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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: itkBSplineDeformableTransform.h,v $
Language: C++
Date: $Date: 2008-04-11 16:28:11 $
Version: $Revision: 1.38 $
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 __itkBSplineDeformableTransform_h
#define __itkBSplineDeformableTransform_h
#include <iostream>
#include "itkTransform.h"
#include "itkImage.h"
#include "itkImageRegion.h"
#include "itkBSplineInterpolationWeightFunction.h"
namespace itk
{
/** \class BSplineDeformableTransform
* \brief Deformable transform using a BSpline representation
*
* This class encapsulates a deformable transform of points from one
* N-dimensional one space to another N-dimensional space.
* The deformation field is modeled using B-splines.
* A deformation is defined on a sparse regular grid of control points
* \f$ \vec{\lambda}_j \f$ and is varied by defining a deformation
* \f$ \vec{g}(\vec{\lambda}_j) \f$ of each control point.
* The deformation \f$ D(\vec{x}) \f$ at any point \f$ \vec{x} \f$
* is obtained by using a B-spline interpolation kernel.
*
* The deformation field grid is defined by a user specified GridRegion,
* GridSpacing and GridOrigin. Each grid/control point has associated with it
* N deformation coefficients \f$ \vec{\delta}_j \f$, representing the N
* directional components of the deformation. Deformation outside the grid
* plus support region for the BSpline interpolation is assumed to be zero.
*
* Additionally, the user can specified an addition bulk transform \f$ B \f$
* such that the transformed point is given by:
* \f[ \vec{y} = B(\vec{x}) + D(\vec{x}) \f]
*
* The parameters for this transform is N x N-D grid of spline coefficients.
* The user specifies the parameters as one flat array: each N-D grid
* is represented by an array in the same way an N-D image is represented
* in the buffer; the N arrays are then concatentated together on form
* a single array.
*
* For efficiency, this transform does not make a copy of the parameters.
* It only keeps a pointer to the input parameters and assumes that the memory
* is managed by the caller.
*
* The following illustrates the typical usage of this class:
* \verbatim
* typedef BSplineDeformableTransform<double,2,3> TransformType;
* TransformType::Pointer transform = TransformType::New();
*
* transform->SetGridRegion( region );
* transform->SetGridSpacing( spacing );
* transform->SetGridOrigin( origin );
*
* // NB: the region must be set first before setting the parameters
*
* TransformType::ParametersType parameters(
* transform->GetNumberOfParameters() );
*
* // Fill the parameters with values
*
* transform->SetParameters( parameters )
*
* outputPoint = transform->TransformPoint( inputPoint );
*
* \endverbatim
*
* An alternative way to set the B-spline coefficients is via array of
* images. The grid region, spacing and origin information is taken
* directly from the first image. It is assumed that the subsequent images
* are the same buffered region. The following illustrates the API:
* \verbatim
*
* TransformType::ImageConstPointer images[2];
*
* // Fill the images up with values
*
* transform->SetCoefficientImages( images );
* outputPoint = transform->TransformPoint( inputPoint );
*
* \endverbatim
*
* Warning: use either the SetParameters() or SetCoefficientImage()
* API. Mixing the two modes may results in unexpected results.
*
* The class is templated coordinate representation type (float or double),
* the space dimension and the spline order.
