itkWarpImageFilter.txx

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkWarpImageFilter.txx,v $
  Language:  C++
  Date:      $Date: 2009-10-29 11:19:10 $
  Version:   $Revision: 1.34 $

  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 __itkWarpImageFilter_txx
#define __itkWarpImageFilter_txx
#include "itkWarpImageFilter.h"

#include "itkImageRegionIterator.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkNumericTraits.h"
#include "itkProgressReporter.h"
#include "itkContinuousIndex.h"
#include "vnl/vnl_math.h"

#include "itkVariableLengthVector.h"
#include "itkPixelBuilder.h"

namespace itk
{

template <class TInputImage,class TOutputImage,class TDeformationField>
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::WarpImageFilter()
{
  // Setup the number of required inputs
  this->SetNumberOfRequiredInputs( 2 );  
  
  // Setup default values
  m_OutputSpacing.Fill( 1.0 );
  m_OutputOrigin.Fill( 0.0 );
  m_OutputDirection.SetIdentity();
  m_OutputSize.Fill(0);
  PixelBuilder<PixelType>::Zero(m_EdgePaddingValue,1);
  m_OutputStartIndex.Fill(0);
  // Setup default interpolator
  typename DefaultInterpolatorType::Pointer interp =
    DefaultInterpolatorType::New();

  m_Interpolator = 
    static_cast<InterpolatorType*>( interp.GetPointer() );
}

template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::PrintSelf(std::ostream& os, Indent indent) const
{

  Superclass::PrintSelf(os, indent);

  os << indent << "OutputSpacing: " << m_OutputSpacing << std::endl;
  os << indent << "OutputOrigin: " << m_OutputOrigin << std::endl;
  os << indent << "OutputDirection: " << m_OutputDirection << std::endl;
  os << indent << "OutputSize: " << m_OutputSize << std::endl;
  os << indent << "OutputStartIndex: " << m_OutputStartIndex << std::endl;
  os << indent << "EdgePaddingValue: "
     << static_cast<typename NumericTraits<PixelType>::PrintType>(m_EdgePaddingValue)
     << std::endl;
  os << indent << "Interpolator: " << m_Interpolator.GetPointer() << std::endl;
  
}


template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::SetOutputSpacing(
  const double* spacing)
{
  SpacingType s(spacing);
  this->SetOutputSpacing( s );
}


template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::SetOutputOrigin(
  const double* origin)
{
  PointType p(origin);
  this->SetOutputOrigin(p);
}

template <class TInputImage,class TOutputImage,class TDeformationField>
void 
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::SetOutputParametersFromImage ( const ImageBaseType * image )
{
  this->SetOutputOrigin ( image->GetOrigin() );
  this->SetOutputSpacing ( image->GetSpacing() );
  this->SetOutputDirection ( image->GetDirection() );
  this->SetOutputStartIndex ( image->GetLargestPossibleRegion().GetIndex() );
  this->SetOutputSize ( image->GetLargestPossibleRegion().GetSize() );
}

template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::SetDeformationField(
  const DeformationFieldType * field )
{
  // const cast is needed because the pipeline is not const-correct.
  DeformationFieldType * input =  
       const_cast< DeformationFieldType * >( field );
  this->ProcessObject::SetNthInput( 1, input );
}


template <class TInputImage,class TOutputImage,class TDeformationField>
typename WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::DeformationFieldType *
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::GetDeformationField(void)
{
  return static_cast<DeformationFieldType *>
    ( this->ProcessObject::GetInput( 1 ));
}


template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::BeforeThreadedGenerateData()
{

  if( !m_Interpolator )
    {
    itkExceptionMacro(<< "Interpolator not set");
    }
  DeformationFieldPointer fieldPtr = this->GetDeformationField();

