Merge pull request #6 from sjfahr/master

Unified optics runs are debugged
WIP: fast QOI
This hotfix branch for fuentes_merge_check is bugged! This commit is so I can change branches to the working one, i.e. the 'local' branch.
I've made sure it works on the 'local' branch and will see if I can fix the 'fuentes'* branch.
It's fixed. The problem was that my 'f.m' file would change the patient_index.txt every DAKOTA iteration. Instead, only the Bash script should. Now I can merge all these changes and overwrite the 'local' branch.
Merge branch 'master' into local

Conflicts:
	analytic/f.m
I don't need the index files to be tracked in the repo.
I regressed and broke it, but then fixed it. It had to do with the 'char' command and getting the patient path right in 'f.m' .