API Reference

Complete API documentation for harmonic analysis of biosignals.

The package is organized by kind — stateful pipeline classes first, then subpackages, then pure-function modules. Each module declares its kind in its docstring header (Module type: Functions / Object / Objects / Data / Subpackage). Not every Python module in the repository has a documentation page yet — pages are added as modules are cleaned up and stabilized.

Objects

Stateful pipeline classes — instantiate and call methods.

• Biotuner object
  • compute_biotuner
  • fit_biotuner()
• BiotunerGroup (BETA)
  • BiotunerGroup
  • Overview
  • Quick Start
  • Main Methods
  • See Also
• Harmonic connectivity
  • harmonic_connectivity
  • wPLI_crossfreq()
  • wPLI_multiband()
  • n_m_phase_locking()
  • cross_frequency_rrci()
  • compute_rhythmic_ratio()
  • rhythmic_ratio_coupling_imaginary()
  • HilbertHuang1D_nopeaks()
  • EMD_time_resolved_harmonicity()
  • temporal_correlation_fdr()
  • compute_cross_spectrum_harmonicity()
• Transitional Harmony
  • transitional_harmony
• Harmonic Sequence
  • biotuner/harmonic_sequence.py
  • TUNING_ATTRS
  • extract_tuning()
  • encode_histograms()
  • encode_scalar_metrics()
  • clear_harmonicity_cache()
  • encode_harmonicity_spectrum()
  • encode_harmonicity_matrices()
  • encode_ji_matrix()
  • histogram_to_ratios()
  • histogram_to_scl()
  • histograms_to_midi()
  • find_optimal_n_states()
  • HarmonicMarkov
  • WassersteinTrajectory
  • HarmonicDMD
  • HarmonicLatentSpace
  • HarmonicTopology
  • HarmonicGrammar
  • HarmonicSequenceAnalyzer

Subpackages

Folders with their own internal structure; each lists its submodules.

• Harmonic Geometry
  • biotuner.harmonic_geometry
  • Medium
  • Pipeline
  • Domain
  • Rectangular
  • Circular
  • PolygonDomain
  • Box3D
  • Sphere
  • RigidPlate
  • ClosedSurface
  • Elastic
  • PlasmaLattice
  • Interference
  • Acoustic
  • Faraday
  • Granular
  • Tracer
  • Streaming
  • Crystallization
  • ReactionDiffusion
  • GeometryData
  • GeomType
  • HarmonicInput
  • HarmonicSequence
  • lissajous_2d()
  • lissajous_3d()
  • lissajous_compound()
  • lissajous_pairwise_grid()
  • lissajous_phase_drift()
  • lissajous_topology()
  • derive_damping_from_linewidth()
  • harmonograph_3d()
  • harmonograph_from_peaks()
  • harmonograph_lateral()
  • harmonograph_rotary()
  • chladni_field_3d_box()
  • chladni_field_circular()
  • chladni_field_polygon()
  • chladni_field_rectangular()
  • chladni_from_input()
  • chladni_nodal_lines()
  • chladni_nodal_surfaces()
  • chladni_temporal()
  • ratios_to_modes()
  • ratios_to_modes_lm()
  • single_spherical_harmonic()
  • spherical_harmonic_field()
  • spherical_harmonic_from_input()
  • spherical_harmonic_mesh()
  • spherical_harmonic_temporal()
  • harmonic_interference_field_2d()
  • interference_field_2d()
  • quasicrystal_field_2d()
  • standing_wave_lattice_2d()
  • vortex_field_2d()
  • extend_harmonic_fit()
  • extend_harmonic_tuning()
  • extend_harmonics()
  • extend_subharmonics()
  • blend_fields()
  • fade_in_components()
  • interpolate_chords()
  • consonance_polygon()
  • epicycloid()
  • hypocycloid()
  • interval_vector_diagram()
  • polygon_chord_pattern()
  • rose_curve()
  • star_polygon()
  • times_table_circle()
  • times_table_from_input()
  • tuning_circle()
  • continued_fraction_rectangles()
  • farey_sequence_layout()
  • ifs_harmonic()
  • stern_brocot_tree()
  • subharmonic_tree()
  • geometry_sequence()
  • lsystem_from_ratios()
  • recursive_polygon()
  • self_similar_tuning()
  • harmonic_knot()
  • harmonic_point_cloud()
  • harmonic_surface()
  • lissajous_tube()
  • lsystem_3d()
  • recursive_polyhedron()
  • MetricsLog
  • compare()
  • geometry_metrics()
  • list_supported_kinds()
  • normalize_metrics()
  • sequence_metrics()
  • Submodules

Functions

Pure-function modules — import what you need.

Peak extraction & extension:

• Peaks Extraction
  • EMD_eeg()
  • SSA_EEG()
  • extract_welch_peaks()
  • compute_FOOOF()
  • HilbertHuang1D()
  • cepstrum()
  • cepstral_peaks()
  • compute_multitaper_psd()
  • sms_partials()
  • pac_frequencies()
  • polycoherence()
  • polyspectrum_frequencies()
  • harmonic_recurrence()
  • endogenous_intermodulations()
  • compute_sidebands()
  • UnivariateTransformerMixin
  • SingularSpectrumAnalysis
• Peaks Extension
  • EEG_harmonics_mult()
  • EEG_harmonics_div()
  • harmonic_fit()
  • intermodulation_spectrum()
  • multi_consonance()

Scale, rhythm & metrics:

