From 3f7fc07c25201c93d1dda3515620a8f9db017fb8 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Tue, 12 Mar 2024 22:47:57 +0100
Subject: [PATCH 1/2] Fix bug

---
 tools/2d_auto_threshold/auto_threshold.py  |   2 +-
 tools/2d_auto_threshold/auto_threshold.xml |   6 ++++--
 tools/2d_auto_threshold/test-data/out3.tif | Bin 87489 -> 87489 bytes
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/2d_auto_threshold/auto_threshold.py b/tools/2d_auto_threshold/auto_threshold.py
index 0aeaa2f5..71f5fabe 100644
--- a/tools/2d_auto_threshold/auto_threshold.py
+++ b/tools/2d_auto_threshold/auto_threshold.py
@@ -43,7 +43,7 @@ def do_thresholding(in_fn, out_fn, th_method, block_size=5, threshold=0, invert_
     parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method')
     parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
     parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value')
-    parser.add_argument('invert_output', default=False, type=bool, help='Values below/above the threshold are labeled with 0/255 if False, and with 255/0 otherwise')
+    parser.add_argument('--invert_output', default=False, action='store_true', help='Values below/above the threshold are labeled with 0/255 by default, and with 255/0 if this argument is used')
     args = parser.parse_args()
 
     do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output)
diff --git a/tools/2d_auto_threshold/auto_threshold.xml b/tools/2d_auto_threshold/auto_threshold.xml
index a8274cfd..c6aaf725 100644
--- a/tools/2d_auto_threshold/auto_threshold.xml
+++ b/tools/2d_auto_threshold/auto_threshold.xml
@@ -2,7 +2,7 @@
     <description>with scikit-image</description>
     <macros>
         <token name="@TOOL_VERSION@">0.18.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -23,7 +23,9 @@
     '$th_method.method_id'
     '$th_method.block_size'
     '$th_method.threshold'
-    '$invert_output'
+    #if $invert_output:
+        --invert_output
+    #end if
     ]]>
     </command>
     <inputs>
diff --git a/tools/2d_auto_threshold/test-data/out3.tif b/tools/2d_auto_threshold/test-data/out3.tif
index e938abd4f67f4baa65fd34fe16a8e447601848ee..3baffa6345d1ddbba0091ac374843b893d1ca12a 100644
GIT binary patch
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From 7672f670ea127338325539247eb695f21e2314ad Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Wed, 13 Mar 2024 00:02:49 +0100
Subject: [PATCH 2/2] Simplify command

---
 tools/2d_auto_threshold/auto_threshold.xml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tools/2d_auto_threshold/auto_threshold.xml b/tools/2d_auto_threshold/auto_threshold.xml
index c6aaf725..cd686e52 100644
--- a/tools/2d_auto_threshold/auto_threshold.xml
+++ b/tools/2d_auto_threshold/auto_threshold.xml
@@ -23,9 +23,7 @@
     '$th_method.method_id'
     '$th_method.block_size'
     '$th_method.threshold'
-    #if $invert_output:
-        --invert_output
-    #end if
+    $invert_output
     ]]>
     </command>
     <inputs>
@@ -74,7 +72,7 @@
                 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
             </when>
         </conditional>
-        <param name="invert_output" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
+        <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
     </inputs>
     <outputs>
        <data format="tiff" name="output" from_work_dir="out.tif" />