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);
}
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);
}
/**
* Loads the mapping between index -> set of detector IDs
*
* If "detector_index", "detector_count" and "detector_list" are all present,
* use these to get the mapping, otherwise spectrum number = detector ID
* (one-to-one)
*
* The spectrum spectrum_index[i] maps to detector_count[i] detectors, whose
* detector IDs are in detector_list starting at the index detector_index[i]
*
* @returns :: map of index -> detector IDs
* @throws std::runtime_error if fails to read data from file
*/
std::map<int, std::set<int>>
LoadMuonNexus2::loadDetectorMapping(const Mantid::NeXus::NXInt &spectrumIndex) {
std::map<int, std::set<int>> mapping;
const int nSpectra = spectrumIndex.dim0();
// Find and open the data group
NXRoot root(getPropertyValue("Filename"));
NXEntry entry = root.openEntry(m_entry_name);
const std::string detectorName = [&entry]() {
// Only the first NXdata found
for (auto &group : entry.groups()) {
std::string className = group.nxclass;
if (className == "NXdata") {
return group.nxname;
}
}
throw std::runtime_error("No NXdata found in file");
}();
NXData dataGroup = entry.openNXData(detectorName);
// Usually for muon data, detector id = spectrum number
// If not, the optional groups "detector_index", "detector_list" and
// "detector_count" will be present to map one to the other
const bool hasDetectorMapping = dataGroup.containsDataSet("detector_index") &&
dataGroup.containsDataSet("detector_list") &&
dataGroup.containsDataSet("detector_count");
if (hasDetectorMapping) {
// Read detector IDs
try {
const auto detIndex = dataGroup.openNXInt("detector_index");
const auto detCount = dataGroup.openNXInt("detector_count");
const auto detList = dataGroup.openNXInt("detector_list");
const int nSpectra = detIndex.dim0();
for (int i = 0; i < nSpectra; ++i) {
const int start = detIndex[i];
const int nDetectors = detCount[i];
std::set<int> detIDs;
for (int jDet = 0; jDet < nDetectors; ++jDet) {
detIDs.insert(detList[start + jDet]);
}
mapping[i] = detIDs;
}
} catch (const ::NeXus::Exception &err) {
// Throw a more user-friendly message
std::ostringstream message;
message << "Failed to read detector mapping: " << err.what();
throw std::runtime_error(message.str());
}
} else {
for (int i = 0; i < nSpectra; ++i) {
mapping[i] = std::set<int>{spectrumIndex[i]};
}
}
return mapping;
}
/** Execute the algorithm.
*/
void LoadILLReflectometry::exec() {
// Retrieve filename
std::string filenameData = getPropertyValue("Filename");
// open the root node
NeXus::NXRoot dataRoot(filenameData);
NXEntry firstEntry = dataRoot.openFirstEntry();
// Load Monitor details: n. monitors x monitor contents
std::vector<std::vector<int>> monitorsData = loadMonitors(firstEntry);
// Load Data details (number of tubes, channels, etc)
loadDataDetails(firstEntry);
std::string instrumentPath = m_loader.findInstrumentNexusPath(firstEntry);
setInstrumentName(firstEntry, instrumentPath);
initWorkSpace(firstEntry, monitorsData);
g_log.debug("Building properties...");
loadNexusEntriesIntoProperties(filenameData);
g_log.debug("Loading data...");
loadDataIntoTheWorkSpace(firstEntry, monitorsData);
// load the instrument from the IDF if it exists
g_log.debug("Loading instrument definition...");
runLoadInstrument();
// 1) Move
// Get distance and tilt angle stored in nexus file
// Mantid way
//// auto angleProp =
/// dynamic_cast<PropertyWithValue<double>*>(m_localWorkspace->run().getProperty("dan.value"));
// Nexus way
double angle =
firstEntry.getFloat("instrument/dan/value"); // detector angle in degrees
double distance = firstEntry.getFloat(
"instrument/det/value"); // detector distance in millimeter
distance /= 1000.0; // convert to meter
g_log.debug() << "Moving detector at angle " << angle << " and distance "
<< distance << std::endl;
placeDetector(distance, angle);
// Set the channel width property
auto channel_width = dynamic_cast<PropertyWithValue<double> *>(
