Mercurial > repos > imgteam > overlay_images
annotate contours.py @ 4:37662cbf44b8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
author | imgteam |
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date | Fri, 17 Nov 2023 23:34:57 +0000 |
parents | b74693340624 |
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b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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1 """ |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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2 Copyright (c) 2017-2023 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University. |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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3 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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4 Distributed under the MIT license. |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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6 """ |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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7 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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8 import numpy as np |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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9 import skimage.morphology as morph |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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10 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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11 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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12 class ContourPaint: |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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13 """Yields masks corresponding to contours of objects. |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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14 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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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. |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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16 :param thickness: The thickness of the contour (width, in pixels). |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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17 :param where: The position of the contour (``inner``, ``center``, or ``outer``). |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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18 """ |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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19 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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20 def __init__(self, fg_mask, thickness, where='center'): |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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21 assert where in ('inner', 'center', 'outer') |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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22 self.fg_mask = fg_mask |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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23 self.where = where |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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24 self.thickness = thickness |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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25 if where == 'inner': |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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26 self.selem_inner = morph.disk(self.thickness) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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27 self.selem_outer = None |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
diff
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28 elif where == 'center': |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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29 self.selem_inner = morph.disk(self.thickness - self.thickness // 2) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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30 self.selem_outer = morph.disk(self.thickness // 2) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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31 elif where == 'outer': |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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32 self.selem_inner = None |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
parents:
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33 self.selem_outer = morph.disk(self.thickness) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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34 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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35 def get_contour_mask(self, mask): |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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36 """Returns the binary mask of the contour of an object. |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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37 |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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38 :param mask: Binary mask of an object. |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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39 :return: Binary mask of the contour |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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40 """ |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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41 if self.selem_inner is not None: |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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42 inner_contour = np.logical_xor(mask, morph.binary_erosion(mask, self.selem_inner)) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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43 else: |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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44 inner_contour = np.zeros(mask.shape, bool) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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45 if self.selem_outer is not None: |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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46 outer_contour = np.logical_and(np.logical_not(self.fg_mask), morph.binary_dilation(mask, self.selem_outer)) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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47 else: |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
imgteam
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48 outer_contour = np.zeros(mask.shape, bool) |
b74693340624
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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49 return np.logical_or(inner_contour, outer_contour) |