1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <string>
#include "H5Include.h"
#include "H5Exception.h"
#include "H5IdComponent.h"
#include "H5PropList.h"
#include "H5Object.h"
#include "H5FaccProp.h"
#include "H5FcreatProp.h"
#include "H5DxferProp.h"
#include "H5DcreatProp.h"
#include "H5CommonFG.h"
#include "H5Group.h"
#include "H5AbstractDs.h"
#include "H5DataSpace.h"
#include "H5DataSet.h"
#include "H5File.h"
#include "H5Alltypes.h"
// There are a few comments that are common to most of the functions
// defined in this file so they are listed here.
// - getLocId is called by all functions, that call a C API, to get
// the location id, which can be either a file id or a group id.
// This function is pure virtual and it's up to H5File and Group
// to call the right getId() - although, as the structure of the
// library at this time, getId() is basically the IdComponent::getId()
// - when a failure returned by the C API, the functions will call
// throwException, which is a pure virtual function and is implemented
// by H5File to throw a FileIException and by Group to throw a
// GroupIException.
// December 2000
#ifndef H5_NO_NAMESPACE
namespace H5 {
#endif
//--------------------------------------------------------------------------
// Function: CommonFG::createGroup
///\brief Creates a new group at this location which can be a file
/// or another group.
///\param name - IN: Name of the group to create
///\param size_hint - IN: Indicates the number of bytes to reserve for
/// the names that will appear in the group
///\return Group instance
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// The optional \a size_hint specifies how much file space to
/// reserve for storing the names that will appear in this new
/// group. If a non-positive value is provided for the \a size_hint
/// then a default size is chosen.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Group CommonFG::createGroup( const char* name, size_t size_hint ) const
{
// Create group creation property list for size_hint
hid_t gcpl_id = H5Pcreate(H5P_GROUP_CREATE);
// If the creation of the property list failed, throw an exception
if( gcpl_id < 0 )
throwException("createGroup", "H5Pcreate failed");
// Set the local heap size hint
if( H5Pset_local_heap_size_hint(gcpl_id, size_hint) < 0) {
H5Pclose(gcpl_id);
throwException("createGroup", "H5Pset_local_heap_size failed");
}
// Call C routine H5Gcreate2 to create the named group, giving the
// location id which can be a file id or a group id
hid_t group_id = H5Gcreate2( getLocId(), name, H5P_DEFAULT, gcpl_id, H5P_DEFAULT );
// Close the group creation property list
H5Pclose(gcpl_id);
// If the creation of the group failed, throw an exception
if( group_id < 0 )
throwException("createGroup", "H5Gcreate2 failed");
// No failure, create and return the Group object
Group group( group_id );
return( group );
}
//--------------------------------------------------------------------------
// Function: CommonFG::createGroup
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Group CommonFG::createGroup( const H5std_string& name, size_t size_hint ) const
{
return( createGroup( name.c_str(), size_hint ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::openGroup
///\brief Opens an existing group in a location which can be a file
/// or another group.
///\param name - IN: Name of the group to open
///\return Group instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Group CommonFG::openGroup( const char* name ) const
{
// Call C routine H5Gopen2 to open the named group, giving the
// location id which can be a file id or a group id
hid_t group_id = H5Gopen2( getLocId(), name, H5P_DEFAULT );
// If the opening of the group failed, throw an exception
if( group_id < 0 )
{
throwException("openGroup", "H5Gopen2 failed");
}
// No failure, create and return the Group object
Group group( group_id );
return( group );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openGroup
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Group CommonFG::openGroup( const H5std_string& name ) const
{
return( openGroup( name.c_str() ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::createDataSet
///\brief Creates a new dataset at this location.
