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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1143 by chuckv, Wed May 30 19:51:07 2007 UTC vs.
Revision 1242 by chuckv, Wed May 14 14:31:48 2008 UTC

# Line 44 | Line 44
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.4 2007-05-30 19:51:07 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.6 2008-05-14 14:31:48 chuckv Exp $
48   *
49   */
50  
51 + /* Standard includes independent of library */
52   #include <iostream>
53   #include <fstream>
54 + #include <list>
55 + #include <algorithm>
56 + #include <iterator>
57   #include "math/ConvexHull.hpp"
58 <
58 > #include "utils/simError.h"
59   using namespace oopse;
60  
61 < ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
61 > /* CGAL version of convex hull first then QHULL */
62 > #ifdef HAVE_CGAL
63 >
64 > #include <CGAL/basic.h>
65 > #include <CGAL/Simple_cartesian.h>
66 > #include <CGAL/Convex_hull_traits_3.h>
67 > #include <CGAL/convex_hull_3.h>
68 > #include <CGAL/double.h>
69 >
70 > #include <CGAL/Quotient.h>
71 > #include <CGAL/MP_Float.h>
72 > #include <CGAL/Lazy_exact_nt.h>
73 >
74 > typedef double RT;
75 > typedef CGAL::Simple_cartesian<RT>                K;
76 > typedef CGAL::Convex_hull_traits_3<K>             Traits;
77 > typedef Traits::Polyhedron_3                      Polyhedron_3;
78 > typedef K::Point_3                                Point;
79 >
80 >
81 > ConvexHull::ConvexHull(){}
82 >
83 > bool ConvexHull::genHull(std::vector<Vector3d> pos)
84 > {
85 >  
86 >  std::vector<Point> points;    
87 >  
88 >  
89 >  // Copy the positon vector into a points vector for cgal.
90 >  for (int i = 0; i < pos.size(); ++i)
91 >    {
92 >      Point pt(pos[i][0],pos[i][1],pos[i][2]);
93 >      points.push_back(pt);
94 >    }
95 >  
96 >  // define object to hold convex hull
97 >  Polyhedron_3 ch_object_;
98 >  // compute convex hull
99 >  CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
100 >  
101 >  for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){
102 >    std::cout<< v.point()<<std::endl;
103 >  }
104 >  
105 >  
106   }
107  
108 < bool ConvexHull::genHull(std::vector<Vector3d> pos) {
109 <  FILE *outfile = stdout;
110 <  FILE *errfile = stderr;
111 <  facetT *facet;
112 <  int exitcode;
113 <  boolT ismalloc = False;
114 <  int curlong,totlong;
108 >
109 >
110 > #else
111 > #ifdef HAVE_QHULL
112 > /* Old options Qt Qu Qg QG0 FA */
113 > ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
114 >                           //ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
115 > {}
116 >
117 > bool ConvexHull::genHull(std::vector<Vector3d> pos)
118 > {
119    
120 +  
121    int numpoints = pos.size();
122 <
123 <  coordT* points;
124 <  points = (coordT*) malloc(sizeof(coordT) * (numpoints*dim_));
125 <
126 <  for (int i=0; i<numpoints; i++) {
127 <    points[dim_ * i] = pos[i][0];
128 <    points[dim_ * i + 1] = pos[i][1];
129 <    points[dim_ * i + 2] = pos[i][2];          
122 >  coordT* pt_array;
123 >  coordT* surfpt_array;
124 >  std::list<int> surface_atoms;
125 >  FILE *outdummy = NULL;
126 >  FILE *errdummy = NULL;
127 >  
128 >  pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
129 >  
130 >  
131 >  for (int i = 0; i < numpoints; i++) {
132 >    pt_array[dim_ * i] = pos[i][0];
133 >    pt_array[dim_ * i + 1] = pos[i][1];
134 >    pt_array[dim_ * i + 2] = pos[i][2];
135    }
136    
137    
80 –  qh_initflags (const_cast<char *>(options_.c_str()));
81 –  qh_init_B (points, numpoints, dim_, ismalloc);
82 –  qh_qhull();
83 –  qh_check_output();
138    
139    
140 +  /*
141 +    qh_initflags(const_cast<char *>(options_.c_str()));
142 +    qh_init_B(pospoints, numpoints, dim_, ismalloc);
143 +    qh_qhull();
144 +    qh_check_output();
145 +
146 +    qh_produce_output();
147 +  */
148 +  boolT ismalloc = False;
149    
150 +  if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
151 +                    const_cast<char *>(options_.c_str()), NULL, stderr)) {
152 +    
153 +    vertexT *vertex, **vertexp;
154 +    facetT *facet;
155 +    setT *vertices;
156 +    unsigned int nf = qh num_facets;
157 +    
158 +    //Matrix idx(nf, dim);
159 +    /*
160 +      int j, i = 0, id = 0;
161 +      
162 +      int id2 = 0;
163 +      coordT *point,**pointp;
164 +      realT dist;
165 +      FORALLfacets {
166 +      j = 0;
167 +      
168 +      if (!facet->simplicial){
169 +      // should never happen with Qt
170 +      sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
171 +      painCave.isFatal = 0;
172 +      simError();
