Mercurial > repos > imgteam > binary2labelimage

comparison binary2label.py @ 3:a041e4e9d449 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
author imgteam
date Mon, 12 May 2025 08:15:32 +0000
parents 938e2358eb80
children
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2:938e2358eb80 3:a041e4e9d449
1 import argparse 1 import argparse
2 import sys
3 import skimage.io
4 from skimage.measure import label
5 import numpy as np
6 import warnings
7 from PIL import Image
8 import skimage.util
9 2
3 import giatools
4 import scipy.ndimage as ndi
5 import tifffile
6
7
8 # Parse CLI parameters
10 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
11 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') 10 parser.add_argument('input', type=str, help='input file')
12 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') 11 parser.add_argument('output', type=str, help='output file (TIFF)')
13 args = parser.parse_args() 12 args = parser.parse_args()
14
15 img_in = skimage.io.imread(args.input_file.name) > 0
16 res = label(img_in)
17 res = skimage.util.img_as_uint(res)
18 13
19 res = Image.fromarray(res) 14 # Read the input image with the original axes
20 res.save(args.out_file.name, "tiff") 15 img = giatools.Image.read(args.input)
16 img = img.normalize_axes_like(
17 img.original_axes,
18 )
19
20 # Make sure the image is truly binary
21 img_arr_bin = (img.data > 0)
22
23 # Perform the labeling
24 img.data = ndi.label(img_arr_bin)[0]
25
26 # Write the result image (same axes as input image)
27 tifffile.imwrite(args.output, img.data, metadata=dict(axes=img.axes))