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Commits (2)
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
......@@ -13,6 +13,8 @@ import re
import argparse
from datetime import datetime
import getpass
import stat
from pathlib import Path
# clusterBaseDir = '/projects/project-nieverge/'
procDir = 'tomoProc'
......@@ -137,7 +139,9 @@ elif args.noLog:
else:
verboseString = ">> %s 2>&1" % (inBaseName + "_alignment.log")
with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scriptFile:
scriptFilePath = Path(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"))
with open(scriptFilePath, "w+") as scriptFile:
scriptFile.write("#!/bin/bash\n\n")
scriptFile.write("# Script file for motioncor2 alignment of tilt series created by mc2FromMDOC.py on %s by %s\n\n" % (datetime.today().strftime('%Y-%m-%d %H:%M'), getpass.getuser()) )
......@@ -162,3 +166,5 @@ with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scr
for imageParams in stackParams:
scriptFile.write("rm %s\n" % (os.path.join(alignedDir, imageParams['filename'])))
scriptFile.write("rmdir %s\n" % (alignedDir))
scriptFilePath.chmod(scriptFilePath.stat().st_mode | stat.S_IEXEC | stat.S_IXGRP )