#ifndef __itkSymmetricLogDomainDemonsRegistrationWithMaskFilter_h
#define __itkSymmetricLogDomainDemonsRegistrationWithMaskFilter_h

#include "plmregister_config.h"
#include "itkLogDomainDeformableRegistrationFilter.h"
#include "itkESMDemonsRegistrationWithMaskFunction.h"

#include "itkMultiplyImageFilter.h"

namespace itk
{

/**
 * \class SymmetricLogDomainDemonsRegistrationWithMaskFilter
 * \brief Deformably register two images using a diffeomorphic demons algorithm
 * and a symmetrized optimization scheme.
 *
 * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
 * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
 * Proc. of MICCAI 2008.
 *
 * Velocity and deformation fields are represented as images whose pixel type are
 * 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 velocity/deformation field type.
 *
 * The input fixed and moving images are set via methods SetFixedImage
 * and SetMovingImage respectively. An initial velocity field maybe set via
 * SetInitialVelocityField or SetInput. If no initial field is set,
 * a zero field is used as the initial condition.
 *
 * The output velocity field can be obtained via methods GetOutput
 * or GetVelocityField.
 *
 * The output deformation field can be obtained via method GetDeformationField.
 *
 * This class make use of the finite difference solver hierarchy. Update
 * for each iteration is computed using a PDEDeformableRegistrationFunction.
 *
 * \warning This filter assumes that the fixed image type, moving image type
 * and velocity field type all have the same number of dimensions.
 *
 * \sa DemonsRegistrationFilter
 * \sa DemonsRegistrationFunction
 * \ingroup DeformableImageRegistration MultiThreaded
 * \author Florence Dru, INRIA and Tom Vercauteren, MKT
 */
template <class TFixedImage, class TMovingImage, class TField>
class ITK_EXPORT SymmetricLogDomainDemonsRegistrationWithMaskFilter
    : public LogDomainDeformableRegistrationFilter<TFixedImage, TMovingImage, TField>
{
public:
  /** Standard class typedefs. */
  typedef SymmetricLogDomainDemonsRegistrationWithMaskFilter                               Self;
  typedef LogDomainDeformableRegistrationFilter<TFixedImage, TMovingImage, TField> 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( SymmetricLogDomainDemonsRegistrationWithMaskFilter, LogDomainDeformableRegistrationFilter );

  /** 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;

  /** Velocity field type. */
  typedef TField                              VelocityFieldType;
  typedef typename VelocityFieldType::Pointer VelocityFieldPointer;

  /** Deformation field type. */
  typedef typename Superclass::DeformationFieldType    DeformationFieldType;
  typedef typename Superclass::DeformationFieldPointer DeformationFieldPointer;

  /** Types inherithed from the superclass */
  typedef typename Superclass::OutputImageType OutputImageType;

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

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

  /** DemonsRegistrationFilterFunction type. */
  typedef ESMDemonsRegistrationWithMaskFunction<FixedImageType,
                                        MovingImageType,
                                        DeformationFieldType>                          DemonsRegistrationFunctionType;
  typedef typename DemonsRegistrationFunctionType::Pointer      DemonsRegistrationFunctionPointer;
  typedef typename DemonsRegistrationFunctionType::GradientType GradientType;

  /** 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;

  virtual void SetUseGradientType( GradientType gtype );

  virtual GradientType GetUseGradientType() 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 length in terms of pixels of
   *  the vectors in the update buffer. */
  virtual void SetMaximumUpdateStepLength(double);

  virtual double GetMaximumUpdateStepLength() const;

  /** Set/Get the number of terms used in the Baker-Campbell-Hausdorff approximation. */
  itkSetMacro( NumberOfBCHApproximationTerms, unsigned int );
  itkGetConstMacro( NumberOfBCHApproximationTerms, unsigned int );
protected:
  SymmetricLogDomainDemonsRegistrationWithMaskFilter();
  ~SymmetricLogDomainDemonsRegistrationWithMaskFilter()
  {
  }
  void PrintSelf(std::ostream& os, Indent indent) const;

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

  /** This method is called before iterating the solution. */
  virtual void Initialize();

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

  /** Method to allow subclasses to get direct access to the backward update
   * buffer */
  virtual VelocityFieldType * GetBackwardUpdateBuffer()
  {
    return m_BackwardUpdateBuffer;
  }

  /** This method allocates storage in m_BackwardUpdateBuffer. */
  virtual void AllocateBackwardUpdateBuffer();

  /** Utility to smooth the BackwardUpdateBuffer using a Gaussian operator.
   * The amount of smoothing is specified by the UpdateFieldStandardDeviations. */
  virtual void SmoothBackwardUpdateField();

  typedef typename VelocityFieldType::RegionType ThreadRegionType;

  /** Does the actual work of calculating change over a region supplied by
   * the multithreading mechanism. */
  virtual TimeStepType ThreadedCalculateChange(const ThreadRegionType & regionToProcess, ThreadIdType threadId);

  /** Apply update. */
#if (ITK_VERSION_MAJOR < 4)
  virtual void ApplyUpdate(TimeStepType dt);
#else
  virtual void ApplyUpdate(const TimeStepType& dt);
#endif

  /** This method returns a pointer to a FiniteDifferenceFunction object that
   * will be used by the filter to calculate updates at image pixels.
   * \returns A FiniteDifferenceObject pointer. */
  itkGetConstReferenceObjectMacro(BackwardDifferenceFunction,
                                  FiniteDifferenceFunctionType );

  /** This method sets the pointer to a FiniteDifferenceFunction object that
   * will be used by the filter to calculate updates at image pixels.
   * \returns A FiniteDifferenceObject pointer. */
  itkSetObjectMacro(BackwardDifferenceFunction, FiniteDifferenceFunctionType );
private:
  SymmetricLogDomainDemonsRegistrationWithMaskFilter(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 *  GetForwardRegistrationFunctionType();

  const DemonsRegistrationFunctionType *  GetForwardRegistrationFunctionType() const;

  DemonsRegistrationFunctionType *  GetBackwardRegistrationFunctionType();

  const DemonsRegistrationFunctionType *  GetBackwardRegistrationFunctionType() const;

  /** Exp and composition typedefs */
  typedef MultiplyImageFilter< VelocityFieldType, itk::Image<TimeStepType,VelocityFieldType::ImageDimension>,
          VelocityFieldType>                   MultiplyByConstantType;

  typedef AddImageFilter<
    VelocityFieldType, VelocityFieldType>                AdderType;

  typedef typename MultiplyByConstantType::Pointer MultiplyByConstantPointer;
  typedef typename AdderType::Pointer              AdderPointer;

  typename FiniteDifferenceFunctionType::Pointer        m_BackwardDifferenceFunction;

  MultiplyByConstantPointer m_Multiplier;
  AdderPointer              m_Adder;
  unsigned int              m_NumberOfBCHApproximationTerms;

  /** The buffer that holds the updates for an iteration of the algorithm. */
  VelocityFieldPointer m_BackwardUpdateBuffer;
};

} // end namespace itk

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

#endif
