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Resonant Fractal Nature Theory — a mathematical framework for coherent patterns on graph-coupled networks.

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© 2026 TNFR project — MIT licensed.DOI 10.5281/zenodo.17602860
docs
grammar
PHYSICS_VERIFICATION.md
API_CONTRACTS.mdCANONICAL_OZ_SEQUENCES.mdEMPIRICAL_CONFRONTATION_EEG.mdREADME.mdSTRUCTURAL_FIELDS_TETRAD.mdSTRUCTURAL_INTERFACE_THEORY.md
theory
APPLIED_STRUCTURAL_ANALYSIS.mdCATALOG_TYPE_HYGIENE_PROGRAMME.mdDISSIPATIVE_AND_OPEN_SYSTEMS.mdEMERGENT_ONTOLOGY.mdEXTENDED_FIELDS_AND_DERIVED_QUANTITIES.mdFUNDAMENTAL_THEORY.mdGAUGE_SYMMETRY_AND_UNIFICATION.mdGLOSSARY.mdMATHEMATICAL_DYNAMICS_BASIS.mdMINIMAL_STRUCTURAL_DEGREES.mdNUCLEUS_A_PRIME_LADDER_ATLAS.mdNUCLEUS_B_EQUIVARIANCE_OBSTRUCTIONS.mdPHYSICAL_REGIME_CORRESPONDENCES.mdREADME.mdREMESH_INFINITY_DERIVATION.mdSTRUCTURAL_CONSERVATION_THEOREM.mdSTRUCTURAL_OPERATORS.mdSTRUCTURAL_STABILITY_AND_DYNAMICS.mdTNFR_BSD_RESEARCH_NOTES.mdTNFR_HODGE_RESEARCH_NOTES.mdTNFR_NAVIER_STOKES_RESEARCH_NOTES.mdTNFR_NUMBER_THEORY.mdTNFR_P_VS_NP_RESEARCH_NOTES.mdTNFR_RIEMANN_RESEARCH_NOTES.mdTNFR_VARIATIONAL_PRINCIPLE.mdTNFR_YANG_MILLS_RESEARCH_NOTES.mdTNFR.pdfUNIFIED_GRAMMAR_RULES.md
factorization-lab
analysis
analyze_patterns.pycertificate_manifest.py
benchmarks
benchmark_analysis.pybenchmark_expansion_suite.pyfull_spectrum_factorization.pypaley_gap_extended.pypaley_gap_smoke.pytest_benchmark_suite.py
demos
experiment_contexts
exp_0b1663cd19b7.jsonexp_0bf0054b7474.jsonexp_75a4c8ca616a.jsonexp_848ee0fd1857.jsonexp_f6fe00562193.jsonexp_fdf3da424e1e.json
failure_telemetry_batch.pyfeedback_integration_demo.pyintegration_demo_snapshots.dbseed_management_integration_demo.pysnapshot_integration_demo.pytrajectory_143.jsontrajectory_77.jsontrajectory_89.jsontrajectory_91.jsontrajectory_97.json
docs
FACTORING_PLAYBOOK.mdFALSE_POSITIVE_TEST_SUITE.mdOPERATOR_CERTIFICATES.mdROADMAP.mdSPECTRAL_ROUTE.md
experiment_contexts
exp_cebe1d9e7d8e.json
notebooks
spectral_history.ipynb
scripts
run_false_positive_tests.py
tests
run_false_positive_test_suite.pytest_cli.pytest_false_positive_methodology.pytest_false_positive_verifier.pytest_feedback_integration.pytest_partitioning.pytest_seed_management.pytest_self_opt_support.pytest_snapshot_system.pytest_spectral_paley.pytest_verification_robustness.py
tnfr_factorization
__init__.pyapi.pycli.pyfailure_telemetry.pyfeedback_adapter.pyfeedback_integration.pypartitioning.pyself_opt_support.pyspectral_paley.py
demo_snapshots.dbLICENSE_SNAPSHOT.mdPACKAGE_SUMMARY.mdREADME.mdseed_management.pysnapshot_system.pytest_certificate_hashing.pytest_installation.pyverification_trajectory_77.json
benchmarks
analyze_tetrad_universality.pyb0star_alpha_canonical_product_graphs.pybenchmark_optimization_tracks.pybenchmark_utils.pyboundary_vibration.pybridge_primes_riemann.pychiral_involution.pycli_utils.pycoherence_projector_sense_index.pycommutant_bridge.pycomposition_arithmetic.pyconfinement_zones_test.pyconservation_law_validation.pydirected_paley_bridge.pyemergent_arithmetic_pulse.pyemergent_atom_dynamics.pyemergent_atomic_shells.pyemergent_base_dimension.pyemergent_dimension_dynamics.pyemergent_fractal_pulse.pyemergent_fractal_simplex_dimension.pyemergent_integers_symmetry.pyemergent_musical_nfr.pyemergent_nfr_geometry.pyemergent_nfr_where.pyemergent_rationals.pyemergent_rhythm.pyemergent_screening.pyemergent_shell_cardinals.pyemergent_shell_ordering.pyemergent_simplex_dimension.pyemergent_substrate_symmetry.pyequivariance_wall.pyexternal_phase_gate_validation.pyfield_methods_battery.pygolden_residue_remesh_bridge.pyintegrated_force_regime_study.pyinverse_spectrum_to_symmetry.pyk_phi_safety_demo.pykuramoto_farey_bridge.pymissing_piece_bridge.pymultichannel_interface_benchmark.pynavier_stokes_recipe_bridge.pynodal_propagator_residue_bridge.pyns_moment_hierarchy_cascade.pyoperational_irreducibility.pypaley_bridge.pyphase_curvature_investigation.pyphase_wall.pyphi_s_confinement_investigation.pyprimes_as_consequence.pypulse_phase_coherence_budget.pyREADME.mdremesh_infinity_riemann_baseline.pyremesh_infinity_riemann_composed.pyremesh_infinity_riemann_modified_graph.pyremesh_infinity_riemann_operator.pyremesh_infinity_riemann_spectral_basis.pyremesh_infinity_riemann_spectral_robustness.pyremesh_infinity_riemann_spectral.pyresidue_phase_vs_riemann.pystructural_interface_benchmark.pytemporal_interface_benchmark.pytetrad_results_aggregate.pyu2_destabilization_irreversibility.pyuniversality_clusters.pyxi_c_fast_experiment.py
