/** Execute the algorithm.
*/
void CreateMDHistoWorkspace::exec()
{
MDHistoWorkspace_sptr ws = this->createEmptyOutputWorkspace();
double* signals = ws->getSignalArray();
double* errors = ws->getErrorSquaredArray();
std::vector<double> signalValues = getProperty("SignalInput");
std::vector<double> errorValues = getProperty("ErrorInput");
size_t binProduct = this->getBinProduct();
std::stringstream stream;
stream << binProduct;
if(binProduct != signalValues.size())
{
throw std::invalid_argument("Expected size of the SignalInput is: " + stream.str() );
}
if(binProduct != errorValues.size())
{
throw std::invalid_argument("Expected size of the ErrorInput is: " + stream.str() );
}
//Copy from property
std::copy(signalValues.begin(), signalValues.end(), signals);
std::vector<double> empty;
//Clean up.
signalValues.swap(empty);
//Copy from property
std::for_each(errorValues.begin(), errorValues.end(), Square());
std::copy(errorValues.begin(), errorValues.end(), errors);
//Clean up
errorValues.swap(empty);
setProperty("OutputWorkspace", ws);
}
void SINQTranspose3D::doTRICS(IMDHistoWorkspace_sptr inWS)
{
double *inVal, *inErr, *outVal, *outErr;
size_t idxIn, idxOut;
unsigned int xdim, ydim, zdim;
boost::shared_ptr<const IMDDimension> x,y,z;
x = inWS->getXDimension();
y = inWS->getYDimension();
z = inWS->getZDimension();
std::vector<IMDDimension_sptr> dimensions;
dimensions.push_back(boost::const_pointer_cast<IMDDimension>(x));
dimensions.push_back(boost::const_pointer_cast<IMDDimension>(z));
dimensions.push_back(boost::const_pointer_cast<IMDDimension>(y));
MDHistoWorkspace_sptr outWS (new MDHistoWorkspace(dimensions));
outWS->setTo(.0,.0,.0);
inVal = inWS->getSignalArray();
inErr = inWS->getErrorSquaredArray();
outVal = outWS->getSignalArray();
outErr = outWS->getErrorSquaredArray();
xdim = static_cast<unsigned int>(x->getNBins());
ydim = static_cast<unsigned int>(y->getNBins());
zdim = static_cast<unsigned int>(z->getNBins());
for(unsigned int xx = 0; xx < xdim; xx++){
for(unsigned int yy= 0; yy < ydim; yy++){
for(unsigned int zz = 0; zz < zdim; zz++){
idxIn = ydim*zdim*xx + zdim*yy + zz; // this works for TRICS
idxOut = outWS->getLinearIndex(xx,zz,yy);
outVal[idxOut] = inVal[idxIn];
outErr[idxOut] = inErr[idxIn];
}
}
}
copyMetaData(inWS, outWS);
// assign the workspace
setProperty("OutputWorkspace",outWS);
}
void SINQTranspose3D::doYXZ(IMDHistoWorkspace_sptr inWS)
{
double *inVal, *inErr, *outVal, *outErr;
size_t idxIn, idxOut;
boost::shared_ptr<const IMDDimension> x,y,z;
x = inWS->getXDimension();
y = inWS->getYDimension();
z = inWS->getZDimension();
std::vector<IMDDimension_sptr> dimensions;
dimensions.push_back(boost::const_pointer_cast<IMDDimension>(y));
dimensions.push_back(boost::const_pointer_cast<IMDDimension>(x));
dimensions.push_back(boost::const_pointer_cast<IMDDimension>(z));
MDHistoWorkspace_sptr outWS (new MDHistoWorkspace(dimensions));
inVal = inWS->getSignalArray();
inErr = inWS->getErrorSquaredArray();
outVal = outWS->getSignalArray();
outErr = outWS->getErrorSquaredArray();
for(unsigned int xx = 0; xx < x->getNBins(); xx++){
for(unsigned int yy= 0; yy < y->getNBins(); yy++){
for(unsigned int zz = 0; zz < z->getNBins(); zz++){
idxIn = inWS->getLinearIndex(xx,yy,zz);
idxOut = outWS->getLinearIndex(yy,xx,zz);
outVal[idxOut] = inVal[idxIn];
outErr[idxOut] = inErr[idxIn];
}
}
}
copyMetaData(inWS, outWS);
// assign the workspace
setProperty("OutputWorkspace",outWS);
}
/** Execute the algorithm.
