redback 1.0.31__py3-none-any.whl → 1.12.0__py3-none-any.whl

redback/priors/csm_shock_and_arnett_two_rphots.prior

@@ -0,0 +1,11 @@
+redshift = Uniform(0.01, 1, 'redshift', latex_label=r'$z$')
+mej = LogUniform(1e-4, 30, 'mej', latex_label = r'$M_{\mathrm{ej}}~(M_\odot)$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+csm_mass = LogUniform(1e-3, 5, 'csm_mass', latex_label=r'$M_{\mathrm{CSM}}~(M_{\odot})$')
+v_min = LogUniform(1e3, 3e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+beta = Uniform(0.4, 0.5, 'beta', latex_label=r'$\\beta$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+shell_radius = Uniform(1e-2, 10, 'shell_radius', latex_label=r'$R_{\mathrm{shell}}~(10^{14}~\mathrm{cm})$')
+shell_width_ratio = Uniform(0.1, 0.5, 'shell_width_ratio', latex_label=r'$\\Delta~R_{\mathrm{shell}}/R_{\mathrm{shell}}$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_{\\gamma}~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,1e5,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/exp_rise_powerlaw_decline.prior

@@ -0,0 +1,6 @@
+t0 = Uniform(58000, 59000, 't0', latex_label = '$t_0$')
+m_peak = Uniform(16, 20, 'm_peak', latex_label = '$m_{peak}$')
+tau_rise = Uniform(0.1, 10.0, 'tau_rise', latex_label = '$\\tau_{rise}$')
+tau_decline = Uniform(0.1, 10.0, 'tau_decline', latex_label = '$\\tau_{decline}$')
+alpha = Uniform(0.1, 5.0, 'alpha', latex_label = '$\\alpha$')
+t_peak = Uniform(59000, 59500, 't_peak', latex_label = '$t_{peak}$')

redback/priors/powerlaw_spectrum_with_absorption_and_emission_lines.prior

@@ -0,0 +1,8 @@
+aa = LogUniform(1e-2, 1e2, name='aa', latex_label=r'$A$')
+alpha = Uniform(minimum=-5, maximum=5, name='alpha', latex_label=r'$\\alpha$')
+lc1 = Uniform(2000, 7000, name='lc1', latex_label=r'$\Lambda_{\mathrm{emission}}$')
+lc2 = Uniform(2000,7000, name='lc2', latex_label=r'$\Lambda_{\mathrm{absorption}}$')
+ls1 = LogUniform(1e-34, 1e-31, name='ls1', latex_label=r'line_stength$_{\mathrm{emission}}$')
+ls2 = LogUniform(1e-34, 1e-31, name='ls2', latex_label=r'line_stength$_{\mathrm{absorption}}$')
+v1 = Uniform(1e3, 1e4, name='v1', latex_label=r'$v_{\mathrm{emission}}$')
+v2 = Uniform(1e3, 1e4, name='v2', latex_label=r'$v_{\mathrm{absorption}}$')

redback/priors/salt2.prior

@@ -0,0 +1,6 @@
+redshift = Uniform(0.1, 0.2, name='redshift', latex_label=r'$z$')
+peak_time = Uniform(10, 20, name='peak_time', latex_label=r'$t_{\mathrm{peak}}~(\mathrm{days})$')
+t0 = Uniform(0, 1, name='t0', latex_label=r'$t_0~(\mathrm{days})$')
+x0 = Uniform(1e-10, 1e-1, name='x0', latex_label=r'$x_0$')
+x1 = Normal(0, 1, name='x1', latex_label=r'$x_1$')
+c = Normal(0, 0.1, name='c', latex_label=r'$c$')

redback/priors/shock_cooling_and_arnett_bolometric.prior

@@ -0,0 +1,11 @@
+log10_mass = Uniform(-2, 3, 'log10_mass', latex_label=r'$\log_{10}~m_{\mathrm{en}} / M_\odot$')
+log10_radius = Uniform(10, 14, 'log10_radius', latex_label=r'$\log_{10}~R_{\mathrm{en}} / {\mathrm{cm}}^{-3}$')
+log10_energy = Uniform(40, 52, 'log10_energy', latex_label=r'$\log_{10}~E_{\mathrm{en}} / {\mathrm{erg}}$')
+nn = Uniform(8, 12, 'nn', latex_label=r'$nn$')
+delta = Uniform(1, 1.5, 'delta', latex_label=r'$\\Delta$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+mej = LogUniform(1e-4, 100, 'mej', latex_label = r'$M_{\mathrm{ej} }~(M_\odot)$')
+vej = LogUniform(1e3, 1e5, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+kappa = Uniform(0.05, 2, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_\\gamma~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,1e5,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/shockcooling_morag.prior

@@ -0,0 +1,6 @@
+redshift = Uniform(0.05, 0.3, 'redshift', latex_label = r'$z$')
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+f_rho_m = Uniform(0.01, 20, 'f_rho_m', latex_label = r'$f_{\\rho_{m}}$')
+radius =  LogUniform(1e-2, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')

redback/priors/shockcooling_morag_and_arnett.prior

@@ -0,0 +1,10 @@
+redshift = Uniform(0.05, 0.3, 'redshift', latex_label = r'$z$')
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+mej = LogUniform(1e-4, 100, 'mej', latex_label = r'$M_{\mathrm{ej} }~(M_\odot)$')
+f_rho = Uniform(0.5, 3, 'f_rho', latex_label = r'$f_{\\rho}$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+radius =  LogUniform(1e-3, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_\\gamma~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,8e3,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/shockcooling_morag_and_arnett_bolometric.prior

@@ -0,0 +1,9 @@
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+mej = LogUniform(1e-4, 100, 'mej', latex_label = r'$M_{\mathrm{ej} }~(M_\odot)$')
+f_rho = Uniform(0.5, 3, 'f_rho', latex_label = r'$f_{\\rho}$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+radius =  LogUniform(1e-3, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_\\gamma~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,8e3,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/shockcooling_morag_bolometric.prior

@@ -0,0 +1,5 @@
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+f_rho_m = Uniform(0.01, 20, 'f_rho_m', latex_label = r'$f_{\\rho_{m}}$')
+radius =  LogUniform(1e-2, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')

redback/priors/shockcooling_sapirandwaxman.prior

@@ -0,0 +1,6 @@
+redshift = Uniform(0.05, 0.3, 'redshift', latex_label = r'$z$')
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+f_rho_m = Uniform(0.01, 20, 'f_rho_m', latex_label = r'$f_{\\rho_{m}}$')
+radius =  LogUniform(1e-2, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')

redback/priors/shockcooling_sapirandwaxman_bolometric.prior

@@ -0,0 +1,5 @@
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = Uniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+f_rho_m = Uniform(0.01, 20, 'f_rho_m', latex_label = r'$f_{\\rho_{m}}$')
+radius =  Uniform(1e-2, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')

redback/priors/shockcooling_sapirwaxman_and_arnett.prior

@@ -0,0 +1,10 @@
+redshift = Uniform(0.05, 0.3, 'redshift', latex_label = r'$z$')
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+mej = LogUniform(1e-4, 100, 'mej', latex_label = r'$M_{\mathrm{ej} }~(M_\odot)$')
+f_rho = Uniform(0.5, 3, 'f_rho', latex_label = r'$f_{\\rho}$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+radius =  LogUniform(1e-3, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_\\gamma~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,8e3,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/shockcooling_sapirwaxman_and_arnett_bolometric.prior

@@ -0,0 +1,9 @@
+v_shock = LogUniform(1e3, 5e4, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+m_env = LogUniform(1e-3, 5, 'm_env', latex_label = r'$M_{\mathrm{env}}~(M_{\odot})$')
+mej = LogUniform(1e-4, 100, 'mej', latex_label = r'$M_{\mathrm{ej} }~(M_\odot)$')
+f_rho = Uniform(0.5, 3, 'f_rho', latex_label = r'$f_{\\rho}$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+radius =  LogUniform(1e-3, 10, 'radius', latex_label=r'$R_{\mathrm{star}}~(10^{13}~\mathrm{cm})$')
+kappa = Uniform(0.01, 1, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_\\gamma~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,8e3,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/shocked_cocoon_and_arnett.prior

