Mercurial > repos > imgteam > 2d_local_threshold

diff auto_local_threshold.py @ 1:c90b91f4a07b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
author imgteam
date Tue, 23 Jul 2019 05:09:04 -0400
parents a20c14eb5f98
children 497dcd834bb3
line wrap: on
line diff
--- a/auto_local_threshold.py	Thu Jul 18 09:22:07 2019 -0400
+++ b/auto_local_threshold.py	Tue Jul 23 05:09:04 2019 -0400
@@ -3,6 +3,7 @@
 import skimage.io
 import skimage.filters
 import skimage.util
+import numpy as np
 
 threshOptions = {
     'gaussian': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='gaussian'),
@@ -20,6 +21,7 @@
     args = parser.parse_args()
 
     img_in = skimage.io.imread(args.input_file.name)
+    img_in = np.reshape(img_in, [img_in.shape[0], img_in.shape[1]])
     thresh = threshOptions[args.thresh_type](img_in, args.block_size)
 
     if args.dark_background: