You don't need GPIOs. Instead analyse the pulse train by hardware. The eCAP modules in the PWMSS subsystems are designed for that purpose. The simplest (and most powerful) solution is to use libpruio. Check out the example pwm_cap.
BR
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So to do that we need to put the Pin PR1_ECAP0_ECAP_CAPIN_APWM_Oin input mode.Where can we find the source code of the libpruio doing that in the pru ?