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annotate anisotropic_diffusion.py @ 2:e6987afa0484 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:29 +0000
parents 17d3cfba9b5a
children 6ad5de2c5b7c
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import sys
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import warnings
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import skimage.io
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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6 import skimage.util
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 from medpy.filter.smoothing import anisotropic_diffusion
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9 parser = argparse.ArgumentParser()
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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12 parser.add_argument('niter', type=int, help='Number of iterations', default=1)
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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13 parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50)
d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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14 parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1)
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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15 parser.add_argument('eqoption', type=int, choices=[1, 2], help='Perona Malik diffusion equation', default=1)
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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16 args = parser.parse_args()
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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18 with warnings.catch_warnings():
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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19 warnings.simplefilter("ignore") # to ignore FutureWarning as well
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile')
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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22 res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption)
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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23 res[res < -1] = -1
e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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24 res[res > +1] = +1
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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26 res = skimage.util.img_as_uint(res) # Attention: precision loss
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d13e26f576bc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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e6987afa0484 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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28 skimage.io.imsave(args.out_file.name, res, plugin='tifffile')