Commit 6d25390c authored by Adrian Nievergelt's avatar Adrian Nievergelt

ignore aligned dir and remove unneccessary commandline switches

parent fd9379ff
...@@ -28,9 +28,9 @@ parser = argparse.ArgumentParser(description = "Generates batch processing scrip ...@@ -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("-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('-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('-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('-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('-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('-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('-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('-b', '--binning', nargs='?', type=int, default=1, help='Output binning. Default 1 (no binning).')
...@@ -94,7 +94,7 @@ mdocDir = os.path.dirname(args.input) ...@@ -94,7 +94,7 @@ mdocDir = os.path.dirname(args.input)
for (dirpath, dirnames, filenames) in os.walk(mdocDir): for (dirpath, dirnames, filenames) in os.walk(mdocDir):
for filename in filenames: 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) subframesDir = os.path.relpath(dirpath, mdocDir)
print("Found subframes in directory \"%s\"" % (subframesDir)) print("Found subframes in directory \"%s\"" % (subframesDir))
break break
......
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