# HG changeset patch
# User imgteam
# Date 1549740553 18000
# Node ID f264ae82f7359e24d2c2665526bee4076b9fcefb

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

diff -r 000000000000 -r f264ae82f735 filter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.xml	Sat Feb 09 14:29:13 2019 -0500
@@ -0,0 +1,44 @@
+<tool id="ip_filter_standard" name="Filter Image" version="0.0.2">
+    <description>applies a standard filter to an image</description>
+    <requirements>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+        <requirement type="package" version="5.3.0">pillow</requirement>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+      <![CDATA[
+        python '$__tool_directory__/filter_image.py' '$input' '$output' $filter_type $radius
+      ]]>
+    </command>
+    <inputs>
+        <param name="filter_type" type="select" label="Image type">
+          <option value="median" selected="True">Median</option>
+          <option value="gaussian">Gaussian Blur</option>
+          <option value="prewitt">Prewitt</option>
+          <option value="sobel">Sobel</option>
+          <option value="scharr">Scharr</option>
+        </param>
+        <param name="radius" type="integer" value="3" label="Radius/Sigma" />
+        <param name="input" type="data" format="tiff" label="Source file" />
+    </inputs>
+    <outputs>
+       <data format="tiff" name="output" />
+    </outputs>
+    <tests>
+      <test>
+        <param name="input" value="sample.tif" />
+        <output name="output" value="res.tif" ftype="tiff" compare="sim_size"/>
+        <param name="filter_type" value="prewitt" />
+        <param name="radius" value="4" />
+      </test>
+    </tests>
+    <help>
+    **What it does**
+
+    Applies a standard filter to an image.
+    </help>
+    <citations>
+       <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r f264ae82f735 filter_image.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_image.py	Sat Feb 09 14:29:13 2019 -0500
@@ -0,0 +1,34 @@
+import argparse
+import sys
+import warnings
+import numpy as np
+import skimage.io
+import skimage.filters
+import skimage.util
+from skimage.morphology import disk
+
+filterOptions = {
+    'median' : lambda img_raw, radius: skimage.filters.median(img_raw, disk(radius)),
+    'gaussian' : lambda img_raw, radius: skimage.filters.gaussian(img_raw, sigma=radius),
+    'prewitt' : lambda img_raw, radius: skimage.filters.prewitt(img_raw),
+    'sobel' : lambda img_raw, radius: skimage.filters.sobel(img_raw),
+    'scharr' : lambda img_raw, radius: skimage.filters.scharr(img_raw),
+}
+
+if __name__ == "__main__":
+    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('filter_type', choices=filterOptions.keys(), help='conversion type')
+    parser.add_argument('radius', default=3.0, type=float, help='Radius/Sigma')
+    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')
diff -r 000000000000 -r f264ae82f735 test-data/res.tif
Binary file test-data/res.tif has changed
diff -r 000000000000 -r f264ae82f735 test-data/sample.tif
Binary file test-data/sample.tif has changed