Mercurial > repos > imgteam > binary2labelimage
comparison 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 | 7f8102bdbfa1 |
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| 2:6e65fd971e13 | 3:9bb446db4a1e |
|---|---|
| 1 import argparse | 1 import argparse |
| 2 import sys | 2 import sys |
| 3 | |
| 3 import skimage.io | 4 import skimage.io |
| 5 import skimage.util | |
| 6 from PIL import Image | |
| 4 from skimage.measure import label | 7 from skimage.measure import label |
| 5 import numpy as np | |
| 6 import warnings | |
| 7 from PIL import Image | |
| 8 import skimage.util | |
| 9 | 8 |
| 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_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') |
| 12 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | 11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') |
| 13 args = parser.parse_args() | 12 args = parser.parse_args() |
| 14 | 13 |
| 15 img_in = skimage.io.imread(args.input_file.name) > 0 | 14 img_in = skimage.io.imread(args.input_file.name) > 0 |
| 16 res = label(img_in) | 15 res = label(img_in) |
| 17 res = skimage.util.img_as_uint(res) | 16 res = skimage.util.img_as_uint(res) |
| 18 | 17 |
| 19 res = Image.fromarray(res) | 18 res = Image.fromarray(res) |