[Numpy-discussion] finding close together points.

Anne Archibald peridot.faceted@gmail....
Mon Nov 16 18:25:26 CST 2009


2009/11/16 Christopher Barker <Chris.Barker@noaa.gov>:
> Anne Archibald wrote:
>> 2009/11/13 Christopher Barker <Chris.Barker@noaa.gov>:
>>> Wow! great -- you sounded interested, but I had no idea you'd run out
>>> and do it! thanks! we'll check it out.
>
> well, it turns out the Python version is unacceptably slow. However, we
> found we could use ckdtree, and use:
>
> tree.query(points,
>             2, # Number of points to return per point given.
>             distance_upper_bound = distance_tolerance,
>            )
>
> This gives us a set of pairs of points closer than our distance
> tolerance -- it includes duplicates, of course, but even when we filter
> those in pure python, it's is nice and speedy.
>
> It looks like it would be pretty easy to add this to the Cython code,
> but it's working now for us, so...

You probably noticed this, but I should remind you that if a point has
more than one nearby neighbor, this may not give you what you wanted.
In particular, if there are three points all within the fixed distance
from each other, you may not find all three pairs this way.

Anne

> Thanks again,
>
> -Chris
>
>
>
> --
> Christopher Barker, Ph.D.
> Oceanographer
>
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>
> Chris.Barker@noaa.gov
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