Index

A

adapt_callback() (in module croak.solver) adjoint_single() (croak.forward.ForwardModel method) AIRY6_RMS_COEFF (in module croak.smearing) airy_amplitude() (in module croak.focal) algorithm (croak.result.RetrievalResult attribute) algorithm_params() (in module croak.retrieve) ALGORITHMS (in module croak.retrieve) amplitude (croak._jax_pulse.Penalties attribute) amplitude_penalty() (croak.pulses.ArrayPulse method) (croak.pulses.ComplexPulse method) (croak.pulses.Pulse method) (in module croak.metrics_jax) amplitude_penalty_grad (croak._jax_pulse.ParamGradFns attribute) amplitude_penalty_grad() (croak.pulses.ArrayPulse method) (croak.pulses.Pulse method) any (croak._jax_pulse.ExtraParamSpec property) aperture_from_scan() (in module croak.collection) aperture_offset() (in module croak.collection) apod (croak.io.MaskWindowSpec attribute) apod_param (croak.io.MaskWindowSpec attribute) APODISATIONS (in module croak.collection) apply_dispersion() (in module croak.dispersion)

apply_marginal_correction() (in module croak.marginal_checks) apply_post_filter() (in module croak.session.pipeline) apply_spectrum_frame() (in module croak.session.pipeline) area (croak.focal.FocalMixture attribute) arms (croak.focal.FocalMixture attribute) arpls_baseline() (in module croak.preprocess) ArrayPulse (class in croak.pulses) assemble_load_data() (in module croak.session.pipeline) assemble_result() (in module croak.solver) assemble_simulated_load_data() (in module croak.session.pipeline) assemble_simulated_tracedata() (in module croak.session.pipeline) attach() (croak.plotting.FrogFilterView method) attached (croak.plotting.FrogFilterView property) (croak.plotting.RetrievalPageView property) augment() (in module croak._jax_pulse) Augmentation (class in croak._jax_pulse) auto_index() (croak.io.FileDatasets method) auto_material() (in module croak.dispersion) auto_taylor() (in module croak.dispersion) auto_third_order_exponent() (in module croak.marginal_checks) ax_phase (croak.plotting.SpectralArtists attribute) (croak.plotting.TemporalArtists attribute)

B

background_subtract() (in module croak.preprocess) base_error (croak.uncertainty.UncertaintyResult attribute) BeamPathMirror (class in croak.session.params) beta() (in module croak.materials) beta1() (in module croak.materials) bias_corrected_interval() (in module croak.uncertainty)

bootstrap_solver_kwargs() (in module croak.session.pipeline) bounds() (croak.pulses.Pulse method) build_parameterisation() (in module croak._jax_pulse) build_tracedata() (in module croak.session.pipeline) build_weights() (in module croak.solver) BUILTIN_COATINGS (in module croak.mirrors) BUILTIN_MIRRORS (in module croak.mirrors)

C

C (in module croak.constants) calibration_curve_scale() (in module croak.preprocess) callback() (croak.progress.ProgressReporter method) can_update() (croak.plotting.RetrievalPageView method) canonical_name() (in module croak.gases) (in module croak.materials) centroid (croak.marginal_checks.MarginalPrediction attribute) centroid() (in module croak.marginal_checks) centroid_is_hard (croak.marginal_checks.MarginalPrediction attribute) chromatic (croak.collection.CollectionAperture attribute) chromatic_delay (croak.collection.TransformPhases attribute) CMAES (class in croak.cmaes) cmap_negwhite() (in module croak.plotting) cmap_pos (croak.plotting.RetrievalPlotData attribute) cmap_white() (in module croak.plotting) collection (croak.focal.FocalMixture attribute) (croak.session.params.RetrieveParams attribute) COLLECTION_MODES (in module croak.collection) CollectionAperture (class in croak.collection) collinear_sd_kernel() (in module croak.smearing) ColorbarSpec (class in croak.plotting) combine_uncertainties() (in module croak.uncertainty) compact (croak.plotting.PlotScale property) COMPACT_BELOW (in module croak.plotting) ComplexPulse (class in croak.pulses) components (croak.uncertainty.UncertaintyResult attribute) compose_dispersion() (in module croak.session.dispersion) compute_mu() (in module croak.metrics) compute_mu_per_freq() (in module croak.metrics) compute_R() (in module croak.metrics) compute_r() (in module croak.metrics) conditional_delay() (croak.smearing.SmearingKernel method) ConvergenceArtists (class in croak.plotting) COPRA (class in croak.copra) copra_alpha (croak.session.params.RetrieveParams attribute) copra_stall_patience (croak.session.params.RetrieveParams attribute) COPRAJax (class in croak.copra_jax) cov (croak.covariance.CovarianceResult attribute) covariance_kwargs() (in module croak.session.pipeline) covariance_uncertainty() (in module croak.covariance) CovarianceResult (class in croak.covariance) coverage_calibration() (in module croak.uncertainty) CoverageResult (class in croak.uncertainty) croak._jax_pulse module croak.cli module croak.cmaes module croak.collection module croak.constants module croak.copra module croak.copra_jax module croak.covariance module croak.delay_origin module croak.dispersion module croak.focal module croak.forward module croak.forward_jax module croak.gases module croak.grid module

