I have scanned a newspaper article which was larger than the scanner glass. Each page was scanned twice: the top and the bottom parts, where the middle part appeared in both images.

Is there a way to quickly match and stitch these scanned images, preferably using CLI? The panorama stitching tools I know require lengthy configuration, which is mostly irrelevant: lens size, focus, angle etc.

Hugin has a solution for this issue, but it isn't practical for batch jobs.