From a91215fd31871dffa74f480240d31be4d96fe943 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 25 Apr 2024 09:26:43 +0200
Subject: [PATCH 1/3] Update `voronoi_tessellation` tool UI

---
 tools/voronoi_tessellation/voronoi_tessellation.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/voronoi_tessellation/voronoi_tessellation.xml b/tools/voronoi_tessellation/voronoi_tessellation.xml
index 1e949cc3..b4f801b4 100644
--- a/tools/voronoi_tessellation/voronoi_tessellation.xml
+++ b/tools/voronoi_tessellation/voronoi_tessellation.xml
@@ -3,7 +3,7 @@
     <macros>
         <import>creators.xml</import>
         <token name="@TOOL_VERSION@">0.22.0</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -31,7 +31,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="png,tiff" label="Input image" help="Must be a label map." />
+        <param name="input" type="data" format="png,tiff" label="Label map" />
     </inputs>
     <outputs>
        <data format="tiff" name="result" from_work_dir="result.tiff" />
@@ -54,7 +54,7 @@
     </tests>
     <help>
 
-        **Computes Voronoi tessellations for labeled images.**
+        **Computes Voronoi tessellations for label maps (labeled images).**
 
         Voronoi tessellations are also known as Vornoi diagrams, or Dirichlet tessellations.
         Zero labels are treated as image background.

From 0e7796234f46c8328f543af6b7e79dabeb1053fe Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 25 Apr 2024 09:28:52 +0200
Subject: [PATCH 2/3] Update `overlay_images` tool UI

---
 tools/overlay_images/overlay_images.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/overlay_images/overlay_images.xml b/tools/overlay_images/overlay_images.xml
index 289834ed..31bb5a12 100644
--- a/tools/overlay_images/overlay_images.xml
+++ b/tools/overlay_images/overlay_images.xml
@@ -4,7 +4,7 @@
         <import>creators.xml</import>
         <import>tests.xml</import>
         <token name="@TOOL_VERSION@">0.0.4</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <creator>
         <expand macro="creators/bmcv"/>
@@ -51,13 +51,13 @@
                 <option value="seg_contour">Segmentation contours over image</option>
             </param>
             <when value="coloc_vis">
-                <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" />
-                <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" />
+                <param name="im1" type="data" format="tiff,png" label="Image 1 (red channel)" />
+                <param name="im2" type="data" format="tiff,png" label="Image 2 (green channel)" />
             </when>
             <when value="blending">
-                <param name="im1" type="data" format="tiff,png" label="Image #1" />
-                <param name="im2" type="data" format="tiff,png" label="Image #2" />
-                <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/>
+                <param name="im1" type="data" format="tiff,png" label="Image 1" />
+                <param name="im2" type="data" format="tiff,png" label="Image 2" />
+                <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: result = (1 - weight) * image1 + weight * image2." />
             </when>
             <when value="seg_contour">
                 <param name="im1" type="data" format="tiff,png" label="Intensity image" />

From 50c4ea6b35090aac53dcad3c3634bd95986e4493 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 25 Apr 2024 10:44:25 +0200
Subject: [PATCH 3/3] Add `repeat_channels` tool

---
 tools/repeat_channels/.shed.yml               |   8 +++
 tools/repeat_channels/creators.xml            |   1 +
 tools/repeat_channels/repeat_channels.py      |  19 ++++++
 tools/repeat_channels/repeat_channels.xml     |  61 ++++++++++++++++++
 tools/repeat_channels/test-data/input1.tif    | Bin 0 -> 70481 bytes
 tools/repeat_channels/test-data/input1_c3.tif | Bin 0 -> 210947 bytes
 tools/repeat_channels/tests.xml               |   1 +
 7 files changed, 90 insertions(+)
 create mode 100644 tools/repeat_channels/.shed.yml
 create mode 120000 tools/repeat_channels/creators.xml
 create mode 100644 tools/repeat_channels/repeat_channels.py
 create mode 100644 tools/repeat_channels/repeat_channels.xml
 create mode 100644 tools/repeat_channels/test-data/input1.tif
 create mode 100644 tools/repeat_channels/test-data/input1_c3.tif
 create mode 120000 tools/repeat_channels/tests.xml

diff --git a/tools/repeat_channels/.shed.yml b/tools/repeat_channels/.shed.yml
new file mode 100644
index 00000000..a9ea49f4
--- /dev/null
+++ b/tools/repeat_channels/.shed.yml
@@ -0,0 +1,8 @@
+categories:
+  - Imaging
+description: Convert single-channel to multi-channel image
+long_description: This tools converts a single-channel image to a multi-channel image by repeating the channel multiple times.
+name: repeat_channels
+owner: imgteam
+homepage_url: https://github.com/bmcv
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/
diff --git a/tools/repeat_channels/creators.xml b/tools/repeat_channels/creators.xml
new file mode 120000
index 00000000..5d2b71e0
--- /dev/null
+++ b/tools/repeat_channels/creators.xml
@@ -0,0 +1 @@
+../../macros/creators.xml
\ No newline at end of file
diff --git a/tools/repeat_channels/repeat_channels.py b/tools/repeat_channels/repeat_channels.py
new file mode 100644
index 00000000..2ce499c1
--- /dev/null
+++ b/tools/repeat_channels/repeat_channels.py
@@ -0,0 +1,19 @@
+import argparse
+
+import giatools.io
+import numpy as np
+import skimage.io
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input', type=str)
+    parser.add_argument('count', type=int)
+    parser.add_argument('output', type=str)
+    args = parser.parse_args()
+
+    im = giatools.io.imread(args.input)
+    im = np.squeeze(im)
+    im = np.dstack([im] * args.count)
+    skimage.io.imsave(args.output, im)
diff --git a/tools/repeat_channels/repeat_channels.xml b/tools/repeat_channels/repeat_channels.xml
new file mode 100644
index 00000000..6350e499
--- /dev/null
+++ b/tools/repeat_channels/repeat_channels.xml
@@ -0,0 +1,61 @@
+<tool id="repeat_channels" name="Convert single-channel to multi-channel image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
+    <description>with NumPy</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">1.26.4</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="1.26.4">numpy</requirement>
+        <requirement type="package" version="0.18.1">scikit-image</requirement>
+        <requirement type="package" version="0.1">giatools</requirement>
+    </requirements>
+    <command><![CDATA[
+    
+    ## Inputs
+    
+    python '$__tool_directory__/repeat_channels.py'
+    '$input'
+    '$count'
+    
+    ## Outputs
+    
+    ./output.tif
+    
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tiff,png" label="Input image (single-channel)" />
+        <param name="count" type="integer" value="3" min="1" label="Number of channels" />
+    </inputs>
+    <outputs>
+        <data format="tiff" name="output" from_work_dir="output.tif" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input1.tif" />
+            <param name="count" value="3" />
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_c3.tif" ftype="tiff" />
+        </test>
+    </tests>
+    <help>
+
+        **Convert single-channel to multi-channel image.**
+
+        This tools converts a single-channel image to a multi-channel image by repeating the channel multiple times.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41586-020-2649-2</citation>
+    </citations>
+</tool>
diff --git a/tools/repeat_channels/test-data/input1.tif b/tools/repeat_channels/test-data/input1.tif
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diff --git a/tools/repeat_channels/tests.xml b/tools/repeat_channels/tests.xml
new file mode 120000
index 00000000..e20d710a
--- /dev/null
+++ b/tools/repeat_channels/tests.xml
@@ -0,0 +1 @@
+../../macros/tests.xml
\ No newline at end of file