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Spike sorting v1 pipeline #651

Merged
merged 156 commits into from
Dec 9, 2023
Merged

Spike sorting v1 pipeline #651

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0752b16
Save LFP as pynwb.ecephys.LFP
khl02007 May 10, 2023
9fb9d7b
Fix formatting
edeno May 10, 2023
5243b21
Fix formatting
edeno May 10, 2023
fc9eac7
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 May 11, 2023
bf7487a
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 May 13, 2023
6a876fd
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 May 21, 2023
fba7523
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 May 22, 2023
2ff1a5f
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Jun 2, 2023
128a0a8
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Jun 5, 2023
75930cd
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Jun 20, 2023
c2adb1d
Add new tables
khl02007 Jul 23, 2023
476ee6d
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Jul 23, 2023
79e842b
Change name of Figurl table
khl02007 Jul 24, 2023
ecc3a0c
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Jul 24, 2023
6f012fb
Merge branch 'master' into spikesorting_v1
khl02007 Jul 24, 2023
8870280
Update pipeline
khl02007 Jul 29, 2023
2834d26
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Aug 2, 2023
379c904
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Aug 7, 2023
8f38db0
Merge branch 'master' into spikesorting_v1
khl02007 Aug 7, 2023
184cb82
Edit merge
khl02007 Aug 7, 2023
e9ffa89
Merge branch 'master' into spikesorting_v1
khl02007 Sep 1, 2023
c1d83eb
Remove methods
khl02007 Sep 7, 2023
af5224c
Minor fix
khl02007 Sep 7, 2023
b10da42
Merge branch 'spikesorting_v1' of github.com:khl02007/nwb_datajoint i…
khl02007 Sep 7, 2023
2a29a87
Save preproc rec as NWB
khl02007 Sep 18, 2023
9c848a9
Add artfiact changes
khl02007 Sep 18, 2023
2a3f002
Minor change
khl02007 Sep 18, 2023
0066f7c
Fix lint
khl02007 Sep 18, 2023
7003e0c
Update artifact and sorting
khl02007 Sep 20, 2023
4567841
Minor update
khl02007 Sep 20, 2023
71aa6e8
Update sorting
khl02007 Sep 21, 2023
64783ab
Start curation
khl02007 Sep 21, 2023
520c587
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Sep 21, 2023
3b054e6
Merge branch 'master' into spikesorting_v1
khl02007 Sep 21, 2023
54b1b4c
Update curation
khl02007 Sep 28, 2023
9f35a11
Update curation
khl02007 Sep 29, 2023
9adb904
Write sorting with curation
khl02007 Sep 30, 2023
45111ca
Finish curation
khl02007 Oct 1, 2023
0268ee8
Remove unused imports
khl02007 Oct 1, 2023
93935dd
Add new schema
khl02007 Oct 1, 2023
3a7f8f1
Update data type
khl02007 Oct 1, 2023
5513598
Update figurl curation
khl02007 Oct 2, 2023
95e6c1a
Modify metric curation
khl02007 Oct 2, 2023
e52aec7
Reorg metric curation
khl02007 Oct 2, 2023
d578e65
Streamline metric
khl02007 Oct 2, 2023
f671fc4
Add to MetricCuration
khl02007 Oct 2, 2023
774d7f0
Add user exposed methods
khl02007 Oct 2, 2023
db73333
Minor update
khl02007 Oct 2, 2023
8a5bc86
Minor edit
khl02007 Oct 2, 2023
652bcee
Update metric methods
khl02007 Oct 5, 2023
b1cd74c
Add docstring
khl02007 Oct 5, 2023
aa975fa
Update metric curation
khl02007 Oct 6, 2023
9765f34
Add comments
khl02007 Oct 6, 2023
5127782
Merge branch 'master' into spikesorting_v1
khl02007 Oct 7, 2023
b7fc7c8
Fix merge
khl02007 Oct 7, 2023
4d9b772
Fix spelling error
khl02007 Oct 7, 2023
59c16c5
Change Curation to CurationV1
