I've set up a .bat file to run hugin.

bat file - pano_fix.bat

rem Build panorama from call
rem Arg 1 - resultant file name
rem Arg 2 - name of files to be used in pano
rem
pto_gen  -o %1.pto %2.jpg 
cpfind -o %1.pto %1.pto
rem hugin_executor  --assistant %1.pto
celeste_standalone -i %1.pto -o %1.pto
cpclean -o %1.pto %1.pto
rem linefind -o %1.pto %1.pto
autooptimiser -a -l -s -m  -o %1.pto %1.pto
pano_modify --canvas=AUTO --crop=AUTO -o --center --straighten %1.pto 
rem hugin_executor --stitching --prefix=prefix %1.pto
nona -m TIFF_m -o %1 %1.pto
enblend -o z%1.tif %100*.tif 
del %1*.tif
rem convert zp_%1.tif -resize 7000x zp_%1r.jpg

Call of file:
pano_fix result afile0*

In using this approach, the specific images to be compiled into the pano 
are given names afile01.jpg afile02.jpg etc. This can easily be done using 
imagemagick commands in the same .bat file which calls the pano constructor.
 

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