Merge remote-tracking branch 'upstream/main' into add_individual_inte…

…nsities

stardis/base.py

@@ -10,9 +10,7 @@
 logger = logging.getLogger(__name__)
 
 
-def run_stardis(
-    config_fname, tracing_lambdas_or_nus, add_config_keys=None, add_config_vals=None
-):
+def run_stardis(config_fname, tracing_lambdas_or_nus, add_config_dict=None):
     """
     Runs a STARDIS simulation.
 
@@ -24,10 +22,8 @@ def run_stardis(
         Numpy array of the frequencies or wavelengths to calculate the
         spectrum for. Must have units attached to it, with dimensions
         of either length or inverse time.
-    add_config_keys : list, optional
-        List of additional keys to add or overwrite for the configuration file.
-    add_config_vals : list, optional
-        List of corresponding additional values to add to the configuration file.
+    add_config_dict : dict, optional
+        Dictionary containing the the keys and values of the configuration to add or overwrite.
 
     Returns
     -------
@@ -37,9 +33,7 @@ def run_stardis(
 
     tracing_nus = tracing_lambdas_or_nus.to(u.Hz, u.spectral())
 
-    config, adata, stellar_model = parse_config_to_model(
-        config_fname, add_config_keys, add_config_vals
-    )
+    config, adata, stellar_model = parse_config_to_model(config_fname, add_config_dict)
     set_num_threads(config.n_threads)
     stellar_plasma = create_stellar_plasma(stellar_model, adata, config)
     stellar_radiation_field = create_stellar_radiation_field(

stardis/io/base.py

@@ -17,7 +17,7 @@
 logger = logging.getLogger(__name__)
 
 
-def parse_config_to_model(config_fname, add_config_keys=None, add_config_vals=None):
+def parse_config_to_model(config_fname, add_config_dict):
     """
     Parses the config and model files and outputs python objects to be passed into run stardis so they can be individually modified in python.
 
@@ -47,28 +47,18 @@ def parse_config_to_model(config_fname, add_config_keys=None, add_config_vals=No
         raise ValueError("Config failed to validate. Check the config file.")
 
     if (
-        not add_config_keys
+        not add_config_dict
     ):  # If a dictionary was passed, update the config with the dictionary
         pass
     else:
         logger.info("Updating config with additional keys and values")
-        if isinstance(add_config_keys, str):
-            # Directly set the config item if add_config_keys is a string
-            config.set_config_item(add_config_keys, add_config_vals)
-        else:
-            # Proceed with iteration if add_config_keys is not a string
-            if len(add_config_keys) != len(add_config_vals):
-                raise ValueError(
-                    "Length of additional config keys and values do not match."
-                )
+        for key, val in add_config_dict.items():
             try:
-                for key, val in zip(add_config_keys, add_config_vals):
-                    config.set_config_item(key, val)
+                config.set_config_item(key, val)
             except:
                 raise ValueError(
-                    f"{add_config_keys} not a valid type. Should be a single string or a list of strings for keys."
+                    f"{key} not a valid type. Should be a string for keys."
                 )
-
         try:
             config_dict = validate_dict(config, schemapath=SCHEMA_PATH)
         except:

stardis/plasma/base.py

@@ -3,7 +3,6 @@
 import logging
 
 from astropy import constants as const, units as u
-from scipy.interpolate import interp1d
 
 from tardis.plasma.base import BasePlasma
 from tardis.plasma.properties.base import (
@@ -118,11 +117,13 @@ class H2PlusDensity(ProcessingPlasmaProperty):
     outputs = ("h2_plus_density",)
 
     def calculate(self, ion_number_density, t_rad):
-        interp_Ks = interp1d(H2_PLUS_K_SAMPLE_TEMPS, H2_PLUS_K_EQUILIBRIUM_CONSTANT)
         h_neutral_density = ion_number_density.loc[1, 0]
         h_plus_density = ion_number_density.loc[1, 1]
+        resampled_Ks = np.interp(
+            t_rad, H2_PLUS_K_SAMPLE_TEMPS, H2_PLUS_K_EQUILIBRIUM_CONSTANT
+        )
         return (
-            h_neutral_density * h_plus_density / interp_Ks(t_rad) * 1e-19
+            h_neutral_density * h_plus_density / resampled_Ks * 1e-19
         )  # scale factor from Stancil 1994 table 1
 
 

stardis/radiation_field/opacities/opacities_solvers/util.py

@@ -4,7 +4,7 @@
 from astropy import units as u, constants as const
 from tardis.util.base import species_string_to_tuple
 
-from scipy.interpolate import interp1d, LinearNDInterpolator
+from scipy.interpolate import LinearNDInterpolator
 
 
 def sigma_file(tracing_lambdas, temperatures, fpath, opacity_source=None):
@@ -83,16 +83,11 @@ def sigma_file(tracing_lambdas, temperatures, fpath, opacity_source=None):
         h_minus_bf_table = pd.read_csv(
             fpath, header=None, comment="#", names=["wavelength", "cross_section"]
         )
-        linear_interp_1d_from_file = interp1d(
+        sigmas = np.interp(
+            tracing_lambdas,
             h_minus_bf_table.wavelength.values,
             h_minus_bf_table.cross_section.values,
-            bounds_error=False,
-            fill_value=(
-                h_minus_bf_table.cross_section.iloc[0],
-                h_minus_bf_table.cross_section.iloc[-1],
-            ),
         )
-        sigmas = linear_interp_1d_from_file(tracing_lambdas)
 
     else:
         raise ValueError(f"Unknown opacity_source: {opacity_source}")