croak.interactions module croak.io module croak.lbfgs module croak.lbfgs_ad module croak.lbfgs_hand module croak.lm module croak.marginal_checks module croak.materials module croak.maths module croak.metrics module croak.metrics_jax module croak.mirrors module croak.optimistix_lbfgs module croak.optimistix_lm module croak.pipeline module croak.plotting module croak.preprocess module croak.processing module croak.progress module croak.pulses module croak.result module croak.retrieve module croak.save module croak.scripting module croak.session.dispersion module croak.session.engine module croak.session.options module croak.session.params module croak.session.pipeline module croak.session.retarget module croak.smearing module croak.solver module croak.truth_metrics module croak.uncertainty module croak.warm_lbfgs module csv_wavelength_unit() (in module croak.io)

D

dataset_path_fields() (croak.session.params.LoadParams static method) DatasetInfo (class in croak.io) datasets (croak.io.FileDatasets attribute) deconvolve_delay() (in module croak.smearing) DEFAULT_N_RADIAL (in module croak.collection) DEFAULT_STAGES (in module croak.session.engine) defringe_carrier() (in module croak.preprocess) delay_convention (croak.io.SimulatedScan attribute) delay_frequency_grid() (in module croak.smearing) delay_origin (croak.session.params.RetrieveParams attribute) DELAY_ORIGINS (in module croak.delay_origin) delays (croak.preprocess.TraceData attribute) (croak.result.RetrievalResult attribute) delta_k (croak.io.MaskWindowSpec attribute) derivative() (in module croak.maths) DESCRIPTIONS (in module croak.materials)

detect_environment() (in module croak.progress) dispersion_phase() (in module croak.dispersion) DispersionParams (class in croak.session.params) draw() (croak.plotting.RetrievalPageView method) (croak.uncertainty.NoiseModel method) draw_convergence() (in module croak.plotting) draw_delay_marginal() (in module croak.plotting) draw_freq_marginal() (in module croak.plotting) draw_measured_lin() (in module croak.plotting) draw_measured_log() (in module croak.plotting) draw_residual() (in module croak.plotting) draw_retrieved_lin() (in module croak.plotting) draw_retrieved_log() (in module croak.plotting) draw_spectral() (in module croak.plotting) draw_spectral_filter() (in module croak.plotting) draw_spectrogram() (in module croak.plotting) draw_temporal() (in module croak.plotting)

E

edge_energy (croak.processing.ProcessedResult attribute) edge_energy_fraction() (in module croak.processing) EDGE_ENERGY_WARN (in module croak.plotting) EDGE_SECOND_MOMENT (in module croak.collection) ENTRIES (in module croak.session.options) Eomega (croak.io.SimulatedScan attribute) (croak.processing.TruthPulse attribute) Eomega_beamlet (croak.io.SimulatedScan attribute) eps_complex_field() (in module croak.truth_metrics) eps_Ew (croak.truth_metrics.TruthErrors attribute) eps_It (croak.truth_metrics.TruthErrors attribute) eps_Iw (croak.truth_metrics.TruthErrors attribute) eps_spectral_intensity() (in module croak.truth_metrics)

eps_temporal_intensity() (in module croak.truth_metrics) error (croak.result.RetrievalResult attribute) errors (croak.result.RetrievalResult attribute) estimate_fwhm_uncertainty() (in module croak.uncertainty) evolve (croak.focal.FocalMixture attribute) evolved_arm_filters() (in module croak.focal) evolved_profile_table() (in module croak.focal) EvolveSpec (class in croak.focal) ew_vjp (croak._jax_pulse.ParamGradFns attribute) ew_vjp() (croak.pulses.ArrayPulse method) (croak.pulses.ComplexPulse method) (croak.pulses.Pulse method) extra_param_centres() (in module croak.session.pipeline) ExtraParamSpec (class in croak._jax_pulse)

