#ifndef __itkMultiResolutionLogDomainDeformableRegistration_h
#define __itkMultiResolutionLogDomainDeformableRegistration_h

#include "itkExponentialDeformationFieldImageFilter2.h"
#include "itkImage.h"
#include "itkImageToImageFilter.h"
#include "itkLogDomainDeformableRegistrationFilter.h"
#include "itkLogDomainDemonsRegistrationFilter.h"
#include "itkMultiResolutionPyramidImageFilter.h"
#include "itkVectorResampleImageFilter.h"

#include <vector>

namespace itk
{
/**
 * \class MultiResolutionLogDomainDeformableRegistration
 * \brief Framework for performing multi-resolution log-domain
 * deformable registration.
 *
 * MultiResolutionLogDomainDeformableRegistration provides a generic framework
 * to peform multi-resolution deformable registration.
 *
 * At each resolution level a LogDomainDeformableRegistrationFilter is used
 * to register two images by computing the velocity field whose exponential will 
 * map a moving image onto a fixed image.
 *
 * 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 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.
 *
 * The internal LogDomainDeformableRegistrationFilter can be set using
 * SetRegistrationFilter. By default a LogDomainDemonsRegistrationFilter is used.
 *
 * The input fixed and moving images are set via methods SetFixedImage
 * and SetMovingImage respectively. An initial velocity field maybe set via
 * SetInitialVelocityField if is matches the characteristics of the coarsest
 * pyramid level. If no such assumption can be made (e.g. the velocity field
 * has the same characteristics as the input images), an initial velocity
 * field can still be set via SetArbitraryInitialVelocityField or
 * SetInput. The filter will then take care of mathching the coarsest level
 * characteristics. If no initial field is set a zero field is used as the
 * initial condition.
 *
 * MultiResolutionPyramidImageFilters are used to downsample the fixed
 * and moving images. A VectorExpandImageFilter is used to upsample
 * the velocity field as we move from a coarse to fine solution.
 *
 * This class is templated over the fixed image type, the moving image type,
 * and the velocity/deformation Field type.
 *
 * \warning This class assumes that the fixed, moving and
 * field image types all have the same number of dimensions.
 *
 * \author Florence Dru, INRIA and Tom Vercauteren, MKT
 *
 * \sa LogDomainDeformableRegistrationFilter
 * \sa LogDomainDemonsRegistrationFilter
 * \sa MultiResolutionPyramidImageFilter
 * \sa VectorExpandImageFilter
 *
 * The current implementation of this class does not support streaming.
 *
 * \ingroup DeformableImageRegistration
 */
template <class TFixedImage, class TMovingImage, class TField, class  TRealType = float>
class ITK_EXPORT MultiResolutionLogDomainDeformableRegistration :
    public ImageToImageFilter <TField, TField>
{
public:
  /** Standard class typedefs */
  typedef MultiResolutionLogDomainDeformableRegistration Self;
  typedef ImageToImageFilter<TField, 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( MultiResolutionLogDomainDeformableRegistration, 
                ImageToImageFilter );

  /** Fixed image type. */
  typedef TFixedImage                            FixedImageType;
  typedef typename FixedImageType::Pointer       FixedImagePointer;
  typedef typename FixedImageType::ConstPointer  FixedImageConstPointer;

  /** Moving image type. */
  typedef TMovingImage                           MovingImageType;
  typedef typename MovingImageType::Pointer      MovingImagePointer;
  typedef typename MovingImageType::ConstPointer MovingImageConstPointer;

  /** Velocity field type. */
  typedef TField                                 VelocityFieldType;
  typedef typename VelocityFieldType::Pointer    VelocityFieldPointer;
  
  /** Deformation field image type. */
  typedef TField                                 DeformationFieldType;
  typedef typename DeformationFieldType::Pointer DeformationFieldPointer;

  /** ImageDimension. */
  itkStaticConstMacro(ImageDimension, unsigned int,
                      FixedImageType::ImageDimension);

  /** Internal float image type. */
  typedef Image<TRealType,itkGetStaticConstMacro(ImageDimension)> FloatImageType;

  /** The internal registration type. */
  typedef LogDomainDeformableRegistrationFilter<FloatImageType, FloatImageType, VelocityFieldType >
                                             RegistrationType;
  typedef typename RegistrationType::Pointer RegistrationPointer;

  /** The default registration type. */
  typedef LogDomainDemonsRegistrationFilter<
    FloatImageType, FloatImageType, VelocityFieldType > DefaultRegistrationType;

  /** The fixed multi-resolution image pyramid type. */
  typedef MultiResolutionPyramidImageFilter<FixedImageType, FloatImageType >
                                                  FixedImagePyramidType;
  typedef typename FixedImagePyramidType::Pointer FixedImagePyramidPointer;

  /** The moving multi-resolution image pyramid type. */
  typedef MultiResolutionPyramidImageFilter<MovingImageType, FloatImageType >
                                                   MovingImagePyramidType;
  typedef typename MovingImagePyramidType::Pointer MovingImagePyramidPointer;
   
  /** The velocity field expander type. */
  typedef VectorResampleImageFilter<VelocityFieldType, VelocityFieldType >
                                               FieldExpanderType;
  typedef typename FieldExpanderType::Pointer  FieldExpanderPointer;

