Getting started
jwspecfit
BroadFitResult
BroadFitResult.best_fit
BroadFitResult.selected_model
BroadFitResult.bic_narrow
BroadFitResult.bic_broad1
BroadFitResult.bic_broad2
BroadFitResult.bic_both
BroadFitResult.all_fits
BroadFitResult.bic_bootstrap
BroadFitResult.bic_hei_bootstrap
BroadFitResult.bic_hei_both
BroadFitResult.bic_hei_broad1
BroadFitResult.bic_hei_broad2
BroadFitResult.bic_hei_off
BroadFitResult.bic_oiii_bootstrap
BroadFitResult.bic_oiii_both
BroadFitResult.bic_oiii_broad1
BroadFitResult.bic_oiii_broad2
BroadFitResult.bic_oiii_off
BroadFitResult.chi2
BroadFitResult.constraints
BroadFitResult.continuum
BroadFitResult.hei_broad_selected
BroadFitResult.hei_selected
BroadFitResult.line_names
BroadFitResult.lines
BroadFitResult.model_flux
BroadFitResult.oiii_broad_selected
BroadFitResult.oiii_selected
BroadFitResult.params
BroadFitResult.residuals
BroadFitResult.spectrum
BroadFitResult.success
DLAResult
DLAResult.log_NHI
DLAResult.log_NHI_err
DLAResult.beta_UV
DLAResult.beta_UV_err
DLAResult.log_F0
DLAResult.log_F0_err
DLAResult.Sigma_HI
DLAResult.samples
DLAResult.wave_fit
DLAResult.flux_fit
DLAResult.flux_err_fit
DLAResult.model_best
DLAResult.z
DLAResult.Av
DLAResult.log_evidence
DLAResult.corner()
DLAResult.fit_x_HI
DLAResult.igm_z_min
DLAResult.is_upper_limit
DLAResult.lam_pivot_A
DLAResult.log_NHI_upper95
DLAResult.lya_params
DLAResult.plot()
DLAResult.summary()
DLAResult.x_HI
DLAResult.x_HI_err
FitResult
FitResult.lines
FitResult.params
FitResult.model_flux
FitResult.continuum
FitResult.residuals
FitResult.chi2
FitResult.spectrum
FitResult.line_names
FitResult.constraints
FitResult.success
FitResult.flux_upper_limit()
FitResult.flux_upper_limits()
FitResult.lya_params
LineResult
LineResult.name
LineResult.rest_wave_A
LineResult.amplitude
LineResult.centroid_A
LineResult.sigma_A
LineResult.flux
LineResult.flux_err
LineResult.ew_A
LineResult.snr_int_err
LineResult.snr_int_cont
LineResult.snr_peak_err
LineResult.snr_peak_cont
LineResult.snr
LineResult.upper_limit()
Peak
Peak.ci68
Peak.ci95
Peak.dchi2
Peak.lines_used
Peak.n_lines_used
Peak.prob
Peak.z
R_from_pixels()
R_prism()
RedshiftResult
RedshiftResult.P_z_coarse
RedshiftResult.P_z_fine
RedshiftResult.chi2_coarse
RedshiftResult.chi2_fine
RedshiftResult.grating
RedshiftResult.is_decisive
RedshiftResult.lines_used
RedshiftResult.peaks
RedshiftResult.plot()
RedshiftResult.spec
RedshiftResult.z_best
RedshiftResult.z_ci68
RedshiftResult.z_ci95
RedshiftResult.z_grid_coarse
RedshiftResult.z_grid_fine
Spectrum
Spectrum.wave_um
Spectrum.flux_ujy
Spectrum.err_ujy
Spectrum.grating
Spectrum.z
Spectrum.R
Spectrum.meta
Spectrum.sci_2d
Spectrum.copy()
Spectrum.dlam_A
Spectrum.err_flam
Spectrum.flux_flam
Spectrum.mask_valid()
Spectrum.n_pix
Spectrum.wave_A
Spectrum.wave_edges_A
compute_D_Lya()
export_lines_txt()
fit_NHI()
fit_lines()
fit_redshift()
fit_with_broad()
