Reading to/Writing from a Dataset

During a dataset I/O operation, the library transfers raw data between memory and the file. The memory can have a data type different than the file data type and can also be a different size (memory is a subset of the dataset elements, or vice versa). Therefore, to perform read or write operations, the application program must specify:

The dataset
The dataset's data type in memory
The dataset's dataspace in memory
The dataset's dataspace in the file
The transfer properties (The data transfer properties control various aspects of the I/O operations like the number of processes participating in a collective I/O request or hints to the library to control caching of raw data. In this tutorial, we use the default transfer properties.)
The data buffer

The steps to read to/write from a dataset are as follows:

Obtain the dataset identifier.
Specify the memory data type.
Specify the memory dataspace.
Specify the file dataspace.
Specify the transfer properties.
Perform the desired operation on the dataset.
Close the dataset.
Close the dataspace/data type, and property list if necessary.

To read to/write from a dataset, the calling program must contain the following call:

   H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id,
           xfer_plist_id, buf );

   H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id,
            xfer_plist_id, buf);

Programming Example

Description

The following example shows how to read and write an existing dataset. It opens the file created in the previous example, obtains the dataset identifier, /dset, writes the dataset to the file, then reads the dataset back from memory. It then closes the dataset and file.
[ Download h5_rdwt.c ]


+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

#include <hdf5.h>
#define FILE "dset.h5"

main() {

   hid_t       file_id, dataset_id;  /* identifiers */
   herr_t      status;
   int         i, j, dset_data[4][6];

   /* Initialize the dataset. */
   for (i = 0; i < 4; i++)
      for (j = 0; j < 6; j++)
         dset_data[i][j] = i * 6 + j + 1;

   /* Open an existing file. */
   file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);

   /* Open an existing dataset. */

   dataset_id = H5Dopen(file_id, "/dset");

   /* Write the dataset. */
   status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                     dset_data);

   status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                    dset_data);

   /* Close the dataset. */
   status = H5Dclose(dataset_id);

   /* Close the file. */
   status = H5Fclose(file_id);
}
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Remarks

H5Fopen opens an existing file and returns a file identifier.

  hid_t H5Fopen (const char *name, unsigned flags, hid_t access_id)

The first argument is the file name.
The second argument is the file access mode. H5F_ACC_RDWR allows a file to be read from and written to.
The third parameter is the identifier for the file access property list. H5P_DEFAULT specifies the default file access property list.

H5Dopen opens an existing dataset with the name specified by the second argument at the location specified by the first parameter, and returns an identifier.

  hid_t H5Dopen (hid_t loc_id, const char *name)

H5Dwrite writes raw data from an application buffer to the specified dataset, converting from the data type and data space of the dataset in memory to the data type and data space of the dataset in the file.

  herr_t H5Dwrite (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, 
                   hid_t file_space_id, hid_t xfer_plist_id, const void * buf)

The first parameter is the identifier of the dataset.
The second parameter is the identifier of the dataset's datatype in memory. H5T_NATIVE_INT is an integer data type for the machine on which the library was compiled.
The third parameter is the identifier of the dataset's dataspace in memory. H5S_ALL indicates that the dataset's dataspace in memory is the same as that in the file.
The fourth parameter is the identifier of the dataset's dataspace in the file. H5S_ALL indicates that the entire dataspace of the dataset in the file is referenced.
The fifth parameter is the identifier of the data transfer propery list. H5P_DEFAULT indicates that the default data transfer property list is used.
The last parameter is the data buffer.

H5Dread reads raw data from the specified dataset to an application buffer, converting from the file datatype and dataspace to the memory datatype and dataspace.
```
  herr_t H5Dread (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, 
                  hid_t file_space_id, hid_t xfer_plist_id, void * buf) 
```
- The first parameter is the identifier of the dataset read from.
- The second parameter is the identifier of the dataset's memory datatype.
- The third parameter is the identifier of the dataset's memory dataspace.
- The fourth parameter is the identifier of the dataset's file dataspace.
- The fifth parameter is the identifier of the data transfer propery list.
- The last parameter is the data buffer.
File Contents
Figure 6.1 shows the contents of 'dset.h5'.
Fig. 6.1 'dset.h5' in DDL
```
      HDF5 "dset.h5" {
      GROUP "/" {
         DATASET "dset" {
            DATATYPE { H5T_STD_I32BE }
            DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }
            DATA {
               1, 2, 3, 4, 5, 6,
               7, 8, 9, 10, 11, 12,
               13, 14, 15, 16, 17, 18,
               19, 20, 21, 22, 23, 24
            }
         }
      }
      }
```
The National Center for Supercomputing Applications
University of Illinois at Urbana-Champaign

hdfhelp@ncsa.uiuc.edu

Last Modified: August 27, 1999

Reading to/Writing from a Dataset

Contents:

Reading to/Writing from a Dataset

Programming Example

Description

Remarks

File Contents

Last Modified: August 27, 1999