Mercurial > repos > imgteam > count_objects
diff count_objects.py @ 0:895a29ebd0c7 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author | imgteam |
---|---|
date | Sat, 09 Feb 2019 14:34:18 -0500 |
parents | |
children | 664232d2a3f7 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/count_objects.py Sat Feb 09 14:34:18 2019 -0500 @@ -0,0 +1,21 @@ +#!/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()