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Is using MicroC/OS the only way to have nios monitor changes to the input states while running? in real time you might say. I'm a noobie thanks
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If I correctly understand what you mean, the answer is no.
You don't need a OS to monitor inputs (you mean something like PIOs, isn't it?). If you want to precisely measure time between input state switching a simple timer and possibly an interrupt, is enough. This would be more more real time than a (supposed) real time OS. All depends if your cpu needs to perform other real time tasks.