F

f_foc (croak.focal.FocalMixture attribute) (croak.io.SimulatedScan attribute) fft() (croak.grid.Grid method) field (croak.result.RetrievalResult property) FileDatasets (class in croak.io) filetype (croak.io.FileDatasets attribute) filter_frog_trace() (in module croak.preprocess) filter_spectrum() (in module croak.preprocess) filter_view_vmax() (in module croak.plotting) finish() (croak.progress.ProgressReporter method) fixed_path_fields() (croak.session.params.LoadParams static method) flim (croak.plotting.RetrievalPlotData attribute) focal (croak.session.params.RetrieveParams attribute) focal_f_mm (croak.session.params.RetrieveParams attribute) focal_mixture() (in module croak.focal) focal_mixture_from_params() (in module croak.session.pipeline) focal_n_azimuth (croak.session.params.RetrieveParams attribute) FocalMixture (class in croak.focal)

FONT_SCALE_MIN (in module croak.plotting) FONT_SCALE_STEP (in module croak.plotting) format_report() (in module croak.progress) ForwardModel (class in croak.forward) frog_error() (in module croak.metrics) (in module croak.metrics_jax) frog_errors (croak.uncertainty.UncertaintyResult attribute) FrogFilterView (class in croak.plotting) from_dict() (croak.session.options.SessionOptions class method) from_intensity() (croak.processing.TruthPulse class method) from_omega() (croak.grid.Grid class method) from_spectrum() (croak.processing.TruthPulse class method) (croak.pulses.ArrayPulse class method) from_toml() (croak.session.options.SessionOptions class method) FULL_SCALE (in module croak.plotting) fwhm (croak.processing.TruthPulse attribute) fwhm() (in module croak.maths) fwhm_to_sigma() (in module croak.maths)

G

gas_model() (in module croak.gases) gas_refractive_index() (in module croak.gases) GASES (in module croak.gases) gauss() (in module croak.maths) gaussian_pulse() (in module croak.pulses) generate_script() (in module croak.scripting) generation_envelope() (in module croak.session.pipeline) geometry (croak.io.SimulatedScan attribute) get_interaction() (in module croak.interactions) get_params() (croak.pulses.ArrayPulse method) (croak.pulses.ComplexPulse method) (croak.pulses.Pulse method)

Grid (class in croak.grid) grid (croak.preprocess.TraceData attribute) (croak.result.RetrievalResult attribute) gridparams_lambda() (in module croak.grid) gridparams_omega() (in module croak.grid) guess_scanaxis_type() (in module croak.io) guess_scanaxis_unit() (in module croak.io) guess_wavelength_unit() (in module croak.io)

H

halfwidth (croak.plotting.RetrievalPlotData attribute) has_dispersion() (in module croak.session.dispersion)

hole_diameter (croak.focal.FocalMixture attribute) (croak.io.MaskWindowSpec attribute)

I

idx_smear (croak._jax_pulse.Augmentation attribute) idx_smear_delta (croak._jax_pulse.Augmentation attribute) idx_tau0 (croak._jax_pulse.Augmentation attribute) idx_thickness (croak._jax_pulse.Augmentation attribute) ifft() (croak.grid.Grid method) initial_guess() (in module croak.pipeline) intensity_omega (croak.result.RetrievalResult property) intensity_t (croak.result.RetrievalResult property) Interaction (class in croak.interactions) interaction (croak.marginal_checks.MarginalPrediction attribute) (croak.preprocess.TraceData attribute) (croak.result.RetrievalResult attribute) (croak.session.params.SimulatedLoadParams attribute)

INTERACTIONS (in module croak.interactions) interval_method (croak.uncertainty.UncertaintyResult attribute) Iomega (croak.io.SimulatedScan attribute) (croak.preprocess.TraceData attribute) Iomega_beamlet (croak.io.SimulatedScan attribute) Iomega_beamlet_reimaged (croak.io.SimulatedScan attribute) It (croak.io.SimulatedScan attribute) (croak.processing.TruthPulse attribute) Iw (croak.processing.TruthPulse attribute)

K

kernel_from_arms() (in module croak.smearing)

keys (croak.plotting.PageSpec property)

