void LoadSINQFocus::loadRunDetails(NXEntry & entry) { API::Run & runDetails = m_localWorkspace->mutableRun(); // int runNum = entry.getInt("run_number"); // std::string run_num = boost::lexical_cast<std::string>(runNum); // runDetails.addProperty("run_number", run_num); std::string start_time = entry.getString("start_time"); //start_time = getDateTimeInIsoFormat(start_time); runDetails.addProperty("run_start", start_time); std::string end_time = entry.getString("end_time"); //end_time = getDateTimeInIsoFormat(end_time); runDetails.addProperty("run_end", end_time); double wavelength = entry.getFloat(m_instrumentPath + "/monochromator/lambda"); runDetails.addProperty<double>("wavelength", wavelength); double energy = entry.getFloat(m_instrumentPath + "/monochromator/energy"); runDetails.addProperty<double>("Ei", energy, true); //overwrite std::string title = entry.getString("title"); runDetails.addProperty("title", title); m_localWorkspace->setTitle(title); }
/** Load logs from Nexus file. Logs are expected to be in * /run/sample group of the file. * @param ws :: The workspace to load the logs to. * @param entry :: The Nexus entry * @param period :: The period of this workspace */ void LoadMuonNexus2::loadLogs(API::MatrixWorkspace_sptr ws, NXEntry &entry, int period) { // Avoid compiler warning (void)period; std::string start_time = entry.getString("start_time"); std::string sampleName = entry.getString("sample/name"); NXMainClass runlogs = entry.openNXClass<NXMainClass>("sample"); ws->mutableSample().setName(sampleName); for (std::vector<NXClassInfo>::const_iterator it = runlogs.groups().begin(); it != runlogs.groups().end(); ++it) { NXLog nxLog = runlogs.openNXLog(it->nxname); Kernel::Property *logv = nxLog.createTimeSeries(start_time); if (!logv) continue; ws->mutableRun().addLogData(logv); } ws->setTitle(entry.getString("title")); if (entry.containsDataSet("notes")) { ws->setComment(entry.getString("notes")); } std::string run_num = std::to_string(entry.getInt("run_number")); // The sample is left to delete the property ws->mutableRun().addLogData( new PropertyWithValue<std::string>("run_number", run_num)); ws->populateInstrumentParameters(); }
void LoadLLB::loadRunDetails(NXEntry &entry) { API::Run &runDetails = m_localWorkspace->mutableRun(); // int runNum = entry.getInt("run_number"); // std::string run_num = boost::lexical_cast<std::string>(runNum); // runDetails.addProperty("run_number", run_num); std::string start_time = entry.getString("start_time"); // start_time = getDateTimeInIsoFormat(start_time); runDetails.addProperty("run_start", start_time); std::string end_time = entry.getString("end_time"); // end_time = getDateTimeInIsoFormat(end_time); runDetails.addProperty("run_end", end_time); double wavelength = entry.getFloat("nxbeam/incident_wavelength"); runDetails.addProperty<double>("wavelength", wavelength); double energy = m_loader.calculateEnergy(wavelength); runDetails.addProperty<double>("Ei", energy, true); // overwrite std::string title = entry.getString("title"); runDetails.addProperty("title", title); m_localWorkspace->setTitle(title); }
/** Log the run details from the file * @param localWorkspace :: The workspace details to use */ void LoadMuonNexus2::loadRunDetails( DataObjects::Workspace2D_sptr localWorkspace) { API::Run &runDetails = localWorkspace->mutableRun(); runDetails.addProperty("run_title", localWorkspace->getTitle(), true); int numSpectra = static_cast<int>(localWorkspace->getNumberHistograms()); runDetails.addProperty("nspectra", numSpectra); m_filename = getPropertyValue("Filename"); NXRoot root(m_filename); NXEntry entry = root.openEntry(m_entry_name); std::string start_time = entry.getString("start_time"); runDetails.addProperty("run_start", start_time); std::string stop_time = entry.getString("end_time"); runDetails.addProperty("run_end", stop_time); if (entry.containsGroup("run")) { NXClass runRun = entry.openNXGroup("run"); if (runRun.containsDataSet("good_total_frames")) { int dum = runRun.getInt("good_total_frames"); runDetails.addProperty("goodfrm", dum); } if (runRun.containsDataSet("number_periods")) { int dum = runRun.getInt("number_periods"); runDetails.addProperty("nperiods", dum); } } { // Duration taken to be stop_time minus stat_time auto start = createFromSanitizedISO8601(start_time); auto end = createFromSanitizedISO8601(stop_time); double duration_in_secs = DateAndTime::secondsFromDuration(end - start); runDetails.addProperty("dur_secs", duration_in_secs); } }
