CGAL users discussion list

["Nico Kruithof" <>]

Hi Benjamin,

I tried your include change, but couldn't see the performance
decrease. Could you have a look at my test program? There is an
enhancement of the polyhedron datastructure in which I add
back-pointers to the Skin_surface_3 object to improve performance.
Maybe you saw something going wrong there. To get the pointers you
should use

typedef CGAL::Polyhedron_3<K,
  CGAL::Skin_surface_polyhedral_items_3<Skin_surface_3> >   Polyhedron;

The optimization used is based on the templates.

Bests,
Nico

On Fri, Nov 21, 2008 at 10:02 AM, Benjamin schwarz
<>
 wrote:
> Hello list,
>
>  I am currently testing the skin package provided in CGAL (thanks a
> lot Nico). My computations seem far less efficient than those
> exhibited in the CGAL manual or in Nico's papers. I guess I did
> something wrong. Maybe another magic compilation variable like
> -DNDEBUG ?
>
>  I pasted the code a few lines below. It only consists in reading
> atom, skin it, get a coarse mesh and refine this mesh twice. The times
> for these four steps on a 28 atoms molecule :
>
> create skin  in : 0.16001
> mesh   skin0 in : 0.012001
> mesh   skin1 in : 11.7727
> mesh   skin2 in : 11.7887
>
> Is this normal ?
>
>  My computer is a bit old : laptop 1.6GHz
>  under linux debian lenny
>  latest cgal installed through dpkg (thanks Sylvain)
>  gcc version 4.3.2 (Debian 4.3.2-1)
>
>  Compilation lines :
>
> g++ -Wall -frounding-math -g -O2 -I/usr/include/qt3 -DCGAL_USE_F2C
> -DCGAL_USE_F2C  -I /home/schwarz/include -O2 -DNDEBUG   -c -o
> test-skins.o test-skins.cpp
>
> g++   -o test-skins test-skins.o  -lCGAL -lCGALcore++ -lCGALQt
> -lCGALimageIO -lCGALPDB -lqt-mt -llapack -lGL -lGLU -llapack -lf77blas
> -lcblas -latlas -lz -lmpfr -lgmpxx -lgmp -lX11
> -lboost_program_options-mt -lm -O2 -lm
>
> ----------My code------------
> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
> #include <CGAL/Polyhedron_incremental_builder_3.h>
> #include <CGAL/Polyhedron_3.h>
> #include <CGAL/IO/Geomview_stream.h>
> #include <CGAL/IO/Polyhedron_geomview_ostream.h>
>
> //#include "skin_surface_writer.h"
>
> #include <CGAL/Skin_surface_3.h>
> #include <CGAL/Polyhedron_3.h>
> #include <CGAL/mesh_skin_surface_3.h>
> #include <CGAL/subdivide_skin_surface_mesh_3.h>
>
> #include <CGAL/Timer.h>
>
> #include <list>
>
> #include <iostream>
> #include <fstream>
>
> typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
> typedef CGAL::Skin_surface_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 K::Point_3                                          Point;
> typedef K::Vector_3                                         Vector;
> typedef CGAL::Polyhedron_3<K>                               Polyhedron;
> typedef Polyhedron::Halfedge_handle                                         
>             Halfedge_handle;
>
>
> int main(int argc, char **argv) {
>  std::list<Weighted_point> l;
>  double                    shrinkfactor = 0.5;
>  CGAL::Timer ben_t;
>
> // first command line arg is a "x y z w" formated file
> std::ifstream in(argv[1],std::ios::in);
> int i=0;
>  double x,y,z,w;
>  while (in>>x) {++i;
>  std::cerr<<"-->"<<x<<std::endl;
>        in >> y; in >> z; in >> w;
>        l.push_back(Weighted_point(Point(x,y,z),w));
>  }
>        std::cerr<<"got "<<i<<" atoms"<<std::endl;
>
>
>  Polyhedron p;
>
>  CGAL::Geomview_stream gv(CGAL::Bbox_3(-100, -100, -100, 100, 100, 100));
>  gv.set_bg_color(CGAL::Color(0, 200, 200));
>  gv.clear();
>
>  int geomId=0;
> double time_coarse = ben_t.time(); ben_t.start();
>         Skin_surface_3 skin_surface(l.begin(), l.end(), shrinkfactor);
> ben_t.stop();time_coarse = ben_t.time() - time_coarse;
>
> double time_meshcoarse = ben_t.time(); ben_t.start();
>        CGAL::mesh_skin_surface_3(skin_surface, p);
> ben_t.stop();time_meshcoarse = ben_t.time() - time_coarse;
>
>  std::cout<<"skin mesh..."<<std::endl;
>  std::cerr<<" done"<<std::endl;
>  gv<<CGAL::Color(100,100,100);
>  gv<<p;
>  gv<<"(name-object g"<<++geomId<<" skin0)";
>
> std::cout<<"mesh subdivide 1..."<<std::endl;
> double time_subdiv1 = ben_t.time(); ben_t.start();
>        CGAL::subdivide_skin_surface_mesh_3(skin_surface, p, 1);
> ben_t.stop();time_subdiv1 = ben_t.time() - time_coarse;
>
>  gv<<CGAL::Color(100,100,200);
>  gv<<p;
>  gv<<"(name-object g"<<++geomId<<" skin1)";
>
> double time_subdiv2 = ben_t.time(); ben_t.start();
>        CGAL::mesh_skin_surface_3(skin_surface, p);
> ben_t.stop();time_subdiv2 = ben_t.time() - time_coarse;
>
>        gv<<CGAL::Color(100,100,200);
>        gv<<p;
>        gv<<"(name-object g"<<++geomId<<" skin2)";
>
>  std::cout<<std::endl;
>  std::cout<<"create skin  in : "<<time_coarse<<std::endl;
>  std::cout<<"mesh   skin0 in : "<<time_meshcoarse<<std::endl;
>  std::cout<<"mesh   skin1 in : "<<time_subdiv1<<std::endl;
>  std::cout<<"mesh   skin2 in : "<<time_subdiv2<<std::endl;
>  std::cout<<"press a key to finish"<<std::endl;
>  char c;std::cin>>c;
>  std::cout<<c<<std::endl;
>  return 0;
> }
>
>
> --
>
>                  --Benjamin SCHWARZ
> ____________________________________________________
> IGBMC
> Département de Biologie et de Génomique Structurales
> Parc d'Innovation, 1 rue Laurent Fries
> BP 10142, 67404 ILLKIRCH CEDEX, France
>
> E-mail : 
> 
> Phone  : 03 88 65 57 95
> ____________________________________________________
> --
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>
#if 1
#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Skin_surface_3.h>
#include <CGAL/Polyhedron_3.h>
#include <CGAL/mesh_skin_surface_3.h>
#include <CGAL/subdivide_skin_surface_mesh_3.h>
#include "skin_surface_writer.h"
#include <list>
#include <fstream>

