bacpipe package

Subpackages

• bacpipe.core package
  • Submodules
  • bacpipe.core.audio_processor module
    • AudioHandler
      • AudioHandler.__init__()
      • AudioHandler.prepare_audio()
  • bacpipe.core.constants module
    • EMBEDDING_DIMENSIONS
    • NEEDS_CHECKPOINT
    • TF_MODELS
    • models_needing_checkpoint
    • supported_models
  • bacpipe.core.experiment_manager module
    • Loader
      • Loader.__init__()
      • Loader.classifier_should_be_run()
      • Loader.embeddings()
      • Loader.get_annotations_parquet()
      • Loader.get_audio_files()
      • Loader.get_embedding_dir()
      • Loader.get_preds_array()
      • Loader.predictions()
      • Loader.read_embedding_file()
      • Loader.save_embedding_file()
      • Loader.update_files()
      • Loader.write_metadata_file()
    • replace_default_kwargs_with_user_kwargs()
    • save_logs()
  • bacpipe.core.workflows module
    • cross_model_evaluation()
    • ensure_models_exist()
    • evaluation_with_settings_already_exists()
    • generate_embeddings()
    • get_model_names()
    • model_specific_evaluation()
    • play()
    • run_pipeline_for_models()
    • run_pipeline_for_single_model()
  • Module contents
• bacpipe.embedding_evaluation package
  • Subpackages
    • bacpipe.embedding_evaluation.clustering package
      • Submodules
      • bacpipe.embedding_evaluation.clustering.cluster module
      • Module contents
    • bacpipe.embedding_evaluation.probing package
      • Submodules
      • bacpipe.embedding_evaluation.probing.dataset_probe module
      • bacpipe.embedding_evaluation.probing.evaluate_probe module
      • bacpipe.embedding_evaluation.probing.inference_probe module
      • bacpipe.embedding_evaluation.probing.probe module
      • bacpipe.embedding_evaluation.probing.train_probe module
      • Module contents
    • bacpipe.embedding_evaluation.visualization package
      • Submodules
      • bacpipe.embedding_evaluation.visualization.dashboard module
      • bacpipe.embedding_evaluation.visualization.dashboard_utils module
      • bacpipe.embedding_evaluation.visualization.tooltips module
      • bacpipe.embedding_evaluation.visualization.visualize module
      • bacpipe.embedding_evaluation.visualization.visualize_embeddings module
      • bacpipe.embedding_evaluation.visualization.visualize_predictions module
      • bacpipe.embedding_evaluation.visualization.visualize_spectrograms module
      • Module contents
  • Submodules
  • bacpipe.embedding_evaluation.benchmark module
    • benchmark()
  • bacpipe.embedding_evaluation.label_embeddings module
    • DefaultLabels
      • DefaultLabels.__init__()
      • DefaultLabels.audio_file_name()
      • DefaultLabels.continuous_timestamp()
      • DefaultLabels.day_of_year()
      • DefaultLabels.default_classifier()
      • DefaultLabels.fill_remaining_labels()
      • DefaultLabels.generate()
      • DefaultLabels.get_datetimes()
      • DefaultLabels.parent_directory()
      • DefaultLabels.time_of_day()
    • assign_global_get_paths_function()
    • build_ground_truth_labels_by_file()
    • collect_ground_truth_labels()
    • concatenate_annotation_files()
    • create_Raven_annotation_table()
    • create_default_labels()
    • ensure_audio_files()
    • fill_all_labels_array()
    • filter_annotations_by_minimum_number_of_occurrences()
    • filter_df_by_filename()
    • fit_labels_to_embedding_timestamps()
    • get_default_labels()
    • get_dim_reduc_path_func()
    • get_dt_filename()
    • get_files_if_no_embeds()
    • get_ground_truth()
    • ground_truth_by_model()
    • load_labels_and_build_dict()
    • make_set_paths_func()
    • model_specific_embedding_path()
    • raven_tables_sanity_check()
  • Module contents
• bacpipe.imgs package
  • Module contents
• bacpipe.model_pipelines package
  • Subpackages
    • bacpipe.model_pipelines.feature_extractors package
      • Submodules
      • bacpipe.model_pipelines.feature_extractors.audiomae module
      • bacpipe.model_pipelines.feature_extractors.audioprotopnet module
      • bacpipe.model_pipelines.feature_extractors.aves_especies module
      • bacpipe.model_pipelines.feature_extractors.avesecho_passt module
      • bacpipe.model_pipelines.feature_extractors.bat module
      • bacpipe.model_pipelines.feature_extractors.batdetect2_clip_avg module
      • bacpipe.model_pipelines.feature_extractors.batdetect2_dets_avg module
      • bacpipe.model_pipelines.feature_extractors.beats module
      • bacpipe.model_pipelines.feature_extractors.biolingual module
      • bacpipe.model_pipelines.feature_extractors.birdaves_especies module
      • bacpipe.model_pipelines.feature_extractors.birdmae module
      • bacpipe.model_pipelines.feature_extractors.birdnet module
      • bacpipe.model_pipelines.feature_extractors.convnext_birdset module
      • bacpipe.model_pipelines.feature_extractors.google_whale module
      • bacpipe.model_pipelines.feature_extractors.hbdet module
      • bacpipe.model_pipelines.feature_extractors.insect459 module
      • bacpipe.model_pipelines.feature_extractors.insect66 module
      • bacpipe.model_pipelines.feature_extractors.mix2 module
      • bacpipe.model_pipelines.feature_extractors.naturebeats module
      • bacpipe.model_pipelines.feature_extractors.perch_bird module
      • bacpipe.model_pipelines.feature_extractors.perch_v2 module
      • bacpipe.model_pipelines.feature_extractors.protoclr module
      • bacpipe.model_pipelines.feature_extractors.rcl_fs_bsed module
      • bacpipe.model_pipelines.feature_extractors.surfperch module
      • bacpipe.model_pipelines.feature_extractors.vggish module
      • Module contents
  • Submodules
  • bacpipe.model_pipelines.model_utils module
    • ModelBaseClass
      • ModelBaseClass.__init__()
      • ModelBaseClass.prepare_inference()
      • ModelBaseClass.preprocessing()
    • check_if_cudnn_tensorflow_compatible()
  • bacpipe.model_pipelines.runner module
    • Classifier
      • Classifier.__init__()
      • Classifier.classify()
      • Classifier.filter_top_k_classifications()
      • Classifier.make_classification_dict()
      • Classifier.run_default_classifier()
      • Classifier.save_Raven_table()
      • Classifier.save_annotation_table()
      • Classifier.save_classifier_outputs()
    • Embedder
      • Embedder.__init__()
      • Embedder.batch_inference()
      • Embedder.embeddings_using_multithreading()
      • Embedder.get_embeddings_for_audio()
      • Embedder.get_embeddings_from_model()
      • Embedder.get_reduced_dimensionality_embeddings()
      • Embedder.init_dataloader()
      • Embedder.run_dimensionality_reduction_pipeline()
      • Embedder.run_inference_pipeline_sequentially()
      • Embedder.run_inference_pipeline_using_multithreading()
  • Module contents
• bacpipe.tests package
  • Submodules
  • bacpipe.tests.conftest module
    • check_if_already_dim_reduced()
    • check_if_already_processed()
    • device()
    • kwargs()
    • only_embed_annotations()
    • overwrite()
    • pytest_addoption()
    • pytest_generate_tests()
  • bacpipe.tests.test_embedding_creation module
    • test_benchmarking()
    • test_embedding_dimensions()
    • test_embedding_generation()
    • test_evaluation()
  • Module contents

Module contents