Mesh Oriented datABase  (version 5.5.1)
An array-based unstructured mesh library
MergeMesh.cpp
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1 #include "moab/MergeMesh.hpp"
2 
3 #include "moab/Skinner.hpp"
5 #include "moab/Range.hpp"
6 #include "moab/CartVect.hpp"
7 
8 #include "Internals.hpp"
9 #include <vector>
10 #include <algorithm>
11 #include <string>
12 #include <vector>
13 #include <cassert>
14 #include <iostream>
15 #include <iomanip>
16 
17 #include <cstdlib>
18 
19 namespace moab
20 {
21 
22 MergeMesh::MergeMesh( Interface* impl, bool printErrorIn )
23  : mbImpl( impl ), mbMergeTag( 0 ), mergeTol( 0.001 ), mergeTolSq( 0.000001 ), printError( printErrorIn )
24 {
25 }
26 
28 {
30  mbMergeTag = NULL;
31 }
32 
34  int elems_size,
35  const double merge_tol,
36  const int do_merge,
37  const int update_sets,
38  Tag merge_tag,
39  bool do_higher_dim )
40 {
41  mergeTol = merge_tol;
42  mergeTolSq = merge_tol * merge_tol;
43  Range tmp_elems;
44  tmp_elems.insert( elems, elems + elems_size );
45  ErrorCode result = merge_entities( tmp_elems, merge_tol, do_merge, update_sets, (Tag)merge_tag, do_higher_dim );
46 
47  return result;
48 }
49 
50 /* This function appears to be not necessary after MOAB conversion
51 
52  void MergeMesh::perform_merge(iBase_TagHandle merge_tag)
53  {
54  // put into a range
55  ErrorCode result = perform_merge((Tag) merge_tag);
56  if (result != MB_SUCCESS)
57  throw MKException(iBase_FAILURE, "");
58  }*/
59 
61  const double merge_tol,
62  const int do_merge,
63  const int,
64  Tag merge_tag,
65  bool merge_higher_dim )
66 {
67  // If merge_higher_dim is true, do_merge must also be true
68  if( merge_higher_dim && !do_merge )
69  {
70  return MB_FAILURE;
71  }
72 
73  mergeTol = merge_tol;
74  mergeTolSq = merge_tol * merge_tol;
75 
76  // get the skin of the entities
77  Skinner skinner( mbImpl );
78  Range skin_range;
79  ErrorCode result = skinner.find_skin( 0, elems, 0, skin_range, false, false );
80  if( MB_SUCCESS != result ) return result;
81 
82  // create a tag to mark merged-to entity; reuse tree_root
83  EntityHandle tree_root = 0;
84  if( 0 == merge_tag )
85  {
86  result = mbImpl->tag_get_handle( "__merge_tag", 1, MB_TYPE_HANDLE, mbMergeTag, MB_TAG_DENSE | MB_TAG_EXCL,
87  &tree_root );
88  if( MB_SUCCESS != result ) return result;
89  }
90  else
91  mbMergeTag = merge_tag;
92 
93  // build a kd tree with the vertices
94  AdaptiveKDTree kd( mbImpl );
95  result = kd.build_tree( skin_range, &tree_root );
96  if( MB_SUCCESS != result ) return result;
97 
98  // find matching vertices, mark them
99  result = find_merged_to( tree_root, kd, mbMergeTag );
100  if( MB_SUCCESS != result ) return result;
101 
102  // merge them if requested
103  if( do_merge )
104  {
105  result = perform_merge( mbMergeTag );
106  if( MB_SUCCESS != result ) return result;
107  }
108 
109  if( merge_higher_dim && deadEnts.size() != 0 )
110  {
111  result = merge_higher_dimensions( elems );
112  if( MB_SUCCESS != result ) return result;
113  }
114 
115  return MB_SUCCESS;
116 }
117 
118 ErrorCode MergeMesh::merge_all( EntityHandle meshset, const double merge_tol )
119 {
120  ErrorCode rval;
121  if( 0 == mbMergeTag )
122  {
123  EntityHandle def_val = 0;
125  &def_val );MB_CHK_ERR( rval );
126  }
127  // get all entities;
128  // get all vertices connected
129  // build a kdtree
130  // find merged to
131  mergeTol = merge_tol;
132  mergeTolSq = merge_tol * merge_tol;
133 
134  // get all vertices
135  Range entities;
136  rval = mbImpl->get_entities_by_handle( meshset, entities, /*recursive*/ true );MB_CHK_ERR( rval );
137  Range sets = entities.subset_by_type( MBENTITYSET );
138  entities = subtract( entities, sets );
139  Range verts;
140  rval = mbImpl->get_connectivity( entities, verts );MB_CHK_ERR( rval );
