An electromagnetic wave having a phase velocity and an amplitude is provided by an electromagnetic wave source to a traveling wave linear accelerator. The traveling wave linear accelerator generates a first output of electrons having a first energy by accelerating an electron beam using the electromagnetic wave. The first output of electrons can be contacted with a target to provide a first beam of x-rays. The electromagnetic wave can be modified by adjusting its amplitude and the phase velocity. The traveling wave linear accelerator then generates a second output of electrons having a second energy by accelerating an electron beam using the modified electromagnetic wave. The second output of electrons can be contacted with a target to provide a second beam of x-rays. A frequency controller can monitor the phase shift of the electromagnetic wave from the input to the output ends of the accelerator and can correct the phase shift of the electromagnetic wave based on the measured phase shift.