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itkPDEDeformableRegistrationFilter.h
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itkPDEDeformableRegistrationFilter.h
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkPDEDeformableRegistrationFilter.h
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 _itkPDEDeformableRegistrationFilter_h_
#define _itkPDEDeformableRegistrationFilter_h_
#include "itkDenseFiniteDifferenceImageFilter.h"
#include "itkPDEDeformableRegistrationFunction.h"
namespace itk {
/**
* \class PDEDeformableRegistrationFilter
* \brief Deformably register two images using a PDE algorithm.
*
* PDEDeformableRegistrationFilter is a base case for filter implementing
* a PDE deformable algorithm that register two images by computing the
* deformation field which will map a moving image onto a fixed image.
*
* A deformation field is represented as a image whose pixel type is some
* vector type with at least N elements, where N is the dimension of
* the fixed image. The vector type must support element access via operator
* []. It is assumed that the vector elements behave like floating point
* scalars.
*
* This class is templated over the fixed image type, moving image type
* and the deformation Field type.
*
* The input fixed and moving images are set via methods SetFixedImage
* and SetMovingImage respectively. An initial deformation field maybe set via
* SetInitialDeformationField or SetInput. If no initial field is set,
* a zero field is used as the initial condition.
*
* The output deformation field can be obtained via methods GetOutput
* or GetDeformationField.
*
* The PDE algorithm is run for a user defined number of iterations.
* Typically the PDE algorithm requires period Gaussin smoothing of the
* deformation field to enforce an elastic-like condition. The amount
* of smoothing is governed by a set of user defined standard deviations
* (one for each dimension).
*
* In terms of memory, this filter keeps two internal buffers: one for storing
* the intermediate updates to the field and one for double-buffering when
* smoothing the deformation field. Both buffers are the same type and size as the
* output deformation field.
*
* This class make use of the finite difference solver hierarchy. Update
* for each iteration is computed using a PDEDeformableRegistrationFunction.
*
* \warning This filter assumes that the fixed image type, moving image type
* and deformation field type all have the same number of dimensions.
*
* \sa PDEDeformableRegistrationFunction.
* \ingroup DeformableImageRegistration
*/
template<class TFixedImage, class TMovingImage, class TDeformationField>
class ITK_EXPORT PDEDeformableRegistrationFilter :
public DenseFiniteDifferenceImageFilter<TDeformationField,TDeformationField>
{
public:
/** Standard class typedefs. */
typedef PDEDeformableRegistrationFilter Self;
typedef DenseFiniteDifferenceImageFilter<
TDeformationField,TDeformationField> Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods) */
itkTypeMacro( PDEDeformableRegistrationFilter,
DenseFiniteDifferenceImageFilter );
/** FixedImage image type. */
typedef TFixedImage FixedImageType;
typedef typename FixedImageType::Pointer FixedImagePointer;
typedef typename FixedImageType::ConstPointer FixedImageConstPointer;
/** MovingImage image type. */
typedef TMovingImage MovingImageType;
typedef typename MovingImageType::Pointer MovingImagePointer;
typedef typename MovingImageType::ConstPointer MovingImageConstPointer;
/** Deformation field type. */
typedef TDeformationField DeformationFieldType;
typedef typename DeformationFieldType::Pointer DeformationFieldPointer;
/** Types inherithed from the superclass */
typedef typename Superclass::OutputImageType OutputImageType;
/** FiniteDifferenceFunction type. */
typedef typename Superclass::FiniteDifferenceFunctionType
FiniteDifferenceFunctionType;
/** PDEDeformableRegistrationFilterFunction type. */
typedef PDEDeformableRegistrationFunction<FixedImageType,MovingImageType,
DeformationFieldType> PDEDeformableRegistrationFunctionType;
/** Inherit some enums and typedefs from the superclass. */
itkStaticConstMacro(ImageDimension, unsigned int,
Superclass::ImageDimension);
/** Set the fixed image. */
void SetFixedImage( const FixedImageType * ptr );
/** Get the fixed image. */
const FixedImageType * GetFixedImage(void) const;
/** Set the moving image. */
void SetMovingImage( const MovingImageType * ptr );
/** Get the moving image. */
const MovingImageType * GetMovingImage(void) const;
/** Set initial deformation field. */
void SetInitialDeformationField( DeformationFieldType * ptr )
{ this->SetInput( ptr ); }
/** Get output deformation field. */
DeformationFieldType * GetDeformationField()
{ return this->GetOutput(); }
/** Get the number of valid inputs. For PDEDeformableRegistration,
* this checks whether the fixed and moving images have been
* set. While PDEDeformableRegistration can take a third input as an
* initial deformation field, this input is not a required input.
