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Don't filter out NaNs for contours #309

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Don't filter out NaNs for contours #309

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c206c83
Don't filter out nans and use CoM from caiman
ethanbb Jul 11, 2024
fa9d7f9
Use previous definition of CoM (add documentation)
ethanbb Jul 24, 2024
16fc63f
remove whitespace
ethanbb Jul 24, 2024
65a38e3
Update ground truths URL
ethanbb Aug 12, 2024
bf1c09e
Merge branch 'master' into contour-nan-fix
ethanbb Sep 3, 2024
279612b
Merge branch 'master' into contour-nan-fix
ethanbb Sep 9, 2024
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5 changes: 3 additions & 2 deletions mesmerize_core/caiman_extensions/cnmf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -268,6 +268,8 @@ def get_contours(
) -> Tuple[List[np.ndarray], List[np.ndarray]]:
"""
Get the contour and center of mass for each spatial footprint
Note, the centers of mass are different from those computed by CaImAn.
They are based on the contours and can be used to compute click targets for visualizations.

Parameters
----------
Expand Down Expand Up @@ -303,10 +305,9 @@ def get_contours(

for contour in contours:
coors = contour["coordinates"]
coors = coors[~np.isnan(coors).any(axis=1)]
coordinates.append(coors)

com = coors.mean(axis=0)
com = np.nanmean(coors, axis=0)
coms.append(com)

return coordinates, coms
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