Skip to content

cigale
cigale
Commit 16147565 authored by Médéric Boquien's avatar Médéric Boquien
Browse files
Options

Cleanup of the Fritz modules to make things more readable and respect the PEP8.

parent 6c5f54d8
Hide whitespace changes
Inline Side-by-side
Showing with 68 additions and 102 deletions
database_builder/__init__.py
View file @ 16147565
......@@ -459,25 +459,21 @@ def build_dl2007(base):
def build_fritz2006(base):
fritz2006_dir = os.path.join(os.path.dirname(__file__), 'fritz2006/')
# Parameters of Fritz+2006
psy = [0.001, 10.100, 20.100, 30.100, 40.100, 50.100, 60.100, 70.100,
80.100, 89.990] # Viewing angle in degrees
opening_angle = ["20", "40", "60"] # Theta = 2*(90 - opening_angle)
80.100, 89.990] # Viewing angle in degrees
opening_angle = ["20", "40", "60"] # Theta = 2*(90 - opening_angle)
gamma = ["0.0", "2.0", "4.0", "6.0"]
beta = ["-1.00", "-0.75", "-0.50", "-0.25", "0.00"]
tau = ["0.1", "0.3", "0.6", "1.0", "2.0", "3.0", "6.0", "10.0"]
r_ratio = ["10","30", "60", "100", "150"]
r_ratio = ["10", "30", "60", "100", "150"]
# Read and convert the wavelength
datafile = open(fritz2006_dir + "ct{}al{}be{}ta{}rm{}.tot".format(opening_angle[0],
gamma[0],
beta[0],
tau[0],
r_ratio[0]))
datafile = open(fritz2006_dir + "ct{}al{}be{}ta{}rm{}.tot"
.format(opening_angle[0], gamma[0], beta[0], tau[0],
r_ratio[0]))
data = "".join(datafile.readlines()[-178:])
datafile.close()
wave = np.genfromtxt(io.BytesIO(data.encode()), usecols=(0))
......@@ -486,55 +482,47 @@ def build_fritz2006(base):
nskip = 28
blocksize = 178
for oa in opening_angle:
for gam in gamma:
for be in beta:
for ta in tau:
for rm in r_ratio:
filename = fritz2006_dir + "ct{}al{}be{}ta{}rm{}.tot".format(
oa,
gam,
be,
ta,
rm)
print("Importing {}...".format(filename))
try :
datafile = open(filename)
except IOError:
continue
data = datafile.readlines()
datafile.close()
for n in range(len(psy)):
block = data[nskip + blocksize * n + 4 * (n + 1) - 1: nskip + blocksize * (n+1) + 4 * (n + 1) - 1]
lumin_therm, lumin_scatt, lumin_agn = np.genfromtxt(io.BytesIO("".join(block).encode()), usecols=(2,3,4), unpack=True)
# Remove NaN
lumin_therm = np.nan_to_num(lumin_therm)
lumin_scatt = np.nan_to_num(lumin_scatt)
lumin_agn = np.nan_to_num(lumin_agn)
# Conversion from erg/s/microns to W/nm
lumin_therm *= 1e-4
lumin_scatt *= 1e-4
lumin_agn *= 1e-4
# Normalization of the lumin_therm to 1W
norm = np.trapz(lumin_therm, x = wave)
lumin_therm = lumin_therm / norm
lumin_scatt = lumin_scatt / norm
lumin_agn = lumin_agn / norm
base.add_fritz2006(Fritz2006(rm,
ta,
be,
gam,
oa,
psy[n],
wave,
lumin_therm,
lumin_scatt,
lumin_agn))
iter_params = ((oa, gam, be, ta, rm)
for oa in opening_angle
for gam in gamma
for be in beta
for ta in tau
for rm in r_ratio)
for params in iter_params:
filename = fritz2006_dir + "ct{}al{}be{}ta{}rm{}.tot".format(*params)
print("Importing {}...".format(filename))
try:
datafile = open(filename)
except IOError:
continue
data = datafile.readlines()
datafile.close()
for n in range(len(psy)):
block = data[nskip + blocksize * n + 4 * (n + 1) - 1:
nskip + blocksize * (n+1) + 4 * (n + 1) - 1]
lumin_therm, lumin_scatt, lumin_agn = np.genfromtxt(
io.BytesIO("".join(block).encode()), usecols=(2, 3, 4),
unpack=True)
# Remove NaN
lumin_therm = np.nan_to_num(lumin_therm)
lumin_scatt = np.nan_to_num(lumin_scatt)
lumin_agn = np.nan_to_num(lumin_agn)
# Conversion from erg/s/microns to W/nm
lumin_therm *= 1e-4
lumin_scatt *= 1e-4
lumin_agn *= 1e-4
# Normalization of the lumin_therm to 1W
norm = np.trapz(lumin_therm, x=wave)
lumin_therm = lumin_therm / norm
lumin_scatt = lumin_scatt / norm
lumin_agn = lumin_agn / norm
base.add_fritz2006(Fritz2006(params[4], params[3], params[2],
params[1], params[0], psy[n], wave,
lumin_therm, lumin_scatt, lumin_agn))
def build_nebular(base):
lines_dir = os.path.join(os.path.dirname(__file__), 'nebular/')
......
pcigale/creation_modules/fritz2006.py
View file @ 16147565
......@@ -65,14 +65,6 @@ class Fritz2006(CreationModule):
"Contribution of the AGN"
"",
None
)),
('attenuation_value_keys', (
'string',
"Keys of the SED information dictionary where the module will "
"look for the attenuation (in W) to re-emit. You can give several "
"keys separated with a & (don't use commas), a re-emission "
"contribution will be added for each key.",
"attenuation"
