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Change Log

All notable changes to this project will be documented in this file.

[2.16.2] = 2023-11-29

  • See release notes on Github
  • Commit code used to create new VBN data release.
  • Update VBN changelog..

[2.16.1] = 2023-11-13

  • See release notes on Github
  • Update testing
  • Update readthedocs configuration
  • Fix bug in trials change time loading.

[2.16.0] = 2023-11-09

  • Python 3.10 and 3.11 support
  • Support for VBO update release.
  • Uspport for new VBO release
  • Various bug fixes.
  • See release notes on Github

[2.14.0] = 2022-12-12

  • Support for updated vbn release containing probe, lfp and behavior only data.
  • Updates to Ophys data in anticipation of a forthcoming updated data release
  • Various notebook updates
  • Python 3.9 support
  • Various bug fixes and quality of life improvements.

[2.13.6] = 2022-08-04

  • bugfix when accessing stimulus presentations table for vcn data
  • updates vbn notebooks

[2.13.5] = 2022-07-27

  • Add support for visual behavior neuropixels data

[2.13.4] = 2022-02-23

  • Bug fix in ecephys
  • Added support for VBN source density jobs.
  • Bug fix for pg8000

[2.13.3] = 2022-02-02

  • Add ability to extract running speed from mulit-stimulus experiments
  • Compatible with pandas 1.4

[2.13.2] = 2022-01-03

  • Fixes bug that caused file paths on windows machines to be incorrect in Visual behavior user-facing classes
  • Updates to support MESO.2
  • Loosens/updates required versions for several dependencies
  • Updates in order to generate valid NWB files for Neuropixels Visual Coding data collected between 2019 and 2021

[2.13.1] = 2021-10-04

  • Fixes bug that was preventing the BehaviorSession from properly instantiating passive sessions.

[2.13.0] = 2021-09-22

  • Major internal refactor to BehaviorSession, BehaviorOphysExperiment classes. Implements DataObject pattern for fetching and serialization of data.

[2.12.4] = 2021-09-21

  • Documentation changes ahead of SWDB 2021
  • Bugfix to CloudCache; it is now possible for multiple users to share a cache.

[2.12.3] = 2021-08-20

  • Reordered columns in Visual Behavior metadata tables to be more helpful

[2.12.2] = 2021-08-13

  • fix to how from_lims API gets OPhys experiment metadata. Preserves relationship between OPhys experiments and failed containers

[2.12.1] = 2021-08-11

  • minor fix to cloud cache

[2.12.0] = 2021-08-11

  • Added ability to specify a static cache directory (use_static_cache=True) to instantiate VisualBehaviorOphysProjectCache.from_local_cache()
  • Added 'experience_level', 'passive' and 'image_set' columns to ophys_experiments_table
  • Added 'ophys_cells_table' metadata table to track the relationship between ophys_experiment_id and cell_specimen_id

[2.11.3] = 2021-08-04

  • Bugfixes related to NWB creation for BehaviorSessions

[2.11.2] = 2021-05-21

  • Fixed mkdir error for non-existing ecephys upload directory

[2.11.1] = 2021-05-20

  • Refactored the schema for the ecephys copy utility to avoid raising an error when a previous output file already exists.

[2.11.0] = 2021-05-13

  • python 3.8 compatibility
  • CloudCache (the class supporting cloud-based data releases) is now smart enough to construct symlinks between files that are identical across dataset versions (rather than downloading duplicate copies of files).
  • VisualBehavioOphysProjectCache supports user-controlled switching between dataset versions.

[2.10.3] = 2021-04-23

  • Adds restriction to require hdmf version to be strictly less than 2.5.0 which accidentally introduced a major version breaking change

[2.10.2] = 2021-03-25

  • This version marks the release of Visual Behavior Optical Physiology data! For more details please visit the: Visual Behavior - Optical Physiology Project Page
  • update documentation to support visual behavior data release
  • Fixes a bug with the dictionary returned by BehaviorSession get get_performance_metrics() method
  • Adds docstrings to the BehaviorSession get_performance_metrics(), get_rolling_performance_df(), and get_reward_rate() methods

[2.10.1] = 2021-03-23

  • changes name of BehaviorProjectCache to VisualBehaviorOphysProjectCache
  • changes VisualBehaviorOphysProjectCache method get_session_table() to get_ophys_session_table()
  • changes VisualBehaviorOphysProjectCache method get_experiment_table() to get_ophys_experiment_table()
  • VisualBehaviorOphysProjectCache is enabled to instantiate from_s3_cache() and from_local_cache()
  • Improvements to BehaviorProjectCache
  • Adds project metadata writer

