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LoadMD.cpp
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LoadMD.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 "MantidMDAlgorithms/LoadMD.h"
#include "MantidAPI/ExperimentInfo.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/IMDEventWorkspace.h"
#include "MantidAPI/IMDWorkspace.h"
#include "MantidAPI/RegisterFileLoader.h"
#include "MantidAPI/WorkspaceHistory.h"
#include "MantidDataObjects/BoxControllerNeXusIO.h"
#include "MantidDataObjects/CoordTransformAffine.h"
#include "MantidDataObjects/MDBoxFlatTree.h"
#include "MantidDataObjects/MDEventFactory.h"
#include "MantidDataObjects/MDHistoWorkspace.h"
#include "MantidGeometry/MDGeometry/IMDDimension.h"
#include "MantidGeometry/MDGeometry/IMDDimensionFactory.h"
#include "MantidGeometry/MDGeometry/MDDimensionExtents.h"
#include "MantidGeometry/MDGeometry/MDFrame.h"
#include "MantidGeometry/MDGeometry/MDFrameFactory.h"
#include "MantidGeometry/MDGeometry/UnknownFrame.h"
#include "MantidKernel/CPUTimer.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/MDUnit.h"
#include "MantidKernel/MDUnitFactory.h"
#include "MantidKernel/Memory.h"
#include "MantidKernel/PropertyWithValue.h"
#include "MantidKernel/System.h"
#include "MantidMDAlgorithms/SetMDFrame.h"
#include <boost/algorithm/string.hpp>
#include <boost/regex.hpp>
#include <nexus/NeXusException.hpp>
#include <vector>
using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::Geometry;
using namespace Mantid::DataObjects;
using file_holder_type = std::unique_ptr<Mantid::DataObjects::BoxControllerNeXusIO>;
namespace Mantid::MDAlgorithms {
DECLARE_NEXUS_HDF5_FILELOADER_ALGORITHM(LoadMD)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
LoadMD::LoadMD()
: m_numDims(0), // uninitialized incorrect value
m_coordSystem(None), m_BoxStructureAndMethadata(true), // this is faster but rarely needed.
m_saveMDVersion(false), m_requiresMDFrameCorrection(false) {}
/**
* Return the confidence with which 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 LoadMD::confidence(Kernel::NexusHDF5Descriptor &descriptor) const {
int confidence = 0;
const std::map<std::string, std::set<std::string>> &allEntries = descriptor.getAllEntries();
if (allEntries.count("NXentry") == 1) {
if (descriptor.isEntry("/MDEventWorkspace") || descriptor.isEntry("/MDHistoWorkspace")) {
confidence = 95;
}
}
return confidence;
}
//----------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm's properties.
*/
void LoadMD::init() {
declareProperty(std::make_unique<FileProperty>("Filename", "", FileProperty::Load, ".nxs"),
"The name of the Nexus file to load, as a full or relative path");
declareProperty(std::make_unique<Kernel::PropertyWithValue<bool>>("MetadataOnly", false),
"Load Box structure and other metadata without events. The "
"loaded workspace will be empty and not file-backed.");
declareProperty(std::make_unique<Kernel::PropertyWithValue<bool>>("BoxStructureOnly", false),
"Load partial information about the boxes and events. Redundant property "
"currently equivalent to MetadataOnly");
declareProperty(std::make_unique<PropertyWithValue<bool>>("FileBackEnd", false),
"Set to true to load the data only on demand.");
setPropertySettings("FileBackEnd", std::make_unique<EnabledWhenProperty>("MetadataOnly", IS_EQUAL_TO, "0"));
declareProperty(std::make_unique<PropertyWithValue<double>>("Memory", -1),
"For FileBackEnd only: the amount of memory (in MB) to allocate to the "
"in-memory cache.\n"
"If not specified, a default of 40% of free physical memory is used.");
setPropertySettings("Memory", std::make_unique<EnabledWhenProperty>("FileBackEnd", IS_EQUAL_TO, "1"));
declareProperty("LoadHistory", true, "If true, the workspace history will be loaded");
declareProperty(std::make_unique<WorkspaceProperty<IMDWorkspace>>("OutputWorkspace", "", Direction::Output),
"Name of the output MDEventWorkspace.");
}
//----------------------------------------------------------------------------------------------
/** Execute the algorithm.
*/
void LoadMD::execLoader() {
m_filename = getPropertyValue("Filename");
convention = Kernel::ConfigService::Instance().getString("Q.convention");
// Start loading
bool fileBacked = this->getProperty("FileBackEnd");
m_BoxStructureAndMethadata = getProperty("MetadataOnly");
bool BoxAndEventInfoOnly = this->getProperty("BoxStructureOnly");
if (m_BoxStructureAndMethadata || BoxAndEventInfoOnly) {
m_BoxStructureAndMethadata = true;
}
// Nexus constructor/destructor throw, so can not be used with scoped pointers
// directly
//(do they lock file because of this and this code is useless?)
std::string for_access;
if (fileBacked) {
for_access = "for Read/Write access";
m_file.reset(new ::NeXus::File(m_filename, NXACC_RDWR));
} else {
for_access = "for Read access";
m_file.reset(new ::NeXus::File(m_filename, NXACC_READ));
}
if (!m_file)
throw Kernel::Exception::FileError("Can not open file " + for_access, m_filename);
// The main entry
const std::shared_ptr<Mantid::Kernel::NexusHDF5Descriptor> fileInfo = getFileInfo();
std::string entryName;
if (fileInfo->isEntry("/MDEventWorkspace", "NXentry")) {
entryName = "MDEventWorkspace";
} else if (fileInfo->isEntry("/MDHistoWorkspace", "NXentry")) {
entryName = "MDHistoWorkspace";
} else {
throw std::runtime_error("Unexpected NXentry name. Expected "
"'MDEventWorkspace' or 'MDHistoWorkspace'.");
}
// Open the entry
m_file->openGroup(entryName, "NXentry");
// Check is SaveMD version 2 was used
m_saveMDVersion = 0;
if (m_file->hasAttr("SaveMDVersion"))
m_file->getAttr("SaveMDVersion", m_saveMDVersion);
if (m_saveMDVersion == 2)
this->loadDimensions2();
else {
// How many dimensions?
std::vector<int32_t> vecDims;
m_file->readData("dimensions", vecDims);
if (vecDims.empty())
throw std::runtime_error("LoadMD:: Error loading number of dimensions.");
m_numDims = vecDims[0];
if (m_numDims == 0)
throw std::runtime_error("LoadMD:: number of dimensions == 0.");
// Now load all the dimension xml
this->loadDimensions();
}
// Coordinate system
this->loadCoordinateSystem();
// QConvention (Inelastic or Crystallography)
this->loadQConvention();
// Display normalization settting
if (fileInfo->isEntry("/" + entryName + "/" + VISUAL_NORMALIZATION_KEY)) {
this->loadVisualNormalization(VISUAL_NORMALIZATION_KEY, m_visualNormalization);
}
if (entryName == "MDEventWorkspace") {
// The type of event
std::string eventType;
m_file->getAttr("event_type", eventType);
if (fileInfo->isEntry("/" + entryName + "/" + VISUAL_NORMALIZATION_KEY_HISTO)) {
this->loadVisualNormalization(VISUAL_NORMALIZATION_KEY_HISTO, m_visualNormalizationHisto);
}
// Use the factory to make the workspace of the right type
IMDEventWorkspace_sptr ws;
if (m_visualNormalizationHisto && m_visualNormalization) {
ws = MDEventFactory::CreateMDWorkspace(m_numDims, eventType, m_visualNormalization.get(),
m_visualNormalizationHisto.get());
} else {
ws = MDEventFactory::CreateMDWorkspace(m_numDims, eventType);
}
// Now the ExperimentInfo
bool lazyLoadExpt = fileBacked;
