LoadMuonNexus1.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 "MantidDataHandling/LoadMuonNexus1.h"

#include "MantidAPI/Axis.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/GroupingLoader.h"
#include "MantidAPI/Progress.h"
#include "MantidAPI/RegisterFileLoader.h"
#include "MantidAPI/SpectrumDetectorMapping.h"
#include "MantidAPI/TableRow.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidDataHandling/ISISRunLogs.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument/Detector.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/Unit.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/UnitLabelTypes.h"
#include "MantidNexus/MuonNexusReader.h"
#include "MantidNexus/NexusClasses.h"
// clang-format off
#include <nexus/NeXusFile.hpp>
#include <nexus/NeXusException.hpp>
// clang-format on

#include <boost/iterator/counting_iterator.hpp>
#include <memory>
#include <boost/scoped_array.hpp>

#include <Poco/Path.h>

#include <cmath>
#include <limits>

namespace Mantid {
namespace DataHandling {
using namespace DataObjects;

// Register the algorithm into the algorithm factory
DECLARE_NEXUS_FILELOADER_ALGORITHM(LoadMuonNexus1)

using namespace Kernel;
using namespace API;
using namespace Mantid::NeXus;
using HistogramData::BinEdges;
using HistogramData::Counts;

/// Empty default constructor
LoadMuonNexus1::LoadMuonNexus1() : LoadMuonNexus() {}

/** Executes the algorithm. Reading in the file and creating and populating
 *  the output workspace
 *
 *  @throw Exception::FileError If the Nexus file cannot be found/opened
 *  @throw std::invalid_argument If the optional properties are set to invalid
 *values
 */
void LoadMuonNexus1::exec() {
  // Retrieve the filename from the properties
  m_filename = getPropertyValue("Filename");
  // Retrieve the entry number
  m_entrynumber = getProperty("EntryNumber");

  NXRoot root(m_filename);
  NXEntry entry = root.openEntry("run/histogram_data_1");
  try {
    NXInfo info = entry.getDataSetInfo("time_zero");
    if (info.stat != NX_ERROR) {
      double dum = root.getFloat("run/histogram_data_1/time_zero");
      setProperty("TimeZero", dum);
    }
  } catch (...) {
  }

  try {
    NXInfo infoResolution = entry.getDataSetInfo("resolution");
    NXInt counts = root.openNXInt("run/histogram_data_1/counts");
    std::string firstGoodBin = counts.attributes("first_good_bin");
    if (!firstGoodBin.empty() && infoResolution.stat != NX_ERROR) {
      double resolution;

      switch (infoResolution.type) {
      case NX_FLOAT32:
        resolution = static_cast<double>(entry.getFloat("resolution"));
        break;
      case NX_INT32:
        resolution = static_cast<double>(entry.getInt("resolution"));
        break;
      default:
        throw std::runtime_error("Unsupported data type for resolution");
      }

      auto bin = static_cast<double>(boost::lexical_cast<int>(firstGoodBin));
      double bin_size = resolution / 1000000.0;

      setProperty("FirstGoodData", bin * bin_size);
    }
  } catch (std::exception &e) {
    g_log.warning() << "Error while loading the FirstGoodData value: "
                    << e.what() << "\n";
  }

  NXEntry nxRun = root.openEntry("run");
  std::string title;
  std::string notes;
  try {
    title = nxRun.getString("title");
    notes = nxRun.getString("notes");
  } catch (...) {
  }
  std::string run_num;
  try {
    run_num = std::to_string(nxRun.getInt("number"));
  } catch (...) {
  }

  MuonNexusReader nxload;
  nxload.readFromFile(m_filename);

  // Read in the instrument name from the Nexus file
  m_instrument_name = nxload.getInstrumentName();
  // Read in the number of spectra in the Nexus file
  m_numberOfSpectra = nxload.t_nsp1;
  if (m_entrynumber != 0) {
    m_numberOfPeriods = 1;
    if (m_entrynumber > nxload.t_nper) {
      throw std::invalid_argument("Invalid Entry Number:Enter a valid number");
    }
  } else {
    // Read the number of periods in this file
    m_numberOfPeriods = nxload.t_nper;
  }

  bool autoGroup = getProperty("AutoGroup");

