Mercurial > repos > imgteam > permutate_axis
changeset 3:ce64e2e4afd2 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
| author | imgteam |
|---|---|
| date | Wed, 17 Dec 2025 15:34:17 +0000 |
| parents | 21168547d572 |
| children | |
| files | permutate_axis.py permutate_axis.xml test-data/galaxyIcon_noText.tif test-data/galaxyIcon_noText.tiff test-data/res.tif test-data/res.tiff |
| diffstat | 6 files changed, 24 insertions(+), 16 deletions(-) [+] |
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--- a/permutate_axis.py Wed Dec 18 09:58:57 2019 +0000 +++ b/permutate_axis.py Wed Dec 17 15:34:17 2025 +0000 @@ -1,32 +1,34 @@ import argparse -import sys import warnings + import numpy as np import skimage.io -import skimage.util +import skimage.util + def permutate_axis(input_image_path, output_image_path, axis, permutate): images = [] raw_image = skimage.io.imread(input_image_path, plugin='tifffile') for i in permutate: - # TODO generalise + # TODO generalise if axis == 0: a_slice = raw_image[i] elif axis == 1: - a_slice = raw_image[:,i] + a_slice = raw_image[:, i] elif axis == 2: - a_slice = raw_image[:,:,i] + a_slice = raw_image[:, :, i] elif axis == 3: - a_slice = raw_image[:,:,:,i] + a_slice = raw_image[:, :, :, i] elif axis == 4: - a_slice = raw_image[:,:,:,:,i] + a_slice = raw_image[:, :, :, :, i] images.append(np.expand_dims(a_slice, axis)) res = np.concatenate(images, axis) with warnings.catch_warnings(): - warnings.simplefilter("ignore") - res = skimage.util.img_as_uint(res) #Attention: precision loss - skimage.io.imsave(output_image_path, res, plugin='tifffile') + warnings.simplefilter("ignore") + res = skimage.util.img_as_uint(res) # Attention: precision loss + skimage.io.imsave(output_image_path, res, plugin='tifffile') + if __name__ == "__main__": parser = argparse.ArgumentParser()
--- a/permutate_axis.xml Wed Dec 18 09:58:57 2019 +0000 +++ b/permutate_axis.xml Wed Dec 17 15:34:17 2025 +0000 @@ -1,5 +1,11 @@ -<tool id="ip_permutate_axis" name="Permutate image" version="0.2"> - <description>along an axis</description> +<tool id="ip_permutate_axis" name="Permutate image axes" version="0.2-2"> + <description></description> + <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="0.14.2">scikit-image</requirement> <requirement type="package" version="1.15.4">numpy</requirement> @@ -9,7 +15,7 @@ <![CDATA[ python '$__tool_directory__/permutate_axis.py' '$input' '$output' $permutate --axis $axis ]]> - </command> + </command> <inputs> <param name="input" type="data" format="tiff" label="Binary Image File"/> <param name="permutate" type="text" value="0,1,2" label="new channel order"> @@ -22,8 +28,8 @@ </outputs> <tests> <test> - <param name="input" value="galaxyIcon_noText.tif"/> - <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/> + <param name="input" value="galaxyIcon_noText.tiff"/> + <output name="output" file="res.tiff" ftype="tiff" compare="sim_size"/> </test> </tests> <help> @@ -32,6 +38,6 @@ Permutates the image along a specified axis. </help> <citations> - <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> </citations> </tool>