Mercurial > repos > iuc > 2d_auto_threshold

annotate auto_threshold.py @ 0:c5a508979531 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/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
author iuc
date Sat, 09 Feb 2019 11:24:40 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
1 import argparse
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
2 import numpy as np
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
3 import os
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
4 import sys
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
5 import warnings
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
6 import skimage.io
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
7 import skimage.filters
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
8 import skimage.util
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
9
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
10 threshOptions = {
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
11 'otsu' : lambda img_raw: skimage.filters.threshold_otsu(img_raw),
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
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
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
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
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
14 'isodata' : lambda img_raw: skimage.filters.threshold_isodata(img_raw),
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
15 'li' : lambda img_raw: skimage.filters.threshold_li(img_raw),
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
16 'yen' : lambda img_raw: skimage.filters.threshold_yen(img_raw),
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
17 }
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
18
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
19 if __name__ == "__main__":
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
20 parser = argparse.ArgumentParser(description='Segment Foci')
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
21 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
22 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
23 parser.add_argument('thresh_type', choices=threshOptions.keys(), help='thresholding method')
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
24 parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark')
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
25 args = parser.parse_args()
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
26
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
27 img_in = skimage.io.imread(args.input_file.name)
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
28 thresh = threshOptions[args.thresh_type](img_in)
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
29
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
30 if args.dark_background:
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
31 res = img_in > thresh
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
32 else:
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
33 res = img_in <= thresh
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
34
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
35 with warnings.catch_warnings():
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
36 warnings.simplefilter("ignore")
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
37 res = skimage.util.img_as_uint(res)
c5a508979531 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
iuc
parents:
diff changeset
38 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")