Currently, the PR #917 works for a 2D notch resonator. In literature seems there is no difference in calibrating a 2D or 3D resonator. Therefore the calibration routine may work in the same way for a 3D resonator. The only difference lies on the $S_{21}$ profile
2D resonator
$$
S_{21}(f) = a^{i\alpha} e^{-2 \pi i f \tau} \left[1 - \frac{Q_l/|Q_c|e^{i\phi}}{1+2iQ_l(f/f_r - 1)}\right]
$$
3D resonator
$$
S_{21}(f) = a^{i\alpha} e^{-2 \pi i f \tau} \left[\frac{2Q_l/|Q_c|e^{i\phi}}{1+2iQ_l(f/f_r - 1)}\right]
$$
Currently, the PR #917 works for a 2D notch resonator. In literature seems there is no difference in calibrating a 2D or 3D resonator. Therefore the calibration routine may work in the same way for a 3D resonator. The only difference lies on the $S_{21}$ profile
2D resonator
$$ S_{21}(f) = a^{i\alpha} e^{-2 \pi i f \tau} \left[1 - \frac{Q_l/|Q_c|e^{i\phi}}{1+2iQ_l(f/f_r - 1)}\right] $$
3D resonator
$$ S_{21}(f) = a^{i\alpha} e^{-2 \pi i f \tau} \left[\frac{2Q_l/|Q_c|e^{i\phi}}{1+2iQ_l(f/f_r - 1)}\right] $$