summaryrefslogtreecommitdiffstats
path: root/hl/src/H5LD.c
blob: 1307fdacf39b2beee261d9bd2de5177ee078288b (plain)
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
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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 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 "H5LDprivate.h"

/*-------------------------------------------------------------------------
 *
 * internal functions
 *
 *-------------------------------------------------------------------------
 */
static herr_t H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid);
static herr_t H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims);
static size_t H5LD_get_dset_type_size(hid_t did, const char *fields);
static herr_t H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims,
                                  const char *fields, void *buf);

/*-------------------------------------------------------------------------
 * Function: H5LD_clean_vector
 *
 * Purpose: Process the vector of info:
 *		1) free the array of pointers to member names in listv[n]
 *		2) close the type id of the last member in listv[n]
 *		3) free the H5LD_memb_t structure itself as pointed to by listv[n]
 *
 * Return: void
 *
 * Programmer:  Vailin Choi; Aug 2010
 *
 *-------------------------------------------------------------------------
 */
void
H5LD_clean_vector(H5LD_memb_t *listv[])
{
    unsigned n; /* Local index variable */

    HDassert(listv);

    /* Go through info for each field stored in listv[] */
    for (n = 0; listv[n] != NULL; n++) {
        if (listv[n]->names) {
            HDfree(listv[n]->names);
            listv[n]->names = NULL;
        } /* end if */

        /* Close the type id of the last member in the field */
        if (!(listv[n]->last_tid < 0)) {
            H5Tclose(listv[n]->last_tid);
            listv[n]->last_tid = -1;
        } /* end if */

        /* Free the H5LD_memb_t structure for the field */
        HDfree(listv[n]);
        listv[n] = NULL;
    } /* end for */
} /* H5LD_clean_vector() */

/*-------------------------------------------------------------------------
 * Function: H5LD_construct_info()
 *
 * Purpose: Get the remaining info for a field:
 *		1) Get the type id of the last member in the field
 *		2) Get the total offset of all the members in the field
 *		3) Get the type size of the last member in the field
 *
 * Return: Success: 0
 *	   Failure: negative
 *
 * Programmer:  Vailin Choi; Aug 2010
 *
 *-------------------------------------------------------------------------
 */
static herr_t
H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid)
{
    hid_t    tmp_tid = -1;     /* Dataset type id */
    unsigned i;                /* Local index variable */
    herr_t   ret_value = FAIL; /* Return value */

    /* Make a copy of the incoming datatype */
    tmp_tid = H5Tcopy(par_tid);

    /* Validate all the members in a field */
    for (i = 0; memb->names[i] != NULL; i++) {
        hid_t memb_tid; /* Type id for a member in a field */
        int   idx;      /* Index # of a member in a compound datatype */

        /* Get the member index and member type id */
        if ((idx = H5Tget_member_index(tmp_tid, memb->names[i])) < 0)
            goto done;
        if ((memb_tid = H5Tget_member_type(tmp_tid, (unsigned)idx)) < 0)
            goto done;

        /* Sum up the offset of all the members in the field */
        memb->tot_offset += H5Tget_member_offset(tmp_tid, (unsigned)idx);
        if (H5Tclose(tmp_tid) < 0)
            goto done;
        tmp_tid = memb_tid;
    } /* end for */

    /* Get the type size of the last member in the field */
    memb->last_tsize = H5Tget_size(tmp_tid);

    /* Save the type id of the last member in the field */
    memb->last_tid = H5Tcopy(tmp_tid);

