Inter individual distance between fishes

I want to calculate inter-individual distances between 5 fishes. I extracted the trajectories and now I have X and Y coordinates of the those trajectories. I have a code with which I could calculate inter-individual distances between fishes for a single X and Y fragment only but there are multiple fragments for a signle video and I have many videos. Hence the code need to run in loop. Can anyone one provide a code which will run in loop for multiple fragments?

[Matt J]

Can't you just wrap the code you already have in a loop?

[Shramana]

I tried but it is not working. This is the code,

% xy = randn(5,2);

x = readmatrix("https://www.mathworks.com/matlabcentral/answers/uploaded_files/1153563/X_fragment1.txt");

y = readmatrix("https://www.mathworks.com/matlabcentral/answers/uploaded_files/1153573/Y_fragment1.txt");

whos

nframes = size(x, 1);

dmean=zeros(nframes, 1);

for i=1:nframes

xy = [x(i,:)', y(i, :)'];

d = pdist2(xy, xy);

% extract the lower triangle

[ii, jj] = meshgrid(1:5, 1:5);

d1 = d(ii>jj); % d21, d31, ..., d61, d32, .., d62, ... d65

dmean(i) = mean(d1);

end

plot(1:nframes, dmean)

xlabel('frame number');

ylabel('mean distance')

Answer 1

[Divyanshu]

Hi Shramana,

I am assuming that the code provided in the comments works fine and gives the desired results for X-Y coordinates of 1 fragment of a video. Here is the sample code to extend it to work for multiple fragments and multiple videos:

%The outermost loop iterates over all the videos I have assumed we have 10
%videos
for vid=1:10
    
    %This is just a sample loop which iterates over 10 videos, you may need to modify the 
    %logic within each iteration and also the path to coordinate-files may get changed for 
    %each iteration, that logic you may need to incorporate in this sample code.
    
    %Below loop iterates over all the frames/fragments of a single video 'vid'
    for i=1:n
        file1 = sprintf("https://www.mathworks.com/matlabcentral/answers/uploaded_files/1153563/X_fragment%d.txt",i);
        file2 = sprintf("https://www.mathworks.com/matlabcentral/answers/uploaded_files/1153563/Y_fragment%d.txt",i);


        %your piece of code
        xy = randn(5,2);
        x = readmatrix(file1);
        y = readmatrix(file2);
        whos
        nframes = size(x, 1);
        dmean=zeros(nframes, 1);
        
        %This loop iterates over all the pair of coordinates for current fragment 'i'
        for i=1:nframes
            xy = [x(i,:)', y(i, :)'];
            d = pdist2(xy, xy);
            % extract the lower triangle
            [ii, jj] = meshgrid(1:5, 1:5);
            d1 = d(ii>jj);  % d21, d31, ..., d61, d32, .., d62, ... d65
            dmean(i) = mean(d1);
        end
        plot(1:nframes, dmean)
        xlabel('frame number');
        ylabel('mean distance')
        
        
    end
end

Moreover, based on the specific usecase the above code can be optimized and nested loops can be avoided.