[Numpy-discussion] finding close together points.

Christopher Barker Chris.Barker@noaa....
Mon Nov 16 18:17:56 CST 2009


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...

Thanks again,

-Chris



-- 
Christopher Barker, Ph.D.
Oceanographer

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Chris.Barker@noaa.gov


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