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I assume that you would like to crop out a rectangle where the tuples (x1,y1) and (x2,y2) define the corners? Also to be clear, I assume origin at top left, x across and y down.
The [] notation is really array slicing in numpy and not an OpenCV function, so the first pair is rows and the second pair columns. This means you need
crop = vis[y1:y2, x1:x2]
Numpy slicing is very flexible, in general with 'basic slicing' like this it returns a view to the same memory buffer so if you modify crop the values in vis will change. This is probably not a problem here, but if it is you can force a copy easily with
crop = vis[y1:y2, x1:x2].copy()
... although obviously this is slightly slower to run.
