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
|
<HTML><HEAD>
<TITLE>HDF5 Tutorial - Creating a Dataset
</TITLE>
</HEAD>
<body bgcolor="#ffffff">
<!-- BEGIN MAIN BODY -->
<A HREF="http://www.ncsa.uiuc.edu/"><img border=0
src="http://www.ncsa.uiuc.edu/Images/NCSAhome/footerlogo.gif"
width=78 height=27 alt="NCSA"><P></A>
[ <A HREF="title.html"><I>HDF5 Tutorial Top</I></A> ]
<H1>
<BIG><BIG><BIG><FONT COLOR="#c101cd">Creating a Dataset</FONT>
</BIG></BIG></BIG></H1>
<hr noshade size=1>
<BODY>
<H2>Contents:</H2>
<UL>
<LI> <A HREF="#def">What is a Dataset</A>?
<LI> Programming Example
<UL>
<LI> <A HREF="#desc">Description</A>
<LI> <A HREF="#rem">Remarks</A>
<LI> <A HREF="#fc">File Contents</A>
<LI> <A HREF="#ddl">Dataset Definition in DDL</A>
</UL>
</UL>
<HR>
<A NAME="def">
<H2>What is a Dataset?</h2>
<P>
A dataset is a multidimensional array of data elements, together with
supporting metadata. To create a dataset, the application program must specify
the location at which to create the dataset, the dataset name, the datatype
and dataspace of the data array, and the dataset creation property list.
<P>
<H3> Datatypes</H3>
A datatype is a collection of datatype properties, all of which can
be stored on disk, and which when taken as a whole, provide complete
information for data conversion to or from that datatype.
<P>
There are two categories of datatypes in HDF5: atomic and compound
datatypes. An <i>atomic datatype</i> is a datatype which cannot be
decomposed into smaller datatype units at the API level.
These include the integer, float, date and time, string, bitfield, and
opaque datatypes.
A <i>compound datatype</i> is a collection of one or more
atomic datatypes and/or small arrays of such datatypes.
<P>
Figure 5.1 shows the HDF5 datatypes. Some of the HDF5 predefined
atomic datatypes are listed in Figures 5.2a and 5.2b.
In this tutorial, we consider only HDF5 predefined integers.
For further information on datatypes, see
<a href="../Datatypes.html">The Datatype Interface (H5T)</a> in the
<cite>HDF5 User's Guide</cite>.
<P>
<B>Fig 5.1</B> <I>HDF5 datatypes</I>
<PRE>
+-- integer
+-- floating point
+---- atomic ----+-- date and time
| +-- character string
HDF5 datatypes --| +-- bitfield
| +-- opaque
|
+---- compound
</PRE>
<table width="100%" border="0" cellpadding="4">
<tr><td valign=top>
<B>Fig. 5.2a</B> <I>Examples of HDF5 predefined datatypes</I>
<table width="95%" border="1" cellpadding="0">
<tr bgcolor="#ffcc99" bordercolor="#FFFFFF">
<td width="20%"><b>Datatype</b></td>
<td width="80%"><b>Description</b></td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_STD_I32LE</code></td>
<td width="80%">Four-byte, little-endian, signed, two's complement integer</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_STD_U16BE</code></td>
<td width="80%">Two-byte, big-endian, unsigned integer</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_IEEE_F32BE</code></td>
<td width="80%">Four-byte, big-endian, IEEE floating point</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_IEEE_F64LE</code></td>
<td width="80%">Eight-byte, little-endian, IEEE floating point</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_C_S1</code></td>
<td width="80%">One-byte, null-terminated string of eight-bit characters</td>
</tr>
</table>
</td><td valign=top>
<B>Fig. 5.2b</B> <I>Examples of HDF5 predefined native datatypes</I>
<table width="95%" border="1" cellpadding="4">
<tr bgcolor="#ffcc99" bordercolor="#FFFFFF">
<td width="20%"><b>Native Datatype</b></td>
<td width="80%"><b>Corresponding C or FORTRAN Type</b></td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><B>C:</B></td>
<td width="80%"> </td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_INT</code></td>
<td width="80%">int</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_FLOAT</code></td>
<td width="80%">float</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_CHAR</code></td>
<td width="80%">char</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_DOUBLE</code></td>
<td width="80%">double</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_LDOUBLE</code></td>
<td width="80%">long double</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><B>FORTRAN:</B></td>
<td width="80%"> </td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_INT</code></td>
<td width="80%">integer</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_REAL</code></td>
<td width="80%">real</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_DOUBLE</code></td>
<td width="80%">double precision</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_CHAR</code></td>
<td width="80%">character</td>
</tr>
</table>
</table>
<H3> Datasets and Dataspaces</H3>
A dataspace describes the dimensionality of the data array. A dataspace
is either a regular N-dimensional array of data points, called a simple
dataspace, or a more general collection of data points organized in
another manner, called a complex dataspace. Figure 5.3 shows HDF5 dataspaces.
