PreprocessDetectorsToMD.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 "MantidMDAlgorithms/PreprocessDetectorsToMD.h"
#include "MantidAPI/AnalysisDataService.h"
#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/NumericAxis.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/SpectrumInfo.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ComponentInfo.h"
#include "MantidGeometry/Instrument/DetectorInfo.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/PropertyWithValue.h"
 
using namespace Mantid;
using namespace Mantid::API;
using namespace Mantid::DataObjects;
 
namespace Mantid::MDAlgorithms {
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(PreprocessDetectorsToMD)
 
PreprocessDetectorsToMD::PreprocessDetectorsToMD() : m_getEFixed(false), m_getIsMasked(false) {}
 
void PreprocessDetectorsToMD::init() {
  auto ws_valid = std::make_shared<Kernel::CompositeValidator>();
  // workspace needs instrument
  ws_valid->add<API::InstrumentValidator>();
  // the validator which checks if the workspace has axis and any units
  // ws_valid->add<API::WorkspaceUnitValidator>("");
 
  declareProperty(std::make_unique<WorkspaceProperty<API::MatrixWorkspace>>("InputWorkspace", "",
                                                                            Kernel::Direction::Input, ws_valid),
                  "Name of an input Matrix Workspace with instrument.");
 
  declareProperty(std::make_unique<WorkspaceProperty<TableWorkspace>>("OutputWorkspace", "", Kernel::Direction::Output),
                  "Name of the output Table workspace with pre-processed "
                  "detectors data. If the workspace exists, it will be "
                  "replaced.");
 
  declareProperty(std::make_unique<Kernel::PropertyWithValue<bool>>("GetMaskState", true, Kernel::Direction::Input),
                  "Returns masked state of the detectors. If this option is "
                  "false, the masked detectors are just dropped from the "
                  "resulting workspace and spectra-to detectors map has to be "
                  "used to analyse the spectra. This is temporary parameter "
                  "and logic necessary until Mantid masks signal by 0 rather "
                  "then NaN.");
 
  declareProperty(std::make_unique<Kernel::PropertyWithValue<bool>>("UpdateMasksInfo", false, Kernel::Direction::Input),
                  "If target workspace already exists as the result of "
                  "previous deployment of this algorithm, the algorithm just "
                  "updated masks states column instead of calculating the "
                  "whole target workspace. The target workspace has to be "
                  "appropriate for the source workspace This is temporary "
                  "parameter and logic necessary until Mantid masks signal by "
                  "0 rather then NaN.");
 
  declareProperty(std::make_unique<Kernel::PropertyWithValue<bool>>("GetEFixed", false, Kernel::Direction::Input),
                  "This option makes sense for Indirect instrument, where each "
                  "detector can have its own energy, defined by correspondent "
                  "crystal-analyzer position.\n"
                  "If this option is selected for other instrument types, the "
                  "value of eFixed is taken from workspace property "
                  "Ei"
                  " or "
                  "eFixed"
                  " if "
                  "Ei"
                  "\n"
                  "is missing and is set to NaN if no such properties are "
                  "defined on the input workspace.");
 
  // declareProperty(new
  // PropertyWithValue<bool>("FakeDetectors",false,Kernel::Direction::Input),
  //  "If selected, generates table workspace with fake detectors, all allocated
  //  in a monitor position.\n"
  //  "Number of detectors is equal to number of spectra and real detectors, if
  //  present are ignored ");
}
 
//----------------------------------------------------------------------------------------------
/* Execute the algorithm.   */
void PreprocessDetectorsToMD::exec() {
  // -------- get Input workspace
  MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
 
  // verify if we want to preprocess real workspace or just update the state of
  // workspace masks
  DataObjects::TableWorkspace_sptr targWS;
  bool updateMasks(false);
  if (this->getProperty("GetMaskState") && this->getProperty("UpdateMasksInfo")) {
    std::string wsName = this->getPointerToProperty("OutputWorkspace")->value();
    if (API::AnalysisDataService::Instance().doesExist(wsName)) {
      targWS =
          std::dynamic_pointer_cast<DataObjects::TableWorkspace>(API::AnalysisDataService::Instance().retrieve(wsName));
      if (targWS) {
        auto *pMasksArray = targWS->getColDataArray<int>("detMask");
        if (pMasksArray)
          updateMasks = true;
        // was this workspace calculated without eFixed and now we need one?
        if (this->getProperty("GetEFixed") && !targWS->getColDataArray<float>("eFixed"))
          updateMasks = false;
      }
    }
  }
 
  if (updateMasks) // just update masks
    this->updateMasksState(inputWS, targWS);
  else // -------- build target workspace:
    targWS = createTableWorkspace(inputWS);
 
  if (this->isDetInfoLost(inputWS))
    this->buildFakeDetectorsPositions(inputWS, targWS);
  else // process real detectors positions
    this->processDetectorsPositions(inputWS, targWS);
 
