/*=========================================================================
  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv

  Authors belong to:
  - University of LYON              http://www.universite-lyon.fr/
  - Léon Bérard cancer center       http://www.centreleonberard.fr
  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr

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

  It is distributed under dual licence

  - BSD        See included LICENSE.txt file
  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkMeanSquaresImageToImageMetricFor3DBLUTFFD.txx,v $
  Language:  C++
  Date:      $Date: 2010/06/14 17:32:07 $
  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.

=========================================================================*/
#ifndef __itkMeanSquaresImageToImageMetricFor3DBLUTFFD_txx
#define __itkMeanSquaresImageToImageMetricFor3DBLUTFFD_txx

// First make sure that the configuration is available.
// This line can be removed once the optimized versions
// gets integrated into the main directories.
#include "itkConfigure.h"

#include "itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx"

#include "itkMeanSquaresImageToImageMetricFor3DBLUTFFD.h"
#include "itkImageRegionConstIteratorWithIndex.h"

namespace itk
{

/**
 * Constructor
 */
template <class TFixedImage, class TMovingImage>
MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
::MeanSquaresImageToImageMetricFor3DBLUTFFD()
{
  itkDebugMacro("Constructor");
}

/**
 * Get the match Measure
 */
template <class TFixedImage, class TMovingImage>
typename MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>::MeasureType
MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
::GetValue( const TransformParametersType & parameters ) const
{

  itkDebugMacro("GetValue( " << parameters << " ) ");

  FixedImageConstPointer fixedImage = this->m_FixedImage;

  if( !fixedImage ) {
    itkExceptionMacro( << "Fixed image has not been assigned" );
  }

  typedef  itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;


  FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );

  typename FixedImageType::IndexType index;

  MeasureType measure = NumericTraits< MeasureType >::Zero;

  this->m_NumberOfPixelsCounted = 0;

  this->SetTransformParameters( parameters );

  while(!ti.IsAtEnd()) {

    index = ti.GetIndex();

    InputPointType inputPoint;
    fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );

    if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
      ++ti;
      continue;
    }

    OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );

    if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
      ++ti;
      continue;
    }

    if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
      const RealType movingValue  = this->m_Interpolator->Evaluate( transformedPoint );
      const RealType fixedValue   = ti.Get();
      this->m_NumberOfPixelsCounted++;
      const RealType diff = movingValue - fixedValue;
      measure += diff * diff;
    }

    ++ti;
  }

  if( !this->m_NumberOfPixelsCounted ) {
    itkExceptionMacro(<<"All the points mapped to outside of the moving image");
  } else {
    measure /= this->m_NumberOfPixelsCounted;
  }

  return measure;

}

/**
 * Get the Derivative Measure
 */
template < class TFixedImage, class TMovingImage>
void
MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
::GetDerivative( const TransformParametersType & parameters,
                 DerivativeType & derivative  ) const
{

  itkDebugMacro("GetDerivative( " << parameters << " ) ");

  if( !this->GetGradientImage() ) {
    itkExceptionMacro(<<"The gradient image is null, maybe you forgot to call Initialize()");
  }

  FixedImageConstPointer fixedImage = this->m_FixedImage;

  if( !fixedImage ) {
    itkExceptionMacro( << "Fixed image has not been assigned" );
  }

  const unsigned int ImageDimension = FixedImageType::ImageDimension;


  typedef  itk::ImageRegionConstIteratorWithIndex<
  FixedImageType> FixedIteratorType;

  typedef  itk::ImageRegionConstIteratorWithIndex<GradientImageType> GradientIteratorType;


  FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );

  typename FixedImageType::IndexType index;

  this->m_NumberOfPixelsCounted = 0;

  this->SetTransformParameters( parameters );

  const unsigned int ParametersDimension = this->GetNumberOfParameters();
  derivative = DerivativeType( ParametersDimension );
  derivative.Fill( NumericTraits<typename DerivativeType::ValueType>::Zero );

  ti.GoToBegin();

  while(!ti.IsAtEnd()) {

    index = ti.GetIndex();

    InputPointType inputPoint;
    fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );

    if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
      ++ti;
      continue;
    }

    OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );

    if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
      ++ti;
      continue;
    }

    if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
      const RealType movingValue  = this->m_Interpolator->Evaluate( transformedPoint );

      TransformJacobianType jacobian;
      this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );

      const RealType fixedValue     = ti.Value();
      this->m_NumberOfPixelsCounted++;
      const RealType diff = movingValue - fixedValue;

