CODEWITHSUNDEEP
pythonscipy
RainisCold
RainisCold

Reputation: 63

How to query the nearest neighbors including the ones at distance zero with Scipy's cKDTree?

I want to find the neighbors within a distance using Scipy cKDTree. Most important, I want the point itself (zero distance) as well. cKDTree. query gives all the neighbors but without zero distance.

Is there a way to do this?

Upvotes: 5

Views: 10766

Answers (1)

mgc
mgc

Reputation: 5443

I can't really reproduce your issue (or it might depends on the method that you are using to query the tree).

Considering this simple snippet of code :

>>> from scipy.spatial import cKDTree
>>> import numpy as np

>>> points_ref = np.array([(1, 1), (3, 3), (4, 4), (5, 4), (6, 6)])
>>> tree = cKDTree(points_ref)

Querying for the nearest neighbors at a distance of 2 around the point (4, 4) with the method cKDTree.query_ball_point can give something like :

>>> idx = tree.query_ball_point((4, 4), 2)
>>> points_ref[idx]
# array([[3, 3], [4, 4], [5, 4]])

Which returns the point with a distance of 0.

Querying for the n-nearest neighbors with the method cKDTree.query also seems to return the point with a distance of 0 :

>>> _, idx = tree.query((3, 3), k=2)
>>> points_ref[idx]
# array([[3, 3], [4, 4]])

Upvotes: 7

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