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comparison anisotropic_diffusion.py @ 1:17d3cfba9b5a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 05:01:04 -0400
parents d13e26f576bc
children e6987afa0484
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0:d13e26f576bc 1:17d3cfba9b5a
12 parser.add_argument('niter', type=int, help='Number of iterations', default=1) 12 parser.add_argument('niter', type=int, help='Number of iterations', default=1)
13 parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50) 13 parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50)
14 parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1) 14 parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1)
15 parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1) 15 parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1)
16 args = parser.parse_args() 16 args = parser.parse_args()
17 17
18 with warnings.catch_warnings(): 18 with warnings.catch_warnings():
19 warnings.simplefilter("ignore") #to ignore FutureWarning as well 19 warnings.simplefilter("ignore") #to ignore FutureWarning as well
20 20
21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile') 21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile')
22 res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) 22 res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption)