/**
    * 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);
    }
Exemple #2
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/**
 * 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();
}
Exemple #3
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/** 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 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);
}
Exemple #5
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/**
 * 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;
}
Exemple #7
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    /**
     *
     * @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);
    }
Exemple #8
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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));
  }
}
/**
 * Fix the detector numbers if the defaults are not correct. Currently checks
 * the isis_vms_compat block and reads them from there if possible.
 *
 * @param det_ids :: An array of prefilled detector IDs
 * @param file :: A reference to the NeXus file opened at the root entry
 * @param spec_ids :: An array of spectrum numbers that the monitors have
 * @param nmonitors :: The size of the det_ids and spec_ids arrays
 */
void LoadNexusMonitors2::fixUDets(boost::scoped_array<detid_t> &det_ids,
                                  ::NeXus::File &file,
                                  const boost::scoped_array<specid_t> &spec_ids,
                                  const size_t nmonitors) const {
  try {
    file.openGroup("isis_vms_compat", "IXvms");
  } catch (::NeXus::Exception &) {
    return;
  }
  // UDET
  file.openData("UDET");
  std::vector<int32_t> udet;
  file.getData(udet);
  file.closeData();
  // SPEC
  file.openData("SPEC");
  std::vector<int32_t> spec;
  file.getData(spec);
  file.closeData();

  // This is a little complicated: Each value in the spec_id array is a value
  // found in the
  // SPEC block of isis_vms_compat. The index that this value is found at then
  // corresponds
  // to the index within the UDET block that holds the detector ID
  std::vector<int32_t>::const_iterator beg = spec.begin();
  for (size_t mon_index = 0; mon_index < nmonitors; ++mon_index) {
    std::vector<int32_t>::const_iterator itr =
        std::find(spec.begin(), spec.end(), spec_ids[mon_index]);
    if (itr == spec.end()) {
      det_ids[mon_index] = -1;
      continue;
    }
    std::vector<int32_t>::difference_type udet_index = std::distance(beg, itr);
    det_ids[mon_index] = udet[udet_index];
  }
  file.closeGroup();
}
Exemple #10
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/**
 * 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();
}
Exemple #11
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/** Loads an entry from a previously-open NXS file as a log entry
 * in the workspace's run.
 *
 * @param file: NXS file handle. MUST BE PASSED BY REFERENCE otherwise there
 *    occurs a segfault.
 * @param entry_name, entry_class: name and class of NXlog to open.
 */
void LoadLogsFromSNSNexus::loadSampleLog(::NeXus::File& file, std::string entry_name, std::string entry_class)
{
  // whether or not to overwrite logs on workspace
  bool overwritelogs = this->getProperty("OverwriteLogs");

  file.openGroup(entry_name, entry_class);

  // Validate the NX log class.
  map<string, 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;
  }


  ::NeXus::Info info;
  //Two possible types of properties:
  vector<double> values;
  vector<int> values_int;

  bool isTimeSeries = false;
  bool isInt = false;

  file.openData("value");

  //Get the units of the property
  std::string units("");
  try
  {
    file.getAttr("units", units);
  }
  catch (::NeXus::Exception &)
  {
    //Ignore missing units field.
    units = "";
  }

  //If there is more than one entry, it is a timeseries
  info = file.getInfo();
  //isTimeSeries = (info.dims[0] > 1);
  isTimeSeries = true;

  Timer timer1;
  try
  {
    //Get the data (convert types if necessary)
    if (file.isDataInt())
    {
      isInt = true;
      file.getDataCoerce(values_int);
//      if (values_int.size() == 1)
//      {
//        WS->mutableRun().addProperty(entry_name, values_int[0], units);
//      }

