What could be the reason for this flickering of this periodic pulse train?

Question

I try to create periodic pulse train for the clock signal in application. I use an arduino nano board. But I noticed in scopes I see flickering pulse train behaviour. It is very hard to explain this by text, so I have uploaded to YouTube:

https://www.youtube.com/watch?v=G51mplB87Cw

As you can see in the video, the pulse train is not very stable it is flickering randomly. When I save the data as CSV or stop the screen I get the following pulse train sometimes I can catch it like below:

So at this particular point above scope shows some pulses are missing.

Here is the code I use to produce the pulses:

const int CLOCK_PIN = 5;

void setup() {
  pinMode(CLOCK_PIN, OUTPUT);

}

void loop() {      

  for (int i=0; i<25; i++) {    

    //digitalWrite(CLOCK_PIN,LOW);
    PORTD &= ~(1 << 5); // clock pin goes low    
    delayMicroseconds(2);    
    //digitalWrite(CLOCK_PIN,HIGH);
    PORTD |= (1 << 5); // lock pin goes high    
    delayMicroseconds(2); 
  }

    delay(50);
 }

I couldn't figure out whether this is scope artefact or related to the code. What could be the reason for this? This is happening both in Auto and Normal trigger mode.

Answer 1

Interrupts are occurring while your code is running. The time required to execute the interrupts is significant compared to your desired delay of 2 microseconds. This disturbs your desired timing.

Your options include disabling interrupts while generating this clock signal, but that is likely to have undesired and unintended consequences. A better idea would be to find some way to generate the clock using only hardware resources rather than a delay loop.

Answer 2

Don't use delayMicroseconds, it's not an accurate way to timing. Although they try, as you can see in the code.
See if you can make your signal with hardware timers.

Answer 3

I'm not sure if @ElliotAlderson has the correct answer, hence here my 2 cents. In the code you posted there shouldn't be running interrupts in the background as you simply don't use one. The delay-functions are blocking ones, not based on interrupt.

My guess is that the flickering is because you toggle for 25 times and then delay for 50ms. Repeating this cycle. Could it be that it is this 50ms you see? --> EDIT: never mind, the delay on the scope trace isn't that long.

As for a fix, I'd use a timer in PWM-mode so you can start it in setup() and let it run without additional code in loop() until it's not needed anymore.