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Develop #685

Merged
merged 97 commits into from
Dec 13, 2023
Merged

Develop #685

merged 97 commits into from
Dec 13, 2023

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k1o0
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@k1o0 k1o0 commented Dec 13, 2023 •
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Release Notes 2.27

features

  • Add full video wheel motion alignment code to ibllib.io.extractors.video_motion module
  • Change FPGA camera extractor to attempt wheel alignment if audio alignment fails
  • Flexible FpgaTrials class allows subclassing for changes in hardware and task
  • Task QC thresholds depend on sound card
  • Extractor classes now return dicts instead of tuple
  • Support extraction of habituationChoiceWorld with FPGA
  • New IBLGlobusPatcher class allows safe and complete deletion of datasets

bugfixes

  • Fix numpy version dependent error in io.extractors.camera.attribute_times
  • Fix for habituationChoiceWorld stim off times occuring outside of trial intervals
  • Improvements to Timeline trials extractor, especially for valve open times
  • trainingPhaseChoiceWorld added to Bpod protocol extractor map fixture
  • Last trial of FPGA sessions now correctly extracted
  • Correct dynamic pipeline extraction of passive choice world trials

other

  • Removed deprecated pyschofit module
  • Deprecated oneibl.globus module in favour of one.remote.globus
  • Deprecated qc.task_extractors in favour of behaviour pipeline tasks

k1o0 and others added 30 commits August 30, 2023 10:50
@k1o0
Deprecate globus module
270fdd4
@k1o0
Use ONE Globus in patcher
0e60893
@k1o0
Add delete_dataset method
d97ccd1
@k1o0
Delete S3 files
64e72f3
@k1o0
Bump ONE version
1889e7c
@mayofaulkner
full session wheel alignment
7d811e0
@mayofaulkner
Merge branch 'release/2.26' into develop
3deb565
@k1o0
Merge branch 'develop' into globusDeprecation
8511bb6
@mayofaulkner
add video wheel alignment to fpga camera extraction
f77bb4a
@mayofaulkner
report server health to data repo not lab
e5b71cf
@mayofaulkner
circular imports
a8850a2
@mayofaulkner
Merge branch 'develop' into wheel_alignment
976b4b0
@mayofaulkner
upload plot to alyx
5c59536
@mayofaulkner
remove circular imports
3cd2ca8
@chris-langfield
Density gain option (#652)
935c0c7 
* add gain option and cleanup docstring

* flake

---------

Co-authored-by: chris-langfield <[email protected]>
@GaelleChapuis
doc probe geometry
6bc95d2
@k1o0
sync extension optional; reduce logging clutter
a497411
@k1o0
flake8
6c04956
@k1o0
Task qc extractor refactor (#649)
68fb8cd 
* Habituation extract phase and position

* Independent task QC method in behaviour tasks

* var names

* flake8

* Initialize settings property
@k1o0
Merge branch 'develop' into globusDeprecation
3d8a626
@mayofaulkner
Merge branch 'develop' into wheel_alignment
7d5bfc1
@mayofaulkner
remove behavior flag, infer from files
b567a3c
@mayofaulkner
restrict to left and right cameras
69972c3
@mayofaulkner
fix glob pattern
659efcf
@mayofaulkner
authenticate alyx
2a66a13
@mayofaulkner
Merge pull request #651 from int-brain-lab/wheel_alignment
fbaea40 
Wheel alignment
@mayofaulkner
save figure with label name
04733ac
@GaelleChapuis
Merge remote-tracking branch 'origin/develop' into docs
9acbf8e
@mayofaulkner
close figure and change processes
10007ec
@mayofaulkner
doc strings to wheel alignment module
c8d6556
k1o0 and others added 29 commits December 8, 2023 13:01
@k1o0
mesoscope trials extractor refactor; fix attribute_times numpy versio…
8aff0ad 
…n bug; FpgaTrials.build_trials method call after sync
@k1o0
Build trials after syncing Bpod clock
6b1416c
@k1o0
Include wheel in Bpod trials dict passed to FpgaTrials
bac2374
@k1o0
Add more fields to qc extractor
ba2553d
@k1o0
Merge pull request #673 from int-brain-lab/HabituationNidq
e0cac72 
Habituation nidq
@mayofaulkner
Merge branch 'probe_plot_fix' into passive_fix
cfbefba
@mayofaulkner
Merge branch 'develop' into passive_fix
30d1d78
@k1o0
Merge branch 'develop' into TrainingTaskQC
c848cea
@k1o0
flake
f3f057c
@mayofaulkner
Merge pull request #681 from int-brain-lab/passive_fix
6075d57 
Passive fix
@k1o0
Merge branch 'develop' into globusDeprecation
d31d7d1
@k1o0
Merge branch 'develop' into globusDeprecation
74e57b8
@k1o0
Skip phase distribution check; handle NaNs in stim move before go cue
f5290b0
@k1o0
use get_bpod_event_times
0ca5082
@k1o0
Merge pull request #665 from int-brain-lab/TrainingTaskQC
beda422 
Training task qc
@k1o0
Increase default protocol period
b31d14e
@k1o0
Merge branch 'develop' into globusDeprecation
da365e6
@k1o0
Test new extractor methods
49ad5a3
@k1o0
Move test_ephys_trials tests to test_ephys_fpga; remove old functions
48cfcd0
@k1o0
Added trainingPhaseChoiceWorld to task protocol extractor map; fix ty…
276603e 
…po in ephysqc
@k1o0
remove prepare_experiment
f617813
@k1o0
Merge pull request #647 from int-brain-lab/globusDeprecation
9e38c64 
Globus deprecation
@k1o0
Merge pull request #684 from int-brain-lab/removeOldFunctions
bb1a851 
remove prepare_experiment
@k1o0
Release notes
ebc9774
@mayofaulkner
randomise session for histology
9fbc0f2
@mayofaulkner
randomise all seeds
8454d8d
@mayofaulkner
Merge pull request #687 from int-brain-lab/random_sessions_for_tests
8c944d2 
randomise session for histology
@k1o0
Update release notes; remove unused time date range function
7c2a821
@k1o0
Remove double import; delete session notes first on teardown
934f9da
@k1o0 k1o0 merged commit d875d82 into master Dec 13, 2023
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6 participants
@k1o0 @mayofaulkner @chris-langfield @GaelleChapuis @oliche @juhuntenburg