Mercurial > repos > thomaswollmann > mergeneighboursinlabelimage
changeset 1:3536648d0a93 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
| author | thomaswollmann |
|---|---|
| date | Wed, 16 Jan 2019 15:35:29 -0500 |
| parents | 66f7e94db2e6 |
| children | |
| files | mergeneighboursinlabelimage.py mergeneighboursinlabelimage.xml test-data/galaxyIcon_noText.tif test-data/out.tiff |
| diffstat | 4 files changed, 17 insertions(+), 12 deletions(-) [+] |
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--- a/mergeneighboursinlabelimage.py Tue Jan 08 08:54:16 2019 -0500 +++ b/mergeneighboursinlabelimage.py Wed Jan 16 15:35:29 2019 -0500 @@ -1,5 +1,3 @@ -#!/usr/bin/python - import argparse import sys import skimage.io @@ -46,6 +44,5 @@ label_image = merge_n(label_image, args.cluster_merge) with warnings.catch_warnings(): warnings.simplefilter("ignore") - res = skimage.util.img_as_uint(res) - skimage.io.imsave("tmp.tiff", res) - os.rename("tmp.tiff", args.output_file.name) + res = skimage.util.img_as_uint(label_image) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
--- a/mergeneighboursinlabelimage.xml Tue Jan 08 08:54:16 2019 -0500 +++ b/mergeneighboursinlabelimage.xml Wed Jan 16 15:35:29 2019 -0500 @@ -1,13 +1,13 @@ -<tool id="mergeneighboursinlabelimage" name="Merge Neighbours in Label" version="0.1"> +<tool id="mergeneighboursinlabelimage" name="Merge Neighbours in Label" version="0.2"> <description>Merge Neighbours in Label Image</description> <requirements> - <requirement type="package" version="0.12.3" >scikit-image</requirement> - <requirement type="package">numpy</requirement> - <requirement type="package">scipy</requirement> + <requirement type="package" version="0.14.0">scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> </requirements> <command> <![CDATA[ - python '$__tool_directory__/mergeneighboursinlabelimage.py '$input' '$output' -c $c + python '$__tool_directory__/mergeneighboursinlabelimage.py' '$input' ./tmp.tiff -c $c + && mv ./tmp.tiff '$output' ]]> </command> <inputs> @@ -16,8 +16,16 @@ </inputs> <outputs> <data format="tiff" name="output"/> - </outputs><help>This tools merges nearby objects in a label image using the minimum pixel distance.</help> + </outputs> + <tests> + <test> + <param name="input" value="galaxyIcon_noText.tif"/> + <param name="c" value="10"/> + <output name="output" file="out.tiff" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help>This tools merges nearby objects in a label image using the minimum pixel distance.</help> <citations> - <citation type="doi">10.7717/peerj.453</citation> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> </citations> </tool>