/*=========================================================================

  Program: GDCM (Grassroots DICOM). A DICOM library

  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#include "vtkGDCMImageReader.h"
#include "vtkGDCMImageWriter.h"
#include "vtkImageData.h"
#include "vtkImageCast.h"
#include "vtkPointData.h"
#include "vtkBitArray.h"
#include "vtkUnsignedCharArray.h"

int main(int argc, char *argv[])
{
  if( argc < 3 )
    {
    return 1;
    }
  const char *filename = argv[1];
  const char *outfilename = argv[2];

  vtkGDCMImageReader *reader = vtkGDCMImageReader::New();
  reader->SetFileName( filename );
  reader->Update();
  //reader->GetOutput()->Print( std::cout );

  vtkDataArray* array = reader->GetOutput()->GetPointData()->GetScalars();
  vtkBitArray *barray = vtkBitArray::SafeDownCast( array );
  if( !barray ) return false;
  vtkIdType nvalues = array->GetNumberOfTuples();
  vtkUnsignedCharArray *uarray = vtkUnsignedCharArray::New();
  uarray->SetNumberOfTuples( nvalues );
  for(vtkIdType i = 0; i < nvalues; ++i)
    {
    uarray->SetValue( i, (unsigned char)barray->GetValue(i) );
    }

  vtkImageData *copy = vtkImageData::New();
  // http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Changes_to_Scalars_Manipulation_Functions#AllocateScalars.28.29
  copy->SetExtent( reader->GetOutput()->GetExtent() );
#if (VTK_MAJOR_VERSION >= 6)
  copy->AllocateScalars(VTK_UNSIGNED_CHAR, 3);
#else
  copy->SetScalarType( VTK_UNSIGNED_CHAR );
  copy->AllocateScalars();
#endif

  //uarray->Print( std::cout );
  //copy->GetPointData()->GetScalars()->Print( std::cout );
  copy->GetPointData()->SetScalars( uarray );
  uarray->Delete();

  vtkGDCMImageWriter *writer = vtkGDCMImageWriter::New();
  writer->SetFileName( outfilename );
  //writer->SetInput( cast->GetOutput() );
#if (VTK_MAJOR_VERSION >= 6)
  writer->SetInputData( copy );
#else
  writer->SetInput( copy );
#endif
  writer->SetImageFormat( reader->GetImageFormat() );
  writer->SetMedicalImageProperties( reader->GetMedicalImageProperties() );
  writer->SetDirectionCosines( reader->GetDirectionCosines() );
  writer->SetShift( reader->GetShift() );
  writer->SetScale( reader->GetScale() );
  writer->SetFileDimensionality( reader->GetFileDimensionality( ) );
  writer->Write();

  reader->Delete();
  copy->Delete();
  writer->Delete();

  return 0;
}