primality-test
benchmarks
comprehensive_benchmark.py
docs
ADVANCED_INTEGRATION.mdmathematical_foundation.mdperformance_analysis.md
examples
advanced_examples.pybasic_usage.py
tnfr_primality
__init__.py__main__.pyadvanced_cli.pyadvanced_core.pycli.pyconstants.pycore.pyoptimized.py
MANIFEST.inPACKAGE_SUMMARY.mdREADME.mdRELEASE_NOTES_v1.0.mdsetup.pytest_installation.py
tests
core_physics
__init__.pytest_conservation_laws.pytest_delta_nfr_computation_paths.pytest_delta_nfr.pytest_dispersion_coherence_sign_invariance.pytest_emergent_constants_guard.pytest_lyapunov_operators.pytest_nodal_equation.pytest_structural_triad.py
data
replay_manifests
sample_run
_manifest_summary.json_manifest.json_partition_files.txt.gz
self_opt_validation
seed_alpha
paley.json
seed_beta
integration.json
seed_gamma
unknown.json
self_optimization
test_run
partitioned
test_run
test_run_p0.jsontest_run_p1.json
_manifest_summary.json_manifest.json
engines
test_pattern_discovery_manifest.pytest_self_optimization_engine.py
mathematics
__init__.pytest_autodiff.pytest_backends.pytest_dissipative_dynamics.pytest_epi.pytest_factory_patterns.pytest_metrics.pytest_navier_stokes_refounded.pytest_number_theory_canonical.pytest_operators.pytest_residue_networks.pytest_riemann_nodal_pulse.pytest_riemann_pulse_coherence.pytest_spaces.pytest_transforms.pytest_validator.py
operators
test_canonical_operators_modern.pytest_grammar_canon.pytest_grammar_canonical_consistency.pytest_grammar_dynamics.pytest_operator_contracts.pytest_operator_strategies.py
parallel
test_fractal_partition_manifest.py
physics
test_conservation_gauge_unification.pytest_dissipative_conservation.pytest_emergent_chemistry.pytest_field_cache_invalidation.pytest_gauge.pytest_phase_transition.pytest_signatures.pytest_spectral_conservation.pytest_structural_diffusion.pytest_structural_integrity.pytest_symplectic_substrate.pytest_tetrad_bounds.pytest_variational.pytest_yang_mills_closure.pytest_yang_mills_derivability.pytest_yang_mills_scaling.pytest_yang_mills_structural_gap.pytest_yang_mills_u6_sweep.py
scripts
test_run_self_opt_validation.pytest_run_self_optimization.py
sdk
__init__.pytest_simple_advanced.py
__init__.pyconftest.pyREADME.mdtest_breast_cancer_phase_gate_demo.pytest_classical_mechanics.pytest_distributed_fft.pytest_external_phase_gate_validation.pytest_factorization_entrypoint.pytest_multichannel_interface.pytest_nodal_optimizer.pytest_phase_gate_api.pytest_replay_register_manifest.pytest_signal_confrontation.pytest_structural_interface_api.pytest_structural_interface_baselines.pytest_structural_interface_benchmark.pytest_temporal_interface.pytest_vectorized_coherence_length_regression.pytest_wine_quality_phase_gate_demo.pyutils.py
examples
01_foundations
01_hello_world.py02_musical_resonance.py03_network_formation.py04_operator_sequences.py05_coherence_evolution.py06_network_topologies.py07_phase_transitions.py08_emergent_phenomena.py09_visualization_suite.py10_simplified_sdk_showcase.py
02_physics_regimes
11_classical_limit_comparison.py115_operator_contract_audit.py12_classical_mechanics_demo.py13_quantum_mechanics_demo.py14_uncertainty_and_interference.py15_train_crossing_demo.py17_conservation_law_demo.py26_gauge_structure_demo.py27_variational_principle_demo.py28_dissipative_systems_demo.py29_lyapunov_stability_demo.py30_self_optimization_demo.py31_mathematical_constants_basis.py33_complex_field_unification.py34_conservation_protocol_suite.py35_tetrad_irreducibility.py36_grammar_violation_detector.py37_operator_tetrad_synergy.py38_grammar_energy_landscape.py39_nodal_equation_decomposition.py
03_riemann_zeta
157_nodal_pulse_phase_attack.py41_von_mangoldt_zeta_demo.py42_riemann_zeros_as_resonances.py43_prime_ladder_hamiltonian_demo.py44_weil_explicit_formula_demo.py45_li_keiper_demo.py46_weil_tnfr_positivity_demo.py47_alpha_sweep_demo.py48_admissible_family_sweep_demo.py49_nodeaware_gauge_sweep_demo.py50_uniform_coercivity_demo.py51_adaptive_coercivity_demo.py52_paley_gap_coercivity_demo.py53_lyapunov_spectral_positivity_demo.py54_hilbert_polya_demo.py55_structural_zero_density_demo.py56_spectral_emergence_demo.py57_admissible_rescaling_demo.py58_oscillatory_correction_demo.py
