Merge pull request BMCV#125 from rmassei/master

Add background_removal tool (skimage)

macros/creators.xml

@@ -5,6 +5,11 @@
         <yield />
     </xml>
 
+    <xml name="creators/rmassei">
+        <person givenName="Riccardo" familyName="Massei"/>
+        <yield/>
+    </xml>
+
     <xml name="creators/alliecreason">
         <person givenName="Allison" familyName="Creason"/>
         <yield/>

tools/background_removal/.shed.yml

@@ -0,0 +1,8 @@
+categories:
+  - Imaging
+description: Background removal filters using scikit-image
+long_description: Tool to perform a background removal using 1) Rolling-Ball Algorithm, 2) Difference of Gaussians and 3) Top-Hat Filter
+name: background_removal
+owner: ufz
+homepage_url: https://github.com/bmcv
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/background_removal

tools/background_removal/background_removal.py

@@ -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()

tools/background_removal/background_removal.xml

@@ -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>

tools/background_removal/creators.xml

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

tools/background_removal/tests.xml

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