コード例 #1
0
ファイル: LoadNXSPE.cpp プロジェクト: mducle/mantid
/** Execute the algorithm.
 */
void LoadNXSPE::exec() {
  std::string filename = getProperty("Filename");
  // quicly check if it's really nxspe
  try {
    ::NeXus::File file(filename);
    std::string mainEntry = (*(file.getEntries().begin())).first;
    file.openGroup(mainEntry, "NXentry");
    file.openData("definition");
    if (identiferConfidence(file.getStrData()) < 1) {
      throw std::invalid_argument("Not NXSPE");
    }
    file.close();
  } catch (...) {
    throw std::invalid_argument("Not NeXus or not NXSPE");
  }

  // Load the data
  ::NeXus::File file(filename);

  std::string mainEntry = (*(file.getEntries().begin())).first;
  file.openGroup(mainEntry, "NXentry");

  file.openGroup("NXSPE_info", "NXcollection");
  std::map<std::string, std::string> entries = file.getEntries();
  std::vector<double> temporary;
  double fixed_energy, psi = 0.;

  if (!entries.count("fixed_energy")) {
    throw std::invalid_argument("fixed_energy field was not found");
  }
  file.openData("fixed_energy");
  file.getData(temporary);
  fixed_energy = temporary.at(0);
  file.closeData();

  if (entries.count("psi")) {
    file.openData("psi");
    file.getData(temporary);
    psi = temporary.at(0);
    file.closeData();
  }

  int kikfscaling = 0;
  if (entries.count("ki_over_kf_scaling")) {
    file.openData("ki_over_kf_scaling");
    std::vector<int> temporaryint;
    file.getData(temporaryint);
    kikfscaling = temporaryint.at(0);
    file.closeData();
  }

  file.closeGroup(); // NXSPE_Info

  file.openGroup("data", "NXdata");
  entries = file.getEntries();

  if (!entries.count("data")) {
    throw std::invalid_argument("data field was not found");
  }
  file.openData("data");
  ::NeXus::Info info = file.getInfo();
  std::size_t numSpectra = static_cast<std::size_t>(info.dims.at(0));
  std::size_t numBins = static_cast<std::size_t>(info.dims.at(1));
  std::vector<double> data;
  file.getData(data);
  file.closeData();

  if (!entries.count("error")) {
    throw std::invalid_argument("error field was not found");
  }
  file.openData("error");
  std::vector<double> error;
  file.getData(error);
  file.closeData();

  if (!entries.count("energy")) {
    throw std::invalid_argument("energy field was not found");
  }
  file.openData("energy");
  std::vector<double> energies;
  file.getData(energies);
  file.closeData();

  if (!entries.count("azimuthal")) {
    throw std::invalid_argument("azimuthal field was not found");
  }
  file.openData("azimuthal");
  std::vector<double> azimuthal;
  file.getData(azimuthal);
  file.closeData();

  if (!entries.count("azimuthal_width")) {
    throw std::invalid_argument("azimuthal_width field was not found");
  }
  file.openData("azimuthal_width");
  std::vector<double> azimuthal_width;
  file.getData(azimuthal_width);
  file.closeData();

  if (!entries.count("polar")) {
    throw std::invalid_argument("polar field was not found");
  }
  file.openData("polar");
  std::vector<double> polar;
  file.getData(polar);
  file.closeData();

  if (!entries.count("polar_width")) {
    throw std::invalid_argument("polar_width field was not found");
  }
  file.openData("polar_width");
  std::vector<double> polar_width;
  file.getData(polar_width);
  file.closeData();

  // distance might not have been saved in all NXSPE files
  std::vector<double> distance;
  if (entries.count("distance")) {
    file.openData("distance");
    file.getData(distance);
    file.closeData();
  }

  file.closeGroup(); // data group
  file.closeGroup(); // Main entry
  file.close();

  // check if dimensions of the vectors are correct
  if ((error.size() != data.size()) || (azimuthal.size() != numSpectra) ||
      (azimuthal_width.size() != numSpectra) || (polar.size() != numSpectra) ||
      (polar_width.size() != numSpectra) ||
      ((energies.size() != numBins) && (energies.size() != numBins + 1))) {
    throw std::invalid_argument(
        "incompatible sizes of fields in the NXSPE file");
  }

  MatrixWorkspace_sptr outputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(
      WorkspaceFactory::Instance().create("Workspace2D", numSpectra,
                                          energies.size(), numBins));
  // Need to get hold of the parameter map
  outputWS->getAxis(0)->unit() = UnitFactory::Instance().create("DeltaE");
  outputWS->setYUnit("SpectraNumber");

