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Fast Fourier Transform Basics and Phase difference

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Sang08

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I have two sine waves with lot of harmonics. I want to find the phase angle difference between the two waves. I was told to Take the FFT of both the waveforms, then find the phase angle difference of the complex FFTs for both signals at the fundamental frequency (and harmonics). How should I go about doing this? Can any one please help.

Thank you,

Sang
 

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