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
|
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html>
<head>
<title>Dataset Interface (H5D)</title>
</head>
<body 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="RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="index.html">Other HDF5 documents and links</a> <br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="H5.user.html"><strong>HDF5 User's Guide:</strong></a>
<br>
<a href="Files.html">Files</a>
Datasets
<a href="Datatypes.html">Datatypes</a>
<a href="Dataspaces.html">Dataspaces</a>
<a href="Groups.html">Groups</a>
<br>
<a href="References.html">References</a>
<a href="Attributes.html">Attributes</a>
<a href="Properties.html">Property Lists</a>
<a href="Errors.html">Error Handling</a>
<br>
<a href="Filters.html">Filters</a>
<a href="Caching.html">Caching</a>
<a href="Chunking.html">Chunking</a>
<a href="MountingFiles.html">Mounting Files</a>
<br>
<a href="Performance.html">Performance</a>
<a href="Debugging.html">Debugging</a>
<a href="Environment.html">Environment</a>
<a href="ddl.html">DDL</a>
</td></tr>
</table>
</center>
<hr>
<h1>The Dataset Interface (H5D)</h1>
<h2>1. Introduction</h2>
<p>The purpose of the dataset interface is to provide a mechanism
to describe properties of datasets and to transfer data between
memory and disk. A dataset is composed of a collection of raw
data points and four classes of meta data to describe the data
points. The interface is hopefully designed in such a way as to
allow new features to be added without disrupting current
applications that use the dataset interface.
<p>The four classes of meta data are:
<dl>
<dt>Constant Meta Data
<dd>Meta data that is created when the dataset is created and
exists unchanged for the life of the dataset. For instance,
the datatype of stored array elements is defined when the
dataset is created and cannot be subsequently changed.
<dt>Persistent Meta Data
<dd>Meta data that is an integral and permanent part of a
dataset but can change over time. For instance, the size in
any dimension can increase over time if such an increase is
allowed when the dataset was created.
<dt>Memory Meta Data
<dd>Meta data that exists to describe how raw data is organized
in the application's memory space. For instance, the data
type of elements in an application array might not be the same
as the datatype of those elements as stored in the HDF5 file.
<dt>Transport Meta Data
<dd>Meta data that is used only during the transfer of raw data
from one location to another. For instance, the number of
processes participating in a collective I/O request or hints
to the library to control caching of raw data.
</dl>
<p>Each of these classes of meta data is handled differently by
the library although the same API might be used to create them.
For instance, the datatype exists as constant meta data and as
memory meta data; the same API (the <code>H5T</code> API) is
used to manipulate both pieces of meta data but they're handled
by the dataset API (the <code>H5D</code> API) in different
manners.
<h2>2. Storage Layout Properties</h2>
<p>The dataset API partitions these terms on three orthogonal axes
(layout, compression, and external storage) and uses a
<em>dataset creation property list</em> to hold the various
settings and pass them through the dataset interface. This is
similar to the way HDF5 files are created with a file creation
property list. A dataset creation property list is always
derived from the default dataset creation property list (use
<code>H5Pcreate()</code> to get a copy of the default property
list) by modifying properties with various
<code>H5Pset_<em>property</em>()</code> functions.
<dl>
<dt><code>herr_t H5Pset_layout (hid_t <em>plist_id</em>,
H5D_layout_t <em>layout</em>)</code>
<dd>The storage layout is a piece of constant meta data that
describes what method the library uses to organize the raw
data on disk. The default layout is contiguous storage.
<br><br>
<dl>
<dt><code>H5D_COMPACT</code> <i><b>(Not yet implemented.)</b></i>
<dd>The raw data is presumably small and can be stored
directly in the object header. Such data is
non-extendible, non-compressible, non-sparse, and cannot
be stored externally. Most of these restrictions are
arbitrary but are enforced because of the small size of
the raw data. Storing data in this format eliminates the
disk seek/read request normally necessary to read raw
data.