@@ -0,0 +1,13 @@
+redshift = Uniform(1e-3,3,name='redshift', latex_label = r'$z$')
+mej_c = Uniform(0.1, 2, 'mej_c', latex_label = r'$M_{\mathrm{cocoon} }~(M_\odot)$')
+vej_c = Uniform(0.01, 0.3, 'vej_c', latex_label = r'$v_{\mathrm{cocoon}}~(c)$')
+eta = Uniform(1, 5, '\\eta', latex_label = r'$\\eta$')
+tshock = Uniform(0.1, 100, 'tshock', latex_label = r'$t_{\mathrm{shock}}~(\mathrm{s})$')
+shocked_fraction = Uniform(0.01, 1, 'shocked_fraction', latex_label = r'$f_{\mathrm{shocked}}$')
+cos_theta_cocoon = Uniform(0.866, 1.0, 'cos_theta_cocoon', latex_label = r'$\cos~\\theta_{\mathrm{cocoon}}$')
+f_nickel = LogUniform(1e-3,1,name='f_nickel', latex_label = r'$f_{\mathrm{Ni}}$')
+mej = LogUniform(0.1, 100, 'mej', latex_label = r'$M_{\mathrm{ej}}~(M_\odot)$')
+vej = LogUniform(1e3, 1e5, 'vej', latex_label = r'$v_{\mathrm{ej}}~(\mathrm{km}/\mathrm{s})$')
+kappa = Uniform(0.05, 2, 'kappa', latex_label = r'$\\kappa~(\mathrm{cm}^{2}/\mathrm{g})$')
+kappa_gamma = LogUniform(1e-4, 1e4, 'kappa_gamma', latex_label = r'$\\kappa_{\\gamma}~(\mathrm{cm}^{2}/\mathrm{g})$')
+temperature_floor = LogUniform(1e3,1e5,name = 'temperature_floor', latex_label = r'$T_{\mathrm{floor}}~(\mathrm{K})$')

redback/priors/synchrotron_ism.prior

@@ -0,0 +1,6 @@
+redshift = Uniform(0.01, 3, 'redshift', latex_label=r'$z$')
+v_s = Uniform(1e3, 3e4, 'vej', latex_label = r'$v_{\mathrm{s}}~(\mathrm{km}/\mathrm{s})$')
+logn0 = Uniform(-5, 2, 'logn0', latex_label=r'$\log_{10}~n_{\mathrm{ism}} / {\mathrm{cm}}^{-3}$')
+logepse = Uniform(-5, 0, 'logepse', latex_label=r'$\log_{10}~\\epsilon_{e}$')
+logepsb = Uniform(-5, 0, 'logepsb', latex_label=r'$\log_{10}~\\epsilon_{B}$')
+p = Uniform(2, 3, 'p', latex_label=r'$p$')

redback/priors/synchrotron_massloss.prior

@@ -0,0 +1,6 @@
+redshift = Uniform(0.01, 3, 'redshift', latex_label=r'$z$')
+v_s = Uniform(1e3, 3e4, 'vej', latex_label = r'$v_{\mathrm{s}}~(\mathrm{km}/\mathrm{s})$')
+log_Mdot_vwind = Uniform(-10, -4, 'log_Mdot_vwind', latex_label = r'$\dot{M}/u_{\mathrm{wind}}~(M_\odot \mathrm{s km year}^{-1})$')
+logepse = Uniform(-5, 0, 'logepse', latex_label=r'$\log_{10}~\\epsilon_{e}$')
+logepsb = Uniform(-5, 0, 'logepsb', latex_label=r'$\log_{10}~\\epsilon_{B}$')
+p = Uniform(2, 3, 'p', latex_label=r'$p$')

redback/priors/synchrotron_pldensity.prior

@@ -0,0 +1,7 @@
+redshift = Uniform(0.01, 3, 'redshift', latex_label=r'$z$')
+v_s = Uniform(1e3, 3e4, 'vej', latex_label = r'$v_{\mathrm{s}}~(\mathrm{km}/\mathrm{s})$')
+logA = Uniform(-5, 5, 'logA', latex_label=r'$A / {\mathrm{cm}}^{-3}$')
+s = Uniform(0, 2, 's', latex_label=r'$s$')
+logepse = Uniform(-5, 0, 'logepse', latex_label=r'$\log_{10}~\\epsilon_{e}$')
+logepsb = Uniform(-5, 0, 'logepsb', latex_label=r'$\log_{10}~\\epsilon_{B}$')
+p = Uniform(2, 3, 'p', latex_label=r'$p$')

