/**
 * Load an NX log entry a group type that has value and time entries.
 * @param file :: A reference to the NeXus file handle opened at the parent
 * group
 * @param entry_name :: The name of the log entry
 * @param entry_class :: The type of the entry
 * @param workspace :: A pointer to the workspace to store the logs
 */
void LoadNexusLogs::loadNXLog(
    ::NeXus::File &file, const std::string &entry_name,
    const std::string &entry_class,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  g_log.debug() << "processing " << entry_name << ":" << entry_class << "\n";

  file.openGroup(entry_name, entry_class);
  // Validate the NX log class.
  std::map<std::string, std::string> entries = file.getEntries();
  if ((entries.find("value") == entries.end()) ||
      (entries.find("time") == entries.end())) {
    g_log.warning() << "Invalid NXlog entry " << entry_name
                    << " found. Did not contain 'value' and 'time'.\n";
    file.closeGroup();
    return;
  }
  // whether or not to overwrite logs on workspace
  bool overwritelogs = this->getProperty("OverwriteLogs");
  try {
    if (overwritelogs || !(workspace->run().hasProperty(entry_name))) {
      Kernel::Property *logValue = createTimeSeries(file, entry_name);
      workspace->mutableRun().addProperty(logValue, overwritelogs);
    }
  } catch (::NeXus::Exception &e) {
    g_log.warning() << "NXlog entry " << entry_name
                    << " gave an error when loading:'" << e.what() << "'.\n";
  }

  file.closeGroup();
}

void
SaveNXTomo::writeImageKeyValue(const DataObjects::Workspace2D_sptr workspace,
                               ::NeXus::File &nxFile, int thisFileInd) {
  // Add ImageKey to instrument/image_key if present, use 0 if not
  try {
    nxFile.openPath("/entry1/tomo_entry/instrument/detector");
  } catch (...) {
    throw std::runtime_error("Unable to create a valid NXTomo file");
  }

  // Set the default key value for this WS
  std::vector<double> keyValue;
  keyValue.push_back(0);

  if (workspace->run().hasProperty("ImageKey")) {
    std::string tmpVal = workspace->run().getLogData("ImageKey")->value();
    try {
      keyValue[0] = boost::lexical_cast<double>(tmpVal);
    } catch (...) {
    }
    // Invalid Cast is handled below
  }

  nxFile.openData("image_key");
  nxFile.putSlab(keyValue, thisFileInd, 1);
  nxFile.closeData();

  nxFile.closeGroup();
}

/** Load the pulse times, if needed. This sets
 * thisBankPulseTimes to the right pointer.
 * */
void LoadBankFromDiskTask::loadPulseTimes(::NeXus::File &file) {
  try {
    // First, get info about the event_time_zero field in this bank
    file.openData("event_time_zero");
  } catch (::NeXus::Exception &) {
    // Field not found error is most likely.
    // Use the "proton_charge" das logs.
    thisBankPulseTimes = m_loader.alg->m_allBanksPulseTimes;
    return;
  }
  std::string thisStartTime;
  size_t thisNumPulses = 0;
  file.getAttr("offset", thisStartTime);
  if (!file.getInfo().dims.empty())
    thisNumPulses = file.getInfo().dims[0];
  file.closeData();

  // Now, we look through existing ones to see if it is already loaded
  // thisBankPulseTimes = NULL;
  for (auto &bankPulseTime : m_loader.m_bankPulseTimes) {
    if (bankPulseTime->equals(thisNumPulses, thisStartTime)) {
      thisBankPulseTimes = bankPulseTime;
      return;
    }
  }

  // Not found? Need to load and add it
  thisBankPulseTimes = boost::make_shared<BankPulseTimes>(boost::ref(file),
                                                          m_framePeriodNumbers);
  m_loader.m_bankPulseTimes.push_back(thisBankPulseTimes);
}

/** Load the event_index field
(a list of size of # of pulses giving the index in the event list for that
pulse)

* @param file :: File handle for the NeXus file
* @param event_index :: ref to the vector
*/
void LoadBankFromDiskTask::loadEventIndex(::NeXus::File &file,
                                          std::vector<uint64_t> &event_index) {
  // Get the event_index (a list of size of # of pulses giving the index in
  // the event list for that pulse)
  file.openData("event_index");
  // Must be uint64
  if (file.getInfo().type == ::NeXus::UINT64)
    file.getData(event_index);
  else {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_index field is not UINT64! It will be skipped.\n";
    m_loadError = true;
  }
  file.closeData();

