Exemplo n.º 1
0
  void MultiplyMD::execEventScalar(typename MDEventWorkspace<MDE, nd>::sptr ws)
  {
    // Get the scalar multiplying
    float scalar = float(m_rhs_scalar->dataY(0)[0]);
    float scalarError = float(m_rhs_scalar->dataE(0)[0]);
    float scalarRelativeErrorSquared = (scalarError * scalarError) / (scalar * scalar);

    // Get all the MDBoxes contained
    MDBoxBase<MDE,nd> * parentBox = ws->getBox();
    std::vector<API::IMDNode *> boxes;
    parentBox->getBoxes(boxes, 1000, true);

    bool fileBackedTarget(false);
    Kernel::DiskBuffer *dbuff(NULL);
    if(ws->isFileBacked())
    {
        fileBackedTarget = true;
        dbuff = ws->getBoxController()->getFileIO();
    }
 

    for (size_t i=0; i<boxes.size(); i++)
    {
      MDBox<MDE,nd> * box = dynamic_cast<MDBox<MDE,nd> *>(boxes[i]);
      if (box)
      {
        typename std::vector<MDE> & events = box->getEvents();
        size_t ic(events.size());
        typename std::vector<MDE>::iterator it = events.begin();
        typename std::vector<MDE>::iterator it_end = events.end();
        for (; it != it_end; it++)
        {
          // Multiply weight by a scalar, propagating error
          float oldSignal = it->getSignal();
          float signal = oldSignal * scalar;
          float errorSquared = signal * signal * (it->getErrorSquared() / (oldSignal * oldSignal) + scalarRelativeErrorSquared);
          it->setSignal(signal);
          it->setErrorSquared(errorSquared);
        }
        box->releaseEvents();
        if(fileBackedTarget && ic>0)
        {
            Kernel::ISaveable *const pSaver(box->getISaveable());
            dbuff->toWrite(pSaver);
        }

      }
    }
    // Recalculate the totals
    ws->refreshCache();
    // Mark file-backed workspace as dirty
    ws->setFileNeedsUpdating(true);
  }
Exemplo n.º 2
0
  void CreateMDWorkspace::finish(typename MDEventWorkspace<MDE, nd>::sptr ws)
  {
    // ------------ Set up the box controller ----------------------------------
    BoxController_sptr bc = ws->getBoxController();
    this->setBoxController(bc);

    // Split to level 1
    ws->splitBox();

    // Do we split more due to MinRecursionDepth?
    int minDepth = this->getProperty("MinRecursionDepth");
    if (minDepth<0) throw std::invalid_argument("MinRecursionDepth must be >= 0.");
    ws->setMinRecursionDepth(size_t(minDepth));
  }
Exemplo n.º 3
0
  void CloneMDWorkspace::doClone(const typename MDEventWorkspace<MDE, nd>::sptr ws)
  {
    std::string outWSName = getPropertyValue("OutputWorkspace");
    Progress prog(this, 0.0, 10.0, 100);
    BoxController_sptr bc = ws->getBoxController();

    if (!bc) throw std::runtime_error("Error with InputWorkspace: no BoxController!");
    if (bc->isFileBacked())
    {
      // Generate a new filename to copy to
      prog.report("Copying File");
      std::string originalFile = bc->getFilename();
      std::string outFilename = getPropertyValue("Filename");
      if (outFilename.empty())
      {
        // Auto-generated name
        Poco::Path path = Poco::Path(originalFile).absolute();
        std::string newName = path.getBaseName() + "_clone." + path.getExtension();
        path.setFileName(newName);
        outFilename = path.toString();
      }

      // Perform the copying
      g_log.notice() << "Cloned workspace file being copied to: " << outFilename << std::endl;
      Poco::File(originalFile).copyTo(outFilename);
      g_log.information() << "File copied successfully." << std::endl;

      // Now load it back
      IAlgorithm_sptr alg = createSubAlgorithm("LoadMD", 0.5, 1.0, false);
      alg->setPropertyValue("Filename", outFilename);
      alg->setPropertyValue("FileBackEnd", "1");
      alg->setPropertyValue("Memory", "0"); //TODO: How much memory?
      alg->setPropertyValue("OutputWorkspace", outWSName);
      alg->executeAsSubAlg();

