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

Zachary Pincus zachary.pincus@yale....
Mon Nov 1 07:14:14 CDT 2010

I use h5py for hdf5 files: it's a lot thinner a wrapper around the  
file format. Basically, h5py is a ctypes interface to the hdf  
libraries, and presents a rather pythonic and "numpy-ish" view of the  

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.


On Nov 1, 2010, at 4:30 AM, Gerrit Holl wrote:

> On 1 November 2010 00:13, John <washakie@gmail.com> wrote:
>> I'm writing to ask what people are generally relying on as a
>> 'toolchain' for reading/writing netcdf and hdf4/5 files.
> I use ScientificPython to read NetCDF and pytables to read and write
> HDF5. I've been quite impressed by the speed of the latter,
> particularly when using indexed searches (as in the pro version).
> There is a bug in the NetCDF 4 library when using HDF-5 at the same
> time. This will affect you unless you use pure Python bindings, but
> there is an easy workaround. See
> http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2010/msg00419.html
> regards,
> Gerrit.
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