text: /*=========================================================================
   *
   *  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 itkLevelSetMotionRegistrationFunction_h
  #define itkLevelSetMotionRegistrationFunction_h
  
  #include "itkPDEDeformableRegistrationFunction.h"
  #include "itkPoint.h"
  #include "itkCovariantVector.h"
  #include "itkLinearInterpolateImageFunction.h"
  #include "itkSmoothingRecursiveGaussianImageFilter.h"
  
  namespace itk
  {
  /**
   * \class LevelSetMotionRegistrationFunction
   *
   * This class encapsulate the PDE which drives the demons registration
   * algorithm. It is used by LevelSetMotionRegistrationFilter to compute the
   * output deformation field which will map a moving image onto a
   * a fixed image.
   *
   * Non-integer moving image values are obtained by using
   * interpolation. The default interpolator is of type
   * LinearInterpolateImageFunction. The user may set other
   * interpolators via method SetMovingImageInterpolator. Note that the input
   * interpolator must derive from baseclass InterpolateImageFunction.
   *
   * This class is templated over the fixed image type, moving image type,
   * and the deformation field type.
   *
   * \warning This filter assumes that the fixed image type, moving image type
   * and deformation field type all have the same number of dimensions.
   *
   * \sa LevelSetMotionRegistrationFilter
   * \ingroup FiniteDifferenceFunctions
   * \ingroup ITKPDEDeformableRegistration
   */
  template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
  class LevelSetMotionRegistrationFunction:
    public PDEDeformableRegistrationFunction< TFixedImage,
                                              TMovingImage,
                                              TDisplacementField >
  {
  public:
    /** Standard class typedefs. */
    typedef LevelSetMotionRegistrationFunction Self;
    typedef PDEDeformableRegistrationFunction< TFixedImage,
                                               TMovingImage, TDisplacementField
                                               > Superclass;
  
    typedef SmartPointer< Self >       Pointer;
    typedef SmartPointer< const Self > ConstPointer;
  
    /** Method for creation through the object factory. */
    itkNewMacro(Self);
  
    /** Run-time type information (and related methods). */
    itkTypeMacro(LevelSetMotionRegistrationFunction,
                 PDEDeformableRegistrationFunction);
  
    /** MovingImage image type. */
    typedef typename Superclass::MovingImageType    MovingImageType;
    typedef typename Superclass::MovingImagePointer MovingImagePointer;
    typedef typename MovingImageType::SpacingType   MovingSpacingType;
  
    /** FixedImage image type. */
    typedef typename Superclass::FixedImageType    FixedImageType;
    typedef typename Superclass::FixedImagePointer FixedImagePointer;
    typedef typename FixedImageType::IndexType     IndexType;
    typedef typename FixedImageType::SizeType      SizeType;
    typedef typename FixedImageType::SpacingType   SpacingType;
  
    /** Deformation field type. */
    typedef typename Superclass::DisplacementFieldType DisplacementFieldType;
    typedef typename Superclass::DisplacementFieldTypePointer
    DisplacementFieldTypePointer;
  
    /** Inherit some enums from the superclass. */
    itkStaticConstMacro(ImageDimension, unsigned
                        int, Superclass::ImageDimension);
  
    /** Inherit some enums from the superclass. */
    typedef typename Superclass::PixelType        PixelType;
    typedef typename Superclass::RadiusType       RadiusType;
    typedef typename Superclass::NeighborhoodType NeighborhoodType;
    typedef typename Superclass::FloatOffsetType  FloatOffsetType;
    typedef typename Superclass::TimeStepType     TimeStepType;
  
    /** Interpolator type. */
    typedef double                                                    CoordRepType;
    typedef InterpolateImageFunction< MovingImageType, CoordRepType > InterpolatorType;
    typedef typename InterpolatorType::Pointer                        InterpolatorPointer;
    typedef typename InterpolatorType::PointType                      PointType;
    typedef LinearInterpolateImageFunction< MovingImageType, CoordRepType >
    DefaultInterpolatorType;
  
    /** Vector types. */
    typedef Vector< double, itkGetStaticConstMacro(ImageDimension) > VectorType;
    typedef CovariantVector< double, itkGetStaticConstMacro(ImageDimension) >
    CovariantVectorType;
  
    /** Moving image gradient calculator type. */
    typedef SmoothingRecursiveGaussianImageFilter< MovingImageType >
    MovingImageSmoothingFilterType;
    typedef typename MovingImageSmoothingFilterType::Pointer
    MovingImageSmoothingFilterPointer;
  
    /** Set the moving image interpolator. */
    void SetMovingImageInterpolator(InterpolatorType *ptr)
    { m_MovingImageInterpolator = ptr; }
  
    /** Get the moving image interpolator. */
    InterpolatorType * GetMovingImageInterpolator(void)
    { return m_MovingImageInterpolator; }
  
    /** Compute the time step that can taken for this iterations.  In
     * this context, the timestep is a function of the maximum gradients. */
    virtual TimeStepType ComputeGlobalTimeStep(void *GlobalData) const ITK_OVERRIDE;
  