*/
virtual std::vector<SmartPointer<DataObject> >::size_type GetNumberOfValidRequiredInputs() const;
/** Set/Get whether the deformation field is smoothed
* (regularized). Smoothing the deformation yields a solution
* elastic in nature. If SmoothDeformationField is on, then the
* deformation field is smoothed with a Gaussian whose standard
* deviations are specified with SetStandardDeviations() */
itkSetMacro( SmoothDeformationField, bool );
itkGetMacro( SmoothDeformationField, bool );
itkBooleanMacro( SmoothDeformationField );
/** Set the Gaussian smoothing standard deviations for the
* deformation field. The values are set with respect to pixel
* coordinates. */
itkSetVectorMacro( StandardDeviations, double, ImageDimension );
virtual void SetStandardDeviations( double value );
/** Get the Gaussian smoothing standard deviations use for smoothing
* the deformation field. */
const double * GetStandardDeviations(void)
{ return (double *) m_StandardDeviations; }
/** Set/Get whether the update field is smoothed
* (regularized). Smoothing the update field yields a solution
* viscous in nature. If SmoothUpdateField is on, then the
* update field is smoothed with a Gaussian whose standard
* deviations are specified with SetUpdateFieldStandardDeviations() */
itkSetMacro( SmoothUpdateField, bool );
itkGetMacro( SmoothUpdateField, bool );
itkBooleanMacro( SmoothUpdateField );
/** Set the Gaussian smoothing standard deviations for the update
* field. The values are set with respect to pixel coordinates. */
itkSetVectorMacro( UpdateFieldStandardDeviations, double, ImageDimension );
virtual void SetUpdateFieldStandardDeviations( double value );
/** Get the Gaussian smoothing standard deviations used for
* smoothing the update field. */
const double * GetUpdateFieldStandardDeviations(void)
{ return (double *) m_UpdateFieldStandardDeviations; }
/** Stop the registration after the current iteration. */
virtual void StopRegistration()
{ m_StopRegistrationFlag = true; }
/** Set/Get the desired maximum error of the Guassian kernel approximate.
* \sa GaussianOperator. */
itkSetMacro( MaximumError, double );
itkGetMacro( MaximumError, double );
/** Set/Get the desired limits of the Gaussian kernel width.
* \sa GaussianOperator. */
itkSetMacro( MaximumKernelWidth, unsigned int );
itkGetMacro( MaximumKernelWidth, unsigned int );
protected:
PDEDeformableRegistrationFilter();
~PDEDeformableRegistrationFilter() {}
void PrintSelf(std::ostream& os, Indent indent) const;
/** Supplies the halting criteria for this class of filters. The
* algorithm will stop after a user-specified number of iterations. */
virtual bool Halt()
{
if ( m_StopRegistrationFlag )
{
return true;
}
return this->Superclass::Halt();
}
/** A simple method to copy the data from the input to the output.
* If the input does not exist, a zero field is written to the output. */
virtual void CopyInputToOutput();
/** Initialize the state of filter and equation before each iteration.
* Progress feeback is implemented as part of this method. */
virtual void InitializeIteration();
/** Utility to smooth the deformation field (represented in the Output)
* using a Guassian operator. The amount of smoothing can be specified
* by setting the StandardDeviations. */
virtual void SmoothDeformationField();
/** Utility to smooth the UpdateBuffer using a Gaussian operator.
* The amount of smoothing can be specified by setting the
* UpdateFieldStandardDeviations. */
virtual void SmoothUpdateField();
/** This method is called after the solution has been generated. In this case,
* the filter release the memory of the internal buffers. */
virtual void PostProcessOutput();
/** This method is called before iterating the solution. */
virtual void Initialize();
/** By default the output deformation field has the same Spacing, Origin
* and LargestPossibleRegion as the input/initial deformation field. If
* the initial deformation field is not set, the output information is
* copied from the fixed image. */
virtual void GenerateOutputInformation();
/** It is difficult to compute in advance the input moving image region
* required to compute the requested output region. Thus the safest
* thing to do is to request for the whole moving image.
*
* For the fixed image and deformation field, the input requested region
* set to be the same as that of the output requested region. */
virtual void GenerateInputRequestedRegion();
private:
PDEDeformableRegistrationFilter(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
/** Standard deviation for Gaussian smoothing */
double m_StandardDeviations[ImageDimension];
double m_UpdateFieldStandardDeviations[ImageDimension];
/** Modes to control smoothing of the update and deformation fields */
bool m_SmoothDeformationField;
bool m_SmoothUpdateField;
/** Temporary deformation field use for smoothing the
* the deformation field. */
DeformationFieldPointer m_TempField;
private:
/** Maximum error for Gaussian operator approximation. */
double m_MaximumError;
/** Limits of Guassian kernel width. */
unsigned int m_MaximumKernelWidth;
/** Flag to indicate user stop registration request. */
bool m_StopRegistrationFlag;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkPDEDeformableRegistrationFilter.txx"
#endif
#endif