Mercurial > repos > imgteam > anisotropic_diffusion

comparison anisotropic_diffusion.py @ 4:6ad5de2c5b7c draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:12:09 +0000
parents e6987afa0484
children
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3:097b803aeb5d 4:6ad5de2c5b7c
1 import argparse 1 import argparse
2 import sys 2 import sys
3 import warnings 3 import warnings
4 4
5 import giatools.io
5 import skimage.io 6 import skimage.io
6 import skimage.util 7 import skimage.util
7 from medpy.filter.smoothing import anisotropic_diffusion 8 from medpy.filter.smoothing import anisotropic_diffusion
8 9
9 parser = argparse.ArgumentParser() 10 parser = argparse.ArgumentParser()
16 args = parser.parse_args() 17 args = parser.parse_args()
17 18
18 with warnings.catch_warnings(): 19 with warnings.catch_warnings():
19 warnings.simplefilter("ignore") # to ignore FutureWarning as well 20 warnings.simplefilter("ignore") # to ignore FutureWarning as well
20 21
21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile') 22 img_in = giatools.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) 23 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
24 res[res > +1] = +1 25 res[res > +1] = +1
25 26
26 res = skimage.util.img_as_uint(res) # Attention: precision loss 27 res = skimage.util.img_as_uint(res) # Attention: precision loss