Newer
Older
// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2019 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source
// & Institut Laue - Langevin
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidDataHandling/LoadNexusProcessed2.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/Workspace.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/DetectorInfo.h"
#include "MantidIndexing/IndexInfo.h"
#include "MantidNexus/NexusClasses.h"
#include "MantidNexusGeometry/AbstractLogger.h"
#include "MantidNexusGeometry/NexusGeometryParser.h"
#include "MantidTypes/SpectrumDefinition.h"
#include <H5Cpp.h>
namespace Mantid {
namespace DataHandling {
using Mantid::API::WorkspaceProperty;
using Mantid::Kernel::Direction;
// Register the algorithm into the AlgorithmFactory
DECLARE_NEXUS_FILELOADER_ALGORITHM(LoadNexusProcessed2)
//----------------------------------------------------------------------------------------------
namespace {
template <typename T>
int countEntriesOfType(const T &entry, const std::string &nxClass) {
int count = 0;
for (const auto &group : entry.groups()) {
if (group.nxclass == nxClass)
++count;
}
return count;
}
template <typename T>
std::vector<Mantid::NeXus::NXClassInfo>
findEntriesOfType(const T &entry, const std::string &nxClass) {
std::vector<Mantid::NeXus::NXClassInfo> result;
for (const auto &group : entry.groups()) {
if (group.nxclass == nxClass)
result.emplace_back(group);
* Determine the format/layout of the instrument block. We use this to
* distinguish between the ESS saving schemes and the Mantid processed nexus
* schemes
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
* @param entry
* @return
*/
InstrumentLayout instrumentFormat(Mantid::NeXus::NXEntry &entry) {
auto result = InstrumentLayout::NotRecognised;
const auto instrumentsCount = countEntriesOfType(entry, "NXinstrument");
if (instrumentsCount == 1) {
// Can now assume nexus format
result = InstrumentLayout::NexusFormat;
if (entry.containsGroup("instrument")) {
auto instr = entry.openNXInstrument("instrument");
if (instr.containsGroup("detector") ||
(instr.containsGroup("physical_detectors") &&
instr.containsGroup("physical_monitors"))) {
result = InstrumentLayout::Mantid; // 1 nxinstrument called instrument,
}
instr.close();
}
entry.close();
}
return result;
}
} // namespace
/// Algorithms name for identification. @see Algorithm::name
const std::string LoadNexusProcessed2::name() const {
return "LoadNexusProcessed";
}
/// Algorithm's version for identification. @see Algorithm::version
int LoadNexusProcessed2::version() const { return 2; }
void LoadNexusProcessed2::readSpectraToDetectorMapping(
Mantid::NeXus::NXEntry &mtd_entry, Mantid::API::MatrixWorkspace &ws) {
m_instrumentLayout = instrumentFormat(mtd_entry);
if (m_instrumentLayout == InstrumentLayout::Mantid) {
// Now assign the spectra-detector map
readInstrumentGroup(mtd_entry, ws);
} else if (m_instrumentLayout == InstrumentLayout::NexusFormat) {
extractMappingInfoNew(mtd_entry);
} else {
g_log.information()
<< "Instrument layout not recognised. Spectra mappings not loaded.";
}
}
void LoadNexusProcessed2::extractMappingInfoNew(
Mantid::NeXus::NXEntry &mtd_entry) {
using namespace Mantid::NeXus;
auto result = findEntriesOfType(mtd_entry, "NXinstrument");
if (result.size() != 1) {
g_log.warning("We are expecting a single NXinstrument. No mappings loaded");
}
auto inst = mtd_entry.openNXInstrument(result[0].nxname);
auto &spectrumNumbers = m_spectrumNumbers;
auto &detectorIds = m_detectorIds;
for (const auto &group : inst.groups()) {
if (group.nxclass == "NXdetector" || group.nxclass == "NXmonitor") {
NXDetector detgroup = inst.openNXDetector(group.nxname);
NXInt spectra_block = detgroup.openNXInt("spectra");
try {
spectra_block.load();
