bugGNU Octave - Bugs: bug #42530, Octave does NOT load any HDF5...

 
 

bug #42530: Octave does NOT load any HDF5 file, just those created by Octave itself (and Matlab?)

Submitter:  None
Submitted:  Tue 10 Jun 2014 06:59:06 AM UTC
   
 
Category:  Documentation Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Documentation
Status:  Fixed Assigned to:  None
Originator Name:  Matthias Brennwald Originator Email:  -email is unavailable-
Open/Closed:  * Closed Release:  * dev
Operating System:  * Any Fixed Release:  9.1.0
Planned Release:  9.1.0
* Mandatory Fields

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Wed 24 Apr 2024 03:31:29 PM UTC, comment #7: 

no comments in a few months, and doc changes were part of 9.1.0 release. considering the doc request complete. closing report.  actual changes to any hdf5 behavior can be tracked elsewhere when that occurs.

Nicholas Jankowski <nrjank>
Group Member
Tue 27 Feb 2024 10:31:49 PM UTC, comment #6: 

made some minor updates to the save and load docstrings in
https://hg.savannah.gnu.org/hgweb/octave/rev/55c8c338aaeb

marking as ready for test in case anything needs refining.

save:

'-7.3'
          Octave does *not* yet implement saving in MATLAB's v7.3 binary
          data format.


load:

'-hdf5'
          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 only read HDF5 files that
          were created by itself with 'save' or with MATLAB's '-v7.3'
          option (which saves in HDF5 format).  This format is only
          available if Octave was built with a link to the HDF5
          libraries.
...

'-7.3'
          Force Octave to assume the file is in MATLAB's v7.3 binary
          data format.  As the v7.3 format is an HDF5 based format,
          those files often can also be opened with the "-hdf5" option.
          Note that Octave *can not* currently save in this format.


Nicholas Jankowski <nrjank>
Group Member
Tue 27 Feb 2024 03:49:53 PM UTC, comment #5: 

also for posterity here's a non-nabble old mailing list thread link that inspired the need for doc updates:
https://lists.gnu.org/archive/html/help-octave/2014-06/msg00036.html

Nicholas Jankowski <nrjank>
Group Member
Tue 27 Feb 2024 03:38:00 PM UTC, comment #4: 

ok, after a bit of testing with 8.4.0 it appears that octave -is- able to load data saved in matlab's 7.3 format.  it loads without error using no options, the -v7.3 option, or the -hdf5 option.  using the -hdf5 option produces errors on other formats, eg. one saved with -v7.

will work up a docstring change for both load and save to try to clarify the current state.

Nicholas Jankowski <nrjank>
Group Member
Mon 26 Feb 2024 10:12:44 PM UTC, comment #3: 

looking at the current status of this request, the help for load does say:


     ‘-hdf5’
          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 only read HDF5 files that
          were created by itself with ‘save’.  This format is only
          available if Octave was built with a link to the HDF5
          libraries.

...

     ‘-v7.3’
     ‘-V7.3’
     ‘-7.3’
          Octave does *not* yet implement MATLAB's v7.3 binary data
          format.


so it seems the first part of the request (that it should mention -hdf5 only works with things octave saved that way) has been satisfied.

Unclear how it should be updated to note that matlab's sv7.3 is hdf5 based and octave can read it.  the note about 7.3 binary, that makes it sound like this format option is unusable. that seems to not be correct.  can someone confirm?


Nicholas Jankowski <nrjank>
Group Member
Wed 11 Jun 2014 03:00:57 PM UTC, comment #2: 

The posters initial problem is https://savannah.gnu.org/bugs/?39491
where we should replace the deprecated H5Giterate with H5Literate.

On the other hand octave can indeed load "simple" .h5 files without attributes. I've created a C project which creates a .h5 file for testing purposes here https://github.com/octave-de/hdf5_tests.

My plan is to add groups which triggers bug 39491 and fix ls-hdf5.cc then.

-- Andy

Andreas Weber <andy1978>
Group Member
Tue 10 Jun 2014 12:26:16 PM UTC, comment #1: 

Thanks for your bug report. I'll summarize here so people don't have to read through the mailing list thread.

The docstring for the load function is vague about what types of HDF5 files it can operate on. Perhaps it should be more explicit that it will load files created by Octave's "save -hdf5" or by Matlab's "save -v7.3" and nothing else.

Mike Miller <mtmiller>
Group Member
Tue 10 Jun 2014 06:59:06 AM UTC, original submission:  
Anonymous

 

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    Follow 9 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2024-04-24 nrjank StatusReady For Test Fixed
        Open/ClosedOpen Closed
        Fixed ReleaseNone 9.1.0
    2024-02-27 nrjank StatusIn Progress Ready For Test
    2024-02-27 nrjank StatusNeed Info In Progress
    2024-02-27 nrjank Planned ReleaseNone 9.1.0
    2024-02-26 nrjank StatusNone Need Info
    2019-03-01 mtmiller Carbon-CopyRemoved 80942 -
    2014-06-10 mtmiller Release3.6.4 dev

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