I knew I was going to have this remark :)
Now correct me if I am wrong, but I think the FFT (which computes the discrete Fourier transform) cannot replace the continous fourier transform in my case, because the optimal periods I find are non-integer values. In the first case, the holes are separated by 7.5 pixels. The FFT could only have told me that they are separated by 7 or 8 pixels, which is not precise enough. Same thing for the tempo, a beat corresponds to 7.1 frames of the video, and a FFT would have told me 7.
If someone knows a way to use the FFT to get non-integer periods (apart from oversampling the signal) I'll gladly change the code.