[AstroPy] astropy and photutils slow

[Stephen Bailey]

What version of numpy and astropy do you have?  (numpy.__version__ and
astropy.__version__).

As another data point, using numpy/1.11.1 and astropy/1.2.1 I get much
faster results than you:

On Tue, Sep 13, 2016 at 12:05 PM, David Nidever <davidnidever at gmail.com>
wrote:

> Hi all,
>
> I'm pretty new to astropy and to python in general.  I've been trying out
> some of the astropy and photutils photometry tools, but I'm finding that
> they
> are running pretty slow.  I wanted to double-check that I'm not doing
> something
> wrong.
>
> Below is an example of running the astropy sigma clipped statistics routine
> on a fake 2Kx4K image (since I'm working on DECam data).  This takes
> almost 20s to run even though similar statistics using numpy take ~0.1s
> or so.
>
> >>> import numpy as np
> >>> from astropy.stats import sigma_clipped_stats
> >>> im = np.random.rand(4096,2048)*10.0+100.0
> >>> timeit mean, median, std = sigma_clipped_stats(im, sigma=3.0, iters=5)
> 1 loop, best of 3: 18.9 s per loop
>

1.84s per loop for me.  Still slow, but not 18.9s.


> It seems like it might be the use of the numpy masked array module that is
> slowing things down.  Just using the masked array median versus the
> normal numpy median takes ~30x longer.
>
> >>> timeit np.median(im)
> 10 loops, best of 3: 109 ms per loop
>

103 ms for me; i.e. this isn't just that I have a super fast machine and
you have a super slow one.


> >>> timeit np.ma.median(im)
> 1 loop, best of 3: 2.71 s per loop
>

104 ms for me.  i.e. with numpy 1.11.1 I don't see a radical difference
between masked array or not.

Stephen


>
> I'm finding similar speed issues with the photutils routines (e.g.
> background2D)
> that I believe also use masked arrays.
>
> Is there something I can do to speed things up?
>
> Thanks!
> David
>
> --
> Dr. David Lee Nidever
> Survey Data Scientist, NOAO
> 950 N. Cherry Ave.
> Tucson, AZ 85719
> (520) 318-8368
>
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