Chaste  Release::2018.1
CmguiMeshWriter.hpp
1 /*
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35 
36 #ifndef CMGUIWRITER_HPP_
37 #define CMGUIWRITER_HPP_
38 
39 #include "AbstractTetrahedralMeshWriter.hpp"
40 #include "OutputFileHandler.hpp"
41 
45 static const char CmguiNodeFileHeader3D[] = " #Fields=1\n\
46  1) coordinates, coordinate, rectangular cartesian, #Components=3\n\
47  x. Value index= 1, #Derivatives= 0\n\
48  y. Value index= 2, #Derivatives= 0\n\
49  z. Value index= 3, #Derivatives= 0\n";
50 
54 static const char CmguiNodeFileHeader2D[] = " #Fields=1\n\
55  1) coordinates, coordinate, rectangular cartesian, #Components=2\n\
56  x. Value index= 1, #Derivatives= 0\n\
57  y. Value index= 2, #Derivatives= 0\n";
58 
59 
63 static const char CmguiNodeFileHeader1D[] = " #Fields=1\n\
64  1) coordinates, coordinate, rectangular cartesian, #Components=1\n\
65  x. Value index= 1, #Derivatives= 0\n";
66 
70 static const char CmguiElementFileHeader3D[] = "Shape. Dimension=3, simplex(2;3)*simplex*simplex\n\
71  #Scale factor sets= 0\n\
72  #Nodes= 4\n";
73 
77 static const char CmguiElementFileHeader3DQuadratic[] = "Shape. Dimension=3, simplex(2;3)*simplex*simplex\n\
78  #Scale factor sets= 0\n\
79  #Nodes= 10\n";
80 
81 
85 static const char CmguiElementFileHeader2D[] = "Shape. Dimension=2, simplex(2)*simplex\n\
86  #Scale factor sets= 0\n\
87  #Nodes= 3\n";
88 
92 static const char CmguiElementFileHeader2DQuadratic[] = "Shape. Dimension=2, simplex(2)*simplex\n\
93  #Scale factor sets= 0\n\
94  #Nodes= 6\n";
95 
99 static const char CmguiElementFileHeader1D[] = "Shape. Dimension=1, line\n\
100  #Scale factor sets= 0\n\
101  #Nodes= 2\n";
102 
106 static const char CmguiElementFileHeader1DQuadratic[] = "Shape. Dimension=1, line\n\
107  #Scale factor sets= 0\n\
108  #Nodes= 3\n";
109 
110 
114 static const char CmguiCoordinatesFileHeader3D[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=3\n\
115  x. l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
116  #Nodes= 4\n\
117  1. #Values=1\n\
118  Value indices: 1\n\
119  Scale factor indices: 1\n\
120  2. #Values=1\n\
121  Value indices: 1\n\
122  Scale factor indices: 2\n\
123  3. #Values=1\n\
124  Value indices: 1\n\
125  Scale factor indices: 3\n\
126  4. #Values=1\n\
127  Value indices: 1\n\
128  Scale factor indices: 4\n\
129  y. l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
130  #Nodes= 4\n\
131  1. #Values=1\n\
132  Value indices: 1\n\
133  Scale factor indices: 1\n\
134  2. #Values=1\n\
135  Value indices: 1\n\
136  Scale factor indices: 2\n\
137  3. #Values=1\n\
138  Value indices: 1\n\
139  Scale factor indices: 3\n\
140  4. #Values=1\n\
141  Value indices: 1\n\
142  Scale factor indices: 4\n\
143  z. l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
144  #Nodes= 4\n\
145  1. #Values=1\n\
146  Value indices: 1\n\
147  Scale factor indices: 1\n\
148  2. #Values=1\n\
149  Value indices: 1\n\
150  Scale factor indices: 2\n\
151  3. #Values=1\n\
152  Value indices: 1\n\
153  Scale factor indices: 3\n\
154  4. #Values=1\n\
155  Value indices: 1\n\
156  Scale factor indices: 4\n";
157 
158 
162 static const char CmguiCoordinatesFileHeader3DQuadratic[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=3\n\
163  x. q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
164  #Nodes= 10\n\
165  1. #Values=1\n\
166  Value indices: 1\n\