))
])
......@@ -81,7 +73,6 @@ class Fritz2006(CreationModule):
('L_AGN', 'Luminosity of the AGN contribution')
])
def _init_code(self):
"""Get the template set out of the database"""
r_ratio = self.parameters["r_ratio"]
......@@ -93,9 +84,7 @@ class Fritz2006(CreationModule):
with Database() as base:
self.fritz2006 = base.get_fritz2006(r_ratio, tau, beta, gamma,
opening_angle, psy)
opening_angle, psy)
def process(self, sed):
"""Add the IR re-emission contributions
......@@ -108,10 +97,9 @@ class Fritz2006(CreationModule):
"""
if 'dust.luminosity' not in sed.info.keys():
sed.add_info('dust.luminosity',1.,True)
sed.add_info('dust.luminosity', 1., True)
luminosity = sed.info['dust.luminosity']
fracAGN = self.parameters["fracAGN"]
sed.add_module(self.name, self.parameters)
......@@ -123,27 +111,15 @@ class Fritz2006(CreationModule):
sed.add_info('psy', self.parameters["psy"])
sed.add_info('fracAGN', self.parameters["fracAGN"])
# Compute the AGN luminosity
L_AGN = fracAGN * (luminosity + 1)
#sed.add_info("L_AGN" + self.postfix, self.parameters["L_AGN"])
sed.add_contribution(
'agn_fritz2006_therm',
self.fritz2006.wave,
L_AGN * self.fritz2006.lumin_therm
)
sed.add_contribution(
'agn_fritz2006_scatt',
self.fritz2006.wave,
L_AGN * self.fritz2006.lumin_scatt
)
sed.add_contribution(
'agn_fritz2006_agn',
self.fritz2006.wave,
L_AGN * self.fritz2006.lumin_agn
)
sed.add_contribution('agn_fritz2006_therm', self.fritz2006.wave,
L_AGN * self.fritz2006.lumin_therm)
sed.add_contribution('agn_fritz2006_scatt', self.fritz2006.wave,
L_AGN * self.fritz2006.lumin_scatt)
sed.add_contribution('agn_fritz2006_agn', self.fritz2006.wave,
L_AGN * self.fritz2006.lumin_agn)
# CreationModule to be returned by get_module
Module = Fritz2006
pcigale/data/__init__.py
View file @ 16147565
......@@ -17,7 +17,7 @@ SqlAlchemy ORM to store the data in a unique SQLite3 database.
import pkg_resources
from sqlalchemy import (create_engine, exc, Column, String, Text,
Float, Integer, PickleType)
Float, PickleType)
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import class_mapper, sessionmaker
import numpy as np
......@@ -187,7 +187,7 @@ class _Fritz2006(BASE):
wave = Column(PickleType)
lumin_therm = Column(PickleType)
lumin_scatt = Column(PickleType)
lumin_agn= Column(PickleType)
lumin_agn = Column(PickleType)
def __init__(self, agn):
self.r_ratio = agn.r_ratio
......@@ -201,6 +201,7 @@ class _Fritz2006(BASE):
self.lumin_scatt = agn.lumin_scatt
self.lumin_agn = agn.lumin_agn
class _NebularLines(BASE):
"""Storage for line templates
"""
......@@ -645,7 +646,7 @@ class Database(object):
lumin_therm : array of float
Luminosity density of the dust torus at each wavelength in W/nm.
lumin_scatt : array of float
Luminosity density of the scattered emission at each wavelength
Luminosity density of the scattered emission at each wavelength
in W/nm.
lumin_agn : array of float
Luminosity density of the central AGN at each wavelength in W/nm.
......@@ -668,12 +669,12 @@ class Database(object):
filter(_Fritz2006.gamma == gamma).
filter(_Fritz2006.opening_angle == opening_angle).
filter(_Fritz2006.psy == psy).
first())
first())
if result:
return Fritz2006(result.r_ratio, result.tau, result.beta,
result.gamma, result.opening_angle, result.psy,
result.wave, result.lumin_therm,
result.lumin_scatt, result.lumin_agn)
result.gamma, result.opening_angle, result.psy,
result.wave, result.lumin_therm,
result.lumin_scatt, result.lumin_agn)
else:
raise DatabaseLookupError(
"The Fritz2006 model is not in the database.")
......
pcigale/data/fritz2006.py
View file @ 16147565
......@@ -12,7 +12,8 @@ class Fritz2006(object):
"""
def __init__(self, r_ratio, tau, beta, gamma, opening_angle, psy, wave, lumin_therm, lumin_scatt, lumin_agn):
def __init__(self, r_ratio, tau, beta, gamma, opening_angle, psy, wave,
lumin_therm, lumin_scatt, lumin_agn):
"""Create a new AGN model
Parameters
......@@ -30,7 +31,7 @@ class Fritz2006(object):
psy : float
Angle between AGN axis and line of sight.
"""
self.r_ratio = r_ratio
self.tau = tau
self.beta = beta
......@@ -40,4 +41,4 @@ class Fritz2006(object):
self.wave = wave
self.lumin_therm = lumin_therm
self.lumin_scatt = lumin_scatt
self.lumin_agn = lumin_agn
\ No newline at end of file
self.lumin_agn = lumin_agn
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment