--- /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")