/**
Create the vtkStructuredGrid from the provided workspace
@param progressUpdating: Reporting object to pass progress information up the stack.
@return fully constructed vtkDataSet.
*/
vtkDataSet* vtkMDHistoQuadFactory::create(ProgressAction& progressUpdating) const
{
vtkDataSet* product = tryDelegatingCreation<MDHistoWorkspace, 2>(m_workspace, progressUpdating);
if(product != NULL)
{
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";
Mantid::Kernel::ReadLock lock(*m_workspace);
CPUTimer tim;
const int nBinsX = static_cast<int>( m_workspace->getXDimension()->getNBins() );
const int nBinsY = static_cast<int>( m_workspace->getYDimension()->getNBins() );
const coord_t maxX = m_workspace-> getXDimension()->getMaximum();
const coord_t minX = m_workspace-> getXDimension()->getMinimum();
const coord_t maxY = m_workspace-> getYDimension()->getMaximum();
const coord_t minY = m_workspace-> getYDimension()->getMinimum();
coord_t incrementX = (maxX - minX) / static_cast<coord_t>(nBinsX);
coord_t incrementY = (maxY - minY) / static_cast<coord_t>(nBinsY);
boost::scoped_ptr<MDHistoWorkspaceIterator> iterator(dynamic_cast<MDHistoWorkspaceIterator*>(createIteratorWithNormalization(m_normalizationOption, m_workspace.get())));
if (!iterator) {
throw std::runtime_error(
"Could not convert IMDIterator to a MDHistoWorkspaceIterator");
}
const int imageSize = (nBinsX ) * (nBinsY );
vtkPoints *points = vtkPoints::New();
points->Allocate(static_cast<int>(imageSize));
vtkFloatArray * signal = vtkFloatArray::New();
signal->Allocate(imageSize);
signal->SetName(vtkDataSetFactory::ScalarName.c_str());
signal->SetNumberOfComponents(1);
//The following represent actual calculated positions.
float signalScalar;
const int nPointsX = nBinsX+1;
const int nPointsY = nBinsY+1;
/* The idea of the next chunk of code is that you should only
create the points that will be needed; so an array of pointNeeded
is set so that all required vertices are marked, and created in a second step. */
// Array of the points that should be created, set to false
bool * pointNeeded = new bool[nPointsX*nPointsY];
memset(pointNeeded, 0, nPointsX*nPointsY*sizeof(bool));
// Array with true where the voxel should be shown
bool * voxelShown = new bool[nBinsX*nBinsY];
double progressFactor = 0.5/double(nBinsX);
double progressOffset = 0.5;
size_t index = 0;
for (int i = 0; i < nBinsX; i++)
{
progressUpdating.eventRaised(progressFactor*double(i));
for (int j = 0; j < nBinsY; j++)
{
index = j + nBinsY*i;
iterator->jumpTo(index);
signalScalar = static_cast<float>(iterator->getNormalizedSignal()); // Get signal normalized as per m_normalizationOption
if (isSpecial( signalScalar ) || !m_thresholdRange->inRange(signalScalar))
{
// out of range
voxelShown[index] = false;
}
else
{
// Valid data
voxelShown[index] = true;
signal->InsertNextValue(static_cast<float>(signalScalar));
// Make sure all 4 neighboring points are set to true
size_t pointIndex = i * nPointsY + j;
pointNeeded[pointIndex] = true;
pointIndex++;
pointNeeded[pointIndex] = true;
pointIndex += nPointsY-1;
pointNeeded[pointIndex] = true;
pointIndex++;
pointNeeded[pointIndex] = true;
}
}
}
std::cout << tim << " to check all the signal values." << std::endl;
// Get the transformation that takes the points in the TRANSFORMED space back into the ORIGINAL (not-rotated) space.
