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Functions181 in github.com/ACCarnall/bagpipes

↓ 17 callersMethodexp
zmet distributed like P(Z) = exp(-z/z_mean), no age dependency.
bagpipes/models/chemical_enrichment_history.py:138
↓ 16 callersMethodplot
(self, show=True, return_y_scale=False, y_scale_spec=None)
bagpipes/input/galaxy.py:238
↓ 9 callersMethod_update_model_components
Generates a model object with the current parameters.
bagpipes/fitting/fitted_model.py:278
↓ 9 callersFunctionupdate_rcParams
()
bagpipes/plotting/general.py:94
↓ 7 callersMethodupdate
(self, param)
bagpipes/models/agn_model.py:22
↓ 6 callersMethodmean
(self)
bagpipes/fitting/noise.py:138
↓ 5 callersFunctionauto_x_ticks
(ax, nticks=5.)
bagpipes/plotting/general.py:179
↓ 4 callersMethod_calzetti
Calculate the ratio A(lambda)/A(V) for the Calzetti et al. (2000) attenuation curve.
bagpipes/models/dust_attenuation_model.py:159
↓ 4 callersMethod_update_model_components
Generates a model object with the current parameters.
bagpipes/fitting/check_priors.py:110
↓ 4 callersFunctionauto_axis_label
(ax, y_scale, z_non_zero=True, log_x=False)
bagpipes/plotting/general.py:249
↓ 4 callersFunctiondeltanu_D
Thermally broadened frequency (in Hz), given a temperature `T` in K (see Dijkstra 2014) and optional turbulent velocity `b` in km/s
bagpipes/models/dla_model.py:21
↓ 3 callersMethod_fit_object
Fit the specified object and update the catalogue.
bagpipes/catalogue/fit_catalogue.py:304
↓ 3 callersFunctiondirichlet
This function samples from a Dirichlet distribution based on N-1 independent random variables (r) in the range (0, 1). The method is that of
bagpipes/fitting/prior.py:9
↓ 3 callersFunctionfix_param_names
(fit_params)
bagpipes/plotting/general.py:207
↓ 3 callersMethodget_advanced_quantities
Calculates advanced derived posterior quantities, these are slower because they require the full model spectra.
bagpipes/fitting/posterior.py:157
↓ 3 callersMethodspectrum
Obtain a 1D spectrum for a given star-formation and chemical enrichment history, ionization parameter and t_bc. parameters -
bagpipes/models/nebular_model.py:67
↓ 3 callersMethodtrans
Get the IGM transmission at a given redshift.
bagpipes/models/igm_model.py:53
↓ 2 callersMethod_calculate_photometry
This method generates predictions for observed photometry. It resamples filter curves onto observed frame wavelengths and integrates
bagpipes/models/model_galaxy.py:504
↓ 2 callersMethod_cardelli
Calculate the ratio A(lambda)/A(V) for the Cardelli et al. (1989) extinction curve.
bagpipes/models/dust_attenuation_model.py:108
↓ 2 callersMethod_interpolate_grid
Interpolates a chosen grid in logU and collapses over star- formation and chemical enrichment history to get 1D models.
bagpipes/models/nebular_model.py:107
↓ 2 callersMethod_smc_gordon
Calculate the ratio A(lambda)/A(V) for the Gordon et al. (2003) Small Magellanic Cloud extinction curve. Warning: this currently dive
bagpipes/models/dust_attenuation_model.py:186
↓ 2 callersFunctionadd_model_photometry
Adds model photometry to the passed axis.
bagpipes/plotting/plot_model_galaxy.py:52
↓ 2 callersFunctionadd_observed_photometry
Adds photometric data to the passed axes.
bagpipes/plotting/plot_galaxy.py:67
↓ 2 callersFunctionadd_spectrum
Add a spectrum to the passed axes. Adds errors if they are included in the spectrum object as a third column.
bagpipes/plotting/plot_spectrum.py:15
↓ 2 callersFunctionadd_z_axis
(ax, z_on_y=False, zvals=[0, 0.5, 1, 2, 4, 10])
bagpipes/plotting/general.py:285
↓ 2 callersMethodgaussian_model
(self, central_wav, sigma_vel, norm)
bagpipes/models/agn_model.py:48
↓ 2 callersFunctionget_Inoue14_trans
Calculate IGM transmission using Inoue et al. (2014) model.
