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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "H5private.h"
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
* File: h5repack.c
* Purpose: Public API functions
*-------------------------------------------------------------------------
*/
static int check_options(pack_opt_t *options);
static int check_objects(const char *fname, pack_opt_t *options);
static const char *get_sfilter(H5Z_filter_t filtn);
static int have_request(pack_opt_t *options);
/*-------------------------------------------------------------------------
* Function: h5repack
*
* Purpose: locate all high-level HDF5 objects in the file
* and compress/chunk them using options
*
* Algorithm: 2 traversals are made to the file; the 1st builds a list of
* the objects, the 2nd makes a copy of them, using the options;
* the reason for the 1st traversal is to check for invalid
* object name requests
*
* Return: 0, ok, -1, fail
*-------------------------------------------------------------------------
*/
int
h5repack(const char *infile, const char *outfile, pack_opt_t *options)
{
/* check input */
if (check_options(options) < 0)
return -1;
/* check for objects in input that are in the file */
if (check_objects(infile, options) < 0)
return -1;
/* copy the objects */
if (copy_objects(infile, outfile, options) < 0)
return -1;
return 0;
} /* end h5repack() */
/*-------------------------------------------------------------------------
* Function: h5repack_init
*
* Purpose: initialize options
*
* Return: 0, ok, -1, fail
*-------------------------------------------------------------------------
*/
int
h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
{
int k, n;
HDmemset(options, 0, sizeof(pack_opt_t));
options->min_comp = 0;
options->verbose = verbose;
options->latest = latest;
options->layout_g = H5D_LAYOUT_ERROR;
options->low_bound = H5F_LIBVER_EARLIEST;
options->high_bound = H5F_LIBVER_LATEST;
options->fin_fapl = H5P_DEFAULT;
options->fout_fapl = H5P_DEFAULT;
for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
options->filter_g[n].filtn = -1;
options->filter_g[n].cd_nelmts = 0;
for (k = 0; k < CD_VALUES; k++)
options->filter_g[n].cd_values[k] = 0;
}
return (options_table_init(&(options->op_tbl)));
} /* end h5repack_init() */
/*-------------------------------------------------------------------------
* Function: h5repack_end
*
* Purpose: free options table
*-------------------------------------------------------------------------
*/
int
h5repack_end(pack_opt_t *options)
{
return options_table_free(options->op_tbl);
} /* end h5repack_end() */
/*-------------------------------------------------------------------------
* Function: h5repack_addfilter
*
* Purpose: add a compression -f option to table
* Example: -f dset:GZIP=6
*
* Return: 0, ok, -1, fail
*-------------------------------------------------------------------------
*/
int
h5repack_addfilter(const char *str, pack_opt_t *options)
{
obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
filter_info_t filter; /* filter info for the current -f option entry */
unsigned n_objs; /* number of objects in the current -f or -l option entry */
int is_glb; /* is the filter global */
/* parse the -f (--filter) option */
if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
return -1;
/* if it applies to all objects */
if (is_glb) {
int n;
n = options->n_filter_g++; /* increase # of global filters */
if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
error_msg("maximum number of filters exceeded for <%s>\n", str);
HDfree(obj_list);
return -1;
}
options->filter_g[n] = filter;
}
else
options_add_filter(obj_list, n_objs, filter, options->op_tbl);
HDfree(obj_list);
return 0;
} /* end h5repack_addfilter() */
/*-------------------------------------------------------------------------
* Function: h5repack_addlayout
*
* Purpose: add a layout option
*
* Return: 0, ok, -1, fail
*-------------------------------------------------------------------------
*/
int
h5repack_addlayout(const char *str, pack_opt_t *options)
{
obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
unsigned n_objs; /*number of objects in the current -t or -c option entry */
pack_info_t pack; /*info about layout to extract from parse */
int j;
int ret_value = -1;
init_packobject(&pack);
if (options->all_layout == 1) {
error_msg("invalid layout input: 'all' option is present with other objects <%s>\n", str);
return ret_value;
}
/* parse the layout option */
obj_list = parse_layout(str, &n_objs, &pack, options);
if (obj_list) {
/* set layout option */
options->layout_g = pack.layout;
/* no individual dataset specified */
if (options->all_layout == 1) {
if (pack.layout == H5D_CHUNKED) {
/* -2 means the NONE option, remove chunking
and set the global layout to contiguous */
if (pack.chunk.rank == -2) /* TODO: fix 'magic number' */
options->layout_g = H5D_CONTIGUOUS;
/* otherwise set the global chunking type */
else {
options->chunk_g.rank = pack.chunk.rank;
for (j = 0; j < pack.chunk.rank; j++)
options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
}
}
}
/* individual dataset specified */
if (options->all_layout == 0)
ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
HDfree(obj_list);
ret_value = 0;
} /* end if obj_list exists */
return ret_value;
} /* end h5repack_addlayout() */
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
* were located in h5repack_copy.c as static prior to bugfix1726.
