Index

A

add() (DistributedExperiment method) (Experiment method) add_xtick_box() (in module vassi.visualization) add_xtick_boxes() (in module vassi.visualization) add_ytick_box() (in module vassi.visualization) add_ytick_boxes() (in module vassi.visualization) adjust_function() (BaseExtractor method) (DataFrameFeatureExtractor method) adjust_lightness() (in module vassi.visualization) aggregate_bouts() (in module vassi.dataset.observations.bouts) allowed_additional_kwargs (BaseExtractor attribute) (DataFrameFeatureExtractor attribute) angular_speed() (in module vassi.features.temporal_features) annotate() (Dataset method) (Dyad method) (Group method) (Individual method) (SampleableMixin method)

AnnotatedDataset (class in vassi.dataset.types.dataset) AnnotatedDyad (class in vassi.dataset.types.dyad) AnnotatedGroup (class in vassi.dataset.types.group) AnnotatedIndividual (class in vassi.dataset.types.individual) AnnotatedMixin (class in vassi.dataset.types.mixins.annotated) AnnotatedSampleableMixin (class in vassi.dataset.types.mixins.annotated_sampleable) annotations (ClassificationResult property) (DatasetClassificationResult property) (GroupClassificationResult property) apply_multiple_to_sliding_windows() (in module vassi.sliding_metrics.sliding_metrics) ArrayToArray (class in vassi.utils) as_absolute() (in module vassi.features.decorators) as_angle() (in module vassi.math) as_dataframe() (in module vassi.features.decorators) as_sign_change_latency() (in module vassi.features.decorators) as_unit_vector() (in module vassi.math) available_resources() (in module vassi.utils)

B

barrier() (DistributedExperiment method) (Experiment method) BaseConfig (class in vassi.config)

BaseExtractor (class in vassi.features.feature_extractor) BaseResult (class in vassi.classification.results) broadcast() (DistributedExperiment method) (Experiment method)

C

catch_time() (in module vassi.logging) categories (ClassificationResult attribute) category_counts (AnnotatedMixin property) cfg (ConfiguredData property) check_observations() (in module vassi.dataset.observations.utils) class_name() (in module vassi.utils) classification_results (DatasetClassificationResult attribute) (GroupClassificationResult attribute) ClassificationResult (class in vassi.classification.results) Classifier (class in vassi.classification.utils) closest_odd_divisible() (in module vassi.utils) collect() (DistributedExperiment method) (Experiment method)

combine() (DatasetClassificationResult class method) (GroupClassificationResult class method) concatenate() (BaseExtractor class method) (DataFrameFeatureExtractor class method) (FeatureExtractor class method) (InstanceCollection class method) config (BaseExtractor property) Config (class in vassi.config) ConfiguredData (class in vassi.data_structures.base) convert_calms21_sequences() (in module vassi.case_studies.calms21.convert) copy() (BaseConfig method) (InstanceCollection method)

D

data (ConfiguredData property) (InstanceCollection property) DataFrameFeature (class in vassi.features.utils) DataFrameFeatureExtractor (class in vassi.features.feature_extractor) Dataset (class in vassi.dataset.types.dataset) DatasetClassificationResult (class in vassi.classification.results) decision_thresholds (PostprocessingParameters attribute)

dimension() (Panel method) DistributedExperiment (class in vassi.distributed) divide() (Panel method) dot_product() (in module vassi.math) download_calm21_dataset() (in module vassi.case_studies.calms21.download) download_social_cichlids_dataset() (in module vassi.case_studies.social_cichlids.download) Dyad (class in vassi.dataset.types.dyad)

E

empty() (BaseExtractor class method) (DataFrameFeatureExtractor class method) (FeatureExtractor class method) encode (AnnotatedMixin property) encode_categories() (in module vassi.dataset.types.mixins.annotated) EncodingFunction (class in vassi.dataset.types.mixins.annotated) ensure_matching_index_columns() (in module vassi.dataset.observations.utils)

ensure_single_index() (in module vassi.dataset.observations.utils) euclidean_distance() (in module vassi.math) exclude_individuals() (Dataset method) Experiment (class in vassi.utils) extent (Panel property) extract() (BaseExtractor method) extract_features() (BaseExtractor method)

