Tone output on Arduino Due

Official Hardware Mega Due
8

This is the current set up of the code now. Since I'm only interested in creating one event per timer cycle I've swaped to a timer that does not use the RC compare reset, and swapped to triggering the interrupt on the RA compare. I was mistaken before, the interrupts were raised on the RC compare.

void set_up_timer(Tc *tc, uint32_t channel, IRQn_Type irq) {
    pmc_set_writeprotect(false);
    pmc_enable_periph_clk((uint32_t)irq);
    // Note using  'TC_CMR_WAVSEL_UP' rather than ' TC_CMR_WAVSEL_UP_RC'
    TC_Configure(tc, channel, TC_CMR_WAVE | TC_CMR_WAVSEL_UP | TC_CMR_TCCLKS_TIMER_CLOCK1);
    TC_SetRA(tc, channel, 500);
    // No need to set RC, only interested in creating one event.
    tc->TC_CHANNEL[channel].TC_IER=TC_IER_CPAS;     // Enable interupt on RA compare
    tc->TC_CHANNEL[channel].TC_IDR=~TC_IER_CPAS;  // Disable all other interupts.
    NVIC_EnableIRQ(irq);
}

void change_speed(uint32_t pulse_period){
  if (pulse_period == 0) {
    // If pulse period set to 0 the timer is checked to see if it is enabled. If so it is disabled.
    if ((TC1->TC_CHANNEL[0].TC_SR & TC_SR_CLKSTA) == TC_SR_CLKSTA){
      TC_Stop(TC1, 0);
    }
  }
  else {
    // If pulse period set to anythin other than 0 the timer is checked to see if it is disabled. If so it is enabled.
    if ((TC1->TC_CHANNEL[0].TC_SR & TC_SR_CLKSTA) != TC_SR_CLKSTA){
      TC_Start(TC1, 0);
    }
  }
}

void TC3_Handler() {
  TC_GetStatus(TC1, 0);
  ...doing stuff here...  
  if (pulse_period != TC1->TC_CHANNEL[0].TC_RA) {
    // If value of RA is not equal to the pulse period it is updated.
    TC1->TC_CHANNEL[0].TC_RA = pulse_period;
  }
  // The following triggers a software reset of the timer.
  TC1->TC_CHANNEL[0].TC_CCR = TC_CCR_SWTRG;
}