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The question I have is that when you set your setpoint that the code will try to go to do you place the setpoint in the motor output or the sync group/parameters slot below it in the motor set output vi.
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I don't understand your question.
Check out the Talon SRX Software Reference Manual to get an idea about what is necessary to leverage the closed-loop feature. It's more then calling the motor-set VI. You have to select your sensor (and may need to software-reverse it), select gains, select the control mode (position or velocity), and then you can set the target and watch it servo.