L

label (croak.plotting.TraceArtists attribute) lam (croak.processing.TruthPulse attribute) lamm_lims (croak.preprocess.TraceData attribute) LBFGS (class in croak.lbfgs) LBFGSAD (class in croak.lbfgs_ad) LBFGSHand (class in croak.lbfgs_hand) legend (croak.plotting.SpectralArtists attribute) (croak.plotting.TemporalArtists attribute) lin_vmax (croak.plotting.RetrievalPlotData attribute) line_phase (croak.plotting.TemporalArtists attribute) line_retr (croak.plotting.SpectralArtists attribute) LineArtists (class in croak.plotting)

list_datasets() (in module croak.io) LM (class in croak.lm) load() (croak.io.FileDatasets method) load_and_clean() (in module croak.preprocess) load_builtin() (in module croak.mirrors) load_coating() (in module croak.mirrors) load_csv() (in module croak.io) load_dataset() (in module croak.io) load_options() (in module croak.save) load_result() (in module croak.save) LoadParams (class in croak.session.params) lower_bounds (croak._jax_pulse.Augmentation attribute) ls_parameterisation() (in module croak._jax_pulse)

M

main() (in module croak.cli) make_forward_adjoint_fns() (in module croak.forward_jax) make_param_grad_fns() (in module croak._jax_pulse) make_param_trace_fn() (in module croak.forward_jax) make_reporter() (in module croak.progress) make_signal_fn() (in module croak.forward_jax) make_spectrum_fn() (in module croak._jax_pulse) make_spline_phase_basis() (in module croak._jax_pulse) make_tabulated_material() (in module croak.materials) make_trace_fn() (in module croak.forward_jax) maketrace() (in module croak.forward) maketrace_jax() (in module croak.forward_jax) marginal (croak.marginal_checks.MarginalPrediction attribute) marginal_peak_delay() (in module croak.preprocess) marginal_peak_delay_jax() (in module croak.delay_origin) MarginalArtists (class in croak.plotting) MarginalPrediction (class in croak.marginal_checks) marginals() (in module croak.processing) mask_diameter (croak.io.SimulatedScan attribute) mask_hole_aperture() (in module croak.collection) mask_transmission() (in module croak.collection) mask_window (croak.io.SimulatedScan attribute) MaskWindowSpec (class in croak.io) match_dataset() (in module croak.io) material (croak.focal.EvolveSpec attribute) material_gdd() (in module croak.dispersion) material_model() (in module croak.materials) material_tod() (in module croak.dispersion) MATERIALS (in module croak.materials) matrix_names (croak.io.FileDatasets property) maxiters (croak.session.params.RetrieveParams attribute) median (croak.uncertainty.UncertaintyResult property) method (croak.uncertainty.UncertaintyResult attribute) MIRROR_AMPLITUDES (in module croak.dispersion) mirror_from_arrays() (in module croak.mirrors) MIRRORS (in module croak.dispersion) MirrorSpec (class in croak.mirrors) mixture_from_nodes() (in module croak.focal) mode (croak.collection.CollectionAperture attribute) module croak._jax_pulse croak.cli croak.cmaes croak.collection croak.constants croak.copra croak.copra_jax croak.covariance croak.delay_origin croak.dispersion croak.focal croak.forward croak.forward_jax croak.gases croak.grid croak.interactions croak.io croak.lbfgs croak.lbfgs_ad croak.lbfgs_hand croak.lm croak.marginal_checks croak.materials croak.maths croak.metrics croak.metrics_jax croak.mirrors croak.optimistix_lbfgs croak.optimistix_lm croak.pipeline croak.plotting croak.preprocess croak.processing croak.progress croak.pulses croak.result croak.retrieve croak.save croak.scripting croak.session.dispersion croak.session.engine croak.session.options croak.session.params croak.session.pipeline croak.session.retarget croak.smearing croak.solver croak.truth_metrics croak.uncertainty croak.warm_lbfgs

moment() (in module croak.maths) mosaic (croak.plotting.PageSpec attribute) mu (croak.result.RetrievalResult attribute) mu_global() (in module croak.metrics_jax) mu_per_freq() (in module croak.metrics_jax)