m_localWorkspace->run().getProperty("monitor1.time_of_flight_0"));
m_localWorkspace->mutableRun().addProperty<double>(
"channel_width", *channel_width, true); // overwrite
// Set the output workspace property
setProperty("OutputWorkspace", m_localWorkspace);
}
/** Log the run details from the file
* @param localWorkspace :: The workspace details to use
*/
void
LoadMuonNexus1::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);
NXRoot root(m_filename);
try {
std::string start_time = root.getString("run/start_time");
runDetails.addProperty("run_start", start_time);
} catch (std::runtime_error &) {
g_log.warning("run/start_time is not available, run_start log not added.");
}
try {
std::string stop_time = root.getString("run/stop_time");
runDetails.addProperty("run_end", stop_time);
} catch (std::runtime_error &) {
g_log.warning("run/stop_time is not available, run_end log not added.");
}
try {
std::string dur = root.getString("run/duration");
runDetails.addProperty("dur", dur);
runDetails.addProperty("durunits", 1); // 1 means second here
runDetails.addProperty("dur_secs", dur);
} catch (std::runtime_error &) {
g_log.warning("run/duration is not available, dur log not added.");
}
// Get sample parameters
NXEntry runSample = root.openEntry("run/sample");
if (runSample.containsDataSet("temperature")) {
float temperature = runSample.getFloat("temperature");
runDetails.addProperty("sample_temp", static_cast<double>(temperature));
}
if (runSample.containsDataSet("magnetic_field")) {
float magn_field = runSample.getFloat("magnetic_field");
runDetails.addProperty("sample_magn_field",
static_cast<double>(magn_field));
}
}
/*
* Load data about the Experiment.
*
* TODO: This is very incomplete. In ISIS they much more info in the nexus file than ILL.
*
* @param entry :: The Nexus entry
*/
void LoadSINQFocus::loadExperimentDetails(NXEntry & entry) {
std::string name = boost::lexical_cast<std::string>(
entry.getFloat("sample/name"));
m_localWorkspace->mutableSample().setName(name);
}
/**
* Load data about the sample
* @param local_workspace :: The workspace to load the logs to.
* @param entry :: The Nexus entry
*/
void LoadISISNexus2::loadSampleData(DataObjects::Workspace2D_sptr local_workspace, NXEntry & entry)
{
/// Sample geometry
NXInt spb = entry.openNXInt("isis_vms_compat/SPB");
// Just load the index we need, not the whole block. The flag is the third value in
spb.load(1, 2);
int geom_id = spb[0];
local_workspace->mutableSample().setGeometryFlag(spb[0]);
NXFloat rspb = entry.openNXFloat("isis_vms_compat/RSPB");
// Just load the indices we need, not the whole block. The values start from the 4th onward
rspb.load(3, 3);
double thick(rspb[0]), height(rspb[1]), width(rspb[2]);
local_workspace->mutableSample().setThickness(thick);
local_workspace->mutableSample().setHeight(height);
local_workspace->mutableSample().setWidth(width);
g_log.debug() << "Sample geometry - ID: " << geom_id << ", thickness: " << thick << ", height: " << height << ", width: " << width << "\n";
}
/** 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();
}
/** 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 logs from Nexus file. Logs are expected to be in
* /raw_data_1/runlog group of the file. Call to this method must be done
* within /raw_data_1 group.
* @param ws :: The workspace to load the logs to.
* @param entry :: Nexus entry
*/
void LoadISISNexus2::loadLogs(DataObjects::Workspace2D_sptr ws, NXEntry & entry)
{
IAlgorithm_sptr alg = createChildAlgorithm("LoadNexusLogs", 0.0, 0.5);
alg->setPropertyValue("Filename", this->getProperty("Filename"));
alg->setProperty<MatrixWorkspace_sptr>("Workspace", ws);
try
{
alg->executeAsChildAlg();
}
catch(std::runtime_error&)
{
g_log.warning() << "Unable to load run logs. There will be no log "
<< "data associated with this workspace\n";
return;
}
// For ISIS Nexus only, fabricate an addtional log containing an array of proton charge information from the periods group.
