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feature/sparse_data
hdf5/doxygen/examples/H5D_struct_chunk_examples.c
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vchoi-hdfgroup.org 582e5f9bbf --Fix doxygen text for H5Pset/get_struct_chunk() and H5Derase() 
--Remove H5Pset_layout() from doxygen examples for the new APIs
--Rename 3 files
2024-08-15 01:27:08 -05:00

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/* -*- c-file-style: "stroustrup" -*- */
#include "hdf5.h"
#include <stdio.h>
#include <stdlib.h>
//! <!-- [H5Dstruct_chunk_iter_cb] -->
int
struct_chunk_cb(const hsize_t *offset, H5D_struct_chunk_info_t *chunk_info, haddr_t *addr,
hsize_t *chunk_size, void *op_data)
{
// Print out info for each structured chunk
printf("offset[0] = %" PRIuHSIZE " offset[1] = %", PRIuHSIZE "\n", offset[0], offset[1]);
printf("addr = %" PRIuHADDR " chunk_size = %" PRIuHSIZE "\n", *addr, *chunk_size);
printf("num_sections = %u section_size[0] = %u section_size[1] = %u\n", chunk_info->num_sections,
chunk_info->section_size[0], chunk_info->section_size[1]);
return EXIT_SUCCESS;
}
//! <!-- [H5Dstruct_chunk_iter_cb] -->
int
main(void)
{
int ret_val = EXIT_SUCCESS;
//! <!-- [get_defined] -->
{
__label__ fail_file, fail_space, fail_dcpl, fail_layout;
__label__ fail_chunk, fail_dcreate, fail_dwrite, fail_defined;
char file_name[] = "sparse.h5";
char dset_name[] = "sparse_dset";
hid_t fid, lcpl, sid, sid1, did;
hsize_t dim[1] = {50};
hsize_t chunk_dim[1] = {5}; /* Chunk size */
int wbuf[50]; /* Write buffer */
// Create a file
if ((fid = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// Create a 1D dataspace
if ((sid = H5Screate_simple(1, dim, NULL)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_space;
}
// Create a dataset creation property list
if ((dcpl = H5Pcreate(H5P_DATASET_CREATE)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dcpl;
}
// Set to sparse chunked dataset
if (H5Pset_struct_chunk(dcpl, 1, chunk_dim, H5D_SPARSE_CHUNK) < 0) {
ret_val = EXIT_FAILURE;
goto fail_chunk;
}
// Create an integer dataset with sparse chunk layout
if ((did = H5Dcreate2(fid, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) ==
H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dcreate;
}
// Initialize sparse data
memset(wbuf, 0, sizeof(wbuf));
wbuf[12] = 12;
wbuf[13] = 13;
wbuf[14] = 14;
wbuf[48] = 48;
wbuf[49] = 49;
// Write sparse data to the dataset
if (H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf) < 0) {
ret_val = EXIT_FAILURE;
goto fail_dwrite;
}
// Get dataspace with the defined elements in the dataset
if ((sid1 = H5Dget_defined(did, H5S_ALL, H5P_DEFAULT)) < 0) {
ret_val = EXIT_FAILURE;
goto fail_defined;
}
// There are 5 defined elements
if ((npoints = H5Sget_select_npoints(sid1)) != 5)
ret_val = EXIT_FAILURE;
H5Sclose(sid1);
fail_defined:
fail_dwrite:
H5Dclose(did);
fail_dcreate:
fail_layout:
fail_chunk:
H5Pclose(dcpl);
fail_dcpl:
H5Sclose(sid);
fail_space:
H5Fclose(fid);
fail_file:;
}
//! <!-- [get_defined] -->
//! <!-- [erase] -->
{
__label__ fail_file, fail_dset, fail_erase, fail_defined;
hid_t fid, sid, did;
hssize_t npoints;
// Open the file
