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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:29:41 -0500
parents 626be11c43fc
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
diff changeset
1 import argparse
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
diff changeset
2 import sys
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
diff changeset
3 import warnings
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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4 import numpy as np
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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5 import skimage.io
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
diff changeset
6 import skimage.util
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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7 from medpy.filter.smoothing import anisotropic_diffusion
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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9 parser = argparse.ArgumentParser()
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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12 parser.add_argument('niter', type=int, help='Number of iterations', default=1)
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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13 parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50)
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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14 parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1)
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
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15 parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1)
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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16 args = parser.parse_args()
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents: 0
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18 with warnings.catch_warnings():
626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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19 warnings.simplefilter("ignore") #to ignore FutureWarning as well
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents: 0
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21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile')
626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents: 0
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22 res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption)
626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents: 0
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23 res[res<-1]=-1
626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents: 0
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24 res[res>1]=1
626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
thomaswollmann
parents:
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26 res = skimage.util.img_as_uint(res) #Attention: precision loss
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626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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626be11c43fc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents: 0
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28 skimage.io.imsave(args.out_file.name, res, plugin='tifffile')