bouter.embedded package

Module contents

class bouter.embedded.EmbeddedExperiment(path, session_id=None, cache_active=False)

Bases: bouter.experiment.Experiment

compute_vigor(vigor_duration_s=0.05, use_polynomial_tailsum=False)

Compute vigor, the proxy of embedded fish forward velocity, a standard deviation calculated on a rolling window of tail curvature. Add it as a column to the dataframe log and return the full dataframe

Parameters

vigor_duration – standard deviation window length in seconds

Returns

get_bout_properties(directionality_duration=0.07, use_polynomial_tailsum=False)

Create dataframe with summary of bouts properties. :param directionality_duration: Window defining initial part of

the bout for the turning angle calculation, in seconds.

Parameters

use_polynomial_tailsum – If the polynomial tail sum is to be used instead of the raw one created by Stytra

Returns

a dataframe giving properties for each bout

get_bouts(vigor_threshold=0.1)

Extract bouts above threshold. :param vigor_threshold: :return:

property n_tail_segments

polynomial_tail_coefficients(n_max_missing=7, degree=3)

Fits a polynomial to the bout shape

Parameters

• n_max_missing –

• degree – the polynomial degree

Returns

polynomial_tailsum()

reconstruct_missing_segments(continue_curvature=None)

property tail_columns

Return names of columns with tracking data from all tracked segments. Careful, the array is not copied!