Here's a quick demonstration of how to capture complete Bode plots with a Linux C program and an Agilent MSO-X 2000 series scope. Really it's just an automated alternative to sitting down with your scope, a pad and a pencil.
Link to more information and the source code: http://geekysuavo.github.io/usbtmc-bode
Dave Jones has a nice video on a quicker way to capture Bode amplitude plots here: http://www.youtube.com/watch?v=uMH2hGvqhlE
Enjoy!
~ Brad.
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Bode plotting with Linux and an Agilent MSO-X | NatokHD