Commit 3a9d8b8a authored by Médéric Boquien's avatar Médéric Boquien

Add the necessary bits in order to allow to fit directly pure BC03 SSP.

parent b487455e
......@@ -20,7 +20,7 @@ import numpy as np
from scipy import interpolate
import scipy.constants as cst
from astropy.table import Table
from import (Database, Filter, M2005, BC03, Fritz2006,
from import (Database, Filter, M2005, BC03, BC03_SSP, Fritz2006,
Dale2014, DL2007, DL2014, NebularLines,
NebularContinuum, Schreiber2016, THEMIS)
......@@ -410,6 +410,48 @@ def build_bc2003(base, res):
def build_bc2003_ssp(base, res):
bc03_dir = os.path.join(os.path.dirname(__file__), 'bc03/')
# Metallicities associated to each key
metallicity = {
"m22": 0.0001,
"m32": 0.0004,
"m42": 0.004,
"m52": 0.008,
"m62": 0.02,
"m72": 0.05
for key, imf in itertools.product(metallicity, ["salp", "chab"]):
ssp_filename = "{}bc2003_{}_{}_{}_ssp.ised_ASCII".format(bc03_dir, res,
key, imf)
color3_filename = "{}bc2003_lr_{}_{}_ssp.3color".format(bc03_dir, key,
color4_filename = "{}bc2003_lr_{}_{}_ssp.4color".format(bc03_dir, key,
print("Importing {}...".format(ssp_filename))
# Read the desired information from the color files
color_table = []
color3_table = np.genfromtxt(color3_filename).transpose()
color4_table = np.genfromtxt(color4_filename).transpose()
color_table.append(color4_table[6]) # Mstar
color_table.append(color4_table[7]) # Mgas
color_table.append(10 ** color3_table[5]) # NLy
color_table = np.array(color_table)
ssp_time, ssp_wave, ssp_lumin = read_bc03_ssp(ssp_filename)
def build_dale2014(base):
models = []
......@@ -860,6 +902,7 @@ def build_base(bc03res='lr'):
print('#' * 78)
print("3- Importing Bruzual and Charlot 2003 SSP\n")
build_bc2003_ssp(base, bc03res)
build_bc2003(base, bc03res)
print('#' * 78)
......@@ -24,6 +24,7 @@ import numpy as np
from .filters import Filter
from .m2005 import M2005
from .bc03 import BC03
from .bc03_ssp import BC03_SSP
from .dale2014 import Dale2014
from .dl2007 import DL2007
from .dl2014 import DL2014
......@@ -116,6 +117,28 @@ class _BC03(BASE):
self.spec_table = ssp.spec_table
class _BC03_SSP(BASE):
"""Storage for Bruzual and Charlot 2003 SSP
__tablename__ = "bc03_ssp"
imf = Column(String, primary_key=True)
metallicity = Column(Float, primary_key=True)
time_grid = Column(PickleType)
wavelength_grid = Column(PickleType)
info_table = Column(PickleType)
spec_table = Column(PickleType)
def __init__(self, ssp):
self.imf = ssp.imf
self.metallicity = ssp.metallicity
self.time_grid = ssp.time_grid
self.wavelength_grid = ssp.wavelength_grid
self.info_table = ssp.info_table
self.spec_table = ssp.spec_table
class _Dale2014(BASE):
"""Storage for Dale et al (2014) infra-red templates
......@@ -444,6 +467,71 @@ class Database(object):
return self._get_parameters(_BC03)
def add_bc03_ssp(self, ssp_bc03):
Add a Bruzual and Charlot 2003 SSP to pcigale database
if self.is_writable:
ssp = _BC03_SSP(ssp_bc03)
except exc.IntegrityError:
raise DatabaseInsertError('The SSP is already in the base.')
raise Exception('The database is not writable.')
def get_bc03_ssp(self, imf, metallicity):
Query the database for the Bruzual and Charlot 2003 SSP corresponding
to the given initial mass function and metallicity.
imf: string
Initial mass function (salp for Salpeter, chab for Chabrier)
metallicity: float
0.02 for Solar metallicity
The BC03 object.
DatabaseLookupError: if the requested SSP is not in the database.
result = self.session.query(_BC03_SSP)\
.filter(_BC03_SSP.imf == imf)\
.filter(_BC03_SSP.metallicity == metallicity)\
if result:
return BC03_SSP(result.imf, result.metallicity, result.time_grid,
result.wavelength_grid, result.info_table,
raise DatabaseLookupError(
"The BC03 SSP for imf <{0}> and metallicity <{1}> is not in "
"the database.".format(imf, metallicity))
def get_bc03_ssp_parameters(self):
"""Get parameters for the Bruzual & Charlot 2003 stellar models.
paramaters: dictionary
dictionary of parameters and their values
return self._get_parameters(_BC03_SSP)
def add_dl2007(self, models):
Add a list of Draine and Li (2007) models to the database.