} catch (std::runtime_error &) { // Throws if dataset zero-sized
detgroup.close();
continue;
}
const size_t nSpecEntries = spectra_block.dim0();
auto data = spectra_block.sharedBuffer();
size_t currentSize = spectrumNumbers.size();
spectrumNumbers.resize(currentSize + nSpecEntries, 0);
// Append spectrum numbers
for (size_t i = 0; i < nSpecEntries; ++i) {
spectrumNumbers[i + currentSize] = data[i];
}
NXInt det_index = detgroup.openNXInt("detector_list");
det_index.load();
size_t nDetEntries = det_index.dim0();
currentSize = detectorIds.size();
data = det_index.sharedBuffer();
detectorIds.resize(currentSize + nDetEntries, 0);
for (size_t i = 0; i < nDetEntries; ++i) {
detectorIds[i + currentSize] = data[i];
}
// Load the number of detectors per spectra
NXInt det_counts = detgroup.openNXInt("detector_count");
det_counts.load();
size_t nDetCounts = det_counts.dim0();
currentSize = detectorCounts.size();
data = det_counts.sharedBuffer();
detectorCounts.resize(currentSize + nDetCounts, 0);
size_t dataSum = 0;
for (size_t i = 0; i < nDetCounts; ++i) {
const int dataVal = data[i];
dataSum += dataVal;
detectorCounts[i + currentSize] = dataVal;
}
if (nDetCounts != nSpecEntries) {
throw std::runtime_error("Bad file. Has different number of entries in "
"spec and detector_count datasets");
}
if (dataSum != nDetEntries) {
throw std::runtime_error("Bad file. detector_counts sum does not match "
"the number of detectors given by number of "
"detector_list entries");
}
detgroup.close();
}
}
inst.close();
}
/**
* Attempt to load nexus geometry. Should fail without exception if not
* possible.
*
* Caveats are:
* 1. Only works for input files where there is a single NXEntry. Does nothing
* otherwise.
* 2. Is only applied after attempted instrument loading in the legacy fashion
* that happens as part of loadEntry. So you will still get warning+error
* messages from that even if this succeeds
*
* @param ws : Input workspace onto which instrument will get attached
* @param nWorkspaceEntries : number of entries
* @param logger : to write to
* @param filename : filename to load from.
* @return true if successful
*/
bool LoadNexusProcessed2::loadNexusGeometry(API::Workspace &ws,
const int nWorkspaceEntries,
Kernel::Logger &logger,
const std::string &filename) {
if (m_instrumentLayout == InstrumentLayout::NexusFormat &&
nWorkspaceEntries == 1) {
if (auto *matrixWs = dynamic_cast<API::MatrixWorkspace *>(&ws)) {
try {
using namespace Mantid::NexusGeometry;
auto instrument = NexusGeometry::NexusGeometryParser::createInstrument(
filename, NexusGeometry::makeLogger(&logger));
matrixWs->setInstrument(
Geometry::Instrument_const_sptr(std::move(instrument)));
auto &detInfo = matrixWs->detectorInfo();
Indexing::IndexInfo info(m_spectrumNumbers);
std::vector<SpectrumDefinition> definitions;
definitions.reserve(m_spectrumNumbers.size());
size_t detCounter = 0;
for (size_t i = 0; i < m_spectrumNumbers.size(); ++i) {
// counts gives number of detectors per spectrum
size_t counts = m_detectorCounts[i];
SpectrumDefinition def;
// Add the number of detectors known to be associated with this
// spectrum
for (size_t j = 0; j < counts; ++j, ++detCounter) {
def.add(detInfo.indexOf(m_detectorIds[detCounter]));
}
definitions.emplace_back(def);
}
info.setSpectrumDefinitions(definitions);
matrixWs->setIndexInfo(info);
return true;
} catch (std::exception &e) {
logger.warning(e.what());
} catch (H5::Exception &e) {
logger.warning(e.getDetailMsg());
}
}
}
return false;
}
int LoadNexusProcessed2::confidence(Kernel::NexusDescriptor &descriptor) const {
if (descriptor.pathExists("/mantid_workspace_1"))
return LoadNexusProcessed::confidence(descriptor) +
1; // incrementally better than v1.
else
return 0;
}
} // namespace DataHandling
} // namespace Mantid