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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.structs.H5G_info_t;
import hdf.hdf5lib.structs.H5O_token_t;
/**
* <p>
* Title: HDF Native Package (Java) Example
* </p>
* <p>
* Description: this example shows how to retrieve HDF file structure using the
* "HDF Native Package (Java)". The example created the group structure and
* datasets, and print out the file structure:
*
* <pre>
* "/" (root)
* integer arrays
* 2D 32-bit integer 20x10
* 3D unsigned 8-bit integer 20x10x5
* float arrays
* 2D 64-bit double 20x10
* 3D 32-bit float 20x10x5
* </pre>
*
* </p>
*/
public class HDF5FileStructure {
private static String fname = "HDF5FileStructure.h5";
private static void FileStructure()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long group_id = HDF5Constants.H5I_INVALID_HID;
// create the file and add groups and dataset into the file
try {
createFile();
}
catch (Exception e) {
e.printStackTrace();
}
// Open file using the default properties.
try {
file_id = H5.H5Fopen(fname, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open the group, obtaining a new handle.
try {
if (file_id >= 0)
group_id = H5.H5Gopen(file_id, "/", HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
try {
printGroup(group_id, "/", "");
}
catch (Exception e) {
e.printStackTrace();
}
// Close the group.
try {
if (group_id >= 0)
H5.H5Gclose(group_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
/**
* Recursively print a group and its members.
*
* @throws Exception
*/
private static void printGroup(long g_id, String gname, String indent) throws Exception
{
if (g_id < 0)
return;
H5G_info_t members = H5.H5Gget_info(g_id);
String objNames[] = new String[(int)members.nlinks];
int objTypes[] = new int[(int)members.nlinks];
int lnkTypes[] = new int[(int)members.nlinks];
H5O_token_t objTokens[] = new H5O_token_t[(int)members.nlinks];
int names_found = 0;
try {
names_found = H5.H5Gget_obj_info_all(g_id, null, objNames, objTypes, lnkTypes, objTokens,
HDF5Constants.H5_INDEX_NAME);
}
catch (Throwable err) {
err.printStackTrace();
}
indent += " ";
for (int i = 0; i < names_found; i++) {
System.out.println(indent + objNames[i]);
long group_id = HDF5Constants.H5I_INVALID_HID;
if (objTypes[i] == HDF5Constants.H5O_TYPE_GROUP) {
// Open the group, obtaining a new handle.
try {
if (g_id >= 0)
group_id = H5.H5Gopen(g_id, objNames[i], HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
if (group_id >= 0)
printGroup(group_id, objNames[i], indent);
// Close the group.
try {
if (group_id >= 0)
H5.H5Gclose(group_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
}
}
/**
* create the file and add groups ans dataset into the file, which is the
* same as javaExample.H5DatasetCreate
*
* @see javaExample.HDF5DatasetCreate
* @throws Exception
*/
private static void createFile() throws Exception
{
long[] dims2D = {20, 10};
long[] dims3D = {20, 10, 5};
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id1 = HDF5Constants.H5I_INVALID_HID;
long dataspace_id2 = HDF5Constants.H5I_INVALID_HID;
long group_id1 = HDF5Constants.H5I_INVALID_HID;
long group_id2 = HDF5Constants.H5I_INVALID_HID;
// Create a new file using default properties.
try {
file_id = H5.H5Fcreate(fname, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Create groups in the file.
try {
if (file_id >= 0) {
group_id1 = H5.H5Gcreate(file_id,
"/"
+ "integer arrays",
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
group_id1 = H5.H5Gcreate(file_id,
"/"
+ "float arrays",
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create the data space for the datasets.
try {
dataspace_id1 = H5.H5Screate_simple(2, dims2D, null);
dataspace_id2 = H5.H5Screate_simple(3, dims3D, null);
}
catch (Exception e) {
e.printStackTrace();
}
// create 2D 32-bit (4 bytes) integer dataset of 20 by 10
try {
if ((file_id >= 0) && (dataspace_id1 >= 0))
dataset_id =
H5.H5Dcreate(file_id,
"/"
+ "integer arrays"
+ "/"
+ "2D 32-bit integer 20x10",
HDF5Constants.H5T_STD_I32LE, dataspace_id1, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
dataset_id = HDF5Constants.H5I_INVALID_HID;
}
catch (Exception e) {
e.printStackTrace();
}
// create 3D 8-bit (1 byte) unsigned integer dataset of 20 by 10 by 5
try {
if ((file_id >= 0) && (dataspace_id2 >= 0))
dataset_id =
H5.H5Dcreate(file_id,
"/"
+ "integer arrays"
+ "/"
+ "3D 8-bit unsigned integer 20x10x5",
HDF5Constants.H5T_STD_I64LE, dataspace_id2, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
dataset_id = HDF5Constants.H5I_INVALID_HID;
}
catch (Exception e) {
e.printStackTrace();
}
// create 2D 64-bit (8 bytes) double dataset of 20 by 10
try {
if ((file_id >= 0) && (dataspace_id1 >= 0))
dataset_id =
H5.H5Dcreate(file_id,
"/"
+ "float arrays"
+ "/"
+ "2D 64-bit double 20x10",
HDF5Constants.H5T_NATIVE_DOUBLE, dataspace_id1, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
dataset_id = HDF5Constants.H5I_INVALID_HID;
}
catch (Exception e) {
e.printStackTrace();
}
// create 3D 32-bit (4 bytes) float dataset of 20 by 10 by 5
try {
if ((file_id >= 0) && (dataspace_id2 >= 0))
dataset_id =
H5.H5Dcreate(file_id,
"/"
+ "float arrays"
+ "/"
+ "3D 32-bit float 20x10x5",
HDF5Constants.H5T_NATIVE_FLOAT, dataspace_id2, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
dataset_id = HDF5Constants.H5I_INVALID_HID;
}
catch (Exception e) {
e.printStackTrace();
}
// Close the data space.
try {
if (dataspace_id1 >= 0)
H5.H5Sclose(dataspace_id1);
dataspace_id1 = HDF5Constants.H5I_INVALID_HID;
if (dataspace_id2 >= 0)
H5.H5Sclose(dataspace_id2);
dataspace_id2 = HDF5Constants.H5I_INVALID_HID;
}
catch (Exception e) {
e.printStackTrace();
}
// Close the groups.
try {
if (group_id1 >= 0)
H5.H5Gclose(group_id1);
if (group_id2 >= 0)
H5.H5Gclose(group_id2);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) { HDF5FileStructure.FileStructure(); }
}
|
