 |
Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
|
|
Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
|
1 /**
2 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
3 * storing and accessing finite element mesh data.
4 *
5 * Copyright 2004 Sandia Corporation. Under the terms of Contract
6 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
7 * retains certain rights in this software.
8 *
9 * This library is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public
11 * License as published by the Free Software Foundation; either
12 * version 2.1 of the License, or (at your option) any later version.
13 *
14 */
15
16 /**
17 * \class ReadVtk
18 * \brief VTK reader from Mesquite
19 * \author Jason Kraftcheck
20 */
21
22 #include <cassert>
23 #include <cstdlib>
24 #include <cstring>
25
26 #include "ReadVtk.hpp"
27 #include "moab/Range.hpp"
28 #include "Internals.hpp"
29 #include "moab/Interface.hpp"
30 #include "moab/ReadUtilIface.hpp"
31 #include "moab/FileOptions.hpp"
32 #include "FileTokenizer.hpp"
33 #include "moab/VtkUtil.hpp"
34 #include "MBTagConventions.hpp"
35
36 // #define MB_VTK_MATERIAL_SETS
37 #ifdef MB_VTK_MATERIAL_SETS
38 #include <map>
39 #endif
40
41 namespace moab
42 {
43
44 #ifdef MB_VTK_MATERIAL_SETS
45
46 class Hash
47 {
48 public:
49 unsigned long value;
50
51 Hash()
52 {
53 this->value = 5381L;
54 }
55
56 Hash( const unsigned char* bytes, size_t len )
57 { // djb2, a hash by dan bernstein presented on comp.lang.c for hashing strings.
58 this->value = 5381L;
59 for( ; len; --len, ++bytes )
60 this->value = this->value * 33 + ( *bytes );
61 }
62
63 Hash( bool duh )
64 {
65 this->value = duh; // Hashing a single bit with a long is stupid but easy.
66 }
67
68 Hash( const Hash& src )
69 {
70 this->value = src.value;
71 }
72
73 Hash& operator=( const Hash& src )
74 {
75 this->value = src.value;
76 return *this;
77 }
78
79 bool operator<( const Hash& other ) const
80 {
81 return this->value < other.value;
82 }
83 };
84
85 // Pass this class opaque data + a handle and it adds the handle to a set
86 // whose opaque data has the same hash. If no set exists for the hash,
87 // it creates one. Each set is tagged with the opaque data.
88 // When entities with different opaque data have the same hash, they
89 // will be placed into the same set.
90 // There will be no collisions when the opaque data is shorter than an
91 // unsigned long, and this is really the only case we need to support.
92 // The rest is bonus. Hash does quite well with strings, even those
93 // with identical prefixes.
94 class Modulator : public std::map< Hash, EntityHandle >
95 {
96 public:
97 Modulator( Interface* iface ) : mesh( iface ) {}
98
99 ErrorCode initialize( std::string tag_name, DataType mb_type, size_t sz, size_t per_elem )
100 {
101 std::vector< unsigned char > default_val;
102 default_val.resize( sz * per_elem );
103 ErrorCode rval = this->mesh->tag_get_handle( tag_name.c_str(), per_elem, mb_type, this->tag,
104 MB_TAG_SPARSE | MB_TAG_BYTES | MB_TAG_CREAT, &default_val[0] );
105 return rval;
106 }
107
108 void add_entity( EntityHandle ent, const unsigned char* bytes, size_t len )
109 {
110 Hash h( bytes, len );
111 EntityHandle mset = this->congruence_class( h, bytes );
112 ErrorCode rval;
113 rval = this->mesh->add_entities( mset, &ent, 1 );MB_CHK_SET_ERR_RET( rval, "Failed to add entities to mesh" );
114 }
115
116 void add_entities( Range& range, const unsigned char* bytes, size_t bytes_per_ent )
117 {
118 for( Range::iterator it = range.begin(); it != range.end(); ++it, bytes += bytes_per_ent )
119 {
120 Hash h( bytes, bytes_per_ent );
121 EntityHandle mset = this->congruence_class( h, bytes );
122 ErrorCode rval;
123 rval = this->mesh->add_entities( mset, &*it, 1 );MB_CHK_SET_ERR_RET( rval, "Failed to add entities to mesh" );
124 }
125 }
126
127 EntityHandle congruence_class( const Hash& h, const void* tag_data )
128 {
129 std::map< Hash, EntityHandle >::iterator it = this->find( h );
130 if( it == this->end() )
131 {
132 EntityHandle mset;
133 Range preexist;
134 ErrorCode rval;
135 rval = this->mesh->get_entities_by_type_and_tag( 0, MBENTITYSET, &this->tag, &tag_data, 1, preexist );MB_CHK_SET_ERR_RET_VAL( rval, "Failed to get entities by type and tag", (EntityHandle)0 );
136 if( preexist.size() )
137 {
138 mset = *preexist.begin();
139 }
140 else
141 {
142 rval = this->mesh->create_meshset( MESHSET_SET, mset );MB_CHK_SET_ERR_RET_VAL( rval, "Failed to create mesh set", (EntityHandle)0 );
143 rval = this->mesh->tag_set_data( this->tag, &mset, 1, tag_data );MB_CHK_SET_ERR_RET_VAL( rval, "Failed to set tag data", (EntityHandle)0 );
144 }
145 ( *this )[h] = mset;
146 return mset;
147 }
148 return it->second;
149 }
150
151 Interface* mesh;
152 Tag tag;
153 };
154 #endif // MB_VTK_MATERIAL_SETS
155
156 ReaderIface* ReadVtk::factory( Interface* iface )
157 {
158 return new ReadVtk( iface );
159 }
160
161 ReadVtk::ReadVtk( Interface* impl ) : mdbImpl( impl ), mPartitionTagName( MATERIAL_SET_TAG_NAME )
162 {
163 mdbImpl->query_interface( readMeshIface );
164 }
165
166 ReadVtk::~ReadVtk()
167 {
168 if( readMeshIface )
169 {
170 mdbImpl->release_interface( readMeshIface );
171 readMeshIface = 0;
172 }
173 }
174
175 const char* const vtk_type_names[] = {
176 "bit", "char", "unsigned_char", "short", "unsigned_short", "int", "unsigned_int",
177 "long", "unsigned_long", "float", "double", "vtkIdType", 0 };
178
179 ErrorCode ReadVtk::read_tag_values( const char* /* file_name */,
180 const char* /* tag_name */,
181 const FileOptions& /* opts */,
182 std::vector< int >& /* tag_values_out */,
183 const SubsetList* /* subset_list */ )
184 {
185 return MB_NOT_IMPLEMENTED;
186 }
187
188 ErrorCode ReadVtk::load_file( const char* filename,
189 const EntityHandle* /* file_set */,
190 const FileOptions& opts,
191 const ReaderIface::SubsetList* subset_list,
192 const Tag* file_id_tag )
193 {
194 ErrorCode result;
195
196 int major, minor;
197 char vendor_string[257];
198 std::vector< Range > element_list;
199 Range vertices;
200
201 if( subset_list )
202 {
203 MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Reading subset of files not supported for VTK" );
204 }
205
206 // Does the caller want a field to be used for partitioning the entities?
207 // If not, we'll assume any scalar integer field named MATERIAL_SET specifies partitions.
208 std::string partition_tag_name;
209 result = opts.get_option( "PARTITION", partition_tag_name );
210 if( result == MB_SUCCESS ) mPartitionTagName = partition_tag_name;
211
212 FILE* file = fopen( filename, "r" );
213 if( !file ) return MB_FILE_DOES_NOT_EXIST;
214
215 // Read file header
216
217 if( !fgets( vendor_string, sizeof( vendor_string ), file ) )
218 {
219 fclose( file );
220 return MB_FAILURE;
221 }
222
223 if( !strchr( vendor_string, '\n' ) || 2 != sscanf( vendor_string, "# vtk DataFile Version %d.%d", &major, &minor ) )
224 {
225 fclose( file );
226 return MB_FAILURE;
227 }
228
229 if( !fgets( vendor_string, sizeof( vendor_string ), file ) )
230 {
231 fclose( file );
232 return MB_FAILURE;
233 }
234
235 // VTK spec says this should not exceed 256 chars.
236 if( !strchr( vendor_string, '\n' ) )
237 {
238 fclose( file );
239 MB_SET_ERR( MB_FAILURE, "Vendor string (line 2) exceeds 256 characters" );
240 }
241
242 // Check file type
243
244 FileTokenizer tokens( file, readMeshIface );
245 const char* const file_type_names[] = { "ASCII", "BINARY", 0 };
246 int filetype = tokens.match_token( file_type_names );
247 switch( filetype )
248 {
249 case 2: // BINARY
250 MB_SET_ERR( MB_FAILURE, "Cannot read BINARY VTK files" );
251 default: // ERROR
252 return MB_FAILURE;
253 case 1: // ASCII
254 break;
255 }
256
257 // Read the mesh
258 if( !tokens.match_token( "DATASET" ) ) return MB_FAILURE;
259 result = vtk_read_dataset( tokens, vertices, element_list );
260 if( MB_SUCCESS != result ) return result;
261
262 if( file_id_tag )
263 {
264 result = store_file_ids( *file_id_tag, vertices, element_list );
265 if( MB_SUCCESS != result ) return result;
266 }
267
268 // Count the number of elements read
269 long elem_count = 0;
270 for( std::vector< Range >::iterator it = element_list.begin(); it != element_list.end(); ++it )
271 elem_count += it->size();
272
273 // Read attribute data until end of file.
274 const char* const block_type_names[] = { "POINT_DATA", "CELL_DATA", 0 };
275 std::vector< Range > vertex_list( 1 );
276 vertex_list[0] = vertices;
277 int blocktype = 0;
278 while( !tokens.eof() )
279 {
280 // Get POINT_DATA or CELL_DATA
281 int new_block_type = tokens.match_token( block_type_names, false );
282 if( tokens.eof() ) break;
283
284 if( !new_block_type )
285 {
286 // If next token was neither POINT_DATA nor CELL_DATA,
287 // then there's another attribute under the current one.
288 if( blocktype )
289 tokens.unget_token();
290 else
291 break;
292 }
293 else
294 {
295 blocktype = new_block_type;
296 long count;
297 if( !tokens.get_long_ints( 1, &count ) ) return MB_FAILURE;
298
299 if( blocktype == 1 && (unsigned long)count != vertices.size() )
300 {
301 MB_SET_ERR( MB_FAILURE, "Count inconsistent with number of vertices at line " << tokens.line_number() );
302 }
303 else if( blocktype == 2 && count != elem_count )
304 {
305 MB_SET_ERR( MB_FAILURE, "Count inconsistent with number of elements at line " << tokens.line_number() );
306 }
307 }
308
309 if( blocktype == 1 )
310 result = vtk_read_attrib_data( tokens, vertex_list );
311 else
312 result = vtk_read_attrib_data( tokens, element_list );
313
314 if( MB_SUCCESS != result ) return result;
315 }
316
317 return MB_SUCCESS;
318 }
319
320 ErrorCode ReadVtk::allocate_vertices( long num_verts,
321 EntityHandle& start_handle_out,
322 double*& x_coord_array_out,
323 double*& y_coord_array_out,
324 double*& z_coord_array_out )
325 {
326 ErrorCode result;
327
328 // Create vertices
329 std::vector< double* > arrays;
330 start_handle_out = 0;
331 result = readMeshIface->get_node_coords( 3, num_verts, MB_START_ID, start_handle_out, arrays );
332 if( MB_SUCCESS != result ) return result;
333
334 x_coord_array_out = arrays[0];
335 y_coord_array_out = arrays[1];
336 z_coord_array_out = arrays[2];
337
338 return MB_SUCCESS;
339 }
340
341 ErrorCode ReadVtk::read_vertices( FileTokenizer& tokens, long num_verts, EntityHandle& start_handle_out )
342 {
343 ErrorCode result;
344 double *x, *y, *z;
345
346 result = allocate_vertices( num_verts, start_handle_out, x, y, z );
347 if( MB_SUCCESS != result ) return result;
348
349 // Read vertex coordinates
350 for( long vtx = 0; vtx < num_verts; ++vtx )
351 {
352 if( !tokens.get_doubles( 1, x++ ) || !tokens.get_doubles( 1, y++ ) || !tokens.get_doubles( 1, z++ ) )
353 return MB_FAILURE;
354 }
355
356 return MB_SUCCESS;
357 }
358
359 ErrorCode ReadVtk::allocate_elements( long num_elements,
360 int vert_per_element,
361 EntityType type,
362 EntityHandle& start_handle_out,
363 EntityHandle*& conn_array_out,
364 std::vector< Range >& append_to_this )
365 {
366 ErrorCode result;
367
368 start_handle_out = 0;
369 result = readMeshIface->get_element_connect( num_elements, vert_per_element, type, MB_START_ID, start_handle_out,
370 conn_array_out );
371 if( MB_SUCCESS != result ) return result;
372
373 Range range( start_handle_out, start_handle_out + num_elements - 1 );
374 append_to_this.push_back( range );
375 return MB_SUCCESS;
376 }
377
378 ErrorCode ReadVtk::vtk_read_dataset( FileTokenizer& tokens, Range& vertex_list, std::vector< Range >& element_list )
379 {
380 const char* const data_type_names[] = {
381 "STRUCTURED_POINTS", "STRUCTURED_GRID", "UNSTRUCTURED_GRID", "POLYDATA", "RECTILINEAR_GRID", "FIELD", 0 };
382 int datatype = tokens.match_token( data_type_names );
383 switch( datatype )
384 {
385 case 1:
386 return vtk_read_structured_points( tokens, vertex_list, element_list );
387 case 2:
388 return vtk_read_structured_grid( tokens, vertex_list, element_list );
389 case 3:
390 return vtk_read_unstructured_grid( tokens, vertex_list, element_list );
391 case 4:
392 return vtk_read_polydata( tokens, vertex_list, element_list );
393 case 5:
394 return vtk_read_rectilinear_grid( tokens, vertex_list, element_list );
395 case 6:
396 return vtk_read_field( tokens );
397 default:
398 return MB_FAILURE;
399 }
400 }
401
402 ErrorCode ReadVtk::vtk_read_structured_points( FileTokenizer& tokens,
403 Range& vertex_list,
404 std::vector< Range >& elem_list )
405 {
406 long i, j, k;
407 long dims[3];
408 double origin[3], space[3];
409 ErrorCode result;
410
411 if( !tokens.match_token( "DIMENSIONS" ) || !tokens.get_long_ints( 3, dims ) || !tokens.get_newline() )
412 return MB_FAILURE;
413
414 if( dims[0] < 1 || dims[1] < 1 || dims[2] < 1 )
415 {
416 MB_SET_ERR( MB_FAILURE, "Invalid dimension at line " << tokens.line_number() );
417 }
418
419 if( !tokens.match_token( "ORIGIN" ) || !tokens.get_doubles( 3, origin ) || !tokens.get_newline() )
420 return MB_FAILURE;
421
422 const char* const spacing_names[] = { "SPACING", "ASPECT_RATIO", 0 };
423 if( !tokens.match_token( spacing_names ) || !tokens.get_doubles( 3, space ) || !tokens.get_newline() )
424 return MB_FAILURE;
425
426 // Create vertices
427 double *x, *y, *z;
428 EntityHandle start_handle = 0;
429 long num_verts = dims[0] * dims[1] * dims[2];
430 result = allocate_vertices( num_verts, start_handle, x, y, z );
431 if( MB_SUCCESS != result ) return result;
432 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
433
434 for( k = 0; k < dims[2]; ++k )
435 for( j = 0; j < dims[1]; ++j )
436 for( i = 0; i < dims[0]; ++i )
437 {
438 *x = origin[0] + i * space[0];
439 ++x;
440 *y = origin[1] + j * space[1];
441 ++y;
442 *z = origin[2] + k * space[2];
443 ++z;
444 }
445
446 return vtk_create_structured_elems( dims, start_handle, elem_list );
447 }
448
449 ErrorCode ReadVtk::vtk_read_structured_grid( FileTokenizer& tokens,
450 Range& vertex_list,
451 std::vector< Range >& elem_list )
452 {
453 long num_verts, dims[3];
454 ErrorCode result;
455
456 if( !tokens.match_token( "DIMENSIONS" ) || !tokens.get_long_ints( 3, dims ) || !tokens.get_newline() )
457 return MB_FAILURE;
458
459 if( dims[0] < 1 || dims[1] < 1 || dims[2] < 1 )
460 {
461 MB_SET_ERR( MB_FAILURE, "Invalid dimension at line " << tokens.line_number() );
462 }
463
464 if( !tokens.match_token( "POINTS" ) || !tokens.get_long_ints( 1, &num_verts ) ||
465 !tokens.match_token( vtk_type_names ) || !tokens.get_newline() )
466 return MB_FAILURE;
467
468 if( num_verts != ( dims[0] * dims[1] * dims[2] ) )
469 {
470 MB_SET_ERR( MB_FAILURE, "Point count not consistent with dimensions at line " << tokens.line_number() );
471 }
472
473 // Create and read vertices
474 EntityHandle start_handle = 0;
475 result = read_vertices( tokens, num_verts, start_handle );
476 if( MB_SUCCESS != result ) return result;
477 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
478
479 return vtk_create_structured_elems( dims, start_handle, elem_list );
480 }
481
482 ErrorCode ReadVtk::vtk_read_rectilinear_grid( FileTokenizer& tokens,
483 Range& vertex_list,
484 std::vector< Range >& elem_list )
485 {
486 int i, j, k;
487 long dims[3];
488 const char* labels[] = { "X_COORDINATES", "Y_COORDINATES", "Z_COORDINATES" };
489 std::vector< double > coords[3];
490 ErrorCode result;
491
492 if( !tokens.match_token( "DIMENSIONS" ) || !tokens.get_long_ints( 3, dims ) || !tokens.get_newline() )
493 return MB_FAILURE;
494
495 if( dims[0] < 1 || dims[1] < 1 || dims[2] < 1 )
496 {
497 MB_SET_ERR( MB_FAILURE, "Invalid dimension at line " << tokens.line_number() );
498 }
499
500 for( i = 0; i < 3; i++ )
501 {
502 long count;
503 if( !tokens.match_token( labels[i] ) || !tokens.get_long_ints( 1, &count ) ||
504 !tokens.match_token( vtk_type_names ) )
505 return MB_FAILURE;
506
507 if( count != dims[i] )
508 {
509 MB_SET_ERR( MB_FAILURE, "Coordinate count inconsistent with dimensions at line " << tokens.line_number() );
510 }
511
512 coords[i].resize( count );
513 if( !tokens.get_doubles( count, &coords[i][0] ) ) return MB_FAILURE;
514 }
515
516 // Create vertices
517 double *x, *y, *z;
518 EntityHandle start_handle = 0;
519 long num_verts = dims[0] * dims[1] * dims[2];
520 result = allocate_vertices( num_verts, start_handle, x, y, z );
521 if( MB_SUCCESS != result ) return result;
522 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
523
524 // Calculate vertex coordinates
525 for( k = 0; k < dims[2]; ++k )
526 for( j = 0; j < dims[1]; ++j )
527 for( i = 0; i < dims[0]; ++i )
528 {
529 *x = coords[0][i];
530 ++x;
531 *y = coords[1][j];
532 ++y;
533 *z = coords[2][k];
534 ++z;
535 }
536
537 return vtk_create_structured_elems( dims, start_handle, elem_list );
538 }
539
540 ErrorCode ReadVtk::vtk_read_polydata( FileTokenizer& tokens, Range& vertex_list, std::vector< Range >& elem_list )
541 {
542 ErrorCode result;
543 long num_verts;
544 const char* const poly_data_names[] = { "VERTICES", "LINES", "POLYGONS", "TRIANGLE_STRIPS", 0 };
545
546 if( !tokens.match_token( "POINTS" ) || !tokens.get_long_ints( 1, &num_verts ) ||
547 !tokens.match_token( vtk_type_names ) || !tokens.get_newline() )
548 return MB_FAILURE;
549
550 if( num_verts < 1 )
551 {
552 MB_SET_ERR( MB_FAILURE, "Invalid point count at line " << tokens.line_number() );
553 }
554
555 // Create vertices and read coordinates
556 EntityHandle start_handle = 0;
557 result = read_vertices( tokens, num_verts, start_handle );
558 if( MB_SUCCESS != result ) return result;
559 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
560
561 int poly_type = tokens.match_token( poly_data_names );
562 switch( poly_type )
563 {
564 case 0:
565 result = MB_FAILURE;
566 break;
567 case 1:
568 MB_SET_ERR( MB_FAILURE, "Vertex element type at line " << tokens.line_number() );
569 break;
570 case 2:
571 MB_SET_ERR( MB_FAILURE, "Unsupported type: polylines at line " << tokens.line_number() );
572 result = MB_FAILURE;
573 break;
574 case 3:
575 result = vtk_read_polygons( tokens, start_handle, elem_list );
576 break;
577 case 4:
578 MB_SET_ERR( MB_FAILURE, "Unsupported type: triangle strips at line " << tokens.line_number() );
579 result = MB_FAILURE;
580 break;
581 }
582
583 return result;
584 }
585
586 ErrorCode ReadVtk::vtk_read_polygons( FileTokenizer& tokens, EntityHandle first_vtx, std::vector< Range >& elem_list )
587 {
588 ErrorCode result;
589 long size[2];
590
591 if( !tokens.get_long_ints( 2, size ) || !tokens.get_newline() ) return MB_FAILURE;
592
593 const Range empty;
594 std::vector< EntityHandle > conn_hdl;
595 std::vector< long > conn_idx;
596 EntityHandle first = 0, prev = 0, handle;
597 for( int i = 0; i < size[0]; ++i )
598 {
599 long count;
600 if( !tokens.get_long_ints( 1, &count ) ) return MB_FAILURE;
601 conn_idx.resize( count );
602 conn_hdl.resize( count );
603 if( !tokens.get_long_ints( count, &conn_idx[0] ) ) return MB_FAILURE;
604
605 for( long j = 0; j < count; ++j )
606 conn_hdl[j] = first_vtx + conn_idx[j];
607
608 result = mdbImpl->create_element( MBPOLYGON, &conn_hdl[0], count, handle );
609 if( MB_SUCCESS != result ) return result;
610
611 if( prev + 1 != handle )
612 {
613 if( first )
614 { // True except for first iteration (first == 0)
615 if( elem_list.empty() || first < elem_list.back().front() ) // Only need new range if order would get
616 // mixed up, or we just began inserting
617 elem_list.push_back( empty );
618 elem_list.back().insert( first, prev );
619 }
620 first = handle;
621 }
622 prev = handle;
623 }
624 if( first )
625 { // True unless no elements (size[0] == 0)
626 if( elem_list.empty() || first < elem_list.back().front() ) // Only need new range if order would get mixed
627 // up, or we just began inserting
628 elem_list.push_back( empty );
629 elem_list.back().insert( first, prev );
630 }
631
632 return MB_SUCCESS;
633 }
634
635 ErrorCode ReadVtk::vtk_read_unstructured_grid( FileTokenizer& tokens,
636 Range& vertex_list,
637 std::vector< Range >& elem_list )
638 {
639 ErrorCode result;
640 long i, num_verts, num_elems[2];
641 EntityHandle tmp_conn_list[27];
642
643 // Poorly formatted VTK legacy format document seems to
644 // lead many to think that a FIELD block can occur within
645 // an UNSTRUCTURED_GRID dataset rather than as its own data
646 // set. So allow for field data between other blocks of
647 // data.
