Index

_

__getitem__() (bacpipe.embedding_evaluation.probing.dataset_probe.ProbeDatasetLoader method), [1], [2] __init__() (bacpipe.core.audio_processor.AudioHandler method), [1], [2] (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Embedder method), [1] (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] (bacpipe.embedding_evaluation.probing.dataset_probe.ProbeDatasetLoader method), [1], [2] (bacpipe.embedding_evaluation.probing.train_probe.KNNProbe method), [1], [2] (bacpipe.embedding_evaluation.probing.train_probe.LinearProbe method), [1], [2] (bacpipe.Loader method) (bacpipe.model_pipelines.feature_extractors.insect66.SpectrogramCNN method), [1] (bacpipe.model_pipelines.model_utils.ModelBaseClass method), [1], [2] (bacpipe.model_pipelines.runner.Classifier method), [1], [2] (bacpipe.model_pipelines.runner.Embedder method), [1], [2]

A

accumulate_data() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader method), [1] accuracy_per_class() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] add_save_button() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] add_styling() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] all_models_page() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2]

apply_clfier_page() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] assign_global_get_paths_function() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] auc() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] audio_file_name() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] AudioHandler (class in bacpipe.core.audio_processor), [1], [2] AugmentMelSTFT (class in bacpipe.model_pipelines.feature_extractors.avesecho_passt), [1]

B

bacpipe module, [1] bacpipe.core module bacpipe.core.audio_processor module, [1], [2] bacpipe.core.constants module, [1] bacpipe.core.experiment_manager module, [1], [2] bacpipe.core.workflows module, [1], [2] bacpipe.embedding_evaluation module bacpipe.embedding_evaluation.benchmark module, [1], [2] bacpipe.embedding_evaluation.clustering module bacpipe.embedding_evaluation.clustering.cluster module, [1], [2] bacpipe.embedding_evaluation.label_embeddings module, [1], [2], [3] bacpipe.embedding_evaluation.probing module bacpipe.embedding_evaluation.probing.dataset_probe module, [1], [2] bacpipe.embedding_evaluation.probing.evaluate_probe module, [1], [2] bacpipe.embedding_evaluation.probing.inference_probe module, [1], [2] bacpipe.embedding_evaluation.probing.probe module, [1], [2] bacpipe.embedding_evaluation.probing.train_probe module, [1], [2] bacpipe.embedding_evaluation.visualization module bacpipe.embedding_evaluation.visualization.dashboard module, [1], [2] bacpipe.embedding_evaluation.visualization.dashboard_utils module, [1] bacpipe.embedding_evaluation.visualization.tooltips module, [1] bacpipe.embedding_evaluation.visualization.visualize module, [1], [2] bacpipe.embedding_evaluation.visualization.visualize_embeddings module, [1] bacpipe.embedding_evaluation.visualization.visualize_predictions module, [1] bacpipe.embedding_evaluation.visualization.visualize_spectrograms module, [1] bacpipe.imgs module bacpipe.model_pipelines module bacpipe.model_pipelines.feature_extractors module bacpipe.model_pipelines.feature_extractors.audiomae module, [1] bacpipe.model_pipelines.feature_extractors.audioprotopnet module, [1] bacpipe.model_pipelines.feature_extractors.aves_especies module, [1]

bacpipe.model_pipelines.feature_extractors.avesecho_passt module, [1] bacpipe.model_pipelines.feature_extractors.bat module, [1] bacpipe.model_pipelines.feature_extractors.batdetect2_clip_avg module, [1] bacpipe.model_pipelines.feature_extractors.batdetect2_dets_avg module, [1] bacpipe.model_pipelines.feature_extractors.beats module, [1] bacpipe.model_pipelines.feature_extractors.biolingual module, [1] bacpipe.model_pipelines.feature_extractors.birdaves_especies module, [1] bacpipe.model_pipelines.feature_extractors.birdmae module, [1] bacpipe.model_pipelines.feature_extractors.birdnet module, [1] bacpipe.model_pipelines.feature_extractors.convnext_birdset module, [1] bacpipe.model_pipelines.feature_extractors.google_whale module, [1] bacpipe.model_pipelines.feature_extractors.hbdet module, [1] bacpipe.model_pipelines.feature_extractors.insect459 module, [1] bacpipe.model_pipelines.feature_extractors.insect66 module, [1] bacpipe.model_pipelines.feature_extractors.mix2 module, [1] bacpipe.model_pipelines.feature_extractors.naturebeats module, [1] bacpipe.model_pipelines.feature_extractors.perch_bird module, [1] bacpipe.model_pipelines.feature_extractors.perch_v2 module, [1] bacpipe.model_pipelines.feature_extractors.protoclr module, [1] bacpipe.model_pipelines.feature_extractors.rcl_fs_bsed module, [1] bacpipe.model_pipelines.feature_extractors.surfperch module, [1] bacpipe.model_pipelines.feature_extractors.vggish module, [1] bacpipe.model_pipelines.model_utils module, [1], [2] bacpipe.model_pipelines.runner module, [1], [2] bacpipe.tests module bacpipe.tests.conftest module, [1] bacpipe.tests.test_embedding_creation module, [1], [2] batch_inference() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] BeatsModel (class in bacpipe.model_pipelines.feature_extractors.beats), [1] benchmark() (in module bacpipe) (in module bacpipe.embedding_evaluation.benchmark), [1], [2] build_ground_truth_labels_by_file() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] build_layout() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] build_model() (bacpipe.model_pipelines.feature_extractors.birdnet.Rebuilder method), [1]

C

change_input_options() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] check_if_already_dim_reduced() (in module bacpipe.tests.conftest), [1] check_if_already_processed() (in module bacpipe.tests.conftest), [1] check_if_cudnn_tensorflow_compatible() (in module bacpipe.model_pipelines.model_utils), [1], [2] Classifier (class in bacpipe.model_pipelines.runner), [1], [2] classifier_predictions() (bacpipe.model_pipelines.feature_extractors.audioprotopnet.Model method), [1] (bacpipe.model_pipelines.feature_extractors.avesecho_passt.Model method), [1] (bacpipe.model_pipelines.feature_extractors.bat.Model method), [1] (bacpipe.model_pipelines.feature_extractors.batdetect2_clip_avg.Model method), [1] (bacpipe.model_pipelines.feature_extractors.birdnet.Model method), [1] (bacpipe.model_pipelines.feature_extractors.convnext_birdset.Model method), [1] (bacpipe.model_pipelines.feature_extractors.google_whale.Model method), [1] (bacpipe.model_pipelines.feature_extractors.perch_v2.Model method), [1] classifier_should_be_run() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) classify() (bacpipe.model_pipelines.runner.Classifier method), [1], [2]

clustering_overview() (in module bacpipe.embedding_evaluation.visualization.visualize), [1], [2] clustering_panel() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] clustering_pipeline() (in module bacpipe) (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] collect_dim_reduced_embeds() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] collect_ground_truth_labels() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] compute_task_metrics() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] concatenate_annotation_files() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] config (in module bacpipe) continuous_timestamp() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] convert_numpy_types() (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] create_default_labels() (in module bacpipe) (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] create_Raven_annotation_table() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] create_specs() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot method), [1] cross_model_evaluation() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2]

D

darken_hex_color_bitwise() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] DashBoard (class in bacpipe.embedding_evaluation.visualization.dashboard), [1], [2] DashBoardHelper (class in bacpipe.embedding_evaluation.visualization.dashboard_utils), [1] data_split_by_labels() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] day_of_year() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3]

default_classifier() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] DefaultLabels (class in bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] DefaultLabels() (in module bacpipe) device() (in module bacpipe.tests.conftest), [1] dummy_image() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot static method), [1]

E

EmbedAndLabelLoader (class in bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] Embedder (class in bacpipe), [1] (class in bacpipe.model_pipelines.runner), [1], [2] EMBEDDING_DIMENSIONS (in module bacpipe.core.constants), [1] EMBEDDING_DIMENSIONS() (in module bacpipe) embedding_panel() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] embeddings() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) embeddings_using_multithreading() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] embeds_array_without_noise() (in module bacpipe.embedding_evaluation.probing.probe), [1], [2]

ensure_audio_files() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] ensure_models_exist() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] eval_clustering() (in module bacpipe) (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] eval_probe() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] eval_with_silhouette() (in module bacpipe) (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] evaluation_with_settings_already_exists() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] extra_repr() (bacpipe.model_pipelines.feature_extractors.avesecho_passt.AugmentMelSTFT method), [1]