#else
#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Polyhedron_incremental_builder_3.h>
#include <CGAL/Polyhedron_3.h>
#include <CGAL/IO/Geomview_stream.h>
#include <CGAL/IO/Polyhedron_geomview_ostream.h>
#include "skin_surface_writer.h"
#include <CGAL/Skin_surface_3.h>
#include <CGAL/Polyhedron_3.h>
#include <CGAL/mesh_skin_surface_3.h>
#include <CGAL/subdivide_skin_surface_mesh_3.h>
#endif

#include <CGAL/Timer.h>
#include <list>
#include <iostream>
#include <fstream>


typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
typedef CGAL::Skin_surface_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 Weighted_point::Point                               Bare_point;
typedef CGAL::Polyhedron_3<K,
  CGAL::Skin_surface_polyhedral_items_3<Skin_surface_3> >   Polyhedron;

int main() {
  std::list<Weighted_point> l;
  FT                        shrinkfactor = 0.5;

 CGAL::Timer timer;
  Weighted_point wp;
  std::ifstream in("data/molecule_tunnel.cin");
  while (in >> wp)
    l.push_front(wp);

  Polyhedron p;

  Skin_surface_3 skin_surface(l.begin(), l.end(), shrinkfactor);
  CGAL::mesh_skin_surface_3(skin_surface, p);

  std::cout << "subdividing ..." << std::endl;
  {
    CGAL::Timer timer;

    timer.start();
    CGAL::subdivide_skin_surface_mesh_3(skin_surface, p);
    timer.stop();
    std::cout << "Elapsed time: " << timer.time() << std::endl;
  }

  std::ofstream out("mesh.off");
  out << p;

  return 0;
}