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/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* 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 itkAdvancedCombinationTransform_h
#define itkAdvancedCombinationTransform_h
#include "itkAdvancedTransform.h"
#include "itkMacro.h"
namespace itk
{
/**
* \class AdvancedCombinationTransform
*
* \brief This class combines two transforms: an 'initial transform'
* with a 'current transform'.
*
* The CombinationTransform class combines an initial transform \f$T_0\f$ with a
* current transform \f$T_1\f$.
*
* Two methods of combining the transforms are supported:
* \li Addition: \f$T(x) = T_0(x) + T_1(x)\f$
* \li Composition: \f$T(x) = T_1( T_0(x) )\f$
*
* The TransformPoint(), the GetJacobian() and the GetInverse() methods
* depend on this setting.
*
* If the transform is used in a registration framework,
* the initial transform is assumed constant, and the current
* transform is assumed to be the transform that is optimised.
* So, the transform parameters of the CombinationTransform are the
* parameters of the CurrentTransform \f$T_1\f$.
*
* Note: It is mandatory to set a current transform. An initial transform
* is not mandatory.
*
* \ingroup Transforms
*/
template <typename TScalarType, unsigned int NDimensions = 3>
class ITK_TEMPLATE_EXPORT AdvancedCombinationTransform : public AdvancedTransform<TScalarType, NDimensions, NDimensions>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(AdvancedCombinationTransform);
/** Standard itk. */
using Self = AdvancedCombinationTransform;
using Superclass = AdvancedTransform<TScalarType, NDimensions, NDimensions>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** New method for creating an object using a factory. */
itkNewMacro(Self);
/** ITK Type info. */
itkTypeMacro(AdvancedCombinationTransform, AdvancedTransform);
/** Input and Output space dimension. */
itkStaticConstMacro(SpaceDimension, unsigned int, NDimensions);
/** Typedefs inherited from Superclass.*/
using typename Superclass::ScalarType;
using typename Superclass::ParametersType;
using typename Superclass::FixedParametersType;
using typename Superclass::ParametersValueType;
using typename Superclass::NumberOfParametersType;
using typename Superclass::DerivativeType;
using typename Superclass::JacobianType;
using typename Superclass::InputVectorType;
using typename Superclass::OutputVectorType;
using typename Superclass::InputCovariantVectorType;
using typename Superclass::OutputCovariantVectorType;
using typename Superclass::InputVnlVectorType;
using typename Superclass::OutputVnlVectorType;
using typename Superclass::InputPointType;
using typename Superclass::OutputPointType;
using typename Superclass::NonZeroJacobianIndicesType;
using typename Superclass::SpatialJacobianType;
using typename Superclass::JacobianOfSpatialJacobianType;
using typename Superclass::SpatialHessianType;
using typename Superclass::JacobianOfSpatialHessianType;
using typename Superclass::InternalMatrixType;
using InverseTransformBaseType = typename Superclass::InverseTransformBaseType;
using typename Superclass::InverseTransformBasePointer;
using typename Superclass::TransformCategoryEnum;
using typename Superclass::MovingImageGradientType;
using typename Superclass::MovingImageGradientValueType;
/** Transform typedefs for the from Superclass. */
using TransformType = typename Superclass::TransformType;
using TransformTypePointer = typename TransformType::Pointer;
using TransformTypeConstPointer = typename TransformType::ConstPointer;
/** Typedefs for the InitialTransform. */
using InitialTransformType = Superclass;
using InitialTransformPointer = typename InitialTransformType::Pointer;
using InitialTransformConstPointer = typename InitialTransformType::ConstPointer;
using InitialTransformInverseTransformBaseType = typename InitialTransformType::InverseTransformBaseType;
using InitialTransformInverseTransformBasePointer = typename InitialTransformType::InverseTransformBasePointer;
/** Typedefs for the CurrentTransform. */
using CurrentTransformType = Superclass;
using CurrentTransformPointer = typename CurrentTransformType::Pointer;
using CurrentTransformConstPointer = typename CurrentTransformType::ConstPointer;
using CurrentTransformInverseTransformBaseType = typename CurrentTransformType::InverseTransformBaseType;
using CurrentTransformInverseTransformBasePointer = typename CurrentTransformType::InverseTransformBasePointer;
/** Set/Get a pointer to the InitialTransform. */
void
SetInitialTransform(InitialTransformType * _arg);
itkGetModifiableObjectMacro(InitialTransform, InitialTransformType);
/** Set/Get a pointer to the CurrentTransform.
