#include "itkTransform.h"
#include "itkTransformFileReader.h"
#include "itkCenteredSimilarity2DTransform.h"
#include "itkTransformFactory.h"
#include "itkSerialTransform.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"

int
main( const int argc, const char* argv[] )
{
  if( argc < 5 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " fixedImageFile  movingImageFile outputImagefile  ";
    std::cerr << " transformFile0 [transformFile1 ...] ";
    return 1;
    }

  const char* argvFixedImagePath = argv[1];
  const char* argvMovingImagePath = argv[2];
  const char* argvOutImagePath = argv[3];
  const int argcTransformList = 4;

  const unsigned int ImageDimension = 2;
  const unsigned int SpaceDimension = ImageDimension;
  typedef double CoordinateRepType;

  typedef unsigned char ReadPixelType;
  typedef itk::Image< ReadPixelType, ImageDimension >  ReadImageType;

  typedef unsigned char WritePixelType;
  typedef itk::Image< WritePixelType, ImageDimension >  WriteImageType;

  typedef itk::ImageFileReader< ReadImageType  > FixedImageReaderType;
  typedef itk::ImageFileReader< ReadImageType > MovingImageReaderType;
  
  FixedImageReaderType::Pointer  fixedImageReader  = FixedImageReaderType::New();
  MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();

  fixedImageReader->SetFileName(  argvFixedImagePath );
  fixedImageReader->Update();
  movingImageReader->SetFileName( argvMovingImagePath );
  
  typedef itk::SerialTransform<CoordinateRepType,ImageDimension> SerialTransformType;
  typedef SerialTransformType::TransformType TransformType;
  SerialTransformType::Pointer serialTransform = SerialTransformType::New();

  typedef itk::CenteredSimilarity2DTransform< CoordinateRepType > SimilarityTransformType;
  itk::TransformFactory<SimilarityTransformType>::RegisterTransform();

  typedef itk::TransformFileReader TransformReaderType;
  typedef TransformReaderType::TransformListType TransformListType;

  for ( int i = argcTransformList; i < argc; ++i )
    {
    TransformReaderType::Pointer transformReader = TransformReaderType::New();  
    transformReader->SetFileName( argv[i] );
    transformReader->Update();
    
    TransformReaderType::TransformListType* tlist = transformReader->GetTransformList();

    TransformReaderType::TransformListType::iterator it = tlist->begin();
    while ( it != tlist->end() )
      {
      // we have to dynamic_cast here because the reader does not store pointers to
      // the concrete transformation classes (ie., with the correct coordinate space
      // dimensions etc.)
      serialTransform->AddTransform( dynamic_cast<TransformType*>( (*it).GetPointer() ) );
      ++it;
      }
    }
  
  typedef itk::ResampleImageFilter<ReadImageType,WriteImageType> ResampleFilterType;
  ResampleFilterType::Pointer resample = ResampleFilterType::New();
  resample->SetTransform( serialTransform );
  resample->SetInput( movingImageReader->GetOutput() );

  ReadImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
  resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetDefaultPixelValue( 0 );  

  typedef itk::ImageFileWriter< WriteImageType >  WriterType;
  WriterType::Pointer writer =  WriterType::New();
  writer->SetFileName( argvOutImagePath );
  writer->SetInput( resample->GetOutput() );

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & err ) 
    { 
    std::cerr << "ExceptionObject caught !" << std::endl; 
    std::cerr << err << std::endl; 
    return -1;
    } 
   
  return 0;
}