summaryrefslogtreecommitdiffstats
path: root/src/H5D.c
blob: b06a9cf7a545067edd676f4ad26639ac8975bc86 (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
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
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
/****************************************************************************
* NCSA HDF								   *
* Software Development Group						   *
* National Center for Supercomputing Applications			   *
* University of Illinois at Urbana-Champaign				   *
* 605 E. Springfield, Champaign IL 61820				   *
*									   *
* For conditions of distribution and use, see the accompanying		   *
* hdf/COPYING file.							   *
*									   *
****************************************************************************/

#ifdef RCSID
static char		RcsId[] = "@(#)$Revision$";
#endif

/* $Id$ */

#include <H5private.h>		/* Generic Functions			*/
#include <H5Iprivate.h>		/* IDs			  	*/
#include <H5ACprivate.h>	/* Cache			  	*/
#include <H5Dprivate.h>		/* Dataset functions			*/
#include <H5Eprivate.h>		/* Error handling		  	*/
#include <H5Gprivate.h>		/* Group headers		  	*/
#include <H5HLprivate.h>		/* Name heap				*/
#include <H5MFprivate.h>	/* File space allocation header		*/
#include <H5MMprivate.h>	/* Memory management			*/
#include <H5Oprivate.h>		/* Object headers		  	*/
#include <H5Pprivate.h>		/* Property lists			*/

#define PABLO_MASK	H5D_mask

/*
 * Define this to be zero or one depending on whether the I/O pipeline should
 * be optimized.
 */
#define H5D_OPTIMIZE_PIPE 1

/*
 * A dataset is the following struct.
 */
struct H5D_t {
    H5G_entry_t		ent;		/*cached object header stuff	*/
    H5T_t		*type;		/*datatype of this dataset	*/
    H5S_t		*space;		/*dataspace of this dataset	*/
    H5D_create_t	*create_parms;	/*creation parameters		*/
    H5O_layout_t	layout;		/*data layout			*/
};

/* Default dataset creation property list */
const H5D_create_t	H5D_create_dflt = {
    H5D_CONTIGUOUS,		/* Layout				*/
    1,				/* Chunk dimensions			*/
    {1, 1, 1, 1, 1, 1, 1, 1,	/* Chunk size.	These default values....*/
     1, 1, 1, 1, 1, 1, 1, 1,	/*...are quite useless.	 Larger chunks..*/
     1, 1, 1, 1, 1, 1, 1, 1,	/*...produce fewer, but larger I/O......*/
     1, 1, 1, 1, 1, 1, 1, 1},	/*...requests.				*/
    {H5F_ADDR_UNDEF,		/* External file list heap address	*/
     0,				/*...slots allocated			*/
     0,				/*...slots used				*/
     NULL}			/*...slot array				*/
};

/* Default dataset transfer property list */
const H5D_xfer_t	H5D_xfer_dflt = {
    1024*1024,			/* Temporary buffer size		*/
    NULL,			/* Type conversion buffer or NULL	*/
    NULL, 			/* Background buffer or NULL		*/
    H5T_BKG_NO,			/* Type of background buffer needed	*/
#ifdef HAVE_PARALLEL
    H5D_XFER_INDEPENDENT,      	/* Independent data transfer      	*/
#endif
};

/* Interface initialization? */
static hbool_t interface_initialize_g = FALSE;
#define INTERFACE_INIT H5D_init_interface
static herr_t H5D_init_interface(void);
static void H5D_term_interface(void);


/*--------------------------------------------------------------------------
NAME
   H5D_init_interface -- Initialize interface-specific information
USAGE
    herr_t H5D_init_interface()
   
RETURNS
   SUCCEED/FAIL
DESCRIPTION
    Initializes any interface-specific data or routines.

--------------------------------------------------------------------------*/
static herr_t
H5D_init_interface(void)
{
    herr_t		    ret_value = SUCCEED;
    FUNC_ENTER(H5D_init_interface, FAIL);

    /* Initialize the atom group for the dataset IDs */
    if ((ret_value = H5I_init_group(H5_DATASET, H5I_DATASETID_HASHSIZE,
				    H5D_RESERVED_ATOMS,
				    (herr_t (*)(void *)) H5D_close)) != FAIL) {
	ret_value = H5_add_exit(H5D_term_interface);
    }
    FUNC_LEAVE(ret_value);
}


/*--------------------------------------------------------------------------
 NAME
    H5D_term_interface
 PURPOSE
    Terminate various H5D objects
 USAGE
    void H5D_term_interface()
 RETURNS
    SUCCEED/FAIL
 DESCRIPTION
    Release the atom group and any other resources allocated.
 GLOBAL VARIABLES
 COMMENTS, BUGS, ASSUMPTIONS
     Can't report errors...
 EXAMPLES
 REVISION LOG
--------------------------------------------------------------------------*/
static void
H5D_term_interface(void)
{
    H5I_destroy_group(H5_DATASET);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dcreate
 *
 * Purpose:	Creates a new dataset named NAME at LOC_ID, opens the
 *		dataset for access, and associates with that dataset constant
 *		and initial persistent properties including the type of each
 *		datapoint as stored in the file (TYPE_ID), the size of the
 *		dataset (SPACE_ID), and other initial miscellaneous
 *		properties (CREATE_PARMS_ID).
 *
 *		All arguments are copied into the dataset, so the caller is
 *		allowed to derive new types, data spaces, and creation
 *		parameters from the old ones and reuse them in calls to
 *		create other datasets.
 *
 * Return:	Success:	The object ID of the new dataset.  At this
 *				point, the dataset is ready to receive its
 *				raw data.  Attempting to read raw data from
 *				the dataset will probably return the fill
 *				value.	The dataset should be closed when
 *				the caller is no longer interested in it.
 *
 *		Failure:	FAIL
 *
 * Errors:
 *		ARGS	  BADTYPE	Not a data space. 
 *		ARGS	  BADTYPE	Not a dataset creation plist. 
 *		ARGS	  BADTYPE	Not a file. 
 *		ARGS	  BADTYPE	Not a type. 
 *		ARGS	  BADVALUE	No name. 
 *		DATASET	  CANTINIT	Can't create dataset. 
 *		DATASET	  CANTREGISTER	Can't register dataset. 
 *
 * Programmer:	Robb Matzke
 *		Wednesday, December  3, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
hid_t
H5Dcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id,
	  hid_t create_parms_id)
{
    H5G_t		   *loc = NULL;
    H5T_t		   *type = NULL;
    H5S_t		   *space = NULL;
    H5D_t		   *new_dset = NULL;
    hid_t		    ret_value = FAIL;
    const H5D_create_t	   *create_parms = NULL;

