elxMissingStructurePenalty.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 elxMissingStructurePenalty_h
#define elxMissingStructurePenalty_h
 
#include "elxIncludes.h"
#include "itkMissingStructurePenalty.h"
 
#include "itkMeshFileReader.h"
#include "itkMeshFileWriter.h"
 
namespace elastix
{

 
template <class TElastix>
class ITK_TEMPLATE_EXPORT MissingStructurePenalty
  : public itk::MissingVolumeMeshPenalty<typename MetricBase<TElastix>::FixedPointSetType,
                                         typename MetricBase<TElastix>::MovingPointSetType>
  , public MetricBase<TElastix>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(MissingStructurePenalty);

  using Self = MissingStructurePenalty;
  using Superclass1 = itk::MissingVolumeMeshPenalty<typename MetricBase<TElastix>::FixedPointSetType,
                                                    typename MetricBase<TElastix>::MovingPointSetType>;
  using Superclass2 = MetricBase<TElastix>;
  using Pointer = itk::SmartPointer<Self>;
  using ConstPointer = itk::SmartPointer<const Self>;

  itkNewMacro(Self);

  itkTypeMacro(MissingStructurePenalty, itk::MissingVolumeMeshPenalty);

  elxClassNameMacro("MissingStructurePenalty");

  using typename Superclass1::FixedMeshType;
  using typename Superclass1::FixedMeshPointer;
  using typename Superclass1::FixedMeshConstPointer;
 
  using typename Superclass1::CoordinateRepresentationType;
  using typename Superclass1::FixedPointSetType;
  using typename Superclass1::FixedPointSetConstPointer;
  using typename Superclass1::FixedMeshContainerType;
  using typename Superclass1::FixedMeshContainerPointer;
  using typename Superclass1::MappedMeshContainerType;
  using typename Superclass1::MappedMeshContainerPointer;
  using typename Superclass1::MovingPointSetType;
  using typename Superclass1::MovingPointSetConstPointer;
  using typename Superclass1::CellInterfaceType;
 
  //  using typename Superclass1::FixedImageRegionType;
  using typename Superclass1::TransformType;
  using typename Superclass1::TransformPointer;
  using typename Superclass1::InputPointType;
  using typename Superclass1::OutputPointType;
  using typename Superclass1::TransformParametersType;
  using typename Superclass1::TransformJacobianType;
  //  using typename Superclass1::RealType;
  using typename Superclass1::FixedImageMaskType;
  using typename Superclass1::FixedImageMaskPointer;
  using typename Superclass1::MovingImageMaskType;
  using typename Superclass1::MovingImageMaskPointer;
  using typename Superclass1::MeasureType;
  using typename Superclass1::DerivativeType;
  using typename Superclass1::ParametersType;
 
  using CoordRepType = typename OutputPointType::CoordRepType;
 
  using typename Superclass1::MeshIdType;
  using CombinationTransformType = itk::AdvancedCombinationTransform<CoordRepType, Self::FixedImageDimension>;
  using InitialTransformType = typename CombinationTransformType::InitialTransformType;

  using typename Superclass2::ElastixType;
  using typename Superclass2::RegistrationType;
  using ITKBaseType = typename Superclass2::ITKBaseType;
  using typename Superclass2::FixedImageType;
  using typename Superclass2::MovingImageType;

  itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
  itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);

  using PointSetType = FixedPointSetType;
  using MeshType = FixedMeshType;
  using ImageType = FixedImageType;

  void
  Initialize() override;

  int
  BeforeAllBase() override;
 
  void
  BeforeRegistration() override;
 
  void
  AfterEachIteration() override;
 
  void
  AfterEachResolution() override;

  unsigned int
  ReadMesh(const std::string & meshFileName, typename FixedMeshType::Pointer & mesh);
 
  void
  WriteResultMesh(const std::string & filename, MeshIdType meshId);
 
  unsigned int
  ReadTransformixPoints(const std::string & filename, typename MeshType::Pointer & mesh);

  void
  SelectNewSamples() override
  {}
 
protected:
  MissingStructurePenalty();
  ~MissingStructurePenalty() override = default;
 
private:
  elxOverrideGetSelfMacro;
 
  unsigned int m_NumberOfMeshes;
};
 
} // end namespace elastix
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "elxMissingStructurePenalty.hxx"
#endif
 
#endif // end #ifndef elxMissingStructurePenalty_h