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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
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1 #include "ReadTetGen.hpp"
2 #include "moab/Interface.hpp"
3 #include "moab/Range.hpp"
4 #include "moab/ReadUtilIface.hpp"
5 #include "moab/FileOptions.hpp"
6 #include "MBTagConventions.hpp"
7 #include <iostream>
8 #include <fstream>
9 #include <sstream>
10 #include <cctype>
11 #include <map>
12
13 namespace moab
14 {
15
16 ReaderIface* ReadTetGen::factory( Interface* moab )
17 {
18 return new ReadTetGen( moab );
19 }
20
21 ReadTetGen::ReadTetGen( Interface* moab ) : mbIface( moab ), readTool( 0 )
22 {
23 moab->query_interface( readTool );
24 }
25
26 ReadTetGen::~ReadTetGen()
27 {
28 if( mbIface && readTool ) mbIface->release_interface( readTool );
29 }
30
31 ErrorCode ReadTetGen::open_file( const std::string& filename,
32 const std::string& basename,
33 const std::string& suffix,
34 const char* exp_suffix,
35 const char* opt_name,
36 const FileOptions& opts,
37 std::ifstream& file_stream,
38 bool file_required )
39 {
40 std::string real_file_name;
41 ErrorCode rval = opts.get_option( opt_name, real_file_name );
42 if( MB_ENTITY_NOT_FOUND == rval || real_file_name.empty() )
43 {
44 if( MB_SUCCESS == rval ) file_required = true;
45 if( suffix == exp_suffix )
46 {
47 real_file_name = filename;
48 }
49 else
50 {
51 real_file_name = basename;
52 real_file_name += ".";
53 real_file_name += exp_suffix;
54 }
55 }
56
57 if( !real_file_name.empty() ) file_stream.open( real_file_name.c_str(), std::ios::in );
58 if( file_required && !file_stream.is_open() )
59 {
60 MB_SET_ERR( MB_FILE_DOES_NOT_EXIST, real_file_name << ": cannot read file" );
61 }
62
63 return MB_SUCCESS;
64 }
65
66 ErrorCode ReadTetGen::read_tag_values( const char* /* file_name */,
67 const char* /* tag_name */,
68 const FileOptions& /* opts */,
69 std::vector< int >& /* tag_values_out */,
70 const SubsetList* /* subset_list */ )
71 {
72 return MB_NOT_IMPLEMENTED;
73 }
74
75 ErrorCode ReadTetGen::load_file( const char* file_name_c,
76 const EntityHandle* /* file_set */,
77 const FileOptions& opts,
78 const ReaderIface::SubsetList* subset_list,
79 const Tag* file_id_tag )
80 {
81 std::ifstream node_file, ele_file, face_file, edge_file;
82 ErrorCode rval;
83
84 if( subset_list )
85 {
86 MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Reading subset of files not supported for TetGen" );
87 }
88
89 std::string suffix, base, filename( file_name_c );
90 size_t dot_idx = filename.find_last_of( '.' );
91 if( dot_idx == std::string::npos )
92 {
93 base = filename;
94 }
95 else
96 {
97 suffix = filename.substr( dot_idx + 1 );
98 for( size_t i = 0; i < suffix.length(); ++i )
99 suffix[i] = (char)tolower( suffix[i] );
100 if( suffix == "node" || suffix == "ele" || suffix == "face" || suffix == "edge" )
101 {
102 base = filename.substr( 0, dot_idx );
103 }
104 else
105 {
106 base = filename;
107 suffix.clear();
108 }
109 }
110
111 rval = open_file( filename, base, suffix, "node", "NODE_FILE", opts, node_file, true );
112 if( MB_SUCCESS != rval ) return rval;
113 rval = open_file( filename, base, suffix, "ele", "ELE_FILE", opts, ele_file );
114 if( MB_SUCCESS != rval ) return rval;
115 rval = open_file( filename, base, suffix, "face", "FACE_FILE", opts, face_file );
116 if( MB_SUCCESS != rval ) return rval;
117 rval = open_file( filename, base, suffix, "edge", "EDGE_FILE", opts, edge_file );
118 if( MB_SUCCESS != rval ) return rval;
119
120 std::vector< Tag > attr_tags[4];