    /* Indicate success */
    ret_value = SUCCEED;

done:
    H5E_BEGIN_TRY
    H5Tclose(tmp_tid);
    H5E_END_TRY

    return (ret_value);
} /* H5LD_construct_info() */

/*-------------------------------------------------------------------------
 * Function: H5LD_construct_vector
 *
 * Purpose: Process the comma-separated list of fields in "fields" as follows:
 * 	Example:
 *		"fields": "a.b.c,d"
 *		listv[0]->tot_offset = total offset of "a" & "b" & "c"
 *		listv[0]->last_tid = type id of "c"
 *		listv[0]->last_tsize = type size of "c"
 *		listv[0]->names[0] = "a"
 *		listv[0]->names[1] = "b"
 *		listv[0]->names[2] = "c"
 *		listv[0]->names[3] = NULL
 *
 *		listv[1]->tot_offset = offset of "d"
 *		listv[1]->last_tid = type id of "d"
 *		listv[1]->last_tsize = type size of "d"
 *		listv[1]->names[0] = "d"
 *		listv[1]->names[1] = NULL
 *
 * Return: Success: # of comma-separated fields in "fields"
 *	   Failure: negative value
 *
 * Programmer:  Vailin Choi; Aug 2010
 *
 *-------------------------------------------------------------------------
 */
int
H5LD_construct_vector(char *fields, H5LD_memb_t *listv[] /*OUT*/, hid_t par_tid)
{
    int     nfields;               /* The # of comma-separated fields in "fields" */
    hbool_t end_of_fields = FALSE; /* end of "fields" */
    char *  fields_ptr;            /* Pointer to "fields" */
    int     ret_value = FAIL;      /* Return value */

    HDassert(listv);
    HDassert(fields);

    fields_ptr = fields;
    nfields    = 0;

    /* Process till end of "fields" */
    while (!end_of_fields) {
        H5LD_memb_t *memb = NULL;       /* Pointer to structure for storing a field's info */
        char *       cur;               /* Pointer to a member in a field */
        size_t       len;               /* Estimated # of members in a field */
        hbool_t      gotcomma  = FALSE; /* A comma encountered */
        hbool_t      gotmember = FALSE; /* Getting member in a field */
        hbool_t      valid     = TRUE;  /* Whether a field being processed is valid or not */
        int          j         = 0;     /* The # of members in a field */

        len = (HDstrlen(fields_ptr) / 2) + 2;

        /* Allocate memory for an H5LD_memb_t for storing a field's info */
        if (NULL == (memb = (H5LD_memb_t *)HDcalloc((size_t)1, sizeof(H5LD_memb_t))))
            goto done;

        /* Allocate memory for an array of pointers to member names */
        if (NULL == (memb->names = (char **)HDcalloc(len, sizeof(char *))))
            goto done;

        memb->names[j] = fields_ptr;
        memb->last_tid = -1;
        cur            = fields_ptr;

        /* Continue processing till: not valid or comma encountered or "fields" ended */
        while (valid && !gotcomma && !end_of_fields) {
            switch (*fields_ptr) {
                case '\0':           /* end of list */
                    if (gotmember) { /* getting something and end of "fields" */
                        *cur++ = '\0';
                        ;
                        memb->names[++j] = NULL;
                    }    /* end if */
                    else /* getting nothing but end of list */
                        valid = FALSE;
                    end_of_fields = TRUE;
                    break;

                case '\\':        /* escape character */
                    ++fields_ptr; /* skip it */
                    if (*fields_ptr == '\0')
                        valid = FALSE;
                    else {
                        *cur++    = *fields_ptr++;
                        gotmember = TRUE;
                    } /* end else */
                    break;

                case '.': /* nested field separator */
                    *fields_ptr++ = *cur++ = '\0';
                    ;
                    if (gotmember) {
                        memb->names[++j] = cur;
                        gotmember        = FALSE;
                    } /* end if */
                    else
                        valid = FALSE;
                    break;

                case ',': /* field separator */
                    *fields_ptr++ = *cur++ = '\0';
                    ;
                    if (gotmember) {
                        memb->names[++j] = NULL;
                        gotmember        = FALSE;
                    } /* end if */
                    else
                        valid = FALSE;
                    gotcomma = TRUE;
                    break;

                default:
                    *cur++    = *fields_ptr++;
                    gotmember = TRUE;
                    break;
            } /* end switch */
        }     /* while (valid && !gotcomma && !end_of_fields) */

        /* If valid, put into listv and continue processing further info */
        if (valid) {
            listv[nfields++] = memb;
            if (H5LD_construct_info(memb, par_tid) < 0)
                goto done;
        } /* end if */
        else {
            if (memb)
                HDfree(memb);
            goto done;
        } /* end else */
    }     /* while !end_of_fields */