• Harmonicity Metrics
  • compute_consonance()
  • euler()
  • tenneyHeight()
  • integral_tenneyHeight()
  • metric_denom()
  • dyad_similarity()
  • peaks_to_harmsim()
  • sum_p_q()
  • sum_distinct_intervals()
  • metric_3()
  • sum_p_q_for_all_intervals()
  • sum_q_for_all_intervals()
  • ratios2harmsim()
  • tuning_cons_matrix()
  • tuning_to_metrics()
  • timepoint_consonance()
  • compute_subharmonics()
  • compute_subharmonic_tension()
  • compute_subharmonics_2lists()
  • consonant_ratios()
  • consonance_peaks()
  • spectral_flatness()
  • spectral_entropy()
  • spectral_spread()
  • higuchi_fd()
• Scale construction
  • oct_subdiv()
  • compare_oct_div()
  • multi_oct_subdiv()
  • harmonic_tuning()
  • euler_fokker_scale()
  • convergents()
  • dissmeasure()
  • diss_curve()
  • compute_harmonic_entropy_domain_integral()
  • compute_harmonic_entropy_simple_weights()
  • harmonic_entropy()
  • tuning_reduction()
  • create_mode()
  • pac_mode()
  • tuning_range_to_MOS()
  • stern_brocot_to_generator_interval()
  • gen_interval_to_stern_brocot()
  • horogram_tree_steps()
  • horogram_tree()
  • phi_convergent_point()
  • Stern_Brocot()
  • generator_interval_tuning()
  • interval_exponents()
  • interval_to_radian()
  • tuning_to_radians()
  • tuning_MOS_info()
  • find_MOS()
  • MOS_metric_harmonic_mean()
  • generator_to_stern_brocot_fractions()
  • measure_symmetry()
• Rhythm construction
  • scale2euclid()
  • invert_ratio()
  • binome2euclid()
  • consonant_euclid()
  • interval_vector()
  • bjorklund()
  • interval_vec_to_string()
  • euclid_string_to_referent()
  • euclid_long_to_short()
  • find_optimal_offsets()
  • euclidean_rhythm()
  • visualize_rhythms()
  • scale2polyrhythm()
  • plot_polyrhythm_piano_roll()
  • plot_polyrhythm_coincidence()
  • plot_polyrhythm_coincidence_matrix()
  • polyrhythm_to_midi()
  • euclid_polyrhythm_to_midi()
  • polyrhythm_to_osc_score()
  • polyrhythm_send_osc()
  • polyrhythm_dump_osc_patterns()
  • scale2polyrhythm_iso()
  • scale2polyrhythm_harmonic()
  • evolve_phase_shift()
  • evolve_metric_modulation()
  • evolve_onset_interpolation()
  • evolve_density_ramp()
  • plot_rhythm_evolution()
  • plot_phase_shift_evolution()
  • scale2polyrhythm_continuous()
  • coincidences_continuous()
  • plot_polyrhythm_score()
  • plot_polyrhythm_phase_wheel()
  • polyrhythm_continuous_to_midi()
  • extract_coincidence_rhythm()
  • second_order_polyrhythm()
  • plot_second_order_polyrhythm()
  • voices_to_midi()
  • frames_to_midi()
  • metric_modulation_to_midi()
  • second_order_polyrhythm_to_midi()
  • beat_envelope()
  • beat_spectrogram()

Spectral analysis:

• Harmonic spectrum
  • compute_global_harmonicity()
  • compute_phase_values()
  • harmonicity_matrices()
  • get_harmonic_ratio()
  • compute_nm_plv()
  • PLV_comod()
  • count_theoretical_harmonic_partners()
  • compute_harmonic_power()
  • compute_phase_spectrum()
  • compute_resonance_values()
  • find_spectral_peaks()
  • harmonic_entropy()
  • harmonic_spectrum_plot_trial_corr()
  • harmonic_spectrum_plot_freq_corr()
  • harmonic_spectrum_plot_avg_corr()

Integrations:

• Biotuner MNE
  • biotuner_mne()

Statistics:

• Stats
  • Typical usage
  • ttest_groups()
  • ancova_groups()
  • compare_all_metrics()
  • correlate_metrics_peaks()
  • plot_stats_comparison()
• Surrogates
  • Typical usage
  • generate_surrogate()
  • generate_surrogate_data()
  • surrogate_group()
  • plot_surrogate_distributions()

Visualization:

• Plot Utils
  • Biotuner Plotting Utilities
  • plot_psd_peaks()
  • plot_emd_peaks()
  • plot_harmonic_peaks()
  • plot_peaks()
  • plot_tuning_dissonance()
  • plot_tuning_entropy()
  • plot_tuning()
  • plot_harmonic_fit()
  • plot_harmonic_position_mappings()
• Plot Config
  • Biotuner Plotting Configuration
  • set_biotuner_style()
  • reset_style()
  • get_color_palette()
  • get_emd_colors()
  • get_band_colors()
  • get_plot_config()
  • update_plot_config()
  • biotuner_style
• Harmonic Sequence Viz
  • biotuner/harmonic_sequence_viz.py
  • plot_histogram_heatmap()
  • plot_wasserstein_flux()
  • plot_wasserstein_matrix()
  • plot_markov_matrix()
  • plot_latent_trajectory()
  • plot_dmd_spectrum()
  • plot_topology_barcode()
  • plot_grammar_interval_heatmap()
  • plot_scenario_overview()
  • plot_comparison_flux()
  • plot_comparison_latent()
  • plot_comparison_summary()
  • plot_tda_grammar_grid()

Helpers:

• Biotuner utilities