  // set up target workspace
  setProperty("OutputWorkspace", targWS);
}
 
std::shared_ptr<DataObjects::TableWorkspace>
PreprocessDetectorsToMD::createTableWorkspace(const API::MatrixWorkspace_const_sptr &inputWS) {
  const size_t nHist = inputWS->getNumberHistograms();
 
  // set the target workspace
  auto targWS = std::make_shared<TableWorkspace>(nHist);
  // detectors positions
  targWS->addColumn("V3D", "DetDirections");
  // sample-detector distance;
  targWS->addColumn("double", "L2");
  // Diffraction angle
  targWS->addColumn("double", "TwoTheta");
  targWS->addColumn("double", "Azimuthal");
  // the detector ID;
  targWS->addColumn("int", "DetectorID");
  // stores spectra index which corresponds to a valid detector index;
  targWS->addColumn("size_t", "detIDMap");
  // stores detector index which corresponds to the workspace index;
  targWS->addColumn("size_t", "spec2detMap");
 
  m_getIsMasked = this->getProperty("GetMaskState");
  if (m_getIsMasked) // as bool is presented in vectors as a class, we are using
                     // int instead of bool
    targWS->addColumn("int", "detMask");
 
  // check if one wants to obtain detector's efixed"
  m_getEFixed = this->getProperty("GetEFixed");
  if (m_getEFixed)
    targWS->addColumn("float", "eFixed");
  targWS->addColumn("double", "DIFA");
  targWS->addColumn("double", "DIFC");
  targWS->addColumn("double", "TZERO");
 
  // will see about that
  // sin^2(Theta)
  //    std::vector<double>      SinThetaSq;
 
  double Efi = getEi(inputWS);
  targWS->logs()->addProperty<double>("Ei", Efi, true);
 
  return targWS;
}
 
void PreprocessDetectorsToMD::processDetectorsPositions(const API::MatrixWorkspace_const_sptr &inputWS,
                                                        DataObjects::TableWorkspace_sptr &targWS) {
  g_log.information() << "Preprocessing detector locations in a target reciprocal space\n";
  //
  Geometry::Instrument_const_sptr instrument = inputWS->getInstrument();
  Geometry::IComponent_const_sptr source = instrument->getSource();
  Geometry::IComponent_const_sptr sample = instrument->getSample();
  if ((!source) || (!sample)) {
    g_log.error() << " Instrument is not fully defined. Can not identify "
                     "source or sample\n";
    throw Kernel::Exception::InstrumentDefinitionError(
        "Instrument not sufficiently defined: failed to get source and/or "
        "sample");
  }
 
  // L1
  try {
    double L1 = source->getDistance(*sample);
    targWS->logs()->addProperty<double>("L1", L1, true);
    g_log.debug() << "Source-sample distance: " << L1 << '\n';
  } catch (Kernel::Exception::NotFoundError &) {
    throw Kernel::Exception::InstrumentDefinitionError("Unable to calculate source-sample distance for workspace",
                                                       inputWS->getTitle());
  }
  // Instrument name
  std::string InstrName = inputWS->getInstrumentName();
  targWS->logs()->addProperty<std::string>("InstrumentName", InstrName,
                                           true); // "The name which should unique identify current instrument");
  targWS->logs()->addProperty<bool>("FakeDetectors", false, true);
 
  // get access to the workspace memory
  auto &sp2detMap = targWS->getColVector<size_t>("spec2detMap");
  auto &detId = targWS->getColVector<int32_t>("DetectorID");
  auto &detIDMap = targWS->getColVector<size_t>("detIDMap");
  auto &L2 = targWS->getColVector<double>("L2");
  auto &TwoTheta = targWS->getColVector<double>("TwoTheta");
  auto &Azimuthal = targWS->getColVector<double>("Azimuthal");
  auto &detDir = targWS->getColVector<Kernel::V3D>("DetDirections");
  auto &DIFA = targWS->getColVector<double>("DIFA");
  auto &DIFC = targWS->getColVector<double>("DIFC");
  auto &TZERO = targWS->getColVector<double>("TZERO");
 
  // Efixed; do we need one and does one exist?
  auto Efi = targWS->getLogs()->getPropertyValueAsType<double>("Ei");
  float *pEfixedArray(nullptr);
  const auto &componentInfo = inputWS->componentInfo();
  const auto &detectorInfo = inputWS->detectorInfo();
  if (m_getEFixed)
    pEfixedArray = targWS->getColDataArray<float>("eFixed");
 
  // check if one needs to generate masked detectors column.
  int *pMasksArray(nullptr);
  if (m_getIsMasked)
    pMasksArray = targWS->getColDataArray<int>("detMask");
 
  size_t div = 100;
  size_t nHist = targWS->rowCount();
  Mantid::API::Progress theProgress(this, 0.0, 1.0, nHist);
  uint32_t liveDetectorsCount(0);
  const auto &spectrumInfo = inputWS->spectrumInfo();
  for (size_t i = 0; i < nHist; i++) {
    sp2detMap[i] = std::numeric_limits<uint64_t>::quiet_NaN();
    detId[i] = std::numeric_limits<int32_t>::quiet_NaN();
    detIDMap[i] = std::numeric_limits<uint64_t>::quiet_NaN();
    L2[i] = std::numeric_limits<double>::quiet_NaN();
    DIFC[i] = std::numeric_limits<double>::quiet_NaN();
    TwoTheta[i] = std::numeric_limits<double>::quiet_NaN();
    Azimuthal[i] = std::numeric_limits<double>::quiet_NaN();
    //     detMask[i]  = true;
 
    if (!spectrumInfo.hasDetectors(i) || spectrumInfo.isMonitor(i))
      continue;
 
    // if masked detectors state is not used, masked detectors just ignored;
    bool maskDetector = spectrumInfo.isMasked(i);
    if (m_getIsMasked)
      *(pMasksArray + liveDetectorsCount) = maskDetector ? 1 : 0;
    else if (maskDetector)
      continue;
 
    // The first detector, for a spectrum of several
    const auto firstDetIndex = spectrumInfo.firstDetectorIndex(i);
 
    // calculate the requested values;
    sp2detMap[i] = liveDetectorsCount;
    detId[liveDetectorsCount] = int32_t(detectorInfo.detid(firstDetIndex));
    detIDMap[liveDetectorsCount] = i;
    L2[liveDetectorsCount] = spectrumInfo.l2(i);
 
    double polar = spectrumInfo.twoTheta(i);
    double azim = spectrumInfo.phi(i);
    TwoTheta[liveDetectorsCount] = polar;
    Azimuthal[liveDetectorsCount] = azim;
 
    std::vector<int> warningDets;
    auto diffConsts = spectrumInfo.diffractometerConstants(i, warningDets);
    // map will create an entry with zero value if not present already
    DIFA[liveDetectorsCount] = diffConsts[Kernel::UnitParams::difa];
    DIFC[liveDetectorsCount] = diffConsts[Kernel::UnitParams::difc];
    TZERO[liveDetectorsCount] = diffConsts[Kernel::UnitParams::tzero];
 
    double sPhi = sin(polar);
    double ez = cos(polar);
    double ex = sPhi * cos(azim);
    double ey = sPhi * sin(azim);
 
    detDir[liveDetectorsCount].setX(ex);
    detDir[liveDetectorsCount].setY(ey);
    detDir[liveDetectorsCount].setZ(ez);
 
    // double sinTheta=sin(0.5*polar);
    // this->SinThetaSq[liveDetectorsCount]  = sinTheta*sinTheta;
 
    // specific code which should work and makes sense
    // for indirect instrument but may be deployed on any code with Ei property
    // defined;
    if (pEfixedArray) {
      // A spectrum of several detectors has no parameters of its own
      if (spectrumInfo.hasUniqueDetector(i)) {
        try {
          const auto eFixed = componentInfo.getNumberParameter(firstDetIndex, "eFixed");
          if (!eFixed.empty())
            Efi = eFixed.front();
        } catch (std::runtime_error &) {
        }
      }
      // set efixed for each existing detector
      *(pEfixedArray + liveDetectorsCount) = static_cast<float>(Efi);
    }
 
    liveDetectorsCount++;
    if (i % div == 0)
      theProgress.report(i, "Preprocessing detectors");
  }
  targWS->logs()->addProperty<uint32_t>("ActualDetectorsNum", liveDetectorsCount, true);
 