try
{
NXClass protonChargeClass = entry.openNXGroup("periods");
NXFloat periodsCharge = protonChargeClass.openNXFloat("proton_charge");
periodsCharge.load();
size_t nperiods = periodsCharge.dim0();
std::vector<double> chargesVector(nperiods);
std::copy(periodsCharge(), periodsCharge() + nperiods, chargesVector.begin());
ArrayProperty<double>* protonLogData = new ArrayProperty<double>("proton_charge_by_period", chargesVector);
ws->mutableRun().addProperty(protonLogData);
}
catch(std::runtime_error&)
{
this->g_log.debug("Cannot read periods information from the nexus file. This group may be absent.");
}
// Populate the instrument parameters.
ws->populateInstrumentParameters();
// Make log creator object and add the run status log
m_logCreator.reset(new ISISRunLogs(ws->run(), m_numberOfPeriods));
m_logCreator->addStatusLog(ws->mutableRun());
}
/**
* Read the instrument group
* @param mtd_entry :: The node for the current workspace
* @param local_workspace :: The workspace to attach the instrument
*/
void LoadNexusProcessed::readInstrumentGroup(NXEntry & mtd_entry, API::MatrixWorkspace_sptr local_workspace)
{
//Instrument information
NXInstrument inst = mtd_entry.openNXInstrument("instrument");
if ( ! inst.containsGroup("detector") )
{
g_log.information() << "Detector block not found. The workspace will not contain any detector information.\n";
return;
}
//Populate the spectra-detector map
NXDetector detgroup = inst.openNXDetector("detector");
//Read necessary arrays from the file
// Detector list contains a list of all of the detector numbers. If it not present then we can't update the spectra
// map
int ndets(-1);
boost::shared_array<int> det_list(NULL);
try
{
NXInt detlist_group = detgroup.openNXInt("detector_list");
ndets = detlist_group.dim0();
detlist_group.load();
det_list.swap(detlist_group.sharedBuffer());
}
catch(std::runtime_error &)
{
g_log.information() << "detector_list block not found. The workspace will not contain any detector information."
<< std::endl;
return;
}
//Detector count contains the number of detectors associated with each spectra
NXInt det_count = detgroup.openNXInt("detector_count");
det_count.load();
//Detector index - contains the index of the detector in the workspace
NXInt det_index = detgroup.openNXInt("detector_index");
det_index.load();
int nspectra = det_index.dim0();
//Spectra block - Contains spectrum numbers for each workspace index
// This might not exist so wrap and check. If it doesn't exist create a default mapping
bool have_spectra(true);
boost::shared_array<int> spectra(NULL);
try
{
NXInt spectra_block = detgroup.openNXInt("spectra");
spectra_block.load();
spectra.swap(spectra_block.sharedBuffer());
}
catch(std::runtime_error &)
{
have_spectra = false;
}
//Now build the spectra list
int *spectra_list = new int[ndets];
API::Axis *axis1 = local_workspace->getAxis(1);
int index=0;
for(int i = 1; i <= nspectra; ++i)
{
int spectrum(-1);
if( have_spectra ) spectrum = spectra[i-1];
else spectrum = i+1 ;
if ((i >= m_spec_min && i < m_spec_max )||(m_list && find(m_spec_list.begin(), m_spec_list.end(),
i) != m_spec_list.end()))
{
if( m_axis1vals.empty() )
{
axis1->spectraNo(index) = spectrum;
}
else
{
axis1->setValue(index, m_axis1vals[i-1]);
}
++index;
}
int offset = det_index[i-1];
int detcount = det_count[i-1];
for(int j = 0; j < detcount; j++)
{
spectra_list[offset + j] = spectrum;
}
}
local_workspace->replaceSpectraMap(new SpectraDetectorMap(spectra_list, det_list.get(), ndets));
delete[] spectra_list;
}
/**
* Load a table
