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

Gary Pajer gary.pajer@gmail....
Wed May 27 13:50:20 CDT 2009

On Wed, May 27, 2009 at 11:34 AM, Davide Cittaro <
davide.cittaro@ifom-ieo-campus.it> wrote:

> Hi all,I have a bunch of spectra listed within a file (mass/intensity
> values). I'm planning to analyze them and match with theoretical spectra...
> In you opinion, which is the best way to store them for an efficient
> analysis?
> In the past this has been done with python arrays (i.e. a spectrum was an
> array of arrays, each peak was a mass/intensity array)...
> Thanks
> d
> /*
> Davide Cittaro

I note that you specifically ask about storage.

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.  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.


> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
> tel.: +39(02)574303007
> e-mail: davide.cittaro@ifom-ieo-campus.it
> */
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