SFI package¶
SFI – Stochastic Force Inference - main entry point
- SFI.enable_logging(level='INFO')[source]¶
Quick helper to turn on SFI log output.
>>> import SFI >>> SFI.enable_logging() # INFO-level messages >>> SFI.enable_logging("DEBUG") # everything
- Parameters:
level (str)
- Return type:
None
Subpackages¶
- SFI.bases package
- SFI.bases
V()X()constant_array()dataset_indicator()extra_scalar()field_component()frame()identity_matrix_basis()linear_basis()monomials_degree()monomials_up_to()named_scalar()named_scalars()ones_basis()per_dataset_scalar()symmetric_matrix_basis()time_fourier()unit_axes()unit_vector_basis()v_components()v_coordinate()v_coordinates()x_components()x_coordinate()x_coordinates()- Submodules
- SFI.bases.constants module
- SFI.bases.linear module
- SFI.bases.monomials module
- SFI.bases.pairs module
- SFI.bases.pairs
angle_coupling()angular_pair_basis()compact_kernels()dyadic_pair_basis()exp_poly_kernels()gaussian_kernels()heading_vector()pair_direction()pair_velocity_difference()parametric_radial_kernel()particle_heading()particle_velocity()pbc_displacement()power_kernels()radial_pair_basis()scalar_pair_basis()vision_gate()wrap_angle()
- SFI.bases.spde module
- SFI.diagnostics package
DiagnosticsReportDynamicsOrderReportassess()classify_dynamics()parametric_four_point_diagnostic()plot_dynamics_order()plot_qq()plot_residual_acf()plot_residual_histogram()plot_summary()- Submodules
- SFI.inference package
- Public classes
BeamSearchStrategyGreedyStepwiseStrategyHillClimbStrategyInferenceResultSFInferenceResultSF.d_v()InferenceResultSF.d_x()InferenceResultSF.dense()InferenceResultSF.dimInferenceResultSF.dot()InferenceResultSF.drop_featuresInferenceResultSF.einsum()InferenceResultSF.elementwisemap()InferenceResultSF.estimate_bytes_per_sample()InferenceResultSF.features_to_rank()InferenceResultSF.flatten_params()InferenceResultSF.labelsInferenceResultSF.load()InferenceResultSF.materialize_params()InferenceResultSF.memory_hint()InferenceResultSF.metaInferenceResultSF.n_featuresInferenceResultSF.needs_vInferenceResultSF.param_covInferenceResultSF.paramsInferenceResultSF.particle_extrasInferenceResultSF.particles_inputInferenceResultSF.pdepthInferenceResultSF.predict_ci()InferenceResultSF.predict_cov()InferenceResultSF.predict_var()InferenceResultSF.rankInferenceResultSF.rank_to_features()InferenceResultSF.required_extrasInferenceResultSF.rootInferenceResultSF.save()InferenceResultSF.sdimsInferenceResultSF.specialize()InferenceResultSF.sqrtm()InferenceResultSF.stack()InferenceResultSF.summary()InferenceResultSF.tensordot()InferenceResultSF.tensorize()InferenceResultSF.vectorize()
LassoStrategyOverdampedLangevinInferenceOverdampedLangevinInference.coeff_block()OverdampedLangevinInference.compare_params_to_exact()OverdampedLangevinInference.compare_to_exact()OverdampedLangevinInference.comparison_scatter()OverdampedLangevinInference.compute_diffusion_constant()OverdampedLangevinInference.compute_diffusion_error()OverdampedLangevinInference.compute_force_error()OverdampedLangevinInference.diagnose()OverdampedLangevinInference.diffusion_comparison_arrays()OverdampedLangevinInference.force_comparison_arrays()OverdampedLangevinInference.get_diffusion_timeop()OverdampedLangevinInference.holdout_score()OverdampedLangevinInference.infer_diffusion()OverdampedLangevinInference.infer_diffusion_linear()OverdampedLangevinInference.infer_force()OverdampedLangevinInference.infer_force_linear()OverdampedLangevinInference.load_results()OverdampedLangevinInference.predict_time_profile()OverdampedLangevinInference.print_report()OverdampedLangevinInference.report_dict()OverdampedLangevinInference.save_results()OverdampedLangevinInference.simulate_bootstrapped_trajectory()OverdampedLangevinInference.sparsify_force()OverdampedLangevinInference.summary()
