WDmodel.viz module

Routines to visualize the DA White Dwarf model atmosphere fit

WDmodel.viz.plot_mcmc_line_fit(spec, linedata, model, cont_model, draws, balmer=None)

Plot a comparison of the normalized hydrogen Balmer lines of the spectrum and model

Note that we fit the full spectrum, not just the lines. The lines are extracted using a coarse continuum fit in WDmodel.fit.pre_process_spectrum(). This fit is purely cosmetic and in no way contributes to the likelihood. It’s particularly useful to detect small velocity offsets or wavelength calibration errors.

Parameters

• spec (numpy.recarray) – The spectrum. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8')]

• linedata (numpy.recarray) – The observations of the spectrum corresponding to the hydrogen Balmer lines. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8'), ('line_mask', 'i4'), ('line_ind', 'i4')]

• model (WDmodel.WDmodel.WDmodel instance) – The DA White Dwarf SED model generator

• cont_model (numpy.recarray) – The continuuum model. Must have the same structure as spec Produced by WDmodel.fit.pre_process_spectrum()

• draws (array-like) – produced by plot_mcmc_spectrum_fit() - see notes for content.

• balmer (array-like, optional) – list of Balmer lines to plot - elements must be in range [1, 6] These correspond to the lines defined in WDmodel.WDmodel.WDmodel._lines. Default is range(1, 7)

Returns

• fig (matplotlib.figure.Figure instance) – The output figure containing the line profile plot

• fig2 (matplotlib.figure.Figure instance) – The output figure containing histograms of the line residuals

See also

WDmodel.viz.plot_mcmc_spectrum_fit()

WDmodel.viz.plot_mcmc_model(spec, phot, linedata, scale_factor, phot_dispersion, objname, outdir, specfile, model, covmodel, cont_model, pbs, params, param_names, samples, samples_lnprob, covtype='Matern32', balmer=None, ndraws=21, everyn=1, savefig=False)

Make all the plots to visualize the full fit of the DA White Dwarf data

Wraps plot_mcmc_spectrum_fit(), plot_mcmc_photometry_res(), plot_mcmc_spectrum_nogp_fit(), plot_mcmc_line_fit() and corner.corner() and saves all the plots to a combined PDF, and optionally individual PDFs.

Parameters

• spec (numpy.recarray) – The spectrum. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8')]

• phot (None or numpy.recarray) – The photometry. Must have dtype=[('pb', 'str'), ('mag', '<f8'), ('mag_err', '<f8')]

• linedata (numpy.recarray) – The observations of the spectrum corresponding to the hydrogen Balmer lines. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8'), ('line_mask', 'i4'), ('line_ind', 'i4')]

• scale_factor (float) – factor by which the flux was scaled for y-axis label

• phot_dispersion (float, optional) – Excess photometric dispersion to add in quadrature with the photometric uncertainties phot.mag_err. Use if the errors are grossly underestimated. Default is 0.

• objname (str) – object name - used to title plots

• outdir (str) – controls where the plot is written out if savefig=True

• specfile (str) – Used in the title, and to set the name of the outfile if savefig=True

• model (WDmodel.WDmodel.WDmodel instance) – The DA White Dwarf SED model generator

• covmodel (WDmodel.covariance.WDmodel_CovModel instance) – The parametrized model for the covariance of the spectrum spec

• cont_model (numpy.recarray) – The continuuum model. Must have the same structure as spec Produced by WDmodel.fit.pre_process_spectrum()

• pbs (dict) – Passband dictionary containing the passbands corresponding to phot.pb and generated by WDmodel.passband.get_pbmodel().