  // Look for the sign that the bank is empty
  if (event_index.size() == 1) {
    if (event_index[0] == 0) {
      // One entry, only zero. This means NO events in this bank.
      m_loadError = true;
      m_loader.alg->getLogger().debug() << "Bank " << entry_name
                                        << " is empty.\n";
    }
  }
}

/**
 * Open the first NXentry of the supplied nexus file.
 *
 * @param handle Object to work on.
 */
void MuonNexusReader::openFirstNXentry(NeXus::File &handle) {
  std::map<string, string> entries = handle.getEntries();
  const auto entry =
      std::find_if(entries.cbegin(), entries.cend(),
                   [](const auto entry) { return entry.second == NXENTRY; });
  if (entry == entries.cend())
    throw std::runtime_error("Failed to find NXentry");
  handle.openGroup(entry->first, NXENTRY);
}

void SaveNXTomo::writeLogValues(const DataObjects::Workspace2D_sptr workspace,
                                ::NeXus::File &nxFile, int thisFileInd) {
  // Add Log information (minus special values - Rotation, ImageKey, Intensity)
  // Unable to add multidimensional string data, storing strings as
  // multidimensional data set of uint8 values
  try {
    nxFile.openPath("/entry1/log_info");
  } catch (...) {
    throw std::runtime_error("Unable to create a valid NXTomo file");
  }

  // Loop through all log values, create it if it doesn't exist. Then append
  // value
  std::vector<Property *> logVals = workspace->run().getLogData();

  for (auto it = logVals.begin(); it != logVals.end(); ++it) {
    auto prop = *it;
    if (prop->name() != "ImageKey" && prop->name() != "Rotation" &&
        prop->name() != "Intensity" && prop->name() != "Axis1" &&
        prop->name() != "Axis2") {
      try {
        nxFile.openData(prop->name());
      } catch (::NeXus::Exception &) {
        // Create the data entry if it doesn't exist yet, and open.
        std::vector<int64_t> infDim;
        infDim.push_back(NX_UNLIMITED);
        infDim.push_back(NX_UNLIMITED);
        nxFile.makeData(prop->name(), ::NeXus::UINT8, infDim, true);
      }

      size_t strSize = prop->value().length();

      char *val = new char[80]();

      // If log value is from FITS file as it should be,
      // it won't be greater than this. Otherwise Shorten it
      if (strSize > 80)
        strSize = 80;

      strncpy(val, prop->value().c_str(), strSize);

      std::vector<int64_t> start, size;
      start.push_back(thisFileInd);
      start.push_back(0);
      size.push_back(1);
      size.push_back(strSize);

      // single item
      nxFile.putSlab(val, start, size);

      nxFile.closeData();
    }
  }
}

/**
 * Open the first NXentry of the supplied nexus file.
 *
 * @param handle Object to work on.
 */
void MuonNexusReader::openFirstNXentry(NeXus::File &handle) {
  std::map<string, string> entries = handle.getEntries();
  bool found = false;
  for (auto &entrie : entries) {
    if (entrie.second == NXENTRY) {
      handle.openGroup(entrie.first, NXENTRY);
      found = true;
      break;
    }
  }
  if (!found)
    throw std::runtime_error("Failed to find NXentry");
}

/**
 * Can we get a histogram (non event data) for every monitor?
 *
 * @param file :: NeXus file object (open)
 * @param monitorNames :: names of monitors of interest
 * @return If there seems to be histograms for all monitors (they have "data")
 **/
bool LoadNexusMonitors2::allMonitorsHaveHistoData(
    ::NeXus::File &file, const std::vector<std::string> &monitorNames) {
  bool res = true;

  try {
    for (std::size_t i = 0; i < m_monitor_count; ++i) {
      file.openGroup(monitorNames[i], "NXmonitor");
      file.openData("data");
      file.closeData();
      file.closeGroup();
    }
  } catch (::NeXus::Exception &) {
    file.closeGroup();
    res = false;
  }
  return res;
}