if ((fid = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// Open the 1-d dataset with sparse chunk layout
if ((did = H5Dopen2(fid, dset_name, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dset;
}
// Deletes defined elements from the dataset
if (H5Derase(did, H5S_ALL, H5P_DEFAULT) < 0) {
ret_val = EXIT_FAILURE;
goto fail_erase;
}
// Get dataspace with the defined elements in the dataset
if ((sid = H5Dget_defined(did, H5S_ALL, H5P_DEFAULT)) < 0) {
ret_val = EXIT_FAILURE;
goto fail_defined;
}
// No defined elements
if ((npoints = H5Sget_select_npoints(sid1)) != 0)
ret_val = EXIT_FAILURE;
H5Sclose(sid);
fail_defined:
fail_erase:
H5Dclose(did);
fail_dset;
H5Fclose(fid);
fail_file:;
}
//! <!-- [erase] -->
//! <!-- [direct_chunk_write] -->
{
__label__ fail_file, fail_space, fail_dcpl, fail_set_chunk, fail_set_layout;
__label__ fail_dcreate, fail_direct_write, fail_dread, fail_shyper;
__label__ fail_calloc0, fail_calloc1, fail_sencode0, fail_encode1;
hid_t fid, sid, did, dcpl;
char file_name[] = "sparse.h5";
char dset_name[] = "sparse_direct_dset";
hsize_t dims[2] = {10, 10};
hsize_t chunk_dims[2] = {5, 5};
const hsize_t start[2], count[2], block[2];
int rbuf[10][10];
size_t encode_size;
hsize_t wr_offset[2] = {0, 0};
H5D_struct_chunk_info_t wr_chk_info;
uint16_t wr_filter_mask[2] = {0, 0};
size_t wr_section_size[2];
void *wr_buf[2];
unsigned char *wr_buf0;
int *wr_buf1;
// Open the file
if ((fid = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// Create a 2D dataspace
if ((sid = H5Screate_simple(2, dim, NULL)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_space;
}
// Create a dataset creation property list
if ((dcpl = H5Pcreate(H5P_DATASET_CREATE)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dcpl;
}
// Set to sparse chunked dataset
if (H5Pset_struct_chunk(dcpl, 1, chunk_dim, H5D_SPARSE_CHUNK) < 0) {
ret_val = EXIT_FAILURE;
goto fail_set_chunk;
}
// Create an integer 2-d dataset with sparse chunk layout
if ((did = H5Dcreate2(fid, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) ==
H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dcreate;
}
// Select the 2 x 3 block in chunk index 0 for writing
start[0] = 3;
start[1] = 2;
block[0] = 2;
block[1] = 3;
count[0] = count[1] = 1;
if (H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, count, block) < 0) {
ret_val = EXIT_FAILURE;
goto fail_shyper;
}
// Get the encoded size for the selection
if (H5Sencode2(sid, NULL, &encode_size, H5P_DEFAULT) < 0) {
ret_val = EXIT_FAILURE;
goto fail_sencode0;
}
// Set up the section size for section 0 and section 1
wr_section_size[0] = encode_size;
wr_section_size[1] = block[0] * block[1] * sizeof(int);
// Allocate buffers for section 0 (encoded selection) and section 1 (data)
if ((wr_buf0 = (unsigned char *)calloc((size_t)1, encode_size)) == NULL) {
ret_val = EXIT_FAILURE;
goto fail_calloc0;
}
if ((wr_buf1 = (int *)calloc((size_t)1, wr_section_size[1])) == NULL) {
ret_val = EXIT_FAILURE;
goto fail_calloc1;
}
// Encode selection into the buffer for section 0
if (H5Sencode2(sid, wr_buf0, &encode_size, H5P_DEFAULT) < 0) {
ret_val = EXIT_FAILURE;
goto fail_sencode1;
}
// Set up data into the buffer for section 1
