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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkInverseDeformationFieldImageFilter.txx,v $
  Language:  C++
  Date:      $Date: 2008-01-20 18:00:40 $
  Version:   $Revision: 1.6 $

  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 _itkInverseDeformationFieldImageFilter_txx
#define _itkInverseDeformationFieldImageFilter_txx

#include "itkInverseDeformationFieldImageFilter.h"
#include "itkObjectFactory.h"
#include "itkProgressReporter.h"
#include "itkThinPlateSplineKernelTransform.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkVectorResampleImageFilter.h"

namespace itk
{

/**
 * Initialize new instance
 */
template <class TInputImage, class TOutputImage>
InverseDeformationFieldImageFilter<TInputImage, TOutputImage>
::InverseDeformationFieldImageFilter()
{
  m_OutputSpacing.Fill(1.0);
  m_OutputOrigin.Fill(0.0);
  for (unsigned int i = 0; i < ImageDimension; i++)
    {
    m_Size[i] = 0;
    }
  
  typedef ThinPlateSplineKernelTransform< 
              double, 
              itkGetStaticConstMacro( ImageDimension ) >  DefaultTransformType;

  m_KernelTransform = DefaultTransformType::New();

  m_SubsamplingFactor = 16;
}


/**
 * Print out a description of self
 *
 * \todo Add details about this class
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage, TOutputImage>
::PrintSelf(std::ostream& os, Indent indent) const
{
  Superclass::PrintSelf(os,indent);

  os << indent << "Size:              " << m_Size << std::endl;
  os << indent << "OutputSpacing:     " << m_OutputSpacing << std::endl;
  os << indent << "OutputOrigin:      " << m_OutputOrigin << std::endl;
  os << indent << "KernelTransform:   " << m_KernelTransform.GetPointer() << std::endl;
  os << indent << "SubsamplingFactor: " << m_SubsamplingFactor << std::endl;

  return;
}



/**
 * Set the output image spacing.
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::SetOutputSpacing(const double* spacing)
{
  SpacingType s(spacing);
  this->SetOutputSpacing( s );
}


/**
 * Set the output image origin.
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::SetOutputOrigin(const double* origin)
{
  OriginPointType p(origin);
  this->SetOutputOrigin( p );
}



/**
 * Sub-sample the input deformation field and prepare the KernelBase
 * BSpline
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::PrepareKernelBaseSpline()
{

  typedef typename KernelTransformType::PointsContainer   LandmarkContainer;
  typedef typename LandmarkContainer::Pointer             LandmarkContainerPointer;

  // Source contains points with physical coordinates of the
  // destination displacement fields (the inverse field)
  LandmarkContainerPointer source = LandmarkContainer::New();

  // Target contains vectors (stored as points) indicating 
  // displacement in the inverse direction.
  LandmarkContainerPointer target = LandmarkContainer::New();


  typedef itk::VectorResampleImageFilter< 
                                InputImageType, 
                                InputImageType  > ResamplerType;

  typename ResamplerType::Pointer resampler = ResamplerType::New();

  const InputImageType * inputImage = this->GetInput();

  resampler->SetInput( inputImage );
  resampler->SetOutputOrigin( inputImage->GetOrigin() );

  typename InputImageType::SpacingType spacing = inputImage->GetSpacing();


  typedef typename InputImageType::RegionType InputRegionType;
  typedef typename InputImageType::SizeType   InputSizeType;
  typedef typename InputImageType::IndexType  InputIndexType;

  InputRegionType region;

  region = inputImage->GetLargestPossibleRegion();

  InputSizeType size = region.GetSize();

  for(unsigned int i=0; i < ImageDimension; i++)
    {
    size[i]    =  static_cast< typename InputSizeType::SizeValueType >( size[i] / m_SubsamplingFactor );
    spacing[i] *= m_SubsamplingFactor;
    }

  InputRegionType subsampledRegion;
  subsampledRegion.SetSize( size );
  subsampledRegion.SetIndex( region.GetIndex() );

  resampler->SetSize( size );
  resampler->SetOutputStartIndex( subsampledRegion.GetIndex() );
  resampler->SetOutputSpacing( spacing );

  resampler->Update();
 

  // allocate a landmark pair for each 
  // pixel in the subsampled field
  const unsigned long numberOfLandmarks = subsampledRegion.GetNumberOfPixels();
  source->Reserve( numberOfLandmarks );
  target->Reserve( numberOfLandmarks );


  const InputImageType * sampledInput = resampler->GetOutput();

  typedef ImageRegionConstIteratorWithIndex< InputImageType > IteratorType;

  unsigned int landmarkId = 0;

  IteratorType ot( sampledInput, subsampledRegion );
  ot.GoToBegin();

