The method is simple enough. I happen to have three guitars with the exact same mini Humbucker pickups. The spacing from the neck and bridge are nearly the same as well. All three are made of different woods. In the studio I plug in direct with only a preamp to get a strong clean tone and play a chord progression of maybe a minute and record all three guitars playing those same chords.
Next I use an analyzer program called Har Bal which can sample the entire waveform and give you a sum total of all the frequencies that wave file produced and it gives you a static shot which can be copied and posted.
I can even open a reference file and compare file A&B - B&C - and A&C so you can see the two waveforms side by side and see exactly where those differences in frequency are produced.
I then do the same thing using overdrive on the guitars using the exact same setting and simply stopping the recorder, unplugging one guitar and plugging in another.
The only thing that may change is the playing dynamics strumming harder on one guitar or another, but that doesn't/shouldn't change the frequency response the analyzer sees.
I can also connect a contact and record the contact mic and pickup at the same time. What you get with that is a wider frequency response in most cases, but it is dependent on where you place the contact mic. I usually just clip it to the bridge and get a decent acoustic tone.
When you overlay the pickup and contact mic you can see where the frequencies from the pickup and contact mic are similar. The Pickups high frequencies will roll off on the high side and the piezo extends up higher so you cant compare the frequencies up above 6K . The Piezo tends to have sharper peaks as well, but like I said the frequencies do align quite well, they just aren't as large from a pickup because the pickups inductance smooth's the peaks.
When I post the pictures and the wave files with no overdrive, and challenge people to use their ears to match the instruments, I got about 50% or better correct identification here on HC last time.. On the driven guitars, I got one out of a dozen, and I cant be sure if that person has good ears or just guessed properly. The three guitars had the same pickups which made identifying them hard, but there was a difference in the amount of bass and brightness that could be heard so there is something to work with. Later I revealed the instruments and wood types and people were surprised that those woods could produce those tones.
I may be in the studio tonight. If so I'll try and remember to make up a fresh batch of files to post. This site has been pretty slow and it may be a fun challenge for everyone. I will again remain neutral until everyone has had a chance to hear and see the differences between the files. Then I'll let you all tell me if I'm hearing things that don't exist, or whether others need to spend more time training their ears.