Index

_

__init__() (deepof.data.Coordinates method), [1], [2] (deepof.data.Project method), [1], [2] (deepof.data.TableDict method), [1], [2] (deepof.hypermodels.Contrastive method), [1], [2] (deepof.hypermodels.VaDE method), [1], [2] (deepof.hypermodels.VQVAE method), [1], [2] (deepof.model_utils.ClusterControl method), [1], [2] (deepof.model_utils.CustomStopper method), [1], [2] (deepof.model_utils.ExponentialLearningRate method), [1], [2] (deepof.model_utils.ProbabilisticDecoder method), [1], [2] (deepof.model_utils.TransformerDecoder method), [1], [2] (deepof.model_utils.TransformerDecoderLayer method), [1], [2] (deepof.model_utils.TransformerEncoder method), [1], [2] (deepof.model_utils.TransformerEncoderLayer method), [1], [2] (deepof.models.Classifier method), [1], [2] (deepof.models.Contrastive method), [1], [2] (deepof.models.GaussianMixtureLatent method), [1], [2] (deepof.models.VaDE method), [1], [2] (deepof.models.VectorQuantizer method), [1], [2] (deepof.models.VQVAE method), [1], [2] (deepof.utils.MouseTrackingImputer method), [1], [2]

_is_point_inside_numba() (in module deepof.utils) _scale_arenas_to_mm() (in module deepof.arena_utils) _scale_rois_to_mm() (in module deepof.arena_utils)

A

add_binned_legends() (in module deepof.visuals_utils) add_polar_bin_labels() (in module deepof.visuals_utils) align_deepof_kinematics_with_unsupervised_labels() (in module deepof.post_hoc), [1] align_trajectories() (in module deepof.utils), [1] angle() (in module deepof.utils), [1] angles (deepof.data.Project property)

animate_skeleton() (in module deepof.visuals), [1] annotate_binwise_stats() (in module deepof.visuals_utils) annotate_time_chunks() (in module deepof.post_hoc), [1] arena_parameter_extraction() (in module deepof.arena_utils) augment_with_neighbors() (in module deepof.annotation_utils), [1] automatically_recognize_arena() (in module deepof.arena_utils)

B

BGR_to_hex() (in module deepof.visuals_utils) binary_moving_median_numba() (in module deepof.utils), [1] body_part_indices (deepof.utils.MouseTrackingImputer attribute), [1] bp2polar() (in module deepof.utils), [1]

bpart_distance() (in module deepof.utils), [1] build() (deepof.hypermodels.Contrastive method) (deepof.hypermodels.VaDE method) (deepof.hypermodels.VQVAE method)

C

calculate_average_arena() (in module deepof.visuals_utils) calculate_close_range() (in module deepof.annotation_utils), [1] calculate_FSTTC() (in module deepof.visuals_utils) calculate_simple_association() (in module deepof.visuals_utils) call() (deepof.model_utils.ClusterControl method) (deepof.model_utils.ProbabilisticDecoder method) (deepof.model_utils.TransformerDecoder method) (deepof.model_utils.TransformerDecoderLayer method) (deepof.model_utils.TransformerEncoder method) (deepof.model_utils.TransformerEncoderLayer method) (deepof.models.Classifier method) (deepof.models.Contrastive method) (deepof.models.GaussianMixtureLatent method) (deepof.models.VaDE method) (deepof.models.VectorQuantizer method) (deepof.models.VQVAE method) chunk_cv_splitter() (in module deepof.post_hoc), [1] chunk_summary_statistics() (in module deepof.post_hoc), [1] Classifier (class in deepof.models), [1] climb_arena() (in module deepof.annotation_utils), [1] close_double_contact() (in module deepof.annotation_utils), [1] close_single_contact() (in module deepof.annotation_utils), [1] closest_side() (in module deepof.arena_utils) cluster_frequencies_regularizer() (in module deepof.model_utils), [1] cluster_transition_matrix() (in module deepof.utils), [1] ClusterControl (class in deepof.model_utils), [1]

cohend() (in module deepof.visuals_utils) cohend_effect_size() (in module deepof.visuals_utils) compute_animal_presence_mask() (in module deepof.utils), [1] compute_areas() (in module deepof.utils), [1] compute_areas_numba() (in module deepof.utils), [1] compute_dist() (in module deepof.utils), [1] compute_kmeans_loss() (in module deepof.model_utils), [1] compute_shannon_entropy() (in module deepof.model_utils), [1] compute_steady_state() (in module deepof.post_hoc), [1] compute_transition_matrix_per_condition() (in module deepof.post_hoc), [1] compute_UMAP() (in module deepof.post_hoc), [1] condition_distance_binning() (in module deepof.post_hoc), [1] connect_mouse() (in module deepof.utils), [1] connectivity (deepof.utils.MouseTrackingImputer attribute), [1] contiguous_segments() (in module deepof.visuals_utils) Contrastive (class in deepof.hypermodels), [1] (class in deepof.models), [1] Coordinates (class in deepof.data), [1] count_all_events() (in module deepof.visuals) count_events() (in module deepof.utils), [1] count_transitions() (in module deepof.utils), [1] create() (deepof.data.Project method) create_bin_pairs() (in module deepof.visuals_utils) create_look_ahead_mask() (in module deepof.model_utils), [1] create_masks() (in module deepof.model_utils), [1] create_padding_mask() (in module deepof.model_utils), [1] CustomStopper (class in deepof.model_utils), [1]