redback/priors/thermal_synchrotron_v2_fluxdensity.prior

@@ -0,0 +1,8 @@
+redshift = Uniform(0.01, 3, 'redshift', latex_label=r'$z$')
+bG_sh = Uniform(0.1, 10, 'bG_sh', latex_label=r'$\\Gamma\\beta$')
+log_Mdot_vwind = Uniform(-10, -4, 'log_Mdot_vwind', latex_label = r'$\dot{M}/u_{\mathrm{wind}}~(M_\odot \mathrm{s km year}^{-1})$')
+n_ism = Uniform(0, 10, 'n_ism', latex_label=r'$n_{\mathrm{ism}} / {\mathrm{cm}}^{-3}$')
+logepse = Uniform(-5, 0, 'logepse', latex_label=r'$\log_{10}~\\epsilon_{e}$')
+logepsb = Uniform(-5, 0, 'logepsb', latex_label=r'$\log_{10}~\\epsilon_{B}$')
+xi = Uniform(0.01, 1., 'xi', latex_label=r'$\\xi_{N}$')
+p = Uniform(2, 3, 'p', latex_label=r'$p$')

redback/priors/thermal_synchrotron_v2_lnu.prior

@@ -0,0 +1,7 @@
+bG_sh = Uniform(0.1, 10, 'bG_sh', latex_label=r'$\\\Gamma\\beta$')
+log_Mdot_vwind = Uniform(-10, -4, 'log_Mdot_vwind', latex_label = r'$\dot{M}/u_{\mathrm{wind}}~(M_\odot \mathrm{s km year}^{-1})$')
+n_ism = Uniform(0, 10, 'n_ism', latex_label=r'$n_{\mathrm{ism}} / {\mathrm{cm}}^{-3}$')
+logepse = Uniform(-5, 0, 'logepse', latex_label=r'$\log_{10}~\\epsilon_{e}$')
+logepsb = Uniform(-5, 0, 'logepsb', latex_label=r'$\log_{10}~\\epsilon_{B}$')
+xi = Uniform(0.01, 1., 'xi', latex_label=r'$\\xi_{N}$')
+p = Uniform(2, 3, 'p', latex_label=r'$p$')

redback/priors.py

@@ -40,12 +40,19 @@ def get_priors(model, times=None, y=None, yerr=None, dt=None, **kwargs):
         return priors
 
     priors = PriorDict()
+
+    if model in redback.model_library.base_models_dict:
+        logger.info(f'Setting up prior for base model {model}.')
+        logger.info(f'You will need to explicitly set a prior on t0 and or extinction if relevant')
+
     try:
         filename = os.path.join(os.path.dirname(__file__), 'priors', f'{model}.prior')
         priors.from_file(filename)
-    except FileNotFoundError as e:
-        logger.warning(e)
-        logger.warning('Returning empty PriorDict.')
+    except FileNotFoundError:
+        logger.warning(f'No prior file found for model {model}. '
+                    f'Perhaps you also want to set up the prior for the base model? '
+                    f'Or you may need to set up your prior explicitly.')
+        logger.info('Returning Empty PriorDict.')
     return priors
 
 

redback/result.py

@@ -136,6 +136,14 @@ class RedbackResult(Result):
         return self.transient.plot_lightcurve(model=model, posterior=self.posterior,
                                               model_kwargs=self.model_kwargs, **kwargs)
 
+    def plot_spectrum(self, model: Union[callable, str] = None, **kwargs: None) -> matplotlib.axes.Axes:
+        """ Reconstructs the transient and calls the specific `plot_spectrum` method.
+        Detailed documentation appears below by running `print(plot_spectrum.__doc__)` """
+        if model is None:
+            model = model_library.all_models_dict[self.model]
+        return self.transient.plot_spectrum(model=model, posterior=self.posterior,
+                                              model_kwargs=self.model_kwargs, **kwargs)
+
     def plot_residual(self, model: Union[callable, str] = None, **kwargs: None) -> matplotlib.axes.Axes:
         """Reconstructs the transient and calls the specific `plot_residual` method.
         Detailed documentation appears below by running `print(plot_residual.__doc__)` """
@@ -168,7 +176,7 @@ class RedbackResult(Result):
     plot_multiband.__doc__ = plot_multiband.__doc__ + redback.transient.Transient.plot_multiband.__doc__
     plot_multiband_lightcurve.__doc__ = \
         plot_multiband_lightcurve.__doc__ + redback.transient.Transient.plot_multiband_lightcurve.__doc__
-
+    plot_spectrum.__doc__ = plot_spectrum.__doc__ + redback.transient.Spectrum.plot_spectrum.__doc__
 
