SaveNexusProcessed.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 +
// SaveNexusProcessed
// @author Ronald Fowler, based on SaveNexus
#include "MantidDataHandling/SaveNexusProcessed.h"
#include "MantidAPI/EnabledWhenWorkspaceIsType.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/IMDEventWorkspace.h"
#include "MantidAPI/IMDHistoWorkspace.h"
#include "MantidAPI/WorkspaceHistory.h"
#include "MantidDataHandling/SaveNexusProcessedHelper.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/GroupingWorkspace.h"
#include "MantidDataObjects/MaskWorkspace.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidGeometry/Crystal/AngleUnits.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include <memory>
#include <utility>
 
using namespace Mantid::API;
 
namespace Mantid::DataHandling {
 
using namespace Kernel;
using namespace API;
using namespace DataObjects;
using Geometry::Instrument_const_sptr;
 
using optional_size_t = Nexus::NexusFileIO::optional_size_t;
 
// Register the algorithm into the algorithm factory
DECLARE_ALGORITHM(SaveNexusProcessed)
 
namespace {
 
void makeMappings(const MatrixWorkspace &ws, const std::vector<int> &ws_indices,
                  std::vector<int32_t> &out_detector_index, std::vector<int32_t> &out_detector_count,
                  std::vector<int32_t> &out_detector_list, int &numberSpec, size_t &numberDetectors) {
 
  // Count the total number of detectors
  numberDetectors =
      std::accumulate(ws_indices.cbegin(), ws_indices.cend(), size_t(0), [&ws](size_t sum, const auto &index) {
        return sum + ws.getSpectrum(static_cast<size_t>(index)).getDetectorIDs().size();
      });
 
  numberSpec = int(ws_indices.size());
  // allocate space for the Nexus Muon format of spectra-detector mapping
  // allow for writing one more than required
  out_detector_index.resize(numberSpec + 1, 0);
  out_detector_count.resize(numberSpec, 0);
  out_detector_list.resize(numberDetectors, 0);
  int id = 0;
 
  // get data from map into Nexus Muon format
  for (int i = 0; i < numberSpec; i++) {
    // Workspace index
    const int si = ws_indices[i];
    // Spectrum there
    const auto &spectrum = ws.getSpectrum(si);
 
    // The detectors in this spectrum
    const auto &detectorgroup = spectrum.getDetectorIDs();
    const auto ndet1 = static_cast<int>(detectorgroup.size());
 
    // points to start of detector list for the next spectrum
    out_detector_index[i + 1] = int32_t(out_detector_index[i] + ndet1);
    out_detector_count[i] = int32_t(ndet1);
 
    std::set<detid_t>::const_iterator it;
    for (it = detectorgroup.begin(); it != detectorgroup.end(); ++it) {
      out_detector_list[id++] = int32_t(*it);
    }
  }
  // Cut the extra entry at the end of detector_index
  out_detector_index.resize(numberSpec);
}
 
} // namespace
 
void SaveNexusProcessed::init() {
  declareProperty(std::make_unique<WorkspaceProperty<Workspace>>("InputWorkspace", "", Direction::Input),
                  "Name of the workspace to be saved");
  // Declare required input parameters for algorithm
  const std::vector<std::string> fileExts{".nxs", ".nx5", ".xml"};
  declareProperty(std::make_unique<FileProperty>("Filename", "", FileProperty::Save, fileExts),
                  "The name of the Nexus file to write, as a full or relative\n"
                  "path");
 
