itkKernelTransform.h

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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 itkKernelTransform_h
#define itkKernelTransform_h

#include "itkTransform.h"
#include "itkMatrix.h"
#include "itkPointSet.h"
#include <deque>
#include <cmath>
#include "vnl/vnl_matrix_fixed.h"
#include "vnl/vnl_matrix.h"
#include "vnl/vnl_vector.h"
#include "vnl/vnl_vector_fixed.h"
#include "vnl/algo/vnl_svd.h"

namespace itk
{
template<typename TParametersValueType,
          unsigned int NDimensions>
class ITK_TEMPLATE_EXPORT KernelTransform :
  public Transform<TParametersValueType, NDimensions, NDimensions>
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(KernelTransform);

  using Self = KernelTransform;
  using Superclass = Transform<TParametersValueType, NDimensions, NDimensions>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  itkTypeMacro(KernelTransform, Transform);

  itkNewMacro(Self);

  static constexpr unsigned int SpaceDimension = NDimensions;

  using ScalarType = typename Superclass::ScalarType;

  using FixedParametersType = typename Superclass::FixedParametersType;
  using ParametersType = typename Superclass::ParametersType;

  using JacobianType = typename Superclass::JacobianType;
  using JacobianPositionType = typename Superclass::JacobianPositionType;
  using InverseJacobianPositionType = typename Superclass::InverseJacobianPositionType;

  using TransformCategoryType = typename Superclass::TransformCategoryType;

  using InputPointType = typename Superclass::InputPointType;
  using OutputPointType = typename Superclass::OutputPointType;

  using InputVectorType = typename Superclass::InputVectorType;
  using OutputVectorType = typename Superclass::OutputVectorType;

  using InputCovariantVectorType = typename Superclass::InputCovariantVectorType;
  using OutputCovariantVectorType = typename Superclass::OutputCovariantVectorType;

  using InputVnlVectorType = typename Superclass::InputVnlVectorType;
  using OutputVnlVectorType = typename Superclass::OutputVnlVectorType;

  using NumberOfParametersType = typename Superclass::NumberOfParametersType;

  using PointSetTraitsType = DefaultStaticMeshTraits<TParametersValueType, NDimensions, NDimensions, TParametersValueType, TParametersValueType>;
  using PointSetType = PointSet<InputPointType, NDimensions, PointSetTraitsType>;

  using PointSetPointer = typename PointSetType::Pointer;
  using PointsContainer = typename PointSetType::PointsContainer;
  using PointsIterator = typename PointSetType::PointsContainerIterator;
  using PointsConstIterator = typename PointSetType::PointsContainerConstIterator;
  using PointIdentifier = typename PointSetType::PointIdentifier;

  using VectorSetType = itk::VectorContainer<SizeValueType, InputVectorType>;
  using VectorSetPointer = typename VectorSetType::Pointer;

  itkGetModifiableObjectMacro(SourceLandmarks, PointSetType); //NOTE: This is used to circumvent the SetTargetLandmarks
  virtual void SetSourceLandmarks(PointSetType *);

  itkGetModifiableObjectMacro(TargetLandmarks, PointSetType); //NOTE: This is used to circumvent the SetTargetLandmarks
  virtual void SetTargetLandmarks(PointSetType *);

  itkGetModifiableObjectMacro(Displacements, VectorSetType);

  void ComputeWMatrix();

  OutputPointType TransformPoint(const InputPointType & thisPoint) const override;

  using Superclass::TransformVector;
  OutputVectorType TransformVector(const InputVectorType &) const override
  {
    itkExceptionMacro( << "TransformVector(const InputVectorType &) is not implemented for KernelTransform");
  }

  OutputVnlVectorType TransformVector(const InputVnlVectorType &) const override
  {
    itkExceptionMacro( << "TransformVector(const InputVnlVectorType &) is not implemented for KernelTransform");
  }

  using Superclass::TransformCovariantVector;
  OutputCovariantVectorType TransformCovariantVector(const InputCovariantVectorType &) const override
  {
    itkExceptionMacro( << "TransformCovariantVector(const InputCovariantVectorType &) is not implemented for KernelTransform");
  }

  using IMatrixType = vnl_matrix_fixed<TParametersValueType, NDimensions, NDimensions>;

  void ComputeJacobianWithRespectToParameters( const InputPointType  & p, JacobianType & jacobian) const override;

  void ComputeJacobianWithRespectToPosition(const InputPointType &,
                                                    JacobianPositionType &) const override
  {
    itkExceptionMacro( "ComputeJacobianWithRespectToPosition not yet implemented "
                       "for " << this->GetNameOfClass() );
  }
  using Superclass::ComputeJacobianWithRespectToPosition;

  void SetParameters(const ParametersType &) override;

  void SetFixedParameters(const FixedParametersType &) override;

  virtual void UpdateParameters() const;

  const ParametersType & GetParameters() const override;

  const FixedParametersType & GetFixedParameters() const override;

  TransformCategoryType GetTransformCategory() const override
  {
    return Self::Spline;
  }

  itkSetClampMacro( Stiffness, double, 0.0, NumericTraits<double>::max() );
  itkGetConstMacro(Stiffness, double);

protected:
  KernelTransform();
  ~KernelTransform() override = default;
  void PrintSelf(std::ostream & os, Indent indent) const override;

public:
  using GMatrixType = vnl_matrix_fixed<TParametersValueType, NDimensions, NDimensions>;

  using LMatrixType = vnl_matrix<TParametersValueType>;

  using KMatrixType = vnl_matrix<TParametersValueType>;

  using PMatrixType = vnl_matrix<TParametersValueType>;

  using YMatrixType = vnl_matrix<TParametersValueType>;

  using WMatrixType = vnl_matrix<TParametersValueType>;

  using DMatrixType = vnl_matrix<TParametersValueType>;

  using AMatrixType = vnl_matrix_fixed<TParametersValueType, NDimensions, NDimensions>;

  using BMatrixType = vnl_vector_fixed<TParametersValueType, NDimensions>;

  using RowMatrixType = vnl_matrix_fixed<TParametersValueType, 1, NDimensions>;

  using ColumnMatrixType = vnl_matrix_fixed<TParametersValueType, NDimensions, 1>;

protected:
  virtual void ComputeG(const InputVectorType & landmarkVector, GMatrixType & gmatrix) const;

  virtual const GMatrixType & ComputeReflexiveG(PointsIterator) const;

  virtual void ComputeDeformationContribution(const InputPointType & inputPoint, OutputPointType & result) const;

  void ComputeK();

  void ComputeL();

  void ComputeP();

  void ComputeY();

  void ComputeD();

  void ReorganizeW();

  double m_Stiffness;

  VectorSetPointer m_Displacements;

  LMatrixType m_LMatrix;

  KMatrixType m_KMatrix;

  PMatrixType m_PMatrix;

  YMatrixType m_YMatrix;

  WMatrixType m_WMatrix;

  DMatrixType m_DMatrix;

  AMatrixType m_AMatrix;

  BMatrixType m_BVector;

  mutable GMatrixType m_GMatrix;

  bool m_WMatrixComputed;

  IMatrixType m_I;

  PointSetPointer m_SourceLandmarks;

  PointSetPointer m_TargetLandmarks;

private:

};
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkKernelTransform.hxx"
#endif

#endif // itkKernelTransform_h