s3.py

from src.skull import SkullStripper
from src import helpers as utils
import os
import time

if __name__ == '__main__':

    from sys import argv

    myargs = utils.getopts(argv)

    want_tissues = False
    want_atlas = False

    if '-i' in myargs:
        input_path = myargs['-i']
        output_path = os.path.dirname(os.path.abspath(input_path))

    if '-o' in myargs:
        output_path = myargs['-o']
        output_path = os.path.abspath(output_path)

    if '-t' in myargs:
        want_tissues = True

    if '-a' in myargs:
        want_atlas = True

    if not os.path.exists(output_path):
        print("The selected output folder doesn't exist, so I am making it \n")
        os.makedirs(output_path)

    start = time.time()
    skull_stripper = SkullStripper(input_path, output_path, want_tissues, want_atlas)
    skull_stripper.strip_skull()
    print('Done (' + str((time.time() - start) / 60.) + ' min)')