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Datajoint pipeline PR into main
branch
#351
Commits on Oct 27, 2023
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Merge pull request #264 from ttngu207/datajoint_pipeline_pyrat
modify `subject` schema to align with pyrat - added pyrat sync routine
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Commits on Oct 31, 2023
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Merge branch 'datajoint_pipeline' of github.com:SainsburyWellcomeCent…
…re/aeon_mecha into datajoint_pipeline
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Merge pull request #268 from JaerongA/datajoint_pipeline
Minor sciviz fix & add pyrat worker to docker-compose
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Commits on Nov 1, 2023
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Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…
…oint_pipeline_pyrat
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added manual table
ExperimentSubject
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deprecate
colony.csv
ingestionThinh Nguyen committedNov 1, 2023 Configuration menu - View commit details
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check and update subject's "available" periodically
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Update aeon/dj_pipeline/subject.py
Co-authored-by: JaerongA <[email protected]>
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Commits on Nov 2, 2023
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Use
acquisition.Experiment
to register new aeon experimentsThinh Nguyen committedNov 2, 2023 Configuration menu - View commit details
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Merge branch 'datajoint_pipeline_pyrat' of https://github.com/ttngu20…
…7/aeon_mecha into datajoint_pipeline_pyrat
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Merge pull request #271 from ttngu207/datajoint_pipeline_pyrat
Added `lab_id` and `available` to pyrat subjects
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Commits on Nov 3, 2023
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Thinh Nguyen committed
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Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…
…oint_pipeline_pyrat
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pyrat schedule to every 12hours
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Merge pull request #274 from ttngu207/datajoint_pipeline_pyrat
minor improvement
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Merge pull request #276 from ttngu207/datajoint_pipeline_pyrat
handles http errors
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Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…
…oint_pipeline_pyrat
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Merge pull request #277 from ttngu207/datajoint_pipeline_pyrat
update sciviz
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Commits on Nov 9, 2023
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update food restriction procedure name
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Merge pull request #279 from ttngu207/datajoint_pipeline_pyrat
update food restriction procedure name
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Merge pull request #284 from JaerongA/dev
Fix epoch ingestion error
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Merge pull request #286 from JaerongA/datajoint_pipeline
build: ➕ add pillow in pyproject.toml
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Merge pull request #287 from JaerongA/datajoint_pipeline
build: ➕ add libtiff5 to apt_requirements.txt
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Merge pull request #289 from JaerongA/datajoint_pipeline
Add experiment devices & schema
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update ingestion for new social experiments
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Commits on Jan 8, 2024
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Merge remote-tracking branch 'upstream/social_schema' into datajoint_…
…pipeline
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fix(load_metadata): resolve pull conflicts (removed dataset.py)
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feat(social01): add new aeon schema for social 01
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feat(streams): incorporate social 0.1 experiments for ingestion
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fix(streams): sanitize column names (remove parenthesis)
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feat(schemas): add schema for social 01 experiment
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Merge branch 'social_schema' into datajoint_pipeline
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rearrange(social01): moved content to
social.py
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refactor(social): refactor binder functions to be more consistent wit…
…h other schema
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Merge branch 'social_schema' into datajoint_pipeline
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fix(acquisition): missing imports
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chore(load_metadata): remove obsolete "ingest_subject" mechanism from…
… colony.csv file
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feat(acquisition): specify devices schema for each experiment in a ta…
…ble instead of hard-coding
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fix(social): bugfix Rfid binder function
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Merge branch 'social_schema' into datajoint_social01
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fix(acquisition): skip Pose reader (this should be manual)
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Merge branch 'social_schema' into datajoint_social01
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fix(social): bugfix setting up RFID binder function
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Merge branch 'social_schema' into datajoint_social01
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fix(schemas): remove duplicated device in social01
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Merge branch 'social_schema' into datajoint_social01
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feat(streams_maker): simplify, improve robustness
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feat(reader): update Pose reader
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Merge branch 'social_schema' into datajoint_social01
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fix(social): bugfix for "Environment" readers
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Merge branch 'social_schema' into datajoint_social01
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Merge pull request #306 from ttngu207/datajoint_social01
Datajoint social01
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feat(acquisition): add
Environment
table to store data from Environ……ment's streams
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chore(tracking): cleanup make call for SLEAP ingestion
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feat(analysis): add Block-level analysis
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fix(social01): bugfix in setting up the readers
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Merge branch 'social_schema' into datajoint_social01
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feat(block_analysis): add analysis and plots for Block
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feat(analysis): add logic for BlockDetection and BlockAnalysis
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feat(get_maintenance_periods): update logic, cleaner & more robust
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fix(block_analysis): minor bugfix
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feat(block_analysis): add example notebook
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Create clone_and_freeze_exp02.py
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Merge pull request #309 from ttngu207/datajoint_social01
Block-level analysis and plots - draft 1
