elxStatisticalShapePenalty.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 elxStatisticalShapePenalty_h
#define elxStatisticalShapePenalty_h
 
#include "elxIncludes.h" // include first to avoid MSVS warning
#include "itkStatisticalShapePointPenalty.h"
 
#include <vnl/vnl_matrix.h>
#include <vnl/vnl_vector.h>
 
namespace elastix
{
using namespace itk;

 
template <typename TElastix>
class ITK_TEMPLATE_EXPORT StatisticalShapePenalty
  : public StatisticalShapePointPenalty<typename MetricBase<TElastix>::FixedPointSetType,
                                        typename MetricBase<TElastix>::MovingPointSetType>
  , public MetricBase<TElastix>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(StatisticalShapePenalty);

  using Self = StatisticalShapePenalty;
  using Superclass1 = StatisticalShapePointPenalty<typename MetricBase<TElastix>::FixedPointSetType,
                                                   typename MetricBase<TElastix>::MovingPointSetType>;
  using Superclass2 = MetricBase<TElastix>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(StatisticalShapePenalty);

  elxClassNameMacro("StatisticalShapePenalty");

  using typename Superclass1::CoordinateRepresentationType;
  using typename Superclass1::FixedPointSetType;
  using typename Superclass1::FixedPointSetConstPointer;
  using typename Superclass1::MovingPointSetType;
  using typename Superclass1::MovingPointSetConstPointer;
 
  //  using typename Superclass1::FixedImageRegionType;
  using typename Superclass1::TransformType;
  using typename Superclass1::TransformPointer;
  using typename Superclass1::InputPointType;
  using typename Superclass1::OutputPointType;
  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 CoordinateType = typename OutputPointType::CoordinateType;
  using VnlVectorType = vnl_vector<CoordinateType>;

  /*typedef itk::AdvancedTransform<
    CoordinateType,
    itkGetStaticConstMacro( FixedImageDimension ),
    itkGetStaticConstMacro( MovingImageDimension ) >  ITKBaseType;
    */
  using CombinationTransformType = itk::AdvancedCombinationTransform<CoordinateType, 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 ImageType = FixedImageType;

  void
  Initialize() override;

  void
  BeforeRegistration() override;
 
  void
  BeforeEachResolution() override;
 
  unsigned int
  ReadShape(const std::string & ShapeFileName, typename PointSetType::Pointer & pointSet);

  void
  SelectNewSamples() override
  {}
 
protected:
  StatisticalShapePenalty() = default;
  ~StatisticalShapePenalty() override = default;
 
private:
  elxOverrideGetSelfMacro;
};
 
} // end namespace elastix
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "elxStatisticalShapePenalty.hxx"
#endif
 
#endif // end #ifndef elxStatisticalShapePenalty_h