supervised_phenotype_scoring

A local web application for anonymised, supervised scoring of birdsong phenotype traits (stereotypy, repeat propensity, …) by human raters.

Songs are extracted from audio recordings, stored in an HDF5 batch, served via a drag-and-drop ranking interface with interactive Plotly comparison panels, and aggregated into per-bird Elo scores with inter-rater reliability statistics.

See the project README on GitHub for installation, configuration, and step-by-step usage.

User Guide

• Usage Guide
  • Preparing a pairings file
  • Single-family workflow
  • Multi-family workflow
  • EC2 deployment for remote scorers
  • Scoring app interface
  • Output files reference

API Reference

• family_spec_generation
  • Public API
  • load_song_results()
  • resolve_audio_path()
  • read_audio_file()
  • bandpass()
  • smooth_envelope()
  • segment_notes()
  • score_song_candidate()
  • make_song_spectrogram()
  • spectrogram_for_plot()
  • plot_segmentation_summary()
  • safe_basename()
  • process_one_file()
  • build_spectrogram_pipeline()
  • load_birds_from_txt()
  • expand_bird_aliases()
  • main()
• prepare_batch
  • Usage
  • load_config()
  • load_existing_batch()
  • load_exclude_set()
  • load_bird_registry()
  • get_audio_duration()
  • plan_snippets()
  • compute_snippet()
  • write_hdf5()
  • main()
• export_batch
  • Usage
  • export_audio()
  • write_public_manifest()
  • main()
• prescreen_app
  • Usage
  • Output CSV columns
  • Labels
  • load_batch()
  • prescreen_csv_path()
  • load_existing_labels()
  • write_labels_csv()
  • read_spec_from_h5()
  • create_app()
  • main()
• run_pipeline
  • Usage
  • Pairings CSV
  • Pass-through options (forwarded to prepare_batch.py / export_batch.py)
  • load_pairings()
  • find_latest_batch_dir()
  • find_prescreen_csv()
  • today_batch_dir()
  • run()
  • phase1()
  • phase2()
  • main()
• ranking_app
  • Usage
  • Dependencies
  • ensure_sortable()
  • ensure_plotly()
  • load_batch()
  • load_previously_flagged()
  • build_session_pool()
  • new_scoring_session()
  • get_session()
  • save_session_to_disk()
  • next_batch()
  • create_app()
  • main()
• analyze_rankings
  • Usage
  • expected_score()
  • update_elo()
  • ranking_to_pairs()
  • load_sessions()
  • flag_fast_rounds()
  • collect_flagged_uids()
  • compute_elo()
  • scorer_ranking()
  • kendall_tau()
  • compute_irr()
  • compute_rank_consistency()
  • bird_averages()
  • role_summary()
  • write_csv()
  • write_flagged_csv()
  • write_consistency_csv()
  • write_summary()
  • plot_bird_elo()
  • plot_snippet_elo()
  • plot_rank_consistency()
  • plot_scorer_agreement()
  • analyze_one_trait()
  • main()
• printout_generator
  • Usage
  • build_bird_page()
  • build_answer_key()
  • main()
• upload_batch
  • Usage
  • Dependencies
  • get_s3_client()
  • upload_file()
  • upload_directory()
  • read_uid_list()
  • upload_manifest()
  • write_hosted_config()
  • main()
• make_test_batch
  • Usage
  • synthetic_spec()
  • synthetic_audio()
  • synthetic_freq_axis()
  • make_bird_list()
  • write_batch()
  • write_fake_sessions()
  • main()

Indices

• Index

• Module Index