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
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
2044
2045
2046
2047
2048
2049
2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
2061
2062
2063
2064
2065
2066
2067
2068
2069
2070
2071
2072
2073
2074
2075
2076
2077
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103
2104
2105
2106
2107
2108
2109
2110
2111
2112
2113
2114
2115
2116
2117
2118
2119
2120
2121
2122
2123
2124
2125
2126
2127
2128
2129
2130
2131
2132
2133
2134
2135
2136
2137
2138
2139
2140
2141
2142
2143
2144
2145
2146
2147
2148
2149
2150
2151
2152
2153
2154
2155
2156
2157
2158
2159
2160
2161
2162
2163
2164
2165
2166
2167
2168
2169
2170
2171
2172
2173
2174
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
2186
2187
2188
2189
2190
2191
2192
2193
2194
2195
2196
2197
2198
2199
2200
2201
2202
2203
2204
2205
2206
2207
2208
2209
2210
2211
2212
2213
2214
2215
2216
2217
2218
2219
2220
2221
2222
2223
2224
2225
2226
2227
2228
2229
2230
2231
2232
2233
2234
2235
2236
2237
2238
2239
2240
2241
2242
2243
2244
2245
2246
2247
2248
2249
2250
2251
2252
2253
2254
2255
2256
2257
2258
2259
2260
2261
2262
2263
2264
2265
2266
2267
2268
2269
2270
2271
2272
2273
2274
2275
2276
2277
2278
2279
2280
2281
2282
2283
2284
2285
2286
2287
2288
2289
2290
2291
2292
2293
2294
2295
2296
2297
2298
2299
2300
2301
2302
2303
2304
2305
2306
2307
2308
2309
2310
2311
2312
2313
2314
2315
2316
2317
2318
2319
2320
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
2331
2332
2333
2334
2335
2336
2337
2338
2339
2340
2341
2342
2343
2344
2345
2346
2347
2348
2349
2350
2351
2352
2353
2354
2355
2356
2357
2358
2359
2360
2361
2362
2363
2364
2365
2366
2367
2368
2369
2370
2371
2372
2373
2374
2375
2376
2377
2378
2379
2380
2381
2382
2383
2384
2385
2386
2387
2388
2389
2390
2391
2392
2393
2394
2395
2396
2397
2398
2399
2400
2401
2402
2403
2404
2405
2406
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
2421
2422
2423
2424
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
|
<HTML>
<!--
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-->
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252">
<META NAME="Generator" CONTENT="Microsoft Word 97">
<TITLE>Introduction to HDF5</TITLE>
</HEAD>
<BODY LINK="#0000ff" VLINK="#800080" bgcolor="#FFFFFF">
<hr>
<center>
<table border=0 width=98%>
<tr><td valign=top align=left>
<a href="../H5.intro.html">Introduction to HDF5</a> <br>
<a href="../H5.user.html">HDF5 User Guide</a>
<!--
<a href="../Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
<a href="../RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="../index.html">Other HDF5 documents and links</a>
</td></tr>
</table>
</center>
<hr>
<h1 ALIGN="CENTER">Introduction to HDF5 -- Example Codes</h1></a>
<a name="IEx-TOC">
<hr>
<center>
<table border=0 width=90%>
<tr><th colspan=3>Table of Contents</th></tr></a>
<tr><td valign=top align=left width=42%>
   
<A href="#CreateExample">1: Creating and writing a
dataset</A><br>
   
<A href="#CheckAndReadExample">2. Reading a hyperslab</A><br>
   
<A href="#WriteSelected">3. Writing selected data</A><br>
   
<A href="#VariableLength">4. Working with variable-length</A><br>
   
   
<A href="#VariableLength">datatypes</A><br>
   
<A href="#Array">5. Working with array datatypes</A><br>
   
<A href="#Compound">6. Working with compound</A><br>
   
   
<A href="#Compound">datatypes</A><br>
   
<A href="#CreateExtendWrite">7. Creating and writing an</a><br>
   
   
<A href="#CreateExtendWrite">extendible dataset</A><br>
</td><td width=6%> </td><td valign=top align=left width=42%>
   
