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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 itkFEMScatteredDataPointSetToImageFilter_h
#define itkFEMScatteredDataPointSetToImageFilter_h

#include "itkPointSetToImageFilter.h"
#include "itkVectorContainer.h"
#include "vnl/vnl_matrix.h"

#include "itkMesh.h"
#include "itkFEMObject.h"
#include "itkFEMElement3DC0LinearTetrahedronStrain.h"
#include "itkFEMElement3DC0LinearHexahedronStrain.h"
#include "itkFEMElement2DC0LinearTriangularStrain.h"
#include "itkFEMElement2DC0LinearQuadrilateralStrain.h"
#include "itkFEMElement2DC0LinearQuadrilateralMembrane.h"
#include "itkFEMRobustSolver.h"
#include "itkFEMLoadNoisyLandmark.h"
#include "itkImageToRectilinearFEMObjectFilter.h"
#include "itkTriangleCell.h"
#include "itkTetrahedronCell.h"
#include "itkQuadrilateralCell.h"
#include "itkHexahedronCell.h"

namespace itk
{
namespace fem
{
/** \class FEMScatteredDataPointSetToImageFilter
 * \brief Scattered data approximation to interpolation
 * in the presence of outliers
 *
 * Given a 2- or 3-D scattered and noisy data, this filter is able to approximate
 * the data while rejecting outliers, and then it advances toward interpolation.
 *
 * This filter also takes the confidence and structrual information into account,
 * if users can provide a scalar to represent the confidence and a tensor
 * to represent the structural information for each feature point.
 *
 * This filter requires a point set, of which each point is associated with a
 * 2-D or 3-D displacement, as input, and outputs a deformation field. Two
 * optional point sets are supported.
 * Confidence point set: this point set defines the confidence associated with
 * each point, which will make the solver behavior like a weighted Least Square
 * Tensor point set: this point set defines a tensor associated with each point,
 * such as a structural tensor.
 *
 * The purpose of this filter is to facilitate the use of the FEMRobustSolver,
 * which does the concrete work on finding the solution. See FEMRobustSolver for
 * details.
 *
 * \code
 *
 *  const unsigned int ParametricDimension = 3;
 *  const unsigned int DataDimension = 3;
 *
 *  typedef int                                           PixelType;
 *  typedef itk::Image<PixelType, ParametricDimension>    InputImageType;
 *  typedef float                                         RealType;
 *  typedef itk::Vector<RealType, DataDimension>          VectorType;
 *  typedef itk::Matrix<RealType, DataDimension,
 *  DataDimension>                                        MatrixType;
 *  typedef itk::Image<VectorType, ParametricDimension>   VectorImageType;
 *  typedef itk::PointSet <VectorType,
 *  ParametricDimension>                                  PointSetType;
 *
 *  typedef itk::PointSet <MatrixType,
 *   ParametricDimension>                                  TensorPointSetType;
 *
 *  typedef itk::PointSet <RealType, ParametricDimension> ConfidencePointSetType;
 *
 *
 *  typedef itk::Mesh< VectorType, ParametricDimension >  MeshType;
 *
 *  typedef itk::FEMScatteredDataPointSetToImageFilter
 *  <PointSetType, MeshType, VectorImageType,
 *  ConfidencePointSetType, TensorPointSetType>           FilterType;
 *
 *  FilterType::Pointer filter = FilterType::New();
 *
 *  filter->SetInput(displacementPointSet);
 *  filter->SetConfidencePointSet(confidencePointSet); //optional
 *  filter->SetTensorPointSet(tensorPointSet); //optional
 *  filter->SetMesh(aITKMesh);
 *  filter->Update();
 *
 *  DeformationField::Pointer = filter->GetOutput();
 *
 * \endcode
 *
 * \author Yixun Liu
 *
 * \par REFERENCE
 * O. Clatz, H. Delingette, I.-F. Talos, A. Golby, R. Kikinis, F. Jolesz,
 * N. Ayache, and S. Warfield, "Robust non-rigid registration to capture brain
 * shift from intra-operative MRI", IEEE Trans. Med. Imag.,
 * 24(11);1417-27, 2005.
 *
 * \par REFERENCE
 * Yixun Liu, Andriy Fedorov, Ron Kikinis and Nikos Chrisochoides,
 * "Real-time Non-rigidRegistration of Medical Images on a Cooperative Parallel
 * Architecture", IEEE International Conference on Bioinformatics & Biomedicine,
 * pp. 401-404, November 2009.
 *
 * \sa FEMRobustSolver
 *
 * \ingroup ITKFEM
 */

