Reducing more memory

Skin_surface_3/examples/Skin_surface_3/makefile

@@ -13,7 +13,7 @@ include $(CGAL_MAKEFILE)
 #                    compiler flags
 #---------------------------------------------------------------------#
 
-CXXFLAGS = -g\
+CXXFLAGS = -O2\
            -I.\
            -Idsrpdb/include\
            -I../../include \
@@ -30,7 +30,7 @@ LIBPATH = \
           $(TESTSUITE_LIBPATH) \
           $(CGAL_LIBPATH)
 
-LDFLAGS = -g \
+LDFLAGS = -O2 \
           $(TESTSUITE_LDFLAGS) \
           $(LONG_NAME_PROBLEM_LDFLAGS) \
           $(CGAL_LDFLAGS)

Skin_surface_3/examples/Skin_surface_3/skin_surface_pdb_reader.C

@@ -17,7 +17,10 @@ typedef CGAL::Regular_triangulation_euclidean_traits_3<K>   Traits;
 typedef CGAL::Skin_surface_3<Traits>                        Skin_surface_3;
 typedef Skin_surface_3::FT                                  FT;
 typedef Skin_surface_3::Weighted_point                      Weighted_point;
-typedef CGAL::Polyhedron_3<K>                               Polyhedron;
+typedef CGAL::Simple_cartesian<float>                       Poly_K;
+typedef Skin_surface_3::Triangulated_mixed_complex          TMC;
+typedef CGAL::Skin_surface_polyhedral_items_3<TMC>          Poly_items;
+typedef CGAL::Polyhedron_3<Poly_K,Poly_items>               Polyhedron;
 
 int main(int argc, char *argv[]) {
   if (argc < 2) {

Skin_surface_3/examples/Skin_surface_3/skin_surface_writer.h

@@ -0,0 +1,55 @@
+#ifndef CGAL_SKIN_SURFACE_WRITER_H
+#define CGAL_SKIN_SURFACE_WRITER_H
+
+#include <fstream>
+#include <CGAL/IO/Polyhedron_iostream.h>
+
+template <class Polyhedron, class SkinSurface>
+/// Write polyhedron with normals:
+void write_polyhedron_with_normals(Polyhedron &p, 
+				   SkinSurface &skin, 
+				   std::ostream &out)
+{
+  typedef typename Polyhedron::Vertex_iterator                  Vertex_iterator;
+  typedef typename Polyhedron::Facet_iterator                   Facet_iterator;
+  typedef typename Polyhedron::Halfedge_around_facet_circulator HFC;
+  typedef typename Polyhedron::Vertex_handle                    Vertex_handle;
+  typedef typename Polyhedron::Traits::Vector_3                 Vector_3;
+
+  // Write header
+  out << "NOFF " << p.size_of_vertices ()
+      << " " << p.size_of_facets()
+      << " " << p.size_of_halfedges()
+      << std::endl;
+
+  // Write vertices
+  typedef CGAL::Skin_surface_subdivision_policy_base_3<Polyhedron, SkinSurface> 
+    Subdivision_policy;
+  Subdivision_policy *policy = get_subdivision_policy(p, skin);
+  for (Vertex_iterator vit = p.vertices_begin();
+       vit != p.vertices_end(); vit ++) {
+    Vector_3 n = policy->normal(vit);
+    n = n/sqrt(n*n);
+    out << vit->point() << " "
+ 	<< n
+	<< std::endl;
+  }
+
+  // Write faces
+  CGAL::Inverse_index<Vertex_handle> index(p.vertices_begin(),
+					   p.vertices_end());
+  for(Facet_iterator fi = p.facets_begin();
+      fi != p.facets_end(); ++fi) {
+    HFC hc = fi->facet_begin();
+    HFC hc_end = hc;
+    std::size_t n = circulator_size( hc);
+    out << n;
+    do {
+      Vertex_handle vh = (*hc).vertex();
+      out << " " << index[vh];
+    } while (++hc != hc_end);
+    out << "\n";
+  }
+}  
+
+#endif // CGAL_SKIN_SURFACE_WRITER_H

Skin_surface_3/include/CGAL/Marching_tetrahedra_traits_skin_surface_3.h

@@ -58,13 +58,14 @@ private:
   typedef typename Triangulation::Geom_traits::Point_3 Triang_point;
   
   // Additional functions, not belonging to the traits concept:
-  HDS_RT value(const Cell_handle &ch, const HDS_point &p) const {
-    return ch->surf->value(p);
-  }
-//   HDS_RT value(const Cell_handle &ch, const Triang_point &p) const {
-//     // NGHK: Remove the to_double later ...
-//     return CGAL::to_double(ch->surf->value(converter(p)));
+//   HDS_RT value(const Cell_handle &ch, const HDS_point &p) const {
+//     return ch->surf->value(p);
 //   }
+  template <class Point>
+  HDS_RT value(const Cell_handle &ch, const Point &p) const {
+    // NGHK: Remove the to_double later ...
+    return ch->surf->value(converter(p));
+  }
 
