combineStack

#!/usr/bin/env python
# remove the necessity to have .py extension

import tifffile
import sys, os
import numpy as np

option_handle_list = ['--imageNumber', '--newName']
option_unique_list = ['--info', '--help']
options = {}




for option_handle in option_handle_list:
    if option_handle in sys.argv:
        options[option_handle[2:]] = sys.argv[sys.argv.index(option_handle) + 1]
    else:
        options[option_handle[2:]] = None

for option_handle in option_unique_list:
    if option_handle in sys.argv:
        options[option_handle[2:]] = True
    else:
        options[option_handle[2:]] = None

if options['info'] != None or options['help'] != None:
    print("Function combineStack, this function can be used to combine stacks of tif files")
    print("USAGE : combineStack [imagePath] [imagePath2]")
    print("")
    print("options")
    print(" --newName: new name of the image")
    exit()


if len(sys.argv) == 1 or not os.path.exists(sys.argv[1]):
    raise ValueError("Incorrect path, the first and second arguments must be the image path")
imagePath = sys.argv[1]

if len(sys.argv) == 1 or not os.path.exists(sys.argv[2]):
    raise ValueError("Incorrect path, the first and second arguments must be the image path")
imagePath2 = sys.argv[2]

if options['newName'] == None:
    newName = "combined.tif"
else:
    newName = options['newName']
y = tifffile.imread(imagePath)
z = tifffile.imread(imagePath2)




tifffile.imsave(newName, np.concatenate((y,z)))