itkKNNGraphAlphaMutualInformationImageToImageMetric.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 __itkKNNGraphAlphaMutualInformationImageToImageMetric_h
#define __itkKNNGraphAlphaMutualInformationImageToImageMetric_h

#include "itkMultiInputImageToImageMetricBase.h"

#include "itkArray.h"
#include "itkListSampleCArray.h"
#include "itkBinaryTreeBase.h"
#include "itkBinaryTreeSearchBase.h"

#include "itkANNkDTree.h"
#include "itkANNbdTree.h"
#include "itkANNBruteForceTree.h"

#include "itkANNStandardTreeSearch.h"
#include "itkANNFixedRadiusTreeSearch.h"
#include "itkANNPriorityTreeSearch.h"

#include "itkArray2D.h"

namespace itk
{
template< class TFixedImage, class TMovingImage >
class KNNGraphAlphaMutualInformationImageToImageMetric :
  public MultiInputImageToImageMetricBase< TFixedImage, TMovingImage >
{
public:

  typedef KNNGraphAlphaMutualInformationImageToImageMetric Self;
  typedef MultiInputImageToImageMetricBase<
    TFixedImage, TMovingImage >                             Superclass;
  typedef SmartPointer< Self >       Pointer;
  typedef SmartPointer< const Self > ConstPointer;

  itkNewMacro( Self );

  itkTypeMacro( KNNGraphAlphaMutualInformationImageToImageMetric,
    MultiInputImageToImageMetricBase );

  typedef typename
    Superclass::CoordinateRepresentationType CoordinateRepresentationType;
  typedef typename Superclass::MovingImageType            MovingImageType;
  typedef typename Superclass::MovingImagePixelType       MovingImagePixelType;
  typedef typename Superclass::MovingImageConstPointer    MovingImageConstPointer;
  typedef typename Superclass::FixedImageType             FixedImageType;
  typedef typename Superclass::FixedImageConstPointer     FixedImageConstPointer;
  typedef typename Superclass::FixedImageRegionType       FixedImageRegionType;
  typedef typename Superclass::TransformType              TransformType;
  typedef typename Superclass::TransformPointer           TransformPointer;
  typedef typename Superclass::InputPointType             InputPointType;
  typedef typename Superclass::OutputPointType            OutputPointType;
  typedef typename Superclass::TransformParametersType    TransformParametersType;
  typedef typename Superclass::TransformJacobianType      TransformJacobianType;
  typedef typename Superclass::InterpolatorType           InterpolatorType;
  typedef typename Superclass::InterpolatorPointer        InterpolatorPointer;
  typedef typename Superclass::RealType                   RealType;
  typedef typename Superclass::GradientPixelType          GradientPixelType;
  typedef typename Superclass::GradientImageType          GradientImageType;
  typedef typename Superclass::GradientImagePointer       GradientImagePointer;
  typedef typename Superclass::GradientImageFilterType    GradientImageFilterType;
  typedef typename Superclass::GradientImageFilterPointer GradientImageFilterPointer;
  typedef typename Superclass::FixedImageMaskType         FixedImageMaskType;
  typedef typename Superclass::FixedImageMaskPointer      FixedImageMaskPointer;
  typedef typename Superclass::MovingImageMaskType        MovingImageMaskType;
  typedef typename Superclass::MovingImageMaskPointer     MovingImageMaskPointer;
  typedef typename Superclass::MeasureType                MeasureType;
  typedef typename Superclass::DerivativeType             DerivativeType;
  typedef typename Superclass::ParametersType             ParametersType;
  typedef typename Superclass::FixedImagePixelType        FixedImagePixelType;
  typedef typename Superclass::MovingImageRegionType      MovingImageRegionType;
  typedef typename Superclass::ImageSamplerType           ImageSamplerType;
  typedef typename Superclass::ImageSamplerPointer        ImageSamplerPointer;
  typedef typename Superclass::ImageSampleContainerType   ImageSampleContainerType;
  typedef typename
    Superclass::ImageSampleContainerPointer ImageSampleContainerPointer;
  typedef typename Superclass::FixedImageLimiterType  FixedImageLimiterType;
  typedef typename Superclass::MovingImageLimiterType MovingImageLimiterType;
  typedef typename
    Superclass::FixedImageLimiterOutputType FixedImageLimiterOutputType;
  typedef typename
    Superclass::MovingImageLimiterOutputType MovingImageLimiterOutputType;
  typedef typename Superclass::NonZeroJacobianIndicesType NonZeroJacobianIndicesType;

