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LoadMuonNexus2.cpp
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LoadMuonNexus2.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidDataHandling/LoadMuonNexus2.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/Progress.h"
#include "MantidAPI/RegisterFileLoader.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidDataHandling/LoadMuonNexus1.h"
#include "MantidDataHandling/LoadMuonNexusV2.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument/Detector.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/DateAndTimeHelpers.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/Unit.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/UnitLabelTypes.h"
#include "MantidNexus/NexusClasses.h"
#include <Poco/Path.h>
#include <memory>
// clang-format off
#include <nexus/NeXusFile.hpp>
#include <nexus/NeXusException.hpp>
// clang-format on
#include <cmath>
#include <numeric>
using Mantid::Types::Core::DateAndTime;
namespace Mantid {
namespace DataHandling {
// Register the algorithm into the algorithm factory
DECLARE_NEXUS_FILELOADER_ALGORITHM(LoadMuonNexus2)
using namespace Kernel;
using namespace DateAndTimeHelpers;
using namespace API;
using Geometry::Instrument;
using Mantid::HistogramData::BinEdges;
using Mantid::HistogramData::Counts;
using Mantid::HistogramData::Histogram;
using namespace Mantid::NeXus;
using Mantid::Types::Core::DateAndTime;
namespace {
inline std::string getLoadAlgName(int confidence1, int confidenceV2) {
return confidence1 > confidenceV2 ? "LoadMuonNexus" : "LoadMuonNexusV2";
}
} // namespace
/// Empty default constructor
LoadMuonNexus2::LoadMuonNexus2() : LoadMuonNexus() {}
/** Executes the right version of the Muon nexus loader
* @throw Exception::FileError If the Nexus file cannot be found/opened
* @throw std::invalid_argument If the optional properties are set to invalid
*values
*/
void LoadMuonNexus2::exec() {
LoadMuonNexus1 load1;
LoadMuonNexusV2 loadV2;
load1.initialize();
loadV2.initialize();
std::string filePath = getPropertyValue("Filename");
Kernel::NexusDescriptor descriptor(filePath);
int confidence1 = load1.confidence(descriptor);
int confidence2 = this->confidence(descriptor);
int confidenceV2 = 0;
// If the file is hdf5 then we can possibly use LoadMuonNexusV2
// To check this we'll have to create an HDF5 descriptor for the file.
if (Kernel::NexusDescriptor::isReadable(filePath,
Kernel::NexusDescriptor::Version5)) {
Kernel::NexusHDF5Descriptor descriptorHDF5(filePath);
confidenceV2 = loadV2.confidence(descriptorHDF5);
};
// if none can load the file throw
if (confidence1 < 80 && confidence2 < 80 && confidenceV2 < 80) {
throw Kernel::Exception::FileError("Cannot open the file ", filePath);
}
// Now pick the correct alg
if (confidence2 > std::max(confidence1, confidenceV2)) {
// Use this loader
doExec();
} else {
// Version 1 or V2
IAlgorithm_sptr childAlg = createChildAlgorithm(
getLoadAlgName(confidence1, confidenceV2), 0, 1, true, 1);
auto loader = std::dynamic_pointer_cast<API::Algorithm>(childAlg);
loader->copyPropertiesFrom(*this);
loader->executeAsChildAlg();
this->copyPropertiesFrom(*loader);
API::Workspace_sptr outWS = loader->getProperty("OutputWorkspace");
setProperty("OutputWorkspace", outWS);
}
}
/** Read in a muon nexus file of the version 2.
