Threshold with Cell Set

07 Mar 2015

In my last blog, I described a new type of unstructured grid which can be used to represent a subset of a structured dataset without explicit connectivity data structures. I mentioned that one very good application of such a dataset is a better implementation of the threshold filter. In the blog, we'll go over such an implementation as shown here and here.

Let's first quickly go over the original VTK implementation as can be found here. First notice that this filter accepts any vtkDataSet and produces an unstructured grid.

// Note that subclasses of vtkUnstructuredGridAlgorithm produce
// vtkUnstructuredGrid in the first output by default.
class VTKFILTERSCORE_EXPORT vtkThreshold : public vtkUnstructuredGridAlgorithm
{

// FillInputPortInformation is overriden to change the required
// input from vtkUnstructuredGrid to vtkDataSet
int vtkThreshold::FillInputPortInformation(int, vtkInformation *info)
{
  info->Set(vtkAlgorithm::INPUT_REQUIRED_DATA_TYPE(), "vtkDataSet");
  return 1;
}

Next, let's quickly take a look at RequestData. I added some comments in the excerpt to make it easier to follow. I also took out pieces that are not very relevant to our discussion. See the full source for details.

int vtkThreshold::RequestData(
  vtkInformation *vtkNotUsed(request),
  vtkInformationVector **inputVector,
  vtkInformationVector *outputVector)
{
  // get the info objects
  vtkInformation *inInfo = inputVector[0]->GetInformationObject(0);
  vtkInformation *outInfo = outputVector->GetInformationObject(0);

  // get the input and output
  vtkDataSet *input = vtkDataSet::SafeDownCast(
    inInfo->Get(vtkDataObject::DATA_OBJECT()));
  vtkUnstructuredGrid *output = vtkUnstructuredGrid::SafeDownCast(
    outInfo->Get(vtkDataObject::DATA_OBJECT()));

  // ...

  // We create an output unstructured grid. This grid will contain
  // the same set of point and cell arrays. But these will be new
  // arrays that contain only the output subset.
  outPD->CopyGlobalIdsOn();
  outPD->CopyAllocate(pd);
  outCD->CopyGlobalIdsOn();
  outCD->CopyAllocate(cd);

  // Create new output points.
  numPts = input->GetNumberOfPoints();
  output->Allocate(input->GetNumberOfCells());

  newPoints = vtkPoints::New();
  // ...
  newPoints->Allocate(numPts);

  // We need this map to find the mapping between input
  // and output point ids so that we can copy the point data.
  pointMap = vtkIdList::New(); //maps old point ids into new
  pointMap->SetNumberOfIds(numPts);
  for (i=0; i < numPts; i++)
    {
    pointMap->SetId(i,-1);
    }

  // ...

  // Check that the scalars of each cell satisfy the threshold criterion
  for (cellId=0; cellId < input->GetNumberOfCells(); cellId++)
    {
    cell = input->GetCell(cellId);
    cellPts = cell->GetPointIds();
    numCellPts = cell->GetNumberOfPoints();

    // Here whether to keep a cell is determined. The answer is stored in
    // the keepCell variable.

    // If we are keeping the cell, copy to the output.
    if (  numCellPts > 0 && keepCell )
      {
      // satisfied thresholding (also non-empty cell, i.e. not VTK_EMPTY_CELL)

      // Go over the points of the cell.
      for (i=0; i < numCellPts; i++)
        {
        ptId = cellPts->GetId(i);
        // If we didn't insert the point already, insert in the output
        if ( (newId = pointMap->GetId(ptId)) < 0 )
          {
          input->GetPoint(ptId, x);
          newId = newPoints->InsertNextPoint(x);
          // Update the point map for future use.
          pointMap->SetId(ptId,newId);
          // Also copy the data.
          outPD->CopyData(pd,ptId,newId);
          }
        // Insert the point to the output cell.
        newCellPts->InsertId(i,newId);
        }
      // ...
      // Insert the new cell to the output
      newCellId = output->InsertNextCell(cell->GetCellType(),newCellPts);
      // Copy the cell data
      outCD->CopyData(cd,cellId,newCellId);
      newCellPts->Reset();
      } // satisfied thresholding
    } // for all cells

  // ..

