update to icon slurm script

cluster/indivICONGPU_v3.slurm

@@ -21,6 +21,7 @@ k2correct="${baseDir}/scripts/processing/correctK2Lines.py"
 mcorrBin="${baseDir}/bin/motioncor2/MotionCor2_1.2.3-Cuda100"
 iconGPU="${baseDir}/bin/ICON_GPU_v1.2.9_CentOS64/bin/ICON-GPU"
 iconMask="${baseDir}/bin/ICON_GPU_v1.2.9_CentOS64/bin/ICONMask3"
+iconPreproc="${baseDir}/bin/ICON_GPU_v1.2.9_CentOS64/bin/ICONPreProcess"
 
 tomoProc="${baseDir}/tomoProc"
 rawDir="${tomoProc}/raw"
@@ -31,6 +32,9 @@ stackDir="${tomoProc}/tiltStacks"
 baseDir=${1%%.*}
 mkdir -p $baseDir
 
-${iconGPU} -i $1 -t $2 -iter 80,160,80 -thr 0 -o ${baseDir} -s 0,3837 -d 1
+
+$iconPreproc -i $1 -t $2 -th 750 -o ${baseDir}_ipp.mrc
+
+${iconGPU} -i ${baseDir}_ipp.mrc -t $2 -iter 80,160,80 -thr 0 -o ${baseDir} -s 0,3837 -d 1
 
 ${iconMask} -i ${baseDir}/reconstruction -t $2 -th 750 -cf ${baseDir}/crossValidation/crossV.frc -ff ${baseDir}/crossValidation/fullRec.frc -o ${baseDir}_icon.rec -s 0,3837