<A href="#ReadExtended">8. Reading data</A><br>
   
<A href="#CreateGroups">9. Creating groups</A><br>
   
<A href="#ReadWriteAttributes">10. Writing and reading
attributes</A><br>
   
<a href="#CreateWriteRefObj">11. Creating and writing
references</a><br>
   
   
<a href="#CreateWriteRefObj">to objects</a><br>
   
<a href="#ReadRefObj">12. Reading references to objects</a><br>
   
<a href="#CreateWriteRefReg">13. Creating and writing
references</a><br>
   
   
<a href="#CreateWriteRefReg">to dataset regions</a><br>
   
<a href="#ReadRefReg">14. Reading references to dataset</a><br>
   
   
<a href="#ReadRefReg">regions</a>
</td></tr>
</table>
</center>
<p>
<hr>
<H4><A NAME="CreateExample">Example 1: How to create a homogeneous multi-dimensional dataset</A> and write it to a file.</A></H4>
<P>This example creates a 2-dimensional HDF 5 dataset of little endian 32-bit integers.
<PRE>
<!-- Insert Example 1, h5_write.c, here. -->
/*
* This example writes data to the HDF5 file.
* Data conversion is performed during write operation.
*/
#include <hdf5.h>
#define FILE "SDS.h5"
#define DATASETNAME "IntArray"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int data[NX][NY]; /* data to write */
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j;
}
/*
* 0 1 2 3 4 5
* 1 2 3 4 5 6
* 2 3 4 5 6 7
* 3 4 5 6 7 8
* 4 5 6 7 8 9
*/
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<A NAME="CheckAndReadExample"> </a>
<H4><A NAME="_Toc429885326">Example 2.</A> How to read a hyperslab from file into memory.</A></H4>
<P>This example reads a hyperslab from a 2-d HDF5 dataset into a 3-d dataset in memory.
<PRE>
<!-- Insert Example 2, h5_read.c, here. -->
/*
* This example reads hyperslab from the SDS.h5 file
* created by h5_write.c program into two-dimensional
* plane of the three-dimensional array.
* Information about dataset in the SDS.h5 file is obtained.
*/
#include "hdf5.h"
#define FILE "SDS.h5"
#define DATASETNAME "IntArray"
#define NX_SUB 3 /* hyperslab dimensions */
#define NY_SUB 4
#define NX 7 /* output buffer dimensions */
#define NY 7
#define NZ 3
#define RANK 2
#define RANK_OUT 3
int
main (void)
{
hid_t file, dataset; /* handles */
hid_t datatype, dataspace;
hid_t memspace;
H5T_class_t class; /* datatype class */
H5T_order_t order; /* data order */
size_t size; /*
* size of the data element
* stored in file
*/
hsize_t dimsm[3]; /* memory space dimensions */
hsize_t dims_out[2]; /* dataset dimensions */
herr_t status;
int data_out[NX][NY][NZ ]; /* output buffer */
hsize_t count[2]; /* size of the hyperslab in the file */
hssize_t offset[2]; /* hyperslab offset in the file */
hsize_t count_out[3]; /* size of the hyperslab in memory */
hssize_t offset_out[3]; /* hyperslab offset in memory */
int i, j, k, status_n, rank;
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++) {
for (k = 0; k < NZ ; k++)
data_out[j][i][k] = 0;
}
}
/*
* Open the file and the dataset.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset = H5Dopen(file, DATASETNAME);
/*
* Get datatype and dataspace handles and then query
* dataset class, order, size, rank and dimensions.
*/
datatype = H5Dget_type(dataset); /* datatype handle */
class = H5Tget_class(datatype);
if (class == H5T_INTEGER) printf("Data set has INTEGER type \n");
order = H5Tget_order(datatype);
if (order == H5T_ORDER_LE) printf("Little endian order \n");
size = H5Tget_size(datatype);
printf(" Data size is %d \n", size);
dataspace = H5Dget_space(dataset); /* dataspace handle */
rank = H5Sget_simple_extent_ndims(dataspace);
status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL);
printf("rank %d, dimensions %lu x %lu \n", rank,
(unsigned long)(dims_out[0]), (unsigned long)(dims_out[1]));
/*
* Define hyperslab in the dataset.
*/
offset[0] = 1;
offset[1] = 2;
count[0] = NX_SUB;
count[1] = NY_SUB;
status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL,
count, NULL);
/*
* Define the memory dataspace.
*/
dimsm[0] = NX;
dimsm[1] = NY;
dimsm[2] = NZ ;
memspace = H5Screate_simple(RANK_OUT,dimsm,NULL);
/*
* Define memory hyperslab.
*/
offset_out[0] = 3;
offset_out[1] = 0;
offset_out[2] = 0;
count_out[0] = NX_SUB;
count_out[1] = NY_SUB;
count_out[2] = 1;
status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL,
count_out, NULL);
/*
* Read data from hyperslab in the file into the hyperslab in
* memory and display.
*/
status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace,
H5P_DEFAULT, data_out);
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++) printf("%d ", data_out[j][i][0]);
printf("\n");
}
/*
* 0 0 0 0 0 0 0
* 0 0 0 0 0 0 0
* 0 0 0 0 0 0 0
* 3 4 5 6 0 0 0
* 4 5 6 7 0 0 0
* 5 6 7 8 0 0 0
* 0 0 0 0 0 0 0
*/
/*
* Close/release resources.
*/
H5Tclose(datatype);
H5Dclose(dataset);
H5Sclose(dataspace);
H5Sclose(memspace);
H5Fclose(file);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="_Toc429885331"><A NAME="WriteSelected"></A>Example 3. Writing selected data from memory to a file.</A></H4>
<P>This example shows how to use the selection capabilities of HDF5 to write selected data to a file. It includes the examples discussed in the text.
<pre>
<!-- Insert Example 3, h5_select.c, here. -->
/*
* This program shows how the H5Sselect_hyperslab and H5Sselect_elements
* functions are used to write selected data from memory to the file.
* Program takes 48 elements from the linear buffer and writes them into
* the matrix using 3x2 blocks, (4,3) stride and (2,4) count.
* Then four elements of the matrix are overwritten with the new values and
* file is closed. Program reopens the file and reads and displays the result.
*/
#include <hdf5.h>
#define FILE "Select.h5"
#define MSPACE1_RANK 1 /* Rank of the first dataset in memory */
#define MSPACE1_DIM 50 /* Dataset size in memory */
#define MSPACE2_RANK 1 /* Rank of the second dataset in memory */
#define MSPACE2_DIM 4 /* Dataset size in memory */
#define FSPACE_RANK 2 /* Dataset rank as it is stored in the file */
#define FSPACE_DIM1 8 /* Dimension sizes of the dataset as it is
stored in the file */
#define FSPACE_DIM2 12
/* We will read dataset back from the file
to the dataset in memory with these
dataspace parameters. */
#define MSPACE_RANK 2
#define MSPACE_DIM1 8
#define MSPACE_DIM2 12
#define NPOINTS 4 /* Number of points that will be selected
and overwritten */
int main (void)
{
hid_t file, dataset; /* File and dataset identifiers */
hid_t mid1, mid2, fid; /* Dataspace identifiers */
hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset
(in memory) */
hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset
(in memory */
hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2};
/* Dimension sizes of the dataset (on disk) */
hssize_t start[2]; /* Start of hyperslab */
hsize_t stride[2]; /* Stride of hyperslab */
hsize_t count[2]; /* Block count */
hsize_t block[2]; /* Block sizes */
hssize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points
from the file dataspace */
herr_t ret;
uint i,j;
int matrix[MSPACE_DIM1][MSPACE_DIM2];
int vector[MSPACE1_DIM];
int values[] = {53, 59, 61, 67}; /* New values to be written */
/*
* Buffers' initialization.
*/
vector[0] = vector[MSPACE1_DIM - 1] = -1;
for (i = 1; i < MSPACE1_DIM - 1; i++) vector[i] = i;
