Mercurial > repos > imgteam > overlay_images
view contours.py @ 7:8dc02c854048 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
author | imgteam |
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date | Thu, 25 Apr 2024 10:57:38 +0000 |
parents | b74693340624 |
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""" Copyright (c) 2017-2023 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University. Distributed under the MIT license. See file LICENSE for detail or copy at https://opensource.org/licenses/MIT """ import numpy as np import skimage.morphology as morph class ContourPaint: """Yields masks corresponding to contours of objects. :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. :param thickness: The thickness of the contour (width, in pixels). :param where: The position of the contour (``inner``, ``center``, or ``outer``). """ def __init__(self, fg_mask, thickness, where='center'): assert where in ('inner', 'center', 'outer') self.fg_mask = fg_mask self.where = where self.thickness = thickness if where == 'inner': self.selem_inner = morph.disk(self.thickness) self.selem_outer = None elif where == 'center': self.selem_inner = morph.disk(self.thickness - self.thickness // 2) self.selem_outer = morph.disk(self.thickness // 2) elif where == 'outer': self.selem_inner = None self.selem_outer = morph.disk(self.thickness) def get_contour_mask(self, mask): """Returns the binary mask of the contour of an object. :param mask: Binary mask of an object. :return: Binary mask of the contour """ if self.selem_inner is not None: inner_contour = np.logical_xor(mask, morph.binary_erosion(mask, self.selem_inner)) else: inner_contour = np.zeros(mask.shape, bool) if self.selem_outer is not None: outer_contour = np.logical_and(np.logical_not(self.fg_mask), morph.binary_dilation(mask, self.selem_outer)) else: outer_contour = np.zeros(mask.shape, bool) return np.logical_or(inner_contour, outer_contour)