Mercurial > repos > imgteam > count_objects
view count_objects.py @ 1:664232d2a3f7 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author | imgteam |
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date | Wed, 18 Dec 2019 05:01:56 -0500 |
parents | 895a29ebd0c7 |
children | 5bf8eb50b280 |
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#!/usr/bin/python import argparse import numpy as np import os import skimage.io from skimage.measure import regionprops parser = argparse.ArgumentParser(description='Count Objects') parser.add_argument('input_file', type=argparse.FileType('r'), help='Label input file') parser.add_argument('output_file', type=argparse.FileType('w'), help='Tabular output file') args = parser.parse_args() img_raw = skimage.io.imread(args.input_file.name) res = len(regionprops(img_raw)) text_file = open(args.output_file.name, "w") text_file.write("objects\n%s" % res) text_file.close()