I realize it should never happen that two electrodes have identical location. However, unless I am making an error in reading the data file, I have come across an example of this in an IBL dataset on the DANDI archive. I still need to double check and confirm that this is the case.
But in any event, here's what happens when you have a duplicated location - and I think this is something that should be fixed.
Note the comment "First channel in this list will always be the primary channel." This is not the case when you have duplicates. And so what ends up happening is that two rows (or maybe columns) of the whitening matrix end up being identical. This in turn causes two channels to be identical signal in the filtered data. And this causes a problem with detection where all spikes are considered non-isolated. Finally this in turn causes the crash of #566
As a follow-up. It seems the IBL dataset is actually okay... you just need to read the rel_x, rel_y fields from the NWB file and not the x, y, z. Still investigating.
I realize it should never happen that two electrodes have identical location. However, unless I am making an error in reading the data file, I have come across an example of this in an IBL dataset on the DANDI archive. I still need to double check and confirm that this is the case.
But in any event, here's what happens when you have a duplicated location - and I think this is something that should be fixed.
Here's the relevant code
https://github.com/MouseLand/Kilosort/blob/d55179f4bed45d4f17e5481283bc3f260212c1c7/preProcess/whiteningLocal.m#L1-L14
Note the comment "First channel in this list will always be the primary channel." This is not the case when you have duplicates. And so what ends up happening is that two rows (or maybe columns) of the whitening matrix end up being identical. This in turn causes two channels to be identical signal in the filtered data. And this causes a problem with detection where all spikes are considered non-isolated. Finally this in turn causes the crash of #566