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annotate scale_image.py @ 4:3179853faae9 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:23 +0000
parents d09507d3fb0e
children 85666e555698
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import sys
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d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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4 import numpy as np
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import skimage.io
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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6 import skimage.transform
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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7 import skimage.util
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8 from PIL import Image
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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11 def scale_image(input_file, output_file, scale, order, antialias):
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d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
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12 Image.MAX_IMAGE_PIXELS = 50000 * 50000
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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13 im = skimage.io.imread(input_file)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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15 # Parse `--scale` argument
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f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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16 if ',' in scale:
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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17 scale = [float(s.strip()) for s in scale.split(',')]
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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18 assert len(scale) <= im.ndim, f'Image has {im.ndim} axes, but scale factors were given for {len(scale)} axes.'
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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19 scale = scale + [1] * (im.ndim - len(scale))
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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21 else:
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f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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22 scale = float(scale)
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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24 # For images with 3 or more axes, the last axis is assumed to correspond to channels
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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25 if im.ndim >= 3:
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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26 scale = [scale] * (im.ndim - 1) + [1]
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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28 # Do the scaling
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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29 res = skimage.transform.rescale(im, scale, order, anti_aliasing=antialias, preserve_range=True)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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31 # Preserve the `dtype` so that both brightness and range of values is preserved
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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32 if res.dtype != im.dtype:
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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33 if np.issubdtype(im.dtype, np.integer):
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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34 res = res.round()
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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35 res = res.astype(im.dtype)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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37 # Save result
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f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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38 skimage.io.imsave(output_file, res)
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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41 if __name__ == "__main__":
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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42 parser = argparse.ArgumentParser()
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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43 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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44 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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45 parser.add_argument('--scale', type=str, required=True)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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46 parser.add_argument('--order', type=int, required=True)
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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47 parser.add_argument('--antialias', default=False, action='store_true')
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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48 args = parser.parse_args()
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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49
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 3
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50 scale_image(args.input_file.name, args.out_file.name, args.scale, args.order, args.antialias)