    FUNC_ENTER(H5Dcreate, FAIL);

    /* Check arguments */
    if (NULL == (loc = H5G_loc(loc_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
    }
    if (!name || !*name) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name");
    }
    if (H5_DATATYPE != H5I_group(type_id) ||
	NULL == (type = H5I_object(type_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type");
    }
    if (H5_DATASPACE != H5I_group(space_id) ||
	NULL == (space = H5I_object(space_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
    }
    if (create_parms_id >= 0) {
	if (H5P_DATASET_CREATE != H5Pget_class(create_parms_id) ||
	    NULL == (create_parms = H5I_object(create_parms_id))) {
	    HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
			  "not a dataset creation property list");
	}
    } else {
	create_parms = &H5D_create_dflt;
    }

    /* build and open the new dataset */
    if (NULL == (new_dset = H5D_create(loc, name, type, space,
				       create_parms))) {
	HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
		      "unable to create dataset");
    }
    /* Register the new datatype and get an ID for it */
    if ((ret_value = H5I_register(H5_DATASET, new_dset)) < 0) {
	H5D_close(new_dset);
	HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
		      "unable to register dataset");
    }
    FUNC_LEAVE(ret_value);
}


/*-------------------------------------------------------------------------
 * Function:	H5Dopen
 *
 * Purpose:	Finds a dataset named NAME at LOC_ID, opens it, and returns
 *		its ID.	 The dataset should be close when the caller is no
 *		longer interested in it.
 *
 * Return:	Success:	A new dataset ID
 *
 *		Failure:	FAIL
 *
 * Errors:
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
hid_t
H5Dopen(hid_t loc_id, const char *name)
{
    H5G_t	*loc = NULL;		/*location holding the dataset	*/
    H5D_t	*dataset = NULL;	/*the dataset			*/
    hid_t	ret_value = FAIL;

    FUNC_ENTER(H5Dopen, FAIL);

    /* Check args */
    if (NULL == (loc = H5G_loc(loc_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
    }
    if (!name || !*name) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name");
    }
    
    /* Find the dataset */
    if (NULL == (dataset = H5D_open(loc, name))) {
	HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found");
    }
    
    /* Create an atom for the dataset */
    if ((ret_value = H5I_register(H5_DATASET, dataset)) < 0) {
	H5D_close(dataset);
	HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
		      "can't register dataset");
    }
    FUNC_LEAVE(ret_value);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dclose
 *
 * Purpose:	Closes access to a dataset (DATASET_ID) and releases
 *		resources used by it. It is illegal to subsequently use that
 *		same dataset ID in calls to other dataset functions.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Errors:
 *		ARGS	  BADTYPE	Not a dataset. 
 *		DATASET	  CANTINIT	Can't free. 
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5Dclose(hid_t dataset_id)
{
    H5D_t		   *dataset = NULL;	/* dataset object to release */

    FUNC_ENTER(H5Dclose, FAIL);

    /* Check args */
    if (H5_DATASET != H5I_group(dataset_id) ||
	NULL == (dataset = H5I_object(dataset_id)) ||
	NULL == dataset->ent.file) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }
    /*
     * Decrement the counter on the dataset.  It will be freed if the count
     * reaches zero.
     */
    if (H5I_dec_ref(dataset_id) < 0) {
	HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free");
    }
    FUNC_LEAVE(SUCCEED);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dget_space
 *
 * Purpose:	Returns a copy of the file data space for a dataset.
 *
 * Return:	Success:	ID for a copy of the data space.  The data
 *				space should be released by calling
 *				H5Sclose().
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Wednesday, January 28, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
hid_t
H5Dget_space (hid_t dataset_id)
{
    H5D_t	*dataset = NULL;
    H5S_t	*copied_space = NULL;
    hid_t	ret_value = FAIL;
    
    FUNC_ENTER (H5Dget_space, FAIL);

    /* Check args */
    if (H5_DATASET!=H5I_group (dataset_id) ||
	NULL==(dataset=H5I_object (dataset_id))) {
	HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }

    /* Copy the data space */
    if (NULL==(copied_space=H5S_copy (dataset->space))) {
	HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		       "unable to copy the data space");
    }

    /* Create an atom */
    if ((ret_value=H5I_register (H5_DATASPACE, copied_space))<0) {
	HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
		       "unable to register data space");
    }

    FUNC_LEAVE (ret_value);
}


/*-------------------------------------------------------------------------
 * Function:	H5Dget_type
 *
 * Purpose:	Returns a copy of the file data type for a dataset.
 *
 * Return:	Success:	ID for a copy of the data type.	 The data
 *				type should be released by calling
 *				H5Tclose().
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Tuesday, February  3, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
hid_t
H5Dget_type (hid_t dataset_id)
{
    
    H5D_t	*dataset = NULL;
    H5T_t	*copied_type = NULL;
    hid_t	ret_value = FAIL;
    
    FUNC_ENTER (H5Dget_type, FAIL);

    /* Check args */
    if (H5_DATASET!=H5I_group (dataset_id) ||
	NULL==(dataset=H5I_object (dataset_id))) {
	HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }

    /* Copy the data type */
    if (NULL==(copied_type=H5T_copy (dataset->type))) {
	HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		       "unable to copy the data type");
    }

    /* Create an atom */
    if ((ret_value=H5I_register (H5_DATATYPE, copied_type))<0) {
	HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
		       "unable to register data type");
    }

    FUNC_LEAVE (ret_value);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dget_create_plist
 *
 * Purpose:	Returns a copy of the dataset creation property list.
 *
 * Return:	Success:	ID for a copy of the dataset creation
 *				property list.  The template should be
 *				released by calling H5Pclose().
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Tuesday, February  3, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
hid_t
H5Dget_create_plist (hid_t dataset_id)
{
    H5D_t		*dataset = NULL;
    H5D_create_t	*copied_parms = NULL;
    hid_t		ret_value = FAIL;
    
    FUNC_ENTER (H5Dget_create_plist, FAIL);

    /* Check args */
    if (H5_DATASET!=H5I_group (dataset_id) ||
	NULL==(dataset=H5I_object (dataset_id))) {
	HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }

    /* Copy the creation property list */
    if (NULL==(copied_parms=H5P_copy (H5P_DATASET_CREATE,
				      dataset->create_parms))) {
	HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		       "unable to copy the creation property list");
    }

    /* Create an atom */
    if ((ret_value=H5I_register ((H5I_group_t)(H5_TEMPLATE_0+
					       H5P_DATASET_CREATE),
				 copied_parms))<0) {
	HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
		       "unable to register creation property list");
    }