Mantid::API::CoordTransform const* transform = NULL;
if (m_useTransform)
transform = m_workspace->getTransformToOriginal();
Mantid::coord_t in[3];
Mantid::coord_t out[3];
in[2] = 0;
// Array with the point IDs (only set where needed)
vtkIdType * pointIDs = new vtkIdType[nPointsX*nPointsY];
index = 0;
for (int i = 0; i < nPointsX; i++)
{
progressUpdating.eventRaised((progressFactor*double(i)) + progressOffset);
in[0] = minX + (static_cast<coord_t>(i) * incrementX); //Calculate increment in x;
for (int j = 0; j < nPointsY; j++)
{
// Create the point only when needed
if (pointNeeded[index])
{
in[1] = minY + (static_cast<coord_t>(j) * incrementY); //Calculate increment in y;
if (transform)
{
transform->apply(in, out);
pointIDs[index] = points->InsertNextPoint(out);
}
else
pointIDs[index] = points->InsertNextPoint(in);
}
index++;
}
}
std::cout << tim << " to create the needed points." << std::endl;
vtkUnstructuredGrid *visualDataSet = vtkUnstructuredGrid::New();
visualDataSet->Allocate(imageSize);
visualDataSet->SetPoints(points);
visualDataSet->GetCellData()->SetScalars(signal);
// ------ Quad creation ----------------
vtkQuad* quad = vtkQuad::New(); // Significant speed increase by creating ONE quad
index = 0;
for (int i = 0; i < nBinsX; i++)
{
for (int j = 0; j < nBinsY; j++)
{
if (voxelShown[index])
{
// The quad will be shown
quad->GetPointIds()->SetId(0, pointIDs[(i)*nPointsY + j]);
quad->GetPointIds()->SetId(1, pointIDs[(i+1)*nPointsY + j]);
quad->GetPointIds()->SetId(2, pointIDs[(i+1)*nPointsY + j+1]);
quad->GetPointIds()->SetId(3, pointIDs[(i)*nPointsY + j+1]);
visualDataSet->InsertNextCell(VTK_QUAD, quad->GetPointIds());
}
index++;
}
}
quad->Delete();
std::cout << tim << " to create and add the quads." << std::endl;
points->Delete();
signal->Delete();
visualDataSet->Squeeze();
delete [] pointIDs;
delete [] voxelShown;
delete [] pointNeeded;
// Hedge against empty data sets
if (visualDataSet->GetNumberOfPoints() <= 0)
{
visualDataSet->Delete();
vtkNullUnstructuredGrid nullGrid;
visualDataSet = nullGrid.createNullData();
}
return visualDataSet;
}
}
/**
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;
}
}
/** Method for creating a 3D or 4D data set
*
* @param timestep :: index of the time step (4th dimension) in the workspace.
* Set to 0 for a 3D workspace.
* @param progressUpdate: Progress updating. passes progress information up the
*stack.
* @return the vtkDataSet created
*/
vtkSmartPointer<vtkDataSet>
vtkMDHistoHexFactory::create3Dor4D(size_t timestep,
ProgressAction &progressUpdate) const {
// Acquire a scoped read-only lock to the workspace (prevent segfault from
// algos modifying ws)
ReadLock lock(*m_workspace);
const size_t nDims = m_workspace->getNonIntegratedDimensions().size();
std::vector<size_t> indexMultiplier(nDims, 0);
// For quick indexing, accumulate these values
// First multiplier
indexMultiplier[0] = m_workspace->getDimension(0)->getNBins();
for (size_t d = 1; d < nDims; d++) {
indexMultiplier[d] =
indexMultiplier[d - 1] * m_workspace->getDimension(d)->getNBins();
}
const int nBinsX = static_cast<int>(m_workspace->getXDimension()->getNBins());
const int nBinsY = static_cast<int>(m_workspace->getYDimension()->getNBins());
const int nBinsZ = static_cast<int>(m_workspace->getZDimension()->getNBins());
