# HG changeset patch
# User thomaswollmann
# Date 1546857490 18000
# Node ID 5f83d67e30f1d90fa193298a31c43d5bce4d8e0d

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f

diff -r 000000000000 -r 5f83d67e30f1 overlay_segmentation_mask.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_segmentation_mask.py	Mon Jan 07 05:38:10 2019 -0500
@@ -0,0 +1,41 @@
+import argparse
+import sys
+import os
+
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+
+#TODO make importable by python script
+
+import skimage.io
+import skimage.measure
+
+parser = argparse.ArgumentParser()
+parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
+parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file')
+parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy
+parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale')
+parser.add_argument('--label', dest='label', action='store_true', help='plot label')
+parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
+parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='thickness')
+parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color')
+args = parser.parse_args()
+img = skimage.io.imread(args.input_file.name)
+label = skimage.io.imread(args.mask_file.name)
+
+fig = plt.figure()
+ax = fig.add_axes([0, 0, 1, 1])
+ax.axis('off')
+
+if args.label:
+    for reg in skimage.measure.regionprops(label):
+        ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=args.label_color)
+
+if args.greyscale:
+    plt.imshow(img, cmap=plt.cm.gray)
+else:
+    plt.imshow(img)
+plt.contour(label, linewidths=args.thickness, colors=args.stroke_color)
+
+fig.canvas.print_png(args.out_file)
\ No newline at end of file
diff -r 000000000000 -r 5f83d67e30f1 overlay_segmentation_mask.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_segmentation_mask.xml	Mon Jan 07 05:38:10 2019 -0500
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool name="Overlay Segmentation Mask" id="ip_overlay_segmentation" version="0.0.6">
+   <description>Overlay Segmentation Mask</description>
+   <requirements>
+     <requirement type="package" version="0.14.0">scikit-image</requirement>
+     <requirement type="package" version="3.0.2">matplotlib</requirement>
+     <requirement type="package" version="5.3.0">pillow</requirement>
+     <requirement type="package" version="0.10.0">tifffile</requirement>
+   </requirements>
+   <stdio>
+     <exit_code level="fatal" range="1:"/>
+   </stdio>
+   <command interpreter="python"><![CDATA[overlay_segmentation_mask.py
+       $greyscale 
+       #if str($label_option.label) == '--label'
+         --label --label_color '$label_option.label_color'
+       #end if
+       --thickness $thickness
+       --stroke_color '$stroke_color'
+       '$input_image' '$input_mask' ./tmp.png 
+       && mv ./tmp.png '$output'
+       ]]>
+   </command>
+   <inputs>
+	    <param name="input_image" type="data" label="Image Source File" format="tif,bmp,jpg,png"/>
+      <param name="input_mask" type="data" label="Mask Source File" format="tif,bmp,jpg,png"/>
+      <param name="greyscale" type="boolean" checked='true' truevalue='--grey' falsevalue='' label="Image Is Greyscale" />
+	    <param name="thickness" size="4" type="float" value="0.3" label="Thickness" />
+	    <param name="stroke_color" type="color" value="#ff0000" label="Stroke Color"/>
+      <conditional name="label_option">
+        <param name="label" type="boolean" checked='false' truevalue='--label' falsevalue='' label="Plot Labels" />
+          <when value=""> </when>
+          <when value="--label">
+      	    <param name="label_color" type="color" value="#ffff00" label="Label Color"/>
+          </when>
+      </conditional>
+   </inputs>
+   <outputs>
+        <data format="png" name="output" />
+   </outputs>
+   <tests>
+   <test> 
+    <conditional name="label_option">
+      <param name="label" value="--label"/>
+      <param name="label_color" value="#ffff00"/>
+    </conditional>
+      <param name="stroke_color" value="#ffaa00"/>
+      <param name="label_option['label']" value="--label"/>
+      <param name="input_image" value="sample.tif"/>
+      <param name="input_mask" value="sample_seg.tif"/>
+      <param name="greyscale" value="--grey"/> 
+      <output name="output" value="outt.png" ftype="png" compare="sim_size"/>
+    </test>
+   </tests>
+   <help>
+This tool overlays a segmentation mask over an image.
+   </help>
+   <citations>
+      <citation type="doi">10.7717/peerj.453</citation>
+   </citations>
+</tool>
diff -r 000000000000 -r 5f83d67e30f1 test-data/outt.png
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diff -r 000000000000 -r 5f83d67e30f1 test-data/sample.tif
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diff -r 000000000000 -r 5f83d67e30f1 test-data/sample_seg.tif
Binary file test-data/sample_seg.tif has changed