D

dcl_loss() (in module deepof.model_utils), [1] deep_unsupervised_embedding() (deepof.data.Coordinates method) deepof module deepof.annotation_utils module, [1] deepof.data module, [1] deepof.deepof_train_embeddings module, [1] deepof.hypermodels module, [1] deepof.model_utils module, [1]

deepof.models module, [1] deepof.post_hoc module, [1] deepof.utils module, [1] deepof.visuals module, [1] deepof.visuals_utils module detect_activity() (in module deepof.annotation_utils), [1] digging() (in module deepof.annotation_utils) display_message() (in module deepof.arena_utils) distances (deepof.data.Project property)

E

edges_to_weighted_adj() (in module deepof.utils), [1] edit_arenas() (deepof.data.Coordinates method) ego (deepof.data.Project property) embedding_model_fitting() (in module deepof.model_utils), [1] embedding_per_video() (in module deepof.model_utils), [1] enforce_skeleton_constraints_numba() (in module deepof.utils), [1] enrichment_across_conditions() (in module deepof.post_hoc), [1] ensure_axis() (in module deepof.visuals_utils)

enumerate_all_bridges() (in module deepof.utils), [1] explain_clusters() (in module deepof.post_hoc) ExponentialLearningRate (class in deepof.model_utils), [1] export_annotated_video() (in module deepof.visuals), [1] extend() (deepof.data.Project method) extend_behaviors_numba() (in module deepof.utils), [1] extract_polygonal_arena_coordinates() (in module deepof.arena_utils) extract_windows() (in module deepof.utils), [1]

F

fc_loss() (in module deepof.model_utils), [1] filter_animal_id_in_table() (in module deepof.utils), [1] filter_columns() (in module deepof.utils), [1] filter_condition() (deepof.data.TableDict method) filter_id() (deepof.data.TableDict method) filter_short_bouts() (in module deepof.utils), [1] filter_short_true_segments() (in module deepof.utils), [1] filter_short_true_segments_numba() (in module deepof.utils), [1] filter_videos() (deepof.data.TableDict method)

find_learning_rate() (in module deepof.model_utils), [1] fit_ellipse_to_polygon() (in module deepof.arena_utils) fit_normative_global_model() (in module deepof.post_hoc), [1] fit_transform() (deepof.utils.MouseTrackingImputer method) following_path() (in module deepof.annotation_utils), [1] format_time_binned_axis() (in module deepof.visuals_utils) frame_corners() (in module deepof.annotation_utils), [1] full_imputation (deepof.utils.MouseTrackingImputer attribute), [1] full_outlier_mask() (in module deepof.utils), [1]

G

gantt_plotter() (in module deepof.visuals) GaussianMixtureLatent (class in deepof.models), [1] generate_behavior_combinations() (in module deepof.visuals_utils) get_aggregated_embedding() (in module deepof.post_hoc) get_angles() (deepof.data.Coordinates method) (deepof.data.Project method) (in module deepof.model_utils), [1] get_angles_at_key() (deepof.data.Coordinates method) get_areas() (deepof.data.Coordinates method) (deepof.data.Project method) get_areas_at_key() (deepof.data.Coordinates method) get_arena() (deepof.data.Project method) get_arenas (deepof.data.Coordinates property) get_arenas() (in module deepof.arena_utils) get_behavior_colors() (in module deepof.visuals_utils) get_behavior_frames_in_roi() (in module deepof.visuals_utils) get_behavior_mask_and_confidence() (in module deepof.utils) get_binned_geometry() (in module deepof.visuals_utils) get_callbacks() (in module deepof.model_utils), [1] get_code_indices() (deepof.models.VectorQuantizer method) get_condition_values() (deepof.data.Coordinates method) get_config() (deepof.model_utils.ClusterControl method) (deepof.model_utils.CustomStopper method) get_contrastive_soft_counts() (in module deepof.post_hoc) get_contrastive_soft_counts_gmm() (in module deepof.post_hoc) get_contrastive_soft_counts_msm_pcca() (in module deepof.post_hoc) get_coords() (deepof.data.Coordinates method) get_coords_at_key() (deepof.data.Coordinates method) get_distances() (deepof.data.Coordinates method) (deepof.data.Project method) get_distances_at_key() (deepof.data.Coordinates method) get_distances_tab() (deepof.data.Project method) get_end_times() (deepof.data.Coordinates method) get_exp_conditions (deepof.data.Coordinates property) get_first_length() (in module deepof.arena_utils)

