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174505ca3c
* 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
347 lines
13 KiB
C
347 lines
13 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/************************************************************
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This example illustrates the concept of the virtual dataset.
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Percival use case. Every fifth 10x10 plane in VDS is stored in
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the corresponding 3D unlimited dataset.
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There are 4 source datasets total.
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This file is intended for use with HDF5 Library version 1.10
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************************************************************/
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/* EIP Add link to the picture */
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#include "hdf5.h"
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#include <stdio.h>
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#include <stdlib.h>
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#define VFILE "vds-percival-unlim.h5"
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#define DATASET "VDS-Percival-unlim"
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#define VDSDIM0 H5S_UNLIMITED
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#define VDSDIM1 10
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#define VDSDIM2 10
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#define DIM0 H5S_UNLIMITED
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#define DIM0_1 10 /* Initial size of the datasets */
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#define DIM1 10
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#define DIM2 10
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#define RANK 3
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#define PLANE_STRIDE 4
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const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5", "d.h5"};
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const char *SRC_DATASET[] = {"A", "B", "C", "D"};
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int
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main(void)
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{
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hid_t vfile, file, src_space, mem_space, vspace, vdset, dset; /* Handles */
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hid_t dcpl;
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herr_t status;
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hsize_t vdsdims[3] = {4 * DIM0_1, VDSDIM1, VDSDIM2}, vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2},
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dims[3] = {DIM0_1, DIM1, DIM2}, extdims[3] = {2 * DIM0_1, DIM1, DIM2},
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chunk_dims[3] = {DIM0_1, DIM1, DIM2}, dims_max[3] = {DIM0, DIM1, DIM2}, vdsdims_out[3],
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vdsdims_max_out[3], start[3], /* Hyperslab parameters */
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stride[3], count[3], src_count[3], block[3];
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hsize_t start_out[3], /* Hyperslab parameter out */
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stride_out[3], count_out[3], block_out[3];
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int i, j, k;
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H5D_layout_t layout; /* Storage layout */
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size_t num_map; /* Number of mappings */
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ssize_t len; /* Length of the string; also a return value */
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char *filename;
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char *dsetname;
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int wdata[DIM0_1 * DIM1 * DIM2];
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int rdata[80][10][10];
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int a_rdata[20][10][10];
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/*
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* Create source files and datasets. This step is optional.
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*/
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for (i = 0; i < PLANE_STRIDE; i++) {
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/*
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* Initialize data for i-th source dataset.
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*/
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for (j = 0; j < DIM0_1 * DIM1 * DIM2; j++)
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wdata[j] = i + 1;
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/*
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* Create the source files and datasets. Write data to each dataset and
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* close all resources.
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*/
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file = H5Fcreate(SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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src_space = H5Screate_simple(RANK, dims, dims_max);
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dcpl = H5Pcreate(H5P_DATASET_CREATE);
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status = H5Pset_chunk(dcpl, RANK, chunk_dims);
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dset = H5Dcreate2(file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT, dcpl, H5P_DEFAULT);
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status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
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status = H5Sclose(src_space);
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status = H5Pclose(dcpl);
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status = H5Dclose(dset);
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status = H5Fclose(file);
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}
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vfile = H5Fcreate(VFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create VDS dataspace. */
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vspace = H5Screate_simple(RANK, vdsdims, vdsdims_max);
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/* Create dataspaces for the source dataset. */
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src_space = H5Screate_simple(RANK, dims, dims_max);
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/* Create VDS creation property */
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dcpl = H5Pcreate(H5P_DATASET_CREATE);
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/* Initialize hyperslab values */
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */
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stride[1] = 1;
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stride[2] = 1;
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count[0] = H5S_UNLIMITED;
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count[1] = 1;
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count[2] = 1;
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src_count[0] = H5S_UNLIMITED;
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src_count[1] = 1;
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src_count[2] = 1;
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block[0] = 1;
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block[1] = DIM1;
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block[2] = DIM2;
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/*
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* Build the mappings
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*
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*/
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status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, src_count, block);
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for (i = 0; i < PLANE_STRIDE; i++) {
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status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block);
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status = H5Pset_virtual(dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space);
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start[0]++;
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}
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H5Sselect_none(vspace);
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/* Create a virtual dataset */
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vdset = H5Dcreate2(vfile, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
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status = H5Sclose(vspace);
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status = H5Sclose(src_space);
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status = H5Pclose(dcpl);
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/* Let's get space of the VDS and its dimension; we should get 40x10x10 */
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vspace = H5Dget_space(vdset);
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H5Sget_simple_extent_dims(vspace, vdsdims_out, vdsdims_max_out);
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printf("VDS dimensions first time \n");
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printf(" Current: ");
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for (i = 0; i < RANK; i++)
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printf(" %d ", (int)vdsdims_out[i]);
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printf("\n");
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/* Let's add data to the source datasets and check new dimensions for VDS */
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for (i = 0; i < PLANE_STRIDE; i++) {
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/*
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* Initialize data for i-th source dataset.
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*/
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for (j = 0; j < DIM0_1 * DIM1 * DIM2; j++)
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wdata[j] = 10 * (i + 1);
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/*
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* Create the source files and datasets. Write data to each dataset and
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* close all resources.
