itkSyNImageRegistrationMethod.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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 itkSyNImageRegistrationMethod_h
#define itkSyNImageRegistrationMethod_h
 
#include "itkImageRegistrationMethodv4.h"
 
#include "itkImageMaskSpatialObject.h"
#include "itkDisplacementFieldTransform.h"
 
namespace itk
{

template <typename TFixedImage,
          typename TMovingImage,
          typename TOutputTransform = DisplacementFieldTransform<double, TFixedImage::ImageDimension>,
          typename TVirtualImage = TFixedImage,
          typename TPointSet = PointSet<unsigned int, TFixedImage::ImageDimension>>
class ITK_TEMPLATE_EXPORT SyNImageRegistrationMethod
  : public ImageRegistrationMethodv4<TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(SyNImageRegistrationMethod);

  using Self = SyNImageRegistrationMethod;
  using Superclass = ImageRegistrationMethodv4<TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  itkNewMacro(Self);

  static constexpr unsigned int ImageDimension = TFixedImage::ImageDimension;

  itkOverrideGetNameOfClassMacro(SyNImageRegistrationMethod);

  using FixedImageType = TFixedImage;
  using FixedImagePointer = typename FixedImageType::Pointer;
  using typename Superclass::FixedImagesContainerType;
  using MovingImageType = TMovingImage;
  using MovingImagePointer = typename MovingImageType::Pointer;
  using typename Superclass::MovingImagesContainerType;
 
  using typename Superclass::PointSetType;
  using PointSetPointer = typename PointSetType::Pointer;
  using typename Superclass::PointSetsContainerType;

  using typename Superclass::ImageMetricType;
  using ImageMetricPointer = typename ImageMetricType::Pointer;
  using MeasureType = typename ImageMetricType::MeasureType;
 
  using ImageMaskSpatialObjectType = ImageMaskSpatialObject<ImageDimension>;
  using typename Superclass::FixedImageMaskType;
  using FixedMaskImageType = typename ImageMaskSpatialObjectType::ImageType;
  using typename Superclass::FixedImageMasksContainerType;
  using typename Superclass::MovingImageMaskType;
  using MovingMaskImageType = typename ImageMaskSpatialObjectType::ImageType;
  using typename Superclass::MovingImageMasksContainerType;
 
  using VirtualImageType = typename Superclass::VirtualImageType;
  using typename Superclass::VirtualImageBaseType;
  using typename Superclass::VirtualImageBaseConstPointer;
 
  using typename Superclass::MultiMetricType;
  using typename Superclass::MetricType;
  using MetricPointer = typename MetricType::Pointer;
  using typename Superclass::PointSetMetricType;
 
  using typename Superclass::InitialTransformType;
  using OutputTransformType = TOutputTransform;
  using OutputTransformPointer = typename OutputTransformType::Pointer;
  using RealType = typename OutputTransformType::ScalarType;
  using DerivativeType = typename OutputTransformType::DerivativeType;
  using DerivativeValueType = typename DerivativeType::ValueType;
  using DisplacementFieldType = typename OutputTransformType::DisplacementFieldType;
  using DisplacementFieldPointer = typename DisplacementFieldType::Pointer;
  using DisplacementVectorType = typename DisplacementFieldType::PixelType;
 
  using typename Superclass::CompositeTransformType;
  using TransformBaseType = typename CompositeTransformType::TransformType;
 
  using typename Superclass::DecoratedOutputTransformType;
  using DecoratedOutputTransformPointer = typename DecoratedOutputTransformType::Pointer;
 
  using DisplacementFieldTransformType = DisplacementFieldTransform<RealType, ImageDimension>;
  using DisplacementFieldTransformPointer = typename DisplacementFieldTransformType::Pointer;
 
  using NumberOfIterationsArrayType = Array<SizeValueType>;

  itkSetMacro(LearningRate, RealType);
  itkGetConstMacro(LearningRate, RealType);

  itkSetMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType);
  itkGetConstMacro(NumberOfIterationsPerLevel, NumberOfIterationsArrayType);

  itkSetMacro(ConvergenceThreshold, RealType);
  itkGetConstMacro(ConvergenceThreshold, RealType);

  itkSetMacro(ConvergenceWindowSize, unsigned int);
  itkGetConstMacro(ConvergenceWindowSize, unsigned int);

  itkSetMacro(DownsampleImagesForMetricDerivatives, bool);
  itkGetConstMacro(DownsampleImagesForMetricDerivatives, bool);

  itkSetMacro(AverageMidPointGradients, bool);
  itkGetConstMacro(AverageMidPointGradients, bool);

  itkSetMacro(GaussianSmoothingVarianceForTheUpdateField, RealType);
  itkGetConstReferenceMacro(GaussianSmoothingVarianceForTheUpdateField, RealType);

  itkSetMacro(GaussianSmoothingVarianceForTheTotalField, RealType);
  itkGetConstReferenceMacro(GaussianSmoothingVarianceForTheTotalField, RealType);

  itkGetModifiableObjectMacro(FixedToMiddleTransform, OutputTransformType);
  itkGetModifiableObjectMacro(MovingToMiddleTransform, OutputTransformType);

  itkSetObjectMacro(FixedToMiddleTransform, OutputTransformType);
  itkSetObjectMacro(MovingToMiddleTransform, OutputTransformType);
 
protected:
  SyNImageRegistrationMethod();
  ~SyNImageRegistrationMethod() override = default;
  void
  PrintSelf(std::ostream & os, Indent indent) const override;

  void
  GenerateData() override;

  virtual void
  StartOptimization();

  void
  InitializeRegistrationAtEachLevel(const SizeValueType) override;
 
  virtual DisplacementFieldPointer
  ComputeUpdateField(const FixedImagesContainerType,
                     const PointSetsContainerType,
                     const TransformBaseType *,
                     const MovingImagesContainerType,
                     const PointSetsContainerType,
                     const TransformBaseType *,
                     const FixedImageMasksContainerType,
                     const MovingImageMasksContainerType,
                     MeasureType &);
  virtual DisplacementFieldPointer
  ComputeMetricGradientField(const FixedImagesContainerType,
                             const PointSetsContainerType,
                             const TransformBaseType *,
                             const MovingImagesContainerType,
                             const PointSetsContainerType,
                             const TransformBaseType *,
                             const FixedImageMasksContainerType,
                             const MovingImageMasksContainerType,
                             MeasureType &);
 
  virtual DisplacementFieldPointer
  ScaleUpdateField(const DisplacementFieldType *);
  virtual DisplacementFieldPointer
  GaussianSmoothDisplacementField(const DisplacementFieldType *, const RealType);
  virtual DisplacementFieldPointer
  InvertDisplacementField(const DisplacementFieldType *, const DisplacementFieldType * = nullptr);
 
  RealType m_LearningRate{ 0.25 };
 
  OutputTransformPointer m_MovingToMiddleTransform{ nullptr };
  OutputTransformPointer m_FixedToMiddleTransform{ nullptr };
 
  RealType     m_ConvergenceThreshold{ static_cast<RealType>(1.0e-6) };
  unsigned int m_ConvergenceWindowSize{ 10 };
 
  NumberOfIterationsArrayType m_NumberOfIterationsPerLevel{};
  bool                        m_DownsampleImagesForMetricDerivatives{ true };
  bool                        m_AverageMidPointGradients{ false };
 
private:
  RealType m_GaussianSmoothingVarianceForTheUpdateField{ 3.0 };
  RealType m_GaussianSmoothingVarianceForTheTotalField{ 0.5 };
};
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkSyNImageRegistrationMethod.hxx"
#endif
 
#endif