CentroidPeaks.cpp

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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidCrystal/CentroidPeaks.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidGeometry/Crystal/EdgePixel.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/ComponentInfo.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidKernel/Unit.h"
#include "MantidKernel/VectorHelper.h"
#include <boost/algorithm/clamp.hpp>
 
using Mantid::DataObjects::PeaksWorkspace;
 
namespace Mantid::Crystal {
 
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(CentroidPeaks)
 
using namespace Mantid::API;
using namespace Mantid::DataObjects;
using namespace Mantid::Geometry;
using namespace Mantid::Kernel;
using namespace Mantid::Crystal;
 
//----------------------------------------------------------------------------------------------
void CentroidPeaks::init() {
  declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("InPeaksWorkspace", "", Direction::Input),
                  "A PeaksWorkspace containing the peaks to centroid.");
 
  declareProperty(std::make_unique<WorkspaceProperty<>>("InputWorkspace", "", Direction::Input),
                  "An input 2D Workspace.");
 
  declareProperty(std::make_unique<PropertyWithValue<int>>("PeakRadius", 10, Direction::Input),
                  "Fixed radius around each peak position in which to calculate the "
                  "centroid.");
 
  declareProperty(std::make_unique<PropertyWithValue<int>>("EdgePixels", 0, Direction::Input),
                  "The number of pixels where peaks are removed at edges. Only "
                  "for instruments with RectangularDetectors. ");
 
  declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("OutPeaksWorkspace", "", Direction::Output),
                  "The output PeaksWorkspace will be a copy of the input PeaksWorkspace "
                  "with the peaks' positions modified by the new found centroids.");
}
 
//----------------------------------------------------------------------------------------------
void CentroidPeaks::integrate() {
 
  Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS = getProperty("InPeaksWorkspace");
 
  Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("OutPeaksWorkspace");
  if (peakWS != inPeakWS)
    peakWS = inPeakWS->clone();
 
  int PeakRadius = getProperty("PeakRadius");
 
  int MinPeaks = -1;
  int MaxPeaks = -1;
  size_t Numberwi = inWS->getNumberHistograms();
  int NumberPeaks = peakWS->getNumberPeaks();
  for (int i = 0; i < NumberPeaks; ++i) {
    Peak &peak = peakWS->getPeaks()[i];
    int pixelID = peak.getDetectorID();
 
    // Find the workspace index for this detector ID
    if (wi_to_detid_map.find(pixelID) != wi_to_detid_map.end()) {
      size_t wi = wi_to_detid_map[pixelID];
      if (MinPeaks == -1 && peak.getRunNumber() == inWS->getRunNumber() && wi < Numberwi)
        MinPeaks = i;
      if (peak.getRunNumber() == inWS->getRunNumber() && wi < Numberwi)
        MaxPeaks = i;
    }
  }
 
  const auto inBlocksize = static_cast<int>(inWS->blocksize());
  int Edge = getProperty("EdgePixels");
  Progress prog(this, MinPeaks, 1.0, MaxPeaks);
  PARALLEL_FOR_IF(Kernel::threadSafe(*inWS, *peakWS))
  for (int i = MinPeaks; i <= MaxPeaks; ++i) {
    PARALLEL_START_INTERRUPT_REGION
    // Get a direct ref to that peak.
    auto &peak = peakWS->getPeak(i);
    int col = peak.getCol();
    int row = peak.getRow();
    int pixelID = peak.getDetectorID();
    auto detidIterator = wi_to_detid_map.find(pixelID);
    if (detidIterator == wi_to_detid_map.end()) {
      continue;
    }
    size_t workspaceIndex = detidIterator->second;
    double TOFPeakd = peak.getTOF();
    const auto &X = inWS->x(workspaceIndex);
    int chan = Kernel::VectorHelper::getBinIndex(X.rawData(), TOFPeakd);
    std::string bankName = peak.getBankName();
    int nCols = 0, nRows = 0;
    sizeBanks(bankName, nCols, nRows);
 
    double intensity = 0.0;
    double chancentroid = 0.0;
 
    int chanstart = std::max(0, chan - PeakRadius);
    int chanend = std::min(static_cast<int>(X.size()), chan + PeakRadius);
    double rowcentroid = 0.0;
    int rowstart = std::max(0, row - PeakRadius);
    int rowend = std::min(nRows - 1, row + PeakRadius);
    double colcentroid = 0.0;
    int colstart = std::max(0, col - PeakRadius);
    int colend = std::min(nCols - 1, col + PeakRadius);
    for (int ichan = chanstart; ichan <= chanend; ++ichan) {
      for (int irow = rowstart; irow <= rowend; ++irow) {
        for (int icol = colstart; icol <= colend; ++icol) {
          if (edgePixel(inst, bankName, icol, irow, Edge))
            continue;
          const auto it = wi_to_detid_map.find(findPixelID(bankName, icol, irow));
          if (it == wi_to_detid_map.end())
            continue;
 
          const auto &histogram = inWS->y(it->second);
 
          intensity += histogram[ichan];
          rowcentroid += irow * histogram[ichan];
          colcentroid += icol * histogram[ichan];
          chancentroid += ichan * histogram[ichan];
        }
      }
    }
    // Set pixelID to change row and col
    row = (int)std::lround(rowcentroid / intensity);
    boost::algorithm::clamp(row, 0, nRows - 1);
    col = (int)std::lround(colcentroid / intensity);
    boost::algorithm::clamp(col, 0, nCols - 1);
    chan = (int)std::lround(chancentroid / intensity);
    boost::algorithm::clamp(chan, 0, inBlocksize);
 
    // Set wavelength to change tof for peak object
    if (!edgePixel(inst, bankName, col, row, Edge)) {
      peak.setDetectorID(findPixelID(bankName, col, row));
      detidIterator = wi_to_detid_map.find(findPixelID(bankName, col, row));
      workspaceIndex = (detidIterator->second);
      Mantid::Kernel::Units::Wavelength wl;
      std::vector<double> timeflight;
      timeflight.emplace_back(inWS->x(workspaceIndex)[chan]);
      double scattering = peak.getScattering();
      double L1 = peak.getL1();
      double L2 = peak.getL2();
      wl.fromTOF(timeflight, timeflight, L1, 0, {{UnitParams::l2, L2}, {UnitParams::twoTheta, scattering}});
      const double lambda = timeflight[0];
      timeflight.clear();
 
      peak.setWavelength(lambda);
      peak.setBinCount(inWS->y(workspaceIndex)[chan]);
    }
    PARALLEL_END_INTERRUPT_REGION
  }
  PARALLEL_CHECK_INTERRUPT_REGION
  removeEdgePeaks(*peakWS);
 
  // Save the output
  setProperty("OutPeaksWorkspace", peakWS);
}
 
//----------------------------------------------------------------------------------------------
void CentroidPeaks::integrateEvent() {
 
  Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS = getProperty("InPeaksWorkspace");
 
  Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("OutPeaksWorkspace");
  if (peakWS != inPeakWS)
    peakWS = inPeakWS->clone();
 
  int PeakRadius = getProperty("PeakRadius");
 
  int MinPeaks = -1;
  int MaxPeaks = -1;
  size_t Numberwi = inWS->getNumberHistograms();
  int NumberPeaks = peakWS->getNumberPeaks();
 
  for (int i = 0; i < NumberPeaks; ++i) {
    auto &peak = peakWS->getPeak(i);
    int pixelID = peak.getDetectorID();
 
    // Find the workspace index for this detector ID
    if (wi_to_detid_map.find(pixelID) != wi_to_detid_map.end()) {
      size_t wi = wi_to_detid_map[pixelID];
      if (MinPeaks == -1 && peak.getRunNumber() == inWS->getRunNumber() && wi < Numberwi)
        MinPeaks = i;
      if (peak.getRunNumber() == inWS->getRunNumber() && wi < Numberwi)
        MaxPeaks = i;
    }
  }
 
  int Edge = getProperty("EdgePixels");
  Progress prog(this, MinPeaks, 1.0, MaxPeaks);
  PARALLEL_FOR_IF(Kernel::threadSafe(*inWS, *peakWS))
  for (int i = MinPeaks; i <= MaxPeaks; ++i) {
    PARALLEL_START_INTERRUPT_REGION
    // Get a direct ref to that peak.
    auto &peak = peakWS->getPeak(i);
    int col = peak.getCol();
    int row = peak.getRow();
    double TOFPeakd = peak.getTOF();
    std::string bankName = peak.getBankName();
    int nCols = 0, nRows = 0;
    sizeBanks(bankName, nCols, nRows);
 
    double intensity = 0.0;
    double tofcentroid = 0.0;
    if (edgePixel(inst, bankName, col, row, Edge))
      continue;
 
    double tofstart = TOFPeakd * std::pow(1.004, -PeakRadius);
    double tofend = TOFPeakd * std::pow(1.004, PeakRadius);
    double rowcentroid = 0.0;
    int rowstart = std::max(0, row - PeakRadius);
    int rowend = std::min(nRows - 1, row + PeakRadius);
    double colcentroid = 0.0;
    int colstart = std::max(0, col - PeakRadius);
    int colend = std::min(nCols - 1, col + PeakRadius);
    for (int irow = rowstart; irow <= rowend; ++irow) {
      for (int icol = colstart; icol <= colend; ++icol) {
        if (edgePixel(inst, bankName, icol, irow, Edge))
          continue;
        auto it1 = wi_to_detid_map.find(findPixelID(bankName, icol, irow));
        size_t workspaceIndex = (it1->second);
        EventList el = eventW->getSpectrum(workspaceIndex);
        el.switchTo(WEIGHTED_NOTIME);
        std::vector<WeightedEventNoTime> events = el.getWeightedEventsNoTime();
 