121 std::vector< int > attr_idx[4];
122 const char* option_names[4] = { "NODE_ATTR_LIST", "EDGE_ATTR_LIST", "TRI_ATTR_LIST", "TET_ATTR_LIST" };
123 const char* group_names[4] = { 0, "CURVE_ID", "SURFACE_ID", "VOLUME_ID" };
124 for( int i = 0; i < 4; ++i )
125 {
126 std::string opt_str;
127 rval = opts.get_str_option( option_names[i], opt_str );
128 if( MB_SUCCESS != rval ) continue;
129 rval = parse_attr_list( opt_str, attr_tags[i], attr_idx[i], group_names[i] );
130 if( MB_SUCCESS != rval )
131 {
132 MB_SET_ERR( MB_TYPE_OUT_OF_RANGE, option_names[i] << ": invalid option value" );
133 }
134 }
135
136 Range tets, tris, edges;
137 std::vector< EntityHandle > nodes;
138 rval = read_node_file( node_file, &attr_tags[0][0], &attr_idx[0][0], attr_tags[0].size(), nodes );
139 if( MB_SUCCESS == rval && ele_file.is_open() ) rval = read_elem_file( MBTET, ele_file, nodes, tets );
140 if( MB_SUCCESS == rval && face_file.is_open() ) rval = read_elem_file( MBTRI, face_file, nodes, tris );
141 if( MB_SUCCESS == rval && edge_file.is_open() ) rval = read_elem_file( MBEDGE, edge_file, nodes, edges );
142
143 if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, &nodes[0], nodes.size() );
144 if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, edges );
145 if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, tris );
146 if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, tets );
147
148 return rval;
149 }
150
151 ErrorCode ReadTetGen::parse_attr_list( const std::string& option_str,
152 std::vector< Tag >& tag_list,
153 std::vector< int >& index_list,
154 const char* group_designator )
155 {
156 std::vector< std::string > name_list;
157 size_t prev_pos = 0;
158 while( prev_pos != std::string::npos )
159 {
160 size_t pos = option_str.find_first_of( ',', prev_pos );
161 name_list.push_back( option_str.substr( prev_pos, pos ) );
162 prev_pos = pos + 1;
163 }
164
165 index_list.resize( name_list.size() );
166 std::map< std::string, int > name_count;
167 for( size_t i = 0; i < name_list.size(); ++i )
168 index_list[i] = name_count[name_list[i]]++;
169
170 for( size_t i = 0; i < name_list.size(); ++i )
171 {
172 if( group_designator && name_list[i] == group_designator )
173 {
174 tag_list[i] = 0;
175 index_list[i] = -1;
176 }
177 else if( name_list.empty() )
178 {
179 tag_list[i] = 0;
180 index_list[i] = 0;
181 }
182 else
183 {
184 ErrorCode rval = mbIface->tag_get_handle( name_list[i].c_str(), name_count[name_list[i]], MB_TYPE_DOUBLE,
185 tag_list[i], MB_TAG_DENSE | MB_TAG_CREAT );
186 if( MB_SUCCESS != rval ) return rval;
187 }
188 }
189
190 return MB_SUCCESS;
191 }
192
193 ErrorCode ReadTetGen::read_line( std::istream& file, std::string& line, int& lineno )
194 {
195 // Loop until we find a non-empty line
196 do
197 {
198 // Read a line
199 line.clear();
200 if( !getline( file, line ) ) return MB_FILE_WRITE_ERROR;
201 ++lineno;
202 // Strip comments from line
203 size_t pos = line.find_first_of( '#' );
204 if( pos != std::string::npos ) line = line.substr( 0, pos );
205 // Strip leading whitespace from line
206 for( pos = 0; pos < line.length() && isspace( line[pos] ); ++pos )
207 ;
208 if( pos == line.length() )
209 line.clear();
210 else if( pos != 0 )
211 line = line.substr( pos );
212 } while( line.empty() );
213
214 return MB_SUCCESS;
215 }
216
217 ErrorCode ReadTetGen::read_line( std::istream& file, double* values_out, int num_values, int& lineno )
218 {
219 // Get a line of text
220 std::string line;
221 ErrorCode rval = read_line( file, line, lineno );
