[Insight-users] converting mesh to binary image

[Moti Freiman]

Hi,
I'm trying to convert a 3d surface (got as some segmentation result) to a
binary image, for comparison between different segmentations.
I build a mesh from points and triangles which I got and save it as a vtk
polygonal data. It performs well and I can visualize it properly using
paraview.
However, when I'm trying to convert it to a 3D binary volume using
itkTriangleMeshToBinaryImageFilter I got the following exception:

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-------------------------------------------------------------------------
ExceptionObject caught !

itk::ExceptionObject (012CFB38)
Location: "void __thiscall itk::TriangleMeshToBinaryImageFilter<class
itk::Mesh<unsigned char,3,class itk::DefaultStaticMeshTraits<unsigned
char,3,3,float,float,unsigned char> >,class itk::Image<unsigned char,3>
>::GenerateData(void)"
File:
e:\libs\insighttoolkit-3.10.0\code\basicfilters\itkTriangleMeshToBinaryImageFilter.txx
Line: 224
Description: itk::ERROR: TriangleMeshToBinaryImageFilter(038FD670): No Image
Indices Found.


Press any key to continue



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-------------------------------------------------------------------------

My code is below,

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code-------------------------------------------------------------------------
#include "itkVTKPolyDataWriter.h"
#include "itkVTKPolyDataReader.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkCastImageFilter.h"


#include "itkMesh.h"
#include "itkTriangleCell.h"
#include <fstream>


#include "itkTriangleMeshToBinaryImageFilter.h"



int main( int argc, char **argv )
{
    char *points_name = NULL, *faces_name = NULL, *output_mesh = NULL,
*input_image = NULL, *output_name = NULL;




    points_name  = argv[1];
    faces_name = argv[2];
    output_mesh  = argv[3];
    input_image = argv[4];
    output_name = argv[5];


    typedef short PixelType;
    typedef unsigned char OutputPixelType;
    const unsigned int          Dimension = 3;


    typedef itk::Mesh <OutputPixelType, Dimension> itkMeshType;

    itkMeshType::Pointer mesh = itkMeshType::New();



    std::fstream pointsReader;
    pointsReader.open (points_name, std::ios::in);
    int i=0;
    while (pointsReader.peek () != EOF)
    {
        itkMeshType::PointType p;
        pointsReader >> p[0] >> p[1] >> p[2];
        mesh->SetPoint (i,p);
        ++i;
    }
    pointsReader.close();

    typedef itkMeshType::CellType CellType;
    typedef itk::TriangleCell < CellType > FaceType;

    typedef CellType::CellAutoPointer CellAutoPointer;



    std::fstream facesReader;
    facesReader.open (faces_name, std::ios::in);

    i=0;
    while (facesReader.peek () != EOF)
    {
        int p[3];
        facesReader >> p[0] >> p[1] >> p[2];

        CellAutoPointer face;
        face.TakeOwnership( new FaceType );

        face->SetPointId (0, p[0]);
        face->SetPointId (1, p[1]);
        face->SetPointId (2, p[2]);

        mesh->SetCell (i,face);
        ++i;
    }
    facesReader.close();
    mesh->Update();






    typedef itk::VTKPolyDataWriter<itkMeshType> itkVTKPolyDataWriterType;

    itkVTKPolyDataWriterType::Pointer meshWriter =
itkVTKPolyDataWriterType::New();
    meshWriter->SetFileName( output_mesh );
    meshWriter->SetInput (mesh);
    try
    {
        meshWriter->Update();
    }
    catch ( itk::ExceptionObject &err)
    {
        std::cout << "ExceptionObject caught !" << std::endl;
        std::cout << err << std::endl;
        return -1;
    }




    typedef itk::Image< PixelType, Dimension > ImageType;
    typedef itk::Image< OutputPixelType, Dimension > OutputImageType;

    typedef itk::ImageFileReader< ImageType > ImageReaderType;





    // Read the input files
    ImageReaderType::Pointer reader = ImageReaderType::New();
    reader->SetFileName( input_image );
    try
    {
        reader->Update();
    }
    catch ( itk::ExceptionObject &err)
    {
        std::cout << "ExceptionObject caught !" << std::endl;
        std::cout << err << std::endl;
        return -1;
    }



    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();





    typedef itk::TriangleMeshToBinaryImageFilter <itkMeshType,
OutputImageType> itkTriangleMeshToBinaryImageFilterType;
    itkTriangleMeshToBinaryImageFilterType::Pointer meshFilter =
itkTriangleMeshToBinaryImageFilterType::New();
    meshFilter->SetTolerance (1.0);
    meshFilter->SetSpacing (orgSpacing);
    meshFilter->SetOrigin(orgOrigin);
    meshFilter->SetSize (orgSize);
    meshFilter->SetIndex (orgIndex);
    meshFilter->SetInput(mesh);


    try
    {
        meshFilter->Update();
    }
    catch ( itk::ExceptionObject &err )
    {
        std::cout << "ExceptionObject caught !" << std::endl;
        std::cout << err << std::endl;
        return -1;
    }




    // Write the output image containing the binary volume.
    typedef itk::ImageFileWriter< OutputImageType > WriterType;
    WriterType::Pointer writer = WriterType::New();
    writer->SetInput( meshFilter->GetOutput() );
    writer->SetFileName( output_name );
    try
    {
        writer->Update();
    }
    catch ( itk::ExceptionObject &err )
    {
        std::cout << "ExceptionObject caught !" << std::endl;
        std::cout << err << std::endl;
        return -1;
    }

    return 0;
}

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code-------------------------------------------------------------------------

Thanks for any help,
Moti
-- 
__
Moti Freiman, Ph.D Student.
Medical Image Processing and Computer-Assisted Surgery Laboratory.
School of Computer Science and Engineering.
The Hebrew University of Jerusalem Givat Ram, Jerusalem 91904, Israel
Phone: +(972)-2-658-5371 (laboratory)
WWW site: http://www.cs.huji.ac.il/~freiman
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