Commit 6af5f535 authored by Adrian Nievergelt's avatar Adrian Nievergelt

tilting inclusion in frame alignment

parent c63069e3
......@@ -23,4 +23,4 @@ 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
$mcorrBin -InFmMotion 1 -Patch 5 5 -Iter 20 -Tilt $2 -InMrc ${correctedDir}/$1 -OutMrc ${alignedDir}/$1
......@@ -85,7 +85,7 @@ with open(inPath[0] + "_1_correctAndAlign.sh", 'w+') as transferFile:
transferFile.write("# Execute on any computer with ssh acceess to cluster (falcon)\n")
transferFile.write("cd \"$(dirname \"$0\")\" # go to script location \n")
for imageParams in stackParams:
transferFile.write("ssh falcon sbatch %s %s %f\n" % (correctAlignSLURM, imageParams['filename'], imageParams['tiltangle']))
transferFile.write("ssh falcon sbatch %s %s \"%f 0.0\" \n" % (correctAlignSLURM, imageParams['filename'], imageParams['tiltangle']))
# write stackup list to
with open(inPath[0] + "_aux0.stackList", 'w+') as transferFile:
......
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