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Node gt matching teun #155

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9233b96
added save_config function
TeunHuijben Jun 14, 2024
094b3e0
added volume attribute to node
TeunHuijben Jun 15, 2024
bad1d87
close_tracks_gaps now works for segments being a dask_array
TeunHuijben Jun 21, 2024
777404a
removed node._volume method, since precomputed area already exists
TeunHuijben Jun 21, 2024
d612e03
added UltrackArray class to utils/array.py
TeunHuijben Jul 11, 2024
cc0b1ed
ran pre-commit
TeunHuijben Jul 11, 2024
4d3b841
added path to database as optional input parameter. If provided, the…
TeunHuijben Jul 16, 2024
dafa92a
adding frontier to database
JoOkuma Jul 29, 2024
dbc2578
hierarchy widget, work in progress
TeunHuijben Jul 30, 2024
57fd803
added non-linear slider for uniform addition of volumes'
TeunHuijben Jul 30, 2024
4e1437d
added documentation to ultrack-array and HierarchyVizWidget
TeunHuijben Jul 31, 2024
6ccbed3
Update ultrack/widgets/ultrackwidget/ultrackwidget.py
TeunHuijben Aug 1, 2024
336a928
Update ultrack/widgets/ultrackwidget/ultrackwidget.py
TeunHuijben Aug 1, 2024
2daaa31
Update ultrack/utils/array.py
TeunHuijben Aug 1, 2024
925c564
implementing Jordaos revisions
TeunHuijben Aug 1, 2024
e4ef936
merged main to branch
TeunHuijben Aug 1, 2024
840c852
revising PR
TeunHuijben Aug 1, 2024
5cb9a38
renaming functions in ultrack-array
TeunHuijben Aug 1, 2024
a1f8c4c
reverting dirty history changes
TeunHuijben Aug 1, 2024
1208da8
redid the changes lost in merge
TeunHuijben Aug 1, 2024
765556a
added indexing test for ultrack-array
TeunHuijben Aug 2, 2024
590fad1
added test for hierarchy widget
TeunHuijben Aug 2, 2024
15b3aaa
Merge branch 'main' into autotune
JoOkuma Aug 16, 2024
8f3daa9
WIP basic autotuning implementation
JoOkuma Aug 16, 2024
4f56337
removing in memory database
JoOkuma Aug 19, 2024
f1f05c5
in memory DB
JoOkuma Aug 19, 2024
1a05547
WIP database centric autotuning
JoOkuma Aug 31, 2024
cc75143
fix db bug
JoOkuma Aug 31, 2024
90aad46
added feature extraction during segmentation
JoOkuma Sep 1, 2024
3a6acc4
added get_nodes_features functionality
JoOkuma Sep 1, 2024
bb97ad8
added manual linking value to ultrack
JoOkuma Sep 1, 2024
5c6ae64
improving documentation
JoOkuma Sep 1, 2024
ad5673a
examples of using node features
JoOkuma Sep 1, 2024
e36082c
added CTC usage
JoOkuma Sep 1, 2024
967ce94
adding ground-truth database
JoOkuma Sep 3, 2024
c0a1001
improving linking codebase
JoOkuma Sep 3, 2024
edb06d5
Merge branch 'autotune' into node-gt-matching
JoOkuma Sep 3, 2024
d6f42ec
Merge branch 'main' into node-gt-matching
JoOkuma Sep 3, 2024
b572f50
WIP auto memory GT linking
JoOkuma Sep 4, 2024
9c78385
bad duplicated link code
JoOkuma Sep 4, 2024
f8109ea
WIP working version of ground-truth matching, missing documentation
JoOkuma Sep 4, 2024
94f3dc5
bug fixing
JoOkuma Sep 4, 2024
cc13a58
Merge branch 'public-main' into node-gt-matching
JoOkuma Oct 2, 2024
76bdceb
addings docs gt matching
JoOkuma Oct 2, 2024
d213a7c
removed unnecessary prints
JoOkuma Oct 3, 2024
f36836a
added image wrapper for feature computation
JoOkuma Oct 6, 2024
b53de0d
fix inverted EDT processing for dask arrays / non-binary masks
JoOkuma Oct 7, 2024
19963ae
Merge branch 'fix-edt' into node-gt-matching
JoOkuma Oct 7, 2024
9b485ba
improved array apply, adding automatic output array creation
JoOkuma Oct 7, 2024
3122daa
Merge branch 'improve-array-apply' into node-gt-matching
JoOkuma Oct 7, 2024
14696e5
undoing wrong removal
JoOkuma Oct 7, 2024
cd119df
Merge branch 'improve-array-apply' into node-gt-matching
JoOkuma Oct 7, 2024
ce6c575
enabling cell division into matching
JoOkuma Oct 10, 2024
b4a5f79
Merge branch 'main' into node-gt-matching
JoOkuma Oct 29, 2024
120f939
merged ultrack-array into ultrackastra/node-gt-matching-teun
Oct 29, 2024
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3 changes: 2 additions & 1 deletion ultrack/imgproc/segmentation.py
Original file line number Diff line number Diff line change
@@ -204,6 +204,7 @@ def inverted_edt(
ArrayLike
Inverted and normalized EDT.
"""
mask = np.asarray(mask)
if axis is None:
dist = edt.edt(mask, anisotropy=voxel_size)
else:
@@ -216,7 +217,7 @@ def inverted_edt(
)
dist = dist / dist.max()
dist = 1.0 - dist
dist[~mask] = 1
dist[mask == 0] = 1
return dist