A functional electrical stimulation system for generating a data file storing stimulation patterns that can be provided to a stimulator is described. The system includes a host computer system for producing a data structure or data file that describes the patterns and a portable stimulator that using the data structure or data file applies electrical pulses to electrodes carried by a patient. The host computer system and the stimulator system each have a memory storing a table having control and pattern generation information with indexes into a table that separately stores electrode characterization data for each electrode used by the portable stimulator.