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you have cylindrical waveguide - so you have one port on the one side and second port on the second side - after calculate, you have S21, S11, S12 and S22 (S21=S12 and S11 = S22). This is your transmitted and return loss.
If you want to get loss about the power, you can calculate:
Transmitted Power (dBm)=Input Power(dBm)-|S21|(dB).
If you want to get loss about Watt, you can Input Power(Watt)-Transmitted Power (Watt)
If you want to get loss about the power, you can calculate:
Transmitted Power (dBm)=Input Power(dBm)-|S21|(dB).
If you want to get loss about Watt, you can Input Power(Watt)-Transmitted Power (Watt)
Added after 8 minutes:
The power will be reflected, transmitted and loss.
1-S11*S11 represent the power except reflection loss.
If waveguide does no has loss, S21*S21=1-S11*S11. However, practical waveguide has loss, 1-S11*S11-S21*S21 represent transmission loss