Re: Loading HDF5 / h5 files

[Matthias Brennwald]

Hi Mike and all

That explains my issues with loading HDF5 files. However, the documentation could be a bit more specific about this. It says the following about loading HDF5 files (https://www.gnu.org/software/octave/doc/interpreter/Simple-File-I_002fO.html):

...Force Octave to assume the file is in HDF5 format. (HDF5 is a free, portable binary format developed by the National Center for Supercomputing Applications at the University of Illinois.) Note that Octave can read HDF5 files not created by itself, but may skip some datasets in formats that it cannot support. This format is only available if Octave was built with a link to the HDF5 libraries...

That somehow fits with your comments above, but is quite misleading without them. It would be good if someone would expand the documentation in this way.

Cheers

Matthias

On 4 June 2014 16:46, Mike Miller <address@hidden> wrote:

On Wed, Jun 4, 2014 at 13:36:15 +0200, Matthias Brennwald wrote:
> Hi All
>
> I am trying to load binary data files into Octave (version 3.6.4 on Mac OS X). The data file specification says the file format is HDF5 / h5. An example for such a file is available here:
> http://www.picarro.com/sites/default/files/CFADS2135-20101206-081426-PressureCal-1.h5
>
> I tried to load the data from this file using the “load” command, but that did not work (see log below). Is this an issue with the file, or with Octave? Anything I could try to make this work better?

Octave's load function reads *particular* HDF5 files, namely files
created by Octave using "save -hdf5" or by Matlab using the "v7.3"
file format I believe (someone please correct if I got that wrong).

The load and save functions are for moving workspace variables between
instances of Octave and Matlab, not for reading generic data files of
arbitrary formats. They are expected to operate only on files created
by Octave itself or by Matlab.

Octave does not currently have functions for reading arbitrary HDF5
files. It could, if someone wants to implement the functions h5read,
h5write, et al.

You could try the third-party h5utils or hdf5oct projects, and let us
know if either of them work for you.

--
mike