*/
void TransformMD::exec() {
Mantid::API::IMDWorkspace_sptr inWS;
Mantid::API::IMDWorkspace_sptr outWS;
inWS = getProperty("InputWorkspace");
outWS = getProperty("OutputWorkspace");
std::string outName = getPropertyValue("OutputWorkspace");
if (boost::dynamic_pointer_cast<MatrixWorkspace>(inWS))
throw std::runtime_error("TransformMD can only transform a "
"MDHistoWorkspace or a MDEventWorkspace.");
if (outWS != inWS) {
// NOT in-place. So first we clone inWS into outWS
IAlgorithm_sptr clone =
this->createChildAlgorithm("CloneMDWorkspace", 0.0, 0.5, true);
clone->setProperty("InputWorkspace", inWS);
clone->executeAsChildAlg();
outWS = clone->getProperty("OutputWorkspace");
}
if (!outWS)
throw std::runtime_error("Invalid output workspace.");
size_t nd = outWS->getNumDims();
m_scaling = getProperty("Scaling");
m_offset = getProperty("Offset");
// Replicate single values
if (m_scaling.size() == 1)
m_scaling = std::vector<double>(nd, m_scaling[0]);
if (m_offset.size() == 1)
m_offset = std::vector<double>(nd, m_offset[0]);
// Check the size
if (m_scaling.size() != nd)
throw std::invalid_argument("Scaling argument must be either length 1 or "
"match the number of dimensions.");
if (m_offset.size() != nd)
throw std::invalid_argument("Offset argument must be either length 1 or "
"match the number of dimensions.");
// Transform the dimensions
outWS->transformDimensions(m_scaling, m_offset);
MDHistoWorkspace_sptr histo =
boost::dynamic_pointer_cast<MDHistoWorkspace>(outWS);
IMDEventWorkspace_sptr event =
boost::dynamic_pointer_cast<IMDEventWorkspace>(outWS);
if (histo) {
// Recalculate all the values since the dimensions changed.
histo->cacheValues();
// Expect first 3 dimensions to be -1 for changing conventions
for (int i = 0; i < static_cast<int>(m_scaling.size()); i++)
if (m_scaling[i] < 0) {
std::vector<int> axes(m_scaling.size()); // vector with ints.
std::iota(std::begin(axes), std::end(axes), 0); // Fill with 0, 1, ...
axes[0] = i;
axes[i] = 0;
if (i > 0)
histo = transposeMD(histo, axes);
signal_t *signals = histo->getSignalArray();
signal_t *errorsSq = histo->getErrorSquaredArray();
signal_t *numEvents = histo->getNumEventsArray();
// Find the extents
size_t nPoints =
static_cast<size_t>(histo->getDimension(0)->getNBins());
size_t mPoints = 1;
for (size_t k = 1; k < histo->getNumDims(); k++) {
mPoints *= static_cast<size_t>(histo->getDimension(k)->getNBins());
}
// other dimensions
for (size_t j = 0; j < mPoints; j++) {
this->reverse(signals + j * nPoints, nPoints);
this->reverse(errorsSq + j * nPoints, nPoints);
this->reverse(numEvents + j * nPoints, nPoints);
}
histo = transposeMD(histo, axes);
}
// Pass on the display normalization from the input workspace
histo->setDisplayNormalization(inWS->displayNormalizationHisto());
this->setProperty("OutputWorkspace", histo);
} else if (event) {
// Call the method for this type of MDEventWorkspace.
