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Commit 4fcb6311 authored by Yannick Roehlly's avatar Yannick Roehlly
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Use ordered dictionaries for parameters 

So that the configuration files and the serialized data have a logical
order.
parent 325f5cd7
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Showing with 327 additions and 306 deletions
pcigale/analysis_modules/common.py
View file @ 4fcb6311
......@@ -4,19 +4,20 @@
# Author: Yannick Roehlly <yannick.roehlly@oamp.fr>
from importlib import import_module
from collections import OrderedDict
class AnalysisModule(object):
"""Abstract class, the pCigale analysis modules are based on.
"""
# parameter_list is a dictionary containing all the parameters used by the
# module. Each parameter name is associate to a tuple (variable type,
# description [string], default value). Each module must define its
# parameter list, unless it does not use any parameter. Using None means
# that there is no description, unit or default value. If None should be
# the default value, use the 'None' string instead.
parameter_list = {}
# parameter_list is a ordered dictionary containing all the parameters
# used by the module. Each parameter name is associate to a tuple
# (variable type, description [string], default value). Each module must
# define its parameter list, unless it does not use any parameter. Using
# None means that there is no description, unit or default value. If None
# should be the default value, use the 'None' string instead.
parameter_list = OrderedDict()
def __init__(self, **kwargs):
"""Instantiate a analysis module
......
pcigale/analysis_modules/psum.py
View file @ 4fcb6311
......@@ -21,6 +21,7 @@ import sys
import atpy
import json
import numpy as np
from collections import OrderedDict
from copy import deepcopy
from scipy import stats
from progressbar import ProgressBar
......@@ -48,56 +49,56 @@ class Module(common.AnalysisModule):
TODO: Description of the PSUM method.
"""
parameter_list = {
"analysed_variables": (
parameter_list = OrderedDict([
("analysed_variables", (
"array of strings",
"List of the variables (in the SEDs info dictionaries) for which "
"the statistical analysis will be done.",
["sfr", "average_sfr"]
),
"save_best_sed": (
)),
("save_best_sed", (
"boolean",
"If true, save the best SED for each observation to a file.",
False
),
"plot_best_sed": (
)),
("plot_best_sed", (
"boolean",
"If true, for each observation save a plot of the best SED "
"and the observed fluxes.",
False
),
"plot_chi2_distribution": (
)),
("plot_chi2_distribution", (
"boolean",
"If true, for each observation and each analysed variable "
"plot the value vs reduced chi-square distribution.",
False
),
"save_pdf": (
)),
("save_pdf", (
"boolean",
"If true, for each observation and each analysed variable "
"save the probability density function.",
False
),
"plot_pdf": (
)),
("plot_pdf", (
"boolean",
"If true, for each observation and each analysed variable "
"plot the probability density function.",
False
),
"pdf_max_bin_number": (
)),
("pdf_max_bin_number", (
"integer",
"Maximum number of bins used to compute the probability density "
"function. This is only used when saving or printing the PDF. "
"If there are less values, the probability is given for each "
"one.",
50
),
"storage_type": (
)),
("storage_type", (
"string",
"Type of storage used to cache the generate SED.",
"memory"
)
}
))
])
def process(self, data_file, column_list, sed_modules,
sed_modules_params, redshift_module_name,
......
pcigale/analysis_modules/savefluxes.py
View file @ 4fcb6311
......@@ -14,6 +14,7 @@ The data file is used only to get the list of fluxes to be computed.
import os
from itertools import product
from collections import OrderedDict
from datetime import datetime
from astropy.table import Table
from progressbar import ProgressBar
......@@ -29,24 +30,24 @@ class Module(common.AnalysisModule):
"""
parameter_list = {
"output_file": (
parameter_list = OrderedDict([
("output_file", (
"string",
"Name of the output file.",
"computed_fluxes.xml"
),
"output_format": (
)),
("output_format", (
"string",
"Format of the output file. Any format supported by astropy.table "
"e.g. votable or ascii.",
"votable"
),
"storage_type": (
)),
("storage_type", (
"string",
"Type of storage used to cache the generate SED.",
"memory"
)
}
))
])
def process(self, data_file, column_list, sed_modules,
sed_modules_params, redshift_module,
......
pcigale/sed/modules/bc03.py
View file @ 4fcb6311
......@@ -4,6 +4,7 @@
# Author: Yannick Roehlly <yannick.roehlly@oamp.fr>
import numpy as np
from collections import OrderedDict
from . import common
from ...data import Database
......@@ -18,40 +19,40 @@ class Module(common.SEDCreationModule):
Bruzual and Charlot (2003) models.