      // Set the output workspace to this
      IMDEventWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
      this->setProperty("OutputWorkspace", outWS);
    }
    else
    {
      // Perform the clone in memory.
      boost::shared_ptr<MDEventWorkspace<MDE,nd> > outWS(new MDEventWorkspace<MDE,nd>(*ws));
      this->setProperty("OutputWorkspace", boost::dynamic_pointer_cast<IMDEventWorkspace>(outWS) );
    }
  }
Exemplo n.º 4
0
void SliceMD::slice(typename MDEventWorkspace<MDE, nd>::sptr ws) {
  // Create the ouput workspace
  typename MDEventWorkspace<OMDE, ond>::sptr outWS(
      new MDEventWorkspace<OMDE, ond>());
  for (size_t od = 0; od < m_binDimensions.size(); od++) {
    outWS->addDimension(m_binDimensions[od]);
  }
  outWS->setCoordinateSystem(ws->getSpecialCoordinateSystem());
  outWS->initialize();
  // Copy settings from the original box controller
  BoxController_sptr bc = ws->getBoxController();

  // store wrute buffer size for the future
  // uint64_t writeBufSize =
  // bc->getFileIO()getDiskBuffer().getWriteBufferSize();
  // and disable write buffer (if any) for input MD Events for this algorithm
  // purposes;
  // bc->setCacheParameters(1,0);

  BoxController_sptr obc = outWS->getBoxController();
  // Use the "number of bins" as the "split into" parameter
  for (size_t od = 0; od < m_binDimensions.size(); od++)
    obc->setSplitInto(od, m_binDimensions[od]->getNBins());
  obc->setSplitThreshold(bc->getSplitThreshold());

  bool bTakeDepthFromInputWorkspace =
      getProperty("TakeMaxRecursionDepthFromInput");
  int tempDepth = getProperty("MaxRecursionDepth");
  size_t maxDepth =
      bTakeDepthFromInputWorkspace ? bc->getMaxDepth() : size_t(tempDepth);
  obc->setMaxDepth(maxDepth);

  // size_t outputSize = writeBufSize;
  // obc->setCacheParameters(sizeof(OMDE),outputSize);

  obc->resetNumBoxes();
  // Perform the first box splitting
  outWS->splitBox();
  size_t lastNumBoxes = obc->getTotalNumMDBoxes();

  // --- File back end ? ----------------
  std::string filename = getProperty("OutputFilename");
  if (!filename.empty()) {

    // First save to the NXS file
    g_log.notice() << "Running SaveMD to create file back-end" << std::endl;
    IAlgorithm_sptr alg = createChildAlgorithm("SaveMD");
    alg->setPropertyValue("Filename", filename);
    alg->setProperty("InputWorkspace", outWS);
    alg->setProperty("MakeFileBacked", true);
    alg->executeAsChildAlg();

    if (!obc->isFileBacked())
      throw std::runtime_error("SliceMD with file-backed output: Can not set "
                               "up file-backed output workspace ");

    auto IOptr = obc->getFileIO();
    size_t outBufSize = IOptr->getWriteBufferSize();
    // the buffer size for resulting workspace; reasonable size is at least 10
    // data chunk sizes (nice to verify)
    if (outBufSize < 10 * IOptr->getDataChunk()) {
      outBufSize = 10 * IOptr->getDataChunk();
      IOptr->setWriteBufferSize(outBufSize);
    }
  }

  // Function defining which events (in the input dimensions) to place in the
  // output
  MDImplicitFunction *function = this->getImplicitFunctionForChunk(NULL, NULL);

  std::vector<API::IMDNode *> boxes;
  // Leaf-only; no depth limit; with the implicit function passed to it.
  ws->getBox()->getBoxes(boxes, 1000, true, function);
  // Sort boxes by file position IF file backed. This reduces seeking time,
  // hopefully.
  bool fileBackedWS = bc->isFileBacked();
  if (fileBackedWS)
    API::IMDNode::sortObjByID(boxes);

  Progress *prog = new Progress(this, 0.0, 1.0, boxes.size());

  // The root of the output workspace
  MDBoxBase<OMDE, ond> *outRootBox = outWS->getBox();

  // if target workspace has events, we should count them as added
  uint64_t totalAdded = outWS->getNEvents();
  uint64_t numSinceSplit = 0;