<br><br>
<dt><code>H5D_CONTIGUOUS</code>
<dd>The raw data is large, non-extendible, non-compressible,
non-sparse, and can be stored externally. This is the
default value for the layout property. The term
<em>large</em> means that it may not be possible to hold
the entire dataset in memory. The non-compressibility is
a side effect of the data being large, contiguous, and
fixed-size at the physical level, which could cause
partial I/O requests to be extremely expensive if
compression were allowed.
<br><br>
<dt><code>H5D_CHUNKED</code>
<dd>The raw data is large and can be extended in any
dimension at any time (provided the data space also allows
the extension). It may be sparse at the chunk level (each
chunk is non-sparse, but there might only be a few chunks)
and each chunk can be compressed and/or stored externally.
A dataset is partitioned into chunks so each chunk is the
same logical size. The chunks are indexed by a B-tree and
are allocated on demand (although it might be useful to be
able to preallocate storage for parts of a chunked array
to reduce contention for the B-tree in a parallel
environment). The chunk size must be defined with
<code>H5Pset_chunk()</code>.
<br><br>
<dt><em>others...</em>
<dd>Other layout types may be defined later without breaking
existing code. However, to be able to correctly read or
modify data stored with one of these new layouts, the
application will need to be linked with a new version of
the library. This happens automatically on systems with
dynamic linking.
</dl>
</dl>
<a name="Dataset_PSetChunk">
<p>Once the general layout is defined, the user can define
</a>
properties of that layout. Currently, the only layout that has
user-settable properties is the <code>H5D_CHUNKED</code> layout,
which needs to know the dimensionality and chunk size.
<dl>
<dt><code>herr_t H5Pset_chunk (hid_t <em>plist_id</em>, int
<em>ndims</em>, hsize_t <em>dim</em>[])</code>
<dd>This function defines the logical size of a chunk for
chunked layout. If the layout property is set to
<code>H5D_CHUNKED</code> and the chunk size is set to
<em>dim</em>. The number of elements in the <em>dim</em> array
is the dimensionality, <em>ndims</em>. One need not call
<code>H5Dset_layout()</code> when using this function since
the chunked layout is implied.
</dl>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Chunked Storage</h4></caption>
<tr>
<td>
<p>This example shows how a two-dimensional dataset
is partitioned into chunks. The library can manage file
memory by moving the chunks around, and each chunk could be
compressed. The chunks are allocated in the file on demand
when data is written to the chunk.
<center>
<img alt="Chunked Storage" src="chunk1.gif">
</center>
<p><code><pre>
size_t hsize[2] = {1000, 1000};
plist = H5Pcreate (H5P_DATASET_CREATE);
H5Pset_chunk (plist, 2, size);
</pre></code>
</td>
</tr>
</table>
</center>
<p>Although it is most efficient if I/O requests are aligned on chunk
boundaries, this is not a constraint. The application can perform I/O
on any set of data points as long as the set can be described by the
data space. The set on which I/O is performed is called the
<em>selection</em>.
<h2>3. Compression Properties</h2>
<p>Chunked data storage
(see <a href="#Dataset_PSetChunk"><code>H5Pset_chunk</code></a>)
allows data compression as defined by the function
<code>H5Pset_deflate</code>.
<!--
<dl>
<dt><code>herr_t H5Pset_compression (hid_t <em>plist_id</em>,
H5Z_method_t <em>method</em>)</code>
<dt><code>H5Z_method_t H5Pget_compression (hid_t
<em>plist_id</em>)</code>
<dd>These functions set and query the compression method that
is used to compress the raw data of a dataset. The
<em>plist_id</em> is a dataset creation property list. The
possible values for the compression method are:
<br><br>
<dl>
<dt><code>H5Z_NONE</code>
<dd>This is the default and specifies that no compression is
to be performed.
<br><br>
<dt><code>H5Z_DEFLATE</code>
<dd>This specifies that a variation of the Lempel-Ziv 1977
(LZ77) encoding is used, the same encoding used by the
free GNU <code>gzip</code> program.
</dl>
-->
<br><br>
<dt><code>herr_t H5Pset_deflate (hid_t <em>plist_id</em>,
int <em>level</em>)</code>
<dt><code>int H5Pget_deflate (hid_t <em>plist_id</em>)</code>
<dd>These functions set or query the deflate level of
dataset creation property list <em>plist_id</em>. The
<code>H5Pset_deflate()</code> sets the compression method to
<code>H5Z_DEFLATE</code> and sets the compression level to
some integer between one and nine (inclusive). One results in
the fastest compression while nine results in the best
compression ratio. The default value is six if
<code>H5Pset_deflate()</code> isn't called. The
<code>H5Pget_deflate()</code> returns the compression level
for the deflate method, or negative if the method is not the
deflate method.
</dl>
<h2>4. External Storage Properties</h2>
<p>Some storage formats may allow storage of data across a set of
non-HDF5 files. Currently, only the <code>H5D_CONTIGUOUS</code> storage
format allows external storage. A set segments (offsets and sizes) in
one or more files is defined as an external file list, or <em>EFL</em>,
and the contiguous logical addresses of the data storage are mapped onto
these segments.
<dl>
<dt><code>herr_t H5Pset_external (hid_t <em>plist</em>, const
char *<em>name</em>, off_t <em>offset</em>, hsize_t
<em>size</em>)</code>
<dd>This function adds a new segment to the end of the external
file list of the specified dataset creation property list. The
segment begins a byte <em>offset</em> of file <em>name</em> and
continues for <em>size</em> bytes. The space represented by this
segment is adjacent to the space already represented by the external
file list. The last segment in a file list may have the size
<code>H5F_UNLIMITED</code>, in which case the external file may be
of unlimited size and no more files can be added to the external files list.
<br><br>
<dt><code>int H5Pget_external_count (hid_t <em>plist</em>)</code>
<dd>Calling this function returns the number of segments in an
external file list. If the dataset creation property list has no
external data then zero is returned.
<br><br>
<dt><code>herr_t H5Pget_external (hid_t <em>plist</em>, int
<em>idx</em>, size_t <em>name_size</em>, char *<em>name</em>, off_t
*<em>offset</em>, hsize_t *<em>size</em>)</code>
<dd>This is the counterpart for the <code>H5Pset_external()</code>
function. Given a dataset creation property list and a zero-based
index into that list, the file name, byte offset, and segment size are
returned through non-null arguments. At most <em>name_size</em>
characters are copied into the <em>name</em> argument which is not
null terminated if the file name is longer than the supplied name
buffer (this is similar to <code>strncpy()</code>).
</dl>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Multiple Segments</h4></caption>
<tr>
<td>
<p>This example shows how a contiguous, one-dimensional dataset
is partitioned into three parts and each of those parts is
stored in a segment of an external file. The top rectangle
represents the logical address space of the dataset
while the bottom rectangle represents an external file.
<center>
<img alt="Multiple Segments" src="extern1.gif">
</center>
<p><code><pre>
plist = H5Pcreate (H5P_DATASET_CREATE);
H5Pset_external (plist, "velocity.data", 3000, 1000);
H5Pset_external (plist, "velocity.data", 0, 2500);
H5Pset_external (plist, "velocity.data", 4500, 1500);
</pre></code>
<p>One should note that the segments are defined in order of the
logical addresses they represent, not their order within the
external file. It would also have been possible to put the
segments in separate files. Care should be taken when setting
up segments in a single file since the library doesn't
automatically check for segments that overlap.
</td>
</tr>
</table>
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Multi-Dimensional</h4></caption>
<tr>
<td>
<p>This example shows how a contiguous, two-dimensional dataset
is partitioned into three parts and each of those parts is
stored in a separate external file. The top rectangle
represents the logical address space of the dataset
while the bottom rectangles represent external files.
