Commit ed02c345 authored by Adrian Nievergelt's avatar Adrian Nievergelt

First try of individual dose-frac frame alignment batch script

parent 013c915d
#!/bin/bash
#SBATCH -J gpu_motioncor # the job's name
#SBATCH -t 00:2:00 # max. wall clock time 5s
#SBATCH -n 1 # number of tasks
#SBATCH -o /projects/project-nieverge/logs/corrAlign_%j.out # output file
#SBATCH --partition=gpu
#SBATCH --gres=gpu:2
#module load cuda/10 #make cuda available to this session's environemt
module load cuda/10.0.130
baseDir='/projects/project-nieverge'
k2correct='${baseDir}/scripts/processing/correctK2Lines.py'
mcorrBin='${baseDir}/bin/motioncor2/MotionCor2_1.2.3-Cuda100'
tomoProc='${baseDir}/tomoProc'
rawDir='${tomoProc}/raw'
correctedDir='${tomoProc}/corrected'
alignedDir='${tomoProc}/aligned'
stackDir='${tomoProc}/tiltStacks'
cd $baseDir
python3 ${k2correct} -i ${rawDir}/$1 -d ${correctedDir} -c 0.5
$mcorrBin -InFmMotion 1 -Patch 5 5 -Iter 20 -InMrc ${correctedDir}/$1 -OutMrc ${alignedDir}/$1
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