  // Connect input image to interpolator
  m_Interpolator->SetInputImage( this->GetInput() );
  typename DeformationFieldType::RegionType defRegion = 
    fieldPtr->GetLargestPossibleRegion();
  typename OutputImageType::RegionType outRegion =
    this->GetOutput()->GetLargestPossibleRegion();
  m_DefFieldSizeSame = outRegion == defRegion;
  if(!m_DefFieldSizeSame)
    {
    m_StartIndex = fieldPtr->GetBufferedRegion().GetIndex();
    for(unsigned i = 0; i < ImageDimension; i++)
      {
      m_EndIndex[i] = m_StartIndex[i] + 
        fieldPtr->GetBufferedRegion().GetSize()[i] - 1;
      }
    }
}

template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::AfterThreadedGenerateData()
{
  // Disconnect input image from interpolator
  m_Interpolator->SetInputImage( NULL );
}


template <class TInputImage,class TOutputImage,class TDeformationField>
typename WarpImageFilter<TInputImage,
                         TOutputImage,
                         TDeformationField>::DisplacementType
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::EvaluateDeformationAtPhysicalPoint(const PointType &point)
{
  DeformationFieldPointer fieldPtr = this->GetDeformationField();
  ContinuousIndex<double,ImageDimension> index;
  fieldPtr->TransformPhysicalPointToContinuousIndex(point,index);
  unsigned int dim;  // index over dimension
  IndexType baseIndex;
  IndexType neighIndex;
  double distance[ImageDimension];

  for( dim = 0; dim < ImageDimension; dim++ )
    {
    baseIndex[dim] = Math::Floor< IndexValueType >( index[dim] );

    if( baseIndex[dim] >=  m_StartIndex[dim] )
      {
      if( baseIndex[dim] <  m_EndIndex[dim] )
        {
        distance[dim] = index[dim] - static_cast<double>( baseIndex[dim] );
        }
      else
        {
        baseIndex[dim] = m_EndIndex[dim];
        distance[dim] = 0.0;
        }
      }
    else
      {
      baseIndex[dim] = m_StartIndex[dim];
      distance[dim] = 0.0;
      }
    }

  DisplacementType output;
  output.Fill(0);

  double totalOverlap = 0.0;
  unsigned int numNeighbors(1 << TInputImage::ImageDimension);

  for( unsigned int counter = 0; counter < numNeighbors; counter++ )
    {
    double overlap = 1.0;          // fraction overlap
    unsigned int upper = counter;  // each bit indicates upper/lower neighbour

    // get neighbor index and overlap fraction
    for( dim = 0; dim < ImageDimension; dim++ )
      {

      if( upper & 1 )
        {
        neighIndex[dim] = baseIndex[dim] + 1;
        overlap *= distance[dim];
        }
      else
        {
        neighIndex[dim] = baseIndex[dim];
        overlap *= 1.0 - distance[dim];
        }

      upper >>= 1;

      }

    // get neighbor value only if overlap is not zero
    if( overlap )
      {
      const DisplacementType input = 
        fieldPtr->GetPixel( neighIndex );
      for(unsigned int k = 0; k < PixelSizeFinder(input); k++ )
        {
        output[k] += overlap * static_cast<double>( input[k] );
        }
      totalOverlap += overlap;
      }

    if( totalOverlap == 1.0 )
      {
      // finished
      break;
      }

    }
  return ( output );
}

template <class PixelType> unsigned int PixelSizeFinder(itk::VariableLengthVector<PixelType> pix)
{
  return pix.Size();
}
template <class PixelType> unsigned int PixelSizeFinder(PixelType pix)
{
  return PixelType::Dimension;
}

template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::ThreadedGenerateData(
  const OutputImageRegionType& outputRegionForThread,
  int threadId )
{

  InputImageConstPointer inputPtr = this->GetInput();
  OutputImagePointer outputPtr = this->GetOutput();
  DeformationFieldPointer fieldPtr = this->GetDeformationField();

  // support progress methods/callbacks
  ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels());
  