    /**
     *
     * @param nxsFile A reference to the open NeXus fileIt should be opened at the
     *                "full_reference_detector" group
     * @param detInfo A reference to the struct that will hold the data from the file
     */
    void LoadDetectorInfo::readLibisisNxs(::NeXus::File & nxsFile, DetectorInfo & detInfo) const
    {
      nxsFile.readData<int32_t>("det_no", detInfo.ids);
      nxsFile.readData<int32_t>("det_type", detInfo.codes);
      nxsFile.readData<double>("delay_time", detInfo.delays);
      const size_t numDets = detInfo.ids.size();

      if(m_moveDets)
      {
        nxsFile.readData<double>("L2", detInfo.l2);
        nxsFile.readData<double>("theta", detInfo.theta);
        nxsFile.readData<double>("phi", detInfo.phi);
      }
      else
      {
        // these will get ignored
        detInfo.l2.resize(numDets, -1.0);
        detInfo.theta.resize(numDets, -1.0);
        detInfo.phi.resize(numDets, -1.0);
      }

      // pressure & wall thickness are global here
      double pressure = -1.0;
      double thickness = -1.0;
      nxsFile.openGroup("det_he3", "NXIXTdet_he3");
      nxsFile.readData<double>("gas_pressure", pressure);
      nxsFile.readData<double>("wall_thickness", thickness);
      nxsFile.closeGroup();
      if(pressure <= 0.0)
      {
        g_log.warning("The data file does not contain correct He3 pressure, "
                      "default value of 10 bar is used instead");
        pressure = 10.0;
      }
      if(thickness <= 0.0)
      {
        g_log.warning("The data file does not contain correct detector's wall "
                      "thickness, default value of 0.8mm is used instead");
        thickness = 0.0008;
      }
      detInfo.pressures.resize(numDets, pressure);
      detInfo.thicknesses.resize(numDets, thickness);
    }

void LoadNexusLogs::loadNPeriods(
    ::NeXus::File &file,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  int value = 1; // Default to 1-period unless
  try {
    file.openGroup("periods", "IXperiods");
    file.openData("number");
    file.getData(&value);
    file.closeData();
    file.closeGroup();
  } catch (::NeXus::Exception &) {
    // Likely missing IXperiods.
    return;
  }

  API::Run &run = workspace->mutableRun();
  const std::string nPeriodsLabel = "nperiods";
  if (!run.hasProperty(nPeriodsLabel)) {
    run.addProperty(new PropertyWithValue<int>(nPeriodsLabel, value));
  }
}

/** Load weight of weigthed events if they exist
 * @param file An NeXus::File object opened at the correct group
 * @returns A new array containing the weights or a nullptr if the weights
 * are not present
 */
std::unique_ptr<float[]>
LoadBankFromDiskTask::loadEventWeights(::NeXus::File &file) {
  try {
    // First, get info about the event_weight field in this bank
    file.openData("event_weight");
  } catch (::NeXus::Exception &) {
    // Field not found error is most likely.
    m_have_weight = false;
    return std::unique_ptr<float[]>();
  }
  // OK, we've got them
  m_have_weight = true;

  // Allocate the array
  auto event_weight = Mantid::Kernel::make_unique<float[]>(m_loadSize[0]);

  ::NeXus::Info weight_info = file.getInfo();
  int64_t weight_dim0 = recalculateDataSize(weight_info.dims[0]);
  if (weight_dim0 < m_loadSize[0] + m_loadStart[0]) {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_weight field is too small to load the desired data.\n";
    m_loadError = true;
  }

  // Check that the type is what it is supposed to be
  if (weight_info.type == ::NeXus::FLOAT32)
    file.getSlab(event_weight.get(), m_loadStart, m_loadSize);
  else {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_weight field is not FLOAT32! It will be skipped.\n";
    m_loadError = true;
  }

  if (!m_loadError) {
    file.closeData();
  }
  return event_weight;
}

/** Try to load the "Veto_pulse" field in DASLogs
 * and convert it to a sample log.
 *
 * @param file :: open nexus file at the DASLogs group
 * @param workspace :: workspace to add to.
 */
void LoadNexusLogs::loadVetoPulses(
    ::NeXus::File &file,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  try {
    file.openGroup("Veto_pulse", "NXgroup");
  } catch (::NeXus::Exception &) {
    // No group. This is common in older files
    return;
  }
  file.openData("veto_pulse_time");