04_riemann_L_twisted
59_dirichlet_l_function_demo.py60_dirichlet_l_continuation_demo.py61_dirichlet_l_hamiltonian_demo.py62_dirichlet_weil_explicit_formula_demo.py63_dirichlet_li_keiper_demo.py64_twisted_weil_positivity_demo.py65_twisted_alpha_sweep_demo.py66_twisted_admissible_family_sweep_demo.py67_twisted_nodeaware_gauge_sweep_demo.py68_twisted_hermite_family_demo.py69_twisted_coercivity_uniform_demo.py70_twisted_paley_gap_coercivity_demo.py71_twisted_lyapunov_spectral_demo.py72_twisted_hilbert_polya_demo.py73_twisted_structural_zero_density_demo.py74_twisted_spectral_emergence_demo.py75_twisted_admissible_rescaling_demo.py76_twisted_oscillatory_correction_demo.py
05_type_hygiene
77_remesh_infinity_residue_split_demo.py78_nuf_type_signature_demo.py79_epi_type_signature_demo.py80_phi_type_signature_demo.py81_dnfr_type_signature_demo.py82_remesh_window_type_signature_demo.py83_delta_phi_max_type_signature_demo.py84_coupling_weights_type_signature_demo.py85_tetrad_closure_signature_demo.py86_currents_closure_signature_demo.py87_aggregates_closure_signature_demo.py88_urules_consistency_signature_demo.py89_operator_catalog_discipline_signature_demo.py
06_navier_stokes
158_navier_stokes_two_face_refounded.py
07_number_theory
100_prime_families_orbits.py101_numbers_as_coupled_network.py102_nodal_flow_primes_equilibria.py116_nuf_emergent_prime_visibility.py146_primality_grammatical_inertness.py147_numbers_as_free_monoid_words.py148_capacity_arm_carries_von_mangoldt.py149_p14_is_the_capacity_arm_operator.py153_structural_frequency_rank_cyclotomy.py40_arithmetic_number_theory.py94_generative_number_construction.py95_primes_from_spectral_waves.py96_spectral_vibration_of_coherence.py97_goldbach_additive_multiplicative.pyemergent_chemistry_particles_demo.py
08_emergent_geometry
103_emergent_substrate_meets_riemann.py106_per_node_polarization_geometry.py107_orthogonal_structure_emergent_geometry.py108_emergent_field_generating_structure.py112_structure_predicts_coherence_flow.py113_overdamped_projection_bridge.py114_substrate_conserved_quantities.py117_emergent_geometry_residue_graph.py118_emergent_vs_classical_operator.py119_phase_sector_directed_residue.py120_symmetry_wall_substrate_vs_spectrum.py121_canonical_symmetry_break_negative.py122_factorization_phase_sector.py123_symmetry_sector_decomposition.py124_emergent_metric_fractal_consistency.py125_node_is_the_emergent_substrate.py126_two_layers_base_fiber.py127_base_is_emergent_not_imposed.py128_base_substrate_coemergence.py129_spectral_gap_base_fiber_clock.py130_operators_break_substrate_charges.py131_coemergent_loop_convergence.py132_geometric_phase_holonomy.py133_psi_topological_defects.py134_spectral_dimension_heat_kernel.py135_arrow_of_time_h_theorem.py136_heat_kernel_coefficients.py137_synchronization_transition.py138_structure_frequency_synchronization.py139_grammar_formal_language.py140_grammar_automaton.py141_grammar_rule_decomposition.py142_grammar_operator_quotient.py143_glyphic_function_sublanguage.py144_branching_combinator.py145_syntactic_monoid_starfree.py150_emergent_grammatical_pattern_parry.py151_grammar_in_emergent_geometry.py152_operator_contract_tetrahedron.py154_conductor_annotated_qr_spectrum.py155_ontological_position_of_numbers.py156_emergence_directness_law.py98_emergent_symplectic_substrate.py99_structural_diffusion.pyunified_fields_showcase.py
09_millennium
109_p_vs_np_coherence_synthesis.py110_bsd_rank_structural_pressure.py111_hodge_discrete_and_honest_gap.py
10_applications
159_empirical_confrontation_pipeline.py90_phase_gate_monitor_demo.py91_breast_cancer_phase_gate_demo.py92_wine_quality_phase_gate_demo.py93_structural_interface_demo.pypytorch_cuda_demo.py
README.md
scripts
replay
__init__.pyregister_manifest.py
__init__.pyREADME.mdrebuild_failure_manifest.pyrun_reproducible_benchmarks.pyrun_self_opt_validation.pyrun_self_optimization.pytnfr_is_prime.pyvalidate_conservation_law.pyverify_internal_references.py
src
core
__init__.pyevaluation.py
tnfr
backends
__init__.pyjax_backend.pynumpy_backend.pyoptimized_numpy.pyREADME.mdtorch_backend.py
cli
