Frequency Counting on a Raspberry PI

I am trying to count a square wave on a Raspberry PI.

I tried a variety of approaches:
http://abyz.co.uk/rpi/pigpio/examples.html (Freq counter 1 and 2)
http://www.dnacoil.com/tools/measuring-light-intensity-with-the-tsl-235-and-a-raspberry-pi/#comment-2850

Both approaches seem to top out around a frequency of 300 which is not useful for direct light conditions .(Ok for low light.)

Data sheet of sensor: TSL235

Is there a better method for getting a square wave, 50% duty cycle on the PI