  // Declare optional parameters (title now optional, was mandatory)
  declareProperty("Title", "", std::make_shared<NullValidator>(), "A title to describe the saved workspace");
  auto mustBePositive = std::make_shared<BoundedValidator<int>>();
  mustBePositive->setLower(0);
 
  declareProperty("WorkspaceIndexMin", 0, mustBePositive,
                  "Index number of first spectrum to write, only for single\n"
                  "period data.");
  declareProperty("WorkspaceIndexMax", Mantid::EMPTY_INT(), mustBePositive,
                  "Index of last spectrum to write, only for single period\n"
                  "data.");
  declareProperty(std::make_unique<ArrayProperty<int>>("WorkspaceIndexList"),
                  "List of spectrum numbers to write, only for single period\n"
                  "data.");
 
  declareProperty("Append", false,
                  "Determines whether .nxs file needs to be\n"
                  "over written or appended");
 
  declareProperty("PreserveEvents", true,
                  "For EventWorkspaces, preserve the events when saving (default).\n"
                  "If false, will save the 2D histogram version of the workspace with the "
                  "current binning parameters.");
  setPropertySettings("PreserveEvents",
                      std::make_unique<EnabledWhenWorkspaceIsType<EventWorkspace>>("InputWorkspace", true));
 
  declareProperty("CompressNexus", false,
                  "For EventWorkspaces, compress the Nexus data field (default False).\n"
                  "This will make smaller files but takes much longer.");
  setPropertySettings("CompressNexus",
                      std::make_unique<EnabledWhenWorkspaceIsType<EventWorkspace>>("InputWorkspace", true));
}
 
void SaveNexusProcessed::getWSIndexList(std::vector<int> &indices, const MatrixWorkspace_const_sptr &matrixWorkspace) {
  const std::vector<int> spec_list = getProperty("WorkspaceIndexList");
  int spec_min = getProperty("WorkspaceIndexMin");
  int spec_max = getProperty("WorkspaceIndexMax");
  const bool list = !spec_list.empty();
  const bool interval = (spec_max != Mantid::EMPTY_INT());
  if (spec_max == Mantid::EMPTY_INT())
    spec_max = 0;
  const auto numberOfHist = static_cast<int>(matrixWorkspace->getNumberHistograms());
 
  if (interval) {
    if (spec_max < spec_min || spec_max > numberOfHist - 1) {
      g_log.error("Invalid WorkspaceIndex min/max properties");
      throw std::invalid_argument("Inconsistent properties defined");
    }
    indices.reserve(1 + spec_max - spec_min);
    for (int i = spec_min; i <= spec_max; i++)
      indices.emplace_back(i);
    if (list) {
      for (auto s : spec_list) {
        if (s < 0)
          continue;
        if (s < spec_min || s > spec_max)
          indices.emplace_back(s);
      }
    }
  } else if (list) {
    spec_max = 0;
    spec_min = numberOfHist - 1;
    for (auto s : spec_list) {
      if (s < 0)
        continue;
      indices.emplace_back(s);
      if (s > spec_max)
        spec_max = s;
      if (s < spec_min)
        spec_min = s;
    }
  } else {
    spec_min = 0;
    spec_max = numberOfHist - 1;
    indices.reserve(1 + spec_max - spec_min);
    for (int i = spec_min; i <= spec_max; i++)
      indices.emplace_back(i);
  }
}
 
void SaveNexusProcessed::doExec(const Workspace_sptr &inputWorkspace, std::shared_ptr<Nexus::NexusFileIO> &nexusFile,
                                const bool keepFile, optional_size_t entryNumber) {
  //
  //
 
  // Retrieve the filename from the properties
  const std::string filename = getPropertyValue("Filename");
  std::string title = getPropertyValue("Title");
  // Do we preserve events?
  const bool PreserveEvents = getProperty("PreserveEvents");
 
  MatrixWorkspace_const_sptr matrixWorkspace = std::dynamic_pointer_cast<const MatrixWorkspace>(inputWorkspace);
  ITableWorkspace_const_sptr tableWorkspace = std::dynamic_pointer_cast<const ITableWorkspace>(inputWorkspace);
  IPeaksWorkspace_const_sptr peaksWorkspace = std::dynamic_pointer_cast<const IPeaksWorkspace>(inputWorkspace);
  OffsetsWorkspace_const_sptr offsetsWorkspace = std::dynamic_pointer_cast<const OffsetsWorkspace>(inputWorkspace);
  MaskWorkspace_const_sptr maskWorkspace = std::dynamic_pointer_cast<const MaskWorkspace>(inputWorkspace);
  if (peaksWorkspace)
    g_log.debug("We have a peaks workspace");
  // check if inputWorkspace is something we know how to save
  if (!matrixWorkspace && !tableWorkspace) {
    // get the workspace name for the error message
    const std::string name = getProperty("InputWorkspace");
 
