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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "h5repack.h"
#include "H5private.h"
#include "h5diff.h"
#include "h5tools.h"
/*-------------------------------------------------------------------------
* local functions
*-------------------------------------------------------------------------
*/
static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
trav_table_t *travt, hid_t fidout);
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
*
* Purpose: duplicate all referenced HDF5 objects in the file
* and create hard links
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
*
*-------------------------------------------------------------------------
*/
int do_copy_refobjs(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in = (-1); /* read group ID */
hid_t grp_out = (-1); /* write group ID */
hid_t dset_in = (-1); /* read dataset ID */
hid_t dset_out = (-1); /* write dataset ID */
hid_t type_in = (-1); /* named type ID */
hid_t dcpl_id = (-1); /* dataset creation property list ID */
hid_t space_id = (-1); /* space ID */
hid_t ftype_id = (-1); /* file data type ID */
hid_t mtype_id = (-1); /* memory data type ID */
size_t msize; /* memory size of memory type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for(i = 0; i < travt->nobjs; i++) {
switch(travt->objs[i].type) {
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_GROUP
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_GROUP:
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
goto error;
if(H5Gclose(grp_out) < 0)
goto error;
if(H5Gclose(grp_in) < 0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_DATASET
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_DATASET:
if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if((space_id = H5Dget_space(dset_in)) < 0)
goto error;
if((ftype_id = H5Dget_type(dset_in)) < 0)
goto error;
if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
goto error;
if((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
goto error;
if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
goto error;
nelmts = 1;
for(k = 0; k < rank; k++)
nelmts *= dims[k];
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
* are not registered in the current configuration
* 1) the external filters GZIP and SZIP might not be available
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
if(h5tools_canreadf(NULL, dcpl_id) == 1) {
/*-------------------------------------------------------------------------
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
dset_out = FAIL;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
hid_t refobj_id;
hobj_ref_t *refbuf = NULL; /* buffer for object references */
hobj_ref_t *buf = NULL;
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (void *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
printf("cannot read into memory\n" );
goto error;
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
refbuf = HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL){
printf("cannot allocate memory\n" );
goto error;
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference(dset_in, H5R_OBJECT, &buf[u])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur
* in the second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
/* create the reference, -1 parameter for objects */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, -1) < 0)
goto error;
if(options->verbose)
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
} /*refname*/
H5Oclose(refobj_id);
} /* u */
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
goto error;
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (void *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
goto error;
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf = HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf("cannot allocate memory\n");
goto error;
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur
* in the second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
hid_t region_id; /* region id of the referenced dataset */
if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
goto error;
/* create the reference, we need the space_id */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
goto error;
if(H5Sclose(region_id) < 0)
goto error;
if(options->verbose)
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
} /*refname*/
H5Oclose(refobj_id);
} /* u */
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
goto error;
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else {
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
} /* end else */
assert(dset_out != FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
if(H5Dclose(dset_out) < 0)
goto error;
} /*can_read*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
goto error;
if(H5Tclose(mtype_id) < 0)
goto error;
if(H5Pclose(dcpl_id) < 0)
goto error;
if(H5Sclose(space_id) < 0)
goto error;
if(H5Dclose(dset_in) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_NAMED_DATATYPE
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if(H5Tclose(type_in) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_LINK
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_LINK:
/*nothing to do */
break;
default:
break;
} /* end switch */
} /* end for */
return 0;
error:
H5E_BEGIN_TRY {
H5Gclose(grp_in);
H5Gclose(grp_out);
H5Pclose(dcpl_id);
H5Sclose(space_id);
H5Dclose(dset_in);
H5Dclose(dset_out);
H5Tclose(ftype_id);
H5Tclose(mtype_id);
H5Tclose(type_in);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: copy_refs_attr
*
* Purpose: duplicate all referenced HDF5 located in attributes
* relative to LOC_IN, which is obtained either from
* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
static int copy_refs_attr(hid_t loc_in,
hid_t loc_out,
pack_opt_t *options,
trav_table_t *travt,
hid_t fidout /* for saving references */
)
{
hid_t attr_id = -1; /* attr ID */
hid_t attr_out = -1; /* attr ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file data type ID */
hid_t mtype_id = -1; /* memory data type ID */
size_t msize; /* memory size of type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* Object info */
int j;
unsigned u;
if(H5Oget_info(loc_in, ".", &oinfo, H5P_DEFAULT) < 0)
goto error;
for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
/*-------------------------------------------------------------------------
* open
*-------------------------------------------------------------------------
*/
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr_id, 255, name) < 0)
goto error;
/* get the file datatype */
if((ftype_id = H5Aget_type(attr_id)) < 0)
goto error;
/* get the dataspace handle */
if((space_id = H5Aget_space(attr_id)) < 0)
goto error;
/* get dimensions */
if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
goto error;
/*-------------------------------------------------------------------------
* elements
*-------------------------------------------------------------------------
*/
nelmts = 1;
for(j = 0; j < rank; j++)
nelmts *= dims[j];
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
hid_t refobj_id;
hobj_ref_t *refbuf = NULL;
unsigned k;
const char* refname;
hobj_ref_t *buf = NULL;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if (nelmts) {
buf = (void *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
refbuf = HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL) {
printf( "cannot allocate memory\n" );
goto error;
} /* end if */
for(k = 0; k < nelmts; k++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference(attr_id, H5R_OBJECT, &buf[k])) < 0)
goto error;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
* second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
/* create the reference */
if(H5Rcreate(&refbuf[k], fidout, refname, H5R_OBJECT, -1) < 0)
goto error;
if(options->verbose)
printf("object <%s> reference created to <%s>\n", name, refname);
}
H5Oclose(refobj_id);
} /* k */
} /*nelmts*/
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
if(H5Aclose(attr_out) < 0)
goto error;
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
const char* refname;
unsigned k;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (void *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf( "cannot read into memory\n" );
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf = HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf( "cannot allocate memory\n" );
goto error;
} /* end if */
for(k = 0; k < nelmts; k++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference(attr_id, H5R_DATASET_REGION, &buf[k])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
* second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
hid_t region_id; /* region id of the referenced dataset */
if((region_id = H5Rget_region(attr_id, H5R_DATASET_REGION, &buf[k])) < 0)
goto error;
/* create the reference, we need the space_id */
if(H5Rcreate(&refbuf[k], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
goto error;
if(H5Sclose(region_id) < 0)
goto error;
if(options->verbose)
printf("object <%s> region reference created to <%s>\n", name, refname);
} /* end if */
H5Oclose(refobj_id);
} /* k */
} /*nelmts */
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
if(H5Aclose(attr_out) < 0)
goto error;
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
goto error;
if(H5Tclose(mtype_id) < 0)
goto error;
if(H5Sclose(space_id) < 0)
goto error;
if(H5Aclose(attr_id) < 0)
goto error;
} /* u */
return 0;
error:
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
H5Tclose(mtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: MapIdToName
*
* Purpose: map a ID from a reference to a dataset name
*
*-------------------------------------------------------------------------
*/
static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt)
{
unsigned int i;
/* linear search */
for(i = 0; i < travt->nobjs; i++) {
if(travt->objs[i].type == H5O_TYPE_DATASET) {
H5O_info_t ref_oinfo; /* Stat for the refobj id */
/* obtain information to identify the referenced object uniquely */
if(H5Oget_info(refobj_id, ".", &ref_oinfo, H5P_DEFAULT) < 0)
return NULL;
if(ref_oinfo.addr == travt->objs[i].objno)
return(travt->objs[i].name);
} /* end if */
} /* i */
return NULL;
}
|
