view binary2label.py @ 4:984358e43242 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533

import argparse
import sys

import skimage.io
import skimage.util
from PIL import Image
from skimage.measure import label

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")