  // Grouping info should be returned if user has set the property
  bool returnGrouping = !getPropertyValue("DetectorGroupingTable").empty();

  // Call private method to validate the optional parameters, if set
  checkOptionalProperties();
  // Calculate the size of a workspace, given its number of periods & spectra to
  // read
  size_t total_specs;
  if (m_interval || m_list) {
    // Remove from list possible duplicate specs
    for (auto it = m_spec_list.begin(); it != m_spec_list.end();) {
      if ((*it >= m_spec_min) && (*it <= m_spec_max)) {
        it = m_spec_list.erase(it);
      } else {
        ++it;
      }
    }
    total_specs = m_spec_list.size();
    if (m_interval) {
      total_specs += (m_spec_max - m_spec_min + 1);
      m_spec_max += 1;
    }
  } else {
    total_specs = m_numberOfSpectra;
    // for nexus return all spectra
    m_spec_min = 1;
    m_spec_max = m_numberOfSpectra + 1; // Add +1 to iterate
  }

  // Read the number of time channels (i.e. bins) from the Nexus file
  const int channelsPerSpectrum = nxload.t_ntc1;
  // Read in the time bin boundaries
  const int lengthIn = channelsPerSpectrum + 1;

  // Try to load dead time info
  loadDeadTimes(root);

  // Create the 2D workspace for the output
  DataObjects::Workspace2D_sptr localWorkspace =
      std::dynamic_pointer_cast<DataObjects::Workspace2D>(
          WorkspaceFactory::Instance().create("Workspace2D", total_specs,
                                              lengthIn, lengthIn - 1));
  localWorkspace->setTitle(title);
  localWorkspace->setComment(notes);
  localWorkspace->mutableRun().addLogData(
      new PropertyWithValue<std::string>("run_number", run_num));

  // Add 'FirstGoodData' to list of logs if possible
  if (existsProperty("FirstGoodData") && existsProperty("TimeZero")) {
    double fgd = getProperty("FirstGoodData");
    double tz = getProperty("TimeZero");
    localWorkspace->mutableRun().addLogData(
        new PropertyWithValue<double>("FirstGoodData", fgd - tz));
  }
  // Set the unit on the workspace to muon time, for now in the form of a Label
  // Unit
  std::shared_ptr<Kernel::Units::Label> lblUnit =
      std::dynamic_pointer_cast<Kernel::Units::Label>(
          UnitFactory::Instance().create("Label"));
  lblUnit->setLabel("Time", Units::Symbol::Microsecond);
  localWorkspace->getAxis(0)->unit() = lblUnit;
  // Set y axis unit
  localWorkspace->setYUnit("Counts");

  WorkspaceGroup_sptr wsGrpSptr = WorkspaceGroup_sptr(new WorkspaceGroup);

  API::Progress progress(this, 0.0, 1.0, m_numberOfPeriods * total_specs);
  // Loop over the number of periods in the Nexus file, putting each period in a
  // separate workspace
  for (int64_t period = 0; period < m_numberOfPeriods; ++period) {
    if (m_entrynumber != 0) {
      period = m_entrynumber - 1;
      if (period != 0) {
        loadRunDetails(localWorkspace);
        runLoadInstrument(localWorkspace);
      }
    }

    if (period == 0) {
      // Only run the Child Algorithms once
      loadRunDetails(localWorkspace);
      runLoadInstrument(localWorkspace);
      runLoadLog(localWorkspace);
      localWorkspace->populateInstrumentParameters();
    } else // We are working on a higher period of a multiperiod raw file
    {
      localWorkspace = std::dynamic_pointer_cast<DataObjects::Workspace2D>(
          WorkspaceFactory::Instance().create(localWorkspace));
      localWorkspace->setTitle(title);
      localWorkspace->setComment(notes);
    }
    addPeriodLog(localWorkspace, period);
    addGoodFrames(localWorkspace, period, nxload.t_nper);