__init__.py__init__.pyiarguments.pyarguments.pyiexecution.pyexecution.pyiinteractive_validator.pyREADME.mdutils.pyutils.pyi
compat
__init__.pydataclass.pyjsonschema_stub.pymatplotlib_stub.pynumpy_stub.pyREADME.md
config
__init__.py__init__.pyiconstants.pyconstants.pyidefaults_core.pydefaults_init.pydefaults_metric.pydefaults.pyfeature_flags.pyfeature_flags.pyiglyph_constants.pyoperator_names.pyoperator_names.pyiphysics_derivation.pyprecision_modes.pypresets.pypresets.pyiREADME.mdsecurity.pythresholds.pytnfr_config.py
constants
__init__.py__init__.pyialiases.pyaliases.pyicanonical.pymetric.pymetric.pyioperational.py
core
__init__.pycontainer.pydefault_implementations.pyexceptions.pyinterfaces.pyREADME.md
dynamics
__init__.py__init__.pyiadaptation.pyadaptation.pyiadaptive_sequences.pyadaptive_sequences.pyiadelic.pyadvanced_cache_optimizer.pyadvanced_fft_arithmetic.pyaliases.pyaliases.pyibifurcation.pycache_aware_fft_engine.pycanonical.pycanonical.pyicomputational_hub.pycoordination.pycoordination.pyidistributed_fft.pydnfr.pydnfr.pyidynamic_limits.pyemergent_centralization.pyemergent_integration_engine.pyfeedback.pyfeedback.pyifft_backend.pyfft_cache_coordinator.pyfft_dispatchers.pyfft_engine.pyfft_workers.pyfused_dnfr.pyhomeostasis.pyhomeostasis.pyiintegrators.pyintegrators.pyilearning.pylearning.pyimetabolism.pymulti_modal_cache.pynbody_tnfr.pynbody.pynodal_optimizer.pyoptimization_orchestrator.pypropagation.pyREADME.mdruntime.pyruntime.pyisampling.pysampling.pyiselectors.pyselectors.pyiself_optimizing_engine.pyspectral_structural_fusion.pystructural_cache.pystructural_clip.pysymplectic.pyunified_backend.pyunified_mathematical_cache_orchestrator.py
engines
computation
__init__.pyfft_engine.pyunified_fft_engine.pyunified_gpu_system.py
constants
__init__.pycanonical.pyoperational.py
integration
__init__.pyemergent_integration.py
pattern_discovery
__init__.pymathematical_patterns.pymulti_modal_cache.py
self_optimization
__init__.pyengine.py
__init__.pyREADME.md
errors
__init__.pycontextual.py
factorization
__init__.py
flatten
README.md
gamma
README.md
glyph_history
README.md
glyph_runtime
README.md
immutable
README.md
initialization
README.md
io
README.md
math
__init__.pyfields_symbolic.pygrammar_validators.pyoptimizer.pyREADME.mdsymbolic.py
mathematics
__init__.pybackend.pybackend.pyidynamics.pydynamics.pyiepi.pyepi.pyigenerators.pygenerators.pyiliouville.pymetrics.pymetrics.pyinumber_theory.pyoperators_factory.pyoperators_factory.pyioperators.pyoperators.pyioptimized_primality.pyprojection.pyprojection.pyiREADME.mdruntime.pyruntime.pyispaces.pyspaces.pyispectral.pytransforms.pytransforms.pyiunified_cache.pyunified_numerical.pyzeta.py
metrics
__init__.py__init__.pyibuffer_cache.pybuffer_cache.pyicache_utils.pycoherence.pycoherence.pyicommon.pycommon.pyicore.pycore.pyidiagnosis.pydiagnosis.pyiemergence.pyexport.pyexport.pyiglyph_timing.pyglyph_timing.pyilearning_metrics.pylearning_metrics.pyilocal_coherence.pyphase_coherence.pyphase_compatibility.pyREADME.mdreporting.pyreporting.pyisense_index.pysense_index.pyitelemetry.pytetrad.pytrig_cache.pytrig_cache.pyitrig.pytrig.pyi
multiscale
__init__.pyhierarchical.pyREADME.md
navier_stokes
__init__.pyconservative_face.pyoperator.py
node
README.md
observers
README.md
operators
network_analysis
__init__.pysource_detection.py
postconditions
__init__.pymutation.py
preconditions
__init__.pycoherence.pydissonance.pyemission.pymutation.pyreception.pyresonance.py
strategies
__init__.pydefaults.pygpu_strategies.pystrategy.py
__init__.py__init__.pyialgebra.pycanonical_patterns.pycascade.pycoherence.pycontraction.pycoupling.pycycle_detection.pydefinitions_base.pydefinitions.pydefinitions.pyidissonance.pyemission.pyexpansion.pygrammar_application.pygrammar_canon.pygrammar_context.pygrammar_core.pygrammar_dynamics.pygrammar_error_factory.pygrammar_memoization.pygrammar_patterns.pygrammar_telemetry.pygrammar_types.pygrammar_u6.pygrammar_validate.pygrammar.pygrammar.pyihamiltonian.pyhealth_analyzer.pyintrospection.pyjitter.pyjitter.pyilifecycle.pymetabolism.pymetrics_basic.pymetrics_core.pymetrics_network.pymetrics_structural.pymetrics_u6.pymetrics.pymutation.pynodal_equation.pyoperator_contracts.pypattern_detection.pypatterns.pyREADME.mdreception.pyrecursivity.pyregistry.pyregistry.pyiremesh.pyremesh.pyiresonance.pyself_organization.pysilence.pystructural_units.pytransition.py
parallel
