Patent Number: 
Section: claims

1. A system comprising:a proton therapy system comprising a plurality of sub-systems including:a super-conducting magnet sub-system;a cryogenic-cooling sub-system;a vacuum sub-system;a radio frequency sub-system; andan ion source;wherein an operation of the proton therapy system comprises a plurality of operation states, the plurality of operation states corresponding to a plurality of power states of the plurality of sub-systems,wherein the proton therapy system is configured to at least partially automatically perform the plurality of operation states in sequence to prepare the proton therapy system to generate and extract a proton beam. 2. The system of claim 1, wherein the plurality of operation states activate the plurality of sub-systems in sequence. 3. The system of claim 1, wherein the plurality of operation states comprise an off state, a first standby state, a second standby state, a radio frequency ready state and a beam ready state. 4. The system of claim 3, wherein the off state comprises a proton therapy system operation state wherein each of the plurality of sub-systems are deactivated except for the cryogenic-cooling sub-system. 5. The system of claim 3, wherein the first standby state comprises a proton therapy system operation state wherein the cryogenic-cooling sub-system and vacuum sub-systems are activated and all other sub-systems of the plurality of sub-systems are deactivated. 6. The system of claim 3, wherein the second standby state comprises a proton therapy system operation state wherein the super conducting magnet sub-system, the cryogenic-cooling sub-system, and the vacuum sub-system are activated and all other sub-systems of the plurality of sub-systems are deactivated. 7. The system of claim 3, wherein the radio frequency ready state comprises a proton therapy system operation state wherein the super conducting magnet sub-system, the cryogenic-cooling sub-system, the vacuum sub-system, and the radio frequency sub-system are activated, and all other sub-systems of the plurality of sub-systems are deactivated. 8. The system of claim 7, wherein the radio frequency sub-system is activated in a reduced power state during the radio frequency ready state. 9. The system of claim 3, wherein the beam ready state comprises a proton therapy system operation state wherein each of the plurality of sub-systems are activated and operating at a plurality of pre-defined set values. 10. The system of claim 1, wherein the plurality of sub-systems further comprises a vertical deflector plate sub-system configured to generate an electric field in a plurality of vertical deflector plates comprised in the cyclotron to influence a trajectory of the proton beam extracted from the proton therapy system. 11. The system of claim 10, wherein the electric field is generated in the plurality of vertical deflector plates by supplying a voltage through the vertical deflector plates. 12. The system of claim 1, wherein the plurality of sub-systems further comprises a phase measurement sub-system comprised in the proton therapy system and configured to correct an effect of beam phase shifts affecting the proton beam. 13. The system of claim 12, wherein the a phase measurement sub-system comprises a non-destructive beam phase detector. 14. The system of claim 12, wherein the a phase measurement sub-system comprises a phase control loop configured to tune a magnetic field generated by the super-conducting magnet sub-system. 15. The system of claim 14, wherein the phase control loop tunes the magnetic field generated by the super-conducting magnet sub-system by measuring the effect of the beam phase shifts affecting the proton beam with respect to a radio frequency generated by the radio frequency sub-system during operation of the proton therapy system. 16. The system of claim 1, wherein the proton therapy system comprises a cyclotron. 17. A method for automatic cyclotron initialization comprising:measuring a temperature of a plurality of components in a super-conducting magnet comprised in a cyclotron;determining a current configuration of the super-conducting magnet based on the temperature;automatically setting a power supply of the super-conducting magnet to the determined current configuration;generating a proton beam in an ion source comprised in the cyclotron with a super-conducting magnet operating with the determined current configuration; andextracting the proton beam. 18. The method of claim 17 further comprising monitoring the extracted proton beam in a phase control loop. 19. The method of claim 18 wherein the extracted proton beam comprises a beam phase, and wherein monitoring the extracted proton beam comprises measuring the beam phase with respect to a radio frequency system of the cyclotron in a phase measurement system. 20. The method of claim 19 wherein monitoring the beam comprises utilizing a signal of a non-destructive beam phase detector. 21. The method of claim 19 wherein monitoring the beam comprises measuring and quantifying an effect of beam phase shifts due to magnetic field drifts. 22. The method of claim 19 further comprising tuning the extracted proton beam monitored in the phase control loop. 23. The method of claim 21 wherein tuning the beam comprises tuning an a beam current stability of the cyclotron by stabilizing the effect of the beam phase shifts due to magnetic field drifts. 24. The method of claim 21 wherein tuning the beam comprises resetting the magnet current to a desired value. 25. A method for automatically refining operation of a cyclotron, the method comprising:centering a proton beam produced by the cyclotron;tuning an extraction efficiency of the proton beam produced by the cyclotron; andrefining positions of a plurality of radial phase slits comprised in the cyclotron,wherein the centering, the tuning and the refining are performed automatically by a control system of the cyclotron. 26. The method according to claim 25 wherein automatically centering the proton beam comprises:measuring an oscillation of a current of the proton beam to determine a precession of the proton beam; andreducing the precession of the proton beam. 27. The method according to claim 26, wherein the oscillation of the current is measured by an internal straight probe. 28. The method according to claim 26, wherein the cyclotron comprises a first plurality of trim rods, and wherein reducing the precession of the radial beam comprises using the first plurality of trim rods to adjust an amplitude and a phase of a first harmonic of the generated magnetic field corresponding to the oscillation of the current of the proton beam. 29. The method according to claim 25, wherein automatically tuning an extraction efficiency comprises analyzing a beam current of the proton beam and resetting values corresponding to a second plurality of trim rods and voltages in a plurality of extraction deflectors to pre-defined values. 30. The method according to claim 29, wherein automatically tuning an extraction efficiency further comprises exciting the precession of the proton beam prior to an extraction of the proton beam with a second plurality of trim rods. 31. The method according to claim 29, wherein automatically tuning an extraction efficiency further comprises adjusting the voltages in a plurality of extraction deflectors, the plurality of extraction deflectors configured to direct a trajectory of the extracted proton beam. 32. The method according to claim 25, wherein the automatically refining positions for the plurality of radial phase slits comprises:determining a plurality of beam current measurements at the plurality of phase slits, the plurality of phase slits being positioned at a first plurality of radial positions;calculating a second plurality of radial positions based on the plurality of beam current measurements; andautomatically re-positioning the phase slits at the second plurality of radial positions.