?? Wouldn't you just look for the time delta between corresponding rising edges, or somesuch?

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I haven't played with the Arduino itself, but the most likely strategy would involve time-stamping like edges of both square waves. Time between these edges for one waveform is the period, and time between these edges for the two different waveforms is the shift. The ratio provides the fractional shift, which could be expressed as percentage or "degrees".

thank you IRstuff and cswilson fellows i will try that.

I would look at the timer/counter section for the micro controller. If you AND phase A with NOT phase B and use that as a gate for a timer/counter. That provides the delay between phase A and phase B. I would use another counter/timer to count the period of the square wave. The trick is to learn how to use the counter timer because they usually count or time at the frequency of the micro controller.

Peter Nachtwey
Delta Computer Systems
http://www.deltamotion.com
http://forum.deltamotion.com/