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itkFastSymmetricForcesDemonsRegistrationFunction.txx
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itkFastSymmetricForcesDemonsRegistrationFunction.txx
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkFastSymmetricForcesDemonsRegistrationFunction.txx
Language: C++
Date: $Date$
Version: $Revision$
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 _itkFastSymmetricForcesDemonsRegistrationFunction_txx_
#define _itkFastSymmetricForcesDemonsRegistrationFunction_txx_
#include "itkFastSymmetricForcesDemonsRegistrationFunction.h"
#include "itkExceptionObject.h"
#include "vnl/vnl_math.h"
namespace itk {
/*
* Default constructor
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::FastSymmetricForcesDemonsRegistrationFunction()
{
RadiusType r;
unsigned int j;
for( j = 0; j < ImageDimension; j++ )
{
r[j] = 0;
}
this->SetRadius(r);
m_TimeStep = 1.0;
m_DenominatorThreshold = 1e-9;
m_IntensityDifferenceThreshold = 0.001;
this->SetMovingImage(NULL);
this->SetFixedImage(NULL);
m_FixedImageSpacing.Fill( 1.0 );
m_FixedImageOrigin.Fill( 0.0 );
m_Normalizer = 0.0;
m_FixedImageGradientCalculator = GradientCalculatorType::New();
typename DefaultInterpolatorType::Pointer interp =
DefaultInterpolatorType::New();
m_MovingImageInterpolator = static_cast<InterpolatorType*>(
interp.GetPointer() );
m_WarpedMovingImageGradientCalculator = MovingGradientCalculatorType::New();
m_MovingImageWarper = WarperType::New();
m_MovingImageWarper->SetInterpolator( m_MovingImageInterpolator );
m_Metric = NumericTraits<double>::max();
m_SumOfSquaredDifference = 0.0;
m_NumberOfPixelsProcessed = 0L;
m_RMSChange = NumericTraits<double>::max();
m_SumOfSquaredChange = 0.0;
}
/*
* Standard "PrintSelf" method.
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::PrintSelf(std::ostream& os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "MovingImageIterpolator: ";
os << m_MovingImageInterpolator.GetPointer() << std::endl;
os << indent << "FixedImageGradientCalculator: ";
os << m_FixedImageGradientCalculator.GetPointer() << std::endl;
os << indent << "DenominatorThreshold: ";
os << m_DenominatorThreshold << std::endl;
os << indent << "IntensityDifferenceThreshold: ";
os << m_IntensityDifferenceThreshold << std::endl;
os << indent << "Metric: ";
os << m_Metric << std::endl;
os << indent << "SumOfSquaredDifference: ";
os << m_SumOfSquaredDifference << std::endl;
os << indent << "NumberOfPixelsProcessed: ";
os << m_NumberOfPixelsProcessed << std::endl;
os << indent << "RMSChange: ";
os << m_RMSChange << std::endl;
os << indent << "SumOfSquaredChange: ";
os << m_SumOfSquaredChange << std::endl;
}
/**
*
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::SetIntensityDifferenceThreshold(double threshold)
{
m_IntensityDifferenceThreshold = threshold;
}
/**
*
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
double
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::GetIntensityDifferenceThreshold() const
{
return m_IntensityDifferenceThreshold;
}
/*
* Set the function state values before each iteration
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::InitializeIteration()
{
if( !this->GetMovingImage() || !this->GetFixedImage() || !m_MovingImageInterpolator )
{
itkExceptionMacro( << "MovingImage, FixedImage and/or Interpolator not set" );
}
// cache fixed image information
m_FixedImageSpacing = this->GetFixedImage()->GetSpacing();
m_FixedImageOrigin = this->GetFixedImage()->GetOrigin();
// compute the normalizer
m_Normalizer = 0.0;
for( unsigned int k = 0; k < ImageDimension; k++ )
{
m_Normalizer += m_FixedImageSpacing[k] * m_FixedImageSpacing[k];
}
m_Normalizer /= static_cast<double>( ImageDimension );
// setup gradient calculator
m_FixedImageGradientCalculator->SetInputImage( this->GetFixedImage() );
m_MovingImageWarper->SetInput( this->GetMovingImage() );
m_MovingImageWarper->SetDeformationField( this->GetDeformationField() );
m_MovingImageWarper->Update();
m_WarpedMovingImageGradientCalculator->SetInputImage( this->m_MovingImageWarper->GetOutput() );
// setup moving image interpolator for further access
m_MovingImageInterpolator->SetInputImage( this->GetMovingImage() );
// initialize metric computation variables
m_SumOfSquaredDifference = 0.0;
m_NumberOfPixelsProcessed = 0L;
m_SumOfSquaredChange = 0.0;
}
/*
* Compute update at a non boundary neighbourhood
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
typename FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::PixelType
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::ComputeUpdate(const NeighborhoodType &it, void * gd,
const FloatOffsetType& itkNotUsed(offset))
{
GlobalDataStruct *globalData = (GlobalDataStruct *)gd;
PixelType update;
IndexType FirstIndex = this->GetFixedImage()->GetLargestPossibleRegion().GetIndex();
IndexType LastIndex = this->GetFixedImage()->GetLargestPossibleRegion().GetIndex() +
this->GetFixedImage()->GetLargestPossibleRegion().GetSize();
IndexType index = it.GetIndex();
// Get fixed image related information
double fixedValue;
CovariantVectorType fixedGradient;
// Note: no need to check the index is within
// fixed image buffer. This is done by the external filter.