167  Scale factor indices: 1\n\
168  2. #Values=1\n\
169  Value indices: 1\n\
170  Scale factor indices: 2\n\
171  3. #Values=1\n\
172  Value indices: 1\n\
173  Scale factor indices: 3\n\
174  4. #Values=1\n\
175  Value indices: 1\n\
176  Scale factor indices: 4\n\
177  5. #Values=1\n\
178  Value indices: 1\n\
179  Scale factor indices: 5\n\
180  6. #Values=1\n\
181  Value indices: 1\n\
182  Scale factor indices: 6\n\
183  7. #Values=1\n\
184  Value indices: 1\n\
185  Scale factor indices: 7\n\
186  8. #Values=1\n\
187  Value indices: 1\n\
188  Scale factor indices: 8\n\
189  9. #Values=1\n\
190  Value indices: 1\n\
191  Scale factor indices: 9\n\
192  10. #Values=1\n\
193  Value indices: 1\n\
194  Scale factor indices: 10\n\
195  y. q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
196  #Nodes= 10\n\
197  1. #Values=1\n\
198  Value indices: 1\n\
199  Scale factor indices: 1\n\
200  2. #Values=1\n\
201  Value indices: 1\n\
202  Scale factor indices: 2\n\
203  3. #Values=1\n\
204  Value indices: 1\n\
205  Scale factor indices: 3\n\
206  4. #Values=1\n\
207  Value indices: 1\n\
208  Scale factor indices: 4\n\
209  5. #Values=1\n\
210  Value indices: 1\n\
211  Scale factor indices: 5\n\
212  6. #Values=1\n\
213  Value indices: 1\n\
214  Scale factor indices: 6\n\
215  7. #Values=1\n\
216  Value indices: 1\n\
217  Scale factor indices: 7\n\
218  8. #Values=1\n\
219  Value indices: 1\n\
220  Scale factor indices: 8\n\
221  9. #Values=1\n\
222  Value indices: 1\n\
223  Scale factor indices: 9\n\
224  10. #Values=1\n\
225  Value indices: 1\n\
226  Scale factor indices: 10\n\
227  z. q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
228  #Nodes= 10\n\
229  1. #Values=1\n\
230  Value indices: 1\n\
231  Scale factor indices: 1\n\
232  2. #Values=1\n\
233  Value indices: 1\n\
234  Scale factor indices: 2\n\
235  3. #Values=1\n\
236  Value indices: 1\n\
237  Scale factor indices: 3\n\
238  4. #Values=1\n\
239  Value indices: 1\n\
240  Scale factor indices: 4\n\
241  5. #Values=1\n\
242  Value indices: 1\n\
243  Scale factor indices: 5\n\
244  6. #Values=1\n\
245  Value indices: 1\n\
246  Scale factor indices: 6\n\
247  7. #Values=1\n\
248  Value indices: 1\n\
249  Scale factor indices: 7\n\
250  8. #Values=1\n\
251  Value indices: 1\n\
252  Scale factor indices: 8\n\
253  9. #Values=1\n\
254  Value indices: 1\n\
255  Scale factor indices: 9\n\
256  10. #Values=1\n\
257  Value indices: 1\n\
258  Scale factor indices: 10\n";
259 
260 
264 static const char CmguiCoordinatesFileHeader2D[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=2\n\
265  x. l.simplex(2)*l.simplex, no modify, standard node based.\n\
266  #Nodes= 3\n\
267  1. #Values=1\n\
268  Value indices: 1\n\
269  Scale factor indices: 1\n\
270  2. #Values=1\n\
271  Value indices: 1\n\
272  Scale factor indices: 2\n\
273  3. #Values=1\n\
274  Value indices: 1\n\
275  Scale factor indices: 3\n\
276  y. l.simplex(2)*l.simplex, no modify, standard node based.\n\
277  #Nodes= 3\n\
278  1. #Values=1\n\
279  Value indices: 1\n\
280  Scale factor indices: 1\n\
281  2. #Values=1\n\
282  Value indices: 1\n\
283  Scale factor indices: 2\n\
284  3. #Values=1\n\
285  Value indices: 1\n\
286  Scale factor indices: 3\n";
287 
288 
293 static const char CmguiCoordinatesFileHeader2DQuadratic[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=2\n\