    /* Indicate success */
    ret_value = nfields;

done:
    listv[nfields] = NULL;
    if (ret_value == FAIL)
        H5LD_clean_vector(listv);

    return (ret_value);
} /* H5LD_construct_vector() */

/*-------------------------------------------------------------------------
 * Function: H5LD_get_dset_dims
 *
 * Purpose: To return the current size for each dimension of the
 *	    dataset's dataspace
 *
 * Return: Success: 0
 *	   Failure: negative value
 *
 * Programmer:  Vailin Choi; March 2010
 *
 *-------------------------------------------------------------------------
 */
static herr_t
H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims)
{
    hid_t  sid       = -1;   /* Dataspace ID */
    herr_t ret_value = FAIL; /* Return Value */

    /* Verify parameter */
    if (cur_dims == NULL)
        goto done;

    /* Get the dataset's dataspace */
    if ((sid = H5Dget_space(did)) < 0)
        goto done;

    /* Get the current dimension size */
    if (H5Sget_simple_extent_dims(sid, cur_dims, NULL) < 0)
        goto done;

    /* Indicate success */
    ret_value = SUCCEED;

done:
    H5E_BEGIN_TRY { H5Sclose(sid); }
    H5E_END_TRY;

    return (ret_value);
} /* H5LD_get_dset_dims() */

/*-------------------------------------------------------------------------
 * Function: H5LD_get_dset_type_size
 *
 * Purpose: To return the size of the dataset's datatype in bytes
 *	null "fields": return the size of the dataset's datatype
 *	non-null "fields": return the size of the dataset's datatype
 *			   with respect to the selection in "fields"
 *
 * Return: Success: size of the dataset's datatype
 *	   Failure: 0 (valid datatypes are never zero size)
 *
 * Programmer:  Vailin Choi; March 2010
 *
 *-------------------------------------------------------------------------
 */
static size_t
H5LD_get_dset_type_size(hid_t did, const char *fields)
{
    hid_t         dset_tid   = -1;   /* Dataset's type identifier */
    hid_t         tid        = -1;   /* Native Type identifier */
    H5LD_memb_t **listv      = NULL; /* Vector for storing information in "fields" */
    char *        dup_fields = NULL; /* A copy of "fields" */
    size_t        ret_value  = 0;    /* Return value */

    /* Get the datatype of the dataset */
    if ((dset_tid = H5Dget_type(did)) < 0)
        goto done;
    if ((tid = H5Tget_native_type(dset_tid, H5T_DIR_DEFAULT)) < 0)
        goto done;

    if (fields == NULL) /* If no "fields" is specified */
        ret_value = H5Tget_size(tid);
    else {                     /* "fields" are specified */
        size_t len;            /* Estimate the number of comma-separated fields in "fields" */
        size_t tot = 0;        /* Data type size of all the fields in "fields" */
        int    n = 0, num = 0; /* Local index variables */

        HDassert(fields && *fields);

        /* Should be a compound datatype if "fields" exists */
        if (H5Tget_class(dset_tid) != H5T_COMPOUND)
            goto done;

        /* Get a copy of "fields" */
        if (NULL == (dup_fields = HDstrdup(fields)))
            goto done;

        /* Allocate memory for a list of H5LD_memb_t pointers to store "fields" info */
        len = (HDstrlen(fields) / 2) + 2;
        if (NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *))))
            goto done;

        /* Process and store info for "fields" */
        if ((num = H5LD_construct_vector(dup_fields, listv /*OUT*/, tid)) < 0)
            goto done;

        /* Sum up the size of all the datatypes in "fields" */
        for (n = 0; n < num; n++)
            tot += listv[n]->last_tsize;

        /* Clean up the vector of H5LD_memb_t structures */
        H5LD_clean_vector(listv);

        /* Return the total size */
        ret_value = tot;
    } /* end else */

done:
    H5E_BEGIN_TRY
    H5Tclose(tid);
    H5Tclose(dset_tid);
    H5E_END_TRY

