redback 1.12.0__py3-none-any.whl → 1.12.1__py3-none-any.whl

redback/transient_models/extinction_models.py

@@ -12,19 +12,29 @@ extinction_afterglow_base_models = ['tophat', 'cocoon', 'gaussian',
                                     'gaussiancore', 'gaussian',
                                     'smoothpowerlaw', 'powerlawcore',
                                     'tophat','tophat_from_emulator',
-                                    'kilonova_afterglow_redback', 'kilonova_afterglow_nakarpiran',
                                     'tophat_redback', 'gaussian_redback', 'twocomponent_redback',
                                     'powerlaw_redback', 'alternativepowerlaw_redback', 'doublegaussian_redback',
                                     'tophat_redback_refreshed', 'gaussian_redback_refreshed',
                                     'twocomponent_redback_refreshed','powerlaw_redback_refreshed',
-                                    'alternativepowerlaw_redback_refreshed', 'doublegaussian_redback_refreshed']
+                                    'alternativepowerlaw_redback_refreshed', 'doublegaussian_redback_refreshed',
+                                    'jetsimpy_tophat', 'jetsimpy_gaussian', 'jetsimpy_powerlaw']
 
+extinction_general_synchrotron_models = ['pwn', 'kilonova_afterglow_redback', 'kilonova_afterglow_nakarpiran',
+                                         'thermal_synchrotron_lnu', 'thermal_synchrotron_fluxdensity',
+                                         'tde_synchrotron', 'synchrotron_massloss', 'synchrotron_ism',
+                                         'synchrotron_pldensity', 'thermal_synchrotron_v2_lnu',
+                                         'thermal_synchrotron_v2_fluxdensity']
+extinction_stellar_interaction_models = ['wr_bh_merger']
 extinction_integrated_flux_afterglow_models = extinction_afterglow_base_models
+
 extinction_supernova_base_models = ['sn_exponential_powerlaw', 'arnett', 'shock_cooling_and_arnett',
                                     'basic_magnetar_powered', 'slsn', 'magnetar_nickel',
                                     'csm_interaction', 'csm_nickel', 'type_1a', 'type_1c',
                                     'general_magnetar_slsn','general_magnetar_driven_supernova', 'sn_fallback',
-                                    'csm_shock_and_arnett', 'shocked_cocoon_and_arnett', 'csm_shock_and_arnett_two_rphots']
+                                    'sn_nickel_fallback', 'shockcooling_morag_and_arnett',
+                                    'shockcooling_sapirandwaxman_and_arnett',
+                                    'csm_shock_and_arnett', 'shocked_cocoon_and_arnett',
+                                    'csm_shock_and_arnett_two_rphots', 'typeII_surrogate_sarin25']
 extinction_kilonova_base_models = ['nicholl_bns', 'mosfit_rprocess', 'mosfit_kilonova',
                                    'power_law_stratified_kilonova','bulla_bns_kilonova',
                                    'bulla_nsbh_kilonova', 'kasen_bns_kilonova','two_layer_stratified_kilonova',
@@ -32,17 +42,23 @@ extinction_kilonova_base_models = ['nicholl_bns', 'mosfit_rprocess', 'mosfit_kil
                                    'one_component_kilonova_model', 'one_component_ejecta_relation',
                                    'one_component_ejecta_relation_projection', 'two_component_bns_ejecta_relation',
                                    'polytrope_eos_two_component_bns', 'one_component_nsbh_ejecta_relation',
-                                   'two_component_nsbh_ejecta_relation','metzger_kilonova_model']
+                                   'two_component_nsbh_ejecta_relation','one_comp_kne_rosswog_heatingrate',
+                                   'two_comp_kne_rosswog_heatingrate','metzger_kilonova_model']
+
 extinction_tde_base_models = ['tde_analytical', 'tde_semianalytical', 'gaussianrise_cooling_envelope',
-                              'cooling_envelope', 'bpl_cooling_envelope']
+                              'cooling_envelope', 'bpl_cooling_envelope', 'tde_fallback',
+                              'fitted', 'fitted_pldecay', 'fitted_expdecay', 'stream_stream_tde']
 extinction_magnetar_driven_base_models = ['basic_mergernova', 'general_mergernova', 'general_mergernova_thermalisation',
                                           'general_mergernova_evolution', 'metzger_magnetar_driven_kilonova_model',
                                           'general_metzger_magnetar_driven', 'general_metzger_magnetar_driven_thermalisation',
                                           'general_metzger_magnetar_driven_evolution']
-extinction_shock_powered_base_models = ['shocked_cocoon', 'shock_cooling', 'csm_shock_breakout']
+extinction_shock_powered_base_models = ['shocked_cocoon', 'shock_cooling', 'csm_shock_breakout',
+                                        'shockcooling_morag', 'shockcooling_sapirandwaxman']
 