    }
    else
    {
      //Try to get as doubles.
      file.getDataCoerce(values);
//      if (values.size() == 1)
//      {
//        WS->mutableRun().addProperty(entry_name, values[0], units);
//      }
    }
  }
  catch (::NeXus::Exception &e)
  {
    g_log.warning() << "NXlog entry " << entry_name << " gave an error when loading 'value' data:'" << e.what() << "'.\n";
    file.closeData();
    file.closeGroup();
    return;
  }
  if (VERBOSE) std::cout << "getDataCoerce took " << timer1.elapsed() << " sec.\n";


  file.closeData();

  if (isTimeSeries)
  {
    // --- Time series property ---

    //Get the times
    vector<double> time_double;
    vector<DateAndTime> times;

    try {
      file.openData("time");
    }
    catch (::NeXus::Exception &e)
    {
      g_log.warning() << "NXlog entry " << entry_name << " gave an error when opening the time field '" << e.what() << "'.\n";
      file.closeGroup();
      return;
    }

    //----- Start time is an ISO8601 string date and time. ------
    std::string start;
    try {
      file.getAttr("start", start);
    }
    catch (::NeXus::Exception &)
    {
      //Some logs have "offset" instead of start
      try {
        file.getAttr("offset", start);
      }
      catch (::NeXus::Exception &)
      {
        g_log.warning() << "NXlog entry " << entry_name << " has no start time indicated.\n";
        file.closeData();
        file.closeGroup();
        return;
      }
    }

    //Convert to date and time
    Kernel::DateAndTime start_time = Kernel::DateAndTime(start);

    std::string time_units;
    file.getAttr("units", time_units);
    if (time_units != "second")
    {
      g_log.warning() << "NXlog entry " << entry_name << " has time units of '" << time_units << "', which are unsupported. 'second' is the only supported time unit.\n";
      file.closeData();
      file.closeGroup();
      return;
    }

    Timer timer2;
    //--- Load the seconds into a double array ---
    try {
      file.getDataCoerce(time_double);
    }
    catch (::NeXus::Exception &e)
    {
      g_log.warning() << "NXlog entry " << entry_name << "'s time field could not be loaded: '" << e.what() << "'.\n";
      file.closeData();
      file.closeGroup();
      return;
    }
    file.closeData();

    if (VERBOSE) std::cout << "getDataCoerce for the seconds field took " << timer2.elapsed() << " sec.\n";

    if (isInt)
    {
      //Make an int TSP
      TimeSeriesProperty<int> * tsp = new TimeSeriesProperty<int>(entry_name);
      tsp->create(start_time, time_double, values_int);
      tsp->setUnits( units );
      WS->mutableRun().addProperty( tsp, overwritelogs );
    }
    else
    {
      //Make a double TSP
      TimeSeriesProperty<double> * tsp = new TimeSeriesProperty<double>(entry_name);

      Timer timer3;
      tsp->create(start_time, time_double, values);
      if (VERBOSE) std::cout << "creating a TSP took  " << timer3.elapsed() << " sec.\n";

      tsp->setUnits( units );
      WS->mutableRun().addProperty( tsp, overwritelogs );
      // Trick to free memory?
      std::vector<double>().swap(time_double);
      std::vector<double>().swap(values);

    }

  }

  file.closeGroup();
}
Exemple #12
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/**
 * 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) {
      auto &dataY = ws->dataY(wsIndex);
      auto &dataE = ws->dataE(wsIndex);
      auto &dataX = ws->dataX(wsIndex);

      for (size_t j = 0; j < axis1Length; ++j) {
        // Data is stored in column-major order so we are translating to
        // row major for Mantid
        const size_t fileDataIndex = j * axis2Length + wsIndex;

        dataY[j] = data[fileDataIndex];
        dataX[j] = axis1Values[j];
        if (!errors.empty())
          dataE[j] = errors[fileDataIndex];
      }
      axis2->setValue(wsIndex, axis2Values[wsIndex]);
    }

    // set the workspace title
    ws->setTitle(nameAttrValueTITLE);

    // use the workspace title to create the workspace name
    std::replace(nameAttrValueTITLE.begin(), nameAttrValueTITLE.end(), ' ',
                 '_');

