Add "Split image along axes" tool (#141)

* Add "Split image along axes" tool

* Add "Split image along axes" tool

* Add tests and fix bugs

* Bump giatools to 0.3.2

* Update split.py

README.md

@@ -26,6 +26,7 @@ If Galaxy Image Analysis helped with the analysis of your data, please do not fo
 - [Scale image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/ip_scale_image) with scikit-image
 - [Show image info](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo) with Bioformats
 - [Slice image into patches](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image)
+- [Split image along axes](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image) with NumPy
 - [Switch axis coordinates](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/imagecoordinates_flipaxis/imagecoordinates_flipaxis)
 
 ### Image conversion

tools/split_image/.shed.yml

@@ -0,0 +1,8 @@
+categories:
+  - Imaging
+description: Split image along axes
+long_description: This tool splits an image along a specific axis (e.g., channels).
+name: split_image
+owner: imgteam
+homepage_url: https://github.com/bmcv
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/

tools/split_image/creators.xml

@@ -0,0 +1 @@
+../../macros/creators.xml

tools/split_image/split.py

@@ -0,0 +1,44 @@
+import argparse
+import math
+
+import giatools
+import giatools.util
+import numpy as np
+import tifffile
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument('input', type=str)
+parser.add_argument('axis', type=str)
+parser.add_argument('output', type=str)
+parser.add_argument('--squeeze', action='store_true', default=False)
+args = parser.parse_args()
+
+# Validate and normalize input parameters
+assert len(args.axis) == 1, 'Axis input must be a single character.'
+axis = args.axis.replace('S', 'C')
+
+# Read input image as TZYXC
+img_in = giatools.Image.read(args.input)
+
+# Determine the axis to split along
+axis_pos = img_in.axes.index(axis)
+
+# Perform the splitting
+arr = np.moveaxis(img_in.data, axis_pos, 0)
+decimals = math.ceil(math.log10(1 + arr.shape[0]))
+output_filename_pattern = f'{args.output}/%0{decimals}d.tiff'
+for img_idx, img in enumerate(arr):
+    img = np.moveaxis(img[None], 0, axis_pos)
+
+    # Optionally, squeeze the image
+    if args.squeeze:
+        s = [axis_pos for axis_pos in range(len(img_in.axes)) if img.shape[axis_pos] == 1 and img_in.axes[axis_pos] not in 'YX']
+        img = np.squeeze(img, axis=tuple(s))
+        img_axes = giatools.util.str_without_positions(img_in.axes, s)
+    else:
+        img_axes = img_in.axes
+
+    # Save the result
+    filename = output_filename_pattern % (img_idx + 1)
+    tifffile.imwrite(filename, img, metadata=dict(axes=img_axes))

tools/split_image/split_image.xml

@@ -0,0 +1,108 @@
+<tool id="ip_split_image" name="Split image along axes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>with NumPy</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">2.2.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">numpy</requirement>
+        <requirement type="package" version="0.3.2">giatools</requirement>
+        <requirement type="package" version="2024.7.24">tifffile</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+
+        mkdir output &&
+        python '$__tool_directory__/split.py'
+
+        '$input'
+        '$axis'
+        output
+
+        $squeeze
+
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tiff,png" label="Image to split" />
+        <param name="axis" type="select" label="Axis to split along">
+            <option value="T">T-axis (split the frames of a temporal image sequence)</option>
+            <option value="Z">Z-axis (split the slices of a 3-D image or image sequence)</option>
+            <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option>
+            <option value="S">S-axis (split the samples of an image or image sequence)</option>
+        </param>
+        <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result imags" help="Only axes with more than one element will be retained in the result images. Does not apply for X and Y axes." />
+    </inputs>
+    <outputs>
+        <collection type="list" name="output" label="Split ${on_string} along ${axis} axis">
+            <discover_datasets directory="output" pattern="__name__" format="tiff" />
+        </collection>
+    </outputs>
+    <tests>
+
+        <!-- PNG tests -->
+        <test>
+            <param name="input" value="rgb1.png" />
+            <param name="axis" value="C" />
+            <param name="squeeze" value="false" />
+            <output_collection name="output" type="list" count="3">
+                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_r.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_g.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+
+        <!-- TIFF tests -->
+        <test>
+            <param name="input" value="zcyx.tiff" />
+            <param name="axis" value="Z" />
+            <param name="squeeze" value="false" />
+            <output_collection name="output" type="list" count="25">
+                <expand macro="tests/intensity_image_diff/element" name="01.tiff" value="zcyx_slice01.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="25.tiff" value="zcyx_slice25.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+
+        <!-- Test squeezing -->
+        <test>
+            <param name="input" value="rgb1.png" />
+            <param name="axis" value="C" />
+            <param name="squeeze" value="true" />
+            <output_collection name="output" type="list" count="3">
+                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_squeezed_r.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_squeezed_g.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+
+        <!-- Test with missing axes -->
+        <test>
+            <param name="input" value="rgb1.png" />
+            <param name="axis" value="Z" />
+            <param name="squeeze" value="false" />
+            <output_collection name="output" type="list" count="1">
+                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+
+    </tests>
+    <help>
+
+        **Splits an image along a specific axis (e.g., channels).**
+
+        This tool splits an image along a specifc axis and yields a collection of images.
+        This can be used, for example, to convert a multi-channel image into a collection of single-channel images.
+
+        The pixel data type of the split image is preserved (will be the same as the input image).
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41586-020-2649-2</citation>
+    </citations>
+</tool>

tools/split_image/tests.xml

@@ -0,0 +1 @@
+../../macros/tests.xml