<center>
<img alt="Multiple Dimensions" src="extern2.gif">
</center>
<p><code><pre>
plist = H5Pcreate (H5P_DATASET_CREATE);
H5Pset_external (plist, "scan1.data", 0, 24);
H5Pset_external (plist, "scan2.data", 0, 24);
H5Pset_external (plist, "scan3.data", 0, 16);
</pre></code>
<p>The library maps the multi-dimensional array onto a linear
address space like normal, and then maps that address space
into the segments defined in the external file list.
</td>
</tr>
</table>
</center>
<p>The segments of an external file can exist beyond the end of the
file. The library reads that part of a segment as zeros. When writing
to a segment that exists beyond the end of a file, the file is
automatically extended. Using this feature, one can create a segment
(or set of segments) which is larger than the current size of the
dataset, which allows to dataset to be extended at a future time
(provided the data space also allows the extension).
<p>All referenced external data files must exist before performing raw
data I/O on the dataset. This is normally not a problem since those
files are being managed directly by the application, or indirectly
through some other library.
<h2>5. Datatype</h2>
<p>Raw data has a constant datatype which describes the datatype
of the raw data stored in the file, and a memory datatype that
describes the datatype stored in application memory. Both data
types are manipulated with the <a
href="Datatypes.html"><code>H5T</code></a> API.
<p>The constant file datatype is associated with the dataset when
the dataset is created in a manner described below. Once
assigned, the constant datatype can never be changed.
<p>The memory datatype is specified when data is transferred
to/from application memory. In the name of data sharability,
the memory datatype must be specified, but can be the same
type identifier as the constant datatype.
<p>During dataset I/O operations, the library translates the raw
data from the constant datatype to the memory datatype or vice
versa. Structured datatypes include member offsets to allow
reordering of struct members and/or selection of a subset of
members and array datatypes include index permutation
information to allow things like transpose operations (<b>the
prototype does not support array reordering</b>) Permutations
are relative to some extrinsic descritpion of the dataset.
<h2>6. Data Space</h2>
<p>The dataspace of a dataset defines the number of dimensions
and the size of each dimension and is manipulated with the
<code>H5S</code> API. The <em>simple</em> dataspace consists of
maximum dimension sizes and actual dimension sizes, which are
usually the same. However, maximum dimension sizes can be the
constant <code>H5D_UNLIMITED</code> in which case the actual
dimension size can be incremented with calls to
<code>H5Dextend()</code>. The maximium dimension sizes are
constant meta data while the actual dimension sizes are
persistent meta data. Initial actual dimension sizes are
supplied at the same time as the maximum dimension sizes when
the dataset is created.
<p>The dataspace can also be used to define partial I/O
operations. Since I/O operations have two end-points, the raw
data transfer functions take two data space arguments: one which
describes the application memory data space or subset thereof
and another which describes the file data space or subset
thereof.
<h2>7. Setting Constant or Persistent Properties</h2>
<p>Each dataset has a set of constant and persistent properties
which describe the layout method, pre-compression
transformation, compression method, datatype, external storage,
and data space. The constant properties are set as described
above in a dataset creation property list whose identifier is
passed to <code>H5Dcreate()</code>.
<dl>
<dt><code>hid_t H5Dcreate (hid_t <em>file_id</em>, const char
*<em>name</em>, hid_t <em>type_id</em>, hid_t
<em>space_id</em>, hid_t <em>create_plist_id</em>)</code>
<dd>A dataset is created by calling <code>H5Dcreate</code> with
a file identifier, a dataset name, a datatype, a dataspace,
and constant properties. The datatype and dataspace are the
type and space of the dataset as it will exist in the file,
which may be different than in application memory.