F

f1_score() (BaseResult method) Feature (class in vassi.features.utils) feature_names (BaseExtractor property) feature_names() (in module vassi.features.utils) FeatureExtractor (class in vassi.features.feature_extractor) filter_sliding_quantile_range() (in module vassi.series_operations) filter_sliding_quantile_range_1d() (in module vassi.series_operations) fit() (Classifier method) (SlidingWindowAggregator method)

fit_classifier() (in module vassi.classification.utils) flatten() (in module vassi.utils) foreground_categories (AnnotatedMixin property) from_cache() (in module vassi.io) from_group() (Group class method) from_groups() (Dataset class method) from_h5() (ClassificationResult class method) (DatasetClassificationResult class method) (GroupClassificationResult class method) from_yaml() (in module vassi.io)

G

get_actor() (in module vassi.dataset.utils) get_ax() (Panel method) get_box_height() (in module vassi.visualization) get_box_width() (in module vassi.visualization) get_feature_names() (in module vassi.features.utils) get_feature_names_out() (SlidingWindowAggregator method) get_inner() (in module vassi.features.decorators) get_instance_range() (in module vassi.visualization) get_interpolated_length() (Trajectory method) get_interval_slice() (in module vassi.data_structures.utils)

get_params() (Classifier method) get_prefix() (in module vassi.features.decorators) get_proximitry_matrix() (in module vassi.dataset.permute) get_random_state() (Experiment method) get_slice() (TimestampedInstanceCollection method) get_trajectory_range() (in module vassi.visualization) get_window_slices() (in module vassi.sliding_metrics.transform) greatest_common_denominator() (in module vassi.data_structures.utils) Group (class in vassi.dataset.types.group) GroupClassificationResult (class in vassi.classification.results)

H

hash_dict() (in module vassi.utils)

height (Panel property)

I

identifiers (NestedSampleableMixin property) include() (in module vassi.dataset.types.dataset) increment_loop() (in module vassi.logging) Individual (class in vassi.dataset.types.individual) individuals (Dataset property) (Group property) (GroupClassificationResult attribute) (NestedSampleableMixin property) infill_observations() (in module vassi.dataset.observations.utils) init_new_classifier() (in module vassi.classification.utils) init_other() (InstanceCollection method) (Trajectory method)

Instance (class in vassi.data_structures.instance) InstanceCollection (class in vassi.data_structures.collection) interpolate() (Trajectory method) interval_contained() (in module vassi.dataset.utils) interval_overlap() (in module vassi.dataset.utils) is_complete (Trajectory property) is_distributed (Experiment property) is_root (DistributedExperiment property) (Experiment property) is_sorted (TimestampedInstanceCollection property) items() (BaseConfig method) (ConfiguredData method)

K

k_fold() (Dataset method) k_fold_predict() (in module vassi.classification.predict) key_timestamp (TimestampedInstanceCollection property)

keypoint_distances() (in module vassi.features.features) keypoints() (in module vassi.features.features) keys() (BaseConfig method) (ConfiguredData method)

L

length (InstanceCollection property) load() (BaseExtractor method) load_calms21_sequences() (in module vassi.case_studies.calms21.convert) load_data() (in module vassi.io)

load_dataset() (in module vassi.io) load_feature_func() (in module vassi.features.feature_extractor) load_trajectories() (in module vassi.io) log_loop() (in module vassi.logging) log_time() (in module vassi.logging)

M

magnitude() (in module vassi.math) max() (in module vassi.sliding_metrics.metrics) mean() (in module vassi.sliding_metrics.metrics) median() (in module vassi.sliding_metrics.metrics) min() (in module vassi.sliding_metrics.metrics) module vassi.case_studies vassi.case_studies.calms21 vassi.case_studies.calms21.convert vassi.case_studies.calms21.download vassi.case_studies.social_cichlids vassi.case_studies.social_cichlids.download vassi.classification vassi.classification.postprocessing vassi.classification.predict vassi.classification.results vassi.classification.utils vassi.classification.visualization vassi.config vassi.data_structures vassi.data_structures.base vassi.data_structures.collection vassi.data_structures.instance vassi.data_structures.timestamped_collection vassi.data_structures.trajectory vassi.data_structures.utils vassi.dataset vassi.dataset.observations vassi.dataset.observations.bouts vassi.dataset.observations.utils vassi.dataset.permute vassi.dataset.types vassi.dataset.types.dataset vassi.dataset.types.dyad vassi.dataset.types.group vassi.dataset.types.individual vassi.dataset.types.mixins vassi.dataset.types.mixins.annotated vassi.dataset.types.mixins.annotated_sampleable vassi.dataset.types.mixins.nested vassi.dataset.types.mixins.sampleable vassi.dataset.utils vassi.distributed vassi.features vassi.features.decorators vassi.features.feature_extractor vassi.features.features vassi.features.temporal_features vassi.features.utils vassi.io vassi.logging vassi.math vassi.series_operations vassi.sliding_metrics vassi.sliding_metrics.metrics vassi.sliding_metrics.sliding_metrics vassi.sliding_metrics.transform vassi.utils vassi.visualization

