diff --git a/species/fit/retrieval.py b/species/fit/retrieval.py index 9de398a..1b3593b 100644 --- a/species/fit/retrieval.py +++ b/species/fit/retrieval.py @@ -2204,22 +2204,22 @@ def _lnlike( log_x_base[item[:-3]] = cube[cube_index[item]] # Create dictionary with cloud parameters - - if "log_kzz" in self.parameters: - cloud_param = [ - "fsed", - "log_kzz", - "sigma_lnorm", - "log_kappa_0", - "opa_index", - "log_p_base", - "albedo", - "log_kappa_abs", - "log_kappa_sca", - "opa_abs_index", - "opa_sca_index", - "lambda_ray", - ] + cloud_param = [ + "fsed", + "log_kzz", + "sigma_lnorm", + "log_kappa_0", + "opa_index", + "log_p_base", + "albedo", + "log_kappa_abs", + "log_kappa_sca", + "opa_abs_index", + "opa_sca_index", + "lambda_ray", + ] + + if any(param_i in self.parameters for param_i in cloud_param): cloud_dict = {} for item in cloud_param: @@ -2444,13 +2444,9 @@ def _lnlike( # that is calculated from the spectrum and the # bolometric flux at each pressure - ln_prior += np.sum( - -0.5 * (f_bol - f_bol_spec) ** 2 / sigma_fbol**2 - ) + ln_prior += np.sum(-0.5 * (f_bol - f_bol_spec) ** 2 / sigma_fbol**2) - ln_prior += ( - -0.5 * f_bol.size * np.log(2.0 * np.pi * sigma_fbol**2) - ) + ln_prior += -0.5 * f_bol.size * np.log(2.0 * np.pi * sigma_fbol**2) # for i in range(i_conv): # for i in range(lowres_radtrans.press.shape[0]): @@ -2997,8 +2993,7 @@ def _lnlike( -0.5 * weight * np.sum( - flux_diff**2 / data_var - + np.log(2.0 * np.pi * data_var) + flux_diff**2 / data_var + np.log(2.0 * np.pi * data_var) ) ) diff --git a/species/util/plot_util.py b/species/util/plot_util.py index d1af5b1..2204088 100644 --- a/species/util/plot_util.py +++ b/species/util/plot_util.py @@ -588,13 +588,13 @@ def update_labels(param: List[str], object_type: str = "planet") -> List[str]: if "T_bottom" in param: index = param.index("T_bottom") - param[index] = r"$T_\mathrm{bottom}$ (K)" + param[index] = r"$T_\mathrm{bot}$ (K)" num_layer = 6 # could make a variable in the future for i in range(num_layer): if f"PTslope_{num_layer - i}" in param: index = param.index(f"PTslope_{num_layer - i}") - param[index] = rf"$(dlnT/dlnP)_\mathrm{{P={i}bar}}$ (K)" + param[index] = rf"dlnT/dlnP$_{i}$ " if "log_p_quench" in param: index = param.index("log_p_quench") @@ -630,7 +630,7 @@ def update_labels(param: List[str], object_type: str = "planet") -> List[str]: if f"fsed_{item}(c)" in param: index = param.index(f"fsed_{item}(c)") - param[index] = rf"$\log\,P_\mathrm{{{cloud_labels[i]}}}$" + param[index] = rf"fsed$_\mathrm{{{cloud_labels[i]}}}$" for i, item_i in enumerate(cloud_species): for j, item_j in enumerate(cloud_species):