  // Load the start date/time as ISO8601 string.
  std::string start_time;
  file.getAttr("start_time", start_time);
  DateAndTime start(start_time);

  // Read the offsets
  std::vector<double> time_double;
  file.getData(time_double);

  // Fake values with zeroes.
  std::vector<double> values(time_double.size(), 0.0);
  TimeSeriesProperty<double> *tsp =
      new TimeSeriesProperty<double>("veto_pulse_time");
  tsp->create(start, time_double, values);
  tsp->setUnits("");

  // Add the log
  workspace->mutableRun().addProperty(tsp);

  file.closeData();
  file.closeGroup();
}

/** Open and load the times-of-flight data
 * @param file An NeXus::File object opened at the correct group
 * @returns A new array containing the time of flights for this bank
 */
std::unique_ptr<float[]> LoadBankFromDiskTask::loadTof(::NeXus::File &file) {
  // Allocate the array
  auto event_time_of_flight =
      Mantid::Kernel::make_unique<float[]>(m_loadSize[0]);

  // Get the list of event_time_of_flight's
  std::string key, tof_unit;
  if (!m_oldNexusFileNames)
    key = "event_time_offset";
  else
    key = "event_time_of_flight";
  file.openData(key);

  // Check that the required space is there in the file.
  ::NeXus::Info tof_info = file.getInfo();
  int64_t tof_dim0 = recalculateDataSize(tof_info.dims[0]);
  if (tof_dim0 < m_loadSize[0] + m_loadStart[0]) {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_time_offset field is too small "
           "to load the desired data.\n";
    m_loadError = true;
  }

  // The Nexus standard does not specify if event_time_offset should be float or
  // integer, so we use the NeXusIOHelper to perform the conversion to float on
  // the fly. If the data field already contains floats, the conversion is
  // skipped.
  auto vec = NeXus::NeXusIOHelper::readNexusSlab<float>(file, key, m_loadStart,
                                                        m_loadSize);
  file.getAttr("units", tof_unit);
  file.closeData();
  // Convert Tof to microseconds
  Kernel::Units::timeConversionVector(vec, tof_unit, "microseconds");
  std::copy(vec.begin(), vec.end(), event_time_of_flight.get());

  return event_time_of_flight;
}

/**
 * Load log entries from the given group
 * @param file :: A reference to the NeXus file handle opened such that the
 * next call can be to open the named group
 * @param entry_name :: The name of the log entry
 * @param entry_class :: The class type of the log entry
 * @param workspace :: A pointer to the workspace to store the logs
 */
void LoadNexusLogs::loadLogs(
    ::NeXus::File &file, const std::string &entry_name,
    const std::string &entry_class,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  file.openGroup(entry_name, entry_class);
  std::map<std::string, std::string> entries = file.getEntries();
  std::map<std::string, std::string>::const_iterator iend = entries.end();
  for (std::map<std::string, std::string>::const_iterator itr = entries.begin();
       itr != iend; ++itr) {
    std::string log_class = itr->second;
    if (log_class == "NXlog" || log_class == "NXpositioner") {
      loadNXLog(file, itr->first, log_class, workspace);
    } else if (log_class == "IXseblock") {
      loadSELog(file, itr->first, workspace);
    } else if (log_class == "NXcollection") {
      int jj = 0;
      ++jj;
    }
  }
  loadVetoPulses(file, workspace);

  file.closeGroup();
}

/** Open and load the times-of-flight data
*/
void LoadBankFromDiskTask::loadTof(::NeXus::File &file) {
  // Allocate the array
  auto temp = new float[m_loadSize[0]];
  delete[] m_event_time_of_flight;
  m_event_time_of_flight = temp;

  // Get the list of event_time_of_flight's
  if (!m_oldNexusFileNames)
    file.openData("event_time_offset");
  else
    file.openData("event_time_of_flight");

  // Check that the required space is there in the file.
  ::NeXus::Info tof_info = file.getInfo();
  int64_t tof_dim0 = recalculateDataSize(tof_info.dims[0]);
  if (tof_dim0 < m_loadSize[0] + m_loadStart[0]) {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name << "'s event_time_offset field is too small "
                                     "to load the desired data.\n";
    m_loadError = true;
  }