khl02007 Oct 9, 2023
00414ff
Fix comments
khl02007 Oct 9, 2023
03c84cb
Update src/spyglass/spikesorting/v1/artifact.py
khl02007 Oct 9, 2023
4ae1bb9
Remove neuroconv from dep and add copied class
khl02007 Oct 10, 2023
f70f2b0
Update init
khl02007 Oct 10, 2023
07db476
Remove unused import
khl02007 Oct 10, 2023
aecaf19
Remove unused import
khl02007 Oct 10, 2023
fc65f30
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Oct 10, 2023
b82b6aa
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Oct 10, 2023
970cfc7
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Oct 10, 2023
dd753b7
Update src/spyglass/spikesorting/v1/artifact.py
khl02007 Oct 10, 2023
9198393
Make ->Session primary key in SortGroup
khl02007 Oct 10, 2023
f5725ed
Make insert1 insert for multi row insertion
khl02007 Oct 12, 2023
6b49897
Remove neuroconv dep
khl02007 Oct 12, 2023
3905209
Update settings.json
khl02007 Oct 18, 2023
65f3edd
Change MetricCuration dep
khl02007 Oct 18, 2023
903cb3e
Add `insert_selection`
khl02007 Oct 19, 2023
68750cd
Update based on comments
khl02007 Oct 19, 2023
56c23bb
Move util
khl02007 Oct 19, 2023
7d3588b
Add insert_selection to SpikeSortingSelection
khl02007 Oct 19, 2023
09fb986
Minor changes to sorting.py
khl02007 Oct 20, 2023
2b9fa3e
Fix id gen
khl02007 Oct 20, 2023
3243e56
Change fetch
khl02007 Oct 20, 2023
51d75a3
Minor change
khl02007 Oct 23, 2023
2249538
Update recording
khl02007 Oct 23, 2023
dc2648a
More changes
khl02007 Oct 23, 2023
7294936
Add dep
khl02007 Oct 24, 2023
3724ae4
Add curation to AnalysisNWB
khl02007 Oct 24, 2023
6afc02b
Minor change
khl02007 Oct 25, 2023
52ab117
Update artifact detection
khl02007 Oct 30, 2023
7fabe29
Minor update
khl02007 Oct 30, 2023
afe7a71
Fix while testing
khl02007 Nov 15, 2023
01da13c
Formatting
khl02007 Nov 15, 2023
af9be6b
Update figurl
khl02007 Nov 15, 2023
e580a39
Add ss v1 tutorial
khl02007 Nov 15, 2023
16d929a
Update merge
khl02007 Nov 16, 2023
1b38679
Update populate
khl02007 Nov 16, 2023
0706b08
Update notebook and merge insert
khl02007 Nov 16, 2023
70be978
Update import issue
khl02007 Nov 27, 2023
aa9d0f1
Fix typo
khl02007 Nov 28, 2023
f5a84a8
Merge branch 'spikesorting_v1' of https://github.com/khl02007/spyglas…
khl02007 Nov 28, 2023
b66d0d0
Fix timestamp extend
khl02007 Nov 28, 2023
11c97cf
Handle ref channel not in sort group
khl02007 Nov 29, 2023
ac32877
Apply black
khl02007 Nov 29, 2023
b9d6b29
Merge branch 'master' of https://github.com/LorenFrankLab/spyglass
khl02007 Nov 29, 2023
d738788
Merge branch 'master' into spikesorting_v1
khl02007 Nov 29, 2023
31d16e6
Add insert metric curation
khl02007 Nov 29, 2023
f189a5d
Fix spelling error
khl02007 Nov 29, 2023
ae74064
Fix concat ref channel
khl02007 Nov 29, 2023
1e20882
Fix insert metric curation
khl02007 Nov 29, 2023
7d947bf
Add SpikeSortingOutput.CuratedSpikeSorting
khl02007 Nov 30, 2023
bf372c6
Sortings -> sorting
khl02007 Nov 30, 2023
ba9eec7
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 1, 2023
fa8edfa
Revert back to sort_group_id int
khl02007 Dec 1, 2023
dbb173d
Merge branch 'spikesorting_v1' of https://github.com/khl02007/spyglas…
khl02007 Dec 1, 2023
fb31546
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 1, 2023
df2bfc8
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 1, 2023
626f8bb
Changes based on comments
khl02007 Dec 5, 2023
1307cdc
Update src/spyglass/spikesorting/merge.py
khl02007 Dec 5, 2023
0d33e99
