[Numpy-discussion] Calculating density based on distance

Thiago Franco Moraes totonixsame at gmail.com
Sat Jan 14 21:23:47 EST 2012

No dia Sábado, 14 de Janeiro de 2012, Benjamin Rootben.root at ou.edu escreveu:
> On Saturday, January 14, 2012, Thiago Franco de Moraes <
totonixsame at gmail.com> wrote:
>> Hi all,
>> I have the following problem:
>> Given a array with dimension Nx3, where N is generally greater than
>> 1.000.000, for each item in this array I have to calculate its density,
>> Where its density is the number of items from the same array with
>> distance less than a given r. The items are the rows from the array.
>> I was not able to think a solution to this using one or two functions of
>> Numpy. Then I wrote this code http://pastebin.com/iQV0bMNy . The problem
>> it so slow. So I tried to implement it in Cython, here the result
>> http://pastebin.com/zTywzjyM , but it is very slow yet.
>> Is there a better and faster way of doing that? Is there something in my
>> Cython implementation I can do to perform better?
>> Thanks!
> Have you looked at scipy.spatial.KDTree?  It can efficiently load up a
data structure that lets you easily determine the spatial relationship
between datapoints.
> Ben Root

Thanks, Ben, I'm going to do that.
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