In this tutorial, we only consider simple dataspaces.
<P>
<B>Fig 5.3</B> <I>HDF5 dataspaces</I>
<PRE>
+-- simple
HDF5 dataspaces --|
+-- complex
</PRE>
The dimensions of a dataset can be fixed (unchanging), or they may be
unlimited, which means that they are extensible. A dataspace can also
describe a portion of a dataset, making it possible to do partial I/O
operations on selections.
<h3>Dataset Creation Property Lists</H3>
When creating a dataset, HDF5 allows the user to specify how raw data is
organized and/or compressed on disk. This information is
stored in a dataset creation property list and passed to the dataset
interface. The raw data on disk can be stored contiguously (in the same
linear way that it is organized in memory), partitioned into chunks,
stored externally, etc. In this tutorial, we use the
default dataset creation property list; that is, contiguous storage layout
and no compression are used. For more information about
dataset creation property lists,
see <a href="../Datasets.html">The Dataset Interface (H5D)</a>
in the <cite>HDF5 User's Guide</cite>.
<P>
In HDF5, datatypes and dataspaces are independent objects which are created
separately from any dataset that they might be attached to. Because of this,
the creation of a dataset requires definition of the datatype and dataspace.
In this tutorial, we use HDF5 predefined datatypes (integer) and consider
only simple dataspaces. Hence, only the creation of dataspace objects is
needed.
<P>
To create an empty dataset (no data written) the following steps need to be
taken:
<OL>
<LI> Obtain the location identifier where the dataset is to be created.
<LI> Define the dataset characteristics and the dataset creation property list.
<UL>
<LI> Define a datatype.
<LI> Define a dataspace.
<LI> Specify the dataset creation property list.
</UL>
<LI> Create the dataset.
<LI> Close the datatype, the dataspace, and the property list if necessary.
<LI> Close the dataset.
</OL>
To create a simple dataspace, the calling program must contain a
call to create and close the dataspace. For example:
<P>
<I>C</I>:
<PRE>
space_id = H5Screate_simple (rank, dims, maxdims);
status = H5Sclose (space_id );
</PRE>
<I>FORTRAN</I>:
<PRE>
CALL h5screate_simple_f (rank, dims, space_id, hdferr, maxdims=max_dims)
<i>or</i>
CALL h5screate_simple_f (rank, dims, space_id, hdferr)
CALL h5sclose_f (space_id, hdferr)
</PRE>
To create a dataset, the calling program must contain calls to create
and close the dataset. For example:
<P>
<I>C</I>:
<PRE>
dset_id = H5Dcreate (hid_t loc_id, const char *name, hid_t type_id,
hid_t space_id, hid_t creation_prp);
status = H5Dclose (dset_id);
</PRE>
<I>FORTRAN</I>:
<PRE>
CALL h5dcreate_f (loc_id, name, type_id, space_id, dset_id, &
hdferr, creation_prp=creat_plist_id)
<i>or</i>
CALL h5dcreate_f (loc_id, name, type_id, space_id, dset_id, hdferr)
CALL h5dclose_f (dset_id, hdferr)
</PRE>
If using the pre-defined datatypes in FORTRAN, then a call must
be made to initialize and terminate access to the pre-defined datatypes:
<PRE>
CALL h5init_types_f (hdferr)
CALL h5close_types_f (hdferr)
</PRE>
<code>h5init_types_f</code> must be called before any HDF5 library
subroutine calls are made;
<code>h5close_types_f</code> must be called after the final HDF5 library
subroutine call.
