Quadcopter using Cyclone II. How to implement gyro inputs and ESC outputs?

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I already have a working quadcopter with a arduino based flight controller with gps hold etc

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My suggestion would be to already use what you have, and just work toward substituting the FPGA controller for the arduino controller.

i.e. revise your goal to become the development of a drop-in replacement for what you already have in your working system.

Not sure if the new inexpensive Altera board with Arduino header might make things easier for that or not.

http://www.altera.com/products/devkits/altera/kit-terasic-cyclone-v-gx-starter.html