ExtractSpectra.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 "MantidAlgorithms/ExtractSpectra.h"
#include "MantidAlgorithms/ExtractSpectra2.h"
 
#include "MantidAPI/Algorithm.hxx"
#include "MantidAPI/NumericAxis.h"
#include "MantidAPI/TextAxis.h"
#include "MantidDataObjects/WorkspaceCreation.h"
#include "MantidIndexing/Extract.h"
#include "MantidIndexing/IndexInfo.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
 
#include <algorithm>
 
namespace {
const double xBoundaryTolerance = 1.0e-15;
} // namespace
 
namespace Mantid::Algorithms {
 
using namespace Kernel;
using namespace API;
using namespace DataObjects;
using namespace HistogramData;
using Types::Event::TofEvent;
 
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(ExtractSpectra)
 
 
const std::string ExtractSpectra::name() const { return "ExtractSpectra"; }
 
int ExtractSpectra::version() const { return 1; }
 
const std::string ExtractSpectra::category() const { return "Transforms\\Splitting"; }
 
const std::string ExtractSpectra::summary() const {
  return "Extracts a list of spectra from a workspace and places them in a new "
         "workspace.";
}
 
std::map<std::string, std::string> ExtractSpectra::validateInputs() {
  std::map<std::string, std::string> helpMessages;
  if (!isDefault("XMin") && !isDefault("XMax")) {
    const double xmin = getProperty("XMin");
    const double xmax = getProperty("XMax");
    if (xmin > xmax) {
      helpMessages["XMin"] = "XMin must be less than XMax";
      helpMessages["XMax"] = "XMax must be greater than XMin";
    }
  }
 
  if (!isDefault("StartWorkspaceIndex")) {
    const int minSpec_i = getProperty("StartWorkspaceIndex");
    auto minSpec = static_cast<size_t>(minSpec_i);
    API::MatrixWorkspace_sptr ws = getProperty("InputWorkspace");
    const size_t numberOfSpectra = ws->indexInfo().globalSize();
    int maxSpec_i = getProperty("EndWorkspaceIndex");
    auto maxSpec = static_cast<size_t>(maxSpec_i);
    if (isEmpty(maxSpec_i))
      maxSpec = numberOfSpectra - 1;
    if (maxSpec < minSpec) {
      helpMessages["StartWorkspaceIndex"] = "StartWorkspaceIndex must be less than or equal to EndWorkspaceIndex";
      helpMessages["EndWorkspaceIndex"] = "EndWorkspaceIndex must be greater than or equal to StartWorkspaceIndex";
    }
  }
 
  return helpMessages;
}
 
void ExtractSpectra::init() {
  declareProperty(std::make_unique<WorkspaceProperty<>>("InputWorkspace", "", Direction::Input), "The input workspace");
  declareProperty(std::make_unique<WorkspaceProperty<>>("OutputWorkspace", "", Direction::Output),
                  "Name of the output workspace");
 
  declareProperty("XMin", EMPTY_DBL(),
                  "An X value that is within the first "
                  "(lowest X value) bin that will be "
                  "retained\n"
                  "(default: workspace min)");
  declareProperty("XMax", EMPTY_DBL(),
                  "An X value that is in the highest X "
                  "value bin to be retained (default: max "
                  "X)");
  auto mustBePositive = std::make_shared<BoundedValidator<int>>();
  mustBePositive->setLower(0);
  declareProperty("StartWorkspaceIndex", 0, mustBePositive,
                  "The index number of the first entry in the Workspace that "
                  "will be loaded\n"
                  "(default: first entry in the Workspace)");
  // As the property takes ownership of the validator pointer, have to take care
  // to pass in a unique pointer to each property.
  declareProperty("EndWorkspaceIndex", EMPTY_INT(), mustBePositive,
                  "The index number of the last entry in the Workspace to be loaded\n"
                  "(default: last entry in the Workspace)");
  declareProperty(std::make_unique<ArrayProperty<size_t>>("WorkspaceIndexList"),
                  "A comma-separated list of individual workspace indices to "
                  "read.  Only used if\n"
                  "explicitly set. The WorkspaceIndexList is only used if the "
                  "DetectorList is empty.");
 
