# HG changeset patch
# User imgteam
# Date 1549738977 18000
# Node ID 6fc65082d1e66c2291170132e8f34b2b4c1d5392

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5

diff -r 000000000000 -r 6fc65082d1e6 auto_threshold.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_threshold.py	Sat Feb 09 14:02:57 2019 -0500
@@ -0,0 +1,38 @@
+import argparse
+import numpy as np
+import os
+import sys
+import warnings
+import skimage.io
+import skimage.filters
+import skimage.util
+
+threshOptions = {
+    'otsu' : lambda img_raw: skimage.filters.threshold_otsu(img_raw),
+    'gaussian_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='gaussian'), # todo reshape 2d
+    'mean_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='mean'), # todo reshape 2d
+    'isodata' : lambda img_raw: skimage.filters.threshold_isodata(img_raw),
+    'li' : lambda img_raw: skimage.filters.threshold_li(img_raw),
+    'yen' : lambda img_raw: skimage.filters.threshold_yen(img_raw),
+}
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Segment Foci')
+    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('thresh_type', choices=threshOptions.keys(), help='thresholding method')
+    parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark')
+    args = parser.parse_args()
+
+    img_in = skimage.io.imread(args.input_file.name)
+    thresh = threshOptions[args.thresh_type](img_in)
+
+    if args.dark_background:
+        res = img_in > thresh
+    else:
+        res = img_in <= thresh
+
+    with warnings.catch_warnings():
+    	warnings.simplefilter("ignore")
+    	res = skimage.util.img_as_uint(res)
+    	skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
diff -r 000000000000 -r 6fc65082d1e6 auto_threshold.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_threshold.xml	Sat Feb 09 14:02:57 2019 -0500
@@ -0,0 +1,49 @@
+<tool id="ip_threshold" name="Auto Threshold" version="0.0.3">
+   <description>applies a standard threshold algorithm 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 '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background
+   ]]>
+   </command>
+   <inputs>
+        <param name="input" type="data" format="tiff" label="Source file" />
+        <param name="thresh_type" type="select" label="Threshold Algorithm">
+          <option value="otsu" selected="True">Otsu</option>
+          <option value="li">Li’s Minimum Cross Entropy</option>
+          <option value="isodata">Isodata</option>
+          <option value="gaussian_adaptive">Adaptive (Gauss)</option>
+          <option value="mean_adaptive">Adaptive (Mean)</option>
+          <option value="yen">Yen</option>
+        </param>
+        <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
+    </inputs>
+    <outputs>
+       <data format="tiff" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sample.tif"/>
+            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
+            <param name="thresh_type" value="gaussian_adaptive"/>
+            <param name="dark_backgroud" value="True"/>
+        </test>
+        <test>
+            <param name="input" value="sample.tif"/>
+            <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
+            <param name="thresh_type" value="otsu"/>
+            <param name="dark_backgroud" value="True"/>
+        </test>
+    </tests>
+    <help>
+        Applies a standard threshold algorithm to an image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 6fc65082d1e6 test-data/out.tif
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diff -r 000000000000 -r 6fc65082d1e6 test-data/out2.tif
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diff -r 000000000000 -r 6fc65082d1e6 test-data/sample.tif
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