  // Go through every box for this chunk.
  // PARALLEL_FOR_IF( !bc->isFileBacked() )
  for (int i = 0; i < int(boxes.size()); i++) {
    MDBox<MDE, nd> *box = dynamic_cast<MDBox<MDE, nd> *>(boxes[i]);
    // Perform the binning in this separate method.
    if (box) {
      // An array to hold the rotated/transformed coordinates
      coord_t outCenter[ond];

      const std::vector<MDE> &events = box->getConstEvents();

      typename std::vector<MDE>::const_iterator it = events.begin();
      typename std::vector<MDE>::const_iterator it_end = events.end();
      for (; it != it_end; it++) {
        // Cache the center of the event (again for speed)
        const coord_t *inCenter = it->getCenter();

        if (function->isPointContained(inCenter)) {
          // Now transform to the output dimensions
          m_transformFromOriginal->apply(inCenter, outCenter);

          // Create the event
          OMDE newEvent(it->getSignal(), it->getErrorSquared(), outCenter);
          // Copy extra data, if any
          copyEvent(*it, newEvent);
          // Add it to the workspace
          outRootBox->addEvent(newEvent);

          numSinceSplit++;
        }
      }
      box->releaseEvents();

      // Ask BC if one needs to split boxes
      if (obc->shouldSplitBoxes(totalAdded, numSinceSplit, lastNumBoxes))
      // if (numSinceSplit > 20000000 || (i == int(boxes.size()-1)))
      {
        // This splits up all the boxes according to split thresholds and sizes.
        Kernel::ThreadScheduler *ts = new ThreadSchedulerFIFO();
        ThreadPool tp(ts);
        outWS->splitAllIfNeeded(ts);
        tp.joinAll();
        // Accumulate stats
        totalAdded += numSinceSplit;
        numSinceSplit = 0;
        lastNumBoxes = obc->getTotalNumMDBoxes();
        // Progress reporting
        if (!fileBackedWS)
          prog->report(i);
      }
      if (fileBackedWS) {
        if (!(i % 10))
          prog->report(i);
      }
    } // is box

  } // for each box in the vector
  prog->report();

  outWS->splitAllIfNeeded(NULL);
  // Refresh all cache.
  outWS->refreshCache();

  g_log.notice() << totalAdded << " " << OMDE::getTypeName()
                 << "'s added to the output workspace." << std::endl;

  if (outWS->isFileBacked()) {
    // Update the file-back-end
    g_log.notice() << "Running SaveMD" << std::endl;
    IAlgorithm_sptr alg = createChildAlgorithm("SaveMD");
    alg->setProperty("UpdateFileBackEnd", true);
    alg->setProperty("InputWorkspace", outWS);
    alg->executeAsChildAlg();
  }
  // return the size of the input workspace write buffer to its initial value
  // bc->setCacheParameters(sizeof(MDE),writeBufSize);
  this->setProperty("OutputWorkspace",
                    boost::dynamic_pointer_cast<IMDEventWorkspace>(outWS));
  delete prog;
}
Exemplo n.º 5
0
void BinMD::binByIterating(typename MDEventWorkspace<MDE, nd>::sptr ws) {
  BoxController_sptr bc = ws->getBoxController();
  // store exisiting write buffer size for the future
  // uint64_t writeBufSize =bc->getDiskBuffer().getWriteBufferSize();
  // and disable write buffer (if any) for input MD Events for this algorithm
  // purposes;
  // bc->setCacheParameters(1,0);

  // Cache some data to speed up accessing them a bit
  indexMultiplier = new size_t[m_outD];
  for (size_t d = 0; d < m_outD; d++) {
    if (d > 0)
      indexMultiplier[d] = outWS->getIndexMultiplier()[d - 1];
    else
      indexMultiplier[d] = 1;
  }
  signals = outWS->getSignalArray();
  errors = outWS->getErrorSquaredArray();
  numEvents = outWS->getNumEventsArray();

  // Start with signal/error/numEvents at 0.0
  outWS->setTo(0.0, 0.0, 0.0);

  // The dimension (in the output workspace) along which we chunk for parallel
  // processing
  // TODO: Find the smartest dimension to chunk against
  size_t chunkDimension = 0;

  // How many bins (in that dimension) per chunk.
  // Try to split it so each core will get 2 tasks:
  int chunkNumBins = int(m_binDimensions[chunkDimension]->getNBins() /
                         (PARALLEL_GET_MAX_THREADS * 2));
  if (chunkNumBins < 1)
    chunkNumBins = 1;

  // Do we actually do it in parallel?
  bool doParallel = getProperty("Parallel");
  // Not if file-backed!
  if (bc->isFileBacked())
    doParallel = false;
  if (!doParallel)
    chunkNumBins = int(m_binDimensions[chunkDimension]->getNBins());

  // Total number of steps
  size_t progNumSteps = 0;
  if (prog)
    prog->setNotifyStep(0.1);
  if (prog)
    prog->resetNumSteps(100, 0.00, 1.0);

  // Run the chunks in parallel. There is no overlap in the output workspace so
  // it is thread safe to write to it..
  // cppcheck-suppress syntaxError
    PRAGMA_OMP( parallel for schedule(dynamic,1) if (doParallel) )
    for (int chunk = 0;
         chunk < int(m_binDimensions[chunkDimension]->getNBins());
         chunk += chunkNumBins) {
      PARALLEL_START_INTERUPT_REGION
      // Region of interest for this chunk.
      std::vector<size_t> chunkMin(m_outD);
      std::vector<size_t> chunkMax(m_outD);
      for (size_t bd = 0; bd < m_outD; bd++) {
        // Same limits in the other dimensions
        chunkMin[bd] = 0;
        chunkMax[bd] = m_binDimensions[bd]->getNBins();
      }
      // Parcel out a chunk in that single dimension dimension
      chunkMin[chunkDimension] = size_t(chunk);
      if (size_t(chunk + chunkNumBins) >
          m_binDimensions[chunkDimension]->getNBins())
        chunkMax[chunkDimension] = m_binDimensions[chunkDimension]->getNBins();
      else
        chunkMax[chunkDimension] = size_t(chunk + chunkNumBins);

      // Build an implicit function (it needs to be in the space of the
      // MDEventWorkspace)
      MDImplicitFunction *function =
          this->getImplicitFunctionForChunk(chunkMin.data(), chunkMax.data());

      // Use getBoxes() to get an array with a pointer to each box
      std::vector<API::IMDNode *> boxes;
      // Leaf-only; no depth limit; with the implicit function passed to it.
      ws->getBox()->getBoxes(boxes, 1000, true, function);

      // Sort boxes by file position IF file backed. This reduces seeking time,
      // hopefully.
      if (bc->isFileBacked())
        API::IMDNode::sortObjByID(boxes);

      // For progress reporting, the # of boxes
      if (prog) {
        PARALLEL_CRITICAL(BinMD_progress) {
          g_log.debug() << "Chunk " << chunk << ": found " << boxes.size()
                        << " boxes within the implicit function.\n";
          progNumSteps += boxes.size();
          prog->setNumSteps(progNumSteps);
        }
      }

      // Go through every box for this chunk.
      for (auto &boxe : boxes) {
        MDBox<MDE, nd> *box = dynamic_cast<MDBox<MDE, nd> *>(boxe);
        // Perform the binning in this separate method.
        if (box && !box->getIsMasked())
          this->binMDBox(box, chunkMin.data(), chunkMax.data());

        // Progress reporting
        if (prog)
          prog->report();
        // For early cancelling of the loop
        if (this->m_cancel)
          break;
      } // for each box in the vector
      PARALLEL_END_INTERUPT_REGION
    } // for each chunk in parallel
    PARALLEL_CHECK_INTERUPT_REGION

    // Now the implicit function
    if (implicitFunction) {
      if (prog)
        prog->report("Applying implicit function.");
      signal_t nan = std::numeric_limits<signal_t>::quiet_NaN();
      outWS->applyImplicitFunction(implicitFunction, nan, nan);
    }

    // return the size of the input workspace write buffer to its initial value
    // bc->setCacheParameters(sizeof(MDE),writeBufSize);
}
Exemplo n.º 6
0
void LoadMD::doLoad(typename MDEventWorkspace<MDE, nd>::sptr ws) {
  // Are we using the file back end?
  bool fileBackEnd = getProperty("FileBackEnd");

  if (fileBackEnd && m_BoxStructureAndMethadata)
    throw std::invalid_argument("Combination of BoxStructureOnly or "
                                "MetaDataOnly were set to TRUE with "
                                "fileBackEnd "
                                ": this is not possible.");

  CPUTimer tim;
  auto prog = new Progress(this, 0.0, 1.0, 100);

  prog->report("Opening file.");
  std::string title;
  try {
    m_file->getAttr("title", title);
  } catch (std::exception &) {
    // Leave the title blank if error on loading
  }
  ws->setTitle(title);

  // Load the WorkspaceHistory "process"
  if (this->getProperty("LoadHistory")) {
    ws->history().loadNexus(m_file.get());
  }

  this->loadAffineMatricies(boost::dynamic_pointer_cast<IMDWorkspace>(ws));

  m_file->closeGroup();
  m_file->close();
  // Add each of the dimension
  for (size_t d = 0; d < nd; d++)
    ws->addDimension(m_dims[d]);