MDBoxFlatTree::loadExperimentInfos(m_file.get(), m_filename, ws, *fileInfo.get(), "MDEventWorkspace", lazyLoadExpt);
// Wrapper to cast to MDEventWorkspace then call the function
CALL_MDEVENT_FUNCTION(this->doLoad, ws);
// Check if a MDFrame adjustment is required
checkForRequiredLegacyFixup(ws);
if (m_requiresMDFrameCorrection) {
setMDFrameOnWorkspaceFromLegacyFile(ws);
}
// Write out the Qconvention
// ki-kf for Inelastic convention; kf-ki for Crystallography convention
std::string pref_QConvention = Kernel::ConfigService::Instance().getString("Q.convention");
g_log.information() << "Convention for Q in Preferences is " << pref_QConvention
<< "; Convention of Q in NeXus file is " << m_QConvention << '\n';
if (pref_QConvention != m_QConvention) {
std::vector<double> scaling(m_numDims);
scaling = qDimensions(ws);
g_log.information() << "Transforming Q\n";
Algorithm_sptr transform_alg = createChildAlgorithm("TransformMD");
transform_alg->setProperty("InputWorkspace", std::dynamic_pointer_cast<IMDWorkspace>(ws));
transform_alg->setProperty("Scaling", scaling);
transform_alg->executeAsChildAlg();
IMDWorkspace_sptr tmp = transform_alg->getProperty("OutputWorkspace");
ws = std::dynamic_pointer_cast<IMDEventWorkspace>(tmp);
}
// Save to output
setProperty("OutputWorkspace", std::dynamic_pointer_cast<IMDWorkspace>(ws));
} else {
// MDHistoWorkspace case.
this->loadHisto();
}
}
/**
* Load a slab of double data into a bare array.
* Checks that the size is correct.
* @param name
* @param data bare pointer to double array
* @param ws
* @param dataType
*/
void LoadMD::loadSlab(const std::string &name, void *data, const MDHistoWorkspace_sptr &ws,
::NeXus::NXnumtype dataType) {
m_file->openData(name);
if (m_file->getInfo().type != dataType)
throw std::runtime_error("Unexpected data type for '" + name + "' data set.'");
int nPoints = 1;
size_t numDims = m_file->getInfo().dims.size();
std::vector<int> size(numDims);
for (size_t d = 0; d < numDims; d++) {
nPoints *= static_cast<int>(m_file->getInfo().dims[d]);
size[d] = static_cast<int>(m_file->getInfo().dims[d]);
}
if (nPoints != static_cast<int>(ws->getNPoints()))
throw std::runtime_error("Inconsistency between the number of points in '" + name +
"' and the number of bins defined by the dimensions.");
std::vector<int> start(numDims, 0);
try {
m_file->getSlab(data, start, size);
} catch (...) {
g_log.debug() << " start: " << start[0] << " size: " << size[0] << '\n';
}
m_file->closeData();
}
//----------------------------------------------------------------------------------------------
/** Perform loading for a MDHistoWorkspace.
* The entry should be open already.
*/
void LoadMD::loadHisto() {
// Create the initial MDHisto.
MDHistoWorkspace_sptr ws;
// If display normalization has been provided. Use that.
if (m_visualNormalization) {
ws = std::make_shared<MDHistoWorkspace>(m_dims, m_visualNormalization.get());
} else {
ws = std::make_shared<MDHistoWorkspace>(m_dims); // Whatever MDHistoWorkspace defaults to.