wr_buf1[0] = 32;
wr_buf1[1] = 33;
wr_buf1[2] = 34;
wr_buf1[3] = 42;
wr_buf1[4] = 43;
wr_buf1[5] = 44;
// Set up the buffer for H5D_write_struct_chunk()
wr_buf[0] = wr_buf0;
wr_buf[1] = wr_buf1;
// Set up chunk info
wr_chk_info.type = H5D_SPARSE_CHUNK;
wr_chk_info.num_sections = 2;
wr_chk_info.filter_mask = wr_filter_mask;
wr_chk_info.section_size = wr_section_size;
wr_chk_info.section_orig_size = wr_section_size;
/* Write the structured chunk at offset [0,0]: chunk index 0 */
if (H5Dwrite_struct_chunk(did, dxpl, wr_offset, &wr_chk_info, wr_buf) < 0) {
ret_val = EXIT_FAILURE;
goto fail_direct_write;
}
/* Read the whole dataset */
if (H5Dread(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl, rbuf) < 0) {
ret_val = EXIT_FAILURE;
goto fail_dread;
}
// Verify elements in rbuf is same as what is written via H5Dwrite_struct_chunk()
if (rbuf[3][2] != wr_buf[1][0] || rbuf[3][3] != wr_buf[1][1] || rbuf[3][4] != wr_buf[1][2] ||
rbuf[4][2] != wr_buf[1][3] || rbuf[4][3] != wr_buf[1][4] || rbuf[4][4] != wr_buf[1][5])
ret_val = EXIT_FAILURE;
fail_direct_write:
fail_dread:
fail_sencode1:
free(wr_buf1);
fail_calloc1:
free(wr_buf0);
fail_calloc0:
fail_sencode0:
fail_shyper:
H5Dclose(did);
fail_dcreate:
fail_set_layout:
fail_set_chunk:
H5Pclose(dcpl);
fail_dcpl:
H5Sclose(sid);
fail_space:
H5Fclose(fid);
fail_file:;
}
//! <!-- [direct_chunk_write] -->
//! <!-- [direct_chunk_read] -->
{
__label__ fail_file, fail_dopen, fail_dwrite, fail_direct_read, fail_dspace;
__label__ fail_shyper, fail_calloc0, fail_calloc1, fail_sencode;
hid_t fid, sid, did, dcpl;
char file_name[] = "sparse.h5";
char dset_name[] = "sparse_direct_dset";
int wbuf[10][10];
size_t encode_size;
const hsize_t start[2], count[2], block[2];
hsize_t rd_offset[2] = {5, 5};
H5D_struct_chunk_info_t rd_chk_info;
uint16_t rd_filter_mask[2] = {0, 0};
size_t rd_section_size[2];
void *rd_buf[2];
unsigned char *rd_buf0;
int *rd_buf1;
// Open the file
if ((fid = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// Open the 2-d dataset with sparse chunk layout
if ((did = H5Dopen2(fid, dset_name, H5P_DEFAULT)) < 0) {
ret_val = EXIT_FAILURE;
goto fail_dopen;
} // Initialize sparse data
memset(wbuf, 0, sizeof(wbuf));
wbuf[7][6] = 76;
wbuf[8][6] = 86;
// Write sparse data to the dataset
if (H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf) < 0) {
ret_val = EXIT_FAILURE;
goto fail_dwrite;
}
// Retrieve the dataset's dataspace
if ((sid = H5Dget_space(did)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_dspace;
}
// Select the 2 x 1 block in chunk index 3 for reading
start[0] = 5;
start[1] = 5;
block[0] = 2;
block[1] = 1;
count[0] = count[1] = 1;
if (H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, count, block) < 0) {
ret_val = EXIT_FAILURE;
goto fail_shyper;
}
// Get the encoded size for the selection
if (H5Sencode2(sid, NULL, &encode_size, H5P_DEFAULT) < 0) {
ret_val = EXIT_FAILURE;
goto fail_sencode;
}
// Set up the section size for section 0 and section 1
rd_section_size[0] = encode_size;
rd_section_size[1] = block[0] * block[1] * sizeof(int);
// Allocate buffers for section 0 (encoded selection) and section 1 (data)
