itkSimplexMesh.h

/*=========================================================================

Program:   Insight Segmentation & Registration Toolkit
Module:    itkSimplexMesh.h
Language:  C++
Date:      $Date$
Version:   $Revision$

Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

This software is distributed WITHOUT ANY WARRANTY; without even 
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#ifndef __itkSimplexMesh_h
#define __itkSimplexMesh_h

#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#include "itkMesh.h"
#include "itkSimplexMeshGeometry.h"
#include "itkVertexCell.h"
#include "itkTriangleCell.h"
#include "itkCellInterface.h"
#include "itkMapContainer.h"
#include "itkFixedArray.h"
#include "itkNumericTraits.h"
#include <itkCovariantVector.h>
#include <vector>
#include <algorithm>
#include <set>

namespace itk
{
/** \class SimplexMesh
 * \brief The class represents a 2-simplex mesh. 
 *
 * A simplex mesh can be used for deformable model segmentation of 3D image data.
 * To create a simplex mesh one needs a triangle mesh, which can be converted 
 * to using the class itkTriangleMeshToSimplexMeshFilter. The back filtering 
 * (from simplex to trinagle mesh)is done through a itkSimplexMeshToTriangleMeshFilter.
 * 
 * \author Thomas Boettger. Division Medical and Biological Informatics, German Cancer Research Center, Heidelberg.
 */
  template <typename TPixelType, unsigned int VDimension = 3,
    typename TMeshTraits = DefaultStaticMeshTraits< TPixelType , VDimension, VDimension, TPixelType , TPixelType , TPixelType >
  >
class SimplexMesh : public Mesh<TPixelType, VDimension, TMeshTraits>
{
public:
  /** Standard typedefs. */
  typedef SimplexMesh                Self;

  /** Standard typedefs. */
  typedef Mesh<TPixelType, VDimension, TMeshTraits>  Superclass;

  /** Standard typedefs. */
  typedef SmartPointer<Self>  Pointer;

  /** Standard typedefs. */
  typedef SmartPointer<const Self>  ConstPointer;

  /** definition for array of indices. */
  typedef typename SimplexMeshGeometry::IndexArray            IndexArray;

  /** definition for a set of neighbor indices */
  typedef std::set<unsigned long>                             NeighborSetType;

  /** */
  typedef typename NeighborSetType::iterator                  NeighborSetIterator;

  /** */
  typedef std::vector<unsigned long>                          NeighborListType;

  /** */
  typedef typename TMeshTraits::PointType                     PointType;

  /** */
  typedef typename TMeshTraits::PointIdentifier               PointIdentifier;

  /** */
  typedef typename PointType::VectorType VectorType;

  /** */ 
  typedef CovariantVector<typename VectorType::ValueType, 3>  CovariantVectorType;

  /** */
  typedef typename Superclass::CellType                       CellType;

  /** */
  typedef typename CellType::CellAutoPointer                  CellAutoPointer;
  /** */
  typedef itk::LineCell<CellType>                             LineType;

  /** map containing a SimplexMeshGeometry data object for each mesh
   * point */
  typedef itk::MapContainer<unsigned long, SimplexMeshGeometry *>   GeometryMapType;

  /** smartpointer def for the geometry map */
  typedef typename GeometryMapType::Pointer GeometryMapPointer;

  /** iterator definition for iterating over a geometry map */
  typedef typename GeometryMapType::Iterator GeometryMapIterator;

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

  /** Standard part of every itk Object. */
  itkTypeMacro(SimplexMesh, Mesh);

  /** Hold on to the type information specified by the template parameters. */
  typedef TMeshTraits                                          MeshTraits;
  typedef typename MeshTraits::PixelType                       PixelType;  
  typedef typename MeshTraits::PointsContainer                 PointsContainer;
  typedef typename Superclass::PointsContainerPointer          PointsContainerPointer;
  typedef typename Superclass::PointsContainer::Iterator       PointsContainerIterator;
  typedef typename Superclass::PointsContainerConstIterator    PointsContainerConstIterator;
  typedef typename Superclass::CellsContainerPointer           CellsContainerPointer;
  typedef typename Superclass::CellsContainerConstPointer      CellsContainerConstPointer;
  typedef typename Superclass::CellsContainerIterator          CellsContainerIterator;
  typedef typename Superclass::CellsContainerConstIterator     CellsContainerConstIterator;

  /** set the map of geometrydata to the new pointer */
  itkSetMacro(GeometryData, GeometryMapPointer );

  /** returns the current map of geometrydata */
  itkGetConstReferenceMacro(GeometryData, GeometryMapPointer );

