[Insight-users] Is it silly to attempt this ?

[Emma Ryan]

Hi,
 
  I am trying to read in a 3D deformationField.vtk file and apply it to a 3D image. To read the deformation field, I use ImageFileReader <deformafieldType>  and then connect the output of this to the warper.

The code for this is available below.  It seems to take forever to read the deformation field file.  Even after 2 hours, the reading is not complete. What is going on ?  Any clues ?

Thanks,
Emma


#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#include "itkImageFileReader.h" 
#include "itkImageFileWriter.h" 

#include "itkImageRegionIterator.h"


#include "itkCastImageFilter.h"
#include "itkWarpImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"

#include "itkSquaredDifferenceImageFilter.h"
#include "itkCheckerBoardImageFilter.h"
#include "itkTimeProbe.h"       

#include "itkImageRegionIteratorWithIndex.h"
#include "itkPointSet.h"
#include <fstream>



int main( int argc, char *argv[] )
{
    if( argc < 4 )
    {
        std::cerr << "Missing Parameters " << std::endl;
        std::cerr << "Usage: " << argv[0];
        std::cerr << " fixedImagefile movingImageFile deformField.vtk ";
        std::cerr << " outputImageFile " << std::endl;
        return 1;
    }

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


    typedef itk::Image< PixelType, Dimension >  FixedImageType;
    typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
    FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New();
    fixedImageReader->SetFileName( argv[1] );

    
    typedef itk::Image< PixelType, Dimension >  MovingImageType;
    typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
    MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
    movingImageReader->SetFileName( argv[2] );

        typedef itk::Vector< float, Dimension >    VectorPixelType;
    typedef itk::Image<  VectorPixelType, Dimension > DeformationFieldType;

    typedef itk::ImageFileReader< DeformationFieldType >  FieldReaderType;
    FieldReaderType::Pointer fieldReader = FieldReaderType::New();

    fieldReader->SetFileName( argv[3] );

   
   try {

    fieldReader->Update();
   }

   catch ( itk::ExceptionObject & err ) 
   {
    std::cerr << "ExceptionObject caught !" << std::endl; 
    std::cerr << err << std::endl; 
    return -1;
    } 


    
    typedef itk::WarpImageFilter<MovingImageType, MovingImageType,DeformationFieldType  >     WarperType;
    typedef itk::LinearInterpolateImageFunction<MovingImageType, double  >  InterpolatorType;
    WarperType::Pointer warper = WarperType::New();
    InterpolatorType::Pointer interpolator = InterpolatorType::New();
    FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();

   
    warper->SetInput( movingImageReader->GetOutput() );
    warper->SetInterpolator( interpolator );
    warper->SetOutputSpacing( fixedImage->GetSpacing() );
    warper->SetOutputOrigin( fixedImage->GetOrigin() );

    warper->SetDeformationField( fieldReader->GetOutput() ); 

  
    typedef  unsigned char  OutputPixelType;
    typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
    typedef itk::CastImageFilter< 
        MovingImageType,
        OutputImageType > CastFilterType;
    typedef itk::ImageFileWriter< OutputImageType >  WriterType;

  
    WriterType::Pointer      writer =  WriterType::New();
    CastFilterType::Pointer  caster =  CastFilterType::New();

    writer->SetFileName( argv[4] );

    
    caster->SetInput( warper->GetOutput() );
    writer->SetInput( caster->GetOutput()   );
    writer->Update();

   
    return 0;
}






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