*
* \ingroup Transforms
*/
template <
class TScalarType = double, // Data type for scalars
unsigned int NDimensions = 3, // Number of dimensions
unsigned int VSplineOrder = 3 > // Spline order
class ITK_EXPORT BSplineDeformableTransform :
public Transform< TScalarType, NDimensions, NDimensions >
{
public:
/** Standard class typedefs. */
typedef BSplineDeformableTransform Self;
typedef Transform< TScalarType, NDimensions, NDimensions > Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** New macro for creation of through the object factory.*/
itkNewMacro( Self );
/** Run-time type information (and related methods). */
itkTypeMacro( BSplineDeformableTransform, Transform );
/** Dimension of the domain space. */
itkStaticConstMacro(SpaceDimension, unsigned int, NDimensions);
/** The BSpline order. */
itkStaticConstMacro(SplineOrder, unsigned int, VSplineOrder);
/** Standard scalar type for this class. */
typedef typename Superclass::ScalarType ScalarType;
/** Standard parameters container. */
typedef typename Superclass::ParametersType ParametersType;
/** Standard Jacobian container. */
typedef typename Superclass::JacobianType JacobianType;
/** Standard vector type for this class. */
typedef Vector<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> InputVectorType;
typedef Vector<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> OutputVectorType;
/** Standard covariant vector type for this class. */
typedef CovariantVector<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> InputCovariantVectorType;
typedef CovariantVector<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> OutputCovariantVectorType;
/** Standard vnl_vector type for this class. */
typedef vnl_vector_fixed<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> InputVnlVectorType;
typedef vnl_vector_fixed<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> OutputVnlVectorType;
/** Standard coordinate point type for this class. */
typedef Point<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> InputPointType;
typedef Point<TScalarType,
itkGetStaticConstMacro(SpaceDimension)> OutputPointType;
/** This method sets the parameters of the transform.
* For a BSpline deformation transform, the parameters are the BSpline
* coefficients on a sparse grid.
*
* The parameters are N number of N-D grid of coefficients. Each N-D grid
* is represented as a flat array of doubles
* (in the same configuration as an itk::Image).
* The N arrays are then concatenated to form one parameter array.
*
* For efficiency, this transform does not make a copy of the parameters.
* It only keeps a pointer to the input parameters. It assumes that the memory
* is managed by the caller. Use SetParametersByValue to force the transform
* to call copy the parameters.
*
* This method wraps each grid as itk::Image's using the user specified
* grid region, spacing and origin.
* NOTE: The grid region, spacing and origin must be set first.
*
*/
void SetParameters(const ParametersType & parameters);
/** This method sets the fixed parameters of the transform.
* For a BSpline deformation transform, the parameters are the following:
* Grid Size, Grid Origin, and Grid Spacing
*
* The fixed parameters are the three times the size of the templated
* dimensions.
* This function has the effect of make the following calls:
* transform->SetGridSpacing( spacing );
* transform->SetGridOrigin( origin );
* transform->SetGridDirection( direction );
* transform->SetGridRegion( bsplineRegion );
*
* This function was added to allow the transform to work with the
* itkTransformReader/Writer I/O filters.
*
*/
void SetFixedParameters(const ParametersType & parameters);
/** This method sets the parameters of the transform.
* For a BSpline deformation transform, the parameters are the BSpline
* coefficients on a sparse grid.
*
* The parameters are N number of N-D grid of coefficients. Each N-D grid
* is represented as a flat array of doubles
* (in the same configuration as an itk::Image).
* The N arrays are then concatenated to form one parameter array.
*
* This methods makes a copy of the parameters while for
* efficiency the SetParameters method does not.
*
* This method wraps each grid as itk::Image's using the user specified
* grid region, spacing and origin.
* NOTE: The grid region, spacing and origin must be set first.
*
*/
void SetParametersByValue(const ParametersType & parameters);
/** This method can ONLY be invoked AFTER calling SetParameters().
* This restriction is due to the fact that the BSplineDeformableTransform
* does not copy the array of paramters internally, instead it keeps a
* pointer to the user-provided array of parameters. This method is also
* in violation of the const-correctness of the parameters since the
* parameter array has been passed to the transform on a 'const' basis but
* the values get modified when the user invokes SetIdentity().
*/
void SetIdentity();
/** Get the Transformation Parameters. */
virtual const ParametersType& GetParameters(void) const;
/** Get the Transformation Fixed Parameters. */
virtual const ParametersType& GetFixedParameters(void) const;
/** Parameters as SpaceDimension number of images. */
typedef typename ParametersType::ValueType PixelType;
typedef Image<PixelType,itkGetStaticConstMacro(SpaceDimension)> ImageType;
typedef typename ImageType::Pointer ImagePointer;
/** Get the array of coefficient images. */
virtual ImagePointer * GetCoefficientImage()
{ return m_CoefficientImage; }
virtual const ImagePointer * GetCoefficientImage() const
{ return m_CoefficientImage; }
/** Set the array of coefficient images.