*/
API::Workspace_sptr LoadNexusProcessed::loadTableEntry(NXEntry & entry)
{
API::ITableWorkspace_sptr workspace;
workspace = Mantid::API::WorkspaceFactory::Instance().createTable("TableWorkspace");
NXData nx_tw = entry.openNXData("table_workspace");
std::vector<double> values;
bool hasNumberOfRowBeenSet = false;
//int numberOfRows = 0;
int columnNumber = 1;
do
{
std::string str = "column_" + boost::lexical_cast<std::string>(columnNumber);
NXInfo info = nx_tw.getDataSetInfo(str.c_str());
if (info.stat == NX_ERROR)
{
break;
}
if ( info.type == NX_FLOAT64 )
{
NXDouble nxDouble = nx_tw.openNXDouble(str.c_str());
std::string columnTitle = nxDouble.attributes("name");
if (!columnTitle.empty())
{
workspace->addColumn("double", columnTitle);
nxDouble.load();
int length = nxDouble.dim0();
if ( !hasNumberOfRowBeenSet )
{
workspace->setRowCount(length);
hasNumberOfRowBeenSet = true;
}
for (int i = 0; i < length; i++)
workspace->cell<double>(i,columnNumber-1) = *(nxDouble() + i);
}
}
else if ( info.type == NX_CHAR )
{
NXChar data = nx_tw.openNXChar(str.c_str());
std::string columnTitle = data.attributes("name");
if (!columnTitle.empty())
{
workspace->addColumn("str", columnTitle);
int nRows = info.dims[0];
if ( !hasNumberOfRowBeenSet )
{
workspace->setRowCount(nRows);
hasNumberOfRowBeenSet = true;
}
int maxStr = info.dims[1];
std::string fromCrap(maxStr,' ');
data.load();
for (int iR = 0; iR < nRows; iR++)
{
for (int i = 0; i < maxStr; i++)
fromCrap[i] = *(data()+i+maxStr*iR);
workspace->cell<std::string>(iR,columnNumber-1) = fromCrap;
}
}
}
columnNumber++;
} while ( 1 );
return boost::static_pointer_cast<API::Workspace>(workspace);
}
/**
* Load data about the run
* @param local_workspace :: The workspace to load the run information in to
* @param entry :: The Nexus entry
*/
void LoadISISNexus2::loadRunDetails(DataObjects::Workspace2D_sptr local_workspace, NXEntry & entry)
{
API::Run & runDetails = local_workspace->mutableRun();
// Charge is stored as a float
m_proton_charge = static_cast<double>(entry.getFloat("proton_charge"));
runDetails.setProtonCharge(m_proton_charge);
std::string run_num = boost::lexical_cast<std::string>(entry.getInt("run_number"));
runDetails.addProperty("run_number", run_num);
//
// Some details are only stored in the VMS compatability block so we'll pull everything from there
// for consistency
NXClass vms_compat = entry.openNXGroup("isis_vms_compat");
// Run header
NXChar char_data = vms_compat.openNXChar("HDR");
char_data.load();
runDetails.addProperty("run_header", std::string(char_data(),80));
// Data details on run not the workspace
runDetails.addProperty("nspectra", static_cast<int>(m_numberOfSpectraInFile));
runDetails.addProperty("nchannels", static_cast<int>(m_numberOfChannelsInFile));
runDetails.addProperty("nperiods", static_cast<int>(m_numberOfPeriodsInFile));
// RPB struct info
NXInt rpb_int = vms_compat.openNXInt("IRPB");
rpb_int.load();
runDetails.addProperty("dur", rpb_int[0]); // actual run duration
runDetails.addProperty("durunits", rpb_int[1]); // scaler for above (1=seconds)
runDetails.addProperty("dur_freq", rpb_int[2]); // testinterval for above (seconds)
runDetails.addProperty("dmp", rpb_int[3]); // dump interval
runDetails.addProperty("dmp_units", rpb_int[4]); // scaler for above
runDetails.addProperty("dmp_freq", rpb_int[5]); // interval for above
runDetails.addProperty("freq", rpb_int[6]); // 2**k where source frequency = 50 / 2**k
// Now double data
NXFloat rpb_dbl = vms_compat.openNXFloat("RRPB");
rpb_dbl.load();