[2.9.0] = 2021-03-08

  • Improvements to BehaviorProjectCache

[2.9.0] = 20201-03-08

  • Updates to Session metadata; refactors implementation to use class rather than dict internally
  • Fixes a bug that was preventing Allen Institute Windows users from accessing gratings images

[2.8.0] = 2021-02-25

  • Created lookup table to get monitor_delay for cases where calculation from data fails
  • If sync timestamp file has more timestamps than eye tracking moving has frame, trim excess timestamps (up to 15)
  • Session API returns both warped and unwarped stimulus images, and both are written to NWB

[2.7.0] = 2021-02-19

  • Refactored behavior and ophys session and data APIs to remove a circular inheritance issue
  • Fixed segmentation mask and roi_mask misregistration in 'BehaviorOphysSession'
  • Replaces BehaviorOphysSession.get_roi_masks() method with roi_masks property
  • Fixes bug which prevented the SDK from loading stimuli dataframes for static gratings
  • Return event detection data through session API
  • Read/write event detection data from/to NWB
  • Time stamps for events in trial_log are set to the exact sync timestamp of the corresponding frame.
  • For behavior-only sessions, sync-like timestamp of the first frame is set to zero.
  • stimulus_templates in Session API returns new object with key of image name
  • Refactored BehaviorOphysSession to inherit methods and properties from BehaviorSession
  • Fixed a test for checking that Behavior and BehaviorOphysSessions contain the same data regardless of which API (LIMS/JSON/NWB) is used. Also fixed resulting failure cases.

[2.6.0] = 2021-02-05

  • Adds ability to write and read behavior only NWB files
  • Adds eye tracking ellipse fits and metadata as new NWB data stream
  • OPhys Behavior data retrieval methods no longer depend on ROIs being ordered identically in different files.

[2.5.0] = 2021-01-29

  • Adds unfiltered running speed as new data stream
  • run_demixing gracefully ignores any ROIs that are not in the input trace file

[2.4.1] = 2021-01-04

  • update deprecated call to scipy.spatial.transform.Rotation.as_dcm() to .as_matrix()

[2.4.0] = 2020-12-21

  • When running raster_plot on a spike_times dataframe, the spike times from each unit are plotted twice. (thank you @dgmurx)
  • improvements and fixes to behavior ophys NWB files.
  • improvements and fixes to BehaviorProjectCache tables including new column "donor_id"
  • implemented a timeout to obtaining an ecephys session. (thank you @wesley-jones)
  • big overhaul of how Behavior and BehaviorOphys classes are structured for the visual behavior project. See AllenInstitute#1789

[2.3.3] = 2020-11-12

Bug Fixes

  • (Internal) Fixed a bug in mesoscope processing where the ophys acquisition frames were being truncated prior to splitting, resulting in many fewer than expected acquisition frames.

[2.3.2] = 2020-10-19

Bug Fixes

  • (Internal) Fixed a running_processing bug for behavior ophys experiments when the input data would have one more encoder entry than timestamp. The behavior of the code now matches what the warning says.

[2.3.1] = 2020-10-13

Bug Fixes

  • (Internal) Fixed a write_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.

[2.3.0] = 2020-10-09

Added

  • Adds load sync data for individual plane sets to relate accurate event timings to mesoscope data.
  • Adds public API method to access the behavior_session_id from an instance of BehaviorOphysSession.

Changes

  • Visual behavior running speed is now low-pass filtered at 10Hz. The raw running speed data is still available. The running speed is corrected for encoder threshold croissing artifacts.
  • Support for stimulus gratings for visual behavior.
  • Updates to some visual behavior pynwb implementations.

Bug Fixes

  • Fixed an eye-tracking sync problem.

[2.2.0] = 2020-09-03

Added

  • AllenSDK HTTP engine streaming requests now include a progress bar.

Changed

  • (Internal) Behavior Ophys Sessions no longer have a dependence on the segmentation_mask_image file (provided by LIMS) when trying to write NWB files.

