[ITK-users] Problems with mesh I/O and conversions in ITK

[Matt McCormick]

Hi Carlos,

When using MeshFileReader/MeshFileWriter, which cell data is being
lost?  Examining a few of the files in the link provided at
nac-brain-atlas-1.0/models/ I am only seeing points.

Thanks,
Matt

On Mon, Apr 14, 2014 at 8:54 AM, Carlos Henrique Villa Pinto
<chvillap at gmail.com> wrote:
> Hi everyone!
> I'm having some problems working with meshes in ITK.
>
> What I'm trying to do (by now) is just a brief test in which I read a .vtk
> mesh file from this database:
> http://www.spl.harvard.edu/publications/item/view/2037, write it again to
> the disk and see if everything is ok. Very simple.
>
> The problem is: if I try to do that using the itk::MeshReader and
> itk::MeshWriter classes, the program doesn't work as expected since the
> written mesh apparently loses all information about the original mesh's
> cells (I'm using Paraview and Slicer for visualization). The same thing
> happens if I use the itk::VTKPolyDataReader and itk::VTKPolyDataWriter
> classes for the mesh I/O. However, if I do the same test reading the .vtk
> mesh file provided by this example:
> http://itk.org/ITKExamples/src/IO/Mesh/ReadMesh/Documentation.html,
> everything works fine in both cases. So I guess it could be a file format
> issue.
>
> I also tried to use VTK instead of ITK for the mesh I/O (the
> vtkPolyDataReader and vtkPolyDataWriter classes). And with that, the program
> works fine even with the meshes from the brain database. But as I intend to
> work with deformable models algorithms in ITK, that approach requires me to
> convert the read vtkPolyData into a ITK simplex mesh, but such conversion
> makes my program crash (either an exception is thrown because of an invalid
> point or the program enters in an infinite loop). I'm using the
> vtkPolyDataToitkMesh class (from InsightApplications) to convert the VTK
> polydata to a ITK triangle mesh, and the
> itk::TriangleMeshToSimplexMeshFilter class to convert the latter to a
> simplex mesh.
>
> Last, but not least: if I just do the following conversions: VTK polydata ->
> ITK triangle mesh -> VTK polydata and try to write the resulting polydata
> (using vtkPolyDataWriter), I get a segmentation fault. No clue about what
> causes it.
>
> The more recent and complete version of my code (VTK + ITK) is below. If
> anyone could help me with any of these issues, I would be very grateful.
>
> =============================================================================================
>
>   // Set the ITK type definitions.
>
>   const int Dimension = 3;
>   typedef double PixelType;
>
>   typedef vtkPolyDataToitkMesh::TriangleMeshType
> TriangleMeshType;
>   typedef itk::DefaultDynamicMeshTraits<PixelType, Dimension, Dimension,
> double, double> SimplexMeshTraits;
>   typedef itk::SimplexMesh<PixelType, Dimension, SimplexMeshTraits>
> SimplexMeshType;
>
>   typedef itk::TriangleMeshToSimplexMeshFilter<TriangleMeshType,
> SimplexMeshType> TriangleToSimplexFilterType;
>   typedef itk::SimplexMeshToTriangleMeshFilter<SimplexMeshType,
> TriangleMeshType> SimplexToTriangleFilterType;
>
>   typedef itk::SimplexMeshVolumeCalculator<SimplexMeshType>
> VolumeCalculatorType;
>
>   typedef itk::VTKPolyDataWriter<TriangleMeshType> WriterType;
>
>   // Read the input VTK polydata.
>
>   vtkSmartPointer<vtkPolyDataReader> reader =
> vtkSmartPointer<vtkPolyDataReader>::New();
>   reader->SetFileName(inputFileName.c_str());
>   reader->Update();
>
>   std::cout << "Polydata read ok\n";
>
>   // Convert the VTK polydata to a ITK mesh.
>
>   vtkPolyDataToitkMesh polyDataToMesh;
>   polyDataToMesh.SetInput(reader->GetOutput());
>   polyDataToMesh.ConvertvtkToitk();
>
>   std::cout << "Conversion to triangle mesh ok\n";
>
>   // Convert the triangle mesh to a simplex mesh.
>
>   TriangleToSimplexFilterType::Pointer triangleToSimplexFilter =
> TriangleToSimplexFilterType::New();
>   triangleToSimplexFilter->SetInput(polyDataToMesh.GetOutput());
>   triangleToSimplexFilter->Update();
>
>   std::cout << "Conversion to simplex mesh ok\n";
>
>   // Compute the simplex mesh volume.
>
>   VolumeCalculatorType::Pointer volumeCalculator =
> VolumeCalculatorType::New();
>   volumeCalculator->SetSimplexMesh(triangleToSimplexFilter->GetOutput());
>   volumeCalculator->Compute();
>
>   std::cout << "Volume calculation ok (value = " <<
> volumeCalculator->GetVolume() << ")\n";
>
>   // Convert the simplex mesh to triangle mesh.
>
>   SimplexToTriangleFilterType::Pointer simplexToTriangleFilter =
> SimplexToTriangleFilterType::New();
>   simplexToTriangleFilter->SetInput(triangleToSimplexFilter->GetOutput());
>   simplexToTriangleFilter->Update();
>
>   std::cout << "Conversion to triangle mesh ok\n";
>
>   // Convert the ITK mesh to VTK polydata.
>
>   itkMeshTovtkPolyData meshToPolyData;
>   meshToPolyData.SetInput(simplexToTriangleFilter->GetOutput());
>   meshToPolyData.ConvertitkTovtk();
>
>   std::cout << "Conversion to polydata ok\n";
>
>   // Write the output polydata.
>
>   vtkSmartPointer<vtkPolyDataWriter> writer =
> vtkSmartPointer<vtkPolyDataWriter>::New();
>   writer->SetFileName(outputFileName.c_str());
>   writer->SetInputData(meshToPolyData.GetOutput());
>   writer->Update();
>
>   std::cout << "Polydata write ok\n";
>
> =============================================================================================
>
> Thanks in advance.
> []s
>
> --
> Carlos Henrique Villa Pinto
> Graduate Student in Computer Science
> Federal University of São Carlos - Brazil
> XCS
>
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