count and send pulses simultaneously

Official Hardware Mega Due
2

Hi everyone,

I'm using an Arduino Due to count and send out pulses. The sending out pulses are suppose to last for 1000 microseconds. How do I keep counting the incoming pulses at the same time?

Here is the code:

int encoderCount = 0;
boolean sampledPin;
boolean lastVal=0;

void setup() {
// put your setup code here, to run once:
pinMode(3,OUTPUT);
pinMode(22,INPUT);
}

void loop() {
// put your main code here, to run repeatedly:

while(true)
{
sampledPin = !!(PIOB->PIO_PDSR & (1<<26));

if(lastVal ^ sampledPin)
{
encoderCount++;
lastVal = sampledPin;
}

if (encoderCount == 3000 )
{
encoderCount = 0;

PIOC->PIO_SODR=1<<28;
delayMicroseconds (1000) ;
PIOC->PIO_CODR=1<<28;
}
}

}