added the code for meshing a union of balls.

TODO: remove unique_hash_map from the construction of the triangulation:

Skin_surface_3/examples/Skin_surface_3/NGHK_skin_surface_simple.C

@@ -20,7 +20,7 @@ typedef CGAL::Polyhedron_3<K,Poly_items>                      Polyhedron;
 int main(int argc, char *argv[]) {
   if (argc < 2) {
     std::cout << "Usage: " << argv[0] << " <cin-file>" << std::endl;
-    return 1;
+    return 0;
   }
 
   std::list<Weighted_point> l;

Skin_surface_3/examples/Skin_surface_3/NGHK_skin_surface_subdiv.C

@@ -20,7 +20,7 @@ typedef CGAL::Polyhedron_3<K,Poly_items>                      Polyhedron;
 int main(int argc, char *argv[]) {
   if (argc < 2) {
     std::cout << "Usage: " << argv[0] << " <cin-file>" << std::endl;
-    return 1;
+    return 0;
   }
 
   std::list<Weighted_point> l;

Skin_surface_3/examples/Skin_surface_3/makefile

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

Skin_surface_3/examples/Skin_surface_3/skin_surface_pdb_reader.C

@@ -22,7 +22,7 @@ typedef CGAL::Polyhedron_3<K,Poly_items>                      Polyhedron;
 int main(int argc, char *argv[]) {
   if (argc < 2) {
     std::cout << "Usage: " << argv[0] << " <pdb-file>" << std::endl;
-    return 1;
+    return 0;
   }
 
   std::list<Weighted_point> l;

Skin_surface_3/examples/Skin_surface_3/skin_surface_subdiv.C

@@ -2,7 +2,6 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Skin_surface_3.h>
 #include <CGAL/Polyhedron_3.h>
-#include <CGAL/Skin_surface_polyhedral_items_3.h>
 #include <CGAL/mesh_skin_surface_3.h>
 #include <CGAL/subdivide_skin_surface_mesh_3.h>
 #include <list>
@@ -16,11 +15,7 @@ typedef CGAL::Skin_surface_3<Traits>                        Skin_surface_3;
 typedef Skin_surface_3::FT                                  FT;
 typedef Skin_surface_3::Weighted_point                      Weighted_point;
 typedef Skin_surface_3::Bare_point                          Bare_point;
-
+typedef CGAL::Polyhedron_3<K>                               Polyhedron;
-// Each facet has a pointer to the tetrahedron of the TMC it is contained in
-typedef Skin_surface_3::Triangulated_mixed_complex          TMC;
-typedef CGAL::Skin_surface_polyhedral_items_3<TMC>          Poly_items;
-typedef CGAL::Polyhedron_3<K,Poly_items>                    Polyhedron;
 
 int main(int argc, char *argv[]) {
   std::list<Weighted_point> l;

Skin_surface_3/examples/Skin_surface_3/skin_surface_subdiv_with_normals.C

@@ -2,13 +2,12 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Skin_surface_3.h>
 #include <CGAL/Polyhedron_3.h>
-#include <CGAL/Skin_surface_polyhedral_items_3.h>
 #include <CGAL/mesh_skin_surface_3.h>
 #include <CGAL/subdivide_skin_surface_mesh_3.h>
 #include <list>
 
 #include <fstream>
-#include <CGAL/IO/Polyhedron_iostream.h>
+#include "skin_surface_writer.h"
 
 typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
 typedef CGAL::Regular_triangulation_euclidean_traits_3<K>   Traits;
@@ -16,69 +15,15 @@ typedef CGAL::Skin_surface_3<Traits>                        Skin_surface_3;
 typedef Skin_surface_3::FT                                  FT;
 typedef Skin_surface_3::Weighted_point                      Weighted_point;
 typedef Skin_surface_3::Bare_point                          Bare_point;
-
+typedef CGAL::Polyhedron_3<K>                               Polyhedron;
-// Each facet has a pointer to the tetrahedron of the TMC it is contained in
-typedef Skin_surface_3::Triangulated_mixed_complex          TMC;
-typedef CGAL::Skin_surface_polyhedral_items_3<TMC>          Poly_items;
-typedef CGAL::Polyhedron_3<K,Poly_items>                    Polyhedron;
-
-
-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;
-
-  // 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 ++) {
-    out << vit->point() << " "
- 	<< policy->normal(vit)
-	<< 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";
-  }
-}  
 
 int main(int argc, char *argv[]) {
   std::list<Weighted_point> l;
   FT                        shrinkfactor = 0.5;
-  if (argc < 2) {
-    std::cout << "Usage: " << argv[0] << " <infile>" << std::endl;
-    exit(0);
-  }
 
-  std::ifstream in(argv[1]);
+  l.push_front(Weighted_point(Bare_point(0,0,0), 1));
-  Weighted_point wp;
+  l.push_front(Weighted_point(Bare_point(0,1,0), 2));
-  while (in >> wp) l.push_front(wp);
+  l.push_front(Weighted_point(Bare_point(0,0,2), 1));
 
   Skin_surface_3 skin_surface(l.begin(), l.end(), shrinkfactor);
 

Skin_surface_3/examples/Skin_surface_3/union_of_balls_simple.C

@@ -1,30 +1,29 @@
-// NGHK: NOT IN USE FOR NOW
-
 // examples/Skin_surface_3/union_of_balls_simple.C
-#include <CGAL/Skin_surface_traits_3.h>
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/skin_surface_3.h>
+#include <CGAL/Union_of_balls_3.h>
 #include <CGAL/Polyhedron_3.h>
-
+// #include <CGAL/mesh_union_of_balls_3.h>
 #include <list>
 
