Abstract: A disk drive includes at least one reference track having a plurality of sectors which are read and averaged in order to compensate for spindle offset. The disk drive has a head position servo system controls a head position actuator and includes a polyphase optical encoder which is initially calibrated by reference to dark current values and recalibrated periodically by reference to the reference track. Preferably, at least two reference tracks are located at the extremes of the radial displacement of the actuator so that variations in gap dimension between a scale mounted to the actuator and a fixed reticle-mask over a photodetector array of the encoder may be measured and compensated for. The method for initializing the drive and for periodically updating its calibration of the encoder and the head position servo is also described.