if ((rd_buf0 = (unsigned char *)calloc((size_t)1, encode_size)) == NULL) {
ret_val = EXIT_FAILURE;
goto fail_calloc0;
}
if ((rd_buf1 = (int *)calloc((size_t)1, rd_section_size[1])) == NULL) {
ret_val = EXIT_FAILURE;
goto fail_calloc1;
}
rd_buf[0] = rd_buf0;
rd_buf[1] = rd_buf1;
rd_chk_info.type = H5D_SPARSE_CHUNK;
rd_chk_info.num_sections = 2;
rd_chk_info.filter_mask = rd_filter_mask;
rd_chk_info.section_size = rd_section_size;
rd_chk_info.section_orig_size = rd_section_size;
// Read the structured chunk at offset [5,5]: chunk index 3
if (H5Dread_struct_chunk(did, dxpl, rd_offset, &rd_chk_info, rd_buf) < 0) {
ret_val = EXIT_FAILURE;
goto fail_direct_read;
}
// Verify elements in rd_buf via H5Dread_struct_chunk() is same as wbuf via H5Dwrite()
if (rd_buf[1][0] != wbuf[7][6] || rd_buf[1][1] != wbuf[8][6])
ret_val = EXIT_FAILURE;
fail_direct_read:
free(rd_buf1);
fail_calloc1:
free(rd_buf0);
fail_calloc0:
fail_shyper;
fail_sencode;
H5Sclose(sid);
fail_dspace:
fail_dwrite:
H5Dclose(did);
fail_dopen:
H5Fclose(fid);
fail_file:;
}
//! <!-- [direct_chunk_read] -->
//! <!-- [direct_chunk_iter] -->
{
__label__ fail_file, fail_dopen;
hid_t fid, sid, did, dcpl;
char file_name[] = "sparse.h5";
char dset_name[] = "sparse_direct_dset";
// Open the file
if ((fid = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// Open the 2-d dataset with sparse chunk layout
if ((did = H5Dopen2(fid, dset_name, H5P_DEFAULT)) < 0) {
ret_val = EXIT_FAILURE;
goto fail_dopen;
}
// Iterate over the structured chunks in the dataset
if (H5Dstruct_chunk_iter(did, H5P_DEFAULT, struct_chunk_cb, NULL) < 0)
ret_val = EXIT_FAILURE;
H5Dclose(did);
fail_dopen:
H5Fclose(fid);
fail_file:;
}
//! <!-- [direct_chunk_iter] -->
//! <!-- [direct_chunk_get_info] -->
{
__label__ fail_file, fail_dopen;
hid_t fid, sid, did, dcpl;
char file_name[] = "sparse.h5";
char dset_name[] = "sparse_direct_dset";
hsize_t offset[2];
haddr_t addr;
hsize_t chunk_size;
// Open the file
if ((fid = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
ret_val = EXIT_FAILURE;
goto fail_file;
}
// Open the 2-d dataset with sparse chunk layout
if ((did = H5Dopen2(fid, dset_name, H5P_DEFAULT)) < 0) {
ret_val = EXIT_FAILURE;
goto fail_dopen;
}
// Get structured chunk info for chunk index 1 which does not exist
if (H5Dget_struct_chunk_info(did, H5S_ALL, 1, offset, NULL, &addr, &chunk_size) < 0) {
ret_val = EXIT_FAILURE;
goto fail_get_info;
}
if (chunk_size != 0 && addr != HADDR_UNDEF) {
ret_val = EXIT_FAILURE;
goto fail_verify_info;
}
// Get structured chunk info for chunk index 3
if (H5Dget_struct_chunk_info(did, H5S_ALL, 3, offset, NULL, NULL, NULL) < 0) {
ret_val = EXIT_FAILURE;
goto fail_get_info;
}
// Use the offset just retrieved to obtain structured chunk info by coordinates
if (H5Dget_struct_chunk_info_by_coord(did, offset, NULL, &addr, &chunk_size) < 0) {
ret_val = EXIT_FAILURE;
goto fail_get_info;
}
if (chunk_size == 0 && addr == HADDR_UNDEF) {
ret_val = EXIT_FAILURE;
goto fail_verify_info;
}
fail_get_info:
fail_verify_info:
fail_get_info:
H5Dclose(did);
fail_dopen:
H5Fclose(fid);
fail_file:;
}
//! <!-- [direct_chunk_get_info] -->
return ret_val;
}
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