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Re: Loading HDF5 / h5 files
From: |
Andreas Weber |
Subject: |
Re: Loading HDF5 / h5 files |
Date: |
Thu, 12 Jun 2014 10:25:38 +0200 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Icedove/24.5.0 |
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