Mercurial > repos > imgteam > 2d_histogram_equalization
changeset 4:99e0ef91ea5e draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 558152251d5d7a1bf77db91aa5388aca7a68ae62
| author | imgteam |
|---|---|
| date | Fri, 20 Feb 2026 09:56:44 +0000 |
| parents | b1c2c210813c |
| children | |
| files | creators.xml histogram_equalization.py histogram_equalization.xml test-data/out.tif test-data/out.tiff test-data/out_clahe.tiff test-data/sample.tif test-data/sample.tiff |
| diffstat | 8 files changed, 43 insertions(+), 10 deletions(-) [+] |
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--- a/creators.xml Wed Apr 24 08:11:54 2024 +0000 +++ b/creators.xml Fri Feb 20 09:56:44 2026 +0000 @@ -5,6 +5,16 @@ <yield /> </xml> + <xml name="creators/kostrykin"> + <person givenName="Leonid" familyName="Kostrykin"/> + <yield/> + </xml> + + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + <xml name="creators/alliecreason"> <person givenName="Allison" familyName="Creason"/> <yield/> @@ -19,5 +29,15 @@ <person givenName="Till" familyName="Korten"/> <yield/> </xml> - + + <xml name="creators/pavanvidem"> + <person givenName="Pavan" familyName="Videm"/> + <yield/> + </xml> + + <xml name="creators/tuncK"> + <person givenName="Tunc" familyName="Kayikcioglu"/> + <yield/> + </xml> + </macros>
--- a/histogram_equalization.py Wed Apr 24 08:11:54 2024 +0000 +++ b/histogram_equalization.py Fri Feb 20 09:56:44 2026 +0000 @@ -2,13 +2,21 @@ import sys import giatools.io +import numpy as np import skimage.exposure import skimage.io import skimage.util + +def rescale(img): + assert np.issubdtype(img.dtype, np.floating), str(img.dtype) # sanity check + img = img - img.min() + return img / img.max() if img.max() != 0 else 1 + + hOptions = { - 'default': lambda img_raw: skimage.exposure.equalize_hist(img_raw), - 'clahe': lambda img_raw: skimage.exposure.equalize_adapthist(img_raw) + 'default': lambda img_raw: rescale(skimage.exposure.equalize_hist(img_raw)), # rescale needed for values to be in [0, 1] + 'clahe': lambda img_raw: skimage.exposure.equalize_adapthist(img_raw), # produces image with values in [0, 1] } if __name__ == "__main__":
--- a/histogram_equalization.xml Wed Apr 24 08:11:54 2024 +0000 +++ b/histogram_equalization.xml Fri Feb 20 09:56:44 2026 +0000 @@ -3,7 +3,7 @@ <macros> <import>creators.xml</import> <import>tests.xml</import> - <token name="@TOOL_VERSION@">0.18.1</token> + <token name="@TOOL_VERSION@">0.25.2</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <creator> @@ -16,11 +16,11 @@ <xref type="bio.tools">scikit-image</xref> <xref type="biii">scikit-image</xref> </xrefs> - <requirements> + <requirements> <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement> - <requirement type="package" version="1.23.3">numpy</requirement> - <requirement type="package" version="2020.10.1">tifffile</requirement> - <requirement type="package" version="0.1">giatools</requirement> + <requirement type="package" version="2.3.5">numpy</requirement> + <requirement type="package" version="2025.5.10">tifffile</requirement> + <requirement type="package" version="0.1.2">giatools</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ @@ -39,9 +39,14 @@ </outputs> <tests> <test> - <param name="input" value="sample.tif"/> + <param name="input" value="sample.tiff"/> <param name="h_type" value="default"/> - <expand macro="tests/intensity_image_diff" name="output" value="out.tif" ftype="tiff"/> + <expand macro="tests/intensity_image_diff" name="output" value="out.tiff" ftype="tiff"/> + </test> + <test> + <param name="input" value="sample.tiff"/> + <param name="h_type" value="clahe"/> + <expand macro="tests/intensity_image_diff" name="output" value="out_clahe.tiff" ftype="tiff"/> </test> </tests> <help>