C++ File::getEntries方法代码示例

/**
 * 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();
}

/**
 * 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);
}

/**
 * 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");
}

/**
 * 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();
}

/** 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)
//.........这里部分代码省略.........

/**
 * 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.........

/**
 * 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++) {
//.........这里部分代码省略.........

/**
 * 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();
}

/**
 * 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
//.........这里部分代码省略.........