Mercurial > repos > thomaswollmann > scale_image

comparison scale_image.py @ 0:2d69cbf0f2d2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:2d69cbf0f2d2
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)