twoD/preprocess

Functions specifically related to preprocessing of 2D recordings

get_preprocessing_relevant_marker_ids

 get_preprocessing_relevant_marker_ids (df:pandas.core.frame.DataFrame,
                                        marker_ids_to_exclude:Optional[Lis
                                        t[str]]=None)

	Type	Default	Details
df	DataFrame		DataFrame with x, y, and likelihood for tracked marker_ids
marker_ids_to_exclude	typing.Optional[typing.List[str]]	None	list of marker_ids to exclude; optional default None
Returns	typing.List[str]

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get_all_unique_marker_ids

 get_all_unique_marker_ids (df:pandas.core.frame.DataFrame)

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smooth_tracked_coords_and_likelihood

 smooth_tracked_coords_and_likelihood (df:pandas.core.frame.DataFrame,
                                       window_length:int,
                                       marker_ids:List[str]=['all'],
                                       polyorder:int=3)

Smoothes the DataFrame basically using the implementation from DLC2kinematics: https://github.com/AdaptiveMotorControlLab/DLC2Kinematics/blob/82e7e60e00e0efb3c51e024c05a5640c91032026/src/dlc2kinematics/preprocess.py#L64 However, with one key change: likelihoods will also be smoothed. In addition, we will not smooth the columns for the tracked LEDs and the MazeCorners.

Note: window_length has to be an odd integer!

	Type	Default	Details
df	DataFrame		DataFrame to smooth
window_length	int		Odd integer (!) of sliding window size in frames to consider for smoothing
marker_ids	typing.List[str]	[‘all’]	List of markers that will be smoothed; optional default [‘all’] to smooth all marker_ids
polyorder	int	3	Order of the polynom used for the savgol filter
Returns	DataFrame

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interpolate_low_likelihood_intervals

 interpolate_low_likelihood_intervals (df:pandas.core.frame.DataFrame,
                                       marker_ids:List[str],
                                       max_interval_length:int,
                                       framerate:float)

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get_low_likelihood_interval_border_idxs

 get_low_likelihood_interval_border_idxs
                                          (likelihood_series:pandas.core.s
                                          eries.Series, framerate:float,
                                          max_interval_length:int, min_lik
                                          elihood_threshold:float=0.5)

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add_new_marker_derived_from_existing_markers

 add_new_marker_derived_from_existing_markers
                                               (df:pandas.core.frame.DataF
                                               rame,
                                               existing_markers:List[str],
                                               new_marker_id:str, likeliho
                                               od_threshold:float=0.5)

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get_corner_coords_with_likelihoods

 get_corner_coords_with_likelihoods (df:pandas.core.frame.DataFrame)

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get_most_reliable_marker_position_with_likelihood

 get_most_reliable_marker_position_with_likelihood
                                                    (df:pandas.core.frame.
                                                    DataFrame,
                                                    marker_id:str, percent
                                                    ile:float=99.95)

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get_translation_vector

 get_translation_vector (coords_to_become_origin:numpy.ndarray)

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evaluate_maze_shape_using_open_corners

 evaluate_maze_shape_using_open_corners (corners_and_likelihoods:Dict,
                                         tolerance:float)

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compute_error_proportion

 compute_error_proportion (query_value:float, target_value:float)

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compute_angle_error

 compute_angle_error (a:numpy.ndarray, b:numpy.ndarray, c:numpy.ndarray)

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compute_distance_ratio_error

 compute_distance_ratio_error (corners_and_likelihoods:Dict,
                               open_corner_marker_id:str, side_id:str)

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get_distance_between_two_points

 get_distance_between_two_points (coords_point_a:numpy.ndarray,
                                  coords_point_b:numpy.ndarray)

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get_conversion_factor_px_to_cm

 get_conversion_factor_px_to_cm (coords_point_a:numpy.ndarray,
                                 coords_point_b:numpy.ndarray,
                                 distance_in_cm:float)

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get_rotation_angle_with_open_corner

 get_rotation_angle_with_open_corner (corners:Dict, side_id:str,
                                      translation_vector:numpy.ndarray,
                                      conversion_factor:float)

Function, that calculates the rotation angle of the maze considering the best matching open corner and the corresponding closed corner on the same side.

Returns: float: angle in radians

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get_rotation_angle_with_closed_corners_only

 get_rotation_angle_with_closed_corners_only (corners:Dict,
                                              translation_vector:numpy.nda
                                              rray,
                                              conversion_factor:float)

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normalize_df

 normalize_df (df:pandas.core.frame.DataFrame, normalization_parameters)

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translate_df

 translate_df (df:pandas.core.frame.DataFrame, translation_vector:<built-
               infunctionarray>)

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rotate_df

 rotate_df (df:pandas.core.frame.DataFrame, rotation_angle:float)

	Type	Details
df	DataFrame	DataFrame with 2D coordinates to be rotated
rotation_angle	float	rotation angle in radians
Returns	DataFrame

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convert_df_to_cm

 convert_df_to_cm (df:pandas.core.frame.DataFrame,
                   conversion_factor:float)

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create_bodypart_objects

 create_bodypart_objects (normalized_df:pandas.core.frame.DataFrame,
                          fps:int)