The response of a speaker is typically measured with a calibrated reference mic. Even the mic isn't trully flat response but it is close and there is a way to offset the measurement results with the Mic's response curve. A sine wave swept from 20hz to 20khz can be used. Pink or white noise can also be used.
For us, the best method is to compare various rigs against your favorite studio headphones or reference monitors. The mist important thing is for your rigs to sound good whether run through direct PA connection, your FRFR stage speakers of choice, or your reference headphones. When you have achieved this, your tones will be accurate and translate well.
On the other hand, if you have a severely colored speaker and compensate in your rigs to correct it, your tones will be unbalanced to everything else (not translate well).
Remember that guitarists are tone snobbs. We have an ideal tone in our heads that we strive to achieve...even with a traditional amp. Unfortunately, once the signal hits the mixer, its out of our hands. Our perfect stage tone is altered. Working with the house eq to get the PA flat for a given room helps. Ultimately, the audience won't care if its not exactly the same....it hardly ever is anyways!
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