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Another issue with encoders to keep in mind is the "sense" of forward and backwards. Especially if using the encoders with jaguar PID loops, but even with cRIO PID loops, the encoders need to be increasing when the motor is going forward, and the control input sense of forward needs to match the encoder. And the jaguar's sense of positive voltage needs to match also. You may need to reverse the A and B lines of the encoder, or the polarity of the motor, to get these things all having the same definition of "forward". If you add limit switches to the mix, the forward and reverse limit switches must also correspond.
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