bagpipes/models/making/igm_inoue2014.py:16
↓ 2 callersFunctionget_bagpipes_spectrum
Makes a bagpipes burst model and returns the spectrum.
bagpipes/models/making/make_cloudy_models.py:103
↓ 2 callersMethodget_photometry
Calculates photometric fluxes. The filters are first re- sampled onto the same wavelength grid with transmission values blueshifted b
bagpipes/filters/filter_set.py:103
↓ 2 callersFunctionhist1d
(samples, ax, smooth=False, label=None, color="orange", percentiles=True, zorder=4, bins=50, lw=2,
bagpipes/plotting/general.py:117
↓ 2 callersFunctionmake_bins
A general function for turning an array of bin midpoints into an array of bin left hand side positions and bin widths. Splits the distance be
bagpipes/utils.py:31
↓ 2 callersFunctionmeasure_index
(ind_dict, spectrum, redshift)
bagpipes/input/spectral_indices.py:6
↓ 2 callersMethodresample_filter_curves
Resamples the filter curves onto a new set of wavelengths and creates a 2D array of filter curves on this sampling.
bagpipes/filters/filter_set.py:84
↓ 2 callersMethodsample
Sample from the prior distribution.
bagpipes/fitting/prior.py:62
↓ 2 callersFunctionsingle_index
Measure spectral indices, either an EW or flux ratio.
bagpipes/input/spectral_indices.py:52
↓ 2 callersMethodupdate
Update the model outputs to reflect new parameter values in the model_components dictionary. Note that only the changing of numerical
bagpipes/models/model_galaxy.py:281
↓ 1 callersMethodVW07
Two component dust law based on Charlot + Fall (2000) model, Stars still embedded in birth clouds (age < 10Myr) have steeper
bagpipes/models/dust_attenuation_model.py:92
↓ 1 callersFunctionVoigt
Approximation of Voigt function of `x` (from Tasitsiomi 2006 or Tepper-Garcia 2006), given a temperature `T` in K and optional turbulent
bagpipes/models/dla_model.py:31
↓ 1 callersMethod_calculate_derived_quantities
(self)
bagpipes/models/star_formation_history.py:123
↓ 1 callersMethod_calculate_effective_wavelengths
Calculates effective wavelengths for each filter curve.
bagpipes/filters/filter_set.py:71
↓ 1 callersMethod_calculate_full_spectrum
This method combines the models for the various emission and absorption processes to generate the internal full galaxy spectrum held
bagpipes/models/model_galaxy.py:343
↓ 1 callersMethod_calculate_min_max_wavelengths
Finds the min and max wavelength values across all of the filter curves.
bagpipes/filters/filter_set.py:49
↓ 1 callersMethod_calculate_spectrum
This method generates predictions for observed spectroscopy. It optionally applies a Gaussian velocity dispersion then resamples onto
bagpipes/models/model_galaxy.py:530
↓ 1 callersMethod_calculate_uvj_mags
Obtain (unnormalised) rest-frame UVJ magnitudes.
bagpipes/models/model_galaxy.py:586
↓ 1 callersMethod_convert_units
Convert between ergs s^-1 cm^-2 A^-1 and microjanskys if there is a difference between the specified input and output units.
bagpipes/input/galaxy.py:179
↓ 1 callersMethod_fit_mpi_serial
Run through the catalogue fitting multiple objects at once on different cores.
bagpipes/catalogue/fit_catalogue.py:201
↓ 1 callersMethod_get_R_curve_wav_sampling
Calculate wavelength sampling for the model to be resampled onto in order to apply variable spectral broadening. Only used if a resol
bagpipes/models/model_galaxy.py:211
↓ 1 callersMethod_get_index_spec_wavs
Generate an appropriate spec_wavs array for covering the spectral indices specified in index_list.
