Mercurial > repos > imgteam > count_objects
comparison count_objects.py @ 0:895a29ebd0c7 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author | imgteam |
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date | Sat, 09 Feb 2019 14:34:18 -0500 |
parents | |
children | 664232d2a3f7 |
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-1:000000000000 | 0:895a29ebd0c7 |
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1 #!/usr/bin/python | |
2 | |
3 import argparse | |
4 import numpy as np | |
5 import os | |
6 import skimage.io | |
7 from skimage.measure import regionprops | |
8 | |
9 parser = argparse.ArgumentParser(description='Count Objects') | |
10 parser.add_argument('input_file', type=argparse.FileType('r'), | |
11 help='Label input file') | |
12 parser.add_argument('output_file', type=argparse.FileType('w'), | |
13 help='Tabular output file') | |
14 args = parser.parse_args() | |
15 | |
16 img_raw = skimage.io.imread(args.input_file.name) | |
17 res = len(regionprops(img_raw)) | |
18 | |
19 text_file = open(args.output_file.name, "w") | |
20 text_file.write("objects\n%s" % res) | |
21 text_file.close() |