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changeset 0:e2c6bedc6b73 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
author imgteam
date Mon, 15 Jul 2024 20:55:08 +0000
parents
children 6e9e98a7be4e
files background_removal.py background_removal.xml creators.xml test-data/input1_output_dog.tif test-data/input1_uint8.tif test-data/input2_output_dog.tif test-data/input2_output_rb.tif test-data/input2_uint16.tif test-data/input3_output_tophat.tif test-data/input3_uint8.tif tests.xml
diffstat 11 files changed, 254 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/background_removal.py	Mon Jul 15 20:55:08 2024 +0000
@@ -0,0 +1,59 @@
+import argparse
+import warnings
+
+import numpy as np
+import skimage.io
+from skimage.filters import difference_of_gaussians
+from skimage.io import imread
+from skimage.morphology import disk, white_tophat
+from skimage.restoration import rolling_ball
+
+
+def process_image(args):
+    image = imread(args.input_image)
+
+    if args.filter == "rolling_ball":
+        background_rolling = rolling_ball(image, radius=args.radius)
+        output_image = image - background_rolling
+
+    elif args.filter == "dog":
+        output_image = difference_of_gaussians(image, low_sigma=0, high_sigma=args.radius)
+
+    elif args.filter == "top_hat":
+        output_image = white_tophat(image, disk(args.radius))
+
+    with warnings.catch_warnings():
+        output_image = convert_image_to_format_of(output_image, image)
+        skimage.io.imsave(args.output, output_image, plugin="tifffile")
+
+
+def convert_image_to_format_of(image, format_image):
+    """
+    Convert the first image to the format of the second image.
+    """
+    if format_image.dtype == image.dtype:
+        return image
+    elif format_image.dtype == np.uint8:
+        return skimage.util.img_as_ubyte(image)
+    elif format_image.dtype == np.uint16:
+        return skimage.util.img_as_uint(image)
+    elif format_image.dtype == np.int16:
+        return skimage.util.img_as_int(image)
+    else:
+        raise ValueError(f'Unsupported image data type: {format_image.dtype}')
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Background removal script using skiimage")
+    parser.add_argument('input_image', help="Input image path")
+    parser.add_argument('filter', choices=['rolling_ball', 'dog', 'top_hat'],
+                        help="Background removal algorithm")
+    parser.add_argument('radius', type=float, help="Radius")
+    parser.add_argument('output', help="Output image path")
+
+    args = parser.parse_args()
+    process_image(args)
+
+
+if __name__ == '__main__':
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/background_removal.xml	Mon Jul 15 20:55:08 2024 +0000
@@ -0,0 +1,72 @@
+<tool id="background_removal" name="Remove image background" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+        <description>with scikit-image</description>  
+    <macros>  
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">0.24.0</token>  
+        <token name="@VERSION_SUFFIX@">0</token>  
+    </macros>  
+    <creator>
+        <expand macro="creators/rmassei"/>
+    </creator>
+    <requirements>
+        <requirement type="package" version="0.24.0">scikit-image</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        python "$__tool_directory__/background_removal.py" $input_image $filter $radius $output
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_image" type="data" format="tiff, jpg, jpeg, png, tif" label="Input Image"/>
+        <param name="filter" type="select" label="Select Filter">
+            <option value="rolling_ball">Rolling-ball algorithm</option>
+            <option value="dog">Difference of Gaussians</option>
+            <option value="top_hat">Top-hat filter</option>
+        </param>
+        <param name="radius" type="float" label="Radius" value="20"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tiff" label="Background substraction output"/>
+    </outputs>
+    <tests>
+        <!-- uint8 tests -->  
+        <test>  
+            <param name="input_image" value="input1_uint8.tif"/>  
+            <param name="filter" value="dog"/>  
+            <param name="radius" value="20"/>  
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_output_dog.tif" ftype="tiff"/>  
+        </test> 
+        <test>
+            <param name="input_image" value="input3_uint8.tif"/>
+            <param name="filter" value="top_hat"/>
+            <param name="radius" value="15"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="input3_output_tophat.tif" ftype="tiff"/>
+        </test>
+        <!-- uint16 tests -->  
+        <test>  
+            <param name="input_image" value="input2_uint16.tif"/>
+            <param name="filter" value="rolling_ball"/>
+            <param name="radius" value="20"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="input2_output_rb.tif" ftype="tiff"/>
+        </test>
+        <test>
+            <param name="input_image" value="input2_uint16.tif"/>
+            <param name="filter" value="dog"/>
+            <param name="radius" value="20"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="input2_output_dog.tif" ftype="tiff"/>
+        </test>
+    </tests>
+    <help>
+        This tool applies different background removal algorithms to an image:
+
+        - Rolling-ball algorithm
+
+        - Difference of Gaussians
+
+        - Top-hat filter
+    </help>
+    <citations>
+        <citation type="doi">10.1109/MC.1983.1654163</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml	Mon Jul 15 20:55:08 2024 +0000
@@ -0,0 +1,28 @@
+<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/rmassei">
+        <person givenName="Riccardo" familyName="Massei"/>
+        <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_output_dog.tif has changed
Binary file test-data/input1_uint8.tif has changed
Binary file test-data/input2_output_dog.tif has changed
Binary file test-data/input2_output_rb.tif has changed
Binary file test-data/input2_uint16.tif has changed
Binary file test-data/input3_output_tophat.tif has changed
Binary file test-data/input3_uint8.tif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml	Mon Jul 15 20:55:08 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>