}
// Now the ExperimentInfo
MDBoxFlatTree::loadExperimentInfos(m_file.get(), m_filename, ws);
// Coordinate system
ws->setCoordinateSystem(m_coordSystem);
// Load the WorkspaceHistory "process"
if (this->getProperty("LoadHistory")) {
ws->history().loadNexus(m_file.get());
}
this->loadAffineMatricies(std::dynamic_pointer_cast<IMDWorkspace>(ws));
if (m_saveMDVersion == 2)
m_file->openGroup("data", "NXdata");
// Load each data slab
this->loadSlab("signal", ws->mutableSignalArray(), ws, ::NeXus::FLOAT64);
this->loadSlab("errors_squared", ws->mutableErrorSquaredArray(), ws, ::NeXus::FLOAT64);
this->loadSlab("num_events", ws->mutableNumEventsArray(), ws, ::NeXus::FLOAT64);
this->loadSlab("mask", ws->mutableMaskArray(), ws, ::NeXus::INT8);
m_file->close();
// Check if a MDFrame adjustment is required
checkForRequiredLegacyFixup(ws);
if (m_requiresMDFrameCorrection) {
setMDFrameOnWorkspaceFromLegacyFile(ws);
}
// Write out the Qconvention
// ki-kf for Inelastic convention; kf-ki for Crystallography convention
std::string pref_QConvention = Kernel::ConfigService::Instance().getString("Q.convention");
g_log.information() << "Convention for Q in Preferences is " << pref_QConvention
<< "; Convention of Q in NeXus file is " << m_QConvention << '\n';
if (pref_QConvention != m_QConvention) {
std::vector<double> scaling(m_numDims);
scaling = qDimensions(ws);
g_log.information() << "Transforming Q\n";
Algorithm_sptr transform_alg = createChildAlgorithm("TransformMD");
transform_alg->setProperty("InputWorkspace", std::dynamic_pointer_cast<IMDWorkspace>(ws));
transform_alg->setProperty("Scaling", scaling);
transform_alg->executeAsChildAlg();
IMDWorkspace_sptr tmp = transform_alg->getProperty("OutputWorkspace");
ws = std::dynamic_pointer_cast<MDHistoWorkspace>(tmp);
}
// Save to output
setProperty("OutputWorkspace", std::dynamic_pointer_cast<IMDWorkspace>(ws));
}
//----------------------------------------------------------------------------------------------
/** Load all the dimensions into this->m_dims */
void LoadMD::loadDimensions() {
m_dims.clear();
// Load each dimension, as their XML representation
for (size_t d = 0; d < m_numDims; d++) {
std::ostringstream mess;
mess << "dimension" << d;
std::string dimXML;
m_file->getAttr(mess.str(), dimXML);
// Use the dimension factory to read the XML
m_dims.emplace_back(createDimension(dimXML));
}
// Since this is an old algorithm we will
// have to provide an MDFrame correction
m_requiresMDFrameCorrection = true;
}
//----------------------------------------------------------------------------------------------
/** Load all the dimensions into this->m_dims
* The dimensions are stored as an nxData array */
void LoadMD::loadDimensions2() {
using namespace Geometry;
m_dims.clear();
std::string axes;
m_file->openGroup("data", "NXdata");
m_file->openData("signal");
m_file->getAttr("axes", axes);
m_file->closeData();
std::vector<std::string> splitAxes;
boost::split(splitAxes, axes, boost::is_any_of(":"));
// Create each dimension from axes data
// We loop axes backwards because Mantid
for (size_t d = splitAxes.size(); d > 0; d--) {
std::string long_name;
std::string units;
std::string frame;
std::vector<double> axis;
m_file->openData(splitAxes[d - 1]);
m_file->getAttr("long_name", long_name);
m_file->getAttr("units", units);
try {
m_file->getAttr("frame", frame);
} catch (std::exception &) {
frame = Mantid::Geometry::UnknownFrame::UnknownFrameName;
m_requiresMDFrameCorrection = true;
}
Geometry::MDFrame_const_uptr mdFrame = Geometry::makeMDFrameFactoryChain()->create(MDFrameArgument(frame, units));
m_file->getData(axis);
m_file->closeData();
m_dims.emplace_back(std::make_shared<MDHistoDimension>(long_name, long_name, *mdFrame,
static_cast<coord_t>(axis.front()),
static_cast<coord_t>(axis.back()), axis.size() - 1));
}
m_file->closeGroup();
m_numDims = m_dims.size();
}
void LoadMD::loadVisualNormalization(const std::string &key,
boost::optional<Mantid::API::MDNormalization> &normalization) {
try {
uint32_t readVisualNormalization(0);
m_file->readData(key, readVisualNormalization);
normalization = static_cast<Mantid::API::MDNormalization>(readVisualNormalization);
} catch (::NeXus::Exception &) {
} catch (std::exception &) {
}
}
/** Load the coordinate system **/
void LoadMD::loadCoordinateSystem() {
// Current version stores the coordinate system
// in its own field. The first version stored it
// as a log value so fallback on that if it can't
// be found.
