A method of inkjet printer operation identifies a problem with an inkjet printer using a comparison of an index for a printhead map identifying inoperative inkjets in a printhead with indexes for clusters of extracted feature descriptors corresponding to printhead maps for printheads having inoperative inkjets stored in a dictionary in a database operatively connected to a controller in the inkjet printer. The dictionary is developed using unsupervised cluster analysis of datasets comprised of printhead maps identifying inoperative inkjets in a plurality of printheads.