648
649 const char* pts_str[] = { "FIELD", "POINTS", 0 };
650 while( 1 == ( i = tokens.match_token( pts_str ) ) )
651 {
652 result = vtk_read_field( tokens );
653 if( MB_SUCCESS != result ) return result;
654 }
655 if( i != 2 ) return MB_FAILURE;
656
657 if( !tokens.get_long_ints( 1, &num_verts ) || !tokens.match_token( vtk_type_names ) || !tokens.get_newline() )
658 return MB_FAILURE;
659
660 if( num_verts < 1 )
661 {
662 MB_SET_ERR( MB_FAILURE, "Invalid point count at line " << tokens.line_number() );
663 }
664
665 // Create vertices and read coordinates
666 EntityHandle first_vertex = 0;
667 result = read_vertices( tokens, num_verts, first_vertex );
668 if( MB_SUCCESS != result ) return result;
669 vertex_list.insert( first_vertex, first_vertex + num_verts - 1 );
670
671 const char* cell_str[] = { "FIELD", "CELLS", 0 };
672 while( 1 == ( i = tokens.match_token( cell_str ) ) )
673 {
674 result = vtk_read_field( tokens );
675 if( MB_SUCCESS != result ) return result;
676 }
677 if( i != 2 ) return MB_FAILURE;
678
679 if( !tokens.get_long_ints( 2, num_elems ) || !tokens.get_newline() ) return MB_FAILURE;
680
681 // Read element connectivity for all elements
682 std::vector< long > connectivity( num_elems[1] );
683 if( !tokens.get_long_ints( num_elems[1], &connectivity[0] ) ) return MB_FAILURE;
684
685 if( !tokens.match_token( "CELL_TYPES" ) || !tokens.get_long_ints( 1, &num_elems[1] ) || !tokens.get_newline() )
686 return MB_FAILURE;
687
688 // Read element types
689 std::vector< long > types( num_elems[0] );
690 if( !tokens.get_long_ints( num_elems[0], &types[0] ) ) return MB_FAILURE;
691
692 // Create elements in blocks of the same type
693 // It is important to preserve the order in
694 // which the elements were read for later reading
695 // attribute data.
696 long id = 0;
697 std::vector< long >::iterator conn_iter = connectivity.begin();
698 while( id < num_elems[0] )
699 {
700 unsigned vtk_type = types[id];
701 if( vtk_type >= VtkUtil::numVtkElemType ) return MB_FAILURE;
702
703 EntityType type = VtkUtil::vtkElemTypes[vtk_type].mb_type;
704 if( type == MBMAXTYPE )
705 {
706 MB_SET_ERR( MB_FAILURE, "Unsupported VTK element type: " << VtkUtil::vtkElemTypes[vtk_type].name << " ("
707 << vtk_type << ")" );
708 }
709
710 int num_vtx = *conn_iter;
711 if( type != MBPOLYGON && type != MBPOLYHEDRON && num_vtx != (int)VtkUtil::vtkElemTypes[vtk_type].num_nodes )
712 {
713 MB_SET_ERR( MB_FAILURE, "Cell " << id << " is of type '" << VtkUtil::vtkElemTypes[vtk_type].name
714 << "' but has " << num_vtx << " vertices" );
715 }
716
717 // Find any subsequent elements of the same type
718 // if polyhedra, need to look at the number of faces to put in the same range
719 std::vector< long >::iterator conn_iter2 = conn_iter + num_vtx + 1;
720 long end_id = id + 1;
721 if( MBPOLYHEDRON != type )
722 {
723 while( end_id < num_elems[0] && (unsigned)types[end_id] == vtk_type && *conn_iter2 == num_vtx )
724 {
725 ++end_id;
726 conn_iter2 += num_vtx + 1;
727 }
728 }
729 else
730 {
731 // advance only if next is polyhedron too, and if number of faces is the same
732 int num_faces = conn_iter[1];
733 while( end_id < num_elems[0] && (unsigned)types[end_id] == vtk_type && conn_iter2[1] == num_faces )
734 {
735 ++end_id;
736 conn_iter2 += num_vtx + 1;
737 }
738 // num_vtx becomes in this case num_faces
739 num_vtx = num_faces; // for polyhedra, this is what we want
740 // trigger vertex adjacency call
741 Range firstFaces;
742 mdbImpl->get_adjacencies( &first_vertex, 1, 2, false, firstFaces );
743 }
744
745 // Allocate element block
746 long num_elem = end_id - id;
747 EntityHandle start_handle = 0;
748 EntityHandle* conn_array;
749
750 // if type is MBVERTEX, skip, we will not create elements with one vertex
751 if( MBVERTEX == type )
752 {
753 id += num_elem;
754 conn_iter += 2 * num_elem; // skip 2 * number of 1-vertex elements
755 continue;
756 }
757
758 result = allocate_elements( num_elem, num_vtx, type, start_handle, conn_array, elem_list );
759 if( MB_SUCCESS != result ) return result;
760
761 EntityHandle* conn_sav = conn_array;
762
763 // Store element connectivity
764 if( type != MBPOLYHEDRON )
765 {
766 for( ; id < end_id; ++id )
767 {
768 if( conn_iter == connectivity.end() )
769 {
770 MB_SET_ERR( MB_FAILURE, "Connectivity data truncated at cell " << id );
771 }
772 // Make sure connectivity length is correct.