N

names() (in module vassi.features.utils)

NestedSampleableMixin (class in vassi.dataset.types.mixins.nested) num_runs (Experiment property)

O

observations (AnnotatedMixin property) optimize_postprocessing_parameters() (in module vassi.classification.postprocessing) optuna_parameter_optimization() (in module vassi.classification.postprocessing)

optuna_score_postprocessing_trial() (in module vassi.classification.postprocessing) orientation_change() (in module vassi.features.temporal_features) OutOfInterval

P

pad_values() (in module vassi.utils) pair() (in module vassi.features.utils) PairedArraysToArray (class in vassi.utils) Panel (class in vassi.visualization) ParameterSuggestionFunction (class in vassi.classification.postprocessing) perform_operation() (in module vassi.utils) performs_run (DistributedExperiment property) (Experiment property) permute_recipients() (in module vassi.dataset.permute) perp() (in module vassi.math) perp_dot_product() (in module vassi.math) plot_classification_timeline() (in module vassi.classification.visualization) plot_confusion_matrix() (in module vassi.classification.visualization) position() (in module vassi.features.features) postprocessing_parameters (PostprocessingParameters attribute) PostprocessingFunction (class in vassi.classification.postprocessing)

PostprocessingParameters (class in vassi.classification.postprocessing) posture_alignment() (in module vassi.features.features) posture_angles() (in module vassi.features.features) posture_segments() (in module vassi.features.features) posture_vectors() (in module vassi.features.features) potential_identifiers (Group property) predict() (Classifier method) (in module vassi.classification.predict) predict_proba() (Classifier method) predictions (ClassificationResult property) (DatasetClassificationResult property) (GroupClassificationResult property) prepare_paired_trajectories() (Dyad class method) projected_velocity() (in module vassi.features.temporal_features) projection() (in module vassi.math) prune_feature_names() (in module vassi.features.utils)

Q

q01() (in module vassi.sliding_metrics.metrics) q05() (in module vassi.sliding_metrics.metrics) q10() (in module vassi.sliding_metrics.metrics)

q90() (in module vassi.sliding_metrics.metrics) q95() (in module vassi.sliding_metrics.metrics) q99() (in module vassi.sliding_metrics.metrics) quantile() (in module vassi.sliding_metrics.metrics)

R

random_state (Experiment property) read_yaml() (BaseExtractor method) recursive_name() (in module vassi.features.utils) rejection() (in module vassi.math) relational_names() (in module vassi.features.utils) remove_cache() (in module vassi.io) remove_overlapping_observations() (in module vassi.dataset.observations.utils)

remove_overlapping_predictions() (BaseResult method) REQUIRED_COLUMNS() (Dataset class method) (Group class method) (SampleableMixin class method) rotate() (in module vassi.math) run (Experiment property) run_k_fold_experiment() (in module vassi.classification.postprocessing)

S

sample() (in module vassi.series_operations) (SampleableMixin method) (Trajectory method) sample_1d() (in module vassi.series_operations) sample_X() (SampleableMixin method) sample_y() (AnnotatedMixin method) SampleableMixin (class in vassi.dataset.types.mixins.sampleable) SamplingFunction (class in vassi.dataset.types.mixins.sampleable) save_data() (in module vassi.io) save_dataset() (in module vassi.io) save_trajectories() (in module vassi.io) save_yaml() (BaseExtractor method) scalar_projection() (in module vassi.math) scalar_rejection() (in module vassi.math) score() (BaseResult method) select() (InstanceCollection method) (NestedSampleableMixin method) select_index() (InstanceCollection method) select_indices() (BaseExtractor method) (DataFrameFeatureExtractor method) (FeatureExtractor method) set_logging_level() (in module vassi.logging) sha1 (BaseExtractor property) (ConfiguredData property) shape (Shaped property)