* Made shared functions as copy_attr() was needed in h5repack_refs.c.
* However copy_attr() may be obsoleted when H5Acopy is available and put back
* others to static in h5repack_copy.c.
*/
/*-------------------------------------------------------------------------
* Function: copy_named_datatype
*
* Purpose: Copies the specified datatype anonymously, and returns an open
* id for that datatype in the output file. The first time this
* is called it scans every named datatype in travt into a
* private stack, afterwards it simply scans that stack. The id
* returned must be closed after it is no longer needed.
* named_datatype_free must be called before the program exits
* to free the stack.
*-------------------------------------------------------------------------
*/
hid_t
copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt,
pack_opt_t *options)
{
named_dt_t *dt = NULL; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info2_t oinfo; /* Object info of input dtype */
int token_cmp;
hid_t ret_value = H5I_INVALID_HID;
if (H5Oget_info3(type_in, &oinfo, H5O_INFO_BASIC) < 0)
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Oget_info failed");
if (*named_dt_head_p) {
/* Search the stack for the datatype. */
for (dt = *named_dt_head_p; dt != NULL; dt = dt->next) {
if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0)
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens");
if (token_cmp == 0)
break; // found it!
}
dt_ret = dt;
}
else {
/* Create the stack */
size_t i;
for (i = 0; i < travt->nobjs; i++) {
if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
/* Push onto the stack */
if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed");
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
/* Update the token/address and id */
HDmemcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t));
dt->id_out = H5I_INVALID_HID;
/* Check if this type is the one requested */
if (H5Otoken_cmp(type_in, &oinfo.token, &dt->obj_token, &token_cmp) < 0)
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens");
if (!token_cmp)
dt_ret = dt;
} /* end if named datatype */
} /* end for each object in traversal table */
} /* end else (create the stack) */
/* Handle the case that the requested datatype was not found. This is
* possible if the datatype was committed anonymously in the input file.
*/
if (!dt_ret) {
/* Push the new datatype onto the stack */
if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed");
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
/* Update the token/address and id */
HDmemcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t));
dt_ret->id_out = H5I_INVALID_HID;
} /* end if requested datatype not found */
/* If the requested datatype does not yet exist in the output file, copy it
* anonymously
*/
if (dt_ret->id_out < 0) {
if (options->use_native == 1)
dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT);
else
dt_ret->id_out = H5Tcopy(type_in);
if (dt_ret->id_out < 0)
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Tget_native_type-H5Tcopy failed");
if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Tcommit_anon failed");
} /* end if named datatype not yet in output file */
/* Set return value */
ret_value = dt_ret->id_out;
/* Increment the ref count on id_out, because the calling function will try
* to close it. (TODO: fix scope envy)
*/
if (H5Iinc_ref(ret_value) < 0)
H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Iinc_ref failed");
done:
return ret_value;
} /* end copy_named_datatype() */
/*-------------------------------------------------------------------------
* Function: named_datatype_free
*
* Purpose: Frees the stack of named datatypes.
