@@ -17,9 +17,10 @@ parser = argparse.ArgumentParser(description = "Generates thumbnails for MRC mic
# 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','--inDir',nargs='?',default='.',help='If specified, automatically process entire directory of mrc files.')
parser.add_argument('-mi','--maxImages',nargs='?',type=float,default=30,help='If more images than specified are in a file, make amontage with a subset of the frames present instead of separate files. Detault is 30 images, minimum 6.')
parser.add_argument('-mi','--maxImages',nargs='?',type=int,default=30,help='If more images than specified are in a file, make amontage with a subset of the frames present instead of separate files. Detault is 30 images, minimum 6.')
parser.add_argument('-sd','--subDirs',action='store_true',help='Include subdirectories when in directory mode.')
parser.add_argument('-et','--excludeTomograms',action='store_true',help='Do not process tomograms (.rec) files.')
parser.add_argument('-r','--resolution',nargs='?',type=int,default=400,help='Default resoltion for still frames. Montages are saved at 60% of this per individual frame.')
# parser.add_argument('-g', '--graph', action='store_true', help='Store a graph of the corrected and uncorrected line intensities for debug purposes.')
...
...
@@ -71,11 +72,11 @@ for inFile in inFileList:
makeMontage=zSlices>args.maxImages
ifmakeMontage:
xOutSize=400;
xOutSize=int(0.4*args.resolution);
montImages=[]
# print("Making a montage")
else:
xOutSize=1000;
xOutSize=args.resolution;
ifmakeMontage:
outputSlices=np.linspace(0,zSlices-1,6).astype(int)# select 6 slices throughout the stack