Mercurial > repos > imgteam > 2d_auto_threshold

comparison auto_threshold.py @ 6:8bccb36e055a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit cb3d628f4c91e996e10dcb35b1168332e692293a
author imgteam
date Wed, 13 Mar 2024 06:15:54 +0000
parents 7db4fc31dbee
children e5c8e7e72373
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5:7db4fc31dbee 6:8bccb36e055a
41 parser.add_argument('im_in', help='Path to the input image') 41 parser.add_argument('im_in', help='Path to the input image')
42 parser.add_argument('im_out', help='Path to the output image (TIFF)') 42 parser.add_argument('im_out', help='Path to the output image (TIFF)')
43 parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method') 43 parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method')
44 parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold') 44 parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
45 parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value') 45 parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value')
46 parser.add_argument('invert_output', default=False, type=bool, help='Values below/above the threshold are labeled with 0/255 if False, and with 255/0 otherwise') 46 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')
47 args = parser.parse_args() 47 args = parser.parse_args()
48 48
49 do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output) 49 do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output)