*-------------------------------------------------------------------------
*/
int
named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
{
named_dt_t *dt = *named_dt_head_p;
int ret_value = -1;
while (dt) {
/* Pop the datatype off the stack and free it */
if (H5Tclose(dt->id_out) < 0 && !ignore_err)
H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed");
dt = dt->next;
HDfree(*named_dt_head_p);
*named_dt_head_p = dt;
}
ret_value = 0;
done:
return (ret_value);
} /* end named_datatype_free() */
/*-------------------------------------------------------------------------
* Function: copy_attr
*
* Purpose: copy attributes located in LOC_IN, which is obtained either from
* loc_id = H5Gopen2( fid, name);
* loc_id = H5Dopen2( fid, name);
* loc_id = H5Topen2( fid, name);
*
* Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
int
copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
hid_t attr_id = H5I_INVALID_HID; /* attr ID */
hid_t attr_out = H5I_INVALID_HID; /* attr ID */
hid_t space_id = H5I_INVALID_HID; /* space ID */
hid_t ftype_id = H5I_INVALID_HID; /* file type ID */
hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */
size_t msize; /* size of type */
void *buf = NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
htri_t is_named; /* Whether the datatype is named */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
H5_timer_t timer; /* Timer for read/write operations */
H5_timevals_t times; /* Elapsed time for each operation */
static double read_time = 0;
static double write_time = 0;
char name[255];
H5O_info2_t oinfo; /* object info */
int j;
unsigned u;
hbool_t is_ref = 0;
H5T_class_t type_class = -1;
int ret_value = 0;
if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed");
/*-------------------------------------------------------------------------
* copy all attributes
*-------------------------------------------------------------------------
*/
for (u = 0; u < (unsigned)oinfo.num_attrs; u++) {
/* 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)
H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed");
if (H5Aget_name(attr_id, (size_t)255, name) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed");
/* get the file datatype */
if ((ftype_id = H5Aget_type(attr_id)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Aget_type failed");
/* Check if the datatype is committed */
if ((is_named = H5Tcommitted(ftype_id)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed");
if (is_named && travt) {
hid_t fidout = H5I_INVALID_HID;
/* Create out file id */
if ((fidout = H5Iget_file_id(loc_out)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Iget_file_id failed");
/* Copy named dt */
if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
H5Fclose(fidout);
H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed");
}
if (H5Fclose(fidout) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Fclose failed");
} /* end if datatype is committed and we have a traversal table */
else {
if (options->use_native == 1)
wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
} /* end else: uncommitted datatype and/or no traversal table */
/* get the dataspace handle */
if ((space_id = H5Aget_space(attr_id)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Aget_space failed");
/* get dimensions */
if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed");
nelmts = 1;
for (j = 0; j < rank; j++)
nelmts *= dims[j];
if ((msize = H5Tget_size(wtype_id)) == 0)
H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed");
/*---------------------------------------------------------------------
* object references are a special case. We cannot just copy the
* buffers, but instead we recreate the reference.
* This is done on a second sweep of the file that just copies the
* referenced objects at copy_refs_attr().