 extinction_model_library = {'kilonova': extinction_kilonova_base_models,
                             'supernova': extinction_supernova_base_models,
+                            'general_synchrotron': extinction_general_synchrotron_models,
+                            'stellar_interaction': extinction_stellar_interaction_models,
                             'afterglow': extinction_afterglow_base_models,
                             'tde': extinction_tde_base_models,
                             'magnetar_driven': extinction_magnetar_driven_base_models,
@@ -52,7 +68,9 @@ extinction_model_library = {'kilonova': extinction_kilonova_base_models,
 model_library = {'supernova': 'supernova_models', 'afterglow': 'afterglow_models',
                  'magnetar_driven': 'magnetar_driven_ejecta_models', 'tde': 'tde_models',
                  'kilonova': 'kilonova_models', 'shock_powered': 'shock_powered_models',
-                 'integrated_flux_afterglow': 'afterglow_models'}
+                 'integrated_flux_afterglow': 'afterglow_models',
+                 'stellar_interaction': 'stellar_interaction_models',
+                 'general_synchrotron': 'general_synchrotron_models'}
 
 def _get_correct_function(base_model, model_type=None):
     """
@@ -79,180 +97,388 @@ def _get_correct_function(base_model, model_type=None):
 
     return function
 
-def _perform_extinction(flux_density, angstroms, av, r_v):
+def _perform_extinction(flux_density, angstroms, av_host, rv_host, av_mw=0.0, rv_mw=3.1,
+                        host_law='fitzpatrick99', mw_law='fitzpatrick99', **kwargs):
     """
-    :param flux_density: flux density in mjy outputted by the model
-    :param angstroms: wavelength in angstroms
-    :param av: absolute mag extinction
-    :param r_v: extinction parameter
-    :return: flux
+    Apply host galaxy and/or Milky Way extinction to flux density
+
+    :param flux_density: flux density in mJy outputted by the model
+    :param angstroms: wavelength in angstroms (observer frame)
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param rv_host: extinction parameter for host galaxy (default 3.1)
+    :param av_mw: V-band extinction from Milky Way in magnitudes
+    :param rv_mw: extinction parameter for Milky Way (default 3.1)
+    :param redshift: source redshift (needed for host extinction)
+    :param host_law: extinction law for host galaxy
+                     ('fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89')
+    :param mw_law: extinction law for Milky Way
+                   ('fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89')
+    :param kwargs: additional parameters for specific extinction laws
+    :return: flux density with extinction applied
     """
-    import extinction  # noqa
+    import extinction
+
+    redshift = kwargs['redshift']
     if isinstance(angstroms, float):
-        angstroms = np.array([angstroms])    
-    mag_extinction = extinction.fitzpatrick99(angstroms, av, r_v=r_v)
-    if av < 10:
-        mask= mag_extinction > 10
-        mag_extinction[mask]=0    
-    flux_density = extinction.apply(mag_extinction, flux_density)
-    return flux_density
-
-def _evaluate_extinction_model(time, av, model_type, **kwargs):
+        angstroms = np.array([angstroms])
+
+    # Available extinction laws
+    extinction_laws = {
+        'fitzpatrick99': extinction.fitzpatrick99,
+        'fm07': extinction.fm07,
+        'calzetti00': extinction.calzetti00,
+        'odonnell94': extinction.odonnell94,
+        'ccm89': extinction.ccm89
+    }
+
+    # Validate extinction laws
+    if host_law not in extinction_laws:
+        raise ValueError(f"Unknown host extinction law: {host_law}. "
+                         f"Available: {list(extinction_laws.keys())}")
+    if mw_law not in extinction_laws:
+        raise ValueError(f"Unknown MW extinction law: {mw_law}. "
+                         f"Available: {list(extinction_laws.keys())}")
+
+    flux_extincted = flux_density.copy() if hasattr(flux_density, 'copy') else np.array(flux_density)
+
+    # Apply host galaxy extinction (in rest frame)
+    if av_host > 0:
+        # Convert observer frame to rest frame wavelengths
+        angstroms_rest = angstroms / (1 + redshift)
+
+        # Get host extinction law function
+        host_extinction_func = extinction_laws[host_law]
+
+        # Calculate extinction - handle different function signatures
+        try:
+            if host_law in ['fitzpatrick99', 'fm07', 'odonnell94', 'ccm89']:
+                mag_extinction_host = host_extinction_func(angstroms_rest, av_host, rv_host)
+            elif host_law == 'calzetti00':
+                # Calzetti law doesn't use R_V parameter
+                mag_extinction_host = host_extinction_func(angstroms_rest, av_host)
+        except Exception as e:
+            raise ValueError(f"Error applying {host_law} extinction law: {e}")
+
+        # Cap extreme extinction values
+        if av_host < 10:
+            mask = mag_extinction_host > 10
+            mag_extinction_host[mask] = 0
+
+        # Apply host extinction
+        flux_extincted = extinction.apply(mag_extinction_host, flux_extincted)
+
+    # Apply Milky Way extinction (in observer frame)
+    if av_mw > 0:
+        # MW extinction applies to observed wavelengths
+        mw_extinction_func = extinction_laws[mw_law]
+
+        # Calculate extinction
+        try:
+            if mw_law in ['fitzpatrick99', 'fm07', 'odonnell94', 'ccm89']:
+                mag_extinction_mw = mw_extinction_func(angstroms, av_mw, rv_mw)
+            elif mw_law == 'calzetti00':
+                mag_extinction_mw = mw_extinction_func(angstroms, av_mw)
+        except Exception as e:
+            raise ValueError(f"Error applying {mw_law} extinction law: {e}")
+
+        # Cap extreme extinction values
+        if av_mw < 10:
+            mask = mag_extinction_mw > 10
+            mag_extinction_mw[mask] = 0
+
+        # Apply MW extinction
+        flux_extincted = extinction.apply(mag_extinction_mw, flux_extincted)
+
+    return flux_extincted
+
+
+def _evaluate_extinction_model(time, av_host, av_mw=0.0, model_type=None, **kwargs):
     """
-    Generalised evaluate extinction function
+    Generalised evaluate extinction function with host and MW extinction
 
