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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: DeformableRegistration6.cxx,v $
  Language:  C++
  Date:      $Date: 2006/05/14 12:16:22 $
  Version:   $Revision: 1.12 $

  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.

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

// This example is based on the example program DeformableRegistration6.cxx
// but using a modified Thin Plate Spline transform.  It is intended as an
// example to support the modified Kernel Transform classes presented in 
// Brooks, R., Arbel. T.  "Improvements to the itk::KernelTransform and its
// subclasses".

#include "itkImageRegistrationMethod.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkImage.h"
#include "itkThinPlateSplineKernelTransform2.h"
#include "itkLBFGSBOptimizer.h"  // this is changed from the example.. this one is more reliable


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

#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkSquaredDifferenceImageFilter.h"




int main( int argc, char *argv[] )
{
  if( argc < 4 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " fixedPointsFile fixedImageFile  movingImageFile outputImagefile  ";
    std::cerr << " [differenceOutputfile] [differenceBeforeRegistration] ";
    std::cerr << " [deformationField] ";
    return 1;
    }
  
  const    unsigned int    ImageDimension = 2;
  typedef  float           PixelType;

  typedef itk::Image< PixelType, ImageDimension >  FixedImageType;
  typedef itk::Image< PixelType, ImageDimension >  MovingImageType;

  const unsigned int SpaceDimension = ImageDimension;
  typedef double CoordinateRepType;

  typedef itk::ThinPlateSplineKernelTransform2<
                            CoordinateRepType,
                            ImageDimension>     TransformType;


  typedef itk::LBFGSBOptimizer       OptimizerType;


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

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

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

  typedef   itk::Point< CoordinateRepType,
                                  ImageDimension >  PointType;
  typedef   TransformType::PointSetType      PointSetType;
  typedef   PointSetType::Pointer            PointSetPointer;
  typedef   PointSetType::PointIdentifier  PointIdType;
  
  
  
  MetricType::Pointer         metric        = MetricType::New();
  OptimizerType::Pointer      optimizer     = OptimizerType::New();
  InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
  RegistrationType::Pointer   registration  = RegistrationType::New();
  

  registration->SetMetric(        metric        );
  registration->SetOptimizer(     optimizer     );
  registration->SetInterpolator(  interpolator  );


  
  TransformType::Pointer  transform = TransformType::New();
  registration->SetTransform( transform );
  
  typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
  typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;

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

  fixedImageReader->SetFileName(  argv[2] );
  movingImageReader->SetFileName( argv[3] );

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

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

  fixedImageReader->Update();

  FixedImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
  
 registration->SetFixedImageRegion( fixedRegion );

  //  Here we define the parameters (ie, the points) of the TPS
 
  PointSetType::Pointer landMarks = PointSetType::New();
  PointType p1;    
  PointSetType::PointsContainer::Pointer landMarkContainer = 
                                   landMarks->GetPoints();

  PointIdType id = itk::NumericTraits< PointIdType >::Zero;

  // Read in the list of landmarks
  std::ifstream infile;
  infile.open( argv[1] );
  int pointCount=0;
  while (!infile.eof())
    {
    infile >>  p1[0] >> p1[1] ;
    landMarkContainer->InsertElement( id, p1 );
	id++;
	pointCount++;
    } 
  infile.close();
  std::cout<<pointCount<<" points read from file"<<std::endl;
  transform->SetSourceLandmarks(landMarks);
  
  transform->SetIdentity();  // copies the source landmarks to the target

  registration->SetInitialTransformParameters( transform->GetParameters() );


