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Replacing NaN with nearest neighbor

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Josh Jones
Josh Jones on 17 Oct 2014
Commented: jie wu on 2 Apr 2020
I am trying to replace NaN's in a vector field with the nearest neighbor. I believe I can use knnsearch to find the indices of the nearest neighbor to each NaN, but am running into problems. Here is what I have so far:
u = median_u; %u & v are 47x47x309
v = median_v;
k = [1 0 -1];
s = [47 47];
u_bad = isnan(u);
v_bad = isnan(v);
bad_u = find(u_bad(:)); %linear indices of NaN's
bad_v = find(v_bad(:));
[u_bad_x, u_bad_y] = ind2sub(s, bad_u); %subscript of NaN
[v_bad_x, v_bad_y] = ind2sub(s, bad_v);
idx = knnsearch(u,[u_bad_x,u_bad_y]);
And this is where I run into problems. I get an error saying that Y in knnsearch must be a matrix with 'X' number of columns. I don't see if the problem is with there being three dimensions for u and v, although I've tried just running it on one 47x47 matrix and get the same error. Thanks in advance for any help.

Accepted Answer

Image Analyst
Image Analyst on 18 Oct 2014
Why use knn? You have the indices of the nan's and non-nan's. Just loop over all nans using the Pythagorean theorem to find the distances from that nan to all other valid numbers. Then sort them and replace it with the value of the closest. It should be trivial. Let me know if you can't figure it out.
  1 Comment
Image Analyst
Image Analyst on 18 Oct 2014
Alright, here's my code. It's well commented so hopefully you'll understand it. Let me know if you don't.
clc; % Clear the command window.
clear all;
workspace; % Make sure the workspace panel is showing.
format long g;
format compact;
% Create a 47 by 47 by 309 array of random numbers.
u = rand(47, 47, 309);
% Get 100 random locations that we can make into nan's
randomLocations = randperm(numel(u), 100);
u(randomLocations) = nan;
% Now find the nan's
nanLocations = isnan(u);
nanLinearIndexes = find(nanLocations)
nonNanLinearIndexes = setdiff(1:numel(u), nanLinearIndexes);
% Get the x,y,z of all other locations that are non nan.
[xGood, yGood, zGood] = ind2sub(size(u), nonNanLinearIndexes);
for index = 1 : length(nanLinearIndexes);
thisLinearIndex = nanLinearIndexes(index);
% Get the x,y,z location
[x,y,z] = ind2sub(size(u), thisLinearIndex);
% Get distances of this location to all the other locations
distances = sqrt((x-xGood).^2 + (y - yGood) .^ 2 + (z - zGood) .^ 2);
[sortedDistances, sortedIndexes] = sort(distances, 'ascend');
% The closest non-nan value will be located at index sortedIndexes(1)
indexOfClosest = sortedIndexes(1);
% Get the u value there.
goodValue = u(xGood(indexOfClosest), yGood(indexOfClosest), zGood(indexOfClosest));
% Replace the bad nan value in u with the good value.
u(x,y,z) = goodValue;
% u should be fixed now - no nans in it.
% Double check. Sum of nans should be zero now.
nanLocations = isnan(u);
numberOfNans = sum(nanLocations(:))

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More Answers (2)

Steven Lord
Steven Lord on 2 Feb 2018
I'm not certain if this will do exactly what you want, but using the fillmissing function with the 'nearest' method may be sufficient for your needs.
jie wu
jie wu on 2 Apr 2020
This 'nearest' element is the 'nearest' in the row or the column same as the 'NaN' locating in.
So this 'nearest' element may not be the 'nearest' one if we take the whole array into account.
The first answer (the accepted one) deal with the case when we consider the whole array.
Is there a built function or more efficient way to do this work? Thanks a lot!

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Yavor Kamer
Yavor Kamer on 6 Jul 2016
Edited: Yavor Kamer on 6 Jul 2016
A quick and dirty* way is to get the indices of the NaN values and replace them with their immediate neighbors (to the left or right). You repeat this until all NaNs are replaced.
*This will not work if one of the end elements is NaN.
nanIDX = find(isnan(vec));
vec(nanIDX) = vec(nanIDX+1);
nanIDX = find(isnan(vec));
An example input/output would look like this:
vecIn = [1 1 NaN 2 NaN 2 3 3 4 NaN NaN 4 4]
vecOut = [1 1 2 2 2 2 3 3 4 4 4 4 4]
  1 Comment
Rami Abousleiman
Rami Abousleiman on 2 Feb 2018
Squeeze your code between these 2 I think it will fix it:
if (isnan(b(end)))
b(end) = inf;
nanIDX = find(isnan(b));
b(nanIDX) = b(nanIDX+1);
nanIDX = find(isnan(b));
nanIDX = find(isinf(b));
nanIDX = flipud(nanIDX);
b(nanIDX) = b(nanIDX-1);
nanIDX = find(isinf(b));

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