294  x. q.simplex(2)*q.simplex, no modify, standard node based.\n\
295  #Nodes= 6\n\
296  1. #Values=1\n\
297  Value indices: 1\n\
298  Scale factor indices: 1\n\
299  2. #Values=1\n\
300  Value indices: 1\n\
301  Scale factor indices: 2\n\
302  3. #Values=1\n\
303  Value indices: 1\n\
304  Scale factor indices: 3\n\
305  4. #Values=1\n\
306  Value indices: 1\n\
307  Scale factor indices: 4\n\
308  5. #Values=1\n\
309  Value indices: 1\n\
310  Scale factor indices: 5\n\
311  6. #Values=1\n\
312  Value indices: 1\n\
313  Scale factor indices: 6\n\
314  y. q.simplex(2)*q.simplex, no modify, standard node based.\n\
315  #Nodes= 6\n\
316  1. #Values=1\n\
317  Value indices: 1\n\
318  Scale factor indices: 1\n\
319  2. #Values=1\n\
320  Value indices: 1\n\
321  Scale factor indices: 2\n\
322  3. #Values=1\n\
323  Value indices: 1\n\
324  Scale factor indices: 3\n\
325  4. #Values=1\n\
326  Value indices: 1\n\
327  Scale factor indices: 4\n\
328  5. #Values=1\n\
329  Value indices: 1\n\
330  Scale factor indices: 5\n\
331  6. #Values=1\n\
332  Value indices: 1\n\
333  Scale factor indices: 6\n";
334 
339 static const char CmguiCoordinatesFileHeader1D[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=1\n\
340  x. l.Lagrange, no modify, standard node based.\n\
341  #Nodes= 2\n\
342  1. #Values=1\n\
343  Value indices: 1\n\
344  Scale factor indices: 1\n\
345  2. #Values=1\n\
346  Value indices: 1\n\
347  Scale factor indices: 2\n";
348 
349 
354 static const char CmguiCoordinatesFileHeader1DQuadratic[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=1\n\
355  x. q.Lagrange, no modify, standard node based.\n\
356  #Nodes= 3\n\
357  1. #Values=1\n\
358  Value indices: 1\n\
359  Scale factor indices: 1\n\
360  2. #Values=1\n\
361  Value indices: 1\n\
362  Scale factor indices: 2\n\
363  3. #Values=1\n\
364  Value indices: 1\n\
365  Scale factor indices: 3\n";
366 
371 static const char CmguiAdditionalFieldHeader3D[] = " field, rectangular cartesian, #Components=1\n\
372  x. l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
373  #Nodes= 4\n\
374  1. #Values=1\n\
375  Value indices: 1\n\
376  Scale factor indices: 1\n\
377  2. #Values=1\n\
378  Value indices: 1\n\
379  Scale factor indices: 2\n\
380  3. #Values=1\n\
381  Value indices: 1\n\
382  Scale factor indices: 3\n\
383  4. #Values=1\n\
384  Value indices: 1\n\
385  Scale factor indices: 4\n";
386 
387 
393 static const char CmguiAdditionalFieldHeader3DQuadratic[] = " field, rectangular cartesian, #Components=1\n\
394  x. q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
395  #Nodes= 10\n\
396  1. #Values=1\n\
397  Value indices: 1\n\
398  Scale factor indices: 1\n\
399  2. #Values=1\n\
400  Value indices: 1\n\
401  Scale factor indices: 2\n\
402  3. #Values=1\n\
403  Value indices: 1\n\
404  Scale factor indices: 3\n\
405  4. #Values=1\n\
406  Value indices: 1\n\
407  Scale factor indices: 4\n\
408  5. #Values=1\n\
409  Value indices: 1\n\
410  Scale factor indices: 5\n\
411  6. #Values=1\n\
412  Value indices: 1\n\
413  Scale factor indices: 6\n\
414  7. #Values=1\n\
415  Value indices: 1\n\
416  Scale factor indices: 7\n\
417  8. #Values=1\n\
418  Value indices: 1\n\
419  Scale factor indices: 8\n\
420  9. #Values=1\n\
421  Value indices: 1\n\
422  Scale factor indices: 9\n\
423  10. #Values=1\n\
424  Value indices: 1\n\
425  Scale factor indices: 10\n";
426 
