view binary2label.py @ 2:6e65fd971e13 draft

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"

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")