Mercurial > repos > imgteam > count_objects

comparison count_objects.py @ 1:664232d2a3f7 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:01:56 -0500
parents 895a29ebd0c7
children 5bf8eb50b280
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0:895a29ebd0c7 1:664232d2a3f7
2 2
3 import argparse 3 import argparse
4 import numpy as np 4 import numpy as np
5 import os 5 import os
6 import skimage.io 6 import skimage.io
7 from skimage.measure import regionprops 7 from skimage.measure import regionprops
8 8
9 parser = argparse.ArgumentParser(description='Count Objects') 9 parser = argparse.ArgumentParser(description='Count Objects')
10 parser.add_argument('input_file', type=argparse.FileType('r'), 10 parser.add_argument('input_file', type=argparse.FileType('r'),
11 help='Label input file') 11 help='Label input file')
12 parser.add_argument('output_file', type=argparse.FileType('w'), 12 parser.add_argument('output_file', type=argparse.FileType('w'),
13 help='Tabular output file') 13 help='Tabular output file')
14 args = parser.parse_args() 14 args = parser.parse_args()
15 15
16 img_raw = skimage.io.imread(args.input_file.name) 16 img_raw = skimage.io.imread(args.input_file.name)
17 res = len(regionprops(img_raw)) 17 res = len(regionprops(img_raw))
18 18
19 text_file = open(args.output_file.name, "w") 19 text_file = open(args.output_file.name, "w")