__init__.pyauto_scaler.pydistributed.pyengine.pymonitoring.pypartitioner.pyREADME.md
performance
guardrails.py
physics
__init__.py_helpers.pycalibration.pycanonical.pycell.pyclassical_mechanics.pyconservation_gauge_unification.pyconservation.pydissipative_conservation.pyemergent_chemistry.pyemergent_particles.pyextended.pyfields.pygauge.pyintegrity.pyinteractions.pylife.pylyapunov.pypatterns.pyphase_transition.pyquantum_mechanics.pyREADME.mdsignatures.pyspectral_conservation.pyspectral_metrics.pystructural_diffusion.pysymplectic_substrate.pytelemetry.pyunified.pyvariational.pyvectorized_ops.py
primality
__init__.py
recipes
__init__.pycookbook.pyREADME.md
riemann
__init__.pyadmissible_family_sweep.pyadmissible_rescaling.pyaggregates_closure_signature.pyalpha_sweep.pyanalytic_continuation_dirichlet.pyanalytic_continuation.pycoercivity_uniform.pycoupling_weights_type_signature.pycurrents_closure_signature.pydelta_phi_max_type_signature.pydirichlet_l.pydnfr_type_signature.pyepi_type_signature.pyhilbert_polya.pyli_keiper.pylyapunov_spectral_positivity.pynodal_pulse.pynodeaware_gauge_sweep.pynuf_type_signature.pyoperator_catalog_discipline_signature.pyoperator.pyoscillatory_correction.pypaley_gap_coercivity.pyphi_type_signature.pyprime_ladder_hamiltonian.pypulse_coherence.pyremesh_infinity_residue_split.pyremesh_window_type_signature.pyspectral_emergence.pystructural_zero_density.pytelemetry.pytetrad_closure_signature.pytwisted_admissible_family_sweep.pytwisted_admissible_rescaling.pytwisted_alpha_sweep.pytwisted_coercivity_uniform.pytwisted_hermite_family.pytwisted_hilbert_polya.pytwisted_li_keiper.pytwisted_lyapunov_spectral_positivity.pytwisted_nodeaware_gauge_sweep.pytwisted_oscillatory_correction.pytwisted_paley_gap_coercivity.pytwisted_prime_ladder_hamiltonian.pytwisted_spectral_emergence.pytwisted_structural_zero_density.pytwisted_weil_explicit_formula.pytwisted_weil_positivity.pyurules_consistency_signature.pyvon_mangoldt.pyweil_explicit_formula.pyweil_positivity.py
schemas
__init__.pygrammar.jsonREADME.md
sdk
__init__.py__init__.pyiadaptive_system.pyadaptive_system.pyibuilders.pybuilders.pyifluent.pyfluent.pyiREADME.mdself_opt.pysimple.pytemplates.pytemplates.pyiutils.py
security
__init__.pycrypto.pydatabase.pyREADME.mdsubprocess.pyvalidation.py
sequencing
__init__.pypatterns.pyREADME.md
services
__init__.pyorchestrator.pyREADME.md
sparse
__init__.pyREADME.mdrepresentations.py
structural
README.md
telemetry
__init__.pycache_metrics.pycache_metrics.pyiconstants.pynu_f.pynu_f.pyiREADME.mdunified_telemetry_system.pyverbosity.pyverbosity.pyi
tools
__init__.pydomain_templates.pyREADME.mdsequence_generator.pytnfr_is_prime_cli_optimized.pytnfr_is_prime_cli.py
topology
__init__.pyasymmetry.pyREADME.md
utils
cache_layers.pycache.pycache.pyicallbacks.pycallbacks.pyichunks.pychunks.pyidata.pydata.pyifast_diameter.pygraph.pygraph.pyiinit.pyinit.pyiio.pyio.pyinumeric.pynumeric.pyiREADME.mdtopology.pyunified_cache.py
validation
__init__.py__init__.pyiaggregator.pybase.pycompatibility.pycompatibility.pyiconfig.pygraph.pygraph.pyihealth.pyinput_validation.pyinterface_baselines.pyinvariants.pymultichannel_interface.pyphase_gate.pyREADME.mdrules.pyrules.pyiruntime.pyruntime.pyisequence_validator.pysignal_confrontation.pysoft_filters.pysoft_filters.pyispectral.pyspectral.pyistructural_interface.pytemporal_interface.pyunified_validation_system.pyvalidator.pywindow.pywindow.pyi
visualization
__init__.pycascade_viz.pyhierarchy.pyREADME.mdsequence_plotter.py
yang_mills
__init__.pyclosure.pyderivability.pyscaling.pystructural_gap.pyu6_sweep.py
__init__.py__init__.pyi_compat.py_version.py_version.pyialias.pyalias.pyibackend_config.pycache.pycache.pyiexecution.pyexecution.pyiflatten.pyflatten.pyigamma.pygamma.pyiglyph_history.pyglyph_history.pyiglyph_runtime.pyglyph_runtime.pyiimmutable.pyimmutable.pyiinitialization.pyinitialization.pyiio.pyio.pyilocking.pylocking.pyinode.pynode.pyiobservers.pyobservers.pyiontosim.pyontosim.pyipy.typedrng.pyrng.pyisecure_config.pyselector.pyselector.pyisense.pysense.pyistructural.pystructural.pyitokens.pytokens.pyitrace.pytrace.pyitypes.pytypes.pyiunits.pyunits.pyi
tetrad_evaluator.py
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FILE: src/tnfr/metrics/trig.py

