Mercurial > repos > imgteam > 2d_simple_filter
comparison filter_image.py @ 0:f264ae82f735 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author | imgteam |
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date | Sat, 09 Feb 2019 14:29:13 -0500 |
parents | |
children | dba87c4b32d3 |
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-1:000000000000 | 0:f264ae82f735 |
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1 import argparse | |
2 import sys | |
3 import warnings | |
4 import numpy as np | |
5 import skimage.io | |
6 import skimage.filters | |
7 import skimage.util | |
8 from skimage.morphology import disk | |
9 | |
10 filterOptions = { | |
11 'median' : lambda img_raw, radius: skimage.filters.median(img_raw, disk(radius)), | |
12 'gaussian' : lambda img_raw, radius: skimage.filters.gaussian(img_raw, sigma=radius), | |
13 'prewitt' : lambda img_raw, radius: skimage.filters.prewitt(img_raw), | |
14 'sobel' : lambda img_raw, radius: skimage.filters.sobel(img_raw), | |
15 'scharr' : lambda img_raw, radius: skimage.filters.scharr(img_raw), | |
16 } | |
17 | |
18 if __name__ == "__main__": | |
19 parser = argparse.ArgumentParser() | |
20 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | |
21 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | |
22 parser.add_argument('filter_type', choices=filterOptions.keys(), help='conversion type') | |
23 parser.add_argument('radius', default=3.0, type=float, help='Radius/Sigma') | |
24 args = parser.parse_args() | |
25 | |
26 img_in = skimage.io.imread(args.input_file.name) | |
27 res = filterOptions[args.filter_type](img_in, args.radius) | |
28 res[res<-1]=-1 | |
29 res[res>1]=1 | |
30 | |
31 with warnings.catch_warnings(): | |
32 warnings.simplefilter("ignore") | |
33 res = skimage.util.img_as_uint(res) #Attention: precision loss | |
34 skimage.io.imsave(args.out_file.name, res, plugin='tifffile') |