N

n (croak.grid.Grid attribute) n_converged (croak.uncertainty.UncertaintyResult attribute) n_params (croak.covariance.CovarianceResult attribute) n_pulse (croak._jax_pulse.Augmentation attribute) n_resamples (croak.uncertainty.UncertaintyResult attribute) n_residuals (croak.covariance.CovarianceResult attribute) name (croak.cmaes.CMAES attribute) (croak.copra.COPRA attribute) (croak.copra_jax.COPRAJax attribute) (croak.lbfgs.LBFGS attribute) (croak.lbfgs_ad.LBFGSAD attribute) (croak.lbfgs_hand.LBFGSHand attribute) (croak.lm.LM attribute) (croak.optimistix_lbfgs.OptxLBFGS attribute) (croak.optimistix_lm.OptxLM attribute) (croak.solver.Retriever attribute) (croak.warm_lbfgs.WarmLBFGS attribute)

names (croak.io.FileDatasets property) nodes (croak.collection.CollectionAperture property) (croak.focal.FocalMixture property) nodes_weights() (croak.smearing.SmearingKernel method) noise_floor (croak.uncertainty.UncertaintyResult attribute) noise_from_background() (in module croak.uncertainty) noise_from_residual() (in module croak.uncertainty) noise_scaled (croak.covariance.CovarianceResult attribute) NoiseModel (class in croak.uncertainty) normalize_spectral_phase() (in module croak.processing) normalize_temporal_phase() (in module croak.processing) nparams (croak.pulses.ArrayPulse property) (croak.pulses.ComplexPulse property) (croak.pulses.Pulse property) npoints (croak.focal.EvolveSpec attribute) null_dim (croak.covariance.CovarianceResult attribute)

O

omega (croak.grid.Grid attribute) (croak.io.SimulatedScan attribute) (croak.marginal_checks.MarginalPrediction attribute) (croak.preprocess.TraceData property) (croak.processing.TruthPulse attribute) (croak.result.RetrievalResult property) omega0 (croak.io.SimulatedScan attribute) omega0_scale (croak.interactions.Interaction attribute) (croak.interactions.SHG attribute)

omega0_trace (croak.plotting.RetrievalPlotData attribute) omega_reference (croak.io.MaskWindowSpec attribute) omega_to_lambda_density() (in module croak.preprocess) OPTIMIZERS (in module croak.dispersion) option_labels (croak.io.FileDatasets property) OptxLBFGS (class in croak.optimistix_lbfgs) OptxLM (class in croak.optimistix_lm) oversample() (in module croak.processing)

P

p (croak.focal.FocalMixture attribute) PageSpec (class in croak.plotting) PanelSpec (class in croak.plotting) parameter_covariance() (in module croak.covariance) Parameterisation (class in croak._jax_pulse) parametric_bootstrap() (in module croak.uncertainty) ParamGradFns (class in croak._jax_pulse) path (croak.io.FileDatasets attribute) peak_power() (croak.processing.TruthPulse method) peak_wavelength() (in module croak.processing) Penalties (class in croak._jax_pulse) penalties (croak._jax_pulse.Parameterisation attribute) percentile_interval() (in module croak.uncertainty) PG (class in croak.interactions) phase (croak._jax_pulse.Penalties attribute) phase_omega (croak.result.RetrievalResult property) phase_penalty() (croak.pulses.ArrayPulse method) (croak.pulses.Pulse method) (in module croak.metrics_jax) phase_penalty_grad (croak._jax_pulse.ParamGradFns attribute) phase_penalty_grad() (croak.pulses.ArrayPulse method) (croak.pulses.Pulse method) phase_t (croak.result.RetrievalResult property) phi (croak.focal.FocalMixture attribute) phi_t (croak.processing.TruthPulse attribute) phi_w (croak.processing.TruthPulse attribute) physical (croak._jax_pulse.Augmentation attribute) planck_taper() (in module croak.maths) plot_convergence() (in module croak.plotting) plot_frog_filter() (in module croak.plotting)

plot_fwhm_distribution() (in module croak.plotting) plot_intensity_band() (in module croak.plotting) plot_marginal() (in module croak.plotting) plot_residual() (in module croak.plotting) plot_retrieval() (in module croak.plotting) plot_retrieval_page() (in module croak.plotting) plot_scale() (in module croak.plotting) plot_simulated_trace() (in module croak.plotting) plot_spectral() (in module croak.plotting) plot_spectrogram() (in module croak.plotting) plot_temporal() (in module croak.plotting) plot_uncertainty() (in module croak.plotting) PlotScale (class in croak.plotting) plus_minus (croak.uncertainty.UncertaintyResult property) point_estimate (croak.uncertainty.UncertaintyResult attribute) position_to_delay() (in module croak.io) post_filter() (in module croak.processing) power_scale (croak.plotting.RetrievalPlotData attribute) predicted_centroid() (in module croak.marginal_checks) predicted_marginal() (in module croak.marginal_checks) PreprocParams (class in croak.session.params) process() (in module croak.session.pipeline) process_mirror_data() (in module croak.mirrors) process_result() (in module croak.processing) processed (croak.plotting.RetrievalPlotData attribute) ProcessedResult (class in croak.processing) profiles (croak.uncertainty.UncertaintyResult attribute) ProgressReporter (class in croak.progress) propagation_label (croak.uncertainty.UncertaintyResult attribute) Pulse (class in croak.pulses)