fixedValue = (double) this->GetFixedImage()->GetPixel( index );
fixedGradient = m_FixedImageGradientCalculator->EvaluateAtIndex( index );
// Get moving image related information
double movingValue;
CovariantVectorType movingGradient;
// use warped moving image to get moving value and gradient fast(er).
movingValue = (double) m_MovingImageWarper->GetOutput()->GetPixel( index );
movingGradient = m_WarpedMovingImageGradientCalculator->EvaluateAtIndex( index );
// unfortunately (since it's a little redundant) we still need the mapped center point coordinates
PointType mappedCenterPoint;
for( unsigned int dim = 0; dim < ImageDimension; dim++ )
{
mappedCenterPoint[dim] = double( index[dim] ) * m_FixedImageSpacing[dim] + m_FixedImageOrigin[dim];
mappedCenterPoint[dim] += it.GetCenterPixel()[dim];
}
/**
* Compute Update.
* In the original equation the denominator is defined as
*
* (g-f)^2 + (moving_grad+fixed_grad)_mag^2
*
* However there is a mismatch in units between the two terms.
* The units for the second term is intensity^2/mm^2 while the
* units for the first term is intensity^2. This mismatch is particularly
* problematic when the fixed image does not have unit spacing.
* In this implemenation, we normalize the first term by a factor K,
* such that denominator = (g-f)^2/K + grad_mag^2
* where K = mean square spacing to compensate for the mismatch in units.
*/
double fixedPlusMovingGradientSquaredMagnitude = 0;
for( unsigned int dim = 0; dim < ImageDimension; dim++ )
{
fixedPlusMovingGradientSquaredMagnitude += vnl_math_sqr( fixedGradient[dim] + movingGradient[dim] );
}
double speedValue = fixedValue - movingValue;
double denominator = vnl_math_sqr( speedValue ) / m_Normalizer + fixedPlusMovingGradientSquaredMagnitude;
if ( vnl_math_abs(speedValue) < m_IntensityDifferenceThreshold || denominator < m_DenominatorThreshold )
{
for( unsigned int j = 0; j < ImageDimension; j++ )
{
update[j] = 0.0;
}
}
else
{
for( unsigned int j = 0; j < ImageDimension; j++ )
{
update[j] = 2 * speedValue * (movingGradient[j] + fixedGradient[j]) / denominator;
}
}
// update the squared change value
PointType newMappedCenterPoint;
double newMovingValue;
bool IsOutsideRegion = 0;
for( unsigned int j = 0; j < ImageDimension; j++ )
{
if ( globalData )
{
globalData->m_SumOfSquaredChange += vnl_math_sqr( update[j] );
newMappedCenterPoint[j] = mappedCenterPoint[j] + update[j];
if ( index[j] < (FirstIndex[j] + 2) || index[j] > (LastIndex[j] - 3) )
{
IsOutsideRegion = 1;
}
}
}
// update the metric with the latest deformable field
if ( globalData )
{
// do not consider voxel on the border (2 voxels) as there are often artefacts
// which falsify the metric
if( !IsOutsideRegion )
{
if( m_MovingImageInterpolator->IsInsideBuffer( newMappedCenterPoint ) )
{
newMovingValue = m_MovingImageInterpolator->Evaluate( newMappedCenterPoint );
}
else
{
newMovingValue = 0;
}
globalData->m_SumOfSquaredDifference += vnl_math_sqr( fixedValue - newMovingValue );
globalData->m_NumberOfPixelsProcessed += 1;
}
}
return update;
}
/*
* Update the metric and release the per-thread-global data.
*/
template <class TFixedImage, class TMovingImage, class TDeformationField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage,TMovingImage,TDeformationField>
::ReleaseGlobalDataPointer( void *gd ) const
{
GlobalDataStruct * globalData = (GlobalDataStruct *) gd;
m_MetricCalculationLock.Lock();
m_SumOfSquaredDifference += globalData->m_SumOfSquaredDifference;
m_NumberOfPixelsProcessed += globalData->m_NumberOfPixelsProcessed;
m_SumOfSquaredChange += globalData->m_SumOfSquaredChange;
if ( m_NumberOfPixelsProcessed )
{
m_Metric = m_SumOfSquaredDifference /
static_cast<double>( m_NumberOfPixelsProcessed );
m_RMSChange = vcl_sqrt( m_SumOfSquaredChange /
static_cast<double>( m_NumberOfPixelsProcessed ) );
}
m_MetricCalculationLock.Unlock();
delete globalData;
}
} // end namespace itk
#endif