[ITK-users] Simplex Mesh Deformable Model doesn't change
Dženan Zukić
dzenanz at gmail.com
Thu Nov 2 11:19:17 EDT 2017
Hi Breno,
can you provide a link via some service which does not require installation
of some adware to download the file? I think that most could storage
providers have a free version (e.g. Dropbox or Google Drive).
Also, we are trying to switch to Discourse <https://discourse.itk.org/>,
can you re-post the message with updated link there?
Regards,
Dženan
On Wed, Nov 1, 2017 at 7:42 PM, bsouza <brufsc at hotmail.com> wrote:
> Dear itk-developers,
>
> I'm trying to use the itkDeformableSimplexMesh3D filter to make a local
> adjustment of a simplex mesh. The mesh that I want to deform using this
> filter is already initialized close to the target structure in the image.
> However, after playing with all parameter values of the filter, it seems
> that there is not significant differences between the input and output
> meshes.
>
> I'm reading the mesh from a file (stl or vtk extension) and I want to
> deform
> it using a brain MRI (nifiti format) image as a reference. After the filter
> application, the result seems to not approximate the mesh to the local
> structure in the image (only occurs a small smoothness of the model). I've
> tried to change the parameters (alpha, beta, gamma, rigidity, number of
> iterations) values to check if some change would occur, but the result
> always seems the same. I would like that deformation to be able to move the
> mesh to closer to the structure in the image. My code is below. Is there
> something wrong with my code? Why it seems that the external force has no
> influence in the mesh deform result?
>
> The image and the mesh I'm using in this test is available in the link
> below
> (I don't know how much time until the link expires):
>
> http://www73.zippyshare.com/v/sqQ6cgjN/file.html
>
> Here is my code:
>
> =================================================================
> enum PARAMS {
> PROGRAM_NAME = 0,
> IMAGE_FILENAME,
> INPUT_MESH_FILENAME,
> OUTPUT_MESH_FILENAME,
> NUM_ARGS
> };
>
>
> using namespace std;
>
> int main( int argc, char *argv[] )
> {
>
> if( argc < NUM_ARGS )
> {
> std::cerr << "\n\n";
> std::cerr << "Usage: " << argv[PROGRAM_NAME] << " imageFileName
> inputMeshFileName ouputMeshFileName";
> std::cerr << "\n\n";
> return 1;
> }
>
> itk::STLMeshIOFactory::RegisterOneFactory();
>
> const int dimension = 3;
>
> typedef float PixelType;
> typedef itk::Image<PixelType, dimension> ImageType;
>
> typedef itk::DefaultDynamicMeshTraits<PixelType, dimension>
> TriangleMeshTraits;
> typedef itk::DefaultDynamicMeshTraits<PixelType, dimension>
> SimplexMeshTraits;
> typedef itk::Mesh<PixelType, dimension, TriangleMeshTraits>
> TriangleMeshType;
> typedef itk::SimplexMesh<PixelType, dimension, SimplexMeshTraits>
> SimplexMeshType;
>
> typedef itk::TriangleMeshToSimplexMeshFilter<TriangleMeshType,
> SimplexMeshType> TriangleToSimplexFilterType;
> typedef itk::SimplexMeshToTriangleMeshFilter<SimplexMeshType,
> TriangleMeshType> SimplexToTriangleFilterType;
>
> typedef itk::DeformableSimplexMesh3DFilter<SimplexMeshType,
> SimplexMeshType> DeformFilterType;
> typedef DeformFilterType::GradientImageType
> GradientType;
>
> typedef itk::GradientAnisotropicDiffusionImageFilter <ImageType,
> ImageType> DiffusionFilterType;
>
> typedef itk::GradientAnisotropicDiffusionImageFilter < ImageType,
> ImageType > GradientAnisotropicImageType;
> typedef itk::GradientMagnitudeRecursiveGaussianImageFilter < ImageType,
> ImageType > GradientMagnitudeType;
> typedef itk::SigmoidImageFilter< ImageType, ImageType > SigmoidImageType;
> typedef itk::GradientRecursiveGaussianImage
> Filter<ImageType,GradientType>