"""
parameter_list = {
"imf": (
parameter_list = OrderedDict([
("imf", (
"string",
"Initial mass function: salp (Salpeter) or chab (Chabrier)",
None
),
"metallicity": (
)),
("metallicity", (
"float",
"Mettalicity, 0.02 for Solar metallicity.",
None
),
"separation_age": (
"integer",
)),
("separation_age", (
"int",
"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).",
10
)
}
out_parameter_list = {
"sfr": "Instantaneous Star Formation Rate in solar mass per year, "
"at the age of the galaxy.",
"average_sfr": "Average SFR in the last 100 Myr (default) of the "
"galaxy history.",
"m_star": "Total mass in stars in Solar mass.",
"m_gas": "Mass returned to the ISM by evolved stars in Solar mass.",
"n_ly": "rate of H-ionizing photons in s^-1, per Solar mass "
"of galaxy.",
"b_4000": "Amplitude of 4000 Å break (Bruzual 2003)",
"b4_vn": "Amplitude of 4000 Å narrow break (Balogh et al. 1999)",
"b4_sdss": "Amplitude of 4000 Å break (Stoughton et al. 2002)",
"b_912": "Amplitude of Lyman discontinuity"
}
))
])
out_parameter_list = OrderedDict([
("sfr", "Instantaneous Star Formation Rate in solar mass per year, "
"at the age of the galaxy."),
("average_sfr", "Average SFR in the last 100 Myr (default) of the "
"galaxy history."),
("m_star", "Total mass in stars in Solar mass."),
("m_gas", "Mass returned to the ISM by evolved stars in Solar mass."),
("n_ly", "rate of H-ionizing photons in s^-1, per Solar mass "
"of galaxy."),
("b_4000", "Amplitude of 4000 Å break (Bruzual 2003)"),
("b4_vn", "Amplitude of 4000 Å narrow break (Balogh et al. 1999)"),
("b4_sdss", "Amplitude of 4000 Å break (Stoughton et al. 2002)"),
("b_912", "Amplitude of Lyman discontinuity")
])
def _init_code(self):
"""Read the SSP from the database."""
......
pcigale/sed/modules/casey2012.py
View file @ 4fcb6311
......@@ -5,6 +5,7 @@
import numpy as np
import scipy.constants as cst
from collections import OrderedDict
from . import common
......@@ -19,35 +20,35 @@ class Module(common.SEDCreationModule):
"""
parameter_list = {
"temperature": (
parameter_list = OrderedDict([
("temperature", (
"float",
"Temperature of the dust in K.",
None
),
"beta": (
)),
("beta", (
"float",
"Emissivity index of the dust.",
None
),
"alpha": (
)),
("alpha", (
"float",
"Mid-infrared powerlaw slope.",
None
),
"attenuation_value_names": (
)),
("attenuation_value_names", (
"list of strings",
"List of attenuation value names (in the SED's info dictionary)."
"A new re-emission contribution will be added for each one.",
None
)
}
out_parameter_list = {
"temperature": "Temperature of the dust in K.",
"beta": "Emissivity index of the dust.",
"alpha": "Mid-infrared powerlaw slope."
}
))
])
out_parameter_list = OrderedDict([
("temperature", "Temperature of the dust in K."),
("beta", "Emissivity index of the dust."),
("alpha", "Mid-infrared powerlaw slope.")
])
def _init_code(self):
......
pcigale/sed/modules/common.py
View file @ 4fcb6311
......@@ -4,6 +4,7 @@
# Author: Yannick Roehlly <yannick.roehlly@oamp.fr>
from importlib import import_module
from collections import OrderedDict
def complete_parameters(given_parameters, parameter_list):
......@@ -14,36 +15,34 @@ def complete_parameters(given_parameters, parameter_list):
have no default value and is not present in given_parameters, raises an
error. If a parameter is present in given_parameters and not in
parameter_list, an exception is also raised.
