rc/2.4.0 #1744
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rc/2.4.0 #1744
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raster_plot now correctly plots each unit once. A unit test checks that the number of plotted lines equals the number of units passed to the raster_plot function.
Codecov Report
@@ Coverage Diff @@
## master #1744 +/- ##
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+ Coverage 36.23% 36.44% +0.21%
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Files 346 350 +4
Lines 33824 33881 +57
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+ Hits 12255 12348 +93
+ Misses 21569 21533 -36
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GH #1756 - Update argschema
This commit removes fields that already exist as part of the pyNWB "Subject" class from the custom behavior ophys subject extension.
Previously dff and fluorescence traces were being stored as ROIs x timepoints Numpy arrays. This commit implements pyNWB best practice by storing the data with the time dimension first.
This is a combination of the following 3 commits: 1) Simplify custom behavior ophys pyNWB extension Previously, the OphysBehaviorMetadata extension included a number of fields that already exist in base pyNWB classes. This commit moves "emission_lambda", "excitation_lambda", "indicator", "location", "session_start_time", and "imaging_rate" fields so that they are stored in pyNWB classes like ImagingPlane and OpticalChannel. This greatly simplifies the OphysBehaviorMetadata extension definition. 2) Add more detailed "doc" description to pyNWB extension fields 3) Address pyNWB NWBFile.modules deprecation warning Trying to access pyNWB processing modules via the "NWBFile.modules" attribute is now deprecated in favor of "NWBFile.processing". This commit implements the favored method for accessing pyNWB processing modules from an NWBFile object.
Previously, ROIs were added to the behavior ophys NWB file incorrectly. ROIs all ended up starting at the 0,0 corner of the whole imaging space. This was caused by feeding the "LIMS formatted ROI" (List[List[bool]]) through the allensdk.brain_observatory.roi_masks.create_roi_mask function twice instead of only once. This happened once in allensdk.internal.api.ophys_lims_api.OphysLimsApi get_cell_specimen_table() method and yet again in the allensdk.brain_observatory.nwb.__init__ add_cell_specimen_table() function. Now, only the OphysLimsApi get_cell_specimen_table() is the only place where LIMS formatted ROIs are deserialized to the allensdk.brain_observatory.roi_masks.RoiMask class. A CellSpecimenTable schema discrepancy was also fixed. 'x' and 'y' fields should be Int not Float based on what the behavior_ophys_write_nwb_strategy from LIMS is passing in.
To better align with best practice guidelines: https://www.nwb.org/best-practices/
This commit adds experiment descriptions to be havior ophys NWB files. These descriptions can be determined based on the behavior ophys "session type" string. Example: "OPHYS_1_images_A" is the first stage of the visual behavior experiments "OPHYS_6_images_A" is the last stage of the visual behavior experiments
GH #1739 - Fix ecephys raster_plot plotting units twice
…hys-nwb-issues 1733 address behavior ophys nwb issues
…l-join-ids Pull data for summary of experiments/sessions even if there are nulls in join ids
- Adds the ability to pass kwargs to the RmaEngine including the timeout kwarg - Adds pytests to verify the kwargs are passed into the RmaEngine - Updates the default timeout for the HttpEngine from 10 to 50 minutes
Previously, the behavior_ophys_nwb_api.py file implemented an `equals` function for comparing two Session objects as well as a `compare_fields` function for checking that attributes of Session objects are also equal. Both these functions have been moved to: allensdk.brain_observatory.session_api_utils Additional, the `equals` function has been renamed to `sessions_are_equal` and the `compare_fields` function has been renamed to `compare_session_fields`.
Renames the `data_fetchers` directory to `data_io`. Data API implementations for sessions and/or project in cases like NWB not only 'fetch' data but also 'save' so 'fetcher' would be too narrow a description. This applies to: - allensdk.brain_observatory.behavior.project_apis.data_fetchers - allensdk.brain_observatory.behavior.session_apis.data_fetchers
This commit will rename the BehaviorDataSession class located in allensdk.brain_observatory.behavior.behavior_data_session to just BehaviorSession (and allensdk.brain_observatory.behavior.behavior_session). This is to bring the naming in line with the BehaviorOphysSession class and also to draw a distinction between a 'session' class that end-users will interact with and a 'data io API' class that loads session data from data sources like LIMS/NWB.