trig.py

Trigonometric helpers shared across metrics and helpers.

This module focuses on mathematical utilities (means, compensated sums, etc.). Caching of cosine/sine values lives in :mod:tnfr.metrics.trig_cache.

Source Code

python
"""Trigonometric helpers shared across metrics and helpers.

This module focuses on mathematical utilities (means, compensated sums, etc.).
Caching of cosine/sine values lives in :mod:`tnfr.metrics.trig_cache`.
"""

from __future__ import annotations

import math
from collections.abc import Iterable, Iterator, Sequence
from itertools import tee
from typing import TYPE_CHECKING, Any, cast, overload

from ..errors import TNFRValueError
from ..mathematics.unified_numerical import np
from ..types import NodeId, Phase, TNFRGraph
from ..utils import cached_import, kahan_sum_nd

if TYPE_CHECKING:  # pragma: no cover - typing only
    from ..node import NodeProtocol

__all__ = (
    "accumulate_cos_sin",
    "_phase_mean_from_iter",
    "_neighbor_phase_mean_core",
    "_neighbor_phase_mean_generic",
    "neighbor_phase_mean_bulk",
    "neighbor_phase_mean_list",
    "neighbor_phase_mean",
)


def accumulate_cos_sin(
    it: Iterable[tuple[float, float] | None],
) -> tuple[float, float, bool]:
    """Accumulate cosine and sine pairs with compensated summation.

    ``it`` yields optional ``(cos, sin)`` tuples. Entries with ``None``
    components are ignored. The returned values are the compensated sums of
    cosines and sines along with a flag indicating whether any pair was
    processed.
    """

    processed = False

    def iter_real_pairs() -> Iterator[tuple[float, float]]:
        nonlocal processed
        for cs in it:
            if cs is None:
                continue
            c, s = cs
            if c is None or s is None:
                continue
            try:
                c_val = float(c)
                s_val = float(s)
            except (TypeError, ValueError):
                continue
            if not (math.isfinite(c_val) and math.isfinite(s_val)):
                continue
            processed = True
            yield (c_val, s_val)

    sum_cos, sum_sin = kahan_sum_nd(iter_real_pairs(), dims=2)

    if not processed:
        return 0.0, 0.0, False

    return sum_cos, sum_sin, True


def _phase_mean_from_iter(
    it: Iterable[tuple[float, float] | None], fallback: float
) -> float:
    """Return circular mean from an iterator of cosine/sine pairs.