    /* Free the array of H5LD_memb_t pointers */
    if (listv)
        HDfree(listv);

    /* Free memory */
    if (dup_fields)
        HDfree(dup_fields);

    return (ret_value);
} /* H5LD_get_dset_type_size() */

/*-------------------------------------------------------------------------
 * Function: H5LD_get_dset_elmts
 *
 * Purpose: To retrieve selected data from the dataset
 *
 * Return: Success: 0
 *	   Failure: negative
 *
 * Programmer:  Vailin Choi; August 2010
 *
 *-------------------------------------------------------------------------
 */
static herr_t
H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, const char *fields,
                    void *buf)
{
    hid_t         dtid = -1, tid = -1; /* Dataset type id */
    hid_t         sid = -1, mid = -1;  /* Dataspace and memory space id */
    hssize_t      snum_elmts;          /* Number of dataset elements in the selection (signed) */
    hsize_t       num_elmts;           /* Number of dataset elements in the selection */
    hsize_t       start[H5S_MAX_RANK]; /* Starting offset */
    hsize_t       count[H5S_MAX_RANK]; /* ??offset */
    H5LD_memb_t **listv      = NULL;   /* Vector for storing information in "fields" */
    char *        dup_fields = NULL;   /* A copy of "fields" */
    char *        sav_buf    = NULL;   /* Saved pointer temporary buffer */
    unsigned      ctr;                 /* Counter for # of curr_dims > prev_dims */
    int           ndims;               /* Number of dimensions for the dataset */
    int           i;                   /* Local index variable */
    herr_t        ret_value = FAIL;    /* Return value */

    /* Verify parameters */
    if (prev_dims == NULL || cur_dims == NULL || buf == NULL)
        goto done;

    /* Get dataset's dataspace */
    if ((sid = H5Dget_space(did)) < 0)
        goto done;

    /* Get the number of dimensions */
    if ((ndims = H5Sget_simple_extent_ndims(sid)) < 0)
        goto done;

    /* Verify that cur_dims must have one dimension whose size is greater than prev_dims */
    HDmemset(start, 0, sizeof start);
    HDmemset(count, 0, sizeof count);
    ctr = 0;
    for (i = 0; i < ndims; i++)
        if (cur_dims[i] > prev_dims[i]) {
            ++ctr;
            count[i] = cur_dims[i] - prev_dims[i];
            start[i] = prev_dims[i];
        }      /* end if */
        else { /* < or = */
            start[i] = 0;
            count[i] = MIN(prev_dims[i], cur_dims[i]);
        } /* end else */
    if (!ctr)
        goto done;

    if (ctr == 1) { /* changes for only one dimension */
        /* Make the selection in the dataset based on "cur_dims" and "prev_dims" */
        if (H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
            goto done;
    }      /* end if */
    else { /* changes for more than one dimensions */
        HDmemset(start, 0, sizeof start);

        /* Make the selection in the dataset based on "cur_dims" and "prev_dims" */
        if (H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, cur_dims, NULL) < 0)
            goto done;
        if (H5Sselect_hyperslab(sid, H5S_SELECT_NOTB, start, NULL, prev_dims, NULL) < 0)
            goto done;
    } /* end else */

    /* Get the number of elements in the selection */
    if (0 == (snum_elmts = H5Sget_select_npoints(sid)))
        goto done;
    num_elmts = (hsize_t)snum_elmts;

    /* Create the memory space for the selection */
    if ((mid = H5Screate_simple(1, &num_elmts, NULL)) < 0)
        goto done;

    /* Get the native datatype size */
    if ((dtid = H5Dget_type(did)) < 0)
        goto done;
    if ((tid = H5Tget_native_type(dtid, H5T_DIR_DEFAULT)) < 0)
        goto done;

    if (fields == NULL) { /* nothing in "fields" */
        /* Read and store all the elements in "buf" */
        if (H5Dread(did, tid, mid, sid, H5P_DEFAULT, buf) < 0)
            goto done;
    }                                                /* end if */
    else {                                           /* "fields" is specified */
        unsigned char *buf_p = (unsigned char *)buf; /* Pointer to the destination buffer */
        char *         tmp_buf;                      /* Temporary buffer for data read */
        size_t         tot_tsize;                    /* Total datatype size */
        size_t         len; /* Estimate the number of comma-separated fields in "fields" */