    // md workspaces should be saved using SaveMD
    if (bool(std::dynamic_pointer_cast<const IMDEventWorkspace>(inputWorkspace)) ||
        bool(std::dynamic_pointer_cast<const IMDHistoWorkspace>(inputWorkspace)))
      g_log.warning() << name << " can be saved using SaveMD\n";
 
    // standard error message
    std::stringstream msg;
    msg << "Workspace \"" << name << "\" not saved because it is not of a type we can presently save.";
 
    throw std::runtime_error(msg.str());
  }
  m_eventWorkspace = std::dynamic_pointer_cast<const EventWorkspace>(matrixWorkspace);
  const std::string workspaceID = inputWorkspace->id();
  if ((workspaceID.find("Workspace2D") == std::string::npos) &&
      (workspaceID.find("RebinnedOutput") == std::string::npos) &&
      (workspaceID.find("WorkspaceSingleValue") == std::string::npos) &&
      (workspaceID.find("GroupingWorkspace") == std::string::npos) && !m_eventWorkspace && !tableWorkspace &&
      !offsetsWorkspace && !maskWorkspace)
    throw Exception::NotImplementedError("SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, "
                                         "EventWorkspace, ITableWorkspace, OffsetsWorkspace, "
                                         "GroupingWorkspace, or MaskWorkspace.");
 
  // Create progress object for initial part - depends on whether events are
  // processed
  if (PreserveEvents && m_eventWorkspace) {
    m_timeProgInit = 0.07; // Events processed 0.05 to 1.0
  } else {
    m_timeProgInit = 1.0; // All work is done in the initial part
  }
  Progress prog_init(this, 0.0, m_timeProgInit, 7);
 
  // If no title's been given, use the workspace title field
  if (title.empty())
    title = inputWorkspace->getTitle();
 
  // get the workspace name to write to file
  const std::string wsName = inputWorkspace->getName();
 
  // If not append, openNexusWrite will open with _CREATES perm and overwrite
  const bool append_to_file = getProperty("Append");
 
  nexusFile->resetProgress(&prog_init);
  nexusFile->openNexusWrite(filename, entryNumber, append_to_file || keepFile);
 
  prog_init.reportIncrement(1, "Opening file");
  if (nexusFile->writeNexusProcessedHeader(title, wsName) != 0)
    throw Exception::FileError("Failed to write to file", filename);
 
  prog_init.reportIncrement(1, "Writing header");
 
  // write instrument data, if present and writer enabled
  if (matrixWorkspace) {
    // Save the instrument names, ParameterMap, sample, run
    matrixWorkspace->saveExperimentInfoNexus(nexusFile->filehandle().get(), saveLegacyInstrument());
    prog_init.reportIncrement(1, "Writing sample and instrument");
 
    // check if all X() are in fact the same array
    const bool uniformSpectra = matrixWorkspace->isCommonBins();
    const bool raggedSpectra = matrixWorkspace->isRaggedWorkspace();
 
    // Retrieve the workspace indices (from params)
    std::vector<int> indices;
    this->getWSIndexList(indices, matrixWorkspace);
 
    prog_init.reportIncrement(1, "Writing data");
    // Write out the data (2D or event)
    if (m_eventWorkspace && PreserveEvents) {
      this->execEvent(nexusFile.get(), uniformSpectra, raggedSpectra, indices);
    } else {
      std::string workspaceTypeGroupName;
      if (offsetsWorkspace)
        workspaceTypeGroupName = "offsets_workspace";
      else if (maskWorkspace)
        workspaceTypeGroupName = "mask_workspace";
      else if (std::dynamic_pointer_cast<const GroupingWorkspace>(inputWorkspace))
        workspaceTypeGroupName = "grouping_workspace";
      else
        workspaceTypeGroupName = "workspace";
 
