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annotate scale_image.py @ 1:3e4231ed875e draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit aeb095d3a95eff1cda6127a8dd757552c0405a11
author imgteam
date Thu, 28 Mar 2019 13:02:18 -0400
parents c4c76f1ebad2
children f3c05a734dd1
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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:
diff changeset
2 import sys
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 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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4 import skimage.transform
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 scipy.misc
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 import warnings
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 import os
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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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
parents:
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9
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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11 def scale_image(input_file, output_file, scale, order=1):
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 with warnings.catch_warnings():
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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13 warnings.simplefilter("ignore")
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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14 Image.MAX_IMAGE_PIXELS = 50000*50000
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 img_in = skimage.io.imread(input_file)
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 if order == 0:
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 interp = 'nearest'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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18 elif order == 1:
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 interp = 'bilinear'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 elif order == 2:
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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21 interp = 'bicubic'
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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23 if ',' in scale:
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 scale = scale[1:-1].split(',')
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 scale = [int(i) for i in scale]
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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26 elif '.' in scale:
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 scale = float(scale)
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 else:
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 scale = int(scale)
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 res = scipy.misc.imresize(img_in, scale, interp=interp)
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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32 skimage.io.imsave(output_file, res)
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
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34
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 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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36 parser = argparse.ArgumentParser()
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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37 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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38 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)')
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 parser.add_argument('scale', type=str, help='fraction scaling factor(float), percentage scaling factor(int), output size(tuple(height,width))') # integer option not implemented in galaxy wrapper
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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40 parser.add_argument('order', type=int, default=1, help='interpolation method')
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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41 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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42
1
3e4231ed875e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit aeb095d3a95eff1cda6127a8dd757552c0405a11
imgteam
parents: 0
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43 scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)