Mercurial > repos > imgteam > binary2labelimage
view binary2label.py @ 2:6e65fd971e13 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author | imgteam |
---|---|
date | Wed, 18 Dec 2019 05:01:27 -0500 |
parents | 6c92ac9ce868 |
children | 9bb446db4a1e |
line wrap: on
line source
import argparse import sys import skimage.io from skimage.measure import label import numpy as np import warnings from PIL import Image import skimage.util parser = argparse.ArgumentParser() parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') args = parser.parse_args() img_in = skimage.io.imread(args.input_file.name) > 0 res = label(img_in) res = skimage.util.img_as_uint(res) res = Image.fromarray(res) res.save(args.out_file.name, "tiff")