/**
 * Apply the created mapping to the workspace
 */
void CreateSimulationWorkspace::applyDetectorMapping() {
  size_t wsIndex(0);
  for (auto iter = m_detGroups.begin(); iter != m_detGroups.end(); ++iter) {
    ISpectrum *spectrum = m_outputWS->getSpectrum(wsIndex);
    spectrum->setSpectrumNo(
        static_cast<specid_t>(wsIndex + 1)); // Ensure a contiguous mapping
    spectrum->clearDetectorIDs();
    spectrum->addDetectorIDs(iter->second);
    ++wsIndex;
  }
}
Esempio n. 2
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/**
*  Only to be used if the KeepUnGrouped property is true, moves the spectra that were not selected
*  to be in a group to the end of the output spectrum
*  @param unGroupedSet :: list of WORKSPACE indexes that were included in a group
*  @param inputWS :: user selected input workspace for the algorithm
*  @param outputWS :: user selected output workspace for the algorithm
*  @param outIndex :: the next spectra index available after the grouped spectra
*/
void GroupDetectors2::moveOthers(const std::set<int64_t> &unGroupedSet, API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS,
         size_t outIndex)
{
  g_log.debug() << "Starting to copy the ungrouped spectra" << std::endl;
  double prog4Copy = (1. - 1.*static_cast<double>(m_FracCompl))/static_cast<double>(unGroupedSet.size());

  std::set<int64_t>::const_iterator copyFrIt = unGroupedSet.begin();
  // go thorugh all the spectra in the input workspace
  for ( ; copyFrIt != unGroupedSet.end(); ++copyFrIt )
  {
    if( *copyFrIt == USED ) continue; //Marked as not to be used
    size_t sourceIndex = static_cast<size_t>(*copyFrIt);

    // The input spectrum we'll copy
    const ISpectrum * inputSpec = inputWS->getSpectrum(sourceIndex);

    // Destination of the copying
    ISpectrum * outputSpec = outputWS->getSpectrum(outIndex);

    // Copy the data
    outputSpec->dataX() = inputSpec->dataX();
    outputSpec->dataY() = inputSpec->dataY();
    outputSpec->dataE() = inputSpec->dataE();

    // Spectrum numbers etc.
    outputSpec->setSpectrumNo(inputSpec->getSpectrumNo());
    outputSpec->clearDetectorIDs();
    outputSpec->addDetectorIDs( inputSpec->getDetectorIDs() );

    // go to the next free index in the output workspace
    outIndex ++;
    // make regular progress reports and check for cancelling the algorithm
    if ( outIndex % INTERVAL == 0 )
    {
      m_FracCompl += INTERVAL*prog4Copy;
      if ( m_FracCompl > 1.0 )
      {
        m_FracCompl = 1.0;
      }
      progress(m_FracCompl);
      interruption_point();
    }
  }
  // Refresh the spectraDetectorMap
  outputWS->generateSpectraMap();

  g_log.debug() << name() << " copied " << unGroupedSet.size()-1 << " ungrouped spectra\n";
}
Esempio n. 3
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void GatherWorkspaces::execEvent() {

  // Every process in an MPI job must hit this next line or everything hangs!
  mpi::communicator included; // The communicator containing all processes
  // The root process needs to create a workspace of the appropriate size
  EventWorkspace_sptr outputWorkspace;
  if (included.rank() == 0) {
    g_log.debug() << "Total number of spectra is " << totalSpec << "\n";
    // Create the workspace for the output
    outputWorkspace = boost::dynamic_pointer_cast<EventWorkspace>(
        API::WorkspaceFactory::Instance().create("EventWorkspace", sumSpec,
                                                 numBins + hist, numBins));
    // Copy geometry over.
    API::WorkspaceFactory::Instance().initializeFromParent(
        eventW, outputWorkspace, true);
    setProperty("OutputWorkspace", outputWorkspace);
    ExperimentInfo_sptr inWS = inputWorkspace;
    outputWorkspace->copyExperimentInfoFrom(inWS.get());
  }

