Mercurial > repos > imgteam > scale_image

comparison scale_image.py @ 0:c4c76f1ebad2 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:46:03 -0500
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children 3e4231ed875e
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-1:000000000000 0:c4c76f1ebad2
1 import argparse
2 import sys
3 import skimage.io
4 import skimage.transform
5 import scipy.misc
6 import warnings
7 import os
8 from PIL import Image
9
10
11 def scale_image(input_file, output_file, scale, order=1):
12 with warnings.catch_warnings():
13 warnings.simplefilter("ignore")
14 Image.MAX_IMAGE_PIXELS = 50000*50000
15 img_in = skimage.io.imread(input_file)
16 if order == 0:
17 interp = 'nearest'
18 elif order == 1:
19 interp = 'bilinear'
20 elif order == 2:
21 interp = 'bicubic'
22
23 if ',' in scale:
24 scale = scale[1:-1].split(',')
25 scale.reverse()
26 scale = [int(i) for i in scale]
27 elif '.' in scale:
28 scale = float(scale)
29 else:
30 scale = int(scale)
31
32 res = scipy.misc.imresize(img_in, scale, interp=interp)
33 skimage.io.imsave(output_file, res)
34
35
36 if __name__ == "__main__":
37 parser = argparse.ArgumentParser()
38 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
39 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)')
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
41 parser.add_argument('order', type=int, default=1, help='interpolation method')
42 args = parser.parse_args()
43
44 scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)