    size_t counter = 0;
    for (auto i = m_spec_min; i < m_spec_max; ++i) {
      // Shift the histogram to read if we're not in the first period
      auto histToRead = static_cast<specnum_t>(i - 1 + period * nxload.t_nsp1);
      auto specNo = i;
      loadData(counter, histToRead, specNo, nxload, lengthIn - 1,
               localWorkspace); // added -1 for NeXus
      counter++;
      progress.report();
    }
    // Read in the spectra in the optional list parameter, if set
    if (m_list) {
      for (auto specid : m_spec_list) {
        auto histToRead =
            static_cast<specnum_t>(specid - 1 + period * nxload.t_nsp1);
        auto specNo = static_cast<specnum_t>(specid);
        loadData(counter, histToRead, specNo, nxload, lengthIn - 1,
                 localWorkspace);
        counter++;
        progress.report();
      }
    }
    // Just a sanity check
    assert(counter == size_t(total_specs));

    Workspace_sptr outWs;

    Workspace_sptr loadedGrouping;

    // Try to load detector grouping info, if needed for auto-grouping or user
    // requested it
    if (autoGroup || returnGrouping) {
      loadedGrouping =
          loadDetectorGrouping(root, localWorkspace->getInstrument());

      if (loadedGrouping && returnGrouping) {
        // Return loaded grouping, if requested
        setProperty("DetectorGroupingTable", loadedGrouping);
      }

      if (!loadedGrouping && autoGroup) {
        // If autoGroup requested and no grouping in the file - show a warning
        g_log.warning(
            "Unable to load grouping from the file. Grouping not applied.");
      }
    }

    if (autoGroup && loadedGrouping) {
      TableWorkspace_sptr groupingTable;

      if (auto table =
              std::dynamic_pointer_cast<TableWorkspace>(loadedGrouping)) {
        groupingTable = table;
      } else if (auto group = std::dynamic_pointer_cast<WorkspaceGroup>(
                     loadedGrouping)) {
        groupingTable =
            std::dynamic_pointer_cast<TableWorkspace>(group->getItem(period));
      }
      std::vector<int> specIDs, detecIDs;
      for (size_t i = 0; i < localWorkspace->getNumberHistograms(); i++) {
        specIDs.emplace_back(localWorkspace->getSpectrum(i).getSpectrumNo());
        detecIDs.emplace_back(localWorkspace->getSpectrum(i).getSpectrumNo());
      }
      API::SpectrumDetectorMapping mapping(specIDs, detecIDs);
      localWorkspace->updateSpectraUsing(mapping);

      Algorithm_sptr groupDet = createChildAlgorithm("MuonGroupDetectors");
      groupDet->setProperty("InputWorkspace", localWorkspace);
      groupDet->setProperty("DetectorGroupingTable", groupingTable);
      groupDet->execute();

      MatrixWorkspace_sptr groupedWs = groupDet->getProperty("OutputWorkspace");

      outWs = groupedWs;
    } else {
      outWs = localWorkspace;
    }

    if (m_numberOfPeriods == 1)
      setProperty("OutputWorkspace", outWs);
    else
      // In case of multiple periods, just add workspace to the group, and we
      // will return the
      // group later
      wsGrpSptr->addWorkspace(outWs);

  } // loop over periods

  if (m_numberOfPeriods > 1) {
    setProperty("OutputWorkspace",
                std::dynamic_pointer_cast<Workspace>(wsGrpSptr));
  }
}

/**
 * Loads dead time table for the detector.
 * @param root :: Root entry of the Nexus to read dead times from
 */
void LoadMuonNexus1::loadDeadTimes(NXRoot &root) {
  // If dead times workspace name is empty - caller doesn't need dead times
  if (getPropertyValue("DeadTimeTable").empty())
    return;

  NXEntry detector = root.openEntry("run/instrument/detector");

  NXInfo infoDeadTimes = detector.getDataSetInfo("deadtimes");
  if (infoDeadTimes.stat != NX_ERROR) {
    NXFloat deadTimesData = detector.openNXFloat("deadtimes");
    deadTimesData.load();

    int numDeadTimes = deadTimesData.dim0();

    std::vector<int> specToLoad;
    std::vector<double> deadTimes;

