changeset 3:4c43875c790c draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f

--- a/concat_channels.py	Mon Nov 13 22:10:47 2023 +0000
+++ b/concat_channels.py	Thu Apr 04 15:25:29 2024 +0000
@@ -1,33 +1,42 @@
 import argparse
-import warnings
 
 import numpy as np
 import skimage.io
 import skimage.util
 
 
-def concat_channels(input_image_paths, output_image_path, axis):
+def concat_channels(input_image_paths, output_image_path, axis, preserve_values):
     images = []
     for image_path in input_image_paths:
+
         raw_image = skimage.io.imread(image_path)
         if len(raw_image.shape) == 2:
             if axis == 0:
                 raw_image = [raw_image]
             else:
                 raw_image = np.expand_dims(raw_image, 2)
+
+        # Preserve values: Convert to `float` dtype without changing the values
+        if preserve_values:
+            raw_image = raw_image.astype(float)
+
+        # Preserve brightness: Scale values to 0..1
+        else:
+            raw_image = skimage.util.img_as_float(raw_image)
+
         images.append(raw_image)
+
+    # Do the concatenation and save
     res = np.concatenate(images, axis)
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore")
-        res = skimage.util.img_as_uint(res)  # Attention: precision loss
-        skimage.io.imsave(output_image_path, res, plugin='tifffile')
+    skimage.io.imsave(output_image_path, res, plugin='tifffile')
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+', help='input file')
-    parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'), help='out file (TIFF)')
-    parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0, 2], help='concatenation axis')
+    parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+')
+    parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'))
+    parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0, 2])
+    parser.add_argument('--preserve_values', default=False, action='store_true')
     args = parser.parse_args()
 
-    concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis)
+    concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis, args.preserve_values)

--- a/concat_channels.xml	Mon Nov 13 22:10:47 2023 +0000
+++ b/concat_channels.xml	Thu Apr 04 15:25:29 2024 +0000
@@ -1,5 +1,12 @@
-<tool id="ip_concat_channels" name="Concatenate images or channels" version="0.2-2">
+<tool id="ip_concat_channels" name="Concatenate images or channels" version="0.3-0" profile="20.05">
     <description></description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -7,40 +14,71 @@
         <xref type="bio.tools">galaxy_image_analysis</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="0.14.2">scikit-image</requirement>
-        <requirement type="package" version="1.15.4">numpy</requirement>
-        <requirement type="package" version="0.15.1">tifffile</requirement>
+        <requirement type="package" version="0.18.3">scikit-image</requirement>
+        <requirement type="package" version="1.24.1">numpy</requirement>
+        <requirement type="package" version="2021.7.2">tifffile</requirement>
     </requirements>
-    <command detect_errors="aggressive">
-    <![CDATA[
-        python '$__tool_directory__/concat_channels.py' 
+    <command detect_errors="aggressive"><![CDATA[
+
+        python '$__tool_directory__/concat_channels.py'
+
         #for $input in $inputs
-            '$input' 
+            '$input'
         #end for
+
+        $mode
+
         -o '$output' --axis '$axis'
-    ]]>
-    </command>
+
+    ]]></command>
     <inputs>
-        <param name="inputs" type="data" multiple="true" format="tiff,png,jpg,bmp" label="Binary Image Files" help="one or multiple binary image fiels"/>
-        <param name="axis" type="select" label="Concatenation Axis">
-            <option value="0">0</option>
-            <option value="2">2</option>
+        <param name="inputs" type="data" multiple="true" format="tiff,png" label="Images to concatenate"/>
+        <param name="axis" type="integer" min="0" value="0" label="Concatenation axis" help="The images will be concatenated along this axis. For a 2-D image, a value of 0 corresponds to horizontal concatenation, and a value of 1 to vertical concatenation. For an RGB image, a value of 2 corresponds to concatenation of the channels of the images."/>
+        <param name="mode" type="select" label="Scaling of values" help="If the brightness is to be preserved (default), then the values will be scaled between 0 and 1, and the pixel type will be float.">
+            <option value="" selected="true">Preserve brightness</option>
+            <option value="--preserve_values">Preserve range of values</option>
         </param>
     </inputs>
     <outputs>
         <data format="tiff" name="output"/>
     </outputs>
     <tests>
+        <!-- Test with "preserve brightness" -->
         <test>
-            <param name="inputs" value="sample1.png,sample2.png"/>
+            <param name="inputs" value="input1_uint8.png,input2_float.tiff"/>
+            <param name="axis" value="0"/>
+            <param name="mode" value=""/>
+            <expand macro="tests/intensity_image_diff" name="output" value="res_preserve_brightness.tiff" ftype="tiff"/>
+        </test>
+        <!-- Test with "preserve range of values" -->
+        <test>
+            <param name="inputs" value="input1_uint8.png,input2_float.tiff"/>
             <param name="axis" value="0"/>
-            <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>
+            <param name="mode" value="--preserve_values"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="res_preserve_values.tiff" ftype="tiff">
+                <!--
+
+                The input files have values ranging between 0 and 255.
+
+                Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
+                values is preserved. The motiviation behind this is that the expectation images are usually checked
+                visually, which means that the `image_diff` comparison is likely to ensure that the brightness of
+                the image is correct, thus it's good to double-check the range of values.
+
+                -->
+                <has_image_mean_intensity min="0" max="255"/>
+            </expand>
         </test>
     </tests>
     <help>
-    **What it does**
+
+        **Concatenates images along arbitrary axes.**
 
