Hello Maxime,
You mentioned the phypepat.html tutorial in your question. The phypepat.html
tutorial shows how to write by pattern in Parallel HDF5.
By "chunk" did you mean "by pattern", or are you looking at another tutorial
example?
I took the example in this tutorial, made it a 'serial' example, and added code
at the end that re-opens the file and reads
by pattern. See the attached example. (Note that reading and writing are very
similar!)
Using hyperslab selection can be confusing. We have a very simple example in
the HDF5 Tutorial that you can play
around with to get a feel for how changing the offset/count/stride/block
affects what gets written. See this topic in the
"Learning the Basics" tutorial:
http://www.hdfgroup.org/HDF5/Tutor/selectsimple.html
I attached the h5_subset.c example from this tutorial.
There is also an example, h5ex_hyper.c, on this page, that you may want to look
at:
http://www.hdfgroup.org/HDF5/examples/api18-c.html
If you still have questions or would like to see more examples, just let me
know! I'd be happy to help.
-Barbara
======================
Barbara Jones
The HDF Group Helpdesk
[email protected]
======================
-----Original Message-----
From: Hdf-forum [mailto:[email protected]] On Behalf Of
Maxime Boissonneault
Sent: Tuesday, February 03, 2015 3:28 PM
To: HDF Users Discussion List
Subject: [Hdf-forum] Question for reading data by pattern
Hi,
I am trying to read data from an HDF5 file, by chunk. I wrote it following the
tutorial here :
http://www.hdfgroup.org/HDF5/Tutor/phypepat.html
However, I have trouble reading the data the same way. Any chance someone has
the corresponding example for reading by chunk ?
Thanks,
--
---------------------------------
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval Ph. D. en physique
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#include "hdf5.h"
#include "stdlib.h"
#define H5FILE_NAME "SDS_pat.h5"
#define DATASETNAME "IntArray"
#define NX 8 /* dataset dimensions */
#define NY 4
#define RANK 2
#define RANK1 1
int
main (int argc, char **argv)
{
/*
* HDF5 APIs definitions
*/
hid_t file_id, dset_id; /* file and dataset identifiers */
hid_t filespace, memspace; /* file and memory dataspace
identifiers */
hsize_t dimsf[2]; /* dataset dimensions */
hsize_t dimsm[1]; /* dataset dimensions */
int *data; /* pointer to data buffer to write */
int rdata[4][2];
hsize_t count[2]; /* hyperslab selection parameters */
hsize_t stride[2];
hsize_t offset[2];
int i,ipat, j;
herr_t status;
file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the dataspace for the dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dimsm[0] = NX;
filespace = H5Screate_simple(RANK, dimsf, NULL);
memspace = H5Screate_simple(RANK1, dimsm, NULL);
/*
* Create the dataset with default properties and close filespace.
*/
dset_id = H5Dcreate(file_id, DATASETNAME, H5T_NATIVE_INT, filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(filespace);
/*
* Write a hyperslab by pattern to the file
*/
count[0] = 4;
count[1] = 2;
stride[0] = 2;
stride[1] = 2;
for (ipat=0; ipat<4; ipat++)
{
if(ipat == 0) {
offset[0] = 0;
offset[1] = 0;
}
if(ipat == 1) {
offset[0] = 1;
offset[1] = 0;
}
if(ipat == 2) {
offset[0] = 0;
offset[1] = 1;
}
if(ipat == 3) {
offset[0] = 1;
offset[1] = 1;
}
/*
* Select hyperslab in the file.
*/
filespace = H5Dget_space(dset_id);
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, stride,
count, NULL);
/*
* Initialize data buffer
*/
data = (int *) malloc(sizeof(int)*dimsm[0]);
for (i=0; i < (int)dimsm[0]; i++) {
data[i] = ipat + 1;
}
status = H5Dwrite(dset_id, H5T_NATIVE_INT, memspace, filespace,
H5P_DEFAULT, data);
free(data);
}
/*
* Close/release resources.