///\param name - IN: Name of the dataset to create
///\param data_type - IN: Datatype of the dataset
///\param data_space - IN: Dataspace for the dataset
///\param create_plist - IN: Creation properly list for the dataset
///\return DataSet instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet CommonFG::createDataSet( const char* name, const DataType& data_type, const DataSpace& data_space, const DSetCreatPropList& create_plist ) const
{
// Obtain identifiers for C API
hid_t type_id = data_type.getId();
hid_t space_id = data_space.getId();
hid_t create_plist_id = create_plist.getId();
// Call C routine H5Dcreate2 to create the named dataset
hid_t dataset_id = H5Dcreate2( getLocId(), name, type_id, space_id, H5P_DEFAULT, create_plist_id, H5P_DEFAULT );
// If the creation of the dataset failed, throw an exception
if( dataset_id < 0 )
{
throwException("createDataSet", "H5Dcreate2 failed");
}
// No failure, create and return the DataSet object
DataSet dataset( dataset_id );
return( dataset );
}
//--------------------------------------------------------------------------
// Function: CommonFG::createDataSet
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet CommonFG::createDataSet( const H5std_string& name, const DataType& data_type, const DataSpace& data_space, const DSetCreatPropList& create_plist ) const
{
return( createDataSet( name.c_str(), data_type, data_space, create_plist ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::openDataSet
///\brief Opens an existing dataset at this location.
///\param name - IN: Name of the dataset to open
///\return DataSet instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet CommonFG::openDataSet( const char* name ) const
{
// Call C function H5Dopen2 to open the specified dataset, giving
// the location id and the dataset's name
hid_t dataset_id = H5Dopen2( getLocId(), name, H5P_DEFAULT );
// If the dataset's opening failed, throw an exception
if(dataset_id < 0)
throwException("openDataSet", "H5Dopen2 failed");
// No failure, create and return the DataSet object
DataSet dataset( dataset_id );
return( dataset );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openDataSet
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataSet CommonFG::openDataSet( const H5std_string& name ) const
{
return( openDataSet( name.c_str() ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::link
///\brief Creates a link of the specified type from \a new_name to
/// \a curr_name.
///\param link_type - IN: Link type; possible values are
/// \li \c H5G_LINK_HARD
/// \li \c H5G_LINK_SOFT
///\param curr_name - IN: Name of the existing object if link is a hard
/// link; can be anything for the soft link
///\param new_name - IN: New name for the object
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// Note that both names are interpreted relative to the
/// specified location.
/// For information on creating hard link and soft link, please
/// refer to the C layer Reference Manual at:
/// http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateHard and
/// http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateSoft
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5L APIs - BMR
//--------------------------------------------------------------------------
void CommonFG::link( H5L_type_t link_type, const char* curr_name, const char* new_name ) const
{
herr_t ret_value;
switch(link_type) {
case H5L_TYPE_HARD:
ret_value = H5Lcreate_hard( getLocId(), curr_name, H5L_SAME_LOC, new_name, H5P_DEFAULT, H5P_DEFAULT );
break;
case H5L_TYPE_SOFT:
ret_value = H5Lcreate_soft( curr_name, getLocId(), new_name, H5P_DEFAULT, H5P_DEFAULT );
break;
default:
throwException("link", "unknown link type");
break;
} /* end switch */
if( ret_value < 0 )
{
throwException("link", "creating link failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::link
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a curr_name and \a new_name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::link( H5L_type_t link_type, const H5std_string& curr_name, const H5std_string& new_name ) const
{
link( link_type, curr_name.c_str(), new_name.c_str() );
}
//--------------------------------------------------------------------------
// Function: CommonFG::unlink
///\brief Removes the specified name at this location.
///\param name - IN: Name of the object to be removed
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5L APIs - BMR
//--------------------------------------------------------------------------
void CommonFG::unlink( const char* name ) const
{
herr_t ret_value = H5Ldelete( getLocId(), name, H5P_DEFAULT );
if( ret_value < 0 )
{
throwException("unlink", "H5Ldelete failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::unlink
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::unlink( const H5std_string& name ) const
{
unlink( name.c_str() );
}
//--------------------------------------------------------------------------
// Function: CommonFG::move
///\brief Renames an object at this location.