for (i = 0; i < MSPACE_DIM1; i++) {
for (j = 0; j < MSPACE_DIM2; j++)
matrix[i][j] = 0;
}
/*
* Create a file.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataspace for the dataset in the file.
*/
fid = H5Screate_simple(FSPACE_RANK, fdim, NULL);
/*
* Create dataset and write it into the file.
*/
dataset = H5Dcreate(file, "Matrix in file", H5T_NATIVE_INT, fid, H5P_DEFAULT);
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, matrix);
/*
* Select hyperslab for the dataset in the file, using 3x2 blocks,
* (4,3) stride and (2,4) count starting at the position (0,1).
*/
start[0] = 0; start[1] = 1;
stride[0] = 4; stride[1] = 3;
count[0] = 2; count[1] = 4;
block[0] = 3; block[1] = 2;
ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block);
/*
* Create dataspace for the first dataset.
*/
mid1 = H5Screate_simple(MSPACE1_RANK, dim1, NULL);
/*
* Select hyperslab.
* We will use 48 elements of the vector buffer starting at the second element.
* Selected elements are 1 2 3 . . . 48
*/
start[0] = 1;
stride[0] = 1;
count[0] = 48;
block[0] = 1;
ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block);
/*
* Write selection from the vector buffer to the dataset in the file.
*
* File dataset should look like this:
* 0 1 2 0 3 4 0 5 6 0 7 8
* 0 9 10 0 11 12 0 13 14 0 15 16
* 0 17 18 0 19 20 0 21 22 0 23 24
* 0 0 0 0 0 0 0 0 0 0 0 0
* 0 25 26 0 27 28 0 29 30 0 31 32
* 0 33 34 0 35 36 0 37 38 0 39 40
* 0 41 42 0 43 44 0 45 46 0 47 48
* 0 0 0 0 0 0 0 0 0 0 0 0
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector);
/*
* Reset the selection for the file dataspace fid.
*/
ret = H5Sselect_none(fid);
/*
* Create dataspace for the second dataset.
*/
mid2 = H5Screate_simple(MSPACE2_RANK, dim2, NULL);
/*
* Select sequence of NPOINTS points in the file dataspace.
*/
coord[0][0] = 0; coord[0][1] = 0;
coord[1][0] = 3; coord[1][1] = 3;
coord[2][0] = 3; coord[2][1] = 5;
coord[3][0] = 5; coord[3][1] = 6;
ret = H5Sselect_elements(fid, H5S_SELECT_SET, NPOINTS,
(const hssize_t **)coord);
/*
* Write new selection of points to the dataset.
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid2, fid, H5P_DEFAULT, values);
/*
* File dataset should look like this:
* 53 1 2 0 3 4 0 5 6 0 7 8
* 0 9 10 0 11 12 0 13 14 0 15 16
* 0 17 18 0 19 20 0 21 22 0 23 24
* 0 0 0 59 0 61 0 0 0 0 0 0
* 0 25 26 0 27 28 0 29 30 0 31 32
* 0 33 34 0 35 36 67 37 38 0 39 40
* 0 41 42 0 43 44 0 45 46 0 47 48
* 0 0 0 0 0 0 0 0 0 0 0 0
*
*/
/*
* Close memory file and memory dataspaces.
*/
ret = H5Sclose(mid1);
ret = H5Sclose(mid2);
ret = H5Sclose(fid);
/*
* Close dataset.
*/
ret = H5Dclose(dataset);
/*
* Close the file.
*/
ret = H5Fclose(file);
/*
* Open the file.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
/*
* Open the dataset.
*/
dataset = dataset = H5Dopen(file,"Matrix in file");
/*
* Read data back to the buffer matrix.
*/
ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, matrix);
/*
* Display the result.
*/
for (i=0; i < MSPACE_DIM1; i++) {
for(j=0; j < MSPACE_DIM2; j++) printf("%3d ", matrix[i][j]);
printf("\n");
}
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="VariableLength"><A NAME="_Toc429885327"></A>Example 4. Working with variable-length datatypes.</A></H4>
<PRE>
/*
* This example shows how to create a dataset with the variable-length
* datatype using user-defined functions for memory management.
*/
#include <hdf5.h>
#define FILE "vltypes.h5"
#define MAX(X,Y) ((X)>(Y)?(X):(Y))
/* 1-D dataset with fixed dimensions */
#define SPACE_NAME "Space"
#define SPACE_RANK 1
#define SPACE_DIM 4
void *vltypes_alloc_custom(size_t size, void *info);
void vltypes_free_custom(void *mem, void *info);
/****************************************************************
**
** vltypes_alloc_custom(): VL datatype custom memory
** allocation routine. This routine just uses malloc to
** allocate the memory and increments the amount of memory
** allocated.
**
****************************************************************/
void *vltypes_alloc_custom(size_t size, void *info)
{
void *ret_value=NULL; /* Pointer to return */
int *mem_used=(int *)info; /* Get the pointer to the memory used */
size_t extra; /* Extra space needed */
/*
* This weird contortion is required on the DEC Alpha to keep the
* alignment correct.
*/
extra=MAX(sizeof(void *),sizeof(int));
if((ret_value=(void *)malloc(extra+size))!=NULL) {
*(int *)ret_value=size;
*mem_used+=size;
} /* end if */
ret_value=((unsigned char *)ret_value)+extra;
return(ret_value);
}
/******************************************************************
** vltypes_free_custom(): VL datatype custom memory
** allocation routine. This routine just uses free to
** release the memory and decrements the amount of memory
** allocated.
** ****************************************************************/
void vltypes_free_custom(void *_mem, void *info)
{
unsigned char *mem;
int *mem_used=(int *)info; /* Get the pointer to the memory used */
size_t extra; /* Extra space needed */
/*
* This weird contortion is required on the DEC Alpha to keep the
* alignment correct.
*/
extra=MAX(sizeof(void *),sizeof(int));
if(_mem!=NULL) {
mem=((unsigned char *)_mem)-extra;
*mem_used-=*(int *)mem;
free(mem);
} /* end if */
}
int main(void)
{
hvl_t wdata[SPACE_DIM]; /* Information to write */
hvl_t rdata[SPACE_DIM]; /* Information read in */
hid_t fid; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t sid; /* Dataspace ID */
hid_t tid; /* Datatype ID */
hid_t xfer_pid; /* Dataset transfer property list ID */
hsize_t dims[] = {SPACE_DIM};
uint i,j; /* counting variables */
int mem_used=0; /* Memory used during allocation */
herr_t ret; /* Generic return value */
/*
* Allocate and initialize VL data to write
*/
for(i=0; i < SPACE_DIM; i++) {
wdata[i].p= (unsigned int *)malloc((i+1)*sizeof(unsigned int));
wdata[i].len=i+1;
for(j=0; j < (i+1); j++)
((unsigned int *)wdata[i].p)[j]=i*10+j;
} /* end for */
/*
* Create file.
*/
fid = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataspace for datasets.
*/
sid = H5Screate_simple(SPACE_RANK, dims, NULL);
/*
* Create a datatype to refer to.
*/
tid = H5Tvlen_create (H5T_NATIVE_UINT);
/*
* Create a dataset.
*/
dataset=H5Dcreate(fid, "Dataset", tid, sid, H5P_DEFAULT);
/*
* Write dataset to disk.
*/
ret=H5Dwrite(dataset, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
/*
* Change to the custom memory allocation routines for reading VL data
*/
xfer_pid=H5Pcreate(H5P_DATASET_XFER);
ret=H5Pset_vlen_mem_manager(xfer_pid, vltypes_alloc_custom,
&mem_used, vltypes_free_custom, &mem_used);
/*
* Read dataset from disk. vltypes_alloc_custom and
* will be used to manage memory.
*/
ret=H5Dread(dataset, tid, H5S_ALL, H5S_ALL, xfer_pid, rdata);
/*
* Display data read in
*/
for(i=0; i < SPACE_DIM; i++) {
printf("%d-th element length is %d \n", i, (unsigned) rdata[i].len);
for(j=0; j < rdata[i].len; j++) {
printf(" %d ",((unsigned int *)rdata[i].p)[j] );
}
printf("\n");
} /* end for */
/*
* Reclaim the read VL data. vltypes_free_custom will be used
* to reclaim the space.
*/
ret=H5Dvlen_reclaim(tid, sid, xfer_pid, rdata);
/*
* Reclaim the write VL data. C language free function will be used
* to reclaim space.