141 
142  // build a kd tree with the vertices
143  AdaptiveKDTree kd( mbImpl );
144  EntityHandle tree_root;
145  rval = kd.build_tree( verts, &tree_root );MB_CHK_ERR( rval );
146  // find matching vertices, mark them
147  rval = find_merged_to( tree_root, kd, mbMergeTag );MB_CHK_ERR( rval );
148 
149  rval = perform_merge( mbMergeTag );MB_CHK_ERR( rval );
150 
151  if( deadEnts.size() != 0 )
152  {
153  rval = merge_higher_dimensions( entities );MB_CHK_ERR( rval );
154  }
155  return MB_SUCCESS;
156 }
158 {
159  // we start with an empty range of vertices that are "merged to"
160  // they are used (eventually) for higher dim entities
161  mergedToVertices.clear();
162  ErrorCode result;
163  if( deadEnts.size() == 0 )
164  {
165  if( printError ) std::cout << "\nWarning: Geometries don't have a common face; Nothing to merge" << std::endl;
166  return MB_SUCCESS; // nothing to merge carry on with the program
167  }
168  if( mbImpl->type_from_handle( *deadEnts.begin() ) != MBVERTEX ) return MB_FAILURE;
169  std::vector< EntityHandle > merge_tag_val( deadEnts.size() );
170  Range deadEntsRange;
171  std::copy( deadEnts.rbegin(), deadEnts.rend(), range_inserter( deadEntsRange ) );
172  result = mbImpl->tag_get_data( merge_tag, deadEntsRange, &merge_tag_val[0] );
173  if( MB_SUCCESS != result ) return result;
174 
175  std::set< EntityHandle >::iterator rit;
176  unsigned int i;
177  for( rit = deadEnts.begin(), i = 0; rit != deadEnts.end(); ++rit, i++ )
178  {
179  assert( merge_tag_val[i] );
180  if( MBVERTEX == TYPE_FROM_HANDLE( merge_tag_val[i] ) ) mergedToVertices.insert( merge_tag_val[i] );
181  result = mbImpl->merge_entities( merge_tag_val[i], *rit, false, false );
182  if( MB_SUCCESS != result )
183  {
184  return result;
185  }
186  }
187  result = mbImpl->delete_entities( deadEntsRange );
188  return result;
189 }
190 // merge vertices according to an input tag
191 // merge them if the tags are equal
192 struct handle_id
193 {
195  int val;
196 };
197 
198 // handle structure comparison function for qsort
199 // if the id is the same , compare the handle.
200 int compare_handle_id( const void* a, const void* b )
201 {
202 
203  handle_id* ia = (handle_id*)a;
204  handle_id* ib = (handle_id*)b;
205  if( ia->val == ib->val )
206  {
207  return ( ia->eh < ib->eh ) ? -1 : 1;
208  }
209  else
210  {
211  return ( ia->val - ib->val );
212  }
213 }
214 
216 {
217  ErrorCode rval;
218  DataType tag_type;
219  rval = mbImpl->tag_get_data_type( user_tag, tag_type );
220  if( rval != MB_SUCCESS || tag_type != MB_TYPE_INTEGER ) return MB_FAILURE;
221 
222  std::vector< int > vals( verts.size() );
223  rval = mbImpl->tag_get_data( user_tag, verts, &vals[0] );
224  if( rval != MB_SUCCESS ) return rval;
225 
226  if( 0 == merge_tag )
227  {
228  EntityHandle def_val = 0;
230  &def_val );
231  if( MB_SUCCESS != rval ) return rval;
232  }
233  else
234  mbMergeTag = merge_tag;
235 
236  std::vector< handle_id > handles( verts.size() );
237  int i = 0;
238  for( Range::iterator vit = verts.begin(); vit != verts.end(); ++vit )
239  {
240  handles[i].eh = *vit;
241  handles[i].val = vals[i];
242  i++;
243  }
244  // std::sort(handles.begin(), handles.end(), compare_handle_id);
245  qsort( &handles[0], handles.size(), sizeof( handle_id ), compare_handle_id );
246  i = 0;
247  while( i < (int)verts.size() - 1 )
248  {
249  handle_id first = handles[i];
250  int j = i + 1;
251  while( j < (int)verts.size() && handles[j].val == first.val )
252  {
253  rval = mbImpl->tag_set_data( mbMergeTag, &( handles[j].eh ), 1, &( first.eh ) );
254  if( rval != MB_SUCCESS ) return rval;
255  deadEnts.insert( handles[j].eh );
256  j++;
257  }
258  i = j;
259  }
260 
261  rval = perform_merge( mbMergeTag );
