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Originally Posted by slijin
I suggest you study the RDK's specs on the limit switch GPIOs to verify that they can actually handle the frequency resolution that effective encoder input demands.
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FWIW, from LM3S2616 datasheet p348:
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Each GPIO port is a separate hardware instantiation of the same physical block. The LM3S2616 microcontroller contains five ports and thus five of these physical GPIO blocks.
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The Jag encoder inputs are on port C, and the limit switches are on port B.