FWIW I had a good experience with Perl-Fu, which is a server run from within the gimp to respond to commands from Perl. (also you can do batch stuff with the Gimp I believe). There are also a bunch of gimp shells I think python-fu and emacs have them, I used pgshell in perl. It let me paste a series of commands on the command line and see them executed so I could confirm my perl program's image manipulation routines would drive gimp correctly. As for grayscale I don't remember, but of course you can convert the image to grayscale, use a single channel as grayscale, or just average the r,g,b yourself. That said I don't quite understand why you are splitting the image into files. Anyway above poster re PDL seems on target but if you really just want pixel values the image magick or gimp will do it for you.
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