  // add logs
  outputWS->mutableRun().addLogData(
      new PropertyWithValue<double>("Ei", fixed_energy));
  outputWS->mutableRun().addLogData(new PropertyWithValue<double>("psi", psi));
  outputWS->mutableRun().addLogData(new PropertyWithValue<std::string>(
      "ki_over_kf_scaling", kikfscaling == 1 ? "true" : "false"));

  // Set Goniometer
  Geometry::Goniometer gm;
  gm.pushAxis("psi", 0, 1, 0, psi);
  outputWS->mutableRun().setGoniometer(gm, true);

  // generate instrument
  Geometry::Instrument_sptr instrument(new Geometry::Instrument("NXSPE"));
  outputWS->setInstrument(instrument);

  Geometry::ObjComponent *source = new Geometry::ObjComponent("source");
  source->setPos(0.0, 0.0, -10.0);
  instrument->add(source);
  instrument->markAsSource(source);
  Geometry::ObjComponent *sample = new Geometry::ObjComponent("sample");
  instrument->add(sample);
  instrument->markAsSamplePos(sample);

  Geometry::Object_const_sptr cuboid(
      createCuboid(0.1, 0.1, 0.1)); // FIXME: memory hog on rendering. Also,
                                    // make each detector separate size
  for (std::size_t i = 0; i < numSpectra; ++i) {
    double r = 1.0;
    if (!distance.empty()) {
      r = distance.at(i);
    }

    Kernel::V3D pos;
    pos.spherical(r, polar.at(i), azimuthal.at(i));

    Geometry::Detector *det =
        new Geometry::Detector("pixel", static_cast<int>(i + 1), sample);
    det->setPos(pos);
    det->setShape(cuboid);
    instrument->add(det);
    instrument->markAsDetector(det);
  }

  Geometry::ParameterMap &pmap = outputWS->instrumentParameters();
  std::vector<double>::iterator itdata = data.begin(), iterror = error.begin(),
                                itdataend, iterrorend;
  API::Progress prog = API::Progress(this, 0.0, 0.9, numSpectra);
  for (std::size_t i = 0; i < numSpectra; ++i) {
    itdataend = itdata + numBins;
    iterrorend = iterror + numBins;
    outputWS->dataX(i) = energies;
    if ((!boost::math::isfinite(*itdata)) || (*itdata <= -1e10)) // masked bin
    {
      outputWS->dataY(i) = std::vector<double>(numBins, 0);
      outputWS->dataE(i) = std::vector<double>(numBins, 0);
      pmap.addBool(outputWS->getDetector(i)->getComponentID(), "masked", true);
    } else {
      outputWS->dataY(i) = std::vector<double>(itdata, itdataend);
      outputWS->dataE(i) = std::vector<double>(iterror, iterrorend);
    }
    itdata = (itdataend);
    iterror = (iterrorend);
    prog.report();
  }

  setProperty("OutputWorkspace", outputWS);
}
コード例 #2
0
/** Execute the algorithm.
 */
void EditInstrumentGeometry::exec() {
  // Lots of things have to do with the input workspace
  MatrixWorkspace_sptr workspace = getProperty("Workspace");
  Geometry::Instrument_const_sptr originstrument = workspace->getInstrument();

  // Get and check the primary flight path
  double l1 = this->getProperty("PrimaryFlightPath");
  if (isEmpty(l1)) {
    // Use the original L1
    if (!originstrument) {
      std::string errmsg(
          "It is not supported that L1 is not given, ",
          "while there is no instrument associated to input workspace.");
      g_log.error(errmsg);
      throw std::runtime_error(errmsg);
    }
    Geometry::IComponent_const_sptr source = originstrument->getSource();
    Geometry::IComponent_const_sptr sample = originstrument->getSample();
    l1 = source->getDistance(*sample);
    g_log.information() << "Retrieve L1 from input data workspace. \n";
  }
  g_log.information() << "Using L1 = " << l1 << "\n";

  // Get spectra number in case they are in a funny order
  std::vector<int32_t> specids = this->getProperty("SpectrumIDs");
  if (specids.empty()) // they are using the order of the input workspace
  {
    size_t numHist = workspace->getNumberHistograms();
    for (size_t i = 0; i < numHist; ++i) {
      specids.push_back(workspace->getSpectrum(i).getSpectrumNo());
      g_log.information() << "Add spectrum "
                          << workspace->getSpectrum(i).getSpectrumNo() << ".\n";
    }
  }

  // Get the detector ids - empsy means ignore it
  const vector<int> vec_detids = getProperty("DetectorIDs");
  const bool renameDetID(!vec_detids.empty());