*
* This is an alternative API for setting the BSpline coefficients
* as an array of SpaceDimension images. The grid region spacing
* and origin is taken from the first image. It is assume that
* the buffered region of all the subsequent images are the same
* as the first image. Note that no error checking is done.
*
* Warning: use either the SetParameters() or SetCoefficientImage()
* API. Mixing the two modes may results in unexpected results.
*
*/
virtual void SetCoefficientImage( ImagePointer images[] );
/** Typedefs for specifying the extend to the grid. */
typedef ImageRegion<itkGetStaticConstMacro(SpaceDimension)> RegionType;
typedef typename RegionType::IndexType IndexType;
typedef typename RegionType::SizeType SizeType;
typedef typename ImageType::SpacingType SpacingType;
typedef typename ImageType::DirectionType DirectionType;
typedef typename ImageType::PointType OriginType;
/** This method specifies the region over which the grid resides. */
virtual void SetGridRegion( const RegionType& region );
itkGetMacro( GridRegion, RegionType );
itkGetConstMacro( GridRegion, RegionType );
/** This method specifies the grid spacing or resolution. */
virtual void SetGridSpacing( const SpacingType& spacing );
itkGetMacro( GridSpacing, SpacingType );
itkGetConstMacro( GridSpacing, SpacingType );
/** This method specifies the grid directions . */
virtual void SetGridDirection( const DirectionType & spacing );
itkGetMacro( GridDirection, DirectionType );
itkGetConstMacro( GridDirection, DirectionType );
/** This method specifies the grid origin. */
virtual void SetGridOrigin( const OriginType& origin );
itkGetMacro( GridOrigin, OriginType );
itkGetConstMacro( GridOrigin, OriginType );
/** Typedef of the bulk transform. */
typedef Transform<ScalarType,itkGetStaticConstMacro(SpaceDimension),
itkGetStaticConstMacro(SpaceDimension)> BulkTransformType;
typedef typename BulkTransformType::ConstPointer BulkTransformPointer;
/** This method specifies the bulk transform to be applied.
* The default is the identity transform.
*/
itkSetConstObjectMacro( BulkTransform, BulkTransformType );
itkGetConstObjectMacro( BulkTransform, BulkTransformType );
/** Transform points by a BSpline deformable transformation. */
OutputPointType TransformPoint(const InputPointType &point ) const;
/** Interpolation weights function type. */
typedef BSplineInterpolationWeightFunction<ScalarType,
itkGetStaticConstMacro(SpaceDimension),
itkGetStaticConstMacro(SplineOrder)> WeightsFunctionType;
typedef typename WeightsFunctionType::WeightsType WeightsType;
typedef typename WeightsFunctionType::ContinuousIndexType
ContinuousIndexType;
/** Parameter index array type. */
typedef Array<unsigned long> ParameterIndexArrayType;
/** Transform points by a BSpline deformable transformation.
* On return, weights contains the interpolation weights used to compute the
* deformation and indices of the x (zeroth) dimension coefficient parameters
* in the support region used to compute the deformation.
* Parameter indices for the i-th dimension can be obtained by adding
* ( i * this->GetNumberOfParametersPerDimension() ) to the indices array.
