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

processing/mc2FromMDOC.py

@@ -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