From 7f01644e3e47e320bdd9d8c1834de4aec82b0ce9 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Wed, 13 Mar 2024 14:42:27 +0100
Subject: [PATCH 1/2] Add `label_to_binary` tool

Squashed commit of the following:

commit 8b2f0909498b4067c5c767a21d129d9f23c610d0
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:39:20 2024 +0000

    Fix

commit baf90b1dd0e87ba3be55800f868abc962aaabdbe
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:37:29 2024 +0000

    Fix

commit 4fd1accfa6271ded8f073ce41d83157d8e304203
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:29:39 2024 +0000

    Fix

commit 58987c434064fa07e8cd48a07764312e128f9e6c
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:20:27 2024 +0000

    Fix requirements

commit 97e2339970c503b769f691d5b0dc89330ae5a7d3
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:14:34 2024 +0000

    Add output

commit 43a9aedddc4c4357da7eadb2616e146051de158a
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:11:02 2024 +0000

    Fix versions

commit 601e1812379b3df2aedeadb93ebbafb6e74c4bd4
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:07:47 2024 +0000

    Fix

commit e1616e428a0dc2bce5efa8fb8fab169bf0c140f4
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 13:04:33 2024 +0000

    Fix

commit c0d79a6362ef3cf1e4da37f8405de81dc8424201
Author: Leonid Kostrykin <void@evoid.de>
Date:   Wed Mar 13 12:54:38 2024 +0000

    Add `label_to_binary` tool
---
 tools/label_to_binary/.shed.yml             |   8 +++
 tools/label_to_binary/label_to_binary.py    |  18 +++++++
 tools/label_to_binary/label_to_binary.xml   |  54 ++++++++++++++++++++
 tools/label_to_binary/test-data/input1.tif  | Bin 0 -> 456 bytes
 tools/label_to_binary/test-data/output1.tif | Bin 0 -> 281 bytes
 5 files changed, 80 insertions(+)
 create mode 100644 tools/label_to_binary/.shed.yml
 create mode 100644 tools/label_to_binary/label_to_binary.py
 create mode 100644 tools/label_to_binary/label_to_binary.xml
 create mode 100644 tools/label_to_binary/test-data/input1.tif
 create mode 100644 tools/label_to_binary/test-data/output1.tif

diff --git a/tools/label_to_binary/.shed.yml b/tools/label_to_binary/.shed.yml
new file mode 100644
index 00000000..d7bcc4a5
--- /dev/null
+++ b/tools/label_to_binary/.shed.yml
@@ -0,0 +1,8 @@
+categories:
+  - Imaging
+description: Convert label map to binary image
+long_description: This tools converts a label map (objects labeled by different labels/values) to a binary image.
+name: label_to_binary 
+owner: imgteam
+homepage_url: https://github.com/bmcv
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/
diff --git a/tools/label_to_binary/label_to_binary.py b/tools/label_to_binary/label_to_binary.py
new file mode 100644
index 00000000..94b712cf
--- /dev/null
+++ b/tools/label_to_binary/label_to_binary.py
@@ -0,0 +1,18 @@
+import argparse
+
+import numpy as np
+import skimage.io
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input', type=str)
+    parser.add_argument('bg_label', type=int)
+    parser.add_argument('output', type=str)
+    args = parser.parse_args()
+
+    im = skimage.io.imread(args.input)
+    im = (im != args.bg_label)
+    im = (im * 255).astype(np.uint8)
+    skimage.io.imsave(args.output, im)
diff --git a/tools/label_to_binary/label_to_binary.xml b/tools/label_to_binary/label_to_binary.xml
new file mode 100644
index 00000000..8b729fd4
--- /dev/null
+++ b/tools/label_to_binary/label_to_binary.xml
@@ -0,0 +1,54 @@
+<tool id="label_to_binary" name="Convert label map to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 
+    <description>with NumPy</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.26.4</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <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>
+    </requirements>
+    <command><![CDATA[
+    
+    ## Inputs
+    
+    python '$__tool_directory__/label_to_binary.py'
+    '$input'
+    '$bg_label'
+    
+    ## Outputs
+    
+    ./output.tif
+    
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
+        <param argument="--bg_label" type="integer" value="0" label="Background label" />
+    </inputs>
+    <outputs>
+        <data format="tiff" name="output" from_work_dir="output.tif" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input1.tif" />
+            <param name="bg_label" value="0" />
+            <output name="output" value="output1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
+        </test>
+    </tests>
+    <help>
+        This tools converts a label map (objects labeled by different labels/values) to a binary image.
+
+        The input image is converted by assigning white (pixel value 255) to image regions corresponding to labeled objects,
+        and black (pixel value 0) to image regions corresponding to image background (by default, this is label 0).
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41586-020-2649-2</citation>
+    </citations>
+</tool>
diff --git a/tools/label_to_binary/test-data/input1.tif b/tools/label_to_binary/test-data/input1.tif
new file mode 100644
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diff --git a/tools/label_to_binary/test-data/output1.tif b/tools/label_to_binary/test-data/output1.tif
new file mode 100644
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GIT binary patch
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From 6c8c96ca614c208587d9b7ba1970b356ebad9f9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 13 Mar 2024 15:21:57 +0100
Subject: [PATCH 2/2] add profile

---
 tools/label_to_binary/label_to_binary.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/label_to_binary/label_to_binary.xml b/tools/label_to_binary/label_to_binary.xml
index 8b729fd4..9d1dedd1 100644
--- a/tools/label_to_binary/label_to_binary.xml
+++ b/tools/label_to_binary/label_to_binary.xml
@@ -1,4 +1,4 @@
-<tool id="label_to_binary" name="Convert label map to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 
+<tool id="label_to_binary" name="Convert label map to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>with NumPy</description>
     <macros>
         <token name="@TOOL_VERSION@">1.26.4</token>