Mercurial > repos > imgteam > 2d_local_threshold
changeset 0:a20c14eb5f98 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
| author | imgteam |
|---|---|
| date | Thu, 18 Jul 2019 09:22:07 -0400 |
| parents | |
| children | c90b91f4a07b |
| files | auto_local_threshold.py auto_local_threshold.xml test-data/out.tif test-data/sample.tif |
| diffstat | 4 files changed, 73 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_local_threshold.py Thu Jul 18 09:22:07 2019 -0400 @@ -0,0 +1,31 @@ +import argparse +import sys +import skimage.io +import skimage.filters +import skimage.util + +threshOptions = { + 'gaussian': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='gaussian'), + 'mean': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='mean'), + 'median': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='median') +} + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Segment Foci') + 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('block_size', type=int, default=5, help='Odd size of pixel neighborhood which is used to calculate the threshold value') + parser.add_argument('thresh_type', choices=threshOptions.keys(), help='thresholding method') + parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark') + args = parser.parse_args() + + img_in = skimage.io.imread(args.input_file.name) + thresh = threshOptions[args.thresh_type](img_in, args.block_size) + + if args.dark_background: + res = img_in > thresh + else: + res = img_in <= thresh + + 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/auto_local_threshold.xml Thu Jul 18 09:22:07 2019 -0400 @@ -0,0 +1,42 @@ +<tool id="ip_localthreshold" name="Local Threshold" version="0.0.1"> + <description>applies a local threshold algorithm to an image</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 '$__tool_directory__/auto_local_threshold.py' '$input' '$output' $block_size $thresh_type $dark_background + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff" label="Source file" /> + <param name="thresh_type" type="select" label="Threshold Algorithm"> + <option value="gaussian" selected="True">Gaussian</option> + <option value="median">Median</option> + <option value="mean">Mean</option> + </param> + <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood which is used to calculate the threshold value" /> + <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" /> + </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="thresh_type" value="gaussian"/> + <param name="block_size" value="429"/> + <param name="dark_backgroud" value="True"/> + </test> + </tests> + <help> + Applies a local threshold algorithm to an image. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>