echo "this will delete all tif files in subfolders\npress enter to continue"
read upscale

#iterate over folders
for dir in ./*/
do

cd $dir

echo $dir

#align images, the "2>/dev/null" part discards warnings
#call it twice since shell is case sensitive
align_image_stack -a OUT *.jpg 2>/dev/null
align_image_stack -a OUT *.JPG 2>/dev/null

#find median, write to base folder
convert *.tif -evaluate-sequence median ../${dir%*/}.jpg

#delete temporary files
rm *.tif

cd ..

done