A Sunday 31 October 2010 11:38:21 Stephan Gerhard escrigué: > Hi Francesc, > > We are trying use PyTables to store fiber data from Neuroimaging in > HDF5. We have a Python list of Numpy arrays, where each array is of a > different first dimension N (N,3). We would like to store this data > in an HDF5 file. We tried to convert it to dtype object, but this > seems to be not supported by HDF5. > > Do you have any idea how we could convert the data into a structure > that is possible to save in HDF5, or maybe using some other feature > of Tables? We need to do random access on a _fiber_ (list element > level) and retrieve its corresponding (N,3) array fast.
Hmm, I'm afraid that PyTables does not have support for writing this into an HDF5-compliant file. However, you may want to use a VLArray object in combination with a ObjectAtom. This will allow you to do what you want, but serializing the list first via Python's cPickle module. The disadvantage of this method is that you won't be able to retrieve the values from a non-python HDF5 application (pickle is a serialization method only available in Python). Finally, if you want to reply to this, please subscribe first to the pytables-users list in: https://lists.sourceforge.net/lists/listinfo/pytables-users and the reply to the list. This may let others to learn (and participate!) from the discussion. Cheers, -- Francesc Alted ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
