Ok, axes.apply_aspect() seems to work.  The other obvious kluge I had found
was to save the figure twice, once before and once after I accessed the axes
position.  

It seems the more elegant solution might be to use a somewhat-complicated
transform, so that that the two endpoints of a Line2d segment can have
coordinates in different coordinate systems (e.g. one end is in data
coordinates on ax1, and the other end is in data coordinates on ax2).  The
"axes zoom effect" is similar to what I'm trying to do: 

http://matplotlib.org/users/annotations_guide.html#zoom-effect-between-axes

Thanks!



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