runDetails.addProperty("gd_prtn_chrg", static_cast<double>(rpb_dbl[7])); // good proton charge (uA.hour)
runDetails.addProperty("tot_prtn_chrg", static_cast<double>(rpb_dbl[8])); // total proton charge (uA.hour)
runDetails.addProperty("goodfrm",rpb_int[9]); // good frames
runDetails.addProperty("rawfrm", rpb_int[10]); // raw frames
runDetails.addProperty("dur_wanted", rpb_int[11]); // requested run duration (units as for "duration" above)
runDetails.addProperty("dur_secs", rpb_int[12]); // actual run duration in seconds
runDetails.addProperty("mon_sum1", rpb_int[13]); // monitor sum 1
runDetails.addProperty("mon_sum2", rpb_int[14]); // monitor sum 2
runDetails.addProperty("mon_sum3",rpb_int[15]); // monitor sum 3
// End date and time is stored separately in ISO format in the "raw_data1/endtime" class
char_data = entry.openNXChar("end_time");
char_data.load();
std::string end_time_iso = std::string(char_data(), 19);
runDetails.addProperty("run_end", end_time_iso);
char_data = entry.openNXChar("start_time");
char_data.load();
std::string start_time_iso = std::string(char_data(), 19);
runDetails.addProperty("run_start", start_time_iso);
runDetails.addProperty("rb_proposal",rpb_int[21]); // RB (proposal) number
vms_compat.close();
}
/**
* 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 data about the run
* @param local_workspace :: The workspace to load the run information in to
* @param entry :: The Nexus entry
*/
void
LoadISISNexus2::loadRunDetails(DataObjects::Workspace2D_sptr &local_workspace,
NXEntry &entry) {
API::Run &runDetails = local_workspace->mutableRun();
// Charge is stored as a float
m_proton_charge = static_cast<double>(entry.getFloat("proton_charge"));
runDetails.setProtonCharge(m_proton_charge);
std::string run_num =
boost::lexical_cast<std::string>(entry.getInt("run_number"));
runDetails.addProperty("run_number", run_num);
//
// Some details are only stored in the VMS comparability block so we'll pull
// everything from there
// for consistency
NXClass vms_compat = entry.openNXGroup("isis_vms_compat");
// Run header
NXChar char_data = vms_compat.openNXChar("HDR");
char_data.load();
// Space-separate the fields
char *nxsHdr = char_data();
char header[86] = {};
const size_t byte = sizeof(char);
const char fieldSep(' ');
size_t fieldWidths[7] = {3, 5, 20, 24, 12, 8, 8};
char *srcStart = nxsHdr;
char *destStart = header;
for (size_t i = 0; i < 7; ++i) {
size_t width = fieldWidths[i];
memcpy(destStart, srcStart, width * byte);
if (i < 6) // no space after last field
{
srcStart += width;
destStart += width;
memset(destStart, fieldSep, byte); // insert separator
destStart += 1;
}
}
runDetails.addProperty("run_header", std::string(header, header + 86));
// Data details on run not the workspace
runDetails.addProperty("nspectra",
static_cast<int>(m_loadBlockInfo.numberOfSpectra));
runDetails.addProperty("nchannels",
static_cast<int>(m_loadBlockInfo.numberOfChannels));
runDetails.addProperty("nperiods",
static_cast<int>(m_loadBlockInfo.numberOfPeriods));
// RPB struct info
NXInt rpb_int = vms_compat.openNXInt("IRPB");
rpb_int.load();
runDetails.addProperty("dur", rpb_int[0]); // actual run duration
runDetails.addProperty("durunits",
rpb_int[1]); // scaler for above (1=seconds)
runDetails.addProperty("dur_freq",
rpb_int[2]); // testinterval for above (seconds)
runDetails.addProperty("dmp", rpb_int[3]); // dump interval
runDetails.addProperty("dmp_units", rpb_int[4]); // scaler for above
runDetails.addProperty("dmp_freq", rpb_int[5]); // interval for above