> GradientFilterType;
>
> typedef itk::ImageFileReader<ImageType> ImageReaderType;
> typedef itk::ImageFileWriter<ImageType> ImageWriterType;
> typedef itk::MeshFileReader<TriangleMeshType> MeshReaderType;
> typedef itk::MeshFileWriter<TriangleMeshType> MeshWriterType;
>
>
> ImageReaderType::Pointer imageReader = ImageReaderType::New();
> imageReader->SetFileName(argv[IMAGE_FILENAME]);
> imageReader->Update();
>
> MeshReaderType::Pointer meshReader = MeshReaderType::New();
> meshReader->SetFileName(argv[INPUT_MESH_FILENAME]);
> meshReader->Update();
>
> std::cout << " starting to Filter Image" << std::endl;
> GradientAnisotropicImageType::Pointer gradientanisotropicfilter =
> GradientAnisotropicImageType::New();
> gradientanisotropicfilter->SetInput(imageReader->GetOutput());
> gradientanisotropicfilter->SetNumberOfIterations(5);
> gradientanisotropicfilter->SetTimeStep(0.0625);
> gradientanisotropicfilter->SetConductanceParameter(3);
> gradientanisotropicfilter->Update();
> std::cout << "GradientAnisotropicDiffusion is DONE!" << std::endl;
>
> GradientMagnitudeType::Pointer gradientmagnitudefilter =
> GradientMagnitudeType::New();
> gradientmagnitudefilter->SetInput( gradientanisotropicfilter->
> GetOutput()
> );
> gradientmagnitudefilter->SetSigma(1.0);
> gradientmagnitudefilter->Update();
> std::cout << "GradientMagnitude is DONE!" << std::endl;
>
> SigmoidImageType::Pointer sigmoidimagefilter = SigmoidImageType::New();
> sigmoidimagefilter->SetInput( gradientmagnitudefilter->GetOutput());
> sigmoidimagefilter->SetOutputMinimum(0);
> sigmoidimagefilter->SetOutputMaximum(1);
> sigmoidimagefilter->SetAlpha(10);
> sigmoidimagefilter->SetBeta(100);
> sigmoidimagefilter->Update();
> std::cout << "Sigmoid is DONE!" << std::endl;
>
> GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
> gradientFilter->SetInput( sigmoidimagefilter->GetOutput() );
> gradientFilter->SetSigma(1.0);
> gradientFilter->Update();
> std::cout << "GradientMagnitude is DONE!" << std::endl;
>
> std::cout << "Gradient filter ok\n";
>
> TriangleToSimplexFilterType::Pointer triangleToSimplexFilter =
> TriangleToSimplexFilterType::New();
> triangleToSimplexFilter->SetInput(meshReader->GetOutput());
> triangleToSimplexFilter->Update();
>
> GradientType::Pointer gradientImage = gradientFilter->GetOutput();
> SimplexMeshType::Pointer simplexMesh =
> triangleToSimplexFilter->GetOutput();
> DeformFilterType::Pointer deformFilter = DeformFilterType::New();
>
> const unsigned int numberOfCycles = 100;
>
> for (unsigned int i = 0; i < numberOfCycles; i++)
> {
> // must disconnect the pipeline
> simplexMesh->DisconnectPipeline();
> deformFilter->SetInput( simplexMesh );
> deformFilter->SetGradient( gradientImage );
> deformFilter->SetAlpha(0.1);
> deformFilter->SetBeta(-0.1);
> deformFilter->SetIterations(5);
> deformFilter->SetRigidity(1);
> deformFilter->Update();
> }
> SimplexMeshType::Pointer deformResult = deformFilter->GetOutput();
>
>
> SimplexToTriangleFilterType::Pointer simplexToTriangleFilter =
> SimplexToTriangleFilterType::New();
> simplexToTriangleFilter->SetInput(deformResult);
> simplexToTriangleFilter->Update();
> TriangleMeshType::Pointer conversionResult =
> simplexToTriangleFilter->GetOutput();
>
> conversionResult->DisconnectPipeline();
>
> MeshWriterType::Pointer meshWriter = MeshWriterType::New();
> meshWriter->SetFileName(argv[OUTPUT_MESH_FILENAME]);
> meshWriter->SetInput(conversionResult);
> meshWriter->Update();
>
> return EXIT_SUCCESS;
> }
>
> =================================================================
>
> I really appreciate any help you can provide me.
>
> Thank you very much,
> Breno
>
>
>
>
> --
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