Methods and systems are presented for calibrating or characterizing a color printer or determining the color response of a color printer to combat spatial non-uniformity, in which color patches are printed on a test page according to an input matrix of input color in a printer-dependent-color space and the test page is measured to provide a corresponding output matrix of output color in a printer-independent-color space. Initial forward and inverse color transforms between the input and the output colors are generated based on the input and the output matrices. The output values are mapped to the input color space based on the initial inverse transform to form a feedback matrix, and spatial non-uniformities present in the printed test page are estimated according to noise values derived from the input matrix and the feedback matrix. The input matrix is modified according to the estimated spatial non-uniformity to form a modified input matrix of input color, and final forward and inverse transforms are generated for the color printer according to the modified input matrix and the output matrix.