Returns an ordered dictionary with the same key order as the parameter
list.
Parameters
----------
given_parameters : dictionary
Parameter dictionary used to configure the module.
parameter_list : dictionary
parameter_list : OrderedDict
Parameter list from the module.
Returns
-------
parameters : dictionary
Dictionary combining the given parameters with the default values for
the missing ones.
parameters : OrderedDict
Ordered dictionary combining the given parameters with the default
values for the missing ones.
Raises
------
KeyError when the given parameters are different from the expected ones.
"""
# For parameters that are present on the parameter_list with a default
# value and that are not in the giver_parameters dictionary, we add them
# with their default value.
# Complete the given parameters with default values when needed.
for key in parameter_list:
if (not key in given_parameters) and (
parameter_list[key][2] is not None):
given_parameters[key] = parameter_list[key][2]
# If the keys of the parameters dictionary are different from the one
# of the parameter_list dictionary, we raises a KeyError. That means
# that a parameter is missing (and has no default value) or that an
# unexpected one was given.
# Check parameter consistency between the parameter list and the given
# parameters.
if not set(given_parameters.keys()) == set(parameter_list.keys()):
missing_parameters = (set(parameter_list.keys())
- set(given_parameters.keys()))
......@@ -61,29 +60,34 @@ def complete_parameters(given_parameters, parameter_list):
raise KeyError("The parameters passed are different from the "
"expected one. " + message)
return given_parameters
# We want the result to be ordered as the parameter_list of the module is.
result = OrderedDict()
for key in parameter_list.keys():
result[key] = given_parameters[key]
return result
class SEDCreationModule(object):
"""Abstract class, the pCigale SED creation modules are based on.
"""
# parameter_list is a dictionary containing all the parameters used by
# the module. Each parameter name is associate to a tuple (variable type,
# description [string], default value). Each module must define its
# parameter list, unless it does not use any parameter. Using None means
# that there is no description or default value. If None should be the
# default value, use the 'None' string instead.
parameter_list = {}
# out_parameter_list is a dictionary containing all the SED parameters
# that are added to the SED info dictionary and for which a statistical
# analysis may be done. Each parameter name is associated with its
# description. In the SED info dictionary, the parameter name in prefixed
# with the name of the module plus an underscore (to allow several
# modules to add a parameter with the same name, for instance a repeated
# module.)
out_parameter_list = {}
# parameter_list is an ordered dictionary containing all the parameters
# used by the module. Each parameter name is associate to a tuple
# (variable type, description [string], default value). Each module must
# define its parameter list, unless it does not use any parameter. Using
# None means that there is no description or default value. If None should
# be the default value, use the 'None' string instead.
parameter_list = OrderedDict()
# out_parameter_list is an ordered dictionary containing all the SED
# parameters that are added to the SED info dictionary and for which a
# statistical analysis may be done. Each parameter name is associated with
# its description. In the SED info dictionary, the parameter name in
# prefixed with the name of the module plus an underscore (to allow
# several modules to add a parameter with the same name, for instance a
# repeated module.)
out_parameter_list = OrderedDict()
# comments is the text that is used to comment the module section in
# the configuration file. For instance, it can be used to give special
......
pcigale/sed/modules/dh2002.py
View file @ 4fcb6311
......@@ -3,6 +3,7 @@
# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
# Author: Yannick Roehlly <yannick.roehlly@oamp.fr>
from collections import OrderedDict
from . import common
from ...data import Database
......@@ -21,21 +22,21 @@ class Module(common.SEDCreationModule):
"""
parameter_list = {
'alpha': (
parameter_list = OrderedDict([
('alpha', (
'float',
"Alpha slope.",
None
),
'attenuation_value_names': (
)),
('attenuation_value_names', (
'array of strings',
"List of attenuation value names (in the SED's info dictionary). "
"A new re-emission contribution will be added for each one.",
None
)
}
))
])
out_parameter_list = {'alpha': 'Alpha slope.'}
out_parameter_list = OrderedDict([('alpha', 'Alpha slope.')])
def _init_code(self):
"""Get the template set out of the database"""
......
