[Insight-users] problem to convert a mesh to a Binary image

[Luis Ibanez]

Hi Noura,

Thanks for the clarification.

The filter that you need then, is called:

       itkTriangleMeshToBinaryImageFilter

http://www.itk.org/Doxygen/html/classitk_1_1TriangleMeshToBinaryImageFilter.html


You will find it in the directory:

            Insight/Code/BasicFilters


    Regards,


        Luis


--------------------------------
On Tue, Feb 16, 2010 at 4:25 AM, Noura AZZABOU
<n.azzabou at institut-myologie.org> wrote:
> Hi Luis,
>
> Thank you for your answer but my problem is the opposite I want to obtain a binary image from the mesh. Indeed, when I used the line code that I posted, the result was not as expected and I obtained a Binary image containing only the pixel belonging to the contour (and not those inside the contour. The result I obtained is similar (but thicker contours) to the one given by
>
> itk::PointSetToImageFilter<MeshType,ImageType> MeshFilterType;
>
> I can send you the resulting image and the corresponding mesh if it makes things more clear.
>
>
> Regards
>
> Noura
>
>
> -----Message d'origine-----
> De : Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Envoyé : 15 February 2010 23:56
> À : Noura AZZABOU
> Cc : insight-users at itk.org
> Objet : Re: [Insight-users] problem to convert a mesh to a Binary image
>
> Hi Noura,
>
> If you only want your binary mask to only have the pixels that
> are touched by the mesh, you can take the current binary mask
> that you got from the rasterization process and you can pass it
> as input to the
>
>               itkSimpleContourExtractorImageFilter
>
> That should give you as output a binary mask that only contains
> the pixelized surface of the mesh.
>
> ---
>
> You can achieve a similar result by eroding the mask and
> subtracting it from the original one.
>
>    Regards,
>
>
>            Luis
>
>
>
> ---------------------------------------------------------------------------------
> On Mon, Feb 15, 2010 at 8:13 AM, Noura AZZABOU
> <n.azzabou at institut-myologie.org> wrote:
>> Hi,
>>
>>
>>
>> I am trying to convert a vtk mesh to a Binary image. I followed the examples
>> given in the ITK software guide.  I used spatial object in order to obtain a
>> Binary image (1 inside the mesh) 0 outside.
>>
>>  Instead of that I obtained an image with 1 for the pixel belonging to the
>> contour and 0 for the rest (inclusing the pixels that are inside the region
>> delimited by the contour)
>>
>>
>>
>> Does any body know if there are some condition on mesh to make the
>> generation of binary image possible.
>>
>>
>>
>> Here is the source code for the binary image generation.
>>
>>
>>
>> Thanks in advance for your help
>>
>>
>>
>>
>>
>>
>>
>> typedef itk::Mesh< double, 3 > MeshType;
>>
>>       typedef itk::MeshSpatialObject< MeshType > SpatialObjectType;
>>
>>       typedef itk::Image< unsigned char, 3 > ImageType;
>>
>>       typedef itk::Image< double, 3> RefImageType;
>>
>>       typedef itk::SpatialObjectToImageFilter< SpatialObjectType, ImageType
>>> MeshFilterType;
>>
>>       typedef itk::VTKPolyDataReader< MeshType > MeshReaderType;
>>
>>       typedef itk::ImageFileWriter< ImageType > ImageWriterType;
>>
>>       typedef itk::ImageFileReader< RefImageType > RefImageReaderType;
>>
>>
>>
>>       /// load vtk mesh
>>
>>       std::cout << "load vtk mesh" << std::endl;
>>
>>       MeshReaderType::Pointer mesh_reader = MeshReaderType::New();
>>
>>       mesh_reader->SetFileName( mesh_path );
>>
>>       mesh_reader->Update();
>>
>>       SpatialObjectType::Pointer mesh = SpatialObjectType::New();
>>
>>       mesh->SetMesh( mesh_reader->GetOutput() );
>>
>>
>>
>>
>>
>>       /// reference image
>>
>>       std::cout << "load reference image" << std::endl;
>>
>>       RefImageReaderType::Pointer ref_image_reader =
>> RefImageReaderType::New();
>>
>>       ref_image_reader->SetFileName( ref_image );
>>
>>       ref_image_reader->Update();
>>
>>       ref_image_reader->GetOutput()->Print(std::cout);
>>
>>
>>
>>       /// image pointer
>>
>>       ImageType::Pointer image;
>>
>>
>>
>>       /// generate output image
>>
>>       std::cout << "generate output image" << std::endl;
>>
>>       MeshFilterType::Pointer mesh_filter = MeshFilterType::New();
>>
>>       mesh_filter->SetOrigin( ref_image_reader->GetOutput()->GetOrigin() );
>>
>>       mesh_filter->SetSize(
>> ref_image_reader->GetOutput()->GetLargestPossibleRegion().GetSize() );
>>
>>       mesh_filter->SetSpacing( ref_image_reader->GetOutput()->GetSpacing()
>> );
>>
>>       //mesh_filter->SetDirection(
>> ref_image_reader->GetOutput()->GetDirection() );
>>
>>       mesh_filter->SetOutsideValue(1);
>>
>>       mesh_filter->SetInsideValue(23);
>>
>>       mesh_filter->SetInput(mesh);
>>
>>       ref_image_reader->Delete();
>>
>>       try
>>
>>       {
>>
>>             mesh_filter->Update();
>>
>>       }
>>
>>       catch( itk::ExceptionObject & excep )
>>
>>       {
>>
>>             std::cerr << "Exception Caught !" << std::endl;
>>
>>             std::cerr << excep << std::endl;
>>
>>       }
>>
>>       // mesh_reader->GetOutput()->Print(std::cout);
>>
>>       // mesh->Print(std::cout);
>>
>>       // mesh->GetMesh()->Print(std::cout);
>>
>>       mesh_filter->GetInput()->Print(std::cout);
>>
>>       mesh_filter->Print(std::cout);
>>
>>
>>
>>       /// save image
>>
>>       std::cout << "save image" << std::endl;
>>
>>       ImageWriterType::Pointer image_writer = ImageWriterType::New();
>>
>>       std::cout << "saving image: " << image_path + "/" + image_name <<
>> std::endl;
>>
>>       image_writer->SetFileName( image_path + "/" + image_name );
>>
>>       image_writer->SetInput( mesh_filter->GetOutput() );
>>
>>       image_writer->Update();
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -----------------------------------------------
>>
>> Noura Azzabou, PhD
>> Labo RMN AIM-CEA
>> Institut de Myologie - Bat Babinski
>> G.H. Pitie-Salpetriere, 83 Bd Hopital
>> 75651 Paris CEDEX 13, France
>> Tél. : 33 (0)1 42 16 58 92
>> Fax : 33 (0) 1 42 16 58 97
>>
>>
>>
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