This commit moved behavior and behavior + ophys session LIMS API related classes from `allensdk.internal.api` to: `allensdk.brain_observatory.behavior.session_apis.data_io` The files moved include: - behavior_data_lims_api: Newer version API for behavior only data from LIMS - behavior_lims_api: Older version API for behavior only data from LIMS - behavior_ophys_api: API for behavior + ophys data from LIMS - ophy_lims_api: API for ophys data from LIMS
It turns out that "BehaviorDataLimsApi" located in allensdk.brain_observatory.behavior.session_apis.data_io.behavior_data_lims_api (previously allensdk.internal.api.behavior_data_lims_api) and the "BehaviorLimsApi" located in allensdk.brain_observatory.bheavior.session_apis.data_io.behavior_lims_api (previously allensdk.internal.api.behavior_lims_api) are historically separate implementations of what *should* be the same class. This commit does the following: - Add the ability to construct a BehaviorDataLimsApi from a foraging_id. This was basically the only unique functionality provided by the BehaviorLimsApi class. - Remove the BehaviorLimsApi class completely. - Spruce up how database connections are created - Rename the BehaviorDataLimsApi to BehaviorLimsApi - Rename behavior_data_lims_api.py to behavior_lims_api.py
This commits fixes imports of the BehaviorOphysLimsApi which previously lived at: allensdk.internal.api.behavior_ophys_api.py Its new location is: allensdk.brain_observatory.behavior.session_apis.data_io.behavior_ophys_lims_api.py
This commit fixes imports for the OphysLimsApi that previously lived at: allensdk.internal.api.ophys_lims_api.py It now lives at: allensdk.brain_observatory.behavior.session_apis.data_io.ophys_lims_api.py
The commit moves the BehaviorOphysJsonApi defined in allensdk.brain_observatory.behavior.write_nwb.__main__ to allensdk.brain_observatory.behavior.session_apis.data_io.behavior_ophys_json_api. This commit also fixes a bug with multiple inheritence and method resolution order. ABC classes should always be inherited last so that the first parent of a class will be able to fill the subclass with defined methods (and not abstract methods).
This commit factors out 'data only' (LIMS/BehaviorOphysJson/NWB) API methods from methods that are required by the OphysSession class. This commit creates a new set of classes (BehaviorDataXforms, BehaviorOphysDataXforms) that transforms data obtained from 'data only' methods into sources for the OphysSession class.
This commits fixes an inheritance order issue that was causing tests to fail. Specifically: - The BehaviorLimsApi inherits from BehaviorDataXforms so BehaviorOphysDataXforms should always be inherited before BehaviorLimsApi - The OphysLimsApi methods should be used before BehaviorLimsApi methods - The BehaviorOphysLimsApi class should not be calling super() in its __init__. Rather it should set and provide self.ophys_experiment_id, self.behavior_session_id, self.lims_db, and self.mtrain_db
This commit aims to improve the clarity of documentation for the db_connection_creator helper function. This includes changing the 'default_credentials' param to 'fallback_credentials'.
This commit standardizes the formatting of LIMS queries for the various behavior APIs. This commit also adds better documentation API methods (including return type and better descriptions of data retrieved by queries).
This is a combination of the following two commits: 1) Add more documentation This commit adds more documentation to brain_observatory.behavior data api methods. 2) Fix a couple of LIMS query typos A set of typos where a semicolon was introduced within a single quote block resulted in a non-functional query. This commit fixes these typos.
…ys-inheritence 1769 modify behavior ophys inheritence
Fix typing.Protocol import in Python 3.8
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This is the PR branch for the 2.4.0 release candidate of AllenSDK. The release date is tentatively ~2020-10-29.