Mercurial > repos > thomaswollmann > mergeneighboursinlabelimage

diff mergeneighboursinlabelimage.py @ 1:3536648d0a93 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:35:29 -0500
parents 66f7e94db2e6
children
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--- a/mergeneighboursinlabelimage.py	Tue Jan 08 08:54:16 2019 -0500
+++ b/mergeneighboursinlabelimage.py	Wed Jan 16 15:35:29 2019 -0500
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import argparse
 import sys
 import skimage.io
@@ -46,6 +44,5 @@
     label_image = merge_n(label_image, args.cluster_merge)
     with warnings.catch_warnings():
     	warnings.simplefilter("ignore")
-    	res = skimage.util.img_as_uint(res)
-    	skimage.io.imsave("tmp.tiff", res)
-    os.rename("tmp.tiff", args.output_file.name)
+    	res = skimage.util.img_as_uint(label_image)
+    	skimage.io.imsave(args.out_file.name, res, plugin="tifffile")