        // Check for events in tof range
        for (const auto &event : events) {
          double tof = event.tof();
          if (tof > tofstart && tof < tofend) {
            double weight = event.weight();
            intensity += weight;
            rowcentroid += irow * weight;
            colcentroid += icol * weight;
            tofcentroid += tof * weight;
          }
        }
      }
    }
    // Set pixelID to change row and col
    row = int(rowcentroid / intensity);
    boost::algorithm::clamp(row, 0, nRows - 1);
    col = int(colcentroid / intensity);
    boost::algorithm::clamp(col, 0, nCols - 1);
    if (!edgePixel(inst, bankName, col, row, Edge)) {
      peak.setDetectorID(findPixelID(bankName, col, row));
 
      // Set wavelength to change tof for peak object
      double tof = tofcentroid / intensity;
      Mantid::Kernel::Units::Wavelength wl;
      std::vector<double> timeflight;
      timeflight.emplace_back(tof);
      double scattering = peak.getScattering();
      double L1 = peak.getL1();
      double L2 = peak.getL2();
      wl.fromTOF(timeflight, timeflight, L1, 0, {{UnitParams::l2, L2}, {UnitParams::twoTheta, scattering}});
      const double lambda = timeflight[0];
      timeflight.clear();
 
      peak.setWavelength(lambda);
      peak.setBinCount(intensity);
    }
    PARALLEL_END_INTERRUPT_REGION
  }
  PARALLEL_CHECK_INTERRUPT_REGION
  removeEdgePeaks(*peakWS);
 
  // Save the output
  setProperty("OutPeaksWorkspace", peakWS);
}
 
//----------------------------------------------------------------------------------------------
void CentroidPeaks::exec() {
  inWS = getProperty("InputWorkspace");
  inst = inWS->getInstrument();
  // For quickly looking up workspace index from det id
  wi_to_detid_map = inWS->getDetectorIDToWorkspaceIndexMap();
 
  eventW = std::dynamic_pointer_cast<const EventWorkspace>(inWS);
  if (eventW) {
    eventW->sortAll(TOF_SORT, nullptr);
    this->integrateEvent();
  } else {
    this->integrate();
  }
}
 
int CentroidPeaks::findPixelID(const std::string &bankName, int col, int row) {
  std::shared_ptr<const IComponent> parent = inst->getComponentByName(bankName);
  if (parent->type() == "RectangularDetector") {
    std::shared_ptr<const RectangularDetector> RDet = std::dynamic_pointer_cast<const RectangularDetector>(parent);
 
    std::shared_ptr<Detector> pixel = RDet->getAtXY(col, row);
    return pixel->getID();
  } else {
    std::string bankName0 = bankName;
    // Only works for WISH
    bankName0.erase(0, 4);
    std::ostringstream pixelString;
    pixelString << inst->getName() << "/" << bankName0 << "/" << bankName << "/tube" << std::setw(3)
                << std::setfill('0') << col << "/pixel" << std::setw(4) << std::setfill('0') << row;
    std::shared_ptr<const Geometry::IComponent> component = inst->getComponentByName(pixelString.str());
    std::shared_ptr<const Detector> pixel = std::dynamic_pointer_cast<const Detector>(component);
    return pixel->getID();
  }
}
 
void CentroidPeaks::removeEdgePeaks(Mantid::DataObjects::PeaksWorkspace &peakWS) {
  int Edge = getProperty("EdgePixels");
  std::vector<int> badPeaks;
  size_t numPeaks = peakWS.getNumberPeaks();
  for (int i = 0; i < static_cast<int>(numPeaks); i++) {
    // Get a direct ref to that peak.
    const auto &peak = peakWS.getPeak(i);
    int col = peak.getCol();
    int row = peak.getRow();
    const std::string &bankName = peak.getBankName();
 
    if (edgePixel(inst, bankName, col, row, Edge)) {
      badPeaks.emplace_back(i);
    }
  }
  peakWS.removePeaks(std::move(badPeaks));
}
 
void CentroidPeaks::sizeBanks(const std::string &bankName, int &nCols, int &nRows) {
  if (bankName == "None")
    return;
  ExperimentInfo expInfo;
  expInfo.setInstrument(inst);
  const auto &compInfo = expInfo.componentInfo();
 
  // Get a single bank
  auto bank = inst->getComponentByName(bankName);
  auto bankID = bank->getComponentID();
  auto allBankDetectorIndexes = compInfo.detectorsInSubtree(compInfo.indexOf(bankID));
 
  nRows = static_cast<int>(compInfo.componentsInSubtree(compInfo.indexOf(bankID)).size() -
                           allBankDetectorIndexes.size() - 1);
  nCols = static_cast<int>(allBankDetectorIndexes.size()) / nRows;
 
  if (nCols * nRows != static_cast<int>(allBankDetectorIndexes.size())) {
    // Need grandchild instead of child
    nRows = static_cast<int>(compInfo.componentsInSubtree(compInfo.indexOf(bankID)).size() -
                             allBankDetectorIndexes.size() - 2);
    nCols = static_cast<int>(allBankDetectorIndexes.size()) / nRows;
  }
}
 
} // namespace Mantid::Crystal