      nexusFile->writeNexusProcessedData2D(matrixWorkspace, uniformSpectra, raggedSpectra, indices,
                                           workspaceTypeGroupName.c_str(), true);
    }
 
    if (saveLegacyInstrument()) {
      nexusFile->filehandle()->openGroup("instrument", "NXinstrument");
      nexusFile->filehandle()->makeGroup("detector", "NXdetector", true);
 
      nexusFile->filehandle()->putAttr("version", 1);
      saveSpectraDetectorMapNexus(*matrixWorkspace, nexusFile->filehandle().get(), indices, NXcompression::LZW);
      saveSpectrumNumbersNexus(*matrixWorkspace, nexusFile->filehandle().get(), indices, NXcompression::LZW);
      nexusFile->filehandle()->closeGroup();
      nexusFile->filehandle()->closeGroup();
    }
 
  } // finish matrix workspace specifics
 
  if (peaksWorkspace) {
    // Save the instrument names, ParameterMap, sample, run
    peaksWorkspace->saveExperimentInfoNexus(nexusFile->filehandle().get());
    prog_init.reportIncrement(1, "Writing sample and instrument");
    peaksWorkspace->saveNexus(nexusFile->filehandle().get());
  } else if (tableWorkspace) {
    nexusFile->writeNexusTableWorkspace(tableWorkspace, "table_workspace");
  }
 
  // Switch to the Cpp API for the algorithm history
  if (trackingHistory()) {
    m_history->fillAlgorithmHistory(this, Mantid::Types::Core::DateAndTime::getCurrentTime(), 0,
                                    Algorithm::g_execCount);
    if (!isChild()) {
      inputWorkspace->history().addHistory(m_history);
    }
    // this is a child algorithm, but we still want to keep the history.
    else if (isRecordingHistoryForChild() && m_parentHistory) {
      m_parentHistory->addChildHistory(m_history);
    }
  }
 
  inputWorkspace->history().saveNexus(nexusFile->filehandle().get());
  nexusFile->closeGroup();
}
 
//-----------------------------------------------------------------------------------------------
void SaveNexusProcessed::exec() {
  Workspace_sptr inputWorkspace = getProperty("InputWorkspace");
 
  // Then immediately open the file
  auto nexusFile = std::make_shared<Mantid::Nexus::NexusFileIO>();
 
  // Perform the execution.
  doExec(inputWorkspace, nexusFile);
 
  // nexusFile->closeNexusFile();
}
 
//-------------------------------------------------------------------------------------
template <class T>
void SaveNexusProcessed::appendEventListData(const std::vector<T> &events, size_t offset, double *tofs, float *weights,
                                             float *errorSquareds, int64_t *pulsetimes) {
  // Do nothing if there are no events.
  if (events.empty())
    return;
 
  const auto it = events.cbegin();
  const auto it_end = events.cend();
 
  // Fill the C-arrays with the fields from all the events, as requested.
  if (tofs) {
    std::transform(it, it_end, std::next(tofs, offset), [](const T &event) { return event.tof(); });
  }
  if (weights) {
    std::transform(it, it_end, std::next(weights, offset),
                   [](const T &event) { return static_cast<float>(event.weight()); });
  }
  if (errorSquareds) {
    std::transform(it, it_end, std::next(errorSquareds, offset),
                   [](const T &event) { return static_cast<float>(event.errorSquared()); });
  }
  if (pulsetimes) {
    std::transform(it, it_end, std::next(pulsetimes, offset),
                   [](const T &event) { return event.pulseTime().totalNanoseconds(); });
  }
}
 
//-----------------------------------------------------------------------------------------------
void SaveNexusProcessed::execEvent(const Mantid::Nexus::NexusFileIO *nexusFile, const bool uniformSpectra,
                                   const bool raggedSpectra, const std::vector<int> &spec) {
  std::vector<int64_t> indices;
  indices.reserve(spec.size() + 1);
  // First we need to index the events in each spectrum
  size_t index = 0;
  for (auto s : spec) {
    indices.emplace_back(index);
    index += m_eventWorkspace->getSpectrum(s).getNumberEvents();
  }
  indices.emplace_back(index);
 
  m_progress = std::make_unique<Progress>(this, m_timeProgInit, 1.0, index * 2);
 
  // Start by writing out the axes and crap
  nexusFile->writeNexusProcessedData2D(m_eventWorkspace, uniformSpectra, raggedSpectra, spec, "event_workspace", false);
 
  // Make a super long list of tofs, weights, etc.
 
