Mercurial > repos > thomaswollmann > anisotropic_diffusion
comparison anisotropic_diffusion.py @ 1:6be26440a8ec draft default tip
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 |
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| 0:9a30c8f0f651 | 1:6be26440a8ec |
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| 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') |