262 
263  return rval;
264 }
266 {
267  AdaptiveKDTreeIter iter;
268 
269  // evaluate vertices in this leaf
270  Range leaf_range, leaf_range2;
271  std::vector< EntityHandle > sorted_leaves;
272  std::vector< double > coords;
273  std::vector< EntityHandle > merge_tag_val, leaves_out;
274 
275  ErrorCode result = tree.get_tree_iterator( tree_root, iter );
276  if( MB_SUCCESS != result ) return result;
277  while( result == MB_SUCCESS )
278  {
279  sorted_leaves.push_back( iter.handle() );
280  result = iter.step();
281  }
282  if( result != MB_ENTITY_NOT_FOUND ) return result;
283  std::sort( sorted_leaves.begin(), sorted_leaves.end() );
284 
285  std::vector< EntityHandle >::iterator it;
286  for( it = sorted_leaves.begin(); it != sorted_leaves.end(); ++it )
287  {
288 
289  leaf_range.clear();
290  result = mbImpl->get_entities_by_handle( *it, leaf_range );
291  if( MB_SUCCESS != result ) return result;
292  coords.resize( 3 * leaf_range.size() );
293  merge_tag_val.resize( leaf_range.size() );
294  result = mbImpl->get_coords( leaf_range, &coords[0] );
295  if( MB_SUCCESS != result ) return result;
296  result = mbImpl->tag_get_data( merge_tag, leaf_range, &merge_tag_val[0] );
297  if( MB_SUCCESS != result ) return result;
298  Range::iterator rit;
299  unsigned int i;
300  bool inleaf_merged, outleaf_merged = false;
301  unsigned int lr_size = leaf_range.size();
302 
303  for( i = 0, rit = leaf_range.begin(); i != lr_size; ++rit, i++ )
304  {
305  if( 0 != merge_tag_val[i] ) continue;
306  CartVect from( &coords[3 * i] );
307  inleaf_merged = false;
308 
309  // check close-by leaves too
310  leaves_out.clear();
311  result =
312  tree.distance_search( from.array(), mergeTol, leaves_out, mergeTol, 1.0e-6, NULL, NULL, &tree_root );
313  leaf_range2.clear();
314  for( std::vector< EntityHandle >::iterator vit = leaves_out.begin(); vit != leaves_out.end(); ++vit )
315  {
316  if( *vit > *it )
317  { // if we haven't visited this leaf yet in the outer loop
318  result = mbImpl->get_entities_by_handle( *vit, leaf_range2, Interface::UNION );
319  if( MB_SUCCESS != result ) return result;
320  }
321  }
322  if( !leaf_range2.empty() )
323  {
324  coords.resize( 3 * ( lr_size + leaf_range2.size() ) );
325  merge_tag_val.resize( lr_size + leaf_range2.size() );
326  result = mbImpl->get_coords( leaf_range2, &coords[3 * lr_size] );
327  if( MB_SUCCESS != result ) return result;
328  result = mbImpl->tag_get_data( merge_tag, leaf_range2, &merge_tag_val[lr_size] );
329  if( MB_SUCCESS != result ) return result;
330  outleaf_merged = false;
331  }
332 
333  // check other verts in this leaf
334  for( unsigned int j = i + 1; j < merge_tag_val.size(); j++ )
335  {
336  EntityHandle to_ent = j >= lr_size ? leaf_range2[j - lr_size] : leaf_range[j];
337 
338  if( *rit == to_ent ) continue;
339 
340  if( ( from - CartVect( &coords[3 * j] ) ).length_squared() < mergeTolSq )
341  {
342  merge_tag_val[j] = *rit;
343  if( j < lr_size )
344  {
345  inleaf_merged = true;
346  }
347  else
348  {
349  outleaf_merged = true;
350  }
351  deadEnts.insert( to_ent );
352  }
353  }
354  if( outleaf_merged )
355  {
356  result = mbImpl->tag_set_data( merge_tag, leaf_range2, &merge_tag_val[leaf_range.size()] );
357  if( MB_SUCCESS != result ) return result;
358  outleaf_merged = false;
359  }
360  if( inleaf_merged )
361  {
362  result = mbImpl->tag_set_data( merge_tag, leaf_range, &merge_tag_val[0] );
363  if( MB_SUCCESS != result ) return result;
364  }
365  }
366  }
367  return MB_SUCCESS;
368 }
369 
370 // Determine which higher dimensional entities should be merged
372 {
373  // apply a different strategy
374  // look at the vertices that were merged to, earlier, and find all entities adjacent to them
375  // elems (input) are used just for initial connectivity