* Make sure to set the CurrentTransform before calling functions like
* TransformPoint(), GetJacobian(), SetParameters() etc.
*/
void
SetCurrentTransform(CurrentTransformType * _arg);
itkGetModifiableObjectMacro(CurrentTransform, CurrentTransformType);
/** Return the number of sub-transforms. */
SizeValueType
GetNumberOfTransforms() const;
/** Get the Nth current transform.
* Exact interface to the ITK4 MultiTransform::GetNthTransform( SizeValueType n )
* \warning The bounds checking is performed.
*/
const TransformTypePointer
GetNthTransform(SizeValueType n) const;
/** Control the way transforms are combined. */
void
SetUseComposition(bool _arg);
itkGetConstMacro(UseComposition, bool);
/** Control the way transforms are combined. */
void
SetUseAddition(bool _arg);
itkGetConstMacro(UseAddition, bool);
/** Method to transform a point. */
OutputPointType
TransformPoint(const InputPointType & point) const override;
/** ITK4 change:
* The following pure virtual functions must be overloaded.
* For now just throw an exception, since these are not used in elastix.
*/
OutputVectorType
TransformVector(const InputVectorType &) const override
{
itkExceptionMacro("TransformVector(const InputVectorType &) is not implemented for AdvancedCombinationTransform");
}
OutputVnlVectorType
TransformVector(const InputVnlVectorType &) const override
{
itkExceptionMacro(
"TransformVector(const InputVnlVectorType &) is not implemented for AdvancedCombinationTransform");
}
OutputCovariantVectorType
TransformCovariantVector(const InputCovariantVectorType &) const override
{
itkExceptionMacro("TransformCovariantVector(const InputCovariantVectorType &) is not implemented for "
"AdvancedCombinationTransform");
}
/** Return the number of parameters that completely define the CurrentTransform. */
NumberOfParametersType
GetNumberOfParameters() const override;
/** Get the number of nonzero Jacobian indices. By default all. */
NumberOfParametersType
GetNumberOfNonZeroJacobianIndices() const override;
/** Get the transformation parameters from the CurrentTransform. */
const ParametersType &
GetParameters() const override;
/** Get the fixed parameters from the CurrentTransform. */
const FixedParametersType &
GetFixedParameters() const override;
/** Set the transformation parameters in the CurrentTransform. */
void
SetParameters(const ParametersType & param) override;
/** Set the transformation parameters in the CurrentTransform.
* This method forces the transform to copy the parameters.
*/
void
SetParametersByValue(const ParametersType & param) override;
/** Set the fixed parameters in the CurrentTransform. */
void
SetFixedParameters(const FixedParametersType & fixedParam) override;
/** Return the inverse \f$T^{-1}\f$ of the transform.
* This is only possible when:
* - both the inverses of the initial and the current transform
* are defined, and Composition is used:
* \f$T^{-1}(y) = T_0^{-1} ( T_1^{-1}(y) )\f$
* - No initial transform is used and the current transform is defined.
* In all other cases this function returns false and does not provide
* an inverse transform. An exception is thrown when no CurrentTransform
* is set.