     :param time: time in days
-    :param av: absolute mag extinction
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param av_mw: V-band extinction from Milky Way in magnitudes
     :param model_type: None, or one of the types implemented
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param kwargs: Must include all parameters for base_model plus:
+        - redshift: source redshift (required for host extinction)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+    :return: flux/magnitude with extinction applied
     """
     base_model = kwargs['base_model']
     if kwargs['base_model'] in ['thin_shell_supernova', 'homologous_expansion_supernova']:
         kwargs['base_model'] = kwargs.get('submodel', 'arnett_bolometric')
+
+    # Extract extinction parameters
+    rv_host = kwargs.pop('rv_host', 3.1)
+    rv_mw = kwargs.pop('rv_mw', 3.1)
+    host_law = kwargs.pop('host_law', 'fitzpatrick99')
+    mw_law = kwargs.pop('mw_law', 'fitzpatrick99')
+
     if kwargs['output_format'] == 'flux_density':
         frequency = kwargs['frequency']
         if isinstance(frequency, float):
             frequency = np.ones(len(time)) * frequency
+
         angstroms = redback.utils.nu_to_lambda(frequency)
+
         temp_kwargs = kwargs.copy()
         temp_kwargs['output_format'] = 'flux_density'
         function = _get_correct_function(base_model=base_model, model_type=model_type)
         flux_density = function(time, **temp_kwargs)
-        r_v = kwargs.get('r_v', 3.1)
-        flux_density = _perform_extinction(flux_density=flux_density, angstroms=angstroms, av=av, r_v=r_v)
+
+        # Apply extinction
+        flux_density = _perform_extinction(
+            flux_density=flux_density,
+            angstroms=angstroms,
+            av_host=av_host,
+            rv_host=rv_host,
+            av_mw=av_mw,
+            rv_mw=rv_mw,
+            host_law=host_law,
+            mw_law=mw_law,
+            **kwargs
+        )
         return flux_density
+
     else:
         temp_kwargs = kwargs.copy()
         temp_kwargs['output_format'] = 'spectra'
         time_obs = time
         function = _get_correct_function(base_model=base_model, model_type=model_type)
         spectra_tuple = function(time, **temp_kwargs)
+
         flux_density = spectra_tuple.spectra
         lambdas = spectra_tuple.lambdas
         time_observer_frame = spectra_tuple.time
-        r_v = kwargs.get('r_v', 3.1)
-        flux_density = _perform_extinction(flux_density=flux_density, angstroms=lambdas, av=av, r_v=r_v)
-        return sed.get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame,
-                                                              spectra=flux_density, lambda_array=spectra_tuple.lambdas,
-                                                              **kwargs)
+
+        # Apply extinction
+        flux_density = _perform_extinction(
+            flux_density=flux_density,
+            angstroms=lambdas,
+            av_host=av_host,
+            rv_host=rv_host,
+            av_mw=av_mw,
+            rv_mw=rv_mw,
+            host_law=host_law,
+            mw_law=mw_law,
+            **kwargs
+        )
+
+        return sed.get_correct_output_format_from_spectra(
+            time=time_obs,
+            time_eval=time_observer_frame,
+            spectra=flux_density,
+            lambda_array=lambdas,
+            **kwargs
+        )
 