  theProgress.report();
  g_log.information() << "Finished preprocessing detector locations. Found: " << liveDetectorsCount
                      << " detectors out of: " << nHist << " histograms\n";
}
void PreprocessDetectorsToMD::updateMasksState(const API::MatrixWorkspace_const_sptr &inputWS,
                                               DataObjects::TableWorkspace_sptr &targWS) {
  auto *pMasksArray = targWS->getColDataArray<int>("detMask");
  if (!pMasksArray)
    throw std::invalid_argument("target workspace " + targWS->getName() +
                                " does not have defined masks column to update");
 
  size_t nHist = targWS->rowCount();
  const size_t nRows = inputWS->getNumberHistograms();
  if (nHist != nRows)
    throw std::invalid_argument(" source workspace " + inputWS->getName() + " and target workspace " +
                                targWS->getName() + " are inconsistent as have different numner of detectors");
 
  uint32_t liveDetectorsCount(0);
  const auto &spectrumInfo = inputWS->spectrumInfo();
  for (size_t i = 0; i < nHist; i++) {
    if (!spectrumInfo.hasDetectors(i) || spectrumInfo.isMonitor(i))
      continue;
 
    // if masked detectors state is not used, masked detectors just ignored;
    bool maskDetector = spectrumInfo.isMasked(i);
    *(pMasksArray + liveDetectorsCount) = maskDetector ? 1 : 0;
 
    liveDetectorsCount++;
  }
}
 
void PreprocessDetectorsToMD::buildFakeDetectorsPositions(const API::MatrixWorkspace_const_sptr &inputWS,
                                                          DataObjects::TableWorkspace_sptr &targWS) {
  UNUSED_ARG(inputWS);
  // set sample-detector position equal to 1;
  targWS->logs()->addProperty<double>("L1", 1., true);
  //
  targWS->logs()->addProperty<std::string>("InstrumentName", "FakeInstrument", true);
  targWS->logs()->addProperty<bool>("FakeDetectors", true, true);
 
  // get access to the workspace memory
  auto &sp2detMap = targWS->getColVector<size_t>("spec2detMap");
  auto &detId = targWS->getColVector<int32_t>("DetectorID");
  auto &detIDMap = targWS->getColVector<size_t>("detIDMap");
  auto &L2 = targWS->getColVector<double>("L2");
  auto &TwoTheta = targWS->getColVector<double>("TwoTheta");
  auto &Azimuthal = targWS->getColVector<double>("Azimuthal");
  auto &detDir = targWS->getColVector<Kernel::V3D>("DetDirections");
  //    auto &detMask    = targWS->getColVector<bool>("detMask");
 
  size_t nHist = targWS->rowCount();
  targWS->logs()->addProperty<uint32_t>("ActualDetectorsNum", uint32_t(nHist), true);
 
  double polar(0);
  // Loop over the spectra
  for (size_t i = 0; i < nHist; i++) {
    sp2detMap[i] = i;
    detId[i] = static_cast<detid_t>(i);
    detIDMap[i] = i;
    L2[i] = 1;
 
    TwoTheta[i] = polar;
    Azimuthal[i] = 0;
    // this->SinThetaSq[i]= 0;
 
    double ez = 1.;
    double ex = 0.;
    double ey = 0.;
 
    detDir[i].setX(ex);
    detDir[i].setY(ey);
    detDir[i].setZ(ez);
  }
  //
}
 
bool PreprocessDetectorsToMD::isDetInfoLost(const Mantid::API::MatrixWorkspace_const_sptr &inWS2D) const {
  auto const *pYAxis = dynamic_cast<API::NumericAxis const *>(inWS2D->getAxis(1));
  // if this is numeric axis, then the detector's information has been lost:
  return pYAxis != nullptr;
}
 
double PreprocessDetectorsToMD::getEi(const API::MatrixWorkspace_const_sptr &inputWS) const {
  double Efi = std::numeric_limits<double>::quiet_NaN();
 
  // is Ei on workspace properties? (it can be defined for some reason if
  // detectors do not have one, and then it would exist as Ei)
  bool EiFound(false);
  try {
    Efi = inputWS->run().getPropertyValueAsType<double>("Ei");
    EiFound = true;
  } catch (Kernel::Exception::NotFoundError &) {
  }
  // try to get Efixed as property on a workspace, obtained for indirect
  // instrument
  bool eFixedFound(false);
  if (!EiFound) {
    try {
      Efi = inputWS->run().getPropertyValueAsType<double>("eFixed");
      eFixedFound = true;
    } catch (Kernel::Exception::NotFoundError &) {
    }
  }
 
  if (!(EiFound || eFixedFound))
    g_log.debug() << " Ei/eFixed requested but have not been found\n";
 
  return Efi;
}
} // namespace Mantid::MDAlgorithms