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 7, 2023
23e3e38
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 7, 2023
e899972
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 7, 2023
6521baf
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 7, 2023
142c09f
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 7, 2023
5225ca8
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 7, 2023
bf27571
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 7, 2023
4f24d23
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 7, 2023
2eccdd7
add util function to get spiking merge_ids from restriction
samuelbray32 Dec 8, 2023
3f55cc3
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 8, 2023
5c554a2
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 8, 2023
b5cf524
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 8, 2023
671b3f3
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 8, 2023
db0278a
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 8, 2023
7bfca04
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 8, 2023
80ef44d
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 8, 2023
634d149
Update src/spyglass/spikesorting/v1/figurl_curation.py
khl02007 Dec 8, 2023
6544ce0
Update src/spyglass/spikesorting/v1/figurl_curation.py
khl02007 Dec 8, 2023
1b2d50f
Update src/spyglass/spikesorting/v1/curation.py
khl02007 Dec 8, 2023
94a31c8
Update src/spyglass/spikesorting/v1/figurl_curation.py
khl02007 Dec 8, 2023
7ed4bfe
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 8, 2023
97a536d
Update src/spyglass/spikesorting/v1/artifact.py
khl02007 Dec 8, 2023
6b9c249
Update src/spyglass/spikesorting/v1/artifact.py
khl02007 Dec 8, 2023
a1fd6cb
Remove custom merge insert
khl02007 Dec 8, 2023
e7a2abb
Update src/spyglass/spikesorting/v1/metric_utils.py
khl02007 Dec 8, 2023
724c504
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 8, 2023
1f91313
Minor fix
khl02007 Dec 8, 2023
2b73a05
Update src/spyglass/spikesorting/v1/figurl_curation.py
khl02007 Dec 8, 2023
32254ec
Update src/spyglass/spikesorting/v1/metric_curation.py
khl02007 Dec 8, 2023
ee709d1
Update src/spyglass/spikesorting/v1/artifact.py
khl02007 Dec 8, 2023
9d85e5d
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 8, 2023
d7f0dbe
Update src/spyglass/spikesorting/v1/figurl_curation.py
khl02007 Dec 8, 2023
453460f
Update src/spyglass/spikesorting/v1/metric_utils.py
khl02007 Dec 8, 2023
c17bf13
Update src/spyglass/spikesorting/v1/metric_utils.py
khl02007 Dec 8, 2023
996a8de
Update src/spyglass/spikesorting/v1/figurl_curation.py
khl02007 Dec 8, 2023
f78e96a
Update name
khl02007 Dec 8, 2023
3592f0d
Merge branch 'spikesorting_v1' of github.com:khl02007/nwb_datajoint i…
khl02007 Dec 8, 2023
586791c
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 8, 2023
8025235
Update src/spyglass/spikesorting/v1/recording.py
khl02007 Dec 8, 2023
7003c07
Lint
khl02007 Dec 8, 2023
b292e8c
Fix changes
khl02007 Dec 9, 2023
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1 change: 0 additions & 1 deletion .vscode/settings.json
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Expand Up @@ -2,7 +2,6 @@
"editor.formatOnSave": true,
"files.trimTrailingWhitespace": true,
"files.trimFinalNewlines": true,
"editor.multiCursorModifier": "ctrlCmd",
"autoDocstring.docstringFormat": "numpy",
"remote.SSH.remoteServerListenOnSocket": true,
"git.confirmSync": false,
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