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FFT phase shift

I am using LabView7.1 and am trying to understand how the FFT measures the phase difference between 2 analog input signals.  The 2 signals have about the same amplitude and their phases will be about the same. I am getting a phase difference of exactly 0.000000 but there should still be a difference. Not sure how the FFT block compares the two signals. Do I need to specify which is the reference signal? If so, how do I go about doing that?

 

Thanks,

SparkEE

phase.JPG

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