How to calculate the phase difference between two square wave (acquired from two channel in one DAQ)

Hello everyone ,
I need a quickly help that as below :
I am trying use PCI-6220 to acquired six signals from one rotation encoder (channel A, channel B,channel Z ,and their non-signals) .The encoder out signals will be square wave and 4000pulses per revolution. I set it rotation at 300rpm speed. I need show every square wave of six out channels in waveform and measure the A-B phase difference to check if the value is correct (designed value should be 90deg) .
I have no idea how to measure or calculate the phase difference of two square wave base on synchronizate to acquire these two square wave from two channel on the PCI-6620....
Anyone can give a idea how to calculate the phase difference with two square wave ?
Thank a lot and Thanks again...
Tim

Tim,
Here is a simple rising edge detector for one channel.
Lynn
Attachments:
Rising edge.vi ‏15 KB

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Attachments:
v603.png ‏320 KB
v603.vi ‏186 KB

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Basic math gives me a bit of pause on this approach. You are sampling at 50 times the frequency of interest so you get 50 samples per cycle. your phase resolution is 1/50th cycle or 7.2 degrees +/- noise. You will need to samlpe faster to reduce phase resolution or average multiple readings (at a time cost that is signifigant)
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I am sampling at 100 times the sine wave's frequency and 200 times the square wave's frequency. Increasing the sampling rate completely solves my problem. But since I am acquiring several other inputs, I cannot afford a sampling rate higher than 5kHz.
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