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HDF5 Tutorial:   Learning The Basics


What is a Datatype?

A datatype is a collection of datatype properties which provide complete information for data conversion to or from that datatype.

Datatypes in HDF5 can be grouped as follows:

Pre-Defined Datatypes

The properties of pre-defined datatypes are:

There are two types of pre-defined datatypes, standard (file) and native:

The following table shows the native types and the standard pre-defined datatypes they correspond to. (Keep in mind that HDF5 can convert between datatypes, so you can specify a buffer of a larger type for a dataset of a given type. For example, you can read a dataset that has a short datatype into a long integer buffer.)

Fig. 1   HDF5 pre-defined native datatypes and corresponding standard (file) type

  C Type   HDF5 Memory Type     HDF5 File Type *
  int   H5T_NATIVE_INT   H5T_STD_I32BE or H5T_STD_I32LE
  short   H5T_NATIVE_SHORT   H5T_STD_I16BE or H5T_STD_I16LE
  long   H5T_NATIVE_LONG   H5T_STD_I32BE, H5T_STD_I32LE,
  H5T_STD_I64BE or H5T_STD_I64LE
  long long     H5T_NATIVE_LLONG   H5T_STD_I64BE or H5T_STD_I64LE
  unsigned int   H5T_NATIVE_UINT   H5T_STD_U32BE or H5T_STD_U32LE
  unsigned short   H5T_NATIVE_USHORT   H5T_STD_U16BE or H5T_STD_U16LE
  unsigned long   H5T_NATIVE_ULONG   H5T_STD_U32BE, H5T_STD_U32LE,
  H5T_STD_U64BE or H5T_STD_U64LE
  unsigned long
  float   H5T_NATIVE_FLOAT   H5T_IEEE_F32BE or H5T_IEEE_F32LE  
  double   H5T_NATIVE_DOUBLE   H5T_IEEE_F64BE or H5T_IEEE_F64LE  

  F90 Type   HDF5 Memory Type   HDF5 File Type *
  integer     H5T_NATIVE_INTEGER   H5T_STD_I32(8,16)BE or H5T_STD_I32(8,16)LE
  real   H5T_NATIVE_REAL   H5T_IEEE_F32BE or H5T_IEEE_F32LE 

* Note that the HDF5 File Types listed are those that are most commonly created.
  The file type created depends on the compiler switches and platforms being
  used. For example, on the Cray an integer is 64-bit, and using H5T_NATIVE_INT (C)
  or H5T_NATIVE_INTEGER (F90) would result in an H5T_STD_I64BE file type.

The following code is an example of when you would use standard pre-defined datatypes vs. native types:

   #include "hdf5.h"

   main() {

      hid_t       file_id, dataset_id, dataspace_id;  
      herr_t      status;
      hsize_t     dims[2]={4,6};
      int         i, j, dset_data[4][6];

      for (i = 0; i < 4; i++)
           for (j = 0; j < 6; j++)
            dset_data[i][j] = i * 6 + j + 1;

      file_id = H5Fcreate ("dtypes.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

      dataspace_id = H5Screate_simple (2, dims, NULL);

      dataset_id = H5Dcreate (file_id, "/dset", H5T_STD_I32BE, dataspace_id, 

      status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, 
                         H5P_DEFAULT, dset_data);

      status = H5Dclose (dataset_id);

      status = H5Fclose (file_id);
By using the native types when reading and writing, the code that reads from or writes to a dataset can be the same for different platforms.

Can native types also be used when creating a dataset? Yes. However, just be aware that the resulting datatype in the file will be one of the standard pre-defined types and may be different than expected.

What happens if you do not use the correct native datatype for a standard (file) datatype? Your data may be incorrect or not what you expect.

Derived Datatypes

ANY pre-defined datatype can be used to derive user-defined datatypes.

To create a datatype derived from a pre-defined type:

Character Strings:

A simple example of creating a derived datatype is using the string datatype, H5T_C_S1 (H5T_FORTRAN_S1), to create strings of more than one character:

The ability to derive datatypes from pre-defined types allows users to create any number of datatypes, from simple to very complex.
- - Last modified: 21 December 2016