try {
uint32_t readCoord(0);
m_file->readData("coordinate_system", readCoord);
m_coordSystem = static_cast<SpecialCoordinateSystem>(readCoord);
} catch (::NeXus::Exception &) {
auto pathOnEntry = m_file->getPath();
try {
m_file->openPath(pathOnEntry + "/experiment0/logs/CoordinateSystem");
int readCoord(0);
m_file->readData("value", readCoord);
m_coordSystem = static_cast<SpecialCoordinateSystem>(readCoord);
} catch (::NeXus::Exception &) {
}
// return to where we started
m_file->openPath(pathOnEntry);
}
}
/** Load the convention for Q **/
void LoadMD::loadQConvention() {
try {
m_file->getAttr("QConvention", m_QConvention);
} catch (std::exception &) {
m_QConvention = "Inelastic";
}
}
//----------------------------------------------------------------------------------------------
/** Do the loading.
*
* The m_file should be open at the entry level at this point.
*
* @param ws :: MDEventWorkspace of the given type
*/
template <typename MDE, size_t nd> 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 = std::make_unique<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(std::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;
auto 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 = std::shared_ptr<DataObjects::BoxControllerNeXusIO>(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);
std::vector<coord_t> boxTemp;
for (size_t i = 0; i < numBoxes; i++) {
prog->report();
auto *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]),
boxTemp);
}
}
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";
}
/**
* Load all of the affine matrices from the file, create the
* appropriate coordinate transform and set those on the workspace.
* @param ws : workspace to set the coordinate transforms on
*/
void LoadMD::loadAffineMatricies(const IMDWorkspace_sptr &ws) {
std::map<std::string, std::string> entries;
m_file->getEntries(entries);
if (entries.find("transform_to_orig") != entries.end()) {
CoordTransform *transform = this->loadAffineMatrix("transform_to_orig");
ws->setTransformToOriginal(transform);
}
if (entries.find("transform_from_orig") != entries.end()) {
CoordTransform *transform = this->loadAffineMatrix("transform_from_orig");
ws->setTransformFromOriginal(transform);
}
}
/**
* Do that actual loading and manipulating of the read data to create
* the affine matrix and then the appropriate transformation. This is
* currently limited to CoordTransformAffine transforms.
* @param entry_name : the entry point in the NeXus file to read
* @return the coordinate transform object
*/
CoordTransform *LoadMD::loadAffineMatrix(const std::string &entry_name) {
m_file->openData(entry_name);
std::vector<coord_t> vec;
m_file->getData<coord_t>(vec);
std::string type;
int inD(0);
int outD(0);
m_file->getAttr("type", type);
m_file->getAttr<int>("rows", outD);
m_file->getAttr<int>("columns", inD);
m_file->closeData();
Matrix<coord_t> mat(vec, outD, inD);
// Adjust dimensions
inD--;
outD--;
CoordTransform *transform = nullptr;
if (("CoordTransformAffine" == type) || ("CoordTransformAligned" == type)) {
auto affine = new CoordTransformAffine(inD, outD);
affine->setMatrix(mat);
transform = affine;
} else {
g_log.information("Do not know how to process coordinate transform " + type);
}
return transform;
}
/**
* Set MDFrames for workspaces from legacy files
* @param ws:: poitner to the workspace which needs to be corrected
*/
void LoadMD::setMDFrameOnWorkspaceFromLegacyFile(const API::IMDWorkspace_sptr &ws) {
g_log.information() << "LoadMD: Encountered a legacy file which has a mismatch between "
"its MDFrames and its Special Coordinate System. "
"Attempting to convert MDFrames.\n";
auto numberOfDimensions = ws->getNumDims();
// Select an MDFrame based on the special coordinates.
