[SciPy-user] [half OT?] best way to store a spectrum

Davide Cittaro davide.cittaro@ifom-ieo-campus...
Wed May 27 14:51:53 CDT 2009

On May 27, 2009, at 8:50 PM, Gary Pajer wrote:
> I note that you specifically ask about storage.

Well, I'm not that fluent with "Engrish"... I mean a way to represent  
a spectra with an appropriate data structure which can help in  
selecting single spectrum regions or peaks...

> I store spectra, too.  Each one has 5,000 - 10,000 data points, and  
> I have sequences of them.  Up until recently I was simply storing  
> them in  numpy arrays.

Did you use arrays with (2,1) shape? or an array for mass and an array  
for intensity?

> When the length of the sequence got up to several hundred I switched  
> to hdf5/PyTables.   The greatest advantage is that I don't worry so  
> much about the structure of my saved datasets.  I was starting to  
> lose sleep.  I can also more conveniently store the small bits of  
> metadata, and other data.  Now I'm looking into h5py to lower (?)  
> the overhead.  My primary need is storage, and I don't need PyTables  
> rich abilites.

Thanks so much. As I will deal with storage issues I will definitely  
take a look to those (I probably need them for other projects ^__^)


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