Mercurial > repos > imgteam > scale_image
annotate scale_image.py @ 2:f3c05a734dd1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author | imgteam |
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date | Mon, 22 Jul 2019 05:04:55 -0400 |
parents | 3e4231ed875e |
children | d09507d3fb0e |
rev | line source |
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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
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1 import argparse |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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2 import sys |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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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:
diff
changeset
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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:
diff
changeset
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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
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6 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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changeset
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7 |
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f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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8 |
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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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changeset
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9 def scale_image(input_file, output_file, scale, order=1): |
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f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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10 Image.MAX_IMAGE_PIXELS = 50000*50000 |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
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changeset
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11 img_in = skimage.io.imread(input_file) |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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12 if order == 0: |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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13 interp = 'nearest' |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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14 elif order == 1: |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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15 interp = 'bilinear' |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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16 elif order == 2: |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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17 interp = 'bicubic' |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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18 if ',' in scale: |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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19 scale = scale[1:-1].split(',') |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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20 scale = [int(i) for i in scale] |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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21 elif '.' in scale: |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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22 scale = float(scale) |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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23 else: |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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24 scale = int(scale) |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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25 res = scipy.misc.imresize(img_in, scale, interp=interp) |
f3c05a734dd1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
1
diff
changeset
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26 skimage.io.imsave(output_file, res) |
0
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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27 |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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28 |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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29 if __name__ == "__main__": |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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30 parser = argparse.ArgumentParser() |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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31 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:
diff
changeset
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32 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
parents:
diff
changeset
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33 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
parents:
diff
changeset
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34 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
parents:
diff
changeset
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35 args = parser.parse_args() |
c4c76f1ebad2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
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36 |
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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37 scale_image(args.input_file.name, args.out_file.name, args.scale, args.order) |