Mercurial > repos > imgteam > 2d_auto_threshold
diff auto_threshold.py @ 7:e5c8e7e72373 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author | imgteam |
---|---|
date | Thu, 04 Apr 2024 15:23:18 +0000 |
parents | 8bccb36e055a |
children | 699a5e9146b3 |
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--- a/auto_threshold.py Wed Mar 13 06:15:54 2024 +0000 +++ b/auto_threshold.py Thu Apr 04 15:23:18 2024 +0000 @@ -27,23 +27,28 @@ } -def do_thresholding(in_fn, out_fn, th_method, block_size=5, threshold=0, invert_output=False): +def do_thresholding(in_fn, out_fn, th_method, block_size, offset, threshold, invert_output=False): img = skimage.io.imread(in_fn) - th = th_methods[th_method](img_raw=img, bz=block_size, thres=threshold) + img = np.squeeze(img) + assert img.ndim == 2 + + th = offset + 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 = 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('im_out', help='Path to the output image (uint8)') 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('offset', type=float, default=0, help='Offset of automatically determined threshold value') + parser.add_argument('threshold', type=float, default=0, help='Manual threshold 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) + do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.offset, args.threshold, args.invert_output)