  for (size_t wi = 0; wi < totalSpec; wi++) {
    if (included.rank() == 0) {
      // How do we accumulate the data?
      std::string accum = this->getPropertyValue("AccumulationMethod");
      std::vector<Mantid::DataObjects::EventList> out_values;
      gather(included, eventW->getEventList(wi), out_values, 0);
      for (int i = 0; i < included.size(); i++) {
        size_t index = wi; // accum == "Add"
        if (accum == "Append")
          index = wi + i * totalSpec;
        outputWorkspace->dataX(index) = eventW->readX(wi);
        outputWorkspace->getOrAddEventList(index) += out_values[i];
        const ISpectrum *inSpec = eventW->getSpectrum(wi);
        ISpectrum *outSpec = outputWorkspace->getSpectrum(index);
        outSpec->clearDetectorIDs();
        outSpec->addDetectorIDs(inSpec->getDetectorIDs());
      }
    } else {
      gather(included, eventW->getEventList(wi), 0);
    }
  }
}
Esempio n. 4
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/**
*  Move the user selected spectra in the input workspace into groups in the output workspace
*  @param inputWS :: user selected input workspace for the algorithm
*  @param outputWS :: user selected output workspace for the algorithm
*  @param prog4Copy :: the amount of algorithm progress to attribute to moving a single spectra
*  @return number of new grouped spectra
*/
size_t GroupDetectors2::formGroups( API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS, 
            const double prog4Copy)
{
  // get "Behaviour" string
  const std::string behaviour = getProperty("Behaviour");
  int bhv = 0;
  if ( behaviour == "Average" ) bhv = 1;

  API::MatrixWorkspace_sptr beh = API::WorkspaceFactory::Instance().create(
    "Workspace2D", static_cast<int>(m_GroupSpecInds.size()), 1, 1);

  g_log.debug() << name() << ": Preparing to group spectra into " << m_GroupSpecInds.size() << " groups\n";

  // where we are copying spectra to, we start copying to the start of the output workspace
  size_t outIndex = 0;
  // Only used for averaging behaviour. We may have a 1:1 map where a Divide would be waste as it would be just dividing by 1
  bool requireDivide(false);
  for ( storage_map::const_iterator it = m_GroupSpecInds.begin(); it != m_GroupSpecInds.end() ; ++it )
  {
    // This is the grouped spectrum
    ISpectrum * outSpec = outputWS->getSpectrum(outIndex);

    // The spectrum number of the group is the key
    outSpec->setSpectrumNo(it->first);
    // Start fresh with no detector IDs
    outSpec->clearDetectorIDs();

    // Copy over X data from first spectrum, the bin boundaries for all spectra are assumed to be the same here
    outSpec->dataX() = inputWS->readX(0);

    // the Y values and errors from spectra being grouped are combined in the output spectrum
    // Keep track of number of detectors required for masking
    size_t nonMaskedSpectra(0);
    beh->dataX(outIndex)[0] = 0.0;
    beh->dataE(outIndex)[0] = 0.0;
    for( std::vector<size_t>::const_iterator wsIter = it->second.begin(); wsIter != it->second.end(); ++wsIter)
    {
      const size_t originalWI = *wsIter;

      // detectors to add to firstSpecNum
      const ISpectrum * fromSpectrum = inputWS->getSpectrum(originalWI);

      // Add up all the Y spectra and store the result in the first one
      // Need to keep the next 3 lines inside loop for now until ManagedWorkspace mru-list works properly
      MantidVec &firstY = outSpec->dataY();
      MantidVec::iterator fYit;
      MantidVec::iterator fEit = outSpec->dataE().begin();
      MantidVec::const_iterator Yit = fromSpectrum->dataY().begin();
      MantidVec::const_iterator Eit = fromSpectrum->dataE().begin();
      for (fYit = firstY.begin(); fYit != firstY.end(); ++fYit, ++fEit, ++Yit, ++Eit)
      {
        *fYit += *Yit;
        // Assume 'normal' (i.e. Gaussian) combination of errors
        *fEit = std::sqrt( (*fEit)*(*fEit) + (*Eit)*(*Eit) );
      }

      // detectors to add to the output spectrum
      outSpec->addDetectorIDs(fromSpectrum->getDetectorIDs() );
      try
      {
        Geometry::IDetector_const_sptr det = inputWS->getDetector(originalWI);
        if( !det->isMasked() ) ++nonMaskedSpectra;
      }
      catch(Exception::NotFoundError&)
      {
        // If a detector cannot be found, it cannot be masked
        ++nonMaskedSpectra;
      }
    }
    if( nonMaskedSpectra == 0 ) ++nonMaskedSpectra; // Avoid possible divide by zero
    if(!requireDivide) requireDivide = (nonMaskedSpectra > 1);
    beh->dataY(outIndex)[0] = static_cast<double>(nonMaskedSpectra);

    // make regular progress reports and check for cancelling the algorithm
    if ( outIndex % INTERVAL == 0 )
    {
      m_FracCompl += INTERVAL*prog4Copy;
      if ( m_FracCompl > 1.0 )
        m_FracCompl = 1.0;
      progress(m_FracCompl);
      interruption_point();
    }
    outIndex ++;
  }
  
  // Refresh the spectraDetectorMap
  outputWS->generateSpectraMap();

  if ( bhv == 1 && requireDivide )
  {
    g_log.debug() << "Running Divide algorithm to perform averaging.\n";
    Mantid::API::IAlgorithm_sptr divide = createChildAlgorithm("Divide");
    divide->initialize();
    divide->setProperty<API::MatrixWorkspace_sptr>("LHSWorkspace", outputWS);
    divide->setProperty<API::MatrixWorkspace_sptr>("RHSWorkspace", beh);
    divide->setProperty<API::MatrixWorkspace_sptr>("OutputWorkspace", outputWS);
    divide->execute();
  }

  g_log.debug() << name() << " created " << outIndex << " new grouped spectra\n";
  return outIndex;
}
Esempio n. 5
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void GatherWorkspaces::exec() {
  // Every process in an MPI job must hit this next line or everything hangs!
  mpi::communicator world; // The communicator containing all processes

  inputWorkspace = getProperty("InputWorkspace");

  // Create a new communicator that includes only those processes that have an
  // input workspace
  const int haveWorkspace(inputWorkspace ? 1 : 0);
  included = world.split(haveWorkspace);

  // If the present process doesn't have an input workspace then its work is
  // done
  if (!haveWorkspace) {
    g_log.information("No input workspace on this process, so nothing to do.");
    return;
  }

  // Get the number of bins in each workspace and check they're all the same
  numBins = inputWorkspace->blocksize();
  std::vector<std::size_t> all_numBins;
  all_gather(included, numBins, all_numBins);
  if (std::count(all_numBins.begin(), all_numBins.end(), numBins) !=
      (int)all_numBins.size()) {
    // All the processes will error out if all the workspaces don't have the
    // same number of bins
    throw Exception::MisMatch<std::size_t>(
        numBins, 0, "All input workspaces must have the same number of bins");
  }
  // Also check that all workspaces are either histogram or not
  // N.B. boost mpi doesn't seem to like me using booleans in the all_gather
  hist = inputWorkspace->isHistogramData();
  std::vector<int> all_hist;
  all_gather(included, hist, all_hist);
  if (std::count(all_hist.begin(), all_hist.end(), hist) !=
      (int)all_hist.size()) {
    // All the processes will error out if we don't have either all histogram or
    // all point-data workspaces
    throw Exception::MisMatch<int>(
        hist, 0,
        "The input workspaces must be all histogram or all point data");
  }

  // How do we accumulate the data?
  std::string accum = this->getPropertyValue("AccumulationMethod");
  // Get the total number of spectra in the combined inputs
  totalSpec = inputWorkspace->getNumberHistograms();
  sumSpec = totalSpec;
  if (accum == "Append") {
    reduce(included, totalSpec, sumSpec, std::plus<std::size_t>(), 0);
  } else if (accum == "Add") {
    // barrier only helps when memory is too low for communication
    // included.barrier();
  }

  eventW = boost::dynamic_pointer_cast<const EventWorkspace>(inputWorkspace);
  if (eventW != NULL) {
    if (getProperty("PreserveEvents")) {
      // Input workspace is an event workspace. Use the other exec method
      this->execEvent();
      return;
    }
  }

  // The root process needs to create a workspace of the appropriate size
  MatrixWorkspace_sptr outputWorkspace;
  if (included.rank() == 0) {
    g_log.debug() << "Total number of spectra is " << sumSpec << "\n";
    // Create the workspace for the output
    outputWorkspace = WorkspaceFactory::Instance().create(
        inputWorkspace, sumSpec, numBins + hist, numBins);
    setProperty("OutputWorkspace", outputWorkspace);
    ExperimentInfo_sptr inWS = inputWorkspace;
    outputWorkspace->copyExperimentInfoFrom(inWS.get());
  }

  for (size_t wi = 0; wi < totalSpec; wi++) {
    if (included.rank() == 0) {
      const ISpectrum *inSpec = inputWorkspace->getSpectrum(wi);
      if (accum == "Add") {
        outputWorkspace->dataX(wi) = inputWorkspace->readX(wi);
        reduce(included, inputWorkspace->readY(wi), outputWorkspace->dataY(wi),
               vplus(), 0);
        reduce(included, inputWorkspace->readE(wi), outputWorkspace->dataE(wi),
               eplus(), 0);
      } else if (accum == "Append") {
        // Copy over data from own input workspace
        outputWorkspace->dataX(wi) = inputWorkspace->readX(wi);
        outputWorkspace->dataY(wi) = inputWorkspace->readY(wi);
        outputWorkspace->dataE(wi) = inputWorkspace->readE(wi);

        const int numReqs(3 * (included.size() - 1));
        mpi::request reqs[numReqs];
        int j(0);

        // Receive data from all the other processes
        // This works because the process ranks are ordered the same in
        // 'included' as
        // they are in 'world', but in general this is not guaranteed. TODO:
        // robustify
        for (int i = 1; i < included.size(); ++i) {
          size_t index = wi + i * totalSpec;
          reqs[j++] = included.irecv(i, 0, outputWorkspace->dataX(index));
          reqs[j++] = included.irecv(i, 1, outputWorkspace->dataY(index));
          reqs[j++] = included.irecv(i, 2, outputWorkspace->dataE(index));
          ISpectrum *outSpec = outputWorkspace->getSpectrum(index);
          outSpec->clearDetectorIDs();
          outSpec->addDetectorIDs(inSpec->getDetectorIDs());
        }

        // Make sure everything's been received before exiting the algorithm
        mpi::wait_all(reqs, reqs + numReqs);
      }
      ISpectrum *outSpec = outputWorkspace->getSpectrum(wi);
      outSpec->clearDetectorIDs();
      outSpec->addDetectorIDs(inSpec->getDetectorIDs());
    } else {
      if (accum == "Add") {
        reduce(included, inputWorkspace->readY(wi), vplus(), 0);
        reduce(included, inputWorkspace->readE(wi), eplus(), 0);
      } else if (accum == "Append") {
        mpi::request reqs[3];

        // Send the spectrum to the root process
        reqs[0] = included.isend(0, 0, inputWorkspace->readX(0));
        reqs[1] = included.isend(0, 1, inputWorkspace->readY(0));
        reqs[2] = included.isend(0, 2, inputWorkspace->readE(0));