template<typename TInputPointSet, typename TInputMesh, typename TOutputImage, typename TInputConfidencePointSet, typename TInputTensorPointSet>
class ITK_TEMPLATE_EXPORT FEMScatteredDataPointSetToImageFilter:
  public PointSetToImageFilter< TInputPointSet, TOutputImage >
{
public:
  typedef FEMScatteredDataPointSetToImageFilter                 Self;
  typedef PointSetToImageFilter<TInputPointSet, TOutputImage>   Superclass;
  typedef SmartPointer<Self>                                    Pointer;
  typedef SmartPointer<const Self>                              ConstPointer;

  /** Method for creation through the object factory. */
  itkNewMacro( Self );

  /** Extract dimension from the output image. */
  itkStaticConstMacro( ImageDimension, unsigned int, TOutputImage::ImageDimension );

  /** Displacement point set typedef support */
  typedef TInputPointSet                                              PointSetType;
  typedef typename PointSetType::PointType                            PointType;
  typedef typename PointSetType::PointsContainer                      PointsContainer;
  typedef typename PointsContainer::ConstIterator                     PointsIterator;
  typedef typename PointSetType::PixelType                            PointDataType;
  typedef typename PointSetType::PointDataContainer                   PointDataContainerType;
  typedef typename PointDataContainerType::ConstIterator              PointDataIterator;

  /** Confidence point set typedef support */
  typedef TInputConfidencePointSet                                            ConfidencePointSetType;
  typedef typename ConfidencePointSetType::PointsContainer::ConstIterator     ConfidencePointsIterator;
  typedef typename ConfidencePointSetType::PixelType                          ConfidencePointDataType;
  typedef typename ConfidencePointSetType::PointDataContainer                 ConfidencePointDataContainerType;

  /** Tensor point set typedef support */
  typedef TInputTensorPointSet                                                TensorPointSetType;
  typedef typename TensorPointSetType::PointsContainer::ConstIterator         TensorPointsIterator;
  typedef typename TensorPointSetType::PixelType                              TensorPointDataType;
  typedef typename TensorPointSetType::PointDataContainer                     TensorPointDataContainerType;
  typedef typename TensorPointDataContainerType::Iterator                     TensorPointDataIterator;

  /** Mesh typedef support */
  typedef TInputMesh                              MeshType;
  typedef typename MeshType::CellType             CellType;
  typedef typename CellType::CellAutoPointer      CellAutoPointer;
  typedef typename MeshType::CellsContainer       CellsContainer;
  typedef typename CellsContainer::ConstIterator  CellIterator;

  typedef TriangleCell<CellType>                  TriangleType;
  typedef TetrahedronCell<CellType>               TetrahedronType;
  typedef QuadrilateralCell<CellType>             QuadrilateralType;
  typedef HexahedronCell<CellType>                HexahedronType;
  typedef typename CellType::PointIdIterator      PointIdIterator;

  /** Image typedef support */
  typedef TOutputImage                                        ImageType;
  typedef typename ImageType::PixelType                       PixelType;
  typedef typename ImageType::RegionType                      RegionType;
  typedef typename ImageType::SizeType                        SizeType;
  typedef typename ImageType::IndexType                       IndexType;
  typedef typename ImageType::SpacingType                     SpacingType;
  typedef ContinuousIndex<SpacePrecisionType, ImageDimension> ContinuousIndexType;

  typedef ImageToRectilinearFEMObjectFilter<ImageType> ImageToRectilinearFEMObjectFilterType;

  /** FEMObject typedef support */
  typedef FEMObject<ImageDimension>                 FEMObjectType;

  /** FEM solver typedef support */
  typedef RobustSolver<ImageDimension>              FEMSolverType;

