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

  Program:   Advanced Normalization Tools
  Module:    $RCSfile: itkSyNDemonsRegistrationFunction.h,v $
  Language:  C++
  Date:      $Date: 2008/11/15 23:46:06 $
  Version:   $Revision: 1.18 $

  Copyright (c) ConsortiumOfANTS. All rights reserved.
  See accompanying COPYING.txt or
 http://sourceforge.net/projects/advants/files/ANTS/ANTSCopyright.txt 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 _itkSyNDemonsRegistrationFunction_h_
#define _itkSyNDemonsRegistrationFunction_h_

#include "itkPDEDeformableRegistrationFunction.h"
#include "itkPoint.h"
#include "itkCovariantVector.h"
#include "itkInterpolateImageFunction.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkCentralDifferenceImageFunction.h"

namespace itk
{
/**
* \class SyNDemonsRegistrationFunction
*
* This class encapsulate the PDE which drives the demons registration
* algorithm. It is used by SyNDemonsRegistrationFilter 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 SyNDemonsRegistrationFilter
* \ingroup FiniteDifferenceFunctions
*/
template <class TFixedImage, class TMovingImage, class TDisplacementField>
class SyNDemonsRegistrationFunction :
  public         AvantsPDEDeformableRegistrationFunction<TFixedImage,
                                                         TMovingImage,
                                                         TDisplacementField>
{
public:
  /** Standard class typedefs. */
  typedef SyNDemonsRegistrationFunction 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( SyNDemonsRegistrationFunction,
                PDEDeformableRegistrationFunction );

  /** MovingImage image type. */
  typedef typename Superclass::MovingImageType    MovingImageType;
  typedef typename Superclass::MovingImagePointer MovingImagePointer;

  /** 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;

  /** Covariant vector type. */
  typedef CovariantVector<double, itkGetStaticConstMacro(ImageDimension)>
    CovariantVectorType;

  /** Fixed image gradient calculator type. */
  typedef CentralDifferenceImageFunction<FixedImageType>
    GradientCalculatorType;
  typedef typename GradientCalculatorType::Pointer GradientCalculatorPointer;

  /** Moving image gradient calculator type. */
  typedef CentralDifferenceImageFunction<MovingImageType, CoordRepType>
    MovingImageGradientCalculatorType;
  typedef typename MovingImageGradientCalculatorType::Pointer
    MovingImageGradientCalculatorPointer;

  /** Set the moving image interpolator. */
  void SetMovingImageInterpolator( InterpolatorType * ptr )
  {
    m_MovingImageInterpolator = ptr;
  }

  /** Get the moving image interpolator. */
  InterpolatorType * GetMovingImageInterpolator(void)
  {
    return m_MovingImageInterpolator;
  }

  /** This class uses a constant timestep of 1. */
  virtual TimeStepType ComputeGlobalTimeStep(void * itkNotUsed(GlobalData) ) const ITK_OVERRIDE
  {
    return m_TimeStep;
  }

  /** 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;
    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;

  virtual PixelType  ComputeUpdateInv(const NeighborhoodType & neighborhood, void *globalData, const FloatOffsetType & offset =
                                        FloatOffsetType(
                                          0.0) ) ITK_OVERRIDE;

  void SetUseSSD( bool b )
  {
    this->m_UseSSD = b;
  }

  /** 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;
  }

  /** Select if the fixed image or moving image gradient is used for
   * the computating the demon forces. The fixed image gradient is used
   * by default. */
  virtual void SetUseMovingImageGradient( bool flag )
  {
    m_UseMovingImageGradient = flag;
  }

  virtual bool GetUseMovingImageGradient() const
  {
    return m_UseMovingImageGradient;
  }

  /** 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;

protected:
  SyNDemonsRegistrationFunction();
  ~SyNDemonsRegistrationFunction()
  {
  }

  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;
    unsigned long m_NumberOfPixelsProcessed;
    double m_SumOfSquaredChange;
    };
private:
  SyNDemonsRegistrationFunction(const Self &); // purposely not implemented
  void operator=(const Self &);                // purposely not implemented

  /** Cache fixed image information. */
  SpacingType m_FixedImageSpacing;
  PointType   m_FixedImageOrigin;
  double      m_Normalizer;

  /** Function to compute derivatives of the fixed image. */
  GradientCalculatorPointer m_FixedImageGradientCalculator;

  /** Function to compute derivatives of the moving image. */
  MovingImageGradientCalculatorPointer m_MovingImageGradientCalculator;
  bool                                 m_UseMovingImageGradient;

  /** Function to interpolate the moving image. */
  InterpolatorPointer m_MovingImageInterpolator;

  /** The global timestep. */
  TimeStepType m_TimeStep;

  /** Threshold below which the denominator term is considered zero. */
  double m_DenominatorThreshold;

  /** Threshold below which two intensity value are assumed to match. */
  double m_IntensityDifferenceThreshold;

  /** 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;

  bool m_UseSSD;
};
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkSyNDemonsRegistrationFunction.cxx"
#endif

#endif