  // Check that the type is what it is supposed to be
  if (tof_info.type == ::NeXus::FLOAT32)
    file.getSlab(m_event_time_of_flight, m_loadStart, m_loadSize);
  else {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_time_offset field is not FLOAT32! It will be skipped.\n";
    m_loadError = true;
  }

  if (!m_loadError) {
    std::string units;
    file.getAttr("units", units);
    if (units != "microsecond") {
      m_loader.alg->getLogger().warning()
          << "Entry " << entry_name << "'s event_time_offset field's units are "
                                       "not microsecond. It will be skipped.\n";
      m_loadError = true;
    }
    file.closeData();
  } // no error
}

/** Open the event_id field and validate the contents
 *
 * @param file :: File handle for the NeXus file
 * @param start_event :: set to the index of the first event
 * @param stop_event :: set to the index of the last event + 1
 * @param event_index ::  (a list of size of # of pulses giving the index in
 *the event list for that pulse)
 */
void LoadBankFromDiskTask::prepareEventId(
    ::NeXus::File &file, int64_t &start_event, int64_t &stop_event,
    const std::vector<uint64_t> &event_index) {
  // Get the list of pixel ID's
  if (m_oldNexusFileNames)
    file.openData("event_pixel_id");
  else
    file.openData("event_id");

  // By default, use all available indices
  start_event = 0;
  ::NeXus::Info id_info = file.getInfo();
  // dims[0] can be negative in ISIS meaning 2^32 + dims[0]. Take that into
  // account
  int64_t dim0 = recalculateDataSize(id_info.dims[0]);
  stop_event = dim0;

  // Handle the time filtering by changing the start/end offsets.
  for (size_t i = 0; i < thisBankPulseTimes->numPulses; i++) {
    if (thisBankPulseTimes->pulseTimes[i] >= m_loader.alg->filter_time_start) {
      start_event = static_cast<int64_t>(event_index[i]);
      break; // stop looking
    }
  }

  if (start_event > dim0) {
    // If the frame indexes are bad then we can't construct the times of the
    // events properly and filtering by time
    // will not work on this data
    m_loader.alg->getLogger().warning()
        << this->entry_name
        << "'s field 'event_index' seems to be invalid (start_index > than "
           "the number of events in the bank)."
        << "All events will appear in the same frame and filtering by time "
           "will not be possible on this data.\n";
    start_event = 0;
    stop_event = dim0;
  } else {
    for (size_t i = 0; i < thisBankPulseTimes->numPulses; i++) {
      if (thisBankPulseTimes->pulseTimes[i] > m_loader.alg->filter_time_stop) {
        stop_event = event_index[i];
        break;
      }
    }
  }
  // We are loading part - work out the event number range
  if (m_loader.chunk != EMPTY_INT()) {
    start_event =
        static_cast<int64_t>(m_loader.chunk - m_loader.firstChunkForBank) *
        static_cast<int64_t>(m_loader.eventsPerChunk);
    // Don't change stop_event for the final chunk
    if (start_event + static_cast<int64_t>(m_loader.eventsPerChunk) <
        stop_event)
      stop_event = start_event + static_cast<int64_t>(m_loader.eventsPerChunk);
  }

  // Make sure it is within range
  if (stop_event > dim0)
    stop_event = dim0;

  m_loader.alg->getLogger().debug()
      << entry_name << ": start_event " << start_event << " stop_event "
      << stop_event << "\n";
}

/**
 * Read histogram data
 * @param histogramEntries map of the file entries that have histogram
 * @param outputGroup pointer to the workspace group
 * @param nxFile Reads data from inside first first top entry
 */
void LoadMcStas::readHistogramData(
    const std::map<std::string, std::string> &histogramEntries,
    WorkspaceGroup_sptr &outputGroup, ::NeXus::File &nxFile) {

  std::string nameAttrValueYLABEL;

  for (const auto &histogramEntry : histogramEntries) {
    const std::string &dataName = histogramEntry.first;
    const std::string &dataType = histogramEntry.second;

    // open second level entry
    nxFile.openGroup(dataName, dataType);

