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' .
I corrected the execute.txt (the script that runs all) and short_execute.txt (the script that does not start/stop DAKMATLAB everytime).
Now both execute scripts will collect the objective functions.
I have a script that writes all of the VTK files.
I added the files for making VOIs. I also am adding a VOI.mat to see if Git can handle a *.mat file.
Added VOI stuff for only Patient 2, 000
I have added the VOI's into the workdir for all Patients and numbers.
I've made corrections for two errors. First, ParaView and MATLAB don't agree on row/column major conventions and I corrected that in fast_temperature_obj_fxn.m . Second, the VTK reader part of fast_temperature_obj_fxn.m needs to know the exact number of VTK files, so I made a text file listing them: VTK_patient_times.txt .
Merge pull request #7 from sjfahr/master

updates