Commit 8fbd5825 authored by Adrian Nievergelt's avatar Adrian Nievergelt
Browse files

ali generator slurm script

parent 822bf8bf
#!/bin/bash
#SBATCH -J makeAli # the job's name
#SBATCH -t 00:20:00 # max. wall clock time 5s
#SBATCH -n 1 # number of tasks
#SBATCH -N 1
#SBATCH -c 10
#SBATCH -o /projects/project-nieverge/logs/makeAli_%j.out # output file
#SBATCH --partition=batch
cd $1
source /sw/apps/imod/current/imodenv
submfg newst.com
submfg ctfcorrection.com
......@@ -37,6 +37,8 @@ parser.add_argument('-i', '--input', nargs='+', default='.', help='Input MDOC fi
parser.add_argument('-cv', '--cudaVer', nargs='?', type=int, default=92, help='Override CUDA version. Default 92. Reduce to a lower value if MotionCor2 does not run properly with the installed graphics card.')
parser.add_argument('-ps', '--patchSize', nargs='?', type=int, default=3, help='Override local alignment patch count. Default 3.')
parser.add_argument('-b', '--binning', nargs='?', type=int, default=1, help='Output binning. Default 1 (no binning).')
parser.add_argument('-bfg', '--bFactorGlobal', nargs='?', type=int, default=800, help='Global bFactor. Default 800.')
parser.add_argument('-bfl', '--bFactorLocal', nargs='?', type=int, default=200, help='Global bFactor. Default 200.')
parser.add_argument('-dw', '--doseWeight', action='store_true', help='Do dose-weighting on alignment.')
parser.add_argument('-ss', '--splitSum', action='store_true', help='Split sum saving for cryoCARE.')
parser.add_argument('-cl', '--correctLines', action='store_true', help='Use correctK2Lines.py script for correcting lines due to drifty camera sensor.')
......@@ -209,12 +211,12 @@ for inputFile in args.input:
doseWeightParams = ""
scriptFile.write("echo Aligning frame stack %s \n" % (os.path.join(sourceDir, imageParams['filename']) ))
scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i \
-InFmMotion 0 -Iter 30 -Tilt %f -Group %i -FtBin %i -PixSize %f%s %s\n\n" %(args.cudaVer,
scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i -Bft %i %i \
-InFmMotion 0 -Iter 10 -Tilt %f -Group %i -FtBin %i -PixSize %f%s %s\n\n" %(args.cudaVer,
os.path.join(sourceDir, imageParams['filename']),
os.path.join(alignedDir, imageParams['filename']),
args.patchSize,
args.patchSize,
args.patchSize, args.patchSize,
args.bFactorGlobal, args.bFactorLocal,
imageParams['tiltangle'],
args.group,
args.binning,
......
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