    // Set the spectrum list that should be loaded
    if (m_interval || m_list) {
      // Load only selected spectra
      specToLoad.insert(specToLoad.end(),
                        boost::counting_iterator<specnum_t>(m_spec_min),
                        boost::counting_iterator<specnum_t>(m_spec_max));
      specToLoad.insert(specToLoad.end(), m_spec_list.begin(),
                        m_spec_list.end());
    } else {
      // Load all the spectra
      // Start from 1 to N+1 to be consistent with
      // the case where spectra are specified
      for (int i = 1; i < numDeadTimes / m_numberOfPeriods + 1; i++)
        specToLoad.emplace_back(i);
    }

    if (numDeadTimes < m_numberOfSpectra) {
      // Check number of dead time entries match the number of
      // spectra in the nexus file
      throw Exception::FileError(
          "Number of dead times specified is less than number of spectra",
          m_filename);

    } else if (numDeadTimes % m_numberOfSpectra) {

      // At least, number of dead times should cover the number of spectra
      throw Exception::FileError(
          "Number of dead times doesn't cover every spectrum in every period",
          m_filename);
    } else {

      if (m_numberOfPeriods == 1) {
        // Simplest case - one dead time for one detector

        // Populate deadTimes
        deadTimes.reserve(specToLoad.size());
        for (auto &spectra : specToLoad) {
          deadTimes.emplace_back(deadTimesData[spectra - 1]);
        }
        // Load into table
        TableWorkspace_sptr table = createDeadTimeTable(specToLoad, deadTimes);
        setProperty("DeadTimeTable", table);

      } else if (numDeadTimes == m_numberOfSpectra) {
        // Multiple periods, but the same dead times for each

        specToLoad.clear();
        for (int i = 1; i < numDeadTimes + 1; i++) {
          specToLoad.emplace_back(i);
        }
        deadTimes.reserve(specToLoad.size());
        for (const auto &spectrum : specToLoad) {
          deadTimes.emplace_back(deadTimesData[spectrum - 1]);
        }
        // Load into table
        TableWorkspace_sptr table = createDeadTimeTable(specToLoad, deadTimes);
        setProperty("DeadTimeTable", table);
      } else {
        // More complex case - different dead times for different periods
        WorkspaceGroup_sptr tableGroup = std::make_shared<WorkspaceGroup>();

        for (int64_t i = 0; i < m_numberOfPeriods; i++) {

          // Populate deadTimes
          deadTimes.reserve(specToLoad.size());
          for (auto spec : specToLoad) {
            auto index = static_cast<int>(spec - 1 + i * m_numberOfSpectra);
            deadTimes.emplace_back(deadTimesData[index]);
          }

          // Load into table
          TableWorkspace_sptr table =
              createDeadTimeTable(specToLoad, deadTimes);

          tableGroup->addWorkspace(table);
        }

        setProperty("DeadTimeTable", tableGroup);
      }
    }
  }
  // It is expected that file might not contain any dead times, so not finding
  // them is not an
  // error
}

/**
 * Loads detector grouping.
 * If no entry in NeXus file for grouping, load it from the IDF.
 * @param root :: Root entry of the Nexus file to read from
 * @param inst :: Pointer to instrument (to use if IDF needed)
 * @returns :: Grouping table - or tables, if per period
 */
Workspace_sptr LoadMuonNexus1::loadDetectorGrouping(
    NXRoot &root, const Geometry::Instrument_const_sptr &inst) {
  NXEntry dataEntry = root.openEntry("run/histogram_data_1");

  NXInfo infoGrouping = dataEntry.getDataSetInfo("grouping");
  if (infoGrouping.stat != NX_ERROR) {
    NXInt groupingData = dataEntry.openNXInt("grouping");
    groupingData.load();

    int numGroupingEntries = groupingData.dim0();

    std::vector<int> specToLoad;
    std::vector<int> grouping;

