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Contolling number of pulses with 16bit timer

Hi,

I'm using ARM processor of TIMER16 bit and getting PWM signal
by varying prescaler register and keepingthe values constant of MR3,
so I had set a time and pulses generated continuously and stopped within that time,
and i'm using a counter loop with this loop the pulses are generated
very randomly.

So can I count for example 100 pulses or 200 etc..within the selected
time and stop.

I tried using IRQ of 16 bit timer, but it's not working correctly.

Kindly give some suggestion on this.