    ``it`` yields optional ``(cos, sin)`` tuples. ``fallback`` is returned if
    no valid pairs are processed.
    """

    sum_cos, sum_sin, processed = accumulate_cos_sin(it)
    if not processed:
        return fallback
    return math.atan2(sum_sin, sum_cos)


def _neighbor_phase_mean_core(
    neigh: Sequence[Any],
    cos_map: dict[Any, float],
    sin_map: dict[Any, float],
    fallback: float,
) -> float:
    """Return circular mean of neighbour phases given trig mappings."""

    def _iter_pairs() -> Iterator[tuple[float, float]]:
        for v in neigh:
            c = cos_map.get(v)
            s = sin_map.get(v)
            if c is not None and s is not None:
                yield c, s

    pairs = _iter_pairs()

    if np is not None:
        cos_iter, sin_iter = tee(pairs, 2)
        cos_arr = np.fromiter((c for c, _ in cos_iter), dtype=float)
        sin_arr = np.fromiter((s for _, s in sin_iter), dtype=float)
        if cos_arr.size:
            mean_cos = float(np.mean(cos_arr))
            mean_sin = float(np.mean(sin_arr))
            return float(np.arctan2(mean_sin, mean_cos))
        return fallback

    sum_cos, sum_sin, processed = accumulate_cos_sin(pairs)
    if not processed:
        return fallback
    return math.atan2(sum_sin, sum_cos)


def _neighbor_phase_mean_generic(
    obj: "NodeProtocol" | Sequence[Any],
    cos_map: dict[Any, float] | None = None,
    sin_map: dict[Any, float] | None = None,
    fallback: float = 0.0,
) -> float:
    """Compute the neighbour phase mean via :func:`_neighbor_phase_mean_core`.

    ``obj`` may be either a node bound to a graph or a sequence of neighbours.
    When ``cos_map`` and ``sin_map`` are ``None`` the function assumes ``obj`` is
    a node and obtains the required trigonometric mappings from the cached
    structures. Otherwise ``obj`` is treated as an explicit neighbour
    sequence and ``cos_map``/``sin_map`` must be provided.
    """

    if cos_map is None or sin_map is None:
        node = cast("NodeProtocol", obj)
        if getattr(node, "G", None) is None:
            raise TypeError("neighbor_phase_mean requires nodes bound to a graph")
        from .trig_cache import get_trig_cache

        trig = get_trig_cache(node.G)
        fallback = trig.theta.get(node.n, fallback)
        cos_map = trig.cos
        sin_map = trig.sin
        neigh = node.G[node.n]
    else:
        neigh = cast(Sequence[Any], obj)

    return _neighbor_phase_mean_core(neigh, cos_map, sin_map, fallback)


def neighbor_phase_mean_list(
    neigh: Sequence[Any],
    cos_th: dict[Any, float],
    sin_th: dict[Any, float],
    fallback: float = 0.0,
) -> float:
    """Return circular mean of neighbour phases from cosine/sine mappings.

    This is a thin wrapper over :func:`_neighbor_phase_mean_generic` that
    operates on explicit neighbour lists.
    """

    return _neighbor_phase_mean_generic(
        neigh, cos_map=cos_th, sin_map=sin_th, fallback=fallback
    )


def neighbor_phase_mean_bulk(
    edge_src: Any,
    edge_dst: Any,
    *,
    cos_values: Any,
    sin_values: Any,
    theta_values: Any,
    node_count: int,
    neighbor_cos_sum: Any | None = None,
    neighbor_sin_sum: Any | None = None,
    neighbor_counts: Any | None = None,
    mean_cos: Any | None = None,
    mean_sin: Any | None = None,
) -> tuple[Any, Any]:
    """Vectorised neighbour phase means for all nodes in a graph.

    Parameters
    ----------
    edge_src, edge_dst:
        Arrays describing the source (neighbour) and destination (node) indices
        for each edge contribution. They must have matching shapes.
    cos_values, sin_values:
        Arrays containing the cosine and sine values of each node's phase. The
        arrays must be indexed using the same positional indices referenced by
        ``edge_src``.
    theta_values:
        Array with the baseline phase for each node. Positions that do not have
        neighbours reuse this baseline as their mean phase.
    node_count:
        Total number of nodes represented in ``theta_values``.

    Optional buffers
    -----------------
    neighbor_cos_sum, neighbor_sin_sum, neighbor_counts, mean_cos, mean_sin:
        Preallocated arrays sized ``node_count`` reused to accumulate the
        neighbour cosine/sine sums, neighbour sample counts, and the averaged
        cosine/sine vectors. When omitted, the helper materialises fresh
        buffers that match the previous semantics.

    Returns
    -------
    tuple[Any, Any]
        tuple ``(mean_theta, has_neighbors)`` where ``mean_theta`` contains the
        circular mean of neighbour phases for every node and ``has_neighbors``
        is a boolean mask identifying which nodes contributed at least one
        neighbour sample.
    """

    if node_count <= 0:
        empty_mean = np.zeros(0, dtype=float)
        return empty_mean, empty_mean.astype(bool)

    edge_src_arr = np.asarray(edge_src, dtype=np.intp)
    edge_dst_arr = np.asarray(edge_dst, dtype=np.intp)

    if edge_src_arr.shape != edge_dst_arr.shape:
        raise TNFRValueError(
            "edge_src and edge_dst must share the same shape",
            context={"src_shape": edge_src_arr.shape, "dst_shape": edge_dst_arr.shape},
        )

    theta_arr = np.asarray(theta_values, dtype=float)
    if theta_arr.ndim != 1 or theta_arr.size != node_count:
        raise TNFRValueError(
            "theta_values must be a 1-D array matching node_count",
            context={"shape": theta_arr.shape, "expected_size": node_count},
        )