  			OptimizerType::BoundSelectionType boundSelect( pointCount*2);
			OptimizerType::BoundValueType upperBound( pointCount*2);
			OptimizerType::BoundValueType lowerBound( pointCount*2);

			boundSelect.Fill( 0 );
			upperBound.Fill( 0.0 );
			lowerBound.Fill( 0.0 );

			optimizer->SetBoundSelection( boundSelect );
			optimizer->SetUpperBound( upperBound );
			optimizer->SetLowerBound( lowerBound );
			optimizer->SetCostFunctionConvergenceFactor( 0.001 );
			optimizer->SetProjectedGradientTolerance( 0.05 );
			optimizer->SetMaximumNumberOfIterations( 500 );
			optimizer->SetMaximumNumberOfEvaluations( 1000 );
			optimizer->SetMaximumNumberOfCorrections( 12 );


  std::cout << "Starting Registration " << std::endl;

  try 
    { 
    registration->StartRegistration(); 
    } 
  catch( itk::ExceptionObject & err ) 
    { 
    std::cerr << "ExceptionObject caught !" << std::endl; 
    std::cerr << err << std::endl; 
    return -1;
    } 
  
  transform->SetParameters( registration->GetLastTransformParameters() );

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

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

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

  resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetDefaultPixelValue( 100 );
  
  typedef  unsigned char  OutputPixelType;

  typedef itk::Image< OutputPixelType, ImageDimension > 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[4] );


  caster->SetInput( resample->GetOutput() );
  writer->SetInput( caster->GetOutput()   );


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


  typedef itk::SquaredDifferenceImageFilter< 
                                  FixedImageType, 
                                  FixedImageType, 
                                  OutputImageType > DifferenceFilterType;

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

  WriterType::Pointer writer2 = WriterType::New();
  writer2->SetInput( difference->GetOutput() );  
  

  // Compute the difference image between the 
  // fixed and resampled moving image.
  if( argc >= 6 )
    {
    difference->SetInput1( fixedImageReader->GetOutput() );
    difference->SetInput2( resample->GetOutput() );
    writer2->SetFileName( argv[5] );
    try
      {
      writer2->Update();
      }
    catch( itk::ExceptionObject & err ) 
      { 
      std::cerr << "ExceptionObject caught !" << std::endl; 
      std::cerr << err << std::endl; 
      return -1;
      } 
    }


  // Compute the difference image between the 
  // fixed and moving image before registration.
  if( argc >= 7 )
    {
    writer2->SetFileName( argv[6] );
    difference->SetInput1( fixedImageReader->GetOutput() );
    difference->SetInput2( movingImageReader->GetOutput() );
    try
      {
      writer2->Update();
      }
    catch( itk::ExceptionObject & err ) 
      { 
      std::cerr << "ExceptionObject caught !" << std::endl; 
      std::cerr << err << std::endl; 
      return -1;
      } 
    }



  // Generate the explicit deformation field resulting from 
  // the registration.

  typedef itk::Vector< float, ImageDimension >  VectorType;
  typedef itk::Image< VectorType, ImageDimension >  DeformationFieldType;

  DeformationFieldType::Pointer field = DeformationFieldType::New();
  field->SetRegions( fixedRegion );
  field->SetOrigin( fixedImage->GetOrigin() );
  field->SetSpacing( fixedImage->GetSpacing() );
  field->Allocate();

  typedef itk::ImageRegionIterator< DeformationFieldType > FieldIterator;
  FieldIterator fi( field, fixedRegion );

  fi.GoToBegin();

  TransformType::InputPointType  fixedPoint;
  TransformType::OutputPointType movingPoint;
  DeformationFieldType::IndexType index;

  VectorType displacement;

  while( ! fi.IsAtEnd() )
    {
    index = fi.GetIndex();
    field->TransformIndexToPhysicalPoint( index, fixedPoint );
    movingPoint = transform->TransformPoint( fixedPoint );
    displacement[0] = movingPoint[0] - fixedPoint[0];
    displacement[1] = movingPoint[1] - fixedPoint[1];
    fi.Set( displacement );
    ++fi;
    }



  typedef itk::ImageFileWriter< DeformationFieldType >  FieldWriterType;
  FieldWriterType::Pointer fieldWriter = FieldWriterType::New();

  fieldWriter->SetInput( field );

  if( argc >= 8 )
    {
    fieldWriter->SetFileName( argv[7] );
    try
      {
      fieldWriter->Update();
      }
    catch( itk::ExceptionObject & excp )
      {
      std::cerr << "Exception thrown " << std::endl;
      std::cerr << excp << std::endl;
      return EXIT_FAILURE;
      }
    }

  return 0;
}