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annotate background_removal.py @ 1:6e9e98a7be4e draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 649a1e6ecb925bed885a8477fe82dfd9dfea8baa
author imgteam
date Tue, 30 Jul 2024 08:08:50 +0000
parents e2c6bedc6b73
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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diff changeset
1 import argparse
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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2 import warnings
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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3
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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4 import numpy as np
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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5 import skimage.io
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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6 from skimage.filters import difference_of_gaussians
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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7 from skimage.io import imread
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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8 from skimage.morphology import disk, white_tophat
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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9 from skimage.restoration import rolling_ball
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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12 def process_image(args):
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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13 image = imread(args.input_image)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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15 if args.filter == "rolling_ball":
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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16 background_rolling = rolling_ball(image, radius=args.radius)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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17 output_image = image - background_rolling
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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18
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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19 elif args.filter == "dog":
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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20 output_image = difference_of_gaussians(image, low_sigma=0, high_sigma=args.radius)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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21
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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22 elif args.filter == "top_hat":
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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23 output_image = white_tophat(image, disk(args.radius))
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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25 with warnings.catch_warnings():
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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26 output_image = convert_image_to_format_of(output_image, image)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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27 skimage.io.imsave(args.output, output_image, plugin="tifffile")
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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30 def convert_image_to_format_of(image, format_image):
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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31 """
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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32 Convert the first image to the format of the second image.
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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33 """
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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34 if format_image.dtype == image.dtype:
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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35 return image
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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36 elif format_image.dtype == np.uint8:
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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37 return skimage.util.img_as_ubyte(image)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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38 elif format_image.dtype == np.uint16:
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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39 return skimage.util.img_as_uint(image)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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40 elif format_image.dtype == np.int16:
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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41 return skimage.util.img_as_int(image)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
imgteam
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42 else:
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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43 raise ValueError(f'Unsupported image data type: {format_image.dtype}')
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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44
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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45
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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46 def main():
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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47 parser = argparse.ArgumentParser(description="Background removal script using skiimage")
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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48 parser.add_argument('input_image', help="Input image path")
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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49 parser.add_argument('filter', choices=['rolling_ball', 'dog', 'top_hat'],
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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50 help="Background removal algorithm")
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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51 parser.add_argument('radius', type=float, help="Radius")
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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52 parser.add_argument('output', help="Output image path")
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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53
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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54 args = parser.parse_args()
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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55 process_image(args)
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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56
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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57
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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58 if __name__ == '__main__':
e2c6bedc6b73 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/background_removal commit 004112ac8c2ebcdb9763096df440227fda174ae3
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59 main()