An encoder system includes a configurable detector array, wherein the configurable detector array includes a plurality of detectors. In an embodiment, the encoder system includes an application-specific integrated circuit (ASIC). The encoder system may also include a memory operable to store a partition map that defines a state for each of the plurality of detectors. In an embodiment, the memory includes a non-volatile memory. The encoder system may also include a controller, such as a microcontroller, operable to read from the memory the partition map and to adjust the partition map according to a misalignment measurement before configuring the configurable detector array. The encoder system may also include an emitter operable to generate a flux modulated by a motion object, wherein the configurable detector array is operable to receive the flux and generate respective current outputs for each of the detectors in response to the flux.