*/
ret=H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, wdata);
/*
* Close Dataset
*/
ret = H5Dclose(dataset);
/*
* Close datatype
*/
ret = H5Tclose(tid);
/*
* Close disk dataspace
*/
ret = H5Sclose(sid);
/*
* Close dataset transfer property list
*/
ret = H5Pclose(xfer_pid);
/*
* Close file
*/
ret = H5Fclose(fid);
}
</PRE>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="Array"><A NAME="_Toc429885327"></A>Example 5. Working with array datatypes.</A></H4>
<PRE>
/*
* This example creates and writes dataset to the HDF5 file.
* Elements of the datasets have an array datatype.
*/
#include <<hdf5.h>
#define FILE "SDS_array_type.h5"
#define DATASETNAME "IntArray"
#define ARRAY_DIM1 5 /* array dimensions and rank */
#define ARRAY_DIM2 4
#define ARRAY_RANK 2
#define SPACE_DIM 10 /* dataset dimensions and rank */
#define RANK 1
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t sdims[] = {SPACE_DIM}; /* dataset dimensions */
hsize_t adims[] = {ARRAY_DIM1, ARRAY_DIM2}; /* array dimensions */
hsize_t adims_out[2];
herr_t status;
int data[SPACE_DIM][ARRAY_DIM1][ARRAY_DIM2]; /* data to write */
int k, i, j;
int array_rank_out;
/*
* Data and output buffer initialization.
*/
for (k = 0; k << SPACE_DIM; k++) {
for (j = 0; j << ARRAY_DIM1; j++) {
for (i = 0; i << ARRAY_DIM2; i++)
data[k][j][i] = k;
}
}
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dataspace = H5Screate_simple(RANK, sdims, NULL);
/*
* Define array datatype for the data in the file.
*/
datatype = H5Tarray_create(H5T_NATIVE_INT, ARRAY_RANK, adims, NULL);
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset);
/*
* Reopen dataset, and return information about its datatype.
*/
dataset = H5Dopen(file, DATASETNAME);
datatype = H5Dget_type(dataset);
array_rank_out = H5Tget_array_ndims(datatype);
status = H5Tget_array_dims(datatype, adims_out, NULL);
printf(" Array datatype rank is %d \n", array_rank_out);
printf(" Array dimensions are %d x %d \n", (int)adims_out[0], (int)adims_out[1]);
H5Tclose(datatype);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
</PRE>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="Compound"><A NAME="_Toc429885327"></A>Example 6. Working with compound datatypes.</A></H4>
<P>This example shows how to create a compound datatype, write an array which has the compound datatype to the file, and read back subsets of fields.
<PRE>
<!-- Insert Example 6, h5_compound.c, here. -->
/*
* This example shows how to create a compound datatype,
* write an array which has the compound datatype to the file,
* and read back fields' subsets.
*/
#include "hdf5.h"
#define FILE "SDScompound.h5"
#define DATASETNAME "ArrayOfStructures"
#define LENGTH 10
#define RANK 1
int
main(void)
{
/* First structure and dataset*/
typedef struct s1_t {
int a;
float b;
double c;
} s1_t;
s1_t s1[LENGTH];
hid_t s1_tid; /* File datatype identifier */
/* Second structure (subset of s1_t) and dataset*/
typedef struct s2_t {
double c;
int a;
} s2_t;
s2_t s2[LENGTH];
hid_t s2_tid; /* Memory datatype handle */
/* Third "structure" ( will be used to read float field of s1) */
hid_t s3_tid; /* Memory datatype handle */
float s3[LENGTH];
int i;
hid_t file, dataset, space; /* Handles */
herr_t status;
hsize_t dim[] = {LENGTH}; /* Dataspace dimensions */
/*
* Initialize the data
*/
for (i = 0; i < LENGTH; i++) {
s1[i].a = i;
s1[i].b = i*i;
s1[i].c = 1./(i+1);
}
/*
* Create the data space.
*/
space = H5Screate_simple(RANK, dim, NULL);
/*
* Create the file.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the memory datatype.
*/
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, "a_name", HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, "c_name", HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
H5Tinsert(s1_tid, "b_name", HOFFSET(s1_t, b), H5T_NATIVE_FLOAT);
/*
* Create the dataset.
*/
dataset = H5Dcreate(file, DATASETNAME, s1_tid, space, H5P_DEFAULT);
/*
* Wtite data to the dataset;
*/
status = H5Dwrite(dataset, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s1);
/*
* Release resources
*/
H5Tclose(s1_tid);
H5Sclose(space);
H5Dclose(dataset);
H5Fclose(file);
/*
* Open the file and the dataset.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset = H5Dopen(file, DATASETNAME);
/*
* Create a datatype for s2
*/
s2_tid = H5Tcreate(H5T_COMPOUND, sizeof(s2_t));
H5Tinsert(s2_tid, "c_name", HOFFSET(s2_t, c), H5T_NATIVE_DOUBLE);
H5Tinsert(s2_tid, "a_name", HOFFSET(s2_t, a), H5T_NATIVE_INT);
/*
* Read two fields c and a from s1 dataset. Fields in the file
* are found by their names "c_name" and "a_name".
*/
status = H5Dread(dataset, s2_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s2);
/*
* Display the fields
*/
printf("\n");
printf("Field c : \n");
for( i = 0; i < LENGTH; i++) printf("%.4f ", s2[i].c);
printf("\n");
printf("\n");
printf("Field a : \n");
for( i = 0; i < LENGTH; i++) printf("%d ", s2[i].a);
printf("\n");
/*
* Create a datatype for s3.
*/
s3_tid = H5Tcreate(H5T_COMPOUND, sizeof(float));
status = H5Tinsert(s3_tid, "b_name", 0, H5T_NATIVE_FLOAT);
/*
* Read field b from s1 dataset. Field in the file is found by its name.
*/
status = H5Dread(dataset, s3_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s3);
/*
* Display the field
*/
printf("\n");
printf("Field b : \n");
for( i = 0; i < LENGTH; i++) printf("%.4f ", s3[i]);
printf("\n");
/*
* Release resources
*/
H5Tclose(s2_tid);
H5Tclose(s3_tid);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="CreateExtendWrite"><A NAME="_Toc429885328"></A>Example 7. Creating and writing an extendible dataset.</A></H4>
<P>This example shows how to create a 3x3 extendible dataset, to extend the dataset to 10x3, then to extend it again to 10x5.
<PRE>
<!-- Insert Example 7, h5_extend_write.c, here. -->
/*
* This example shows how to work with extendible dataset.
* In the current version of the library dataset MUST be
* chunked.
*
*/
#include "hdf5.h"
#define FILE "SDSextendible.h5"
#define DATASETNAME "ExtendibleArray"
#define RANK 2
#define NX 10
#define NY 5
int
main (void)
{
hid_t file; /* handles */
hid_t dataspace, dataset;
hid_t filespace;
hid_t cparms;
hsize_t dims[2] = { 3, 3}; /*
* dataset dimensions
* at the creation time
*/
hsize_t dims1[2] = { 3, 3}; /* data1 dimensions */
hsize_t dims2[2] = { 7, 1}; /* data2 dimensions */
hsize_t dims3[2] = { 2, 2}; /* data3 dimensions */
hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
hsize_t chunk_dims[2] ={2, 5};
hsize_t size[2];
hssize_t offset[2];
herr_t status;
int data1[3][3] = { {1, 1, 1}, /* data to write */
{1, 1, 1},
{1, 1, 1} };
int data2[7] = { 2, 2, 2, 2, 2, 2, 2};
int data3[2][2] = { {3, 3},
{3, 3} };
/*
* Create the data space with unlimited dimensions.
*/
dataspace = H5Screate_simple(RANK, dims, maxdims);
/*
* Create a new file. If file exists its contents will be overwritten.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Modify dataset creation properties, i.e. enable chunking.
*/
cparms = H5Pcreate (H5P_DATASET_CREATE);
status = H5Pset_chunk( cparms, RANK, chunk_dims);
/*
* Create a new dataset within the file using cparms
* creation properties.
*/
dataset = H5Dcreate(file, DATASETNAME, H5T_NATIVE_INT, dataspace,
cparms);
/*
