[AstroPy] Sigma clipping along an axis?

[Lisa Fogarty]

Hi Erik,

Yes, the Boolean array with False for clipped data is exactly what I
wanted. This works well, thank-you! I like the feature in sigma_clip of
being able to define the centre function and variance function - it makes
NaN handling easy which I was previously worried about.

Thank-you again for your answer! I will submit a feature request as you
suggest.

Yours,
Lisa.




On Tue, Apr 30, 2013 at 9:48 AM, Erik Tollerud <erik.tollerud at gmail.com>wrote:

> So what do you want as the output?  If you want only the *values* that
> are clipped/not clipped, you can't get an array back, because each of
> the 60x60 sub-arrays will give you *different* lengths of clipped
> arrays back.  So perhaps you want the mask of clipped arrays?  If so,
> most straightforward is probably (unfortunately) nested for loops:
>
>
> from astropy.stats import sigma_clip
>
> frames = *your 60x60xN array*
>
> masks = [[sigma_clip(subarrj, ...)[1]  for  subarrj in subarri] for
> subarri in frames] #gmail will probably break this into multiple
> line... but it's supposed to be all one line
>
> maskarr = np.array(masks)
>
>
> After that, maskarr will be a 60x60xN boolean array that is *False*
> where the data was clipped, and *True* where it is valid.
>
> There's also probably a way to adjust the astropy.stats.sigma_clip
> function to do this automatically and in a more numpy-optimized way.
> Feel free to add this as an issue for
> astropy (https://github.com/astropy/astropy/issues).
>
>
> On Mon, Apr 29, 2013 at 7:21 PM, Lisa Fogarty
> <l.fogarty at physics.usyd.edu.au> wrote:
> > Hi All,
> >
> > I would like to perform a sigma-clipped sum of several data frames (60x60
> > pixels each). I have put the frames into a 3D array - so if I have N
> frames
> > the array is 60x60xN. I therefore want to sigma clip along the z-axis. As
> > far as I can see the astropy.stats.sigma_clip function ravels the data
> > before performing the sigma clip (i.e. it clips in the whole array,
> where I
> > want to clip pixel-by-pixel). Is there a pythonic way I can accomplish
> what
> > I want to do?
> >
> > Many thanks,
> > Lisa.
> >
> > --
> > Dr Lisa Fogarty | Postdoctoral Research Associate, SIfA, Sydney Institute
> > for Astronomy
> > School of Physics | Faculty of Science
> >
> > THE UNIVERSITY OF SYDNEY
> > Rm 464, Physics Building A29 | The University of Sydney | NSW | 2006
> > | AUSTRALIA
> >
> > T +61 2 935 13112
> > E  l.fogarty at physics.usyd.edu.au | W
> http://sydney.edu.au/science/physics
> >
> > _______________________________________________
> > AstroPy mailing list
> > AstroPy at scipy.org
> > http://mail.scipy.org/mailman/listinfo/astropy
> >
>
>
>
> --
> Erik
>



-- 
Dr Lisa Fogarty | Postdoctoral Research Associate, SIfA, Sydney Institute
for Astronomy
School of Physics | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 464, Physics Building A29 | The University of Sydney | NSW | 2006
| AUSTRALIA

T +61 2 935 13112
E  l.fogarty at physics.usyd.edu.au | W
http://sydney.edu.au/science/**physics<http://sydney.edu.au/science/physics>
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