Creating an HDF5 file

What is an HDF5 file?

An HDF5 file is a binary file which contains scientific data and supporting metadata. The two primary objects stored in an HDF5 file are groups and datasets. Groups and datasets will be discussed in the other sessions.

To create a file, the program application must specify a file name, file access mode, file creation property list, and file access property list.

File Creation Property List:
The file creation property list is used to control the file metadata. File metadata contains information about the size of the user-block, the size of various file data structures used by the HDF5 library, etc.
The user-block is a fixed length block of data located at the beginning of the file which is ignored by the HDF5 library and may be used to store any data information found to be useful to applications.
For more details, see the HDF5 documentation. In this tutorial, the default file metadata is used.
File Access Property List:
The file access property list is used to control different methods of performing I/O on files. See the HDF5 User's Guide for details. The default file access property is used in this tutorial.

The steps to create and close an HDF5 file are as follows:

Specify the file creation and access property lists if necessary.
Create a file.
Close the file and close the property lists if necessary.

To create an HDF5 file, the calling program must contain the following calls:

   file_id = H5Fcreate(filename, access_mode, create_id, access_id);

   H5Fclose(file_id);

Programming Example

Description

The following example demonstrates how to create and close an HDF5 file. It creates a file called 'file.h5', and then closes the file.
[ Download h5_crtfile.c ]

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

main() {

   hid_t       file_id;   /* file identifier */
   herr_t      status;

   /* Create a new file using default properties. */
   file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

   /* Terminate access to the file. */
   status = H5Fclose(file_id); 
}
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Remarks

The include file 'hdf5.h' contains definitions and declarations, and it must be included in any file that uses the HDF5 library.
H5Fcreate creates an HDF5 file and returns the file identifier.
```
 hid_t H5Fcreate (const char *name, unsigned flags, hid_t create_id, 
                  hid_t access_id) 
```
- The first parameter specifies the name of the file to be created.
- The second parameter specifies the file access mode. H5F_ACC_TRUNC will truncate a file if it already exists.
- The third parameter specifies the file creation property list. H5P_DEFAULT indicates that the default file creation property list is used.
- The last parameter of H5Fcreate specifies the file access property list. H5P_DEFAULT indicates that the default file access property list is used.
When a file is no longer accessed by a program, H5Fclose must be called to release the resource used by the file. This call is mandatory.
```
    herr_t H5Fclose (hid_t file_id) 
```
The root group is automatically created when a file is created. Every file has a root group and the path name of the root group is '/'.

File Contents

HDF has developed tools to examine the contents of HDF5 files. The tool used in this tutorial is the HDF5 dumper, h5dump. h5dump is a tool that displays the file contents in human readable form to an ASCII file in DDL. DDL (Data Description Language) is a language that describes HDF5 objects in Backus-Naur Form. To view the file contents, type:

   h5dump <filename>

Figure 4.1 describes the file contents of 'file.h5' using a directed graph. Each HDF5 object is represented by a rectangle and the arrows indicate the structure of the contents. In Fig. 4.2, 'file.h5' contains a group object named '/' (the root group).

Fig. 4.1 Contents of 'file.h5'

Figure 4.2 is the text-description of 'file.h5' generated by h5dump. The HDF5 file called 'file.h5' contains a group called '/'.

Fig. 4.2 'file.h5' in DDL


         HDF5 "file.h5" {
         GROUP "/" {
         }
         }

File Definition in DDL

Figure 4.3 is the simplified DDL file definition for creating an HDF5 file. For simplicity, a simplified DDL is used in this tutorial. A complete and more rigorous DDL can be found in the HDF5 User's Guide. See the References section of this tutorial.

Fig. 4.3 HDF5 File Definition

The explanation of the symbols used in the DDL:


        ::=               defined as
        <tname>           a token with the name tname
        <a> | <b>         one of <a> or <b>
        <a>*              zero or more occurrences of <a>

The simplified DDL file definition:

        <file> ::= HDF5 "<file_name>" { <root_group> }

        <root_group> ::= GROUP "/" { <group_attribute>* <group_member>* }

        <group_attribute> ::= <attribute>

        <group_member> ::= <group> | <dataset>

The National Center for Supercomputing Applications
University of Illinois at Urbana-Champaign

hdfhelp@ncsa.uiuc.edu