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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 05:39:54 -0500
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2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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diff changeset
1 import argparse
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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2 import sys
2d69cbf0f2d2 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
2d69cbf0f2d2 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
2d69cbf0f2d2 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
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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6 import warnings
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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7 import os
2d69cbf0f2d2 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
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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9
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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10
2d69cbf0f2d2 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):
2d69cbf0f2d2 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():
2d69cbf0f2d2 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")
2d69cbf0f2d2 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
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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15 img_in = skimage.io.imread(input_file)
2d69cbf0f2d2 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:
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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17 interp = 'nearest'
2d69cbf0f2d2 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:
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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19 interp = 'bilinear'
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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20 elif order == 2:
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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21 interp = 'bicubic'
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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22
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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23 if ',' in scale:
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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24 scale = scale[1:-1].split(',')
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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25 scale.reverse()
2d69cbf0f2d2 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]
2d69cbf0f2d2 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:
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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28 scale = float(scale)
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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29 else:
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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30 scale = int(scale)
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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2d69cbf0f2d2 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)
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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33 skimage.io.imsave(output_file, res)
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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34
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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36 if __name__ == "__main__":
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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37 parser = argparse.ArgumentParser()
2d69cbf0f2d2 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')
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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39 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)')
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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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
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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41 parser.add_argument('order', type=int, default=1, help='interpolation method')
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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42 args = parser.parse_args()
2d69cbf0f2d2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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2d69cbf0f2d2 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)