A method is provided for calibrating a free-space-coupled fiber-optic transmission system 23, 30. The method uses signal content in the measured coupled power at frequencies equal to the sum, difference, and first harmonics of the frequencies of control-related dither signals to infer and correct errors in the kinematical model used to apply the dithers 109. The technique can operate independently or simultaneously with dither-based functions such as alignment control and power attenuation to provide continuous tracking of model terms 100. The calibration method does not require that any calibration-specific signals be injected into the system, or that the operation of primary functions be halted for the purpose of calibration 300.
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