Bug Fixes

  • (Internal) response_time of a trial in behavior-only or behavior + ophys sessions is now the first lick of the trial (for non-"aborted" trials). If no lick occurred or if the trial is "aborted", response_time is NaN.
  • Resolve ImportError: cannot import name 'MultiContainerInterface' from 'hdmf.container' errors by removing explicit version bounds on the hdmf package.
  • The optical physiology 2-photon trace demixer has been modified to be more memory friendly and should no longer result in out of memory errors when trying to demix very large movie stacks.
  • (Internal) Docker image definitions have been updated so that internal continuous integration tests can work properly

[2.1.0] = 2020-07-16

Added

  • Behavior Ophys NWB File writing capability fixes for updated PyNWB and HDMF versions
  • Added warning if using outdated Visual Coding Neuropixels NWB files
  • Added documentation file for Visual Behavior terms in AllenSDK for quick lookup

[2.0.0] = 2020-06-11

Added

  • CCF locations for ecephys neuropixels electrodes have been added to their respective nwb electrodes tables
  • Examples for accessing eye tracking ellipse fit and screen gaze location data have been added to ecephys example notebooks

Changed

  • pynwb and hdmf version pinning has been relaxed
  • The organization of data for ecephys neuropixels Neurodata Without Borders (NWB) files has been significantly changed to conform with NWB specifications and best practices

Important Note: Due to newer versions of pynwb/hdmf having issues reading previously released Visual Coding Neuropixels NWB files and due to the significant reorganization of their NWB file contents, this release contains breaking changes that necessitate a major version revision. NWB files released prior to 6/11/2020 are not guaranteed to work with the 2.0.0 version of AllenSDK. If you cannot or choose not to re-download the updated NWB files, you can continue using a prior version of AllenSDK (< 2.0.0) to access them. However, no further features or bugfixes for AllenSDK (< 2.0.0) are planned. Data released for other projects (Cell Types, Mouse Connectivity, etc.) are NOT affected and will NOT need to be re-downloaded

[1.8.0] = 2020-06-06

Added

  • The biophysical module can now run both current and legacy all-active models.
  • Internal users can now access date_of_acquisition for behavior-only Session data.
  • A pull request template was added to the repository.

Changed

  • The CSV log was removed from BehaviorProjectCache (internal users).
  • Duplicated demixer module was deprecated, and test coverage was added.
  • Docker image for AllenSDK was updated.

Bug Fixes

  • Internal LIMS data served to BehaviorDataSession class now all use the same timestamp source

[1.7.1] = 2020-05-5

Bug Fixes

  • Time sync tests were failing because of removed content. Tests were running only on nightly.
  • Notebook tests failing on nightly because of down server, switched tests to production server.

[1.7.0] = 2020-04-29

Added

  • Internal users can now access eye_tracking ellipse fit data from behavior + ophys Session objects
  • A new mixin for managing processing parameters for Session objects
  • Added support for additional sync file line labels

Changed

  • Monitor delay calculation is updated to properly handle photodiode streams that end on a rising edge. We are no longer providing a default delay value in case of error.

Bug Fixes

  • experiment_table from behavior project cache has NaNs in the 'imaging_depth' column for MultiScope experiments due to incorrect join in behavior_project_lims_api.py and 4 other places where ophys_sessions was incorrectly queried for imaging_depth_id
  • get_keys method for sync datasets was returning the wrong line labels and creating incorrect key, value pairs for data loading from sync files

[1.6.0] = 2020-03-23

Added

  • tutorial for optotagging for ecephys notebook
  • get_receptive_field() method in ecephys receptive field mapping

Changed

  • remove redundant sham_change column in behavior sessions.trials table
  • versions for NWB output for ecephys and ophys behavior.
  • monitor delay is now calculated for BehaviorOphysLimsApi rather than defaulting to 0.0351

Bug Fixes

  • Fixed a bug where auto-rewarded trials were not properly attributed in the rewards property of a visual behavior
  • return None rather than raise exception if no container id was returned from lims id for given ophys id
  • Project caches no longer accept arbitrary keywords
  • matplotloib.pyplot.hist parameter normed no longer supported

[1.5.0] = 2020-02-10

Added

  • Users have an option to provide credentials for accessing the database either explicitly via public API or by setting up the environment variables

Changed

  • Allow users to modify BehaviorDataSession and BehaviorOphysSession data

Bug Fixes

  • morphology.apply_affine correctly rescales radii
  • invalid extracellular electrophysiology spikes no longer show up as spikes at time -1
  • (internal) When loading a behavior session, behavior and eye tracking video frame times are assessed from the correct lines

[1.3.0] = 2019-12-12

Added

  • Improved Neuropixels data download performance by enabling asynchronous transfers. Data downloads will now raise timeout errors when data cannot be retrieved in a reasonable timeframe.