773 if( *conn_iter != num_vtx )
774 {
775 MB_SET_ERR( MB_FAILURE, "Cell " << id << " is of type '" << VtkUtil::vtkElemTypes[vtk_type].name
776 << "' but has " << num_vtx << " vertices" );
777 }
778 ++conn_iter;
779
780 for( i = 0; i < num_vtx; ++i, ++conn_iter )
781 {
782 if( conn_iter == connectivity.end() )
783 {
784 MB_SET_ERR( MB_FAILURE, "Connectivity data truncated at cell " << id );
785 }
786
787 conn_array[i] = *conn_iter + first_vertex;
788 }
789
790 const unsigned* order = VtkUtil::vtkElemTypes[vtk_type].node_order;
791 if( order )
792 {
793 assert( num_vtx * sizeof( EntityHandle ) <= sizeof( tmp_conn_list ) );
794 memcpy( tmp_conn_list, conn_array, num_vtx * sizeof( EntityHandle ) );
795 for( int j = 0; j < num_vtx; ++j )
796 conn_array[order[j]] = tmp_conn_list[j];
797 }
798
799 conn_array += num_vtx;
800 }
801 }
802 else // type == MBPOLYHEDRON
803 {
804 // in some cases, we may need to create new elements; will it screw the tags?
805 // not if the file was not from moab
806 ErrorCode rv = MB_SUCCESS;
807 for( ; id < end_id; ++id )
808 {
809 if( conn_iter == connectivity.end() )
810 {
811 MB_SET_ERR( MB_FAILURE, "Connectivity data truncated at polyhedra cell " << id );
812 }
813 ++conn_iter;
814 // iterator is now at number of faces
815 // we should check it is indeed num_vtx
816 int num_faces = *conn_iter;
817 if( num_faces != num_vtx ) MB_SET_ERR( MB_FAILURE, "Connectivity data wrong at polyhedra cell " << id );
818
819 EntityHandle connec[20]; // we bet we will have only 20 vertices at most, in a
820 // face in a polyhedra
821 for( int j = 0; j < num_faces; j++ )
822 {
823 conn_iter++;
824 int numverticesInFace = (int)*conn_iter;
825 if( numverticesInFace > 20 )
826 MB_SET_ERR( MB_FAILURE,
827 "too many vertices in face index " << j << " for polyhedra cell " << id );
828 // need to find the face, but first fill with vertices
829 for( int k = 0; k < numverticesInFace; k++ )
830 {
831 connec[k] = first_vertex + *( ++conn_iter ); //
832 }
833 Range adjFaces;
834 // find a face with these vertices; if not, we need to create one, on the fly :(
835 rv = mdbImpl->get_adjacencies( connec, numverticesInFace, 2, false, adjFaces );MB_CHK_ERR( rv );
836 if( adjFaces.size() >= 1 )
837 {
838 conn_array[j] = adjFaces[0]; // get the first face found
839 }
840 else
841 {
842 // create the face; tri, quad or polygon
843 EntityType etype = MBTRI;
844 if( 4 == numverticesInFace ) etype = MBQUAD;
845 if( 4 < numverticesInFace ) etype = MBPOLYGON;
846
847 rv = mdbImpl->create_element( etype, connec, numverticesInFace, conn_array[j] );MB_CHK_ERR( rv );
848 }
849 }
850
851 conn_array += num_vtx; // advance for next polyhedra
852 conn_iter++; // advance to the next field
853 }
854 }
855
856 // Notify MOAB of the new elements
857 result = readMeshIface->update_adjacencies( start_handle, num_elem, num_vtx, conn_sav );
858 if( MB_SUCCESS != result ) return result;
859 }
860
861 return MB_SUCCESS;
862 }
863
864 ErrorCode ReadVtk::vtk_create_structured_elems( const long* dims,
865 EntityHandle first_vtx,
866 std::vector< Range >& elem_list )
867 {
868 ErrorCode result;
869 // int non_zero[3] = {0, 0, 0}; // True if dim > 0 for x, y, z respectively
870 long elem_dim = 0; // Element dimension (2->quad, 3->hex)
871 long num_elems = 1; // Total number of elements
872 long vert_per_elem; // Element connectivity length
873 long edims[3] = { 1, 1, 1 }; // Number of elements in each grid direction
874
875 // Populate above data
876 for( int d = 0; d < 3; d++ )
877 {
878 if( dims[d] > 1 )
879 {
880 // non_zero[elem_dim] = d;
881 ++elem_dim;
882 edims[d] = dims[d] - 1;
883 num_elems *= edims[d];
884 }
885 }
886 vert_per_elem = 1 << elem_dim;
887
888 // Get element type from element dimension
889 EntityType type;
890 switch( elem_dim )
891 {
892 case 1:
893 type = MBEDGE;
894 break;
895 case 2:
896 type = MBQUAD;
897 break;
898 case 3:
899 type = MBHEX;
900 break;
901 default:
902 MB_SET_ERR( MB_FAILURE, "Invalid dimension for structured elements: " << elem_dim );
903 }
904
905 // Allocate storage for elements
906 EntityHandle start_handle = 0;
907 EntityHandle* conn_array;
908 result = allocate_elements( num_elems, vert_per_elem, type, start_handle, conn_array, elem_list );
909 if( MB_SUCCESS != result ) return MB_FAILURE;
910
911 EntityHandle* conn_sav = conn_array;
912
913 // Offsets of element vertices in grid relative to corner closest to origin
914 long k = dims[0] * dims[1];
915 const long corners[8] = { 0, 1, 1 + dims[0], dims[0], k, k + 1, k + 1 + dims[0], k + dims[0] };
916
917 // Populate element list
918 for( long z = 0; z < edims[2]; ++z )
919 for( long y = 0; y < edims[1]; ++y )
920 for( long x = 0; x < edims[0]; ++x )
921 {
922 const long index = x + y * dims[0] + z * ( dims[0] * dims[1] );
923 for( long j = 0; j < vert_per_elem; ++j, ++conn_array )
924 *conn_array = index + corners[j] + first_vtx;
925 }
926
927 // Notify MOAB of the new elements
928 result = readMeshIface->update_adjacencies( start_handle, num_elems, vert_per_elem, conn_sav );
929 if( MB_SUCCESS != result ) return result;
930
931 return MB_SUCCESS;
932 }
933
934 ErrorCode ReadVtk::vtk_read_field( FileTokenizer& tokens )
935 {
936 // This is not supported yet.