get_line_list()
igm_transmission()
load_result()
lya_model()
observable_lines()
plot_2d_1d()
plot_fit()
plot_fit_interactive()
plot_spectrum_interactive()
read_dict()
read_fits()
read_npz()
resolve_R()
save_result()
show_lines()
sigma_inst_A()
tau_DLA()
tau_IGM_DW()
ConstraintSet
fit_continuum()
voigt_H()
observed_wave_A()
observed_wave_um()
rest_wave_A()
skewed_gaussian_binned()
asymmetric_gaussian()
build_model()
gaussian_binned()
pixel_weight()
R_grating()
sigma_inst_kms()
jwspecmcmc
sampler="nuts"
sampler="emcee"
sampler="nautilus"
GaussianPrior
GaussianPrior.hi
GaussianPrior.lo
GaussianPrior.log_prob()
GaussianPrior.mean
GaussianPrior.sample()
GaussianPrior.std
LogUniformPrior
LogUniformPrior.hi
LogUniformPrior.lo
LogUniformPrior.log_prob()
LogUniformPrior.sample()
MCMCBroadFitResult
MCMCBroadFitResult.bic_both
MCMCBroadFitResult.bic_broad1
MCMCBroadFitResult.bic_broad2
MCMCBroadFitResult.bic_hei_both
MCMCBroadFitResult.bic_hei_broad1
MCMCBroadFitResult.bic_hei_broad2
MCMCBroadFitResult.bic_hei_off
MCMCBroadFitResult.bic_narrow
MCMCBroadFitResult.bic_oiii_both
MCMCBroadFitResult.bic_oiii_broad1
MCMCBroadFitResult.bic_oiii_broad2
MCMCBroadFitResult.bic_oiii_off
MCMCBroadFitResult.chains
MCMCBroadFitResult.constraints
MCMCBroadFitResult.continuum
MCMCBroadFitResult.convergence
MCMCBroadFitResult.doublet_flux_posterior()
MCMCBroadFitResult.doublet_snr()
MCMCBroadFitResult.flat_chains
MCMCBroadFitResult.flat_chains_free
MCMCBroadFitResult.flat_log_prob
MCMCBroadFitResult.flux_ratio_posterior()
MCMCBroadFitResult.flux_upper_limit()
MCMCBroadFitResult.flux_upper_limits()
MCMCBroadFitResult.hei_broad_selected
MCMCBroadFitResult.hei_selected
MCMCBroadFitResult.line_names
MCMCBroadFitResult.lines
MCMCBroadFitResult.mcmc_result
MCMCBroadFitResult.model_flux
MCMCBroadFitResult.oiii_broad_selected
MCMCBroadFitResult.oiii_selected
MCMCBroadFitResult.params
MCMCBroadFitResult.sampler_meta
MCMCBroadFitResult.sampler_name
MCMCBroadFitResult.selected_model
MCMCBroadFitResult.spectrum
MCMCBroadFitResult.to_fit_result()
MCMCLineResult
MCMCLineResult.amplitude
MCMCLineResult.amplitude_err
MCMCLineResult.centroid_A
MCMCLineResult.centroid_err
MCMCLineResult.ew_A
MCMCLineResult.flux
MCMCLineResult.flux_err
MCMCLineResult.flux_posterior
MCMCLineResult.name
MCMCLineResult.rest_wave_A
MCMCLineResult.sigma_A
MCMCLineResult.sigma_err
MCMCLineResult.snr
MCMCResult
MCMCResult.chains
MCMCResult.constraints
MCMCResult.continuum
MCMCResult.convergence
MCMCResult.doublet_flux_posterior()
MCMCResult.doublet_snr()
MCMCResult.flat_chains
MCMCResult.flat_chains_free
MCMCResult.flat_log_prob
MCMCResult.flux_ratio_posterior()
MCMCResult.flux_upper_limit()
MCMCResult.flux_upper_limits()
MCMCResult.line_names
MCMCResult.lines
MCMCResult.lya_params
MCMCResult.model_flux
MCMCResult.params
MCMCResult.sampler_meta
MCMCResult.sampler_name