    // ensure that specified name is given to workspace (eventWS) when added to
    // outputGroup
    std::string nameOfGroupWS = getProperty("OutputWorkspace");
    std::string nameUserSee = nameAttrValueTITLE + "_" + nameOfGroupWS;
    std::string extraProperty =
        "Outputworkspace_dummy_" + std::to_string(m_countNumWorkspaceAdded);
    declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
        extraProperty, nameUserSee, Direction::Output));
    setProperty(extraProperty, boost::static_pointer_cast<Workspace>(ws));
    m_countNumWorkspaceAdded++; // need to increment to ensure extraProperty are
                                // unique

    // Make Mantid store the workspace in the group
    outputGroup->addWorkspace(ws);
  }
  nxFile.closeGroup();

} // finish
Exemple #13
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/**
 * Read Event Data
 * @param eventEntries map of the file entries that have events
 * @param nxFile Reads data from inside first top entry
 * @return Names of workspaces to include in the output group
 */
std::vector<std::string> LoadMcStas::readEventData(
    const std::map<std::string, std::string> &eventEntries,
    ::NeXus::File &nxFile) {

  // vector to store output workspaces
  std::vector<std::string> scatteringWSNames;

  std::string filename = getPropertyValue("Filename");
  auto entries = nxFile.getEntries();
  const bool errorBarsSetTo1 = getProperty("ErrorBarsSetTo1");

  // will assume that each top level entry contain one mcstas
  // generated IDF and any event data entries within this top level
  // entry are data collected for that instrument
  // This code for loading the instrument is for now adjusted code from
  // ExperimentalInfo.

  // Close data folder and go back to top level. Then read and close the
  // Instrument folder.
  nxFile.closeGroup();

  Geometry::Instrument_sptr instrument;

  // Initialize progress reporting
  int reports = 2;
  const double progressFractionInitial = 0.1;
  Progress progInitial(this, 0.0, progressFractionInitial, reports);

  std::string instrumentXML;
  progInitial.report("Loading instrument");
  try {
    nxFile.openGroup("instrument", "NXinstrument");
    nxFile.openGroup("instrument_xml", "NXnote");
    nxFile.readData("data", instrumentXML);
    nxFile.closeGroup();
    nxFile.closeGroup();
  } catch (...) {
    g_log.warning()
        << "\nCould not find the instrument description in the Nexus file:"
        << filename << " Ignore eventdata from the Nexus file\n";
    return scatteringWSNames;
    ;
  }

  try {
    std::string instrumentName = "McStas";
    Geometry::InstrumentDefinitionParser parser(filename, instrumentName,
                                                instrumentXML);
    std::string instrumentNameMangled = parser.getMangledName();

    // Check whether the instrument is already in the InstrumentDataService
    if (InstrumentDataService::Instance().doesExist(instrumentNameMangled)) {
      // If it does, just use the one from the one stored there
      instrument =
          InstrumentDataService::Instance().retrieve(instrumentNameMangled);
    } else {
      // Really create the instrument
      instrument = parser.parseXML(nullptr);
      // Add to data service for later retrieval
      InstrumentDataService::Instance().add(instrumentNameMangled, instrument);
    }
  } catch (Exception::InstrumentDefinitionError &e) {
    g_log.warning()
        << "When trying to read the instrument description in the Nexus file: "
        << filename << " the following error is reported: " << e.what()
        << " Ignore eventdata from the Nexus file\n";
    return scatteringWSNames;
    ;
  } catch (...) {
    g_log.warning()
        << "Could not parse instrument description in the Nexus file: "
        << filename << " Ignore eventdata from the Nexus file\n";
    return scatteringWSNames;
    ;
  }
  // Finished reading Instrument. Then open new data folder again
  nxFile.openGroup("data", "NXdetector");