Changed

  • Updated AllenSDK readme and contributing documentation

Bug Fixes

[1.0.0] = 2019-10-3

Added

  • Support for Brain Observatory - Visual Coding Neuropixels data.
  • AllenInstitute#447 Implemented improved eye tracking module based on DeepLabCut

Changed

  • Python 2.x is no longer supported.
  • statsmodels is now pinned at 0.9.0

Bug Fixes

[0.16.3] = 2019-5-22

Bug Fixes

[0.16.2] = 2019-4-23

Added

Changed

Bug Fixes

[0.16.1] = 2019-3-12

Added

Changed

  • Update pytest version number (now requires pytest>=4.1.1)
  • Update numpy version number (now requires numpy>=1.15.1)
  • Removed deprecated functions from BrainObservatoryNwbDataSet
  • Updated documentation

Bug Fixes

[0.16.0] = 2018-10-04

Added

  • BrainObservatoryCache.get_ophys_experiment_events
  • BrainObservatoryCache.get_ophys_experiments and get_experiment_containers accept reporter_lines argument
  • BrainObservatoryCache.ge_ophys_experiment_analysis
  • Cache subclasses can have their manifest locations set via environment variable

[0.14.5] = 2018-06-14

Changed

  • bumped lower limit of pandas to 0.17, removed upper limit
  • changed CellTypesCache cell data structure to be less nested, more flat. Requires update to manifest and re-download of cells.json.
  • simplified MouseConnectivityCache data structure. Requires update to manifest and re-download of experiments.json.
  • stopped using deprecated function in SimpleTree

Added

  • regression tests for Brain Observatory analysis

[0.14.4] - 2018-01-30

Changed

  • Numerous Python 2/3 compatibility fixes
  • Improved spike filtering in ephys.ephys_features

[0.14.3] - 2017-10-19

Added

  • CellTypesCache.get_cells has a new species argument.

Changed

  • MouseConnectivityCache downloads structure masks instead of computing them.

[0.14.2] - 2017-08-17

Added

  • ABS-64; Jupyterhub Dockerfiles
  • PR #13; Manifest error check

Changed

ABS-132; changed to Allen Institute Software License ABS-129; StructureTree converts color hex triplet to 8-bit color triplet ABS-125; update expected data for unmocked tests PBS-358; update extract_trace module to deal with motion border case ABS-85; allow variable long square start time in ephys feature extractor

[0.13.2] - 2017-06-15

Added

  • BrainObservatoryNwbDataSet.get_demixed_traces
  • BrainObservatoryNwbDataSet.get_pupil_location
  • BrainObservatoryNwbDataSet.get_pupil_size
  • BrainObservatoryApi.get_cell_specimen_id_mapping
  • allensdk.brain_observatory.receptive_field_analysis
  • allensdk.brain_observatory.demixer

Changed

  • BrainObservatoryCache.get_ophys_experiments returns "acquisition_age_days" instead of "age_days". The new field describes the age of the animal on the day of experiment acquisition.
  • BrainObservatoryCache.get_experiment_containers no longer returns "age_days".
  • BrainObservatoryCache.get_ophys_experiments accepts a list of cell_specimen_ids for additional filtering
  • json_utilities uses simplejson for better NaN handling

[0.13.1] - 2017-03-20

Fixed

  • issue #42: Caching behavior in MouseConnectivityCache for CCF volumes fixed
  • GLIF examples, documentation fixed

[0.13.0] - 2017-03-16

Added

  • ReferenceSpace is a new class for relating structure graphs and annotation volumes.
  • Standardized caching and paging decorators

Changed

  • Ontology has been deprecated in favor of StructureTree.
  • MouseConnectivityCache uses StructureTree internally (ontology-based methods are deprecated)
  • CellTypesCache and MouseConnectivityCache use cacher decorator
  • GlifApi has stateless methods now. Old methods are deprecated.

Fixed

  • Github issue #35 - MouseConnectivityCache's manifest now uses CCF-version- and resolution-specific file names for masks. The masks now live inside the CCF version directory. Users must download a new manifest.

[0.12.4] - 2016-10-28

Fixed

  • Github issues #23, #28 - added a new dependency "requests_toolbelt" and upgraded API database for more reliable large file downloads.
  • Github issue #26 - better documentation for structure unionize records.
  • Github issue #25 - documentation errors in brain observatory analysis.

Changed

  • New CCF annotation volume with complete cortical areas and layers.
  • Mouse Connectivity structure unionize records have been computed for new CCF. Previous records are available here: https://download.alleninstitute.org/informatics-archive/june-2016/mouse_projection/
  • Github issue #27 - MouseConnectivityCache.get_structure_unionizes returns only requested structures, not all descendants. Added a separate argument for descendant inclusion.

Added

  • MouseConnectivityCache has a new constructor argument for specifying CCF version.