runDetails.addProperty("freq",
rpb_int[6]); // 2**k where source frequency = 50 / 2**k
// Now double data
NXFloat rpb_dbl = vms_compat.openNXFloat("RRPB");
rpb_dbl.load();
runDetails.addProperty(
"gd_prtn_chrg",
static_cast<double>(rpb_dbl[7])); // good proton charge (uA.hour)
runDetails.addProperty(
"tot_prtn_chrg",
static_cast<double>(rpb_dbl[8])); // total proton charge (uA.hour)
runDetails.addProperty("goodfrm", rpb_int[9]); // good frames
runDetails.addProperty("rawfrm", rpb_int[10]); // raw frames
runDetails.addProperty(
"dur_wanted",
rpb_int[11]); // requested run duration (units as for "duration" above)
runDetails.addProperty("dur_secs",
rpb_int[12]); // actual run duration in seconds
runDetails.addProperty("mon_sum1", rpb_int[13]); // monitor sum 1
runDetails.addProperty("mon_sum2", rpb_int[14]); // monitor sum 2
runDetails.addProperty("mon_sum3", rpb_int[15]); // monitor sum 3
// End date and time is stored separately in ISO format in the
// "raw_data1/endtime" class
char_data = entry.openNXChar("end_time");
char_data.load();
std::string end_time_iso = std::string(char_data(), 19);
runDetails.addProperty("run_end", end_time_iso);
char_data = entry.openNXChar("start_time");
char_data.load();
std::string start_time_iso = std::string(char_data(), 19);
runDetails.addProperty("run_start", start_time_iso);
runDetails.addProperty("rb_proposal", rpb_int[21]); // RB (proposal) number
vms_compat.close();
}
/**
* 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;
}
}
/**Method takes input parameters which describe monitor loading and analyze
*them against spectra/monitor block information in the file.
* The result is the option if monitors can be loaded together with spectra or
*mast be treated separately
* and additional information on how to treat monitor spectra.
*
*@param entry :: entry to the NeXus file, opened at root folder
*@param spectrum_index :: array of spectra indexes of the data present in
*the file
*@param ndets :: size of the spectrum index array
*@param n_vms_compat_spectra :: number of data entries containing common time
*bins (e.g. all spectra, or all spectra and monitors or some spectra (this is
*not fully supported)
*@param monitors :: map connecting monitor spectra ID against
*monitor group name in the file.
*@param excludeMonitors :: input property indicating if it is requested to
*exclude monitors from the target workspace
*@param separateMonitors :: input property indicating if it is requested to
*load monitors separately (and exclude them from target data workspace this way)
*
*@param OvelapMonitors :: output property containing the list of monitors
*ID for monitors, which are also included with spectra.
*@return excludeMonitors :: indicator if monitors should or mast be excluded
*from the main data workspace if they can not be loaded with the data
* (contain different number of time channels)
*
*/
bool LoadISISNexus2::findSpectraDetRangeInFile(
NXEntry &entry, boost::shared_array<int> &spectrum_index, int64_t ndets,
int64_t n_vms_compat_spectra, std::map<int64_t, std::string> &monitors,
bool excludeMonitors, bool separateMonitors,
std::map<int64_t, std::string> &OvelapMonitors) {
OvelapMonitors.clear();
size_t nmons = monitors.size();
if (nmons > 0) {
NXInt chans = entry.openNXInt(m_monitors.begin()->second + "/data");
m_monBlockInfo = DataBlock(chans);
m_monBlockInfo.numberOfSpectra = nmons; // each monitor is in separate group
// so number of spectra is equal to
// number of groups.
// identify monitor ID range.