  output->SetPoints(newPoints);
  newPoints->Delete();

  output->Squeeze();

  return 1;
}

In our new filter, much of this will remain the same. In fact, to quickly develop it, I copied vtkThreshold to vtkThreshold3 and made a few changes. First, I change the filter to produce a vtkCellSet:

class vtkThreshold3 : public vtkUnstructuredGridBaseAlgorithm
{

int vtkThreshold3::RequestDataObject(
  vtkInformation *vtkNotUsed(request),
  vtkInformationVector **vtkNotUsed(inputVector),
  vtkInformationVector *outputVector)
{
  vtkInformation* info = outputVector->GetInformationObject(0);
  vtkCellSet *output = vtkCellSet::SafeDownCast(
    info->Get(vtkDataObject::DATA_OBJECT()));

  if (!output)
    {
    vtkCellSet* newOutput = vtkCellSet::New();
    info->Set(vtkDataObject::DATA_OBJECT(), newOutput);
    newOutput->Delete();
    }

  return 1;
}

Next, I changed the part of the code that creates new points and cells to instead keep track of the ids of the cells that we want to threshold. So the following code

// If we are keeping the cell, copy to the output.
if (  numCellPts > 0 && keepCell )
  {
  // satisfied thresholding (also non-empty cell, i.e. not VTK_EMPTY_CELL)

  // Go over the points of the cell.
  for (i=0; i < numCellPts; i++)
    {
    ptId = cellPts->GetId(i);
    // If we didn't insert the point already, insert in the output
    if ( (newId = pointMap->GetId(ptId)) < 0 )
      {
      input->GetPoint(ptId, x);
      newId = newPoints->InsertNextPoint(x);
      // Update the point map for future use.
      pointMap->SetId(ptId,newId);
      // Also copy the data.
      outPD->CopyData(pd,ptId,newId);
      }
    // Insert the point to the output cell.
    newCellPts->InsertId(i,newId);
    }
  // ...
  // Insert the new cell to the output
  newCellId = output->InsertNextCell(cell->GetCellType(),newCellPts);
  // Copy the cell data
  outCD->CopyData(cd,cellId,newCellId);
  newCellPts->Reset();
  } // satisfied thresholding

changes to

if (  numCellPts > 0 && keepCell )
  {
  ids->InsertNextValue(cellId);
  } // satisfied thresholding

And the ids are used in creating the cell set as follows

vtkIdTypeArray* ids = vtkIdTypeArray::New();
ids->Allocate(input->GetNumberOfCells());
output->GetImplementation()->SetCellIds(ids);
ids->Delete();

Finally, we have to create an instance of vtkPoints for the output unstructured grid. This has to be handled specially in the cases where the input does not have its own vtkPoints (for example vtkImageData). Here is the code:

vtkImageData* inputImage = vtkImageData::SafeDownCast(input);
if (inputImage)
  {
  vtkNew<vtkImageData> img;
  img->CopyStructure(inputImage);

  vtkNew<vtkImagePointsArray<double> > ptsArray;
  ptsArray->InitializeArray(img.GetPointer());
  ptsArray->SetName("pts");

  vtkNew<vtkPoints> points;
  points->SetData(ptsArray.GetPointer());

  output->SetPoints(points.GetPointer());
  }

This is it! The output of this filter acts as an unstructured grid but does not store cells or points explicitly. As a bonus, the filter actually got simpler and performs better. We can exercise this filter as follows.

vtkNew<vtkRTAnalyticSource> source;
source->SetWholeExtent(-50, 50, -50, 50, -50, 50);

vtkNew<vtkThreshold3> threshold;
threshold->ThresholdByLower(200);
threshold->SetInputConnection(source->GetOutputPort());
threshold->Update();
cerr << "Threshold " << timer->GetElapsedTime() << endl;
cerr << threshold->GetOutput()->GetNumberOfCells() << endl;

vtkNew<vtkContourFilter> contour;
contour->SetValue(0, 150);
contour->SetInputConnection(threshold->GetOutputPort());
contour->Update();
cerr << "Contour " << timer->GetElapsedTime() << endl;
cerr << contour->GetOutput()->GetNumberOfPoints() << endl;

Careful readers probably noticed that there is a flaw in this approach: the output of the threshold filter contains all of the points of the input. Therefore, any point-based filters such as glyph and point statistics will incorrectly produce results based on all input points. With the current VTK data model, there is no easy way of fixing this issue. In the near future, we will add support for masking (blanking) of points and cells to all datasets. With this feature in place, one could easily keep track of all points touched by the output grid during tresholding and mask all others. In fact, if masking support was in the data model, we wouldn't have to create a new unstructured grid but directly mask cells and points that are not needed. A blog for another time.

Berk Geveci About Archive Feed

Threshold with Cell Set

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