    FUNC_LEAVE (ret_value);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dread
 *
 * Purpose:	Reads (part of) a DATASET from the file into application
 *		memory BUF. The part of the dataset to read is defined with
 *		MEM_SPACE_ID and FILE_SPACE_ID.	 The data points are
 *		converted from their file type to the MEM_TYPE_ID specified. 
 *		Additional miscellaneous data transfer properties can be
 *		passed to this function with the XFER_PARMS_ID argument.
 *
 *		The FILE_SPACE_ID can be the constant H5S_ALL which indicates
 *		that the entire file data space is to be referenced.
 *
 *		The MEM_SPACE_ID can be the constant H5S_ALL in which case
 *		the memory data space is the same as the file data space
 *		defined when the dataset was created.
 *
 *		The number of elements in the memory data space must match
 *		the number of elements in the file data space.
 *
 *		The XFER_PARMS_ID can be the constant H5P_DEFAULT in which
 *		case the default data transfer properties are used.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Errors:
 *		ARGS	  BADTYPE	Not a data space. 
 *		ARGS	  BADTYPE	Not a data type. 
 *		ARGS	  BADTYPE	Not a dataset. 
 *		ARGS	  BADTYPE	Not xfer parms. 
 *		ARGS	  BADVALUE	No output buffer. 
 *		DATASET	  READERROR	Can't read data. 
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5Dread(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
	hid_t file_space_id, hid_t xfer_parms_id, void *buf/*out*/)
{
    H5D_t		   *dataset = NULL;
    const H5T_t		   *mem_type = NULL;
    const H5S_t		   *mem_space = NULL;
    const H5S_t		   *file_space = NULL;
    const H5D_xfer_t	   *xfer_parms = NULL;

    FUNC_ENTER(H5Dread, FAIL);

    /* check arguments */
    if (H5_DATASET != H5I_group(dataset_id) ||
	NULL == (dataset = H5I_object(dataset_id)) ||
	NULL == dataset->ent.file) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }
    if (H5_DATATYPE != H5I_group(mem_type_id) ||
	NULL == (mem_type = H5I_object(mem_type_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
    }
    if (H5S_ALL != mem_space_id) {
	if (H5_DATASPACE != H5I_group(mem_space_id) ||
	    NULL == (mem_space = H5I_object(mem_space_id))) {
	    HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
	}
    }
    if (H5S_ALL != file_space_id) {
	if (H5_DATASPACE != H5I_group(file_space_id) ||
	    NULL == (file_space = H5I_object(file_space_id))) {
	    HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
	}
    }
    if (H5P_DEFAULT == xfer_parms_id) {
	xfer_parms = &H5D_xfer_dflt;
    } else if (H5P_DATASET_XFER != H5Pget_class(xfer_parms_id) ||
	       NULL == (xfer_parms = H5I_object(xfer_parms_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
    }
    if (!buf) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer");
    }

    /* read raw data */
    if (H5D_read(dataset, mem_type, mem_space, file_space, xfer_parms,
		 buf/*out*/) < 0) {
	HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data");
    }
    FUNC_LEAVE(SUCCEED);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dwrite
 *
 * Purpose:	Writes (part of) a DATASET from application memory BUF to the
 *		file.  The part of the dataset to write is defined with the
 *		MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
 *		are converted from their current type (MEM_TYPE_ID) to their
 *		file data type.	 Additional miscellaneous data transfer
 *		properties can be passed to this function with the
 *		XFER_PARMS_ID argument.
 *
 *		The FILE_SPACE_ID can be the constant H5S_ALL which indicates
 *		that the entire file data space is to be referenced.
 *
 *		The MEM_SPACE_ID can be the constant H5S_ALL in which case
 *		the memory data space is the same as the file data space
 *		defined when the dataset was created.
 *
 *		The number of elements in the memory data space must match
 *		the number of elements in the file data space.
 *
 *		The XFER_PARMS_ID can be the constant H5P_DEFAULT in which
 *		case the default data transfer properties are used.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Errors:
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5Dwrite(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
	 hid_t file_space_id, hid_t xfer_parms_id, const void *buf)
{
    H5D_t		   *dataset = NULL;
    const H5T_t		   *mem_type = NULL;
    const H5S_t		   *mem_space = NULL;
    const H5S_t		   *file_space = NULL;
    const H5D_xfer_t	   *xfer_parms = NULL;

    FUNC_ENTER(H5Dwrite, FAIL);

    /* check arguments */
    if (H5_DATASET != H5I_group(dataset_id) ||
	NULL == (dataset = H5I_object(dataset_id)) ||
	NULL == dataset->ent.file) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }
    if (H5_DATATYPE != H5I_group(mem_type_id) ||
	NULL == (mem_type = H5I_object(mem_type_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
    }
    if (H5S_ALL != mem_space_id) {
	if (H5_DATASPACE != H5I_group(mem_space_id) ||
	    NULL == (mem_space = H5I_object(mem_space_id))) {
	    HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
	}
    }
    if (H5S_ALL != file_space_id) {
	if (H5_DATASPACE != H5I_group(file_space_id) ||
	    NULL == (file_space = H5I_object(file_space_id))) {
	    HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
	}
    }
    if (H5P_DEFAULT == xfer_parms_id) {
	xfer_parms = &H5D_xfer_dflt;
    } else if (H5P_DATASET_XFER != H5Pget_class(xfer_parms_id) ||
	       NULL == (xfer_parms = H5I_object(xfer_parms_id))) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
    }
    if (!buf) {
	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer");
    }

    /* write raw data */
    if (H5D_write(dataset, mem_type, mem_space, file_space, xfer_parms,
		  buf) < 0) {
	HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't write data");
    }
    FUNC_LEAVE(SUCCEED);
}

/*-------------------------------------------------------------------------
 * Function:	H5Dextend
 *
 * Purpose:	This function makes sure that the dataset is at least of size
 *		SIZE. The dimensionality of SIZE is the same as the data
 *		space of the dataset being changed.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Friday, January 30, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5Dextend (hid_t dataset_id, const hsize_t *size)
{
    H5D_t	*dataset = NULL;
    
    FUNC_ENTER (H5Dextend, FAIL);

    /* Check args */
    if (H5_DATASET!=H5I_group (dataset_id) ||
	NULL==(dataset=H5I_object (dataset_id))) {
	HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
    }
    if (!size) {
	HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified");
    }

    /* Increase size */
    if (H5D_extend (dataset, size)<0) {
	HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		       "unable to extend dataset");
    }

