rc/2.3.0 #1703
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rc/2.3.0 #1703
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Codecov Report
@@ Coverage Diff @@
## master #1703 +/- ##
==========================================
- Coverage 36.83% 36.16% -0.67%
==========================================
Files 346 346
Lines 34714 33814 -900
==========================================
- Hits 12786 12229 -557
+ Misses 21928 21585 -343
Continue to review full report at Codecov.
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Implements corrections and filtering to the running speed data. Recomputes 'delta theta', or 'dx' due to raw data issues Corrects for artifacts ocurring when the encoder wraps at the maximum/minimum voltages, which produced transient spikes in speed. Reduces noise by implementing a 10Hz lowpass filter by default; unfiltered, artifact-corrected speed is available by using new session methods prefixed with `raw_` ( `raw_running_speed`, `raw_running_df`).
…pendencies in stimulus_processing.py (#1678) * GH #1666, Adds support for gratings stimuli in stimulus_processing and concurrency in naming Due to an assumption that all stimuli have 'images' keys stimulus_processing module was breaking when a grating stimuli was loaded. This adds support for grating stimuli in the form of adding required data to stimulus_processing to be able to recreate gratings and eliminates image key dependency. This also adds test coverage for stimulus_processing that was sorely lacking. Lastly trials_processing names of grating stimuli were changed to be concurrent to the stimulus_processing format. Resolves: #1666 See Also: #1667
Added an opt out to the trimming that occurs in get_synchronized_frame_times. Also fixed issue where no trimming would occur if the first element was a discontiguity.
Adds phase and spatial frequency columns to behavior_ophys_api get_stimulus_presentations. Fixes the regression test that was failing by making two apis (data_api and lims_api) congruent.
Fixes breaking regression of get_stimulus_presentations test between data api and lims api
This commit is a combination of the following: 1. Move some extension fields to augmented pynwb Subject class This commit moves subject related fields from our custom extension class to an extended version (BehaviorSubject) of the pynwb Subject class. 2. Rename OphysBehaviorTaskParametersSchema to BehaviorTaskParametersSchema Because the fields in the OphysBehaviorTaskParametersSchema were already describing parameters for a more encompassing behavior only schema, we need only rename it and regenerate our extensions. 3. Update naming and organization of pynwb extensions Previously the AllenSDK behavior + ophys pyNWB extension was called "AIBS_ophys_behavior". In order to follow new recommended pyNWB extension naming conventions, the extension has been renamed to "ndx-aibs-behavior-ophys". 4. Fix failing tests
…unning-speed GH #1671: Filtered+corrected running speed
…king-mismatch GH-1682/feature/eye tracking mismatch
…nwb-extension Gh 1702 create behavior nwb extension
Resamples the single ophys (2p) frame time stream to properly distribute across mesoscope plane groups. The mesoscope jumps between plane groups as it, acquires data, necessitating the resampling of the combined time stream. Data that does not acquire multiple planes in parallel is unaffected.
…esampling GH #1654: Mesoscope time resampling
Gh 1654/mesoscope time test
…est-fail Integration test
Also updates LIMS fetch API and abstract base classes.
…-id-in-BehaviorOphysSession GH #1491: Add behavior_session_id to BehaviorOphysSession
Codecov Report
@@ Coverage Diff @@
## master #1703 +/- ##
==========================================
- Coverage 36.83% 36.16% -0.67%
==========================================
Files 346 346
Lines 34714 33814 -900
==========================================
- Hits 12786 12229 -557
+ Misses 21928 21585 -343
Continue to review full report at Codecov.
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This is the release candidate for release 2.3.0, tentatively slated for release on September 19th 2020. All new features should target this branch (urgent bugfixes ought to instead target master).
Please see the confluence guide for more information on the release process.
Before merge
__init__.pyMerge!
After merge