How can I calculate the distances of a set of 3d points with each other using python?

Question

I have a set of 3D points, where I need to find the distances of every point with all other points. So far I came up with the code as below to calculate the distances between tw

Answer 1

How about two loops instead of one?

distances = []
for i in xrange(npoints-1):
    for j in range(i+1, npoints):
        distances.append(np.linalg.norm(x[i]-x[j])

Answer 2

For each of your npoints points, there are exactly npoints - 1 other points to compare with, for distance. And, the distance between x[m] and x[n] is the same as the distance between x[n] and x[m], so that cuts the total number of distances in half. The itertools package has a nice way to handle this:

import numpy as np
import scipy as sp
import itertools as its

npoints = 10
nCombos = (npoints * (npoints - 1))/2
x = sp.randn(npoints,3)
rij_mat = np.zeros(nCombos)

ii = 0
for i1, i2 in its.combinations(range(npoints), 2):
    rij_mat[ii] = np.linalg.norm(x[i1]-x[i2])
    ii += 1

print "the distances are..."
print rij_mat

If you're a really careful person, you might check at the end that ii == nCombos.

Since you called your output matrix rij_mat, maybe you intended it to be a 2-dimensional matrix? Then you'd want something like:

import numpy as np
import scipy as sp
import itertools as its

npoints = 10

x = sp.randn(npoints,3)
rij_mat = np.zeros((npoints, npoints))

for i1, i2 in its.combinations(range(npoints), 2):
    rij_mat[i2, i1] = rij_mat[i1, i2] = np.linalg.norm(x[i1]-x[i2])

print "the distances are..."
print rij_mat