  declareProperty(std::make_unique<ArrayProperty<detid_t>>("DetectorList"),
                  "A comma-separated list of individual detector IDs to read.  "
                  "Only used if\n"
                  "explicitly set. When specifying the WorkspaceIndexList and "
                  "DetectorList property,\n"
                  "the latter is being selected.");
}
 
void ExtractSpectra::exec() {
  m_inputWorkspace = getProperty("InputWorkspace");
  m_isHistogramData = m_inputWorkspace->isHistogramData();
  m_commonBoundaries = m_inputWorkspace->isCommonBins();
  this->checkProperties();
 
  if (m_workspaceIndexList.empty()) {
    MatrixWorkspace_sptr out = getProperty("OutputWorkspace");
    // No spectra extracted, but not in-place, clone input before cropping.
    if (out != m_inputWorkspace)
      m_inputWorkspace = m_inputWorkspace->clone();
  } else {
    auto extract = std::make_shared<ExtractSpectra2>();
    setupAsChildAlgorithm(extract);
    extract->setWorkspaceInputProperties(
        "InputWorkspace", m_inputWorkspace, IndexType::WorkspaceIndex,
        std::vector<int64_t>(m_workspaceIndexList.begin(), m_workspaceIndexList.end()));
    extract->execute();
    m_inputWorkspace = extract->getProperty("OutputWorkspace");
  }
  setProperty("OutputWorkspace", m_inputWorkspace);
 
  // don't trim x-range if those values are not specified
  if (isDefault("XMin") && isDefault("XMax"))
    return;
 
  eventW = std::dynamic_pointer_cast<EventWorkspace>(m_inputWorkspace);
  if (eventW)
    this->execEvent();
  else
    this->execHistogram();
}
 
void ExtractSpectra::execHistogram() {
  auto size = static_cast<int>(m_inputWorkspace->getNumberHistograms());
  auto croppedCommonXHistogram = getCroppedXHistogram(*m_inputWorkspace);
  Progress prog(this, 0.0, 1.0, size);
  for (int i = 0; i < size; ++i) {
    if (m_commonBoundaries) {
      this->cropCommon(*m_inputWorkspace, croppedCommonXHistogram, i);
    } else {
      this->cropRagged(*m_inputWorkspace, i);
    }
    propagateBinMasking(*m_inputWorkspace, i);
    prog.report();
  }
}
 
const Kernel::cow_ptr<Mantid::HistogramData::HistogramX>
ExtractSpectra::getCroppedXHistogram(const API::MatrixWorkspace &workspace) {
  const auto hist = workspace.histogram(0);
  auto begin = m_minXIndex;
  auto end = histXMaxIndex();
 
  auto cropped(hist);
  cropped.resize(end - begin);
 
  auto xEnd = hist.xMode() == Histogram::XMode::Points ? end : end + 1;
  cropped.mutableX().assign(hist.x().begin() + begin, hist.x().begin() + xEnd);
  return cropped.sharedX();
}
 
void ExtractSpectra::cropCommon(API::MatrixWorkspace &workspace,
                                Kernel::cow_ptr<Mantid::HistogramData::HistogramX> XHistogram, int index) {
  const auto hist = workspace.histogram(index);
  auto begin = m_minXIndex;
  auto end = histXMaxIndex();
 
  auto cropped(hist);
  cropped.resize(end - begin);
 
  cropped.setSharedX(XHistogram);
 
  if (cropped.sharedY())
    cropped.mutableY().assign(hist.y().begin() + begin, hist.y().begin() + end);
  if (cropped.sharedE())
    cropped.mutableE().assign(hist.e().begin() + begin, hist.e().begin() + end);
  if (cropped.sharedDx())
    cropped.mutableDx().assign(hist.dx().begin() + begin, hist.dx().begin() + end);
 
