My hands are typing words.
Added the scripts that track the registration
I added the temperature-based objective function
The Bash script to run all DAKMATLAB runs is now written.
Added a hopefully quicker script to run DAKOTA-MATLAB codes. Unless DAKMATLAB must be re-initialized between runs.
Adding scripts that should use the unified optical parameters, and then be able to write the VTKs.
Added scripts for mu_eff calculations
Did some major repo management; deleted old stuff and added/moved needed stuff
Merge branch 'master' of https://github.com/fuentesdt/optpp_pds
Tried to debug. Didn't
Not finished, but... I've fixed the bug so now the system optimizes with the unified optics. Furthermore, I've begun working on how to script all patients. The quickest way is to introduce a 'patient_index.txt' that tracks what patient path to use.
I added the indices for the patients. The index from patient_index.txt should match the line number of the desired path from the patient_paths.txt file.
These new files are SJF's unified optics runs. Also, the unified optics runs are debugged.
Merge pull request #6 from sjfahr/master

Unified optics runs are debugged