*/
H5Dclose(dset_id);
H5Sclose(filespace);
H5Sclose(memspace);
H5Fclose(file_id);
/***************************************************
* Re-open the file and read by pattern in a loop
***************************************************/
file_id = H5Fopen (H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
dset_id = H5Dopen (file_id, DATASETNAME, H5P_DEFAULT);
count[0] = 4;
count[1] = 2;
stride[0] = 2;
stride[1] = 2;
for (ipat=0; ipat<4; ipat++)
{
if(ipat == 0) {
offset[0] = 0;
offset[1] = 0;
}
if(ipat == 1) {
offset[0] = 1;
offset[1] = 0;
}
if(ipat == 2) {
offset[0] = 0;
offset[1] = 1;
}
if(ipat == 3) {
offset[0] = 1;
offset[1] = 1;
}
memspace = H5Screate_simple(RANK1, dimsm, NULL);
filespace = H5Dget_space(dset_id);
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, stride,
count, NULL);
status = H5Dread(dset_id, H5T_NATIVE_INT, memspace, filespace,
H5P_DEFAULT, rdata);
printf ("\nData Pattern %i:\n", ipat);
for (i=0;i<4; i++)
for (j=0;j<2; j++)
printf (" %i", rdata[i][j]);
printf ("\n");
}
status = H5Dclose(dset_id);
status = H5Sclose(filespace);
status = H5Sclose(memspace);
status = H5Fclose(file_id);
return 0;
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* This example illustrates how to read/write a subset of data (a slab)
* from/to a dataset in an HDF5 file. It is used in the HDF5 Tutorial.
*/
#include "hdf5.h"
#define FILE "subset.h5"
#define DATASETNAME "IntArray"
#define RANK 2
#define DIM0_SUB 3 /* subset dimensions */
#define DIM1_SUB 4
#define DIM0 8 /* size of dataset */
#define DIM1 10
int
main (void)
{
hsize_t dims[2], dimsm[2];
int data[DIM0][DIM1]; /* data to write */
int sdata[DIM0_SUB][DIM1_SUB]; /* subset to write */
int rdata[DIM0][DIM1]; /* buffer for read */
hid_t file_id, dataset_id; /* handles */
hid_t dataspace_id, memspace_id;
herr_t status;
hsize_t count[2]; /* size of subset in the file */
hsize_t offset[2]; /* subset offset in the file */
hsize_t stride[2];
hsize_t block[2];
int i, j;
/*****************************************************************
* Create a new file with default creation and access properties.*
* Then create a dataset and write data to it and close the file *
* and dataset. *
*****************************************************************/
file_id = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dims[0] = DIM0;
dims[1] = DIM1;
dataspace_id = H5Screate_simple (RANK, dims, NULL);
dataset_id = H5Dcreate2 (file_id, DATASETNAME, H5T_STD_I32BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for (j = 0; j < DIM0; j++) {
for (i = 0; i < DIM1; i++)
if (i< (DIM1/2))
data[j][i] = 1;
else
data[j][i] = 2;
}
status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
printf ("\nData Written to File:\n");
for (i = 0; i<DIM0; i++){
for (j = 0; j<DIM1; j++)
printf (" %i", data[i][j]);
printf ("\n");
}
status = H5Sclose (dataspace_id);
status = H5Dclose (dataset_id);
status = H5Fclose (file_id);
/*****************************************************
* Reopen the file and dataset and write a subset of *
* values to the dataset.
*****************************************************/
file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT);
dataset_id = H5Dopen2 (file_id, DATASETNAME, H5P_DEFAULT);
/* Specify size and shape of subset to write. */
offset[0] = 1;
offset[1] = 2;
count[0] = DIM0_SUB;
count[1] = DIM1_SUB;
stride[0] = 1;
stride[1] = 1;
block[0] = 1;
block[1] = 1;
/* Create memory space with size of subset. Get file dataspace
and select subset from file dataspace. */
dimsm[0] = DIM0_SUB;
dimsm[1] = DIM1_SUB;
memspace_id = H5Screate_simple (RANK, dimsm, NULL);
dataspace_id = H5Dget_space (dataset_id);
status = H5Sselect_hyperslab (dataspace_id, H5S_SELECT_SET, offset,
stride, count, block);
/* Write a subset of data to the dataset, then read the
entire dataset back from the file. */
printf ("\nWrite subset to file specifying:\n");
printf (" offset=1x2 stride=1x1 count=3x4 block=1x1\n");
for (j = 0; j < DIM0_SUB; j++) {
for (i = 0; i < DIM1_SUB; i++)
sdata[j][i] = 5;
}
status = H5Dwrite (dataset_id, H5T_NATIVE_INT, memspace_id,
dataspace_id, H5P_DEFAULT, sdata);
status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, rdata);
printf ("\nData in File after Subset is Written:\n");
for (i = 0; i<DIM0; i++){
for (j = 0; j<DIM1; j++)
printf (" %i", rdata[i][j]);
printf ("\n");
}
status = H5Sclose (memspace_id);
status = H5Sclose (dataspace_id);
status = H5Dclose (dataset_id);
status = H5Fclose (file_id);
}
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