67.6.16.6 Detecting a Missing Index Pulse
To detect a missing index pulse due contamination, dust, etc., the TC_SR0.CPCS flag can be used. It is also possible to assert the interrupt line if the TC_SR0.CPCS flag is enabled as a source of the interrupt by writing a ‘1’ to TC_IER0.CPCS.
The TC_RC0.RC field must be written with the nominal number of counts per revolution provided by the rotary encoder, plus a margin to eliminate potential noise (ex: if the nominal count per revolution is 1024, then TC_RC0.RC=1026).
If the index pulse is missing, the timer value is not cleared and the nominal value is exceeded, then the comparator on the RC triggers an event, TC_SR0.CPCS=1, and the interrupt line is asserted if TC_IER0.CPCS=1.
The missing index pulse detection is only valid if the bit TC_QISR.DIRCHG=0.