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 MissingStructurePenalty :
  public
  itk::MissingVolumeMeshPenalty<
  typename MetricBase< TElastix >::FixedPointSetType,
  typename MetricBase< TElastix >::MovingPointSetType >,
  public MetricBase< TElastix >
{
public:
 
  typedef MissingStructurePenalty Self;
  typedef itk::MissingVolumeMeshPenalty<
    typename MetricBase< TElastix >::FixedPointSetType,
    typename MetricBase< TElastix >::MovingPointSetType > Superclass1;
  typedef MetricBase< TElastix >          Superclass2;
  typedef itk::SmartPointer< Self >       Pointer;
  typedef itk::SmartPointer< const Self > ConstPointer;
 
  itkNewMacro( Self );
 
  itkTypeMacro( MissingStructurePenalty,
    itk::MissingVolumeMeshPenalty );
 
  elxClassNameMacro( "MissingStructurePenalty" );
 
  typedef typename Superclass1::FixedMeshType         FixedMeshType;
  typedef typename Superclass1::FixedMeshPointer      FixedMeshPointer;
  typedef typename Superclass1::FixedMeshConstPointer FixedMeshConstPointer;
 
  typedef typename Superclass1::CoordinateRepresentationType CoordinateRepresentationType;
  typedef typename Superclass1::FixedPointSetType            FixedPointSetType;
  typedef typename Superclass1::FixedPointSetConstPointer    FixedPointSetConstPointer;
  typedef typename Superclass1::FixedMeshContainerType       FixedMeshContainerType;
  typedef typename Superclass1::FixedMeshContainerPointer    FixedMeshContainerPointer;
  typedef typename Superclass1::MappedMeshContainerType      MappedMeshContainerType;
  typedef typename Superclass1::MappedMeshContainerPointer   MappedMeshContainerPointer;
  typedef typename Superclass1::MovingPointSetType           MovingPointSetType;
  typedef typename Superclass1::MovingPointSetConstPointer   MovingPointSetConstPointer;
  typedef typename Superclass1::CellInterfaceType            CellInterfaceType;
 
  //  typedef typename Superclass1::FixedImageRegionType       FixedImageRegionType;
  typedef typename Superclass1::TransformType           TransformType;
  typedef typename Superclass1::TransformPointer        TransformPointer;
  typedef typename Superclass1::InputPointType          InputPointType;
  typedef typename Superclass1::OutputPointType         OutputPointType;
  typedef typename Superclass1::TransformParametersType TransformParametersType;
  typedef typename Superclass1::TransformJacobianType   TransformJacobianType;
  //  typedef typename Superclass1::RealType                   RealType;
  typedef typename Superclass1::FixedImageMaskType     FixedImageMaskType;
  typedef typename Superclass1::FixedImageMaskPointer  FixedImageMaskPointer;
  typedef typename Superclass1::MovingImageMaskType    MovingImageMaskType;
  typedef typename Superclass1::MovingImageMaskPointer MovingImageMaskPointer;
  typedef typename Superclass1::MeasureType            MeasureType;
  typedef typename Superclass1::DerivativeType         DerivativeType;
  typedef typename Superclass1::ParametersType         ParametersType;
 
  typedef typename OutputPointType::CoordRepType CoordRepType;
 
  typedef typename Superclass1::MeshIdType MeshIdType;
  typedef itk::Object ObjectType;
 
  typedef itk::AdvancedCombinationTransform< CoordRepType,
    itkGetStaticConstMacro( FixedImageDimension ) >   CombinationTransformType;
  typedef typename
    CombinationTransformType::InitialTransformType InitialTransformType;
 
  typedef typename Superclass2::ElastixType          ElastixType;
  typedef typename Superclass2::ElastixPointer       ElastixPointer;
  typedef typename Superclass2::ConfigurationType    ConfigurationType;
  typedef typename Superclass2::ConfigurationPointer ConfigurationPointer;
  typedef typename Superclass2::RegistrationType     RegistrationType;
  typedef typename Superclass2::RegistrationPointer  RegistrationPointer;
  typedef typename Superclass2::ITKBaseType          ITKBaseType;
  typedef typename Superclass2::FixedImageType       FixedImageType;
  typedef typename Superclass2::MovingImageType      MovingImageType;
 
  itkStaticConstMacro( FixedImageDimension, unsigned int,
    FixedImageType::ImageDimension );
  itkStaticConstMacro( MovingImageDimension, unsigned int,
    MovingImageType::ImageDimension );
 
  typedef FixedPointSetType PointSetType;
  typedef FixedMeshType     MeshType;
  typedef FixedImageType    ImageType;
 
  void Initialize( void ) override;
 
  int BeforeAllBase( void ) override;
 
  void BeforeRegistration( void ) override;
 
  void AfterEachIteration( void ) override;
 
  void AfterEachResolution( void ) override;
 
  unsigned int ReadMesh(
  const std::string & meshFileName,
  typename FixedMeshType::Pointer & mesh );
 
  void WriteResultMesh( const char * filename, MeshIdType meshId );
 
  unsigned int ReadTransformixPoints( const std::string & filename, typename MeshType::Pointer & mesh );
 
  void SelectNewSamples( void ) override{}
 
protected:
 
  MissingStructurePenalty();
  ~MissingStructurePenalty() override {}
 
private:
 
  MissingStructurePenalty( const Self & );  // purposely not implemented
  void operator=( const Self & );           // purposely not implemented
 
  unsigned int m_NumberOfMeshes;
};
 
} // end namespace elastix
 
#ifndef ITK_MANUAL_INSTANTIATION
#include "elxMissingStructurePenalty.hxx"
#endif
 
#endif // end #ifndef __elxMissingStructurePenalty_H__