Q

quadrature (croak.focal.EvolveSpec attribute)

quadrature_hole_diameter() (in module croak.collection) quadrature_nodes_weights() (in module croak.forward)

R

r (croak.focal.FocalMixture attribute) random_gaussian_spectrum() (in module croak.pulses) rank (croak.covariance.CovarianceResult attribute) raw_direct (croak.session.params.SimulatedLoadParams attribute) raw_fft() (in module croak.grid) raw_ifft() (in module croak.grid) read_nk_csv() (in module croak.materials) read_simulated_mask_window() (in module croak.io) read_simulated_scan() (in module croak.io) read_simulated_truth_keys() (in module croak.io) read_simulated_wavelength_range() (in module croak.io) read_simulated_window_keys() (in module croak.io) read_simulated_z_positions() (in module croak.io) recentre_trace() (in module croak.delay_origin) recentring() (in module croak.delay_origin) reduce_to_1d() (in module croak.io) reduced_chisq (croak.covariance.CovarianceResult attribute) reduced_moments() (in module croak.focal) reduced_weight() (croak.focal.FocalMixture method) reference_wavelength (croak.io.MaskWindowSpec attribute) refractive_index() (in module croak.materials) reg_amp (croak.session.params.RetrieveParams attribute) REG_DEFAULTS (in module croak.solver) reg_defaults() (in module croak.session.params) reg_family() (in module croak.session.params) reg_spectrum (croak.session.params.RetrieveParams attribute) register_material() (in module croak.materials) register_mirror() (in module croak.dispersion) regrid() (in module croak.preprocess) resample_spectrum() (in module croak.preprocess) resampling_bootstrap() (in module croak.uncertainty) reset() (croak.plotting.RetrievalPageView method)

residual_vector() (in module croak.metrics_jax) ResidualArtists (class in croak.plotting) residuals() (in module croak.processing) resolve_guess() (in module croak.session.pipeline) (in module croak.solver) resolve_tanh_width() (in module croak.collection) resolve_time_direction() (in module croak.processing) result (croak.plotting.RetrievalPlotData attribute) result_from_saved() (in module croak.save) retarget() (in module croak.session.retarget) RETRIEVAL_COLORBARS (in module croak.plotting) RETRIEVAL_OVERVIEW (in module croak.plotting) RETRIEVAL_PAGES (in module croak.plotting) RETRIEVAL_PANELS (in module croak.plotting) retrieval_plot_data() (in module croak.plotting) RetrievalPageView (class in croak.plotting) RetrievalPlotData (class in croak.plotting) RetrievalResult (class in croak.result) retrieve() (in module croak.retrieve) retrieve_from_tracedata() (in module croak.pipeline) RetrieveParams (class in croak.session.params) Retriever (class in croak.solver) reverse_trace (croak.session.params.LoadParams attribute) rms_width (croak.marginal_checks.MarginalPrediction attribute) rms_width() (in module croak.marginal_checks) ROOM_TEMPERATURE_K (in module croak.gases) run() (croak.solver.Retriever method) run_cmaes() (in module croak.cmaes) run_copra() (in module croak.copra) run_copra_jax() (in module croak.copra_jax) run_retrieval() (in module croak.session.pipeline) run_session() (in module croak.session.engine) run_uncertainty() (in module croak.session.pipeline)