F

fill_all_labels_array() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] fill_remaining_labels() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] filter_annotations_by_minimum_number_of_occurrences() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] filter_df_by_filename() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] filter_top_k_classifications() (bacpipe.model_pipelines.runner.Classifier static method), [1], [2] fit() (bacpipe.embedding_evaluation.probing.train_probe.KNNProbe method), [1], [2]

fit_labels_to_embedding_timestamps() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] forward() (bacpipe.embedding_evaluation.probing.train_probe.KNNProbe method), [1], [2] (bacpipe.embedding_evaluation.probing.train_probe.LinearProbe method), [1], [2] (bacpipe.model_pipelines.feature_extractors.audiomae.PatchEmbed_new method), [1] (bacpipe.model_pipelines.feature_extractors.avesecho_passt.AugmentMelSTFT method), [1] (bacpipe.model_pipelines.feature_extractors.protoclr.Normalization method), [1]

G

generate() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] generate_annotations_for_probing_task() (in module bacpipe.embedding_evaluation.probing.dataset_probe), [1], [2] generate_bar_plot() (in module bacpipe.embedding_evaluation.visualization.visualize), [1], [2] generate_embeddings() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] get_annotations_parquet() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) get_audio_files() (bacpipe.core.experiment_manager.Loader static method), [1], [2] (bacpipe.Loader static method) (in module bacpipe) get_classes() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader method), [1] get_clustering_models() (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] get_data() (bacpipe.embedding_evaluation.visualization.visualize_embeddings.EmbedAndLabelLoader method), [1] (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader method), [1] get_datetimes() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] get_default_labels() (in module bacpipe) (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] get_dim_reduc_path_func() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] get_dt_filename() (in module bacpipe) (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] get_embedding_dir() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method)

get_embeddings() (bacpipe.model_pipelines.feature_extractors.beats.BeatsModel method), [1] get_embeddings_for_audio() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] get_embeddings_from_model() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] get_files_if_no_embeds() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] get_ground_truth() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] get_labels_for_plot() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] get_mean_detection_features() (in module bacpipe.model_pipelines.feature_extractors.batdetect2_dets_avg), [1] get_model_names() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] get_nr_of_clusters() (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] get_output_shape() (bacpipe.model_pipelines.feature_extractors.audiomae.PatchEmbed_new method), [1] get_preds_array() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) get_reduced_dimensionality_embeddings() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] get_timestamps_per_embedding() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader method), [1] ground_truth_by_model() (in module bacpipe) (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3]

H

handle_click() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1]

handle_selection() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1]

I

init_dataloader() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] init_embed_figure() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1]

init_interactive_embed_plot() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] init_plot() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] init_widget() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] iterate_through_subtasks() (in module bacpipe.embedding_evaluation.visualization.visualize), [1], [2]

K

KNNProbe (class in bacpipe.embedding_evaluation.probing.train_probe), [1], [2]

kwargs() (in module bacpipe.tests.conftest), [1]

L

LinearProbe (class in bacpipe.embedding_evaluation.probing.train_probe), [1], [2] load_audio() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot method), [1] load_classification() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader method), [1]

load_labels_and_build_dict() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] load_results() (in module bacpipe.embedding_evaluation.visualization.visualize_predictions), [1] Loader (class in bacpipe) (class in bacpipe.core.experiment_manager), [1], [2]

