itkKNNGraphAlphaMutualInformationImageToImageMetric.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 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 <typename TFixedImage, typename TMovingImage>
class ITK_TEMPLATE_EXPORT KNNGraphAlphaMutualInformationImageToImageMetric
  : public MultiInputImageToImageMetricBase<TFixedImage, TMovingImage>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(KNNGraphAlphaMutualInformationImageToImageMetric);

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

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(KNNGraphAlphaMutualInformationImageToImageMetric);

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

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

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

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

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

  using BinaryKNNTreeSearchType = BinaryTreeSearchBase<ListSampleType>;
  using BinaryKNNTreeSearchPointer = typename BinaryKNNTreeSearchType::Pointer;
  using ANNStandardTreeSearchType = ANNStandardTreeSearch<ListSampleType>;
  using ANNFixedRadiusTreeSearchType = ANNFixedRadiusTreeSearch<ListSampleType>;
  using ANNPriorityTreeSearchType = ANNPriorityTreeSearch<ListSampleType>;
 
  using IndexArrayType = typename BinaryKNNTreeSearchType::IndexArrayType;
  using DistanceArrayType = typename BinaryKNNTreeSearchType::DistanceArrayType;
 
  using typename Superclass::DerivativeValueType;
  using TransformJacobianValueType = typename TransformJacobianType::ValueType;


  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
  SetANNStandardTreeSearch(unsigned int kNearestNeighbors, double errorBound);

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

  void
  SetANNPriorityTreeSearch(unsigned int kNearestNeighbors, double errorBound);


  void
  Initialize() override;

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

  MeasureType
  GetValue(const ParametersType & parameters) const override;

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

  itkSetClampMacro(Alpha, double, 0.0, 1.0);

  itkGetConstReferenceMacro(Alpha, double);

  itkSetClampMacro(AvoidDivisionBy, double, 0.0, 1.0);

  itkGetConstReferenceMacro(AvoidDivisionBy, double);
 
protected:
  KNNGraphAlphaMutualInformationImageToImageMetric();

  ~KNNGraphAlphaMutualInformationImageToImageMetric() override = default;

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

  BinaryKNNTreePointer m_BinaryKNNTreeFixed{ nullptr };
  BinaryKNNTreePointer m_BinaryKNNTreeMoving{ nullptr };
  BinaryKNNTreePointer m_BinaryKNNTreeJoint{ nullptr };
 
  BinaryKNNTreeSearchPointer m_BinaryKNNTreeSearcherFixed{ nullptr };
  BinaryKNNTreeSearchPointer m_BinaryKNNTreeSearcherMoving{ nullptr };
  BinaryKNNTreeSearchPointer m_BinaryKNNTreeSearcherJoint{ nullptr };
 
  double m_Alpha{ 0.99 };
  double m_AvoidDivisionBy{ 1e-10 };
 
private:
  using typename Superclass::FixedImagePointType;
  using typename Superclass::MovingImagePointType;
  using typename Superclass::MovingImageDerivativeType;
  using typename Superclass::MovingImageContinuousIndexType;
  using TransformJacobianContainerType = std::vector<TransformJacobianType>;
  // typedef std::vector<ParameterIndexArrayType>           TransformJacobianIndicesContainerType;
  using TransformJacobianIndicesContainerType = std::vector<NonZeroJacobianIndicesType>;
  using SpatialDerivativeType = vnl_matrix<double>;
  using SpatialDerivativeContainerType = std::vector<SpatialDerivativeType>;

  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