    cos_arr = np.asarray(cos_values, dtype=float)
    sin_arr = np.asarray(sin_values, dtype=float)
    if cos_arr.ndim != 1 or cos_arr.size != node_count:
        raise TNFRValueError(
            "cos_values must be a 1-D array matching node_count",
            context={"shape": cos_arr.shape, "expected_size": node_count},
        )
    if sin_arr.ndim != 1 or sin_arr.size != node_count:
        raise TNFRValueError(
            "sin_values must be a 1-D array matching node_count",
            context={"shape": sin_arr.shape, "expected_size": node_count},
        )

    edge_count = edge_dst_arr.size

    def _coerce_buffer(buffer: Any | None, *, name: str) -> tuple[Any, bool]:
        if buffer is None:
            return None, False
        arr = np.array(buffer, dtype=float, copy=False)
        if arr.ndim != 1 or arr.size != node_count:
            raise TNFRValueError(
                f"{name} must be a 1-D array sized node_count",
                context={"name": name, "shape": arr.shape, "expected_size": node_count},
            )
        arr.fill(0.0)
        return arr, True

    neighbor_cos_sum, has_cos_buffer = _coerce_buffer(
        neighbor_cos_sum, name="neighbor_cos_sum"
    )
    neighbor_sin_sum, has_sin_buffer = _coerce_buffer(
        neighbor_sin_sum, name="neighbor_sin_sum"
    )
    neighbor_counts, has_count_buffer = _coerce_buffer(
        neighbor_counts, name="neighbor_counts"
    )

    if edge_count:
        cos_bincount = np.bincount(
            edge_dst_arr,
            weights=cos_arr[edge_src_arr],
            minlength=node_count,
        )
        sin_bincount = np.bincount(
            edge_dst_arr,
            weights=sin_arr[edge_src_arr],
            minlength=node_count,
        )
        count_bincount = np.bincount(
            edge_dst_arr,
            minlength=node_count,
        ).astype(float, copy=False)

        if not has_cos_buffer:
            neighbor_cos_sum = cos_bincount
        else:
            np.copyto(neighbor_cos_sum, cos_bincount)

        if not has_sin_buffer:
            neighbor_sin_sum = sin_bincount
        else:
            np.copyto(neighbor_sin_sum, sin_bincount)

        if not has_count_buffer:
            neighbor_counts = count_bincount
        else:
            np.copyto(neighbor_counts, count_bincount)
    else:
        if neighbor_cos_sum is None:
            neighbor_cos_sum = np.zeros(node_count, dtype=float)
        if neighbor_sin_sum is None:
            neighbor_sin_sum = np.zeros(node_count, dtype=float)
        if neighbor_counts is None:
            neighbor_counts = np.zeros(node_count, dtype=float)

    has_neighbors = neighbor_counts > 0.0

    mean_cos, _ = _coerce_buffer(mean_cos, name="mean_cos")
    mean_sin, _ = _coerce_buffer(mean_sin, name="mean_sin")

    if mean_cos is None:
        mean_cos = np.zeros(node_count, dtype=float)
    if mean_sin is None:
        mean_sin = np.zeros(node_count, dtype=float)

    if edge_count:
        with np.errstate(divide="ignore", invalid="ignore"):
            np.divide(
                neighbor_cos_sum,
                neighbor_counts,
                out=mean_cos,
                where=has_neighbors,
            )
            np.divide(
                neighbor_sin_sum,
                neighbor_counts,
                out=mean_sin,
                where=has_neighbors,
            )

    mean_theta = np.where(has_neighbors, np.arctan2(mean_sin, mean_cos), theta_arr)
    return mean_theta, has_neighbors


@overload
def neighbor_phase_mean(obj: "NodeProtocol", n: None = ...) -> Phase: ...


@overload
def neighbor_phase_mean(obj: TNFRGraph, n: NodeId) -> Phase: ...


def neighbor_phase_mean(
    obj: "NodeProtocol" | TNFRGraph, n: NodeId | None = None
) -> Phase:
    """Circular mean of neighbour phases for ``obj``.

    Parameters
    ----------
    obj:
        Either a :class:`~tnfr.node.NodeProtocol` instance bound to a graph or a
        :class:`~tnfr.types.TNFRGraph` from which the node ``n`` will be wrapped.
    n:
        Optional node identifier. Required when ``obj`` is a graph. Providing a
        node identifier for a node object raises :class:`TypeError`.
    """

    NodeNX = cached_import("tnfr.node", "NodeNX")
    if NodeNX is None:
        raise ImportError("NodeNX is unavailable")
    if n is None:
        if hasattr(obj, "nodes"):
            raise TypeError(
                "neighbor_phase_mean requires a node identifier when passing a graph"
            )
        node = obj
    else:
        if hasattr(obj, "nodes"):
            node = NodeNX(obj, n)
        else:
            raise TypeError(
                "neighbor_phase_mean received a node and an explicit identifier"
            )
    return _neighbor_phase_mean_generic(node)