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
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 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 illustrates the concept of virtual dataset.
The program creates three 1-dim source datasets and writes
data to them. Then it creates a 2-dim virtual dataset and
maps the first three rows of the virtual dataset to the data
in the source datasets. Elements of a row are mapped to all
elements of the corresponding source dataset.
The fourth row is not mapped and will be filled with the fill
values when virtual dataset is read back.
The program closes all datasets, and then reopens the virtual
dataset, and finds and prints its creation properties.
Then it reads the values.
This file is intended for use with HDF5 Library version 1.10
************************************************************/
/* EIP Add link to the picture */
#include "hdf5.h"
#include <stdio.h>
#include <stdlib.h>
#define FILE "vds.h5"
#define DATASET "VDS"
#define VDSDIM1 6
#define VDSDIM0 4
#define DIM0 6
#define RANK1 1
#define RANK2 2
const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5"};
const char *SRC_DATASET[] = {"A", "B", "C"};
int
main(void)
{
hid_t file, space, src_space, vspace, dset; /* Handles */
hid_t dcpl;
herr_t status;
hsize_t vdsdims[2] = {VDSDIM0, VDSDIM1}, /* Virtual datasets dimension */
dims[1] = {DIM0}, /* Source datasets dimensions */
start[2], /* Hyperslab parameters */
stride[2], count[2], block[2];
hsize_t start_out[2], stride_out[2], count_out[2], block_out[2];
int wdata[DIM0], /* Write buffer for source dataset */
rdata[VDSDIM0][VDSDIM1], /* Read buffer for virtual dataset */
i, j, k, l;
int fill_value = -1; /* Fill value for VDS */
H5D_layout_t layout; /* Storage layout */
size_t num_map; /* Number of mappings */
ssize_t len; /* Length of the string; also a return value */
char * filename;
char * dsetname;
hsize_t nblocks;
hsize_t * buf; /* Buffer to hold hyperslab coordinates */
/*
* Create source files and datasets. This step is optional.
*/
for (i = 0; i < 3; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0; j++)
wdata[j] = i + 1;
/*
* Create the source files and datasets. Write data to each dataset and
* close all resources.
*/
file = H5Fcreate(SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
space = H5Screate_simple(RANK1, dims, NULL);
dset = H5Dcreate2(file, SRC_DATASET[i], H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
status = H5Sclose(space);
status = H5Dclose(dset);
status = H5Fclose(file);
}
/* Create file in which virtual dataset will be stored. */
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create VDS dataspace. */
space = H5Screate_simple(RANK2, vdsdims, NULL);
/* Set VDS creation property. */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fill_value);
/* Initialize hyperslab values. */
start[0] = 0;
start[1] = 0;
count[0] = 1;
count[1] = 1;
block[0] = 1;
block[1] = VDSDIM1;
/*
* Build the mappings.
* Selections in the source datasets are H5S_ALL.
* In the virtual dataset we select the first, the second and the third rows
* and map each row to the data in the corresponding source dataset.
*/
src_space = H5Screate_simple(RANK1, dims, NULL);
for (i = 0; i < 3; i++) {
start[0] = (hsize_t)i;
/* Select i-th row in the virtual dataset; selection in the source datasets is the same. */
status = H5Sselect_hyperslab(space, H5S_SELECT_SET, start, NULL, count, block);
status = H5Pset_virtual(dcpl, space, SRC_FILE[i], SRC_DATASET[i], src_space);
}
/* Create a virtual dataset. */
dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT);
status = H5Sclose(space);
status = H5Sclose(src_space);
status = H5Dclose(dset);
status = H5Fclose(file);
/*
* Now we begin the read section of this example.
*/
/*
* Open the file and virtual dataset.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen2(file, DATASET, H5P_DEFAULT);
/*
* Get creation property list and mapping properties.
*/
dcpl = H5Dget_create_plist(dset);
/*
* Get storage layout.
*/
layout = H5Pget_layout(dcpl);
if (H5D_VIRTUAL == layout)
printf(" Dataset has a virtual layout \n");
else
printf(" Wrong layout found \n");
/*
* Find the number of mappings.
*/
status = H5Pget_virtual_count(dcpl, &num_map);
printf(" Number of mappings is %lu\n", (unsigned long)num_map);
/*
* Get mapping parameters for each mapping.
*/
for (i = 0; i < (int)num_map; i++) {
printf(" Mapping %d \n", i);
printf(" Selection in the virtual dataset ");
/* Get selection in the virttual dataset */
vspace = H5Pget_virtual_vspace(dcpl, (size_t)i);
/* Make sure that this is a hyperslab selection and then print information. */
if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) {
nblocks = H5Sget_select_hyper_nblocks(vspace);
buf = (hsize_t *)malloc(sizeof(hsize_t) * 2 * RANK2 * nblocks);
status = H5Sget_select_hyper_blocklist(vspace, (hsize_t)0, nblocks, buf);
for (l = 0; l < nblocks; l++) {
printf("(");
for (k = 0; k < RANK2 - 1; k++)
printf("%d,", (int)buf[k]);
printf("%d ) - (", (int)buf[k]);
for (k = 0; k < RANK2 - 1; k++)
printf("%d,", (int)buf[RANK2 + k]);
printf("%d)\n", (int)buf[RANK2 + k]);
}
/* We also can use new APIs to get start, stride, count and block */
if (H5Sis_regular_hyperslab(vspace)) {
status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu] \n", (unsigned long long)start_out[0],
(unsigned long long)start_out[1]);
printf(" stride = [%llu, %llu] \n", (unsigned long long)stride_out[0],
(unsigned long long)stride_out[1]);
printf(" count = [%llu, %llu] \n", (unsigned long long)count_out[0],
(unsigned long long)count_out[1]);
printf(" block = [%llu, %llu] \n", (unsigned long long)block_out[0],
(unsigned long long)block_out[1]);
}
}
/* Get source file name. */
len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0);
filename = (char *)malloc((size_t)len * sizeof(char) + 1);
H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1);
printf(" Source filename %s\n", filename);
/* Get source dataset name. */
len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0);
dsetname = (char *)malloc((size_t)len * sizeof(char) + 1);
H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1);
printf(" Source dataset name %s\n", dsetname);
/* Get selection in the source dataset. */
printf(" Selection in the source dataset ");
src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i);
/* Make sure it is ALL selection and then print the coordinates. */
if (H5Sget_select_type(src_space) == H5S_SEL_ALL) {
printf("(0) - (%d) \n", DIM0 - 1);
}
H5Sclose(vspace);
H5Sclose(src_space);
free(filename);
free(dsetname);
free(buf);
}
/*
* Read the data using the default properties.
*/
status = H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata[0]);
/*
* Output the data to the screen.
*/
printf(" VDS Data:\n");
for (i = 0; i < VDSDIM0; i++) {
printf(" [");
for (j = 0; j < VDSDIM1; j++)
printf(" %3d", rdata[i][j]);
printf("]\n");
}
/*
* Close and release resources.
*/
status = H5Pclose(dcpl);
status = H5Dclose(dset);
status = H5Fclose(file);
return 0;
}
|
