File I/O with HDF5¶
The class hdf_file facilitates I/O of data to hdf
files. This class implements a simple way to read and write basic data
types and O₂scl data types. All files created by the
o2scl_hdf::hdf_file class are normal HDF5 files, and can
be manipulated in the usual way, for example with h5dump
command-line tool. Users can easily mix code which performs I/O with
o2scl_hdf::hdf_file and other O₂scl functions
with their own HDF code. The caveat is that O₂scl
cannot parse generic HDF5 files, so that HDF files which contain data
not output through O₂scl cannot always be read by O₂scl.
HDF5 files which are written by O₂scl can be viewed and
manipulated on the command line using the acol utility. See
The acol Command Line Utility for more information.
Objects are stored by referring to their dataset name. I/O for basic
objects is provided directly in the hdf_file class.
Some classes also provide their own I/O functions named hdf_output
and hdf_input based on the hdf_file class. Some
of the current classes which provide I/O are table,
table_units, table3d,
tensor_grid, hist, and
hist_2d.
O₂scl formats complicated data types for HDF I/O by
combining basic data into groups. For that reason, one cannot use
O₂scl to read or write HDF files where groups have the same
name as a dataset in the current HDF id. All O₂scl groups
in HDF files come with a fixed-length string named
o2scl_type, which refers to the type of object which has been
written to the HDF file as a group.
Note
Vector I/O from HDF5 files can be performed directly only if
the vector object provides a pointer to a contiguous chunk
of memory. This works for std::vector objects, because
the C++ standard guarantees this. It is not necessarily
possible for uBlas vector objects (nor desirable for vectors
built upon slices of matrices or tensors), and thus HDF5 I/O
with uBlas vectors or matrices requires an extra copy.
Note
There are some current limitations regarding the matching of error handling policies between O₂scl and the HDF library. HDF functions do not always call the O₂scl error handler and thus do not always throw O₂scl exceptions.
Todo
(Future) Create an HDF file I/O example