get_gmm_params (deepof.models.VaDE property) get_graph_dataset() (deepof.data.Coordinates method) get_hard_counts() (in module deepof.model_utils), [1] get_hparams() (deepof.hypermodels.Contrastive method) (deepof.hypermodels.VaDE method) (deepof.hypermodels.VQVAE method) get_k_nearest_neighbors() (in module deepof.model_utils), [1] get_pairwise_distances() (in module deepof.post_hoc) get_point_polygon_distance() (in module deepof.utils) get_point_polygon_distance_numba() (in module deepof.utils) get_quality() (deepof.data.Coordinates method) get_recurrent_block() (in module deepof.model_utils), [1] get_recurrent_decoder() (in module deepof.models), [1] get_recurrent_encoder() (in module deepof.models) get_roi_data() (in module deepof.visuals) get_square_shape_for_gridlike_plot() (in module deepof.visuals_utils) get_start_times() (deepof.data.Coordinates method) get_supervised_behaviors_in_roi() (in module deepof.visuals_utils) get_supervised_parameters() (deepof.data.Coordinates method) get_table_keys() (deepof.data.Coordinates method) get_table_lengths() (deepof.data.Coordinates method) get_TCN_decoder() (in module deepof.models), [1] get_TCN_encoder() (in module deepof.models), [1] get_time_on_cluster() (in module deepof.post_hoc), [1] get_total_Frames() (in module deepof.utils), [1] get_training_set() (deepof.data.TableDict method) get_transformer_decoder() (in module deepof.models), [1] get_transformer_encoder() (in module deepof.models), [1] get_transitions() (in module deepof.post_hoc), [1] get_unsupervised_behaviors_in_roi() (in module deepof.visuals_utils) get_vade() (in module deepof.models), [1] get_videos() (deepof.data.Coordinates method) get_vqvae() (in module deepof.models), [1] gmm_compute() (in module deepof.utils), [1] gmm_model_selection() (in module deepof.utils), [1]

H

hard_loss() (in module deepof.model_utils), [1] heatmap() (in module deepof.visuals) (in module deepof.visuals_utils)

hex_to_BGR() (in module deepof.visuals_utils)

I

immobility() (in module deepof.annotation_utils), [1] in_field_of_view() (in module deepof.utils) in_field_of_view_numba() (in module deepof.utils)

infer_column_types() (in module deepof.utils) infer_scalar_cols() (in module deepof.utils) is_display_available() (in module deepof.data) iterative_imputation() (in module deepof.utils), [1]

K

KeyErrorMessage (class in deepof.utils)

kleinberg() (in module deepof.utils), [1] kleinberg_core_numba() (in module deepof.utils), [1]

L

lin_interp_limit (deepof.utils.MouseTrackingImputer attribute), [1] load_exp_conditions() (deepof.data.Coordinates method) (deepof.data.Project method)

load_precompiled_model() (in module deepof.utils) load_project() (in module deepof.data), [1] load_table() (in module deepof.utils), [1] log_hyperparameters() (in module deepof.model_utils), [1]

M

mask_outliers() (in module deepof.utils), [1] max_behaviour() (in module deepof.annotation_utils), [1] merge() (deepof.data.TableDict method) metrics (deepof.models.Contrastive property) (deepof.models.VaDE property) (deepof.models.VQVAE property) module deepof deepof.annotation_utils, [1] deepof.data, [1] deepof.deepof_train_embeddings, [1] deepof.hypermodels, [1] deepof.model_utils, [1] deepof.models, [1] deepof.post_hoc, [1] deepof.utils, [1] deepof.visuals, [1] deepof.visuals_utils

mouse_body_estimation_samples (deepof.utils.MouseTrackingImputer attribute), [1] mouse_in_roi() (in module deepof.utils), [1] MouseTrackingImputer (class in deepof.utils), [1] moving_average() (in module deepof.utils), [1] multi_step_paired_smoothing() (in module deepof.utils), [1]

N

n_iterations (deepof.utils.MouseTrackingImputer attribute), [1]

nce_loss() (in module deepof.model_utils), [1] new_dict_same_header() (deepof.data.TableDict method)

O

on_batch_end() (deepof.model_utils.ExponentialLearningRate method) on_epoch_end() (deepof.model_utils.CustomStopper method)

output_videos_per_cluster() (in module deepof.visuals) outside_ellipse() (in module deepof.annotation_utils), [1]

