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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 04:59:02 -0500
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35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
parents:
diff changeset
1 import argparse
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
parents:
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2 import sys
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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3 import skimage.io
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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4 import skimage.transform
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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5 import scipy.misc
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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6 import warnings
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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7 import os
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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8 from PIL import Image
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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9
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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10
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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11 def scale_image(input_file, output_file, scale, order=1):
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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12 with warnings.catch_warnings():
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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13 warnings.simplefilter("ignore")
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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14 Image.MAX_IMAGE_PIXELS = 50000*50000
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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15 img_in = skimage.io.imread(input_file)
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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16 if order == 0:
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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17 interp = 'nearest'
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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18 elif order == 1:
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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19 interp = 'bilinear'
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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20 elif order == 2:
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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21 interp = 'bicubic'
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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22
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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23 if ',' in scale:
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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24 scale = scale[1:-1].split(',')
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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25 scale.reverse()
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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26 scale = [int(i) for i in scale]
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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27 elif '.' in scale:
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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28 scale = float(scale)
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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29 else:
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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30 scale = int(scale)
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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32 res = scipy.misc.imresize(img_in, scale, interp=interp)
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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33 skimage.io.imsave(output_file, res)
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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35
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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36 if __name__ == "__main__":
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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37 parser = argparse.ArgumentParser()
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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38 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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39 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)')
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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40 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
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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41 parser.add_argument('order', type=int, default=1, help='interpolation method')
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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42 args = parser.parse_args()
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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43
35ad679613a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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44 scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)