Nearest neighbour for one dataset

Hello,

I have one dataset consiting of 3d points. I want to find out within that dataset, which point is closest to which in 3d? Eg; [1 2 3; 3 4 5;6 7 8;8 9 10]... And what are some neat tricks to visualize such results?

Thanks!

Answer 1

[Walter Roberson]

https://www.mathworks.com/help/stats/knnsearch.html

To visualize, you could construct a directed graph using digraph() and plot it with coordinates https://www.mathworks.com/help/matlab/ref/graph.plot.html#buzeikk

[AB]

Hello Walter,

I looked at it. Thanks. I have one question though. The knnsearch works for 2 matrices X and Y. If I have the same dataset as X and Y, will it not count the nearest neighbour for a point in X as the same point in Y. How can I get rid of this?

Thanks!

[Walter Roberson]

%calculate distances of each point to each other point
dists = squareform( pdist(X) );
%set diagonal to inf so point is not its own closest neighbor
dist(1:size(dists,1)+1:end) = inf;
%find index of closest point
[~, minidx] = min(dists, [], 2);

Now for the K'th point, X(K,:), minidx(K) is the row index of its closest neighbour.

For large number of points, the above might not be as efficient as what knnsearch does, but for modest number of points it is probably more efficient.