#ifndef __itkNCCRegistrationFunction2_h
#define __itkNCCRegistrationFunction2_h

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

namespace itk
{

/**
 * \class NCCRegistrationFunction2
 *
 * This class encapsulate the PDE which drives the demons registration
 * algorithm. It is used by NCCRegistrationFilter 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 NCCRegistrationFilter
 * \ingroup FiniteDifferenceFunctions
 */
template <class TFixedImage, class TMovingImage, class TDeformationField>
class ITK_EXPORT NCCRegistrationFunction2 :
  public PDEDeformableRegistrationFunction<TFixedImage,
                                           TMovingImage, TDeformationField>
{
public:
  /** Standard class typedefs. */
  typedef NCCRegistrationFunction2 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( NCCRegistrationFunction2,
                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::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;

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

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

  /** 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
  {
    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
  {
    GlobalDataStruct *global = new GlobalDataStruct();

    return global;
  }

  /** Release memory for global data structure. */
  virtual void ReleaseGlobalDataPointer( void *GlobalData ) const
  {
    delete (GlobalDataStruct *) GlobalData;
  }

  /** 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) );

  /** Set/Get SubtractMean boolean. If true, the sample mean is subtracted
   * from the sample values in the cross-correlation formula.
   * Default value is false. */
  void SetSubtractMean( bool e)
  {
    m_SubtractMean = e;
  }
  bool GetSubtractMean() const
  {
    return m_SubtractMean;
  }
protected:
  NCCRegistrationFunction2();
  ~NCCRegistrationFunction2()
  {
  }
  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
   * iterators for the fixed image. */
  struct GlobalDataStruct
    {
    FixedImageNeighborhoodIteratorType m_FixedImageIterator;
    };
private:
  NCCRegistrationFunction2(const Self &); // purposely not implemented
  void operator=(const Self &);           // purposely not implemented

  /** Cache fixed image information. */
  SpacingType m_FixedImageSpacing;

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

  /** 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;

  mutable double m_MetricTotal;

  bool m_SubtractMean;
};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkNCCRegistrationFunction2.hxx"
#endif

#endif
