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

 Program:   Insight Segmentation & Registration Toolkit
 Module:    $RCSfile: itkDiffeomorphicDemonsRegistrationWithMaskFilter.h,v $
 Language:  C++
 Date:      $Date: 2008-07-05 00:07:02 $
 Version:   $Revision: 1.1 $

 Copyright (c) Insight Software Consortium. All rights reserved.
 See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 __itkDiffeomorphicDemonsRegistrationWithMaskFilter_h
#define __itkDiffeomorphicDemonsRegistrationWithMaskFilter_h

#include "itkPDEDeformableRegistrationFilter.h"
#include "itkESMDemonsRegistrationWithMaskFunction.h"

#include "itkMultiplyByConstantImageFilter.h"
#include "itkExponentialDeformationFieldImageFilter.h"
#include "itkWarpVectorImageFilter.h"
#include "itkVectorLinearInterpolateNearestNeighborExtrapolateImageFunction.h"
#include "itkAddImageFilter.h"
#include "itkSpatialObject.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 DemonsRegistrationFilter. 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
 * SetInitialDeformationField 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 GetDeformationField.
 *
 * 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:
 * http://hdl.handle.net/1926/510
 *
 * \sa DemonsRegistrationFilter
 * \sa DemonsRegistrationFunction
 * \ingroup DeformableImageRegistration MultiThreaded
 */
template <class TFixedImage, class TMovingImage, class TDeformationField>
class ITK_EXPORT DiffeomorphicDemonsRegistrationWithMaskFilter :
  public PDEDeformableRegistrationFilter<TFixedImage, TMovingImage,
    TDeformationField>
  {
public:
  /** Standard class typedefs. */
  typedef DiffeomorphicDemonsRegistrationWithMaskFilter Self;
  typedef PDEDeformableRegistrationFilter<
    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( DiffeomorphicDemonsRegistrationWithMaskFilter,
    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;

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

  /** 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::GradientType GradientType;
  
   /** Inherit some enums from the superclass. */
  itkStaticConstMacro(ImageDimension, unsigned int, Superclass::ImageDimension);
  
  typedef itk::SpatialObject<itkGetStaticConstMacro(ImageDimension)>  MaskType;


  /** 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;

  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 );
  itkGetMacro( 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;

  virtual void SetMovingImageMask( MaskType *mask);

  virtual void SetFixedImageMask(MaskType *mask);

  virtual const MaskType * GetMovingImageMask() const;

  virtual const MaskType * GetFixedImageMask() const;

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

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

private:
  DiffeomorphicDemonsRegistrationWithMaskFilter(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;

  /** Exp and composition typedefs */
  typedef MultiplyByConstantImageFilter<
    DeformationFieldType,
    TimeStepType, DeformationFieldType>                MultiplyByConstantType;

  typedef ExponentialDeformationFieldImageFilter<
    DeformationFieldType, DeformationFieldType>        FieldExponentiatorType;

  typedef WarpVectorImageFilter<
    DeformationFieldType,
    DeformationFieldType, DeformationFieldType>        VectorWarperType;

  typedef VectorLinearInterpolateNearestNeighborExtrapolateImageFunction<
    DeformationFieldType, double>                      FieldInterpolatorType;

  typedef AddImageFilter<
    DeformationFieldType,
    DeformationFieldType, DeformationFieldType>        AdderType;

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

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

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

#endif
