Take FFT to find time period for eclipsing binaries

[CassiopeiaA]

I am trying to use Kepler Data for Eclipsing Binaries to estimate time period, and then other parameters such as mass, eccentricity, semi-major axis, distance, etc. of the binary systems. I want to write code in MATLAB which will use FFT to find the time period. The available data has the following columns:

bjd(date) | phase | raw_flux | raw_err | corr_flux | corr_err | dtr_flux | dtr_err

My question : Does this data require any cleaning? And If I want to take the FFT of the data to find time period, which data should I use? (If there is another method for finding time, please do suggest)

 

[mfb]

The signal is not a sine curve, so you would have to look for a whole tower of spectra for frequencies n, 2n, 3n, ... I'm not sure how useful that is. Fitting the individual transits and then getting the period out of those timestamps could be more reliable. This is even more important if the stars are variable on their own.