view binary2label.py @ 3:9bb446db4a1e draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:33 +0000
parents 6e65fd971e13
children
line wrap: on
line source

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")