*/
bool
GetInverse(Self * inverse) const;
/** Return whether the transform is linear (or actually: affine)
* Returns true when both initial and current transform are linear */
bool
IsLinear() const override;
/** Special handling for combination transform. If all transforms
* are linear, then return category Linear. Otherwise if all
* transforms set to optimize are DisplacementFields, then
* return DisplacementField category. */
TransformCategoryEnum
GetTransformCategory() const override;
/** Whether the advanced transform has nonzero matrices. */
bool
GetHasNonZeroSpatialHessian() const override;
bool
HasNonZeroJacobianOfSpatialHessian() const;
/** Compute the (sparse) Jacobian of the transformation. */
void
GetJacobian(const InputPointType & inputPoint,
JacobianType & j,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const override;
/** Compute the inner product of the Jacobian with the moving image gradient. */
void
EvaluateJacobianWithImageGradientProduct(const InputPointType & inputPoint,
const MovingImageGradientType & movingImageGradient,
DerivativeType & imageJacobian,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const override;
/** Compute the spatial Jacobian of the transformation. */
void
GetSpatialJacobian(const InputPointType & inputPoint, SpatialJacobianType & sj) const override;
/** Compute the spatial Hessian of the transformation. */
void
GetSpatialHessian(const InputPointType & inputPoint, SpatialHessianType & sh) const override;
/** Compute the Jacobian of the spatial Jacobian of the transformation. */
void
GetJacobianOfSpatialJacobian(const InputPointType & inputPoint,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const override;
/** Compute both the spatial Jacobian and the Jacobian of the
* spatial Jacobian of the transformation.
*/
void
GetJacobianOfSpatialJacobian(const InputPointType & inputPoint,
SpatialJacobianType & sj,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const override;
/** Compute the Jacobian of the spatial Hessian of the transformation. */
void
GetJacobianOfSpatialHessian(const InputPointType & inputPoint,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const override;
/** Compute both the spatial Hessian and the Jacobian of the
* spatial Hessian of the transformation.
*/
void
GetJacobianOfSpatialHessian(const InputPointType & inputPoint,
SpatialHessianType & sh,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const override;
protected:
/** Constructor. */
AdvancedCombinationTransform();
/** Destructor. */
~AdvancedCombinationTransform() override = default;
/** Set the SelectedTransformPointFunction and the
* SelectedGetJacobianFunction.
*/
void
UpdateCombinationMethod();
/** ************************************************
* Methods to transform a point.
*/
/** ADDITION: \f$T(x) = T_0(x) + T_1(x) - x\f$ */
OutputPointType
TransformPointUseAddition(const InputPointType & point) const;
/** COMPOSITION: \f$T(x) = T_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
OutputPointType
TransformPointUseComposition(const InputPointType & point) const;
/** CURRENT ONLY: \f$T(x) = T_1(x)\f$ */
OutputPointType
TransformPointNoInitialTransform(const InputPointType & point) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
OutputPointType
TransformPointNoCurrentTransform(const InputPointType & point) const;
/** ************************************************
* Methods to compute the sparse Jacobian.
*/
/** ADDITION: \f$J(x) = J_1(x)\f$ */
void
GetJacobianUseAddition(const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const;
/** COMPOSITION: \f$J(x) = J_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
void
GetJacobianUseComposition(const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const;
/** CURRENT ONLY: \f$J(x) = J_1(x)\f$ */
void
GetJacobianNoInitialTransform(const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
void
GetJacobianNoCurrentTransform(const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const;
/** ************************************************
* Methods to compute the inner product of the Jacobian with the moving image gradient.
*/
/** ADDITION: \f$J(x) = J_1(x)\f$ */
void
EvaluateJacobianWithImageGradientProductUseAddition(const InputPointType &,
const MovingImageGradientType &,
DerivativeType &,
NonZeroJacobianIndicesType &) const;
/** COMPOSITION: \f$J(x) = J_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
void
EvaluateJacobianWithImageGradientProductUseComposition(const InputPointType &,
const MovingImageGradientType &,
DerivativeType &,
NonZeroJacobianIndicesType &) const;
/** CURRENT ONLY: \f$J(x) = J_1(x)\f$ */
void
EvaluateJacobianWithImageGradientProductNoInitialTransform(const InputPointType &,
const MovingImageGradientType &,
DerivativeType &,
NonZeroJacobianIndicesType &) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
void
EvaluateJacobianWithImageGradientProductNoCurrentTransform(const InputPointType &,
const MovingImageGradientType &,
DerivativeType &,
NonZeroJacobianIndicesType &) const;
/** ************************************************
* Methods to compute the spatial Jacobian.