    FUNC_LEAVE (SUCCEED);
}

/*-------------------------------------------------------------------------
 * Function:	H5D_create
 *
 * Purpose:	Creates a new dataset with name NAME in file F and associates
 *		with it a datatype TYPE for each element as stored in the
 *		file, dimensionality information or dataspace SPACE, and
 *		other miscellaneous properties CREATE_PARMS.  All arguments
 *		are deep-copied before being associated with the new dataset,
 *		so the caller is free to subsequently modify them without
 *		affecting the dataset.
 *
 * Return:	Success:	Pointer to a new dataset
 *
 *		Failure:	NULL
 *
 * Errors:
 *		DATASET	  CANTINIT	Can't update dataset header. 
 *		DATASET	  CANTINIT	Problem with the dataset name. 
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
H5D_t *
H5D_create(H5G_t *loc, const char *name, const H5T_t *type, const H5S_t *space,
	   const H5D_create_t *create_parms)
{
    H5D_t		*new_dset = NULL;
    H5D_t		*ret_value = NULL;
    intn		i, ndims;
    hsize_t		max_dim[H5O_LAYOUT_NDIMS];
    H5O_efl_t		*efl = NULL;
    H5F_t		*f = H5G_fileof (loc);

    FUNC_ENTER(H5D_create, NULL);

    /* check args */
    assert (f);
    assert (loc);
    assert (name && *name);
    assert (type);
    assert (space);
    assert (create_parms);

    /* Initialize the dataset object */
    new_dset = H5MM_xcalloc(1, sizeof(H5D_t));
    H5F_addr_undef(&(new_dset->ent.header));
    new_dset->type = H5T_copy(type);
    new_dset->space = H5S_copy(space);
    new_dset->create_parms = H5P_copy (H5P_DATASET_CREATE, create_parms);
    efl = &(new_dset->create_parms->efl);

    /* Total raw data size */
    new_dset->layout.type = new_dset->create_parms->layout;
    new_dset->layout.ndims = H5S_get_ndims(space) + 1;
    assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim));
    new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(type);

    switch (new_dset->create_parms->layout) {
    case H5D_CONTIGUOUS:
	/*
	 * The maximum size of the dataset cannot exceed the storage size.
	 * Also, only the slowest varying dimension of a simple data space
	 * can be extendible.
	 */
	if ((ndims=H5S_get_dims(space, new_dset->layout.dim, max_dim)) < 0) {
	    HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
			"unable to initialize contiguous storage");
	}
	for (i=1; i<ndims; i++) {
	    if (max_dim[i]>new_dset->layout.dim[i]) {
		HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
			     "only the first dimension can be extendible");
	    }
	}
	if (efl->nused>0) {
	    hsize_t max_points = H5S_get_npoints_max (space);
	    hsize_t max_storage = H5O_efl_total_size (efl);

	    if (H5S_UNLIMITED==max_points) {
		if (H5O_EFL_UNLIMITED!=max_storage) {
		    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
				 "unlimited data space but finite storage");
		}
	    } else if (max_points * H5T_get_size (type) < max_points) {
		HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
			     "data space * type size overflowed");
	    } else if (max_points * H5T_get_size (type) > max_storage) {
		HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
			     "data space size exceeds external storage size");
	    }
	} else if (max_dim[0]>new_dset->layout.dim[0]) {
	    HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL,
			 "extendible contiguous non-external dataset");
	}
	break;

    case H5D_CHUNKED:
	/*
	 * Chunked storage allows any type of data space extension, so we
	 * don't even bother checking.
	 */
	if (new_dset->create_parms->chunk_ndims != H5S_get_ndims(space)) {
	    HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL,
		   "dimensionality of chunks doesn't match the data space");
	}
	if (efl->nused>0) {
	    HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
			 "external storage not supported with chunked layout");
	}
	for (i=0; i<new_dset->layout.ndims-1; i++) {
	    new_dset->layout.dim[i] = new_dset->create_parms->chunk_size[i];
	}
	break;

    default:
	HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
    }

    /* Create (open for write access) an object header */
    if (H5O_create(f, 96, &(new_dset->ent)) < 0) {
	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
		    "unable to create dataset object header");
    }

    /* Update the type and space header messages */
    if (H5O_modify(&(new_dset->ent), H5O_DTYPE, 0,
		   (H5O_FLAG_CONSTANT|H5O_FLAG_SHARED),
		   new_dset->type) < 0 ||
	H5S_modify(&(new_dset->ent), new_dset->space) < 0) {
	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
		    "can't update type or space header messages");
    }

    /*
     * Initialize storage.  We assume that external storage is already
     * initialized by the caller, or at least will be before I/O is
     * performed.
     */
    if (0==efl->nused) {
	if (H5F_arr_create(f, &(new_dset->layout)) < 0) {
	    HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
			"unable to initialize storage");
	}
    } else {
	H5F_addr_undef (&(new_dset->layout.addr));
    }

    /* Update layout message */
    if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT,
		    &(new_dset->layout)) < 0) {
	HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
		     "unable to update layout message");
    }

    /* Update external storage message */
    if (efl->nused>0) {
	size_t heap_size = H5HL_ALIGN (1);
	for (i=0; i<efl->nused; i++) {
	    heap_size += H5HL_ALIGN (strlen (efl->slot[i].name)+1);
	}
	if (H5HL_create (f, heap_size, &(efl->heap_addr))<0 ||
	    (size_t)(-1)==H5HL_insert (f, &(efl->heap_addr), 1, "")) {
	    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
			 "unable to create external file list name heap");
	}
	if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT,
			efl)<0) {
	    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
			 "unable to update external file list message");
	}
    }

    /* Give the dataset a name */
    if (H5G_insert(loc, name, &(new_dset->ent)) < 0) {
	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset");
    }

    /* Success */
    ret_value = new_dset;

  done:
    if (!ret_value && new_dset) {
	if (new_dset->type) H5T_close(new_dset->type);
	if (new_dset->space) H5S_close(new_dset->space);
	if (new_dset->create_parms) {
	    H5P_close (H5P_DATASET_CREATE, new_dset->create_parms);
	    new_dset->create_parms = NULL;
	}
	if (H5F_addr_defined(&(new_dset->ent.header))) {
	    H5O_close(&(new_dset->ent));
	}
	new_dset->ent.file = NULL;
	H5MM_xfree(new_dset);
    }
    FUNC_LEAVE(ret_value);
}

