It really takes half an hour??? What hardware are you using?
Anyway, the biggest improvement on this code is to stop calculating the mean of M every time round the loop. Do it once before you loop. That would take your complexity down from O(N*N) to O(N).
Mav = mean(M);
Oh, and of course if M is a matrix then mean(M) is going to be a 1280-length vector. I suppose that takes your current complexity up to just about O(N^3). Do you even get the right answer? Or are you expecting that? I'd have thought you do this:
Mav = mean(M(:));
Next, you could stop dividing by numel(M) every iteration and do it once after the loop:
avg = avg / numel(M);
But then, why not dispense with the loop altogether and let MatLab deal with it?
avg = mean(abs(mean(M(:)) - M(:)));
I bet that'll do your 500 data sets in a couple of seconds flat.