173 +      }
174 +                        
175 +      vertices = qh_facet3vertex(facet);
176 +      FOREACHvertex_(vertices){
177 +      id = qh_pointid(vertex->point);
178 +      surface_atoms.push_back(id);
179 +      //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
180 +      }
181 +      qh_settempfree(&vertices);
182 +      
183 +      FOREACHpoint_(facet->coplanarset){
184 +      vertex= qh_nearvertex (facet, point, &dist);
185 +      //id= qh_pointid (vertex->point);
186 +      id2= qh_pointid (point);
187 +      surface_atoms.push_back(id2);
188 +      //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
189 +      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
190 +      //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
191 +                                        
192 +      }
193 +      
194 +      }
195 +                
196 + */
197 +                
198 +                
199 +  }
200 +
201 +
202 +
203 +
204    qh_getarea(qh facet_list);
205 <  volume_ = qh totvol;                                                  
206 <  area_ = qh totarea;                                          
205 >  volume_ = qh totvol;
206 >  area_ = qh totarea;
207 >  //    FILE *newGeomFile;
208    
209    
210 +  /*
211 +    FORALLfacets {
212 +    for (int k=0; k < qh hull_dim; k++)
213 +    printf ("%6.2g ", facet->normal[k]);
214 +    printf ("\n");
215 +    }
216 +  */
217    
218 +  int curlong,totlong;
219 +  //    geomviewHull("junk.off");
220    qh_freeqhull(!qh_ALL);
221 <  qh_memfreeshort (&curlong, &totlong);
221 >  qh_memfreeshort(&curlong, &totlong);
222    if (curlong || totlong)
223 <    fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
224 <             totlong, curlong);
223 >    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
224 >              << totlong << curlong << std::endl;
225 >  free(pt_array);
226 >  /*
227 >    int j = 0;
228 >    surface_atoms.sort();
229 >    surface_atoms.unique();
230 >    surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
231 >    for(std::list<int>::iterator list_iter = surface_atoms.begin();
232 >    list_iter != surface_atoms.end(); list_iter++)
233 >    {
234 >    int i = *list_iter;
235 >    //surfpt_array[dim_ * j] = pos[i][0];
236 >    //surfpt_array[dim_ * j + 1] = pos[i][1];
237 >    //surfpt_array[dim_ * j + 2] = pos[i][2];
238 >    std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
239 >    j++;
240 >    }
241 >  */    
242    
243 <  
243 >  /*    
244 >        std::string deloptions_ = "qhull d Qt";
245 >        facetT *facet, *neighbor;
246 >        ridgeT *ridge, **ridgep;
247 >        
248 >        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
249 >        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
250 >        
251 >        qh visit_id++;
252 >        FORALLfacets {
253 >        if (!facet->upperdelaunay) {
254 >        facet->visitid= qh visit_id;
255 >        qh_makeridges(facet);
256 >        FOREACHridge_(facet->ridges) {
257 >        neighbor= otherfacet_(ridge, facet);
258 >        if (neighbor->visitid != qh visit_id) {
259 >        
260 >        FOREACHvertex_(ridge->vertices)
261 >        int id2 = qh_pointid (vertex->point);
262 >        std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
263 >        }
264 >        }
265 >        }
266 >        
267 >
268 >
269 >        
270 >        }
271 >
272 >        qh_freeqhull(!qh_ALL);
273 >        qh_memfreeshort(&curlong, &totlong);
274 >        if (curlong || totlong)
275 >        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
276 >        << totlong << curlong << std::endl;
277 >        free(surfpt_array);
278 >  */            
279    return true;
280   }
281  
282  
283 < RealType ConvexHull::getVolume() {
283 >
284 > RealType ConvexHull::getVolume()
285 > {
286    return volume_;
287   }
288  
289 < void ConvexHull::geomviewHull(const std::string& geomFileName) {
289 > void ConvexHull::geomviewHull(const std::string& geomFileName)
290 > {
291 >
292 >  FILE *newGeomFile;
293    
110 –  std::ofstream newGeomFile;
111 –  
294    //create new .md file based on old .md file
295 <  newGeomFile.open(geomFileName.c_str());
295 >  newGeomFile = fopen(geomFileName.c_str(), "w");
296 >  qh_findgood_all(qh facet_list);
297 >  for (int i = 0; i < qh_PRINTEND; i++)
298 >    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
299    
300 <  
116 <  newGeomFile.close();
300 >  fclose(newGeomFile);
301   }
302 + #endif //QHULL
303 + #endif //CGAL
304 +
305 +
306 +

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