Mercurial > repos > imgteam > label_to_binary
changeset 0:5da15c3bafed draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ commit 0a64a49d4a0ac3438544244a8b871be2fc144766
| author | imgteam |
|---|---|
| date | Wed, 13 Mar 2024 14:55:31 +0000 |
| parents | |
| children | |
| files | label_to_binary.py label_to_binary.xml test-data/input1.tif test-data/output1.tif |
| diffstat | 4 files changed, 72 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/label_to_binary.py Wed Mar 13 14:55:31 2024 +0000 @@ -0,0 +1,18 @@ +import argparse + +import numpy as np +import skimage.io + + +if __name__ == '__main__': + + parser = argparse.ArgumentParser() + parser.add_argument('input', type=str) + parser.add_argument('bg_label', type=int) + parser.add_argument('output', type=str) + args = parser.parse_args() + + im = skimage.io.imread(args.input) + im = (im != args.bg_label) + im = (im * 255).astype(np.uint8) + skimage.io.imsave(args.output, im)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/label_to_binary.xml Wed Mar 13 14:55:31 2024 +0000 @@ -0,0 +1,54 @@ +<tool id="label_to_binary" name="Convert label map to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> + <description>with NumPy</description> + <macros> + <token name="@TOOL_VERSION@">1.26.4</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> + <requirements> + <requirement type="package" version="1.26.4">numpy</requirement> + <requirement type="package" version="0.18.1">scikit-image</requirement> + </requirements> + <command><![CDATA[ + + ## Inputs + + python '$__tool_directory__/label_to_binary.py' + '$input' + '$bg_label' + + ## Outputs + + ./output.tif + + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff,png" label="Input image (label map)" /> + <param argument="--bg_label" type="integer" value="0" label="Background label" /> + </inputs> + <outputs> + <data format="tiff" name="output" from_work_dir="output.tif" /> + </outputs> + <tests> + <test> + <param name="input" value="input1.tif" /> + <param name="bg_label" value="0" /> + <output name="output" value="output1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + </test> + </tests> + <help> + This tools converts a label map (objects labeled by different labels/values) to a binary image. + + The input image is converted by assigning white (pixel value 255) to image regions corresponding to labeled objects, + and black (pixel value 0) to image regions corresponding to image background (by default, this is label 0). + </help> + <citations> + <citation type="doi">10.1038/s41586-020-2649-2</citation> + </citations> +</tool>