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Measure Phase with Pluto

Hi,

I would like to measure what I believe is instantaneous phase with the Pluto. 

I am using the Pluto with MATLAB.

1. I am sending a 2GHz signal to the Plutos RX and taking a measurement and storing the data

2. I am sending a 2GHz 90° signal to the Plutos RX and taking a measurement and storing the data

I would like to post process the data to be able to detect the phase shift between (1) and (2).

I believe I can take the FFT of each data set to detect a peak in the frequency domain.

Then from the FFT I can do angle(FFT) - This will show me phase with respect to frequency. 

Is this the best way to process the data to obtain the phase difference?

Many thanks,

Zain