# HG changeset patch
# User imgteam
# Date 1563785683 14400
# Node ID a85f2165267776a4e1e04c009b441154c019b920

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d

diff -r 000000000000 -r a85f21652677 2d_split_binaryimage_by_watershed.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2d_split_binaryimage_by_watershed.py	Mon Jul 22 04:54:43 2019 -0400
@@ -0,0 +1,26 @@
+import argparse
+import sys
+import skimage.io
+from skimage.morphology import watershed
+from skimage.feature import peak_local_max
+from scipy import ndimage as ndi
+import skimage.util
+ 
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Split binaryimage by watershed')
+    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('min_distance', type=int, default=100, help='Minimum distance to next object')
+    args = parser.parse_args()
+
+    img_in = skimage.io.imread(args.input_file.name)
+    distance = ndi.distance_transform_edt(img_in)
+    local_maxi = peak_local_max(distance, 
+                                indices=False, 
+                                min_distance=args.min_distance, 
+                                labels=img_in)
+    markers = ndi.label(local_maxi)[0]
+    res = watershed(-distance, markers, mask=img_in)
+
+    res = skimage.util.img_as_uint(res)
+    skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
diff -r 000000000000 -r a85f21652677 2d_split_binaryimage_by_watershed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2d_split_binaryimage_by_watershed.xml	Mon Jul 22 04:54:43 2019 -0400
@@ -0,0 +1,35 @@
+<tool id="ip_2d_split_binaryimage_by_watershed" name="Split objects" version="0.0.1"> 
+   <description>Split binary image by using watershed</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>
+        <requirement type="package" version="1.2.1">scipy</requirement>
+   </requirements>
+   <command detect_errors="aggressive">
+   <![CDATA[
+   python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
+   ]]> 
+   </command>
+   <inputs>
+        <param name="input" type="data" format="tiff" label="Source file" /> 
+        <param name="min_distance" type="integer" value="5" label="Minimum distance between two objects." />
+    </inputs>
+    <outputs>
+       <data format="tiff" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="in.tif"/>
+            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
+            <param name="min_distance" value="10"/>
+        </test>
+    </tests>
+    <help>
+        Split binary image by using distance transform and watershed.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r a85f21652677 test-data/in.tif
Binary file test-data/in.tif has changed
diff -r 000000000000 -r a85f21652677 test-data/out.tif
Binary file test-data/out.tif has changed