/** 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);
}
}
/**
Create the vtkStructuredGrid from the provided workspace
@param progressUpdating: Reporting object to pass progress information up the
stack.
@return fully constructed vtkDataSet.
*/
vtkSmartPointer<vtkDataSet>
vtkMDLineFactory::create(ProgressAction &progressUpdating) const {
auto product = tryDelegatingCreation<IMDEventWorkspace, 1>(m_workspace,
progressUpdating);
if (product != nullptr) {
return product;
} else {
g_log.warning() << "Factory " << this->getFactoryTypeName()
<< " is being used. You are viewing data with less than "
"three dimensions in the VSI. \n";
IMDEventWorkspace_sptr imdws =
doInitialize<IMDEventWorkspace, 1>(m_workspace);
// Acquire a scoped read-only lock to the workspace (prevent segfault from
// algos modifying ws)
Mantid::Kernel::ReadLock lock(*imdws);
const size_t nDims = imdws->getNumDims();
size_t nNonIntegrated = imdws->getNonIntegratedDimensions().size();
/*
Write mask array with correct order for each internal dimension.
*/
auto masks = Mantid::Kernel::make_unique<bool[]>(nDims);
for (size_t i_dim = 0; i_dim < nDims; ++i_dim) {
bool bIntegrated = imdws->getDimension(i_dim)->getIsIntegrated();
masks[i_dim] =
!bIntegrated; // TRUE for unmaksed, integrated dimensions are masked.
}
// Ensure destruction in any event.
boost::scoped_ptr<IMDIterator> it(
createIteratorWithNormalization(m_normalizationOption, imdws.get()));
// Create 2 points per box.
vtkNew<vtkPoints> points;
points->SetNumberOfPoints(it->getDataSize() * 2);
// One scalar per box
vtkNew<vtkFloatArray> signals;
signals->Allocate(it->getDataSize());
signals->SetName(vtkDataSetFactory::ScalarName.c_str());
signals->SetNumberOfComponents(1);
size_t nVertexes;
auto visualDataSet = vtkSmartPointer<vtkUnstructuredGrid>::New();
visualDataSet->Allocate(it->getDataSize());
vtkNew<vtkIdList> linePointList;
linePointList->SetNumberOfIds(2);
Mantid::API::CoordTransform const *transform = NULL;
if (m_useTransform) {
transform = imdws->getTransformToOriginal();
}
Mantid::coord_t out[1];
auto useBox = std::vector<bool>(it->getDataSize());
double progressFactor = 0.5 / double(it->getDataSize());
double progressOffset = 0.5;
size_t iBox = 0;
do {
progressUpdating.eventRaised(double(iBox) * progressFactor);
Mantid::signal_t signal_normalized = it->getNormalizedSignal();
if (std::isfinite(signal_normalized) &&
m_thresholdRange->inRange(signal_normalized)) {
useBox[iBox] = true;
signals->InsertNextValue(static_cast<float>(signal_normalized));
auto coords = std::unique_ptr<coord_t[]>(
it->getVertexesArray(nVertexes, nNonIntegrated, masks.get()));
// Iterate through all coordinates. Candidate for speed improvement.
for (size_t v = 0; v < nVertexes; ++v) {
coord_t *coord = coords.get() + v * 1;
size_t id = iBox * 2 + v;
if (m_useTransform) {
transform->apply(coord, out);
points->SetPoint(id, out[0], 0, 0);
} else {
points->SetPoint(id, coord[0], 0, 0);
}
}
} // valid number of vertexes returned
else {
useBox[iBox] = false;
}
++iBox;
} while (it->next());
for (size_t ii = 0; ii < it->getDataSize(); ++ii) {
progressUpdating.eventRaised((double(ii) * progressFactor) +
progressOffset);
if (useBox[ii] == true) {
vtkIdType pointIds = ii * 2;
linePointList->SetId(0, pointIds + 0); // xyx
linePointList->SetId(1, pointIds + 1); // dxyz
visualDataSet->InsertNextCell(VTK_LINE, linePointList.GetPointer());
} // valid number of vertexes returned
}
signals->Squeeze();
points->Squeeze();
visualDataSet->SetPoints(points.GetPointer());
visualDataSet->GetCellData()->SetScalars(signals.GetPointer());
visualDataSet->Squeeze();
// Hedge against empty data sets
if (visualDataSet->GetNumberOfPoints() <= 0) {
vtkNullUnstructuredGrid nullGrid;
visualDataSet = nullGrid.createNullData();
}
vtkSmartPointer<vtkDataSet> dataset = visualDataSet;
return dataset;
}
}
/**
Create the vtkStructuredGrid from the provided workspace
@param progressUpdating: Reporting object to pass progress information up the stack.