• params (dict) – dictionary of parameters with keywords value, fixed, scale, bounds for each. Same format as returned from WDmodel.io.read_params()

• param_names (array-like) – Ordered list of free parameter names

• samples (array-like) – Samples from the flattened Markov Chain with shape (N, len(param_names))

• samples_lnprob (array-like) – Log Posterior corresponding to samples from the flattened Markov Chain with shape (N,)

• covtype ({'Matern32', 'SHO', 'Exp', 'White'}) – stationary kernel type used to parametrize the covariance in WDmodel.covariance.WDmodel_CovModel

• balmer (array-like, optional) – list of Balmer lines to plot - elements must be in range [1, 6] These correspond to the lines defined in WDmodel.WDmodel.WDmodel._lines. Default is range(1, 7)

• ndraws (int, optional) – Number of draws to make from the Markov Chain to overplot. Higher numbers provide a better sense of the uncertainty in the model at the cost of speed and a larger, slower to render output plot.

• everyn (int, optional) – If the posterior function was evaluated using only every nth observation from the data, this should be specified to visually indicate the observations used.

• savefig (bool) – if True, save the individual figures

Returns

• model_spec (numpy.recarray) – The model spectrum. Has dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8'), ('norm_flux', '<f8')] and same shape as input spec. The norm_flux attribute has the model flux without the Gaussian process prediction applied.

• SED_model (numpy.recarray) – The SED model spectrum. Has dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8')]

• model_mags (None or numpy.recarray) – If there is observed photometry, this contains the model magnitudes. Has dtype=[('pb', 'str'), ('mag', '<f8')]

WDmodel.viz.plot_mcmc_photometry_res(objname, phot, phot_dispersion, model, pbs, draws)

Plot the observed DA white dwarf photometry as well as the “best-fit” model magnitudes

Parameters

• objname (str) – object name - used to title plots

• phot (None or numpy.recarray) – The photometry. Must have dtype=[('pb', 'str'), ('mag', '<f8'), ('mag_err', '<f8')]

• phot_dispersion (float, optional) – Excess photometric dispersion to add in quadrature with the photometric uncertainties phot.mag_err. Use if the errors are grossly underestimated. Default is 0.

• model (WDmodel.WDmodel.WDmodel instance) – The DA White Dwarf SED model generator

• pbs (dict) – Passband dictionary containing the passbands corresponding to phot.pb and generated by WDmodel.passband.get_pbmodel().

• draws (array-like) – produced by plot_mcmc_spectrum_fit() - see notes for content.

Returns

• fig (matplotlib.figure.Figure instance) – The output figure

• mag_draws (array-like) – The magnitudes corresponding to the parameters draws from the Markov Chain used in fig

Notes

Each element of mag_draws contains

• wres - the difference between the observed and synthetic magnitudes

• model_mags - the model magnitudes corresponding to the current model parameters

• mu - the flux normalization parameter that must be added to the model_mags

See also

WDmodel.viz.plot_mcmc_spectrum_fit()

WDmodel.viz.plot_mcmc_spectrum_fit(spec, objname, specfile, scale_factor, model, covmodel, result, param_names, samples, ndraws=21, everyn=1)

Plot the spectrum of the DA White Dwarf and the “best fit” model

The full fit parametrizes the covariance model using a stationary Gaussian process as defined by WDmodel.covariance.WDmodel_CovModel. The posterior function constructed in WDmodel.likelihood.WDmodel_Posterior is evaluated by the sampler in the WDmodel.fit.fit_model() method. The median value is reported as the best-fit value for each of the fit parameters in WDmodel.likelihood.WDmodel_Likelihood.parameter_names.

Parameters

• spec (numpy.recarray) – The spectrum. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8')]

• objname (str) – object name - used to title plots

• outdir (str) – controls where the plot is written out if save=True

• specfile (str) – Used in the title, and to set the name of the outfile if save=True

• scale_factor (float) – factor by which the flux was scaled for y-axis label

• model (WDmodel.WDmodel.WDmodel instance) – The DA White Dwarf SED model generator

• covmodel (WDmodel.covariance.WDmodel_CovModel instance) – The parametrized model for the covariance of the spectrum spec

• result (dict) – dictionary of parameters with keywords value, fixed, scale, bounds for each. Same format as returned from WDmodel.io.read_params()

• param_names (array-like) – Ordered list of free parameter names

• samples (array-like) – Samples from the flattened Markov Chain with shape (N, len(param_names))

• ndraws (int, optional) – Number of draws to make from the Markov Chain to overplot. Higher numbers provide a better sense of the uncertainty in the model at the cost of speed and a larger, slower to render output plot.