///\param src - IN: Object's original name
///\param dst - IN: Object's new name
///\exception H5::FileIException or H5::GroupIException
///\note
/// Exercise care in moving groups as it is possible to render
/// data in a file inaccessible with Group::move. Please refer
/// to the Group Interface in the HDF5 User's Guide at:
/// http://www.hdfgroup.org/HDF5/doc/UG/UG_frame09Groups.html
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5L APIs - BMR
//--------------------------------------------------------------------------
void CommonFG::move( const char* src, const char* dst ) const
{
herr_t ret_value = H5Lmove( getLocId(), src, H5L_SAME_LOC, dst, H5P_DEFAULT, H5P_DEFAULT );
if( ret_value < 0 )
{
throwException("move", "H5Lmove failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::move
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a src and \a dst.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::move( const H5std_string& src, const H5std_string& dst ) const
{
move( src.c_str(), dst.c_str() );
}
#ifndef H5_NO_DEPRECATED_SYMBOLS
//--------------------------------------------------------------------------
// Function: CommonFG::getObjinfo
///\brief Returns information about an object.
///\param name - IN: Name of the object
///\param follow_link - IN: Link flag
///\param statbuf - OUT: Buffer to return information about the object
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// For more information, please refer to the C layer Reference
/// Manual at:
/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5G.html#Group-GetObjinfo
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::getObjinfo( const char* name, hbool_t follow_link, H5G_stat_t& statbuf ) const
{
herr_t ret_value = H5Gget_objinfo( getLocId(), name, follow_link, &statbuf );
if( ret_value < 0 )
{
throwException("getObjinfo", "H5Gget_objinfo failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::getObjinfo
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::getObjinfo( const H5std_string& name, hbool_t follow_link, H5G_stat_t& statbuf ) const
{
getObjinfo( name.c_str(), follow_link, statbuf );
}
//--------------------------------------------------------------------------
// Function: CommonFG::getObjinfo
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above functions in that it doesn't have
/// the paramemter \a follow_link.
// Programmer Binh-Minh Ribler - Nov, 2005
// Note: need to modify to use H5Oget_info and H5Lget_info - BMR
//--------------------------------------------------------------------------
void CommonFG::getObjinfo( const char* name, H5G_stat_t& statbuf ) const
{
herr_t ret_value = H5Gget_objinfo( getLocId(), name, 0, &statbuf );
if( ret_value < 0 )
{
throwException("getObjinfo", "H5Gget_objinfo failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::getObjinfo
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - Nov, 2005
//--------------------------------------------------------------------------
void CommonFG::getObjinfo( const H5std_string& name, H5G_stat_t& statbuf ) const
{
getObjinfo( name.c_str(), statbuf );
}
#endif /* H5_NO_DEPRECATED_SYMBOLS */
//--------------------------------------------------------------------------
// Function: CommonFG::getLinkval
///\brief Returns the name of the object that the symbolic link points to.
///\param name - IN: Symbolic link to the object
///\param size - IN: Maximum number of characters of value to be returned
///\return Name of the object
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5std_string CommonFG::getLinkval( const char* name, size_t size ) const
{
H5L_info_t linkinfo;
char *value_C; // value in C string
size_t val_size = size;
H5std_string value = "";
herr_t ret_value;
// if user doesn't provide buffer size, determine it
if (size == 0)
{
ret_value = H5Lget_info(getLocId(), name, &linkinfo, H5P_DEFAULT);
if( ret_value < 0 )
{
throwException("getLinkval", "H5Lget_info to find buffer size failed");
}
val_size = linkinfo.u.val_size;
}
// if link has value, retrieve the value, otherwise, return null string
if (val_size > 0)
{
value_C = new char[val_size+1]; // temporary C-string for C API
ret_value = H5Lget_val(getLocId(), name, value_C, val_size, H5P_DEFAULT);
if( ret_value < 0 )
{
throwException("getLinkval", "H5Lget_val failed");
}
value = H5std_string(value_C);
delete []value_C;
}
return(value);
}
//--------------------------------------------------------------------------
// Function: CommonFG::getLinkval
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5std_string CommonFG::getLinkval( const H5std_string& name, size_t size ) const
{
return( getLinkval( name.c_str(), size ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::setComment
///\brief Sets or resets the comment for an object specified by its name.