  // create and prepare an event workspace ready to receive the mcstas events
  progInitial.report("Set up EventWorkspace");
  EventWorkspace_sptr eventWS(new EventWorkspace());
  // initialize, where create up front number of eventlists = number of
  // detectors
  eventWS->initialize(instrument->getNumberDetectors(), 1, 1);
  // Set the units
  eventWS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
  eventWS->setYUnit("Counts");
  // set the instrument
  eventWS->setInstrument(instrument);
  // assign detector ID to eventlists

  std::vector<detid_t> detIDs = instrument->getDetectorIDs();

  for (size_t i = 0; i < instrument->getNumberDetectors(); i++) {
    eventWS->getSpectrum(i).addDetectorID(detIDs[i]);
    // spectrum number are treated as equal to detector IDs for McStas data
    eventWS->getSpectrum(i).setSpectrumNo(detIDs[i]);
  }
  // the one is here for the moment for backward compatibility
  eventWS->rebuildSpectraMapping(true);

  bool isAnyNeutrons = false;
  // to store shortest and longest recorded TOF
  double shortestTOF(0.0);
  double longestTOF(0.0);

  // create vector container all the event output workspaces needed
  const size_t numEventEntries = eventEntries.size();
  std::string nameOfGroupWS = getProperty("OutputWorkspace");
  const auto eventDataTotalName = "EventData_" + nameOfGroupWS;
  std::vector<std::pair<EventWorkspace_sptr, std::string>> allEventWS = {
      {eventWS, eventDataTotalName}};
  // if numEventEntries > 1 also create separate event workspaces
  const bool onlySummedEventWorkspace =
      getProperty("OutputOnlySummedEventWorkspace");
  if (!onlySummedEventWorkspace && numEventEntries > 1) {
    for (const auto &eventEntry : eventEntries) {
      const std::string &dataName = eventEntry.first;
      // create container to hold partial event data
      // plus the name users will see for it
      const auto ws_name = dataName + "_" + nameOfGroupWS;
      allEventWS.emplace_back(eventWS->clone(), ws_name);
    }
  }

  Progress progEntries(this, progressFractionInitial, 1.0, numEventEntries * 2);

  // Refer to entry in allEventWS. The first non-summed workspace index is 1
  auto eventWSIndex = 1u;
  // Loop over McStas event data components
  for (const auto &eventEntry : eventEntries) {
    const std::string &dataName = eventEntry.first;
    const std::string &dataType = eventEntry.second;

    // open second level entry
    nxFile.openGroup(dataName, dataType);
    std::vector<double> data;
    nxFile.openData("events");
    progEntries.report("read event data from nexus");

    // Need to take into account that the nexus readData method reads a
    // multi-column data entry
    // into a vector
    // The number of data column for each neutron is here hardcoded to (p, x,
    // y,  n, id, t)
    // Thus  we have
    // column  0 : p 	neutron wight
    // column  1 : x 	x coordinate
    // column  2 : y 	y coordinate
    // column  3 : n 	accumulated number of neutrons
    // column  4 : id 	pixel id
    // column  5 : t 	time

    // get info about event data
    ::NeXus::Info id_info = nxFile.getInfo();
    if (id_info.dims.size() != 2) {
      g_log.error() << "Event data in McStas nexus file not loaded. Expected "
                       "event data block to be two dimensional\n";
      return scatteringWSNames;
      ;
    }
    int64_t nNeutrons = id_info.dims[0];
    int64_t numberOfDataColumn = id_info.dims[1];
    if (nNeutrons && numberOfDataColumn != 6) {
      g_log.error() << "Event data in McStas nexus file expecting 6 columns\n";
      return scatteringWSNames;
      ;
    }
    if (!isAnyNeutrons && nNeutrons > 0)
      isAnyNeutrons = true;

    std::vector<int64_t> start(2);
    std::vector<int64_t> step(2);