S

samples (croak.uncertainty.UncertaintyResult attribute) save_options() (in module croak.save) save_result() (in module croak.save) save_uncertainty() (in module croak.save) scalecurve (croak.preprocess.TraceData attribute) scaled() (croak.smearing.SmearingKernel method) scaled_rc() (in module croak.plotting) scales (croak._jax_pulse.Augmentation attribute) SD (class in croak.interactions) sech() (in module croak.maths) sech_pulse() (in module croak.pulses) SessionOptions (class in croak.session.options) SessionResult (class in croak.session.engine) set_params() (croak.pulses.ArrayPulse method) (croak.pulses.ComplexPulse method) (croak.pulses.Pulse method) SHG (class in croak.interactions) shiftnorm() (in module croak.processing) si_power() (in module croak.plotting) sig3() (in module croak.plotting) sigma_smear (croak.covariance.CovarianceResult attribute) sigma_smear_delta (croak.covariance.CovarianceResult attribute) sigma_spectrum (croak.marginal_checks.MarginalPrediction attribute) sigma_tau0 (croak.covariance.CovarianceResult attribute) sigma_thickness (croak.covariance.CovarianceResult attribute) signal() (croak.interactions.Interaction method) (croak.interactions.PG method) (croak.interactions.SD method) (croak.interactions.SHG method) signal_adjoint() (croak.interactions.Interaction method) (croak.interactions.PG method) (croak.interactions.SD method) (croak.interactions.SHG method) signal_position (croak.focal.FocalMixture property) signal_single() (croak.forward.ForwardModel method) signal_smeared() (croak.forward.ForwardModel method) signed_pcolormesh() (in module croak.plotting) SIMULATED_TRUTH_SOURCES (in module croak.io) SIMULATED_WINDOW_KEYS (in module croak.io) SimulatedLoadParams (class in croak.session.params) SimulatedScan (class in croak.io) smear_layout (croak.session.params.RetrieveParams attribute) smear_scale (croak.result.RetrievalResult attribute) (croak.session.params.RetrieveParams attribute) smear_scale_delta (croak.result.RetrievalResult attribute)

smeared_shifts() (croak.interactions.Interaction method) (croak.interactions.PG method) (croak.interactions.SD method) smeared_signal() (croak.interactions.Interaction method) (croak.interactions.PG method) (croak.interactions.SD method) smearing_kernel() (in module croak.session.pipeline) SmearingKernel (class in croak.smearing) solver (croak.session.params.RetrieveParams attribute) spectral (croak._jax_pulse.Penalties attribute) spectral_autoconvolution() (in module croak.marginal_checks) SPECTRAL_AXES (in module croak.plotting) spectral_axis (croak.plotting.RetrievalPlotData attribute) spectral_filter() (croak.focal.FocalMixture method) spectral_fwhm() (in module croak.processing) spectral_penalty() (croak.pulses.ArrayPulse method) (in module croak.metrics_jax) spectral_penalty_grad (croak._jax_pulse.ParamGradFns attribute) spectral_penalty_grad() (croak.pulses.ArrayPulse method) spectral_target_amplitude() (in module croak.solver) SpectralArtists (class in croak.plotting) spectrogram (croak.plotting.RetrievalPlotData property) spectrogram() (in module croak.processing) SpectrogramArtists (class in croak.plotting) spectrum (croak.result.RetrievalResult attribute) spectrum() (croak.pulses.ArrayPulse method) (croak.pulses.ComplexPulse method) (croak.pulses.Pulse method) spectrum_fn (croak._jax_pulse.Parameterisation attribute) spectrum_frame_p (croak.session.params.RetrieveParams attribute) spectrum_on_grid() (croak.processing.TruthPulse method) spectrum_source (croak.session.params.SimulatedLoadParams attribute) square_boxcars_delay_width() (in module croak.smearing) square_boxcars_kernel() (in module croak.smearing) square_boxcars_spacing() (in module croak.smearing) stage_boundaries (croak.result.RetrievalResult attribute) stall_patience (croak.copra_jax.COPRAJax attribute) static_phase (croak.collection.TransformPhases attribute) statistic (croak.uncertainty.UncertaintyResult attribute) std (croak.uncertainty.UncertaintyResult property) std() (croak.uncertainty.NoiseModel method) stderr (croak.covariance.CovarianceResult property) suggested_tau_exclude() (in module croak.preprocess) summary() (croak.uncertainty.CoverageResult method) (croak.uncertainty.UncertaintyResult method) synthetic_experiment() (in module croak.uncertainty)

