[Insight-users] translating image volume using affine transformation

[michiel mentink]

Dear all,

I'm trying to make a simple function that translates a dicom volume by a
certain amount.
It first opens all dicom slides of an mri scan.

To do this, I pasted DicomSeriesReadImageWrite2.cxx and
ResampleImageFilter.cxx and adjusted
the latter so it accepts 3 dimensions instead of two and uses integer
instead of unsigned char.

The function compiles and a .vtk volume is written. However, there's no
image data in the file.
It does display all pixels with value 100, as I set by:
filter->SetDefaultPixelValue( 100 );

questions:
1) am I too naive to think that the ResampleImageFilter can easily be
extended from 2 to 3 dimensions?
2) if not, what did I do wrong?

I pasted the source code below.

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkOrientedImage.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"

#include "itkAffineTransform.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
// Software Guide : EndCodeSnippet

int main( int argc, char* argv[] )
{

  if( argc < 3 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " DicomDirectory  outputFileName  [seriesName]"
              << std::endl;
    return EXIT_FAILURE;
    }

  typedef signed short    PixelType;
  const unsigned int      Dimension = 3;

  typedef itk::OrientedImage< PixelType, Dimension >         ImageType;

  typedef itk::ImageSeriesReader< ImageType >        ReaderType;
  ReaderType::Pointer reader = ReaderType::New();

  typedef itk::GDCMImageIO       ImageIOType;
  ImageIOType::Pointer dicomIO = ImageIOType::New();

  reader->SetImageIO( dicomIO );

  typedef itk::GDCMSeriesFileNames NamesGeneratorType;
  NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();

  nameGenerator->SetUseSeriesDetails( true );
  nameGenerator->AddSeriesRestriction("0008|0021" );

  nameGenerator->SetDirectory( argv[1] );

  try
    {
    std::cout << std::endl << "The directory: " << std::endl;
    std::cout << std::endl << argv[1] << std::endl << std::endl;
    std::cout << "Contains the following DICOM Series: ";
    std::cout << std::endl << std::endl;

    typedef std::vector< std::string >    SeriesIdContainer;

    const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();

    SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
    SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
    while( seriesItr != seriesEnd )
      {
      std::cout << seriesItr->c_str() << std::endl;
      seriesItr++;
      }

    std::string seriesIdentifier;

    if( argc > 3 ) // If no optional series identifier
      {
      seriesIdentifier = argv[3];
      }
    else
      {
      seriesIdentifier = seriesUID.begin()->c_str();
      }

    std::cout << std::endl << std::endl;
    std::cout << "Now reading series: " << std::endl << std::endl;
    std::cout << seriesIdentifier << std::endl;
    std::cout << std::endl << std::endl;

    typedef std::vector< std::string >   FileNamesContainer;
    FileNamesContainer fileNames;

    fileNames = nameGenerator->GetFileNames( seriesIdentifier );
    reader->SetFileNames( fileNames );
    try
      {
      reader->Update();
      }
    catch (itk::ExceptionObject &ex)
      {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
      }
    }
  catch (itk::ExceptionObject &ex)
    {
    std::cout << ex << std::endl;
    return EXIT_FAILURE;
    }
//  return EXIT_SUCCESS;

//////////////////////////////////////////////////////////////////////////////////////
// FROM HERE ADJUSTED ResampleImageFilter.cxx CODE
/////////////////////////////////////////////////////////////////////////////////////

//  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::Image< PixelType, Dimension >   OutputImageType;
  // typedef itk::ImageFileReader< InputImageType  >  ReaderType;

  typedef itk::ImageFileWriter< ImageType >  WriterType;
  WriterType::Pointer writer = WriterType::New();


  writer->SetFileName( argv[2] );

//  typedef itk::ResampleImageFilter<ImageType,OutputImageType> FilterType;
  typedef itk::ResampleImageFilter<ImageType,ImageType> FilterType;
  FilterType::Pointer filter = FilterType::New();

  typedef itk::AffineTransform< double, Dimension >  TransformType;
  TransformType::Pointer transform = TransformType::New();
  filter->SetTransform( transform );


  typedef itk::NearestNeighborInterpolateImageFunction<ImageType, double >
InterpolatorType;
  InterpolatorType::Pointer interpolator = InterpolatorType::New();
  filter->SetInterpolator( interpolator );


  filter->SetDefaultPixelValue( 100 ); // if pixel in output image not
defined, what value?


  double spacing[ Dimension ];
  spacing[0] = 0.29; // pixel spacing in millimeters along X
  spacing[1] = 0.29; // pixel spacing in millimeters along Y
  spacing[2] = 3.3;

  filter->SetOutputSpacing( spacing );

  double origin[ Dimension ];
  origin[0] = 0.0;  // X space coordinate of origin
  origin[1] = 0.0;  // Y space coordinate of origin
  origin[2] = 0.0;

  filter->SetOutputOrigin( origin );
  ImageType::DirectionType direction;
  direction.SetIdentity();
  filter->SetOutputDirection( direction );
  ImageType::SizeType   size;

  size[0] = 560;  // number of pixels along X
  size[1] = 560;  // number of pixels along Y
  size[2] = 300;

  filter->SetSize( size );
  filter->SetInput( reader->GetOutput() );
//  writer->SetInput( filter->GetOutput() );
//  writer->Update();
  TransformType::OutputVectorType translation;
  translation[0] = 0;  // X translation in millimeters
  translation[1] = 0;  // Y translation in millimeters
  translation[2] = 0;

  transform->Translate( translation );
  // Software Guide : EndCodeSnippet

   writer->SetInput( filter->GetOutput() );

    std::cout  << "Writing the image as " << std::endl << std::endl;
    std::cout  << argv[2] << std::endl << std::endl;
    writer->Update();

}
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