    // read the event data in blocks. 1 million event is 1000000*6*8 doubles
    // about 50Mb
    int64_t nNeutronsInBlock = 1000000;
    int64_t nOfFullBlocks = nNeutrons / nNeutronsInBlock;
    int64_t nRemainingNeutrons = nNeutrons - nOfFullBlocks * nNeutronsInBlock;
    // sum over number of blocks + 1 to cover the remainder
    for (int64_t iBlock = 0; iBlock < nOfFullBlocks + 1; iBlock++) {
      if (iBlock == nOfFullBlocks) {
        // read remaining neutrons
        start[0] = nOfFullBlocks * nNeutronsInBlock;
        start[1] = 0;
        step[0] = nRemainingNeutrons;
        step[1] = numberOfDataColumn;
      } else {
        // read neutrons in a full block
        start[0] = iBlock * nNeutronsInBlock;
        start[1] = 0;
        step[0] = nNeutronsInBlock;
        step[1] = numberOfDataColumn;
      }
      const int64_t nNeutronsForthisBlock =
          step[0]; // number of neutrons read for this block
      data.resize(nNeutronsForthisBlock * numberOfDataColumn);

      // Check that the type is what it is supposed to be
      if (id_info.type == ::NeXus::FLOAT64) {
        nxFile.getSlab(&data[0], start, step);
      } else {
        g_log.warning()
            << "Entry event field is not FLOAT64! It will be skipped.\n";
        continue;
      }

      // populate workspace with McStas events
      const detid2index_map detIDtoWSindex_map =
          allEventWS[0].first->getDetectorIDToWorkspaceIndexMap(true);

      progEntries.report("read event data into workspace");
      for (int64_t in = 0; in < nNeutronsForthisBlock; in++) {
        const int detectorID =
            static_cast<int>(data[4 + numberOfDataColumn * in]);
        const double detector_time = data[5 + numberOfDataColumn * in] *
                                     1.0e6; // convert to microseconds
        if (in == 0 && iBlock == 0) {
          shortestTOF = detector_time;
          longestTOF = detector_time;
        } else {
          if (detector_time < shortestTOF)
            shortestTOF = detector_time;
          if (detector_time > longestTOF)
            longestTOF = detector_time;
        }

        const size_t workspaceIndex =
            detIDtoWSindex_map.find(detectorID)->second;

        int64_t pulse_time = 0;
        auto weightedEvent = WeightedEvent();
        if (errorBarsSetTo1) {
          weightedEvent = WeightedEvent(detector_time, pulse_time,
                                        data[numberOfDataColumn * in], 1.0);
        } else {
          weightedEvent = WeightedEvent(
              detector_time, pulse_time, data[numberOfDataColumn * in],
              data[numberOfDataColumn * in] * data[numberOfDataColumn * in]);
        }
        allEventWS[0].first->getSpectrum(workspaceIndex) += weightedEvent;
        if (!onlySummedEventWorkspace && numEventEntries > 1) {
          allEventWS[eventWSIndex].first->getSpectrum(workspaceIndex) +=
              weightedEvent;
        }
      }
      eventWSIndex++;
    } // end reading over number of blocks of an event dataset

    nxFile.closeData();
    nxFile.closeGroup();

  } // end reading over number of event datasets

  // Create a default TOF-vector for histogramming, for now just 2 bins
  // 2 bins is the standard. However for McStas simulation data it may make
  // sense to
  // increase this number for better initial visual effect

  auto axis = HistogramData::BinEdges{shortestTOF - 1, longestTOF + 1};

