Question: quad detected complex time domain data arrays imput into fft for spectral data output

Have quadrature detected time domain complex data arrays.  Trying to fft array to get frequency domain arrays.  Arrays returned are always sinusoidal in nature rotating between + and - y axis.  Can not phase correct these sinusoidal frequency arrays.  Any ideas how to pretreat time domain arrays before fft or posttreat frequency domain arrays after fft in order to determine phase correction angles that will allow combination of real and imaginary frequency domain data points that are only in + y axis.

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