  workspace.setHistogram(index, cropped);
}
 
void ExtractSpectra::cropRagged(MatrixWorkspace &workspace, int index) {
  auto &Y = workspace.mutableY(index);
  auto &E = workspace.mutableE(index);
  const size_t size = Y.size();
  size_t startX = this->getXMinIndex(index);
  if (startX > size)
    startX = size;
  for (size_t i = 0; i < startX; ++i) {
    Y[i] = 0.0;
    E[i] = 0.0;
  }
  size_t endX = this->getXMaxIndex(index);
  if (endX > 0 && m_isHistogramData)
    endX -= 1;
  for (size_t i = endX; i < size; ++i) {
    Y[i] = 0.0;
    E[i] = 0.0;
  }
}
 
namespace { // anonymous namespace
template <class T> void filterEventsHelper(std::vector<T> &events, const double xmin, const double xmax) {
  events.erase(std::remove_if(events.begin(), events.end(),
                              [xmin, xmax](const T &event) {
                                const double tof = event.tof();
                                return bool(tof < xmin || tof > xmax);
                              }),
               events.end());
}
} // namespace
 
void ExtractSpectra::execEvent() {
  // use min/max from workspace if the values aren't supplied by the user
  const double minX_val = isDefault("XMin") ? eventW->getTofMin() : getProperty("XMin");
  const double maxX_val = isDefault("XMax") ? eventW->getTofMax() : getProperty("XMax");
 
  BinEdges binEdges(2);
  if (m_commonBoundaries) {
    auto &oldX = m_inputWorkspace->x(0);
    binEdges = BinEdges(oldX.begin() + m_minXIndex, oldX.begin() + m_maxXIndex);
  }
  if (m_maxXIndex - m_minXIndex < 2) {
    // create new output X axis
    binEdges = {minX_val, maxX_val};
  }
 
  Progress prog(this, 0.0, 1.0, eventW->getNumberHistograms());
  PARALLEL_FOR_IF(Kernel::threadSafe(*eventW))
  for (int i = 0; i < static_cast<int>(eventW->getNumberHistograms()); ++i) {
    PARALLEL_START_INTERRUPT_REGION
    EventList &el = eventW->getSpectrum(i);
 
    if (!el.empty()) {
      switch (el.getEventType()) {
      case TOF: {
        filterEventsHelper(el.getEvents(), minX_val, maxX_val);
        break;
      }
      case WEIGHTED: {
        filterEventsHelper(el.getWeightedEvents(), minX_val, maxX_val);
        break;
      }
      case WEIGHTED_NOTIME: {
        filterEventsHelper(el.getWeightedEventsNoTime(), minX_val, maxX_val);
        break;
      }
      }
    }
 
    // If the X axis is NOT common, then keep the initial X axis, just clear the
    // events, otherwise:
    if (m_commonBoundaries) {
      const auto oldDx = el.pointStandardDeviations();
      el.setHistogram(binEdges);
      if (oldDx) {
        auto end = histXMaxIndex();
        el.setPointStandardDeviations(oldDx.begin() + m_minXIndex, oldDx.begin() + end);
      }
    }
    propagateBinMasking(*eventW, i);
    prog.report();
    PARALLEL_END_INTERRUPT_REGION
  }
  PARALLEL_CHECK_INTERRUPT_REGION
}
 
void ExtractSpectra::propagateBinMasking(MatrixWorkspace &workspace, const int i) const {
  auto end = histXMaxIndex();
  if (workspace.hasMaskedBins(i)) {
    MatrixWorkspace::MaskList filteredMask;
    for (const auto &mask : workspace.maskedBins(i)) {
      const size_t maskIndex = mask.first;
      if (maskIndex >= m_minXIndex && maskIndex < end)
        filteredMask[maskIndex - m_minXIndex] = mask.second;
    }
    if (filteredMask.size() > 0)
      workspace.setMaskedBins(i, filteredMask);
    else
      workspace.setUnmaskedBins(i);
  }
}
 
