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    <p>You should be doing things differently anyway. Unfortunatly the <code>cKDTree</code> which is much faster does not have the necessary features, but even the other <code>KDTree</code> should give you a vast speed increase (and solve it much more elegantly)</p> <pre><code>from scipy.spatial import KDTree from itertools import chain tree = KDTree(circles) # unfortunatly only a list of lists, because there may be a different amount # also the point itself is included every time. connections = tree.query_ball_tree(tree, 2*r) # if all you want is a list of lists of what connects with what # connections is already what you need. The rest creates a connectivity matrix: repeats = [len(l) for l in connections] x_point = np.arange(len(circles)).repeat(repeats) y_point = np.fromiter(chain(*connections), dtype=np.intp) # or construct a sparse matrix here instead, scipy.sparse has some graph tools # maybe it even has a better thing to do this. connected = np.zeros((len(circles),) * 2, dtype=bool) connected[x_point, y_point] = True </code></pre> <p>While it doesn't use <code>cKDTree</code> unfortunatly, this still saves you the <code>O(N^2)</code> complexity... Of course if <code>len(circles)</code> is small, that does not matter, but then you can just use broadcasting, (or also <code>distance_matrix</code> from <code>scipy.spatial</code>):</p> <pre><code>distances = np.sqrt(((circles[:,None,:] - circles)**2).sum(-1)) connected = distances &lt; (2 * r) # if you need the list of lists/arrays here you can do: connections = [np.flatnonzero(c) for c in connected] </code></pre> <p>But note that the second method is a memory hungry monster and only any good if <code>circles</code> is small.</p>
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    1. POCreate a loop that runs function (with parameters which are indices of data set) on all items of the data set?
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    1. COThank you for your help. I'm getting this error though: NameError: name 'x_point' is not defined
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    2. COThank you! Unfortunately, I am still getting a NameError with r being undefined, and therefore x_point and y_point being undefined, and the code not working.
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    3. CO@Amanc well, `r` is your radius (or maybe `2*r`), its your job to define it.
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