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Commit 86a4ee80 authored by Adrian Nievergelt's avatar Adrian Nievergelt

script to do icon processing

parent 25463191
#!/bin/bash
#SBATCH -J iconGPU-reconst # the job's name
#SBATCH -t 30:00:00 # max. wall clock time 5s
#SBATCH -n 1 # number of tasks
#SBATCH -N 1
#SBATCH -c 2
#SBATCH -o /projects/project-nieverge/logs/iconGPU-reconst_%j.out # output file
#SBATCH --partition=gpu
#SBATCH --gres=gpu:2
#module load cuda/10 #make cuda available to this session's environemt
numNodes=16
totalSlices=3837 # zero referenced
module load cuda/9.2.148
module load fftw/3.3.4
baseDir="/projects/project-nieverge"
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"
tomoProc="${baseDir}/tomoProc"
rawDir="${tomoProc}/raw"
correctedDir="${tomoProc}/corrected"
alignedDir="${tomoProc}/aligned"
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
${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
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