Commit 8a77773a authored by Adrian Nievergelt's avatar Adrian Nievergelt

Merge branch 'master' of git.mpi-cbg.de:nieverge/scripts

parents 13d2032c 6d25390c
......@@ -28,9 +28,9 @@ parser = argparse.ArgumentParser(description = "Generates batch processing scrip
# parser.add_argument("-f", "--file", help="create overlay for a single file",
parser.add_argument('-i', '--input', nargs='?', default='.', help='Input MDOC file to process.')
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('-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 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).')
......@@ -95,7 +95,7 @@ if mdocDir == "":
mdocDir = "."
for (dirpath, dirnames, filenames) in os.walk(mdocDir):
for filename in filenames:
if filename == stackParams[0]['filename']:
if filename == stackParams[0]['filename'] and not dirpath.endswith(alignedDir):
subframesDir = os.path.relpath(dirpath, mdocDir)
print("Found subframes in directory \"%s\"" % (subframesDir))
break
......
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