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HDF5 Tutorial:   Learning The Basics
Creating a Dataset

Contents:


What is a Dataset?

A dataset is a multidimensional array of data elements, together with supporting metadata. To create a dataset, the application program must specify the location at which to create the dataset, the dataset name, the datatype and dataspace of the data array, and the property lists.

Datatypes

A datatype is a collection of properties, all of which can be stored on disk, and which, when taken as a whole, provide complete information for data conversion to or from that datatype.

There are two categories of datatypes in HDF5:

Figure 5.1 shows the HDF5 pre-defined datatypes. Some of the HDF5 predefined atomic datatypes are listed in Figures 5.2a and 5.2b.

In this tutorial, we consider only HDF5 predefined integers.

For further information on datatypes, see The Datatype Interface (H5T) in the HDF5 User's Guide, in addition to the Datatypes tutorial topic.

Fig 5.1   HDF5 datatypes


                                          +--  integer
                                          +--  floating point
                        +---- atomic  ----+--  date and time
                        |                 +--  character string
       HDF5 datatypes --|                 +--  bitfield
                        |                 +--  opaque
                        |
                        +---- compound

Fig. 5.2a   Examples of HDF5 predefined datatypes
Datatype Description
H5T_STD_I32LE Four-byte, little-endian, signed, two's complement integer
H5T_STD_U16BE Two-byte, big-endian, unsigned integer
H5T_IEEE_F32BE Four-byte, big-endian, IEEE floating point
H5T_IEEE_F64LE Eight-byte, little-endian, IEEE floating point
H5T_C_S1 One-byte, null-terminated string of eight-bit characters

Fig. 5.2b   Examples of HDF5 predefined native datatypes
Native Datatype Corresponding C or FORTRAN Type
C:  
H5T_NATIVE_INT int
H5T_NATIVE_FLOAT float
H5T_NATIVE_CHAR char
H5T_NATIVE_DOUBLE double
H5T_NATIVE_LDOUBLE long double
FORTRAN:  
H5T_NATIVE_INTEGER integer
H5T_NATIVE_REAL real
H5T_NATIVE_DOUBLE double precision
H5T_NATIVE_CHARACTER character

Datasets and Dataspaces

A dataspace describes the dimensionality of the data array. A dataspace is either a regular N-dimensional array of data points, called a simple dataspace, or a more general collection of data points organized in another manner, called a complex dataspace. Figure 5.3 shows HDF5 dataspaces. In this tutorial, we only consider simple dataspaces.

Fig 5.3   HDF5 dataspaces


                         +-- simple
       HDF5 dataspaces --|
                         +-- complex

The dimensions of a dataset can be fixed (unchanging), or they may be unlimited, which means that they are extensible. A dataspace can also describe a portion of a dataset, making it possible to do partial I/O operations on selections.

Property Lists

Property lists are a mechanism for modifying the default behavior when creating or accessing objects. For more information on property lists see the Property List tutorial topic.

The following property lists can be specified when creating a dataset:


Steps to Create a Dataset

To create an empty dataset (no data written) the following steps need to be taken:

In HDF5, datatypes and dataspaces are independent objects which are created separately from any dataset that they might be attached to. Because of this, the creation of a dataset requires the definition of the datatype and dataspace. In this tutorial, we use the HDF5 predefined datatypes (integer) and consider only simple dataspaces. Hence, only the creation of dataspace objects is needed.

High Level APIs

The High Level HDF5 Lite APIs (H5LT) include functions that simplify and condense the steps for creating datasets in HDF5. The examples in the following section use the standard APIs. For a quick start you may prefer to look at the HDF5 Lite APIs at this time.

If you plan to work with images, please look at the High Level HDF5 Image APIs (H5IM), as well.

Programming Example

Description

The following example shows how to create an empty dataset. It creates a file called dset.h5 in the C version (dsetf.h5 in Fortran), defines the dataset dataspace, creates a dataset which is a 4x6 integer array, and then closes the dataspace, the dataset, and the file.

See HDF5 Introductory Examples for the examples used in the Learning the Basics tutorial. There are examples for several other languages, including Java.

For details on compiling an HDF5 application: [ Compile Information ]

Remarks