Mercurial > repos > thomaswollmann > anisotropic_diffusion
diff anisotropic_diffusion.py @ 1:626be11c43fc draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
| author | thomaswollmann |
|---|---|
| date | Wed, 12 Dec 2018 04:48:49 -0500 |
| parents | babb41158e9f |
| children |
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--- a/anisotropic_diffusion.py Tue Feb 21 09:10:52 2017 -0500 +++ b/anisotropic_diffusion.py Wed Dec 12 04:48:49 2018 -0500 @@ -15,12 +15,14 @@ parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1) args = parser.parse_args() -img_in = skimage.io.imread(args.input_file.name) -res = anisotropic_diffusion(img_raw, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) -res[res<-1]=-1 -res[res>1]=1 +with warnings.catch_warnings(): + warnings.simplefilter("ignore") #to ignore FutureWarning as well -with warnings.catch_warnings(): - warnings.simplefilter("ignore") + img_in = skimage.io.imread(args.input_file.name, plugin='tifffile') + res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) + res[res<-1]=-1 + res[res>1]=1 + res = skimage.util.img_as_uint(res) #Attention: precision loss -skimage.io.imsave(args.out_file.name, res, plugin='tifffile') + + skimage.io.imsave(args.out_file.name, res, plugin='tifffile')