Commit 561c2019 authored by Adrian Nievergelt's avatar Adrian Nievergelt

update to icon slurm script

parent 86a4ee80
File mode changed from 100644 to 100755
File mode changed from 100644 to 100755
......@@ -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
File mode changed from 100644 to 100755
File mode changed from 100644 to 100755
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