        /* should be a compound datatype if "fields" exists */
        if (H5Tget_class(tid) != H5T_COMPOUND)
            goto done;

        /* Get the total size of the dataset's datatypes */
        if (0 == (tot_tsize = H5LD_get_dset_type_size(did, NULL)))
            goto done;

        /* Allocate memory for reading in the elements in the dataset selection */
        if (NULL == (sav_buf = tmp_buf = (char *)HDcalloc((size_t)num_elmts, tot_tsize)))
            goto done;

        /* Read the dataset elements in the selection */
        if (H5Dread(did, tid, mid, sid, H5P_DEFAULT, tmp_buf) < 0)
            goto done;

        /* Make a copy of "fields" */
        if (NULL == (dup_fields = HDstrdup(fields)))
            goto done;

        /* Allocate memory for the vector of H5LD_memb_t pointers */
        len = (HDstrlen(fields) / 2) + 2;
        if (NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *))))
            goto done;

        /* Process and store information for "fields" */
        if (H5LD_construct_vector(dup_fields, listv, tid) < 0)
            goto done;

        /* Copy data for each dataset element in the selection */
        for (i = 0; i < (int)num_elmts; i++) {
            int j; /* Local index variable */

            /* Copy data for "fields" to the input buffer */
            for (j = 0; listv[j] != NULL; j++) {
                HDmemcpy(buf_p, tmp_buf + listv[j]->tot_offset, listv[j]->last_tsize);
                buf_p += listv[j]->last_tsize;
            } /* end for */
            tmp_buf += tot_tsize;
        } /* end for */

        /* Clean up the vector of H5LD_memb_t structures */
        H5LD_clean_vector(listv);
    } /* end else */

    /* Indicate success */
    ret_value = SUCCEED;

done:
    H5E_BEGIN_TRY
    H5Tclose(dtid);
    H5Tclose(tid);
    H5Sclose(sid);
    H5Sclose(mid);
    H5E_END_TRY

    /* Free the array of H5LD_memb_t pointers */
    if (listv)
        HDfree(listv);

    /* Free memory */
    if (dup_fields)
        HDfree(dup_fields);
    if (sav_buf)
        HDfree(sav_buf);

    return (ret_value);
} /* H5LD_get_dset_elmts() */

/*-------------------------------------------------------------------------
 *
 * Public functions
 *
 *-------------------------------------------------------------------------
 */

/*-------------------------------------------------------------------------
 * Function: H5LDget_dset_dims
 *
 * Purpose: To retrieve the current dimension sizes for a dataset
 *
 * Return: Success: 0
 *	   Failure: negative value
 *
 * Programmer:  Vailin Choi; March 2010
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5LDget_dset_dims(hid_t did, hsize_t *cur_dims)
{
    return (H5LD_get_dset_dims(did, cur_dims));
} /* H5LDget_dset_dims() */

/*-------------------------------------------------------------------------
 * Function: H5LDget_dset_type_size
 *
 * Purpose:  To return the size in bytes of the datatype for the dataset
 *
 * Return: Success: size in bytes of the dataset's datatype
 *	   Failure: 0 (valid datatypes are never zero size)
 *
 * Programmer:  Vailin Choi; March 2010
 *
 *-------------------------------------------------------------------------
 */
size_t
H5LDget_dset_type_size(hid_t did, const char *fields)
{
    return (H5LD_get_dset_type_size(did, fields));
} /* H5LDget_dset_type_size() */

/*-------------------------------------------------------------------------
 * Function: H5LDget_dset_elmts
 *
 * Purpose: To retrieve selected data from the dataset
 *
 * Return: Success: 0
 *	   Failure: negative value
 *
 * Programmer:  Vailin Choi; March 2010
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5LDget_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, const char *fields,
                   void *buf)
{
    return (H5LD_get_dset_elmts(did, prev_dims, cur_dims, fields, buf));
} /* H5LDget_dset_elmts() */