*
* @throw Exception::FileError If the Nexus file cannot be found/opened
* @throw std::invalid_argument If the optional properties are set to invalid
*values
*/
void LoadMuonNexus2::doExec() {
// Create the root Nexus class
NXRoot root(getPropertyValue("Filename"));
int64_t iEntry = getProperty("EntryNumber");
if (iEntry >= static_cast<int64_t>(root.groups().size())) {
throw std::invalid_argument("EntryNumber is out of range");
}
// Open the data entry
m_entry_name = root.groups()[iEntry].nxname;
NXEntry entry = root.openEntry(m_entry_name);
// Read in the instrument name from the Nexus file
m_instrument_name = entry.getString("instrument/name");
// Read the number of periods in this file
if (entry.containsGroup("run")) {
try {
m_numberOfPeriods = entry.getInt("run/number_periods");
} catch (::NeXus::Exception &) {
// assume 1
m_numberOfPeriods = 1;
}
} else {
m_numberOfPeriods = 1;
}
// Need to extract the user-defined output workspace name
Property *ws = getProperty("OutputWorkspace");
std::string localWSName = ws->value();
// If multiperiod, will need to hold the Instrument & Sample for copying
std::shared_ptr<Instrument> instrument;
std::shared_ptr<Sample> sample;
std::string detectorName;
// Only the first NXdata found
for (auto &group : entry.groups()) {
std::string className = group.nxclass;
if (className == "NXdata") {
detectorName = group.nxname;
break;
}
}
NXData dataGroup = entry.openNXData(detectorName);
Mantid::NeXus::NXInt spectrum_index = dataGroup.openNXInt("spectrum_index");
spectrum_index.load();
m_numberOfSpectra = spectrum_index.dim0();
// Load detector mapping
const auto &detMapping = loadDetectorMapping(spectrum_index);
// Call private method to validate the optional parameters, if set
checkOptionalProperties();
NXFloat raw_time = dataGroup.openNXFloat("raw_time");
raw_time.load();
int nBins = raw_time.dim0();
std::vector<double> timeBins;
timeBins.assign(raw_time(), raw_time() + nBins);
timeBins.emplace_back(raw_time[nBins - 1] + raw_time[1] - raw_time[0]);
// Calculate the size of a workspace, given its number of periods & spectra to
// read
int total_specs;
if (m_interval || m_list) {
total_specs = static_cast<int>(m_spec_list.size());
if (m_interval) {
total_specs += static_cast<int>((m_spec_max - m_spec_min + 1));
} else {
m_spec_max = -1; // to stop entering the min - max loop
}
} else {
total_specs = static_cast<int>(m_numberOfSpectra);
// for nexus return all spectra
m_spec_min = 1;
m_spec_max = m_numberOfSpectra; // was +1?
}
// Create the 2D workspace for the output
DataObjects::Workspace2D_sptr localWorkspace =
std::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create("Workspace2D", total_specs,
nBins + 1, nBins));
// Set the unit on the workspace to muon time, for now in the form of a Label
// Unit
std::shared_ptr<Kernel::Units::Label> lblUnit =
std::dynamic_pointer_cast<Kernel::Units::Label>(
UnitFactory::Instance().create("Label"));
lblUnit->setLabel("Time", Units::Symbol::Microsecond);
localWorkspace->getAxis(0)->unit() = lblUnit;
// Set y axis unit
localWorkspace->setYUnit("Counts");
// g_log.error()<<" number of perioids= "<<m_numberOfPeriods<<'\n';
WorkspaceGroup_sptr wsGrpSptr = WorkspaceGroup_sptr(new WorkspaceGroup);
if (entry.containsDataSet("title")) {
wsGrpSptr->setTitle(entry.getString("title"));
}
if (entry.containsDataSet("notes")) {
wsGrpSptr->setComment(entry.getString("notes"));
}
if (m_numberOfPeriods > 1) {
setProperty("OutputWorkspace",
std::dynamic_pointer_cast<Workspace>(wsGrpSptr));
}
// period_index is currently unused
// Mantid::NeXus::NXInt period_index = dataGroup.openNXInt("period_index");
// period_index.load();
Mantid::NeXus::NXInt counts = dataGroup.openIntData();
counts.load();
NXInstrument instr = entry.openNXInstrument("instrument");
if (instr.containsGroup("detector_fb")) {
NXDetector detector = instr.openNXDetector("detector_fb");
if (detector.containsDataSet("time_zero")) {
double dum = detector.getFloat("time_zero");
setProperty("TimeZero", dum);
}
if (detector.containsDataSet("first_good_time")) {
double dum = detector.getFloat("first_good_time");
setProperty("FirstGoodData", dum);
}
}
API::Progress progress(this, 0.0, 1.0, m_numberOfPeriods * total_specs);
// Loop over the number of periods in the Nexus file, putting each period in a
// separate workspace
for (int period = 0; period < m_numberOfPeriods; ++period) {
if (period == 0) {
// Only run the Child Algorithms once
loadRunDetails(localWorkspace);