431 static const char CmguiAdditionalFieldHeader2D[] = " field, rectangular cartesian, #Components=1\n\
432  x. l.simplex(2)*l.simplex, no modify, standard node based.\n\
433  #Nodes= 3\n\
434  1. #Values=1\n\
435  Value indices: 1\n\
436  Scale factor indices: 1\n\
437  2. #Values=1\n\
438  Value indices: 1\n\
439  Scale factor indices: 2\n\
440  3. #Values=1\n\
441  Value indices: 1\n\
442  Scale factor indices: 3\n";
443 
448 static const char CmguiAdditionalFieldHeader2DQuadratic[] = " field, rectangular cartesian, #Components=1\n\
449  x. q.simplex(2)*q.simplex, no modify, standard node based.\n\
450  #Nodes= 6\n\
451  1. #Values=1\n\
452  Value indices: 1\n\
453  Scale factor indices: 1\n\
454  2. #Values=1\n\
455  Value indices: 1\n\
456  Scale factor indices: 2\n\
457  3. #Values=1\n\
458  Value indices: 1\n\
459  Scale factor indices: 3\n\
460  4. #Values=1\n\
461  Value indices: 1\n\
462  Scale factor indices: 4\n\
463  5. #Values=1\n\
464  Value indices: 1\n\
465  Scale factor indices: 5\n\
466  6. #Values=1\n\
467  Value indices: 1\n\
468  Scale factor indices: 6\n";
469 
470 
475 static const char CmguiAdditionalFieldHeader1D[] = " field, rectangular cartesian, #Components=1\n\
476  x. l.Lagrange, no modify, standard node based.\n\
477  #Nodes= 2\n\
478  1. #Values=1\n\
479  Value indices: 1\n\
480  Scale factor indices: 1\n\
481  2. #Values=1\n\
482  Value indices: 1\n\
483  Scale factor indices: 2\n";
484 
489 static const char CmguiAdditionalFieldHeader1DQuadratic[] = " field, rectangular cartesian, #Components=1\n\
490  x. q.Lagrange, no modify, standard node based.\n\
491  #Nodes= 2\n\
492  1. #Values=1\n\
493  Value indices: 1\n\
494  Scale factor indices: 1\n\
495  2. #Values=1\n\
496  Value indices: 1\n\
497  Scale factor indices: 2\n\
498  3. #Values=1\n\
499  Value indices: 1\n\
500  Scale factor indices: 3\n";
501 
502 
514 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
515 class CmguiMeshWriter : public AbstractTetrahedralMeshWriter<ELEMENT_DIM,SPACE_DIM>
516 {
517 protected:
518 
522  std::vector<std::string> mAdditionalFieldNames;
523 
524 
529  std::vector<std::string> mRegionNames;// {tissue, bath, whatever}
530 
537  std::string mGroupName;
538 
543  std::string mElementFileHeader;
544 
550  std::string mCoordinatesFileHeader;
551 
556  std::string mAdditionalFieldHeader;
557 
562  unsigned mNumNodesPerElement;
563 
567  std::vector<unsigned> mReordering;
568 
574  std::ios_base::openmode GetOpenMode(bool append);
575 
582  out_stream OpenNodeFile(bool append = false);
583 
590  std::vector<boost::shared_ptr<std::ofstream> > OpenElementFiles(bool append = false);
591 
598  void WriteNodeFileHeader(out_stream& rpNodeFile);
599 
605  void WriteElementsFileHeader(std::vector<boost::shared_ptr<std::ofstream> >& rElemFiles);
606 
607 
611  void CreateFilesWithHeaders();
612 
616  void AppendLocalDataToFiles();
617 
621  void WriteFilesFooter();
622 
623 public:
624 
632  CmguiMeshWriter(const std::string& rDirectory,
633  const std::string& rBaseName,
634  bool cleanDirectory=true);
635 
639  void WriteFiles();
640 
646  void SetAdditionalFieldNames(std::vector<std::string>& rFieldNames);
647 
653  void SetRegionNames(std::vector<std::string>& rRegionNames);
654 
658  virtual ~CmguiMeshWriter()
659  {}
660 
661  // A method called CompareCmguiFiles() has been removed, please use FileComparison class instead.
