Spike sorting v1 pipeline (LorenFrankLab#651)

* Save LFP as pynwb.ecephys.LFP

* Fix formatting

* Fix formatting

* Add new tables

* Change name of Figurl table

* Update pipeline

* Edit merge

* Remove methods

* Minor fix

* Save preproc rec as NWB

* Add artfiact changes

* Minor change

* Fix lint

* Update artifact and sorting

* Minor update

* Update sorting

* Start curation

* Update curation

* Update curation

* Write sorting with curation

* Finish curation

* Remove unused imports

* Add new schema

* Update data type

* Update figurl curation

* Modify metric curation

* Reorg metric curation

* Streamline metric

* Add to MetricCuration

* Add user exposed methods

* Minor update

* Minor edit

* Update metric methods

* Add docstring

* Update metric curation

* Add comments

* Fix merge

* Fix spelling error

* Change Curation to CurationV1

* Fix comments

* Update src/spyglass/spikesorting/v1/artifact.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Remove neuroconv from dep and add copied class

* Update init

* Remove unused import

* Remove unused import

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/artifact.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Make ->Session primary key in SortGroup

* Make insert1 insert for multi row insertion

* Remove neuroconv dep

* Update settings.json

* Change MetricCuration dep

* Add `insert_selection`

* Update based on comments

* Move util

* Add insert_selection to SpikeSortingSelection

* Minor changes to sorting.py

* Fix id gen

* Change fetch

* Minor change

* Update recording

* More changes

* Add dep

* Add curation to AnalysisNWB

* Minor change

* Update artifact detection

* Minor update

* Fix while testing

* Formatting

* Update figurl

* Add ss v1 tutorial

* Update merge

* Update populate

* Update notebook and merge insert

* Update import issue

* Fix typo

* Fix timestamp extend

* Handle ref channel not in sort group

* Apply black

* Add insert metric curation

* Fix spelling error

* Fix concat ref channel

* Fix insert metric curation

* Add SpikeSortingOutput.CuratedSpikeSorting

* Sortings -> sorting

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Revert back to sort_group_id int

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Changes based on comments

* Update src/spyglass/spikesorting/merge.py

Co-authored-by: Eric Denovellis <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* add util function to get spiking merge_ids from restriction

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/figurl_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/figurl_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/figurl_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/artifact.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/artifact.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Remove custom merge insert

* Update src/spyglass/spikesorting/v1/metric_utils.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Minor fix

* Update src/spyglass/spikesorting/v1/figurl_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/artifact.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/figurl_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_utils.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/metric_utils.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/figurl_curation.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update name

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/v1/recording.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Lint

* Fix changes

---------

Co-authored-by: Eric Denovellis <[email protected]>
Co-authored-by: Chris Brozdowski <[email protected]>
Co-authored-by: Eric Denovellis <[email protected]>
Co-authored-by: Sam Bray <[email protected]>

.vscode/settings.json

@@ -2,7 +2,6 @@
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     "files.trimTrailingWhitespace": true,
     "files.trimFinalNewlines": true,
-    "editor.multiCursorModifier": "ctrlCmd",
     "autoDocstring.docstringFormat": "numpy",
     "remote.SSH.remoteServerListenOnSocket": true,
     "git.confirmSync": false,