Index

A

add_shades() (in module neurokin.utils.experiments.neural_correlates_plot)

average_block() (in module neurokin.utils.neural.processing)

B

bin_feature() (in module neurokin.utils.features_extraction.feature_extraction)

C

calculate_power_spectral_density() (in module neurokin.utils.neural.processing) check_correct_columns_extraction() (in module neurokin.utils.kinematics.kinematics_processing) check_time_cutoff() (in module neurokin.utils.experiments.neural_correlates) compute_acceleration() (in module neurokin.utils.features_extraction.commons) compute_angle() (in module neurokin.utils.features_extraction.commons) compute_angle_acceleration() (in module neurokin.utils.features_extraction.commons) compute_angle_correlation() (in module neurokin.utils.features_extraction.commons) compute_angle_phase() (in module neurokin.utils.features_extraction.commons) compute_angle_velocity() (in module neurokin.utils.features_extraction.commons) compute_ci() (in module neurokin.utils.experiments.neural_states_helper) compute_duration() (in module neurokin.utils.experiments.neural_states_helper) compute_events_percentage() (in module neurokin.utils.experiments.neural_states_helper) compute_feature() (neurokin.utils.features_extraction.core.FeatureExtraction method) (neurokin.utils.features_extraction.core.MyFeat method) (neurokin.utils.features_extraction.core.MyFeat2 method)

compute_gait_cycles_bounds() (neurokin.kinematic_data.KinematicDataRun method) compute_percentage() (in module neurokin.utils.experiments.neural_states_helper) compute_phase_at_max_amplitude() (in module neurokin.utils.features_extraction.commons) compute_psd_for_row() (in module neurokin.utils.experiments.neural_correlates) compute_recording_duration() (neurokin.neural_data.NeuralData method) compute_speed() (in module neurokin.utils.features_extraction.commons) compute_tang_acceleration() (in module neurokin.utils.features_extraction.commons) compute_velocity() (in module neurokin.utils.features_extraction.commons) condense_distribution_event_types() (in module neurokin.utils.experiments.neural_states_helper) convert_DLC_like_to_df() (neurokin.kinematic_data.KinematicDataRun method) create_empty_df() (in module neurokin.utils.kinematics.import_export) create_events_dataset() (neurokin.locomotion_states.NeuralCorrelatesStates method) create_exclusion_mask() (in module neurokin.utils.experiments.neural_correlates) create_psd_dataset() (neurokin.locomotion_states.NeuralCorrelatesStates method) create_raw_neural_dataset() (neurokin.locomotion_states.NeuralCorrelatesStates method)

E

export_neural_data_to_bin() (in module neurokin.utils.neural.exporting) extract_features() (in module neurokin.utils.features_extraction.feature_extraction) (neurokin.kinematic_data.KinematicDataRun method)

extraction_target (neurokin.utils.features_extraction.core.MyFeat attribute) (neurokin.utils.features_extraction.core.MyFeat2 attribute)

F

FeatureExtraction (class in neurokin.utils.features_extraction.core) filter_marker_df() (neurokin.kinematic_data.KinematicDataRun method)

find_closest_index() (in module neurokin.utils.neural.processing) find_closest_smaller_index() (in module neurokin.utils.neural.processing)

G

gait_param_to_csv() (neurokin.kinematic_data.KinematicDataRun method) get_average_amplitudes() (in module neurokin.utils.neural.processing) get_c3d_labels() (in module neurokin.utils.kinematics.import_export) get_csv_first_block_len() (in module neurokin.utils.experiments.neural_correlates) get_event_timestamps_freezing_active() (in module neurokin.utils.experiments.neural_correlates) get_event_timestamps_freezing_rest() (in module neurokin.utils.experiments.neural_correlates) get_event_timestamps_gait() (in module neurokin.utils.experiments.neural_correlates) get_event_timestamps_nlm_active() (in module neurokin.utils.experiments.neural_correlates) get_event_timestamps_nlm_rest() (in module neurokin.utils.experiments.neural_correlates) get_events_dict() (in module neurokin.utils.experiments.neural_correlates) get_extractor_obj() (in module neurokin.utils.features_extraction.feature_extraction) get_first_block_df() (in module neurokin.utils.experiments.neural_correlates) get_first_last_frame_from_csv() (in module neurokin.utils.experiments.neural_correlates) get_freeze_ts_bound() (in module neurokin.utils.experiments.neural_correlates) get_group_split() (in module neurokin.utils.experiments.neural_states_helper) get_idxs_events_to_exclude() (in module neurokin.utils.experiments.neural_correlates) get_median_distance() (in module neurokin.utils.neural.processing)

get_neural_ch() (in module neurokin.utils.experiments.neural_correlates) get_neural_correlate_psd() (in module neurokin.utils.experiments.neural_correlates) get_neural_correlates_dict() (in module neurokin.utils.experiments.neural_correlates) get_peak_boundaries_scipy() (in module neurokin.utils.kinematics.event_detection) get_per_animal_psds_df() (in module neurokin.utils.experiments.neural_states_helper) get_polygon_corners() (in module neurokin.utils.experiments.spider_factory) get_psd_single_event_type() (in module neurokin.utils.experiments.neural_correlates) get_runs_list() (in module neurokin.utils.experiments.neural_states_helper) get_single_neural_type() (in module neurokin.utils.experiments.neural_correlates) get_spectrogram_data() (in module neurokin.utils.neural.processing) get_start_of_gait() (in module neurokin.utils.experiments.neural_correlates) get_state_graph_stats() (in module neurokin.utils.experiments.neural_states_helper) get_stim_timestamps() (in module neurokin.utils.neural.processing) get_timestamps_stim_blocks() (in module neurokin.utils.neural.processing) get_toe_lift_landing() (in module neurokin.utils.kinematics.event_detection) get_ts_from_exclusion_mask() (in module neurokin.utils.experiments.neural_correlates) get_unilateral_df() (in module neurokin.utils.kinematics.kinematics_processing)

