Code

NWB revisions - PR 2 of 3#71

Code

Merged

sidhulyalkar merged 157 commits intodatajoint:maindatajoint/element-array-ephys:mainfrom CBroz1:rkCBroz1/element-array-ephys:rkCopy head branch name to clipboardOct 19, 2022

+2,872-256

Commits

Commits on Aug 18, 2021

• added NWB export

  

  Thinh Nguyen

  committed
  f740aef

Commits on Sep 19, 2021

• copied ephys to ephys-no-curation, added recording_duration, make

  

  Thinh Nguyen

  committed
  042cc46

• remove Curation

  

  Thinh Nguyen

  committed
  a39a9b1

• make clustering_output_dir user-input optional, auto infer

  

  Thinh Nguyen

  committed
  590310e

• minor bug fix

  

  Thinh Nguyen

  committed
  adfad95

Commits on Sep 20, 2021

• improve kilosort loading routine - add validate() method

  

  Thinh Nguyen

  committed
  b7c0845

• helper for ProbeInsertion - auto_generate_entries(session_key)

  

  Thinh Nguyen

  committed
  de84ce0

Commits on Sep 21, 2021

• no-curation, store processed data in user-specified processed_data_dir if provided

  

  Thinh Nguyen

  committed
  4397dd7

• using find_full_path for session dir as well - improve robustness

  

  Thinh Nguyen

  committed
  5420ae0

• Update ephys_no_curation.py

  

  Thinh Nguyen

  committed
  70e93b3

Commits on Sep 22, 2021

• bugfix

  

  Thinh Nguyen

  committed
  a7e7554

Commits on Sep 23, 2021

• automate ClusteringTask insertion

  

  Thinh Nguyen

  committed
  0d56456

Commits on Sep 30, 2021

• triggering Kilosort with ecephys_spike_sorting package

  

  Thinh Nguyen

  committed
  047bfa1

• remove _required_packages_paths

  

  Thinh Nguyen

  committed
  60105da

• minor stylistic improvements

  

  Thinh Nguyen

  committed
  a9326ea

• Apply suggestions from code review

  Show description for 149ef3f
  

  Thinh Nguyen

  and

  dimitri-yatsenko

  authored
  149ef3f

Commits on Oct 1, 2021

• typo fix

  

  Thinh Nguyen

  committed
  9f98195

• Merge branch 'no-curation' of https://github.com/ttngu207/element-array-ephys into no-curation

  

  Thinh Nguyen

  committed
  a24bd1a

• handles a weird windows/unix path incompatibility (even with pathlib)

  

  Thinh Nguyen

  committed
  ba28637

• fix missing clustering_method

  

  Thinh Nguyen

  committed
  5cdc994

• flag to create spike sorting output dir

  

  Thinh Nguyen

  committed
  6c646bb

• Update kilosort_trigger.py

  

  Thinh Nguyen

  committed
  dd01fd2

• minor tweak/improvements in kilosort triggering

  

  Thinh Nguyen

  committed
  f699ce7

• bugfix in triggering ecephys_spike_sorting

  

  Thinh Nguyen

  committed
  6bf0eb1

• handle cases where fileTimeSecs is not available

  

  Thinh Nguyen

  committed
  6788180

Commits on Oct 2, 2021

• bugfix

  

  Thinh Nguyen

  committed
  d63561f

• missing generate module json

  

  Thinh Nguyen

  committed
  375e437

• change default noise_template_use_rf to False

  

  Thinh Nguyen

  committed
  c593baf

Commits on Oct 4, 2021

• minor bugfix

  

  Thinh Nguyen

  committed
  69c5e51

• add kilosort 2.5 as default content

  

  Thinh Nguyen

  committed
  a6cae12

• make variable naming consistent

  

  Thinh Nguyen

  committed
  a0ea9f7

• include clustering_method into the calculation of param_set_hash

  

  Thinh Nguyen

  committed
  acdab12

• updating kilosort_repository depending on which KSVer to be used

  

  Thinh Nguyen

  committed
  38c5be6

• bugfix

  

  Thinh Nguyen

  committed
  28c4452

• bugfix, convert path to string

  

  Thinh Nguyen

  committed
  94aade7

Commits on Oct 5, 2021

• log the folder creation

  

  Thinh Nguyen

  committed
  ae966aa

• add debugging lines

  

  Thinh Nguyen

  committed
  b9f4e92

• bugfix - no dir created

  

  Thinh Nguyen

  committed
  044c389

Commits on Oct 6, 2021

• Update kilosort.py

  

  Thinh Nguyen

  committed
  0f0c212

• new version 0.1.0b1

  

