itkSyNImageRegistrationMethod.h

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/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  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 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 SyNImageRegistrationMethod
: public ImageRegistrationMethodv4<TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet>
{
public:
  typedef SyNImageRegistrationMethod                                                  Self;
  typedef ImageRegistrationMethodv4<TFixedImage, TMovingImage, TOutputTransform,
                                                       TVirtualImage, TPointSet>      Superclass;
  typedef SmartPointer<Self>                                                          Pointer;
  typedef SmartPointer<const Self>                                                    ConstPointer;

  itkNewMacro( Self );

  itkStaticConstMacro( ImageDimension, unsigned int, TFixedImage::ImageDimension );

  itkTypeMacro( SyNImageRegistrationMethod, SimpleImageRegistrationMethod );

  typedef TFixedImage                                                 FixedImageType;
  typedef typename FixedImageType::Pointer                            FixedImagePointer;
  typedef typename Superclass::FixedImagesContainerType               FixedImagesContainerType;
  typedef TMovingImage                                                MovingImageType;
  typedef typename MovingImageType::Pointer                           MovingImagePointer;
  typedef typename Superclass::MovingImagesContainerType              MovingImagesContainerType;

  typedef typename Superclass::PointSetType                           PointSetType;
  typedef typename PointSetType::Pointer                              PointSetPointer;
  typedef typename Superclass::PointSetsContainerType                 PointSetsContainerType;

  typedef typename Superclass::ImageMetricType                        ImageMetricType;
  typedef typename ImageMetricType::Pointer                           ImageMetricPointer;
  typedef typename ImageMetricType::MeasureType                       MeasureType;

  typedef ImageMaskSpatialObject<ImageDimension>                      ImageMaskSpatialObjectType;
  typedef typename Superclass::FixedImageMaskType                     FixedImageMaskType;
  typedef typename ImageMaskSpatialObjectType::ImageType              FixedMaskImageType;
  typedef typename Superclass::FixedImageMasksContainerType           FixedImageMasksContainerType;
  typedef typename Superclass::MovingImageMaskType                    MovingImageMaskType;
  typedef typename ImageMaskSpatialObjectType::ImageType              MovingMaskImageType;
  typedef typename Superclass::MovingImageMasksContainerType          MovingImageMasksContainerType;

  typedef typename Superclass::VirtualImageType                       VirtualImageType;
  typedef typename Superclass::VirtualImageBaseType                   VirtualImageBaseType;
  typedef typename Superclass::VirtualImageBaseConstPointer           VirtualImageBaseConstPointer;

  typedef typename Superclass::MultiMetricType                        MultiMetricType;
  typedef typename Superclass::MetricType                             MetricType;
  typedef typename MetricType::Pointer                                MetricPointer;
  typedef typename Superclass::PointSetMetricType                     PointSetMetricType;

  typedef typename Superclass::InitialTransformType                   InitialTransformType;
  typedef TOutputTransform                                            OutputTransformType;
  typedef typename OutputTransformType::Pointer                       OutputTransformPointer;
  typedef typename OutputTransformType::ScalarType                    RealType;
  typedef typename OutputTransformType::DerivativeType                DerivativeType;
  typedef typename DerivativeType::ValueType                          DerivativeValueType;
  typedef typename OutputTransformType::DisplacementFieldType         DisplacementFieldType;
  typedef typename DisplacementFieldType::Pointer                     DisplacementFieldPointer;
  typedef typename DisplacementFieldType::PixelType                   DisplacementVectorType;

  typedef typename Superclass::CompositeTransformType                 CompositeTransformType;
  typedef typename CompositeTransformType::TransformType              TransformBaseType;

  typedef typename Superclass::DecoratedOutputTransformType           DecoratedOutputTransformType;
  typedef typename DecoratedOutputTransformType::Pointer              DecoratedOutputTransformPointer;

  typedef DisplacementFieldTransform<RealType, ImageDimension>        DisplacementFieldTransformType;
  typedef typename DisplacementFieldTransformType::Pointer            DisplacementFieldTransformPointer;

  typedef Array<SizeValueType>                                        NumberOfIterationsArrayType;

  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();
  virtual ~SyNImageRegistrationMethod();
  virtual void PrintSelf( std::ostream & os, Indent indent ) const ITK_OVERRIDE;

  virtual void  GenerateData() ITK_OVERRIDE;

  virtual void StartOptimization();

  virtual void InitializeRegistrationAtEachLevel( const SizeValueType ) ITK_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 * = ITK_NULLPTR );

  RealType                                                        m_LearningRate;

  OutputTransformPointer                                          m_MovingToMiddleTransform;
  OutputTransformPointer                                          m_FixedToMiddleTransform;

  RealType                                                        m_ConvergenceThreshold;
  unsigned int                                                    m_ConvergenceWindowSize;

  NumberOfIterationsArrayType                                     m_NumberOfIterationsPerLevel;
  bool                                                            m_DownsampleImagesForMetricDerivatives;
  bool                                                            m_AverageMidPointGradients;

private:
  SyNImageRegistrationMethod( const Self & ) ITK_DELETE_FUNCTION;
  void operator=( const Self & ) ITK_DELETE_FUNCTION;

  RealType                                                        m_GaussianSmoothingVarianceForTheUpdateField;
  RealType                                                        m_GaussianSmoothingVarianceForTheTotalField;
};
} // end namespace itk

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

#endif