for (auto it = monitors.begin(); it != monitors.end(); it++) {
int64_t mon_id = static_cast<int64_t>(it->first);
if (m_monBlockInfo.spectraID_min > mon_id)
m_monBlockInfo.spectraID_min = mon_id;
if (m_monBlockInfo.spectraID_max < mon_id)
m_monBlockInfo.spectraID_max = mon_id;
}
if (m_monBlockInfo.spectraID_max - m_monBlockInfo.spectraID_min + 1 !=
static_cast<int64_t>(nmons)) {
g_log.warning() << "When trying to find the range of monitor spectra: "
"non-consequent monitor ID-s in the monitor block. "
"Unexpected situation for the loader\n";
}
// at this stage we assume that the only going to load monitors
m_loadBlockInfo = m_monBlockInfo;
}
if (ndets == 0) {
separateMonitors = false; // only monitors in the main workspace. No
// detectors. Will be loaded in the main workspace
// Possible function exit point
return separateMonitors;
}
// detectors are present in the file
NXData nxData = entry.openNXData("detector_1");
NXInt data = nxData.openIntData();
m_detBlockInfo = DataBlock(data);
// We assume again that this spectrum list ID increase monotonically
m_detBlockInfo.spectraID_min = spectrum_index[0];
m_detBlockInfo.spectraID_max = spectrum_index[ndets - 1];
if (m_detBlockInfo.spectraID_max - m_detBlockInfo.spectraID_min + 1 !=
static_cast<int64_t>(m_detBlockInfo.numberOfSpectra)) {
g_log.warning() << "When trying to find the range of monitor spectra: "
"non-consequent spectra ID-s in the detectors block. "
"Unexpected situation for the loader\n";
}
m_loadBlockInfo = m_detBlockInfo;
// now we are analyzing what is actually going or can be loaded
bool removeMonitors = excludeMonitors || separateMonitors;
if (((m_detBlockInfo.numberOfPeriods != m_monBlockInfo.numberOfPeriods) ||
(m_detBlockInfo.numberOfChannels != m_monBlockInfo.numberOfChannels)) &&
nmons > 0) {
// detectors and monitors have different characteristics. Can be loaded only
// to separate workspaces.
if (!removeMonitors) {
g_log.warning() << " Performing separate loading as can not load spectra "
"and monitors in the single workspace:\n";
g_log.warning() << " Monitors data contain :"
<< m_monBlockInfo.numberOfChannels
<< " time channels and: "
<< m_monBlockInfo.numberOfPeriods << " period(s)\n";
g_log.warning() << " Spectra data contain :"
<< m_detBlockInfo.numberOfChannels
<< " time channels and: "
<< m_detBlockInfo.numberOfPeriods << " period(s)\n";
}
separateMonitors = true;
removeMonitors = true;
}
int64_t spectraID_min =
std::min(m_monBlockInfo.spectraID_min, m_detBlockInfo.spectraID_min);
int64_t spectraID_max =
std::max(m_monBlockInfo.spectraID_max, m_detBlockInfo.spectraID_max);
size_t totNumOfSpectra =
m_monBlockInfo.numberOfSpectra + m_detBlockInfo.numberOfSpectra;
if (!removeMonitors) {
m_loadBlockInfo.numberOfSpectra = totNumOfSpectra;
m_loadBlockInfo.spectraID_min = spectraID_min;
m_loadBlockInfo.spectraID_max = spectraID_max;
}
if (separateMonitors)
m_loadBlockInfo = m_detBlockInfo;
// verify integrity of the monitor and detector information
if ((totNumOfSpectra == static_cast<size_t>(n_vms_compat_spectra)) &&
(spectraID_max - spectraID_min + 1 ==
static_cast<int64_t>(n_vms_compat_spectra))) {
// all information written in the file is correct, there are no spurious
// spectra and detectors & monitors form continuous block on HDD
return separateMonitors;
}
// something is wrong and we need to analyze spectra map. Currently we can
// identify and manage the case when all monitor's spectra are written
// together with detectors
// make settings for this situation
m_detBlockInfo.numberOfSpectra -= m_monBlockInfo.numberOfSpectra;
m_loadBlockInfo.numberOfSpectra -= m_monBlockInfo.numberOfSpectra;
std::map<int64_t, std::string> remaining_monitors;
if (removeMonitors) {
for (auto it = monitors.begin(); it != monitors.end(); it++) {
if (it->first >= m_detBlockInfo.spectraID_min &&
it->first <= m_detBlockInfo.spectraID_max) { // monitors ID-s are
// included with spectra
// ID-s -- let's try not
// to load it twice.
OvelapMonitors.insert(*it);
} else {
remaining_monitors.insert(*it);
}
}
}
monitors.swap(remaining_monitors);
return separateMonitors;
}