pulsar_spectra modules
catalogue
Loads all the data required by vcstools from the data directory.
- pulsar_spectra.catalogue.all_flux_from_atnf(query=None)[source]
Queries the ATNF database for flux info for all pulsar at all frequencies.
- Parameters
- querypsrqpy object, optional
A previous psrqpy.QueryATNF query. Can be supplied to prevent performing a new query.
- Returns
- jname_cat_dictdict
Catalgoues dictionary with the keys in the format jname_cat_dict[jname][ref][‘Frequency MHz’, ‘Flux Density mJy’, ‘Flux Density error mJy’]
'jname'strThe pulsar’s Jname.
'ref'strThe reference label.
'Frequency MHz'The observing frequency in MHz.
'Flux Density mJy'The flux density in mJy.
'Flux Density error mJy'The error of the flux density in mJy.
- pulsar_spectra.catalogue.collect_catalogue_fluxes(only_use=None, exclude=None, query=None)[source]
Collect the fluxes from all of the catalogues recorded in this repo.
- Parameters
- only_uselist, optional
A list of reference labels (in the format ‘Author_year’) of all the papers you want to use.
- excludelist, optional
A list of reference labels (in the format ‘Author_year’) of all the papers you want to exclude.
- querypsrqpy object, optional
A previous psrqpy.QueryATNF query. Can be supplied to prevent performing a new query.
- Returns
- jname_cat_list[jname]dict
Catalgoues dictionary with the keys:
'jname'strThe pulsar’s Jname.
Each dictionary contains a list of lists with the following:
- Frequency MHzlist
The observing frequency in MHz.
- Flux Density mJylist
The flux density in mJy.
- Flux Density error mJylist
The error of the flux density in mJy.
- reflist
The reference label (in the format ‘Author_year’).
- pulsar_spectra.catalogue.convert_antf_ref(ref_code, ref_dict=None)[source]
Converts an ATNF psrcat reference code to a reference in the format “Author Year”
- Parameters
- ref_codestr
An ATNF psrcat reference code as found from psrqpy.get_references(updaterefcache=True) and https://www.atnf.csiro.au/research/pulsar/psrcat/psrcat_ref.html.
- ref_dictdict, optional
A previous psrqpy.get_references query. Can be supplied to prevent performing a new query.
- Returns
- refstr
Reference in the format “Author Year”.
- pulsar_spectra.catalogue.convert_cat_list_to_dict(jname_cat_list)[source]
- Returns
- jname_cat_dictdict
Catalgoues dictionary with the keys in the format jname_cat_dict[jname][ref][‘Frequency MHz’, ‘Flux Density mJy’, ‘Flux Density error mJy’]
'jname'strThe pulsar’s Jname.
'ref'strThe reference label.
'Frequency MHz'The observing frequency in MHz.
'Flux Density mJy'The flux density in mJy.
'Flux Density error mJy'The error of the flux density in mJy.
- pulsar_spectra.catalogue.flux_from_atnf(pulsar, query=None, ref_dict=None, assumed_error=0.5)[source]
Queries the ATNF database for flux info on a particular pulsar at all frequencies.
- Parameters
- pulsarstr
The Jname of the pulsar.
- querypsrqpy object, optional
A previous psrqpy.QueryATNF query. Can be supplied to prevent performing a new query.
- ref_dictdict, optional
A previous psrqpy.get_references query. Can be supplied to prevent performing a new query.
- assumed_errorfloat, optional
If no error found, apply this factor to flux to make an assumed error.
Default: 0.5.
- Returns
- freq_alllist
All frequencies in Hz with flux values on ATNF.
- flux_alllist
The flux values corresponding to the freq_all list in mJy.
- flux_err_alllist
The uncertainty in the flux_all values.
- referenceslist
The reference keys from: https://www.atnf.csiro.au/research/pulsar/psrcat/psrcat_ref.html
models
Spectral models from Jankowski et al. 2018 and references within
- pulsar_spectra.models.broken_power_law(v, vb, a1, a2, b, v0)[source]
Broken power law:
\[\begin{split}S_v = b \left\{\begin{matrix} x^{a_1} & \mathrm{if} x ≤ x_b \\ x^{a_2}x_b^{a_1-a_2} & \mathrm{otherwise'} \end{matrix}\right.\end{split}\]where \(x=\frac{v}{1.3e9},x_b=\frac{v_b}{1.3e9}\)
- Parameters
- vlist
Frequency in Hz.
- v_bfloat
The frequency of the break in Hz.
- a_1float
The spectral index before the break.
- a_2float
The spectral index after the break.
- bfloat
Constant.