*---------------------------------------------------------------------
*/
type_class = H5Tget_class(wtype_id);
is_ref = (type_class == H5T_REFERENCE);
if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
hid_t base_type = H5I_INVALID_HID;
base_type = H5Tget_super(ftype_id);
is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
if (H5Tclose(base_type) < 0)
H5TOOLS_ERROR((-1), "H5Tclose base_type failed");
} /* end if type_class is variable length or array */
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(wtype_id);
for (j = 0; j < nmembers; j++) {
hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j);
H5T_class_t mtclass = H5Tget_class(mtid);
if (H5Tclose(mtid) < 0)
H5TOOLS_ERROR((-1), "H5Tclose mtid failed");
if (mtclass == H5T_REFERENCE) {
is_ref = 1;
break;
}
} /* end for each member */
} /* end if type_class is H5T_COMPOUND */
read_time = 0;
write_time = 0;
if (!is_ref) {
/*-----------------------------------------------------------------
* read to memory
*-----------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
if (buf == NULL) {
H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
} /* end if */
if (options->verbose == 2) {
H5_timer_init(&timer);
H5_timer_start(&timer);
}
if (H5Aread(attr_id, wtype_id, buf) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Aread failed");
if (options->verbose == 2) {
H5_timer_stop(&timer);
H5_timer_get_times(timer, ×);
read_time += times.elapsed;
}
/*-----------------------------------------------------------------
* copy
*-----------------------------------------------------------------
*/
if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Acreate2 failed on ,%s>", name);
if (options->verbose == 2) {
H5_timer_init(&timer);
H5_timer_start(&timer);
}
if (H5Awrite(attr_out, wtype_id, buf) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Awrite failed");
if (options->verbose == 2) {
H5_timer_stop(&timer);
H5_timer_get_times(timer, ×);
write_time += times.elapsed;
}
/*close*/
if (H5Aclose(attr_out) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed");
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf);
HDfree(buf);
buf = NULL;
} /*H5T_REFERENCE*/
if (options->verbose > 0) {
if (options->verbose == 2)
HDprintf(FORMAT_OBJ_ATTR_TIME, "attr", read_time, write_time, name);
else
HDprintf(FORMAT_OBJ_ATTR, "attr", name);
}
/*---------------------------------------------------------------------
* close
*---------------------------------------------------------------------
*/
if (H5Sclose(space_id) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed");
space_id = H5I_INVALID_HID;
if (H5Tclose(wtype_id) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed");
wtype_id = H5I_INVALID_HID;
if (H5Tclose(ftype_id) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed");
ftype_id = H5I_INVALID_HID;
if (H5Aclose(attr_id) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed");
attr_id = H5I_INVALID_HID;
} /* for u (each attribute) */
done:
H5E_BEGIN_TRY
{
if (buf) {
/* Check if we have VL data and string in the attribute's
* datatype that must be reclaimed
*/
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf);
/* Free buf */
HDfree(buf);
}
H5Aclose(attr_out);
H5Sclose(space_id);
H5Tclose(wtype_id);
H5Tclose(ftype_id);
H5Aclose(attr_id);
}
H5E_END_TRY;
return ret_value;
} /* end copy_attr() */
/*-----------------------------------------------------------------------------
* Function: check_options
*
* Purpose: print options, checks for invalid options
*
* Return: void, return -1 on error
*-----------------------------------------------------------------------------
*/
static int
check_options(pack_opt_t *options)
{
unsigned int i;
int k, j, has_cp = 0, has_ck = 0;
char slayout[30];
int ret_value = 0;
/*-------------------------------------------------------------------------
* Objects to layout
*-------------------------------------------------------------------------
*/
if (options->verbose > 0 && have_request(options)) {
if (options->all_layout == 1) {
HDprintf("All objects to modify layout are...\n");
switch (options->layout_g) {
case H5D_COMPACT:
strcpy(slayout, "compact");
break;
case H5D_CONTIGUOUS:
strcpy(slayout, "contiguous");
break;
case H5D_CHUNKED:
strcpy(slayout, "chunked");
break;
case H5D_VIRTUAL:
strcpy(slayout, "virtual");
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
H5TOOLS_GOTO_ERROR((-1), "invalid layout");
break;
default:
strcpy(slayout, "invalid layout\n");
H5TOOLS_GOTO_DONE((-1));
}
HDprintf(" Apply %s layout to all", slayout);
if (H5D_CHUNKED == options->layout_g) {
HDprintf("with dimension [ ");
for (j = 0; j < options->chunk_g.rank; j++)
HDprintf("%d ", (int)options->chunk_g.chunk_lengths[j]);
HDprintf("]");
}
HDprintf("\n");
}
else
HDprintf("No all objects to modify layout\n");
} /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
char *name = options->op_tbl->objs[i].path;
if (options->op_tbl->objs[i].chunk.rank > 0) {
if (options->verbose > 0) {
HDprintf(" <%s> with chunk size ", name);
for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
HDprintf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
HDprintf("\n");
}
has_ck = 1;
}
else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */
if (options->verbose > 0)
HDprintf(" <%s> %s\n", name, "NONE (contiguous)");
has_ck = 1;
}
} /* end for each object in options */
if (options->all_layout == 1 && has_ck)
H5TOOLS_GOTO_ERROR((-1), "invalid chunking input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
* Objects to filter
*-------------------------------------------------------------------------
*/
if (options->verbose > 0 && have_request(options)) {
if (options->all_filter == 1) {
HDprintf("All objects to apply filter are...\n");
for (k = 0; k < options->n_filter_g; k++) {
H5Z_filter_t filtn = options->filter_g[k].filtn;
if (filtn < 0) {
HDprintf(" Unknown\n");
continue;
}
switch (filtn) {
case H5Z_FILTER_NONE:
HDprintf(" Uncompress all\n");
break;
case H5Z_FILTER_SHUFFLE:
case H5Z_FILTER_FLETCHER32:
HDprintf(" All with %s\n", get_sfilter(filtn));
break;
case H5Z_FILTER_SZIP:
case H5Z_FILTER_DEFLATE:
HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn),
options->filter_g[k].cd_values[0]);
break;
default:
HDprintf(" User Defined %d\n", filtn);
break;
} /* end switch */
} /* end for each filter */
} /* end if options->all_filter == 1 (TODO: meaning) */
else
HDprintf("No all objects to apply filter\n");
} /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
pack_info_t pack = options->op_tbl->objs[i];
char *name = pack.path;
for (j = 0; j < pack.nfilters; j++) {
if (options->verbose > 0) {
if (pack.filter[j].filtn >= 0) {
if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) {
HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn),
pack.filter[j].filtn);
}
else {
HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
}
}
}
has_cp = 1;
} /* end for each filter */
} /* end for each object in options table */
if (options->all_filter == 1 && has_cp)
H5TOOLS_GOTO_ERROR((-1), "invalid compression input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
* Check options for the latest format
*-------------------------------------------------------------------------
*/
if (options->grp_compact < 0)
H5TOOLS_GOTO_ERROR((-1), "invalid maximum number of links to store as header messages");
if (options->grp_indexed < 0)
H5TOOLS_GOTO_ERROR((-1), "invalid minimum number of links to store in the indexed format");
if (options->grp_indexed > options->grp_compact)
H5TOOLS_GOTO_ERROR((-1), "minimum indexed size is greater than the maximum compact size");
for (i = 0; i < 8; i++)
if (options->msg_size[i] < 0)
H5TOOLS_GOTO_ERROR((-1), "invalid shared message size");
/*------------------------------------------------------------------------
* Verify new user userblock options; file name must be present
*------------------------------------------------------------------------
*/
if (options->ublock_filename != NULL && options->ublock_size == 0) {
if (options->verbose > 0) {
HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
options->ublock_filename);
options->ublock_size = 1024;
}
}
if (options->ublock_filename == NULL && options->ublock_size != 0)
H5TOOLS_GOTO_ERROR((-1), "file name missing for user block");
/*------------------------------------------------------------------------
* Verify alignment options; threshold is zero default but alignment not
*------------------------------------------------------------------------
*/
if (options->alignment == 0 && options->threshold != 0)
H5TOOLS_GOTO_ERROR((-1), "alignment for H5Pset_alignment missing");
done:
return ret_value;
} /* end check_options() */
/*-------------------------------------------------------------------------
* Function: check_objects
*
* Purpose: Locate all HDF5 objects in the file and compare with user-supplied
* list.