  // ensure that specified name is given to workspace (eventWS) when added to
  // outputGroup
  for (auto eventWS : allEventWS) {
    const auto ws = eventWS.first;
    ws->setAllX(axis);
    AnalysisDataService::Instance().addOrReplace(eventWS.second, ws);
    scatteringWSNames.emplace_back(eventWS.second);
  }
  return scatteringWSNames;
}
Exemple #14
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/**
 * Load an SE log entry
 * @param file :: A reference to the NeXus file handle opened at the parent
 * group
 * @param entry_name :: The name of the log entry
 * @param workspace :: A pointer to the workspace to store the logs
 */
void LoadNexusLogs::loadSELog(
    ::NeXus::File &file, const std::string &entry_name,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  // Open the entry
  file.openGroup(entry_name, "IXseblock");
  std::string propName = entry_name;
  if (workspace->run().hasProperty(propName)) {
    propName = "selog_" + propName;
  }
  // There are two possible entries:
  //   value_log - A time series entry. This can contain a corrupt value entry
  //   so if it does use the value one
  //   value - A single value float entry
  Kernel::Property *logValue(nullptr);
  std::map<std::string, std::string> entries = file.getEntries();
  if (entries.find("value_log") != entries.end()) {
    try {
      try {
        file.openGroup("value_log", "NXlog");
      } catch (::NeXus::Exception &) {
        file.closeGroup();
        throw;
      }
      logValue = createTimeSeries(file, propName);
      file.closeGroup();
    } catch (::NeXus::Exception &e) {
      g_log.warning() << "IXseblock entry '" << entry_name
                      << "' gave an error when loading "
                      << "a time series:'" << e.what() << "'. Skipping entry\n";
      file.closeGroup(); // value_log
      file.closeGroup(); // entry_name
      return;
    }
  } else if (entries.find("value") != entries.end()) {
    try {
      // This may have a larger dimension than 1 bit it has no time field so
      // take the first entry
      file.openData("value");
      ::NeXus::Info info = file.getInfo();
      if (info.type == ::NeXus::FLOAT32) {
        boost::scoped_array<float> value(new float[info.dims[0]]);
        file.getData(value.get());
        file.closeData();
        logValue = new Kernel::PropertyWithValue<double>(
            propName, static_cast<double>(value[0]), true);
      } else {
        file.closeGroup();
        return;
      }
    } catch (::NeXus::Exception &e) {
      g_log.warning() << "IXseblock entry " << entry_name
                      << " gave an error when loading "
                      << "a single value:'" << e.what() << "'.\n";
      file.closeData();
      file.closeGroup();
      return;
    }
  } else {
    g_log.warning() << "IXseblock entry " << entry_name
                    << " cannot be read, skipping entry.\n";
    file.closeGroup();
    return;
  }
  workspace->mutableRun().addProperty(logValue);
  file.closeGroup();
}
Exemple #15
0
/**
 * Return the confidence with with this algorithm can load the file
 * @param eventEntries map of the file entries that have events
 * @param outputGroup pointer to the workspace group
 * @param nxFile Reads data from inside first first top entry
 */
void LoadMcStas::readEventData(
    const std::map<std::string, std::string> &eventEntries,
    WorkspaceGroup_sptr &outputGroup, ::NeXus::File &nxFile) {
  std::string filename = getPropertyValue("Filename");
  auto entries = nxFile.getEntries();

  // will assume that each top level entry contain one mcstas
  // generated IDF and any event data entries within this top level
  // entry are data collected for that instrument
  // This code for loading the instrument is for now adjusted code from
  // ExperimentalInfo.

  // Close data folder and go back to top level. Then read and close the
  // Instrument folder.
  nxFile.closeGroup();

  Geometry::Instrument_sptr instrument;

  // Initialize progress reporting
  int reports = 2;
  const double progressFractionInitial = 0.1;
  Progress progInitial(this, 0.0, progressFractionInitial, reports);

  try {
    nxFile.openGroup("instrument", "NXinstrument");
    std::string instrumentXML;
    nxFile.openGroup("instrument_xml", "NXnote");
    nxFile.readData("data", instrumentXML);
    nxFile.closeGroup();
    nxFile.closeGroup();

    progInitial.report("Loading instrument");

    Geometry::InstrumentDefinitionParser parser;
    std::string instrumentName = "McStas";
    parser.initialize(filename, instrumentName, instrumentXML);
    std::string instrumentNameMangled = parser.getMangledName();

