Python alternative for calculating pairwise distance between two sets of 2d points

Question

In Matlab there exists the pdist2 command. Given the matrix mx2 and the matrix nx2, each row of matrices represents a 2d point. Now I want to create a mxn matrix such that (i,j) element represents the distance from ith point of mx2 matrix to jth point of nx2 matrix. I simply call the command pdist2(M,N).

I am looking for an alternative to this in python. I can of course write 2 for loops but since I am working with 2 numpy arrays, using for loops is not always the best choice. Is there an optimized command for this in the python universe? Basically I am asking for python alternative to MATLAB's pdist2.

Answer 1

You're looking for the cdist scipy function. It will calculate the pair-wise distances (euclidean by default) between two sets of n-dimensional matrices.

from scipy.spatial.distance import cdist
import numpy as np

X = np.arange(10).reshape(-1,2)
Y = np.arange(10).reshape(-1,2)

cdist(X, Y)

[[  0.           2.82842712   5.65685425   8.48528137  11.3137085 ]
 [  2.82842712   0.           2.82842712   5.65685425   8.48528137]
 [  5.65685425   2.82842712   0.           2.82842712   5.65685425]
 [  8.48528137   5.65685425   2.82842712   0.           2.82842712]
 [ 11.3137085    8.48528137   5.65685425   2.82842712   0.        ]]