Mercurial > repos > imgteam > 2d_auto_threshold

comparison auto_threshold.py @ 0:d4da97f51700 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:27:36 -0500
parents
children 4853fc2b50bf
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-1:000000000000 0:d4da97f51700
1 import argparse
2 import numpy as np
3 import os
4 import sys
5 import warnings
6 import skimage.io
7 import skimage.filters
8 import skimage.util
9
10 threshOptions = {
11 'otsu' : lambda img_raw: skimage.filters.threshold_otsu(img_raw),
12 'gaussian_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='gaussian'), # todo reshape 2d
13 'mean_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='mean'), # todo reshape 2d
14 'isodata' : lambda img_raw: skimage.filters.threshold_isodata(img_raw),
15 'li' : lambda img_raw: skimage.filters.threshold_li(img_raw),
16 'yen' : lambda img_raw: skimage.filters.threshold_yen(img_raw),
17 }
18
19 if __name__ == "__main__":
20 parser = argparse.ArgumentParser(description='Segment Foci')
21 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
22 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
23 parser.add_argument('thresh_type', choices=threshOptions.keys(), help='thresholding method')
24 parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark')
25 args = parser.parse_args()
26
27 img_in = skimage.io.imread(args.input_file.name)
28 thresh = threshOptions[args.thresh_type](img_in)
29
30 if args.dark_background:
31 res = img_in > thresh
32 else:
33 res = img_in <= thresh
34
35 with warnings.catch_warnings():
36 warnings.simplefilter("ignore")
37 res = skimage.util.img_as_uint(res)
38 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")