Hello Jonathon,
Your UAV is flying at constant altitude, but is the ground surface planar,
i.e. flat?
You are essentially collecting images to stitch in mosaic mode, in which
case the surface should ideally be planar, but that does depend on the
altitude and the variation in elevation of the surface.
If the variation in elevation is small and altitude is large, stitching in
mosaic mode should give a reasonable result.
Others who frequent this forum have done quite a bit of work in perfecting
methods of stitching shots of large maps which are not exactly flat due to
creases from folds. Some of the experience with that may be applicable,
not sure.
A tutorial on hugin's mosaic mode is here
<
http://hugin.sourceforge.net/tutorials/Mosaic-mode/en.shtml> if that is
of any help to you.
An alternate approach is to use a GIS, such as GRASS, which has features
specifically for your work.
Cheers,
--
Regards,
Terry Duell