  Thinh Nguyen

  committed
  67341d8

Commits on Oct 7, 2021

• improve clusteringtask and waveform ingestion routine

  

  Thinh Nguyen

  committed
  c2ee64f

• minor cleanup

  

  Thinh Nguyen

  committed
  dc7ddd9

• stage tracking and resumable kilosort run

  

  Thinh Nguyen

  committed
  408532c

• minor bugfix

  

  Thinh Nguyen

  committed
  55bec01

• bugfix logging for kilosort triggering

  

  Thinh Nguyen

  committed
  f34e95d

• duration for each module run

  

  Thinh Nguyen

  committed
  19b704b

Commits on Oct 8, 2021

• check ap.bin file validity before triggering kilosort (based on filesize)

  

  Thinh Nguyen

  committed
  beaf765

Commits on Oct 11, 2021

• Apply suggestions from code review

  Show description for 74e3ead
  

  Thinh Nguyen

  and

  dimitri-yatsenko

  authored
  74e3ead

• stylistic improvements, addressing code review comments

  

  Thinh Nguyen

  committed
  e8ffe17

Commits on Nov 2, 2021

• handle NWB export with multiple curated clusterings from one session

  

  Thinh Nguyen

  committed
  d07f830

• Update nwb.py

  

  Thinh Nguyen

  committed
  19616ef

• minor bugfix

  

  Thinh Nguyen

  committed
  09c1e60

• Merge pull request #2 from ttngu207/nwb-export

  Show description for 3ebdf23
  

  Thinh Nguyen

  authored
  3ebdf23

• add nwb export to no-curation ephys

  

  Thinh Nguyen

  committed
  b25f065

Commits on Nov 9, 2021

• first prototype for running the ecephys_pipeline with OpenEphys

  

  Thinh Nguyen

  committed
  49ca0be

• bugfix for running kilosort for Open Ephys data

  

  Thinh Nguyen

  committed
  199a2ba

Commits on Nov 11, 2021

• specify additional recording-info as part of the params

  

  Thinh Nguyen

  committed
  58b5984

Commits on Nov 18, 2021

• add neuropixels UHD probe type

  

  Thinh Nguyen

  committed
  ddc3b94

• triggering kilosort analysis for open-ephys

  

  Thinh Nguyen

  committed
  df599fb

Commits on Nov 19, 2021

• first prototype for pykilosort

  

  Thinh Nguyen

  committed
  819ff19

• use_C_waves=False for OpenEphys

  

  Thinh Nguyen

  committed
  81d99c8

Commits on Nov 22, 2021

• using fork of pyopenephys

  

  Thinh Nguyen

  committed
  96931a4

• minor bugfix in running pykilosort

  

  Thinh Nguyen

  committed
  b6f8f99

• update openephys loader

  

  Thinh Nguyen

  committed
  4250220

• fix package requirement formatting error

  

  Thinh Nguyen

  committed
  af2b18b

• handles format differences between npx1 vs 3A

  

  Thinh Nguyen

  committed
  e325a30

Commits on Nov 23, 2021

• supporting neuropixels UHD in ephys.EphysRecording

  

  Thinh Nguyen

  committed
  db3027b

• bugfix in electrode sites design for Neuropixels UHD probe

  

  Thinh Nguyen

  committed
  f55a6a7

• search recording channels for Open Ephys based on channel names

  

  Thinh Nguyen

  committed
  d105419

• bugfix openephys loader

  

  Thinh Nguyen

  committed
  0d16e7e

• bugfix - extract recording datetime (instead of using experiment datetime)

  

  Thinh Nguyen

  committed
  c213325

• bugfix, timedelta as seconds

  

  Thinh Nguyen

  committed
  adffe34

• handles extraction of connected channels for NP_PROBE format in OpenEphys

  

  Thinh Nguyen

  committed
  43d6614

Commits on Nov 25, 2021

• clusters extraction - check cluster_group.tsv and cluster_KSLabel.tsv

  

  Thinh Nguyen

  committed
  da10c66

• bugfix in triggering pykilosort

  

  Thinh Nguyen

  committed
  02069c9

• handle missing sample_rate from pykilosort params.py

  

  Thinh Nguyen

  committed
  142459d

• for pykilosort's probe, provide both Nchan and NchanTOT

  

  Thinh Nguyen

  committed
  1c39568

Commits on Nov 26, 2021

• openephys loader - handles signalchain and processor as single element or list

  

  Thinh Nguyen

  committed
  2022e91

• handles multi-probe for older OE version

  

  Thinh Nguyen

  committed
  02c4b67

Commits on Nov 29, 2021

• NWB export fix, specifying which ephys module

  

  Thinh Nguyen

  committed
  8dff08b

• version bump

  

