From e4c60ea470d5a2757c7e803a6da97f9ba4d167ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 15 Mar 2022 13:24:42 +0000
Subject: [PATCH] add passing segment_traps arguments
---
aliby/tile/traps.py | 26 ++++++++++++++++++++------
1 file changed, 20 insertions(+), 6 deletions(-)
diff --git a/aliby/tile/traps.py b/aliby/tile/traps.py
index 5d3e25fe..94d6c4cd 100644
--- a/aliby/tile/traps.py
+++ b/aliby/tile/traps.py
@@ -24,14 +24,28 @@ def stretch_image(image):
return image
-def segment_traps(image, tile_size, downscale=0.4):
+def segment_traps(
+ image,
+ tile_size,
+ downscale=0.4,
+ disk_radius_frac=None,
+ square_size=None,
+ min_frac_tilesize=None,
+):
+ if disk_radius_frac is None:
+ disk_radius_frac = 0.01
+ if square_size is None:
+ square_size = 3
+ if min_frac_tilesize is None:
+ min_frac_tilesize = 0.8
+
# Make image go between 0 and 255
img = image # Keep a memory of image in case need to re-run
- # stretched = stretch_image(image)
- # img = stretch_image(image)
# TODO Optimise the hyperparameters
- disk_radius = int(min([0.01 * x for x in img.shape]))
- min_area = 0.2 * (tile_size ** 2)
+
+ disk_radius = int(min([disk_radius_frac * x for x in img.shape]))
+ min_area = min_frac_tilesize * (tile_size ** 2)
+
if downscale != 1:
img = transform.rescale(image, downscale)
# entropy_image = entropy(img_as_ubyte(img), disk(disk_radius))
@@ -41,7 +55,7 @@ def segment_traps(image, tile_size, downscale=0.4):
# apply threshold
thresh = threshold_otsu(entropy_image)
- bw = closing(entropy_image > thresh, square(3))
+ bw = closing(entropy_image > thresh, square(square_size))
# remove artifacts connected to image border
cleared = clear_border(bw)
--
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