Allensdk

- 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

- 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.

- 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.

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

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

- 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 https://github.com/AllenInstitute/AllenSDK/pull/1789