[AstroPy] Missing some statistical method for your astronomy analyses in Python?

Thomas Robitaille thomas.robitaille@gmail....
Tue Jan 15 04:29:58 CST 2013


I think this is something that should be brought up with the Numpy
developers, and it would probably benefit everyone to have a faster
median calculation function (not just astronomers). At the moment,
Numpy just uses a quicksort, but if one could achieve speedups of 5x,
then I think the Numpy devs might be interested.

Cheers,
Tom

On 15 January 2013 10:51, Jerome Caron <jerome_caron_astro@ymail.com> wrote:
> Dear Christoph
> I think the calculation of median values in Numpy is not optimal. I don't
> know if there are other libraries that do better?
> On my machine I get these results:
>>>> data = numpy.random.rand(5000,5000)
>>>> t0=time.time();print numpy.ma.median(data);print time.time()-t0
> 0.499845739822
> 15.1949999332
>>>> t0=time.time();print numpy.median(data);print time.time()-t0
> 0.499845739822
> 4.32100009918
>>>> t0=time.time();print aspylib.astro.get_median(data);print time.time()-t0
> [ 0.49984574]
> 0.90499997139
>>>>
> The median calculation in Aspylib is using C code from Nicolas Devillard
> (can be found here: http://ndevilla.free.fr/median/index.html) interfaced
> with ctypes.
> It could be easily re-used for other, more official packages. I think the
> code also finds quantiles efficiently.
> Kind regards
> Jerome Caron
>
> De : Christoph Deil <deil.christoph@googlemail.com>
> À : "astropy@scipy.org list" <astropy@scipy.org>
> Envoyé le : Mardi 15 janvier 2013 8h42
> Objet : [AstroPy] Missing some statistical method for your astronomy
> analyses in Python?
>
> Dear all,
>
> we would like to know which statistical methods you want to use for you
> astronomy work with Python that are not readily available e.g. in scipy or
> one of the existing scientific Python packages like e.g. statsmodels,
> scikit-learn, astroML, …
>
> Please visit the wiki page for what has already been suggested, then reply
> to this email or make an addition to the
> https://github.com/astropy/astropy/wiki/What-methods-do-we-want-in-astropy.stats?
> wiki page directly.
>
> The plan is to add these methods either to astropy.stats or, if they are not
> astronomy-specific, to one of the existing scientific Python packages.
>
> Christoph
>
> PS: This discussion started as a thread on astropy-dev (
> https://groups.google.com/d/topic/astropy-dev/Zwgafam171E/discussion ), but
> it was suggested to also ask here.
>
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