    // Set the spectrum list that should be loaded
    if (m_interval || m_list) {
      // Load only selected spectra
      specToLoad.insert(specToLoad.end(),
                        boost::counting_iterator<specnum_t>(m_spec_min),
                        boost::counting_iterator<specnum_t>(m_spec_max));
      specToLoad.insert(specToLoad.end(), m_spec_list.begin(),
                        m_spec_list.end());
    } else {
      // Load all the spectra
      // Start from 1 to N+1 to be consistent with
      // the case where spectra are specified
      for (int i = 1; i < m_numberOfSpectra + 1; i++)
        specToLoad.emplace_back(i);
    }

    if (numGroupingEntries < m_numberOfSpectra) {
      // Check number of dead time entries match the number of
      // spectra in the nexus file
      throw Exception::FileError(
          "Number of grouping entries is less than number of spectra",
          m_filename);

    } else if (numGroupingEntries % m_numberOfSpectra) {
      // At least the number of entries should cover all the spectra
      throw Exception::FileError("Number of grouping entries doesn't cover "
                                 "every spectrum in every period",
                                 m_filename);

    } else {

      if (m_numberOfPeriods == 1) {
        // Simplest case - one grouping entry per spectrum
        grouping.reserve(grouping.size() + specToLoad.size());
        if (!m_entrynumber) {
          // m_entrynumber = 0 && m_numberOfPeriods = 1 means that user did not
          // select
          // any periods but there is only one in the dataset
          for (auto spec : specToLoad) {
            grouping.emplace_back(groupingData[spec - 1]);
          }
        } else {
          // User selected an entry number
          for (auto &spec : specToLoad) {
            int index =
                spec - 1 +
                static_cast<int>((m_entrynumber - 1) * m_numberOfSpectra);
            grouping.emplace_back(groupingData[index]);
          }
        }

        TableWorkspace_sptr table =
            createDetectorGroupingTable(specToLoad, grouping);

        if (table->rowCount() != 0)
          return table;

      } else if (numGroupingEntries == m_numberOfSpectra) {
        // Multiple periods - same grouping for each
        specToLoad.clear();
        for (int i = 1; i < m_numberOfSpectra + 1; i++) {
          specToLoad.emplace_back(i);
        }
        for (const auto &spectrum : specToLoad) {
          grouping.emplace_back(groupingData[spectrum - 1]);
        }
        // Load into table
        TableWorkspace_sptr table =
            createDetectorGroupingTable(specToLoad, grouping);
        if (table->rowCount() != 0)
          return table;
      } else {
        // More complex case - grouping information for every period

        WorkspaceGroup_sptr tableGroup = std::make_shared<WorkspaceGroup>();

        for (int i = 0; i < m_numberOfPeriods; i++) {

          // Get the grouping
          grouping.clear();
          for (auto &spec : specToLoad) {
            int index = spec - 1 + i * static_cast<int>(m_numberOfSpectra);
            grouping.emplace_back(groupingData[index]);
          }

          // Set table for period i
          TableWorkspace_sptr table =
              createDetectorGroupingTable(specToLoad, grouping);

          // Add table to group
          if (table->rowCount() != 0)
            tableGroup->addWorkspace(table);
        }

        if (tableGroup->size() != 0) {
          if (tableGroup->size() != static_cast<size_t>(m_numberOfPeriods))
            throw Exception::FileError("Zero grouping for some of the periods",
                                       m_filename);

          return tableGroup;
        }
      }
    }
  }
  // If we reach this point, no/zero grouping found.
  // Try to load from IDF instead
  const std::string mainFieldDirection = getProperty("MainFieldDirection");
  API::GroupingLoader groupLoader(inst, mainFieldDirection);
  try {
    const auto idfGrouping = groupLoader.getGroupingFromIDF();
    g_log.warning("Loading grouping from IDF");
    return idfGrouping->toTable();
  } catch (const std::runtime_error &) {
    g_log.warning("Loading dummy grouping");
    auto dummyGrouping = std::make_shared<Grouping>();
    if (inst->getNumberDetectors() != 0) {
      dummyGrouping = groupLoader.getDummyGrouping();
    } else {
      // Make sure it uses the right number of detectors
      std::ostringstream oss;
      oss << "1-" << m_numberOfSpectra;
      dummyGrouping->groups.emplace_back(oss.str());
      dummyGrouping->description = "Dummy grouping";
      dummyGrouping->groupNames.emplace_back("all");
    }
    return dummyGrouping->toTable();
  }
}