  // Initialize all the arrays
  int64_t num = index;
  double *tofs = nullptr;
  float *weights = nullptr;
  float *errorSquareds = nullptr;
  int64_t *pulsetimes = nullptr;
 
  // overall event type.
  EventType type = m_eventWorkspace->getEventType();
  bool writeTOF = true;
  bool writePulsetime = false;
  bool writeWeight = false;
  bool writeError = false;
 
  switch (type) {
  case TOF:
    writePulsetime = true;
    break;
  case WEIGHTED:
    writePulsetime = true;
    writeWeight = true;
    writeError = true;
    break;
  case WEIGHTED_NOTIME:
    writeWeight = true;
    writeError = true;
    break;
  }
 
  // --- Initialize the combined event arrays ----
  if (writeTOF)
    tofs = new double[num];
  if (writeWeight)
    weights = new float[num];
  if (writeError)
    errorSquareds = new float[num];
  if (writePulsetime)
    pulsetimes = new int64_t[num];
 
  // --- Fill in the combined event arrays ----
  PARALLEL_FOR_NO_WSP_CHECK()
  for (int wi = 0; wi < static_cast<int>(spec.size()); wi++) {
    PARALLEL_START_INTERRUPT_REGION
    const DataObjects::EventList &el = m_eventWorkspace->getSpectrum(spec[wi]);
 
    // This is where it will land in the output array.
    // It is okay to write in parallel since none should step on each other.
    size_t offset = indices[wi];
 
    switch (el.getEventType()) {
    case TOF:
      appendEventListData(el.getEvents(), offset, tofs, weights, errorSquareds, pulsetimes);
      break;
    case WEIGHTED:
      appendEventListData(el.getWeightedEvents(), offset, tofs, weights, errorSquareds, pulsetimes);
      break;
    case WEIGHTED_NOTIME:
      appendEventListData(el.getWeightedEventsNoTime(), offset, tofs, weights, errorSquareds, pulsetimes);
      break;
    }
    m_progress->reportIncrement(el.getNumberEvents(), "Copying EventList");
 
    PARALLEL_END_INTERRUPT_REGION
  }
  PARALLEL_CHECK_INTERRUPT_REGION
 
  /*Default = DONT compress - much faster*/
  bool CompressNexus = getProperty("CompressNexus");
 
  // Write out to the NXS file.
  nexusFile->writeNexusProcessedDataEventCombined(m_eventWorkspace, indices, tofs, weights, errorSquareds, pulsetimes,
                                                  CompressNexus);
 
  // Free mem.
  delete[] tofs;
  delete[] weights;
  delete[] errorSquareds;
  delete[] pulsetimes;
}
 
//-----------------------------------------------------------------------------------------------
void SaveNexusProcessed::setOtherProperties(IAlgorithm *alg, const std::string &propertyName,
                                            const std::string &propertyValue, int perioidNum) {
  if (propertyName == "Append") {
    if (perioidNum != 1) {
      alg->setPropertyValue(propertyName, "1");
    } else
      alg->setPropertyValue(propertyName, propertyValue);
  } else
    Algorithm::setOtherProperties(alg, propertyName, propertyValue, perioidNum);
}
 
bool SaveNexusProcessed::processGroups() {
  // Then immediately open the file
  auto nexusFile = std::make_shared<Mantid::Nexus::NexusFileIO>();
 