* Extend the dataset. This call assures that dataset is at least 3 x 3.
*/
size[0] = 3;
size[1] = 3;
status = H5Dextend (dataset, size);
/*
* Select a hyperslab.
*/
filespace = H5Dget_space (dataset);
offset[0] = 0;
offset[1] = 0;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
dims1, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data1);
/*
* Extend the dataset. Dataset becomes 10 x 3.
*/
dims[0] = dims1[0] + dims2[0];
size[0] = dims[0];
size[1] = dims[1];
status = H5Dextend (dataset, size);
/*
* Select a hyperslab.
*/
filespace = H5Dget_space (dataset);
offset[0] = 3;
offset[1] = 0;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
dims2, NULL);
/*
* Define memory space
*/
dataspace = H5Screate_simple(RANK, dims2, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data2);
/*
* Extend the dataset. Dataset becomes 10 x 5.
*/
dims[1] = dims1[1] + dims3[1];
size[0] = dims[0];
size[1] = dims[1];
status = H5Dextend (dataset, size);
/*
* Select a hyperslab
*/
filespace = H5Dget_space (dataset);
offset[0] = 0;
offset[1] = 3;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
dims3, NULL);
/*
* Define memory space.
*/
dataspace = H5Screate_simple(RANK, dims3, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data3);
/*
* Resulting dataset
*
* 3 3 3 2 2
* 3 3 3 2 2
* 3 3 3 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
*/
/*
* Close/release resources.
*/
H5Dclose(dataset);
H5Sclose(dataspace);
H5Sclose(filespace);
H5Fclose(file);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="ReadExtended"><A NAME="_Toc429885329"></A>Example 8. Reading data.</A></H4>
<P>This example shows how to read information the chunked dataset written by <A HREF="#CreateExtendWrite">Example 7</A>.
<PRE>
<!-- Insert Example 8, h5_chunk_read.c, here. -->
/*
* This example shows how to read data from a chunked dataset.
* We will read from the file created by h5_extend_write.c
*/
#include "hdf5.h"
#define FILE "SDSextendible.h5"
#define DATASETNAME "ExtendibleArray"
#define RANK 2
#define RANKC 1
#define NX 10
#define NY 5
int
main (void)
{
hid_t file; /* handles */
hid_t dataset;
hid_t filespace;
hid_t memspace;
hid_t cparms;
hsize_t dims[2]; /* dataset and chunk dimensions*/
hsize_t chunk_dims[2];
hsize_t col_dims[1];
hsize_t count[2];
hssize_t offset[2];
herr_t status, status_n;
int data_out[NX][NY]; /* buffer for dataset to be read */
int chunk_out[2][5]; /* buffer for chunk to be read */
int column[10]; /* buffer for column to be read */
int rank, rank_chunk;
hsize_t i, j;
/*
* Open the file and the dataset.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset = H5Dopen(file, DATASETNAME);
/*
* Get dataset rank and dimension.
*/
filespace = H5Dget_space(dataset); /* Get filespace handle first. */
rank = H5Sget_simple_extent_ndims(filespace);
status_n = H5Sget_simple_extent_dims(filespace, dims, NULL);
printf("dataset rank %d, dimensions %lu x %lu\n",
rank, (unsigned long)(dims[0]), (unsigned long)(dims[1]));
/*
* Get creation properties list.
*/
cparms = H5Dget_create_plist(dataset); /* Get properties handle first. */
/*
* Check if dataset is chunked.
*/
if (H5D_CHUNKED == H5Pget_layout(cparms)) {
/*
* Get chunking information: rank and dimensions
*/
rank_chunk = H5Pget_chunk(cparms, 2, chunk_dims);
printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk,
(unsigned long)(chunk_dims[0]), (unsigned long)(chunk_dims[1]));
}
/*
* Define the memory space to read dataset.
*/
memspace = H5Screate_simple(RANK,dims,NULL);
/*
* Read dataset back and display.
*/
status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace,
H5P_DEFAULT, data_out);
printf("\n");
printf("Dataset: \n");
for (j = 0; j < dims[0]; j++) {
for (i = 0; i < dims[1]; i++) printf("%d ", data_out[j][i]);
printf("\n");
}
/*
* dataset rank 2, dimensions 10 x 5
* chunk rank 2, dimensions 2 x 5
* Dataset:
* 1 1 1 3 3
* 1 1 1 3 3
* 1 1 1 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
*/
/*
* Read the third column from the dataset.
* First define memory dataspace, then define hyperslab
* and read it into column array.
*/
col_dims[0] = 10;
memspace = H5Screate_simple(RANKC, col_dims, NULL);
/*
* Define the column (hyperslab) to read.
*/
offset[0] = 0;
offset[1] = 2;
count[0] = 10;
count[1] = 1;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
count, NULL);
status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace,
H5P_DEFAULT, column);
printf("\n");
printf("Third column: \n");
for (i = 0; i < 10; i++) {
printf("%d \n", column[i]);
}
/*
* Third column:
* 1
* 1
* 1
* 0
* 0
* 0
* 0
* 0
* 0
* 0
*/
/*
* Define the memory space to read a chunk.
*/
memspace = H5Screate_simple(rank_chunk,chunk_dims,NULL);
/*
* Define chunk in the file (hyperslab) to read.
*/
offset[0] = 2;
offset[1] = 0;
count[0] = chunk_dims[0];
count[1] = chunk_dims[1];
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
count, NULL);
/*
* Read chunk back and display.
*/
status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace,
H5P_DEFAULT, chunk_out);
printf("\n");
printf("Chunk: \n");
for (j = 0; j < chunk_dims[0]; j++) {
for (i = 0; i < chunk_dims[1]; i++) printf("%d ", chunk_out[j][i]);
printf("\n");
}
/*
* Chunk:
* 1 1 1 0 0
* 2 0 0 0 0
*/
/*
* Close/release resources.
*/
H5Pclose(cparms);
H5Dclose(dataset);
H5Sclose(filespace);
H5Sclose(memspace);
H5Fclose(file);
return 0;
)
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="CreateGroups"><A NAME="_Toc429885330"></A>Example 9. Creating groups.</A></H4>
<P>This example shows how to create and access a group in an
HDF5 file and to place a dataset within this group.
It also illustrates the usage of the <code>H5Giterate</code>,
<code>H5Glink</code>, and <code>H5Gunlink</code> functions.
<PRE>
<!-- Insert Example 9, h5_group.c, here. -->
/*
* This example creates a group in the file and dataset in the group.
* Hard link to the group object is created and the dataset is accessed
* under different names.
* Iterator function is used to find the object names in the root group.
*/
#include "hdf5.h"
#define FILE "group.h5"
#define RANK 2
herr_t file_info(hid_t loc_id, const char *name, void *opdata);
/* Operator function */
int
main(void)
{
hid_t file;
hid_t grp;
hid_t dataset, dataspace;
hid_t plist;
herr_t status;
hsize_t dims[2];
hsize_t cdims[2];
int idx;
/*
* Create a file.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a group in the file.
*/
grp = H5Gcreate(file, "/Data", 0);
/*
* Create dataset "Compressed Data" in the group using absolute
* name. Dataset creation property list is modified to use
* GZIP compression with the compression effort set to 6.
* Note that compression can be used only when dataset is chunked.
*/
dims[0] = 1000;
dims[1] = 20;
cdims[0] = 20;
cdims[1] = 20;
dataspace = H5Screate_simple(RANK, dims, NULL);
plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(plist, 2, cdims);
H5Pset_deflate( plist, 6);
dataset = H5Dcreate(file, "/Data/Compressed_Data", H5T_NATIVE_INT,
dataspace, plist);
/*
* Close the dataset and the file.
*/
H5Sclose(dataspace);
H5Dclose(dataset);
H5Fclose(file);
/*
* Now reopen the file and group in the file.
*/
file = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);
grp = H5Gopen(file, "Data");
/*
