Mercurial > repos > thomaswollmann > anisotropic_diffusion
changeset 1:6be26440a8ec draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit d93e1dd276027cfc3fb518236110395a23d96f66
| author | thomaswollmann |
|---|---|
| date | Wed, 16 Jan 2019 15:33:19 -0500 |
| parents | 9a30c8f0f651 |
| children | |
| files | anisotropic_diffusion.py anisotropic_diffusion.xml test-data/galaxyIcon_noText.png test-data/galaxyIcon_noText.tif test-data/res.tif |
| diffstat | 5 files changed, 17 insertions(+), 15 deletions(-) [+] |
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--- a/anisotropic_diffusion.py Tue Feb 21 09:11:07 2017 -0500 +++ b/anisotropic_diffusion.py Wed Jan 16 15:33:19 2019 -0500 @@ -15,12 +15,14 @@ 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") #to ignore FutureWarning as well -with warnings.catch_warnings(): - warnings.simplefilter("ignore") + 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') + + skimage.io.imsave(args.out_file.name, res, plugin='tifffile')
--- a/anisotropic_diffusion.xml Tue Feb 21 09:11:07 2017 -0500 +++ b/anisotropic_diffusion.xml Wed Jan 16 15:33:19 2019 -0500 @@ -1,9 +1,9 @@ <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> + <requirement type="package" version="0.14.0" >scikit-image</requirement> + <requirement type="package" version="0.3.0">medpy</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> </requirements> <command> <![CDATA[ @@ -11,7 +11,7 @@ ]]> </command> <inputs> - <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file"/> + <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"/> @@ -25,16 +25,16 @@ </outputs> <tests> <test> - <param name="input" value="galaxyIcon_noText.png" /> + <param name="input" value="galaxyIcon_noText.tif" /> <param name="niter" value="100" /> - <param name="kappa" value="50" /> + <param name="kappa" value="50" /> <param name="gamma" value="0.1" /> <param name="eqoption" value="1" /> - <output name="output" ftype="tiff" /> + <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/> </test> </tests> <help>Edge-preserving, Anisotropic image diffusion.</help> <citations> - <citation type="doi">10.1109/34.56205</citation> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> </citations> </tool>