M

macro_accuracy() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] macro_f1() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] make_classification_dict() (bacpipe.model_pipelines.runner.Classifier static method), [1], [2] make_set_paths_func() (in module bacpipe) (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] make_sidebar() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] micro_accuracy() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] micro_f1() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] Model (class in bacpipe.model_pipelines.feature_extractors.audiomae), [1] (class in bacpipe.model_pipelines.feature_extractors.audioprotopnet), [1] (class in bacpipe.model_pipelines.feature_extractors.aves_especies), [1] (class in bacpipe.model_pipelines.feature_extractors.avesecho_passt), [1] (class in bacpipe.model_pipelines.feature_extractors.bat), [1] (class in bacpipe.model_pipelines.feature_extractors.batdetect2_clip_avg), [1] (class in bacpipe.model_pipelines.feature_extractors.batdetect2_dets_avg), [1] (class in bacpipe.model_pipelines.feature_extractors.beats), [1] (class in bacpipe.model_pipelines.feature_extractors.biolingual), [1] (class in bacpipe.model_pipelines.feature_extractors.birdaves_especies), [1] (class in bacpipe.model_pipelines.feature_extractors.birdmae), [1] (class in bacpipe.model_pipelines.feature_extractors.birdnet), [1] (class in bacpipe.model_pipelines.feature_extractors.convnext_birdset), [1] (class in bacpipe.model_pipelines.feature_extractors.google_whale), [1] (class in bacpipe.model_pipelines.feature_extractors.hbdet), [1] (class in bacpipe.model_pipelines.feature_extractors.insect459), [1] (class in bacpipe.model_pipelines.feature_extractors.insect66), [1] (class in bacpipe.model_pipelines.feature_extractors.mix2), [1] (class in bacpipe.model_pipelines.feature_extractors.naturebeats), [1] (class in bacpipe.model_pipelines.feature_extractors.perch_bird), [1] (class in bacpipe.model_pipelines.feature_extractors.perch_v2), [1] (class in bacpipe.model_pipelines.feature_extractors.protoclr), [1] (class in bacpipe.model_pipelines.feature_extractors.rcl_fs_bsed), [1] (class in bacpipe.model_pipelines.feature_extractors.surfperch), [1] (class in bacpipe.model_pipelines.feature_extractors.vggish), [1] model_page() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] model_specific_embedding_path() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] model_specific_evaluation() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] ModelBaseClass (class in bacpipe.model_pipelines.model_utils), [1], [2] models_needing_checkpoint (in module bacpipe), [1] (in module bacpipe.core.constants), [1] models_needing_checkpoint() (in module bacpipe) module bacpipe, [1] bacpipe.core bacpipe.core.audio_processor, [1], [2] bacpipe.core.constants, [1] bacpipe.core.experiment_manager, [1], [2] bacpipe.core.workflows, [1], [2] bacpipe.embedding_evaluation bacpipe.embedding_evaluation.benchmark, [1], [2] bacpipe.embedding_evaluation.clustering bacpipe.embedding_evaluation.clustering.cluster, [1], [2] bacpipe.embedding_evaluation.label_embeddings, [1], [2], [3] bacpipe.embedding_evaluation.probing bacpipe.embedding_evaluation.probing.dataset_probe, [1], [2] bacpipe.embedding_evaluation.probing.evaluate_probe, [1], [2] bacpipe.embedding_evaluation.probing.inference_probe, [1], [2] bacpipe.embedding_evaluation.probing.probe, [1], [2] bacpipe.embedding_evaluation.probing.train_probe, [1], [2] bacpipe.embedding_evaluation.visualization bacpipe.embedding_evaluation.visualization.dashboard, [1], [2] bacpipe.embedding_evaluation.visualization.dashboard_utils, [1] bacpipe.embedding_evaluation.visualization.tooltips, [1] bacpipe.embedding_evaluation.visualization.visualize, [1], [2] bacpipe.embedding_evaluation.visualization.visualize_embeddings, [1] bacpipe.embedding_evaluation.visualization.visualize_predictions, [1] bacpipe.embedding_evaluation.visualization.visualize_spectrograms, [1] bacpipe.imgs bacpipe.model_pipelines bacpipe.model_pipelines.feature_extractors bacpipe.model_pipelines.feature_extractors.audiomae, [1] bacpipe.model_pipelines.feature_extractors.audioprotopnet, [1] bacpipe.model_pipelines.feature_extractors.aves_especies, [1] bacpipe.model_pipelines.feature_extractors.avesecho_passt, [1] bacpipe.model_pipelines.feature_extractors.bat, [1] bacpipe.model_pipelines.feature_extractors.batdetect2_clip_avg, [1] bacpipe.model_pipelines.feature_extractors.batdetect2_dets_avg, [1] bacpipe.model_pipelines.feature_extractors.beats, [1] bacpipe.model_pipelines.feature_extractors.biolingual, [1] bacpipe.model_pipelines.feature_extractors.birdaves_especies, [1] bacpipe.model_pipelines.feature_extractors.birdmae, [1] bacpipe.model_pipelines.feature_extractors.birdnet, [1] bacpipe.model_pipelines.feature_extractors.convnext_birdset, [1] bacpipe.model_pipelines.feature_extractors.google_whale, [1] bacpipe.model_pipelines.feature_extractors.hbdet, [1] bacpipe.model_pipelines.feature_extractors.insect459, [1] bacpipe.model_pipelines.feature_extractors.insect66, [1] bacpipe.model_pipelines.feature_extractors.mix2, [1] bacpipe.model_pipelines.feature_extractors.naturebeats, [1] bacpipe.model_pipelines.feature_extractors.perch_bird, [1] bacpipe.model_pipelines.feature_extractors.perch_v2, [1] bacpipe.model_pipelines.feature_extractors.protoclr, [1] bacpipe.model_pipelines.feature_extractors.rcl_fs_bsed, [1] bacpipe.model_pipelines.feature_extractors.surfperch, [1] bacpipe.model_pipelines.feature_extractors.vggish, [1] bacpipe.model_pipelines.model_utils, [1], [2] bacpipe.model_pipelines.runner, [1], [2] bacpipe.tests bacpipe.tests.conftest, [1] bacpipe.tests.test_embedding_creation, [1], [2]