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*/
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file = H5Fopen(SRC_FILE[i], H5F_ACC_RDWR, H5P_DEFAULT);
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dset = H5Dopen2(file, SRC_DATASET[i], H5P_DEFAULT);
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status = H5Dset_extent(dset, extdims);
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src_space = H5Dget_space(dset);
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start[0] = DIM0_1;
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start[1] = 0;
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start[2] = 0;
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count[0] = 1;
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count[1] = 1;
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count[2] = 1;
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block[0] = DIM0_1;
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block[1] = DIM1;
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block[2] = DIM2;
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mem_space = H5Screate_simple(RANK, dims, NULL);
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status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, count, block);
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status = H5Dwrite(dset, H5T_NATIVE_INT, mem_space, src_space, H5P_DEFAULT, wdata);
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status = H5Sclose(src_space);
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status = H5Dclose(dset);
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status = H5Fclose(file);
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}
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status = H5Dclose(vdset);
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status = H5Fclose(vfile);
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/*
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* Now we begin the read section of this example.
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*/
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/*
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* Open file and dataset using the default properties.
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*/
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vfile = H5Fopen(VFILE, H5F_ACC_RDONLY, H5P_DEFAULT);
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vdset = H5Dopen2(vfile, DATASET, H5P_DEFAULT);
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/*
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* Get creation property list and mapping properties.
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*/
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dcpl = H5Dget_create_plist(vdset);
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/*
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* Get storage layout.
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*/
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layout = H5Pget_layout(dcpl);
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if (H5D_VIRTUAL == layout)
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printf(" Dataset has a virtual layout \n");
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else
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printf(" Wrong layout found \n");
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/*
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* Find number of mappings.
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*/
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status = H5Pget_virtual_count(dcpl, &num_map);
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printf(" Number of mappings is %lu\n", (unsigned long)num_map);
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/*
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* Get mapping parameters for each mapping.
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*/
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for (i = 0; i < (int)num_map; i++) {
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printf(" Mapping %d \n", i);
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printf(" Selection in the virtual dataset \n");
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/* Get selection in the virtual dataset */
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vspace = H5Pget_virtual_vspace(dcpl, (size_t)i);
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if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) {
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if (H5Sis_regular_hyperslab(vspace)) {
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status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out);
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printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0],
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(unsigned long long)start_out[1], (unsigned long long)start_out[2]);
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printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0],
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(unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
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printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0],
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(unsigned long long)count_out[1], (unsigned long long)count_out[2]);
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printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0],
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(unsigned long long)block_out[1], (unsigned long long)block_out[2]);
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}
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}
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/* Get source file name */
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len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0);
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filename = (char *)malloc((size_t)len * sizeof(char) + 1);
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H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1);
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printf(" Source filename %s\n", filename);
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/* Get source dataset name */
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len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0);
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dsetname = (char *)malloc((size_t)len * sizeof(char) + 1);
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H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1);
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printf(" Source dataset name %s\n", dsetname);
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/* Get selection in the source dataset */
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printf(" Selection in the source dataset \n");
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src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i);
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if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) {
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if (H5Sis_regular_hyperslab(src_space)) {
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status = H5Sget_regular_hyperslab(src_space, start_out, stride_out, count_out, block_out);
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printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0],
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(unsigned long long)start_out[1], (unsigned long long)start_out[2]);
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printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0],
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(unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
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printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0],
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(unsigned long long)count_out[1], (unsigned long long)count_out[2]);
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printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0],
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(unsigned long long)block_out[1], (unsigned long long)block_out[2]);
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}
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}
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H5Sclose(vspace);
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H5Sclose(src_space);
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free(filename);
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free(dsetname);
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}
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/*
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* Read data from VDS.
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*/
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vspace = H5Dget_space(vdset);
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H5Sget_simple_extent_dims(vspace, vdsdims_out, vdsdims_max_out);
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printf("VDS dimensions second time \n");
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printf(" Current: ");
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for (i = 0; i < RANK; i++)
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printf(" %d ", (int)vdsdims_out[i]);
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printf("\n");
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/* Read all VDS data */
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/* EIP We should be able to do it by using H5S_ALL instead of making selection
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* or using H5Sselect_all from vspace.
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*/
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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count[0] = 1;
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count[1] = 1;
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count[2] = 1;
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block[0] = vdsdims_out[0];
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block[1] = vdsdims_out[1];
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block[2] = vdsdims_out[2];
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status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, NULL, count, block);
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mem_space = H5Screate_simple(RANK, vdsdims_out, NULL);
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status = H5Dread(vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT, rdata);
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printf(" All data: \n");
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for (i = 0; i < (int)vdsdims_out[0]; i++) {
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for (j = 0; j < (int)vdsdims_out[1]; j++) {
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printf("(%d, %d, 0)", i, j);
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for (k = 0; k < (int)vdsdims_out[2]; k++)
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printf(" %d ", rdata[i][j][k]);
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printf("\n");
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}
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}
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/* Read VDS, but only data mapeed to dataset a.h5 */
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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stride[0] = PLANE_STRIDE;
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stride[1] = 1;
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stride[2] = 1;
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count[0] = 2 * DIM0_1;
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count[1] = 1;
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count[2] = 1;
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block[0] = 1;
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block[1] = vdsdims_out[1];
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block[2] = vdsdims_out[2];
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dims[0] = 2 * DIM0_1;
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status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block);
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mem_space = H5Screate_simple(RANK, dims, NULL);
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status = H5Dread(vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT, a_rdata);
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printf(" All data: \n");
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for (i = 0; i < 2 * DIM0_1; i++) {
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for (j = 0; j < (int)vdsdims_out[1]; j++) {
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printf("(%d, %d, 0)", i, j);
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for (k = 0; k < (int)vdsdims_out[2]; k++)
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printf(" %d ", a_rdata[i][j][k]);
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printf("\n");
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}
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}
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/*
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* Close and release resources.
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*/
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status = H5Sclose(mem_space);
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status = H5Pclose(dcpl);
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status = H5Dclose(vdset);
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status = H5Fclose(vfile);
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return 0;
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}
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