Once you have this mean periodic signal you can substract it from each segment which leaves only the noise. The mean you obtain is an estimate of the periodic signal as measured by the sensor (you can not use the reference signal which is created and measured by the sensors as the sensors are not ideal and can suffer for instance from nonlinearities or other artefacts). Taking the mean over the different periods point-wise, the noise will be forced to its mean value (likely to be zero) while the mean of the periodic part is unchanged due to periodicity.
The periodic signal should be the same from segment to segment while the noise is different. Measure several periods with the sensor, partition the measured signal in segment where its length is equal to the period. In this sense you also know the period length.
Nevertheless, if you use the Fourier transform you can detect the frequency of the measured periodic signal. Even if your sensors are not ideal they will not measure the exact phase, amplitude or frequency. Typically in practice it is a good idea to measure a periodic signal with a known period length. You need to perform a reference measurement of a signal you know.
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