1. A computer-implemented method for inversion of measured geophysical data to determine a physical properties model for a subsurface region, comprising: (a) obtaining measured geophysical data from a geophysical survey of the subsurface region; (b) inverting the measured data by iterative inversion involving simultaneous encoded-source simulation of survey data representing a plurality of survey sources or receivers if source-receiver reciprocity is used, wherein source or receiver signatures in the simulation are encoded, resulting in a simulated simultaneous encoded-source or encoded-receiver gather of geophysical data, the inversion process involving updating an assumed physical properties model to reduce misfit between the simulated simultaneous encoded-source or encoded-receiver gather and a corresponding simultaneous encoded-source or encoded-receiver gather survey data encoded with the same encoding functions used in the simulation; wherein in one or more of the iterations, different encoding functions are used compared to the preceding iteration; and (c) downloading the updated physical properties model or saving it to computer storage.