  /** FEM element typedef support */
  typedef Element3DC0LinearTetrahedronStrain        FEMTetrahedronType;
  typedef Element3DC0LinearHexahedronStrain         FEMHexahedronType;
  typedef Element2DC0LinearTriangularStrain         FEM2DTriangleType;
  typedef Element2DC0LinearQuadrilateralStrain      FEM2DQuadrilateralType;

  /** FEM node typedef support */
  typedef Element::Node                             NodeType;

  /** FEM Load typedef support */
  typedef LoadNoisyLandmark                         LoadType;

  /** FEM material typedef support */
  typedef MaterialLinearElasticity                  MaterialType;
  typedef MaterialType::Pointer                     MaterialPointerType;

  /** FEM element typedef support */
  typedef Element::VectorType                       FEMVectorType;
  typedef Element::MatrixType                       FEMMatrixType;

  /** FEM container typedef support */
  typedef typename FEMObjectType::LoadContainerType        LoadContainerType;
  typedef typename FEMObjectType::NodeContainerType        NodeContainerType;
  typedef typename FEMObjectType::ElementContainerType     ElementContainerType;
  typedef typename FEMObjectType::MaterialContainerType    MaterialContainerType;

  /** Helper functions */
  itkSetConstObjectMacro(ConfidencePointSet, ConfidencePointSetType);

  itkSetConstObjectMacro(TensorPointSet, TensorPointSetType);

  itkSetObjectMacro(Mesh, MeshType);
  itkGetModifiableObjectMacro(Mesh, MeshType);

  itkSetObjectMacro(FEMSolver, FEMSolverType);
  itkGetModifiableObjectMacro(FEMSolver, FEMSolverType);

  /** Get/Set the number of voxels/pixels in each dimension used during the mesh generation */
  itkGetConstReferenceMacro(PixelsPerElement, ContinuousIndexType);
  itkSetMacro(PixelsPerElement, ContinuousIndexType);

  /** Set/Get the spacing of the rectilinear element */
  void SetElementSpacing(const SpacingType & elementSpacing);
  itkGetConstReferenceMacro(SpacingPerElement, SpacingType);

  /** Get the number of element in each dimension of the generated mesh */
  itkGetConstReferenceMacro(NumberOfElements, SizeType);

protected:

  FEMScatteredDataPointSetToImageFilter();
  virtual ~FEMScatteredDataPointSetToImageFilter();

  /** Generate 2D/3D rectilinear mesh */
  void GenerateRectilinearMesh();

  /** Generate a 2D quadrilateral mesh */
  void Generate2DQuadrilateralMesh();

  /** generate 3D hexahedral mesh */
  void Generate3DHexahedralMesh();

  /** Initialize FEMObject from a mesh and feature points */
  void InitializeFEMObject(FEMObjectType * femObject);

  /** Initialize Materials */
  void InitializeMaterials(FEMObjectType * femObject);

  /** Initialize Nodes */
  void InitializeNodes(FEMObjectType * femObject);

  /** Initialize Elements */
  void InitializeElements(FEMObjectType * femObject);

  /** Initialize Loads */
  void InitializeLoads(FEMObjectType * femObject);

  /** Run the solver and call ProduceDeformationField to produce deformation field */
  void GenerateData() ITK_OVERRIDE;

  void ProduceDeformationField();

  void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

private:

  ITK_DISALLOW_COPY_AND_ASSIGN(FEMScatteredDataPointSetToImageFilter);

  typename FEMObjectType::Pointer      m_FEMObject;
  typename FEMSolverType::Pointer      m_FEMSolver;
  typename FEMSolverType::ConstPointer m_FEMDeformedObject;
  typename MeshType::Pointer           m_Mesh;

  typename ConfidencePointSetType::ConstPointer m_ConfidencePointSet;
  typename TensorPointSetType::ConstPointer     m_TensorPointSet;

  /** Rectilinear mesh */
  SizeType                 m_NumberOfElements;
  ContinuousIndexType      m_PixelsPerElement;
  SpacingType              m_SpacingPerElement;

  /** Material */
  MaterialPointerType m_Material;
};

}// end namespace fem
}// end namespace itk

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

#endif
