I've done a lot of work with OpenEXR at previous $job
so I can talk you through some of that stuff but, to be honest, we were using
Apple's Shake and/or custom tools to do most of our manipulation.
Fortunately, since Apple have decided to give up on Shake it's now dropped down in price to about $200. Unfortunately that's only for Macs. Unless things have changed the Linux version is still about $4000 per licence.
Also, Shake is unlike any Image Manipulation program you've ever come across - it's designed for compositing over a timeline and the interface is a DAG. You drop IO Nodes ((multiple) FileIn and (multiple) FileOut) into the script and then start dropping in other nodes (image mult, blur etc etc) in. Writing your own plugins is pretty easy and very powerful - they can either be a collection of collapsed nodes or written in C++.
Open Source wise there's a couple of GPL compositing tools that might help - Cinelerra
(of which there are several different forks - it's a bit complicated) or the tool previous known as FilmGimp and no known as CinePaint
If you want - I can talk you through some of that or, if what you want is some standard pipeline software, then code to read OpenEXRs is actually pretty easy and I can help you with that.