[Numpy-discussion] Calculating density based on distance

Thiago Franco Moraes totonixsame@gmail....
Sat Jan 14 20:23:47 CST 2012


No dia Sábado, 14 de Janeiro de 2012, Benjamin Rootben.root@ou.edu escreveu:
>
>
> On Saturday, January 14, 2012, Thiago Franco de Moraes <
totonixsame@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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