Mercurial > repos > imgteam > 2d_histogram_equalization
changeset 0:70316d792fc9 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
| author | imgteam |
|---|---|
| date | Tue, 23 Jul 2019 14:07:07 -0400 |
| parents | |
| children | 77f7159d775a |
| files | histogram_equalization.py histogram_equalization.xml test-data/out.tif test-data/sample.tif |
| diffstat | 4 files changed, 60 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/histogram_equalization.py Tue Jul 23 14:07:07 2019 -0400 @@ -0,0 +1,23 @@ +import argparse +import os +import sys +import skimage.io +import skimage.exposure +import skimage.util + +hOptions = { + 'default' : lambda img_raw: skimage.exposure.equalize_hist(img_raw), + 'clahe' : lambda img_raw: skimage.exposure.equalize_adapthist(img_raw) +} + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Histogram equalization') + 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)') + parser.add_argument('h_type', choices=hOptions.keys(), help='histogram equalization method') + args = parser.parse_args() + + img_in = skimage.io.imread(args.input_file.name) + res = hOptions[args.h_type](img_in) + res = skimage.util.img_as_uint(res) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/histogram_equalization.xml Tue Jul 23 14:07:07 2019 -0400 @@ -0,0 +1,37 @@ +<tool id="ip_histogram_equalization" name="Histogram equalization" version="0.0.1"> + <description>automatic histogram equalization</description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="5.3.0">pillow</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/histogram_equalization.py' '$input' '$output' $h_type + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff" label="Source file" /> + <param name="h_type" type="select" label="Histogram Equalization Algorithm"> + <option value="default">Stretching</option> + <option value="clahe" selected="True">CLAHE</option> + </param> + </inputs> + <outputs> + <data format="tiff" name="output" /> + </outputs> + <tests> + <test> + <param name="input" value="sample.tif"/> + <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> + <param name="h_type" value="default"/> + </test> + </tests> + <help> + Applies histogram equalization to an image. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>