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When padding a PSF with (odd, odd) dimension to (even, even) dimension, the center of the PSF should be placed to the center-right of the array. Otherwise the peak value could be shifted to the end of the array after applying np.fft.fftshift(e.g. Correct padding: [0,0,1,2,3,2,1,0] -> [3,2,1,0,0,0,1,2], Incorrect padding: [0,1,2,3,2,1,0,0] - > [2,1,0,0, 0,1,2,3]). This corresponds to a one pixel offset since the np.fft.fft assume the first component of the array as the origin.