im-processor.py

#!/usr/bin/env python3

import os, sys
import time

cleanerpath = '"' + sys.argv[1].replace('"','').replace("'","") + '"'
	#Input image folder name:
imagefolder = sys.argv[2].replace('"','').replace("'","").rstrip('/')  + "/"
    #Output folder name:
outfolder = sys.argv[3].replace('"','').replace("'","").rstrip('/') + "/"
filelist = [files for root, dirs, files in os.walk(imagefolder)][0]

start = time.time()

def runIM(file, out):
    try:
        command = ' '.join(["bash", cleanerpath, "-g", "-e none", "-f 25", "-o 10", "-T -b white", 
                   '"'+imagefolder + file+'"', '"' + out + file.replace(".tif","") + '.processed.tif"'])
        print(command)
        os.system(command)
    except:
        print('Preprocessing failed on ', file)
            
if not os.path.exists(outfolder):
    os.makedirs(outfolder)            


for f in filelist:
    if f[0] != '.':
    	runIM(f, outfolder)

end = time.time()
    
print("Time elapsed = ",(end-start)/60, "minutes.")