  // Get individual detector geometries ordered by input spectrum Numbers
  const std::vector<double> l2s = this->getProperty("L2");
  const std::vector<double> tths = this->getProperty("Polar");
  std::vector<double> phis = this->getProperty("Azimuthal");

  // empty list of L2 and 2-theta is not allowed
  if (l2s.empty()) {
    throw std::runtime_error("User must specify L2 for all spectra. ");
  }
  if (tths.empty()) {
    throw std::runtime_error("User must specify 2theta for all spectra.");
  }

  // empty list of phi means that they are all zero
  if (phis.empty()) {
    phis.assign(l2s.size(), 0.);
  }

  // Validate
  for (size_t ib = 0; ib < l2s.size(); ib++) {
    g_log.information() << "Detector " << specids[ib] << "  L2 = " << l2s[ib]
                        << "  2Theta = " << tths[ib] << '\n';
    if (specids[ib] < 0) {
      // Invalid spectrum Number : less than 0.
      stringstream errmsgss;
      errmsgss << "Detector ID = " << specids[ib] << " cannot be less than 0.";
      throw std::invalid_argument(errmsgss.str());
    }
    if (l2s[ib] <= 0.0) {
      throw std::invalid_argument("L2 cannot be less or equal to 0");
    }
  }

  // Keep original instrument and set the new instrument, if necessary
  const auto spec2indexmap = workspace->getSpectrumToWorkspaceIndexMap();

  // ??? Condition: spectrum has 1 and only 1 detector
  size_t nspec = workspace->getNumberHistograms();

  // Initialize another set of L2/2-theta/Phi/DetectorIDs vector ordered by
  // workspace index
  std::vector<double> storL2s(nspec, 0.);
  std::vector<double> stor2Thetas(nspec, 0.);
  std::vector<double> storPhis(nspec, 0.);
  vector<int> storDetIDs(nspec, 0);

  // Map the properties from spectrum Number to workspace index
  for (size_t i = 0; i < specids.size(); i++) {
    // Find spectrum's workspace index
    auto it = spec2indexmap.find(specids[i]);
    if (it == spec2indexmap.end()) {
      stringstream errss;
      errss << "Spectrum Number " << specids[i] << " is not found. "
            << "Instrument won't be edited for this spectrum. \n";
      g_log.error(errss.str());
      throw std::runtime_error(errss.str());
    }

    // Store and set value
    size_t workspaceindex = it->second;

    storL2s[workspaceindex] = l2s[i];
    stor2Thetas[workspaceindex] = tths[i];
    storPhis[workspaceindex] = phis[i];
    if (renameDetID)
      storDetIDs[workspaceindex] = vec_detids[i];

    g_log.debug() << "workspace index = " << workspaceindex
                  << " is for Spectrum " << specids[i] << '\n';
  }

  // Generate a new instrument
  // Name of the new instrument
  std::string name = std::string(getProperty("InstrumentName"));
  if (name.empty()) {
    // Use the original L1
    if (!originstrument) {
      std::string errmsg(
          "It is not supported that InstrumentName is not given, ",
          "while there is no instrument associated to input workspace.");
      g_log.error(errmsg);
      throw std::runtime_error(errmsg);
    }
    name = originstrument->getName();
  }

  // Create a new instrument from scratch any way.
  auto instrument = boost::make_shared<Geometry::Instrument>(name);
  if (!bool(instrument)) {
    stringstream errss;
    errss << "Trying to use a Parametrized Instrument as an Instrument.";
    g_log.error(errss.str());
    throw std::runtime_error(errss.str());
  }

  // Set up source and sample information
  Geometry::ObjComponent *samplepos =
      new Geometry::ObjComponent("Sample", instrument.get());
  instrument->add(samplepos);
  instrument->markAsSamplePos(samplepos);
  samplepos->setPos(0.0, 0.0, 0.0);

  Geometry::ObjComponent *source =
      new Geometry::ObjComponent("Source", instrument.get());
  instrument->add(source);
  instrument->markAsSource(source);
  source->setPos(0.0, 0.0, -1.0 * l1);

  // Add/copy detector information
  auto indexInfo = workspace->indexInfo();
  std::vector<detid_t> detIDs;
  for (size_t i = 0; i < workspace->getNumberHistograms(); i++) {
    // Create a new detector.
    //    (Instrument will take ownership of pointer so no need to delete.)
    detid_t newdetid;
    if (renameDetID)
      newdetid = storDetIDs[i];
    else
      newdetid = detid_t(i) + 100;
    Geometry::Detector *detector =
        new Geometry::Detector("det", newdetid, samplepos);

    // Set up new detector parameters related to new instrument
    double l2 = storL2s[i];
    double tth = stor2Thetas[i];
    double phi = storPhis[i];

