Mercurial > repos > thomaswollmann > anisotropic_diffusion

comparison anisotropic_diffusion.py @ 1:6be26440a8ec draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:33:19 -0500
parents 9a30c8f0f651
children
comparison
equal deleted inserted replaced
0:9a30c8f0f651 1:6be26440a8ec
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 img_in = skimage.io.imread(args.input_file.name) 18 with warnings.catch_warnings():
19 res = anisotropic_diffusion(img_raw, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) 19 warnings.simplefilter("ignore") #to ignore FutureWarning as well
20 res[res<-1]=-1
21 res[res>1]=1
22 20
23 with warnings.catch_warnings(): 21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile')
24 warnings.simplefilter("ignore") 22 res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption)
23 res[res<-1]=-1
24 res[res>1]=1
25
25 res = skimage.util.img_as_uint(res) #Attention: precision loss 26 res = skimage.util.img_as_uint(res) #Attention: precision loss
26 skimage.io.imsave(args.out_file.name, res, plugin='tifffile') 27
28 skimage.io.imsave(args.out_file.name, res, plugin='tifffile')