        // Make sure the sends have completed before exiting the algorithm
        mpi::wait_all(reqs, reqs + 3);
      }
    }
  }
}
Esempio n. 6
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/** Executes the algorithm
 *
 */
void SumSpectra::exec()
{
  // Try and retrieve the optional properties
  m_MinSpec = getProperty("StartWorkspaceIndex");
  m_MaxSpec = getProperty("EndWorkspaceIndex");
  const std::vector<int> indices_list = getProperty("ListOfWorkspaceIndices");

  keepMonitors = getProperty("IncludeMonitors");

  // Get the input workspace
  MatrixWorkspace_const_sptr localworkspace = getProperty("InputWorkspace");

  numberOfSpectra = static_cast<int>(localworkspace->getNumberHistograms());
  this->yLength = static_cast<int>(localworkspace->blocksize());

  // Check 'StartSpectrum' is in range 0-numberOfSpectra
  if ( m_MinSpec > numberOfSpectra )
  {
    g_log.warning("StartWorkspaceIndex out of range! Set to 0.");
    m_MinSpec = 0;
  }

  if (indices_list.empty())
  {
    //If no list was given and no max, just do all.
    if ( isEmpty(m_MaxSpec) ) m_MaxSpec = numberOfSpectra-1;
  }

  //Something for m_MaxSpec was given but it is out of range?
  if (!isEmpty(m_MaxSpec) && ( m_MaxSpec > numberOfSpectra-1 || m_MaxSpec < m_MinSpec ))
  {
    g_log.warning("EndWorkspaceIndex out of range! Set to max Workspace Index");
    m_MaxSpec = numberOfSpectra;
  }

  //Make the set of indices to sum up from the list
  this->indices.insert(indices_list.begin(), indices_list.end());

  //And add the range too, if any
  if (!isEmpty(m_MaxSpec))
  {
    for (int i = m_MinSpec; i <= m_MaxSpec; i++)
      this->indices.insert(i);
  }

  //determine the output spectrum id
  m_outSpecId = this->getOutputSpecId(localworkspace);
  g_log.information() << "Spectra remapping gives single spectra with spectra number: "
                      << m_outSpecId << "\n";

  m_CalculateWeightedSum = getProperty("WeightedSum");

 
  EventWorkspace_const_sptr eventW = boost::dynamic_pointer_cast<const EventWorkspace>(localworkspace);
  if (eventW)
  {
    m_CalculateWeightedSum = false;
    this->execEvent(eventW, this->indices);
  }
  else
  {
    //-------Workspace 2D mode -----

    // Create the 2D workspace for the output
    MatrixWorkspace_sptr outputWorkspace = API::WorkspaceFactory::Instance().create(localworkspace,
                                                           1,localworkspace->readX(0).size(),this->yLength);
    size_t numSpectra(0); // total number of processed spectra
    size_t numMasked(0);  // total number of the masked and skipped spectra
    size_t numZeros(0);   // number of spectra which have 0 value in the first column (used in special cases of evaluating how good Puasonian statistics is)
  
    Progress progress(this, 0, 1, this->indices.size());

    // This is the (only) output spectrum
    ISpectrum * outSpec = outputWorkspace->getSpectrum(0);

    // Copy over the bin boundaries
    outSpec->dataX() = localworkspace->readX(0);

    //Build a new spectra map
    outSpec->setSpectrumNo(m_outSpecId);
    outSpec->clearDetectorIDs();

    if (localworkspace->id() == "RebinnedOutput")
    {
      this->doRebinnedOutput(outputWorkspace, progress,numSpectra,numMasked,numZeros);
    }
    else
    {
      this->doWorkspace2D(localworkspace, outSpec, progress,numSpectra,numMasked,numZeros);
    }