# -*- coding: utf-8 -*-
# Copyright (C) 2013 Centre de données Astrophysiques de Marseille
# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
# Author: Yannick Roehlly
import numpy as np
class BC03_SSP(object):
def __init__(self, imf, metallicity, time_grid, wavelength_grid,
info_table, spec_table):
if imf in ['salp', 'chab']:
self.imf = imf
raise ValueError('IMF must be either sal for Salpeter or '
'cha for Chabrier.')
self.metallicity = metallicity
self.time_grid = time_grid
self.wavelength_grid = wavelength_grid
self.info_table = info_table
self.spec_table = spec_table
Bruzual and Charlot (2003) stellar emission module for an SSP
This module implements the Bruzual and Charlot (2003) Single Stellar
from collections import OrderedDict
import numpy as np
from . import SedModule
from import Database
class BC03SSP(SedModule):
parameter_list = OrderedDict([
("imf", (
"cigale_list(dtype=int, options=0. & 1.)",
"Initial mass function: 0 (Salpeter) or 1 (Chabrier).",
("metallicity", (
"cigale_list(options=0.0001 & 0.0004 & 0.004 & 0.008 & 0.02 & "
"Metalicity. Possible values are: 0.0001, 0.0004, 0.004, 0.008, "
"0.02, 0.05.",
("separation_age", (
"cigale_list(dtype=int, minvalue=0)",
"Age [Myr] of the separation between the young and the old star "
"populations. The default value in 10^7 years (10 Myr). Set "
"to 0 not to differentiate ages (only an old population).",
def _init_code(self):
"""Read the SSP from the database."""
self.imf = int(self.parameters["imf"])
self.metallicity = float(self.parameters["metallicity"])
self.separation_age = int(self.parameters["separation_age"])
with Database() as database:
if self.imf == 0:
self.ssp = database.get_bc03_ssp('salp', self.metallicity)
elif self.imf == 1:
self.ssp = database.get_bc03_ssp('chab', self.metallicity)
raise Exception("IMF #{} unknown".format(self.imf))
def process(self, sed):
"""Add the convolution of a Bruzual and Charlot SSP to the SED
sed: pcigale.sed.SED
SED object.
if 'ssp.index' in
index =['ssp.index']
raise Exception('The stellar models do not correspond to pure SSP.')
if self.ssp.time_grid[index] <= self.separation_age:
spec_young = self.ssp.spec_table[:, index]
info_young = self.ssp.info_table[:, index]
spec_old = np.zeros_like(spec_young)
info_old = np.zeros_like(info_young)
spec_old = self.ssp.spec_table[:, index]
info_old = self.ssp.info_table[:, index]
spec_young = np.zeros_like(spec_old)
info_young = np.zeros_like(info_old)
info_all = info_young + info_old
info_young = dict(zip(["m_star", "m_gas", "n_ly"], info_young))
info_old = dict(zip(["m_star", "m_gas", "n_ly"], info_old))
info_all = dict(zip(["m_star", "m_gas", "n_ly"], info_all))
# We compute the Lyman continuum luminosity as it is important to
# compute the energy absorbed by the dust before ionising gas.
wave = self.ssp.wavelength_grid
w = np.where(wave <= 91.1)
lum_lyc_young, lum_lyc_old = np.trapz([spec_young[w], spec_old[w]],
# We do similarly for the total stellar luminosity
lum_young, lum_old = np.trapz([spec_young, spec_old], wave)
sed.add_module(, self.parameters)
sed.add_info("stellar.imf", self.imf)
sed.add_info("stellar.metallicity", self.metallicity)
sed.add_info("stellar.old_young_separation_age", self.separation_age)
sed.add_info("stellar.age", self.ssp.time_grid[index])
sed.add_info("stellar.m_star_young", info_young["m_star"], True)
sed.add_info("stellar.m_gas_young", info_young["m_gas"], True)
sed.add_info("stellar.n_ly_young", info_young["n_ly"], True)
sed.add_info("stellar.lum_ly_young", lum_lyc_young, True)
sed.add_info("stellar.lum_young", lum_young, True)
sed.add_info("stellar.m_star_old", info_old["m_star"], True)
sed.add_info("stellar.m_gas_old", info_old["m_gas"], True)
sed.add_info("stellar.n_ly_old", info_old["n_ly"], True)
sed.add_info("stellar.lum_ly_old", lum_lyc_old, True)
sed.add_info("stellar.lum_old", lum_old, True)
sed.add_info("stellar.m_star", info_all["m_star"], True)
sed.add_info("stellar.m_gas", info_all["m_gas"], True)
sed.add_info("stellar.n_ly", info_all["n_ly"], True)
sed.add_info("stellar.lum_ly", lum_lyc_young + lum_lyc_old, True)
sed.add_info("stellar.lum", lum_young + lum_old, True)
sed.add_contribution("stellar.old", wave, spec_old)
sed.add_contribution("stellar.young", wave, spec_young)
# SedModule to be returned by get_module
Module = BC03SSP
Simple module to reduce the SFH to a single SSP
This module implements a star formation history (SFH) through a single SSP.
from collections import OrderedDict
import numpy as np
from . import SedModule
class SSP(SedModule):
"""Instantaneous burst corresponding to a model-provided SSP
This module sets the SED star formation history (SFH) as a single stellar
parameter_list = OrderedDict([
("index", (
"cigale_list(dtype=int, minvalue=0)",
"Index of the SSP to use.",
def _init_code(self):
self.index = int(self.parameters["index"])
def process(self, sed):
"""Add a double decreasing exponential Star Formation History.
sed: pcigale.sed.SED object
sed.add_module(, self.parameters)
# Add the sfh and the output parameters to the SED.
sed.sfh = np.array([0.])
sed.add_info("ssp.index", self.index)
# SedModule to be returned by get_module
Module = SSP
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