-typedef CGAL::Skin_surface_traits_3<>                    Skin_surface_traits;
+typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
-typedef Skin_surface_traits::Regular_traits              Regular_traits;
+typedef CGAL::Regular_triangulation_euclidean_traits_3<K>   Traits;
-typedef Regular_traits::Bare_point                       Reg_point;
+typedef CGAL::Union_of_balls_3<Traits>                      Union_of_balls_3;
-typedef Regular_traits::Weighted_point                   Reg_weighted_point;
+typedef Union_of_balls_3::FT                                FT;
-typedef CGAL::Polyhedron_3<Skin_surface_traits::Polyhedron_traits> Polyhedron;
+typedef Union_of_balls_3::Weighted_point                    Weighted_point;
+typedef Union_of_balls_3::Bare_point                        Bare_point;
+typedef CGAL::Polyhedron_3<K>                               Polyhedron;
 
 int main(int argc, char *argv[]) {
-  return 0;
+  std::list<Weighted_point> l;
 
-  std::list<Reg_weighted_point> l;
+  l.push_front(Weighted_point(Bare_point(0,0,0), 1));
+  l.push_front(Weighted_point(Bare_point(0,1,0), 2));
+  l.push_front(Weighted_point(Bare_point(0,0,2), 1));
 
-  l.push_front(Reg_weighted_point(Reg_point(0,0,0), 1));
+  Union_of_balls_3 union_of_balls(l.begin(), l.end());
-  l.push_front(Reg_weighted_point(Reg_point(0,1,0), 2));
-  l.push_front(Reg_weighted_point(Reg_point(0,0,2), 1));
 
-  Polyhedron p;
+//   Polyhedron p;
-  Skin_surface_traits skin_surface_traits(1);
+//   CGAL::mesh_union_of_balls_3(union_of_balls, p);
-  CGAL::skin_surface_3(l.begin(), l.end(), p, skin_surface_traits);
 
   return 0;
 }

Skin_surface_3/include/CGAL/Skin_surface_3.h

@@ -17,8 +17,8 @@
 //
 // Author(s)     : Nico Kruithof <Nico@cs.rug.nl>
 
-#ifndef CGAL_CGAL_SKIN_SURFACE_3_H
+#ifndef CGAL_SKIN_SURFACE_3_H
-#define CGAL_CGAL_SKIN_SURFACE_3_H
+#define CGAL_SKIN_SURFACE_3_H
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Exact_predicates_exact_constructions_kernel.h>
@@ -289,4 +289,4 @@ construct_bounding_box(Regular &regular)
 
 CGAL_END_NAMESPACE
 
-#endif // CGAL_CGAL_SKIN_SURFACE_TRAITS_3_H
+#endif // CGAL_SKIN_SURFACE_3_H

Skin_surface_3/include/CGAL/Skin_surface_refinement_traits_3.h

@@ -176,8 +176,8 @@ private:
 protected:
   Skin_surface const &skin;
   SS_vertex_map triang_vertex_signs;
-  T2P_converter const t2p_converter;
+  T2P_converter t2p_converter;
-  P2T_converter const p2t_converter;
+  P2T_converter p2t_converter;
 };
 
 template <class Polyhedron_3, class SkinSurface_3>
@@ -225,13 +225,13 @@ public:
   
   P_point to_surface(P_vertex_handle vh) 
   {
-    SS_cell_handle ch = Base::skin.locate(Base::p2t_converter(vh->point()));
+    SS_cell_handle ch = Base::skin.locate(p2t_converter(vh->point()));
     return to_surface_along_transversal_segment(vh->point(),ch);
   }
   
   P_vector normal(P_vertex_handle vh) 
   {
-    SS_cell_handle ch = Base::skin.locate(Base::p2t_converter(vh->point()));
+    SS_cell_handle ch = Base::skin.locate(p2t_converter(vh->point()));
     return ch->surf->gradient(vh->point());
   }
 };

Skin_surface_3/include/CGAL/Triangulated_mixed_complex_observer_3.h

@@ -188,9 +188,9 @@ public:
 		     const Surface_RT &s,
 		     const int orient) {
     Q[1] = Q[3] = Q[4] = 0;
-    Q[0] = Q[2] = Q[5] = orient*(1-s);
+    Q[0] = Q[2] = Q[5] = orient/s;
     
-    surf = new Quadratic_surface(Q, c, s*(1-s)*w);
+    surf = new Quadratic_surface(Q, c, w);
   }
 
   void create_hyperboloid(const Surface_point &c,
@@ -198,18 +198,18 @@ public:
 			  const Surface_vector &t,
 			  const Surface_RT &s,
 			  const int orient) {
-    Surface_RT den = t*t;
+    Surface_RT den = t*t*s*(1-s);
     
-    Q[0] = orient*(-  t.x()*t.x()/den + (1-s));
+    Q[0] = orient*(-  t.x()*t.x()/den + 1/s);
     
     Q[1] = orient*(-2*t.y()*t.x()/den);
-    Q[2] = orient*(-  t.y()*t.y()/den + (1-s));
+    Q[2] = orient*(-  t.y()*t.y()/den + 1/s);
     
     Q[3] = orient*(-2*t.z()*t.x()/den);
     Q[4] = orient*(-2*t.z()*t.y()/den);
-    Q[5] = orient*(-  t.z()*t.z()/den + (1-s));
+    Q[5] = orient*(-  t.z()*t.z()/den + 1/s);
     
-    surf = new Quadratic_surface(Q, c, s*(1-s)*w);
+    surf = new Quadratic_surface(Q, c, w);
   }
 
   Surface_RT Q[6];