    /** Return a pointer to a global data structure that is passed to
     * this object from the solver at each calculation.  */
    virtual void * GetGlobalDataPointer() const ITK_OVERRIDE
    {
      GlobalDataStruct *global = new GlobalDataStruct();
  
      global->m_SumOfSquaredDifference  = 0.0;
      global->m_NumberOfPixelsProcessed = 0L;
      global->m_SumOfSquaredChange      = 0;
      global->m_MaxL1Norm            = NumericTraits< double >::NonpositiveMin();
      return global;
    }
  
    /** Release memory for global data structure. */
    virtual void ReleaseGlobalDataPointer(void *GlobalData) const ITK_OVERRIDE;
  
    /** Set the object's state before each iteration. */
    virtual void InitializeIteration() ITK_OVERRIDE;
  
    /** This method is called by a finite difference solver image filter at
     * each pixel that does not lie on a data set boundary */
    virtual PixelType  ComputeUpdate( const NeighborhoodType & neighborhood,
                                      void *globalData,
                                      const FloatOffsetType & offset =
                                        FloatOffsetType(0.0) ) ITK_OVERRIDE;
  
    /** Get the metric value. The metric value is the mean square difference
     * in intensity between the fixed image and transforming moving image
     * computed over the the overlapping region between the two images. */
    virtual double GetMetric() const
    { return m_Metric; }
  
    /** Get the rms change in deformation field. */
    virtual double GetRMSChange() const
    { return m_RMSChange; }
  
    /** Set/Get the parameter alpha.  Alpha is added to the calculated
     * gradient magnitude prior to normalizing the gradient to protect
     * against numerical instability as the gradient magnitude
     * approaches zero.  This should be set as a small fraction of the
     * intensity dynamic range, for instance 0.04%. Default is the
     * absolute (not percentage) value of 0.1. */
    virtual void SetAlpha(double);
  
    virtual double GetAlpha() const;
  
    /** Set/Get the threshold below which the absolute difference of
     * intensity yields a match. When the intensities match between a
     * moving and fixed image pixel, the update vector (for that
     * iteration) will be the zero vector. Default is 0.001. */
    virtual void SetIntensityDifferenceThreshold(double);
  
    virtual double GetIntensityDifferenceThreshold() const;
  
    /** Set/Get the threshold below which the gradient magnitude is
     * considered the zero vector. Default is 1e-9. */
    virtual void SetGradientMagnitudeThreshold(double);
  
    virtual double GetGradientMagnitudeThreshold() const;
  
    /** Set/Get the standard deviation used for smoothing the moving
     * image prior to calculating gradients. */
    virtual void SetGradientSmoothingStandardDeviations(double);
  
    virtual double GetGradientSmoothingStandardDeviations() const;
  
    /** Use the image spacing information in calculations. Use this option if you
     * want derivatives in physical space. Default is UseImageSpacing ON, due to a
     * backward compatibility state. */
    void SetUseImageSpacing(bool);
  
    bool GetUseImageSpacing() const;
  
  protected:
    LevelSetMotionRegistrationFunction();
    ~LevelSetMotionRegistrationFunction() {}
    void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
  
    /** FixedImage image neighborhood iterator type. */
    typedef ConstNeighborhoodIterator< FixedImageType >
    FixedImageNeighborhoodIteratorType;
  
    /** A global data type for this class of equation. Used to store
     * information for computing the metric. */
    struct GlobalDataStruct {
      double m_SumOfSquaredDifference;
      SizeValueType m_NumberOfPixelsProcessed;
      double m_SumOfSquaredChange;
      double m_MaxL1Norm;
    };
  
  private:
    LevelSetMotionRegistrationFunction(const Self &); //purposely not implemented
    void operator=(const Self &);                     //purposely not implemented
  
    /** Cache fixed image information. */
    SpacingType m_FixedImageSpacing;
    PointType   m_FixedImageOrigin;
  
    /** Function to compute derivatives of the moving image. */
    MovingImageSmoothingFilterPointer m_MovingImageSmoothingFilter;
  
    /** Function to interpolate the moving image. */
    InterpolatorPointer m_MovingImageInterpolator;
    InterpolatorPointer m_SmoothMovingImageInterpolator;
  
    /** Stabilization factor for normalizing gradients to protect
     * against small gradient magnitudes */
    double m_Alpha;
  
    /** Threshold below which the gradient is considered zero. */
    double m_GradientMagnitudeThreshold;
  
    /** Threshold below which two intensity value are assumed to match. */
    double m_IntensityDifferenceThreshold;
  
    /** Smoothing parameter for gradient calculation */
    double m_GradientSmoothingStandardDeviations;
  
    /** The metric value is the mean square difference in intensity between
     * the fixed image and transforming moving image computed over the
     * the overlapping region between the two images. */
    mutable double        m_Metric;
    mutable double        m_SumOfSquaredDifference;
    mutable SizeValueType m_NumberOfPixelsProcessed;
    mutable double        m_RMSChange;
    mutable double        m_SumOfSquaredChange;
  
    /** Mutex lock to protect modification to metric. */
    mutable SimpleFastMutexLock m_MetricCalculationLock;
  
    bool m_UseImageSpacing;
  };
  } // end namespace itk
  
  #ifndef ITK_MANUAL_INSTANTIATION
  #include "itkLevelSetMotionRegistrationFunction.hxx"
  #endif
  
  #endif
  