Shaped (class in vassi.features.feature_extractor) shift() (in module vassi.math) sign_change_latency() (in module vassi.series_operations) sign_change_latency_1d() (in module vassi.series_operations) signed_angle() (in module vassi.math) size (SampleableMixin property) slice_window() (TimestampedInstanceCollection method) (Trajectory method) sliding_max() (in module vassi.sliding_metrics.sliding_metrics) sliding_mean() (in module vassi.sliding_metrics.sliding_metrics) sliding_median() (in module vassi.sliding_metrics.sliding_metrics) sliding_min() (in module vassi.sliding_metrics.sliding_metrics) sliding_quantile() (in module vassi.sliding_metrics.sliding_metrics) sliding_quantiles() (in module vassi.sliding_metrics.sliding_metrics) SlidingWindowAggregator (class in vassi.sliding_metrics.transform) smooth() (ClassificationResult method) (in module vassi.series_operations) smooth_1d() (in module vassi.series_operations) SmoothingFunction (class in vassi.utils) sort() (TimestampedInstanceCollection method) speed() (in module vassi.features.temporal_features) split() (Dataset method) start() (Panel method) subsample() (SampleableMixin method) subtract() (in module vassi.math) summarize_experiment() (in module vassi.classification.postprocessing)

T

target (NestedSampleableMixin property) target_angles() (in module vassi.features.features) target_vectors() (in module vassi.features.features) target_velocity() (in module vassi.features.temporal_features) threshold() (ClassificationResult method) TimestampedInstanceCollection (class in vassi.data_structures.timestamped_collection) timestamps (ClassificationResult attribute) (TimestampedInstanceCollection property) timestep (Trajectory property) to_cache() (in module vassi.io) to_dataset() (DatasetClassificationResult method) to_h5() (ClassificationResult method) (DatasetClassificationResult method) (GroupClassificationResult method)

to_int_seed() (in module vassi.utils) to_observations() (in module vassi.dataset.observations.utils) to_predictions() (in module vassi.classification.utils) to_scalars() (in module vassi.utils) to_y() (in module vassi.dataset.observations.utils) to_yaml() (in module vassi.io) ToArray (class in vassi.utils) Trajectory (class in vassi.data_structures.trajectory) transform() (SlidingWindowAggregator method) translation() (in module vassi.features.temporal_features)

U

unit_vector() (in module vassi.math)

unsigned_angle() (in module vassi.math)

V

validate() (InstanceCollection method) validate_data() (InstanceCollection method) (Trajectory method) validate_keys() (in module vassi.data_structures.utils) validate_predictions() (in module vassi.classification.utils) validate_timestamps() (in module vassi.data_structures.utils) validated_length() (in module vassi.data_structures.utils) values() (BaseConfig method) (ConfiguredData method) vassi.case_studies module vassi.case_studies.calms21 module vassi.case_studies.calms21.convert module vassi.case_studies.calms21.download module vassi.case_studies.social_cichlids module vassi.case_studies.social_cichlids.download module vassi.classification module vassi.classification.postprocessing module vassi.classification.predict module vassi.classification.results module vassi.classification.utils module vassi.classification.visualization module vassi.config module vassi.data_structures module vassi.data_structures.base module vassi.data_structures.collection module vassi.data_structures.instance module vassi.data_structures.timestamped_collection module vassi.data_structures.trajectory module vassi.data_structures.utils module vassi.dataset module vassi.dataset.observations module vassi.dataset.observations.bouts module vassi.dataset.observations.utils module vassi.dataset.permute module

vassi.dataset.types module vassi.dataset.types.dataset module vassi.dataset.types.dyad module vassi.dataset.types.group module vassi.dataset.types.individual module vassi.dataset.types.mixins module vassi.dataset.types.mixins.annotated module vassi.dataset.types.mixins.annotated_sampleable module vassi.dataset.types.mixins.nested module vassi.dataset.types.mixins.sampleable module vassi.dataset.utils module vassi.distributed module vassi.features module vassi.features.decorators module vassi.features.feature_extractor module vassi.features.features module vassi.features.temporal_features module vassi.features.utils module vassi.io module vassi.logging module vassi.math module vassi.series_operations module vassi.sliding_metrics module vassi.sliding_metrics.metrics module vassi.sliding_metrics.sliding_metrics module vassi.sliding_metrics.transform module vassi.utils module vassi.visualization module velocity() (in module vassi.features.temporal_features)

W

width (Panel property) with_duration() (in module vassi.dataset.observations.utils)

with_loop() (in module vassi.logging) wrap_angle() (in module vassi.math) writeable() (in module vassi.data_structures.utils)

Y

y_pred_numeric (ClassificationResult attribute) y_proba (ClassificationResult attribute)

y_proba_smoothed (ClassificationResult property) y_true_numeric (ClassificationResult property)