*
* Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
static int
check_objects(const char *fname, pack_opt_t *options)
{
hid_t fid = H5I_INVALID_HID;
hid_t did = H5I_INVALID_HID;
hid_t sid = H5I_INVALID_HID;
unsigned int i;
int ifil;
trav_table_t *travt = NULL;
int ret_value = 0;
/* nothing to do */
if (options->op_tbl->nelems == 0)
H5TOOLS_GOTO_DONE(0);
/*-------------------------------------------------------------------------
* open the file
*-------------------------------------------------------------------------
*/
if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, options->fin_fapl,
(options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0)) < 0)
H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
/*-------------------------------------------------------------------------
* get the list of objects in the file
*-------------------------------------------------------------------------
*/
/* Initialize indexing options */
h5trav_set_index(sort_by, sort_order);
/* init table */
trav_table_init(fid, &travt);
/* get the list of objects in the file */
if (h5trav_gettable(fid, travt) < 0)
H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed");
/*-------------------------------------------------------------------------
* compare with user supplied list
*-------------------------------------------------------------------------
*/
if (options->verbose > 0)
HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs);
for (i = 0; i < options->op_tbl->nelems; i++) {
pack_info_t obj = options->op_tbl->objs[i];
char *name = obj.path;
if (options->verbose > 0)
HDprintf(" <%s>", name);
/* the input object names are present in the file and are valid */
if (h5trav_getindext(name, travt) < 0)
H5TOOLS_GOTO_ERROR((-1), "%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose > 0 ? "\n" : ""), name, fname);
if (options->verbose > 0)
HDprintf("...Found\n");
for (ifil = 0; ifil < obj.nfilters; ifil++) {
if (obj.filter[ifil].filtn < 0)
H5TOOLS_GOTO_ERROR((-1), "invalid filter");
/* check for extra filter conditions */
switch (obj.filter[ifil].filtn) {
/* chunk size must be smaller than pixels per block */
case H5Z_FILTER_SZIP: {
int j;
hsize_t csize = 1;
unsigned ppb = obj.filter[ifil].cd_values[0];
hsize_t dims[H5S_MAX_RANK];
int rank;
if (obj.chunk.rank > 0) {
rank = obj.chunk.rank;
for (j = 0; j < rank; j++)
csize *= obj.chunk.chunk_lengths[j];
}
else {
if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed");
if ((sid = H5Dget_space(did)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed");
if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed");
HDmemset(dims, 0, sizeof dims);
if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed");
for (j = 0; j < rank; j++)
csize *= dims[j];
if (H5Sclose(sid) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed");
if (H5Dclose(did) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed");
}
if (csize < ppb) {
HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
H5TOOLS_GOTO_DONE(0);
}
} /* end case SZIP */
break;
default:
break;
} /* end switch */
} /* for ifil (each user-defined filter) */
} /* for i (each object in options traversal table) */
done:
H5E_BEGIN_TRY
{
H5Sclose(sid);
H5Dclose(did);
H5Fclose(fid);
}
H5E_END_TRY;
if (travt)
trav_table_free(travt);
return ret_value;
} /* end check_objects() */
/*-------------------------------------------------------------------------
* Function: have_request
*
* Purpose: check if a filter or layout was requested
*
* Return: 1 yes, 0 no
*-------------------------------------------------------------------------
*/
static int
have_request(pack_opt_t *options)
{
if (options->all_filter || options->all_layout || options->op_tbl->nelems)
return 1;
return 0;
} /* end have_request() */
/*-------------------------------------------------------------------------
* Function: get_sfilter
*
* Purpose: return the filter as a string name
*
* Return: name of filter, exit on error
*-------------------------------------------------------------------------
*/
static const char *
get_sfilter(H5Z_filter_t filtn)
{
if (filtn < 0)
return NULL;
else if (filtn == H5Z_FILTER_NONE)
return "NONE";
else if (filtn == H5Z_FILTER_DEFLATE)
return "GZIP";
else if (filtn == H5Z_FILTER_SZIP)
return "SZIP";
else if (filtn == H5Z_FILTER_SHUFFLE)
return "SHUFFLE";
else if (filtn == H5Z_FILTER_FLETCHER32)
return "FLETCHER32";
else if (filtn == H5Z_FILTER_NBIT)
return "NBIT";
else if (filtn == H5Z_FILTER_SCALEOFFSET)
return "SOFF";
else
return "UD";
} /* end get_sfilter() */
|