High brightness electron bunches will be guided in the future Free Electron Laser (SwissFEL) at the Paul Scherrer Institute (PSI) by several hundred magnets. The SwissFEL machine imposes very strict requirements not only at the field quality but also at the mechanical and magnetic alignments of these magnets. To ensure that the magnet specifications are met, and to develop reliable procedures for aligning magnets in the SwissFEL and correcting their field errors during machine operations, the PSI magnet test system was upgraded. The upgraded system is a high precision measurement setup based on Hall probe, rotating coil, vibrating wire and moving wire techniques. It is fully automated and integrated in the PSI controls. The paper describes the main controls components of the new magnet test setup and their performance.