Frequently I need to change the projection of an image, or transform
the image to be in a different region of the existing projection.
However I haven't been able to get this to work with EXR (32 bit)
files. According to the documentation however, this should be
possible.

Here is an example 90x90 rectilinear nadir shot:
http://df.arcs.org.au/quickshare/2f41ffc997134ced/Nadir_recti.exr
I tried to transform it to an equirectangular image without moving it
at all with this file:http://df.arcs.org.au/quickshare/
9f4b76a5411bf677/Nadir-ZnN.pto
This was the result after hacking the make file:
http://df.arcs.org.au/quickshare/20c83fc6f724fd57/Nadir-ZnN0000.exr
(all black)
I also tried to transform it to equirectangular image and moving pitch
-90 with this pto file: 
http://df.arcs.org.au/quickshare/2076ceafc68bba43/Nadir-equi.pto
By default both pto files attempt to make a TIFF_m output.

I have found that Hugin creates a completely black output image of too
small a file size.
Modifying the pto.mk file or running nona from the command line
haven't worked for me either (I struggled to find enough
documentation).
This may be related to the issue discussed here:
http://groups.google.com/group/hugin-ptx/browse_thread/thread/4bc638b17e5bf799

Any solution would be good, however I was hoping for either a command
line instruction I could run on my file, or a pto.mk template where I
could edit the name of the source file and have it transform the
image.

Why do I need to do this?
Images that have XYZ translations can only be stitched in the centre
180 degrees of an Equi. So I stitch that part of the image (usually
the nadir), edit it in an image editor if necessary, and then attempt
to transform it to be along the bottom of a traditional (horizon runs
along the middle of the image) 360x180 equirectangular. This is
following the advice on this web page:
http://wiki.panotools.org/Hugin_FAQ#Patching_nadir_shots_using_XYZ_mosaic_mode_cuts_the_photos_in_half
Sometimes I transform the nadir to be 90 degrees to the right of its
previous position for editing as per this web page by Peter Nyfeler:
http://wiki.panotools.org/Edit_zenith_and_nadir_in_one_go_with_PTGui

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