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Re: Loading HDF5 / h5 files


From: Markus Appel
Subject: Re: Loading HDF5 / h5 files
Date: Thu, 12 Jun 2014 19:35:17 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Thunderbird/24.5.0

On 06/12/2014 10:25 AM, Andreas Weber wrote:
Hi Markus,

On 12.06.2014 10:14, Markus Appel wrote:
On 06/11/2014 04:54 PM, Andreas Weber wrote:
Hi Matthias,

On 04.06.2014 13:36, Matthias Brennwald wrote:
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
...
octave:23> load CFADS2135-20101206-081426-PressureCal-1.h5
error: load: error while reading hdf5 item results
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
    #000: H5Gdeprec.c line 780 in H5Giterate(): group iteration failed
I think you've hit this bug:
https://savannah.gnu.org/bugs/?39491

Until the bug is fixed, can you use h5dump to extract the fields you
need and read it with octave as workaround?

I started to look at that bug and exchanged all deprecated HDF functions
from octave code, but I cannot properly test/finish it and put into a
proper patch for the next few weeks. Anyway, it seems that it doesn't
help in reading the hdf file in question (though I could be wrong), but
I presume that the "compound data" type which is used in there is not
implemented in the octave routines.

Can you share your work anyway? I've also started to replace H5Giterate
and want to see if we had the same approach.

Andy


I posted my progress here: http://savannah.gnu.org/bugs/?39491

Markus



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