/*-------------------------------------------------------------------------
 * Function:	H5D_open
 *
 * Purpose:	Finds a dataset named NAME in file F and builds a descriptor
 *		for it, opening it for access.
 *
 * Return:	Success:	Pointer to a new dataset descriptor.
 *
 *		Failure:	NULL
 *
 * Errors:
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
H5D_t *
H5D_open(H5G_t *loc, const char *name)
{
    H5D_t	*dataset = NULL;	/*the dataset which was found	*/
    H5D_t	*ret_value = NULL;	/*return value			*/
    intn	i;
    H5F_t	*f = NULL;
    
    FUNC_ENTER(H5D_open, NULL);

    /* check args */
    assert (loc);
    assert (name && *name);
    
    f = H5G_fileof (loc);
    dataset = H5MM_xcalloc(1, sizeof(H5D_t));
    dataset->create_parms = H5P_copy (H5P_DATASET_CREATE, &H5D_create_dflt);
    H5F_addr_undef(&(dataset->ent.header));

    /* Open the dataset object */
    if (H5G_find(loc, name, NULL, &(dataset->ent)) < 0) {
	HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found");
    }
    if (H5O_open(&(dataset->ent)) < 0) {
	HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open");
    }
    
    /* Get the type and space */
    if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL)) ||
	NULL==(dataset->space=H5S_read(f, &(dataset->ent)))) {
	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
		    "unable to load type or space info from dataset header");
    }
    
    /*
     * Get the raw data layout info.  It's actually stored in two locations:
     * the storage message of the dataset (dataset->storage) and certain
     * values are copied to the dataset create plist so the user can query
     * them.
     */
    if (NULL==H5O_read(&(dataset->ent), H5O_LAYOUT, 0, &(dataset->layout))) {
	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
		    "unable to read data layout message");
    }
    switch (dataset->layout.type) {
    case H5D_CONTIGUOUS:
	dataset->create_parms->layout = H5D_CONTIGUOUS;
	break;

    case H5D_CHUNKED:
	/*
	 * Chunked storage.  The creation plist's dimension is one less than
	 * the chunk dimension because the chunk includes a dimension for the
	 * individual bytes of the data type.
	 */
	dataset->create_parms->layout = H5D_CHUNKED;
	dataset->create_parms->chunk_ndims = dataset->layout.ndims - 1;
	for (i = 0; i < dataset->layout.ndims - 1; i++) {
	    dataset->create_parms->chunk_size[i] = dataset->layout.dim[i];
	}
	break;

    default:
	HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
    }

    /* Get the external file list message, which might not exist */
    if (NULL==H5O_read (&(dataset->ent), H5O_EFL, 0,
			&(dataset->create_parms->efl)) &&
	!H5F_addr_defined (&(dataset->layout.addr))) {
	HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
		     "storage address is undefined an no external file list");
    }

    /* Success */
    ret_value = dataset;

  done:
    if (!ret_value && dataset) {
	if (H5F_addr_defined(&(dataset->ent.header))) {
	    H5O_close(&(dataset->ent));
	}
	if (dataset->type) {
	    H5T_close(dataset->type);
	}
	if (dataset->space) {
	    H5S_close(dataset->space);
	}
	if (dataset->create_parms) {
	    H5P_close (H5P_DATASET_CREATE, dataset->create_parms);
	}
	dataset->ent.file = NULL;
	H5MM_xfree(dataset);
    }
    FUNC_LEAVE(ret_value);
}

/*-------------------------------------------------------------------------
 * Function:	H5D_close
 *
 * Purpose:	Insures that all data has been saved to the file, closes the
 *		dataset object header, and frees all resources used by the
 *		descriptor.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Errors:
 *		DATASET	  CANTINIT	Couldn't free the type or space,
 *					but the dataset was freed anyway. 
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5D_close(H5D_t *dataset)
{
    uintn		    free_failed;

    FUNC_ENTER(H5D_close, FAIL);

    /* check args */
    assert(dataset && dataset->ent.file);

    /*
     * Release dataset type and space - there isn't much we can do if one of
     * these fails, so we just continue.
     */
    free_failed = (H5T_close(dataset->type) < 0 ||
		   H5S_close(dataset->space) < 0 ||
		   H5P_close (H5P_DATASET_CREATE, dataset->create_parms)); 

    /* Close the dataset object */
    H5O_close(&(dataset->ent));

    /*
     * Free memory.  Before freeing the memory set the file pointer to NULL.
     * We always check for a null file pointer in other H5D functions to be
     * sure we're not accessing an already freed dataset (see the assert()
     * above).
     */
    dataset->ent.file = NULL;
    H5MM_xfree(dataset);

    if (free_failed) {
	HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
		      "couldn't free the type or space, but the dataset was "
		      "freed anyway.");
    }
    FUNC_LEAVE(SUCCEED);
}

/*-------------------------------------------------------------------------
 * Function:	H5D_read
 *
 * Purpose:	Reads (part of) a DATASET into application memory BUF. See
 *		H5Dread() for complete details.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
	 const H5S_t *file_space, const H5D_xfer_t *xfer_parms,
	 void *buf/*out*/)
{
    hsize_t		nelmts;			/*number of elements	*/
    size_t		smine_start;		/*strip mine start loc	*/
    size_t		smine_nelmts;		/*elements per strip	*/
    uint8		*tconv_buf = NULL;	/*data type conv buffer	*/
    uint8		*bkg_buf = NULL;	/*background buffer	*/
    H5T_conv_t		tconv_func = NULL;	/*conversion function	*/
    hid_t		src_id = -1, dst_id = -1;/*temporary type atoms */
    const H5S_conv_t	*sconv_func = NULL;	/*space conversion funcs*/
    H5S_number_t	numbering;		/*element numbering info*/
    H5T_cdata_t		*cdata = NULL;		/*type conversion data	*/
    herr_t		ret_value = FAIL;
    herr_t		status;
    size_t		src_type_size;		/*size of source type	*/
    size_t		dst_type_size;		/*size of destination type*/
    size_t		target_size;		/*desired buffer size	*/
    size_t		request_nelmts;		/*requested strip mine	*/
    H5T_bkg_t		need_bkg;		/*type of background buf*/
#ifdef HAVE_PARALLEL
    int	access_mode_saved = -1;
#endif

    FUNC_ENTER(H5D_read, FAIL);

    /* check args */
    assert(dataset && dataset->ent.file);
    assert(mem_type);
    assert(xfer_parms);
    assert(buf);
    if (!file_space) file_space = dataset->space;
    if (!mem_space) mem_space = file_space;
    nelmts = H5S_get_npoints(mem_space);