@return fully constructed vtkDataSet.
*/
vtkDataSet* vtkMDQuadFactory::create(ProgressAction& progressUpdating) const
{
vtkDataSet* product = tryDelegatingCreation<IMDEventWorkspace, 2>(m_workspace, progressUpdating);
if(product != NULL)
{
return product;
}
else
{
IMDEventWorkspace_sptr imdws = this->castAndCheck<IMDEventWorkspace, 2>(m_workspace);
// Acquire a scoped read-only lock to the workspace (prevent segfault from algos modifying ws)
Mantid::Kernel::ReadLock lock(*imdws);
const size_t nDims = imdws->getNumDims();
size_t nNonIntegrated = imdws->getNonIntegratedDimensions().size();
/*
Write mask array with correct order for each internal dimension.
*/
bool* masks = new bool[nDims];
for(size_t i_dim = 0; i_dim < nDims; ++i_dim)
{
bool bIntegrated = imdws->getDimension(i_dim)->getIsIntegrated();
masks[i_dim] = !bIntegrated; //TRUE for unmaksed, integrated dimensions are masked.
}
//Ensure destruction in any event.
boost::scoped_ptr<IMDIterator> it(imdws->createIterator());
// Create 4 points per box.
vtkPoints *points = vtkPoints::New();
points->SetNumberOfPoints(it->getDataSize() * 4);
// One scalar per box
vtkFloatArray * signals = vtkFloatArray::New();
signals->Allocate(it->getDataSize());
signals->SetName(m_scalarName.c_str());
signals->SetNumberOfComponents(1);
size_t nVertexes;
vtkUnstructuredGrid *visualDataSet = vtkUnstructuredGrid::New();
visualDataSet->Allocate(it->getDataSize());
vtkIdList * quadPointList = vtkIdList::New();
quadPointList->SetNumberOfIds(4);
Mantid::API::CoordTransform* transform = NULL;
if (m_useTransform)
{
transform = imdws->getTransformToOriginal();
}
Mantid::coord_t out[2];
bool* useBox = new bool[it->getDataSize()];
double progressFactor = 0.5/double(it->getDataSize());
double progressOffset = 0.5;
size_t iBox = 0;
do
{
progressUpdating.eventRaised(progressFactor * double(iBox));
Mantid::signal_t signal_normalized= it->getNormalizedSignal();
if (!isSpecial( signal_normalized ) && m_thresholdRange->inRange(signal_normalized))
{
useBox[iBox] = true;
signals->InsertNextValue(static_cast<float>(signal_normalized));
coord_t* coords = it->getVertexesArray(nVertexes, nNonIntegrated, masks);
delete [] coords;
coords = it->getVertexesArray(nVertexes, nNonIntegrated, masks);
//Iterate through all coordinates. Candidate for speed improvement.
for(size_t v = 0; v < nVertexes; ++v)
{
coord_t * coord = coords + v*2;
size_t id = iBox*4 + v;
if(m_useTransform)
{
transform->apply(coord, out);
points->SetPoint(id, out[0], out[1], 0);
}
else
{
points->SetPoint(id, coord[0], coord[1], 0);
}
}
// Free memory
delete [] coords;
} // valid number of vertexes returned
else
{
useBox[iBox] = false;
}
++iBox;
} while (it->next());
delete[] masks;
for(size_t ii = 0; ii < it->getDataSize() ; ++ii)
{
progressUpdating.eventRaised((progressFactor * double(ii)) + progressOffset);
if (useBox[ii] == true)
{
vtkIdType pointIds = vtkIdType(ii * 4);
quadPointList->SetId(0, pointIds + 0); //xyx
quadPointList->SetId(1, pointIds + 1); //dxyz
quadPointList->SetId(2, pointIds + 3); //dxdyz
quadPointList->SetId(3, pointIds + 2); //xdyz
visualDataSet->InsertNextCell(VTK_QUAD, quadPointList);
} // valid number of vertexes returned
}
delete[] useBox;
signals->Squeeze();
points->Squeeze();
visualDataSet->SetPoints(points);
visualDataSet->GetCellData()->SetScalars(signals);
visualDataSet->Squeeze();
signals->Delete();
points->Delete();
quadPointList->Delete();
return visualDataSet;
}
}