376  ErrorCode result;
377  Range verts;
378  result = mbImpl->get_connectivity( elems, verts );
379  if( MB_SUCCESS != result ) return result;
380 
381  // all higher dim entities that will be merged will be connected to the vertices that were
382  // merged earlier; we will look at these vertices only
383  Range mergedToVertsRange;
384  std::copy( mergedToVertices.rbegin(), mergedToVertices.rend(), range_inserter( mergedToVertsRange ) );
385  Range vertsOfInterest = intersect( mergedToVertsRange, verts );
386  // Go through each dimension
387  Range possibleEntsToMerge, conn, matches, moreDeadEnts;
388 
389  for( int dim = 1; dim < 3; dim++ )
390  {
391  moreDeadEnts.clear();
392  possibleEntsToMerge.clear();
393  result = mbImpl->get_adjacencies( vertsOfInterest, dim, false, possibleEntsToMerge, Interface::UNION );
394  if( MB_SUCCESS != result ) return result;
395  // Go through each possible entity and see if it shares vertices with another entity of same
396  // dimension
397  for( Range::iterator pit = possibleEntsToMerge.begin(); pit != possibleEntsToMerge.end(); ++pit )
398  {
399  EntityHandle eh = *pit; // possible entity to be matched
400  conn.clear();
401  // Get the vertices connected to it in a range
402 
403  result = mbImpl->get_connectivity( &eh, 1, conn );
404  if( MB_SUCCESS != result ) return result;
405  matches.clear();
406  // now retrieve all entities connected to all conn vertices
407  result = mbImpl->get_adjacencies( conn, dim, false, matches, Interface::INTERSECT );
408  if( MB_SUCCESS != result ) return result;
409  if( matches.size() > 1 )
410  {
411  for( Range::iterator matchIt = matches.begin(); matchIt != matches.end(); ++matchIt )
412  {
413  EntityHandle to_remove = *matchIt;
414  if( to_remove != eh )
415  {
416  moreDeadEnts.insert( to_remove );
417  result = mbImpl->merge_entities( eh, to_remove, false, false );
418  if( result != MB_SUCCESS ) return result;
419  possibleEntsToMerge.erase( to_remove );
420  }
421  }
422  }
423  }
424  // Delete the entities of dimension dim
425  result = mbImpl->delete_entities( moreDeadEnts );
426  if( result != MB_SUCCESS ) return result;
427  }
428  return MB_SUCCESS;
429 #if 0
430  Range skinEnts, adj, matches, moreDeadEnts;
431  ErrorCode result;
432  Skinner skinner(mbImpl);
433  //Go through each dimension
434  for (int dim = 1; dim < 3; dim++)
435  {
436  skinEnts.clear();
437  moreDeadEnts.clear();
438  result = skinner.find_skin(0, elems, dim, skinEnts, false, false);
439  //Go through each skin entity and see if it shares adjacancies with another entity
440  for (Range::iterator skinIt = skinEnts.begin();
441  skinIt != skinEnts.end(); ++skinIt)
442  {
443  adj.clear();
444  //Get the adjacencies 1 dimension lower
445  result = mbImpl->get_adjacencies(&(*skinIt), 1, dim - 1, false, adj);
446  if (result != MB_SUCCESS)
447  return result;
448  //See what other entities share these adjacencies
449  matches.clear();
450  result = mbImpl->get_adjacencies(adj, dim, false, matches,
452  if (result != MB_SUCCESS)
453  return result;
454  //If there is more than one entity, then we have some to merge and erase
455  if (matches.size() > 1)
456  {
457  for (Range::iterator matchIt = matches.begin();
458  matchIt != matches.end(); ++matchIt)
459  {
460  if (*matchIt != *skinIt)
461  {
462  moreDeadEnts.insert(*matchIt);
463  result = mbImpl->merge_entities(*skinIt, *matchIt, false, false);
464  if (result != MB_SUCCESS)
465  return result;
466  skinEnts.erase(*matchIt);
467  }
468  }
469  }
470  }
471  //Delete the entities
472  result = mbImpl->delete_entities(moreDeadEnts);
473  if (result != MB_SUCCESS)
474  return result;
475  }
476  return MB_SUCCESS;
477 #endif
478 }
479 
480 } // End namespace moab