AllRunContAngle

#!/bin/bash
#set -ex

#~ ImageNames=" BLSWa_8bit_500_500_500   "
ImageNames=$(ls *.mhd | sed 's/.mhd//g')
echo $ImageNames

################


#msSrc=/opt/contactAngleAhmedAlratrout2017/apps
#source $msSrc/contactAngle/bashrc
# Figure out Paths assuming this file is in src/ContactAngle folder
myCurrentDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )/../../src" && pwd )
: ${msSrc:=$myCurrentDIR} ; export msSrc
[ -n "$WM_PROJECT" ] || echo "WM_PROJECT not set, sourcing $msSrc/script/bashrc"
[ -n "$WM_PROJECT" ] || source $msSrc/script/bashrc


for ImageName in $ImageNames ; do
 echo "analysing $ImageName"
 if [ -d $ImageName ] ; then 
   echo "folder $ImageName exist, delete to rerun"
 else
   mkdir $ImageName
   if [ -d system ]; then cp -r system $ImageName/;
   else                   cp -r $msSrc/ContAngle/tutorial/system $ImageName/; fi
   
   cp $ImageName.* $ImageName/

   sed -i 's/subvolume/'"$ImageName"'/g' $ImageName/system/meshingDict



   echo "(cd $ImageName/ && voxelToSurfaceML) "

  (cd $ImageName/ && voxelToSurfaceML )
  (cd $ImageName/ && surfaceAddLayerToCL)
  (cd $ImageName/ && calcContactAngleUnifKc )
  (cd $ImageName/ && more contactAngles.txt >>Kc.txt)
  (cd $ImageName/ && more Kc.txt >> *_Layered_Smooth.vtk)
  echo $?

 fi
done