# HG changeset patch
# User imgteam
# Date 1721076908 0
# Node ID e2c6bedc6b734e1216dee23bc5bcb82845226c81
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
diff -r 000000000000 -r e2c6bedc6b73 background_removal.py
--- /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()
diff -r 000000000000 -r e2c6bedc6b73 background_removal.xml
--- /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 @@
+
+ with scikit-image
+
+ creators.xml
+ tests.xml
+ 0.24.0
+ 0
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+ This tool applies different background removal algorithms to an image:
+
+ - Rolling-ball algorithm
+
+ - Difference of Gaussians
+
+ - Top-hat filter
+
+
+ 10.1109/MC.1983.1654163
+
+
diff -r 000000000000 -r e2c6bedc6b73 creators.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml Mon Jul 15 20:55:08 2024 +0000
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input1_output_dog.tif
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input1_uint8.tif
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input2_output_dog.tif
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input2_output_rb.tif
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input2_uint16.tif
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input3_output_tophat.tif
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diff -r 000000000000 -r e2c6bedc6b73 test-data/input3_uint8.tif
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diff -r 000000000000 -r e2c6bedc6b73 tests.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml Mon Jul 15 20:55:08 2024 +0000
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