* Access "Compressed_Data" dataset in the group.
*/
dataset = H5Dopen(grp, "Compressed_Data");
if( dataset < 0) printf(" Dataset is not found. \n");
printf("\"/Data/Compressed_Data\" dataset is open \n");
/*
* Close the dataset.
*/
status = H5Dclose(dataset);
/*
* Create hard link to the Data group.
*/
status = H5Glink(file, H5G_LINK_HARD, "Data", "Data_new");
/*
* We can access "Compressed_Data" dataset using created
* hard link "Data_new".
*/
dataset = H5Dopen(file, "/Data_new/Compressed_Data");
if( dataset < 0) printf(" Dataset is not found. \n");
printf("\"/Data_new/Compressed_Data\" dataset is open \n");
/*
* Close the dataset.
*/
status = H5Dclose(dataset);
/*
* Use iterator to see the names of the objects in the file
* root directory.
*/
idx = H5Giterate(file, "/", NULL, file_info, NULL);
/*
* Unlink name "Data" and use iterator to see the names
* of the objects in the file root direvtory.
*/
if (H5Gunlink(file, "Data") < 0)
printf(" H5Gunlink failed \n");
else
printf("\"Data\" is unlinked \n");
idx = H5Giterate(file, "/", NULL, file_info, NULL);
/*
* Close the file.
*/
status = H5Fclose(file);
return 0;
}
/*
* Operator function.
*/
herr_t
file_info(hid_t loc_id, const char *name, void *opdata)
{
hid_t grp;
/*
* Open the group using its name.
*/
grp = H5Gopen(loc_id, name);
/*
* Display group name.
*/
printf("\n");
printf("Name : ");
puts(name);
H5Gclose(grp);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="_Toc429885332"><A NAME="ReadWriteAttributes">Example 10</A>. Writing and reading attributes.</A></H4>
<P>This example shows how to create HDF5 attributes, to attach them to a dataset, and to read through all of the attributes of a dataset.
<pre>
<!-- Insert Example 10, h5_attribute.c, here. -->
/*
* This program illustrates the usage of the H5A Interface functions.
* It creates and writes a dataset, and then creates and writes array,
* scalar, and string attributes of the dataset.
* Program reopens the file, attaches to the scalar attribute using
* attribute name and reads and displays its value. Then index of the
* third attribute is used to read and display attribute values.
* The H5Aiterate function is used to iterate through the dataset attributes,
* and display their names. The function is also reads and displays the values
* of the array attribute.
*/
#include <stdlib.h>
#include <hdf5.h>
#define FILE "Attributes.h5"
#define RANK 1 /* Rank and size of the dataset */
#define SIZE 7
#define ARANK 2 /* Rank and dimension sizes of the first dataset attribute */
#define ADIM1 2
#define ADIM2 3
#define ANAME "Float attribute" /* Name of the array attribute */
#define ANAMES "Character attribute" /* Name of the string attribute */
herr_t attr_info(hid_t loc_id, const char *name, void *opdata);
/* Operator function */
int
main (void)
{
hid_t file, dataset; /* File and dataset identifiers */
hid_t fid; /* Dataspace identifier */
hid_t attr1, attr2, attr3; /* Attribute identifiers */
hid_t attr;
hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */
hid_t atype; /* Attribute type */
hsize_t fdim[] = {SIZE};
hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */
float matrix[ADIM1][ADIM2]; /* Attribute data */
herr_t ret; /* Return value */
uint i,j; /* Counters */
int idx; /* Attribute index */
char string_out[80]; /* Buffer to read string attribute back */
int point_out; /* Buffer to read scalar attribute back */
/*
* Data initialization.
*/
int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */
int point = 1; /* Value of the scalar attribute */
char string[] = "ABCD"; /* Value of the string attribute */
for (i=0; i < ADIM1; i++) { /* Values of the array attribute */
for (j=0; j < ADIM2; j++)
matrix[i][j] = -1.;
}
/*
* Create a file.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the dataspace for the dataset in the file.
*/
fid = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(fid, RANK, fdim, NULL);
/*
* Create the dataset in the file.
*/
dataset = H5Dcreate(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector);
/*
* Create dataspace for the first attribute.
*/
aid1 = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL);
/*
* Create array attribute.
*/
attr1 = H5Acreate(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT);
/*
* Write array attribute.
*/
ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix);
/*
* Create scalar attribute.
*/
aid2 = H5Screate(H5S_SCALAR);
attr2 = H5Acreate(dataset, "Integer attribute", H5T_NATIVE_INT, aid2,
H5P_DEFAULT);
/*
* Write scalar attribute.
*/
ret = H5Awrite(attr2, H5T_NATIVE_INT, &point);
/*
* Create string attribute.
*/
aid3 = H5Screate(H5S_SCALAR);
atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 4);
attr3 = H5Acreate(dataset, ANAMES, atype, aid3, H5P_DEFAULT);
/*
* Write string attribute.
*/
ret = H5Awrite(attr3, atype, string);
/*
* Close attribute and file dataspaces.
*/
ret = H5Sclose(aid1);
ret = H5Sclose(aid2);
ret = H5Sclose(aid3);
ret = H5Sclose(fid);
/*
* Close the attributes.
*/
ret = H5Aclose(attr1);
ret = H5Aclose(attr2);
ret = H5Aclose(attr3);
/*
* Close the dataset.
*/
ret = H5Dclose(dataset);
/*
* Close the file.
*/
ret = H5Fclose(file);
/*
* Reopen the file.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
/*
* Open the dataset.
*/
dataset = H5Dopen(file,"Dataset");
/*
* Attach to the scalar attribute using attribute name, then read and
* display its value.
*/
attr = H5Aopen_name(dataset,"Integer attribute");
ret = H5Aread(attr, H5T_NATIVE_INT, &point_out);
printf("The value of the attribute \"Integer attribute\" is %d \n", point_out);
ret = H5Aclose(attr);
/*
* Attach to the string attribute using its index, then read and display the value.
*/
attr = H5Aopen_idx(dataset, 2);
atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 4);
ret = H5Aread(attr, atype, string_out);
printf("The value of the attribute with the index 2 is %s \n", string_out);
ret = H5Aclose(attr);
ret = H5Tclose(atype);
/*
* Get attribute info using iteration function.
*/
idx = H5Aiterate(dataset, NULL, attr_info, NULL);
/*
* Close the dataset and the file.
*/
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
/*
* Operator function.
*/
herr_t
attr_info(hid_t loc_id, const char *name, void *opdata)
{
hid_t attr, atype, aspace; /* Attribute, datatype and dataspace identifiers */
int rank;
hsize_t sdim[64];
herr_t ret;
int i;
size_t npoints; /* Number of elements in the array attribute. */
float *float_array; /* Pointer to the array attribute. */
/*
* Open the attribute using its name.
*/
attr = H5Aopen_name(loc_id, name);
/*
* Display attribute name.
*/
printf("\n");
printf("Name : ");
puts(name);
/*
* Get attribute datatype, dataspace, rank, and dimensions.
*/
atype = H5Aget_type(attr);
aspace = H5Aget_space(attr);
rank = H5Sget_simple_extent_ndims(aspace);
ret = H5Sget_simple_extent_dims(aspace, sdim, NULL);
/*
* Display rank and dimension sizes for the array attribute.
*/
if(rank > 0) {
printf("Rank : %d \n", rank);
printf("Dimension sizes : ");
for (i=0; i < rank; i++) printf("%d ", (int)sdim[i]);
printf("\n");
}
/*
* Read array attribute and display its type and values.
*/
if (H5T_FLOAT == H5Tget_class(atype)) {
printf("Type : FLOAT \n");