STLSQStrategySparseScorerSparsityResultSparsityStrategyUnderdampedLangevinInferenceUnderdampedLangevinInference.coeff_block()UnderdampedLangevinInference.compare_params_to_exact()UnderdampedLangevinInference.compare_to_exact()UnderdampedLangevinInference.comparison_scatter()UnderdampedLangevinInference.compute_diffusion_constant()UnderdampedLangevinInference.compute_diffusion_error()UnderdampedLangevinInference.compute_force_error()UnderdampedLangevinInference.diagnose()UnderdampedLangevinInference.diffusion_comparison_arrays()UnderdampedLangevinInference.force_comparison_arrays()UnderdampedLangevinInference.get_diffusion_timeop()UnderdampedLangevinInference.holdout_score()UnderdampedLangevinInference.infer_diffusion()UnderdampedLangevinInference.infer_diffusion_linear()UnderdampedLangevinInference.infer_force()UnderdampedLangevinInference.infer_force_linear()UnderdampedLangevinInference.load_results()UnderdampedLangevinInference.predict_time_profile()UnderdampedLangevinInference.print_report()UnderdampedLangevinInference.report_dict()UnderdampedLangevinInference.save_results()UnderdampedLangevinInference.simulate_bootstrapped_trajectory()UnderdampedLangevinInference.sparsify_force()UnderdampedLangevinInference.summary()
load_model()load_results()overlap_metrics()predictive_nmse()save_model()save_results()- Subpackages
- Submodules
- SFI.integrate package
- Public API
ConstOperandExprOperandIntegrandTermTimeOperandadd()integrate()make_minibatch_parametric_integrator()make_parametric_integrator()scale()stream()timeop()velocity()- Submodules
- SFI.langevin package
- SFI.langevin
CompositeNoiseConservedNoiseNoiseModelOverdampedProcessOverdampedProcess.DOverdampedProcess.FOverdampedProcess.diffusion_sfOverdampedProcess.extras_globalOverdampedProcess.extras_localOverdampedProcess.force_sfOverdampedProcess.initialize()OverdampedProcess.metadataOverdampedProcess.set_extras()OverdampedProcess.set_params()OverdampedProcess.simulate()OverdampedProcess.theta_DOverdampedProcess.theta_F
UnderdampedProcessUnderdampedProcess.DUnderdampedProcess.FUnderdampedProcess.diffusion_sfUnderdampedProcess.extras_globalUnderdampedProcess.extras_localUnderdampedProcess.force_sfUnderdampedProcess.initialize()UnderdampedProcess.metadataUnderdampedProcess.set_extras()UnderdampedProcess.set_params()UnderdampedProcess.simulate()UnderdampedProcess.theta_DUnderdampedProcess.theta_F
WhiteNoise- Submodules
- SFI.statefunc package
BasisBasis.d_v()Basis.d_x()Basis.dense()Basis.dimBasis.dot()Basis.einsum()Basis.elementwisemap()Basis.estimate_bytes_per_sample()Basis.features_to_rank()Basis.labelsBasis.memory_hint()Basis.n_featuresBasis.needs_vBasis.particle_extrasBasis.particles_inputBasis.pdepthBasis.rankBasis.rank_to_features()Basis.required_extrasBasis.rootBasis.sdimsBasis.specialize()Basis.sqrtm()Basis.stack()Basis.tensordot()Basis.tensorize()Basis.to_psf()Basis.vectorize()
InteractorInteractor.d_v()Interactor.d_x()Interactor.dense()Interactor.dimInteractor.dispatch()Interactor.dispatch_pairs()Interactor.dispatch_pairs_from_extras()Interactor.dot()Interactor.einsum()Interactor.elementwisemap()Interactor.estimate_bytes_per_sample()Interactor.features_to_rank()Interactor.memory_hint()Interactor.n_featuresInteractor.needs_vInteractor.particle_extrasInteractor.particles_inputInteractor.pdepthInteractor.rankInteractor.rank_to_features()Interactor.required_extrasInteractor.rootInteractor.sdimsInteractor.specialize()Interactor.sqrtm()Interactor.stack()Interactor.tensordot()Interactor.tensorize()Interactor.vectorize()
PSFPSF.bind()PSF.d_theta()PSF.d_v()PSF.d_x()PSF.dense()PSF.dimPSF.dot()PSF.drop_featuresPSF.einsum()PSF.elementwisemap()PSF.estimate_bytes_per_sample()PSF.features_to_rank()PSF.flatten_params()PSF.labelsPSF.memory_hint()PSF.n_featuresPSF.needs_vPSF.particle_extrasPSF.particles_inputPSF.pdepthPSF.rankPSF.rank_to_features()PSF.required_extrasPSF.rootPSF.sdimsPSF.specialize()PSF.sqrtm()PSF.stack()PSF.templatePSF.tensordot()PSF.tensorize()PSF.unflatten_params()PSF.vectorize()