 @citation_wrapper('redback')
-def extinction_with_function(time, av, **kwargs):
+def extinction_with_function(time, av_host, **kwargs):
     """
     Extinction model when using your own specified function
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type=None, **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type=None, **kwargs)
     return output
 
 @citation_wrapper('redback')
-def extinction_with_supernova_base_model(time, av, **kwargs):
+def extinction_with_supernova_base_model(time, av_host, **kwargs):
     """
     Extinction with models implemented in supernova_models
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type='supernova', **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='supernova', **kwargs)
     return output
 
 @citation_wrapper('redback')
-def extinction_with_kilonova_base_model(time, av, **kwargs):
+def extinction_with_kilonova_base_model(time, av_host, **kwargs):
     """
     Extinction with models implemented in kilonova_models
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type='kilonova', **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='kilonova', **kwargs)
     return output
 
 @citation_wrapper('redback')
-def extinction_with_tde_base_model(time, av, **kwargs):
+def extinction_with_tde_base_model(time, av_host, **kwargs):
     """
     Extinction with models implemented in tde_models
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type='tde', **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='tde', **kwargs)
     return output
 
 @citation_wrapper('redback')
-def extinction_with_shock_powered_base_model(time, av, **kwargs):
+def extinction_with_shock_powered_base_model(time, av_host, **kwargs):
     """
-    Extinction with models implemented in tde_models
+    Extinction with models implemented in shock_powered_models
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type='shock_powered', **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='shock_powered', **kwargs)
     return output
 
 @citation_wrapper('redback')
-def extinction_with_magnetar_driven_base_model(time, av, **kwargs):
+def extinction_with_magnetar_driven_base_model(time, av_host, **kwargs):
     """
     Extinction with models implemented in magnetar_driven_ejecta_models
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: set by output format kwarg - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
+    """
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='magnetar_driven', **kwargs)
+    return output
+
+@citation_wrapper('redback')
+def extinction_with_stellar_interaction_base_model(time, av_host, **kwargs):
+    """
+    Extinction with models implemented in stellar_interaction_models
+
+    :param time: time in observer frame in days
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type='magnetar_driven', **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='stellar_interaction', **kwargs)
     return output
 
+@citation_wrapper('redback')
+def extinction_with_general_synchrotron_base_model(time, av_host, **kwargs):
+    """
+    Extinction with models implemented in general_synchrotron_models
+
+    :param time: time in observer frame in days
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
+    """
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='general_synchrotron', **kwargs)
+    return output
 
 @citation_wrapper('https://ui.adsabs.harvard.edu/abs/2021arXiv210601556S/abstract')
-def extinction_with_afterglow_base_model(time, av, **kwargs):
+def extinction_with_afterglow_base_model(time, av_host, **kwargs):
     """
     Extinction with models implemented in afterglow_models
 
     :param time: time in observer frame in days
-    :param av: absolute mag extinction
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-        and r_v, default is 3.1
-    :return: flux_density or magnitude depending on kwargs['output_format']
-        Note that only sed varient models can take magnitude as an output
+    :param av_host: V-band extinction from host galaxy in magnitudes
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
+        Note that only sed variant models can take magnitude as an output
     """
-    output = _evaluate_extinction_model(time=time, av=av, model_type='afterglow', **kwargs)
+    output = _evaluate_extinction_model(time=time, av_host=av_host, model_type='afterglow', **kwargs)
     return output
 
