itkMattesMutualInformationImageToImageMetric.h

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkMattesMutualInformationImageToImageMetric.h,v $
  Language:  C++
  Date:      $Date: 2009-11-02 18:46:33 $
  Version:   $Revision: 1.29 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 __itkMattesMutualInformationImageToImageMetric_h
#define __itkMattesMutualInformationImageToImageMetric_h

// First make sure that the configuration is available.
// This line can be removed once the optimized versions
// gets integrated into the main directories.
#include "itkConfigure.h"

#ifdef ITK_USE_OPTIMIZED_REGISTRATION_METHODS
#include "itkOptMattesMutualInformationImageToImageMetric.h"
#else

#include "itkImageToImageMetric.h"
#include "itkCovariantVector.h"
#include "itkPoint.h"
#include "itkIndex.h"
#include "itkBSplineKernelFunction.h"
#include "itkBSplineDerivativeKernelFunction.h"
#include "itkCentralDifferenceImageFunction.h"
#include "itkBSplineInterpolateImageFunction.h"
#include "itkBSplineDeformableTransform.h"
#include "itkArray2D.h"

namespace itk
{

template <class TFixedImage,class TMovingImage >
class ITK_EXPORT MattesMutualInformationImageToImageMetric :
    public ImageToImageMetric< TFixedImage, TMovingImage >
{
public:

  typedef MattesMutualInformationImageToImageMetric           Self;
  typedef ImageToImageMetric< TFixedImage, TMovingImage >     Superclass;
  typedef SmartPointer<Self>                                  Pointer;
  typedef SmartPointer<const Self>                            ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(MattesMutualInformationImageToImageMetric, ImageToImageMetric);

  typedef typename Superclass::TransformType            TransformType;
  typedef typename Superclass::TransformPointer         TransformPointer;
  typedef typename Superclass::TransformJacobianType    TransformJacobianType;
  typedef typename Superclass::InterpolatorType         InterpolatorType;
  typedef typename Superclass::MeasureType              MeasureType;
  typedef typename Superclass::DerivativeType           DerivativeType;
  typedef typename Superclass::ParametersType           ParametersType;
  typedef typename Superclass::FixedImageType           FixedImageType;
  typedef typename Superclass::MovingImageType          MovingImageType;
  typedef typename Superclass::FixedImageConstPointer   FixedImageConstPointer;
  typedef typename Superclass::MovingImageConstPointer  MovingImageCosntPointer;
  typedef typename Superclass::InputPointType           InputPointType;
  typedef typename Superclass::OutputPointType          OutputPointType;

  typedef typename Superclass::CoordinateRepresentationType
  CoordinateRepresentationType;

  typedef typename FixedImageType::IndexType           FixedImageIndexType;
  typedef typename FixedImageType::OffsetValueType     OffsetValueType;
  typedef typename FixedImageIndexType::IndexValueType FixedImageIndexValueType;
  typedef typename MovingImageType::IndexType          MovingImageIndexType;
  typedef typename TransformType::InputPointType       FixedImagePointType;
  typedef typename TransformType::OutputPointType      MovingImagePointType;

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

  virtual void Initialize(void) throw ( ExceptionObject );

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

  MeasureType GetValue( const ParametersType& parameters ) const;

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

  itkSetClampMacro( NumberOfSpatialSamples, unsigned long,
                    1, NumericTraits<unsigned long>::max() );
  itkGetConstReferenceMacro( NumberOfSpatialSamples, unsigned long); 

  itkSetClampMacro( NumberOfHistogramBins, unsigned long,
                    5, NumericTraits<unsigned long>::max() );
  itkGetConstReferenceMacro( NumberOfHistogramBins, unsigned long);   

  void ReinitializeSeed();
  void ReinitializeSeed(int);  

  itkSetMacro(UseAllPixels,bool);
  itkGetConstReferenceMacro(UseAllPixels,bool);
  itkBooleanMacro(UseAllPixels);

  itkSetMacro(UseExplicitPDFDerivatives,bool);
  itkGetConstReferenceMacro(UseExplicitPDFDerivatives,bool);
  itkBooleanMacro(UseExplicitPDFDerivatives);

  itkSetMacro(UseCachingOfBSplineWeights,bool);
  itkGetConstReferenceMacro(UseCachingOfBSplineWeights,bool);
  itkBooleanMacro(UseCachingOfBSplineWeights);

protected:

  MattesMutualInformationImageToImageMetric();
  virtual ~MattesMutualInformationImageToImageMetric() {};
  void PrintSelf(std::ostream& os, Indent indent) const;


  class FixedImageSpatialSample
    {
    public:
    FixedImageSpatialSample():FixedImageValue(0.0)
      { FixedImagePointValue.Fill(0.0); }
    ~FixedImageSpatialSample() {};
  
    FixedImagePointType           FixedImagePointValue;
    double                        FixedImageValue;
    unsigned int                  FixedImageParzenWindowIndex;
    };
  
  typedef std::vector<FixedImageSpatialSample>  
  FixedImageSpatialSampleContainer;

  FixedImageSpatialSampleContainer    m_FixedImageSamples;

  virtual void SampleFixedImageDomain( 
    FixedImageSpatialSampleContainer& samples);

  virtual void SampleFullFixedImageDomain( 
    FixedImageSpatialSampleContainer& samples);

  virtual void TransformPoint( unsigned int sampleNumber,
                               const ParametersType& parameters,
                               MovingImagePointType& mappedPoint,
                               bool& sampleWithinSupportRegion,
                               double& movingImageValue ) const;

private:

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


  typedef float                       PDFValueType;
  typedef std::vector<PDFValueType>   MarginalPDFType;

  mutable MarginalPDFType             m_FixedImageMarginalPDF;

  mutable MarginalPDFType             m_MovingImageMarginalPDF;

  typedef double                      PRatioType;
  typedef Array2D< PRatioType >       PRatioArrayType;
  mutable PRatioArrayType             m_PRatioArray;

  mutable DerivativeType              m_MetricDerivative;

  typedef Image<PDFValueType,2>                 JointPDFType;
  typedef JointPDFType::IndexType               JointPDFIndexType;
  typedef JointPDFType::PixelType               JointPDFValueType;
  typedef JointPDFType::RegionType              JointPDFRegionType;
  typedef JointPDFType::SizeType                JointPDFSizeType;
  typedef Image<PDFValueType,3>                 JointPDFDerivativesType;
  typedef JointPDFDerivativesType::IndexType    JointPDFDerivativesIndexType;
  typedef JointPDFDerivativesType::PixelType    JointPDFDerivativesValueType;
  typedef JointPDFDerivativesType::RegionType   JointPDFDerivativesRegionType;
  typedef JointPDFDerivativesType::SizeType     JointPDFDerivativesSizeType;

  typename JointPDFType::Pointer                m_JointPDF;
  typename JointPDFDerivativesType::Pointer     m_JointPDFDerivatives;

  unsigned long                                 m_NumberOfSpatialSamples;
  unsigned long                                 m_NumberOfParameters;

  unsigned long  m_NumberOfHistogramBins;
  double         m_MovingImageNormalizedMin;
  double         m_FixedImageNormalizedMin;
  double         m_MovingImageTrueMin;
  double         m_MovingImageTrueMax;
  double         m_FixedImageBinSize;
  double         m_MovingImageBinSize;

  typedef BSplineKernelFunction<3>           CubicBSplineFunctionType;
  typedef BSplineDerivativeKernelFunction<3> CubicBSplineDerivativeFunctionType;

  typename CubicBSplineFunctionType::Pointer   m_CubicBSplineKernel;
  typename CubicBSplineDerivativeFunctionType::Pointer 
  m_CubicBSplineDerivativeKernel;

  virtual void ComputeFixedImageParzenWindowIndices( 
                   FixedImageSpatialSampleContainer& samples );

  typedef CovariantVector< double,
                           itkGetStaticConstMacro(MovingImageDimension) >
                                                         ImageDerivativesType;

  virtual void ComputeImageDerivatives( const MovingImagePointType& mappedPoint,
                                        ImageDerivativesType& gradient ) const;

  bool m_InterpolatorIsBSpline;

  typedef
  BSplineInterpolateImageFunction<MovingImageType,
                                  CoordinateRepresentationType> 
                                                      BSplineInterpolatorType;

  typename BSplineInterpolatorType::Pointer m_BSplineInterpolator;

  typedef CentralDifferenceImageFunction<MovingImageType,
                                         CoordinateRepresentationType> 
                                                       DerivativeFunctionType;

  typename DerivativeFunctionType::Pointer m_DerivativeCalculator;


  virtual void ComputePDFDerivatives( unsigned int sampleNumber,
                                      int movingImageParzenWindowIndex,
                                      const ImageDerivativesType&
                                                movingImageGradientValue,
                                      double cubicBSplineDerivativeValue
                                      ) const;

  bool m_TransformIsBSpline;

  long m_NumParametersPerDim;

  unsigned long m_NumBSplineWeights;

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

  enum { DeformationSplineOrder = 3 };

  typedef BSplineDeformableTransform<
    CoordinateRepresentationType,
    ::itk::GetImageDimension<FixedImageType>::ImageDimension,
    DeformationSplineOrder> BSplineTransformType;
  typedef typename BSplineTransformType::WeightsType 
  BSplineTransformWeightsType;
  typedef typename BSplineTransformType::ParameterIndexArrayType 
  BSplineTransformIndexArrayType;

  typename BSplineTransformType::Pointer m_BSplineTransform;

  typedef typename BSplineTransformWeightsType::ValueType    WeightsValueType;
  typedef          Array2D<WeightsValueType>                 BSplineTransformWeightsArrayType;
  typedef typename BSplineTransformIndexArrayType::ValueType IndexValueType;
  typedef          Array2D<IndexValueType>                   BSplineTransformIndicesArrayType;
  typedef          std::vector<MovingImagePointType>         MovingImagePointArrayType;
  typedef          std::vector<bool>                         BooleanArrayType;

  BSplineTransformWeightsArrayType      m_BSplineTransformWeightsArray;
  BSplineTransformIndicesArrayType      m_BSplineTransformIndicesArray;
  MovingImagePointArrayType             m_PreTransformPointsArray;
  BooleanArrayType                      m_WithinSupportRegionArray;
  
  typedef FixedArray<unsigned long, 
                     ::itk::GetImageDimension<FixedImageType>::ImageDimension>
                                                          ParametersOffsetType;
  ParametersOffsetType                  m_ParametersOffset;

  bool             m_UseAllPixels;

  virtual void PreComputeTransformValues();

  bool             m_ReseedIterator;
  int              m_RandomSeed;
  
  // Selection of explicit or implicit computation of PDF derivatives
  // with respect to Transform parameters.
  bool             m_UseExplicitPDFDerivatives;

  // Variables needed for optionally caching values when using a BSpline transform.
  bool                                    m_UseCachingOfBSplineWeights;
  mutable BSplineTransformWeightsType     m_Weights;
  mutable BSplineTransformIndexArrayType  m_Indices;

};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMattesMutualInformationImageToImageMetric.txx"
#endif

#endif

#endif