-    This tool concatenates images.
+        This can be used, for example, to spatially concatenate images, or along their channels.
+
+        This tool either preserves the image brightness, or the range of values.
+        In general, both cannot be preserved when concatenating images of different pixel types (e.g., uint8 and uint16).
+
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml	Thu Apr 04 15:25:29 2024 +0000
@@ -0,0 +1,23 @@
+<macros>
+
+    <xml name="creators/bmcv">
+        <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        <yield />
+    </xml>
+
+    <xml name="creators/alliecreason">
+        <person givenName="Allison" familyName="Creason"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/bugraoezdemir">
+        <person givenName="Bugra" familyName="Oezdemir"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/thawn">
+        <person givenName="Till" familyName="Korten"/>
+        <yield/>
+    </xml>
+    
+</macros>

Binary file test-data/input1_uint8.png has changed

Binary file test-data/input2_float.tiff has changed

Binary file test-data/out.tiff has changed

Binary file test-data/res.tiff has changed

Binary file test-data/res_preserve_brightness.tiff has changed

Binary file test-data/res_preserve_values.tiff has changed

Binary file test-data/sample1.png has changed

Binary file test-data/sample2.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml	Thu Apr 04 15:25:29 2024 +0000
@@ -0,0 +1,95 @@
+<macros>
+
+    <!-- Macros for verification of image outputs -->
+
+    <xml
+        name="tests/binary_image_diff"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="mae"
+        token_eps="0.01">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0">
+            <assert_contents>
+                <has_image_n_labels n="2"/>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <xml
+        name="tests/label_image_diff"
+        tokens="name,value,ftype,metric,eps,pin_labels"
+        token_metric="iou"
+        token_eps="0.01"
+        token_pin_labels="0">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <xml
+        name="tests/intensity_image_diff"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="rms"
+        token_eps="0.01">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <!-- Variants of the above for verification of collection elements -->
+
+    <xml
+        name="tests/binary_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="mae"
+        token_eps="0.01">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0">
+            <assert_contents>
+                <has_image_n_labels n="2"/>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+    <xml
+        name="tests/label_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="iou"
+        token_eps="0.01"
+        token_pin_labels="0">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+    <xml
+        name="tests/intensity_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="rms"
+        token_eps="0.01">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+</macros>