elxBSplineTransformWithDiffusion.h

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/*======================================================================

  This file is part of the elastix software.

  Copyright (c) University Medical Center Utrecht. All rights reserved.
  See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
  details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE. See the above copyright notices for more information.

======================================================================*/

#ifndef __elxBSplineTransformWithDiffusion_H__
#define __elxBSplineTransformWithDiffusion_H__

/* For easy changing the BSplineOrder: */
#define __VSplineOrder 3

#include "itkAdvancedBSplineDeformableTransform.h"
#include "itkAdvancedCombinationTransform.h"
//#include "itkBSplineCombinationTransform.h"
#include "itkBSplineResampleImageFilterBase.h"
#include "itkBSplineUpsampleImageFilter.h"

#include "itkImageRegionConstIterator.h"

#include "elxIncludes.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
{
using namespace itk;


template < class TElastix >
class BSplineTransformWithDiffusion
  : public
  DeformationFieldRegulizer<
    AdvancedCombinationTransform<
    //BSplineCombinationTransform<
    ITK_TYPENAME elx::TransformBase<TElastix>::CoordRepType,
    elx::TransformBase<TElastix>::FixedImageDimension > >,
    //elx::TransformBase<TElastix>::FixedImageDimension, __VSplineOrder > >,
  public
  TransformBase<TElastix>
{
public:

  typedef BSplineTransformWithDiffusion               Self;
  typedef DeformationFieldRegulizer<
    AdvancedCombinationTransform<
    //BSplineCombinationTransform<
    typename elx::TransformBase<TElastix>::CoordRepType,
    elx::TransformBase<TElastix>::FixedImageDimension > >
    //elx::TransformBase<TElastix>::FixedImageDimension, __VSplineOrder > >
                                                      Superclass1;
  typedef elx::TransformBase<TElastix>                Superclass2;

  typedef AdvancedBSplineDeformableTransform<
    typename elx::TransformBase<TElastix>::CoordRepType,
    elx::TransformBase<TElastix>::FixedImageDimension,
    __VSplineOrder >                          BSplineTransformType;

  typedef SmartPointer<Self>                  Pointer;
  typedef SmartPointer<const Self>            ConstPointer;

  itkNewMacro( Self );

  itkTypeMacro( BSplineTransformWithDiffusion, 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::BulkTransformType          BulkTransformType;
  typedef typename BSplineTransformType::BulkTransformPointer       BulkTransformPointer;
  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 ElastixType::FixedImageType            FixedImageELXType;
  typedef typename ElastixType::MovingImageType           MovingImageELXType;

  typedef Image< short,
    itkGetStaticConstMacro( SpaceDimension ) >      DummyImageType;
  typedef ImageRegionConstIterator<
    DummyImageType >                                DummyIteratorType;
  typedef typename BSplineTransformType::Pointer    BSplineTransformPointer;
  typedef typename Superclass1::Superclass          GenericDeformationFieldRegulizer;

  typedef ImageFileReader< VectorImageType >        VectorReaderType;
  typedef typename VectorImageType::PixelType       VectorType;
  typedef ImageRegionIterator<
    VectorImageType >                               VectorImageIteratorType;
  typedef FixedImageELXType                         GrayValueImageType;
  typedef typename GrayValueImageType::PixelType    GrayValuePixelType;
  typedef ImageRegionIterator<
    GrayValueImageType >                            GrayValueImageIteratorType;
  typedef MaximumImageFilter<
    GrayValueImageType, GrayValueImageType,
    GrayValueImageType >                            MaximumImageFilterType;
  typedef VectorMeanDiffusionImageFilter<
    VectorImageType, GrayValueImageType >           DiffusionFilterType;
  typedef typename VectorImageType::SizeType        RadiusType;
  typedef ResampleImageFilter<
    MovingImageELXType, GrayValueImageType,
    CoordRepType >                                  ResamplerType1;
  typedef ResampleImageFilter<
    GrayValueImageType, GrayValueImageType,
    CoordRepType >                                  ResamplerType2;
  typedef BSplineInterpolateImageFunction<
    GrayValueImageType >                            InterpolatorType;
  typedef ImageFileReader< GrayValueImageType >     GrayValueImageReaderType;
  typedef ImageFileWriter< GrayValueImageType >     GrayValueImageWriterType;
  typedef ImageFileWriter< VectorImageType >        DeformationFieldWriterType;

  virtual void BeforeRegistration( void );

  virtual void BeforeEachResolution( void );

  virtual void AfterEachIteration( void );

  virtual void AfterRegistration( void );

  virtual void SetInitialGrid( bool upsampleGridOption );

  virtual void IncreaseScale( void );

  virtual void ReadFromFile( void );

  virtual void WriteToFile( const ParametersType & param ) const;

  void DiffuseDeformationField( void );

  virtual OutputPointType TransformPoint( const InputPointType  & point ) const;

protected:

  BSplineTransformWithDiffusion();
  virtual ~BSplineTransformWithDiffusion() {};

  SpacingType   m_GridSpacingFactor;

private:

  BSplineTransformWithDiffusion( const Self& ); // purposely not implemented
  void operator=( const Self& );                // purposely not implemented

  typename DiffusionFilterType::Pointer   m_Diffusion;
  typename VectorImageType::Pointer       m_DeformationField;
  typename VectorImageType::Pointer       m_DiffusedField;
  typename GrayValueImageType::Pointer    m_GrayValueImage1;
  typename GrayValueImageType::Pointer    m_GrayValueImage2;
  typename GrayValueImageType::Pointer    m_MovingSegmentationImage;
  typename GrayValueImageType::Pointer    m_FixedSegmentationImage;
  typename GrayValueImageReaderType::Pointer  m_MovingSegmentationReader;
  typename GrayValueImageReaderType::Pointer  m_FixedSegmentationReader;
  std::string                             m_MovingSegmentationFileName;
  std::string                             m_FixedSegmentationFileName;
  typename ResamplerType1::Pointer        m_Resampler1;
  typename ResamplerType2::Pointer        m_Resampler2;
  typename InterpolatorType::Pointer      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 class BSplineTransformWithDiffusion


} // end namespace elastix

#ifndef ITK_MANUAL_INSTANTIATION
#include "elxBSplineTransformWithDiffusion.hxx"
#endif

#endif // end #ifndef __elxBSplineTransformWithDiffusion_H__