# HG changeset patch
# User thomaswollmann
# Date 1487686252 18000
# Node ID babb41158e9f0edb9709d0b5f2f54c752bce8242

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8

diff -r 000000000000 -r babb41158e9f anisotropic_diffusion.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anisotropic_diffusion.py	Tue Feb 21 09:10:52 2017 -0500
@@ -0,0 +1,26 @@
+import argparse
+import sys
+import warnings
+import numpy as np
+import skimage.io
+import skimage.util
+from medpy.filter.smoothing import anisotropic_diffusion
+
+parser = argparse.ArgumentParser()
+parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
+parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
+parser.add_argument('niter', type=int, help='Number of iterations', default=1)
+parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50)
+parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1)
+parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1)
+args = parser.parse_args()
+
+img_in = skimage.io.imread(args.input_file.name)
+res = anisotropic_diffusion(img_raw, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption)
+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')
diff -r 000000000000 -r babb41158e9f anisotropic_diffusion.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anisotropic_diffusion.xml	Tue Feb 21 09:10:52 2017 -0500
@@ -0,0 +1,40 @@
+<tool id="anisotropic_diffusion" name="Anisotropic Diffusion" version="0.1">
+  <description>Edge-preserving, Anisotropic diffusion</description>
+  <requirements>
+    <requirement type="package" version="0.12.3" >scikit-image</requirement>
+    <requirement type="package" version="0.2.2">medpy</requirement>
+    <requirement type="package" version="1.12">numpy</requirement>
+  </requirements>
+  <command>
+        <![CDATA[
+        python "$__tool_directory__/anisotropic_diffusion.py" '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption'
+        ]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file"/>
+    <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/>
+    <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/>
+    <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
+    <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation">
+        <option value="1" selected="True">Favour high contrast edges</option>
+        <option value="2">Favour wide regions</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tiff" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+	    <param name="input" value="galaxyIcon_noText.png" />
+	    <param name="niter" value="100" />
+            <param name="kappa" value="50" />
+	    <param name="gamma" value="0.1" />
+	    <param name="eqoption" value="1" />
+	    <output name="output" ftype="tiff" />
+    </test>
+  </tests>
+  <help>Edge-preserving, Anisotropic image diffusion.</help>
+  <citations>
+      <citation type="doi">10.1109/34.56205</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r babb41158e9f test-data/galaxyIcon_noText.png
Binary file test-data/galaxyIcon_noText.png has changed
diff -r 000000000000 -r babb41158e9f test-data/res.tif
Binary file test-data/res.tif has changed