ParamSpecParamSuiteParamSuite.coerce()ParamSuite.defaults()ParamSuite.from_specs()ParamSuite.has_defaultsParamSuite.materialize()ParamSuite.merge()ParamSuite.merge_many()ParamSuite.parse()ParamSuite.sizeParamSuite.specsParamSuite.stamp()ParamSuite.tree_flatten()ParamSuite.tree_unflatten()ParamSuite.vectorize()ParamSuite.zeros()
RankSFSF.d_v()SF.d_x()SF.dense()SF.dimSF.dot()SF.drop_featuresSF.einsum()SF.elementwisemap()SF.estimate_bytes_per_sample()SF.features_to_rank()SF.labelsSF.memory_hint()SF.n_featuresSF.needs_vSF.paramsSF.particle_extrasSF.particles_inputSF.pdepthSF.rankSF.rank_to_features()SF.required_extrasSF.rootSF.sdimsSF.specialize()SF.sqrtm()SF.stack()SF.tensordot()SF.tensorize()SF.vectorize()
StateExprStateExpr.d_v()StateExpr.d_x()StateExpr.dense()StateExpr.dimStateExpr.dot()StateExpr.einsum()StateExpr.elementwisemap()StateExpr.estimate_bytes_per_sample()StateExpr.features_to_rank()StateExpr.memory_hint()StateExpr.n_featuresStateExpr.needs_vStateExpr.particle_extrasStateExpr.particles_inputStateExpr.pdepthStateExpr.rankStateExpr.rank_to_features()StateExpr.required_extrasStateExpr.rootStateExpr.sdimsStateExpr.specialize()StateExpr.sqrtm()StateExpr.stack()StateExpr.tensordot()StateExpr.tensorize()StateExpr.vectorize()
make_basis()make_interactor()make_psf()make_sf()set_jit()- Subpackages
- Submodules
- SFI.trajectory package
FunctionExtraTimeSeriesExtraTrajectoryCollectionTrajectoryCollection.Teff()TrajectoryCollection.concat()TrajectoryCollection.dataset_index()TrajectoryCollection.datasetsTrajectoryCollection.degrade()TrajectoryCollection.from_arrays()TrajectoryCollection.from_columns()TrajectoryCollection.from_dataframe()TrajectoryCollection.from_dataset()TrajectoryCollection.iter_slices()TrajectoryCollection.load()TrajectoryCollection.merge()TrajectoryCollection.peek_X()TrajectoryCollection.peek_dX()TrajectoryCollection.peek_dt()TrajectoryCollection.peek_mask()TrajectoryCollection.peek_row()TrajectoryCollection.save()TrajectoryCollection.split_time()TrajectoryCollection.to_array()TrajectoryCollection.to_arrays()TrajectoryCollection.velocity_array()TrajectoryCollection.weightsTrajectoryCollection.with_weights()
TrajectoryDatasetTrajectoryDataset.NTrajectoryDataset.TTrajectoryDataset.Teff()TrajectoryDataset.XTrajectoryDataset.build_extras()TrajectoryDataset.dTrajectoryDataset.dtTrajectoryDataset.dynamic_maskTrajectoryDataset.extras_globalTrajectoryDataset.extras_localTrajectoryDataset.from_arrays()TrajectoryDataset.make_batch_producer()TrajectoryDataset.make_producer()TrajectoryDataset.maskTrajectoryDataset.materialize_time()TrajectoryDataset.metaTrajectoryDataset.split_time()TrajectoryDataset.tTrajectoryDataset.to_arrays()TrajectoryDataset.uuidTrajectoryDataset.valid_indices()
function_extra()time_series_extra()- Submodules
- SFI.utils package
as_default_float()default_float_dtype()fd_velocity()model_summary()print_model_comparison()solve_or_pinv()sqrtm_psd()stable_pinv()- Submodules
- SFI.utils.formatting module
- SFI.utils.maths module
- SFI.utils.neighbors module
- SFI.utils.plotting module
SFI_COLORSanimate_particles()animate_spde_comparison()axisvector()comparison_scatter()dark_ax()dark_fig()phase2d()phase2d_scalar()phase3d()plot_field()plot_field_error()plot_nematic_director()plot_pareto_front()plot_particles()plot_particles_field()plot_profile_1d()plot_recovery_bar()plot_recovery_bar_multi()plot_recovery_matrix()plot_rods()plot_spde_snapshot()plot_tensor_field()plot_time_profile_comparison()spatial_acorr2d()stamp_fig()stamp_output()stream_field()timeseries()timeseries_colored()trajectory_scatter()wrap_positions()