GroupingWorkspace", groupingWS);
  }
  etConv->setProperty("ReductionProperties", getPropertyValue("ReductionProperties"));
  std::string tibWsName = this->getPropertyValue("OutputWorkspace") + "_tib";
  etConv->executeAsChildAlg();
  MatrixWorkspace_sptr outputWS = etConv->getProperty("OutputWorkspace");
  MatrixWorkspace_sptr tibWS = etConv->getProperty("OutputTibWorkspace");

  if (tibWS && showIntermedWS) {
    this->declareProperty(std::make_unique<WorkspaceProperty<>>("SampleTibWorkspace", tibWsName, Direction::Output));
    this->setProperty("SampleTibWorkspace", tibWS);
  }

  Workspace_sptr absSampleWS = this->loadInputData("AbsUnitsSample", false);

  progress.report("Absolute units reduction...");

  // Perform absolute normalisation if necessary
  if (absSampleWS) {
    std::string absWsName = outputWsName + "_absunits";

    // Collect the other workspaces first.
    MatrixWorkspace_sptr absSampleMonWS = this->getProperty("AbsUnitsSampleInputMonitorWorkspace");
    Workspace_sptr absDetVanWS = this->loadInputData("AbsUnitsDetectorVanadium", false);
    MatrixWorkspace_sptr absDetVanMonWS = this->getProperty("AbsUnitsDetectorVanadiumInputMonitorWorkspace");
    MatrixWorkspace_sptr absGroupingWS = this->loadGroupingFile("AbsUnits");

    // Run the absolute normalisation reduction
    auto absUnitsRed = createChildAlgorithm("DgsAbsoluteUnitsReduction");
    absUnitsRed->setProperty("InputWorkspace", absSampleWS);
    absUnitsRed->setProperty("InputMonitorWorkspace", absSampleMonWS);
    absUnitsRed->setProperty("DetectorVanadiumWorkspace", absDetVanWS);
    absUnitsRed->setProperty("DetectorVanadiumMonitorWorkspace", absDetVanMonWS);
    absUnitsRed->setProperty("GroupingWorkspace", absGroupingWS);
    absUnitsRed->setProperty("MaskWorkspace", maskWS);
    absUnitsRed->setProperty("ReductionProperties", getPropertyValue("ReductionProperties"));
    absUnitsRed->executeAsChildAlg();
    MatrixWorkspace_sptr absUnitsWS = absUnitsRed->getProperty("OutputWorkspace");
    //!!! There is Property outputMaskWorkspace to get masks? It looks like one
    // is using wrong property for masks
    MatrixWorkspace_sptr absMaskWS = absUnitsRed->getProperty("OutputWorkspace");

    auto mask = createChildAlgorithm("MaskDetectors");
    mask->setProperty("Workspace", outputWS);
    mask->setProperty("MaskedWorkspace", absMaskWS);
    mask->executeAsChildAlg();
    outputWS = mask->getProperty("Workspace");

    // Do absolute normalisation
    outputWS = divide(outputWS, absUnitsWS);

    if (showIntermedWS) {
      this->declareProperty(std::make_unique<WorkspaceProperty<>>("AbsUnitsWorkspace", absWsName, Direction::Output));
      this->setProperty("AbsUnitsWorkspace", absUnitsWS);
      this->declareProperty(std::make_unique<WorkspaceProperty<>>(
          "AbsUnitsDiagMask", outputWsName + "_absunits_diagmask", Direction::Output));
      this->setProperty("AbsUnitsDiagMask", absMaskWS);
    }
  }

  progress.report();

  // Convert from DeltaE to powder S(Q,W)
  const bool doPowderConvert = this->getProperty("DoPowderDataConversion");
  if (doPowderConvert) {
    g_log.notice() << "Converting to powder S(Q,W)\n";
    // Collect information
    std::string sqwWsName = outputWsName + "_pd_sqw";
    std::vector<double> qBinning = this->getProperty("PowderMomTransferRange");
    const auto initialEnergy = outputWS->run().getPropertyValueAsType<double>("Ei");

    auto sofqw = createChildAlgorithm("SofQW3");
    sofqw->setProperty("InputWorkspace", outputWS);
    sofqw->setProperty("QAxisBinning", qBinning);
    sofqw->setProperty("EMode", "Direct");
    sofqw->setProperty("EFixed", initialEnergy);
    sofqw->executeAsChildAlg();
    MatrixWorkspace_sptr sqwWS = sofqw->getProperty("OutputWorkspace");
    this->declareProperty(std::make_unique<WorkspaceProperty<>>("PowderSqwWorkspace", sqwWsName, Direction::Output));
    this->setProperty("PowderSqwWorkspace", sqwWS);

    const bool saveProcNexus = this->getProperty("SavePowderNexusFile");
    if (saveProcNexus) {
      std::string saveProcNexusFilename = this->getProperty("SavePowderNexusFilename");
      if (saveProcNexusFilename.empty()) {
        saveProcNexusFilename = sqwWsName + ".nxs";
      }
      auto saveNxs = createChildAlgorithm("SaveNexus");
      saveNxs->setProperty("InputWorkspace", sqwWS);
      saveNxs->setProperty("Filename", saveProcNexusFilename);
      saveNxs->executeAsChildAlg();
    }
  }

  progress.report();

  this->setProperty("OutputWorkspace", outputWS);
}

} // namespace Mantid::WorkflowAlgorithms