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Creating and manipulating datatypes which describe elements of a dataset (H5T)

* Use of these functions is deprecated in Release 1.8.0.

The Datatype interface, H5T, provides a mechanism to describe the storage format of individual data points of a data set and is hopefully designed in such a way as to allow new features to be easily added without disrupting applications that use the data type interface. A dataset (the H5D interface) is composed of a collection or raw data points of homogeneous type organized according to the data space (the H5S interface).

A datatype is a collection of datatype 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. The interface provides functions to set and query properties of a datatype.

A data point is an instance of a datatype, which is an instance of a type class. We have defined a set of type classes and properties which can be extended at a later time. The atomic type classes are those which describe types which cannot be decomposed at the datatype interface level; all other classes are compound.

See HDF5 Datatypes in the HDF5 User’s Guide for more information.

List of pre-defined datatypes in HDF5

Creating variable-length string datatypes 

As the term implies, variable-length strings are strings of varying lengths; they can be arbitrarily long, anywhere from 1 character to thousands of characters.

HDF5 provides the ability to create a variable-length string datatype. Like all string datatypes, this type is based on the atomic string datatype: H5T_C_S1 in C or H5T_FORTRAN_S1 in Fortran. While these datatypes default to one character in size, they can be resized to specific fixed lengths or to variable length.

Variable-length strings will transparently accommodate ASCII strings or UTF-8 strings. This characteristic is set with H5T_SET_CSET  in the process of creating the datatype.

The following HDF5 calls create a C-style variable-length string datatype, vls_type_c_id:

    vls_type_c_id = H5Tcopy(H5T_C_S1)
    status        = H5Tset_size(vls_type_c_id, H5T_VARIABLE) 

In a C environment, variable-length strings will always be NULL-terminated, so the buffer to hold such a string must be one byte larger than the string itself to accommodate the NULL terminator.

In Fortran, strings are normally of fixed length. Variable-length strings come into play only when data is shared with a C application that uses them. For such situations, the datatype class H5T_STRING is predefined by the HDF5 library to accommodate variable-length strings. The first HDF5 call below creates a Fortran string, vls_type_f_id, that will handle variable-length string data. The second call sets the string padding value to space padding:

    h5tcopy_f(H5T_STRING, vls_type_f_id, hdferr)
    h5tset_strpad_f(vls_type_f_id, H5T_STR_SPACEPAD_F, hdferr) 

While Fortran-style strings are generally space-padded, they may be NULL-terminated in cases where the data is also used in a C environment.

Note:   Under the covers, variable-length strings are stored in a heap, potentially impacting efficiency in the following ways:

  • Heap storage requires more space than regular raw data storage.
  • Heap access generally reduces I/O efficiency because it requires individual read or write operations for each data element rather than one read or write per dataset or per data selection.
  • Chunking and filters, including compression, are not available for heaps.

--- Last Modified: September 13, 2019 | 01:16 PM