itkMissingStructurePenalty.h

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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 itkMissingStructurePenalty_h
#define itkMissingStructurePenalty_h
 
#include "itkSingleValuedPointSetToPointSetMetric.h"
#include "itkPoint.h"
#include "itkPointSet.h"
#include "itkImage.h"
#include "itkMesh.h"
#include "itkVectorContainer.h"
#include "vnl_adjugate_fixed.h"
 
namespace itk
{

template <typename TFixedPointSet, typename TMovingPointSet>
class ITK_TEMPLATE_EXPORT MissingVolumeMeshPenalty
  : public SingleValuedPointSetToPointSetMetric<TFixedPointSet, TMovingPointSet>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(MissingVolumeMeshPenalty);

  using Self = MissingVolumeMeshPenalty;
  using Superclass = SingleValuedPointSetToPointSetMetric<TFixedPointSet, TMovingPointSet>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;


  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(MissingVolumeMeshPenalty);

  using typename Superclass::TransformType;
  using typename Superclass::TransformPointer;
  using typename Superclass::ParametersType;
  using typename Superclass::TransformJacobianType;
 
  using typename Superclass::MeasureType;
  using typename Superclass::DerivativeType;
  using typename Superclass::DerivativeValueType;
 
  using typename Superclass::InputPointType;
  using typename Superclass::OutputPointType;
  using CoordinateType = typename OutputPointType::CoordinateType;
  using VnlVectorType = vnl_vector<CoordinateType>;
 
  using typename Superclass::NonZeroJacobianIndicesType;

  itkStaticConstMacro(FixedPointSetDimension, unsigned int, Superclass::FixedPointSetDimension);
  itkStaticConstMacro(MovingPointSetDimension, unsigned int, Superclass::MovingPointSetDimension);

  using DummyMeshPixelType = unsigned char;
  using MeshTraitsType =
    DefaultStaticMeshTraits<DummyMeshPixelType, FixedPointSetDimension, FixedPointSetDimension, CoordinateType>;
  using FixedMeshType = Mesh<DummyMeshPixelType, FixedPointSetDimension, MeshTraitsType>;
  using FixedMeshPointIdentifier = typename FixedMeshType::PointIdentifier;
 
  using FixedMeshConstPointer = typename FixedMeshType::ConstPointer;
  using FixedMeshPointer = typename FixedMeshType::Pointer;
  using CellInterfaceType = typename MeshTraitsType::CellType;
 
  using MeshPointType = typename FixedMeshType::PointType;
  using VectorType = typename FixedMeshType::PointType::VectorType;
  using VectorConstPointer = typename VectorType::const_pointer;
  using SubVectorType = itk::Vector<typename VectorType::ValueType, FixedPointSetDimension - 1>;
 
  using MeshPointsContainerType = typename FixedMeshType::PointsContainer;
  using MeshPointsContainerPointer = typename MeshPointsContainerType::Pointer;
  using MeshPointsContainerConstPointer = typename MeshPointsContainerType::ConstPointer;
  using MeshPointsContainerConstIteratorType = typename FixedMeshType::PointsContainerConstIterator;
  using MeshPointsContainerIteratorType = typename FixedMeshType::PointsContainerIterator;
 
  using MeshPointDataContainerType = typename FixedMeshType::PointDataContainer;
  using MeshPointDataContainerConstPointer = typename FixedMeshType::PointDataContainerConstPointer;
  using MeshPointDataContainerPointer = typename FixedMeshType::PointDataContainerPointer;
  // typedef typename FixedMeshType::PointDataContainerConstIterator     MeshPointDataContainerConstIteratorType;
  using MeshPointDataContainerConstIteratorType = typename FixedMeshType::PointDataContainerIterator;
 
  using MeshIdType = unsigned int;
  using FixedMeshContainerType = VectorContainer<MeshIdType, FixedMeshConstPointer>;
  using FixedMeshContainerPointer = typename FixedMeshContainerType::Pointer;
  using FixedMeshContainerConstPointer = typename FixedMeshContainerType::ConstPointer;
  using FixedMeshContainerElementIdentifier = typename FixedMeshContainerType::ElementIdentifier;
 
  using MappedMeshContainerType = VectorContainer<MeshIdType, FixedMeshPointer>;
  using MappedMeshContainerPointer = typename MappedMeshContainerType::Pointer;
  using MappedMeshContainerConstPointer = typename MappedMeshContainerType::ConstPointer;
 
  using MeshPointsDerivativeValueType = Array<DerivativeValueType>;
 
  itkSetConstObjectMacro(FixedMeshContainer, FixedMeshContainerType);
  itkGetConstObjectMacro(FixedMeshContainer, FixedMeshContainerType);
 
  itkSetObjectMacro(MappedMeshContainer, MappedMeshContainerType);
  itkGetModifiableObjectMacro(MappedMeshContainer, MappedMeshContainerType);

  void
  Initialize() override;

  // \todo: currently not used
  // itkSetConstObjectMacro( FixedImageMask, FixedImageMaskType );

  // itkGetConstObjectMacro( FixedImageMask, FixedImageMaskType );

  MeasureType
  GetValue(const ParametersType & parameters) const override;

  void
  GetDerivative(const ParametersType & parameters, DerivativeType & Derivative) const override;

  void
  GetValueAndDerivative(const ParametersType & parameters,
                        MeasureType &          Value,
                        DerivativeType &       Derivative) const override;
 
protected:
  MissingVolumeMeshPenalty();
  ~MissingVolumeMeshPenalty() override = default;

  // void PrintSelf(std::ostream& os, Indent indent) const;

  FixedMeshConstPointer m_FixedMesh{};
 
  mutable FixedMeshContainerConstPointer m_FixedMeshContainer{};
  mutable MappedMeshContainerPointer     m_MappedMeshContainer{};
 
private:
  void
  SubVector(const VectorType & fullVector, SubVectorType & subVector, const unsigned int leaveOutIndex) const;
};
 
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkMissingStructurePenalty.hxx"
#endif
 
#endif