///\param name - IN: Name of the object
///\param comment - IN: New comment
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// If \a comment is an empty string or a null pointer, the comment
/// message is removed from the object.
/// Comments should be relatively short, null-terminated, ASCII
/// strings. They can be attached to any object that has an
/// object header, e.g., data sets, groups, named data types,
/// and data spaces, but not symbolic links.
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
void CommonFG::setComment( const char* name, const char* comment ) const
{
herr_t ret_value = H5Oset_comment_by_name( getLocId(), name, comment, H5P_DEFAULT );
if( ret_value < 0 )
{
throwException("setComment", "H5Oset_comment_by_name failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::setComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name and \a comment.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::setComment( const H5std_string& name, const H5std_string& comment ) const
{
setComment( name.c_str(), comment.c_str() );
}
//--------------------------------------------------------------------------
// Function: CommonFG::removeComment
///\brief Removes the comment from an object specified by its name.
///\param name - IN: Name of the object
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - May 2005
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
void CommonFG::removeComment(const char* name) const
{
herr_t ret_value = H5Oset_comment_by_name(getLocId(), name, NULL, H5P_DEFAULT);
if( ret_value < 0 )
{
throwException("removeComment", "H5Oset_comment_by_name failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::removeComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - May 2005
//--------------------------------------------------------------------------
void CommonFG::removeComment(const H5std_string& name) const
{
removeComment (name.c_str());
}
//--------------------------------------------------------------------------
// Function: CommonFG::getComment
///\brief Retrieves comment for the specified object and its comment's
/// length.
///\param name - IN: Name of the object
///\param bufsize - IN: Length of the comment to retrieve
///\return Comment string
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
// 2007: QAK modified to use H5O APIs; however the first parameter is
// no longer just file or group, this function should be moved
// to another class to accommodate attribute, dataset, and named
// datatype. - BMR
//--------------------------------------------------------------------------
H5std_string CommonFG::getComment( const char* name, size_t bufsize ) const
{
// bufsize is default to 256
// temporary variable
hid_t loc_id = getLocId(); // temporary variable
// temporary C-string for the object's comment; bufsize already including
// null character
char* comment_C = new char[bufsize];
ssize_t ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, bufsize, H5P_DEFAULT);
// if the actual length of the comment is longer than bufsize and bufsize
// was the default value, i.e., not given by the user, then call
// H5Oget_comment_by_name again with the correct value.
// If the call to H5Oget_comment_by_name returned an error, skip this block
// and throw an exception below.
if (ret_value >= 0 && (size_t)ret_value > bufsize && bufsize == 256)
{
size_t new_size = ret_value;
delete []comment_C;
comment_C = new char[new_size]; // new_size including null terminator
ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, new_size, H5P_DEFAULT);
}
// if H5Oget_comment_by_name returns SUCCEED, return the string comment,
// otherwise, throw an exception
if( ret_value < 0 )
{
throwException("getComment", "H5Oget_comment_by_name failed");
}
H5std_string comment = H5std_string(comment_C);
delete []comment_C;
return (comment);
}
//--------------------------------------------------------------------------
// Function: CommonFG::getComment
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5std_string CommonFG::getComment( const H5std_string& name, size_t bufsize ) const
{
return( getComment( name.c_str(), bufsize ));
}
//--------------------------------------------------------------------------
// Function: CommonFG::mount
///\brief Mounts the file \a child onto this group.
///\param name - IN: Name of the group
///\param child - IN: File to mount
///\param plist - IN: Property list to use
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::mount( const char* name, H5File& child, PropList& plist ) const
{
// Obtain identifiers for C API
hid_t plist_id = plist.getId();
hid_t child_id = child.getId();
// Call C routine H5Fmount to do the mouting
herr_t ret_value = H5Fmount( getLocId(), name, child_id, plist_id );
// Raise exception if H5Fmount returns negative value
if( ret_value < 0 )
{
throwException("mount", "H5Fmount failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::mount
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::mount( const H5std_string& name, H5File& child, PropList& plist ) const
{
mount( name.c_str(), child, plist );
}
//--------------------------------------------------------------------------
// Function: CommonFG::unmount
///\brief Unmounts the specified file.
///\param name - IN: Name of the file to unmount
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::unmount( const char* name ) const
{
// Call C routine H5Fmount to do the mouting
herr_t ret_value = H5Funmount( getLocId(), name );
// Raise exception if H5Funmount returns negative value
if( ret_value < 0 )
{
throwException("unmount", "H5Funmount failed");
}
}
//--------------------------------------------------------------------------
// Function: CommonFG::unmount
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void CommonFG::unmount( const H5std_string& name ) const
{
unmount( name.c_str() );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openDataType
///\brief Opens the named generic datatype at this location.
///\param name - IN: Name of the datatype to open
///\return DataType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataType CommonFG::openDataType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openDataType", "H5Topen2 failed");
// No failure, create and return the DataType object
DataType data_type(type_id);
return(data_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openDataType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
DataType CommonFG::openDataType( const H5std_string& name ) const
{
return( openDataType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openArrayType
///\brief Opens the named array datatype at this location.
///\param name - IN: Name of the array datatype to open
///\return ArrayType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - Jul, 2005
//--------------------------------------------------------------------------
ArrayType CommonFG::openArrayType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openArrayType", "H5Topen2 failed");
// No failure, create and return the ArrayType object
ArrayType array_type (type_id);
return(array_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openArrayType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - Jul, 2005
//--------------------------------------------------------------------------
ArrayType CommonFG::openArrayType( const H5std_string& name ) const
{
return( openArrayType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openCompType
///\brief Opens the named compound datatype at this location.
///\param name - IN: Name of the compound datatype to open
///\return CompType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
CompType CommonFG::openCompType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openCompType", "H5Topen2 failed");
// No failure, create and return the CompType object
CompType comp_type(type_id);
return(comp_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openCompType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
CompType CommonFG::openCompType( const H5std_string& name ) const
{
return( openCompType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openEnumType
///\brief Opens the named enumeration datatype at this location.
///\param name - IN: Name of the enumeration datatype to open
///\return EnumType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
EnumType CommonFG::openEnumType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openEnumType", "H5Topen2 failed");
// No failure, create and return the EnumType object
EnumType enum_type(type_id);
return(enum_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openEnumType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
EnumType CommonFG::openEnumType( const H5std_string& name ) const
{
return( openEnumType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openIntType
///\brief Opens the named integer datatype at this location.
///\param name - IN: Name of the integer datatype to open
///\return IntType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
IntType CommonFG::openIntType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openIntType", "H5Topen2 failed");
// No failure, create and return the IntType object
IntType int_type(type_id);
return(int_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openIntType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
IntType CommonFG::openIntType( const H5std_string& name ) const
{
return( openIntType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openFloatType
///\brief Opens the named floating-point datatype at this location.
///\param name - IN: Name of the floating-point datatype to open
///\return FloatType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
FloatType CommonFG::openFloatType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openFloatType", "H5Topen2 failed");
// No failure, create and return the FloatType object
FloatType float_type(type_id);
return(float_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openFloatType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
FloatType CommonFG::openFloatType( const H5std_string& name ) const
{
return( openFloatType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openStrType
///\brief Opens the named string datatype at this location.
