On Thu, 2010-06-03 at 23:36 -0700, tetsu yatsu wrote:
> In Hugin, I would use the Align... button first, before running the
> nona commands. Is there a step here that does alignment that I'm
> missing?

Yes. Autopano only generates control points. Use autooptimiser to set
the image positions.

Between autopano-complete and nona, try this:
        autooptimiser -a -l -s -o panoproject.pto panoproject.pto

This page provides more details:
http://wiki.panotools.org/Panorama_scripting_in_a_nutshell#Optimising_positions_and_geometry

-James


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