*/
/** ADDITION: \f$J(x) = J_1(x)\f$ */
void
GetSpatialJacobianUseAddition(const InputPointType & inputPoint, SpatialJacobianType & sj) const;
/** COMPOSITION: \f$J(x) = J_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
void
GetSpatialJacobianUseComposition(const InputPointType & inputPoint, SpatialJacobianType & sj) const;
/** CURRENT ONLY: \f$J(x) = J_1(x)\f$ */
void
GetSpatialJacobianNoInitialTransform(const InputPointType & inputPoint, SpatialJacobianType & sj) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
void
GetSpatialJacobianNoCurrentTransform(const InputPointType & inputPoint, SpatialJacobianType & sj) const;
/** ************************************************
* Methods to compute the spatial Hessian.
*/
/** ADDITION: \f$J(x) = J_1(x)\f$ */
void
GetSpatialHessianUseAddition(const InputPointType & inputPoint, SpatialHessianType & sh) const;
/** COMPOSITION: \f$J(x) = J_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
void
GetSpatialHessianUseComposition(const InputPointType & inputPoint, SpatialHessianType & sh) const;
/** CURRENT ONLY: \f$J(x) = J_1(x)\f$ */
void
GetSpatialHessianNoInitialTransform(const InputPointType & inputPoint, SpatialHessianType & sh) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
void
GetSpatialHessianNoCurrentTransform(const InputPointType & inputPoint, SpatialHessianType & sh) const;
/** ************************************************
* Methods to compute the Jacobian of the spatial Jacobian.
*/
/** ADDITION: \f$J(x) = J_1(x)\f$ */
void
GetJacobianOfSpatialJacobianUseAddition(const InputPointType & inputPoint,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialJacobianUseAddition(const InputPointType & inputPoint,
SpatialJacobianType & sj,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** COMPOSITION: \f$J(x) = J_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
void
GetJacobianOfSpatialJacobianUseComposition(const InputPointType & inputPoint,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialJacobianUseComposition(const InputPointType & inputPoint,
SpatialJacobianType & sj,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** CURRENT ONLY: \f$J(x) = J_1(x)\f$ */
void
GetJacobianOfSpatialJacobianNoInitialTransform(const InputPointType & inputPoint,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialJacobianNoInitialTransform(const InputPointType & inputPoint,
SpatialJacobianType & sj,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
void
GetJacobianOfSpatialJacobianNoCurrentTransform(const InputPointType & inputPoint,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialJacobianNoCurrentTransform(const InputPointType & inputPoint,
SpatialJacobianType & sj,
JacobianOfSpatialJacobianType & jsj,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** ************************************************
* Methods to compute the Jacobian of the spatial Hessian.
*/
/** ADDITION: \f$J(x) = J_1(x)\f$ */
void
GetJacobianOfSpatialHessianUseAddition(const InputPointType & inputPoint,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialHessianUseAddition(const InputPointType & inputPoint,
SpatialHessianType & sh,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** COMPOSITION: \f$J(x) = J_1( T_0(x) )\f$
* \warning: assumes that input and output point type are the same.
*/
void
GetJacobianOfSpatialHessianUseComposition(const InputPointType & inputPoint,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialHessianUseComposition(const InputPointType & inputPoint,
SpatialHessianType & sh,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** CURRENT ONLY: \f$J(x) = J_1(x)\f$ */
void
GetJacobianOfSpatialHessianNoInitialTransform(const InputPointType & inputPoint,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialHessianNoInitialTransform(const InputPointType & inputPoint,
SpatialHessianType & sh,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
/** NO CURRENT TRANSFORM SET: throw an exception. */
void
GetJacobianOfSpatialHessianNoCurrentTransform(const InputPointType & inputPoint,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
void
GetJacobianOfSpatialHessianNoCurrentTransform(const InputPointType & inputPoint,
SpatialHessianType & sh,
JacobianOfSpatialHessianType & jsh,
NonZeroJacobianIndicesType & nonZeroJacobianIndices) const;
private:
// Private using-declarations, to avoid `-Woverloaded-virtual` warnings from GCC (GCC 11.4).
