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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

/** \brief read DICOM CT and PET series into  volumes and then save these volumes in another
*  file format (MetaImage).
*/
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkMetaDataDictionary.h"
#include "itkMetaDataObject.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"

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

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


 // define the pixel type and dimension of the image to be read. 
  typedef signed short    PixelType;
  const unsigned int      Dimension = 3;


  typedef itk::Image< PixelType, Dimension >         ImageType;
 
//use the image type for instantiating the type of the series reader and
// for constructing one object of its type.

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

// A GDCMImageIO object is created and connected to the reader to
// to process the Dicom format image
  typedef itk::GDCMImageIO       ImageIOType;
  ImageIOType::Pointer dicomIO = ImageIOType::New();
  
  reader->SetImageIO( dicomIO );

// read a DICOM series. (identify from a given directory the set of
// filenames that belong together to the same volumetric image) we call the 
// \code{SetUseSeriesDetails(true)} function that tells the GDCMSereiesFileNames 
// object to use additional DICOM information to distinguish unique volumes
//  within the directory.  

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

  nameGenerator->SetUseSeriesDetails( true );
  nameGenerator->SetDirectory( argv[1] );  

  try
    {
    std::cout << std::endl << "The image directory: " << std::endl;
    std::cout << argv[1] << std::endl;
	
// GDCMSeriesFileNames object first identifies the list of DICOM series
// that are present in the given directory. 
    typedef std::vector< std::string >    SeriesIdContainer;
    const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
    
    SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
    SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
	
	std::string seriesIdentifier;
    typedef std::vector< std::string >   FileNamesContainer;
    FileNamesContainer fileNames;
	
	typedef itk::ImageFileWriter< ImageType > WriterType;
    WriterType::Pointer writer = WriterType::New();
	
	int k = 2;
	 do {
	  seriesIdentifier = seriesItr->c_str();
	  std::cout << std::endl;
      std::cout << "Now reading series: " << std::endl;
      std::cout << seriesIdentifier << std::endl;
      std::cout << std::endl;
	 
	  fileNames = nameGenerator->GetFileNames( seriesIdentifier );
	  reader->SetFileNames( fileNames );
	  try{
        reader->Update();
       }catch (itk::ExceptionObject &ex) {
        std::cout << ex << std::endl;
        return EXIT_FAILURE;
       }
	
	writer->SetFileName( argv[k] );

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

    std::cout  << "Writing the image as " << std::endl;
    std::cout  << argv[k] << std::endl << std::endl;
	try
	{
       writer->Update();   
	}catch (itk::ExceptionObject &ex)
	{
       std::cout << ex << std::endl;
       return EXIT_FAILURE;
	}
	  
	seriesItr++;
	k++;
	  
      } while( seriesItr != seriesEnd );

    } catch (itk::ExceptionObject &ex) 
	{
      std::cout << ex << std::endl;
    return EXIT_FAILURE;
    }

  return EXIT_SUCCESS;

}