Converting x,y coordinates into a format for getAffineTransform?
No I think there is something else that is the problem.  Docs say: cv2.getAffineTransform Calculates an affine transform from three pairs of the corresponding points.
The problem is you are giving it 125 pairs of points.  It only wants 3 pairs of point correspondences.  This is of course the number of correspondences needed to solve the linear system of equations.  If you are looking to estimate an affine transformation from noisy correspondences then you will need to use something like weighted least squares or RANSAC.  To estimate affine transform from noisy data with a prepackaged algorithm it looks like cv2.estimateRigidTransform might work setting fullAffine = True
I'm trying to use the cv2.getAffineTransform(src,dst) function in openCV, but it crashes because my inputs are arrays containing 125 pairs of x,y coordinates and getAffineTransform wants its input to have three columns. Can I just concat a row full of zeros onto my array or is there a special transformation I should do?