  OutputPixelType value;
  Point<double, ImageDimension> sourcePoint;
  Point<double, ImageDimension> targetPoint;

  while( !ot.IsAtEnd() )
    {
    value = ot.Get();
    sampledInput->TransformIndexToPhysicalPoint( ot.GetIndex(), sourcePoint );

    source->InsertElement( landmarkId,  sourcePoint );

    for(unsigned int i=0; i < ImageDimension; i++)
      {
      targetPoint[i] = -value[i];
      }
    target->InsertElement( landmarkId, targetPoint );  // revert direction of displacement

    ++landmarkId;
    ++ot;
    }

  itkDebugMacro( << "Number of Landmarks created = " <<  numberOfLandmarks );

  m_KernelTransform->GetTargetLandmarks()->SetPoints( target );
  m_KernelTransform->GetSourceLandmarks()->SetPoints( source );

  itkDebugMacro( << "Before ComputeWMatrix() ");
  
  m_KernelTransform->ComputeWMatrix();
  
  itkDebugMacro( << "After ComputeWMatrix() ");

}




/**
 * GenerateData
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::GenerateData()
{

  // First subsample the input deformation field in order to create
  // the KernelBased spline.
  this->PrepareKernelBaseSpline();

  itkDebugMacro(<<"Actually executing");

  // Get the output pointers
  OutputImageType *  outputPtr = this->GetOutput();

  outputPtr->SetBufferedRegion( outputPtr->GetRequestedRegion() );
  outputPtr->Allocate();

  // Create an iterator that will walk the output region for this thread.
  typedef ImageRegionIteratorWithIndex< 
                                  TOutputImage> OutputIterator;

  OutputImageRegionType region = outputPtr->GetRequestedRegion();

  OutputIterator outIt( outputPtr, region );

  // Define a few indices that will be used to translate from an input pixel
  // to an output pixel
  IndexType outputIndex;         // Index to current output pixel

  typedef typename KernelTransformType::InputPointType  InputPointType;
  typedef typename KernelTransformType::OutputPointType OutputPointType;

  InputPointType outputPoint;    // Coordinates of current output pixel

  // Support for progress methods/callbacks
  ProgressReporter progress(this, 0, region.GetNumberOfPixels(), 10);
        
  outIt.GoToBegin();

  // Walk the output region
  while ( !outIt.IsAtEnd() )
    {
    // Determine the index of the current output pixel
    outputIndex = outIt.GetIndex();
    outputPtr->TransformIndexToPhysicalPoint( outputIndex, outputPoint );


    // Compute corresponding inverse displacement vector
    OutputPointType interpolation = 
                        m_KernelTransform->TransformPoint( outputPoint );

    OutputPixelType inverseDisplacement;

    for(unsigned int i=0; i < ImageDimension; i++)
      {
      inverseDisplacement[i] = interpolation[i];
      }

    outIt.Set( inverseDisplacement ); // set inverse displacement.
    ++outIt;
    progress.CompletedPixel();
    }

  return;
}


/** 
 * Inform pipeline of necessary input image region
 *
 * Determining the actual input region is non-trivial, especially
 * when we cannot assume anything about the transform being used.
 * So we do the easy thing and request the entire input image.
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::GenerateInputRequestedRegion()
{
  // call the superclass's implementation of this method
  Superclass::GenerateInputRequestedRegion();

  if ( !this->GetInput() )
    {
    return;
    }

  // get pointers to the input and output
  InputImagePointer  inputPtr  = 
    const_cast< InputImageType *>( this->GetInput() );

  // Request the entire input image
  InputImageRegionType inputRegion;
  inputRegion = inputPtr->GetLargestPossibleRegion();
  inputPtr->SetRequestedRegion(inputRegion);

  return;
}


/** 
 * Inform pipeline of required output region
 */
template <class TInputImage, class TOutputImage>
void 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::GenerateOutputInformation()
{
  // call the superclass' implementation of this method
  Superclass::GenerateOutputInformation();

  // get pointers to the input and output
  OutputImagePointer outputPtr = this->GetOutput();
  if ( !outputPtr )
    {
    return;
    }

  // Set the size of the output region
  typename TOutputImage::RegionType outputLargestPossibleRegion;
  outputLargestPossibleRegion.SetSize( m_Size );
  outputPtr->SetLargestPossibleRegion( outputLargestPossibleRegion );

  // Set spacing and origin
  outputPtr->SetSpacing( m_OutputSpacing );
  outputPtr->SetOrigin( m_OutputOrigin );

  return;
}



/** 
 * Verify if any of the components has been modified.
 */
template <class TInputImage, class TOutputImage>
unsigned long 
InverseDeformationFieldImageFilter<TInputImage,TOutputImage>
::GetMTime( void ) const
{
  unsigned long latestTime = Object::GetMTime(); 

  if( m_KernelTransform )
    {
    if( latestTime < m_KernelTransform->GetMTime() )
      {
      latestTime = m_KernelTransform->GetMTime();
      }
    }

  return latestTime;
}



} // end namespace itk

#endif