void ExtractSpectra::checkProperties() {
  m_minXIndex = this->getXMinIndex();
  m_maxXIndex = this->getXMaxIndex();
  const size_t xSize = m_inputWorkspace->x(0).size();
  if (m_minXIndex > 0 || m_maxXIndex < xSize) {
    if (m_minXIndex > m_maxXIndex) {
      throw std::out_of_range("XMin must be less than XMax");
    }
    m_croppingInX = true;
    if (m_commonBoundaries && !std::dynamic_pointer_cast<EventWorkspace>(m_inputWorkspace) &&
        (m_minXIndex == m_maxXIndex || (m_isHistogramData && m_maxXIndex == m_minXIndex + 1))) {
      m_minXIndex--;
      m_maxXIndex = m_minXIndex + 1;
      if (m_isHistogramData) {
        m_maxXIndex += 1;
      }
    }
  }
  if (!m_commonBoundaries) {
    m_minXIndex = 0;
    m_maxXIndex = static_cast<int>(m_inputWorkspace->x(0).size());
  }
 
  // The hierarchy of inputs is (one is being selected):
  // 1. DetectorList
  // 2. WorkspaceIndexList
  // 3. Start and stop index
  std::vector<detid_t> detectorList = getProperty("DetectorList");
  if (!detectorList.empty()) {
    m_workspaceIndexList = m_inputWorkspace->getIndicesFromDetectorIDs(detectorList);
  } else {
    m_workspaceIndexList = getProperty("WorkspaceIndexList");
 
    if (m_workspaceIndexList.empty()) {
      int minSpec_i = getProperty("StartWorkspaceIndex");
      auto minSpec = static_cast<size_t>(minSpec_i);
      const size_t numberOfSpectra = m_inputWorkspace->indexInfo().globalSize();
      int maxSpec_i = getProperty("EndWorkspaceIndex");
      auto maxSpec = static_cast<size_t>(maxSpec_i);
      if (isEmpty(maxSpec_i))
        maxSpec = numberOfSpectra - 1;
      if (maxSpec - minSpec + 1 != numberOfSpectra) {
        m_workspaceIndexList.reserve(maxSpec - minSpec + 1);
        for (size_t i = minSpec; i <= maxSpec; ++i)
          m_workspaceIndexList.emplace_back(i);
      }
    }
  }
} // namespace Algorithms
 
size_t ExtractSpectra::getXMinIndex(const size_t wsIndex) {
  double minX_val = getProperty("XMin");
  size_t xIndex = 0;
  if (!isEmpty(minX_val)) { // A value has been passed to the algorithm, check
                            // it and maybe store it
    const auto &X = m_inputWorkspace->x(wsIndex);
    if (m_commonBoundaries && minX_val > X.back()) {
      std::stringstream msg;
      msg << "XMin is greater than the largest X value (" << minX_val << " > " << X.back() << ")";
      throw std::out_of_range(msg.str());
    }
    // Reduce cut-off value slightly to allow for rounding errors
    // when trying to exactly hit a bin boundary.
    minX_val -= std::abs(minX_val * xBoundaryTolerance);
    xIndex = std::lower_bound(X.begin(), X.end(), minX_val) - X.begin();
  }
  return xIndex;
}
 
size_t ExtractSpectra::getXMaxIndex(const size_t wsIndex) {
  const auto &X = m_inputWorkspace->x(wsIndex);
  size_t xIndex = X.size();
  // get the value that the user entered if they entered one at all
  double maxX_val = getProperty("XMax");
  if (!isEmpty(maxX_val)) { // we have a user value, check it and maybe store it
    if (m_commonBoundaries && maxX_val < X.front()) {
      std::stringstream msg;
      msg << "XMax is less than the smallest X value (" << maxX_val << " < " << X.front() << ")";
      throw std::out_of_range(msg.str());
    }
    // Increase cut-off value slightly to allow for rounding errors
    // when trying to exactly hit a bin boundary.
    maxX_val += std::abs(maxX_val * xBoundaryTolerance);
    xIndex = std::upper_bound(X.begin(), X.end(), maxX_val) - X.begin();
  }
  return xIndex;
}
 
size_t ExtractSpectra::histXMaxIndex() const {
  if (m_isHistogramData) {
    return m_maxXIndex - 1;
  }
  return m_maxXIndex;
}
 
} // namespace Mantid::Algorithms