Sounds like a fairly ambitious first project!
I assume your 7200 edges/rev come from an encoder with 2 channels in quadrature which each provide 1800 cycles/rev. You can clock in analog data at 1800 scans/rev with either of the two encoder channels, but will probably need an external quadrature decoder circuit to produce 7200 scans/rev. Either method can be done with screwdriver and wire or else by using another counter from the 6602 and the RTSI bus. Here are two approaches in detail, but you could mix-and-match as needed.
Note also that if you can be sure that your reference encoder will be uni-directional, you wouldn't need to measure position -- position could be determined by the array index of the analog scan data. This would simplify things greatly.
1800 scans/rev, screwdriver & wire
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Wire both encoder channels to your 6602 breakout box and configure your counter for the 4x quadrature option. Send a wire from one of the encoder channel connections at your 6602 breakout box to a PFI pin at your E-series board breakout box. Config the analog acquisition to use an external scan clock and specify the correct PFI pin -- there are built-in examples that will guide you. Now one edge of one encoder channel acts as a scan clock for your analog acquisition. Inside the 6602 breakout box, route the same signal to one of the default gate pins and configure your encoder counter gate to use that pin as its gate signal. Note that there will be a race condition governing whether the encoder value updates from the encoder inputs before or after the value is latched by the gate.
7200 scans/rev, extra counter & RTSI
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Make sure you have a RTSI connector between your two acquisition boards inside your PC. Build a quadrature decoder circuit that will convert your two encoder channels into a clock and direction output. (Consider the LSI 7084 decoder chip or similar). Setup your "encoder" counter for buffered position measurement. Use "Counter Set Attribute" to define "up down" as "digital" (don't use it to define "encoder type"). The clock output goes to the counter SOURCE and the direction output goes to the counter UP_DOWN pin.
Use "Adjacent Counters.vi" to identify the counter considered adjacent to your encoder counter. Configure it for "retriggerable pulse generation". Use "Counter Gate (NI-TIO).vi" to specify "other counter source" as the gating signal. Configure the output pulse specs to be short duration (make sure total of delay + pulse width is less than the minimum period of the incoming encoder clock signals). Use "Route Signal.vi" to send this counter's output onto the RTSI bus, say RTSI 0.
Now configure the analog acq. to use RTSI 0 as its external scan clock. Also configure the encoder counter to use RTSI 0 as its gate signal. Voila! Now your quadrature decoder clock output acts as a scan clock for analog acquisition and a "gate" to buffer your encoder measurement. The short delay helps ensure that the clock updates the position measurement before the gate fires to latch the value.
Respond if you need clearer explanation. There's a fair amount of decent info "out there" if you scour the online help and this website. Good luck!
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