///\param name - IN: Name of the string datatype to open
///\return StrType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
StrType CommonFG::openStrType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openStrType", "H5Topen2 failed");
// No failure, create and return the StrType object
StrType str_type(type_id);
return(str_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openStrType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
StrType CommonFG::openStrType( const H5std_string& name ) const
{
return( openStrType( name.c_str()) );
}
//--------------------------------------------------------------------------
// Function: CommonFG::openVarLenType
///\brief Opens the named variable length datatype at this location.
///\param name - IN: Name of the variable length datatype to open
///\return VarLenType instance
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - Jul, 2005
//--------------------------------------------------------------------------
VarLenType CommonFG::openVarLenType( const char* name ) const
{
// Call C function H5Topen2 to open the named datatype in this group,
// given either the file or group id
hid_t type_id = H5Topen2(getLocId(), name, H5P_DEFAULT);
// If the datatype's opening failed, throw an exception
if( type_id < 0 )
throwException("openVarLenType", "H5Topen2 failed");
// No failure, create and return the VarLenType object
VarLenType varlen_type(type_id);
return(varlen_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::openVarLenType
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - Jul, 2005
//--------------------------------------------------------------------------
VarLenType CommonFG::openVarLenType( const H5std_string& name ) const
{
return( openVarLenType( name.c_str()) );
}
#ifndef H5_NO_DEPRECATED_SYMBOLS
//--------------------------------------------------------------------------
// Function: CommonFG::iterateElems
///\brief Iterates a user's function over the entries of a group.
///\param name - IN : Name of group to iterate over
///\param idx - IN/OUT: Starting (IN) and ending (OUT) entry indices
///\param op - IN : User's function to operate on each entry
///\param op_data - IN/OUT: Data associated with the operation
///\return The return value of the first operator that returns non-zero,
/// or zero if all members were processed with no operator
/// returning non-zero.
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int CommonFG::iterateElems( const char* name, int *idx, H5G_iterate_t op , void* op_data )
{
int ret_value = H5Giterate( getLocId(), name, idx, op, op_data );
if( ret_value < 0 )
{
throwException("iterateElems", "H5Giterate failed");
}
return( ret_value );
}
//--------------------------------------------------------------------------
// Function: CommonFG::iterateElems
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function in that it takes an
/// \c H5std_string for \a name.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int CommonFG::iterateElems( const H5std_string& name, int *idx, H5G_iterate_t op , void* op_data )
{
return( iterateElems( name.c_str(), idx, op, op_data ));
}
#endif /* H5_NO_DEPRECATED_SYMBOLS */
//--------------------------------------------------------------------------
// Function: CommonFG::getNumObjs
///\brief Returns the number of objects in this group.
///\return Number of objects
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - January, 2003
//--------------------------------------------------------------------------
hsize_t CommonFG::getNumObjs() const
{
H5G_info_t ginfo; /* Group information */
herr_t ret_value = H5Gget_info(getLocId(), &ginfo);
if(ret_value < 0)
{
throwException("getNumObjs", "H5Gget_info failed");
}
return (ginfo.nlinks);
}
//--------------------------------------------------------------------------
// Function: CommonFG::getObjnameByIdx
///\brief Returns the name of an object in this group, given the
/// object's index.
///\param idx - IN: Transient index of the object
///\return Object name
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// The value of idx can be any nonnegative number less than the
/// total number of objects in the group, which is returned by
/// the function \c CommonFG::getNumObjs. Note that this is a
/// transient index; thus, an object may have a different index
/// each time the group is opened.