*/
virtual void TransformPoint( const InputPointType & inputPoint,
OutputPointType & outputPoint,
WeightsType & weights,
ParameterIndexArrayType & indices,
bool & inside ) const;
virtual void GetJacobian( const InputPointType & inputPoint,
WeightsType & weights,
ParameterIndexArrayType & indices
) const;
/** Get number of weights. */
unsigned long GetNumberOfWeights() const
{ return m_WeightsFunction->GetNumberOfWeights(); }
/** Method to transform a vector -
* not applicable for this type of transform. */
virtual OutputVectorType TransformVector(const InputVectorType &) const
{
itkExceptionMacro(<< "Method not applicable for deformable transform." );
return OutputVectorType();
}
/** Method to transform a vnl_vector -
* not applicable for this type of transform */
virtual OutputVnlVectorType TransformVector(const InputVnlVectorType &) const
{
itkExceptionMacro(<< "Method not applicable for deformable transform. ");
return OutputVnlVectorType();
}
/** Method to transform a CovariantVector -
* not applicable for this type of transform */
virtual OutputCovariantVectorType TransformCovariantVector(
const InputCovariantVectorType &) const
{
itkExceptionMacro(<< "Method not applicable for deformable transfrom. ");
return OutputCovariantVectorType();
}
/** Compute the Jacobian Matrix of the transformation at one point */
virtual const JacobianType& GetJacobian(const InputPointType &point ) const;
/** Return the number of parameters that completely define the Transfom */
virtual unsigned int GetNumberOfParameters(void) const;
/** Return the number of parameters per dimension */
unsigned int GetNumberOfParametersPerDimension(void) const;
/** Return the region of the grid wholly within the support region */
itkGetConstReferenceMacro( ValidRegion, RegionType );
/** Indicates that this transform is linear. That is, given two
* points P and Q, and scalar coefficients a and b, then
*
* T( a*P + b*Q ) = a * T(P) + b * T(Q)
*/
virtual bool IsLinear() const { return false; }
unsigned int GetNumberOfAffectedWeights() const;
protected:
/** Print contents of an BSplineDeformableTransform. */
void PrintSelf(std::ostream &os, Indent indent) const;
BSplineDeformableTransform();
virtual ~BSplineDeformableTransform();
/** Allow subclasses to access and manipulate the weights function. */
itkSetObjectMacro( WeightsFunction, WeightsFunctionType );
itkGetObjectMacro( WeightsFunction, WeightsFunctionType );
/** Wrap flat array into images of coefficients. */
void WrapAsImages();
/** Convert an input point to a continuous index inside the BSpline grid */
void TransformPointToContinuousIndex(
const InputPointType & point, ContinuousIndexType & index ) const;
private:
BSplineDeformableTransform(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
/** The bulk transform. */
BulkTransformPointer m_BulkTransform;
/** Variables defining the coefficient grid extend. */
RegionType m_GridRegion;
SpacingType m_GridSpacing;
DirectionType m_GridDirection;
OriginType m_GridOrigin;
DirectionType m_PointToIndex;
DirectionType m_IndexToPoint;
RegionType m_ValidRegion;
/** Variables defining the interpolation support region. */
unsigned long m_Offset;
bool m_SplineOrderOdd;
SizeType m_SupportSize;
IndexType m_ValidRegionLast;
/** Array holding images wrapped from the flat parameters. */
ImagePointer m_WrappedImage[NDimensions];
/** Array of images representing the B-spline coefficients
* in each dimension. */
ImagePointer m_CoefficientImage[NDimensions];
/** Jacobian as SpaceDimension number of images. */
typedef typename JacobianType::ValueType JacobianPixelType;
typedef Image<JacobianPixelType,
itkGetStaticConstMacro(SpaceDimension)> JacobianImageType;
typename JacobianImageType::Pointer m_JacobianImage[NDimensions];
/** Keep track of last support region used in computing the Jacobian
* for fast resetting of Jacobian to zero.
*/
mutable IndexType m_LastJacobianIndex;
/** Keep a pointer to the input parameters. */
const ParametersType * m_InputParametersPointer;
/** Internal parameters buffer. */
ParametersType m_InternalParametersBuffer;
/** Pointer to function used to compute Bspline interpolation weights. */
typename WeightsFunctionType::Pointer m_WeightsFunction;
/** Check if a continuous index is inside the valid region. */
bool InsideValidRegion( const ContinuousIndexType& index ) const;
}; //class BSplineDeformableTransform
} // namespace itk
// Define instantiation macro for this template.
#define ITK_TEMPLATE_BSplineDeformableTransform(_, EXPORT, x, y) namespace itk { \
_(3(class EXPORT BSplineDeformableTransform< ITK_TEMPLATE_3 x >)) \
namespace Templates { typedef BSplineDeformableTransform< ITK_TEMPLATE_3 x > \
BSplineDeformableTransform##y; } \
}
#if ITK_TEMPLATE_EXPLICIT
# include "Templates/itkBSplineDeformableTransform+-.h"
#endif
#if ITK_TEMPLATE_TXX
# include "itkBSplineDeformableTransform.txx"
#endif
#endif /* __itkBSplineDeformableTransform_h */
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