elxBSplineTransformWithDiffusion.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
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 *  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.
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#ifndef elxBSplineTransformWithDiffusion_h
#define elxBSplineTransformWithDiffusion_h
 
/* For easy changing the BSplineOrder: */
#define __VSplineOrder 3
 
#include "elxIncludes.h" // include first to avoid MSVS warning
#include "itkAdvancedBSplineDeformableTransform.h"
#include "itkAdvancedCombinationTransform.h"
// #include "itkBSplineCombinationTransform.h"
#include "itkBSplineResampleImageFilterBase.h"
#include "itkBSplineUpsampleImageFilter.h"
 
#include "itkImageRegionConstIterator.h"

#include "itkDeformationFieldRegulizer.h"
#include "itkVectorMeanDiffusionImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkMaximumImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkBSplineInterpolateImageFunction.h"
 
namespace elastix
{

 
template <typename TElastix>
class ITK_TEMPLATE_EXPORT BSplineTransformWithDiffusion
  : public itk::DeformationFieldRegulizer<itk::AdvancedCombinationTransform<
      // BSplineCombinationTransform<
      typename elx::TransformBase<TElastix>::CoordinateType,
      elx::TransformBase<TElastix>::FixedImageDimension>>
  ,
    // elx::TransformBase<TElastix>::FixedImageDimension, __VSplineOrder > >,
    public TransformBase<TElastix>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(BSplineTransformWithDiffusion);

  using Self = BSplineTransformWithDiffusion;
  using Superclass1 = itk::DeformationFieldRegulizer<
    itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordinateType,
                                      elx::TransformBase<TElastix>::FixedImageDimension>>;
  using Superclass2 = elx::TransformBase<TElastix>;

  using BSplineTransformType =
    itk::AdvancedBSplineDeformableTransform<typename elx::TransformBase<TElastix>::CoordinateType,
                                            elx::TransformBase<TElastix>::FixedImageDimension,
                                            3>;
 
  using Pointer = itk::SmartPointer<Self>;
  using ConstPointer = itk::SmartPointer<const Self>;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(BSplineTransformWithDiffusion);

  elxClassNameMacro("BSplineTransformWithDiffusion");

  itkStaticConstMacro(SpaceDimension, unsigned int, Superclass2::FixedImageDimension);

  itkStaticConstMacro(SplineOrder, unsigned int, __VSplineOrder);

  using typename Superclass1::ScalarType;
  using typename Superclass1::ParametersType;
  using typename Superclass1::JacobianType;
  using typename Superclass1::InputVectorType;
  using typename Superclass1::OutputVectorType;
  using typename Superclass1::InputCovariantVectorType;
  using typename Superclass1::OutputCovariantVectorType;
  using typename Superclass1::InputVnlVectorType;
  using typename Superclass1::OutputVnlVectorType;
  using typename Superclass1::InputPointType;
  using typename Superclass1::OutputPointType;

  using PixelType = typename BSplineTransformType::PixelType;
  using ImageType = typename BSplineTransformType::ImageType;
  using ImagePointer = typename BSplineTransformType::ImagePointer;
  using RegionType = typename BSplineTransformType::RegionType;
  using IndexType = typename BSplineTransformType::IndexType;
  using SizeType = typename BSplineTransformType::SizeType;
  using SpacingType = typename BSplineTransformType::SpacingType;
  using OriginType = typename BSplineTransformType::OriginType;
  using WeightsFunctionType = typename BSplineTransformType::WeightsFunctionType;
  using WeightsType = typename BSplineTransformType::WeightsType;
  using ContinuousIndexType = typename BSplineTransformType::ContinuousIndexType;
  using ParameterIndexArrayType = typename BSplineTransformType::ParameterIndexArrayType;

  using typename Superclass2::ElastixType;
  using typename Superclass2::ParameterMapType;
  using typename Superclass2::RegistrationType;
  using typename Superclass2::CoordinateType;
  using typename Superclass2::FixedImageType;
  using typename Superclass2::MovingImageType;
  using ITKBaseType = typename Superclass2::ITKBaseType;
  using CombinationTransformType = typename Superclass2::CombinationTransformType;

  using typename Superclass1::IntermediaryDFTransformType;
  using typename Superclass1::VectorImageType;
  using VectorImagePointer = typename VectorImageType::Pointer;