/**
 * Creates Dead Time Table using all the data between begin and end.
 * @param specToLoad :: vector containing the spectrum numbers to load
 * @param deadTimes :: vector containing the corresponding dead times
 * @return Dead Time Table create using the data
 */
TableWorkspace_sptr
LoadMuonNexus1::createDeadTimeTable(std::vector<int> specToLoad,
                                    std::vector<double> deadTimes) {
  TableWorkspace_sptr deadTimeTable = std::dynamic_pointer_cast<TableWorkspace>(
      WorkspaceFactory::Instance().createTable("TableWorkspace"));

  deadTimeTable->addColumn("int", "spectrum");
  deadTimeTable->addColumn("double", "dead-time");

  for (size_t i = 0; i < specToLoad.size(); i++) {
    TableRow row = deadTimeTable->appendRow();
    row << specToLoad[i] << deadTimes[i];
  }

  return deadTimeTable;
}

/**
 * Creates Detector Grouping Table using all the data between begin and end.
 *
 * @param specToLoad :: Vector containing the spectrum list to load
 * @param grouping :: Vector containing corresponding grouping
 * @return Detector Grouping Table create using the data
 */
TableWorkspace_sptr
LoadMuonNexus1::createDetectorGroupingTable(std::vector<int> specToLoad,
                                            std::vector<int> grouping) {
  auto detectorGroupingTable = std::dynamic_pointer_cast<TableWorkspace>(
      WorkspaceFactory::Instance().createTable("TableWorkspace"));

  detectorGroupingTable->addColumn("vector_int", "Detectors");

  std::map<int, std::vector<int>> groupingMap;

  for (size_t i = 0; i < specToLoad.size(); i++) {
    // Add detector ID to the list of group detectors. Detector ID is always
    // spectra index + 1
    groupingMap[grouping[i]].emplace_back(specToLoad[i]);
  }

  for (auto &group : groupingMap) {
    if (group.first != 0) // Skip 0 group
    {
      TableRow newRow = detectorGroupingTable->appendRow();
      newRow << group.second;
    }
  }

  return detectorGroupingTable;
}

/** Load in a single spectrum taken from a NeXus file
 *  @param hist ::     The workspace index
 *  @param i ::        The spectrum number
 *  @param specNo ::   The spectrum number
 *  @param nxload ::   A reference to the MuonNeXusReader object
 *  @param lengthIn :: The number of elements in a spectrum
 *  @param localWorkspace :: A pointer to the workspace in which the data will
 * be stored
 */
void LoadMuonNexus1::loadData(
    size_t hist, specnum_t &i, specnum_t specNo, MuonNexusReader &nxload,
    const int64_t lengthIn,
    const DataObjects::Workspace2D_sptr &localWorkspace) {
  // Read in a spectrum
  // Put it into a vector, discarding the 1st entry, which is rubbish
  // But note that the last (overflow) bin is kept
  // For Nexus, not sure if above is the case, hence give all data for now

  // Create and fill another vector for the X axis
  auto timeChannels = new float[lengthIn + 1]();
  nxload.getTimeChannels(timeChannels, static_cast<int>(lengthIn + 1));
  // Put the read in array into a vector (inside a shared pointer)

  localWorkspace->setHistogram(
      hist, BinEdges(timeChannels, timeChannels + lengthIn + 1),
      Counts(nxload.counts + i * lengthIn,
             nxload.counts + i * lengthIn + lengthIn));

  localWorkspace->getSpectrum(hist).setSpectrumNo(specNo);
  // Muon v1 files: always a one-to-one mapping between spectra and detectors
  localWorkspace->getSpectrum(hist).setDetectorID(static_cast<detid_t>(specNo));
  // Clean up
  delete[] timeChannels;
}

