def ion_count(self, atomic_num, shell_num):
"""Generates fractional abundance of ions of a specific element and
shell, in a form that can be used by a table widget
Parameters
----------
atomic_num : int
Atomic number of element
shell_num : int
Shell number (note: starts from 1, not 0 which is what simulation
model use)
Returns
-------
pandas.DataFrame
Dataframe containing ion specie and fractional abundance for a
specific element, against each ion number
"""
ion_num_density = self.ion_number_density[shell_num - 1].loc[atomic_num]
element_num_density = self.number_density.loc[atomic_num, shell_num - 1]
ion_count_data = ion_num_density / element_num_density # Normalization
ion_count_data.index.name = "Ion"
ion_count_data.fillna(0, inplace=True)
return pd.DataFrame(
{
"Species": ion_count_data.index.map(
lambda x: species_tuple_to_string((atomic_num, x))
),
"Frac. Ab. (Z={})".format(atomic_num): ion_count_data.map(
"{:.6e}".format
),
}
)
def get_last_line_counts(
self,
selected_species,
filter_mode=FILTER_MODES[0],
group_mode=GROUP_MODES[0],
):
"""
Get packet counts of each last line interaction of a species.
Parameters
----------
selected_species : str
Valid symbol of a species (e.g Si II) selected from the species
data returned by :code:`get_species_interactions` (see Notes section)
filter_mode : str, optional
Filter mode of the LastLineInteraction object to use for fetching
the data of last lines interacted (more details in Notes section).
Allowed values are given by the class variable :code:`FILTER_MODES`
(default value is :code:`FILTER_MODES[0]`)
group_mode : str, optional
Group mode to use for grouping last line interactions by excitation
lines, de-excitation lines or both. Allowed values are given by the
class variable :code:`GROUP_MODES` (default value is
:code:`GROUP_MODES[0]` i.e. both)
Returns
-------
pd.DataFrame
DataFrame containing last line interactions and corresponding
packet counts.
Notes
-----
This method depends on tardis.analysis.LastLineInteraction object for
doing computations. So there is a member variable in this class -
:code:`line_interaction_analysis` which is a dictionary of such objects
(each of them differ in how they filter the selected wavelength range).
Thus we have to specify which object to use by specifying the
filter_mode parameter.
This method should always be called after calling
:code:`get_species_interactions` method which sets a wavelength
range on LastLineInteraction object. So selected_species should
be one present within that range, otherwise it will result an error.
"""
if selected_species:
selected_species_tuple = species_string_to_tuple(selected_species)
try:
# Get selected species' rows from last_line_in dataframe
current_last_lines_in = (
self.line_interaction_analysis[filter_mode].last_line_in.
xs(
key=selected_species_tuple,
level=["atomic_number", "ion_number"],
drop_level=False,
).reset_index())
# Get selected species' rows from last_line_out dataframe
current_last_lines_out = (
self.line_interaction_analysis[filter_mode].last_line_out.
xs(
key=selected_species_tuple,
level=["atomic_number", "ion_number"],
drop_level=False,
).reset_index())
assert (current_last_lines_in.empty
& current_last_lines_out.empty == False)
except (KeyError, AssertionError): # selected_species is invalid
allowed_species = [
species_tuple_to_string(species)
for species in self.line_interaction_analysis[filter_mode].
