Very slow function, excessive overhead?

I've got a function that looks at a n x 2 array (1st column time vector, 2nd column flag vector) and it's running incredibly slow. As you can see, line 17 takes almost all of the runtime. I've read that this could be related to overhead, but I don't actually know what that means or how to improve it. Any ideas on what could be causing this?

Answer 1

[Walter Roberson]

You are not assigning to flag within your loop, so you should use

flagrows = size(flag,1);
while i < flagrows
    
end

The end for a loop does get "charged" the cost of the loop overhead, which in this case is doing more computations than required.

[Jesse]

Thank you! That did the trick. I didn't realize how computationally heavy the "size" function could be. It makes sense though, when you call it nearly 400 thousand times.

[Walter Roberson]

you used length(flag(:, 1)) which starts by extracting the first column and then taking the length of the column. That sequence involves copying data and then checking the size. That is a lot more work then just checking the size of the original data.

Answer 2

[Torsten]

The inner while loop is not necessary: if flag(i,2)-flag(i-1,2) == 1, then of course flag(i,2)-flag(i-1,2) ~== -1. Thus the incrementation i = i+1 will always happen. This is strange since you increment i again after you quit the if-clause.

Preallocating "events" as zeros(size(flag,1),3) and finally cutting it by events = events(1:j-1,:) might speed up the function also.

[Jesse]

I'm trying to find the start and end point of each flag "event". the outer loop finds when flag goes from 0 to 1, and the inner loop finds whent the flag goes from 1 to 0.