Substrate processing apparatus including a wafer transport apparatus with a transport arm including an end effector, an arm pose deterministic feature integral to the substrate transport apparatus and disposed so that a static detection sensor of the substrate processing apparatus detects at least one edge of the at least one arm pose deterministic feature on the fly with radial motion of the transport arm, and a controller configured so that detection of the edge effects a determination of a proportion factor identifying at least a thermal expansion variance of the transport arm on the fly and includes a kinematic effects resolver configured to determine, from the detection of the edge on the fly, a discrete relation between the determined proportion factor and each different discrete variance respective to each different link of the transport arm determining at least the thermal expansion variance of the transport arm on the fly.