itkPCAMetric.h

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 *
 *  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 itkPCAMetric_h
#define itkPCAMetric_h
 
#include "itkAdvancedImageToImageMetric.h"
 
#include "itkSmoothingRecursiveGaussianImageFilter.h"
#include "itkImageRandomCoordinateSampler.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkExtractImageFilter.h"
#include <vector>
 
namespace itk
{
template <typename TFixedImage, typename TMovingImage>
class ITK_TEMPLATE_EXPORT PCAMetric : public AdvancedImageToImageMetric<TFixedImage, TMovingImage>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(PCAMetric);

  using Self = PCAMetric;
  using Superclass = AdvancedImageToImageMetric<TFixedImage, TMovingImage>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;
 
  using typename Superclass::FixedImageRegionType;
  using FixedImageSizeType = typename FixedImageRegionType::SizeType;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(PCAMetric);

  itkSetMacro(UseZeroAverageDisplacementConstraint, bool);
  itkSetMacro(GridSize, FixedImageSizeType);
  itkSetMacro(TransformIsStackTransform, bool);
  itkSetMacro(NumEigenValues, unsigned int);

  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::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::MovingImageDerivativeScalesType;
  using typename Superclass::DerivativeValueType;
  using typename Superclass::ThreadInfoType;
 
  using MatrixType = vnl_matrix<RealType>;
  using DerivativeMatrixType = vnl_matrix<DerivativeValueType>;
 
  //    using MatrixType = vnl_matrix< double >;
  //    using DerivativeMatrixType = vnl_matrix< double >;

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

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

  MeasureType
  GetValue(const ParametersType & parameters) const override;

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

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

 
  void
  Initialize() override;
 
protected:
  PCAMetric();
  ~PCAMetric() override = default;
  void
  PrintSelf(std::ostream & os, Indent indent) const override;


  using typename Superclass::FixedImageIndexType;
  using typename Superclass::FixedImageIndexValueType;
  using typename Superclass::MovingImageIndexType;
  using typename Superclass::FixedImagePointType;
  using FixedImageContinuousIndexType =
    typename itk::ContinuousIndex<CoordinateRepresentationType, FixedImageDimension>;
  using typename Superclass::MovingImagePointType;
  using typename Superclass::MovingImageContinuousIndexType;
  using typename Superclass::BSplineInterpolatorType;
  using typename Superclass::MovingImageDerivativeType;
  using typename Superclass::NonZeroJacobianIndicesType;

  void
  EvaluateTransformJacobianInnerProduct(const TransformJacobianType &     jacobian,
                                        const MovingImageDerivativeType & movingImageDerivative,
                                        DerivativeType &                  imageJacobian) const override;

  void
  ThreadedGetSamples(ThreadIdType threadID);
 
  void
  ThreadedComputeDerivative(ThreadIdType threadID);

  void
  AfterThreadedGetSamples(MeasureType & value) const;
 
  void
  AfterThreadedComputeDerivative(DerivativeType & derivative) const;

  static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION
  GetSamplesThreaderCallback(void * arg);
 
  static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION
  ComputeDerivativeThreaderCallback(void * arg);

  void
  LaunchGetSamplesThreaderCallback() const;
 
  void
  LaunchComputeDerivativeThreaderCallback() const;

  void
  InitializeThreadingParameters() const override;
 
private:
  struct PCAMetricMultiThreaderParameterType
  {
    Self * m_Metric;
  };
 
  PCAMetricMultiThreaderParameterType m_PCAMetricThreaderParameters{};
 
  struct PCAMetricGetSamplesPerThreadStruct
  {
    SizeValueType                    st_NumberOfPixelsCounted;
    MatrixType                       st_DataBlock;
    std::vector<FixedImagePointType> st_ApprovedSamples;
    DerivativeType                   st_Derivative;
  };
 
  itkPadStruct(ITK_CACHE_LINE_ALIGNMENT, PCAMetricGetSamplesPerThreadStruct, PaddedPCAMetricGetSamplesPerThreadStruct);
 
  itkAlignedTypedef(ITK_CACHE_LINE_ALIGNMENT,
                    PaddedPCAMetricGetSamplesPerThreadStruct,
                    AlignedPCAMetricGetSamplesPerThreadStruct);
 
  mutable std::vector<AlignedPCAMetricGetSamplesPerThreadStruct> m_PCAMetricGetSamplesPerThreadVariables{};
 
  unsigned int m_G{};
  unsigned int m_LastDimIndex{};

  bool m_UseZeroAverageDisplacementConstraint{ true };

  FixedImageSizeType m_GridSize{};

  bool m_TransformIsStackTransform{ false };

  unsigned int m_NumEigenValues{ 6 };

  mutable std::vector<unsigned int> m_PixelStartIndex{};
  mutable MatrixType                m_Atmm{};
  mutable DerivativeMatrixType      m_vSAtmm{};
  mutable DerivativeMatrixType      m_CSv{};
  mutable DerivativeMatrixType      m_Sv{};
  mutable DerivativeMatrixType      m_vdSdmu_part1{};
};
 
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkPCAMetric.hxx"
#endif
 
#endif // end #ifndef itkPCAMetric_h