/*=========================================================================
  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
===========================================================================**/
#ifndef __clitkTransformToDeformationFieldSource_txx
#define __clitkTransformToDeformationFieldSource_txx
#include "clitkTransformToDeformationFieldSource.h"

#include "itkIdentityTransform.h"
#include "itkProgressReporter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkImageLinearIteratorWithIndex.h"

namespace clitk
{
/**
 * Constructor
 */
  template <class TOutputImage, class TTransformPrecisionType>
  TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>::TransformToDeformationFieldSource()
{
  this->m_OutputSpacing.Fill(1.0);
  this->m_OutputOrigin.Fill(0.0);
  this->m_OutputDirection.SetIdentity();

  SizeType size;
  size.Fill( 0 );
  this->m_OutputRegion.SetSize( size );

  IndexType index;
  index.Fill( 0 );
  this->m_OutputRegion.SetIndex( index );

  this->m_Transform
    = itk::IdentityTransform<TTransformPrecisionType, ImageDimension>::New();
} // end Constructor

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

  os << indent << "OutputRegion: " << this->m_OutputRegion << std::endl;
  os << indent << "OutputSpacing: " << this->m_OutputSpacing << std::endl;
  os << indent << "OutputOrigin: " << this->m_OutputOrigin << std::endl;
  os << indent << "OutputDirection: " << this->m_OutputDirection << std::endl;
  os << indent << "Transform: " << this->m_Transform.GetPointer() << std::endl;
} // end PrintSelf()

/**
 * Set the output image size.
 */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::SetOutputSize( const SizeType & size )
{
  this->m_OutputRegion.SetSize( size );
}

/**
 * Get the output image size.
 */
template <class TOutputImage, class TTransformPrecisionType>
const typename TransformToDeformationFieldSource<TOutputImage,
  TTransformPrecisionType>
  ::SizeType &
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::GetOutputSize()
{
  return this->m_OutputRegion.GetSize();
}

/**
 * Set the output image index.
 */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::SetOutputIndex( const IndexType & index )
{
  this->m_OutputRegion.SetIndex( index );
}

/**
 * Get the output image index.
 */
template <class TOutputImage, class TTransformPrecisionType>
const typename TransformToDeformationFieldSource<TOutputImage,
  TTransformPrecisionType>
  ::IndexType &
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::GetOutputIndex()
{
  return this->m_OutputRegion.GetIndex();
}

/**
 * Set the output image spacing.
 */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::SetOutputSpacing( const double *spacing )
{
  SpacingType s( spacing );

  this->SetOutputSpacing( s );
} // end SetOutputSpacing()

/**
 * Set the output image origin.
 */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::SetOutputOrigin( const double *origin )
{
  OriginType p( origin );

  this->SetOutputOrigin( p );
}

/** Helper method to set the output parameters based on this image */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::SetOutputParametersFromImage ( const ImageBaseType *image )
{
  if ( !image )
    {
    itkExceptionMacro(<< "Cannot use a null image reference");
    }

  this->SetOutputOrigin( image->GetOrigin() );
  this->SetOutputSpacing( image->GetSpacing() );
  this->SetOutputDirection( image->GetDirection() );
  this->SetOutputRegion( image->GetLargestPossibleRegion() );
} // end SetOutputParametersFromImage()

/**
 * Set up state of filter before multi-threading.
 * InterpolatorType::SetInputImage is not thread-safe and hence
 * has to be set up before ThreadedGenerateData
 */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::BeforeThreadedGenerateData( void )
{
  if ( !this->m_Transform )
    {
    itkExceptionMacro(<< "Transform not set");
    }
} // end BeforeThreadedGenerateData()

/**
 * ThreadedGenerateData
 */
template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::ThreadedGenerateData(
  const OutputImageRegionType & outputRegionForThread,
  int threadId )
{
  // Check whether we can use a fast path for resampling. Fast path
  // can be used if the transformation is linear. Transform respond
  // to the IsLinear() call.
  if ( this->m_Transform->IsLinear() )
    {
    this->LinearThreadedGenerateData( outputRegionForThread, threadId );
    return;
    }

  // Otherwise, we use the normal method where the transform is called
  // for computing the transformation of every point.
  this->NonlinearThreadedGenerateData( outputRegionForThread, threadId );
} // end ThreadedGenerateData()

template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::NonlinearThreadedGenerateData(
  const OutputImageRegionType & outputRegionForThread,
  int threadId )
{
  // Get the output pointer
  OutputImagePointer outputPtr = this->GetOutput();