  /** Set the fixed image. */
  virtual void SetFixedImage( const FixedImageType * ptr );

  /** Get the fixed image. */
  const FixedImageType * GetFixedImage(void) const;

  /** Set the moving image. */
  virtual void SetMovingImage( const MovingImageType * ptr );

  /** Get the moving image. */
  const MovingImageType * GetMovingImage(void) const;

  /** Set initial velocity field to be used as is (no smoothing, no
   *  subsampling at the coarsest level of the pyramid. */
  virtual void SetInitialVelocityField( VelocityFieldType * ptr )
    {
    this->m_InitialVelocityField=ptr;
    }

  /** Set initial velocity field. No assumption is made on the
   *  input. It will therefore be smoothed and resampled to match the
   *  images characteristics at the coarsest level of the pyramid. */
  virtual void SetArbitraryInitialVelocityField( VelocityFieldType * ptr )
    {
    this->SetInput( ptr ); 
    }

  /** Get output velocity field. */
  VelocityFieldType * GetVelocityField() { return this->GetOutput(); }

  /** Get output deformation field. */
  DeformationFieldPointer GetDeformationField();

  /** Get output inverse deformation field. */
  DeformationFieldPointer GetInverseDeformationField();

  /** Get the number of valid inputs.  For
   * MultiResolutionLogDomainDeformableRegistration, this checks whether the
   * fixed and moving images have been set. While
   * MultiResolutionLogDomainDeformableRegistration can take a third input
   * as an initial velocity field, this input is not a required input. */
  virtual std::vector<SmartPointer<DataObject> >::size_type GetNumberOfValidRequiredInputs() const;

  /** Set the internal registrator. */
  itkSetObjectMacro( RegistrationFilter, RegistrationType );

  /** Get the internal registrator. */
  itkGetObjectMacro( RegistrationFilter, RegistrationType );
  
  /** Set the fixed image pyramid. */
  itkSetObjectMacro( FixedImagePyramid, FixedImagePyramidType );

  /** Get the fixed image pyramid. */
  itkGetObjectMacro( FixedImagePyramid, FixedImagePyramidType );

  /** Set the moving image pyramid. */
  itkSetObjectMacro( MovingImagePyramid, MovingImagePyramidType );

  /** Get the moving image pyramid. */
  itkGetObjectMacro( MovingImagePyramid, MovingImagePyramidType );

  /** Set number of multi-resolution levels. */
  virtual void SetNumberOfLevels( unsigned int num );

  /** Get number of multi-resolution levels. */
  itkGetConstReferenceMacro( NumberOfLevels, unsigned int );

  /** Get the current resolution level being processed. */
  itkGetConstReferenceMacro( CurrentLevel, unsigned int );

  /** Set number of iterations per multi-resolution levels. */
  itkSetVectorMacro( NumberOfIterations, unsigned int, m_NumberOfLevels );

  /** Set the moving image pyramid. */
  itkSetObjectMacro( FieldExpander, FieldExpanderType );

  /** Get the moving image pyramid. */
  itkGetObjectMacro( FieldExpander, FieldExpanderType );

  /** Get number of iterations per multi-resolution levels. */
  virtual const unsigned int * GetNumberOfIterations() const
  { return &(m_NumberOfIterations[0]); }

  /** Stop the registration after the current iteration. */
  virtual void StopRegistration();

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

  /** Exponential type */
  typedef ExponentialDeformationFieldImageFilter2< 
    VelocityFieldType, DeformationFieldType >      FieldExponentiatorType;
  
  typedef typename FieldExponentiatorType::Pointer FieldExponentiatorPointer;

  itkSetObjectMacro( Exponentiator, FieldExponentiatorType );
  itkGetObjectMacro( Exponentiator, FieldExponentiatorType );

  /** Generate output data by performing the registration
   * at each resolution level. */
  virtual void GenerateData();

  /** The current implementation of this class does not support
   * streaming. As such it requires the largest possible region
   * for the moving, fixed and input velocity field. */
  virtual void GenerateInputRequestedRegion();

  /** By default, the output velocity field has the same
   * spacing, origin and LargestPossibleRegion as the input/initial
   * velocity field. If the initial velocity field is not set, the output
   * information is copied from the fixed image. */
  virtual void GenerateOutputInformation();

  /** The current implementation of this class does not supprot
   * streaming. As such it produces the output for the largest
   * possible region. */
  virtual void EnlargeOutputRequestedRegion( DataObject *ptr );

  /** This method returns true to indicate that the registration should
   * terminate at the current resolution level. */
  virtual bool Halt();

private:
  MultiResolutionLogDomainDeformableRegistration(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented
  
  RegistrationPointer        m_RegistrationFilter;
  FixedImagePyramidPointer   m_FixedImagePyramid;
  MovingImagePyramidPointer  m_MovingImagePyramid;
  FieldExpanderPointer       m_FieldExpander;
  VelocityFieldPointer       m_InitialVelocityField;

  unsigned int               m_NumberOfLevels;
  unsigned int               m_CurrentLevel;
  std::vector<unsigned int>  m_NumberOfIterations;

  /** Flag to indicate user stop registration request. */
  bool                      m_StopRegistrationFlag;

  FieldExponentiatorPointer m_Exponentiator;
};


} // end namespace itk

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


#endif