  typedef typename Superclass::FixedImageVectorType             FixedImageVectorType;
  typedef typename Superclass::FixedImageMaskVectorType         FixedImageMaskVectorType;
  typedef typename Superclass::FixedImageRegionVectorType       FixedImageRegionVectorType;
  typedef typename Superclass::MovingImageVectorType            MovingImageVectorType;
  typedef typename Superclass::MovingImageMaskVectorType        MovingImageMaskVectorType;
  typedef typename Superclass::InterpolatorVectorType           InterpolatorVectorType;
  typedef typename Superclass::FixedImageInterpolatorVectorType FixedImageInterpolatorVectorType;

  itkStaticConstMacro( FixedImageDimension, unsigned int, FixedImageType::ImageDimension );
  itkStaticConstMacro( MovingImageDimension, unsigned int, MovingImageType::ImageDimension );

  typedef Array< double >                           MeasurementVectorType;
  typedef typename MeasurementVectorType::ValueType MeasurementVectorValueType;
  typedef typename Statistics::ListSampleCArray<
    MeasurementVectorType, double >                   ListSampleType;
  typedef typename ListSampleType::Pointer ListSamplePointer;

  typedef BinaryTreeBase< ListSampleType >    BinaryKNNTreeType;
  typedef typename BinaryKNNTreeType::Pointer BinaryKNNTreePointer;
  typedef ANNkDTree< ListSampleType >         ANNkDTreeType;
  typedef ANNbdTree< ListSampleType >         ANNbdTreeType;
  typedef ANNBruteForceTree< ListSampleType > ANNBruteForceTreeType;

  typedef BinaryTreeSearchBase< ListSampleType >     BinaryKNNTreeSearchType;
  typedef typename BinaryKNNTreeSearchType::Pointer  BinaryKNNTreeSearchPointer;
  typedef ANNStandardTreeSearch< ListSampleType >    ANNStandardTreeSearchType;
  typedef ANNFixedRadiusTreeSearch< ListSampleType > ANNFixedRadiusTreeSearchType;
  typedef ANNPriorityTreeSearch< ListSampleType >    ANNPriorityTreeSearchType;

  typedef typename BinaryKNNTreeSearchType::IndexArrayType    IndexArrayType;
  typedef typename BinaryKNNTreeSearchType::DistanceArrayType DistanceArrayType;

  typedef typename DerivativeType::ValueType        DerivativeValueType;
  typedef typename TransformJacobianType::ValueType TransformJacobianValueType;

  void SetANNkDTree( unsigned int bucketSize, std::string splittingRule );

  void SetANNkDTree( unsigned int bucketSize, std::string splittingRuleFixed,
    std::string splittingRuleMoving, std::string splittingRuleJoint );

  void SetANNbdTree( unsigned int bucketSize, std::string splittingRule,
    std::string shrinkingRule );

  void SetANNbdTree( unsigned int bucketSize, std::string splittingRuleFixed,
    std::string splittingRuleMoving, std::string splittingRuleJoint,
    std::string shrinkingRuleFixed, std::string shrinkingRuleMoving,
    std::string shrinkingRuleJoint );

  void SetANNBruteForceTree( void );

  void SetANNStandardTreeSearch( unsigned int kNearestNeighbors,
    double errorBound );

  void SetANNFixedRadiusTreeSearch( unsigned int kNearestNeighbors,
    double errorBound, double squaredRadius );

  void SetANNPriorityTreeSearch( unsigned int kNearestNeighbors,
    double errorBound );

  virtual void Initialize( void ) throw ( ExceptionObject );

  void GetDerivative( const TransformParametersType & parameters,
    DerivativeType & Derivative ) const;

