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.


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.


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.


(Future) Create an HDF file I/O example