Mercurial > repos > thomaswollmann > count_objects
diff count_objects.py @ 0:f02a2d0f407c draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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date | Wed, 16 Jan 2019 15:34:44 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/count_objects.py Wed Jan 16 15:34:44 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()