[Insight-users] DICOM Reader Rescale Writer

[Ignacio García Fenoll]

Good evening, insight-users!!

I am trying to get a program that firstly read DICOM series from a
directory, later extract all the images without considering headings and at
last copy the image series (all the images png for example) into a new
directory. When I read the errors, the compilator shows that there is an
incompatibility of types, but I am not able to find what is the matter with
that. Could you help me?

This is my code:

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"

#include <list>
#include <fstream>
#include <vector>
#include <itksys/SystemTools.hxx>



int main( int argc, char* argv[] )
{
  if( argc < 3 )
    {
    std::cerr << "Usage: " << argv[0] <<
      " DicomDirectory  OutputPngSeriesDirectory" << 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::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 );
  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;
    }

  typedef signed short InputPixelType;
  const unsigned int   InputDimension = 2;

  typedef itk::Image< InputPixelType, InputDimension > InputImageType;


  typedef itk::ImageFileReader< InputImageType > ReaderType2;

  ReaderType::Pointer reader2 = ReaderType2::New();
  reader2->SetFileName(reader->GetOutput() );

  typedef itk::GDCMImageIO           ImageIOType;

  ImageIOType::Pointer gdcmImageIO = ImageIOType::New();

  reader2->SetImageIO( gdcmImageIO );


  try
    {
    reader2->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "exception in file reader " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }



  typedef unsigned char WritePixelType;

  typedef itk::Image< WritePixelType, 2 > WriteImageType;

  typedef itk::RescaleIntensityImageFilter<
               InputImageType, WriteImageType > RescaleFilterType;

  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

  rescaler->SetOutputMinimum(   0 );
  rescaler->SetOutputMaximum( 255 );


  typedef itk::ImageFileWriter< WriteImageType >  Writer2Type;

  Writer2Type::Pointer writer2 = Writer2Type::New();

  writer2->SetFileName( argv[2] );

  rescaler->SetInput( reader2->GetOutput() );
  writer2->SetInput( rescaler->GetOutput() );


  try
    {
    writer2->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }


  const char * outputDirectory = argv[2];

  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( reader2->GetOutput() );
  seriesWriter->SetImageIO( gdcmIO );

  namesGenerator->SetOutputDirectory( outputDirectory );

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

  seriesWriter->SetMetaDataDictionaryArray(
                        reader2->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;
}


Thank you very much!! I would be very grateful if you could help me a bit!!

Regards!

-- 
Ignacio García Fenoll
Grupo de Imágenes Médicas
Departamento de Teoría de la Señal y Comunicaciones
Universidad de Sevilla
e-mail: igfenoll at gmail.com
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