    // Check whether the instrument is already in the InstrumentDataService
    if (InstrumentDataService::Instance().doesExist(instrumentNameMangled)) {
      // If it does, just use the one from the one stored there
      instrument =
          InstrumentDataService::Instance().retrieve(instrumentNameMangled);
    } else {
      // Really create the instrument
      instrument = parser.parseXML(NULL);
      // Add to data service for later retrieval
      InstrumentDataService::Instance().add(instrumentNameMangled, instrument);
    }
  } catch (...) {
    // Loader should not stop if there is no IDF.xml
    g_log.warning()
        << "\nCould not find the instrument description in the Nexus file:"
        << filename << " Ignore evntdata from data file" << std::endl;
    return;
  }
  // Finished reading Instrument. Then open new data folder again
  nxFile.openGroup("data", "NXdetector");

  // create and prepare an event workspace ready to receive the mcstas events
  progInitial.report("Set up EventWorkspace");
  EventWorkspace_sptr eventWS(new EventWorkspace());
  // initialize, where create up front number of eventlists = number of
  // detectors
  eventWS->initialize(instrument->getNumberDetectors(), 1, 1);
  // Set the units
  eventWS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
  eventWS->setYUnit("Counts");
  // set the instrument
  eventWS->setInstrument(instrument);
  // assign detector ID to eventlists

  std::vector<detid_t> detIDs = instrument->getDetectorIDs();

  for (size_t i = 0; i < instrument->getNumberDetectors(); i++) {
    eventWS->getEventList(i).addDetectorID(detIDs[i]);
    // spectrum number are treated as equal to detector IDs for McStas data
    eventWS->getEventList(i).setSpectrumNo(detIDs[i]);
  }
  // the one is here for the moment for backward compatibility
  eventWS->rebuildSpectraMapping(true);

  bool isAnyNeutrons = false;
  // to store shortest and longest recorded TOF
  double shortestTOF(0.0);
  double longestTOF(0.0);

  const size_t numEventEntries = eventEntries.size();
  Progress progEntries(this, progressFractionInitial, 1.0, numEventEntries * 2);
  for (auto eit = eventEntries.begin(); eit != eventEntries.end(); ++eit) {
    std::string dataName = eit->first;
    std::string dataType = eit->second;

    // open second level entry
    nxFile.openGroup(dataName, dataType);
    std::vector<double> data;
    nxFile.openData("events");
    progEntries.report("read event data from nexus");

    // Need to take into account that the nexus readData method reads a
    // multi-column data entry
    // into a vector
    // The number of data column for each neutron is here hardcoded to (p, x,
    // y,  n, id, t)
    // Thus  we have
    // column  0 : p 	neutron wight
    // column  1 : x 	x coordinate
    // column  2 : y 	y coordinate
    // column  3 : n 	accumulated number of neutrons
    // column  4 : id 	pixel id
    // column  5 : t 	time

    // get info about event data
    ::NeXus::Info id_info = nxFile.getInfo();
    if (id_info.dims.size() != 2) {
      g_log.error() << "Event data in McStas nexus file not loaded. Expected "
                       "event data block to be two dimensional" << std::endl;
      return;
    }
    int64_t nNeutrons = id_info.dims[0];
    int64_t numberOfDataColumn = id_info.dims[1];
    if (nNeutrons && numberOfDataColumn != 6) {
      g_log.error() << "Event data in McStas nexus file expecting 6 columns"
                    << std::endl;
      return;
    }
    if (isAnyNeutrons == false && nNeutrons > 0)
      isAnyNeutrons = true;

    std::vector<int64_t> start(2);
    std::vector<int64_t> step(2);