npoints = H5Sget_simple_extent_npoints(aspace);
float_array = (float *)malloc(sizeof(float)*(int)npoints);
ret = H5Aread(attr, atype, float_array);
printf("Values : ");
for( i = 0; i < (int)npoints; i++) printf("%f ", float_array[i]);
printf("\n");
free(float_array);
}
/*
* Release all identifiers.
*/
H5Tclose(atype);
H5Sclose(aspace);
H5Aclose(attr);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="CreateWriteRefObj">Example 11</A>. Creating and storing references to objects.</A></H4>
This example creates a group and two datasets and a named datatype
in the group. References to these four objects are stored in the dataset
in the root group.
<PRE>
#include <hdf5.h>
#define FILE1 "trefer1.h5"
/* 1-D dataset with fixed dimensions */
#define SPACE1_NAME "Space1"
#define SPACE1_RANK 1
#define SPACE1_DIM1 4
/* 2-D dataset with fixed dimensions */
#define SPACE2_NAME "Space2"
#define SPACE2_RANK 2
#define SPACE2_DIM1 10
#define SPACE2_DIM2 10
int
main(void) {
hid_t fid1; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t group; /* Group ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hsize_t dims1[] = {SPACE1_DIM1};
hobj_ref_t *wbuf; /* buffer to write to disk */
int *tu32; /* Temporary pointer to int data */
int i; /* counting variables */
const char *write_comment="Foo!"; /* Comments for group */
herr_t ret; /* Generic return value */
/* Compound datatype */
typedef struct s1_t {
unsigned int a;
unsigned int b;
float c;
} s1_t;
/* Allocate write buffers */
wbuf=(hobj_ref_t *)malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
tu32=malloc(sizeof(int)*SPACE1_DIM1);
/* Create file */
fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create dataspace for datasets */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
/* Create a group */
group=H5Gcreate(fid1,"Group1",-1);
/* Set group's comment */
ret=H5Gset_comment(group,".",write_comment);
/* Create a dataset (inside Group1) */
dataset=H5Dcreate(group,"Dataset1",H5T_STD_U32LE,sid1,H5P_DEFAULT);
for(i=0; i < SPACE1_DIM1; i++)
tu32[i] = i*3;
/* Write selection to disk */
ret=H5Dwrite(dataset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Create another dataset (inside Group1) */
dataset=H5Dcreate(group,"Dataset2",H5T_NATIVE_UCHAR,sid1,H5P_DEFAULT);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Create a datatype to refer to */
tid1 = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
/* Insert fields */
ret=H5Tinsert (tid1, "a", HOFFSET(s1_t,a), H5T_NATIVE_INT);
ret=H5Tinsert (tid1, "b", HOFFSET(s1_t,b), H5T_NATIVE_INT);
ret=H5Tinsert (tid1, "c", HOFFSET(s1_t,c), H5T_NATIVE_FLOAT);
/* Save datatype for later */
ret=H5Tcommit (group, "Datatype1", tid1);
/* Close datatype */
ret = H5Tclose(tid1);
/* Close group */
ret = H5Gclose(group);
/* Create a dataset to store references */
dataset=H5Dcreate(fid1,"Dataset3",H5T_STD_REF_OBJ,sid1,H5P_DEFAULT);
/* Create reference to dataset */
ret = H5Rcreate(&wbuf[0],fid1,"/Group1/Dataset1",H5R_OBJECT,-1);
/* Create reference to dataset */
ret = H5Rcreate(&wbuf[1],fid1,"/Group1/Dataset2",H5R_OBJECT,-1);
/* Create reference to group */
ret = H5Rcreate(&wbuf[2],fid1,"/Group1",H5R_OBJECT,-1);
/* Create reference to named datatype */
ret = H5Rcreate(&wbuf[3],fid1,"/Group1/Datatype1",H5R_OBJECT,-1);
/* Write selection to disk */
ret=H5Dwrite(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);
/* Close disk dataspace */
ret = H5Sclose(sid1);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Close file */
ret = H5Fclose(fid1);
free(wbuf);
free(tu32);
return 0;
}
</PRE>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="ReadRefObj">Example 12</A>. Reading references to objects.</A></H4>
This example opens and reads dataset <code>Dataset3</code> from
the file created in Example 11. Then the program dereferences the references
to dataset <code>Dataset1</code>, the group and the named datatype,
and opens those objects.
The program reads and displays the dataset's data, the group's comment, and
the number of members of the compound datatype.
<PRE>
#include <stdlib.h>
#include <hdf5.h>
#define FILE1 "trefer1.h5"
/* dataset with fixed dimensions */
#define SPACE1_NAME "Space1"
#define SPACE1_RANK 1
#define SPACE1_DIM1 4
int
main(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dataset, /* Dataset ID */
dset2; /* Dereferenced dataset ID */
hid_t group; /* Group ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hobj_ref_t *rbuf; /* buffer to read from disk */
int *tu32; /* temp. buffer read from disk */
int i; /* counting variables */
char read_comment[10];
herr_t ret; /* Generic return value */
/* Allocate read buffers */
rbuf = malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
tu32 = malloc(sizeof(int)*SPACE1_DIM1);
/* Open the file */
fid1 = H5Fopen(FILE1, H5F_ACC_RDWR, H5P_DEFAULT);
/* Open the dataset */
dataset=H5Dopen(fid1,"/Dataset3");
/* Read selection from disk */
ret=H5Dread(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);
/* Open dataset object */
dset2 = H5Rdereference(dataset,H5R_OBJECT,&rbuf[0]);
/* Check information in referenced dataset */
sid1 = H5Dget_space(dset2);
ret=H5Sget_simple_extent_npoints(sid1);
/* Read from disk */
ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);
printf("Dataset data : \n");
for (i=0; i < SPACE1_DIM1 ; i++) printf (" %d ", tu32[i]);
printf("\n");
printf("\n");
/* Close dereferenced Dataset */
ret = H5Dclose(dset2);
/* Open group object */
group = H5Rdereference(dataset,H5R_OBJECT,&rbuf[2]);
/* Get group's comment */
ret=H5Gget_comment(group,".",10,read_comment);
printf("Group comment is %s \n", read_comment);
printf(" \n");
/* Close group */
ret = H5Gclose(group);
/* Open datatype object */
tid1 = H5Rdereference(dataset,H5R_OBJECT,&rbuf[3]);
/* Verify correct datatype */
{
H5T_class_t tclass;
tclass= H5Tget_class(tid1);
if ((tclass == H5T_COMPOUND))
printf ("Number of compound datatype members is %d \n", H5Tget_nmembers(tid1));
printf(" \n");
}
/* Close datatype */
ret = H5Tclose(tid1);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Close file */
ret = H5Fclose(fid1);
/* Free memory buffers */
free(rbuf);
free(tu32);
return 0;
}
</PRE>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="CreateWriteRefReg">Example 13</A>. Creating and writing a reference to a region.</A></H4>
This example creates a dataset in the file. Then it creates a dataset
to store references to the dataset regions (selections).
The first selection is a 6 x 6 hyperslab.
The second selection is a point selection in the same dataset.
References to both selections are created and stored in the buffer,
and then written to the dataset in the file.
<pre>
#include <stdlib.h>
#include <hdf5.h>
#define FILE2 "trefer2.h5"
#define SPACE1_NAME "Space1"
#define SPACE1_RANK 1
#define SPACE1_DIM1 4
/* Dataset with fixed dimensions */
#define SPACE2_NAME "Space2"
#define SPACE2_RANK 2
#define SPACE2_DIM1 10
#define SPACE2_DIM2 10
/* Element selection information */
#define POINT1_NPOINTS 10
int
main(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dset1, /* Dataset ID */
dset2; /* Dereferenced dataset ID */
hid_t sid1, /* Dataspace ID #1 */
sid2; /* Dataspace ID #2 */
hsize_t dims1[] = {SPACE1_DIM1},