222 if( MB_SUCCESS != rval ) return rval;
223
224 // Tokenize line as doubles
225 std::stringstream str( line );
226 for( int i = 0; i < num_values; ++i )
227 {
228 double v;
229 if( !( str >> v ) )
230 {
231 MB_SET_ERR( MB_FAILURE, "Error reading node data at line " << lineno );
232 }
233 values_out[i] = v;
234 }
235
236 // Check that we're at the end of the line
237 int junk;
238 if( ( str >> junk ) || !str.eof() )
239 {
240 MB_SET_ERR( MB_FAILURE, "Unexpected trailing data for line " << lineno << " of node data" );
241 }
242
243 return MB_SUCCESS;
244 }
245
246 ErrorCode ReadTetGen::read_node_file( std::istream& file,
247 const Tag* attr_tag_list,
248 const int* attr_tag_index,
249 int attr_tag_list_len,
250 std::vector< EntityHandle >& nodes )
251 {
252 int lineno = 0;
253 ErrorCode rval;
254
255 double header_vals[4];
256 rval = read_line( file, header_vals, 4, lineno );
257 if( MB_SUCCESS != rval ) return rval;
258
259 const int num_vtx = (int)header_vals[0];
260 const int dim = (int)header_vals[1];
261 const int num_attr = (int)header_vals[2];
262 const int bdry_flag = (int)header_vals[3];
263 if( num_vtx < 1 || dim < 2 || dim > 3 || num_attr < 0 || bdry_flag < 0 || bdry_flag > 1 )
264 {
265 MB_SET_ERR( MB_FAILURE, "Invalid header line for node data" );
266 }
267 if( attr_tag_list_len > num_attr ) attr_tag_list_len = num_attr;
268
269 // Allocate space for tag data
270 std::map< Tag, int > tag_size;
271 std::map< Tag, std::vector< double > > tag_data;
272 for( int i = 0; i < attr_tag_list_len; ++i )
273 {
274 if( !attr_tag_list[i] || attr_tag_index[i] < 0 ) continue;
275 std::vector< double >& data = tag_data[attr_tag_list[i]];
276 // Increase tag size by one value per vertex for each time
277 // we encounter it in the list.
278 data.resize( data.size() + num_vtx );
279 ++tag_size[attr_tag_list[i]];
280 }
281 std::vector< double* > attr_data( attr_tag_list_len );
282 std::vector< int > attr_size( attr_tag_list_len );
283 for( int i = 0; i < attr_tag_list_len; ++i )
284 {
285 if( !attr_tag_list[i] || attr_tag_index[i] < 0 )
286 {
287 attr_data[i] = 0;
288 attr_size[i] = 0;
289 }
290 else
291 {
292 attr_data[i] = &( tag_data[attr_tag_list[i]] )[0];
293 attr_size[i] = tag_size[attr_tag_list[i]];
294 }
295 }
296
297 // Allocate vertices
298 std::vector< double* > coords;
299 EntityHandle start_handle;
300 rval = readTool->get_node_coords( dim, num_vtx, 1, start_handle, coords );
301 if( MB_SUCCESS != rval ) return rval;
302
303 // Read data line for each node
304 nodes.reserve( num_vtx );
305 std::vector< double > data( 1 + dim + num_attr + bdry_flag );
306 std::vector< int > ids( num_vtx );
307 for( int i = 0; i < num_vtx; ++i )
308 {
309 rval = read_line( file, &data[0], data.size(), lineno );
310 if( MB_SUCCESS != rval ) return rval;
311
312 // Get ID
313 ids[i] = (int)data[0];
314 if( ids[i] >= (int)nodes.size() ) nodes.resize( ids[i] + 1 );
315 nodes[ids[i]] = start_handle + i;
316
317 // Get coordinates
318 // Cppcheck warning (false positive): variable coords is assigned a value that is never used
319 for( int j = 0; j < dim; ++j )
320 coords[j][i] = data[j + 1];
321
322 // Get attribute data
323 for( int j = 0; j < attr_tag_list_len; ++j )
324 if( attr_data[j] ) attr_data[j][i * attr_size[j] + attr_tag_index[j]] = data[j + 1 + dim];
325
326 // Discard boundary bit
327 }
328
329 // Store tag data
330 Range node_range;
331 node_range.insert( start_handle, start_handle + num_vtx - 1 );
332 for( std::map< Tag, std::vector< double > >::iterator i = tag_data.begin(); i != tag_data.end(); ++i )
