#ifndef __itkDiffeomorphicDemonsRegistrationTensorFilter_h
#define __itkDiffeomorphicDemonsRegistrationTensorFilter_h

#include "itkPDEDeformableRegistrationFilter.h"
#include "itkESMDemonsRegistrationTensorFunction.h"

#include "itkMultiplyImageFilter.h"
#include "itkExponentialDisplacementFieldImageFilter.h"
#include "itkWarpVectorImageFilter.h"
#include "itkVectorLinearInterpolateNearestNeighborExtrapolateImageFunction.h"
#include "itkAddImageFilter.h"

namespace itk
{

/** \class DiffeomorphicDemonsRegistrationTensorFilter
 * \brief Deformably register two tensor images using a diffeomorphic demons
 * algorithm.
 *
 * This class was contributed by Thomas Yeo, INRIA, based on a variation of
 * the DiffeomorphicDemonsRegistrationFilter. The modification is to use
 * tensors instead of scalars.
 *
 * DiffeomorphicDemonsRegistrationTensorFilter implements the demons deformable
 * algorithm that register two images by computing the deformation field which
 * will map a moving image onto a fixed image.
 *
 * A deformation field is represented as a image whose pixel type is some
 * vector type with at least N elements, where N is the dimension of
 * the fixed image. The vector type must support element access via operator
 * []. It is assumed that the vector elements behave like floating point
 * scalars.
 *
 * This class is templated over the fixed image type, moving image type
 * and the deformation field type.
 *
 * The input fixed and moving images are set via methods SetFixedImage
 * and SetMovingImage respectively. An initial deformation field maybe set via
 * SetInitialDisplacementField or SetInput. If no initial field is set,
 * a zero field is used as the initial condition.
 *
 * The output deformation field can be obtained via methods GetOutput
 * or GetDisplacementField.
 *
 * This class make use of the finite difference solver hierarchy. Update
 * for each iteration is computed in ESMDemonsRegistrationTensorFunction.
 *
 * \warning This filter assumes that the fixed image type, moving image type
 * and deformation field type all have the same number of dimensions.
 *
 * \sa DiffeomorphicDemonsRegistrationFilter
 * \sa ESMDemonsRegistrationTensorFunction
 * \ingroup DeformableImageRegistration MultiThreaded
 * \author Thomas Yeo.
 */
template < class TFixedImage, class TMovingImage, class TDisplacementField, class TSolverPrecision>
class ITK_EXPORT DiffeomorphicDemonsRegistrationTensorFilter :
public PDEDeformableRegistrationFilter<TFixedImage, TMovingImage,
TDisplacementField>
{
public:
  /** Standard class typedefs. */
  typedef DiffeomorphicDemonsRegistrationTensorFilter Self;
  typedef PDEDeformableRegistrationFilter<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( DiffeomorphicDemonsRegistrationTensorFilter,
      PDEDeformableRegistrationFilter );

  /** FixedImage image type. */
  typedef    typename Superclass::FixedImageType FixedImageType;
  typedef typename Superclass::FixedImagePointer FixedImagePointer;

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

  /** Displacement field type. */
  typedef typename Superclass::DisplacementFieldType DisplacementFieldType;
  typedef typename Superclass::DisplacementFieldPointer
  DisplacementFieldPointer;

  /** FiniteDifferenceFunction type. */
  typedef typename Superclass::FiniteDifferenceFunctionType
  FiniteDifferenceFunctionType;

  /** Take timestep type from the FiniteDifferenceFunction. */
  typedef typename FiniteDifferenceFunctionType::TimeStepType TimeStepType;

  /** DemonsRegistrationFilterFunction type. */
  typedef ESMDemonsRegistrationTensorFunction<FixedImageType,
  MovingImageType, DisplacementFieldType, TSolverPrecision> DemonsRegistrationFunctionType;

  /** Exp and composition typedefs */
  typedef MultiplyImageFilter<DisplacementFieldType,
    itk::Image <TimeStepType,TFixedImage::ImageDimension>, DisplacementFieldType> MultiplyByConstantType;
  typedef ExponentialDisplacementFieldImageFilter<DisplacementFieldType,
  DisplacementFieldType> FieldExponentiatorType;

  typedef WarpVectorImageFilter< DisplacementFieldType, DisplacementFieldType,
  DisplacementFieldType> VectorWarperType;
  typedef VectorLinearInterpolateNearestNeighborExtrapolateImageFunction
  <DisplacementFieldType, double> FieldInterpolatorType;
  typedef AddImageFilter<DisplacementFieldType, DisplacementFieldType, DisplacementFieldType>
  AdderType;

  typedef typename MultiplyByConstantType::Pointer MultiplyByConstantPointer;
  typedef typename FieldExponentiatorType::Pointer FieldExponentiatorPointer;
  typedef typename VectorWarperType::Pointer VectorWarperPointer;
  typedef typename FieldInterpolatorType::Pointer FieldInterpolatorPointer;
  typedef typename FieldInterpolatorType::OutputType FieldInterpolatorOutputType;
  typedef typename AdderType::Pointer AdderPointer;

  /** 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.
   * This value is calculated for the current iteration */
  virtual double GetMetric() const;

  /** Get the number of pixels processed (the number in the overlap region). */
  virtual unsigned long GetNumberOfPixelsProcessed() const;

  /** Get the rms change in the deformation field. */
  virtual const double &GetRMSChange() const;

  /** Set/Get types of available image forces */
  typedef typename DemonsRegistrationFunctionType::GradientType GradientType;
  virtual void SetUseGradientType( GradientType gtype );
  virtual GradientType GetUseGradientType() const;

  /** Set/Get types of rotation we use to optimize the registration wrt tensor
   * reorientation */
  typedef typename DemonsRegistrationFunctionType::RotationType RotationType;
  virtual void SetUseRotationType( RotationType rtype );
  virtual RotationType GetUseRotationType() 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 maximum update step length. In Thirion this is 0.5.
   *  Setting it to 0 implies no restriction (beware of numerical
   *  instability in this case. */
  virtual void SetMaximumUpdateStepLength(double);
  virtual double GetMaximumUpdateStepLength() const;

  /** Set/Get whether or not we precondition the solver. */
  virtual void SetPreconditionSolver( bool preconditionSolver )
  { this->DownCastDifferenceFunctionType()->SetPreconditionSolver(preconditionSolver);}
  virtual bool GetPreconditionSolver() const
  { return this->DownCastDifferenceFunctionType()->GetPreconditionSolver();}


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

  /** Initialize the state of filter and equation before each iteration. */
  virtual void InitializeIteration();

  /** This method allocates storage in m_UpdateBuffer.  It is called from
   * FiniteDifferenceFilter::GenerateData(). */
  virtual void AllocateUpdateBuffer();

  /** Solve update (if necessary) and apply it update. */
  virtual void ApplyUpdate(const TimeStepType &dt);

private:
  DiffeomorphicDemonsRegistrationTensorFilter(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented

  /** Downcast the DifferenceFunction using a dynamic_cast to ensure that it is of the correct type.
   * this method will throw an exception if the function is not of the expected type. */
  DemonsRegistrationFunctionType *  DownCastDifferenceFunctionType();
  const DemonsRegistrationFunctionType *  DownCastDifferenceFunctionType() const;

  MultiplyByConstantPointer m_Multiplier;
  FieldExponentiatorPointer m_Exponentiator;
  VectorWarperPointer m_Warper;
  AdderPointer m_Adder;
};

} // end namespace itk

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

#endif
