yasar - 9 months ago 106
Python Question

# Distance calculation on matrix using numpy

I am trying to implement a K-means algorithm in Python (I know there is libraries for that, but I want to learn how to implement it myself.) Here is the function I am havin problem with:

def AssignPoints(points, centroids):
"""
Takes two arguments:
points is a numpy array such that points.shape = m , n where m is number of examples,
and n is number of dimensions.

centroids is numpy array such that centroids.shape = k , n where k is number of centroids.
k < m should hold.

Returns:
numpy array A such that A.shape = (m,) and A[i] is index of the centroid which points[i] is assigned to.
"""

m ,n = points.shape
temp = []
for i in xrange(n):
temp.append(np.subtract.outer(points[:,i],centroids[:,i]))
distances = np.hypot(*temp)
return distances.argmin(axis=1)


Purpose of this function, given m points in n dimensional space, and k centroids in n dimensional space, produce a numpy array of (x1 x2 x3 x4 ... xm) where x1 is the index of centroid which is closest to first point. This was working fine, until I tried it with 4 dimensional examples. When I try to put 4 dimensional examples, I get this error:

  File "/path/to/the/kmeans.py", line 28, in AssignPoints
distances = np.hypot(*temp)
ValueError: invalid number of arguments


How can I fix this, or if I can't, how do you suggest I calculate what I am trying to calculate here?

def AssignPoints(points, centroids):
m ,n = points.shape
temp = []
for i in xrange(n):
temp.append(np.subtract.outer(points[:,i],centroids[:,i]))
for i in xrange(len(temp)):
temp[i] = temp[i] ** 2
return distances.argmin(axis=1)


Try this:

np.sqrt(((points[np.newaxis] - centroids[:,np.newaxis]) ** 2).sum(axis=2)).argmin(axis=0)


Or:

diff = points[np.newaxis] - centroids[:,np.newaxis]
norm = np.sqrt((diff*diff).sum(axis=2))
closest = norm.argmin(axis=0)


And don't ask what's it doing :D

Edit: nah, just kidding. The broadcasting in the middle (points[np.newaxis] - centroids[:,np.newaxis]) is "making" two 3D arrays from the original ones. The result is such that each "plane" contains the difference between all the points and one of the centroids. Let's call it diffs.

Then we do the usual operation to calculate the euclidean distance (square root of the squares of differences): np.sqrt((diffs ** 2).sum(axis=2)). We end up with a (k, m) matrix where row 0 contain the distances to centroids[0], etc. So, the .argmin(axis=0) gives you the result you wanted.