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itkPDEDeformableRegistrationFilter.hxx
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itkPDEDeformableRegistrationFilter.hxx
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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef itkPDEDeformableRegistrationFilter_hxx
#define itkPDEDeformableRegistrationFilter_hxx
#include "itkPDEDeformableRegistrationFilter.h"
#include "itkImageRegionIterator.h"
#include "itkImageLinearIteratorWithIndex.h"
#include "itkDataObject.h"
#include "itkGaussianOperator.h"
#include "itkVectorNeighborhoodOperatorImageFilter.h"
#include "itkMath.h"
#include "itkMath.h"
namespace itk
{
/**
* Default constructor
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::PDEDeformableRegistrationFilter()
{
this->SetNumberOfRequiredInputs(2);
// Primary input is optional in this filter
this->RemoveRequiredInputName( "Primary" );
this->SetNumberOfIterations(10);
unsigned int j;
for ( j = 0; j < ImageDimension; j++ )
{
m_StandardDeviations[j] = 1.0;
m_UpdateFieldStandardDeviations[j] = 1.0;
}
m_TempField = DisplacementFieldType::New();
m_MaximumError = 0.1;
m_MaximumKernelWidth = 30;
m_StopRegistrationFlag = false;
m_SmoothDisplacementField = true;
m_SmoothUpdateField = false;
}
/*
* Set the fixed image.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetFixedImage(
const FixedImageType *ptr)
{
this->ProcessObject::SetNthInput( 1, const_cast< FixedImageType * >( ptr ) );
}
/*
* Get the fixed image.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
const typename PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::FixedImageType *
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetFixedImage() const
{
return dynamic_cast< const FixedImageType * >
( this->ProcessObject::GetInput(1) );
}
/*
* Set the moving image.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetMovingImage(
const MovingImageType *ptr)
{
this->ProcessObject::SetNthInput( 2, const_cast< MovingImageType * >( ptr ) );
}
/*
* Get the moving image.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
const typename PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::MovingImageType *
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetMovingImage() const
{
return dynamic_cast< const MovingImageType * >
( this->ProcessObject::GetInput(2) );
}
/*
*
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
std::vector< SmartPointer< DataObject > >::size_type
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetNumberOfValidRequiredInputs() const
{
typename std::vector< SmartPointer< DataObject > >::size_type num = 0;
if ( this->GetFixedImage() )
{
num++;
}
if ( this->GetMovingImage() )
{
num++;
}
return num;
}
/**
* Set the standard deviations.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetStandardDeviations(
double value)
{
unsigned int j;
for ( j = 0; j < ImageDimension; j++ )
{
if ( Math::NotExactlyEquals(value, m_StandardDeviations[j]) )
{
break;
}
}
if ( j < ImageDimension )
{
this->Modified();
for ( j = 0; j < ImageDimension; j++ )
{
m_StandardDeviations[j] = value;
}
}
}
/*
* Set the standard deviations.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetUpdateFieldStandardDeviations(
double value)
{
unsigned int j;
for ( j = 0; j < ImageDimension; j++ )
{
if ( Math::NotExactlyEquals(value, m_UpdateFieldStandardDeviations[j]) )
{
break;
}
}
if ( j < ImageDimension )
{
this->Modified();
for ( j = 0; j < ImageDimension; j++ )
{
m_UpdateFieldStandardDeviations[j] = value;
