Cooling Fan RPM Sensing

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i'm using pwm on brushless cooling fan computer. put 680uf capacitor on pwm output smooth out voltage time gets fan. however, rpm sensing doesn't work out @ all! using pulsein() function read rpm. @ full speed works, @ low speed reads part of time, @ medium speed shows rpm being faster full speed. makes no sense. there possible way make work pwm?

unless pwm interferes pulsein(), can't think of atm.  see code?  waiting go high low or low high?  taking multiple readings , averaging them?


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