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For really low resolution encoders, counting ticks may not work well. But measuring time between ticks can fix that problem. Gives really good resolution for low resolution encoders.
Actually, if coded, it can get even fancier by accounting for rotational velocity and guessing the location between clicks.
I didn't understand what you mean by 'guessing' the location of clicks. Can it be much more difficult then using a timer and just pulling out the current count value every time the pin changes? If the timer overflows then assume the rotation has stopped.
But what happens if the wheel is moving so slowly that the timer overflows when measuring a tick (or if the motor stops)?
If the timer overflows then assume the rotation has stopped.