/**
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;
}
}
/** 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 do4D :: if true, create a 4D dataset, else to 3D
* @param progressUpdate: Progress updating. passes progress information up the stack.
* @return the vtkDataSet created
*/
vtkDataSet* vtkMDHistoHexFactory::create3Dor4D(size_t timestep, bool do4D, ProgressAction & progressUpdate) const
{
// Acquire a scoped read-only lock to the workspace (prevent segfault from algos modifying ws)
ReadLock lock(*m_workspace);
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 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();
coord_t incrementX = (maxX - minX) / static_cast<coord_t>(nBinsX);
coord_t incrementY = (maxY - minY) / static_cast<coord_t>(nBinsY);
coord_t incrementZ = (maxZ - minZ) / static_cast<coord_t>(nBinsZ);
const int imageSize = (nBinsX ) * (nBinsY ) * (nBinsZ );
vtkPoints *points = vtkPoints::New();
points->Allocate(static_cast<int>(imageSize));
vtkFloatArray * signal = vtkFloatArray::New();
signal->Allocate(imageSize);
signal->SetName(m_scalarName.c_str());
signal->SetNumberOfComponents(1);
double signalScalar;
const int nPointsX = nBinsX+1;
const int nPointsY = nBinsY+1;
const int nPointsZ = nBinsZ+1;
CPUTimer tim;
/* 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*nPointsZ];
memset(pointNeeded, 0, nPointsX*nPointsY*nPointsZ*sizeof(bool));
// Array with true where the voxel should be shown
bool * voxelShown = new bool[nBinsX*nBinsY*nBinsZ];
double progressFactor = 0.5/double(nBinsZ);
double progressOffset = 0.5;
size_t index = 0;
for (int z = 0; z < nBinsZ; z++)
{
//Report progress updates for the first 50%
progressUpdate.eventRaised(double(z)*progressFactor);
for (int y = 0; y < nBinsY; y++)
{
for (int x = 0; x < nBinsX; x++)
{
/* NOTE: It is very important to match the ordering of the two arrays
* (the one used in MDHistoWorkspace and voxelShown/pointNeeded).
* If you access the array in the wrong way and can't cache it on L1/L2 cache, I got a factor of 8x slowdown.
*/
//index = x + (nBinsX * y) + (nBinsX*nBinsY*z);
if (do4D)
signalScalar = m_workspace->getSignalNormalizedAt(x,y,z, timestep);
else
signalScalar = m_workspace->getSignalNormalizedAt(x,y,z);
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 8 neighboring points are set to true
size_t pointIndex = x + (nPointsX * y) + (nPointsX*nPointsY*z); //(Note this index is different then the other one)
pointNeeded[pointIndex] = true; pointIndex++;
pointNeeded[pointIndex] = true; pointIndex += nPointsX-1;
pointNeeded[pointIndex] = true; pointIndex++;
pointNeeded[pointIndex] = true; pointIndex += nPointsX*nPointsY - nPointsX - 1;
pointNeeded[pointIndex] = true; pointIndex++;
pointNeeded[pointIndex] = true; pointIndex += nPointsX-1;
pointNeeded[pointIndex] = true; pointIndex++;
pointNeeded[pointIndex] = true;
}
index++;
}
}
}
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* transform = NULL;
if (m_useTransform)
transform = m_workspace->getTransformToOriginal();
Mantid::coord_t in[3];
Mantid::coord_t out[3];
// Array with the point IDs (only set where needed)
vtkIdType * pointIDs = new vtkIdType[nPointsX*nPointsY*nPointsZ];
index = 0;
progressFactor = 0.5/static_cast<double>(nPointsZ);
for (int z = 0; z < nPointsZ; z++)
{
//Report progress updates for the last 50%
progressUpdate.eventRaised(double(z)*progressFactor + progressOffset);
in[2] = (minZ + (static_cast<coord_t>(z) * incrementZ)); //Calculate increment in z;
for (int y = 0; y < nPointsY; y++)
{
in[1] = (minY + (static_cast<coord_t>(y) * incrementY)); //Calculate increment in y;
for (int x = 0; x < nPointsX; x++)
{
// Create the point only when needed
if (pointNeeded[index])
{
in[0] = (minX + (static_cast<coord_t>(x) * incrementX)); //Calculate increment in x;
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);
// ------ Hexahedron creation ----------------
// It is approx. 40 x faster to create the hexadron only once, and reuse it for each voxel.
vtkHexahedron *theHex = vtkHexahedron::New();
index = 0;
for (int z = 0; z < nBinsZ; z++)
{
for (int y = 0; y < nBinsY; y++)
{
for (int x = 0; x < nBinsX; x++)
{
if (voxelShown[index])
{
//Only create topologies for those cells which are not sparse.
// create a hexahedron topology
vtkIdType id_xyz = pointIDs[(x) + (y)*nPointsX + z*nPointsX*nPointsY];
vtkIdType id_dxyz = pointIDs[(x+1) + (y)*nPointsX + z*nPointsX*nPointsY];
vtkIdType id_dxdyz = pointIDs[(x+1) + (y+1)*nPointsX + z*nPointsX*nPointsY];
vtkIdType id_xdyz = pointIDs[(x) + (y+1)*nPointsX + z*nPointsX*nPointsY];
vtkIdType id_xydz = pointIDs[(x) + (y)*nPointsX + (z+1)*nPointsX*nPointsY];
vtkIdType id_dxydz = pointIDs[(x+1) + (y)*nPointsX + (z+1)*nPointsX*nPointsY];
vtkIdType id_dxdydz = pointIDs[(x+1) + (y+1)*nPointsX + (z+1)*nPointsX*nPointsY];
vtkIdType id_xdydz = pointIDs[(x) + (y+1)*nPointsX + (z+1)*nPointsX*nPointsY];
//create the hexahedron
theHex->GetPointIds()->SetId(0, id_xyz);
theHex->GetPointIds()->SetId(1, id_dxyz);
theHex->GetPointIds()->SetId(2, id_dxdyz);
theHex->GetPointIds()->SetId(3, id_xdyz);
theHex->GetPointIds()->SetId(4, id_xydz);
theHex->GetPointIds()->SetId(5, id_dxydz);
theHex->GetPointIds()->SetId(6, id_dxdydz);
theHex->GetPointIds()->SetId(7, id_xdydz);
visualDataSet->InsertNextCell(VTK_HEXAHEDRON, theHex->GetPointIds());
}
index++;
}
}
}
theHex->Delete();
std::cout << tim << " to create and add the hexadrons." << std::endl;
points->Delete();
signal->Delete();
visualDataSet->Squeeze();
delete [] pointIDs;
delete [] voxelShown;
delete [] pointNeeded;
return visualDataSet;
}