   Converter converter;
   HDS_RT iso_value;

Skin_surface_3/include/CGAL/Skin_surface_3.h

@@ -133,11 +133,12 @@ public:
       std::cerr << "Vertices: " << _tmc.number_of_vertices() << std::endl;
       std::cerr << "Cells:    " << _tmc.number_of_cells() << std::endl;
     }
-//     std::ofstream out("vertices.txt");
-//     for (typename Triangulated_mixed_complex::Finite_vertices_iterator 
-// 	   vit = _tmc.finite_vertices_begin();
-// 	 vit != _tmc.finite_vertices_end(); vit ++) {
-//       out << vit->point().x().exact() << std::endl;
+
+//     std::ofstream out("edgelength.txt");
+//     for (typename Triangulated_mixed_complex::Finite_edges_iterator 
+// 	   eit = _tmc.finite_edges_begin();
+// 	 eit != _tmc.finite_edges_end(); eit ++) {
+//       out << sqrt(_tmc.segment(eit).squared_length()) << std::endl;
 //     }
   }
   const Triangulated_mixed_complex &triangulated_mixed_complex() const {

Skin_surface_3/include/CGAL/Skin_surface_traits_3.h

@@ -108,24 +108,6 @@ public:
     return P2T_converter();
   }
 
-  // NGHK: Not in current implementation
-//   template <class Kernel>
-//   Construct_weighted_circumcenter_3<
-//     Regular_triangulation_euclidean_traits_3<Kernel> >
-//   construct_weighted_circumcenter_3_object() const {
-//     return Regular_triangulation_euclidean_traits_3<Kernel>().
-//       construct_weighted_circumcenter_3_object();
-//   }
-
-  // NGHK: Not in current implementation
-//   template <class Kernel>
-//   In_smallest_orthogonal_sphere_3<
-//     Regular_triangulation_euclidean_traits_3<Kernel> >
-//   in_smallest_orthogonal_sphere_3_object() const {
-//     return Regular_triangulation_euclidean_traits_3<Kernel>().
-//       in_smallest_orthogonal_sphere_3_object();
-//   }
-
   Regular_RT shrink_factor() const {
     return shrink;
   }

Skin_surface_3/include/CGAL/triangulate_mixed_complex_3.h

@@ -95,8 +95,16 @@ private:
   typedef Compute_anchor_3<Regular>                       Compute_anchor;
   typedef std::pair<Rt_Simplex,Rt_Simplex>                Symb_anchor;
 
-  typedef std::map<Rt_Simplex, Rt_Simplex>       Anchor_map;
-  typedef typename Anchor_map::iterator          Anchor_map_iterator;
+  // You might get type differences here:
+  struct Anchor_map_iterator_tmp;
+  typedef std::map<Rt_Simplex, Anchor_map_iterator_tmp>     Anchor_map;
+  struct Anchor_map_iterator_tmp : Anchor_map::iterator {
+    Anchor_map_iterator_tmp() 
+      : Anchor_map::iterator() {}
+    Anchor_map_iterator_tmp(typename Anchor_map::iterator const &it) 
+      : Anchor_map::iterator(it) {}
+  };
+  typedef typename Anchor_map::iterator                     Anchor_map_iterator;
 public:
 
   Mixed_complex_triangulator_3(
@@ -165,19 +173,25 @@ private:
   void construct_anchor_vor(Rt_Simplex const &sVor);
   void construct_anchors();
   Rt_Simplex get_anchor_del(Rt_Simplex const &sDel) {
-    return find_anchor(anchor_del2, sDel);
+    return find_anchor(anchor_del2, sDel)->first;
   }
   Rt_Simplex get_anchor_vor(Rt_Simplex const &sVor) {
-    return find_anchor(anchor_vor2, sVor);
+    return find_anchor(anchor_vor2, sVor)->first;
   }  
-  Rt_Simplex find_anchor(Anchor_map &a_map, Rt_Simplex const&s) {
-    Anchor_map_iterator it = a_map.find(s);
+  Anchor_map_iterator find_anchor(Anchor_map &a_map, Rt_Simplex const&s) {
+    return find_anchor(a_map, a_map.find(s));
+  }
+  Anchor_map_iterator find_anchor(Anchor_map &a_map,
+				  Anchor_map_iterator const&it) {
     CGAL_assertion(it != a_map.end());
-    if (it->second == s) return s;
-
-    Rt_Simplex result = find_anchor(a_map,it->second);
-    it->second = result;
-    return result;
+    Anchor_map_iterator it2 = it->second;
+    while (it2 != it2->second) {
+      it->second = it2->second;
+      // NGHK: changed the type for the map-iterator-hack
+      it2->second = it;
+      it2 = it->second;
+    }
+    return it2;
   }
   void construct_vertices();
   
