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hdf5/examples/h5_vds-percival-unlim.c
luzpaz 174505ca3c
Fix typos found in the rest of the hdf5 code-base (#1985) 
* Fix typos found in the rest of the hdf5 code-base

* Typo in tool.cmake

* Revert "Typo in tool.cmake"

This reverts commit 06b8403d99.

* Fix clang-format styling
2022-08-10 13:57:26 -07:00

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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://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 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 virtual 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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