using Superclass::TransformCovariantVector;
using Superclass::TransformVector;
/** Exception text. */
static constexpr const char * NoCurrentTransformSet = "No current transform set in the AdvancedCombinationTransform";
/** Declaration of members. */
InitialTransformPointer m_InitialTransform{ nullptr };
CurrentTransformPointer m_CurrentTransform{ nullptr };
/** Typedefs for function pointers. */
using TransformPointFunctionPointer = OutputPointType (Self::*)(const InputPointType &) const;
using GetSparseJacobianFunctionPointer = void (Self::*)(const InputPointType &,
JacobianType &,
NonZeroJacobianIndicesType &) const;
using EvaluateJacobianWithImageGradientProductFunctionPointer = void (Self::*)(const InputPointType &,
const MovingImageGradientType &,
DerivativeType &,
NonZeroJacobianIndicesType &) const;
using GetSpatialJacobianFunctionPointer = void (Self::*)(const InputPointType &, SpatialJacobianType &) const;
using GetSpatialHessianFunctionPointer = void (Self::*)(const InputPointType &, SpatialHessianType &) const;
using GetJacobianOfSpatialJacobianFunctionPointer = void (Self::*)(const InputPointType &,
JacobianOfSpatialJacobianType &,
NonZeroJacobianIndicesType &) const;
using GetJacobianOfSpatialJacobianFunctionPointer2 = void (Self::*)(const InputPointType &,
SpatialJacobianType &,
JacobianOfSpatialJacobianType &,
NonZeroJacobianIndicesType &) const;
using GetJacobianOfSpatialHessianFunctionPointer = void (Self::*)(const InputPointType &,
JacobianOfSpatialHessianType &,
NonZeroJacobianIndicesType &) const;
using GetJacobianOfSpatialHessianFunctionPointer2 = void (Self::*)(const InputPointType &,
SpatialHessianType &,
JacobianOfSpatialHessianType &,
NonZeroJacobianIndicesType &) const;
/** A pointer to one of the following functions:
* - TransformPointUseAddition,
* - TransformPointUseComposition,
* - TransformPointNoCurrentTransform
* - TransformPointNoInitialTransform.
*/
TransformPointFunctionPointer m_SelectedTransformPointFunction{ &Self::TransformPointNoCurrentTransform };
/** A pointer to one of the following functions:
* - GetJacobianUseAddition,
* - GetJacobianUseComposition,
* - GetJacobianNoCurrentTransform
* - GetJacobianNoInitialTransform.
*/
// GetJacobianFunctionPointer m_SelectedGetJacobianFunction;
/** More of these. Set everything to have no current transform. */
GetSparseJacobianFunctionPointer m_SelectedGetSparseJacobianFunction{ &Self::GetJacobianNoCurrentTransform };
EvaluateJacobianWithImageGradientProductFunctionPointer m_SelectedEvaluateJacobianWithImageGradientProductFunction{
&Self::EvaluateJacobianWithImageGradientProductNoInitialTransform
};
GetSpatialJacobianFunctionPointer m_SelectedGetSpatialJacobianFunction{ &Self::GetSpatialJacobianNoCurrentTransform };
GetSpatialHessianFunctionPointer m_SelectedGetSpatialHessianFunction{ &Self::GetSpatialHessianNoCurrentTransform };
GetJacobianOfSpatialJacobianFunctionPointer m_SelectedGetJacobianOfSpatialJacobianFunction{
&Self::GetJacobianOfSpatialJacobianNoCurrentTransform
};
GetJacobianOfSpatialJacobianFunctionPointer2 m_SelectedGetJacobianOfSpatialJacobianFunction2{
&Self::GetJacobianOfSpatialJacobianNoCurrentTransform
};
GetJacobianOfSpatialHessianFunctionPointer m_SelectedGetJacobianOfSpatialHessianFunction{
&Self::GetJacobianOfSpatialHessianNoCurrentTransform
};
GetJacobianOfSpatialHessianFunctionPointer2 m_SelectedGetJacobianOfSpatialHessianFunction2{
&Self::GetJacobianOfSpatialHessianNoCurrentTransform
};
/** How to combine the transformations. Composition by default. */
bool m_UseAddition{ false };
bool m_UseComposition{ true };
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkAdvancedCombinationTransform.hxx"
#endif
#endif // end #ifndef itkAdvancedCombinationTransform_h
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