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Solves issue #680 for tardis.util.base #1085

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Mar 9, 2020
Merged

Solves issue #680 for tardis.util.base #1085

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90 changes: 47 additions & 43 deletions tardis/util/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,12 +77,12 @@ def int_to_roman(i):

Parameters
----------
i: int
i : int
Integer to be converted into roman numerals

Returns
-------
: str
str
Returns roman numeral representation of i in str format.
"""
result = []
Expand All @@ -98,12 +98,12 @@ def roman_to_int(roman_string):

Parameters
----------
roman_string: str
roman_string : str
Roman numeral to be converted into an integer

Returns
-------
: int
int
Returns integer representation of roman_string
"""

Expand Down Expand Up @@ -131,26 +131,26 @@ def calculate_luminosity(

Parameters
----------
spec_fname: file or str
spec_fname : file or str
File or file name to be read
distance: float
distance : float
Distance to star
wavelength_column: int, optional(default = 0)
wavelength_column : int, optional(default = 0)
Column index in which the wavelength is stored
wavelength_unit: float, optional(default = u.angstrom)
wavelength_unit : float, optional(default = u.angstrom)
Dictates units used for calculating wavelength.
flux_column: int, optional(default = 1)
flux_column : int, optional(default = 1)
Column index in which the flux is stored
flux_unit: str, optional(default = u.Unit('erg / (Angstrom cm2 s)')
flux_unit : str, optional(default = u.Unit('erg / (Angstrom cm2 s)')
Dictates units used for flux

Returns
-------
luminosity.value: float
luminosity.value : float
Returned luminosity value of star.
wavelength.min()
wavelength.min() : float
Minimum value of wavelength of light
wavelength.max()
wavelength.max() : float
Maximum value of wavelength of light
"""
#BAD STYLE change to parse quantity
Expand All @@ -170,21 +170,25 @@ def create_synpp_yaml(radial1d_mdl, fname, shell_no=0, lines_db=None):

Parameters
----------
radial1d_mdl: Radial1DModel
radial1d_mdl : Radial1DModel
Inputted object that will be read into YAML file
fname: str
fname : str
File name for the synpp yaml
shell_no: int, optional(default = 0)
shell_no : int, optional(default = 0)
Number of shells
lines_db: file, optional(default = None)

lines_db : file, optional(default = None)

Raises
------
ValueError
If the current dataset does not contain necessary reference files
"""

logger.warning('Currently only works with Si and a special setup')
if radial1d_mdl.atom_data.synpp_refs is not None:
raise ValueError(
'The current atom dataset does not contain the '
'necesarry reference files (please contact the authors)')
'necessary reference files (please contact the authors)')

radial1d_mdl.atom_data.synpp_refs['ref_log_tau'] = -99.0
for key, value in radial1d_mdl.atom_data.synpp_refs.iterrows():
Expand Down Expand Up @@ -253,14 +257,14 @@ def intensity_black_body(nu, T):

Parameters
----------
nu: float
nu : float
Frequency of light
T: float
T : float
Temperature in kelvin

Returns
-------
Intensity: float
Intensity : float
Returns the intensity of the black body
"""
beta_rad = 1 / (k_B_cgs * T)
Expand All @@ -276,16 +280,16 @@ def species_tuple_to_string(species_tuple, roman_numerals=True):

Parameters
----------
species_tuple: tuple
species_tuple : tuple
Tuple of 2 values indicated atomic number and number of
electrons missing

roman_numerals: bool, optional(default = TRUE)
roman_numerals : bool, optional(default = TRUE)
Indicates whether the returned ion number is in roman numerals

Returns
-------
element_symbol, roman_ion_number: str
element_symbol, roman_ion_number : str
Returns corresponding string representation of given tuple
"""
atomic_number, ion_number = species_tuple
Expand All @@ -303,12 +307,12 @@ def species_string_to_tuple(species_string):

Parameters
----------
species_string: str
species_string : str
String containing species symbol (e.g. Si II, Fe III)

Returns
-------
atomic_number, ion_number: tuple
atomic_number, ion_number : tuple
Returns tuple of length 2 indicating atomic number and ion number

Raises
Expand Down Expand Up @@ -353,17 +357,17 @@ def parse_quantity(quantity_string):

Parameters
----------
quantity_string: str
quantity_string : str
String to be converted into astropy.Quantity

Returns
-------
q: ~u.Quantity
q : ~u.Quantity
Corresponding astropy.Quantity object for passed string

Raises
------
MalformedQuantitiyError
MalformedQuantityError
If string is not properly formatted for Astropy Quantity
"""

Expand Down Expand Up @@ -394,12 +398,12 @@ def element_symbol2atomic_number(element_string):

Parameters
----------
element_string: str
element_string : str
Inputted element symbol

Returns
-------
: int
int
Returned atomic number
"""
reformatted_element_string = reformat_element_symbol(element_string)
Expand All @@ -414,12 +418,12 @@ def atomic_number2element_symbol(atomic_number):

Parameters
----------
atomic_number: int
atomic_number : int
Inputted atomic number

Returns
-------
: str
str
Returned corresponding element symbol
"""
return ATOMIC_NUMBER2SYMBOL[atomic_number]
Expand All @@ -432,12 +436,12 @@ def reformat_element_symbol(element_string):

Parameters
----------
element_string: str
element_string : str
Inputted element symbol

Returns
-------
: str
str
Returned reformatted element symbol
"""

Expand All @@ -451,16 +455,16 @@ def quantity_linspace(start, stop, num, **kwargs):

Parameters
----------
start: ~astropy.Quantity
start : ~astropy.Quantity
Starting value of the sequence
stop: ~astropy.Quantity
stop : ~astropy.Quantity
End value of the sequence
num: ~int
num : int
Number of samples to generate

Returns
-------
: ~astropy.Quantity
~astropy.Quantity
Returns num evenly spaced characters of type astropy.Quantity

Raises
Expand All @@ -482,14 +486,14 @@ def convert_abundances_format(fname, delimiter=r'\s+'):

Parameters
----------
fname: file, str
fname : file, str
File or file name that contains abundance info
delimiter: str, optional(default = '\\s+')
delimiter : str, optional(default = '\\s+')
Determines the separator for splitting file

Returns
-------
: DataFrame
DataFrame
Corresponding data frame
"""
df = pd.read_csv(fname, delimiter=delimiter, comment='#', header=None)
Expand Down