last_line_in.groupby(["atomic_number", "ion_number"
]).groups.keys()
]
raise ValueError(
"Invalid value of selected_species, it must be one present "
"within the currently selected wavelength range in your "
f"LineInfoWidget instance, which are {allowed_species}")
last_line_interaction_string = []
interacting_packets_count = []
if group_mode == "both":
# Group by both exc. line ids and de-exc. line ids
current_last_lines_in[
"line_id_out"] = current_last_lines_out.line_id
grouped_line_interactions = current_last_lines_in.groupby(
["line_id", "line_id_out"])
# Iterate over each group's key and size and append them to list
for (
line_id,
count,
) in grouped_line_interactions.size().iteritems():
current_line_in = self.lines_data.loc[line_id[0]]
current_line_out = self.lines_data.loc[line_id[1]]
last_line_interaction_string.append(
f"exc. {int(current_line_in.level_number_lower):02d}-"
f"{int(current_line_in.level_number_upper):02d} "
f"({current_line_in.wavelength:.2f} A) "
f"de-exc. {int(current_line_out.level_number_upper):02d}-"
f"{int(current_line_out.level_number_lower):02d} "
f"({current_line_out.wavelength:.2f} A)")
interacting_packets_count.append(count)
elif group_mode == "exc":
grouped_line_interactions = current_last_lines_in.groupby(
"line_id")
# Iterate over each group's key and size and append them to list
for (
line_id,
count,
) in grouped_line_interactions.size().iteritems():
current_line_in = self.lines_data.loc[line_id]
last_line_interaction_string.append(
f"exc. {int(current_line_in.level_number_lower):02d}-"
f"{int(current_line_in.level_number_upper):02d} "
f"({current_line_in.wavelength:.2f} A)")
interacting_packets_count.append(count)
elif group_mode == "de-exc":
grouped_line_interactions = current_last_lines_out.groupby(
"line_id")
# Iterate over each group's key and size and append them to list
for (
line_id,
count,
) in grouped_line_interactions.size().iteritems():
current_line_out = self.lines_data.loc[line_id]
last_line_interaction_string.append(
f"de-exc. {int(current_line_out.level_number_upper):02d}-"
f"{int(current_line_out.level_number_lower):02d} "
f"({current_line_out.wavelength:.2f} A)")
interacting_packets_count.append(count)
else:
raise ValueError(
"Invalid value passed to group_mode argument. "
f"Allowed values are {self.GROUP_MODES}")
else: # species_selected is None
# qgrid cannot show empty dataframe properly,
# so create one row with empty strings
interacting_packets_count = [""]
last_line_interaction_string = [""]
last_line_counts = pd.Series(interacting_packets_count)
last_line_counts.name = "No. of packets"
last_line_counts.index = pd.Index(last_line_interaction_string,
name="Last Line Interaction")
return last_line_counts.sort_values(ascending=False).to_frame()
def get_species_interactions(self,
wavelength_range,
filter_mode=FILTER_MODES[0]):
"""
Get fractional species interactions in specified wavelength range.
Fractional species interactions means fraction of packets present in
the specified wavelength range which experienced their last interaction
with a species. The packets to consider are filtered by the specified
filter mode.
Parameters
----------
wavelength_range : list-like or None
A list of two float values to specify the wavelength range - first
for the range start and second for the range end. None specifies
that no wavelength range is selected and will return empty dataframe
filter_mode : str, optional
Filter mode of the LastLineInteraction object to use for filtering
the selected wavelength range (more details in Notes section).
Allowed values are given by the class variable :code:`FILTER_MODES`
(default value is :code:`FILTER_MODES[0]`)
Returns
-------
pandas.DataFrame
Dataframe containing species symbols and corresponding fractions
of packets interacting with them
Notes
-----
This method depends on tardis.analysis.LastLineInteraction object for
doing computations. So there is a member variable in this class -
:code:`line_interaction_analysis` which is a dictionary of such objects
(each of them differ in how they filter the selected wavelength range).
Thus we have to specify which object to use by specifying the
filter_mode parameter.
"""
if wavelength_range:
self.line_interaction_analysis[filter_mode].wavelength_start = (
wavelength_range[0] * u.AA)
self.line_interaction_analysis[filter_mode].wavelength_end = (
wavelength_range[1] * u.AA)
# Obtain species group from last_line_in dataframe
selected_species_group = self.line_interaction_analysis[
filter_mode].last_line_in.groupby(
["atomic_number", "ion_number"])
if selected_species_group.groups:
selected_species_symbols = [
species_tuple_to_string(item)
for item in selected_species_group.groups.keys()
]
# Normalize each group's count to find fractions of interactions
fractional_species_interactions = (
selected_species_group.size() /
self.line_interaction_analysis[filter_mode].last_line_in.
shape[0])
else: # No species could be selected in specified wavelength_range
# qgrid cannot show empty dataframe properly,
# so create one row with empty strings
selected_species_symbols = [""]
fractional_species_interactions = pd.Series([""])
else: # wavelength_range is None
selected_species_symbols = [""]
fractional_species_interactions = pd.Series([""])
fractional_species_interactions.index = pd.Index(
selected_species_symbols, name="Species")
fractional_species_interactions.name = "Fraction of packets interacting"
return fractional_species_interactions.sort_values(
ascending=False).to_frame()
def test_species_tuple_to_string(species_tuple, roman_numerals,
species_string):
assert species_tuple_to_string(
species_tuple, roman_numerals=roman_numerals) == species_string
def test_species_tuple_to_string(species_tuple, roman_numerals, species_string):
assert species_tuple_to_string(species_tuple, roman_numerals=roman_numerals) == species_string