• everyn (int, optional) – If the posterior function was evaluated using only every nth observation from the data, this should be specified to visually indicate the observations used.

Returns

• fig (matplotlib.figure.Figure instance) – The output figure

• draws (array-like) – The actual draws from the Markov Chain used in fig

Notes

It’s faster to draw samples from the posterior in one location, and pass along the same samples to all the methods in WDmodel.viz.

Consequently, most require draws as an input. This makes all the plots connected, and none will return if an error is thrown here, but this is the correct behavior as all of them are visualizing one aspect of the same fit.

Each element of draws contains

• smoothedmod - the model spectrum

• wres - the prediction from the Gaussian process

• wres_err - the diagonal of the covariance matrix for the prediction from the Gaussian process

• full_mod - the full model SED, in order to compute the synthetic photometry

• out_draw - the dictionary of model parameters from this draw. Same format as result.

WDmodel.viz.plot_mcmc_spectrum_nogp_fit(spec, objname, specfile, scale_factor, cont_model, draws, covtype='Matern32', everyn=1)

Plot the spectrum of the DA White Dwarf and the “best fit” model without the Gaussian process

Unlike plot_mcmc_spectrum_fit() this version does not apply the prediction from the Gaussian process to the spectrum model to match the observed spectrum. This visualization is useful to indicate if the Gaussian process - i.e. the kernel choice covtype used to parametrize the covariance is - is appropriate.

Parameters

• spec (numpy.recarray) – The spectrum. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8')]

• objname (str) – object name - used to title plots

• outdir (str) – controls where the plot is written out if save=True

• specfile (str) – Used in the title, and to set the name of the outfile if save=True

• scale_factor (float) – factor by which the flux was scaled for y-axis label

• cont_model (numpy.recarray) – The continuuum model. Must have the same structure as spec Produced by WDmodel.fit.pre_process_spectrum()

• draws (array-like) – produced by plot_mcmc_spectrum_fit() - see notes for content.

• covtype ({'Matern32', 'SHO', 'Exp', 'White'}) – stationary kernel type used to parametrize the covariance in WDmodel.covariance.WDmodel_CovModel

• everyn (int, optional) – If the posterior function was evaluated using only every nth observation from the data, this should be specified to visually indicate the observations used.

Returns

fig – The output figure

Return type

matplotlib.figure.Figure instance

See also

WDmodel.viz.plot_mcmc_spectrum_fit()

WDmodel.viz.plot_minuit_spectrum_fit(spec, objname, outdir, specfile, scale_factor, model, result, save=True)

Plot the MLE fit of the spectrum with the model, assuming uncorrelated noise.

Parameters

• spec (numpy.recarray) – The spectrum. Must have dtype=[('wave', '<f8'), ('flux', '<f8'), ('flux_err', '<f8')]

• objname (str) – object name - used to title plots

• outdir (str) – controls where the plot is written out if save=True

• specfile (str) – Used in the title, and to set the name of the outfile if save=True

• scale_factor (float) – factor by which the flux was scaled for y-axis label

• model (WDmodel.WDmodel.WDmodel instance) – The DA White Dwarf SED model generator

• result (dict) – dictionary of parameters with keywords value, fixed, scale, bounds for each. Same format as returned from WDmodel.io.read_params()

• save (bool) – if True, save the file

Returns

fig

Return type

matplotlib.figure.Figure instance

Notes

The MLE fit uses iminuit.Minuit.migrad() to fit the spectrum with the model. This fit doesn’t try to account for the covariance in the data, and is not expected to be great - just fast, and capable of setting a reasonable initial guess. If it is apparent from the plot that this fit is very far off, refine the initial guess to the fitter.