CALL_MDEVENT_FUNCTION(this->doTransform, outWS);
Progress *prog2 = nullptr;
ThreadScheduler *ts = new ThreadSchedulerFIFO();
ThreadPool tp(ts, 0, prog2);
event->splitAllIfNeeded(ts);
// prog2->resetNumSteps( ts->size(), 0.4, 0.6);
tp.joinAll();
event->refreshCache();
// Set the special coordinate system.
IMDEventWorkspace_sptr inEvent =
boost::dynamic_pointer_cast<IMDEventWorkspace>(inWS);
event->setCoordinateSystem(inEvent->getSpecialCoordinateSystem());
if (m_scaling[0] < 0) {
// Only need these 2 algorithms for transforming with negative number
std::vector<double> extents;
std::vector<std::string> names, units;
for (size_t d = 0; d < nd; d++) {
Geometry::IMDDimension_const_sptr dim = event->getDimension(d);
// Find the extents
extents.push_back(dim->getMinimum());
extents.push_back(dim->getMaximum());
names.push_back(std::string(dim->getName()));
units.push_back(dim->getUnits());
}
Algorithm_sptr create_alg = createChildAlgorithm("CreateMDWorkspace");
create_alg->setProperty("Dimensions", static_cast<int>(nd));
create_alg->setProperty("EventType", event->getEventTypeName());
create_alg->setProperty("Extents", extents);
create_alg->setProperty("Names", names);
create_alg->setProperty("Units", units);
create_alg->setPropertyValue("OutputWorkspace", "__none");
create_alg->executeAsChildAlg();
Workspace_sptr none = create_alg->getProperty("OutputWorkspace");
AnalysisDataService::Instance().addOrReplace(outName, event);
AnalysisDataService::Instance().addOrReplace("__none", none);
Mantid::API::BoxController_sptr boxController = event->getBoxController();
std::vector<int> splits;
for (size_t d = 0; d < nd; d++) {
splits.push_back(static_cast<int>(boxController->getSplitInto(d)));
}
Algorithm_sptr merge_alg = createChildAlgorithm("MergeMD");
merge_alg->setPropertyValue("InputWorkspaces", outName + ",__none");
merge_alg->setProperty("SplitInto", splits);
merge_alg->setProperty(
"SplitThreshold",
static_cast<int>(boxController->getSplitThreshold()));
merge_alg->setProperty("MaxRecursionDepth", 13);
merge_alg->executeAsChildAlg();
event = merge_alg->getProperty("OutputWorkspace");
AnalysisDataService::Instance().remove("__none");
}
this->setProperty("OutputWorkspace", event);
}
}
/** 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 = boost::make_shared<MDHistoWorkspace>(m_dims,
m_visualNormalization.get());
} else {
ws = boost::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(boost::dynamic_pointer_cast<IMDWorkspace>(ws));
if (m_saveMDVersion == 2)
m_file->openGroup("data", "NXdata");
// Load each data slab
this->loadSlab("signal", ws->getSignalArray(), ws, ::NeXus::FLOAT64);
this->loadSlab("errors_squared", ws->getErrorSquaredArray(), ws,
::NeXus::FLOAT64);
this->loadSlab("num_events", ws->getNumEventsArray(), ws, ::NeXus::FLOAT64);
this->loadSlab("mask", ws->getMaskArray(), 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",
boost::dynamic_pointer_cast<IMDWorkspace>(ws));
transform_alg->setProperty("Scaling", scaling);
transform_alg->executeAsChildAlg();
IMDWorkspace_sptr tmp = transform_alg->getProperty("OutputWorkspace");
ws = boost::dynamic_pointer_cast<MDHistoWorkspace>(tmp);
}
// Save to output
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<IMDWorkspace>(ws));
}