[Insight-users] How to properly use itkTriangleMeshToImageFilter?

[Amardeep Singh]

Dear Luis

Thank you very much for your quick reply.

What I actually want to do is iterate over a part of my image and 
extract a circular neighborhood
at every point and postprocess these extracted circles. Using the 
itkMesh was a first try to get
the circular neighborhood. However, I think it might be too slow for my 
task as it would be applied very frequently.
So, I need to come up with something else, anyway, I guess. Any ideas?

I added the following line to my code:
reader->GetOutput()->TransformIndexToPhysicalPoint(idx, center);

where "idx" is the Index in my image where I want my sphere to be and 
"center" is the center of the sphere (RegularSphereMeshSource).
Like this, I manage to place the sphere where I want it to be. I was not 
aware that the center is set in world coordinates.
Thanks a lot for your help!

Best regards
Amardeep

Luis Ibanez wrote:
>
> Hi Amardeep,
>
> I think that this typically happens when the image parameters
> are such that the image is not overlapping with your input mesh
> in Physical space.
>
>
> You should choose the
>
>     * Origin
>     * Spacing
>     * Number of pixels
>
> of you image to create a grid on top of the Physical space that
> is occupied by the Mesh.
>
> Have you looked at your Mesh, and found the bounds of the
> mesh nodes in space ?
>
> Can you please post to the mailing list what the BoundingBox
> of your mesh is ?
>
> These values can be used to select proper parameters for the
> output image that contains the rasterization of the Mesh.
>
>
> The image parameters should match the extent of the input Mesh,
> not the extent of an image that you read from disk. Unless your
> Mesh was extracted from that image that you are reading from
> disk...
>
>
>
> You could get a feeling for these parameters by loading your
> Mesh into ParaView (or any other visualization tool).
>
>
>     Please let us know,
>
>
>        Thanks
>
>
>             Luis
>
>
> --------------------------------------------------------------------------------
> On Thu, Jul 2, 2009 at 3:34 PM, Amardeep Singh <amar.singh at gmx.de 
> <mailto:amar.singh at gmx.de>> wrote:
>
>     Dear ITK Users
>
>     I would like to use the "itkTriangleMeshToImageFilter". In a first
>     experiment, I just want to create
>     a sphere using the "itkRegularSphereMeshSource", binarize it and
>     save the output. I take the size, origin and spacing
>     of the resulting image from an image that I read from the harddisk
>     (just for convenience).
>     Unfortunately, I get the following error:
>
>     Start Processing!
>     [-90, 126, -72]          <--- origin
>     [182, 218, 182]        <--- size of image
>     [1, 1, 1]                    <--- spacing of image
>     [0, 0, 0]                    <--- index
>     Exception caught !
>
>     itk::ExceptionObject (0x81a3b00)
>     Location: "void itk::TriangleMeshToBinaryImageFilter<TInputMesh,
>     TOutputImage>::GenerateData() [with TInputMesh = itk::Mesh<float,
>     3u, itk::DefaultStaticMeshTraits<float, 3u, 3u, float, float,
>     float> >, TOutputImage = itk::Image<unsigned char, 3u>]"
>     File:
>     /workspace/InsightToolkit-3.14.0/Code/BasicFilters/itkTriangleMeshToBinaryImageFilter.txx
>     Line: 224
>     Description: itk::ERROR:
>     TriangleMeshToBinaryImageFilter(0x8141ec8): No Image Indices Found.
>
>     Above, I have included output, indicating the origin, size,
>     spacing and index of the largest region of the image that I read
>     from the harddisk. These are the values that I pass to the
>     "itkTriangleMeshToImageFilter", so they should be fine, I think.
>     There has been a similar posting on the mailing list
