# HG changeset patch
# User thomaswollmann
# Date 1546955656 18000
# Node ID 66f7e94db2e63115161697e2a63489a07f3c04a2

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259

diff -r 000000000000 -r 66f7e94db2e6 mergeneighboursinlabelimage.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergeneighboursinlabelimage.py	Tue Jan 08 08:54:16 2019 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/python
+
+import argparse
+import sys
+import skimage.io
+import skimage.util
+from skimage.measure import regionprops
+import scipy.spatial.distance
+import numpy as np
+import warnings
+
+def merge_n(img, dist=50):
+    props = regionprops(img)
+    found = False
+    for i in range(0, len(props)):
+        i_coords = props[i].coords
+        for q in range(0, len(props)):
+            if i==q:
+                continue
+            q_coords = props[q].coords
+            iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean'))
+            if iq_dist <= dist:
+                props[q].label = props[i].label
+                for a_point in range(0, q_coords.shape[0]):
+                    img[q_coords[a_point, 0], q_coords[a_point, 1]] = props[i].label
+                found = True
+    if found:
+        merge_n(img, dist)
+    return img
+
+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(
+        '-c',
+        dest='cluster_merge',
+        type=int,
+        required=False,
+        default=50,
+        help='Distance in pixel of clusters which are merged',
+    )
+    args = parser.parse_args()
+
+    label_image = skimage.io.imread(args.input_file.name)
+    label_image = merge_n(label_image, args.cluster_merge)
+    with warnings.catch_warnings():
+    	warnings.simplefilter("ignore")
+    	res = skimage.util.img_as_uint(res)
+    	skimage.io.imsave("tmp.tiff", res)
+    os.rename("tmp.tiff", args.output_file.name)
diff -r 000000000000 -r 66f7e94db2e6 mergeneighboursinlabelimage.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergeneighboursinlabelimage.xml	Tue Jan 08 08:54:16 2019 -0500
@@ -0,0 +1,23 @@
+<tool id="mergeneighboursinlabelimage" name="Merge Neighbours in Label" version="0.1">
+  <description>Merge Neighbours in Label Image</description>
+  <requirements>
+    <requirement type="package" version="0.12.3" >scikit-image</requirement>
+    <requirement type="package">numpy</requirement>
+    <requirement type="package">scipy</requirement>
+  </requirements>
+  <command>
+        <![CDATA[
+        python '$__tool_directory__/mergeneighboursinlabelimage.py '$input' '$output' -c $c
+        ]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="tiff,png,jpg,bmp" label="Label Image File"/>
+    <param  label="Distance in pixel of objects which are merged" name="c" type="integer" value="50"/>
+  </inputs>
+  <outputs>
+    <data format="tiff" name="output"/>
+  </outputs><help>This tools merges nearby objects in a label image using the minimum pixel distance.</help>
+  <citations>
+      <citation type="doi">10.7717/peerj.453</citation>
+  </citations>
+</tool>