[Numpy-discussion] Calculating density based on distance

[Thiago Franco de Moraes]

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!