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hdf5/examples/h5_vds-percival-unlim.c

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/************************************************************
This example illustrates the concept of the virtual dataset.
Percival use case. Every fifth 10x10 plane in VDS is stored in
the corresponding 3D unlimited dataset.
There are 4 source datasets total.
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 VFILE "vds-percival-unlim.h5"
#define DATASET "VDS-Percival-unlim"
#define VDSDIM0 H5S_UNLIMITED
#define VDSDIM1 10
#define VDSDIM2 10
#define DIM0 H5S_UNLIMITED
#define DIM0_1 10 /* Initial size of the datasets */
#define DIM1 10
#define DIM2 10
#define RANK 3
#define PLANE_STRIDE 4
const char *SRC_FILE[] = {
"a.h5",
"b.h5",
"c.h5",
"d.h5"
};
const char *SRC_DATASET[] = {
"A",
"B",
"C",
"D"
};
int
main (void)
{
hid_t vfile, file, src_space, mem_space, vspace,
vdset, dset; /* Handles */
hid_t dcpl;
herr_t status;
hsize_t vdsdims[3] = {4*DIM0_1, VDSDIM1, VDSDIM2},
vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2},
dims[3] = {DIM0_1, DIM1, DIM2},
extdims[3] = {2*DIM0_1, DIM1, DIM2},
chunk_dims[3] = {DIM0_1, DIM1, DIM2},
dims_max[3] = {DIM0, DIM1, DIM2},
vdsdims_out[3],
vdsdims_max_out[3],
start[3], /* Hyperslab parameters */
stride[3],
count[3],
src_count[3],
block[3];
hsize_t start_out[3], /* Hyperslab parameter out */
stride_out[3],
count_out[3],
block_out[3];
int i, j, k;
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;
int wdata[DIM0_1*DIM1*DIM2];
int rdata[80][10][10];
int a_rdata[20][10][10];
/*
* Create source files and datasets. This step is optional.
*/
for (i=0; i < PLANE_STRIDE; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0_1*DIM1*DIM2; 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);
src_space = H5Screate_simple (RANK, dims, dims_max);
dcpl = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_chunk (dcpl, RANK, chunk_dims);
dset = H5Dcreate2 (file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata);
status = H5Sclose (src_space);
status = H5Pclose (dcpl);
status = H5Dclose (dset);
status = H5Fclose (file);
}
vfile = H5Fcreate (VFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create VDS dataspace. */
vspace = H5Screate_simple (RANK, vdsdims, vdsdims_max);
/* Create dataspaces for the source dataset. */
src_space = H5Screate_simple (RANK, dims, dims_max);
/* Create VDS creation property */
dcpl = H5Pcreate (H5P_DATASET_CREATE);
/* Initialize hyperslab values */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */
stride[1] = 1;
stride[2] = 1;
count[0] = H5S_UNLIMITED;
count[1] = 1;
count[2] = 1;
src_count[0] = H5S_UNLIMITED;
src_count[1] = 1;
src_count[2] = 1;
block[0] = 1;
block[1] = DIM1;
block[2] = DIM2;
/*
* Build the mappings
*
*/
status = H5Sselect_hyperslab (src_space, H5S_SELECT_SET, start, NULL, src_count, block);
for (i=0; i < PLANE_STRIDE; i++) {
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
status = H5Pset_virtual (dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space);
start[0]++;
}
H5Sselect_none(vspace);
/* Create a virtual dataset */
vdset = H5Dcreate2 (vfile, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Sclose (vspace);
status = H5Sclose (src_space);
status = H5Pclose (dcpl);
/* Let's get space of the VDS and its dimension; we should get 40x10x10 */
vspace = H5Dget_space (vdset);
H5Sget_simple_extent_dims (vspace, vdsdims_out, vdsdims_max_out);
printf ("VDS dimensions first time \n");
printf (" Current: ");
for (i=0; i<RANK; i++)
printf (" %d ", (int)vdsdims_out[i]);
printf ("\n");
/* Let's add data to the source datasets and check new dimensions for VDS */
for (i=0; i < PLANE_STRIDE; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0_1*DIM1*DIM2; j++) wdata[j] = 10*(i+1);
/*
* Create the source files and datasets. Write data to each dataset and
* close all resources.