MCMCResult.spectrum
MCMCResult.to_fit_result()
PriorSet
PriorSet.log_prior()
PriorSet.n_dim
PriorSet.priors
PriorSet.sample()
UniformPrior
UniformPrior.hi
UniformPrior.lo
UniformPrior.log_prob()
UniformPrior.sample()
load_mcmc_result()
plot_corner()
plot_flux_posterior()
plot_traces()
priors_from_bounds()
save_mcmc_result()
effective_sample_size()
gelman_rubin()
summarise_convergence()
make_jax_log_likelihood()
LikelihoodSpec
log_likelihood()
log_probability()
Prior
run_emcee()
run_nautilus()
run_nuts()
jwspecabund
AbundanceResult
AbundanceResult.ArO
AbundanceResult.ArO_err
AbundanceResult.Av
AbundanceResult.Av_err
AbundanceResult.Av_posterior
AbundanceResult.CO
AbundanceResult.CO_err
AbundanceResult.CO_posterior
AbundanceResult.NO
AbundanceResult.NO_err
AbundanceResult.NO_icf_name
AbundanceResult.NO_posterior
AbundanceResult.NO_tiers
AbundanceResult.NeO
AbundanceResult.NeO_err
AbundanceResult.OH
AbundanceResult.OH_err
AbundanceResult.OH_posterior
AbundanceResult.SO
AbundanceResult.SO_err
AbundanceResult.Te_high
AbundanceResult.Te_high_err
AbundanceResult.Te_low
AbundanceResult.Te_low_err
AbundanceResult.alt_results
AbundanceResult.chi2
AbundanceResult.diagnostics
AbundanceResult.excluded_lines
AbundanceResult.failures
AbundanceResult.icf_method
AbundanceResult.icf_values
AbundanceResult.ionic
AbundanceResult.ionic_ul_details
AbundanceResult.ionic_upper_limits
AbundanceResult.logU
AbundanceResult.logU_err
AbundanceResult.lya_f_esc
AbundanceResult.lya_f_esc_details
AbundanceResult.lya_f_esc_err
AbundanceResult.lya_f_esc_posterior
AbundanceResult.method
AbundanceResult.ne
AbundanceResult.ne_high
AbundanceResult.ne_low
AbundanceResult.ne_mid
AbundanceResult.ratios_used
AbundanceResult.summary()
Te_low_from_high()
cardelli_extinction()
compute_Av_balmer_pair()
compute_Av_from_balmer()
compute_Av_multi_balmer()
compute_NO_martinez25()
compute_Te_NII()
compute_Te_OIII()
compute_Te_OIII_1666()
compute_abundances()
compute_ionic_abundances()
compute_line_ratios()
compute_lya_escape_fraction()
compute_lya_escape_fraction_mc()
compute_ne()
compute_ne_CIII()
compute_ne_NIV()
compute_total_abundances()
dust_correct_fluxes()
forward_model()
hbeta_emissivity_aller84()
icf_argon()
icf_neon()
icf_nitrogen()
icf_sulfur()
log_U_from_N43()
log_U_from_O32()
salim_attenuation()
sanders25_metallicity()
ciii_ratio_at_density()
niv_ratio_at_density()
icf_carbon()
compute_NO_martinez25_locked()
icf_NpNpp_OpOpp()
icf_NpOp()
icf_NppNppp_Opp()
icf_NppOpp()
icf_NpppOpp()
Visualisation
plot_fit
plot_2d_1d
plot_spectrum_interactive
plot_fit_interactive
plot_corner
plot_traces
plot_flux_posterior
Methodology
_extract_fluxes(result)
(fluxes, errors, is_mcmc)
_extract_posteriors(result)
{name: flux_posterior_array}
_filter_low_snr()
_run_direct()
_run_direct_mcmc()
icf_method="direct_sum"
icf_method="martinez25"
"auto"
icf_method="izotov06"
Project