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
|
/************************************************************
This example shows how to read and write bitfield
datatypes to an attribute. The program first writes bit
fields to an attribute with a dataspace of DIM0xDIM1, then
closes the file. Next, it reopens the file, reads back
the data, and outputs it to the screen.
This file is intended for use with HDF5 Library verion 1.6
************************************************************/
package examples.datatypes;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.Datatype;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.h5.H5Datatype;
import ncsa.hdf.object.h5.H5File;
import ncsa.hdf.object.h5.H5ScalarDS;
public class H5ObjectEx_T_BitAttribute {
private static String FILENAME = "H5ObjectEx_T_BitAttribute.h5";
private static String DATASETNAME = "DS1";
private static String ATTRIBUTENAME = "A1";
private static final int DIM0 = 4;
private static final int DIM1 = 7;
private static final int RANK = 2;
private static void CreateDataset() {
H5File file = null;
H5ScalarDS dset = null;
int dataspace_id = -1;
int dataset_id = -1;
int attribute_id = -1;
long[] dims = { DIM0, DIM1 };
int[][] dset_data = new int[DIM0][DIM1];
final H5Datatype typeInt = new H5Datatype(Datatype.CLASS_INTEGER, 4, Datatype.ORDER_LE, -1);
// Initialize data.
for (int indx = 0; indx < DIM0; indx++)
for (int jndx = 0; jndx < DIM1; jndx++) {
dset_data[indx][jndx] = 0;
dset_data[indx][jndx] |= (indx * jndx - jndx) & 0x03; /* Field "A" */
dset_data[indx][jndx] |= (indx & 0x03) << 2; /* Field "B" */
dset_data[indx][jndx] |= (jndx & 0x03) << 4; /* Field "C" */
dset_data[indx][jndx] |= ((indx + jndx) & 0x03) << 6; /* Field "D" */
}
// Create a new file using default properties.
try {
file = new H5File(FILENAME, FileFormat.CREATE);
file.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataset with a scalar dataspace.
try {
dset = (H5ScalarDS) file.createScalarDS(DATASETNAME, null, typeInt, dims, null, null, 0, null);
dataset_id = dset.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
dataspace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the attribute and write the array data to it.
try {
if ((dataset_id >= 0) && (dataspace_id >= 0))
attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME,
HDF5Constants.H5T_STD_B8BE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the dataset.
try {
if (attribute_id >= 0)
H5.H5Awrite(attribute_id, HDF5Constants.H5T_NATIVE_B8, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
dset.close(dataset_id);
}
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();
}
// Close the file.
try {
file.close();
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset() {
H5File file = null;
H5ScalarDS dset = null;
int dataspace_id = -1;
int dataset_id = -1;
int attribute_id = -1;
long[] dims = { DIM0, DIM1 };
int[][] dset_data;
// Open an existing file.
try {
file = new H5File(FILENAME, FileFormat.READ);
file.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
dset = (H5ScalarDS) file.get(DATASETNAME);
dataset_id = dset.open();
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Get dataspace and allocate memory for read buffer.
try {
if (attribute_id >= 0)
dataspace_id = H5.H5Aget_space(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataspace_id >= 0)
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate array of pointers to two-dimensional arrays (the
// elements of the dataset.
dset_data = new int[(int) dims[0]][(int) (dims[1])];
// Read data.
try {
if (attribute_id >= 0)
H5.H5Aread(attribute_id, HDF5Constants.H5T_NATIVE_B8, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
System.out.println(ATTRIBUTENAME + ":");
for (int indx = 0; indx < dims[0]; indx++) {
System.out.print(" [");
for (int jndx = 0; jndx < dims[1]; jndx++) {
System.out.print("{" + (dset_data[indx][jndx] & 0x03) + ", ");
System.out.print(((dset_data[indx][jndx] >> 2) & 0x03) + ", ");
System.out.print(((dset_data[indx][jndx] >> 4) & 0x03) + ", ");
System.out.print(((dset_data[indx][jndx] >> 6) & 0x03) + "}");
}
System.out.println("]");
}
System.out.println();
// End access to the dataset and release resources used by it.
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
dset.close(dataset_id);
}
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();
}
// Close the file.
try {
file.close();
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
H5ObjectEx_T_BitAttribute.CreateDataset();
// Now we begin the read section of this example. Here we assume
// the dataset and array have the same name and rank, but can have
// any size. Therefore we must allocate a new array to read in
// data using malloc().
H5ObjectEx_T_BitAttribute.ReadDataset();
}
}
|