>     ("http://www.nabble.com/converting-mesh-to-binary-image-td21170657.html"),
>     but the solution to the problem was not made explicit,
>     unfortunately. Please, find my source code attached.
>     Does anyone know how to resolve this problem?
>     Thank you very much!
>
>     Best regards
>     Amardeep
>
>
>     #include "itkImageRegionIterator.h"
>     #include "itkImageFileReader.h"
>     #include "itkImageFileWriter.h"
>     #include "itkTriangleMeshToBinaryImageFilter.h"
>     #include "itkDefaultStaticMeshTraits.h"
>     #include "itkMesh.h"
>     #include "itkRegularSphereMeshSource.h"
>
>     #include "iostream"
>
>
>     int main(int argc, char *argv[] )
>     {
>       std::cout << "Start Processing!" << std::endl;
>
>       typedef unsigned char BinaryPixelType;
>       typedef float PixelType;
>       typedef itk::DefaultStaticMeshTraits<float, 3, 3,float,float>
>     TriangleMeshTraits;
>       typedef itk::Mesh<float,3, TriangleMeshTraits> TriangleMeshType;
>       typedef itk::RegularSphereMeshSource<TriangleMeshType>
>      SphereMeshSourceType;
>       typedef SphereMeshSourceType::PointType PointType;
>
>       typedef itk::Image<BinaryPixelType, 3>      BinaryImageType;
>       typedef itk::Image<PixelType, 3> ImageType;
>
>       typedef itk::TriangleMeshToBinaryImageFilter<TriangleMeshType,
>     BinaryImageType> TriangleMeshToBinaryImageFilterType;
>
>      
>       TriangleMeshToBinaryImageFilterType::Pointer triangleMeshToImage
>     = TriangleMeshToBinaryImageFilterType::New();
>       SphereMeshSourceType::Pointer sphere = SphereMeshSourceType::New();
>       sphere->SetScale(5);
>       sphere->SetResolution(5);
>
>       typedef itk::ImageFileReader<ImageType> ReaderType;
>       typedef itk::ImageFileWriter<BinaryImageType> WriterType;
>
>       ReaderType::Pointer reader = ReaderType::New();
>       reader->SetFileName("/test_image.nii.gz");
>       try
>       {
>         reader->Update();
>       }
>       catch( itk::ExceptionObject & excep )
>       {
>         std::cerr << "Exception caught !" << std::endl;
>         std::cerr << excep << std::endl;
>       }
>
>       PointType center;
>       center[0] = 10;
>       center[1] = 10;
>       center[2] = 10;
>       sphere->SetCenter(center);
>       triangleMeshToImage->SetInput(sphere->GetOutput());
>
>       ImageType::Pointer orgImage = reader->GetOutput();
>       const ImageType::PointType orgOrigin = orgImage->GetOrigin();
>       const ImageType::SizeType orgSize =
>     orgImage->GetLargestPossibleRegion().GetSize();
>       const ImageType::SpacingType orgSpacing = orgImage->GetSpacing();
>       const ImageType::IndexType orgIndex =
>     orgImage->GetLargestPossibleRegion().GetIndex();
>
>       std::cout << orgOrigin << std::endl;
>       std::cout << orgSize << std::endl;
>       std::cout << orgSpacing << std::endl;
>       std::cout << orgIndex << std::endl;
>
>       triangleMeshToImage->SetTolerance (1.0);
>       triangleMeshToImage->SetSpacing (orgSpacing);
>       triangleMeshToImage->SetOrigin(orgOrigin);
>       triangleMeshToImage->SetSize (orgSize);
>       triangleMeshToImage->SetIndex (orgIndex);
>
>       WriterType::Pointer writer = WriterType::New();
>
>       writer->SetFileName("/test_output.nii.gz");
>       writer->SetInput(triangleMeshToImage->GetOutput());
>
>       try
>       {
>           sphere->Update();
>           triangleMeshToImage->Update();
>           writer->Update();
>       }
>       catch( itk::ExceptionObject & excep )
>       {
>         std::cerr << "Exception caught !" << std::endl;
>         std::cerr << excep << std::endl;
>       }
>
>       return 0;
>
>     }
>
>
>
>
>
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