[SciPy-User] HDF4, HDF5, netcdf solutions -- PyNIO/PyNGL or CDAT or ??

Robert Kern robert.kern@gmail....
Mon Nov 1 15:19:02 CDT 2010

On Mon, Nov 1, 2010 at 15:01, Dav Clark <dav@alum.mit.edu> wrote:
> On Nov 1, 2010, at 5:14 AM, Zachary Pincus wrote:
>> Where pytables tries to present its own interface, h5py just gives you
>> the hdf5 file. This means that pytables can do a lot of neat things
>> (like the indexed searching), but it also means that (at least last I
>> checked) pytables isn't the best tool for reading in hdf5 files not
>> created by pytables -- for that, you'd want h5py.
> Every time I've had an issue with pytables reading a non-pytables created file, I've submitted a bug and it got fixed usually in a few days. At the time, I was using HDF5 as a transfer layer between matlab's rudimentary hdf5 support and python w/ pytables. (Thanks Francesc!)

I just wanted to add that in my experience, you can read just about
any HDF5 file with PyTables except for a few with some more exotic
features. If you absolutely need to write an HDF5 file according to a
strict standard without any extra bits, you may need h5py. However,
many other readers of your standard probably won't care about the
extra bits PyTables includes. You just have to be a little bit careful
to make sure that you aren't relying on any PyTables features, like
Python-pickled attributes.

Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco

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