}
}
}
/*
* Standard PrintSelf method.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "Smooth deformation field: "
<< ( m_SmoothDisplacementField ? "on" : "off" ) << std::endl;
unsigned int j = 0;
os << indent << "Standard deviations: [" << m_StandardDeviations[j];
for ( j = 1; j < ImageDimension; j++ )
{
os << ", " << m_StandardDeviations[j];
}
os << "]" << std::endl;
os << indent << "Smooth update field: "
<< ( m_SmoothUpdateField ? "on" : "off" ) << std::endl;
j = 0;
os << indent << "Update field standard deviations: [" << m_UpdateFieldStandardDeviations[j];
for ( j = 1; j < ImageDimension; j++ )
{
os<< ", " << m_UpdateFieldStandardDeviations[j];
}
os << "]" << std::endl;
os << indent << "StopRegistrationFlag: ";
os << m_StopRegistrationFlag << std::endl;
os << indent << "MaximumError: ";
os << m_MaximumError << std::endl;
os << indent << "MaximumKernelWidth: ";
os << m_MaximumKernelWidth << std::endl;
}
/*
* Set the function state values before each iteration
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::InitializeIteration()
{
MovingImageConstPointer movingPtr = this->GetMovingImage();
FixedImageConstPointer fixedPtr = this->GetFixedImage();
if ( !movingPtr || !fixedPtr )
{
itkExceptionMacro(<< "Fixed and/or moving image not set");
}
// update variables in the equation object
PDEDeformableRegistrationFunctionType *f =
dynamic_cast< PDEDeformableRegistrationFunctionType * >
( this->GetDifferenceFunction().GetPointer() );
if ( !f )
{
itkExceptionMacro(<< "FiniteDifferenceFunction not of type PDEDeformableRegistrationFilterFunction");
}
f->SetFixedImage(fixedPtr);
f->SetMovingImage(movingPtr);
this->Superclass::InitializeIteration();
}
/*
* Override the default implemenation for the case when the
* initial deformation is not set.
* If the initial deformation is not set, the output is
* fill with zero vectors.
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::CopyInputToOutput()
{
typename Superclass::InputImageType::ConstPointer inputPtr = this->GetInput();
if ( inputPtr )
{
this->Superclass::CopyInputToOutput();
}
else
{
typename Superclass::PixelType zeros;
for ( unsigned int j = 0; j < ImageDimension; j++ )
{
zeros[j] = 0;
}
typename OutputImageType::Pointer output = this->GetOutput();
ImageRegionIterator< OutputImageType > out( output, output->GetRequestedRegion() );
while ( !out.IsAtEnd() )
{
out.Value() = zeros;
++out;
}
}
}
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::GenerateOutputInformation()
{
typename DataObject::Pointer output;
if ( this->GetInput(0) )
{
// Initial deformation field is set.
// Copy information from initial field.
this->Superclass::GenerateOutputInformation();
}
else if ( this->GetFixedImage() )
{
// Initial deforamtion field is not set.
// Copy information from the fixed image.
for ( unsigned int idx = 0; idx <
this->GetNumberOfIndexedOutputs(); ++idx )
{
output = this->GetOutput(idx);
if ( output )
{
output->CopyInformation( this->GetFixedImage() );
}
}
}
}
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::GenerateInputRequestedRegion()
{
// call the superclass's implementation
Superclass::GenerateInputRequestedRegion();
// request the largest possible region for the moving image
MovingImagePointer movingPtr =
const_cast< MovingImageType * >( this->GetMovingImage() );
if ( movingPtr )
{
movingPtr->SetRequestedRegionToLargestPossibleRegion();
}
// just propagate up the output requested region for
// the fixed image and initial deformation field.