T

t (croak.grid.Grid attribute) (croak.io.SimulatedScan attribute) (croak.processing.TruthPulse attribute) (croak.result.RetrievalResult property) t_profile (croak.uncertainty.UncertaintyResult attribute) TAPER_COLLAR_BINS (in module croak.preprocess) taper_loss (croak.preprocess.TraceData attribute) tau (croak.io.SimulatedScan attribute) tau0 (croak.result.RetrievalResult attribute) tau0_bound_fs (croak.session.params.RetrieveParams attribute) tau_fwhm (croak.io.SimulatedScan attribute) tau_lims (croak.preprocess.TraceData attribute) temporal (croak._jax_pulse.Penalties attribute) TemporalArtists (class in croak.plotting) theta (croak.focal.FocalMixture attribute) thickness (croak.focal.EvolveSpec attribute) (croak.result.RetrievalResult attribute) thickness_bootstrap() (in module croak.uncertainty) thickness_central (croak.uncertainty.UncertaintyResult attribute) thickness_sigma (croak.uncertainty.UncertaintyResult attribute) thicknesses (croak.uncertainty.UncertaintyResult attribute) third_order_scale() (in module croak.preprocess) time_reversal_ambiguous (croak.interactions.Interaction attribute) (croak.interactions.SHG attribute)

time_window_mask() (in module croak._jax_pulse) tl_init (croak.session.params.RetrieveParams attribute) to_1d() (in module croak.io) to_dict() (croak.session.options.SessionOptions method) to_toml() (croak.session.options.SessionOptions method) trace (croak.io.SimulatedScan attribute) (croak.preprocess.TraceData attribute) (croak.result.RetrievalResult attribute) trace() (croak.forward.ForwardModel method) trace_error() (in module croak.metrics) TraceArtists (class in croak.plotting) TraceData (class in croak.preprocess) tracedb (croak.plotting.RetrievalPlotData attribute) transfer_function() (in module croak.session.dispersion) transform_phases() (in module croak.collection) TransformPhases (class in croak.collection) transmission (croak.collection.CollectionAperture attribute) truth (croak.plotting.RetrievalPlotData attribute) truth_errors() (in module croak.truth_metrics) truth_init (croak.session.params.RetrieveParams attribute) truth_source (croak.session.params.SimulatedLoadParams attribute) TruthErrors (class in croak.truth_metrics) TruthPulse (class in croak.processing) tshift() (croak.grid.Grid method)

U

u (croak.covariance.CovarianceResult attribute) u0 (croak._jax_pulse.Augmentation attribute) (croak._jax_pulse.Parameterisation attribute) UncertaintyParams (class in croak.session.params) UncertaintyResult (class in croak.uncertainty) uniform_core_indices() (in module croak.preprocess) uniform_delay_core (croak.session.params.SimulatedLoadParams attribute) UNIT_FACTORS (in module croak.io) unit_to_si() (in module croak.io) unpack (croak._jax_pulse.Augmentation attribute) unregister_material() (in module croak.materials) unregister_mirror() (in module croak.dispersion) update() (croak.plotting.FrogFilterView method) (croak.plotting.RetrievalPageView method)

update_convergence() (in module croak.plotting) update_convergence_curve() (in module croak.plotting) update_delay_marginal() (in module croak.plotting) update_freq_marginal() (in module croak.plotting) update_measured_lin() (in module croak.plotting) update_measured_log() (in module croak.plotting) update_residual() (in module croak.plotting) update_retrieved_lin() (in module croak.plotting) update_retrieved_log() (in module croak.plotting) update_spectral() (in module croak.plotting) update_spectral_filter() (in module croak.plotting) update_spectrogram() (in module croak.plotting) update_temporal() (in module croak.plotting)

V

valid_range_m (croak.mirrors.MirrorSpec property)

vector_names (croak.io.FileDatasets property)

W

warm_start (croak.uncertainty.UncertaintyResult attribute) WarmLBFGS (class in croak.warm_lbfgs) wavelength (croak.result.RetrievalResult property) weight (croak.collection.CollectionAperture attribute) weight_amp (croak.collection.TransformPhases attribute) weight_sq (croak.collection.TransformPhases attribute) weighting (croak.collection.CollectionAperture attribute) (croak.io.MaskWindowSpec attribute)

WEIGHTINGS (in module croak.collection) width_bracket (croak.marginal_checks.MarginalPrediction attribute) width_is_hard (croak.marginal_checks.MarginalPrediction attribute) window_def_prefix() (in module croak.io) window_key (croak.io.SimulatedScan attribute) (croak.session.params.SimulatedLoadParams attribute) window_type (croak.io.MaskWindowSpec attribute) with_() (croak.session.options.SessionOptions method) wlfreq() (in module croak.maths)

Z

z_index (croak.io.SimulatedScan attribute) (croak.session.params.SimulatedLoadParams attribute) z_mask (croak.collection.CollectionAperture attribute) (croak.io.MaskWindowSpec attribute)

z_positions (croak.io.SimulatedScan attribute) z_thickness_um (croak.session.params.SimulatedLoadParams attribute)