bagpipes/models/model_galaxy.py:247
↓ 1 callersMethod_get_wavelength_sampling
Calculate the optimal wavelength sampling for the model given the required resolution values specified in the config file. The way th
bagpipes/models/model_galaxy.py:133
↓ 1 callersMethod_lnlike_indices
Calculates the log-likelihood for spectral indices.
bagpipes/fitting/fitted_model.py:270
↓ 1 callersMethod_lnlike_line_fluxes
Calculates the log-likelihood for spectral indices.
bagpipes/fitting/fitted_model.py:258
↓ 1 callersMethod_lnlike_phot
Calculates the log-likelihood for photometric data.
bagpipes/fitting/fitted_model.py:195
↓ 1 callersMethod_lnlike_spec
Calculates the log-likelihood for spectroscopic data. This includes options for fitting flexible spectral calibration and covariant n
bagpipes/fitting/fitted_model.py:203
↓ 1 callersMethod_load_filter_curves
Loads filter files for the specified filt_list and truncates any zeros from either of their edges.
bagpipes/filters/filter_set.py:29
↓ 1 callersMethod_mask
Set the error spectrum to infinity in masked regions.
bagpipes/input/galaxy.py:214
↓ 1 callersMethod_print_results
Print the 16th, 50th, 84th percentiles of the posterior.
bagpipes/fitting/fit.py:311
↓ 1 callersMethod_process_fit_instructions
(self)
bagpipes/fitting/fitted_model.py:50
↓ 1 callersMethod_process_fit_instructions
(self)
bagpipes/fitting/check_priors.py:47
↓ 1 callersFunction_read_multinest_data
Read MultiNest data. By default, Fortran drops the "E" symbol for 3-digit exponent output (e.g., '0.148232-104'). This impacts the outpu
bagpipes/fitting/fit.py:47
↓ 1 callersMethod_resample_in_age
Resamples the intermediate stellar grids to the age sampling which is set in the config file. This has to be done carefully as summin
bagpipes/models/stellar_model.py:44
↓ 1 callersMethod_resample_in_wavelength
Resamples the raw stellar grids to the input wavs.
bagpipes/models/stellar_model.py:26
↓ 1 callersMethod_resample_in_wavelength
Resample the raw grid to the input wavelengths.
bagpipes/models/igm_model.py:34
↓ 1 callersMethod_resample_live_frac_grid
(self)
bagpipes/models/star_formation_history.py:172
↓ 1 callersMethod_set_constants
Calculate constant factors used in the lnlike function.
bagpipes/fitting/fitted_model.py:115
↓ 1 callersMethod_set_redshift
Sets the corrrect redshift (range) in self.fit_instructions for the object being fitted.
bagpipes/catalogue/fit_catalogue.py:271
↓ 1 callersMethod_setup_catalogue
Set up the initial blank output catalogue.
bagpipes/catalogue/fit_catalogue.py:393
↓ 1 callersMethod_setup_grids
Loads Cloudy nebular continuum grid and resamples to the input wavelengths. Loads nebular line grids and adds line fluxes to the corr
bagpipes/models/nebular_model.py:26
↓ 1 callersMethod_setup_vars
Set up list of variables to go in the output catalogue.
bagpipes/catalogue/fit_catalogue.py:383
↓ 1 callersFunctionadd_calibration
(fit, ax)
bagpipes/plotting/plot_calibration.py:37
↓ 1 callersFunctionadd_full_spectrum
(model, ax, color="darkorange", lw=1)
bagpipes/plotting/plot_model_galaxy.py:102
↓ 1 callersFunctionadd_observed_photometry_linear
Adds photometric data to the passed axes without doing any manipulation of the axes or labels.
bagpipes/plotting/plot_galaxy.py:117
↓ 1 callersFunctionadd_photometry_posterior
(fit, ax, zorder=4, y_scale=None, color1=None, color2=None, skip_no_obs=False,
bagpipes/plotting/plot_spectrum_posterior.py:44
↓ 1 callersFunctionadd_sfh
Creates a plot of sfr(t) for a given star-formation history.
