itkDeformableSimplexMesh3DFilter.h

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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
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 *  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.
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 *=========================================================================*/
/*=========================================================================
 *
 *  Portions of this file are subject to the VTK Toolkit Version 3 copyright.
 *
 *  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
 *
 *  For complete copyright, license and disclaimer of warranty information
 *  please refer to the NOTICE file at the top of the ITK source tree.
 *
 *=========================================================================*/
#ifndef itkDeformableSimplexMesh3DFilter_h
#define itkDeformableSimplexMesh3DFilter_h

#include "itkMeshToMeshFilter.h"
#include "itkSimplexMesh.h"
#include "itkSphereSpatialFunction.h"
#include "itkFloodFilledSpatialFunctionConditionalIterator.h"
#include "itkVectorGradientMagnitudeImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkArray.h"

#include <set>

namespace itk
{
template< typename TInputMesh, typename TOutputMesh >
class DeformableSimplexMesh3DFilter:public MeshToMeshFilter< TInputMesh, TOutputMesh >
{
public:
  typedef DeformableSimplexMesh3DFilter Self;

  typedef MeshToMeshFilter< TInputMesh, TOutputMesh > Superclass;

  typedef SmartPointer< Self >       Pointer;
  typedef SmartPointer< const Self > ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(DeformableSimplexMesh3DFilter, MeshToMeshFilter);

  typedef TInputMesh  InputMeshType;
  typedef TOutputMesh OutputMeshType;

  typedef typename InputMeshType::PointsContainerPointer         InputPointsContainerPointer;
  typedef typename InputMeshType::PointsContainer                InputPointsContainer;
  typedef typename InputMeshType::PointsContainer::ConstIterator InputPointsContainerConstIterator;

  typedef typename SimplexMeshGeometry::PointType              PointType;
  typedef typename PointType::VectorType                       VectorType;
  typedef CovariantVector< typename VectorType::ValueType, 3 > CovariantVectorType;
  typedef typename InputMeshType::PixelType                    PixelType;

  typedef CovariantVector< PixelType, 3 > GradientType;
  typedef Image< GradientType, 3 >        GradientImageType;
  typedef Image< unsigned char, 3 >       BinaryOutput;
  typedef Image< float, 3 >               MagnitudeOutput;

  typedef typename GradientImageType::Pointer        GradientImagePointer;
  typedef typename GradientImageType::IndexType      GradientIndexType;
  typedef typename GradientImageType::PixelType      GradientPixelType;
  typedef typename GradientIndexType::IndexValueType GradientIndexValueType;
  typedef typename GradientImageType::SizeType       GradientImageSizeType;

  /* Mesh pointer definition. */
  typedef typename InputMeshType::Pointer  InputMeshPointer;
  typedef typename OutputMeshType::Pointer OutputMeshPointer;

  typedef typename InputMeshType::PointType                  MeshPointType;
  typedef typename InputMeshType::CellsContainerPointer      CellsContainerPointer;
  typedef typename InputMeshType::CellsContainer::Iterator   CellsContainerIterator;
  typedef typename InputMeshType::NeighborListType           InputNeighbors;
  typedef typename InputMeshType::NeighborListType::iterator InputNeighborsIterator;

  typedef std::set< IdentifierType >                            NeighborSetType;
  typedef std::set< IdentifierType >                            IndexSetType;
  typedef itk::MapContainer< IdentifierType, NeighborSetType >  VertexNeighborListType;
  typedef typename NeighborSetType::iterator                    NeighborSetIterator;
  typedef typename IndexSetType::iterator                       IndexSetIterator;

  typedef typename InputMeshType::GeometryMapType GeometryMapType;
  typedef typename GeometryMapType::Pointer       GeometryMapPointer;
  typedef typename GeometryMapType::Iterator      GeometryMapIterator;

  void SetGradient( const GradientImageType * gradientImage );

  const GradientImageType * GetGradient() const;

  itkSetMacro(Iterations, int);
  itkGetConstMacro(Iterations, int);

  itkSetMacro(Alpha, double);

  itkGetConstMacro(Alpha, double);

  itkSetMacro(Beta, double);

  itkGetConstMacro(Beta, double);

  itkSetMacro(Gamma, double);

  itkGetConstMacro(Gamma, double);

  itkSetMacro(Damping, double);

  itkGetConstMacro(Damping, double);

  itkSetMacro(Rigidity, unsigned int);

  itkGetConstMacro(Rigidity, unsigned int);

  itkSetObjectMacro(Data, GeometryMapType);
  itkGetModifiableObjectMacro(Data, GeometryMapType);

  itkGetConstMacro(ImageWidth, int);
  itkGetConstMacro(ImageHeight, int);
  itkGetConstMacro(ImageDepth, int);

  itkGetConstMacro(Step, int);

protected:
  DeformableSimplexMesh3DFilter();
  ~DeformableSimplexMesh3DFilter();
  DeformableSimplexMesh3DFilter(const Self &) ITK_DELETE_FUNCTION;
  void operator=(const Self &) ITK_DELETE_FUNCTION;

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

  virtual void GenerateData() ITK_OVERRIDE;

  virtual void Initialize();

  virtual void ComputeGeometry();

  virtual void ComputeDisplacement();

  virtual void ComputeInternalForce(SimplexMeshGeometry *data);

  virtual void ComputeExternalForce(SimplexMeshGeometry *data, const GradientImageType *gradient);

  virtual void ComputeOutput();

  virtual void UpdateReferenceMetrics();

  bool L_Func(const double r, const double d, const double phi, double & output);

  PointType ComputeBarycentricCoordinates(PointType p, SimplexMeshGeometry *data);

  double m_Alpha;

  double m_Beta;

  double m_Gamma;
  double m_Damping;

  unsigned int m_Rigidity;

  // definition of internal parameters
  int m_Step;

  int m_ImageWidth;

  int m_ImageHeight;

  int m_ImageDepth;

  int m_Iterations;

  GeometryMapPointer m_Data;

}; // end of class
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkDeformableSimplexMesh3DFilter.hxx"
#endif

#endif //itkDeformableSimplexMesh3DFilter_h