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

[Luis Ibanez]

Hi Emma,

The source code that you posted seems to be reasonable.


However, a duration of 2 hours for warping an image
sounds like an excesive time.


1) How big is your image ?
      pixels along X
      pixels along Y
      pixels along Z


2) How much RAM do you have ?


3) Have you checked if your computer
    is not swapping memory ?

    (you can check this on Windows by looking
     at the Task Manager, or in Linux by using
     the top tool, or the system information tool.)


Please let us know,


   Thanks


    Luis


----------------
Emma Ryan wrote:
> 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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