Mercurial > repos > imgteam > split_labelmap

comparison split_labelmap.py @ 3:0e7be7c35f15 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:13:26 +0000
parents 9db1c22dbe17
children
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2:7a2e2e3cf836 3:0e7be7c35f15
1 import argparse 1 import argparse
2 import warnings 2 import warnings
3 3
4 import giatools.io
4 import numpy as np 5 import numpy as np
5 import scipy 6 import scipy
6 import skimage.draw 7 import skimage.draw
7 import skimage.io 8 import skimage.io
8 from imageio import imread as io_imread
9 from skimage.measure import regionprops 9 from skimage.measure import regionprops
10 10
11 # split_label_image takes a label image and outputs a similar file with the given name where the labeled 11 # split_label_image takes a label image and outputs a similar file with the given name where the labeled
12 # parts of the image that touch (or overlap) are separated by at least 1 pixel (at most 2). 12 # parts of the image that touch (or overlap) are separated by at least 1 pixel (at most 2).
13 13
14 14
15 def split_labelmap(labelmap, outputfile): 15 def split_labelmap(labelmap, outputfile):
16 16
17 # Information from the label map. 17 # Information from the label map.
18 label_img = io_imread(labelmap) 18 label_img = giatools.io.imread(labelmap)
19 xtot, ytot = label_img.shape 19 xtot, ytot = label_img.shape
20 props = regionprops(label_img) 20 props = regionprops(label_img)
21 N = len(props) 21 N = len(props)
22 22
23 # Creating the backgrounds. 23 # Creating the backgrounds.