Mercurial > repos > imgteam > 2d_auto_threshold
view auto_threshold.py @ 1:4853fc2b50bf draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
author | imgteam |
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date | Tue, 23 Jul 2019 05:09:26 -0400 |
parents | d4da97f51700 |
children | 81f0cbca04a7 |
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import argparse import numpy as np import sys import skimage.io import skimage.filters import skimage.util threshOptions = { 'otsu': lambda img_raw: skimage.filters.threshold_otsu(img_raw), 'gaussian_adaptive': lambda img_raw: skimage.filters.threshold_local(img_raw, 3, method='gaussian'), 'mean_adaptive': lambda img_raw: skimage.filters.threshold_local(img_raw, 3, method='mean'), 'isodata': lambda img_raw: skimage.filters.threshold_isodata(img_raw), 'li': lambda img_raw: skimage.filters.threshold_li(img_raw), 'yen': lambda img_raw: skimage.filters.threshold_yen(img_raw), } if __name__ == "__main__": parser = argparse.ArgumentParser(description='Segment Foci') parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') parser.add_argument('thresh_type', choices=threshOptions.keys(), help='thresholding method') parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark') args = parser.parse_args() img_in = skimage.io.imread(args.input_file.name) img_in = np.reshape(img_in, [img_in.shape[0], img_in.shape[1]]) thresh = threshOptions[args.thresh_type](img_in) if args.dark_background: res = img_in > thresh else: res = img_in <= thresh res = skimage.util.img_as_uint(res) skimage.io.imsave(args.out_file.name, res, plugin="tifffile")