Mercurial > repos > imgteam > 2d_local_threshold
changeset 3:be2d3ce89c0f draft default tip
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
| author | imgteam |
|---|---|
| date | Sat, 19 Feb 2022 15:17:19 +0000 |
| parents | 497dcd834bb3 |
| children | |
| files | auto_local_threshold.py auto_local_threshold.xml |
| diffstat | 2 files changed, 7 insertions(+), 4 deletions(-) [+] |
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--- a/auto_local_threshold.py Wed Dec 18 05:00:26 2019 -0500 +++ b/auto_local_threshold.py Sat Feb 19 15:17:19 2022 +0000 @@ -1,9 +1,10 @@ import argparse import sys -import skimage.io + +import numpy as np import skimage.filters +import skimage.io import skimage.util -import numpy as np threshOptions = { 'gaussian': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='gaussian'), @@ -24,7 +25,7 @@ img_in = np.reshape(img_in, [img_in.shape[0], img_in.shape[1]]) thresh = threshOptions[args.thresh_type](img_in, args.block_size) - if args.dark_background: + if args.dark_background: res = img_in > thresh else: res = img_in <= thresh
--- a/auto_local_threshold.xml Wed Dec 18 05:00:26 2019 -0500 +++ b/auto_local_threshold.xml Sat Feb 19 15:17:19 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="ip_localthreshold" name="Local Threshold" version="0.0.2"> +<tool id="ip_localthreshold" name="Local Threshold" version="0.0.3" profile="20.05"> <description>applies a local threshold algorithm to an image</description> <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> @@ -35,6 +35,8 @@ </tests> <help> Applies a local threshold algorithm to an image. + + Note: This tool is deprecated and may not be supported in future. Please use the tool "Auto Threshold" instead. </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>