Mercurial > repos > imgteam > overlay_images

comparison contours.py @ 2:b74693340624 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
author imgteam
date Thu, 10 Aug 2023 07:29:34 +0000
parents
children
comparison
equal deleted inserted replaced
1:bf590a9733ed 2:b74693340624
1 """
2 Copyright (c) 2017-2023 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University.
3
4 Distributed under the MIT license.
5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
6 """
7
8 import numpy as np
9 import skimage.morphology as morph
10
11
12 class ContourPaint:
13 """Yields masks corresponding to contours of objects.
14
15 :param fg_mask: Binary mask of the image foreground. Any contour never overlaps the image foreground except of those image regions corresponding to the contoured object itself.
16 :param thickness: The thickness of the contour (width, in pixels).
17 :param where: The position of the contour (``inner``, ``center``, or ``outer``).
18 """
19
20 def __init__(self, fg_mask, thickness, where='center'):
21 assert where in ('inner', 'center', 'outer')
22 self.fg_mask = fg_mask
23 self.where = where
24 self.thickness = thickness
25 if where == 'inner':
26 self.selem_inner = morph.disk(self.thickness)
27 self.selem_outer = None
28 elif where == 'center':
29 self.selem_inner = morph.disk(self.thickness - self.thickness // 2)
30 self.selem_outer = morph.disk(self.thickness // 2)
31 elif where == 'outer':
32 self.selem_inner = None
33 self.selem_outer = morph.disk(self.thickness)
34
35 def get_contour_mask(self, mask):
36 """Returns the binary mask of the contour of an object.
37
38 :param mask: Binary mask of an object.
39 :return: Binary mask of the contour
40 """
41 if self.selem_inner is not None:
42 inner_contour = np.logical_xor(mask, morph.binary_erosion(mask, self.selem_inner))
43 else:
44 inner_contour = np.zeros(mask.shape, bool)
45 if self.selem_outer is not None:
46 outer_contour = np.logical_and(np.logical_not(self.fg_mask), morph.binary_dilation(mask, self.selem_outer))
47 else:
48 outer_contour = np.zeros(mask.shape, bool)
49 return np.logical_or(inner_contour, outer_contour)