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; }
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); }