333 {
334 rval = mbIface->tag_set_data( i->first, node_range, &i->second[0] );
335 if( MB_SUCCESS != rval ) return rval;
336 }
337 Tag idtag = mbIface->globalId_tag();
338
339 rval = mbIface->tag_set_data( idtag, node_range, &ids[0] );
340 if( MB_SUCCESS != rval ) return rval;
341
342 return MB_SUCCESS;
343 }
344
345 ErrorCode ReadTetGen::read_elem_file( EntityType type,
346 std::istream& file,
347 const std::vector< EntityHandle >& nodes,
348 Range& elems )
349 {
350 int lineno = 0;
351 ErrorCode rval;
352
353 int node_per_elem, have_group_id, dim;
354 double header_vals[3];
355 switch( type )
356 {
357 case MBTET:
358 rval = read_line( file, header_vals, 3, lineno );
359 node_per_elem = (int)header_vals[1];
360 have_group_id = (int)header_vals[2];
361 dim = 3;
362 break;
363 case MBTRI:
364 rval = read_line( file, header_vals, 2, lineno );
365 node_per_elem = 3;
366 have_group_id = (int)header_vals[1];
367 dim = 2;
368 break;
369 case MBEDGE:
370 rval = read_line( file, header_vals, 1, lineno );
371 node_per_elem = 2;
372 have_group_id = 0;
373 dim = 1;
374 break;
375 default:
376 rval = MB_FAILURE;
377 break;
378 }
379 if( MB_SUCCESS != rval ) return rval;
380 const int num_elem = (int)header_vals[0];
381 if( num_elem < 1 || node_per_elem < 2 || have_group_id < 0 || have_group_id > 1 )
382 {
383 MB_SET_ERR( MB_FAILURE, "Invalid header line for element data" );
384 }
385
386 // Create group map
387 std::map< double, EntityHandle > groups;
388 Tag dim_tag, id_tag;
389 id_tag = mbIface->globalId_tag();
390
391 const int negone = -1;
392 rval = mbIface->tag_get_handle( GEOM_DIMENSION_TAG_NAME, 1, MB_TYPE_INTEGER, dim_tag, MB_TAG_SPARSE | MB_TAG_CREAT,
393 &negone );
394 if( MB_SUCCESS != rval ) return rval;
395
396 // Allocate elements
397 EntityHandle start_handle, *conn_array;
398 rval = readTool->get_element_connect( num_elem, node_per_elem, type, 1, start_handle, conn_array );
399 if( MB_SUCCESS != rval ) return rval;
400 elems.insert( start_handle, start_handle + num_elem - 1 );
401
402 // Read data line for each node
403 std::vector< double > data( 1 + node_per_elem + have_group_id );
404 std::vector< int > ids( num_elem );
405 for( int i = 0; i < num_elem; ++i )
406 {
407 rval = read_line( file, &data[0], data.size(), lineno );
408 if( MB_SUCCESS != rval ) return rval;
409
410 // Get ID
411 ids[i] = (int)data[0];
412
413 // Get connectivity
414 for( int j = 0; j < node_per_elem; ++j )
415 conn_array[node_per_elem * i + j] = nodes[(int)data[j + 1]];
416
417 // Grouping
418 if( have_group_id && 0.0 != data[node_per_elem + 1] )
419 {
420 double id = data[node_per_elem + 1];
421 EntityHandle grp = groups[id];
422 if( 0 == grp )
423 {
424 rval = mbIface->create_meshset( MESHSET_SET, grp );
425 if( MB_SUCCESS != rval ) return rval;
426 elems.insert( grp );
427 rval = mbIface->tag_set_data( dim_tag, &grp, 1, &dim );
428 if( MB_SUCCESS != rval ) return rval;
429 int iid = (int)id;
430 rval = mbIface->tag_set_data( id_tag, &grp, 1, &iid );
431 if( MB_SUCCESS != rval ) return rval;
432 groups[id] = grp;
433 }
434 EntityHandle handle = start_handle + i;
435 rval = mbIface->add_entities( grp, &handle, 1 );
436 if( MB_SUCCESS != rval ) return rval;
437 }
438 }
439
440 // Store id data
441 Range elems2;
442 elems2.insert( start_handle, start_handle + num_elem - 1 );
443 rval = mbIface->tag_set_data( id_tag, elems2, &ids[0] );
444 if( MB_SUCCESS != rval ) return rval;
445
446 return MB_SUCCESS;
447 }
448
449 } // namespace moab
1.9.1.