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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/************************************************************
This example shows how to read and write data to an
external dataset. The program first writes integers to an
external dataset with dataspace dimensions of DIM_XxDIM_Y,
then closes the file. Next, it reopens the file, reads
back the data, and outputs the name of the external data
file and the data to the screen.
************************************************************/
package examples.datasets;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
public class H5Ex_D_External {
private static String FILENAME = "H5Ex_D_External.h5";
private static String EXTERNALNAME = "H5Ex_D_External.data";
private static String DATASETNAME = "DS1";
private static final int DIM_X = 4;
private static final int DIM_Y = 7;
private static final int RANK = 2;
private static final int NAME_BUF_SIZE = 32;
private static void writeExternal() {
long file_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
// Initialize the dataset.
for (int indx = 0; indx < DIM_X; indx++)
for (int jndx = 0; jndx < DIM_Y; jndx++)
dset_data[indx][jndx] = indx * jndx - jndx;
// Create a new file using default properties.
try {
file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
filespace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset creation property list.
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
}
catch (Exception e) {
e.printStackTrace();
}
// set the external file.
try {
if (dcpl_id >= 0)
H5.H5Pset_external(dcpl_id, EXTERNALNAME, 0, HDF5Constants.H5F_UNLIMITED);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the HDF5Constants.dataset.
try {
if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0))
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id,
HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the dataset.
try {
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
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();
}
// Terminate access to the data space.
try {
if (filespace_id >= 0)
H5.H5Sclose(filespace_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dcpl_id >= 0)
H5.H5Pclose(dcpl_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void readExternal() {
long file_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];
String[] Xname = new String[1];
// Open file using the default properties.
try {
file_id = H5.H5Fopen(FILENAME, 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, DATASETNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Retrieve the dataset creation property list.
try {
if (dataset_id >= 0)
dcpl_id = H5.H5Dget_create_plist(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Retrieve and print the name of the external file.
long[] Xsize = new long[NAME_BUF_SIZE];
try {
if (dcpl_id >= 0)
H5.H5Pget_external(dcpl_id, 0, Xsize.length, Xname, Xsize);
}
catch (Exception e) {
e.printStackTrace();
}
System.out.println(DATASETNAME + " is stored in file: " + Xname[0]);
// Read the data using the default properties.
try {
if (dataset_id >= 0)
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
System.out.println(DATASETNAME + ":");
for (int indx = 0; indx < DIM_X; indx++) {
System.out.print(" [ ");
for (int jndx = 0; jndx < DIM_Y; jndx++)
System.out.print(dset_data[indx][jndx] + " ");
System.out.println("]");
}
System.out.println();
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dcpl_id >= 0)
H5.H5Pclose(dcpl_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) {
H5Ex_D_External.writeExternal();
H5Ex_D_External.readExternal();
}
}
|