const int imageSize = (nBinsX) * (nBinsY) * (nBinsZ);
vtkSmartPointer<vtkStructuredGrid> visualDataSet =
vtkSmartPointer<vtkStructuredGrid>::New();
visualDataSet->SetDimensions(nBinsX + 1, nBinsY + 1, nBinsZ + 1);
// Array with true where the voxel should be shown
double progressFactor = 0.5 / double(imageSize);
std::size_t offset = 0;
if (nDims == 4) {
offset = timestep * indexMultiplier[2];
}
std::unique_ptr<MDHistoWorkspaceIterator> iterator(
dynamic_cast<MDHistoWorkspaceIterator *>(createIteratorWithNormalization(
m_normalizationOption, m_workspace.get())));
vtkNew<vtkMDHWSignalArray<double>> signal;
signal->SetName(vtkDataSetFactory::ScalarName.c_str());
signal->InitializeArray(std::move(iterator), offset, imageSize);
visualDataSet->GetCellData()->SetScalars(signal.GetPointer());
for (vtkIdType index = 0; index < imageSize; ++index) {
progressUpdate.eventRaised(double(index) * progressFactor);
double signalScalar = signal->GetValue(index);
bool maskValue = (!std::isfinite(signalScalar) ||
!m_thresholdRange->inRange(signalScalar));
if (maskValue) {
visualDataSet->BlankCell(index);
}
}
vtkNew<vtkPoints> points;
Mantid::coord_t in[2];
const coord_t maxX = m_workspace->getXDimension()->getMaximum();
const coord_t minX = m_workspace->getXDimension()->getMinimum();
const coord_t maxY = m_workspace->getYDimension()->getMaximum();
const coord_t minY = m_workspace->getYDimension()->getMinimum();
const coord_t maxZ = m_workspace->getZDimension()->getMaximum();
const coord_t minZ = m_workspace->getZDimension()->getMinimum();
const coord_t incrementX = (maxX - minX) / static_cast<coord_t>(nBinsX);
const coord_t incrementY = (maxY - minY) / static_cast<coord_t>(nBinsY);
const coord_t incrementZ = (maxZ - minZ) / static_cast<coord_t>(nBinsZ);
const vtkIdType nPointsX = nBinsX + 1;
const vtkIdType nPointsY = nBinsY + 1;
const vtkIdType nPointsZ = nBinsZ + 1;
vtkFloatArray *pointsarray = vtkFloatArray::SafeDownCast(points->GetData());
if (pointsarray == NULL) {
throw std::runtime_error("Failed to cast vtkDataArray to vtkFloatArray.");
} else if (pointsarray->GetNumberOfComponents() != 3) {
throw std::runtime_error("points array must have 3 components.");
}
float *it = pointsarray->WritePointer(0, nPointsX * nPointsY * nPointsZ * 3);
// Array with the point IDs (only set where needed)
progressFactor = 0.5 / static_cast<double>(nPointsZ);
double progressOffset = 0.5;
for (int z = 0; z < nPointsZ; z++) {
// Report progress updates for the last 50%
progressUpdate.eventRaised(double(z) * progressFactor + progressOffset);
in[1] = (minZ + (static_cast<coord_t>(z) *
incrementZ)); // Calculate increment in z;
for (int y = 0; y < nPointsY; y++) {
in[0] = (minY + (static_cast<coord_t>(y) *
incrementY)); // Calculate increment in y;
for (int x = 0; x < nPointsX; x++) {
it[0] = (minX + (static_cast<coord_t>(x) *
incrementX)); // Calculate increment in x;
it[1] = in[0];
it[2] = in[1];
std::advance(it, 3);
}
}
}
visualDataSet->SetPoints(points.GetPointer());
visualDataSet->Register(NULL);
visualDataSet->Squeeze();
// Hedge against empty data sets
if (visualDataSet->GetNumberOfPoints() <= 0) {
vtkNullStructuredGrid nullGrid;
visualDataSet = nullGrid.createNullData();
}
vtkSmartPointer<vtkDataSet> dataset = visualDataSet;
return dataset;
}