      // Get the gradient by NearestNeighboorInterpolation:
      // which is equivalent to round up the point components.
      typedef typename OutputPointType::CoordRepType CoordRepType;
      typedef ContinuousIndex<CoordRepType,MovingImageType::ImageDimension>
      MovingImageContinuousIndexType;

      MovingImageContinuousIndexType tempIndex;
      this->m_MovingImage->TransformPhysicalPointToContinuousIndex( transformedPoint, tempIndex );

      typename MovingImageType::IndexType mappedIndex;
      mappedIndex.CopyWithRound( tempIndex );

      const GradientPixelType gradient =
        this->GetGradientImage()->GetPixel( mappedIndex );

      for(unsigned int par=0; par<ParametersDimension; par++) {
        RealType sum = NumericTraits< RealType >::Zero;
        for(unsigned int dim=0; dim<ImageDimension; dim++) {
          sum += 2.0 * diff * jacobian( dim, par ) * gradient[dim];
        }
        derivative[par] += sum;
      }
    }

    ++ti;
  }

  if( !this->m_NumberOfPixelsCounted ) {
    itkExceptionMacro(<<"All the points mapped to outside of the moving image");
  } else {
    for(unsigned int i=0; i<ParametersDimension; i++) {
      derivative[i] /= this->m_NumberOfPixelsCounted;
    }
  }

}


/*
 * Get both the match Measure and theDerivative Measure
 */
template <class TFixedImage, class TMovingImage>
void
MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
::GetValueAndDerivative(const TransformParametersType & parameters,
                        MeasureType & value, DerivativeType  & derivative) const
{

  itkDebugMacro("GetValueAndDerivative( " << parameters << " ) ");

  if( !this->GetGradientImage() ) {
    itkExceptionMacro(<<"The gradient image is null, maybe you forgot to call Initialize()");
  }

  FixedImageConstPointer fixedImage = this->m_FixedImage;

  if( !fixedImage ) {
    itkExceptionMacro( << "Fixed image has not been assigned" );
  }

  const unsigned int ImageDimension = FixedImageType::ImageDimension;

  typedef  itk::ImageRegionConstIteratorWithIndex<
  FixedImageType> FixedIteratorType;

  typedef  itk::ImageRegionConstIteratorWithIndex<GradientImageType> GradientIteratorType;


  FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );

  typename FixedImageType::IndexType index;

  MeasureType measure = NumericTraits< MeasureType >::Zero;

  this->m_NumberOfPixelsCounted = 0;

  this->SetTransformParameters( parameters );

  const unsigned int ParametersDimension = this->GetNumberOfParameters();
  derivative = DerivativeType( ParametersDimension );
  derivative.Fill( NumericTraits<typename DerivativeType::ValueType>::Zero );

  ti.GoToBegin();

  while(!ti.IsAtEnd()) {

    index = ti.GetIndex();

    InputPointType inputPoint;
    fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );

    if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
      ++ti;
      continue;
    }

    OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );

    if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
      ++ti;
      continue;
    }

    if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
      const RealType movingValue  = this->m_Interpolator->Evaluate( transformedPoint );

      TransformJacobianType jacobian;
      this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );

      const RealType fixedValue     = ti.Value();
      this->m_NumberOfPixelsCounted++;

      const RealType diff = movingValue - fixedValue;

      measure += diff * diff;

      // Get the gradient by NearestNeighboorInterpolation:
      // which is equivalent to round up the point components.
      typedef typename OutputPointType::CoordRepType CoordRepType;
      typedef ContinuousIndex<CoordRepType,MovingImageType::ImageDimension>
      MovingImageContinuousIndexType;

      MovingImageContinuousIndexType tempIndex;
      this->m_MovingImage->TransformPhysicalPointToContinuousIndex( transformedPoint, tempIndex );

      typename MovingImageType::IndexType mappedIndex;
      mappedIndex.CopyWithRound( tempIndex );

      const GradientPixelType gradient =
        this->GetGradientImage()->GetPixel( mappedIndex );

      for(unsigned int par=0; par<ParametersDimension; par++) {
        RealType sum = NumericTraits< RealType >::Zero;
        for(unsigned int dim=0; dim<ImageDimension; dim++) {
          sum += 2.0 * diff * jacobian( dim, par ) * gradient[dim];
        }
        derivative[par] += sum;
      }
    }

    ++ti;
  }

  if( !this->m_NumberOfPixelsCounted ) {
    itkExceptionMacro(<<"All the points mapped to outside of the moving image");
  } else {
    for(unsigned int i=0; i<ParametersDimension; i++) {
      derivative[i] /= this->m_NumberOfPixelsCounted;
    }
    measure /= this->m_NumberOfPixelsCounted;
  }

  value = measure;

}

} // end namespace itk


#endif

#endif