    // Pointer to sqrt function
    MantidVec& YError = outSpec->dataE();
    typedef double (*uf)(double);
    uf rs=std::sqrt;
    //take the square root of all the accumulated squared errors - Assumes Gaussian errors
    std::transform(YError.begin(), YError.end(), YError.begin(), rs);

    outputWorkspace->generateSpectraMap();
    // set up the summing statistics
    outputWorkspace->mutableRun().addProperty("NumAllSpectra",int(numSpectra),"",true);
    outputWorkspace->mutableRun().addProperty("NumMaskSpectra",int(numMasked),"",true);
    outputWorkspace->mutableRun().addProperty("NumZeroSpectra",int(numZeros),"",true);


    // Assign it to the output workspace property
    setProperty("OutputWorkspace", outputWorkspace);

  }
}
Esempio n. 7
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void GroupDetectors::exec()
{
  // Get the input workspace
  const MatrixWorkspace_sptr WS = getProperty("Workspace");

  std::vector<size_t> indexList = getProperty("WorkspaceIndexList");
  std::vector<specid_t> spectraList = getProperty("SpectraList");
  const std::vector<detid_t> detectorList = getProperty("DetectorList");

  // Could create a Validator to replace the below
  if ( indexList.empty() && spectraList.empty() && detectorList.empty() )
  {
    g_log.information(name() +
      ": WorkspaceIndexList, SpectraList, and DetectorList properties are all empty, no grouping done");
    return;
  }

  // Bin boundaries need to be the same, so check if they actually are
  if (!API::WorkspaceHelpers::commonBoundaries(WS))
  {
    g_log.error("Can only group if the histograms have common bin boundaries");
    throw std::runtime_error("Can only group if the histograms have common bin boundaries");
  }

  // If the spectraList property has been set, need to loop over the workspace looking for the
  // appropriate spectra number and adding the indices they are linked to the list to be processed
  if ( ! spectraList.empty() )
  {
    WS->getIndicesFromSpectra(spectraList,indexList);
  }// End dealing with spectraList
  else if ( ! detectorList.empty() )
  {
    // Dealing with DetectorList
    //convert from detectors to workspace indices
    WS->getIndicesFromDetectorIDs(detectorList, indexList);
  }

  if ( indexList.empty() )
  {
      g_log.warning("Nothing to group");
      return;
  }

  const size_t vectorSize = WS->blocksize();

  const specid_t firstIndex = static_cast<specid_t>(indexList[0]);
  ISpectrum * firstSpectrum = WS->getSpectrum(firstIndex);

  setProperty("ResultIndex",firstIndex);

  // loop over the spectra to group
  Progress progress(this, 0.0, 1.0, static_cast<int>(indexList.size()-1));
  for (size_t i = 0; i < indexList.size()-1; ++i)
  {
    // The current spectrum
    const size_t currentIndex = indexList[i+1];
    ISpectrum * spec = WS->getSpectrum(currentIndex);

    // Add the current detector to belong to the first spectrum
    firstSpectrum->addDetectorIDs(spec->getDetectorIDs());

    // Add up all the Y spectra and store the result in the first one
    // Need to keep the next 3 lines inside loop for now until ManagedWorkspace mru-list works properly
    MantidVec &firstY = WS->dataY(firstIndex);
    MantidVec::iterator fYit;
    MantidVec::iterator fEit = firstSpectrum->dataE().begin();
    MantidVec::iterator Yit = spec->dataY().begin();
    MantidVec::iterator Eit = spec->dataE().begin();
    for (fYit = firstY.begin(); fYit != firstY.end(); ++fYit, ++fEit, ++Yit, ++Eit)
    {
      *fYit += *Yit;
      // Assume 'normal' (i.e. Gaussian) combination of errors
      *fEit = sqrt( (*fEit)*(*fEit) + (*Eit)*(*Eit) );
    }

    // Now zero the now redundant spectrum and set its spectraNo to indicate this (using -1)
    // N.B. Deleting spectra would cause issues for ManagedWorkspace2D, hence the the approach taken here
    spec->dataY().assign(vectorSize,0.0);
    spec->dataE().assign(vectorSize,0.0);
    spec->setSpectrumNo(-1);
    spec->clearDetectorIDs();
    progress.report();
  }

}