# HG changeset patch
# User imgteam
# Date 1563454318 14400
# Node ID dba87c4b32d31311bd866b766c027a7b46e3e3a0
# Parent  f264ae82f7359e24d2c2665526bee4076b9fcefb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit 8e0d09b4c4eadfaaf125f4a0ae7dcbd1bee5ee51

diff -r f264ae82f735 -r dba87c4b32d3 filter.xml
--- a/filter.xml	Sat Feb 09 14:29:13 2019 -0500
+++ b/filter.xml	Thu Jul 18 08:51:58 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="ip_filter_standard" name="Filter Image" version="0.0.2">
+<tool id="ip_filter_standard" name="Filter Image" version="0.0.3">
     <description>applies a standard filter to an image</description>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
diff -r f264ae82f735 -r dba87c4b32d3 filter_image.py
--- a/filter_image.py	Sat Feb 09 14:29:13 2019 -0500
+++ b/filter_image.py	Thu Jul 18 08:51:58 2019 -0400
@@ -6,6 +6,7 @@
 import skimage.filters
 import skimage.util
 from skimage.morphology import disk
+from skimage import img_as_uint
 
 filterOptions = {
     'median' : lambda img_raw, radius: skimage.filters.median(img_raw, disk(radius)),
@@ -24,11 +25,5 @@
     args = parser.parse_args()
 
     img_in = skimage.io.imread(args.input_file.name)
-    res = filterOptions[args.filter_type](img_in, args.radius)
-    res[res<-1]=-1
-    res[res>1]=1
-
-    with warnings.catch_warnings():
-    	warnings.simplefilter("ignore")
-    	res = skimage.util.img_as_uint(res) #Attention: precision loss
-    	skimage.io.imsave(args.out_file.name, res, plugin='tifffile')
+    res = img_as_uint(filterOptions[args.filter_type](img_in, args.radius))
+    skimage.io.imsave(args.out_file.name, res, plugin='tifffile')
diff -r f264ae82f735 -r dba87c4b32d3 test-data/res.tif
Binary file test-data/res.tif has changed