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[Ianic <>]

I am still in the process of getting the neighbors list for all cells and
facets of a 3D mesh. Here is the code that I've written (I simply added it
to an example with a liver image):


...
typedef Tr::Cell_handle Cell_handle;
typedef C3t3::Cell_iterator Cell_iterator;
typedef Tr::Facet Facet;
typedef C3t3::Facet_iterator Facet_iterator;
typedef Tr::Facet_circulator Facet_circulator;
typedef Tr::Edge Edge;
typedef Tr::Vertex_handle Vertex_handle;
...

  //---------------------------
  // A mesh connectivity file
  //---------------------------
  std::ofstream neigh_file;
  neigh_file.open("liver.neigh");

  //---------------------------
  // 1.0 Cell connectivity
  //---------------------------

  // Enumerating cells
  std::map<Cell_handle, int> C;
  int icell = 1;
  for( Cell_iterator cit = c3t3.cells_begin() ;
       cit != c3t3.cells_end() ;
       ++cit )
    C[cit] = icell++;

  // Writing cell connectivity data
  neigh_file << "Cell neighbours" << std::endl
     << c3t3.number_of_cells() << std::endl;

  for( Cell_iterator cit = c3t3.cells_begin() ;
       cit != c3t3.cells_end() ;
       ++cit ) {
    const Cell_handle& c = cit;
    for ( int i=0 ; i<4 ; ++i ) {
      const Cell_handle& neighbor = c->neighbor(i);
      if ( c3t3.is_in_complex(neighbor) )
        neigh_file << C[neighbor] << " ";
      else
        neigh_file << -1 << " ";
    }
    neigh_file << std::endl;
  }

  //---------------------------
  // 2.0 Facet connectivity
  //---------------------------

  // Enumerating facets
  std::map<Facet, int> F;
  int ifacet = 1;
  for( Facet_iterator fit = c3t3.facets_begin() ;
       fit != c3t3.facets_end() ;
       ++fit )
    F[*fit] = ifacet++;

  // Writing facet connectivity data
  neigh_file << "Facet neighbours" << std::endl
     << c3t3.number_of_facets() << std::endl;

  std::vector<int> vert;
  vert.resize(3);
  std::vector<Edge> edge;
  edge.resize(3);

  for( Facet_iterator fit = c3t3.facets_begin();
       fit != c3t3.facets_end();
       ++fit ) {
  
    const Cell_handle& cell = fit->first;
    int indexInCell = fit->second;
    vert[0] = (indexInCell+1)%4;
    vert[1] = (indexInCell+2)%4;
    vert[2] = (indexInCell+3)%4;

    edge[0] = Edge(cell, vert[1], vert[2]);
    edge[1] = Edge(cell, vert[2], vert[0]);
    edge[2] = Edge(cell, vert[0], vert[1]);

    for (unsigned int i = 0; i < edge.size(); ++i) {
      Facet_circulator fc = c3t3.triangulation().incident_facets(edge[i],
*fit);
      Facet_circulator done(fc);
      do {
        if ( c3t3.is_in_complex(*fc) )
          neigh_file << F[*fc] << " ";
      } while (++fc != done);
    }
    neigh_file << std::endl;
  }
  neigh_file << "End" << std::endl;
  neigh_file.close();

The cell neighbors list seems to be correct, though I am still wondering
what the neighbor(i) holds for a boundary cell, a NULL pointer?

The facet code doesn't work. The idea essentially is that I take all 3 edges
of each facet, circulate over their incident facets that belong to a c3t3
complex (should be 2) and for each edge I write out the facet number which
is not the current one (this check is omitted in this code just now).
However, when I run this code, I get lots of zeros from this line:

neigh_file << F[*fc] << " ";

Why does it happen? Can it be because I assign IDs to facets using typedef
C3t3::Facet_iterator, while when I go over the edge facets, I use typedef
Tr::Facet_circulator?
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