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catalystneuro / tye-lab-to-nwb

NWB Conversion project for the Tye lab at the Salk Institute.
MIT License
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Remove `ignore_timestamps_errors` flag #43

Closed weiglszonja closed 10 months ago

weiglszonja commented 10 months ago

Using ignore_timestamps_errors currently does not guarantee that data has no gaps in it. https://github.com/NeuralEnsemble/python-neo/issues/1336 I think it is better to remove completely and if we see this error we can turn it on for investigating.

CodyCBakerPhD commented 10 months ago

Wasn't this needed for a separate session https://github.com/catalystneuro/tye-lab-to-nwb/issues/29?

weiglszonja commented 10 months ago

Yes, but now since it's turned on by default in convert_session.py, we won't know whether other sessions have this issue but they were silently ignored. I hope only #29 needed this flag and the other files are fine, but we don't know.. that is the problem. as @samuelgarcia told me, the OpenEphysRawIO doesn't check for gaps when ignore_timestamps_errors=True is turned on, so for being safe it is better to collect the affected sessions first and investigate.

CodyCBakerPhD commented 10 months ago

Ah, so perhaps it should be a session-level parameter and should be turned off by default then enabled on that one session that needed it?

I know the conversion is done now, but just for precedence and future design of this kind of thing

weiglszonja commented 10 months ago

Yeah exactly for future proofing

samuelgarcia commented 10 months ago

The main problem with the option ignore_timestamps_errors=True in OpenEphysRawIO is that they are no garanty that gaps are the same across channels. Wich is a bit dangerous because the get_analogsignal_chunk rely on the fact that channels have no gaps and are aligned.

If there is a high user demand no reading this formats when they are gaps I would need to improve the IO.