diff auto_threshold.py @ 0:6fc65082d1e6 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_threshold.py	Sat Feb 09 14:02:57 2019 -0500
@@ -0,0 +1,38 @@
+import argparse
+import numpy as np
+import os
+import sys
+import warnings
+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),
+}
+
+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('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)
+
+    if args.dark_background:
+        res = img_in > thresh
+    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")