Uhh...if I remember correctly then the Fourier transform is: F(w) = <f(x), cos(2 pi w x)> + i <f(x), sin (2 pi w x) > (where <_, _> is the inner product betw

Uhh...if I remember correctly then the Fourier transform is: F(w) = <f(x), cos(2 pi w x)> + i <f(x), sin (2 pi w x) > (where <_, _> is the inner product between functions, x is a time and w is a frequency). So the imaginary component is not the phase but how much of your function is explained by a sine wave. To get the phase you should take the angle of each complex number (and to get the amplitude you take the magnitude).