// Note that for None, we select a General Coordinate System,
// unless the name is "Unknown frame"
std::string selectedFrame;
switch (m_coordSystem) {
case Mantid::Kernel::QLab:
selectedFrame = Mantid::Geometry::QLab::QLabName;
break;
case Mantid::Kernel::QSample:
selectedFrame = Mantid::Geometry::QSample::QSampleName;
break;
case Mantid::Kernel::HKL:
selectedFrame = Mantid::Geometry::HKL::HKLName;
break;
default:
selectedFrame = Mantid::Geometry::GeneralFrame::GeneralFrameName;
}
// Get the old frames just in case something goes wrong. In this case we
// reset the frames.
std::vector<std::string> oldFrames(numberOfDimensions, Mantid::Geometry::GeneralFrame::GeneralFrameName);
for (size_t index = 0; index < numberOfDimensions; ++index) {
oldFrames[index] = ws->getDimension(index)->getMDFrame().name();
}
// We want to set only up to the first three dimensions to the selected Frame;
// Everything else will be set to a General Frame
std::vector<std::string> framesToSet(numberOfDimensions, Mantid::Geometry::GeneralFrame::GeneralFrameName);
auto fillUpTo = numberOfDimensions > 3 ? 3 : numberOfDimensions;
std::fill_n(framesToSet.begin(), fillUpTo, selectedFrame);
try {
// Set the MDFrames for each axes
Algorithm_sptr setMDFrameAlg = this->createChildAlgorithm("SetMDFrame");
int axesCounter = 0;
for (auto &frame : framesToSet) {
setMDFrameAlg->setProperty("InputWorkspace", ws);
setMDFrameAlg->setProperty("MDFrame", frame);
setMDFrameAlg->setProperty("Axes", std::vector<int>(1, axesCounter));
++axesCounter;
setMDFrameAlg->executeAsChildAlg();
}
} catch (...) {
g_log.warning() << "LoadMD: An issue occured while trying to correct "
"MDFrames. Trying to revert to original.\n";
// Revert to the old frames.
Algorithm_sptr setMDFrameAlg = this->createChildAlgorithm("SetMDFrame");
int axesCounter = 0;
for (auto &oldFrame : oldFrames) {
setMDFrameAlg->setProperty("InputWorkspace", ws);
setMDFrameAlg->setProperty("MDFrame", oldFrame);
setMDFrameAlg->setProperty("Axes", std::vector<int>(1, axesCounter));
++axesCounter;
setMDFrameAlg->executeAsChildAlg();
}
}
}
/**
* Check for required legacy fix up for certain file types. Namely the case
* where
* all MDFrames were stored as MDFrames
*/
void LoadMD::checkForRequiredLegacyFixup(const API::IMDWorkspace_sptr &ws) {
// Check if the special coordinate is not none
auto isQBasedSpecialCoordinateSystem = true;
if (m_coordSystem == Mantid::Kernel::SpecialCoordinateSystem::None) {
isQBasedSpecialCoordinateSystem = false;
}
// Check if all MDFrames are of type Unknown frame
auto containsOnlyUnkownFrames = true;
for (size_t index = 0; index < ws->getNumDims(); ++index) {
if (ws->getDimension(index)->getMDFrame().name() != Mantid::Geometry::UnknownFrame::UnknownFrameName) {
containsOnlyUnkownFrames = false;
break;
}
}
// Check if a fix up is required
if (isQBasedSpecialCoordinateSystem && containsOnlyUnkownFrames) {
m_requiresMDFrameCorrection = true;
}
}
/**
* Find scaling for Q dimensions
*/
std::vector<double> LoadMD::qDimensions(const API::IMDWorkspace_sptr &ws) {
std::vector<double> scaling(m_numDims);
for (size_t d = 0; d < m_numDims; d++) {
std::string dimd = ws->getDimension(d)->getName();
// Assume the Q dimensions are those that have names starting with [
// such as [H,0.5H,0], or Q_ such as Q_sample_x.
// The change in sign should apply only to those.
boost::regex re("\\[.*|Q_");
if (boost::regex_search(dimd.begin(), dimd.begin() + 2, re))
scaling[d] = -1.0;
else
scaling[d] = 1.0;
}
return scaling;
}
const std::string LoadMD::VISUAL_NORMALIZATION_KEY = "visual_normalization";
const std::string LoadMD::VISUAL_NORMALIZATION_KEY_HISTO = "visual_normalization_histo";
} // namespace Mantid::MDAlgorithms