Commit f66549cb authored by Adrian Nievergelt's avatar Adrian Nievergelt

added automated logging for alignment

parent a307a180
......@@ -36,6 +36,7 @@ parser.add_argument('-ps', '--patchSize', nargs='?', type=int, default=3, help='
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.')
parser.add_argument('-v', '--verbose', action='store_true', help='Allow verbose output from motioncor2 during script run.')
parser.add_argument('-nl', '--noLog', action='store_true', help='Allow verbose output from motioncor2 during script run.')
parser.add_argument('-kf', '--keepFrames', action='store_true', help='Keep temporary individual aligned frames.')
parser.add_argument('-psf', '--pixelSizeFactor', nargs='?', type=float, default=1, help='Correction factor for pixel size, set to 0.5 for super resolution with binned mdoc.')
......@@ -129,8 +130,10 @@ with open(tiltFileName, "w+") as tiltFile:
if args.verbose:
verboseString = ""
else:
elif args.noLog:
verboseString = " &>/dev/null"
else:
verboseString = " &>%s" % (inBaseName + "_alignment.log")
with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scriptFile:
scriptFile.write("#!/bin/bash\n\n")
......
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