This is an old post, preserved for reference.
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I built a Simple Arduino Frequency Counter last year, and it's been quite a useful project. Over the time it's been in use, I've been tinkering with it to improve the display and accuracy. This started off with a simple display of the frequency in Hz. I modified the code slightly to add some commas to make it easier to read:
I've altered that slightly, and now what it does is enable an interrupt on change on a pin. When that is triggered, it stores the start time. It then changes the interrupt to go to a different routine, and when that is called, counts pulses and stores the time of the last pulse. It then waits one second again and calculates the frequency, based on the time between the first and last pulse, to improve accuracy. As per the follow up to that forum post, I've taken into account ignoring the initial isr call as this may happen if the pin is high when the interrupt is enabled. I've done this with a third isr, again trying to keep the code in there down. The new code can be downloaded here.