 def read_in_result(
         filename: str = None, outdir: str = None, label: str = None,

redback/sampler.py

@@ -12,7 +12,7 @@ from redback.result import RedbackResult
 from redback.utils import logger
 from redback.transient.afterglow import Afterglow
 from redback.transient.prompt import PromptTimeSeries
-from redback.transient.transient import OpticalTransient, Transient
+from redback.transient.transient import OpticalTransient, Transient, Spectrum
 
 
 dirname = os.path.dirname(__file__)
@@ -40,11 +40,13 @@ def fit_model(
     :param resume: Whether to resume the run from a checkpoint if available.
     :param save_format: The format to save the result in. (Default value = 'json'_
     :param model_kwargs: Additional keyword arguments for the model.
-    :param kwargs: Additional parameters that will be passed to the sampler
+    :param clean: If True, rerun the fitting, if false try to use previous results in the output directory.
     :param plot: If True, create corner and lightcurve plot
+    :param kwargs: Additional parameters that will be passed to the sampler
     :return: Redback result object, transient specific data object
     """
     if isinstance(model, str):
+        modelname = model
         model = all_models_dict[model]
 
     if transient.data_mode in ["flux_density", "magnitude"]:
@@ -53,12 +55,22 @@ def fit_model(
                 f"Transient data mode {transient.data_mode} is inconsistent with "
                 f"output format {model_kwargs['output_format']}. These should be the same.")
 
-    prior = prior or bilby.prior.PriorDict(filename=f"{dirname}/Priors/{model}.prior")
+    if prior is None:
+        prior = bilby.prior.PriorDict(filename=f"{dirname}/priors/{modelname}.prior")
+        logger.warning(f"No prior given. Using default priors for {modelname}")
+    else:
+        prior = prior
     outdir = outdir or f"{transient.directory_structure.directory_path}/{model.__name__}"
     Path(outdir).mkdir(parents=True, exist_ok=True)
     label = label or transient.name
 
-    if isinstance(transient, Afterglow):
+    if isinstance(transient, Spectrum):
+        return _fit_spectrum(transient=transient, model=model, outdir=outdir, label=label, sampler=sampler,
+                             nlive=nlive, prior=prior, walks=walks,
+                             resume=resume, save_format=save_format, model_kwargs=model_kwargs,
+                             plot=plot, **kwargs)
+
+    elif isinstance(transient, Afterglow):
         return _fit_grb(
             transient=transient, model=model, outdir=outdir, label=label, sampler=sampler, nlive=nlive, prior=prior,
             walks=walks, use_photon_index_prior=use_photon_index_prior, resume=resume, save_format=save_format,
@@ -82,7 +94,37 @@ def fit_model(
     else:
         raise ValueError(f'Source type {transient.__class__.__name__} not known')
 
+def _fit_spectrum(transient, model, outdir, label, likelihood=None, sampler='dynesty', nlive=3000, prior=None, walks=1000,
+                  resume=True, save_format='json', model_kwargs=None, plot=True, **kwargs):
+    x, y, y_err = transient.angstroms, transient.flux_density, transient.flux_density_err
+    likelihood = likelihood or GaussianLikelihood(x=x, y=y, sigma=y_err, function=model, kwargs=model_kwargs)
+
+    meta_data = dict(model=model.__name__, transient_type=transient.__class__.__name__.lower())
+    transient_kwargs = {k.lstrip("_"): v for k, v in transient.__dict__.items()}
+    meta_data.update(transient_kwargs)
+    model_kwargs = redback.utils.check_kwargs_validity(model_kwargs)
+    meta_data['model_kwargs'] = model_kwargs
+    nthreads = kwargs.get('nthreads', 1)
+
+    result = None
+    if not kwargs.get("clean", False):
+        try:
+            result = redback.result.read_in_result(
+                outdir=outdir, label=label, extension=kwargs.get("extension", "json"), gzip=kwargs.get("gzip", False))
+            plt.close('all')
+            return result
+        except Exception:
+            pass
 
