Mercurial > repos > thomaswollmann > anisotropic_diffusion
comparison anisotropic_diffusion.py @ 0:9a30c8f0f651 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
| author | thomaswollmann |
|---|---|
| date | Tue, 21 Feb 2017 09:11:07 -0500 |
| parents | |
| children | 6be26440a8ec |
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| -1:000000000000 | 0:9a30c8f0f651 |
|---|---|
| 1 import argparse | |
| 2 import sys | |
| 3 import warnings | |
| 4 import numpy as np | |
| 5 import skimage.io | |
| 6 import skimage.util | |
| 7 from medpy.filter.smoothing import anisotropic_diffusion | |
| 8 | |
| 9 parser = argparse.ArgumentParser() | |
| 10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | |
| 11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | |
| 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) | |
| 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) | |
| 16 args = parser.parse_args() | |
| 17 | |
| 18 img_in = skimage.io.imread(args.input_file.name) | |
| 19 res = anisotropic_diffusion(img_raw, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) | |
| 20 res[res<-1]=-1 | |
| 21 res[res>1]=1 | |
| 22 | |
| 23 with warnings.catch_warnings(): | |
| 24 warnings.simplefilter("ignore") | |
| 25 res = skimage.util.img_as_uint(res) #Attention: precision loss | |
| 26 skimage.io.imsave(args.out_file.name, res, plugin='tifffile') |