>>Anyway, the code for the ISR is big,
>
> That is always a bad sign ...
>

This is not a true statement. I have several times developed systems that 
required accurate timing for complex functions ( multiple simultaneous 
software UARTs, software video generation) in which nearly all CPU time, and 
a large proportion of code were in a (timer) interrupt handler. One useful 
trick here is that you may be able compute the correct outputs for interrupt 
N+1 during interrupt N, save them, and them output them at the very start of 
interrupt N+1. This can result in (on a PIC at least!) ZERO jitter.

Bob Ammerman
RAm Systems


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