Mercurial > repos > thomaswollmann > anisotropic_diffusion
changeset 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 |
| files | anisotropic_diffusion.py anisotropic_diffusion.xml test-data/galaxyIcon_noText.png test-data/res.tif |
| diffstat | 4 files changed, 66 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/anisotropic_diffusion.py Tue Feb 21 09:11:07 2017 -0500 @@ -0,0 +1,26 @@ +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() + +img_in = skimage.io.imread(args.input_file.name) +res = anisotropic_diffusion(img_raw, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) +res[res<-1]=-1 +res[res>1]=1 + +with warnings.catch_warnings(): + warnings.simplefilter("ignore") + 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 Tue Feb 21 09:11:07 2017 -0500 @@ -0,0 +1,40 @@ +<tool id="anisotropic_diffusion" name="Anisotropic Diffusion" version="0.1"> + <description>Edge-preserving, Anisotropic diffusion</description> + <requirements> + <requirement type="package" version="0.12.3" >scikit-image</requirement> + <requirement type="package" version="0.2.2">medpy</requirement> + <requirement type="package" version="1.12">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,png,jpg,bmp" 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.png" /> + <param name="niter" value="100" /> + <param name="kappa" value="50" /> + <param name="gamma" value="0.1" /> + <param name="eqoption" value="1" /> + <output name="output" ftype="tiff" /> + </test> + </tests> + <help>Edge-preserving, Anisotropic image diffusion.</help> + <citations> + <citation type="doi">10.1109/34.56205</citation> + </citations> +</tool>