diff count_objects.py @ 0:895a29ebd0c7 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

--- /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()