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 *
 *  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 __itkPhysicsBasedNonRigidRegistrationMethod_h
#define __itkPhysicsBasedNonRigidRegistrationMethod_h


#include "itkMaskFeaturePointSelectionFilter.h"
#include "itkBlockMatchingImageFilter.h"
#include "itkFEMScatteredDataPointSetToImageFilter.h"
#include "itkConceptChecking.h"


namespace itk
{
namespace fem
{

/** \class PhysicsBasedNonRigidRegistrationMethod
 * \brief Perform a non-rigid registration of two 3D images using a set of
 * feature points, block matching and linear elastic model.
 *
 * PhysicsBasedNonRigidRegistrationMethod takes a fixed image, a moving
 * image with an optional mask and a mesh as inputs and generates a
 * dense deformation field image as an output.
 *
 * This filter is intended to be used for driving the process of Physics-
 * Based Non-Rigid Registration. It computes feature points from the
 * moving image, then computes displacements of the feature points in the
 * fixed image via block-matching, then computes deformation field of a
 * whole image using linear elastic model[ M. Bierling, Displacement
 * estimation by hierarchical block matching, Proc. SPIE Vis. Comm. and
 * Image Proc., vol. 1001, pp. 942-951, 1988. ].
 *
 * The filter is templated over fixed image, moving image, mask, mesh and
 * deformation field image.
 *
 * \author Andriy Kot, Center for Real-Time Computing, Old Dominion University,
 * Norfolk, VA
 *
 * \ingroup ITKFEMRegistration
 */


template <typename TFixedImage, typename TMovingImage, typename TMaskImage, typename TMesh, typename TDeformationField>
class PhysicsBasedNonRigidRegistrationMethod : public ImageToImageFilter<TMovingImage, TDeformationField>
{
public:
  typedef PhysicsBasedNonRigidRegistrationMethod               Self;
  typedef ImageToImageFilter<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( PhysicsBasedNonRigidRegistrationMethod, ImageToImageFilter );

  typedef TMovingImage                       MovingImageType;
  typedef TFixedImage                        FixedImageType;
  typedef TMaskImage                         MaskImageType;
  typedef TMesh                              MeshType;
  typedef TDeformationField                  DeformationFieldType;

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

  /** Not input specific typedefs */
  typedef ImageRegion< ImageDimension >  ImageRegionType;
  typedef Size< ImageDimension >         ImageSizeType;
  typedef Index< ImageDimension >        ImageIndexType;

  /** Typedefs for the components filters. */
  typedef MaskFeaturePointSelectionFilter< MovingImageType, MaskImageType >  FeatureSelectionFilterType;
  typedef BlockMatchingImageFilter< FixedImageType, MovingImageType >        BlockMatchingFilterType;
  typedef FEMScatteredDataPointSetToImageFilter<
    typename BlockMatchingFilterType::DisplacementsType,
    MeshType,
    DeformationFieldType,
    typename BlockMatchingFilterType::SimilaritiesType,
    typename FeatureSelectionFilterType::FeaturePointsType // tensors are optional pixel values of feature points pointset
  >  FEMFilterType;

  /** set fraction of eligible points to select */
  itkSetMacro(SelectFraction, double);
  itkGetConstMacro(SelectFraction, double);

  /** set/get non-connectivity */
  itkSetMacro(NonConnectivity, unsigned int);
  itkGetConstMacro(NonConnectivity, unsigned int);

  /** set/get half size */
  itkSetMacro(BlockRadius, ImageSizeType);
  itkGetConstReferenceMacro(BlockRadius, ImageSizeType);

  /** set/get half window */
  itkSetMacro(SearchRadius, ImageSizeType);
  itkGetConstReferenceMacro(SearchRadius, ImageSizeType);

  /** set/get number of approximation steps */
  itkSetMacro(ApproximationSteps, unsigned int);
  itkGetMacro(ApproximationSteps, unsigned int);

  /** set/get number of outlier rejection steps */
  itkSetMacro(OutlierRejectionSteps, unsigned int);
  itkGetMacro(OutlierRejectionSteps, unsigned int);

  /** set/get fixed image */
  itkSetInputMacro(FixedImage, FixedImageType);
  itkGetInputMacro(FixedImage, FixedImageType);

  /** set/get moving image */
  itkSetInputMacro(MovingImage, MovingImageType);
  itkGetInputMacro(MovingImage, MovingImageType);

  /** set/get moving image */
  itkSetInputMacro(MaskImage, MaskImageType);
  itkGetInputMacro(MaskImage, MaskImageType);

  /** set/get moving image */
  itkSetInputMacro(Mesh, MeshType);
  itkGetInputMacro(Mesh, MeshType);

  /** get FEMFilter */
  itkGetConstObjectMacro(FEMFilter, FEMFilterType);

#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  /* Currently only the 3D implementation is available due to a narrow
     definition of the filter in the original proposal
     and lack of available resources. */
  itkConceptMacro( FixedImageDimensionShouldBe3,
                   ( Concept::SameDimension< TFixedImage::ImageDimension, 3u > ) );
  itkConceptMacro( MovingImageDimensionShouldBe3,
                   ( Concept::SameDimension< TMovingImage::ImageDimension, 3u > ) );
  itkConceptMacro( MaskImageDimensionShouldBe3,
                   ( Concept::SameDimension< TMaskImage::ImageDimension, 3u > ) );
  itkConceptMacro( MeshDimensionShouldBe3,
                   ( Concept::SameDimension< TMesh::PointType::PointDimension, 3u > ) );
  itkConceptMacro( DeformationFieldImageDimensionShouldBe3,
                   ( Concept::SameDimension< TDeformationField::ImageDimension, 3u > ) );
  // End concept checking
#endif

protected:
  PhysicsBasedNonRigidRegistrationMethod();
  virtual ~PhysicsBasedNonRigidRegistrationMethod();
  virtual void PrintSelf( std::ostream & os, Indent indent ) const;
  virtual void GenerateData();

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

  // algorithm parameters
  double         m_SelectFraction;
  unsigned int   m_NonConnectivity;
  ImageSizeType  m_BlockRadius;
  ImageSizeType  m_SearchRadius;
  unsigned int   m_ApproximationSteps;
  unsigned int   m_OutlierRejectionSteps;

  typename FeatureSelectionFilterType::Pointer m_FeatureSelectionFilter;
  typename BlockMatchingFilterType::Pointer    m_BlockMatchingFilter;
  typename FEMFilterType::Pointer              m_FEMFilter;
};

}
}  // end namespace itk::fem

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

#endif