    /*
     * Locate the type conversion function and data space conversion
     * functions, and set up the element numbering information. If a data
     * type conversion is necessary then register data type atoms. Data type
     * conversion is necessary if the user has set the `need_bkg' to a high
     * enough value in xfer_parms since turning off data type conversion also
     * turns off background preservation.
     */
    if (nelmts!=H5S_get_npoints (file_space)) {
	HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
		     "src and dest data spaces have different sizes");
    }
    if (0==nelmts) HRETURN (SUCCEED);
    if (NULL == (tconv_func = H5T_find(dataset->type, mem_type,
				       xfer_parms->need_bkg, &cdata))) {
	HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
		    "unable to convert between src and dest data types");
    } else if (H5T_conv_noop!=tconv_func) {
	if ((src_id=H5I_register(H5_DATATYPE, H5T_copy(dataset->type)))<0 ||
	    (dst_id=H5I_register(H5_DATATYPE, H5T_copy(mem_type)))<0) {
	    HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
			"unable to register types for conversion");
	}
    }
    if (NULL==(sconv_func=H5S_find (mem_space, file_space))) {
	HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
		     "unable to convert from file to memory data space");
    }
	
#ifdef HAVE_PARALLEL
    /*
     * Check if collective data transfer requested.
     */
    if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){
	/* verify that the file can support collective access. */
	/* The check may not be necessarily since collective access */
	/* can always be simulated by independent access. */
	/* Nevertheless, must check driver is MPIO before using those */
	/* access_mode which exists only for MPIO case. */
	if (dataset->ent.file->shared->access_parms.driver == H5F_LOW_MPIO){
	    /* Supports only no conversion, type or space, for now. */
	    if (H5T_conv_noop==tconv_func &&
		NULL!=sconv_func->read) {
		/* 
		 * -AKC-
		 * "plant" the collective access mode into the file information
		 * so that the lower level mpio routines know to use collective
		 * access.
		 * This is not thread-safe, is a klutch for now.
		 * Should change all the I/O routines to pass along the xfer
		 * property list to the low level I/O for proper execution.
		 * Make it to work now.  Must fix it later.
		 * -AKC-
		 */
#ifdef AKC
		printf("%s: collective access requested\n", FUNC);
		printf("%s: current f->access_mode = %x\n", FUNC,
		    dataset->ent.file->shared->access_parms.u.mpio.access_mode);
#endif
		access_mode_saved = dataset->ent.file->shared->access_parms.u.mpio.access_mode;
		dataset->ent.file->shared->access_parms.u.mpio.access_mode = H5ACC_COLLECTIVE;
		status = (sconv_func->read)(dataset->ent.file, &(dataset->layout),
					     &(dataset->create_parms->efl),
					     H5T_get_size (dataset->type), file_space,
					     mem_space, buf/*out*/);
		if (status>=0) goto succeed;
		HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
		    "collective read failed");
	    }
	}
	HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
		 "collective access not permissible");
    }
#endif /*HAVE_PARALLEL*/

    
    /*
     * If there is no type conversion then try reading directly into the
     * application's buffer.  This saves at least one mem-to-mem copy.
     */
    if (H5D_OPTIMIZE_PIPE &&
	H5T_conv_noop==tconv_func &&
	NULL!=sconv_func->read) {
	status = (sconv_func->read)(dataset->ent.file, &(dataset->layout),
				    &(dataset->create_parms->efl),
				    H5T_get_size (dataset->type), file_space,
				    mem_space, buf/*out*/);
	if (status>=0) goto succeed;
#ifdef H5D_DEBUG
	fprintf (stderr, "H5D: input pipe optimization failed "
		 "(falling through)\n");
#endif
	H5E_clear ();
    }
    
	
    /*
     * This is the general case.  Figure out the strip mine size.
     */
    src_type_size = H5T_get_size(dataset->type);
    dst_type_size = H5T_get_size(mem_type);
    target_size = xfer_parms->buf_size;
    request_nelmts = target_size / MAX(src_type_size, dst_type_size);
    if (request_nelmts<=0) {
	HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		     "temporary buffer max size is too small");
    }
    if (sconv_func->init) {
	smine_nelmts = (sconv_func->init)(&(dataset->layout), mem_space,
					  file_space, request_nelmts,
					  &numbering/*out*/);
	if (smine_nelmts<=0) {
	    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
			 "unable to initialize element numbering information");
	}
    } else {
	smine_nelmts = request_nelmts;
	HDmemset (&numbering, 0, sizeof numbering);
    }

    /*
     * Get a temporary buffer for type conversion unless the app has already
     * supplied one through the xfer properties. Instead of allocating a
     * buffer which is the exact size, we allocate the target size.  The
     * malloc() is usually less resource-intensive if we allocate/free the
     * same size over and over.
     */
    if (cdata->need_bkg) {
	need_bkg = MAX (cdata->need_bkg, xfer_parms->need_bkg);
    } else {
	need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
    }
    if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
	tconv_buf = H5MM_xmalloc (target_size);
    }
    if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
	bkg_buf = H5MM_xmalloc (smine_nelmts * dst_type_size);
    }

#ifdef H5D_DEBUG
    {
	/* Strip mine diagnostics.... */
	size_t buffer_size = smine_nelmts * MAX (src_type_size, dst_type_size);
	if (smine_nelmts<nelmts) {
	    fprintf (stderr, "H5D: strip mine");
	    if (smine_nelmts!=request_nelmts) {
		fprintf (stderr, " got %lu of %lu",
			 (unsigned long)smine_nelmts,
			 (unsigned long)request_nelmts);
	    }
	    if (buffer_size!=target_size) {
		fprintf (stderr, " (%1.1f%% of buffer)",
			 100.0*(double)buffer_size/(double)target_size);
	    }
	    fprintf (stderr, " %1.1f iterations\n",
		     (double)nelmts/(double)smine_nelmts);
	}
    }
#endif

    /* Start strip mining... */
    for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
	smine_nelmts = MIN (smine_nelmts, nelmts-smine_start);
	
	/*
	 * Gather the data from disk into the data type conversion
	 * buffer. Also gather data from application to background buffer
	 * if necessary.
	 */
	if ((sconv_func->fgath)(dataset->ent.file, &(dataset->layout),
				&(dataset->create_parms->efl), 
				H5T_get_size (dataset->type), file_space,
				&numbering, smine_start, smine_nelmts,
				tconv_buf/*out*/)!=smine_nelmts) {
	    HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed");
	}
	if ((H5D_OPTIMIZE_PIPE && H5T_BKG_YES==need_bkg) ||
	    (!H5D_OPTIMIZE_PIPE && need_bkg)) {
	    if ((sconv_func->mgath)(buf, H5T_get_size (mem_type), mem_space,
				    &numbering, smine_start, smine_nelmts,
				    bkg_buf/*out*/)!=smine_nelmts) {
		HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed");
	    }
	}