N

NEEDS_CHECKPOINT (in module bacpipe.core.constants), [1]

NEEDS_CHECKPOINT() (in module bacpipe) Normalization (class in bacpipe.model_pipelines.feature_extractors.protoclr), [1]

O

only_embed_annotations() (in module bacpipe.tests.conftest), [1]

overwrite() (in module bacpipe.tests.conftest), [1]

P

parent_directory() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] PatchEmbed_new (class in bacpipe.model_pipelines.feature_extractors.audiomae), [1] play() (in module bacpipe), [1] (in module bacpipe.core.workflows), [1], [2] play_audio() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot method), [1] plot_classification_heatmap() (in module bacpipe.embedding_evaluation.visualization.visualize_predictions), [1] plot_classification_results() (in module bacpipe.embedding_evaluation.visualization.visualize_predictions), [1] plot_clusterings() (in module bacpipe.embedding_evaluation.visualization.visualize), [1], [2] plot_comparison() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] plot_embedding_points() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] plot_embeddings() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] plot_embeddings_px() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] plot_overview_metrics() (in module bacpipe.embedding_evaluation.visualization.visualize), [1], [2] plot_per_class_metrics() (in module bacpipe.embedding_evaluation.visualization.visualize_predictions), [1] plot_widget() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] predictions() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) PredictionsLoader (class in bacpipe.embedding_evaluation.visualization.visualize_predictions), [1] prepare_audio() (bacpipe.core.audio_processor.AudioHandler method), [1], [2] (bacpipe.Embedder method) prepare_inference() (bacpipe.model_pipelines.model_utils.ModelBaseClass method), [1], [2] prepare_probe_inference() (in module bacpipe) (in module bacpipe.embedding_evaluation.probing.inference_probe), [1], [2] (in module bacpipe.embedding_evaluation.probing.probe), [1], [2] preprocess() (bacpipe.model_pipelines.feature_extractors.audiomae.Model method), [1] (bacpipe.model_pipelines.feature_extractors.audioprotopnet.Model method), [1] (bacpipe.model_pipelines.feature_extractors.aves_especies.Model method), [1] (bacpipe.model_pipelines.feature_extractors.avesecho_passt.Model method), [1] (bacpipe.model_pipelines.feature_extractors.bat.Model method), [1] (bacpipe.model_pipelines.feature_extractors.batdetect2_clip_avg.Model method), [1] (bacpipe.model_pipelines.feature_extractors.batdetect2_dets_avg.Model method), [1] (bacpipe.model_pipelines.feature_extractors.beats.Model method), [1] (bacpipe.model_pipelines.feature_extractors.biolingual.Model method), [1] (bacpipe.model_pipelines.feature_extractors.birdmae.Model method), [1] (bacpipe.model_pipelines.feature_extractors.birdnet.Model method), [1] (bacpipe.model_pipelines.feature_extractors.convnext_birdset.Model method), [1] (bacpipe.model_pipelines.feature_extractors.hbdet.Model method), [1] (bacpipe.model_pipelines.feature_extractors.insect459.Model method), [1] (bacpipe.model_pipelines.feature_extractors.insect66.Model method), [1] (bacpipe.model_pipelines.feature_extractors.mix2.Model method), [1] (bacpipe.model_pipelines.feature_extractors.naturebeats.Model method), [1] (bacpipe.model_pipelines.feature_extractors.perch_v2.Model method), [1] (bacpipe.model_pipelines.feature_extractors.protoclr.Model method), [1] (bacpipe.model_pipelines.feature_extractors.rcl_fs_bsed.Model method), [1]

preprocessing() (bacpipe.model_pipelines.model_utils.ModelBaseClass method), [1], [2] probe_dataset_loader() (in module bacpipe.embedding_evaluation.probing.dataset_probe), [1], [2] ProbeDatasetLoader (class in bacpipe.embedding_evaluation.probing.dataset_probe), [1], [2] probing_panel() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] probing_pipeline() (in module bacpipe) (in module bacpipe.embedding_evaluation.probing.probe), [1], [2] pytest_addoption() (in module bacpipe.tests.conftest), [1] pytest_generate_tests() (in module bacpipe.tests.conftest), [1]