    // grap title to use to e.g. create workspace name
    std::string nameAttrValueTITLE;
    nxFile.getAttr("filename", nameAttrValueTITLE);

    if (nxFile.hasAttr("ylabel")) {
      nxFile.getAttr("ylabel", nameAttrValueYLABEL);
    }

    // Find the axis names
    auto nxdataEntries = nxFile.getEntries();
    std::string axis1Name, axis2Name;
    for (auto &nxdataEntry : nxdataEntries) {
      if (nxdataEntry.second == "NXparameters")
        continue;
      if (nxdataEntry.first == "ncount")
        continue;
      nxFile.openData(nxdataEntry.first);

      if (nxFile.hasAttr("axis")) {
        int axisNo(0);
        nxFile.getAttr("axis", axisNo);
        if (axisNo == 1)
          axis1Name = nxdataEntry.first;
        else if (axisNo == 2)
          axis2Name = nxdataEntry.first;
        else
          throw std::invalid_argument("Unknown axis number");
      }
      nxFile.closeData();
    }

    std::vector<double> axis1Values, axis2Values;
    nxFile.readData<double>(axis1Name, axis1Values);
    if (axis2Name.length() == 0) {
      axis2Name = nameAttrValueYLABEL;
      axis2Values.push_back(0.0);
    } else {
      nxFile.readData<double>(axis2Name, axis2Values);
    }

    const size_t axis1Length = axis1Values.size();
    const size_t axis2Length = axis2Values.size();
    g_log.debug() << "Axis lengths=" << axis1Length << " " << axis2Length
                  << '\n';

    // Require "data" field
    std::vector<double> data;
    nxFile.readData<double>("data", data);

    // Optional errors field
    std::vector<double> errors;
    try {
      nxFile.readData<double>("errors", errors);
    } catch (::NeXus::Exception &) {
      g_log.information() << "Field " << dataName
                          << " contains no error information.\n";
    }

    // close second level entry
    nxFile.closeGroup();

    MatrixWorkspace_sptr ws = WorkspaceFactory::Instance().create(
        "Workspace2D", axis2Length, axis1Length, axis1Length);
    Axis *axis1 = ws->getAxis(0);
    axis1->title() = axis1Name;
    // Set caption
    auto lblUnit = boost::make_shared<Units::Label>();
    lblUnit->setLabel(axis1Name, "");
    axis1->unit() = lblUnit;

    Axis *axis2 = new NumericAxis(axis2Length);
    axis2->title() = axis2Name;
    // Set caption
    lblUnit = boost::make_shared<Units::Label>();
    lblUnit->setLabel(axis2Name, "");
    axis2->unit() = lblUnit;

    ws->setYUnit(axis2Name);
    ws->replaceAxis(1, axis2);

    for (size_t wsIndex = 0; wsIndex < axis2Length; ++wsIndex) {
//.........这里部分代码省略.........

/**
 * Writes a single workspace into the file
 * @param workspace the workspace to get data from
 * @param nxFile the nexus file to save data into
 */
void SaveNXTomo::writeSingleWorkspace(const Workspace2D_sptr workspace,
                                      ::NeXus::File &nxFile) {
  try {
    nxFile.openPath("/entry1/tomo_entry/data");
  } catch (...) {
    throw std::runtime_error("Unable to create a valid NXTomo file");
  }

  int numFiles = 0;
  nxFile.getAttr<int>("NumFiles", numFiles);

  // Change slab start to after last data position
  m_slabStart[0] = numFiles;
  m_slabSize[0] = 1;

  // Set the rotation value for this WS
  std::vector<double> rotValue;
  rotValue.push_back(0);

  if (workspace->run().hasProperty("Rotation")) {
    std::string tmpVal = workspace->run().getLogData("Rotation")->value();
    try {
      rotValue[0] = boost::lexical_cast<double>(tmpVal);
    } catch (...) {
    }
    // Invalid Cast is handled below
  }

  nxFile.openData("rotation_angle");
  nxFile.putSlab(rotValue, numFiles, 1);
  nxFile.closeData();

  // Copy data out, remake data with dimension of old size plus new elements.
  // Insert previous data.
  nxFile.openData("data");

  double *dataArr = new double[m_spectraCount];

  for (int64_t i = 0; i < m_dimensions[1]; ++i) {
    for (int64_t j = 0; j < m_dimensions[2]; ++j) {
      dataArr[i * m_dimensions[1] + j] =
          workspace->dataY(i * m_dimensions[1] + j)[0];
    }
  }

  nxFile.putSlab(dataArr, m_slabStart, m_slabSize);

  nxFile.closeData();

  nxFile.putAttr("NumFiles", numFiles + 1);

  nxFile.closeGroup();

