An X-ray system configured to strike an electron beam pulse against a target and for providing alternating X-ray pulses of first and second energies with controlled dose per pulse comprising a linear accelerator having resonance with a bandwidth, a control processor, a power supply, a modulator, a pulse transformer, a magnetron, a mechanical tuner, wherein the control processor is configured to send control signals to the power supply and to the modulator, wherein the modulator is configured to receive an output from the power supply and to output a high voltage to the pulse transformer, the pulse transformer being configured to supply high energy pulses to the magnetron, wherein the magnetron is configured to supply the linear accelerator with RF energy at alternating first and second RF power levels with corresponding first and second frequencies, wherein the mechanical tuner is configured to control the resonance frequency of the magnetron, an electron gun driver, operating independently of the magnetron by being responsive to a further control signal from the control processor, said further control signal being synchronized with a control signal sent from the control processor to the modulator, the electron gun driver configured to supply to the linear accelerator alternating pulses (310, 315) of first and second beam currents with the pulses of each different beam current synchronized to occur within an envelope created by an RF pulse (300, 305) of the corresponding RF power levels, wherein the linear accelerator has an effective Q between 2000 and 4000, and wherein the bandwidth of the resonance of the linear accelerator allows coupling of the magnetron output to the linear accelerator at the first and second RF power levels such that the first and second energies of the X-ray pulses are at least 1 MeV apart and less than 5 MeV apart with controlled dose per pulse for pulses of both first and second energies. a linear accelerator having resonance with a bandwidth, a control processor, a power supply, a modulator, a pulse transformer, a magnetron, a mechanical tuner, wherein the control processor is configured to send control signals to the power supply and to the modulator, wherein the modulator is configured to receive an output from the power supply and to output a high voltage to the pulse transformer, the pulse transformer being configured to supply high energy pulses to the magnetron, wherein the magnetron is configured to supply the linear accelerator with RF energy at alternating first and second RF power levels with corresponding first and second frequencies, wherein the mechanical tuner is configured to control the resonance frequency of the magnetron, an electron gun driver, operating independently of the magnetron by being responsive to a further control signal from the control processor, said further control signal being synchronized with a control signal sent from the control processor to the modulator, the electron gun driver configured to supply to the linear accelerator alternating pulses (310, 315) of first and second beam currents with the pulses of each different beam current synchronized to occur within an envelope created by an RF pulse (300, 305) of the corresponding RF power levels, wherein the linear accelerator has an effective Q between 2000 and 4000, and wherein the bandwidth of the resonance of the linear accelerator allows coupling of the magnetron output to the linear accelerator at the first and second RF power levels such that the first and second energies of the X-ray pulses are at least 1 MeV apart and less than 5 MeV apart with controlled dose per pulse for pulses of both first and second energies.