- v0float
Reference frequency.
- Returns
- S_vlist
The flux density predicted by the model.
- pulsar_spectra.models.high_frequency_cut_off_power_law(v, vc, b, v0)[source]
Power law with high-frequency cut-off off:
\[S_v = bx^{-2} \left ( 1 - \frac{x}{x_c} \right ), x < x_c\]where \(x=\frac{v}{1.3e9},x_c=\frac{v_c}{1.3e9}\)
- Parameters
- vlist
Frequency in Hz.
- v_clist
Cut off frequency in Hz.
- bfloat
Constant.
- v0float
Reference frequency.
- Returns
- S_vlist
The flux density predicted by the model.
- pulsar_spectra.models.log_parabolic_spectrum(v, a, b, c, v0)[source]
Log-parabolic spectrum:
\[\mathrm{log}_{10} S_v = ax^2 + bx +c\]where \(x=\mathrm{log}_{10} \left ( \frac{v}{1.3e9} \right )\)
- Parameters
- vlist
Frequency in Hz.
- afloat
Curvature parameter.
- bfloat
The spectral index for \(a = 0\).
- cfloat
Constant.
- v0float
Reference frequency.
- Returns
- S_vlist
The flux density predicted by the model.
- pulsar_spectra.models.low_frequency_turn_over_power_law(v, vc, a, b, beta, v0)[source]
power law with low-frequency turn-over:
\[S_v = bx^{a} exp\left ( \frac{a}{\beta} x_c^{-\beta} \right )\]where \(x=\frac{v}{1.3e9},x_c=\frac{v_c}{1.3e9}\)
- Parameters
- vlist
Frequency in Hz.
- v_clist
Trun-over frequency in Hz.
- afloat
The spectral index.
- bfloat
Constant.
- betafloat
The smoothness of the turn-over.
- v0float
Reference frequency.
- Returns
- S_vlist
The flux density predicted by the model.
- pulsar_spectra.models.model_settings(print_models=False)[source]
Holds metadata about spectral models such as common names and default fit parameters.
- Parameters
- print_modelsboolean, optional
If true, will print the models dictionary which is useful for debuging new models. Default False.
- Returns
- model_dictdict
Returns a dictionary in the format
{model_name: [model_function, short_name, start_params, mod_limits]}
spectral_fit
Function used to fit different spectral models to the fluxs_mJy densities of pulsars
- pulsar_spectra.spectral_fit.estimate_flux_density(est_freq, model, iminuit_result)[source]
Estimate a pulsar’s flux density using a previous spectra fit.
- Parameters
- est_freqfloat or list
A single or list of frequencies to estimate flux at (in MHz).
- modelfunction
The pulsar spectra model function from
pulsar_spectra.models().- miminuit.Minuit
The Minuit class after being fit in
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().
- Returns
- fitted_fluxfloat or list
The estimated flux density of the pulsar at the input frequencies.
- fitted_flux_errfloat or list
The estimated flux density errors of the pulsar at the input frequencies.
- pulsar_spectra.spectral_fit.find_best_spectral_fit(pulsar, freqs_MHz, fluxs_mJy, flux_errs_mJy, ref_all, plot_all=False, plot_best=False, plot_compare=False, plot_error=True, alternate_style=False, axis=None, secondary_fit=False, fit_range=None)[source]
Fit pulsar spectra with iminuit.
- Parameters
- pulsarstr
The Jname of the pulsar to be fit.
- freqs_MHzlist
A list of the frequencies in MHz.
- fluxs_mJylist
A list of the flux density in mJy.
- flux_errs_mJylist
A list of the uncertainty of the flux density in mJy.
- ref_alllist
A list of the reference label (in the format ‘Author_year’).
- plot_allboolean, optional
If you want to plot the result of all fits.
Default: False.- plot_bestboolean, optional
If you want to only plot the best fit.
Default: False.- plot_compareboolean, optional
If you want to make a single plot with the result of all fits.
Default: False.- plot_errorboolean, optional
If you want to include the fit error in the plot.
Default: True.- alternate_styleboolean, optional
Plot with the alternate plot style based on Jankowski 2018.
Default: False.- axisAxes, optional
The axes with which the spectrum will be plotted.
Default: None.- secondary_fitboolean, optional
Plot model with an alternate style and without markers. Does not work for comparison plots.
Default: False.- fit_rangetuple, optional
Frequency range to plot the second model over.
Default: None.
- Returns
- model_namestr
The best fit model name from
pulsar_spectra.models().- miminuit.Minuit
The Minuit class after being fit in
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().- fit_infostr
The string to label the fit with from
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().- p_bestfloat
The probability that the best-fit model is actually the best-fit model.
