C++ File::openData方法代码示例

    /**
    * 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);
    }

/** 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();
}

/** 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";
    }
  }
}

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);
}

/** 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
}

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();
    }
  }
}

/**
 * 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();
}

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;
}

/** 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;
}

//.........这里部分代码省略.........
  // 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;

/** 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";
}

/**
 * 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();
}

/**
 * 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;
}