[Insight-users] output image with different grey levels

[Giorgos Pichis]

Hi Luis,
Here is the code I used. It is the example ResampleImageFilter5 with a
change in the transform.
The images were dicom mammography 3d images.
The same problem appeared when I used .vtk 3d images . I didnt changed
the input and output pixel type

Thanks ,
Giorgos


#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkSimilarity3DTransform.h"

int main( int argc, char * argv[] )
{
  if( argc < 5 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << "  inputImageFile  outputImageFile  degrees
scale" << std::endl;
    return EXIT_FAILURE;
    }

  const     unsigned int   Dimension = 3;
  typedef   unsigned char  InputPixelType;
  typedef   unsigned char  OutputPixelType;

  typedef itk::Image< InputPixelType,  Dimension >   InputImageType;
  typedef itk::Image< OutputPixelType, Dimension >   OutputImageType;

  typedef itk::ImageFileReader< InputImageType  >  ReaderType;
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( argv[1] );
  writer->SetFileName( argv[2] );
    typedef itk::Similarity3DTransform< double >  TransformType;
  TransformType::Pointer transform = TransformType::New();

  typedef TransformType::ParametersType ParametersType;
  ParametersType parameters;
   double angleInDegrees = atof( argv[3] );

   double scale          = atof( argv[4] );

  transform->SetScale(scale);
  typedef itk::ResampleImageFilter<
                  InputImageType, OutputImageType >  FilterType;

  FilterType::Pointer filter = FilterType::New();


  typedef itk::LinearInterpolateImageFunction<
                       InputImageType, double >  InterpolatorType;
  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  filter->SetInterpolator( interpolator );

  filter->SetDefaultPixelValue( 0 );

  reader->Update();
  const InputImageType::SpacingType&
    spacing = reader->GetOutput()->GetSpacing();
  const InputImageType::PointType&
    origin  = reader->GetOutput()->GetOrigin();
  InputImageType::SizeType size =
      reader->GetOutput()->GetLargestPossibleRegion().GetSize();

  filter->SetOutputOrigin( origin );
  filter->SetOutputSpacing( spacing );
  filter->SetSize( size );


  filter->SetInput( reader->GetOutput() );
  writer->SetInput( filter->GetOutput() );
  TransformType::InputPointType rotationCenter;
  rotationCenter[0] = origin[0] + spacing[0] * size[0] / 2.0;
  rotationCenter[1] = origin[1] + spacing[1] * size[1] / 2.0;
  rotationCenter[2] = origin[2] + spacing[2] * size[2] / 2.0;
  transform->SetCenter( rotationCenter );

  typedef TransformType::VersorType VersorType;
  typedef VersorType::VectorType VectorType;
  VersorType rotation;
  VectorType axis;
  axis[0]=0.0;
  axis[1]=0.0;
  axis[2]=1.0;
   double degreesToRadians = atan(1.0) / 45.0;
    const double angle = angleInDegrees * degreesToRadians;
 rotation.Set (axis, angle);
  transform->SetRotation( rotation );

  TransformType::OutputVectorType translation;

  translation[0] =   0.0;
  translation[1] =   0.0;
  translation[2] =   0.0;
  transform->SetTranslation (translation);


  filter->SetTransform( transform );

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception catched !" << std::endl;
    std::cerr << excep << std::endl;
    }
  return EXIT_SUCCESS;
}


On Fri, Mar 28, 2008 at 6:18 PM, Luis Ibanez <luis.ibanez at kitware.com>
wrote:

> Hi Giorgos,
>
> 1) How different are the intensities of the output image ?
>
> 2) What Transform are you using ?
>
> 3) What interpolator are you using ?
>
> 4) What image type did you defined for the input ?
>
> 5) What image type did you defined for the output ?
>
> 6) What is the modality of the input image ?
>
> ...
>
> 7) Please post your code to the list.
>
>
>   Thanks
>
>
>      Luis
>
>
> -----------------------
> Giorgos Pichis wrote:
> > Hi there,
> > I tried to resample a 3d image (.vtk) with a transformation,
> > but the output image (  writer->SetInput(filter->GetOutput() );   )
> > had different intensity values than the input image.
> > Do you know what might be the problem?
> > Thanks
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
>
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