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jvshields committed Aug 19, 2024
1 parent 65d7449 commit 3f8b9cf
Showing 1 changed file with 33 additions and 35 deletions.
68 changes: 33 additions & 35 deletions tardis/io/atom_data/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -546,9 +546,9 @@ def prepare_continuum_interaction_data(self, continuum_interaction_species):
)

level_idxs2continuum_idx = self.photo_ion_levels_idx.copy()
level_idxs2continuum_idx["continuum_idx"] = (
self.level2continuum_edge_idx
)
level_idxs2continuum_idx[
"continuum_idx"
] = self.level2continuum_edge_idx
self.level_idxs2continuum_idx = level_idxs2continuum_idx.set_index(
["source_level_idx", "destination_level_idx"]
)
Expand Down Expand Up @@ -582,33 +582,31 @@ def prepare_macro_atom_data(
self.macro_atom_references = self.macro_atom_references.loc[
self.macro_atom_references["count_down"] > 0
]
self.macro_atom_references.loc[:, "count_total"] = (
self.macro_atom_references["count_down"]
)
self.macro_atom_references.loc[:, "block_references"] = (
np.hstack(
(
0,
np.cumsum(
self.macro_atom_references["count_down"].values[
:-1
]
),
)
self.macro_atom_references.loc[
:, "count_total"
] = self.macro_atom_references["count_down"]
self.macro_atom_references.loc[
:, "block_references"
] = np.hstack(
(
0,
np.cumsum(
self.macro_atom_references["count_down"].values[:-1]
),
)
)

elif line_interaction_type == "macroatom":
self.macro_atom_references.loc[:, "block_references"] = (
np.hstack(
(
0,
np.cumsum(
self.macro_atom_references[
"count_total"
].values[:-1]
),
)
self.macro_atom_references.loc[
:, "block_references"
] = np.hstack(
(
0,
np.cumsum(
self.macro_atom_references["count_total"].values[
:-1
]
),
)
)

Expand Down Expand Up @@ -726,12 +724,12 @@ def _init_indices(self):
& (self.lines.ion_number == species[1])
)
self.lines_idx[species] = lines_idx
self.lines_level_number_lower[species] = (
self.lines.level_number_lower.values[lines_idx].astype(int)
)
self.lines_level_number_upper[species] = (
self.lines.level_number_upper.values[lines_idx].astype(int)
)
self.lines_level_number_lower[
species
] = self.lines.level_number_lower.values[lines_idx].astype(int)
self.lines_level_number_upper[
species
] = self.lines.level_number_upper.values[lines_idx].astype(int)

self.A_uls[species] = self.atom_data.lines.A_ul.values[lines_idx]
self.B_uls[species] = self.atom_data.lines.B_ul.values[lines_idx]
Expand Down Expand Up @@ -766,9 +764,9 @@ def _create_collision_coefficient_matrix(self):
line,
) in collision_group.get_group(species).iterrows():
# line.columns : delta_e, g_ratio, temperatures ...
C_ul_matrix[level_number_lower, level_number_upper, :] = (
line.values[2:]
)
C_ul_matrix[
level_number_lower, level_number_upper, :
] = line.values[2:]
delta_E_matrix[level_number_lower, level_number_upper] = line[
"delta_e"
]
Expand Down

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