/**  Log the run details from the file
 * @param localWorkspace :: The workspace details to use
 */
void LoadMuonNexus1::loadRunDetails(
    const DataObjects::Workspace2D_sptr &localWorkspace) {
  API::Run &runDetails = localWorkspace->mutableRun();

  runDetails.addProperty("run_title", localWorkspace->getTitle(), true);

  auto numSpectra = static_cast<int>(localWorkspace->getNumberHistograms());
  runDetails.addProperty("nspectra", numSpectra);

  NXRoot root(m_filename);
  try {
    std::string start_time = root.getString("run/start_time");
    runDetails.addProperty("run_start", start_time);
  } catch (std::runtime_error &) {
    g_log.warning("run/start_time is not available, run_start log not added.");
  }

  try {
    std::string stop_time = root.getString("run/stop_time");
    runDetails.addProperty("run_end", stop_time);
  } catch (std::runtime_error &) {
    g_log.warning("run/stop_time is not available, run_end log not added.");
  }

  try {
    std::string dur = root.getString("run/duration");
    runDetails.addProperty("dur", dur);
    runDetails.addProperty("durunits", 1); // 1 means second here
    runDetails.addProperty("dur_secs", dur);
  } catch (std::runtime_error &) {
    g_log.warning("run/duration is not available, dur log not added.");
  }

  // Get sample parameters
  NXEntry runSample = root.openEntry("run/sample");

  if (runSample.containsDataSet("temperature")) {
    float temperature = runSample.getFloat("temperature");
    runDetails.addProperty("sample_temp", static_cast<double>(temperature));
  }

  if (runSample.containsDataSet("magnetic_field")) {
    float magn_field = runSample.getFloat("magnetic_field");
    runDetails.addProperty("sample_magn_field",
                           static_cast<double>(magn_field));
  }
}

/// Run the LoadLog Child Algorithm
void LoadMuonNexus1::runLoadLog(
    const DataObjects::Workspace2D_sptr &localWorkspace) {
  IAlgorithm_sptr loadLog = createChildAlgorithm("LoadMuonLog");
  // Pass through the same input filename
  loadLog->setPropertyValue("Filename", m_filename);
  // Set the workspace property to be the same one filled above
  loadLog->setProperty<MatrixWorkspace_sptr>("Workspace", localWorkspace);

  // Now execute the Child Algorithm. Catch and log any error, but don't stop.
  try {
    loadLog->execute();
  } catch (std::runtime_error &) {
    g_log.error("Unable to successfully run LoadMuonLog Child Algorithm");
  } catch (std::logic_error &) {
    g_log.error("Unable to successfully run LoadMuonLog Child Algorithm");
  }

  if (!loadLog->isExecuted())
    g_log.error("Unable to successfully run LoadMuonLog Child Algorithm");

  NXRoot root(m_filename);

  // Get main field direction
  std::string mainFieldDirection = "Longitudinal"; // default
  try {
    NXChar orientation = root.openNXChar("run/instrument/detector/orientation");
    // some files have no data there
    orientation.load();

    if (orientation[0] == 't') {
      auto p =
          std::make_unique<Kernel::TimeSeriesProperty<double>>("fromNexus");
      std::string start_time = root.getString("run/start_time");
      p->addValue(start_time, -90.0);
      localWorkspace->mutableRun().addLogData(std::move(p));
      mainFieldDirection = "Transverse";
    }
  } catch (...) {
    // no data - assume main field was longitudinal
  }

  // set output property and add to workspace logs
  auto &run = localWorkspace->mutableRun();
  setProperty("MainFieldDirection", mainFieldDirection);
  run.addProperty("main_field_direction", mainFieldDirection);

  ISISRunLogs runLogs(run);
  runLogs.addStatusLog(run);
}

/**
 * Add the 'period i' log to a workspace.
 * @param localWorkspace A workspace to add the log to.
 * @param period A period for this workspace.
 */
void LoadMuonNexus1::addPeriodLog(
    const DataObjects::Workspace2D_sptr &localWorkspace, int64_t period) {
  auto &run = localWorkspace->mutableRun();
  ISISRunLogs runLogs(run);
  if (period == 0) {
    runLogs.addPeriodLogs(1, run);
  } else {
    run.removeLogData("period 1");
    runLogs.addPeriodLog(static_cast<int>(period) + 1, run);
  }
}

void LoadMuonNexus1::addGoodFrames(
    const DataObjects::Workspace2D_sptr &localWorkspace, int64_t period,
    int nperiods) {

