parser.add_argument('-d','--outDir',nargs='?',default='.',help='Optional output directory to write scripts to.')
parser.add_argument('-dp','--dataPath',nargs='?',default='.',help='Optional override to use if the data is mounted in a different network base path.')
parser.add_argument('-cp','--clusterPath',nargs='?',default='/projects/project-nieverge/',help='Destination path of the HPC filesystem data directory.')
parser.add_argument('-cv','--cudaVer',nargs='?',type=int,default=92,help='Override CUDA version. Default 9.2')
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('-dw','--doseWeight',action='store_true',help='Do dose-weighting on alignment.')
...
...
@@ -111,7 +111,7 @@ with open(tiltFileName, "w+") as tiltFile:
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()))
scriptFile.write('cd "$(dirname "$0")"\n')
...
...
@@ -129,7 +129,8 @@ with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scr