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CNMF seems to be merging components despite setting do_merge = False
- How you installed Caiman (pure conda, conda + compile, colab, ..): conda
When running cnm.fit(images)
I have noticed that this gets logged:
[cnmf.py: fit():603] [3681004] merging
I have set do_merge = False
and del_duplicates = True
(to avoid merging the ROIs in the overlapping strides of the patches). In addition to that, I have noticed that if even if I set do_merge = False
the number of ROIs I get vary depending on the value of merge_thr
, so I think that many components are being merged together.
In cnmf.py line 603:
logging.info("merging")
self.estimates.merged_ROIs = [0]
And in line 642:
while len(self.estimates.merged_ROIs) > 0:
self.merge_comps(Yr, mx=np.Inf)
So it seems like merge_comps (which in turn calls merge_components) gets always called regardless of the do_merge parameter. Also, the max_merge_area
does not seem to be passed, and in my experience it does not affect the merging even if do_merge = True
Am I missing something? Or is there a reason why some components would need to be merged even if the do_merge flag is set to False?