[Insight-users] replacing the pixels of a DICOM image by a RAW FILE

[Stéphane CALANDE]

If someone is interrested, here is the code of a program that takes as input
:

> a repertory of a DICOM series
> a volume .MHD having the same resolution, spacing, origin, number of
slices,... than the series (containing )
> an output directory

an that gives, as output, a DICOM Series with the headers of the first DICOM
series but with the pixels of the volume MHD

(It's a modification of the code
"Examples/IO/DicomSeriesReadSeriesWrite.cxx")

++

Stéphane


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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif


#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
#include <vector>
#include <itksys/SystemTools.hxx>

int main( int argc, char* argv[] )
{
  if( argc < 4 )
    {
    std::cerr << "Usage: " << argv[0] <<
      " DicomDirectory_having_good_headers
MHD_volume_to_convert_to_DICOMseies OutputDicomDirectory" << std::endl;
    return EXIT_FAILURE;
    }


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

  typedef itk::Image< PixelType, Dimension >      ImageType;
  typedef itk::ImageSeriesReader< ImageType >     ReaderType;
  typedef itk::ImageFileReader< ImageType >       ReaderMHDType;
  typedef itk::GDCMImageIO                        ImageIOType;
  typedef itk::GDCMSeriesFileNames                NamesGeneratorType;


  ImageIOType::Pointer gdcmIO = ImageIOType::New();
  NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();


  namesGenerator->SetInputDirectory( argv[1] );

  const ReaderType::FileNamesContainer & filenames =
                            namesGenerator->GetInputFileNames();


  unsigned int numberOfFilenames =  filenames.size();
  std::cout << numberOfFilenames << std::endl;
  for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
    {
    std::cout << "filename # " << fni << " = ";
    std::cout << filenames[fni] << std::endl;
    }

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

  reader->SetImageIO( gdcmIO ); // ici on précise qu'on est en train de lire
une image au format DICOM
  reader->SetFileNames( filenames );

  try
    {
    reader->Update();
    }
  catch (itk::ExceptionObject &excp)
    {
    std::cerr << "Exception thrown while writing the image" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

    // à partir d'ici, reader->getOutput = le volume chargé en mémoire
contenant toutes les slices

    // ici on va loader le volume MHD

    ReaderMHDType::Pointer readerMHD = ReaderMHDType::New();
    readerMHD->SetFileName( argv[2] );

  const char * outputDirectory = argv[3];

  itksys::SystemTools::MakeDirectory( outputDirectory );

  typedef signed short    OutputPixelType;
  const unsigned int      OutputDimension = 2;

  typedef itk::Image< OutputPixelType, OutputDimension >    Image2DType;

  typedef itk::ImageSeriesWriter<
                             ImageType, Image2DType >  SeriesWriterType;

  SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();

  seriesWriter->SetInput( readerMHD->GetOutput() ); // ici on écrit le
volume du fichier MHD au lieu de l'original
  seriesWriter->SetImageIO( gdcmIO ); // ici on précise qu'on va écrire une
image au format DICOM

  namesGenerator->SetOutputDirectory( outputDirectory );

  seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );

  // l'instruction qui suit est très importante, elle copie toutes les infos
provenant des headers DICOM (renseignements patients,...)
  // et ici, on prend bien le bon reader (celui de la série DICOM qu'on a
chargé au tout début)
  seriesWriter->SetMetaDataDictionaryArray(
                        reader->GetMetaDataDictionaryArray() );

  try
    {
    seriesWriter->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown while writing the series " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

  return EXIT_SUCCESS;
}
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