P

pca() (deepof.data.TableDict method) plot_arena() (in module deepof.visuals) (in module deepof.visuals_utils) plot_binned_groups() (in module deepof.visuals_utils) plot_binned_line() (in module deepof.visuals_utils) plot_cluster_detection_performance() (in module deepof.visuals) plot_distance_between_conditions() (in module deepof.visuals), [1] plot_effectsize_histogram() (in module deepof.visuals_utils) plot_embeddings() (in module deepof.visuals), [1] plot_enrichment() (in module deepof.visuals), [1] plot_gantt() (in module deepof.visuals), [1] plot_heatmaps() (in module deepof.visuals), [1] plot_lr_vs_loss() (in module deepof.model_utils), [1] plot_mouse_roi_interaction() (in module deepof.visuals)

plot_normative_log_likelihood() (in module deepof.visuals), [1] plot_shap_swarm_per_cluster() (in module deepof.visuals) plot_stationary_entropy() (in module deepof.visuals), [1] plot_transitions() (in module deepof.visuals), [1] point_in_polygon() (in module deepof.utils), [1] point_in_polygon_numba() (in module deepof.utils), [1] polygon_area_numba() (in module deepof.utils), [1] positional_encoding() (in module deepof.model_utils), [1] postprocess_df_bins() (in module deepof.visuals_utils) preprocess() (deepof.data.TableDict method) preprocess_tables() (deepof.data.Project method) pretrain() (deepof.models.VaDE method) ProbabilisticDecoder (class in deepof.model_utils), [1] process_df() (in module deepof.visuals_utils) Project (class in deepof.data), [1]

R

random_projection() (deepof.data.TableDict method) recluster() (in module deepof.post_hoc), [1] remove_outliers() (in module deepof.utils), [1] rename_track_bps() (in module deepof.utils), [1] reset_supervised_parameters() (deepof.data.Coordinates method) retrieve_corners_from_image() (in module deepof.arena_utils) return_mouse_roi_interaction() (in module deepof.visuals) return_supervised_summary() (in module deepof.visuals) return_transitions() (in module deepof.visuals)

RGB_to_hex() (in module deepof.visuals_utils) rolling_speed() (in module deepof.utils), [1] rolling_window() (in module deepof.utils), [1] rotate() (in module deepof.annotation_utils), [1] (in module deepof.utils), [1] rotate_all_numba() (in module deepof.utils), [1] rotate_numba() (in module deepof.utils), [1] row_nanargmax() (in module deepof.utils) rts_smoother_numba() (in module deepof.utils), [1]

S

sample_windows_from_data() (deepof.data.TableDict method) save() (deepof.data.Coordinates method) scale_table() (in module deepof.utils), [1] scale_tables() (deepof.data.Project method) scale_units() (in module deepof.visuals_utils) seconds_to_time() (in module deepof.visuals_utils) select_contrastive_loss() (in module deepof.model_utils), [1] separation_between_conditions() (in module deepof.post_hoc), [1] set_missing_animals() (in module deepof.utils), [1] set_pretrain_mode() (deepof.models.VaDE method) set_supervised_parameters() (deepof.data.Coordinates method)

set_up_project_directory() (deepof.data.Project method) signed_angle() (in module deepof.utils) simplify_polygon() (in module deepof.arena_utils) skeleton_constraints (deepof.utils.MouseTrackingImputer attribute), [1] smooth_boolean_array() (in module deepof.utils), [1] smooth_mult_trajectory() (in module deepof.utils), [1] sniff_around() (in module deepof.annotation_utils), [1] sniff_object() (in module deepof.annotation_utils), [1] stationary_lookaround() (in module deepof.annotation_utils), [1] str2bool() (in module deepof.utils), [1] supervised_annotation() (deepof.data.Coordinates method) supervised_tagging() (in module deepof.annotation_utils), [1]

T

tab2polar() (in module deepof.utils), [1] TableDict (class in deepof.data), [1] test_step() (deepof.models.Contrastive method) (deepof.models.VaDE method) (deepof.models.VQVAE method) time_to_seconds() (in module deepof.visuals_utils) train_step() (deepof.models.Contrastive method) (deepof.models.VaDE method) (deepof.models.VQVAE method)

train_supervised_cluster_detectors() (in module deepof.post_hoc), [1] TransformerDecoder (class in deepof.model_utils), [1] TransformerDecoderLayer (class in deepof.model_utils), [1] TransformerEncoder (class in deepof.model_utils), [1] TransformerEncoderLayer (class in deepof.model_utils), [1] tune_search() (in module deepof.model_utils), [1]

U

umap() (deepof.data.TableDict method)

V

VaDE (class in deepof.hypermodels), [1] (class in deepof.models), [1] validate_custom_bins() (in module deepof.visuals_utils)

validate_parameter() (in module deepof.utils) VectorQuantizer (class in deepof.models), [1] VQVAE (class in deepof.hypermodels), [1] (class in deepof.models), [1]