Cue light tools

Methods for analyzing animal behaviours associated with cue-light states through.

Analyze

class simba.cue_light_tools.cue_light_analyzer.CueLightAnalyzer(config_path: Union[str, PathLike], in_dir: Union[str, PathLike], cue_light_names: List[str])[source]

Bases: ConfigReader

Analyze when cue lights are in ON and OFF states. Results are stored in the project_folder/csv/cue_lights cue lights directory.

Parameters

config_path (str) – path to SimBA project config file in Configparser format
in_dir (str) – directory holding pose-estimation data. E.g., project_folder/csv/outlier_corrected_movement_location
cue_light_names (List[str]) – Names of cue light ROIs, as defined in the SimBA ROI interface.

Note

Cue light tutorials.

Examples

>>> cue_light_analyzer = CueLightAnalyzer(config_path='MyProjectConfig', in_dir='project_folder/csv/outlier_corrected_movement_location', cue_light_names=['Cue_light'])
>>> cue_light_analyzer.run()

CLF Statistics

class simba.cue_light_tools.cue_light_clf_statistics.CueLightClfAnalyzer(config_path: Union[str, PathLike], pre_window: int, post_window: int, cue_light_names: List[str], clf_list: List[str])[source]

Bases: ConfigReader

Compute aggregate statistics when classified behaviors are occurring in relation to the cue light ON and OFF states.

Parameters

config_path (str) – path to SimBA project config file in Configparser format
pre_window (int) – Time period (in millisecond) before the onset of each cue light to compute aggregate classification statistics within.
post_window (int) – Time period (in millisecond) after the offset of each cue light to compute aggregate classification statistics within.
cue_light_names (List[str]) – Names of cue lights, as defined in the SimBA ROI interface.
list (List[str]) – Names of the classifiers we want to compute aggregate statistics for.

Note

Cue light tutorials.

Examples

>>> cue_light_clf_analyzer = CueLightClfAnalyzer(config_path='MyProjectConfig', pre_window=1000, post_window=1000, cue_light_names=['Cue_light'], clf_list=['Attack'])
>>> cue_light_clf_analyzer.analyze_clf()
>>> cue_light_clf_analyzer.organize_results()
>>> cue_light_clf_analyzer.save_data()

analyze_clf()[source]

Method to calculate classifier data during cue lights periods

Returns: Attribute – results
Return type: dict

organize_results()[source]

Method to organize classifier data into a summary dataframe.

Returns: Attribute – results_df
Return type: pd.DataFrame

save_data()[source]

Method to save cue light classification data to disk. Results are stored in the project_folder/logs directory of the SimBA project.

Return type: None

GUI

class simba.cue_light_tools.cue_light_menues.CueLightAnalyzerMenu(config_path: Union[str, PathLike])[source]

Bases: ConfigReader, PopUpMixin

Launch cue light analysis GUI in SimBA.

Parameters: config_path (str) – path to SimBA project config file in Configparser format

Note

Cue light tutorials.

Examples

>>> cue_light_gui = CueLightAnalyzerMenu(config_path='MySimBAConfigPath')
>>> cue_light_gui.main_frm.mainloop()

Movement statistics

class simba.cue_light_tools.cue_light_movement_statistics.CueLightMovementAnalyzer(config_path: Union[str, PathLike], pre_window: int, post_window: int, cue_light_names: List[str], threshold: float, roi_setting: bool)[source]

Bases: ConfigReader

Compute aggregate statistics of animal movement in relation to the cue light ON and OFF states.

Parameters

config_path (str) – path to SimBA project config file in Configparser format
pre_window (int) – Time period (in millisecond) before the onset of each cue light to compute aggregate classification statistics within.
post_window (int) – Time period (in millisecond) after the offset of each cue light to compute aggregate classification statistics within.
cue_light_names (List[str]) – Names of cue lights, as defined in the SimBA ROI interface.
threshold (float) – The body-part post-estimation probability threshold. SimBA omits movement calculations for frames where the body-part probability threshold is lower than the user-specified threshold.
roi_setting (bool) – If True, SimBA calculates movement statistics within non-light cue ROIs.

Examples

>>> cue_light_movement_analyzer = CueLightMovementAnalyzer(config_path='MyProjectConfig', cue_light_names=['Cue_light'], pre_window=1000, post_window=1000, threshold=0.0, roi_setting=True)
>>> cue_light_movement_analyzer.calculate_whole_session_movement()
>>> cue_light_movement_analyzer.organize_results()
>>> cue_light_movement_analyzer.save_results()

calculate_whole_session_movement()[source]

Method to calculate movement in relation to cue-light(s) onsets.

Returns: Attribute – roi_results
Return type: dict

organize_results()[source]

Method to organize movement results into dataframe

Returns: Attribute – results_roi_df
Return type: pd.DataFrame

save_results()[source]

Method to save movement cue light results into the SimBA project folder. Results are stored in the project_folder/logs directory of the SimBA project.

Return type: None

Tools

simba.cue_light_tools.cue_light_tools.find_frames_when_cue_light_on(data_df: DataFrame, cue_light_names: List[str], fps: int, prior_window_frames_cnt: int, post_window_frames_cnt: int)[source]: Private multiprocess helper for finding cue-light states. Called by meth:simba.cue_light_tools.cue_light_analyzer.CueLightAnalyzer.

Visualize

class simba.cue_light_tools.cue_light_visualizer.CueLightVisualizer(config_path: Union[str, PathLike], cue_light_names: List[str], video_path: str, frame_setting: bool, video_setting: bool)[source]

Bases: ConfigReader

Visualize SimBA computed cue-light ON and OFF states and the aggregate statistics of ON and OFF states.

Parameters

config_path (str) – path to SimBA project config file in Configparser format.
cue_light_names (List[str]) – Names of cue lights, as defined in the SimBA ROI interface.
video_path (str) – Path to video which user wants to create visualizations of cue light states and aggregate statistics for.
frame_setting (bool) – If True, creates individual frames in png format.
video_setting (bool) – If True, creates compressed videos in mp4 format.

Examples

>>> cue_light_visualizer = CueLightVisualizer(config_path='SimBAConfig', cue_light_names=['Cue_light'], video_path='VideoPath', video_setting=True, frame_setting=False)
>>> cue_light_visualizer.run()

run()[source]: Method to create cue light visualizations. Results are stored in the project_folder/frames/output/cue_lights directory of the SimBA project.