  /** Get the first free id for new cells */
  itkSetMacro(LastCellId, unsigned long);

  /** Set the id value valid for new cells */
  itkGetConstMacro(LastCellId, unsigned long);

  /**
   * copy all necessary information from passed object
   * to the mesh
   */
  virtual void CopyInformation(const DataObject *data);


  /**
   * Add a new edge to the simplex mesh by specifying the ids of the start 
   * and end point of the edge
   * Note: This can destroy the simplex mesh structure! Better use the 
   * simplex mesh modification or creation filters
   */
  unsigned long AddEdge(unsigned long startPointId, unsigned long endPointId);


  /**
   * Add a new simplex mesh cell to the mesh by passing an AutoPointer of a 
   * previously created simplex mesh cell
   * 
   * Note: This can destroy the simplex mesh structure! You should use the 
   * simplex mesh modification or creation filters.
   */
  unsigned long AddFace(CellAutoPointer &cellPointer);

  /**
   * Replaces the cell specified by replaceIndex with the new cell passed by its
   * AutoPopinter
   */
    unsigned long ReplaceFace(unsigned long replaceIndex, CellAutoPointer &cellPointer);

  /** 
   * Get the three direct neighbors of a point 
   */  
  IndexArray GetNeighbors(unsigned long pointId) const;

  /** 
   * Get all neighbor points with a specified radius  
   */  
  NeighborListType* GetNeighbors(unsigned long pointId, unsigned int radius, NeighborListType* list = NULL) const;

  /** 
   * Add a neighbor to a point. 
   * Note: This can destroy the simplex mesh topology! 
   * Better use te simplex mesh creation filters.
   */  
  void AddNeighbor(unsigned long pointId, unsigned long neighborId);

  /** 
   * Replace a neighbor of a specific point by a new one
   */  
  void ReplaceNeighbor(unsigned long pointId, unsigned long oldNeighborId,unsigned long newNeighborIdx);

  /** 
   * Swap the order of two neighbors  
   */
  void SwapNeighbors(unsigned long pointId, unsigned long firstNeighborId,unsigned long secondNeighborId);

  /**
   * Set the geometry data for a specified point
   */
  void SetGeometryData(unsigned long pointId, SimplexMeshGeometry*);

  /**
   * Set the geometry data for a specified point
   */
  void SetBarycentricCoordinates(unsigned long idx, PointType values);

  /**
   * Set the barycentric coordinates for a specified point
   */
  PointType GetBarycentricCoordinates(unsigned long idx) const;

  /**
   * Set the reference metrics for a specified point
   */
  void SetReferenceMetrics(unsigned long idx, PointType values);

  /**
   *  Return the reference metrics for the specified point
   */
  PointType GetReferenceMetrics(unsigned long idx) const;

  /**
   * Set the simplex angle for the specified point
   */
  void SetPhi(unsigned long idx, double values);

  /**
   * Get the simplex angle for the specified point
   */
  double GetPhi(unsigned long idx) const;

  /**
   * Set the mean curvature for the specified point
   */
  void SetMeanCurvature(unsigned long idx, double values);

  /**
   * Get the mean curvature for the specified point
   */
  double GetMeanCurvature(unsigned long idx) const;

  /**
   * Set the circum circles radius for the specified point
   */
  void SetRadius(unsigned long idx, double values);

  /**
   * Get the circum circles radius for the specified point
   */
  double GetRadius(unsigned long idx) const;

  /**
   * Set the distance to the foot point for the specified point
   */
  void SetDistance(unsigned long idx, double values);

  /**
   * Get the distance to the foot point for the specified point
   */
  double GetDistance(unsigned long idx) const;

  /** compute the normal vector in the specified mesh point */
  CovariantVectorType ComputeNormal(unsigned long idx ) const;

protected:
  //  /** Constructor for use by New() method. */
  SimplexMesh();
  virtual ~SimplexMesh();
  void PrintSelf(std::ostream& os, Indent indent) const;

  /** 
   * The map stores a SimplexMeshGeometry object for each mesh point
   */
  GeometryMapPointer m_GeometryData;

  /**
   * The last cell id is the index which is used for insertion of new
   * cells. It increases during mesh creation. This is done because
   * one cannot rely on the size of the map or the highest index when 
   * cells are removed.
   */
  unsigned long m_LastCellId;

private:
  SimplexMesh(const Self&); //purposely not implemented
  //  void operator=(const Self&); //purposely not implemented
}; // End Class:  SimplexMesh

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkSimplexMesh.txx"
#endif

#endif