  // If we have arrived here then a WorkspaceGroup was passed to the
  // InputWorkspace property. Pull out the unrolled workspaces and append an
  // entry for each one. We only have a single input workspace property declared
  // so there will only be a single list of unrolled workspaces
  const auto &workspaces = m_unrolledInputWorkspaces[0];
  if (!workspaces.empty()) {
    for (size_t entry = 0; entry < workspaces.size(); entry++) {
      const Workspace_sptr ws = workspaces[entry];
      if (ws->isGroup()) {
        throw std::runtime_error("NeXus files do not "
                                 "support nested groups of groups");
      }
      this->doExec(ws, nexusFile, entry > 0 /*keepFile*/, entry);
      g_log.information() << "Saving group index " << entry << "\n";
    }
  }
 
  nexusFile->closeNexusFile();
 
  return true;
}
 
void SaveNexusProcessed::saveSpectraDetectorMapNexus(const MatrixWorkspace &ws, Nexus::File *file,
                                                     const std::vector<int> &wsIndices,
                                                     const NXcompression compression) const {
 
  std::vector<int32_t> detector_index;
  std::vector<int32_t> detector_count;
  std::vector<int32_t> detector_list;
  int numberSpec = 0;
  size_t nDetectors = 0;
  /*Make the mappings needed for writing to disk*/
  makeMappings(ws, wsIndices, detector_index, detector_count, detector_list, numberSpec, nDetectors);
  if (nDetectors == 0)
    return;
 
  // write data as Nexus sections detector{index,count,list}
  Nexus::DimVector dims(1, numberSpec);
  file->writeCompData("detector_index", detector_index, dims, compression, dims);
  file->writeCompData("detector_count", detector_count, dims, compression, dims);
  dims.front() = static_cast<int>(nDetectors);
  file->writeCompData("detector_list", detector_list, dims, compression, dims);
  // Get all the positions
  try {
    std::vector<double> detPos(nDetectors * 3);
    Geometry::Instrument_const_sptr inst = ws.getInstrument();
    Geometry::IComponent_const_sptr sample = inst->getSample();
    if (sample) {
      Kernel::V3D sample_pos = sample->getPos();
      for (size_t i = 0; i < nDetectors; i++) {
        double R, Theta, Phi;
        try {
          Geometry::IDetector_const_sptr det = inst->getDetector(detector_list[i]);
          Kernel::V3D pos = det->getPos() - sample_pos;
          pos.getSpherical(R, Theta, Phi);
          R = det->getDistance(*sample);
          Theta = ws.detectorTwoTheta(*det) * Geometry::rad2deg;
        } catch (...) {
          R = 0.;
          Theta = 0.;
          Phi = 0.;
        }
        // Need to get R & Theta through these methods to be correct for grouped
        // detectors
        detPos[3 * i] = R;
        detPos[3 * i + 1] = Theta;
        detPos[3 * i + 2] = Phi;
      }
    } else
      for (size_t i = 0; i < 3 * nDetectors; i++)
        detPos[i] = 0.;
 
    dims.front() = static_cast<int>(nDetectors);
    dims.emplace_back(3);
    file->writeCompData("detector_positions", detPos, dims, compression, dims);
  } catch (...) {
    g_log.error("Unknown error caught when saving detector positions.");
  }
}
 
void SaveNexusProcessed::saveSpectrumNumbersNexus(const API::MatrixWorkspace &ws, Nexus::File *file,
                                                  const std::vector<int> &wsIndices,
                                                  const NXcompression compression) const {
  const auto numberSpec = int(wsIndices.size());
  std::vector<int32_t> spectra;
  spectra.reserve(static_cast<size_t>(numberSpec));
  for (const auto index : wsIndices) {
    const auto &spectrum = ws.getSpectrum(static_cast<size_t>(index));
    spectra.emplace_back(static_cast<int32_t>(spectrum.getSpectrumNo()));
  }
 
  const Nexus::DimVector dims(1, numberSpec);
  file->writeCompData("spectra", spectra, dims, compression, dims);
}
 
} // namespace Mantid::DataHandling