937 // Parse the data but throw it away because
938 // Mesquite has no internal representation for it.
939
940 // Could save this in tags, but the only useful thing that
941 // could be done with the data is to write it back out
942 // with the modified mesh. As there's no way to save the
943 // type of a tag in Mesquite, it cannot be written back
944 // out correctly either.
945 // FIXME: Don't know what to do with this data.
946 // For now, read it and throw it out.
947
948 long num_arrays;
949 if( !tokens.get_string() || // Name
950 !tokens.get_long_ints( 1, &num_arrays ) )
951 return MB_FAILURE;
952
953 for( long i = 0; i < num_arrays; ++i )
954 {
955 /*const char* name =*/tokens.get_string();
956
957 long dims[2];
958 if( !tokens.get_long_ints( 2, dims ) || !tokens.match_token( vtk_type_names ) ) return MB_FAILURE;
959
960 long num_vals = dims[0] * dims[1];
961
962 for( long j = 0; j < num_vals; j++ )
963 {
964 double junk;
965 if( !tokens.get_doubles( 1, &junk ) ) return MB_FAILURE;
966 }
967 }
968
969 return MB_SUCCESS;
970 }
971
972 ErrorCode ReadVtk::vtk_read_attrib_data( FileTokenizer& tokens, std::vector< Range >& entities )
973 {
974 const char* const type_names[] = { "SCALARS", "COLOR_SCALARS", "VECTORS", "NORMALS", "TEXTURE_COORDINATES",
975 "TENSORS", "FIELD", 0 };
976
977 int type = tokens.match_token( type_names );
978 const char* tmp_name = tokens.get_string();
979 if( !type || !tmp_name ) return MB_FAILURE;
980
981 std::string name_alloc( tmp_name );
982 const char* name = name_alloc.c_str();
983 switch( type )
984 {
985 case 1:
986 return vtk_read_scalar_attrib( tokens, entities, name );
987 case 2:
988 return vtk_read_color_attrib( tokens, entities, name );
989 case 3:
990 return vtk_read_vector_attrib( tokens, entities, name );
991 case 4:
992 return vtk_read_vector_attrib( tokens, entities, name );
993 case 5:
994 return vtk_read_texture_attrib( tokens, entities, name );
995 case 6:
996 return vtk_read_tensor_attrib( tokens, entities, name );
997 case 7:
998 return vtk_read_field_attrib( tokens, entities, name );
999 }
1000
1001 return MB_FAILURE;
1002 }
1003
1004 ErrorCode ReadVtk::vtk_read_tag_data( FileTokenizer& tokens,
1005 int type,
1006 size_t per_elem,
1007 std::vector< Range >& entities,
1008 const char* name )
1009 {
1010 ErrorCode result;
1011 DataType mb_type;
1012 if( type == 1 )
1013 {
1014 mb_type = MB_TYPE_BIT;
1015 }
1016 else if( type >= 2 && type <= 9 )
1017 {
1018 mb_type = MB_TYPE_INTEGER;
1019 }
1020 else if( type == 10 || type == 11 )
1021 {
1022 mb_type = MB_TYPE_DOUBLE;
1023 }
1024 else if( type == 12 )
1025 {
1026 mb_type = MB_TYPE_INTEGER;
1027 }
1028 else
1029 return MB_FAILURE;
1030
1031 #ifdef MB_VTK_MATERIAL_SETS
1032 size_t size;
1033 if( type == 1 )
1034 {
1035 size = sizeof( bool );
1036 }
1037 else if( type >= 2 && type <= 9 )
1038 {
1039 size = sizeof( int );
1040 }
1041 else if( type == 10 || type == 11 )
1042 {
1043 size = sizeof( double );
1044 }
1045 else /* (type == 12) */
1046 {
1047 size = 4; // Could be 4 or 8, but we don't know. Hope it's 4 because MOAB doesn't support
1048 // 64-bit ints.
1049 }
1050 Modulator materialMap( this->mdbImpl );
1051 result = materialMap.initialize( this->mPartitionTagName, mb_type, size, per_elem );MB_CHK_SET_ERR( result, "MaterialMap tag (" << this->mPartitionTagName << ") creation failed." );
1052 bool isMaterial = size * per_elem <= 4 && // Must have int-sized values (ParallelComm requires it)
1053 !this->mPartitionTagName.empty() && // Must have a non-empty field name...
1054 !strcmp( name, this->mPartitionTagName.c_str() ); // ... that matches our spec.