    Kernel::V3D pos;
    pos.spherical(l2, tth, phi);
    detector->setPos(pos);

    // Add new detector to spectrum and instrument
    // Good and do some debug output
    g_log.debug() << "Orignal spectrum " << indexInfo.spectrumNumber(i)
                  << "has " << indexInfo.detectorIDs(i).size()
                  << " detectors. \n";

    detIDs.push_back(newdetid);
    instrument->add(detector);
    instrument->markAsDetector(detector);

  } // ENDFOR workspace index
  indexInfo.setDetectorIDs(std::move(detIDs));
  workspace->setIndexInfo(indexInfo);

  // Add the new instrument
  workspace->setInstrument(instrument);
}
コード例 #3
0
/** Executes the algorithm. Reading in the file and creating and populating
 *  the output workspace
 *
 *  @throw FileError Thrown if unable to parse XML file
 */
void LoadInstrumentFromNexus::exec()
{
  // Retrieve the filename from the properties
  m_filename = getPropertyValue("Filename");

  // Get the input workspace
  const MatrixWorkspace_sptr localWorkspace = getProperty("Workspace");

  // open Nexus file
  MuonNexusReader nxload;
  if (nxload.readFromFile(m_filename.c_str()) != 0)
  {
    g_log.error("Unable to open file " + m_filename);
    throw Exception::FileError("Unable to open File:" , m_filename);
  }
  progress(0.5);
  // Create a new Instrument with the right name and add it to the workspace
  Geometry::Instrument_sptr instrument(new Geometry::Instrument(nxload.getInstrumentName()));
  localWorkspace->setInstrument(instrument);

  // Add dummy source and samplepos to instrument
  // The L2 and 2-theta values from nexus file assumed to be relative to sample position

  Geometry::ObjComponent *samplepos = new Geometry::ObjComponent("Unknown",instrument.get());
  instrument->add(samplepos);
  instrument->markAsSamplePos(samplepos);
  samplepos->setPos(0.0,0.0,0.0);

  Geometry::ObjComponent *source = new Geometry::ObjComponent("Unknown",instrument.get());
  instrument->add(source);
  instrument->markAsSource(source);
  double l1;
  // If user has provided an L1, use that
  if ( ! Kernel::ConfigService::Instance().getValue("instrument.L1", l1) )
  {
    // Otherwise try and get it from the nexus file - but not there at present!
    // l1 = nxload.ivpb.i_l1;
    // Default to 10 if the file doesn't have it set
    if (l1 == 0)  l1 = 10.0;
  }
  source->setPos(0.0,-1.0*l1,0.0);
    progress(1.0);

  // add detectors
  /* **** Ignoring all this for the moment - the sample Nexus files do not contain most of these values

  const int numDetector = nxload.i_det;    // number of detectors
  const int* const detID = nxload.udet;    // detector IDs
  const float* const r = nxload.len2;      // distance from sample
  const float* const angle = nxload.tthe;  // angle between indicent beam and direction from sample to detector (two-theta)

  for (int i = 0; i < numDetector; ++i)
  {
    // Create a new detector. Instrument will take ownership of pointer so no need to delete.
    Geometry::Detector *detector = new Geometry::Detector("det",samplepos);
    Kernel::V3D pos;
    pos.spherical(r[i], angle[i], 0.0);
    detector->setPos(pos);

    // set detector ID, add copy to instrument and mark it
    detector->setID(detID[i]);
    instrument->add(detector);
    instrument->markAsDetector(detector);
  }

  // Now mark the up the monitors
  const int numMonitors = nxload.i_mon;     // The number of monitors
  const int* const monIndex = nxload.mdet;  // Index into the udet array for each monitor
  for (int j = 0; j < numMonitors; ++j)
  {
    const int detectorToMark = detID[monIndex[j]-1];
    Geometry::Detector *det = dynamic_cast<Geometry::Detector*>(instrument->getDetector(detectorToMark));
    det->markAsMonitor();
    g_log.information() << "Detector with ID " << detectorToMark << " marked as a monitor." << std::endl;
  }

  // Information to the user about what info is extracted from nexus file
  g_log.information() << "SamplePos component added with position set to (0,0,0).\n"
    << "Detector components added with position coordinates assumed to be relative to the position of the sample; \n"
    << "L2 and two-theta values were read from nexus file and used to set the r and theta spherical coordinates; \n"
    << "the remaining spherical coordinate phi was set to zero.\n"
    << "Source component added with position set to (0,-" << l1 << ",0). In standard configuration, with \n"
    << "the beam along y-axis pointing from source to sample, this implies the source is " << l1 << "m in front \n"
    << "of the sample. This value can be changed via the 'instrument.l1' configuration property.\n";
  */

  return;
}