+    result = result or bilby.run_sampler(
+        likelihood=likelihood, priors=prior, label=label, sampler=sampler, nlive=nlive,
+        outdir=outdir, plot=plot, use_ratio=False, walks=walks, resume=resume,
+        maxmcmc=10 * walks, result_class=RedbackResult, meta_data=meta_data,
+        nthreads=nthreads, save_bounds=False, nsteps=nlive, nwalkers=walks, save=save_format, **kwargs)
+    plt.close('all')
+    if plot:
+        result.plot_spectrum(model=model)
+    return result
 
 def _fit_grb(transient, model, outdir, label, likelihood=None, sampler='dynesty', nlive=3000, prior=None, walks=1000,
              use_photon_index_prior=False, resume=True, save_format='json', model_kwargs=None, plot=True, **kwargs):

redback/sed.py

@@ -203,7 +203,7 @@ def blackbody_to_flux_density(temperature, r_photosphere, dl, frequency):
     :param dl: luminosity_distance in cm
     :param frequency: frequency to calculate in Hz - Must be same length as time array or a single number.
                       In source frame
-    :return: flux_density
+    :return: flux_density in erg/s/Hz/cm^2
     """
     # adding units back in to ensure dimensions are correct
     frequency = frequency * uu.Hz
@@ -248,6 +248,53 @@ class _SED(object):
         # convert to mJy
         return flux_density.to(uu.mJy)
 
+def boosted_bolometric_luminosity(temperature, radius, lambda_cut):
+    """
+    Compute the boosted bolometric luminosity for a blackbody with temperature T (K)
+    and radius R (cm) to account for missing blue flux.
+
+    It uses:
+        L_bb = 4π R² σ_SB T⁴,
+    F_tot = σ_SB T⁴, and integrates the flux density redward of lambda_cut.
+
+    Parameters
+    ----------
+    temperature : float
+        Temperature (K)
+    radius : float
+        Photospheric radius (cm)
+    lambda_cut : float
+        Cutoff wavelength in centimeters (i.e. converted from angstroms by multiplying by 1e-8)
+
+    Returns
+    -------
+    L_boosted : float
+        The corrected bolometric luminosity (erg/s)
+    """
+    from scipy.integrate import quad
+    sigma_SB = sigma_sb  # Stefan–Boltzmann constant in cgs
+
+    # Compute pure-blackbody bolometric luminosity.
+    L_bb = 4.0 * np.pi * radius ** 2 * sigma_SB * temperature ** 4
+    # Total flux per unit area (erg/s/cm^2)
+    F_tot = sigma_SB * temperature ** 4
+
+    # Define the Planck function B_lambda (in erg/s/cm^2/cm/sr)
+    def planck_lambda(lam, T):
+        h = planck  # erg s
+        c = speed_of_light  # cm/s
+        k = boltzmann_constant  # erg/K
+        return (2.0 * h * c ** 2) / (lam ** 5) / (np.exp(h * c / (lam * k * T)) - 1.0)
+
+    # Integrand: π * B_lambda gives flux per unit wavelength (erg/s/cm²/cm)
+    integrand = lambda lam, T: np.pi * planck_lambda(lam, T)
+    # Integrate from lambda_cut to infinity to get the red flux.
+    F_red, integration_error = quad(integrand, lambda_cut, np.inf, args=(temperature,))
+    # Compute boost factor.
+    Boost = F_tot / F_red
+    # Corrected luminosity.
+    return Boost * L_bb, L_bb
+
 
 class CutoffBlackbody(_SED):
 

redback/simulate_transients.py

@@ -76,7 +76,7 @@ class SimulateGenericTransient(object):
         injection_kwargs = self.parameters.copy()
         if 'bands' in model_kwargs.keys():
             injection_kwargs['bands'] = self.subset_bands
-            injection_kwargs['output_format'] = 'magnitude'
+            injection_kwargs['output_format'] = model_kwargs['output_format']
         if 'frequency' in model_kwargs.keys():
             injection_kwargs['frequency'] = self.subset_frequency
             injection_kwargs['output_format'] = 'flux_density'
@@ -534,6 +534,10 @@ class SimulateOpticalTransient(object):
         Function to wrap user models into sncosmo model format for full functionality.
         :return: sncosmo source
         """
+        # Ensure sncosmo_kwargs is a dictionary
+        if self.sncosmo_kwargs is None:
+            self.sncosmo_kwargs = {}
+
         self.sncosmo_kwargs['max_time'] = self.sncosmo_kwargs.get('max_time', 100)
         self.parameters['wavelength_observer_frame'] = self.parameters.get('wavelength_observer_frame',
                                                                           np.geomspace(100,60000,100))