  // Coordinate system
  ws->setCoordinateSystem(m_coordSystem);

  // ----------------------------------------- Box Structure
  // ------------------------------
  prog->report("Reading box structure from HDD.");
  MDBoxFlatTree FlatBoxTree;
  int nDims = static_cast<int>(nd); // should be safe
  FlatBoxTree.loadBoxStructure(m_filename, nDims, MDE::getTypeName());

  BoxController_sptr bc = ws->getBoxController();
  bc->fromXMLString(FlatBoxTree.getBCXMLdescr());

  prog->report("Restoring box structure and connectivity");
  std::vector<API::IMDNode *> boxTree;
  FlatBoxTree.restoreBoxTree(boxTree, bc, fileBackEnd,
                             m_BoxStructureAndMethadata);
  size_t numBoxes = boxTree.size();

  // ---------------------------------------- DEAL WITH BOXES
  // ------------------------------------
  if (fileBackEnd) { // TODO:: call to the file format factory
    auto loader = boost::shared_ptr<API::IBoxControllerIO>(
        new DataObjects::BoxControllerNeXusIO(bc.get()));
    loader->setDataType(sizeof(coord_t), MDE::getTypeName());
    bc->setFileBacked(loader, m_filename);
    // boxes have been already made file-backed when restoring the boxTree;
    // How much memory for the cache?
    {
      // TODO: Clean up, only a write buffer now
      double mb = getProperty("Memory");

      // Defaults have changed, default disk buffer size should be 10 data
      // chunks TODO: find optimal, 100 may be better.
      if (mb <= 0)
        mb = double(10 * loader->getDataChunk() * sizeof(MDE)) /
             double(1024 * 1024);

      // Express the cache memory in units of number of events.
      uint64_t cacheMemory =
          static_cast<uint64_t>((mb * 1024. * 1024.) / sizeof(MDE)) + 1;

      // Set these values in the diskMRU
      bc->getFileIO()->setWriteBufferSize(cacheMemory);

      g_log.information() << "Setting a DiskBuffer cache size of " << mb
                          << " MB, or " << cacheMemory << " events.\n";
    }
  } // Not file back end
  else if (!m_BoxStructureAndMethadata) {
    // ---------------------------------------- READ IN THE BOXES
    // ------------------------------------
    // TODO:: call to the file format factory
    auto loader =
        file_holder_type(new DataObjects::BoxControllerNeXusIO(bc.get()));
    loader->setDataType(sizeof(coord_t), MDE::getTypeName());

    loader->openFile(m_filename, "r");

    const std::vector<uint64_t> &BoxEventIndex = FlatBoxTree.getEventIndex();
    prog->setNumSteps(numBoxes);

    for (size_t i = 0; i < numBoxes; i++) {
      prog->report();
      MDBox<MDE, nd> *box = dynamic_cast<MDBox<MDE, nd> *>(boxTree[i]);
      if (!box)
        continue;

      if (BoxEventIndex[2 * i + 1] >
          0) // Load in memory NOT using the file as the back-end,
      {
        boxTree[i]->reserveMemoryForLoad(BoxEventIndex[2 * i + 1]);
        boxTree[i]->loadAndAddFrom(
            loader.get(), BoxEventIndex[2 * i],
            static_cast<size_t>(BoxEventIndex[2 * i + 1]));
      }
    }
    loader->closeFile();
  } else // box structure and metadata only
  {
  }
  g_log.debug() << tim
                << " to create all the boxes and fill them with events.\n";

  // Box of ID 0 is the head box.
  ws->setBox(boxTree[0]);
  // Make sure the max ID is ok for later ID generation
  bc->setMaxId(numBoxes);

  // end-of bMetaDataOnly
  // Refresh cache
  // TODO:if(!fileBackEnd)ws->refreshCache();
  ws->refreshCache();
  g_log.debug() << tim << " to refreshCache(). " << ws->getNPoints()
                << " points after refresh.\n";

  g_log.debug() << tim << " to finish up.\n";
  delete prog;
}
Exemplo n.º 7
0
void SaveMD::doSaveEvents(typename MDEventWorkspace<MDE, nd>::sptr ws) {
  std::string filename = getPropertyValue("Filename");
  bool update = getProperty("UpdateFileBackEnd");
  bool MakeFileBacked = getProperty("MakeFileBacked");

  bool wsIsFileBacked = ws->isFileBacked();
  if (update && MakeFileBacked)
    throw std::invalid_argument(
        "Please choose either UpdateFileBackEnd or MakeFileBacked, not both.");

  if (MakeFileBacked && wsIsFileBacked)
    throw std::invalid_argument(
        "You picked MakeFileBacked but the workspace is already file-backed!");

  BoxController_sptr bc = ws->getBoxController();

  if (!wsIsFileBacked) { // Erase the file if it exists
    Poco::File oldFile(filename);
    if (oldFile.exists())
      oldFile.remove();
  }

  auto prog = new Progress(this, 0.0, 0.05, 1);
  if (update) // workspace has its own file and ignores any changes to the
              // algorithm parameters
  {
    if (!ws->isFileBacked())
      throw std::runtime_error(" attempt to update non-file backed workspace");
    filename = bc->getFileIO()->getFileName();
  }

  //-----------------------------------------------------------------------------------------------------
  // create or open WS group and put there additional information about WS and
  // its dimensions
  int nDims = static_cast<int>(nd);
  bool data_exist;
  auto file = file_holder_type(MDBoxFlatTree::createOrOpenMDWSgroup(
      filename, nDims, MDE::getTypeName(), false, data_exist));

  // Save each NEW ExperimentInfo to a spot in the file
  MDBoxFlatTree::saveExperimentInfos(file.get(), ws);
  if (!update || !data_exist) {
    MDBoxFlatTree::saveWSGenericInfo(file.get(), ws);
  }
  file->closeGroup();
  file->close();

  MDBoxFlatTree BoxFlatStruct;
  //-----------------------------------------------------------------------------------------------------
  if (update) // the workspace is already file backed;
  {
    // remove all boxes from the DiskBuffer. DB will calculate boxes positions
    // on HDD.
    bc->getFileIO()->flushCache();
    // flatten the box structure; this will remember boxes file positions in the
    // box structure
    BoxFlatStruct.initFlatStructure(ws, filename);
  } else // not file backed;
  {
    // the boxes file positions are unknown and we need to calculate it.
    BoxFlatStruct.initFlatStructure(ws, filename);
    // create saver class
    auto Saver = boost::shared_ptr<API::IBoxControllerIO>(
        new DataObjects::BoxControllerNeXusIO(bc.get()));
    Saver->setDataType(sizeof(coord_t), MDE::getTypeName());
    if (MakeFileBacked) {
      // store saver with box controller
      bc->setFileBacked(Saver, filename);
      // get access to boxes array
      std::vector<API::IMDNode *> &boxes = BoxFlatStruct.getBoxes();
      // calculate the position of the boxes on file, indicating to make them
      // saveable and that the boxes were not saved.
      BoxFlatStruct.setBoxesFilePositions(true);
      prog->resetNumSteps(boxes.size(), 0.06, 0.90);
      for (auto &boxe : boxes) {
        auto saveableTag = boxe->getISaveable();
        if (saveableTag) // only boxes can be saveable
        {
          // do not spend time on empty boxes
          if (boxe->getDataInMemorySize() == 0)
            continue;
          // save boxes directly using the boxes file postion, precalculated in
          // boxFlatStructure.
          saveableTag->save();
          // remove boxes data from memory. This will actually correctly set the
          // tag indicatin that data were not loaded.
          saveableTag->clearDataFromMemory();
          // put boxes into write buffer wich will save them when necessary
          // Saver->toWrite(saveTag);
          prog->report("Saving Box");
        }
      }
      // remove everything from diskBuffer;  (not sure if it really necessary
      // but just in case , should not make any harm)
      Saver->flushCache();
      // drop NeXus on HDD (not sure if it really necessary but just in case )
      Saver->flushData();
    } else // just save data, and finish with it
    {
      Saver->openFile(filename, "w");
      BoxFlatStruct.setBoxesFilePositions(false);
      std::vector<API::IMDNode *> &boxes = BoxFlatStruct.getBoxes();
      std::vector<uint64_t> &eventIndex = BoxFlatStruct.getEventIndex();
      prog->resetNumSteps(boxes.size(), 0.06, 0.90);
      for (size_t i = 0; i < boxes.size(); i++) {
        if (eventIndex[2 * i + 1] == 0)
          continue;
        boxes[i]->saveAt(Saver.get(), eventIndex[2 * i]);
        prog->report("Saving Box");
      }
      Saver->closeFile();
    }
  }

  // -------------- Save Box Structure  -------------------------------------
  // OK, we've filled these big arrays of data representing flat box structrre.
  // Save them.
  progress(0.91, "Writing Box Data");
  prog->resetNumSteps(8, 0.92, 1.00);

  // Save box structure;
  BoxFlatStruct.saveBoxStructure(filename);

  delete prog;

  ws->setFileNeedsUpdating(false);
}
Exemplo n.º 8
0
  void BinToMDHistoWorkspace::do_centerpointBin(typename MDEventWorkspace<MDE, nd>::sptr ws)
  {
    bool DODEBUG = true;

    CPUTimer tim;

    // Number of output binning dimensions found
    size_t outD = binDimensions.size();

    //Since the costs are not known ahead of time, use a simple FIFO buffer.
    ThreadScheduler * ts = new ThreadSchedulerFIFO();

    // Create the threadpool with: all CPUs, a progress reporter
    ThreadPool tp(ts, 0, prog);

    // Big efficiency gain is obtained by grouping a few bins per task.
    size_t binsPerTask = 100;

    // For progress reporting, the approx  # of tasks
    if (prog)
      prog->setNumSteps( int(outWS->getNPoints()/100) );

    // The root-level box.
    IMDBox<MDE,nd> * rootBox = ws->getBox();

    // This is the limit to loop over in each dimension
    size_t * index_max = new size_t[outD];
    for (size_t bd=0; bd<outD; bd++) index_max[bd] = binDimensions[bd]->getNBins();

    // Cache a calculation to convert indices x,y,z,t into a linear index.
    size_t * index_maker = new size_t[outD];
    Utils::NestedForLoop::SetUpIndexMaker(outD, index_maker, index_max);

    int numPoints = int(outWS->getNPoints());

    // Run in OpenMP with dynamic scheduling and a smallish chunk size (binsPerTask)
    // Right now, not parallel for file-backed systems.
    bool fileBacked = (ws->getBoxController()->getFile() != NULL);
    PRAGMA_OMP(parallel for schedule(dynamic, binsPerTask) if (!fileBacked)  )
    for (int i=0; i < numPoints; i++)
    {
      PARALLEL_START_INTERUPT_REGION

      size_t linear_index = size_t(i);
      // nd >= outD in all cases so this is safe.
      size_t index[nd];

      // Get the index at each dimension for this bin.
      Utils::NestedForLoop::GetIndicesFromLinearIndex(outD, linear_index, index_maker, index_max, index);

      // Construct the bin and its coordinates
      MDBin<MDE,nd> bin;
      for (size_t bd=0; bd<outD; bd++)
      {
        // Index in this binning dimension (i_x, i_y, etc.)
        size_t idx = index[bd];
        // Dimension in the MDEventWorkspace
        size_t d = dimensionToBinFrom[bd];
        // Corresponding extents
        bin.m_min[d] = binDimensions[bd]->getX(idx);
        bin.m_max[d] = binDimensions[bd]->getX(idx+1);
      }
      bin.m_index = linear_index;

      bool dimensionsUsed[nd];
      for (size_t d=0; d<nd; d++)
        dimensionsUsed[d] = (d<3);

      // Check if the bin is in the ImplicitFunction (if any)
      bool binContained = true;
      if (implicitFunction)
      {
        binContained = implicitFunction->isPointContained(bin.m_min); //TODO. Correct argument passed to this method?
      }

      if (binContained)
      {
        // Array of bools set to true when a dimension is fully contained (binary splitting only)
        bool fullyContained[nd];
        for (size_t d=0; d<nd; d++)
          fullyContained[d] = false;

        // This will recursively bin into the sub grids
        rootBox->centerpointBin(bin, fullyContained);

        // Save the data into the dense histogram
        outWS->setSignalAt(linear_index, bin.m_signal);
        outWS->setErrorAt(linear_index, bin.m_errorSquared);
      }

      // Report progress but not too often.
      if (((linear_index % 100) == 0) && prog ) prog->report();

      PARALLEL_END_INTERUPT_REGION
    } // (for each linear index)
    PARALLEL_CHECK_INTERUPT_REGION

    if (DODEBUG) std::cout << tim << " to run the openmp loop.\n";

    delete [] index_max;
    delete [] index_maker;
  }
Exemplo n.º 9
0
  void BinToMDHistoWorkspace::binByIterating(typename MDEventWorkspace<MDE, nd>::sptr ws)
  {
    BoxController_sptr bc = ws->getBoxController();

    // Start with signal at 0.0
    outWS->setTo(0.0, 0.0);

    // Cache some data to speed up accessing them a bit
    indexMultiplier = new size_t[outD];
    for (size_t d=0; d<outD; d++)
    {
      if (d > 0)
        indexMultiplier[d] = outWS->getIndexMultiplier()[d-1];
      else
        indexMultiplier[d] = 1;
    }
    signals = outWS->getSignalArray();
    errors = outWS->getErrorSquaredArray();

    // The dimension (in the output workspace) along which we chunk for parallel processing
    // TODO: Find the smartest dimension to chunk against
    size_t chunkDimension = 0;

    // How many bins (in that dimension) per chunk.
    // Try to split it so each core will get 2 tasks:
    int chunkNumBins =  int(binDimensions[chunkDimension]->getNBins() / (Mantid::Kernel::ThreadPool::getNumPhysicalCores() * 2));
    if (chunkNumBins < 1) chunkNumBins = 1;

    // Do we actually do it in parallel?
    bool doParallel = getProperty("Parallel");
    // Not if file-backed!
    if (bc->isFileBacked()) doParallel = false;
    if (!doParallel)
      chunkNumBins = int(binDimensions[chunkDimension]->getNBins());

    // Total number of steps
    size_t progNumSteps = 0;
    if (prog) prog->setNotifyStep(0.1);
    if (prog) prog->resetNumSteps(100, 0.00, 1.0);

    // Run the chunks in parallel. There is no overlap in the output workspace so it is
    // thread safe to write to it..
    PRAGMA_OMP( parallel for schedule(dynamic,1) if (doParallel) )
    for(int chunk=0; chunk < int(binDimensions[chunkDimension]->getNBins()); chunk += chunkNumBins)
    {
      PARALLEL_START_INTERUPT_REGION
      // Region of interest for this chunk.
      size_t * chunkMin = new size_t[outD];
      size_t * chunkMax = new size_t[outD];
      for (size_t bd=0; bd<outD; bd++)
      {
        // Same limits in the other dimensions
        chunkMin[bd] = 0;
        chunkMax[bd] = binDimensions[bd]->getNBins();
      }
      // Parcel out a chunk in that single dimension dimension
      chunkMin[chunkDimension] = size_t(chunk);
      if (size_t(chunk+chunkNumBins) > binDimensions[chunkDimension]->getNBins())
        chunkMax[chunkDimension] = binDimensions[chunkDimension]->getNBins();
      else
        chunkMax[chunkDimension] = size_t(chunk+chunkNumBins);

      // Build an implicit function (it needs to be in the space of the MDEventWorkspace)
      MDImplicitFunction * function = this->getImplicitFunctionForChunk(chunkMin, chunkMax);

      // Use getBoxes() to get an array with a pointer to each box
      std::vector<IMDBox<MDE,nd>*> boxes;
      // Leaf-only; no depth limit; with the implicit function passed to it.
      ws->getBox()->getBoxes(boxes, 1000, true, function);

      // Sort boxes by file position IF file backed. This reduces seeking time, hopefully.
      if (bc->isFileBacked())
        IMDBox<MDE, nd>::sortBoxesByFilePos(boxes);

      // For progress reporting, the # of boxes
      if (prog)
      {
        PARALLEL_CRITICAL(BinToMDHistoWorkspace_progress)
        {
          std::cout << "Chunk " << chunk << ": found " << boxes.size() << " boxes within the implicit function." << std::endl;
          progNumSteps += boxes.size();
          prog->setNumSteps( progNumSteps );
        }
      }

      // Go through every box for this chunk.
      for (size_t i=0; i<boxes.size(); i++)
      {
        MDBox<MDE,nd> * box = dynamic_cast<MDBox<MDE,nd> *>(boxes[i]);
        // Perform the binning in this separate method.
        if (box)
          this->binMDBox(box, chunkMin, chunkMax);

        // Progress reporting
        if (prog) prog->report();

      }// for each box in the vector
      PARALLEL_END_INTERUPT_REGION
    } // for each chunk in parallel
    PARALLEL_CHECK_INTERUPT_REGION



    // Now the implicit function
    if (implicitFunction)
    {
      prog->report("Applying implicit function.");
      signal_t nan = std::numeric_limits<signal_t>::quiet_NaN();
      outWS->applyImplicitFunction(implicitFunction, nan, nan);
    }
  }