bouter.free package

Module contents

class bouter.free.FreelySwimmingExperiment(path, session_id=None, cache_active=False)

Bases: bouter.experiment.Experiment

property camera_px_in_mm

Return camera pixel size in millimeters

Parameters

exp –

Returns

compute_velocity(max_interpolate=2, recalculate_vel=False, scale=None, median_vel=False, window_size=7)

Compute the squared total swimming velocity for each fish. Add them as new columns to the dataframe log and return the complete dataframe.

Parameters

• max_interpolate – number of points to interpolate if surrounded by NaNs in tracking

• recalculate_vel –

• scale – mm per pixel, recalculated by default

Returns

get_bout_properties(continuity=None)

Makes a summary of all extracted bouts with basic kinematic parameters and timing.

Parameters

continuity –

Returns

a dataframe containing all bouts

get_bouts(scale=None, threshold=1, **kwargs)

Extracts all bouts from a freely-swimming tracking experiment

Parameters

• exp – the experiment object

• scale – mm per pixel, recalculated by default

• threshold – velocity threshold in mm/s

Returns

tuple: (list of single bout dataframes, list of boolean arrays marking if the bout i follows bout i-1)

property n_fish

property n_tail_segments

reconstruct_missing_segments(continue_curvature=None)

property tail_columns

Return a nested list of names of columns with tracking data from all tracked segments. One list for each fish tracked during the experiment.