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How many bits are you are using for I and Q channels? How many are for fractional and integer parts?
Which are maximum and minimum values for I and Q channels?.
However, if the I Q channels bit size (N) don't grow, you should be able to use the arctan core without problems assuming a signed fixed point format b_N-1. b_N-2 ... b_0, any scale value is canceled after doing Q/I.
Be careful with divider circuit, because it can introduce overflows.
Fixed point division is performed correctly by doing
(Q<<Nf)/I
Where Nf is the fractional bits size.
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My "channel" is basically a stream of 8bit symbols representing signed integers 1,-1,3,-3 (16QAM). These values are upsampled & filtered with a nyquist filter, therefore causing their amplitudes to vary around their nominal values. The divider prior to the arctan will therefore be dividing 8bit symbols with one another and then sending the output to the arctan as an argument (which need to be between -1 & 1).