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Commit 16147565 authored by Médéric Boquien's avatar Médéric Boquien
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Cleanup of the Fritz modules to make things more readable and respect the PEP8.

parent 6c5f54d8
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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
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