/** * Load a given period into the workspace * @param period :: The period number to load (starting from 1) * @param entry :: The opened root entry node for accessing the monitor and data nodes * @param local_workspace :: The workspace to place the data in */ void LoadISISNexus2::loadPeriodData(int64_t period, NXEntry & entry, DataObjects::Workspace2D_sptr local_workspace) { int64_t hist_index = 0; int64_t period_index(period - 1); int64_t first_monitor_spectrum = 0; if( !m_monitors.empty() ) { first_monitor_spectrum = m_monitors.begin()->first; hist_index = first_monitor_spectrum - 1; for(std::map<int64_t,std::string>::const_iterator it = m_monitors.begin(); it != m_monitors.end(); ++it) { NXData monitor = entry.openNXData(it->second); NXInt mondata = monitor.openIntData(); m_progress->report("Loading monitor"); mondata.load(1,static_cast<int>(period-1)); // TODO this is just wrong MantidVec& Y = local_workspace->dataY(hist_index); Y.assign(mondata(),mondata() + m_numberOfChannels); MantidVec& E = local_workspace->dataE(hist_index); std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt); local_workspace->getAxis(1)->spectraNo(hist_index) = static_cast<specid_t>(it->first); NXFloat timeBins = monitor.openNXFloat("time_of_flight"); timeBins.load(); local_workspace->dataX(hist_index).assign(timeBins(),timeBins() + timeBins.dim0()); hist_index++; } if (first_monitor_spectrum > 1) { hist_index = 0; } } if( m_have_detector ) { NXData nxdata = entry.openNXData("detector_1"); NXDataSetTyped<int> data = nxdata.openIntData(); data.open(); //Start with thelist members that are lower than the required spectrum const int * const spec_begin = m_spec.get(); std::vector<int64_t>::iterator min_end = m_spec_list.end(); if( !m_spec_list.empty() ) { // If we have a list, by now it is ordered so first pull in the range below the starting block range // Note the reverse iteration as we want the last one if( m_range_supplied ) { min_end = std::find_if(m_spec_list.begin(), m_spec_list.end(), std::bind2nd(std::greater<int>(), m_spec_min)); } for( std::vector<int64_t>::iterator itr = m_spec_list.begin(); itr < min_end; ++itr ) { // Load each int64_t spectra_no = (*itr); // For this to work correctly, we assume that the spectrum list increases monotonically int64_t filestart = std::lower_bound(spec_begin,m_spec_end,spectra_no) - spec_begin; m_progress->report("Loading data"); loadBlock(data, static_cast<int64_t>(1), period_index, filestart, hist_index, spectra_no, local_workspace); } } if( m_range_supplied ) { // When reading in blocks we need to be careful that the range is exactly divisible by the blocksize // and if not have an extra read of the left overs const int64_t blocksize = 8; const int64_t rangesize = (m_spec_max - m_spec_min + 1) - m_monitors.size(); const int64_t fullblocks = rangesize / blocksize; int64_t read_stop = 0; int64_t spectra_no = m_spec_min; if (first_monitor_spectrum == 1) {// this if crudely checks whether the monitors are at the begining or end of the spectra spectra_no += static_cast<int>(m_monitors.size()); } // For this to work correctly, we assume that the spectrum list increases monotonically int64_t filestart = std::lower_bound(spec_begin,m_spec_end,spectra_no) - spec_begin; if( fullblocks > 0 ) { read_stop = (fullblocks * blocksize);// + m_monitors.size(); //RNT: I think monitors are excluded from the data //for( ; hist_index < read_stop; ) for(int64_t i = 0; i < fullblocks; ++i) { loadBlock(data, blocksize, period_index, filestart, hist_index, spectra_no, local_workspace); filestart += blocksize; } } int64_t finalblock = rangesize - (fullblocks * blocksize); if( finalblock > 0 ) { loadBlock(data, finalblock, period_index, filestart, hist_index, spectra_no, local_workspace); } } //Load in the last of the list indices for( std::vector<int64_t>::iterator itr = min_end; itr < m_spec_list.end(); ++itr ) { // Load each int64_t spectra_no = (*itr); // For this to work correctly, we assume that the spectrum list increases monotonically int64_t filestart = std::lower_bound(spec_begin,m_spec_end,spectra_no) - spec_begin; loadBlock(data, 1, period_index, filestart, hist_index, spectra_no, local_workspace); } } try { const std::string title = entry.getString("title"); local_workspace->setTitle(title); // write the title into the log file (run object) local_workspace->mutableRun().addProperty("run_title", title, true); } catch (std::runtime_error &) { g_log.debug() << "No title was found in the input file, " << getPropertyValue("Filename") << std::endl; } }
/** * Load a given period into the workspace * @param period :: The period number to load (starting from 1) * @param entry :: The opened root entry node for accessing the monitor and data * nodes * @param local_workspace :: The workspace to place the data in * @param update_spectra2det_mapping :: reset spectra-detector map to the one * calculated earlier. (Warning! -- this map has to be calculated correctly!) */ void LoadISISNexus2::loadPeriodData(int64_t period, NXEntry &entry, DataObjects::Workspace2D_sptr &local_workspace, bool update_spectra2det_mapping) { int64_t hist_index = 0; int64_t period_index(period - 1); // int64_t first_monitor_spectrum = 0; for (auto block = m_spectraBlocks.begin(); block != m_spectraBlocks.end(); ++block) { if (block->isMonitor) { NXData monitor = entry.openNXData(block->monName); NXInt mondata = monitor.openIntData(); m_progress->report("Loading monitor"); mondata.load(1, static_cast<int>(period - 1)); // TODO this is just wrong MantidVec &Y = local_workspace->dataY(hist_index); Y.assign(mondata(), mondata() + m_monBlockInfo.numberOfChannels); MantidVec &E = local_workspace->dataE(hist_index); std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt); if (update_spectra2det_mapping) { // local_workspace->getAxis(1)->setValue(hist_index, // static_cast<specid_t>(it->first)); auto spec = local_workspace->getSpectrum(hist_index); specid_t specID = m_specInd2specNum_map.at(hist_index); spec->setDetectorIDs( m_spec2det_map.getDetectorIDsForSpectrumNo(specID)); spec->setSpectrumNo(specID); } NXFloat timeBins = monitor.openNXFloat("time_of_flight"); timeBins.load(); local_workspace->dataX(hist_index) .assign(timeBins(), timeBins() + timeBins.dim0()); hist_index++; } else if (m_have_detector) { NXData nxdata = entry.openNXData("detector_1"); NXDataSetTyped<int> data = nxdata.openIntData(); data.open(); // Start with the list members that are lower than the required spectrum const int *const spec_begin = m_spec.get(); // When reading in blocks we need to be careful that the range is exactly // divisible by the block-size // and if not have an extra read of the left overs const int64_t blocksize = 8; const int64_t rangesize = block->last - block->first + 1; const int64_t fullblocks = rangesize / blocksize; int64_t spectra_no = block->first; // For this to work correctly, we assume that the spectrum list increases // monotonically int64_t filestart = std::lower_bound(spec_begin, m_spec_end, spectra_no) - spec_begin; if (fullblocks > 0) { for (int64_t i = 0; i < fullblocks; ++i) { loadBlock(data, blocksize, period_index, filestart, hist_index, spectra_no, local_workspace); filestart += blocksize; } } int64_t finalblock = rangesize - (fullblocks * blocksize); if (finalblock > 0) { loadBlock(data, finalblock, period_index, filestart, hist_index, spectra_no, local_workspace); } } } try { const std::string title = entry.getString("title"); local_workspace->setTitle(title); // write the title into the log file (run object) local_workspace->mutableRun().addProperty("run_title", title, true); } catch (std::runtime_error &) { g_log.debug() << "No title was found in the input file, " << getPropertyValue("Filename") << std::endl; } }