  Thinh Nguyen

  committed
  6107e8e

• fix NWB export - null waveforms - back to version 0.1.0b1

  

  Thinh Nguyen

  committed
  dae36d1

• version bump

  

  Thinh Nguyen

  committed
  8657d58

• include probe as part of the electrode_group name for uniqueness

  

  Thinh Nguyen

  committed
  aa47c8a

Commits on Dec 7, 2021

• bugfix in assigning unit electrode indices

  ttngu207

  committed
  31bba8c

• Merge pull request #3 from ttngu207/nwb-export

  Show description for f9a4754
  

  Thinh Nguyen

  authored
  f9a4754

Commits on Jan 24, 2022

• all three ephys files up to date

  A-Baji

  committed
  f2881ca

• applied requested changes

  A-Baji

  committed
  c56cd18

• Merge pull request datajoint#4 from A-Baji/no-curation

  Show description for 9dd6b42
  

  Thinh Nguyen

  authored
  9dd6b42

Commits on Jan 26, 2022

• DEPRECATING NWB EXPORT

  

  Thinh Nguyen

  committed
  4951b39

• Merge branch 'main' of https://github.com/datajoint/element-array-ephys into no-curation

  

  Thinh Nguyen

  committed
  b4832ea

Commits on Jan 27, 2022

• minor bugfix

  

  Thinh Nguyen

  committed
  d66368c

• name tweak

  

  Thinh Nguyen

  committed
  779b2fb

• Apply suggestions from code review

  Show description for f4052cc
  

  Thinh Nguyen

  and

  dimitri-yatsenko

  authored
  f4052cc

Commits on Jan 31, 2022

• rename sess_dir -> session_dir

  

  Thinh Nguyen

  committed
  03cab02

• Update requirements.txt

  

  Thinh Nguyen

  authored
  cb1a041

• Update requirements.txt

  

  Thinh Nguyen

  authored
  7320f9f

• Update requirements.txt

  

  Thinh Nguyen

  authored
  f0b3d4a

Commits on Feb 18, 2022

• handle older open ephys format for single probe

  

  Thinh Nguyen

  authored
  bdcfa46

• remove unintended prototyping work

  

  Thinh Nguyen

  authored
  83649f5

Commits on Feb 25, 2022

• delete nwb export - rename ephys module -> ephys_acute

  

  Thinh Nguyen

  committed
  c2f8aea

Commits on Mar 14, 2022

• Update __init__.py

  

  Thinh Nguyen

  authored
  e0a9a4f

Commits on Mar 16, 2022

• bugfix

  

  Thinh Nguyen

  authored
  769de13

Commits on Mar 25, 2022

• configurable paramset_idx for auto ClusteringTask generation

  

  Thinh Nguyen

  authored
  39c8579

Commits on May 12, 2022

• Update openephys.py

  

  Thinh Nguyen

  committed
  85c7c8b

Commits on May 20, 2022

• update openephys loader - handle new open ephys format

  

  Thinh Nguyen

  committed
  11a12ba

• handles new probe naming in latest Open Ephys format

  

  Thinh Nguyen

  committed
  cd5fe70

Commits on May 23, 2022

• Apply suggestions from code review

  Show description for af864d7
  

  Thinh Nguyen

  and

  dimitri-yatsenko

  authored
  af864d7

• added assertion - safeguard against failed loading of continuous.dat

  

  Thinh Nguyen

  committed
  47babf3

• Merge branch 'no-curation' of https://github.com/ttngu207/element-array-ephys into no-curation

  

  Thinh Nguyen

  committed
  7fecff1

• Merge remote-tracking branch 'upstream/run_kilosort' into no-curation

  

  Thinh Nguyen

  committed
  ddd4095

• Merge pull request datajoint#69 from ttngu207/no-curation

  Show description for 364f80e
  kabilar

  authored
  364f80e

• Update requirements.txt

  

  Thinh Nguyen

  committed
  a578d85

• kilosort2 also as part of the contents for ClusteringMethod

  

  Thinh Nguyen

  committed
  f4b917d

Commits on May 24, 2022

• bugfix for LFP electrode mapping

  

  Thinh Nguyen

  committed
  f11e016

• Merge pull request datajoint#70 from ttngu207/no-curation

  Show description for 747c15f
  sidhulyalkar

  authored
  747c15f

Commits on May 25, 2022

• WIP: nwb bugfix

  CBroz1

  committed
  49bba8a

Commits on May 26, 2022

• WIP: NWB fix - prevent SQL err by restricting key

  CBroz1

  committed
  b62fd12

• update open ephys loader to handle "STREAM" in latest format

  

