Mercurial > repos > imgteam > 2d_auto_threshold
changeset 1:4853fc2b50bf draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
| author | imgteam |
|---|---|
| date | Tue, 23 Jul 2019 05:09:26 -0400 |
| parents | d4da97f51700 |
| children | 81f0cbca04a7 |
| files | auto_threshold.py auto_threshold.xml |
| diffstat | 2 files changed, 12 insertions(+), 15 deletions(-) [+] |
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--- a/auto_threshold.py Sat Feb 09 14:27:36 2019 -0500 +++ b/auto_threshold.py Tue Jul 23 05:09:26 2019 -0400 @@ -1,19 +1,17 @@ import argparse import numpy as np -import os -import sys -import warnings +import sys import skimage.io import skimage.filters import skimage.util threshOptions = { - 'otsu' : lambda img_raw: skimage.filters.threshold_otsu(img_raw), - 'gaussian_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='gaussian'), # todo reshape 2d - 'mean_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='mean'), # todo reshape 2d - 'isodata' : lambda img_raw: skimage.filters.threshold_isodata(img_raw), - 'li' : lambda img_raw: skimage.filters.threshold_li(img_raw), - 'yen' : lambda img_raw: skimage.filters.threshold_yen(img_raw), + 'otsu': lambda img_raw: skimage.filters.threshold_otsu(img_raw), + 'gaussian_adaptive': lambda img_raw: skimage.filters.threshold_local(img_raw, 3, method='gaussian'), + 'mean_adaptive': lambda img_raw: skimage.filters.threshold_local(img_raw, 3, method='mean'), + 'isodata': lambda img_raw: skimage.filters.threshold_isodata(img_raw), + 'li': lambda img_raw: skimage.filters.threshold_li(img_raw), + 'yen': lambda img_raw: skimage.filters.threshold_yen(img_raw), } if __name__ == "__main__": @@ -25,6 +23,7 @@ args = parser.parse_args() img_in = skimage.io.imread(args.input_file.name) + img_in = np.reshape(img_in, [img_in.shape[0], img_in.shape[1]]) thresh = threshOptions[args.thresh_type](img_in) if args.dark_background: @@ -32,7 +31,5 @@ else: res = img_in <= thresh - with warnings.catch_warnings(): - warnings.simplefilter("ignore") - res = skimage.util.img_as_uint(res) - skimage.io.imsave(args.out_file.name, res, plugin="tifffile") + res = skimage.util.img_as_uint(res) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
--- a/auto_threshold.xml Sat Feb 09 14:27:36 2019 -0500 +++ b/auto_threshold.xml Tue Jul 23 05:09:26 2019 -0400 @@ -1,6 +1,6 @@ -<tool id="ip_threshold" name="Auto Threshold" version="0.0.3"> +<tool id="ip_threshold" name="Auto Threshold" version="0.0.4"> <description>applies a standard threshold algorithm to an image</description> - <requirements> + <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>