    // read the event data in blocks. 1 million event is 1000000*6*8 doubles
    // about 50Mb
    int64_t nNeutronsInBlock = 1000000;
    int64_t nOfFullBlocks = nNeutrons / nNeutronsInBlock;
    int64_t nRemainingNeutrons = nNeutrons - nOfFullBlocks * nNeutronsInBlock;
    // sum over number of blocks + 1 to cover the remainder
    for (int64_t iBlock = 0; iBlock < nOfFullBlocks + 1; iBlock++) {
      if (iBlock == nOfFullBlocks) {
        // read remaining neutrons
        start[0] = nOfFullBlocks * nNeutronsInBlock;
        start[1] = 0;
        step[0] = nRemainingNeutrons;
        step[1] = numberOfDataColumn;
      } else {
        // read neutrons in a full block
        start[0] = iBlock * nNeutronsInBlock;
        start[1] = 0;
        step[0] = nNeutronsInBlock;
        step[1] = numberOfDataColumn;
      }
      const int64_t nNeutronsForthisBlock =
          step[0]; // number of neutrons read for this block
      data.resize(nNeutronsForthisBlock * numberOfDataColumn);

      // Check that the type is what it is supposed to be
      if (id_info.type == ::NeXus::FLOAT64) {
        nxFile.getSlab(&data[0], start, step);
      } else {
        g_log.warning()
            << "Entry event field is not FLOAT64! It will be skipped.\n";
        continue;
      }

      // populate workspace with McStas events
      const detid2index_map detIDtoWSindex_map =
          eventWS->getDetectorIDToWorkspaceIndexMap(true);

      progEntries.report("read event data into workspace");
      for (int64_t in = 0; in < nNeutronsForthisBlock; in++) {
        const int detectorID =
            static_cast<int>(data[4 + numberOfDataColumn * in]);
        const double detector_time = data[5 + numberOfDataColumn * in] *
                                     1.0e6; // convert to microseconds
        if (in == 0 && iBlock == 0) {
          shortestTOF = detector_time;
          longestTOF = detector_time;
        } else {
          if (detector_time < shortestTOF)
            shortestTOF = detector_time;
          if (detector_time > longestTOF)
            longestTOF = detector_time;
        }

        const size_t workspaceIndex =
            detIDtoWSindex_map.find(detectorID)->second;

        int64_t pulse_time = 0;
        // eventWS->getEventList(workspaceIndex) +=
        // TofEvent(detector_time,pulse_time);
        // eventWS->getEventList(workspaceIndex) += TofEvent(detector_time);
        eventWS->getEventList(workspaceIndex) += WeightedEvent(
            detector_time, pulse_time, data[numberOfDataColumn * in], 1.0);
      }
    } // end reading over number of blocks of an event dataset

    // nxFile.getData(data);
    nxFile.closeData();
    nxFile.closeGroup();

  } // end reading over number of event datasets

  // Create a default TOF-vector for histogramming, for now just 2 bins
  // 2 bins is the standard. However for McStas simulation data it may make
  // sense to
  // increase this number for better initial visual effect
  Kernel::cow_ptr<MantidVec> axis;
  MantidVec &xRef = axis.access();
  xRef.resize(2, 0.0);
  // if ( nNeutrons > 0)
  if (isAnyNeutrons) {
    xRef[0] = shortestTOF - 1; // Just to make sure the bins hold it all
    xRef[1] = longestTOF + 1;
  }
  // Set the binning axis
  eventWS->setAllX(axis);

  // ensure that specified name is given to workspace (eventWS) when added to
  // outputGroup
  std::string nameOfGroupWS = getProperty("OutputWorkspace");
  std::string nameUserSee = std::string("EventData_") + nameOfGroupWS;
  std::string extraProperty =
      "Outputworkspace_dummy_" +
      boost::lexical_cast<std::string>(m_countNumWorkspaceAdded);
  declareProperty(new WorkspaceProperty<Workspace>(extraProperty, nameUserSee,
                                                   Direction::Output));
  setProperty(extraProperty, boost::static_pointer_cast<Workspace>(eventWS));
  m_countNumWorkspaceAdded++; // need to increment to ensure extraProperty are
                              // unique

  outputGroup->addWorkspace(eventWS);
}