[Numpy-discussion] fast numpy i/o

Derek Homeier derek@astro.physik.uni-goettingen...
Tue Jun 21 13:24:08 CDT 2011


On 21.06.2011, at 7:58PM, Neal Becker wrote:

> I think, in addition, that hdf5 is the only one that easily interoperates with 
> matlab?
> 
> speaking of hdf5, I see:
> 
> pyhdf5io  0.7 - Python module containing high-level hdf5 load and save 
> functions.
> h5py  2.0.0 - Read and write HDF5 files from Python
> 
> Any thoughts on the relative merits of these?

In my experience, HDF5 access usually approaches disk access speed, and random access to sub-datasets should be significantly faster than reading in the entire file, though I have not been able to test this. 
I have not heard about pyhdf5io (how does it work together with numpy?) - as alternative to h5py I'd rather recommend pytables, though I prefer the former for its cleaner/simpler interface (but that probably depends on your programming habits). 

HTH,
						Derek



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