R

raven_tables_sanity_check() (in module bacpipe.embedding_evaluation.label_embeddings), [1], [2], [3] read_embedding_file() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) rebuild_layer() (bacpipe.model_pipelines.feature_extractors.birdnet.Rebuilder method), [1] Rebuilder (class in bacpipe.model_pipelines.feature_extractors.birdnet), [1] remove_noise_indices() (bacpipe.embedding_evaluation.visualization.visualize_embeddings.EmbedAndLabelLoader method), [1] reorder_by_most_occurrance() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader static method), [1] reorder_embeddings_by_clustering_performance() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] replace_default_kwargs_with_user_kwargs() (in module bacpipe.core.experiment_manager), [1], [2] return_rows_cols() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] run_clustering() (in module bacpipe) (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] run_default_classifier() (bacpipe.model_pipelines.runner.Classifier method), [1], [2]

run_dimensionality_reduction_pipeline() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] run_inference_pipeline_sequentially() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] run_inference_pipeline_using_multithreading() (bacpipe.Embedder method), [1] (bacpipe.model_pipelines.runner.Embedder method), [1], [2] run_pipeline_for_models() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] run_pipeline_for_single_model() (in module bacpipe) (in module bacpipe.core.workflows), [1], [2] run_probe_inference() (in module bacpipe) (in module bacpipe.embedding_evaluation.probing.inference_probe), [1], [2] (in module bacpipe.embedding_evaluation.probing.probe), [1], [2]

S

save_annotation_table() (bacpipe.model_pipelines.runner.Classifier method), [1], [2] save_classifier_outputs() (bacpipe.model_pipelines.runner.Classifier method), [1], [2] save_clustering_performance() (in module bacpipe.embedding_evaluation.clustering.cluster), [1], [2] save_embedding_file() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method) save_embedding_plot() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] save_logs() (in module bacpipe.core.experiment_manager), [1], [2] save_probe_results() (in module bacpipe.embedding_evaluation.probing.evaluate_probe), [1], [2] save_Raven_table() (bacpipe.model_pipelines.runner.Classifier method), [1], [2] save_selected_points() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1]

set_axis_lims_dep_sr() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot method), [1] set_colorbar_or_legend() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] set_figsize_for_comparison() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] set_legend() (in module bacpipe.embedding_evaluation.visualization.visualize_embeddings), [1] settings (in module bacpipe) spectrogram_panel() (bacpipe.embedding_evaluation.visualization.dashboard.DashBoard method), [1], [2] SpectrogramCNN (class in bacpipe.model_pipelines.feature_extractors.insect66), [1] SpectrogramPlot (class in bacpipe.embedding_evaluation.visualization.visualize_spectrograms), [1] supported_models (in module bacpipe), [1] (in module bacpipe.core.constants), [1] supported_models() (in module bacpipe)

T

test_benchmarking() (in module bacpipe.tests.test_embedding_creation), [1], [2] test_embedding_dimensions() (in module bacpipe.tests.test_embedding_creation), [1], [2] test_embedding_generation() (in module bacpipe.tests.test_embedding_creation), [1], [2] test_evaluation() (in module bacpipe.tests.test_embedding_creation), [1], [2] TF_MODELS (in module bacpipe.core.constants), [1]

TF_MODELS() (in module bacpipe) time_of_day() (bacpipe.embedding_evaluation.label_embeddings.DefaultLabels method), [1], [2], [3] train_knn_probe() (in module bacpipe.embedding_evaluation.probing.train_probe), [1], [2] train_linear_probe() (in module bacpipe.embedding_evaluation.probing.train_probe), [1], [2] train_probe() (in module bacpipe.embedding_evaluation.probing.train_probe), [1], [2] transform_presence_into_hour_heatmap() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader static method), [1]

U

update_files() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method)

update_main_plot() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1] update_spectrogram() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot method), [1] update_text() (bacpipe.embedding_evaluation.visualization.visualize_spectrograms.SpectrogramPlot method), [1]

V

verify_threshold() (bacpipe.embedding_evaluation.visualization.visualize_predictions.PredictionsLoader static method), [1] visualise_results_across_models() (in module bacpipe.embedding_evaluation.visualization.visualize), [1], [2]

visualize_using_dashboard() (in module bacpipe) (in module bacpipe.embedding_evaluation.visualization.dashboard), [1], [2]

W

widget() (bacpipe.embedding_evaluation.visualization.dashboard_utils.DashBoardHelper method), [1]

write_metadata_file() (bacpipe.core.experiment_manager.Loader method), [1], [2] (bacpipe.Loader method)