  // iterator for the output image
  ImageRegionIteratorWithIndex<OutputImageType> outputIt(
    outputPtr, outputRegionForThread );
  IndexType index;
  PointType point;
  DisplacementType displacement;
  if(this->m_DefFieldSizeSame)
    {
    // iterator for the deformation field
    ImageRegionIterator<DeformationFieldType> 
      fieldIt(fieldPtr, outputRegionForThread );

    while( !outputIt.IsAtEnd() )
      {
      // get the output image index
      index = outputIt.GetIndex();
      outputPtr->TransformIndexToPhysicalPoint( index, point );

      // get the required displacement
      displacement = fieldIt.Get();

      // compute the required input image point
      for(unsigned int j = 0; j < ImageDimension; j++ )
        {
        point[j] += displacement[j];
        }

      // get the interpolated value
      if( m_Interpolator->IsInsideBuffer( point ) )
        {
        PixelType value = 
          static_cast<PixelType>(m_Interpolator->Evaluate( point ) );
        outputIt.Set( value );
        }
      else
        {
        outputIt.Set( m_EdgePaddingValue );
        }   
      ++outputIt;
      ++fieldIt; 
      progress.CompletedPixel();
      }
    } 
  else 
    {
    while( !outputIt.IsAtEnd() )
      {
      // get the output image index
      index = outputIt.GetIndex();
      outputPtr->TransformIndexToPhysicalPoint( index, point );

      displacement = this->EvaluateDeformationAtPhysicalPoint(point);
      // compute the required input image point
      for(unsigned int j = 0; j < ImageDimension; j++ )
        {
        point[j] += displacement[j];
        }

      // get the interpolated value
      if( m_Interpolator->IsInsideBuffer( point ) )
        {
        PixelType value = 
          static_cast<PixelType>(m_Interpolator->Evaluate( point ) );
        outputIt.Set( value );
        }
      else
        {
        outputIt.Set( m_EdgePaddingValue );
        }   
      ++outputIt;
      progress.CompletedPixel();
      }
    }
}


template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::GenerateInputRequestedRegion()
{

  // call the superclass's implementation
  Superclass::GenerateInputRequestedRegion();

  // request the largest possible region for the input image
  InputImagePointer inputPtr = 
    const_cast< InputImageType * >( this->GetInput() );

  if( inputPtr )
    {
    inputPtr->SetRequestedRegionToLargestPossibleRegion();
    }

  // just propagate up the output requested region for the 
  // deformation field.
  DeformationFieldPointer fieldPtr = this->GetDeformationField();
  OutputImagePointer outputPtr = this->GetOutput();
  if(fieldPtr.IsNotNull() )
    {
    fieldPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
    if(!fieldPtr->VerifyRequestedRegion())
      {
      fieldPtr->SetRequestedRegion(fieldPtr->GetLargestPossibleRegion());
      }
    }
}


template <class TInputImage,class TOutputImage,class TDeformationField>
void
WarpImageFilter<TInputImage,TOutputImage,TDeformationField>
::GenerateOutputInformation()
{
  // call the superclass's implementation of this method
  Superclass::GenerateOutputInformation();

  OutputImagePointer outputPtr = this->GetOutput();

  outputPtr->SetSpacing( m_OutputSpacing );
  outputPtr->SetOrigin( m_OutputOrigin );
  outputPtr->SetDirection( m_OutputDirection );

  DeformationFieldPointer fieldPtr = this->GetDeformationField();
  if( this->m_OutputSize[0] == 0 && 
      fieldPtr.IsNotNull())
    {
    outputPtr->SetLargestPossibleRegion( fieldPtr->
                                         GetLargestPossibleRegion() );
    }
  else
    {
    OutputImageRegionType region;
    region.SetSize(this->m_OutputSize);
    region.SetIndex(this->m_OutputStartIndex);
    outputPtr->SetLargestPossibleRegion(region);
    }
}


} // end namespace itk

#endif