elxBSplineTransformWithDiffusion.h

Go to the documentation of this file.

/*=========================================================================
 *
 *  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 __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< class TElastix >
class BSplineTransformWithDiffusion :
  public
  itk::DeformationFieldRegulizer<
  itk::AdvancedCombinationTransform<
  //BSplineCombinationTransform<
  typename elx::TransformBase< TElastix >::CoordRepType,
  elx::TransformBase< TElastix >::FixedImageDimension > >,
  //elx::TransformBase<TElastix>::FixedImageDimension, __VSplineOrder > >,
  public
  TransformBase< TElastix >
{
public:
 
  typedef BSplineTransformWithDiffusion Self;
  typedef itk::DeformationFieldRegulizer<
    itk::AdvancedCombinationTransform<
    //BSplineCombinationTransform<
    typename elx::TransformBase< TElastix >::CoordRepType,
    elx::TransformBase< TElastix >::FixedImageDimension > >
    //elx::TransformBase<TElastix>::FixedImageDimension, __VSplineOrder > >
    Superclass1;
  typedef elx::TransformBase< TElastix > Superclass2;
 
  typedef itk::AdvancedBSplineDeformableTransform<
    typename elx::TransformBase< TElastix >::CoordRepType,
    elx::TransformBase< TElastix >::FixedImageDimension,
    __VSplineOrder >                                  BSplineTransformType;
 
  typedef itk::SmartPointer< Self >       Pointer;
  typedef itk::SmartPointer< const Self > ConstPointer;
 
  itkNewMacro( Self );
 
  itkTypeMacro( BSplineTransformWithDiffusion, itk::DeformationFieldRegulizer );
 
  elxClassNameMacro( "BSplineTransformWithDiffusion" );
 
  itkStaticConstMacro( SpaceDimension, unsigned int, Superclass2::FixedImageDimension );
 
  itkStaticConstMacro( SplineOrder, unsigned int, __VSplineOrder );
 
  typedef typename Superclass1::ScalarType                ScalarType;
  typedef typename Superclass1::ParametersType            ParametersType;
  typedef typename Superclass1::JacobianType              JacobianType;
  typedef typename Superclass1::InputVectorType           InputVectorType;
  typedef typename Superclass1::OutputVectorType          OutputVectorType;
  typedef typename Superclass1::InputCovariantVectorType  InputCovariantVectorType;
  typedef typename Superclass1::OutputCovariantVectorType OutputCovariantVectorType;
  typedef typename Superclass1::InputVnlVectorType        InputVnlVectorType;
  typedef typename Superclass1::OutputVnlVectorType       OutputVnlVectorType;
  typedef typename Superclass1::InputPointType            InputPointType;
  typedef typename Superclass1::OutputPointType           OutputPointType;
 
  typedef typename BSplineTransformType::PixelType               PixelType;
  typedef typename BSplineTransformType::ImageType               ImageType;
  typedef typename BSplineTransformType::ImagePointer            ImagePointer;
  typedef typename BSplineTransformType::RegionType              RegionType;
  typedef typename BSplineTransformType::IndexType               IndexType;
  typedef typename BSplineTransformType::SizeType                SizeType;
  typedef typename BSplineTransformType::SpacingType             SpacingType;
  typedef typename BSplineTransformType::OriginType              OriginType;
  typedef typename BSplineTransformType::WeightsFunctionType     WeightsFunctionType;
  typedef typename BSplineTransformType::WeightsType             WeightsType;
  typedef typename BSplineTransformType::ContinuousIndexType     ContinuousIndexType;
  typedef typename BSplineTransformType::ParameterIndexArrayType ParameterIndexArrayType;
 
  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::CoordRepType             CoordRepType;
  typedef typename Superclass2::FixedImageType           FixedImageType;
  typedef typename Superclass2::MovingImageType          MovingImageType;
  typedef typename Superclass2::ITKBaseType              ITKBaseType;
  typedef typename Superclass2::CombinationTransformType CombinationTransformType;
 
  typedef typename Superclass1::IntermediaryDFTransformType IntermediaryDFTransformType;
  typedef typename Superclass1::VectorImageType             VectorImageType;
  typedef typename VectorImageType::Pointer                 VectorImagePointer;
 
  typedef typename ElastixType::FixedImageType  FixedImageELXType;
  typedef typename ElastixType::MovingImageType MovingImageELXType;
 
  typedef itk::Image< short,
    itkGetStaticConstMacro( SpaceDimension ) >      DummyImageType;
  typedef itk::ImageRegionConstIterator<
    DummyImageType >                                DummyIteratorType;
  typedef typename BSplineTransformType::Pointer BSplineTransformPointer;
  typedef typename Superclass1::Superclass       GenericDeformationFieldRegulizer;
 
  typedef itk::ImageFileReader< VectorImageType > VectorReaderType;
  typedef typename VectorImageType::PixelType     VectorType;
  typedef itk::ImageRegionIterator<
    VectorImageType >                               VectorImageIteratorType;
  typedef FixedImageELXType                      GrayValueImageType;
  typedef typename GrayValueImageType::Pointer   GrayValueImagePointer;
  typedef typename GrayValueImageType::PixelType GrayValuePixelType;
  typedef itk::ImageRegionIterator<
    GrayValueImageType >                            GrayValueImageIteratorType;
  typedef itk::MaximumImageFilter<
    GrayValueImageType, GrayValueImageType,
    GrayValueImageType >                            MaximumImageFilterType;
  typedef itk::VectorMeanDiffusionImageFilter<
    VectorImageType, GrayValueImageType >           DiffusionFilterType;
  typedef typename DiffusionFilterType::Pointer DiffusionFilterPointer;
  typedef typename VectorImageType::SizeType    RadiusType;
  typedef itk::ResampleImageFilter<
    MovingImageELXType, GrayValueImageType,
    CoordRepType >                                  ResamplerType1;
  typedef typename ResamplerType1::Pointer ResamplerPointer1;
  typedef itk::ResampleImageFilter<
    GrayValueImageType, GrayValueImageType,
    CoordRepType >                                  ResamplerType2;
  typedef typename ResamplerType2::Pointer ResamplerPointer2;
  typedef itk::BSplineInterpolateImageFunction<
    GrayValueImageType >                            InterpolatorType;
  typedef typename InterpolatorType::Pointer         InterpolatorPointer;
  typedef itk::ImageFileReader< GrayValueImageType > GrayValueImageReaderType;
  typedef typename GrayValueImageReaderType::Pointer GrayValueImageReaderPointer;
  typedef itk::ImageFileWriter< GrayValueImageType > GrayValueImageWriterType;
  typedef itk::ImageFileWriter< VectorImageType >    DeformationFieldWriterType;
 
  void BeforeRegistration( void ) override;
 
  void BeforeEachResolution( void ) override;
 
  void AfterEachIteration( void ) override;
 
  void AfterRegistration( void ) override;
 
  virtual void SetInitialGrid( bool upsampleGridOption );
 
  virtual void IncreaseScale( void );
 
  void ReadFromFile( void ) override;
 
  void WriteToFile( const ParametersType & param ) const override;
 
  void DiffuseDeformationField( void );
 
  OutputPointType TransformPoint( const InputPointType  & point ) const override;
 
protected:
 
  BSplineTransformWithDiffusion();
  ~BSplineTransformWithDiffusion() override {}
 
  SpacingType m_GridSpacingFactor;
 
private:
 
  BSplineTransformWithDiffusion( const Self & ); // purposely not implemented
  void operator=( const Self & );                // purposely not implemented
 
  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__