  Thinh Nguyen

  committed
  07604e2

Commits on May 31, 2022

• WIP: nwb line length, Readme mention of

  CBroz1

  committed
  e1c9b35

Commits on Jun 1, 2022

• added loading of electrode location for new openephys format

  

  Thinh Nguyen

  committed
  4e367d7

• Merge pull request datajoint#73 from ttngu207/no-curation

  Show description for 9272ee6
  sidhulyalkar

  authored
  9272ee6

Commits on Jun 3, 2022

• more robust loading of openephys format

  

  Thinh Nguyen

  committed
  67039ac

• Merge pull request datajoint#77 from ttngu207/no-curation

  Show description for d298b07
  

  Thinh Nguyen

  authored
  d298b07

• Update README.md

  Show description for 720e355
  

  CBroz1

  and

  dimitri-yatsenko

  authored
  720e355

Commits on Jun 7, 2022

• improve logic for running kilosort modules in a resumable fashion

  

  Thinh Nguyen

  committed
  9a59e57

• code cleanup, minor bugfix

  

  Thinh Nguyen

  committed
  b97566e

Commits on Jun 9, 2022

• bugfix, match new implementation for openephys

  

  Thinh Nguyen

  committed
  3f1ee37

Commits on Jun 15, 2022

• Issue datajoint#11

  CBroz1

  committed
  4a3e0bf

• Merge branch 'rk' of https://github.com/CBroz1/element-array-ephys into rk

  CBroz1

  committed
  bd6d7e4

• Issue datajoint#63

  CBroz1

  committed
  d102f6f

Commits on Jun 16, 2022

• Add Code of Conduct

  CBroz1

  committed
  e43e5d5

Commits on Jun 17, 2022

• Add contact info to Code of Conduct

  CBroz1

  committed
  70e0b1c

Commits on Jun 30, 2022

• improve kilosort calls, handle spaces in paths

  

  Thinh Nguyen

  authored
  0c77826

• remove space escaping character

  

  Thinh Nguyen

  authored
  b71b459

Commits on Jul 19, 2022

• improve error message

  

  Thinh Nguyen

  committed
  a3c5c2f

• Merge branch 'no-curation' of https://github.com/ttngu207/element-array-ephys into no-curation

  

  Thinh Nguyen

  committed
  fd331bd

Commits on Jul 21, 2022

• Merge branch 'run_kilosort' of https://github.com/datajoint/element-array-ephys into rk

  CBroz1

  committed
  13d74ad

• WIP: version bump pynwb to 2.0

  CBroz1

  committed
  0221848

Commits on Jul 22, 2022

• Merge pull request datajoint#86 from CBroz1/rk

  Show description for d9c3887
  kabilar

  authored
  d9c3887

Commits on Jul 25, 2022

• Merge pull request datajoint#88 from ttngu207/no-curation

  Show description for ad8436e
  kabilar

  authored
  ad8436e

• implement data compression using mtscomp for openephys and spikeglx neuropixels data

  

  Thinh Nguyen

  committed
  b2bd0ee

Commits on Aug 12, 2022

• garbage collect openephys objects

  

  Thinh Nguyen

  committed
  97f3d21

Commits on Aug 15, 2022

• garbage collect openephys objects

  

  Thinh Nguyen

  committed
  d8aea04

• Merge pull request datajoint#89 from ttngu207/no-curation

  Show description for c153e7f
  sidhulyalkar

  authored
  c153e7f

Commits on Aug 30, 2022

• Update kilosort_triggering.py

  

  Thinh Nguyen

  committed
  f9f18d0

Commits on Sep 2, 2022

• bugfix in running catgt

  

  Thinh Nguyen

  committed
  5905392

• enable catgt run

  

  Thinh Nguyen

  committed
  987231b

• bugfix

  

  Thinh Nguyen

  committed
  aed42ca

• bugfix

  

  Thinh Nguyen

  committed
  fbdbe24

• missing_ok arg only available in python 3.8+

  

  Thinh Nguyen

  committed
  35da39b

• bugfix - path search for catgt output

  

  Thinh Nguyen

  committed
  c33d1b0

• improve error handling

  

  Thinh Nguyen

  committed
  f60ba3d

• Merge pull request datajoint#90 from ttngu207/no-curation

  Show description for 23ca7ca
  

  Thinh Nguyen

  authored
  23ca7ca

Commits on Sep 14, 2022

• Update kilosort_triggering.py

  

  Thinh Nguyen

  committed
  71d87ae

• Merge pull request datajoint#91 from ttngu207/no-curation

  Show description for 6757ef7
  

  Thinh Nguyen

  authored
  6757ef7

Commits on Sep 15, 2022

• Ensure Path type for get_spikeglx_meta_filepath

  CBroz1

  committed
  0e94252