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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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;
/**
* <p>
* Title: HDF Native Package (Java) Example
* </p>
* <p>
* Description: this example shows how to select a subset using the
* "HDF Native Package (Java)". The example creates an integer dataset, and read
* subset of the dataset:
*
* <pre>
* "/" (root)
* 2D 32-bit integer 20x10
* </pre>
*
* The whole 20x10 data set is
*
* <pre>
* 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009
* 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109
* 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209
* 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309
* 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409
* 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509
* 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609
* 1700, 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709
* 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1808, 1809
* 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909
* 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
* 2100, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109
* 2200, 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209
* 2300, 2301, 2302, 2303, 2304, 2305, 2306, 2307, 2308, 2309
* 2400, 2401, 2402, 2403, 2404, 2405, 2406, 2407, 2408, 2409
* 2500, 2501, 2502, 2503, 2504, 2505, 2506, 2507, 2508, 2509
* 2600, 2601, 2602, 2603, 2604, 2605, 2606, 2607, 2608, 2609
* 2700, 2701, 2702, 2703, 2704, 2705, 2706, 2707, 2708, 2709
* 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809
* 2900, 2901, 2902, 2903, 2904, 2905, 2906, 2907, 2908, 2909
* </pre>
*
* Subset: start=(4, 2), size=(5, 3) and stride=(3, 2). The subset values are:
*
* <pre>
* 1402,1404,1406
* 1702,1704,1706
* 2002,2004,2006
* 2302,2304,2306
* 2602,2604,2606
* </pre>
*
* </p>
*
* @author Peter X. Cao
* @version 2.4
*/
public class HDF5SubsetSelect {
private static String fname = "HDF5SubsetSelect.h5";
private static String dsname = "2D 32-bit integer 20x10";
private static long[] dims2D = {20, 10};
private static void SubsetSelect()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long memspace_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 dataset using the default properties.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, dsname, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate array of pointers to two-dimensional arrays (the
// elements of the dataset.
int[][] dataRead = new int[5][3];
// Define and select the hyperslab to use for reading.
try {
if (dataset_id >= 0) {
filespace_id = H5.H5Dget_space(dataset_id);
long[] start = {4, 2};
long[] stride = {3, 2};
long[] count = {5, 3};
long[] block = null;
if (filespace_id >= 0) {
H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count,
block);
memspace_id = H5.H5Screate_simple(2, count, null);
// Read the data using the previously defined hyperslab.
if ((dataset_id >= 0) && (filespace_id >= 0) && (memspace_id >= 0))
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, memspace_id, filespace_id,
HDF5Constants.H5P_DEFAULT, dataRead);
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// print out the data values
System.out.println("\n\nSubset Data Values");
for (int i = 0; i < 5; i++) {
System.out.print("\n" + dataRead[i][0]);
for (int j = 1; j < 3; j++) {
System.out.print("," + dataRead[i][j]);
}
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (filespace_id >= 0)
H5.H5Sclose(filespace_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_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 file_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = 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 the data space for the dataset.
try {
dataspace_id = H5.H5Screate_simple(2, dims2D, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset.
try {
if ((file_id >= 0) && (dataspace_id >= 0))
dataset_id = H5.H5Dcreate(file_id, dsname, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
}
catch (Exception e) {
e.printStackTrace();
}
// set the data values
int[] dataIn = new int[20 * 10];
for (int i = 0; i < 20; i++) {
for (int j = 0; j < 10; j++) {
dataIn[i * 10 + j] = 1000 + i * 100 + j;
}
}
// Write the data to the dataset.
try {
if (dataset_id >= 0)
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dataIn);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
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) { HDF5SubsetSelect.SubsetSelect(); }
}
|