Dataset names within a group must be unique:
<code>H5Dcreate</code> returns an error if a dataset with the
name specified in <code><em>name</em></code> already exists
at the location specified in <code><em>file_id</em></code>.
The <em>create_plist_id</em> is a <code>H5P_DATASET_CREATE</code>
property list created with <code>H5Pcreate()</code> and
initialized with the various functions described above.
<code>H5Dcreate()</code> returns a dataset handle for success
or negative for failure. The handle should eventually be
closed by calling <code>H5Dclose()</code> to release resources
it uses.
<br><br>
<dt><code>hid_t H5Dopen (hid_t <em>file_id</em>, const char
*<em>name</em>)</code>
<dd>An existing dataset can be opened for access by calling this
function. A dataset handle is returned for success or a
negative value is returned for failure. The handle should
eventually be closed by calling <code>H5Dclose()</code> to
release resources it uses.
<br><br>
<dt><code>herr_t H5Dclose (hid_t <em>dataset_id</em>)</code>
<dd>This function closes a dataset handle and releases all
resources it might have been using. The handle should not be
used in subsequent calls to the library.
<br><br>
<dt><code>herr_t H5Dextend (hid_t <em>dataset_id</em>,
hsize_t <em>dim</em>[])</code>
<dd>This function extends a dataset by increasing the size in
one or more dimensions. Not all datasets can be extended.
</dl>
<h2>8. Querying Constant or Persistent Properties</h2>
<p>Constant or persistent properties can be queried with a set of
three functions. Each function returns an identifier for a copy
of the requested properties. The identifier can be passed to
various functions which modify the underlying object to derive a
new object; the original dataset is completely unchanged. The
return values from these functions should be properly destroyed
when no longer needed.
<dl>
<dt><code>hid_t H5Dget_type (hid_t <em>dataset_id</em>)</code>
<dd>Returns an identifier for a copy of the dataset permanent
datatype or negative for failure.
<dt><code>hid_t H5Dget_space (hid_t <em>dataset_id</em>)</code>
<dd>Returns an identifier for a copy of the dataset permanent
data space, which also contains information about the current
size of the dataset if the data set is extendable with
<code>H5Dextend()</code>.
<dt><code>hid_t H5Dget_create_plist (hid_t
<em>dataset_id</em>)</code>
<dd>Returns an identifier for a copy of the dataset creation
property list. The new property list is created by examining
various permanent properties of the dataset. This is mostly a
catch-all for everything but type and space.
</dl>
<h2>9. Setting Memory and Transfer Properties</h2>
<p>A dataset also has memory properties which describe memory
within the application, and transfer properties that control
various aspects of the I/O operations. The memory can have a
datatype different than the permanent file datatype (different
number types, different struct member offsets, different array
element orderings) and can also be a different size (memory is a
subset of the permanent dataset elements, or vice versa). The
transfer properties might provide caching hints or collective
I/O information. Therefore, each I/O operation must specify
memory and transfer properties.
<p>The memory properties are specified with <em>type_id</em> and
<em>space_id</em> arguments while the transfer properties are
specified with the <em>transfer_id</em> property list for the
<code>H5Dread()</code> and <code>H5Dwrite()</code> functions
(these functions are described below).
<dl>
<dt><code>herr_t H5Pset_buffer (hid_t <em>xfer_plist</em>,
hsize_t <em>max_buf_size</em>, void *<em>tconv_buf</em>, void
*<em>bkg_buf</em>)</code>
<dt><code>hsize_t H5Pget_buffer (hid_t <em>xfer_plist</em>, void
**<em>tconv_buf</em>, void **<em>bkg_buf</em>)</code>
<dd>Sets or retrieves the maximum size in bytes of the temporary
buffer used for datatype conversion in the I/O pipeline. An
application-defined buffer can also be supplied as the
<em>tconv_buf</em> argument, otherwise a buffer will be
allocated and freed on demand by the library. A second
temporary buffer <em>bkg_buf</em> can also be supplied and
should be the same size as the <em>tconv_buf</em>. The
default values are 1MB for the maximum buffer size, and null
pointers for each buffer indicating that they should be
allocated on demand and freed when no longer needed. The
<code>H5Pget_buffer()</code> function returns the maximum
buffer size or zero on error.
