Change name of blackbody function. Hook up RadiationField.source_func…

…tion to raytrace.

stardis/base.py

@@ -75,10 +75,10 @@ def run_stardis(config_fname, tracing_lambdas_or_nus):
 
     if True:  # change to checking source function from config
         from stardis.radiation_field.source_functions.blackbody import (
-            bb_nu,
+            blackbody_flux_at_nu,
         )
 
-        stellar_radiation_field = RadiationField(tracing_nus, bb_nu, stellar_model)
+        stellar_radiation_field = RadiationField(tracing_nus, blackbody_flux_at_nu, stellar_model)
 
     calc_alphas(
         stellar_plasma=stellar_plasma,
@@ -92,9 +92,9 @@ def run_stardis(config_fname, tracing_lambdas_or_nus):
     return STARDISOutput(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.opacities.opacities,
-        stellar_radiation_field.opacities.opacities["alpha_line_at_nu_gammas"],
-        stellar_radiation_field.opacities.opacities["alpha_line_at_nu_doppler_widths"],
+        stellar_radiation_field.opacities.opacities_dict,
+        stellar_radiation_field.opacities.opacities_dict["alpha_line_at_nu_gammas"],
+        stellar_radiation_field.opacities.opacities_dict["alpha_line_at_nu_doppler_widths"],
         stellar_radiation_field.F_nu,
         stellar_radiation_field.frequencies,
     )

stardis/radiation_field/base.py

@@ -6,6 +6,7 @@ class RadiationField:
     """
     Class containing information about the radiation field.
     ###TODO Radiation field temperature should be a separate attribute, for the case of differing gas and radiation.
+    ###TODO Implement a source function class. Doesn't need to be done until we have another source function than just blackbody. 
 
     Parameters
     ----------

stardis/radiation_field/opacities/base.py

@@ -2,22 +2,21 @@ class Opacities:
     """
     Holds opacity information.
 
-    ###TODO: Change to dict that holds each of the sources of opacity separately. Then have a method that combines them all to return the total opacity.
     Paramaters
     ----------
-    opacities : dict
+    opacities_dict : dict
         Python dictionary to contain each of the sources of opacity by name as well as their contribution at each frequency specified in the radiation field.
     total_alphas : numpy.ndarray
         Array of the total opacity at each frequency specified in the radiation field at each depth points.
         Added as an attribute when calc_total_alphas() is called.
     """
 
     def __init__(self):
-        self.opacities = {}
+        self.opacities_dict = {}
 
     ###TODO: Better implementation for this
     def calc_total_alphas(self):
-        for i, item in enumerate(self.opacities.items()):
+        for i, item in enumerate(self.opacities_dict.items()):
             if "gammas" not in item[0] and "doppler" not in item[0]:
                 if i == 0:
                     self.total_alphas = item[1]

stardis/radiation_field/opacities/opacities_solvers/base.py

@@ -560,49 +560,49 @@ def calc_alphas(
         stellar_radiation_field.frequencies,
         opacity_config.file,
     )
-    stellar_radiation_field.opacities.opacities["alpha_file"] = alpha_file
+    stellar_radiation_field.opacities.opacities_dict["alpha_file"] = alpha_file
 
     alpha_bf = calc_alpha_bf(
         stellar_plasma,
         stellar_model,
         stellar_radiation_field.frequencies,
         opacity_config.bf,
     )
-    stellar_radiation_field.opacities.opacities["alpha_bf"] = alpha_bf
+    stellar_radiation_field.opacities.opacities_dict["alpha_bf"] = alpha_bf
 
     alpha_ff = calc_alpha_ff(
         stellar_plasma,
         stellar_model,
         stellar_radiation_field.frequencies,
         opacity_config.ff,
     )
-    stellar_radiation_field.opacities.opacities["alpha_ff"] = alpha_ff
+    stellar_radiation_field.opacities.opacities_dict["alpha_ff"] = alpha_ff
 
     alpha_rayleigh = calc_alpha_rayleigh(
         stellar_plasma,
         stellar_model,
         stellar_radiation_field.frequencies,
         opacity_config.rayleigh,
     )
-    stellar_radiation_field.opacities.opacities["alpha_rayleigh"] = alpha_rayleigh
+    stellar_radiation_field.opacities.opacities_dict["alpha_rayleigh"] = alpha_rayleigh
 
     alpha_electron = calc_alpha_electron(
         stellar_plasma,
         stellar_model,
         stellar_radiation_field.frequencies,
         opacity_config.disable_electron_scattering,
     )
-    stellar_radiation_field.opacities.opacities["alpha_electron"] = alpha_electron
+    stellar_radiation_field.opacities.opacities_dict["alpha_electron"] = alpha_electron
 
     alpha_line_at_nu, gammas, doppler_widths = calc_alpha_line_at_nu(
         stellar_plasma,
         stellar_model,
         stellar_radiation_field.frequencies,
         opacity_config.line,
     )
-    stellar_radiation_field.opacities.opacities["alpha_line_at_nu"] = alpha_line_at_nu
-    stellar_radiation_field.opacities.opacities["alpha_line_at_nu_gammas"] = gammas
-    stellar_radiation_field.opacities.opacities[
+    stellar_radiation_field.opacities.opacities_dict["alpha_line_at_nu"] = alpha_line_at_nu
+    stellar_radiation_field.opacities.opacities_dict["alpha_line_at_nu_gammas"] = gammas
+    stellar_radiation_field.opacities.opacities_dict[
         "alpha_line_at_nu_doppler_widths"
     ] = doppler_widths
     alphas = stellar_radiation_field.opacities.calc_total_alphas()

stardis/radiation_field/radiation_field_solvers/base.py

@@ -1,6 +1,6 @@
 import numba
 import numpy as np
-from stardis.radiation_field.source_functions.blackbody import bb_nu
+# from stardis.radiation_field.source_functions.blackbody import blackbody_flux_at_nu
 
 
 @numba.njit
@@ -41,6 +41,7 @@ def single_theta_trace(
     alphas,
     tracing_nus,
     theta,
+    source_function
 ):
     """
     Performs ray tracing at an angle following van Noort 2001 eq 14.
@@ -71,7 +72,8 @@ def single_theta_trace(
     taus = mean_alphas.T * geometry_dist_to_next_depth_point / np.cos(theta)
     no_of_depth_gaps = len(geometry_dist_to_next_depth_point)
 
-    source = bb_nu(tracing_nus, temps)
+    ###TODO: Generalize this for source functions other than blackbody that may require args other than frequency and temperature
+    source = source_function(tracing_nus, temps)
     delta_source = source[1:] - source[:-1]
     I_nu_theta = np.ones((no_of_depth_gaps + 1, len(tracing_nus))) * np.nan
     I_nu_theta[0] = source[0]  # the innermost depth point is the photosphere
@@ -145,6 +147,7 @@ def raytrace(stellar_model, stellar_radiation_field, no_of_thetas=20):
             stellar_radiation_field.opacities.total_alphas,
             stellar_radiation_field.frequencies,
             theta,
+            stellar_radiation_field.source_function
         )
 
     return stellar_radiation_field.F_nu

stardis/radiation_field/source_functions/blackbody.py

@@ -8,7 +8,7 @@
 
 
 @numba.njit
-def bb_nu(tracing_nus, temps):
+def blackbody_flux_at_nu(tracing_nus, temps):
     """
     Planck blackbody intensity distribution w.r.t. frequency.