- p_categorystr
Category based on the quality of spectral fit, as defined in Jankowski et al. (2018).
- pulsar_spectra.spectral_fit.huber_loss_function(sq_resi, k=1.345)[source]
Robust loss function which penalises outliers, as detailed in Jankowski et al (2018).
- Parameters
- sq_resifloat or list
A single or list of the squared residuals.
- kfloat, optional
A constant that defines at which distance the loss function starts to penalize outliers.
Default: 1.345.
- Returns
- rhofloat or list
The modified squared residuals.
- pulsar_spectra.spectral_fit.iminuit_fit_spectral_model(freqs_MHz, fluxs_mJy, flux_errs_mJy, ref, model_name='simple_power_law', start_params=None, mod_limits=None, plot=False, plot_error=True, save_name='fit.png', alternate_style=False, axis=None, secondary_fit=False, fit_range=None)[source]
Fit pulsar spectra with iminuit.
- Parameters
- freqs_MHzlist
A list of the frequencies in MHz.
- fluxs_mJylist
A list of the flux density in mJy.
- flux_errs_mJylist
A list of the uncertainty of the flux density in mJy.
- reflist
A list of the reference label (in the format ‘Author_year’).
- model_namefunction, optional
One of the model names from
pulsar_spectra.models.model_settings(). Default:pulsar_spectra.models.simple_power_law().- start_paramstuple, optional
A tuple of the starting paramaters for each input to the model that iminuit will use as an initial estimate. If none provided, will use the defaults from
pulsar_spectra.models.model_settings().- mod_limitslist of `tuple`s, optional
A list of tuples where each tuples is the minimum and maximum limits that will be applied to the model by iminuit. If none provided, will use the defaults from
pulsar_spectra.models.model_settings().- plotboolean, optional
If you want to plot the result of the fit.
Default: False.- plot_errorboolean, optional
If you want to include the fit error in the plot.
Default: True.- save_namestr, optional
The name of the saved plot.
Default: “fit.png”.- alternate_styleboolean, optional
If you want to use the alternate plot style.
Default: False.- axisAxes, optional
The axes with which the spectrum will be plotted.
None.- secondary_fitboolean, optional
Plot model with an alternate style and without markers.
Default: False.- fit_rangetuple, optional
Frequency range to plot the second model over.
Default: None.
- Returns
- aicfloat
The Akaike information criterion of the fit.
- miminuit.Minuit
The Minuit class after being fit in
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().- fit_infostr
The string to label the fit with from
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().
- pulsar_spectra.spectral_fit.plot_fit(freqs_MHz, fluxs_mJy, flux_errs_mJy, ref, model, iminuit_result, fit_info, plot_error=True, save_name='fit.png', alternate_style=False, axis=None, secondary_fit=False, fit_range=None)[source]
Create a plot of the pulsar spectral fit.
- Parameters
- freqs_MHzlist
A list of the frequencies in MHz.
- fluxs_mJylist
A list of the flux density in mJy.
- flux_errs_mJylist
A list of the uncertainty of the flux density in mJy.
- reflist
A list of the reference label (in the format ‘Author_year’).
- modelfunction
One of the model functions from
pulsar_spectra.models().- iminuit_resultiminuit.Minuit
The Minuit class after being fit in
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().- fit_infostr
The string to label the fit with from
pulsar_spectra.spectral_fit.iminuit_fit_spectral_model().- plot_errorboolean, optional
If you want to include the fit error in the plot.
Default: True.- save_namestr, optional
The name of the saved plot.
Default: “fit.png”.- alternate_styleboolean, optional
Plot with the alternate plot style based on Jankowski 2018.
Default: False.- axisAxes, optional
The axes with which the spectrum will be plotted.
None.- secondary_fitboolean, optional
Plot model with an alternate style and without markers.
Default: False.- fit_rangetuple, (float, float) optional
Frequency range to plot the second model over in MHz, eg. (100, 3000).
Default: None, will use input frequency range.
- pulsar_spectra.spectral_fit.robust_cost_function(f_y, y, sigma_y, k=1.345)[source]
Robust cost function. The negative log-likelihood of a Gaussian likelihood with Huber loss.
- Parameters
- f_ylist
A list of predicted values according to the model.
- ylist
A list of measured values at the same frequency as the model values.
- sigma_ylist
A list of uncertainties corresponding to the measured values y.
- kfloat, optional
A constant that defines at which distance the loss function starts to penalize outliers.
Default: 1.345.
- Returns
- betafloat
The cost of the model fit.