</dl>
<p>If the maximum size of the temporary I/O pipeline buffers is
too small to hold the entire I/O request, then the I/O request
will be fragmented and the transfer operation will be strip
mined. However, certain restrictions apply to the strip
mining. For instance, when performing I/O on a hyperslab of a
simple data space the strip mining is in terms of the slowest
varying dimension. So if a 100x200x300 hyperslab is requested,
the temporary buffer must be large enough to hold a 1x200x300
sub-hyperslab.
<p>To prevent strip mining from happening, the application should
use <code>H5Pset_buffer()</code> to set the size of the
temporary buffer so it's large enough to hold the entire
request.
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example</h4></caption>
<tr>
<td>
<p>This example shows how to define a function that sets
a dataset transfer property list so that strip mining
does not occur. It takes an (optional) dataset transfer
property list, a dataset, a data space that describes
what data points are being transfered, and a datatype
for the data points in memory. It returns a (new)
dataset transfer property list with the temporary
buffer size set to an appropriate value. The return
value should be passed as the fifth argument to
<code>H5Dread()</code> or <code>H5Dwrite()</code>.
<p><code><pre>
1 hid_t
2 disable_strip_mining (hid_t xfer_plist, hid_t dataset,
3 hid_t space, hid_t mem_type)
4 {
5 hid_t file_type; /* File datatype */
6 size_t type_size; /* Sizeof larger type */
7 size_t size; /* Temp buffer size */
8 hid_t xfer_plist; /* Return value */
9
10 file_type = H5Dget_type (dataset);
11 type_size = MAX(H5Tget_size(file_type), H5Tget_size(mem_type));
12 H5Tclose (file_type);
13 size = H5Sget_npoints(space) * type_size;
14 if (xfer_plist<0) xfer_plist = H5Pcreate (H5P_DATASET_XFER);
15 H5Pset_buffer(xfer_plist, size, NULL, NULL);
16 return xfer_plist;
17 }
</pre></code>
</td>
</tr>
</table>
</center>
<h2>10. Querying Memory or Transfer Properties</h2>
<p>Unlike constant and persistent properties, a dataset cannot be
queried for it's memory or transfer properties. Memory
properties cannot be queried because the application already
stores those properties separate from the buffer that holds the
raw data, and the buffer may hold multiple segments from various
datasets and thus have more than one set of memory properties.
The transfer properties cannot be queried from the dataset
because they're associated with the transfer itself and not with
the dataset (but one can call
<code>H5Pget_<em>property</em>()</code> to query transfer
properties from a tempalate).
<h2>11. Raw Data I/O</h2>
<p>All raw data I/O is accomplished through these functions which
take a dataset handle, a memory datatype, a memory data space,
a file data space, transfer properties, and an application
memory buffer. They translate data between the memory datatype
and space and the file datatype and space. The data spaces can
be used to describe partial I/O operations.
<dl>
<dt><code>herr_t H5Dread (hid_t <em>dataset_id</em>, hid_t
<em>mem_type_id</em>, hid_t <em>mem_space_id</em>, hid_t
<em>file_space_id</em>, hid_t <em>xfer_plist_id</em>,
void *<em>buf</em>/*out*/)</code>
<dd>Reads raw data from the specified dataset into <em>buf</em>
converting from file datatype and space to memory datatype
and space.
<br><br>
<dt><code>herr_t H5Dwrite (hid_t <em>dataset_id</em>, hid_t
<em>mem_type_id</em>, hid_t <em>mem_space_id</em>, hid_t
<em>file_space_id</em>, hid_t <em>xfer_plist_id</em>,
const void *<em>buf</em>)</code>
<dd>Writes raw data from an application buffer <em>buf</em> to
the specified dataset converting from memory datatype and
space to file datatype and space.
