How is the signal frequency measured in Atmega?

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How is the signal frequency measured in Atmega? In particular, how is the signal frequency (sinus) measured in Atmega8?

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You need to read the signal using an ADC pin of the ATMega8, sample it at the desired rate, and apply a FFT algorithm to determine the sine wave frequency.

Another way might be explained here: http://www.atmel.com/Images/doc8365.pdf

Best regards, Alex Tofan