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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 a compact
dataset. The program first writes integers to a compact
dataset with dataspace dimensions of DIM_XxDIM_Y, then
closes the file. Next, it reopens the file, reads back
the data, and outputs it to the screen.
************************************************************/
package examples.datasets;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
public class H5Ex_D_Compact {
private static String FILENAME = "H5Ex_D_Compact.h5";
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;
// Values for the status of space allocation
enum H5D_layout {
H5D_LAYOUT_ERROR(-1), H5D_COMPACT(0), H5D_CONTIGUOUS(1), H5D_CHUNKED(2), H5D_VIRTUAL(3), H5D_NLAYOUTS(4);
private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>();
static {
for (H5D_layout s : EnumSet.allOf(H5D_layout.class))
lookup.put(s.getCode(), s);
}
private int code;
H5D_layout(int layout_type) {
this.code = layout_type;
}
public int getCode() {
return this.code;
}
public static H5D_layout get(int code) {
return lookup.get(code);
}
}
private static void writeCompact() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long[] dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
// Initialize data.
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 layout to compact.
try {
if (dcpl_id >= 0)
H5.H5Pset_layout(dcpl_id, H5D_layout.H5D_COMPACT.getCode());
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset. We will use all default properties for this example.
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 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, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (dcpl_id >= 0)
H5.H5Pclose(dcpl_id);
}
catch (Exception e) {
e.printStackTrace();
}
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();
}
}
private static void readCompact() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
int[][] dset_data = new int[DIM_X][DIM_Y];
// Open file and dataset using the default properties.
try {
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
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();
}
// Print the storage layout.
try {
if (dcpl_id >= 0) {
int layout_type = H5.H5Pget_layout(dcpl_id);
System.out.print("Storage layout for " + DATASETNAME + " is: ");
switch (H5D_layout.get(layout_type)) {
case H5D_COMPACT:
System.out.println("H5D_COMPACT");
break;
case H5D_CONTIGUOUS:
System.out.println("H5D_CONTIGUOUS");
break;
case H5D_CHUNKED:
System.out.println("H5D_CHUNKED");
break;
case H5D_VIRTUAL:
System.out.println("H5D_VIRTUAL");
break;
case H5D_LAYOUT_ERROR:
break;
case H5D_NLAYOUTS:
break;
default:
break;
}
System.out.println();
}
}
catch (Exception e) {
e.printStackTrace();
}
// 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("Data for " + DATASETNAME + " is: ");
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();
// End access to the dataset and release resources used by it.
try {
if (dcpl_id >= 0)
H5.H5Pclose(dcpl_id);
}
catch (Exception e) {
e.printStackTrace();
}
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();
}
}
public static void main(String[] args) {
H5Ex_D_Compact.writeCompact();
H5Ex_D_Compact.readCompact();
}
}
|