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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 *         http://www.apache.org/licenses/LICENSE-2.0.txt
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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 ITK_TEMPLATE_EXPORT DeformableSimplexMesh3DFilter:public MeshToMeshFilter< TInputMesh, TOutputMesh >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(DeformableSimplexMesh3DFilter);

  using Self = DeformableSimplexMesh3DFilter;

  using Superclass = MeshToMeshFilter< TInputMesh, TOutputMesh >;

  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkNewMacro(Self);

  itkTypeMacro(DeformableSimplexMesh3DFilter, MeshToMeshFilter);

  using InputMeshType = TInputMesh;
  using OutputMeshType = TOutputMesh;

  using InputPointsContainerPointer = typename InputMeshType::PointsContainerPointer;
  using InputPointsContainer = typename InputMeshType::PointsContainer;
  using InputPointsContainerConstIterator = typename InputMeshType::PointsContainer::ConstIterator;

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

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

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

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

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

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

  using GeometryMapType = typename InputMeshType::GeometryMapType;
  using GeometryMapPointer = typename GeometryMapType::Pointer;
  using GeometryMapIterator = typename GeometryMapType::Iterator;

  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() override = default;
  void PrintSelf(std::ostream & os, Indent indent) const override;

  void GenerateData() 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