finding nearest neighbor for python numpy.ndarray in 3d-space

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I have a numpy.ndarray of 3d-points, i.e. the np.shape of it is (4350,3) and such a second numpy.ndarray of 3d-points of np.shape (10510,3). Now I am trying to find the right python-package to calculate the nearest neighbors in the second array of the points in the first array as quickly as possible.

I've found a quite similar question here: find the k nearest neighbours of a point in 3d space with python numpy but I don't understand how to use the solution there for my problem.

I'd very, very much appreciate your help on this!

nearest-neighbor numpy-ndarray python-3.x numpy python
1 Answers

Here is the KDTree way :

from scipy.spatial import KDTree

data= np.random.rand(10510,3)
sample= np.random.rand(4350,3)
kdtree=KDTree(data)

Then dist,points=kdtree.query(sample,2) will give you the 2 best neighbors for the 4350 candidates in about one second.

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