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retaining label in tardis atom data #347

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retaining label in tardis atom data #347

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0aa307d
retaining label in tardis atom data
AyushiDaksh Jul 7, 2023
ecfd112
Add label in lines data and old tardis levels data
AyushiDaksh Jul 7, 2023
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16 changes: 9 additions & 7 deletions carsus/io/output/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -343,10 +343,10 @@ def _get_all_levels_data(self):
levels = pd.concat([gf_levels, ch_levels, cf_levels], sort=True)
levels['g'] = 2*levels['j'] + 1
levels['g'] = levels['g'].astype(np.int)
levels = levels.drop(columns=['j', 'label', 'method'])
levels = levels.drop(columns=['j', 'method'])
levels = levels.reset_index()
levels = levels.rename(columns={'ion_charge': 'ion_number'})
levels = levels[['atomic_number', 'ion_number', 'g', 'energy',
levels = levels[['atomic_number', 'ion_number', 'label', 'g', 'energy',
'ds_id', 'priority']]
levels['energy'] = u.Quantity(levels['energy'], 'cm-1').to(
'eV', equivalencies=u.spectral()).value
Expand Down Expand Up @@ -398,7 +398,7 @@ def _get_all_levels_data(self):
levels['ion_number'] == ion[1])
levels = levels.drop(levels[mask].index)

levels = levels[['atomic_number', 'ion_number', 'g', 'energy',
levels = levels[['atomic_number', 'ion_number', 'label', 'g', 'energy',
'ds_id']]
levels = levels.reset_index()

Expand Down Expand Up @@ -551,22 +551,24 @@ def create_levels_lines(self, lines_loggf_threshold=-3,

levels["level_number"] = levels["level_number"].astype(np.int)

levels = levels[['atomic_number', 'ion_number', 'g', 'energy',
levels = levels[['atomic_number', 'ion_number', 'label', 'g', 'energy',
'metastable', 'level_number', 'ds_id']]

# Join atomic_number, ion_number, level_number_lower,
# level_number_upper on lines
lower_levels = levels.rename(
columns={
"level_number": "level_number_lower",
"label": "label_lower",
"g": "g_l"}
).loc[:, ["atomic_number", "ion_number", "level_number_lower", "g_l"]]
).loc[:, ["atomic_number", "ion_number", "level_number_lower", "label_lower", "g_l"]]

upper_levels = levels.rename(
columns={
"level_number": "level_number_upper",
"label": "label_upper",
"g": "g_u"}
).loc[:, ["level_number_upper", "g_u"]]
).loc[:, ["level_number_upper", "label_upper", "g_u"]]

lines = lines.join(lower_levels, on="lower_level_id").join(
upper_levels, on="upper_level_id")
Expand Down Expand Up @@ -875,7 +877,7 @@ def levels_prepared(self):
"""

levels_prepared = self.levels.loc[:, [
"atomic_number", "ion_number", "level_number",
"atomic_number", "ion_number", "level_number", "label",
"energy", "g", "metastable"]].copy()

levels_prepared = levels_prepared.set_index(
Expand Down
9 changes: 6 additions & 3 deletions carsus/io/output/tardis_.py
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Original file line number Diff line number Diff line change
Expand Up @@ -475,6 +475,7 @@ def _get_all_levels_data(self):
Level.level_id.label('level_id'),
Level.atomic_number.label('atomic_number'),
Level.ion_charge.label('ion_number'),
Level.label.label('label'),
Level.g.label('g'),
).
join(
Expand Down Expand Up @@ -681,13 +682,15 @@ def create_levels_lines(
lower_levels = levels.rename(
columns={
"level_number": "level_number_lower",
"label": "label_lower",
"g": "g_l"}
).loc[:, ["atomic_number", "ion_number", "level_number_lower", "g_l"]]
).loc[:, ["atomic_number", "ion_number", "level_number_lower", "label_lower", "g_l"]]
upper_levels = levels.rename(
columns={
"level_number": "level_number_upper",
"label": "label_upper",
"g": "g_u"}
).loc[:, ["level_number_upper", "g_u"]]
).loc[:, ["level_number_upper", "label_upper", "g_u"]]
lines = lines.join(lower_levels, on="lower_level_id").join(upper_levels, on="upper_level_id")

# Calculate absorption oscillator strength f_lu and emission oscillator strength f_ul
Expand Down Expand Up @@ -729,7 +732,7 @@ def levels_prepared(self):
"""

levels_prepared = self.levels.loc[:, [
"atomic_number", "ion_number", "level_number",
"atomic_number", "ion_number", "level_number", "label",
"energy", "g", "metastable"]].copy()

# Set index
Expand Down