Refactor artifacts detection + add sturation detection

[samuelgarcia]

@JoeZiminski @oliche

This refactor the artifact detection and blanking

• with a main multi method function : detect_artifact_periods()
• return periods with the new base_period_dtype instead list of list
• SilencedPeriodsRecording also use this new dtype
• DetectArtifactAndSilentPeriodsRecording (replace SilencedArtifactsRecording) do detect and silence at the same
  time to be used in preprocess dict (@chrishalcrow this is for you)
• refactor the method of Pierre based on envleope
• incorporate the method of @oliche and @JoeZiminski to detect saturation

Could also be done in this PR:

• add a margin_ms option in SilentPeriodsRecording to ewxtend the zeroing with a mragin : do we need this ?

To be done in 2 futures PR:

• handle margin and taper on border of SilentPeriod (more tricky that it appear when period is at border...)
• rewrite RemoveArtifactsRecording based on SilencedPeriodsRecording and the new dtype

[yger]

@samuelgarcia do not forget, in this PR, to change DetectThresholdCrossing(recording, ...) to DetectThresholdCrossing(envelope, ...) in the detec_period_artefacts_by_envelope

[samuelgarcia]

Hi @oliche @JoeZiminski
I copy paste and clean a bit your PR #4301 into this one.
Have a look and tell if this is OK.

I think we do not need to scaled traces at each chunk we could only could the unscaled threhold in the init and then we could avoid the costly convertion to float32 or float64.

Also I put the unit in uV to be more SI friendly.

[samuelgarcia]

@alejoe91 @chrishalcrow ready to review on my side

[samuelgarcia]

add detect_artifact_method detect_artifact_kwargs

[chrishalcrow]

Suggested change

	* 'saturation' using detect_artifact_periods_by_envelope()
	* 'envelope' using detect_saturation_periods()
	* 'saturation' using detect_saturation_periods()
	* 'envelope' using detect_artifact_periods_by_envelope()

[chrishalcrow]

Suggested change

	# from spikeinterface.core.core_tools import define_function_handling_dict_from_class
	# from spikeinterface.preprocessing.silence_periods import SilencedPeriodsRecording

[chrishalcrow]

oups

[chrishalcrow]

Hello, trying this out on real data with saturation. I get this output

artifact_periods=array([(0, 637721, 638769), (0, 638955, 639206), (0, 923219, 923602),
       (0, 923605, 923606), (0, 923607, 923835)],

Are these periods inclusive? And if they are, should the last pair be merged?

[chrishalcrow]

Is it assumed that saturation_threshold_uV is symmetric around 0uV? E.g. you'll get saturation at $\pm 1200$uV? Is this always the case?

[alejoe91]

I think that's how saturation works, at least for int16. Maybe we can make a symmetric arguments?

[JoeZiminski]

Hey @samuelgarcia thanks for this! will check this out tomorrow. I accidentally did not push two tidy-up commits to #4301, do you mind if I push to your branch to add some changes? I think it is mostly superficial stuff like docstrings etc.

[samuelgarcia]

Hello, trying this out on real data with saturation. I get this output

artifact_periods=array([(0, 637721, 638769), (0, 638955, 639206), (0, 923219, 923602),
       (0, 923605, 923606), (0, 923607, 923835)],

Are these periods inclusive? And if they are, should the last pair be merged?

Yes, the last pair should be merged.
Let us check. the _collapse_events() is done for this purpose.
@JoeZiminski can you look at this ?

[samuelgarcia]

Hey @samuelgarcia thanks for this! will check this out tomorrow. I accidentally did not push two tidy-up commits to #4301, do you mind if I push to your branch to add some changes? I think it is mostly superficial stuff like docstrings etc.

yes of course. push anything you want