Mercurial > repos > imgteam > anisotropic_diffusion
changeset 0:d13e26f576bc draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:30:00 -0500 |
| parents | |
| children | 17d3cfba9b5a |
| files | anisotropic_diffusion.py anisotropic_diffusion.xml test-data/galaxyIcon_noText.tif test-data/res.tif |
| diffstat | 4 files changed, 72 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/anisotropic_diffusion.py Sat Feb 09 14:30:00 2019 -0500 @@ -0,0 +1,28 @@ +import argparse +import sys +import warnings +import numpy as np +import skimage.io +import skimage.util +from medpy.filter.smoothing import anisotropic_diffusion + +parser = argparse.ArgumentParser() +parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') +parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') +parser.add_argument('niter', type=int, help='Number of iterations', default=1) +parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50) +parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1) +parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1) +args = parser.parse_args() + +with warnings.catch_warnings(): + warnings.simplefilter("ignore") #to ignore FutureWarning as well + + 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')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/anisotropic_diffusion.xml Sat Feb 09 14:30:00 2019 -0500 @@ -0,0 +1,44 @@ +<tool id="ip_anisotropic_diffusion" name="Anisotropic Diffusion" version="0.1"> + <description>Edge-preserving, Anisotropic diffusion</description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="0.3.0">medpy</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/anisotropic_diffusion.py' '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff" label="Image file"/> + <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/> + <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/> + <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/> + <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation"> + <option value="1" selected="True">Favour high contrast edges</option> + <option value="2">Favour wide regions</option> + </param> + </inputs> + <outputs> + <data format="tiff" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="galaxyIcon_noText.tif" /> + <param name="niter" value="100" /> + <param name="kappa" value="50" /> + <param name="gamma" value="0.1" /> + <param name="eqoption" value="1" /> + <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help> + **What it does** + + Edge-preserving, Anisotropic image diffusion + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>