  using FixedImageELXType = typename ElastixType::FixedImageType;
  using MovingImageELXType = typename ElastixType::MovingImageType;

  using DummyImageType = itk::Image<short, Self::SpaceDimension>;
  using BSplineTransformPointer = typename BSplineTransformType::Pointer;
  using GenericDeformationFieldRegulizer = typename Superclass1::Superclass;

  using VectorReaderType = itk::ImageFileReader<VectorImageType>;
  using VectorType = typename VectorImageType::PixelType;
  using VectorImageIteratorType = itk::ImageRegionIterator<VectorImageType>;
  using GrayValueImageType = FixedImageELXType;
  using GrayValueImagePointer = typename GrayValueImageType::Pointer;
  using GrayValuePixelType = typename GrayValueImageType::PixelType;
  using GrayValueImageIteratorType = itk::ImageRegionIterator<GrayValueImageType>;
  using MaximumImageFilterType = itk::MaximumImageFilter<GrayValueImageType, GrayValueImageType, GrayValueImageType>;
  using DiffusionFilterType = itk::VectorMeanDiffusionImageFilter<VectorImageType, GrayValueImageType>;
  using DiffusionFilterPointer = typename DiffusionFilterType::Pointer;
  using RadiusType = typename VectorImageType::SizeType;
  using ResamplerType1 = itk::ResampleImageFilter<MovingImageELXType, GrayValueImageType, CoordinateType>;
  using ResamplerPointer1 = typename ResamplerType1::Pointer;
  using ResamplerType2 = itk::ResampleImageFilter<GrayValueImageType, GrayValueImageType, CoordinateType>;
  using ResamplerPointer2 = typename ResamplerType2::Pointer;
  using InterpolatorType = itk::BSplineInterpolateImageFunction<GrayValueImageType>;
  using InterpolatorPointer = typename InterpolatorType::Pointer;
  using GrayValueImageReaderType = itk::ImageFileReader<GrayValueImageType>;
  using GrayValueImageReaderPointer = typename GrayValueImageReaderType::Pointer;

  void
  BeforeRegistration() override;

  void
  BeforeEachResolution() override;

  void
  AfterEachIteration() override;

  void
  AfterRegistration() override;

  virtual void
  SetInitialGrid(bool upsampleGridOption);

  virtual void
  IncreaseScale();

  void
  ReadFromFile() override;

  void
  DiffuseDeformationField();

  OutputPointType
  TransformPoint(const InputPointType & point) const override;

 
protected:
  BSplineTransformWithDiffusion();
  ~BSplineTransformWithDiffusion() override = default;

  SpacingType m_GridSpacingFactor;
 
private:
  elxOverrideGetSelfMacro;

  ParameterMapType
  CreateDerivedTransformParameterMap() const override;

  void
  WriteDerivedTransformDataToFile() const override;

  DiffusionFilterPointer      m_Diffusion;
  VectorImagePointer          m_DeformationField;
  VectorImagePointer          m_DiffusedField;
  GrayValueImagePointer       m_GrayValueImage1;
  GrayValueImagePointer       m_GrayValueImage2;
  GrayValueImagePointer       m_MovingSegmentationImage;
  GrayValueImagePointer       m_FixedSegmentationImage;
  GrayValueImageReaderPointer m_MovingSegmentationReader;
  GrayValueImageReaderPointer m_FixedSegmentationReader;
  std::string                 m_MovingSegmentationFileName;
  std::string                 m_FixedSegmentationFileName;
  ResamplerPointer1           m_Resampler1;
  ResamplerPointer2           m_Resampler2;
  InterpolatorPointer         m_Interpolator;
  RegionType                  m_DeformationRegion;
  OriginType                  m_DeformationOrigin;
  SpacingType                 m_DeformationSpacing;

  bool               m_WriteDiffusionFiles;
  bool               m_AlsoFixed;
  bool               m_ThresholdBool;
  GrayValuePixelType m_ThresholdHU;
  bool               m_UseMovingSegmentation;
  bool               m_UseFixedSegmentation;

  ParametersType m_BSplineParameters;

  BSplineTransformPointer m_BSplineTransform;
};
 
} // end namespace elastix
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "elxBSplineTransformWithDiffusion.hxx"
#endif
 
#endif // end #ifndef elxBSplineTransformWithDiffusion_h