bagpipes/plotting/plot_sfh.py:36
↓ 1 callersFunctionadd_sfh_posterior
(fit, ax, colorscheme="bw", z_axis=True, zorder=4, label=None, zvals=[0, 0.5, 1, 2, 4, 1
bagpipes/plotting/plot_sfh_posterior.py:39
↓ 1 callersFunctionadd_spectrum_posterior
(fit, ax, zorder=4, y_scale=None)
bagpipes/plotting/plot_spectrum_posterior.py:104
↓ 1 callersFunctioncompile_cloudy_grid
(path)
bagpipes/models/making/make_cloudy_models.py:277
↓ 1 callersMethoddelta
Delta function metallicity history, default unless specified.
bagpipes/models/chemical_enrichment_history.py:43
↓ 1 callersFunctiondla_trans
Lyman-alpha optical depth given a neutral hydrogen column density `N_HI` in cm^-2, temperature `T` in K, and optional turbulent velocity
bagpipes/models/dla_model.py:65
↓ 1 callersFunctionextract_cloudy_results
Loads individual cloudy results from the output files and converts the units to L_sol/A for continuum, L_sol for lines.
bagpipes/models/making/make_cloudy_models.py:221
↓ 1 callersMethodfit
Run through the catalogue fitting each object. Parameters ---------- verbose : bool - optional Set to True to g
bagpipes/catalogue/fit_catalogue.py:134
↓ 1 callersMethodget_basic_quantities
Calculates basic posterior quantities, these are fast as they are derived only from the SFH model, not the spectral model.
bagpipes/fitting/posterior.py:127
↓ 1 callersMethodget_basic_quantities
Calculates basic prior quantities, these are fast as they are derived only from the SFH model, not the spectral model.
bagpipes/fitting/check_priors.py:159
↓ 1 callersMethodget_dirichlet_tx
Calculate tx vals for any Dirichlet distributed params.
bagpipes/fitting/posterior.py:90
↓ 1 callersFunctioninterp_discont
Interpolates separately on both sides of a discontinuity, not over it
bagpipes/models/igm_model.py:8
↓ 1 callersMethodiyer2019
(self, sfr, param)
bagpipes/models/star_formation_history.py:297
↓ 1 callersMethodline_fluxes
Obtain line fluxes for a given star-formation and chemical enrichment history, ionization parameter and t_bc. parameters ---
bagpipes/models/nebular_model.py:87
↓ 1 callersMethodlnlike
Returns the log-likelihood for a given parameter vector.
bagpipes/fitting/fitted_model.py:133
↓ 1 callersFunctionmake_cloudy_input_file
Makes an instructions file for cloudy.
bagpipes/models/making/make_cloudy_models.py:140
↓ 1 callersFunctionmake_cloudy_sed_file
Saves a bagpipes spectrum in the correct format to the cloudy sed files directory.
bagpipes/models/making/make_cloudy_models.py:122
↓ 1 callersFunctionmake_hist_arrays
convert x and y arrays for a line plot to a histogram plot.
bagpipes/plotting/general.py:109
↓ 1 callersMethodmassformed_at_redshift
(self, redshift)
bagpipes/models/star_formation_history.py:183
↓ 1 callersFunctionmpi_combine_array
Combines array sections from different cores.
bagpipes/models/making/make_cloudy_models.py:68
↓ 1 callersFunctionmpi_split_array
Distributes array elements to cores when using mpi.
bagpipes/models/making/make_cloudy_models.py:33
↓ 1 callersMethodplot
(self, show=True, color="default")
bagpipes/models/model_galaxy.py:591
↓ 1 callersMethodplot_1d_posterior
(self, show=False, save=True)
bagpipes/fitting/fit.py:335
↓ 1 callersMethodplot_calibration
(self, show=False, save=True)
bagpipes/fitting/fit.py:345
↓ 1 callersMethodplot_corner
(self, show=False, save=True)
bagpipes/fitting/fit.py:332
↓ 1 callersFunctionplot_galaxy
Make a quick plot of the data loaded into a galaxy object.
bagpipes/plotting/plot_galaxy.py:16
↓ 1 callersMethodplot_sfh_posterior
(self, show=False, save=True, colorscheme="bw")
bagpipes/fitting/fit.py:338
↓ 1 callersMethodplot_spectrum_posterior
(self, show=False, save=True)
bagpipes/fitting/fit.py:342
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