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




#include "itkImageRegistrationMethod.h"
#include "itkTranslationTransform.h"
#include "itkGradientDifferenceImageToImageMetric.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkImage.h"

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

#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkCommand.h"

class CommandIterationUpdate : public itk::Command 
{
public:
  typedef  CommandIterationUpdate   Self;
  typedef  itk::Command             Superclass;
  typedef itk::SmartPointer<Self>  Pointer;
  itkNewMacro( Self );

protected:
  CommandIterationUpdate() {};
 

public:
  typedef itk::RegularStepGradientDescentOptimizer     OptimizerType;
  typedef const OptimizerType                         *OptimizerPointer;

  void Execute(itk::Object *caller, const itk::EventObject & event)
    {
    Execute( (const itk::Object *)caller, event);
    }

  void Execute(const itk::Object * object, const itk::EventObject & event)
    {
    OptimizerPointer optimizer = 
                         dynamic_cast< OptimizerPointer >( object );
    if( ! itk::IterationEvent().CheckEvent( &event ) )
      {
      return;
      }
      std::cout << optimizer->GetCurrentIteration() << " = ";
      std::cout << optimizer->GetValue() << " : ";
      std::cout << optimizer->GetCurrentPosition() << std::endl;
  }
   
};


int main( int argc, char *argv[] )
{
  if( argc < 3 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " fixedImageFile  movingImageFile ";
    std::cerr << "outputImagefile" << std::endl;
    std::cerr << "[initialTx] [initialTy]" << std::endl;
    return EXIT_FAILURE;
    }
  
  const    unsigned int    Dimension = 3;
  typedef  float  PixelType;
  
  typedef itk::Image< PixelType, Dimension >  FixedImageType;
  typedef itk::Image< PixelType, Dimension >  MovingImageType;

  typedef itk::TranslationTransform< double, Dimension > TransformType;

  typedef itk::RegularStepGradientDescentOptimizer       OptimizerType;

  typedef itk::LinearInterpolateImageFunction< 
                                    MovingImageType,
                                    double             > InterpolatorType;

  typedef itk::ImageRegistrationMethod< 
                                    FixedImageType, 
                                    MovingImageType   >  RegistrationType;

  typedef itk::GradientDifferenceImageToImageMetric< 
                                      FixedImageType, 
                                      MovingImageType >  MetricType;

  TransformType::Pointer      transform     = TransformType::New();
  OptimizerType::Pointer      optimizer     = OptimizerType::New();
  InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
  RegistrationType::Pointer   registration  = RegistrationType::New();

  registration->SetOptimizer(     optimizer     );
  registration->SetTransform(     transform     );
  registration->SetInterpolator(  interpolator  );

  MetricType::Pointer         metric        = MetricType::New();
  
  metric->SetDerivativeDelta( 0.5 );

  registration->SetMetric( metric  );

  typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
  typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;

  FixedImageReaderType::Pointer  fixedImageReader  = FixedImageReaderType::New();
  MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();

  fixedImageReader->SetFileName(  argv[1] );
  movingImageReader->SetFileName( argv[2] );

  registration->SetFixedImage(    fixedImageReader->GetOutput()    );
  registration->SetMovingImage(   movingImageReader->GetOutput()   );

  fixedImageReader->Update(); // This is needed to make the BufferedRegion below valid.

  registration->SetFixedImageRegion( 
       fixedImageReader->GetOutput()->GetBufferedRegion() );

  typedef RegistrationType::ParametersType ParametersType;
  ParametersType initialParameters( transform->GetNumberOfParameters() );

  initialParameters[0] = 0.0;  // Initial offset in mm along X
  initialParameters[1] = 0.0;  // Initial offset in mm along Y
  initialParameters[2] = 0.0;  // Initial offset in mm along Z//
  
  if( argc > 4 )
    {
    initialParameters[0] = atof( argv[4] );
    }

  if( argc > 5 )
    {
    initialParameters[1] = atof( argv[5] );
    }

  std::cout << "Initial parameters = " << initialParameters << std::endl;

  registration->SetInitialTransformParameters( initialParameters ); 

  optimizer->SetMaximumStepLength( 1.0 );
  optimizer->SetMinimumStepLength( 0.001 );
  optimizer->SetNumberOfIterations( 200 );
  optimizer->SetGradientMagnitudeTolerance( 1e-40 ); //1e-40

  optimizer->MaximizeOn();


  CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
  optimizer->AddObserver( itk::IterationEvent(), observer );

  try 
    { 
    registration->StartRegistration(); 
    } 
  catch( itk::ExceptionObject & err ) 
    { 
    std::cout << "ExceptionObject caught !" << std::endl; 
    std::cout << err << std::endl; 
    return EXIT_FAILURE;
    } 


  ParametersType finalParameters = registration->GetLastTransformParameters();
  
  const double TranslationAlongX = finalParameters[0];
  const double TranslationAlongY = finalParameters[1];
  const double TranslationAlongZ = finalParameters[2];//
  
  const unsigned int numberOfIterations = optimizer->GetCurrentIteration();
  
  const double bestValue = optimizer->GetValue();

  std::cout << "Registration done !" << std::endl;
  std::cout << "Stopping condition   = " << optimizer->GetStopCondition() << std::endl;
  std::cout << "Number of iterations = " << numberOfIterations << std::endl;
  std::cout << "Translation along X  = " << TranslationAlongX << std::endl;
  std::cout << "Translation along Y  = " << TranslationAlongY << std::endl;
  std::cout << "Optimal metric value = " << bestValue << std::endl;



  typedef itk::ResampleImageFilter<
                            MovingImageType, 
                            FixedImageType >    ResampleFilterType;

  TransformType::Pointer finalTransform = TransformType::New();

  finalTransform->SetParameters( finalParameters );

  ResampleFilterType::Pointer resample = ResampleFilterType::New();

  resample->SetTransform( finalTransform );
  resample->SetInput( movingImageReader->GetOutput() );

  FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();

  resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetOutputDirection( fixedImage->GetDirection() );
  resample->SetDefaultPixelValue( 100 );



  typedef  float  OutputPixelType;

  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
  
  typedef itk::CastImageFilter< 
                        FixedImageType,
                        OutputImageType > CastFilterType;
                    
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;

  WriterType::Pointer      writer =  WriterType::New();
  CastFilterType::Pointer  caster =  CastFilterType::New();


  writer->SetFileName( argv[3] );
  
  caster->SetInput( resample->GetOutput() );
  writer->SetInput( caster->GetOutput()   );
  writer->Update();


  return EXIT_SUCCESS;
}