itkDeformableSimplexMesh3DFilter.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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.
 *
 *=========================================================================*/
/*=========================================================================
 *
 *  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_MOVE(DeformableSimplexMesh3DFilter);

  using Self = DeformableSimplexMesh3DFilter;

  using Superclass = MeshToMeshFilter<TInputMesh, TOutputMesh>;

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

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(DeformableSimplexMesh3DFilter);

  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 * gradientImage);

  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