@@ -256,27 +270,32 @@ Mixed_complex_triangulator_3<
   TriangulatedMixedComplexObserver_3>::
 construct_anchor_del(Rt_Simplex const &sDel) {
   Rt_Simplex s = compute_anchor_obj.anchor_del(sDel);
-  anchor_del2.insert(std::pair<Rt_Simplex,Rt_Simplex>(sDel, s));
+  anchor_del2[sDel] = Anchor_map_iterator();
+
+  Anchor_map_iterator it = anchor_del2.find(sDel);
+  Anchor_map_iterator it2 = anchor_del2.find(s);
+  CGAL_assertion(it != anchor_del2.end());
+  CGAL_assertion(it2 != anchor_del2.end());
+  it->second = it2;
 
   // degenerate simplices:
   if (compute_anchor_obj.is_degenerate()) {
-    s = find_anchor(anchor_del2, sDel);
+    it = find_anchor(anchor_del2, it);
     typename Compute_anchor::Simplex_iterator degenerate_it;
     for (degenerate_it = compute_anchor_obj.equivalent_anchors_begin();
 	 degenerate_it != compute_anchor_obj.equivalent_anchors_end(); 
 	 degenerate_it++) {
-      Anchor_map_iterator it = anchor_del2.find(*degenerate_it);
-      CGAL_assertion(it != anchor_del2.end());
-      Anchor_map_iterator it2 = anchor_del2.find(it->second);
+      Anchor_map_iterator tmp;
+      it2 = anchor_del2.find(*degenerate_it);
       CGAL_assertion(it2 != anchor_del2.end());
       // Merge sets:
-      while (it != it2) {
-	it->second = s;
-	it = it2;
-	it2 = anchor_del2.find(it->second);
+      while (it2 != it2->second) {
+	tmp = it2->second;
+	it2->second = it->second;
+	it2 = tmp;
 	CGAL_assertion(it2 != anchor_del2.end());
       }
-      it->second = s;
+      it2->second = it->second;
     }
   }
 }
@@ -292,30 +311,36 @@ Mixed_complex_triangulator_3<
   TriangulatedMixedComplexObserver_3>::
 construct_anchor_vor(Rt_Simplex const &sVor) {
   Rt_Simplex s = compute_anchor_obj.anchor_vor(sVor);
-  anchor_vor2.insert(std::pair<Rt_Simplex,Rt_Simplex>(sVor, s));
+  anchor_vor2[sVor] = Anchor_map_iterator();
+
+  Anchor_map_iterator it = anchor_vor2.find(sVor);
+  Anchor_map_iterator it2 = anchor_vor2.find(s);
+  CGAL_assertion(it != anchor_vor2.end());
+  CGAL_assertion(it2 != anchor_vor2.end());
+  it->second = it2;
 
   // degenerate simplices:
   if (compute_anchor_obj.is_degenerate()) {
-    s = find_anchor(anchor_vor2, sVor);
+    it = find_anchor(anchor_vor2, it);
     typename Compute_anchor::Simplex_iterator degenerate_it;
     for (degenerate_it = compute_anchor_obj.equivalent_anchors_begin();
 	 degenerate_it != compute_anchor_obj.equivalent_anchors_end(); 
 	 degenerate_it++) {
+      Anchor_map_iterator tmp;
+      it2 = anchor_vor2.find(*degenerate_it);
       // Possibly not found for 2 Voronoi vertices with the same center,
       // If the first vertex is inserted and the second is already found.
       // see compute_anchor_obj.anchor_vor(Cell_handle)
-      Anchor_map_iterator it = anchor_vor2.find(*degenerate_it);
-      if (it != anchor_vor2.end()) {
-	Anchor_map_iterator it2 = anchor_vor2.find(it->second);
+      if (it2 != anchor_vor2.end()) {
 	CGAL_assertion(it2 != anchor_vor2.end());
 	// Merge sets:
-	while (it != it2) {
-	  it->second = s;
-	  it = it2;
-	  it2 = anchor_vor2.find(it->second);
+	while (it2 != it2->second) {
+	  tmp = it2->second;
+	  it2->second = it->second;
+	  it2 = tmp;
 	  CGAL_assertion(it2 != anchor_vor2.end());
 	}
-	it->second = s;
+	it2->second = it->second;
       }
     }
   }