662 };
663 
664 #endif /*CMGUIWRITER_HPP_*/
CmguiMeshWriter::mAdditionalFieldHeader
std::string mAdditionalFieldHeader
Definition: CmguiMeshWriter.hpp:556
CmguiMeshWriter::OpenNodeFile
out_stream OpenNodeFile(bool append=false)
Definition: CmguiMeshWriter.cpp:163
CmguiMeshWriter::~CmguiMeshWriter
virtual ~CmguiMeshWriter()
Definition: CmguiMeshWriter.hpp:658
CmguiMeshWriter::SetRegionNames
void SetRegionNames(std::vector< std::string > &rRegionNames)
Definition: CmguiMeshWriter.cpp:157
CmguiMeshWriter::mCoordinatesFileHeader
std::string mCoordinatesFileHeader
Definition: CmguiMeshWriter.hpp:550
CmguiMeshWriter::OpenElementFiles
std::vector< boost::shared_ptr< std::ofstream > > OpenElementFiles(bool append=false)
Definition: CmguiMeshWriter.cpp:170
CmguiMeshWriter::WriteElementsFileHeader
void WriteElementsFileHeader(std::vector< boost::shared_ptr< std::ofstream > > &rElemFiles)
Definition: CmguiMeshWriter.cpp:239
CmguiMeshWriter::mRegionNames
std::vector< std::string > mRegionNames
Definition: CmguiMeshWriter.hpp:529
CmguiMeshWriter::GetOpenMode
std::ios_base::openmode GetOpenMode(bool append)
Definition: CmguiMeshWriter.cpp:361
CmguiMeshWriter::mElementFileHeader
std::string mElementFileHeader
Definition: CmguiMeshWriter.hpp:543
CmguiMeshWriter::mNumNodesPerElement
unsigned mNumNodesPerElement
Definition: CmguiMeshWriter.hpp:562
CmguiMeshWriter::mReordering
std::vector< unsigned > mReordering
Definition: CmguiMeshWriter.hpp:567
CmguiMeshWriter::mGroupName
std::string mGroupName
Definition: CmguiMeshWriter.hpp:537
CmguiMeshWriter::SetAdditionalFieldNames
void SetAdditionalFieldNames(std::vector< std::string > &rFieldNames)
Definition: CmguiMeshWriter.cpp:151
CmguiMeshWriter::mAdditionalFieldNames
std::vector< std::string > mAdditionalFieldNames
Definition: CmguiMeshWriter.hpp:522
CmguiMeshWriter::CmguiMeshWriter
CmguiMeshWriter(const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true)
Definition: CmguiMeshWriter.cpp:48
CmguiMeshWriter::WriteNodeFileHeader
void WriteNodeFileHeader(out_stream &rpNodeFile)
Definition: CmguiMeshWriter.cpp:206