runLoadInstrument(localWorkspace);
loadLogs(localWorkspace, entry, period);
} else // We are working on a higher period of a multiperiod raw file
{
localWorkspace = std::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(localWorkspace));
}
std::string outws;
if (m_numberOfPeriods > 1) {
std::string outputWorkspace = "OutputWorkspace";
std::stringstream suffix;
suffix << (period + 1);
outws = outputWorkspace + "_" + suffix.str();
std::string WSName = localWSName + "_" + suffix.str();
declareProperty(std::make_unique<WorkspaceProperty<Workspace>>(
outws, WSName, Direction::Output));
if (wsGrpSptr)
wsGrpSptr->addWorkspace(localWorkspace);
}
// create spectrum -> index correspondence
std::map<int, int> index_spectrum;
for (int i = 0; i < m_numberOfSpectra; ++i) {
index_spectrum[spectrum_index[i]] = i;
}
int wsIndex = 0;
localWorkspace->mutableX(0) = timeBins;
for (auto spec = static_cast<int>(m_spec_min);
spec <= static_cast<int>(m_spec_max); ++spec) {
int i = index_spectrum[spec]; // if spec not found i is 0
localWorkspace->setHistogram(
wsIndex, loadData(localWorkspace->binEdges(0), counts, period, i));
localWorkspace->getSpectrum(wsIndex).setSpectrumNo(spectrum_index[i]);
localWorkspace->getSpectrum(wsIndex).setDetectorIDs(detMapping.at(i));
wsIndex++;
progress.report();
}
// Read in the spectra in the optional list parameter, if set
if (m_list) {
for (auto spec : m_spec_list) {
int k = index_spectrum[spec]; // if spec not found k is 0
localWorkspace->setHistogram(
wsIndex, loadData(localWorkspace->binEdges(0), counts, period, k));
localWorkspace->getSpectrum(wsIndex).setSpectrumNo(spectrum_index[k]);
localWorkspace->getSpectrum(wsIndex).setDetectorIDs(detMapping.at(k));
wsIndex++;
progress.report();
}
}
// Just a sanity check
assert(wsIndex == total_specs);
bool autogroup = getProperty("AutoGroup");
if (autogroup) {
g_log.warning(
"Autogrouping is not implemented for muon NeXus version 2 files");
}
// Assign the result to the output workspace property
if (m_numberOfPeriods > 1)
setProperty(outws, std::static_pointer_cast<Workspace>(localWorkspace));
else {
setProperty("OutputWorkspace",
std::dynamic_pointer_cast<Workspace>(localWorkspace));
}
} // loop over periods
}
/** loadData
* Load the counts data from an NXInt into a workspace
*/
Histogram LoadMuonNexus2::loadData(const BinEdges &edges,
const Mantid::NeXus::NXInt &counts,
int period, int spec) {
int nBins = 0;
const int *data = nullptr;
if (counts.rank() == 3) {
nBins = counts.dim2();
data = &counts(period, spec, 0);
} else if (counts.rank() == 2) {
nBins = counts.dim1();
data = &counts(spec, 0);
} else {
throw std::runtime_error("Data have unsupported dimensionality");
}
return Histogram(edges, Counts(data, data + nBins));
}
/** 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(const 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(
const DataObjects::Workspace2D_sptr &localWorkspace) {
API::Run &runDetails = localWorkspace->mutableRun();
runDetails.addProperty("run_title", localWorkspace->getTitle(), true);
auto 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);
}
}
/**
* Return the confidence with with this algorithm can load the file
* @param descriptor A descriptor for the file
* @returns An integer specifying the confidence level. 0 indicates it will not
* be used
*/
int LoadMuonNexus2::confidence(Kernel::NexusDescriptor &descriptor) const {
const auto &firstEntryNameType = descriptor.firstEntryNameType();
const std::string root = "/" + firstEntryNameType.first;
if (!descriptor.pathExists(root + "/definition"))
return 0;
bool upperIDF(true);
if (descriptor.pathExists(root + "/IDF_version"))
upperIDF = true;
else {
if (descriptor.pathExists(root + "/idf_version"))
upperIDF = false;
else
return 0;
}
try {
std::string versionField = "idf_version";
if (upperIDF)
versionField = "IDF_version";
auto &file = descriptor.data();
file.openPath(root + "/" + versionField);
int32_t version = 0;
file.getData(&version);
if (version != 2)
return 0;
file.openPath(root + "/definition");
std::string def = file.getStrData();
if (def == "muonTD" || def == "pulsedTD") {
// If all this succeeded then we'll assume this is an ISIS Muon NeXus file
// version 2
return 81;
}
} catch (...) {
}
return 0;
}
/**
* 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 nDet = detIndex.dim0();
for (int i = 0; i < nDet; ++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;
}
} // namespace DataHandling
} // namespace Mantid