  // Get handle to nexus file
  ::NeXus::File handle(m_filename, NXACC_READ);

  // For single-period datasets, read /run/instrument/beam/frames_good
  if (nperiods == 1) {

    try {

      handle.openPath("run/instrument/beam");
      try {
        handle.openData("frames_good");
      } catch (::NeXus::Exception &) {
        // If it's not there, read "frames" instead and assume they are good
        g_log.warning("Could not read /run/instrument/beam/frames_good");
        handle.openData("frames");
        g_log.warning("Using run/instrument/beam/frames instead");
      }

      // read frames_period_daq
      boost::scoped_array<int> dataVals(new int[1]);
      handle.getData(dataVals.get());

      auto &run = localWorkspace->mutableRun();
      run.addProperty("goodfrm", dataVals[0]);

    } catch (::NeXus::Exception &) {
      g_log.warning("Could not read number of good frames");
    }

  } else {
    // For multi-period datasets, read entries in
    // /run/instrument/beam/frames_period_daq
    try {

      handle.openPath("run/instrument/beam/");
      handle.openData("frames_period_daq");

      ::NeXus::Info info = handle.getInfo();
      // Check that frames_period_daq contains values for
      // every period
      if (period >= info.dims[0]) {
        std::ostringstream error;
        error << "goodfrm not found for period " << period;
        throw std::runtime_error(error.str());
      }
      if (nperiods != info.dims[0]) {
        std::ostringstream error;
        error << "Inconsistent number of period entries found (";
        error << info.dims[0];
        error << "!=" << nperiods << ")";
        throw std::runtime_error(error.str());
      }

      // read frames_period_daq
      boost::scoped_array<int> dataVals(new int[info.dims[0]]);
      handle.getData(dataVals.get());

      auto &run = localWorkspace->mutableRun();
      if (period == 0) {
        // If this is the first period
        // localWorkspace will not contain goodfrm
        run.addProperty("goodfrm", dataVals[0]);

      } else {
        // If period > 0, we need to remove
        // previous goodfrm log value
        run.removeLogData("goodfrm");
        run.addProperty("goodfrm", dataVals[period]);
      }
    } catch (::NeXus::Exception &) {
      g_log.warning("Could not read /run/instrument/beam/frames_period_daq");
    }
  } // else

  handle.close();
}

/**
 * Return the confidence with with this algorithm can load the file
 * @param descriptor A descriptor for the file
 * @returns An integer specifying the confidence level. 0 indicates it will not
 * be used
 */
int LoadMuonNexus1::confidence(Kernel::NexusDescriptor &descriptor) const {
  const auto &firstEntryNameType = descriptor.firstEntryNameType();
  const std::string root = "/" + firstEntryNameType.first;
  if (!descriptor.pathExists(root + "/analysis"))
    return 0;

  bool upperIDF(true);
  if (descriptor.pathExists(root + "/IDF_version"))
    upperIDF = true;
  else {
    if (descriptor.pathExists(root + "/idf_version"))
      upperIDF = false;
    else
      return 0;
  }

  try {
    std::string versionField = "idf_version";
    if (upperIDF)
      versionField = "IDF_version";

    auto &file = descriptor.data();
    file.openPath(root + "/" + versionField);
    int32_t version = 0;
    file.getData(&version);
    if (version != 1)
      return 0;

    file.openPath(root + "/analysis");
    std::string def = file.getStrData();
    if (def == "muonTD" || def == "pulsedTD") {
      // If all this succeeded then we'll assume this is an ISIS Muon NeXus file
      // version 2
      return 81;
    }
  } catch (...) {
  }
  return 0;
}

} // namespace DataHandling
} // namespace Mantid