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but there is still some shakyness in the wheels.
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Jlyon, I think you need to better explain that. I would put the RIO encoders into 4X mode and retest so you can compare apples to apples.
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or the input could be lagging behind by four ticks
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4 Ticks? That sounds pretty accurate to me. Unless your encoders are very low resolution.
Please read section 16.9 if the observation is that the Talon encoders are "behind" the RIO encoders only when encoders are spinning. In which case do the math to see what 20ms of lag (at your RPM) should do in terms of encoder difference If that's a problem tweak the status frame rate to be faster (section 20.5).
If you problem is that there is error between Rio and Talon when the encoders are still then the root-cause has nothing to do with the frame rate.
If you're using LabVIEW (you didn't mention what language you were using) avoid calling Motor-Enable continuously since that will re-set the sensor position.