allensdk.brain_observatory.behavior.data_objects.running_speed.multi_stim_running_processing module

allensdk.brain_observatory.behavior.data_objects.running_speed.multi_stim_running_processing.multi_stim_running_df_from_raw_data(sync_path: str, behavior_stimulus_file: BehaviorStimulusFile, mapping_stimulus_file: MappingStimulusFile, replay_stimulus_file: ReplayStimulusFile, use_lowpass_filter: bool, zscore_threshold: float, behavior_start_frame: int) → Tuple[DataFrame, DataFrame]

Derive running speed data frames from sync file and pickle files

Parameters:

sync_path: str

The path to the sync file

behavior_stimulus_file: BehaviorStimulusFile

stimulus file for the behavior stimulus block

mapping_stimulus_file: MappingStimulusFile

stimulus file for the mapping stimulus block

replay_stimulus_file: ReplayStimulusFile

stimulus file for the replay stimulus block

use_lowpass_filter: bool

whther or not to apply a low pass filter to the running speed results

zscore_threshold: float

The threshold to use for removing outlier running speeds which might be noise and not true signal

behavior_start_frame: int

the frame on which behavior data starts

Returns:

Tuple[pd.DataFrame, pd.DataFrame]

concatenated velocity data, raw data

Notes

velocities pd.DataFrame:

columns:

“velocity”: computed running speed “net_rotation”: dx in radians “frame_indexes”: frame indexes into

the full vsync times list

raw data pd.DataFrame:

Dataframe with an index of timestamps and the following columns:

“vsig”: voltage signal from the encoder “vin”: the theoretical maximum voltage that the encoder

will reach prior to “wrapping”. This should theoretically be 5V (after crossing 5V goes to 0V, or vice versa). In practice the encoder does not always reach this value before wrapping, which can cause transient spikes in speed at the voltage “wraps”.

“frame_time”: list of the vsync times “dx”: angular change, computed during data collection

The raw data are provided so that the user may compute their own speed from source, if desired.