Mercurial > repos > imgteam > binary2labelimage
changeset 0:b97a362ff321 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:30:31 -0500 |
| parents | |
| children | 6c92ac9ce868 |
| files | binary2label.py binary2label.xml test-data/galaxyIcon_noText.tif test-data/label.tif |
| diffstat | 4 files changed, 49 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/binary2label.py Sat Feb 09 14:30:31 2019 -0500 @@ -0,0 +1,18 @@ +import argparse +import sys +import skimage.io +from skimage.measure import label +import numpy as np +import warnings +from PIL import Image + +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)') +args = parser.parse_args() + +img_in = skimage.io.imread(args.input_file.name) > 0 +res = label(img_in).astype(np.int32) + +res = Image.fromarray(res) +res.save(args.out_file.name, "tiff") \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/binary2label.xml Sat Feb 09 14:30:31 2019 -0500 @@ -0,0 +1,31 @@ +<tool id="ip_binary_to_labelimage" name="Binary 2 Label" version="0.2"> + <description>Converts Binary to Label Image</description> + <requirements> + <requirement type="package" version="0.12.3">scikit-image</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/binary2label.py' '$input' '$output' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/> + </inputs> + <outputs> + <data format="tiff" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="galaxyIcon_noText.tif" /> + <output name="output" value="label.tif" ftype="tiff" /> + </test> + </tests> + <help> + **What it does** + + This tool assigns every object an own grey value. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>