*/
file = H5Fopen (SRC_FILE[i], H5F_ACC_RDWR, H5P_DEFAULT);
dset = H5Dopen2 (file, SRC_DATASET[i], H5P_DEFAULT);
status = H5Dset_extent (dset, extdims);
src_space = H5Dget_space (dset);
start[0] = DIM0_1;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = 1;
block[0] = DIM0_1;
block[1] = DIM1;
block[2] = DIM2;
mem_space = H5Screate_simple(RANK, dims, NULL);
status = H5Sselect_hyperslab (src_space, H5S_SELECT_SET, start, NULL, count, block);
status = H5Dwrite (dset, H5T_NATIVE_INT, mem_space, src_space, H5P_DEFAULT,
wdata);
status = H5Sclose (src_space);
status = H5Dclose (dset);
status = H5Fclose (file);
}
status = H5Dclose (vdset);
status = H5Fclose (vfile);
/*
* Now we begin the read section of this example.
*/
/*
* Open file and dataset using the default properties.
*/
vfile = H5Fopen (VFILE, H5F_ACC_RDONLY, H5P_DEFAULT);
vdset = H5Dopen2 (vfile, DATASET, H5P_DEFAULT);
/*
* Get creation property list and mapping properties.
*/
dcpl = H5Dget_create_plist (vdset);
/*
* 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 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 \n");
/* Get selection in the virttual dataset */
vspace = H5Pget_virtual_vspace (dcpl, (size_t)i);
if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(vspace)) {
status = H5Sget_regular_hyperslab (vspace, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
/* 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 \n");
src_space = H5Pget_virtual_srcspace (dcpl, (size_t)i);
if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(src_space)) {
status = H5Sget_regular_hyperslab (src_space, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
H5Sclose(vspace);
H5Sclose(src_space);
free(filename);
free(dsetname);
}
/*
* Read data from VDS.
*/
vspace = H5Dget_space (vdset);
H5Sget_simple_extent_dims (vspace, vdsdims_out, vdsdims_max_out);
printf ("VDS dimensions second time \n");
printf (" Current: ");
for (i=0; i<RANK; i++)
printf (" %d ", (int)vdsdims_out[i]);
printf ("\n");
/* Read all VDS data */
/* EIP We should be able to do it by using H5S_ALL instead of making selection
* or using H5Sselect_all from vspace.
*/
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = 1;
block[0] = vdsdims_out[0];
block[1] = vdsdims_out[1];
block[2] = vdsdims_out[2];
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, NULL, count, block);
mem_space = H5Screate_simple(RANK, vdsdims_out, NULL);
status = H5Dread (vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT,
rdata);
printf (" All data: \n");
for (i=0; i < (int)vdsdims_out[0]; i++) {
for (j=0; j < (int)vdsdims_out[1]; j++) {
printf ("(%d, %d, 0)", i, j);
for (k=0; k < (int)vdsdims_out[2]; k++)
printf (" %d ", rdata[i][j][k]);
printf ("\n");
}
}
/* Read VDS, but only data mapeed to dataset a.h5 */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = PLANE_STRIDE;
stride[1] = 1;
stride[2] = 1;
count[0] = 2*DIM0_1;
count[1] = 1;
count[2] = 1;
block[0] = 1;
block[1] = vdsdims_out[1];
block[2] = vdsdims_out[2];
dims[0] = 2*DIM0_1;
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
mem_space = H5Screate_simple(RANK, dims, NULL);
status = H5Dread (vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT,
a_rdata);
printf (" All data: \n");
for (i=0; i < 2*DIM0_1; i++) {
for (j=0; j < (int)vdsdims_out[1]; j++) {
printf ("(%d, %d, 0)", i, j);
for (k=0; k < (int)vdsdims_out[2]; k++)
printf (" %d ", a_rdata[i][j][k]);
printf ("\n");
}
}
/*
* Close and release resources.
*/
status = H5Sclose(mem_space);
status = H5Pclose (dcpl);
status = H5Dclose (vdset);
status = H5Fclose (vfile);
return 0;
}
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