dims2[] = {SPACE2_DIM1, SPACE2_DIM2};
hssize_t start[SPACE2_RANK]; /* Starting location of hyperslab */
hsize_t stride[SPACE2_RANK]; /* Stride of hyperslab */
hsize_t count[SPACE2_RANK]; /* Element count of hyperslab */
hsize_t block[SPACE2_RANK]; /* Block size of hyperslab */
hssize_t coord1[POINT1_NPOINTS][SPACE2_RANK];
/* Coordinates for point selection */
hdset_reg_ref_t *wbuf; /* buffer to write to disk */
int *dwbuf; /* Buffer for writing numeric data to disk */
int i; /* counting variables */
herr_t ret; /* Generic return value */
/* Allocate write & read buffers */
wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
dwbuf=malloc(sizeof(int)*SPACE2_DIM1*SPACE2_DIM2);
/* Create file */
fid1 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create dataspace for datasets */
sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL);
/* Create a dataset */
dset2=H5Dcreate(fid1,"Dataset2",H5T_STD_U8LE,sid2,H5P_DEFAULT);
for(i=0; i < SPACE2_DIM1*SPACE2_DIM2; i++)
dwbuf[i]=i*3;
/* Write selection to disk */
ret=H5Dwrite(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,dwbuf);
/* Close Dataset */
ret = H5Dclose(dset2);
/* Create dataspace for the reference dataset */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
/* Create a dataset */
dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);
/* Create references */
/* Select 6x6 hyperslab for first reference */
start[0]=2; start[1]=2;
stride[0]=1; stride[1]=1;
count[0]=6; count[1]=6;
block[0]=1; block[1]=1;
ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,stride,count,block);
/* Store first dataset region */
ret = H5Rcreate(&wbuf[0],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
/* Select sequence of ten points for second reference */
coord1[0][0]=6; coord1[0][1]=9;
coord1[1][0]=2; coord1[1][1]=2;
coord1[2][0]=8; coord1[2][1]=4;
coord1[3][0]=1; coord1[3][1]=6;
coord1[4][0]=2; coord1[4][1]=8;
coord1[5][0]=3; coord1[5][1]=2;
coord1[6][0]=0; coord1[6][1]=4;
coord1[7][0]=9; coord1[7][1]=0;
coord1[8][0]=7; coord1[8][1]=1;
coord1[9][0]=3; coord1[9][1]=3;
ret = H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(const hssize_t **)coord1);
/* Store second dataset region */
ret = H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
/* Write selection to disk */
ret=H5Dwrite(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);
/* Close all objects */
ret = H5Sclose(sid1);
ret = H5Dclose(dset1);
ret = H5Sclose(sid2);
/* Close file */
ret = H5Fclose(fid1);
free(wbuf);
free(dwbuf);
return 0;
}
</pre>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<H4><A NAME="ReadRefReg">Example 14</A>. Reading a reference to a region.</A></H4>
This example reads a dataset containing dataset region references.
It reads data from the dereferenced dataset and displays the number of
elements and raw data. Then it reads two selections:
a hyperslab selection and a point selection. The program queries a
number of points in the hyperslab and the coordinates and displays them.
Then it queries a number of selected points and their coordinates and
displays the information.
<PRE>
#include <stdlib.h>
#include <hdf5.h>
#define FILE2 "trefer2.h5"
#define NPOINTS 10
/* 1-D dataset with fixed dimensions */
#define SPACE1_NAME "Space1"
#define SPACE1_RANK 1
#define SPACE1_DIM1 4
/* 2-D dataset with fixed dimensions */
#define SPACE2_NAME "Space2"
#define SPACE2_RANK 2
#define SPACE2_DIM1 10
#define SPACE2_DIM2 10
int
main(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dset1, /* Dataset ID */
dset2; /* Dereferenced dataset ID */
hid_t sid1, /* Dataspace ID #1 */
sid2; /* Dataspace ID #2 */
hsize_t * coords; /* Coordinate buffer */
hsize_t low[SPACE2_RANK]; /* Selection bounds */
hsize_t high[SPACE2_RANK]; /* Selection bounds */
hdset_reg_ref_t *rbuf; /* buffer to to read disk */
int *drbuf; /* Buffer for reading numeric data from disk */
int i, j; /* counting variables */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
/* Allocate write & read buffers */
rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
drbuf=calloc(sizeof(int),SPACE2_DIM1*SPACE2_DIM2);
/* Open the file */
fid1 = H5Fopen(FILE2, H5F_ACC_RDWR, H5P_DEFAULT);
/* Open the dataset */
dset1=H5Dopen(fid1,"/Dataset1");
/* Read selection from disk */
ret=H5Dread(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);
/* Try to open objects */
dset2 = H5Rdereference(dset1,H5R_DATASET_REGION,&rbuf[0]);
/* Check information in referenced dataset */
sid1 = H5Dget_space(dset2);
ret=H5Sget_simple_extent_npoints(sid1);
printf(" Number of elements in the dataset is : %d\n",ret);
/* Read from disk */
ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,drbuf);
for(i=0; i < SPACE2_DIM1; i++) {
for (j=0; j < SPACE2_DIM2; j++) printf (" %d ", drbuf[i*SPACE2_DIM2+j]);
printf("\n"); }
/* Get the hyperslab selection */
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);
/* Verify correct hyperslab selected */
ret = H5Sget_select_npoints(sid2);
printf(" Number of elements in the hyperslab is : %d \n", ret);
ret = H5Sget_select_hyper_nblocks(sid2);
coords=malloc(ret*SPACE2_RANK*sizeof(hsize_t)*2); /* allocate space for the hyperslab blocks */
ret = H5Sget_select_hyper_blocklist(sid2,0,ret,coords);
printf(" Hyperslab coordinates are : \n");
printf (" ( %lu , %lu ) ( %lu , %lu ) \n", \
(unsigned long)coords[0],(unsigned long)coords[1],(unsigned long)coords[2],(unsigned long)coords[3]);
free(coords);
ret = H5Sget_select_bounds(sid2,low,high);
/* Close region space */
ret = H5Sclose(sid2);
/* Get the element selection */
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[1]);
/* Verify correct elements selected */
ret = H5Sget_select_elem_npoints(sid2);
printf(" Number of selected elements is : %d\n", ret);
/* Allocate space for the element points */
coords= malloc(ret*SPACE2_RANK*sizeof(hsize_t));
ret = H5Sget_select_elem_pointlist(sid2,0,ret,coords);
printf(" Coordinates of selected elements are : \n");
for (i=0; i < 2*NPOINTS; i=i+2)
printf(" ( %lu , %lu ) \n", (unsigned long)coords[i],(unsigned long)coords[i+1]);
free(coords);
ret = H5Sget_select_bounds(sid2,low,high);
/* Close region space */
ret = H5Sclose(sid2);
/* Close first space */
ret = H5Sclose(sid1);
/* Close dereferenced Dataset */
ret = H5Dclose(dset2);
/* Close Dataset */
ret = H5Dclose(dset1);
/* Close file */
ret = H5Fclose(fid1);
/* Free memory buffers */
free(rbuf);
free(drbuf);
return 0;
}
</PRE>
<P>
<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
<hr>
<center>
<table border=0 width=98%>
<tr><td valign=top align=left>
<a href="../H5.intro.html">Introduction to HDF5</a> <br>
<a href="../H5.user.html">HDF5 User Guide</a>
<!--
<a href="../Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
<a href="../RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="../index.html">Other HDF5 documents and links</a>
</td></tr>
</table>
</center>
<hr>
<address>
<table width=100% border=0>
<tr><td align=left valign=top>
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
<br>
Last modified: 15 February 2001
<br>
Describes HDF5 Release 1.4.4, June 2002
</td><td align=right valign=top>
<a href="../Copyright.html">Copyright</a>
</td></tr>
</table>
</BODY>
</HTML>
|