DisplacementFieldPointer inputPtr =
const_cast< DisplacementFieldType * >( this->GetInput() );
DisplacementFieldPointer outputPtr = this->GetOutput();
FixedImagePointer fixedPtr =
const_cast< FixedImageType * >( this->GetFixedImage() );
if ( inputPtr )
{
inputPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
}
if ( fixedPtr )
{
fixedPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
}
}
/*
* Release memory of internal buffers
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::PostProcessOutput()
{
this->Superclass::PostProcessOutput();
m_TempField->Initialize();
}
/*
* Initialize flags
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::Initialize()
{
this->Superclass::Initialize();
m_StopRegistrationFlag = false;
}
/*
* Smooth deformation using a separable Gaussian kernel
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::SmoothDisplacementField()
{
DisplacementFieldPointer field = this->GetOutput();
// copy field to TempField
m_TempField->SetOrigin( field->GetOrigin() );
m_TempField->SetSpacing( field->GetSpacing() );
m_TempField->SetDirection( field->GetDirection() );
m_TempField->SetLargestPossibleRegion(
field->GetLargestPossibleRegion() );
m_TempField->SetRequestedRegion(
field->GetRequestedRegion() );
m_TempField->SetBufferedRegion( field->GetBufferedRegion() );
m_TempField->Allocate();
typedef typename DisplacementFieldType::PixelType VectorType;
typedef typename VectorType::ValueType ScalarType;
typedef GaussianOperator< ScalarType, ImageDimension > OperatorType;
typedef VectorNeighborhoodOperatorImageFilter<
DisplacementFieldType,
DisplacementFieldType > SmootherType;
OperatorType *oper = new OperatorType;
typename SmootherType::Pointer smoother = SmootherType::New();
typedef typename DisplacementFieldType::PixelContainerPointer
PixelContainerPointer;
PixelContainerPointer swapPtr;
// graft the output field onto the mini-pipeline
smoother->GraftOutput(m_TempField);
for ( unsigned int j = 0; j < ImageDimension; j++ )
{
// smooth along this dimension
oper->SetDirection(j);
double variance = itk::Math::sqr(m_StandardDeviations[j]);
oper->SetVariance(variance);
oper->SetMaximumError(m_MaximumError);
oper->SetMaximumKernelWidth(m_MaximumKernelWidth);
oper->CreateDirectional();
// todo: make sure we only smooth within the buffered region
smoother->SetOperator(*oper);
smoother->SetInput(field);
smoother->Update();
if ( j + 1 < ImageDimension )
{
// swap the containers
swapPtr = smoother->GetOutput()->GetPixelContainer();
smoother->GraftOutput(field);
field->SetPixelContainer(swapPtr);
smoother->Modified();
}
}
// graft the output back to this filter
m_TempField->SetPixelContainer( field->GetPixelContainer() );
this->GraftOutput( smoother->GetOutput() );
delete oper;
}
/*
* Smooth deformation using a separable Gaussian kernel
*/
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDisplacementField >
::SmoothUpdateField()
{
// The update buffer will be overwritten with new data.
DisplacementFieldPointer field = this->GetUpdateBuffer();
typedef typename DisplacementFieldType::PixelType VectorType;
typedef typename VectorType::ValueType ScalarType;
typedef GaussianOperator< ScalarType, ImageDimension > OperatorType;
typedef VectorNeighborhoodOperatorImageFilter<
DisplacementFieldType,
DisplacementFieldType > SmootherType;
OperatorType opers[ImageDimension];
typename SmootherType::Pointer smoothers[ImageDimension];
for ( unsigned int j = 0; j < ImageDimension; j++ )
{
// smooth along this dimension
opers[j].SetDirection(j);
double variance = itk::Math::sqr(this->GetUpdateFieldStandardDeviations()[j]);
//double variance = itk::Math::sqr( 1.0 );
opers[j].SetVariance(variance);
opers[j].SetMaximumError( this->GetMaximumError() );
opers[j].SetMaximumKernelWidth( this->GetMaximumKernelWidth() );
opers[j].CreateDirectional();
smoothers[j] = SmootherType::New();
smoothers[j]->SetOperator(opers[j]);
smoothers[j]->ReleaseDataFlagOn();
if ( j > 0 )
{
smoothers[j]->SetInput( smoothers[j - 1]->GetOutput() );
}
}
smoothers[0]->SetInput(field);
smoothers[ImageDimension - 1]->GetOutput()
->SetRequestedRegion( field->GetBufferedRegion() );
smoothers[ImageDimension - 1]->Update();
// field to contain the final smoothed data, do the equivalent of a graft
field->SetPixelContainer( smoothers[ImageDimension - 1]->GetOutput()
->GetPixelContainer() );
field->SetRequestedRegion( smoothers[ImageDimension - 1]->GetOutput()
->GetRequestedRegion() );
field->SetBufferedRegion( smoothers[ImageDimension - 1]->GetOutput()
->GetBufferedRegion() );
field->SetLargestPossibleRegion( smoothers[ImageDimension - 1]->GetOutput()
->GetLargestPossibleRegion() );
field->CopyInformation( smoothers[ImageDimension - 1]->GetOutput() );
}
} // end namespace itk
#endif