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fix(foraging): bugfix, duplicated code in resolving merge conflict
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update(dj_pipeline): remove obsolete tables
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update(report): disable
report
schema for nowThinh Nguyen committedJan 30, 2024 Configuration menu - View commit details
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chore(dj_pipeline): remove obsolete tables, helper functions
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refactor(reader): minor tweak in PoseReader
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Merge pull request #313 from JaerongA/datajoint_pipeline
Bug fix & add block analysis plots
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Merge pull request #315 from JaerongA/datajoint_pipeline
fix: 🐛 fix type hinting issue using 'from future import annotations
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feat(acqusition): add tables to store Experiment Notes and to extract…
… ActiveRegions
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feat(social): update binder function for social0.2
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Merge branch 'social_schema' into datajoint_social01
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Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…
…oint_social01
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fix(subject): set ref_weight to -1 if not available
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Merge pull request #316 from ttngu207/datajoint_social01
Major cleanup - removing obsolete tables and previous analysis routines - update worker
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Merge pull request #317 from JaerongA/datajoint_pipeline
Add block analysis to sciviz
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Merge pull request #318 from JaerongA/datajoint_pipeline
docs: 📝 update sciviz README.md
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fix(block_analysis): SubjectState is not a reliable indication of sub…
…jects in the block, use identities from SLEAP data
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Merge pull request #319 from ttngu207/datajoint_social01
SubjectState is not a reliable indication of subjects in the block, use identities from SLEAP data
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Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…
…oint_pipeline
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feat(worker): update worker for social01 and social02
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feat(block_analysis): Ensure the relevant streams ingestion are caugh…
…t up before each block analysis
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chore(worker): minor worker tuning
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update(worker): fine tune workers
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Merge pull request #321 from ttngu207/datajoint_pipeline
social0.2 ingestion and worker setup for automation
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Merge pull request #322 from JaerongA/datajoint_pipeline
feat: ✨ add a cronjob script for dj workers
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fix: bugfix in specsheet and tune worker
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Merge pull request #323 from ttngu207/datajoint_pipeline
fix: bugfix in specsheet and tune worker
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Merge branch 'datajoint_pipeline' of https://github.com/JaerongA/aeon…
…_mecha into datajoint_pipeline
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Merge pull request #325 from JaerongA/datajoint_pipeline
chore: 🔊 Create a logger for a cron job
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cron job runs a different version of docker-compose which yields version incompatibility issue
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Merge pull request #326 from JaerongA/datajoint_pipeline
fix: 🐛 specify docker path
Thinh Nguyen authoredFeb 6, 2024 Configuration menu - View commit details
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fix(social02): bugfix social schema reader
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update: more robust check for subjects in a given block
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Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…
…oint_pipeline
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Update social_experiments_block_analysis.ipynb
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Merge pull request #329 from ttngu207/datajoint_pipeline
update: more robust check for subjects in a given block
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fix(reader): bugfix csv reader dropping column when the csv file is e…
…mpty
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feat(block_analysis): add BlockSubject analysis based on Jai's initia…
…l work
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feat(metadata): explicitly extract and store frame rate for video source
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fix(block_analysis): minor bugfix
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Merge pull request #336 from ttngu207/datajoint_pipeline
add BlockSubjectPatch analysis & other minor fixes
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Merge pull request #339 from JaerongA/datajoint_pipeline
feat: ✨ add SocialExperiment page in sciviz
Thinh Nguyen authoredMar 11, 2024 Configuration menu - View commit details
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Merge pull request #341 from JaerongA/datajoint_pipeline
fix: 🐛 fix KeyError in BlockDetection
Thinh Nguyen authoredMar 20, 2024 Configuration menu - View commit details
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Merge pull request #342 from SainsburyWellcomeCentre/io-reorg
Introduce explicit object model for device streams
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Merge pull request #338 from SainsburyWellcomeCentre/add-license
Add BSD-3 license to project
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Merge pull request #346 from SainsburyWellcomeCentre/sciviz-local-setup
Update SciViz local setup
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update(schemas): update social schemas to use the refactored Stream, …
…StreamGroup and Device
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Merge pull request #347 from ttngu207/datajoint_pipeline
Update ingestion - using new Stream/Device io
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Merge pull request #348 from ttngu207/datajoint_pipeline
feat(dj): ingest data by searching multiple directories in specified order
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Merge pull request #349 from ttngu207/datajoint_pipeline
feat(acquisition): refactor Epoch & Metadata ingestion
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Merge pull request #350 from ttngu207/datajoint_pipeline
fix(tracking): bugfix searching for SLEAP model config file for multi-dir
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Merge pull request #352 from ttngu207/datajoint_pipeline
fix(acquisition): remove debugging codeblock
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Merge pull request #353 from ttngu207/datajoint_pipeline
feat(block_analysis): retrieve patch offset
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Merge pull request #355 from ttngu207/datajoint_pipeline
update(tracking): raise error if no SLEAP data found
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Merge pull request #360 from ttngu207/datajoint_pipeline
fix first chunk starting before epoch start & disable automatic BlockDetection
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Merge pull request #361 from ttngu207/datajoint_pipeline
Improve block analysis - skip subjects with no position data, bugfix Block detection
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Merge pull request #363 from ttngu207/datajoint_pipeline
BlockSubjectPatch analysis, patch preference plot and SciViz update
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