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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkLevelSetMotionRegistrationFunction.h,v $
  Language:  C++
  Date:      $Date: 2005/04/29 15:58:31 $
  Version:   $Revision: 1.3 $

  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 _itkLevelSetMotionRegistrationFunction_h_
#define _itkLevelSetMotionRegistrationFunction_h_

#include "itkPDEDeformableRegistrationFunction.h"
#include "itkPoint.h"
#include "itkVector.h"
#include "itkCovariantVector.h"
#include "itkInterpolateImageFunction.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
*/
template<class TFixedImage, class TMovingImage, class TDeformationField>
class ITK_EXPORT LevelSetMotionRegistrationFunction :
    public PDEDeformableRegistrationFunction< TFixedImage,
                                              TMovingImage, 
TDeformationField>
{
public:
  /** Standard class typedefs. */
  typedef LevelSetMotionRegistrationFunction    Self;
  typedef PDEDeformableRegistrationFunction< TFixedImage,
                                             TMovingImage, TDeformationField 
 >    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::DeformationFieldType    DeformationFieldType;
  typedef typename Superclass::DeformationFieldTypePointer
  DeformationFieldTypePointer;

  /** 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;

  /** Return a pointer to a global data structure that is passed to
   * this object from the solver at each calculation.  */
  virtual void *GetGlobalDataPointer() const
  {
    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;

  /** Set the object's state before each iteration. */
  virtual void InitializeIteration();

  /** 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));

  /** 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;
  
protected:
  LevelSetMotionRegistrationFunction();
  ~LevelSetMotionRegistrationFunction() {}
  void PrintSelf(std::ostream& os, Indent indent) const;

  /** 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;
    unsigned long   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 unsigned long           m_NumberOfPixelsProcessed;
  mutable double                  m_RMSChange;
  mutable double                  m_SumOfSquaredChange;

  /** Mutex lock to protect modification to metric. */
  mutable SimpleFastMutexLock     m_MetricCalculationLock;

};


} // end namespace itk

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

#endif