</dl>
<p>In the name of sharability, the memory datatype must be
supplied. However, it can be the same identifier as was used to
create the dataset or as was returned by
<code>H5Dget_type()</code>; the library will not implicitly
derive memory datatypes from constant datatypes.
<p>For complete reads of the dataset one may supply
<code>H5S_ALL</code> as the argument for the file data space.
If <code>H5S_ALL</code> is also supplied as the memory data
space then no data space conversion is performed. This is a
somewhat dangerous situation since the file data space might be
different than what the application expects.
<h2>12. Examples</h2>
<p>The examples in this section illustrate some common dataset
practices.
<p>This example shows how to create a dataset which is stored in
memory as a two-dimensional array of native <code>double</code>
values but is stored in the file in Cray <code>float</code>
format using LZ77 compression. The dataset is written to the
HDF5 file and then read back as a two-dimensional array of
<code>float</code> values.
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example 1</h4></caption>
<tr>
<td>
<p><code><pre>
1 hid_t file, data_space, dataset, properties;
2 double dd[500][600];
3 float ff[500][600];
4 hsize_t dims[2], chunk_size[2];
5
6 /* Describe the size of the array */
7 dims[0] = 500;
8 dims[1] = 600;
9 data_space = H5Screate_simple (2, dims);
10
11
12 /*
13 * Create a new file using with read/write access,
14 * default file creation properties, and default file
15 * access properties.
16 */
17 file = H5Fcreate ("test.h5", H5F_ACC_RDWR, H5P_DEFAULT,
18 H5P_DEFAULT);
19
20 /*
21 * Set the dataset creation plist to specify that
22 * the raw data is to be partitioned into 100x100 element
23 * chunks and that each chunk is to be compressed with
24 * LZ77.
25 */
26 chunk_size[0] = chunk_size[1] = 100;
27 properties = H5Pcreate (H5P_DATASET_CREATE);
28 H5Pset_chunk (properties, 2, chunk_size);
29 H5Pset_deflate (properties, 9);
30
31 /*
32 * Create a new dataset within the file. The datatype
33 * and data space describe the data on disk, which may
34 * be different than the format used in the application's
35 * memory.
36 */
37 dataset = H5Dcreate (file, "dataset", H5T_CRAY_FLOAT,
38 data_space, properties);
39
40 /*
41 * Write the array to the file. The datatype and data
42 * space describe the format of the data in the `dd'
43 * buffer. The raw data is translated to the format
44 * required on disk defined above. We use default raw
45 * data transfer properties.
46 */
47 H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
48 H5P_DEFAULT, dd);
49
50 /*
51 * Read the array as floats. This is similar to writing
52 * data except the data flows in the opposite direction.
53 */
54 H5Dread (dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
55 H5P_DEFAULT, ff);
56
64 H5Dclose (dataset);
65 H5Sclose (data_space);
66 H5Pclose (properties);
67 H5Fclose (file);
</pre></code>
</td>
</tr>
</table>
</center>
<p>This example uses the file created in Example 1 and reads a
hyperslab of the 500x600 file dataset. The hyperslab size is
100x200 and it is located beginning at element
<200,200>. We read the hyperslab into an 200x400 array in
memory beginning at element <0,0> in memory. Visually,
the transfer looks something like this:
<center>
<img alt="Raw Data Transfer" src="dataset_p1.gif">
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example 2</h4></caption>
<tr>
<td>
<p><code><pre>
1 hid_t file, mem_space, file_space, dataset;
2 double dd[200][400];
3 hssize_t offset[2];
4 hsize size[2];
5
6 /*
7 * Open an existing file and its dataset.
8 */
9 file = H5Fopen ("test.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
10 dataset = H5Dopen (file, "dataset");
11
12 /*
13 * Describe the file data space.
14 */
15 offset[0] = 200; /*offset of hyperslab in file*/
16 offset[1] = 200;
17 size[0] = 100; /*size of hyperslab*/
18 size[1] = 200;
19 file_space = H5Dget_space (dataset);
20 H5Sselect_hyperslab (file_space, H5S_SELECT_SET, offset, NULL, size, NULL);
21
22 /*
23 * Describe the memory data space.
24 */
25 size[0] = 200; /*size of memory array*/
26 size[1] = 400;
27 mem_space = H5Screate_simple (2, size);
28
29 offset[0] = 0; /*offset of hyperslab in memory*/
30 offset[1] = 0;
31 size[0] = 100; /*size of hyperslab*/
32 size[1] = 200;
33 H5Sselect_hyperslab (mem_space, H5S_SELECT_SET, offset, NULL, size, NULL);
34
35 /*
36 * Read the dataset.
37 */
38 H5Dread (dataset, H5T_NATIVE_DOUBLE, mem_space,
39 file_space, H5P_DEFAULT, dd);
40
41 /*
42 * Close/release resources.
43 */
44 H5Dclose (dataset);
45 H5Sclose (mem_space);
46 H5Sclose (file_space);
47 H5Fclose (file);
</pre></code>
</td>
</tr>
</table>
</center>
<p>If the file contains a compound data structure one of whose
members is a floating point value (call it "delta") but the
application is interested in reading an array of floating point
values which are just the "delta" values, then the application
should cast the floating point array as a struct with a single
"delta" member.
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example 3</h4></caption>
<tr>
<td>
<p><code><pre>
1 hid_t file, dataset, type;
2 double delta[200];
3
4 /*
5 * Open an existing file and its dataset.
6 */
7 file = H5Fopen ("test.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
8 dataset = H5Dopen (file, "dataset");
9
10 /*
11 * Describe the memory datatype, a struct with a single
12 * "delta" member.
13 */
14 type = H5Tcreate (H5T_COMPOUND, sizeof(double));
15 H5Tinsert (type, "delta", 0, H5T_NATIVE_DOUBLE);
16
17 /*
18 * Read the dataset.
19 */
20 H5Dread (dataset, type, H5S_ALL, H5S_ALL,
21 H5P_DEFAULT, dd);
22
23 /*
24 * Close/release resources.
25 */
26 H5Dclose (dataset);
27 H5Tclose (type);
28 H5Fclose (file);
</pre></code>
</td>
</tr>
</table>
</center>
<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="RM_H5Front.html">HDF5 Reference Manual</a> <br>
<a href="index.html">Other HDF5 documents and links</a> <br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="H5.user.html"><strong>HDF5 User's Guide:</strong></a>
<br>
<a href="Files.html">Files</a>
Datasets
<a href="Datatypes.html">Datatypes</a>
<a href="Dataspaces.html">Dataspaces</a>
<a href="Groups.html">Groups</a>
<br>
<a href="References.html">References</a>
<a href="Attributes.html">Attributes</a>
<a href="Properties.html">Property Lists</a>
<a href="Errors.html">Error Handling</a>
<br>
<a href="Filters.html">Filters</a>
<a href="Caching.html">Caching</a>
<a href="Chunking.html">Chunking</a>
<a href="MountingFiles.html">Mounting Files</a>
<br>
<a href="Performance.html">Performance</a>
<a href="Debugging.html">Debugging</a>
<a href="Environment.html">Environment</a>
<a href="ddl.html">DDL</a>
</td></tr>
</table>
</center>
<hr>
<address>
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
</address>
<!-- Created: Tue Dec 2 09:17:09 EST 1997 -->
<!-- hhmts start -->
Last modified: 2 March 2001
<!-- hhmts end -->
<br>
Describes HDF5 Release 1.5, Unrealeased Development Branch
</body>
</html>
|