  MeasureType GetValue( const TransformParametersType & parameters ) const;

  void GetValueAndDerivative( const TransformParametersType & parameters,
    MeasureType & Value, DerivativeType & Derivative ) const;

  itkSetClampMacro( Alpha, double, 0.0, 1.0 );

  itkGetConstReferenceMacro( Alpha, double );

  itkSetClampMacro( AvoidDivisionBy, double, 0.0, 1.0 );

  itkGetConstReferenceMacro( AvoidDivisionBy, double );

protected:

  KNNGraphAlphaMutualInformationImageToImageMetric();

  virtual ~KNNGraphAlphaMutualInformationImageToImageMetric() {}

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

  BinaryKNNTreePointer m_BinaryKNNTreeFixed;
  BinaryKNNTreePointer m_BinaryKNNTreeMoving;
  BinaryKNNTreePointer m_BinaryKNNTreeJoint;

  BinaryKNNTreeSearchPointer m_BinaryKNNTreeSearcherFixed;
  BinaryKNNTreeSearchPointer m_BinaryKNNTreeSearcherMoving;
  BinaryKNNTreeSearchPointer m_BinaryKNNTreeSearcherJoint;

  double m_Alpha;
  double m_AvoidDivisionBy;

private:

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

  typedef typename Superclass::FixedImagePointType            FixedImagePointType;
  typedef typename Superclass::MovingImagePointType           MovingImagePointType;
  typedef typename Superclass::MovingImageDerivativeType      MovingImageDerivativeType;
  typedef typename Superclass::MovingImageContinuousIndexType MovingImageContinuousIndexType;
  typedef std::vector< TransformJacobianType >                TransformJacobianContainerType;
  //typedef std::vector<ParameterIndexArrayType>           TransformJacobianIndicesContainerType;
  typedef std::vector< NonZeroJacobianIndicesType > TransformJacobianIndicesContainerType;
  typedef Array2D< double >                         SpatialDerivativeType;
  typedef std::vector< SpatialDerivativeType >      SpatialDerivativeContainerType;

  virtual void ComputeListSampleValuesAndDerivativePlusJacobian(
    const ListSamplePointer & listSampleFixed,
    const ListSamplePointer & listSampleMoving,
    const ListSamplePointer & listSampleJoint,
    const bool & doDerivative,
    TransformJacobianContainerType & jacobians,
    TransformJacobianIndicesContainerType & jacobiansIndices,
    SpatialDerivativeContainerType & spatialDerivatives ) const;

  virtual void EvaluateMovingFeatureImageDerivatives(
    const MovingImagePointType & mappedPoint,
    SpatialDerivativeType & featureGradients ) const;

  virtual void UpdateDerivativeOfGammas(
    const SpatialDerivativeType & D1sparse,
    const SpatialDerivativeType & D2sparse_M,
    const SpatialDerivativeType & D2sparse_J,
    //const ParameterIndexArrayType & D1indices,
    //const ParameterIndexArrayType & D2indices_M,
    //const ParameterIndexArrayType & D2indices_J,
    const NonZeroJacobianIndicesType & D1indices,
    const NonZeroJacobianIndicesType & D2indices_M,
    const NonZeroJacobianIndicesType & D2indices_J,
    const MeasurementVectorType & diff_M,
    const MeasurementVectorType & diff_J,
    const MeasureType & distance_M,
    const MeasureType & distance_J,
    DerivativeType & dGamma_M,
    DerivativeType & dGamma_J ) const;

};

} // end namespace itk

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

#endif // end #ifndef __itkKNNGraphAlphaMutualInformationImageToImageMetric_h