Mercurial > repos > imgteam > 2d_auto_threshold
view auto_threshold.py @ 6:8bccb36e055a draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit cb3d628f4c91e996e10dcb35b1168332e692293a
author | imgteam |
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date | Wed, 13 Mar 2024 06:15:54 +0000 |
parents | 7db4fc31dbee |
children | e5c8e7e72373 |
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""" Copyright 2017-2024 Biomedical Computer Vision Group, Heidelberg University. Distributed under the MIT license. See file LICENSE for detail or copy at https://opensource.org/licenses/MIT """ import argparse import numpy as np import skimage.filters import skimage.io import skimage.util import tifffile th_methods = { 'manual': lambda thres, **kwargs: thres, 'otsu': lambda img_raw, **kwargs: skimage.filters.threshold_otsu(img_raw), 'li': lambda img_raw, **kwargs: skimage.filters.threshold_li(img_raw), 'yen': lambda img_raw, **kwargs: skimage.filters.threshold_yen(img_raw), 'isodata': lambda img_raw, **kwargs: skimage.filters.threshold_isodata(img_raw), 'loc_gaussian': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='gaussian'), 'loc_median': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='median'), 'loc_mean': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='mean') } def do_thresholding(in_fn, out_fn, th_method, block_size=5, threshold=0, invert_output=False): img = skimage.io.imread(in_fn) th = th_methods[th_method](img_raw=img, bz=block_size, thres=threshold) res = img > th if invert_output: res = np.logical_not(res) tifffile.imwrite(out_fn, skimage.util.img_as_ubyte(res)) if __name__ == "__main__": parser = argparse.ArgumentParser(description='Automatic Image Thresholding') parser.add_argument('im_in', help='Path to the input image') parser.add_argument('im_out', help='Path to the output image (TIFF)') parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method') parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold') parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value') parser.add_argument('--invert_output', default=False, action='store_true', help='Values below/above the threshold are labeled with 0/255 by default, and with 255/0 if this argument is used') args = parser.parse_args() do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output)