  // Create an iterator that will walk the output region for this thread.
  typedef itk::ImageRegionIteratorWithIndex<TOutputImage> OutputIteratorType;
  OutputIteratorType outIt( outputPtr, outputRegionForThread );

  // Define a few variables that will be used to translate from an input pixel
  // to an output pixel
  PointType outputPoint;         // Coordinates of output pixel
  PointType transformedPoint;    // Coordinates of transformed pixel
  PixelType deformation;         // the difference

  // Support for progress methods/callbacks
  itk::ProgressReporter progress( this, threadId,
                            outputRegionForThread.GetNumberOfPixels() );

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

    // Compute corresponding input pixel position
    transformedPoint = this->m_Transform->TransformPoint( outputPoint );

    // Compute the deformation
    for ( unsigned int i = 0; i < SpaceDimension; ++i )
      {
      deformation[i] = static_cast<PixelValueType>(
        transformedPoint[i] - outputPoint[i] );
      }

    // Set it
    outIt.Set( deformation );

    // Update progress and iterator
    progress.CompletedPixel();
    ++outIt;
    }
} // end NonlinearThreadedGenerateData()

template <class TOutputImage, class TTransformPrecisionType>
void
TransformToDeformationFieldSource<TOutputImage, TTransformPrecisionType>
  ::LinearThreadedGenerateData(
  const OutputImageRegionType & outputRegionForThread,
  int threadId )
{
  // Get the output pointer
  OutputImagePointer outputPtr = this->GetOutput();

  // Create an iterator that will walk the output region for this thread.
  typedef itk::ImageLinearIteratorWithIndex<TOutputImage> OutputIteratorType;
  OutputIteratorType outIt( outputPtr, outputRegionForThread );

  outIt.SetDirection( 0 );

  // Define a few indices that will be used to translate from an input pixel
  // to an output pixel
  PointType outputPoint;         // Coordinates of current output pixel
  PointType transformedPoint;    // Coordinates of transformed pixel
  PixelType deformation;         // the difference

  IndexType index;

  // Support for progress methods/callbacks
  itk::ProgressReporter progress( this, threadId,
                            outputRegionForThread.GetNumberOfPixels() );

  // Determine the position of the first pixel in the scanline
  outIt.GoToBegin();
  index = outIt.GetIndex();
  outputPtr->TransformIndexToPhysicalPoint( index, outputPoint );

  // Compute corresponding transformed pixel position
  transformedPoint = this->m_Transform->TransformPoint( outputPoint );

  // Compare with the ResampleImageFilter

  // Compute delta
  PointType outputPointNeighbour;
  PointType transformedPointNeighbour;
  typedef typename PointType::VectorType VectorType;
  VectorType delta;
  ++index[0];
  outputPtr->TransformIndexToPhysicalPoint( index, outputPointNeighbour );
  transformedPointNeighbour = this->m_Transform->TransformPoint(
    outputPointNeighbour );
  delta = transformedPointNeighbour - transformedPoint
          - ( outputPointNeighbour - outputPoint );

  // loop over the vector image
  while ( !outIt.IsAtEnd() )
    {
    // Get current point
    index = outIt.GetIndex();
    outputPtr->TransformIndexToPhysicalPoint( index, outputPoint );

    // Compute transformed point
    transformedPoint = this->m_Transform->TransformPoint( outputPoint );

    while ( !outIt.IsAtEndOfLine() )
      {
      // Compute the deformation
      for ( unsigned int i = 0; i < SpaceDimension; ++i )
        {
        deformation[i] = static_cast<PixelValueType>(
          transformedPoint[i] - outputPoint[i] );
        }

      // Set it
      outIt.Set( deformation );

      // Update stuff
      progress.CompletedPixel();
      ++outIt;
      transformedPoint += delta;
      }

    outIt.NextLine();
    }
} // end LinearThreadedGenerateData()

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

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

  outputPtr->SetLargestPossibleRegion( m_OutputRegion );

  outputPtr->SetSpacing( m_OutputSpacing );
  outputPtr->SetOrigin( m_OutputOrigin );
  outputPtr->SetDirection( m_OutputDirection );
} // end GenerateOutputInformation()

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

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

  return latestTime;
} // end GetMTime()
} // end namespace clitk

#endif // end #ifndef _clitkTransformToDeformationFieldSource_txx