See the programming example below for an illustration of the use of
these calls.
<P>
<H2> Programming Example</H2>
<A NAME="desc">
<H3><U>Description</U></H3>
The following example shows how to create an empty dataset.
It creates a file called <code>dset.h5</code> in the C version
(<code>dsetf.h5</code> in Fortran), defines the dataset dataspace, creates a
dataset which is a 4x6 integer array, and then closes the dataspace,
the dataset, and the file. <BR>
<UL>
[ <A HREF="examples/h5_crtdat.c">C Example</A> ]
-- <code>h5_crtdat.c</code><BR>
[ <A HREF="examples/dsetexample.f90">Fortran Example</A> ]
-- <code>dsetexample.f90</code><BR>
[ <A HREF="examples/java/CreateDataset.java">Java Example</A> ]
-- <code>CreateDataset.java</code>
</UL>
<B>NOTE:</B> To download a tar file of the examples, including a Makefile,
please go to the <A HREF="references.html">References</A> page of this tutorial.
<A NAME="rem">
<H3><U>Remarks</U></H3>
<UL>
<LI><code>H5Screate_simple</code>/<code>h5screate_simple_f</code>
creates a new simple dataspace and returns a dataspace identifier.
<PRE>
<I>C</I>:
hid_t H5Screate_simple (int rank, const hsize_t * dims,
const hsize_t * maxdims)
<I>FORTRAN</I>:
h5screate_simple_f (rank, dims, space_id, hdferr, maxdims)
rank INTEGER
dims(*) INTEGER(HSIZE_T)
space_id INTEGER(HID_T)
hdferr INTEGER
(Valid values: 0 on success and -1 on failure)
maxdims(*) INTEGER(HSIZE_T), OPTIONAL
</PRE>
<UL>
<LI> The <I>rank</I> parameter specifies the rank, i.e., the number of
dimensions, of the dataset.
<LI> The <I>dims</I> parameter specifies the size of the dataset.
<LI>The <I>maxdims</I> parameter specifies the upper limit on the
size of the dataset.
If this parameter is NULL in C (or not specified in FORTRAN),
then the upper limit is the same as the dimension
sizes specified by the <I>dims</I> parameter.
<LI>The function returns the dataspace identifier in C if successful;
otherwise it returns a negative value.
In FORTRAN, the dataspace identifier
is returned in the <I>space_id</I> parameter. If the call is successul
then a 0 is returned in <I>hdferr</I>; otherwise a -1 is returned.
</UL>
<P>
<LI><code>H5Dcreate</code>/<code>h5dcreate_f</code> creates a dataset
at the specified location and returns a dataset identifier.
<PRE>
<I>C</I>:
hid_t H5Dcreate (hid_t loc_id, const char *name, hid_t type_id,
hid_t space_id, hid_t creation_prp)
<I>FORTRAN</I>:
h5dcreate_f (loc_id, name, type_id, space_id, dset_id, &
hdferr, creation_prp)
loc_id INTEGER(HID_T)
name CHARACTER(LEN=*)
type_id INTEGER(HID_T)
space_id INTEGER(HID_T)
dset_id INTEGER(HID_T)
hdferr INTEGER
(Valid values: 0 on success and -1 on failure)
creation_prp INTEGER(HID_T), OPTIONAL
</PRE>
<UL>
<LI> The <I>loc_id</I> parameter is the location identifier.
<P>
<LI> The <I>name</I> parameter is the name of the dataset to create.
<P>
<LI> The <I>type_id</I> parameter specifies the datatype identifier.
<P>
<LI> The <I>space_id</I> parameter is the dataspace identifier.
<P>
<LI> The <I>creation_prp</I> parameter specifies the
dataset creation property list.
<code>H5P_DEFAULT</code> in C and <code>H5P_DEFAULT_F</code> in FORTRAN
specify the default dataset creation property list.
This parameter is optional in FORTRAN; if it is omitted,
the default dataset creation property list will be used.
