A method and apparatus are provided for compensating for spatial non-uniformities in a printer by deriving a true spatial non-uniformity tone response curve (TRC) that characterizes the printer in terms of color output variation for each addressable pixel location in a spatial range. The “true average” tone response curve is determined for a color channel. A prediction of the true response as a function of the spatial location is derived by printing and scanning a specially designed halftone-independent target of binary patterns. The predicted tone response curve for each color channel and halftone is predicted using a binary printer model, wherein the “predicted tone response curve” provides a model based approximation of the actual response for each addressable pixel location in the spatial range. Also stored is an “average predicted tone response” by averaging the “predicted tone response curve” over the spatial range of the printer.