I

import_binary_to_float32() (in module neurokin.utils.neural.importing) import_c3d() (in module neurokin.utils.kinematics.import_export)

import_dlc_df() (in module neurokin.utils.kinematics.import_export) import_open_ephys_channel_data() (in module neurokin.utils.neural.importing) import_tdt_channel_data() (in module neurokin.utils.neural.importing)

K

keys2string() (in module neurokin.utils.helper.load_config)

KinematicDataRun (class in neurokin.kinematic_data)

L

load_dataset() (in module neurokin.utils.experiments.neural_states_helper) load_kinematics() (neurokin.kinematic_data.KinematicDataRun method)

load_open_ephys() (neurokin.neural_data.NeuralData method) load_tdt_data() (neurokin.neural_data.NeuralData method) lowpass_array() (in module neurokin.utils.kinematics.event_detection)

M

mean_psds() (in module neurokin.utils.experiments.neural_states_helper) median_distance() (in module neurokin.utils.kinematics.event_detection) module neurokin neurokin.kinematic_data neurokin.locomotion_states neurokin.neural_data neurokin.utils neurokin.utils.experiments neurokin.utils.experiments.neural_correlates neurokin.utils.experiments.neural_correlates_plot neurokin.utils.experiments.neural_states_helper neurokin.utils.experiments.spider_factory neurokin.utils.features_extraction neurokin.utils.features_extraction.commons neurokin.utils.features_extraction.core neurokin.utils.features_extraction.feature_extraction neurokin.utils.helper neurokin.utils.helper.load_config neurokin.utils.kinematics neurokin.utils.kinematics.event_detection neurokin.utils.kinematics.import_export neurokin.utils.kinematics.kinematics_processing neurokin.utils.neural neurokin.utils.neural.exporting neurokin.utils.neural.importing neurokin.utils.neural.neural_plot neurokin.utils.neural.processing

MyFeat (class in neurokin.utils.features_extraction.core) MyFeat2 (class in neurokin.utils.features_extraction.core)

N

NeuralCorrelatesStates (class in neurokin.locomotion_states) NeuralData (class in neurokin.neural_data) neurokin module neurokin.kinematic_data module neurokin.locomotion_states module neurokin.neural_data module neurokin.utils module neurokin.utils.experiments module neurokin.utils.experiments.neural_correlates module neurokin.utils.experiments.neural_correlates_plot module neurokin.utils.experiments.neural_states_helper module neurokin.utils.experiments.spider_factory module neurokin.utils.features_extraction module neurokin.utils.features_extraction.commons module

neurokin.utils.features_extraction.core module neurokin.utils.features_extraction.feature_extraction module neurokin.utils.helper module neurokin.utils.helper.load_config module neurokin.utils.kinematics module neurokin.utils.kinematics.event_detection module neurokin.utils.kinematics.import_export module neurokin.utils.kinematics.kinematics_processing module neurokin.utils.neural module neurokin.utils.neural.exporting module neurokin.utils.neural.importing module neurokin.utils.neural.neural_plot module neurokin.utils.neural.processing module

P

parse_raw() (in module neurokin.utils.neural.processing) pick_sync_data() (neurokin.neural_data.NeuralData method) plot_prep_psds_dataset() (neurokin.locomotion_states.NeuralCorrelatesStates method) plot_prep_states_distribution() (neurokin.locomotion_states.NeuralCorrelatesStates method) plot_psd_single_state() (in module neurokin.utils.experiments.neural_correlates_plot)

plot_spectrogram() (in module neurokin.utils.neural.neural_plot) plot_spider_single_trace() (in module neurokin.utils.experiments.spider_factory) plot_step_partition() (neurokin.kinematic_data.KinematicDataRun method) plot_welch() (in module neurokin.utils.neural.neural_plot) print_step_partition() (neurokin.kinematic_data.KinematicDataRun method)

R

read_config() (in module neurokin.utils.helper.load_config) run_feat_extraction() (neurokin.utils.features_extraction.core.FeatureExtraction method)

running_mean() (in module neurokin.utils.neural.processing) running_mean_2D() (in module neurokin.utils.neural.processing)

S

save_data() (in module neurokin.utils.experiments.neural_states_helper) save_dataset() (neurokin.locomotion_states.NeuralCorrelatesStates method) shift_correct() (in module neurokin.utils.kinematics.kinematics_processing)

simply_mean_data_binarize() (in module neurokin.utils.neural.processing) spider_factory() (in module neurokin.utils.experiments.spider_factory) stepwise_gait_features_to_csv() (neurokin.kinematic_data.KinematicDataRun method)

T

tilt_correct() (in module neurokin.utils.kinematics.kinematics_processing) time_to_frame_in_roi() (in module neurokin.utils.experiments.neural_correlates) time_to_sample() (in module neurokin.utils.neural.importing)

transpose_start_of_gait() (in module neurokin.utils.experiments.neural_correlates) traspose_idxs() (in module neurokin.utils.experiments.neural_correlates) trim_equal_len() (in module neurokin.utils.neural.processing)