1055 #endif // MB_VTK_MATERIAL_SETS
1056
1057 // Get/create tag
1058 Tag handle;
1059 result = mdbImpl->tag_get_handle( name, per_elem, mb_type, handle, MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( result, "Tag name conflict for attribute \"" << name << "\" at line " << tokens.line_number() );
1060
1061 std::vector< Range >::iterator iter;
1062
1063 if( type == 1 )
1064 {
1065 for( iter = entities.begin(); iter != entities.end(); ++iter )
1066 {
1067 bool* data = new bool[iter->size() * per_elem];
1068 if( !tokens.get_booleans( per_elem * iter->size(), data ) )
1069 {
1070 delete[] data;
1071 return MB_FAILURE;
1072 }
1073
1074 bool* data_iter = data;
1075 Range::iterator ent_iter = iter->begin();
1076 for( ; ent_iter != iter->end(); ++ent_iter )
1077 {
1078 unsigned char bits = 0;
1079 for( unsigned j = 0; j < per_elem; ++j, ++data_iter )
1080 bits |= (unsigned char)( *data_iter << j );
1081 #ifdef MB_VTK_MATERIAL_SETS
1082 if( isMaterial ) materialMap.add_entity( *ent_iter, &bits, 1 );
1083 #endif // MB_VTK_MATERIAL_SETS
1084 result = mdbImpl->tag_set_data( handle, &*ent_iter, 1, &bits );
1085 if( MB_SUCCESS != result )
1086 {
1087 delete[] data;
1088 return result;
1089 }
1090 }
1091 delete[] data;
1092 }
1093 }
1094 else if( ( type >= 2 && type <= 9 ) || type == 12 )
1095 {
1096 std::vector< int > data;
1097 for( iter = entities.begin(); iter != entities.end(); ++iter )
1098 {
1099 data.resize( iter->size() * per_elem );
1100 if( !tokens.get_integers( iter->size() * per_elem, &data[0] ) ) return MB_FAILURE;
1101 #ifdef MB_VTK_MATERIAL_SETS
1102 if( isMaterial ) materialMap.add_entities( *iter, (unsigned char*)&data[0], per_elem * size );
1103 #endif // MB_VTK_MATERIAL_SETS
1104 result = mdbImpl->tag_set_data( handle, *iter, &data[0] );
1105 if( MB_SUCCESS != result ) return result;
1106 }
1107 }
1108 else if( type == 10 || type == 11 )
1109 {
1110 std::vector< double > data;
1111 for( iter = entities.begin(); iter != entities.end(); ++iter )
1112 {
1113 data.resize( iter->size() * per_elem );
1114 if( !tokens.get_doubles( iter->size() * per_elem, &data[0] ) ) return MB_FAILURE;
1115 #ifdef MB_VTK_MATERIAL_SETS
1116 if( isMaterial ) materialMap.add_entities( *iter, (unsigned char*)&data[0], per_elem * size );
1117 #endif // MB_VTK_MATERIAL_SETS
1118 result = mdbImpl->tag_set_data( handle, *iter, &data[0] );
1119 if( MB_SUCCESS != result ) return result;
1120 }
1121 }
1122
1123 return MB_SUCCESS;
1124 }
1125
1126 ErrorCode ReadVtk::vtk_read_scalar_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
1127 {
1128 int type = tokens.match_token( vtk_type_names );
1129 if( !type ) return MB_FAILURE;
1130
1131 long size;
1132 const char* tok = tokens.get_string();
1133 if( !tok ) return MB_FAILURE;
1134
1135 const char* end = 0;
1136 size = strtol( tok, (char**)&end, 0 );
1137 if( *end )
1138 {
1139 size = 1;
1140 tokens.unget_token();
1141 }
1142
1143 // VTK spec says cannot be greater than 4--do we care?
1144 if( size < 1 )
1145 { //|| size > 4)
1146 MB_SET_ERR( MB_FAILURE, "Scalar count out of range [1,4] at line " << tokens.line_number() );
1147 }
1148
1149 if( !tokens.match_token( "LOOKUP_TABLE" ) || !tokens.match_token( "default" ) ) return MB_FAILURE;
1150
1151 return vtk_read_tag_data( tokens, type, size, entities, name );
1152 }
1153
1154 ErrorCode ReadVtk::vtk_read_color_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
1155 {
1156 long size;
1157 if( !tokens.get_long_ints( 1, &size ) || size < 1 ) return MB_FAILURE;
1158
1159 return vtk_read_tag_data( tokens, 10, size, entities, name );
1160 }
1161
1162 ErrorCode ReadVtk::vtk_read_vector_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
1163 {
1164 int type = tokens.match_token( vtk_type_names );
1165 if( !type ) return MB_FAILURE;
1166
1167 return vtk_read_tag_data( tokens, type, 3, entities, name );
1168 }
1169
1170 ErrorCode ReadVtk::vtk_read_texture_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
1171 {
1172 int type, dim;
1173 if( !tokens.get_integers( 1, &dim ) || !( type = tokens.match_token( vtk_type_names ) ) ) return MB_FAILURE;
1174
1175 if( dim < 1 || dim > 3 )
1176 {
1177 MB_SET_ERR( MB_FAILURE, "Invalid dimension (" << dim << ") at line " << tokens.line_number() );
1178 }
1179
1180 return vtk_read_tag_data( tokens, type, dim, entities, name );
1181 }
1182
1183 ErrorCode ReadVtk::vtk_read_tensor_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
1184 {
1185 int type = tokens.match_token( vtk_type_names );
1186 if( !type ) return MB_FAILURE;
1187
1188 return vtk_read_tag_data( tokens, type, 9, entities, name );
1189 }
1190
1191 ErrorCode ReadVtk::vtk_read_field_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* )
1192 {
1193 long num_fields;
1194 if( !tokens.get_long_ints( 1, &num_fields ) ) return MB_FAILURE;
1195
1196 long i;
1197 for( i = 0; i < num_fields; ++i )
1198 {
1199 const char* tok = tokens.get_string();
1200 if( !tok ) return MB_FAILURE;
1201
1202 std::string name_alloc( tok );
1203
1204 long num_comp;
1205 if( !tokens.get_long_ints( 1, &num_comp ) ) return MB_FAILURE;
1206
1207 long num_tuples;
1208 if( !tokens.get_long_ints( 1, &num_tuples ) ) return MB_FAILURE;
1209
1210 int type = tokens.match_token( vtk_type_names );
1211 if( !type ) return MB_FAILURE;
1212
1213 ErrorCode result = vtk_read_tag_data( tokens, type, num_comp, entities, name_alloc.c_str() );MB_CHK_SET_ERR( result, "Error reading data for field \"" << name_alloc << "\" (" << num_comp << " components, "
1214 << num_tuples << " tuples, type " << type
1215 << ") at line " << tokens.line_number() );
1216 }
1217
1218 return MB_SUCCESS;
1219 }
1220
1221 ErrorCode ReadVtk::store_file_ids( Tag tag, const Range& verts, const std::vector< Range >& elems )
1222 {
1223 ErrorCode rval;
1224
1225 rval = readMeshIface->assign_ids( tag, verts );
1226 if( MB_SUCCESS != rval ) return rval;
1227
1228 int id = 0;
1229 for( size_t i = 0; i < elems.size(); ++i )
1230 {
1231 rval = readMeshIface->assign_ids( tag, elems[i], id );
1232 id += elems[i].size();
1233 }
1234
1235 return MB_SUCCESS;
1236 }
1237
1238 } // namespace moab
1.9.1.