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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
author imgteam
date Thu, 17 Oct 2024 10:47:14 +0000
parents ac497ba6819d
children
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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diff changeset
1 import argparse
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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2 import sys
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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4 import giatools.io
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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5 import numpy as np
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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6 import skimage.io
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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7 import skimage.transform
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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8 import skimage.util
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9 from PIL import Image
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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parents: 2
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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12 def scale_image(input_file, output_file, scale, order, antialias):
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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13 Image.MAX_IMAGE_PIXELS = 50000 * 50000
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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14 im = giatools.io.imread(input_file)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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16 # Parse `--scale` argument
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ac497ba6819d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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17 if ',' in scale:
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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18 scale = [float(s.strip()) for s in scale.split(',')]
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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19 assert len(scale) <= im.ndim, f'Image has {im.ndim} axes, but scale factors were given for {len(scale)} axes.'
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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20 scale = scale + [1] * (im.ndim - len(scale))
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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22 else:
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ac497ba6819d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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23 scale = float(scale)
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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25 # For images with 3 or more axes, the last axis is assumed to correspond to channels
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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26 if im.ndim >= 3:
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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27 scale = [scale] * (im.ndim - 1) + [1]
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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29 # Do the scaling
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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30 res = skimage.transform.rescale(im, scale, order, anti_aliasing=antialias, preserve_range=True)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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32 # Preserve the `dtype` so that both brightness and range of values is preserved
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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33 if res.dtype != im.dtype:
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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34 if np.issubdtype(im.dtype, np.integer):
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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35 res = res.round()
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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36 res = res.astype(im.dtype)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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38 # Save result
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ac497ba6819d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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39 skimage.io.imsave(output_file, res)
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 if __name__ == "__main__":
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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43 parser = argparse.ArgumentParser()
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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44 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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45 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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46 parser.add_argument('--scale', type=str, required=True)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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47 parser.add_argument('--order', type=int, required=True)
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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48 parser.add_argument('--antialias', default=False, action='store_true')
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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49 args = parser.parse_args()
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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50
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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51 scale_image(args.input_file.name, args.out_file.name, args.scale, args.order, args.antialias)