# HG changeset patch
# User imgteam
# Date 1713946293 0
# Node ID 699a5e9146b3d6f17a21e2d37590dbbc952a6fd5
# Parent  e5c8e7e72373669790e094e5427945bda8e1af5e
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c86a1b93cb7732f7331a981d13465653cc1a2790

diff -r e5c8e7e72373 -r 699a5e9146b3 auto_threshold.py
--- a/auto_threshold.py	Thu Apr 04 15:23:18 2024 +0000
+++ b/auto_threshold.py	Wed Apr 24 08:11:33 2024 +0000
@@ -7,12 +7,13 @@
 
 import argparse
 
+import giatools.io
 import numpy as np
 import skimage.filters
-import skimage.io
 import skimage.util
 import tifffile
 
+
 th_methods = {
     'manual': lambda thres, **kwargs: thres,
 
@@ -28,7 +29,7 @@
 
 
 def do_thresholding(in_fn, out_fn, th_method, block_size, offset, threshold, invert_output=False):
-    img = skimage.io.imread(in_fn)
+    img = giatools.io.imread(in_fn)
     img = np.squeeze(img)
     assert img.ndim == 2
 
diff -r e5c8e7e72373 -r 699a5e9146b3 auto_threshold.xml
--- a/auto_threshold.xml	Thu Apr 04 15:23:18 2024 +0000
+++ b/auto_threshold.xml	Wed Apr 24 08:11:33 2024 +0000
@@ -4,7 +4,7 @@
         <import>creators.xml</import>
         <import>tests.xml</import>
         <token name="@TOOL_VERSION@">0.18.1</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
         <xml name="inputs/offset">
             <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." />
         </xml>
@@ -22,6 +22,7 @@
     <requirements> 
         <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
         <requirement type="package" version="2020.10.1">tifffile</requirement>
+        <requirement type="package" version="0.1">giatools</requirement>
     </requirements>
     <command detect_errors="aggressive">
     <![CDATA[
@@ -124,6 +125,13 @@
             <param name="invert_output" value="True"/>
             <expand macro="tests/binary_image_diff" name="output" value="out4.tif" ftype="tiff"/>
         </test>
+        <!-- Tests for irregular files -->
+        <test>
+            <param name="input" value="sample2.tif"/>
+            <param name="method_id" value="otsu"/>
+            <param name="invert_output" value="False"/>
+            <expand macro="tests/binary_image_diff" name="output" value="out5.tif" ftype="tiff"/>
+        </test>
         <!-- Tests for multi-channel images -->
         <test expect_failure="true">
             <param name="input" value="rgb.png"/>
diff -r e5c8e7e72373 -r 699a5e9146b3 test-data/out5.tif
Binary file test-data/out5.tif has changed
diff -r e5c8e7e72373 -r 699a5e9146b3 test-data/sample2.tif
Binary file test-data/sample2.tif has changed