CGAL users discussion list

["Benjamin schwarz" <>]

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
____________________________________________________