Dear Alexander,
Please see if the attached example C code helps. It is an example from
HDF web site.
Best,
Ekin
On 03/21/2012 01:55 PM, Alexander Beck-Ratzka wrote:
Hi Folks,
I am a newby in HDF5, and after having already successfully written (and also
plotted) one singel time step of a variable into an HDF5 dataset, I would like
to know how I can write time series of a 3-d variable into one single HDF5
dataset? Do I need to have the tiem as fouhrth dimension?
An explaing example in C would be welcome.
Best wishes
Alexander
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--
*Ekin Akoglu*
Research Assistant
Institute of Marine Sciences
Middle East Technical University
P.O. Box 28, 33731
Erdemli, Mersin
Turkey
Web: www.ims.metu.edu.tr
Email: [email protected] <mailto:[email protected]>
Phone: +90 324 521 34 34
GSM: +90 506 554 03 90
Fax: +90 324 521 23 27
/************************************************************
This example shows how to read and write array datatypes
to a dataset. The program first writes integers arrays of
dimension ADIM0xADIM1 to a dataset with a dataspace of
DIM0, then closes the file. Next, it reopens the file,
reads back the data, and outputs it to the screen.
This file is intended for use with HDF5 Library version 1.8
************************************************************/
#include "hdf5.h"
#include <stdio.h>
#include <stdlib.h>
#define FILE "h5ex_t_array.h5"
#define DATASET "DS1"
#define DIM0 4
#define ADIM0 3
#define ADIM1 5
int
main (void)
{
hid_t file, filetype, memtype, space, dset;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0},
adims[2] = {ADIM0, ADIM1};
int wdata[DIM0][ADIM0][ADIM1], /* Write buffer */
***rdata, /* Read buffer */
ndims,
i, j, k;
/*
* Initialize data. i is the element in the dataspace, j and k the
* elements within the array datatype.
*/
for (i=0; i<DIM0; i++)
for (j=0; j<ADIM0; j++)
for (k=0; k<ADIM1; k++)
wdata[i][j][k] = i * j - j * k + i * k;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create array datatypes for file and memory.
*/
filetype = H5Tarray_create (H5T_STD_I64LE, 2, adims);
memtype = H5Tarray_create (H5T_NATIVE_INT, 2, adims);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the dataset and write the array data to it.
*/
dset = H5Dcreate (file, DATASET, filetype, space, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Dwrite (dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata[0][0]);
/*
* Close and release resources.
*/
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (filetype);
status = H5Tclose (memtype);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the dataset and array have the same name and rank, but can have
* any size. Therefore we must allocate a new array to read in
* data using malloc().
*/
/*
* Open file and dataset.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET, H5P_DEFAULT);
/*
* Get the datatype and its dimensions.
*/
filetype = H5Dget_type (dset);
ndims = H5Tget_array_dims (filetype, adims);
/*
* Get dataspace and allocate memory for read buffer. This is a
* three dimensional dataset when the array datatype is included so
* the dynamic allocation must be done in steps.
*/
space = H5Dget_space (dset);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
/*
* Allocate array of pointers to two-dimensional arrays (the
* elements of the dataset.
*/
rdata = (int ***) malloc (dims[0] * sizeof (int **));
/*
* Allocate two dimensional array of pointers to rows in the data
* elements.
*/
rdata[0] = (int **) malloc (dims[0] * adims[0] * sizeof (int *));
/*
* Allocate space for integer data.
*/
rdata[0][0] = (int *) malloc (dims[0] * adims[0] * adims[1] * sizeof (int));
/*
* Set the members of the pointer arrays allocated above to point
* to the correct locations in their respective arrays.
*/
for (i=0; i<dims[0]; i++) {
rdata[i] = rdata[0] + i * adims[0];
for (j=0; j<adims[0]; j++)
rdata[i][j] = rdata[0][0] + (adims[0] * adims[1] * i) +
(adims[1] * j);
}
/*
* Create the memory datatype.
*/
memtype = H5Tarray_create (H5T_NATIVE_INT, 2, adims);
/*
* Read the data.
*/
status = H5Dread (dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
rdata[0][0]);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n", DATASET, i);
for (j=0; j<adims[0]; j++) {
printf (" [");
for (k=0; k<adims[1]; k++)
printf (" %3d", rdata[i][j][k]);
printf ("]\n");
}
printf("\n");
}
/*
* Close and release resources.
*/
free (rdata[0][0]);
free (rdata[0]);
free (rdata);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (filetype);
status = H5Tclose (memtype);
status = H5Fclose (file);
return 0;
}
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Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