// Programmer Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
H5std_string CommonFG::getObjnameByIdx(hsize_t idx) const
{
// call H5Lget_name_by_idx with name as NULL to get its length
ssize_t name_len = H5Lget_name_by_idx(getLocId(), ".", H5_INDEX_NAME, H5_ITER_INC, idx, NULL, 0, H5P_DEFAULT);
if(name_len < 0)
{
throwException("getObjnameByIdx", "H5Lget_name_by_idx failed");
}
// now, allocate C buffer to get the name
char* name_C = new char[name_len+1];
name_len = H5Lget_name_by_idx(getLocId(), ".", H5_INDEX_NAME, H5_ITER_INC, idx, name_C, name_len+1, H5P_DEFAULT);
// clean up and return the string
H5std_string name = H5std_string(name_C);
delete []name_C;
return (name);
}
//--------------------------------------------------------------------------
// Function: CommonFG::getObjnameByIdx
///\brief Retrieves the name of an object in this group, given the
/// object's index.
///\param idx - IN: Transient index of the object
///\param name - IN/OUT: Retrieved name of the object
///\param size - IN: Length to retrieve
///\return Actual size of the object name or 0, if object has no name
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// The value of idx can be any nonnegative number less than the
/// total number of objects in the group, which is returned by
/// the function \c CommonFG::getNumObjs. Note that this is a
/// transient index; thus, an object may have a different index
/// each time the group is opened.
// Programmer Binh-Minh Ribler - January, 2003
//--------------------------------------------------------------------------
ssize_t CommonFG::getObjnameByIdx(hsize_t idx, H5std_string& name, size_t size) const
{
char* name_C = new char[size];
ssize_t name_len = H5Lget_name_by_idx(getLocId(), ".", H5_INDEX_NAME, H5_ITER_INC, idx, name_C, size, H5P_DEFAULT);
if(name_len < 0)
{
throwException("getObjnameByIdx", "H5Lget_name_by_idx failed");
}
name = H5std_string(name_C);
delete []name_C;
return (name_len);
}
#ifndef H5_NO_DEPRECATED_SYMBOLS
//--------------------------------------------------------------------------
// Function: CommonFG::getObjTypeByIdx
///\brief Returns the type of an object in this group, given the
/// object's index.
///\param idx - IN: Transient index of the object
///\return Object type
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - January, 2003
//--------------------------------------------------------------------------
H5G_obj_t CommonFG::getObjTypeByIdx(hsize_t idx) const
{
H5G_obj_t obj_type = H5Gget_objtype_by_idx(getLocId(), idx);
if (obj_type == H5G_UNKNOWN)
{
throwException("getObjTypeByIdx", "H5Gget_objtype_by_idx failed");
}
return (obj_type);
}
//--------------------------------------------------------------------------
// Function: CommonFG::getObjTypeByIdx
///\brief This is an overloaded member function, provided for convenience.
/// It differs from the above function because it also provides
/// the returned object type in text.
///\param idx - IN: Transient index of the object
///\param type_name - IN: Object type in text
///\return Object type
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - January, 2003
//--------------------------------------------------------------------------
H5G_obj_t CommonFG::getObjTypeByIdx(hsize_t idx, H5std_string& type_name) const
{
H5G_obj_t obj_type = H5Gget_objtype_by_idx(getLocId(), idx);
switch (obj_type)
{
case H5G_LINK: type_name = H5std_string("symbolic link"); break;
case H5G_GROUP: type_name = H5std_string("group"); break;
case H5G_DATASET: type_name = H5std_string("dataset"); break;
case H5G_TYPE: type_name = H5std_string("datatype"); break;
case H5G_UNKNOWN:
default:
{
throwException("getObjTypeByIdx", "H5Gget_objtype_by_idx failed");
}
}
return (obj_type);
}
#endif /* H5_NO_DEPRECATED_SYMBOLS */
//--------------------------------------------------------------------------
// Function: CommonFG default constructor
///\brief Default constructor.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
CommonFG::CommonFG() {}
//--------------------------------------------------------------------------
// Function: CommonFG destructor
///\brief Noop destructor.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
CommonFG::~CommonFG() {}
#ifndef H5_NO_NAMESPACE
}
#endif
|