 @citation_wrapper('https://ui.adsabs.harvard.edu/abs/2021arXiv210601556S/abstract')
 def extinction_afterglow_galactic_dust_to_gas_ratio(time, lognh, factor=2.21, **kwargs):
     """
-    Extinction with afterglow models and a dust-to-gas ratio
+    Extinction with afterglow models using galactic dust-to-gas ratio
 
     :param time: time in observer frame in days
     :param lognh: log10 hydrogen column density
-    :param factor: factor to convert nh to av i.e., av = nh/factor
-    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model']
-    :return: set by output format kwarg - 'flux_density', 'magnitude', 'flux' with extinction applied
+    :param factor: factor to convert nh to av i.e., av = nh/factor (default 2.21)
+    :param kwargs: Must be all the parameters required by the base_model specified using kwargs['base_model'] plus:
+        - redshift: source redshift (required)
+        - av_mw: MW V-band extinction in magnitudes (default 0.0)
+        - rv_host: host R_V parameter (default 3.1)
+        - rv_mw: MW R_V parameter (default 3.1)
+        - host_law: host extinction law (default 'fitzpatrick99')
+        - mw_law: MW extinction law (default 'fitzpatrick99')
+        Available extinction laws: 'fitzpatrick99', 'fm07', 'calzetti00', 'odonnell94', 'ccm89'
+    :return: set by kwargs['output_format'] - 'flux_density', 'magnitude', 'flux', 'spectra' with extinction applied
     """
     factor = factor * 1e21
     nh = 10 ** lognh
     av = nh / factor
-    output = extinction_with_afterglow_base_model(time=time, av=av, **kwargs)
+    output = extinction_with_afterglow_base_model(time=time, av_host=av, **kwargs)
     return output
 
 

redback/transient_models/gaussianprocess_models.py

@@ -1,4 +1,3 @@
-import george.modeling
 from redback.transient_models import phenomenological_models as pm
 
 def calculate_flux_with_labels(time, t0, tau_rise, tau_fall, labels, **kwargs):
@@ -32,14 +31,4 @@ def calculate_flux_with_labels(time, t0, tau_rise, tau_fall, labels, **kwargs):
     # Construct the result dictionary with labels
     flux_results = {f'{label}': flux_matrix[i] for i, label in enumerate(labels)}
 
-    return flux_results
-
-class BazinGPModel(george.modeling.Model):
-    def __init__(self, band_labels):
-        self.parameter_names = ['t0', 'tau_rise', 'tau_fall']
-        self.band_labels = band_labels
-        for label in band_labels:
-            self.parameter_names.extend([f'a_{label}', f'b_{label}'])
-
-        def get_flux(self, t):
-            return calculate_flux_with_labels(t, **self.get_parameter_vector())
+    return flux_results

redback/transient_models/kilonova_models.py

@@ -738,7 +738,7 @@ def bulla_bns_kilonova(time, redshift, mej_dyn, mej_disk, phi, costheta_obs, **k
             spectra = output.spectra / (4 * np.pi * dl ** 2) # to erg/s/cm^2/Angstrom
             spectra = spectra * uu.erg / (uu.s * uu.cm ** 2 * uu.Angstrom)
             time_obs = time
-            return get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame / day_to_s,
+            return get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame,
                                                    spectra=spectra, lambda_array=lambda_observer_frame,
                                                    **kwargs)
 
@@ -791,7 +791,7 @@ def bulla_nsbh_kilonova(time, redshift, mej_dyn, mej_disk, costheta_obs, **kwarg
             spectra = output.spectra / (4 * np.pi * dl ** 2) # to erg/s/cm^2/Angstrom
             spectra = spectra * uu.erg / (uu.s * uu.cm ** 2 * uu.Angstrom)
             time_obs = time
-            return get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame / day_to_s,
+            return get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame,
                                                    spectra=spectra, lambda_array=lambda_observer_frame,
                                                    **kwargs)
 
@@ -842,7 +842,7 @@ def kasen_bns_kilonova(time, redshift, mej, vej, chi, **kwargs):
             spectra = output.spectra / (4 * np.pi * dl ** 2) # to erg/s/cm^2/Angstrom
             spectra = spectra * uu.erg / (uu.s * uu.cm ** 2 * uu.Angstrom)
             time_obs = time
-            return get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame / day_to_s,
+            return get_correct_output_format_from_spectra(time=time_obs, time_eval=time_observer_frame,
                                                    spectra=spectra, lambda_array=lambda_observer_frame,
                                                    **kwargs)
 @citation_wrapper('https://ui.adsabs.harvard.edu/abs/2020ApJ...891..152H/abstract')