/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkDiffeomorphicDemonsRegistrationWithMaskFilter_h
#define itkDiffeomorphicDemonsRegistrationWithMaskFilter_h

#include "itkPDEDeformableRegistrationWithMaskFilter.h"
#include "itkESMDemonsRegistrationFunction.h"

#include "itkMultiplyImageFilter.h"
#include "itkExponentialDisplacementFieldImageFilter.h"

namespace itk
{
/** \class DiffeomorphicDemonsRegistrationWithMaskFilter
 * \brief Deformably register two images using a diffeomorphic demons algorithm.
 *
 * This class was contributed by Tom Vercauteren, INRIA & Mauna Kea Technologies,
 * based on a variation of the DemonsRegistrationWithMaskFilter. The basic modification
 * is to use diffeomorphism exponentials.
 *
 * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
 * "Non-parametric Diffeomorphic Image Registration with the Demons Algorithm",
 * Proc. of MICCAI 2007.
 *
 * DiffeomorphicDemonsRegistrationWithMaskFilter 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 DemonsRegistrationFunction.
 *
 * \author Tom Vercauteren, INRIA & Mauna Kea Technologies
 *
 * \warning This filter assumes that the fixed image type, moving image type
 * and deformation field type all have the same number of dimensions.
 *
 * This implementation was taken from the Insight Journal paper:
 * https://hdl.handle.net/1926/510
 *
 * \sa DemonsRegistrationWithMaskFilter
 * \sa DemonsRegistrationFunction
 * \ingroup DeformableImageRegistration MultiThreaded
 * \ingroup ITKPDEDeformableRegistration
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
class ITK_TEMPLATE_EXPORT DiffeomorphicDemonsRegistrationWithMaskFilter:
        public PDEDeformableRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
{
public:
  /** Standard class typedefs. */
  typedef DiffeomorphicDemonsRegistrationWithMaskFilter                                           Self;
  typedef PDEDeformableRegistrationWithMaskFilter< 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(DiffeomorphicDemonsRegistrationWithMaskFilter, PDEDeformableRegistrationWithMaskFilter);

  /** 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;

  /** Deformation field type. */
  typedef typename Superclass::DisplacementFieldType    DisplacementFieldType;
  typedef typename Superclass::DisplacementFieldPointer DisplacementFieldPointer;
#ifdef ITKV3_COMPATIBILITY
  typedef typename Superclass::DeformationFieldType    DeformationFieldType;
  typedef typename Superclass::DeformationFieldPointer DeformationFieldPointer;
#endif

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

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

  /** DemonsRegistrationWithMaskFilterFunction type. */
  typedef ESMDemonsRegistrationFunction< FixedImageType, MovingImageType,
                                         DisplacementFieldType > DemonsRegistrationFunctionType;
  typedef typename DemonsRegistrationFunctionType::GradientType GradientType;

  itkStaticConstMacro(
    ImageDimension, unsigned int, FixedImageType::ImageDimension);

  /** 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 const double & GetRMSChange() const ITK_OVERRIDE;

  virtual void SetUseGradientType(GradientType gtype);

  virtual GradientType GetUseGradientType() const;

  /** Use a first-order approximation of the exponential.
   *  This amounts to using an update rule of the type
   *  s <- s o (Id + u) instead of s <- s o exp(u) */
  itkSetMacro(UseFirstOrderExp, bool);
  itkGetConstMacro(UseFirstOrderExp, bool);
  itkBooleanMacro(UseFirstOrderExp);

  /** 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;

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

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

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

  /** Apply update. */
  virtual void ApplyUpdate(const TimeStepType& dt) ITK_OVERRIDE;

private:
  ITK_DISALLOW_COPY_AND_ASSIGN(DiffeomorphicDemonsRegistrationWithMaskFilter);

  /** 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;

  /** Exp and composition typedefs */
  typedef MultiplyImageFilter< DisplacementFieldType,
    itk::Image<TimeStepType, 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;

  MultiplyByConstantPointer m_Multiplier;
  FieldExponentiatorPointer m_Exponentiator;
  VectorWarperPointer       m_Warper;
  AdderPointer              m_Adder;
  bool                      m_UseFirstOrderExp;
};
} // end namespace itk

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

#endif