	/*
	 * Perform data type conversion.
	 */
	cdata->command = H5T_CONV_CONV;
	cdata->ncalls++;
	if ((tconv_func)(src_id, dst_id, cdata, smine_nelmts, tconv_buf,
			 bkg_buf)<0) {
	    HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
			"data type conversion failed");
	}
	cdata->nelmts += smine_nelmts;

	/*
	 * Scatter the data into memory.
	 */
	if ((sconv_func->mscat)(tconv_buf, H5T_get_size (mem_type), mem_space,
				&numbering, smine_start, smine_nelmts,
				buf/*out*/)<0) {
	    HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "scatter failed");
	}
    }
    
 succeed:
    ret_value = SUCCEED;
    
 done:
    if (src_id >= 0) H5I_dec_ref(src_id);
    if (dst_id >= 0) H5I_dec_ref(dst_id);
    if (tconv_buf && NULL==xfer_parms->tconv_buf) {
	H5MM_xfree(tconv_buf);
    }
    if (bkg_buf && NULL==xfer_parms->bkg_buf) {
	H5MM_xfree (bkg_buf);
    }
#ifdef HAVE_PARALLEL
    /*
     * Check if collective data transfer requested.
     * If so, need to restore the access mode.  Shouldnot needed.
     */
    if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){
	dataset->ent.file->shared->access_parms.u.mpio.access_mode = access_mode_saved;
    }
#endif /*HAVE_PARALLEL*/
    FUNC_LEAVE(ret_value);
}


/*-------------------------------------------------------------------------
 * Function:	H5D_write
 *
 * Purpose:	Writes (part of) a DATASET to a file from application memory
 *		BUF. See H5Dwrite() for complete details.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Thursday, December  4, 1997
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
	  const H5S_t *file_space, const H5D_xfer_t *xfer_parms,
	  const void *buf)
{
    hsize_t		nelmts;			/*total number of elmts	*/
    size_t		smine_start;		/*strip mine start loc	*/
    size_t		smine_nelmts;		/*elements per strip	*/
    uint8		*tconv_buf = NULL;	/*data type conv buffer	*/
    uint8		*bkg_buf = NULL;	/*background buffer	*/
    H5T_conv_t		tconv_func = NULL;	/*conversion function	*/
    hid_t		src_id = -1, dst_id = -1;/*temporary type atoms */
    const H5S_conv_t	*sconv_func = NULL;	/*space conversion funcs*/
    H5S_number_t	numbering;		/*element numbering info*/
    H5T_cdata_t		*cdata = NULL;		/*type conversion data	*/
    herr_t		ret_value = FAIL, status;
    size_t		src_type_size;		/*size of source type	*/
    size_t		dst_type_size;		/*size of destination type*/
    size_t		target_size;		/*desired buffer size	*/
    size_t		request_nelmts;		/*requested strip mine	*/
    H5T_bkg_t		need_bkg;		/*type of background buf*/
#ifdef HAVE_PARALLEL
    int	access_mode_saved = -1;
#endif

    FUNC_ENTER(H5D_write, FAIL);

    /* check args */
    assert(dataset && dataset->ent.file);
    assert(mem_type);
    assert(xfer_parms);
    assert(buf);
    if (!file_space) file_space = dataset->space;
    if (!mem_space) mem_space = file_space;
    nelmts = H5S_get_npoints(mem_space);

    /*
     * Locate the type conversion function and data space conversion
     * functions, and set up the element numbering information. If a data
     * type conversion is necessary then register data type atoms. Data type
     * conversion is necessary if the user has set the `need_bkg' to a high
     * enough value in xfer_parms since turning off data type conversion also
     * turns off background preservation.
     */
    if (nelmts!=H5S_get_npoints (file_space)) {
	HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
		     "src and dest data spaces have different sizes");
    }
    if (0==nelmts) HRETURN (SUCCEED);
    if (NULL == (tconv_func = H5T_find(mem_type, dataset->type,
				       xfer_parms->need_bkg, &cdata))) {
	HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
		    "unable to convert between src and dest data types");
    } else if (H5T_conv_noop!=tconv_func) {
	if ((src_id = H5I_register(H5_DATATYPE, H5T_copy(mem_type)))<0 ||
	    (dst_id = H5I_register(H5_DATATYPE, H5T_copy(dataset->type)))<0) {
	    HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
			"unable to register types for conversion");
	}
    }
    if (NULL==(sconv_func=H5S_find (mem_space, file_space))) {
	HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
		     "unable to convert from memory to file data space");
    }
    
#ifdef HAVE_PARALLEL
    /*
     * Check if collective data transfer requested.
     */
    if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){
	/* verify that the file can support collective access. */
	/* The check may not be necessarily since collective access */
	/* can always be simulated by independent access. */
	/* Nevertheless, must check driver is MPIO before using those */
	/* access_mode which exists only for MPIO case. */
	if (dataset->ent.file->shared->access_parms.driver == H5F_LOW_MPIO){
	    /* Supports only no conversion, type or space, for now. */
	    if (H5T_conv_noop==tconv_func &&
		NULL!=sconv_func->write) {
		/* 
		 * -AKC-
		 * "plant" the collective access mode into the file information
		 * so that the lower level mpio routines know to use collective
		 * access.
		 * This is not thread-safe, is a klutch for now.
		 * Should change all the I/O routines to pass along the xfer
		 * property list to the low level I/O for proper execution.
		 * Make it to work now.  Must fix it later.
		 * -AKC-
		 */
#ifdef AKC
		printf("%s: collective access requested\n", FUNC);
		printf("%s: current f->access_mode = %x\n", FUNC,
		    dataset->ent.file->shared->access_parms.u.mpio.access_mode);
#endif
		access_mode_saved = dataset->ent.file->shared->access_parms.u.mpio.access_mode;
		dataset->ent.file->shared->access_parms.u.mpio.access_mode = H5ACC_COLLECTIVE;
		status = (sconv_func->write)(dataset->ent.file, &(dataset->layout),
					     &(dataset->create_parms->efl),
					     H5T_get_size (dataset->type), file_space,
					     mem_space, buf);
		if (status>=0) goto succeed;
		HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
		    "collective write failed");
	    }
	}
	HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
		 "collective access not permissible");
    }
#endif /*HAVE_PARALLEL*/