<P>
<LI> The C function returns the dataset identifier if successful and
a negative value otherwise. The FORTRAN call returns the
dataset identifier in <I>dset_id</I>. If it is successful, then 0 is
returned in <I>hdferr</I>; otherwise a -1 is returned.
</UL>
<P>
<LI><code>H5Dcreate</code>/<code>h5dcreate_f</code> creates an empty array
and initializes the data to 0.
<P>
<LI> When a dataset is no longer accessed by a program,
<code>H5Dclose</code>/<code>h5dclose_f</code> must be called to release
the resource used by the dataset. This call is mandatory.
<PRE>
<I>C</I>:
hid_t H5Dclose (hid_t dset_id)
<I>FORTRAN</I>:
h5dclose_f (dset_id, hdferr)
dset_id INTEGER(HID_T)
hdferr INTEGER
(Valid values: 0 on success and -1 on failure)
</PRE>
</UL>
<A NAME="fc">
<H3><U>File Contents</U></H3>
The contents of the file <code>dset.h5</code> (<code>dsetf.h5</code>
for FORTRAN) are shown in <B>Figure 5.4</B> and <B>Figures 5.5a </B>
and <B>5.5b</B>.
<P>
<table border="0">
<tr align=left><td>
<B>Figure 5.4</B> <I>Contents of <code>dset.h5</code> ( <code>dsetf.h5</code>)</i>
</td></tr><tr align=center><td>
<IMG src="img002.gif"> </PRE>
</td></tr></table>
<table width="100%" border="1" cellspacing="4" bordercolor="#FFFFFF">
<tr bordercolor="#FFFFFF">
<td width="50%"><b>Figure 5.5a</b> <i><code>dset.h5</code> in DDL</i> </td>
<td width="50%"><b>Figure 5.5b</b> <i><code>dsetf.h5</code> in DDL</i> </td>
</tr>
<tr bordercolor="#000000">
<td width="35%">
<PRE>
HDF5 "dset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }
DATA {
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0
}
}
}
}
</PRE>
</td>
<td width="35%">
<pre>
HDF5 "dsetf.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 6, 4 ) / ( 6, 4 ) }
DATA {
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0
}
}
}
}
</pre>
</td>
</tr>
</table>
<p>
Note in Figures 5.5a and 5.5b that
<code>H5T_STD_I32BE</code>, a 32-bit Big Endian integer,
is an HDF atomic datatype.
<A NAME="ddl">
<h3><U>Dataset Definition in DDL</U></H3>
The following is the simplified DDL dataset definition:
<P>
<B>Fig. 5.6</B> <I>HDF5 Dataset Definition</I>
<PRE>
<dataset> ::= DATASET "<dataset_name>" { <datatype>
<dataspace>
<data>
<dataset_attribute>* }
<datatype> ::= DATATYPE { <atomic_type> }
<dataspace> ::= DATASPACE { SIMPLE <current_dims> / <max_dims> }
<dataset_attribute> ::= <attribute>
</PRE>
<!-- BEGIN FOOTER INFO -->
<P><hr noshade size=1>
<font face="arial,helvetica" size="-1">
<a href="http://www.ncsa.uiuc.edu/"><img border=0
src="http://www.ncsa.uiuc.edu/Images/NCSAhome/footerlogo.gif"
width=78 height=27 alt="NCSA"><br>
The National Center for Supercomputing Applications</A><br>
<a href="http://www.uiuc.edu/">University of Illinois
at Urbana-Champaign</a><br>
<br>
<!-- <A HREF="helpdesk.mail.html"> -->
<A HREF="mailto:hdfhelp@@ncsa.uiuc.edu">
hdfhelp@@ncsa.uiuc.edu</A>
<br>
Describes HDF5 Release 1.2.2, June 2000
<BR> <H6>Last Modified: April 5, 2000</H6><BR>
<!-- modified by Barbara Jones - bljones@@ncsa.uiuc.edu -->
<!-- modified by Frank Baker - fbaker@@ncsa.uiuc.edu -->
</FONT>
<BR>
<!-- <A HREF="mailto:hdfhelp@@ncsa.uiuc.edu"> -->
</BODY>
</HTML>
|