[0.12.2] - 2016-9-1

Fixed

  • Github issue #16 (jinja2 requirement)
  • Github pull request #21 (spurious "i" typo) in r_neuropil.py

[0.12.1] - 2016-8-17

Changed

  • neuropil subtraction algorithm (brain_observatory.r_neuropil) faster and more robust
  • formatting changes for better PEP8 compliance
  • preparation for Python 3 support
  • updated Dockerfiles

Fixed

  • Github issue #17 (scipy requirement)

[0.12.0] - 2016-6-9

Added

  • Support for the Allen Brain Observatory data (BrainObservatoryCache and BrainObservatoryApi classes).
  • Code for neurpil subtraction, dF/F estimation, and tuning analysis.
  • New ephys feature extractor (ephys_features.py, ephys_extractor.py). The old one is still there (feature_extractor.py) but should be considered deprecated.

[0.11.0] - 2016-3-3

Added

  • CellTypesCache.get_cells has a new argument 'reporter_status', which accepts one or more ReporterStatus values.
  • CellTypesApi.save_reconstruction_marker and CellTypesCache.get_reconstruction_marker download and open files containing positions that mark special points in reconstruction (truncation, early termination of reconstruction, etc).
  • swc.read_marker_file for reading in marker files
  • Morphology has new methods for manipulating the morphology tree structure
  • allensdk.model.biophysical package supports active and passive models

Changed

  • Morphology compartments are now Compartment objects that behave like dictionaries
  • Compartment.children stores references to immediate descendant Compartments
  • spike times in NWB files are stored in "analysis/spike_times" instead of "analysis/aibs_spike_times"
  • NwbDataSet looks for spike times in both locations ("spike_times" first)
  • glif_neuron_methods.py function names have been changed to be more standardized
  • allensdk.model.biophysical_perisomatic package renamed to allensdk.model.biophysical
  • NEURON dependency updated to 7.4 release 1370

Fixed

  • MouseConnectivityCache.get_structure_mask bug fixed (github issue 8)
  • CellTypesApi.get_ephys_sweeps returns sweeps in sweep number order (github issue 11)
  • NwbDataSet.set_spike_times added maxshape(None,) to create_dataset (github issue 7)

[0.10.1] - 2015-9-24

Added

  • MouseConnectivityCache.get_projection_matrix, method for building a signal matrix from injection structure to projection structure.
  • CellTypesCache.get_morphology_features, method for retrieving morphology features for all cells
  • CellTypesCache.get_all_features, method for retrieving both morphology and ephys features for all cells in a single table
  • new RmaTemplate class enables construction of queries with jinja2 template library.
  • Jupyter notebook examples added to documentation.

Fixed

  • Api.retrieve_parsed_json_over_http respects post parameter.
  • improved installation of dependencies.

Changed

  • Ontology.get_child_ids and Ontology.get_descendant_ids accept a list of ids instead of a variable length argument list.
  • API Access/Data API Client documentation better reflects new 0.10.x allensdk.api.query modules.
  • Cache.wrap method defaults to save_as_json=False.
  • Cache.wrap method defaults to returning json rather than a pandas dataframe (new parameter return_dataframe=False).
  • BiophysicalApi.cache_data throws an exception if no data is found for a neuronal model id.
  • Replaced brainscales Dockerfile with neuralenseble Dockerfiles.

[0.10.1] - 2015-x-x

Added

  • MouseConnectivityCache.get_projection_matrix, method for building a signal matrix from injection structure to projection structure.
  • CellTypesCache.get_morphology_features, method for retrieving morphology features for all cells
  • CellTypesCache.get_all_features, method for retrieving both morphology and ephys features for all cells in a single table

Changed

  • Ontology.get_child_ids and Ontology.get_descendant_ids accept a list of ids instead of a variable length argument list.

[0.10.0] - 2015-8-20

Added

  • Manifest and Cache classes for keeping track of files
  • MouseConnectivityApi class for downloading data from the Mouse Connectivity Atlas
  • MouseConnectivityCache fclass or keeping track of files
  • CellTypesCache for keeping track of cell types files
  • Ontology class for manipulating structures
  • Rma class for formalizing API queries
  • GridDataApi for downloading expression and projection grid volumes
  • EphysFeatureExtractor module for computing ephys features used in Cell Types Database

Fixed

  • json_utilities has better numpy data type serialization support

[0.9.1] - 2015-5-13

Changed

  • Documentation updated

Fixed

  • Installation/Makefile bug

[0.9.0] - 2015-5-12

Added

  • Everything: initial release!