Solved the setup matlab workspace bug

The script works in MATLAB. I.e., I read in one 'TmpDataInput.mat' and return an objective function. But it doesn't work as part of DAKOTA and 'brainsearch.py' . Upon executing: 

'dakota workdir/Patient0006/007/opt/dakota_q_newton_heating.in'

it gets stuck on the first iteration with the following error. One thing I notice is there are double backslashes on some of the paths, suggesting path errors:

blocking fork: python ./brainsearch.py --param_file  ./workdir/Patient0006/007/opt/optpp_pds.in.1 ./workdir/Patient0006/007/opt/optpp_pds.out.1
opening database//Patient0006/007/vtk/referenceBased//temperature.0001.vtk
mrti data from database//Patient0006/007/vtk/referenceBased/ setupfile ./workdir/Patient0006/007/opt/setup.ini
/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/python2.7/site-packages/scipy/io/matlab/mio.py:266: FutureWarning: Using oned_as default value ('column') This will change to 'row' in future versions
  oned_as=oned_as)
pre-processing with setupworkspace.m

As for the bugs:
1. Some numerical data from the .mat file are actually strings, so I converted them.
2. Some numerical data were singles and I needed double precision
3. I had some path errors.