  // Write additional log information, intensity and image key
  writeLogValues(workspace, nxFile, numFiles);
  writeIntensityValue(workspace, nxFile, numFiles);
  writeImageKeyValue(workspace, nxFile, numFiles);

  ++numFiles;

  delete[] dataArr;
}

bool MuonNexusReader::readMuonLogData(NeXus::File &handle) {
  const string NAME("name");
  const string VALUES("values");
  const string TIME("time");

  // read name of Log data
  string dataName;
  handle.readData(NAME, dataName);

  // read data values
  try {
    handle.openData(VALUES);
  } catch (NeXus::Exception &) {
    g_log.warning() << "No " << VALUES << " set in " << handle.getPath()
                    << "\n";
    return false;
  }

  std::vector<float> values;
  std::vector<std::string> stringValues;
  bool isNumeric(false);

  NeXus::Info info = handle.getInfo();
  if (info.type == NX_FLOAT32 && info.dims.size() == 1) {
    isNumeric = true;
    boost::scoped_array<float> dataVals(new float[info.dims[0]]);
    handle.getData(dataVals.get());
    values.assign(dataVals.get(), dataVals.get() + info.dims[0]);
    stringValues.resize(info.dims[0]); // Leave empty
  } else if (info.type == NX_CHAR && info.dims.size() == 2) {
    boost::scoped_array<char> dataVals(
        new char[info.dims[0] * info.dims[1] + 1]);
    handle.getData(dataVals.get());
    dataVals[info.dims[0] * info.dims[1]] = 0;
    for (int i = 0; i < info.dims[0]; ++i) {
      std::string str(&dataVals[i * info.dims[1]],
                      &dataVals[(i + 1) * info.dims[1]]);
      stringValues.push_back(str);
    }
    values.resize(info.dims[0]); // Leave empty
  } else {
    // Leave both empty
    values.resize(info.dims[0]);
    stringValues.resize(info.dims[0]);
  }
  handle.closeData();

  // read time values
  try {
    handle.openData(TIME);
  } catch (NeXus::Exception &) {
    g_log.warning() << "No " << TIME << " set in " << handle.getPath() << "\n";
    return false;
  }

  info = handle.getInfo();
  boost::scoped_array<float> timeVals(new float[info.dims[0]]);
  if (info.type == NX_FLOAT32 && info.dims.size() == 1) {
    handle.getData(timeVals.get());
  } else {
    throw std::runtime_error(
        "Error in MuonNexusReader: expected float array for log times");
  }
  handle.closeData();

  // Add loaded values to vectors

  logNames.push_back(dataName);

  std::vector<float> tmp(timeVals.get(), timeVals.get() + info.dims[0]);
  logTimes.push_back(tmp);

  logType.push_back(isNumeric);
  logValues.push_back(values);
  logStringValues.push_back(stringValues);

  return true;
}

    /**
    * Update the detector information from a NeXus file
    * @param nxFile :: Handle to a NeXus file where the root group has been opened
    */
    void UpdateInstrumentFromFile::updateFromNeXus(::NeXus::File & nxFile)
    {
      try
      {
        nxFile.openGroup("isis_vms_compat","IXvms");
      }
      catch(::NeXus::Exception&)
      {
        throw std::runtime_error("Unknown NeXus flavour. Cannot update instrument positions using this type of file");
      }
      // Det ID
      std::vector<int32_t> detID;
      nxFile.openData("UDET");
      nxFile.getData(detID);
      nxFile.closeData();
      // Position information
      std::vector<float> l2, theta,phi;
      nxFile.openData("LEN2");
      nxFile.getData(l2);
      nxFile.closeData();
      nxFile.openData("TTHE");
      nxFile.getData(theta);
      nxFile.closeData();
      nxFile.openData("UT01");
      nxFile.getData(phi);
      nxFile.closeData();

      g_log.information() << "Setting detector postions from NeXus file.\n";
      setDetectorPositions(detID, l2, theta, phi);
    }