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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: HomogeneousImageRegistration.cxx,v $
  Language:  C++
  Date:      $Date: 2007-03-14 12:37:08 $
  Version:   $Revision: 1.1 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 notices for more information.

=========================================================================

  This example provided by Rupert Brooks, McGill University.  This example 
  based closely on Examples/Registration/ImageRegistration3.cxx

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



#include "itkImageRegistrationMethod.h"
// note use of Homogeneous Transform
#include "itkHomogeneousTransform.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkSubtractImageFilter.h"
#include "itkRescaleIntensityImageFilter.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 [differenceImage]" << std::endl;
    return 1;
    }
  
  const    unsigned int    Dimension = 2;
  typedef  unsigned short  PixelType;
  
  typedef itk::Image< PixelType, Dimension >  FixedImageType;
  typedef itk::Image< PixelType, Dimension >  MovingImageType;

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

  typedef itk::RegularStepGradientDescentOptimizer       OptimizerType;

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

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

  typedef itk::MeanSquaresImageToImageMetric< 
                                      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();
  
  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;
  
  transform->SetIdentity();

  // set the centre to be the centre of the image
  TransformType::InputPointType centre;
  FixedImageType::SizeType size=fixedImageReader->GetOutput()->GetLargestPossibleRegion().GetSize();
  centre[0]=size[0]/2;
  centre[1]=size[1]/2;
  transform->SetCenter(centre);

  ParametersType initialParameters=transform->GetParameters();

  registration->SetInitialTransformParameters( initialParameters );

  typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
  const double baseScale = 2500.0;

  optimizerScales[0] = baseScale;
  optimizerScales[1] = baseScale;
  optimizerScales[2] = baseScale;
  optimizerScales[3] = baseScale;
  optimizerScales[4] = 1;
  optimizerScales[5] = 1;
  optimizerScales[6] = baseScale*10000;  // the transform is particularly sensitive
  optimizerScales[7] = baseScale*10000;  // to the elation parameters

  optimizer->SetScales( optimizerScales );
 
  optimizer->SetMaximumStepLength( 4.00 );  
  optimizer->SetMinimumStepLength( 0.01 );
  optimizer->SetNumberOfIterations( 200 );

  optimizer->MaximizeOff();


  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 -1;
    } 


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

  std::cout << "Registration done !" << std::endl;
  std::cout << "Number of iterations = " << numberOfIterations << std::endl;
  std::cout << "Parameters: "<<finalParameters;
  std::cout << "Optimal metric value = " << bestValue << std::endl;


  // Prepare the resampling filter in order to map the moving image.
  //
  typedef itk::ResampleImageFilter< 
                            MovingImageType, 
                            FixedImageType >    ResampleFilterType;

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

  finalTransform->SetParameters( finalParameters );
  finalTransform->SetCenter(transform->GetCenter()); //you need the center to be the same,
                                                     // or the transform is not really the same

  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->SetDefaultPixelValue( 0 );


  // Prepare a writer and caster filters to send the resampled moving image to
  // a file
  //
  typedef  unsigned char  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();



  typedef itk::Image< float, Dimension > DifferenceImageType;

  typedef itk::SubtractImageFilter< 
                           FixedImageType, 
                           FixedImageType, 
                           DifferenceImageType > DifferenceFilterType;

  DifferenceFilterType::Pointer difference = DifferenceFilterType::New();

  typedef  unsigned char  OutputPixelType;

  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
  
  typedef itk::RescaleIntensityImageFilter< 
                                  DifferenceImageType, 
                                  OutputImageType >   RescalerType;

  RescalerType::Pointer intensityRescaler = RescalerType::New();

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

  difference->SetInput1( fixedImageReader->GetOutput() );
  difference->SetInput2( resample->GetOutput() );

  resample->SetDefaultPixelValue( 1 );

  intensityRescaler->SetInput( difference->GetOutput() );  

  typedef itk::ImageFileWriter< OutputImageType >  WriterType;

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

  writer2->SetInput( intensityRescaler->GetOutput() );


  try
    {
    // Compute the difference image between the 
    // fixed and moving image after registration.
    if( argc > 4 )
      {
      writer2->SetFileName( argv[4] );
      writer2->Update();
      }

    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Error while writing difference images" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }






  return 0;
}