    
    /*
     * If there is no type conversion then try writing directly from
     * application buffer to file.
     */
    if (H5D_OPTIMIZE_PIPE &&
	H5T_conv_noop==tconv_func &&
	NULL!=sconv_func->write) {
	status = (sconv_func->write)(dataset->ent.file, &(dataset->layout),
				     &(dataset->create_parms->efl),
				     H5T_get_size (dataset->type), file_space,
				     mem_space, buf);
	if (status>=0) goto succeed;
#ifdef H5D_DEBUG
	fprintf (stderr, "H5D: output pipe optimization failed "
		 "(falling through)\n");
#endif
	H5E_clear ();
    }


    /*
     * This is the general case.  Figure out the strip mine size.
     */
    src_type_size = H5T_get_size(mem_type);
    dst_type_size = H5T_get_size(dataset->type);
    target_size = xfer_parms->buf_size;
    request_nelmts = target_size / MAX (src_type_size, dst_type_size);
    if (request_nelmts<=0) {
	HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		     "temporary buffer max size is too small");
    }
    if (sconv_func->init) {
	smine_nelmts = (sconv_func->init)(&(dataset->layout), mem_space,
					  file_space, request_nelmts,
					  &numbering/*out*/);
	if (smine_nelmts<=0) {
	    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
			 "unable to initialize element numbering information");
	}
    } else {
	smine_nelmts = request_nelmts;
	HDmemset (&numbering, 0, sizeof numbering);
    }

    /*
     * Get a temporary buffer for type conversion unless the app has already
     * supplied one through the xfer properties.  Instead of allocating a
     * buffer which is the exact size, we allocate the target size. The
     * malloc() is usually less resource-intensive if we allocate/free the
     * same size over and over.
     */
    if (cdata->need_bkg) {
	need_bkg = MAX (cdata->need_bkg, xfer_parms->need_bkg);
    } else {
	need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
    }
    if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
	tconv_buf = H5MM_xmalloc (target_size);
    }
    if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
	bkg_buf = H5MM_xmalloc (smine_nelmts * dst_type_size);
    }

#ifdef H5D_DEBUG
    {
	/* Strip mine diagnostics.... */
	size_t buffer_size = smine_nelmts * MAX (src_type_size, dst_type_size);
	if (smine_nelmts<nelmts) {
	    fprintf (stderr, "H5D: strip mine");
	    if (smine_nelmts!=request_nelmts) {
		fprintf (stderr, " got %lu of %lu",
			 (unsigned long)smine_nelmts,
			 (unsigned long)request_nelmts);
	    }
	    if (buffer_size!=target_size) {
		fprintf (stderr, " (%1.1f%% of buffer)",
			 100.0*(double)buffer_size/(double)target_size);
	    }
	    fprintf (stderr, " %1.1f iterations\n",
		     (double)nelmts/(double)smine_nelmts);
	}
    }
#endif

    /* Start strip mining... */
    for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
	smine_nelmts = MIN (smine_nelmts, nelmts-smine_start);

	/*
	 * Gather data from application buffer into the data type conversion
	 * buffer. Also gather data from the file into the background buffer
	 * if necessary.
	 */
	if ((sconv_func->mgath)(buf, H5T_get_size (mem_type), mem_space,
				&numbering, smine_start, smine_nelmts,
				tconv_buf/*out*/)!=smine_nelmts) {
	    HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed");
	}
	if ((H5D_OPTIMIZE_PIPE && H5T_BKG_YES==need_bkg) ||
	    (!H5D_OPTIMIZE_PIPE && need_bkg)) {
	    if ((sconv_func->fgath)(dataset->ent.file, &(dataset->layout),
				    &(dataset->create_parms->efl),
				    H5T_get_size (dataset->type), file_space,
				    &numbering, smine_start, smine_nelmts,
				    bkg_buf/*out*/)!=smine_nelmts) {
		HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
			     "file gather failed");
	    }
	}

	/*
	 * Perform data type conversion.
	 */
	cdata->command = H5T_CONV_CONV;
	cdata->ncalls++;
	if ((tconv_func) (src_id, dst_id, cdata, smine_nelmts, tconv_buf,
			  bkg_buf)<0) {
	    HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
			"data type conversion failed");
	}
	cdata->nelmts += smine_nelmts;

	/*
	 * Scatter the data out to the file.
	 */
	if ((sconv_func->fscat)(dataset->ent.file, &(dataset->layout),
				&(dataset->create_parms->efl),
				H5T_get_size (dataset->type), file_space,
				&numbering, smine_start, smine_nelmts,
				tconv_buf)<0) {
	    HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed");
	}
    }

 succeed:
    ret_value = SUCCEED;
    
 done:
    if (src_id >= 0) H5I_dec_ref(src_id);
    if (dst_id >= 0) H5I_dec_ref(dst_id);
    if (tconv_buf && NULL==xfer_parms->tconv_buf) {
	H5MM_xfree(tconv_buf);
    }
    if (bkg_buf && NULL==xfer_parms->bkg_buf) {
	H5MM_xfree (bkg_buf);
    }
#ifdef HAVE_PARALLEL
    /*
     * Check if collective data transfer requested.
     * If so, need to restore the access mode.  Shouldnot needed.
     */
    if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){
	dataset->ent.file->shared->access_parms.u.mpio.access_mode = access_mode_saved;
    }
#endif /*HAVE_PARALLEL*/
    FUNC_LEAVE(ret_value);
}


/*-------------------------------------------------------------------------
 * Function:	H5D_extend
 *
 * Purpose:	Increases the size of a dataset.
 *
 * Return:	Success:	SUCCEED
 *
 *		Failure:	FAIL
 *
 * Programmer:	Robb Matzke
 *		Friday, January 30, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
herr_t
H5D_extend (H5D_t *dataset, const hsize_t *size)
{
    herr_t	changed;

    FUNC_ENTER (H5D_extend, FAIL);

    /* Check args */
    assert (dataset);
    assert (size);

    /*
     * Restrictions on extensions were checked when the dataset was created.
     * All extensions are allowed here since none should be able to muck
     * things up.
     */
    /*void*/

    /* Increase the size of the data space */
    if ((changed=H5S_extend (dataset->space, size))<0) {
	HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
		       "unable to increase size of data space");
    }

    /* Save the new dataspace in the file if necessary */
    if (changed>0 &&
	H5S_modify (&(dataset->ent), dataset->space)<0) {
	HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
		       "unable to update file with new dataspace");
    }

    FUNC_LEAVE (SUCCEED);
}