#5 in System theory books
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Reddit mentions of System Identification: A Frequency Domain Approach
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I would recommend Frequency Identification, which is explained quite well in Schoukens et al. (http://www.amazon.com/System-Identification-Frequency-Domain-Approach/dp/0470640375) Their accompanying Matlab examples are free to download and actually explain the procedure quite nicely.
Basically, one puts noise on the input, and measures noise on the output. This will give you the transfer function. More interesting things happen if you want to do this while the quad rotor is flying.