pcigale/sed/modules/dl2007.py
View file @ 4fcb6311
......@@ -4,6 +4,7 @@
# Author: Médéric Boquien <mederic.boquien@oamp.fr>
from . import common
from collections import OrderedDict
import numpy as np
from pcigale.data import Database
......@@ -22,39 +23,41 @@ class Module(common.SEDCreationModule):
"""
parameter_list = {
'qpah': (
parameter_list = OrderedDict([
('qpah', (
'float',
"Mass fraction of PAH",
None
),
'umin': (
)),
('umin', (
'float',
"Minimum radiation field",
None
),
'umax': (
)),
('umax', (
'float',
"Maximum radiation field",
None
),
'gamma': (
)),
('gamma', (
'float',
"Fraction illuminated from Umin to Umax",
None
),
'attenuation_value_names': (
)),
('attenuation_value_names', (
'list of strings',
"List of attenuation value names (in the SED's info dictionary). "
"A new re-emission contribution will be added for each one.",
None
)
}
out_parameter_list = {'qpah': 'Mass fraction of PAH',
'umin': 'Minimum radiation field',
'umax': 'Maximum radiation field',
'gamma': 'Fraction illuminated from Umin to Umax'}
))
])
out_parameter_list = OrderedDict([
('qpah', 'Mass fraction of PAH'),
('umin', 'Minimum radiation field'),
('umax', 'Maximum radiation field'),
('gamma', 'Fraction illuminated from Umin to Umax')
])
def _init_code(self):
"""Get the model out of the database"""
......
pcigale/sed/modules/dustatt_calzleit.py
View file @ 4fcb6311
......@@ -4,6 +4,7 @@
# Author: Yannick Roehlly <yannick.roehlly@oamp.fr>
import numpy as np
from collections import OrderedDict
from . import common
from ...data import Database
......@@ -167,77 +168,77 @@ class Module(common.SEDCreationModule):
"""
parameter_list = {
"E_BVs_young": (
parameter_list = OrderedDict([
("E_BVs_young", (
"float",
"E(B-V)*, the colour excess of the stellar continuum light for "
"the young population.",
None
),
"E_BVs_old_factor": (
)),
("E_BVs_old_factor", (
"float",
"Reduction factor for the E(B-V)* of the old population compared "
"to the young one (<1).",
None
),
"young_contribution_name": (
)),
("young_contribution_name", (
"string",
"Name of the contribution containing the spectrum of the "
"young population.",
"m2005_young"
),
"old_contribution_name": (
)),
("old_contribution_name", (
"string",
"Name of the contribution containing the spectrum of the "
"old population. If it is set to 'None', only one population "
"is considered.",
"m2005_old"
),
"uv_bump_wavelength": (
)),
("uv_bump_wavelength", (
"float",
"Central wavelength of the UV bump in nm.",
217.5
),
"uv_bump_width": (
)),
("uv_bump_width", (
"float",
"Width (FWHM) of the UV bump in nm.",
None
),
"uv_bump_amplitude": (
)),
("uv_bump_amplitude", (
"float",
"Amplitude of the UV bump in nm.",
None
),
"powerlaw_slope": (
)),
("powerlaw_slope", (
"float",
"Slope delta of the power law modifying the attenuation curve.",
None
),
"filters": (
)),
("filters", (
"list of strings",
"List of the filters for which the attenuation will be computed.",
['V_B90', 'FUV']
)
}
out_parameter_list = {
"NAME_E_BVs_young": "E(B-V)*, the colour excess of the stellar "
"continuum light for the young population.",
"NAME_E_BVs_old": "E(B-V)*, the colour excess of the stellar "
"continuum light for the old population.",
"NAME_attenuation_young": "Amount of luminosity attenuated from the "
"young population in W.",
"NAME_E_BVs_old_factor": "Ratio of the old population E(B-V)* to the "
"young one.",
"NAME_attenuation_old": "Amount of luminosity attenuated from the "
"old population in W.",
"NAME_attenuation": "Total amount of luminosity attenuated in W.",
"NAME_uv_bump_wavelength": "Central wavelength of UV bump in nm.",
"NAME_uv_bump_width": "Width of the UV bump in nm.",
"NAME_uv_bump_amplitude": "Amplitude of the UV bump in nm.",
"NAME_powerlaw_slope": "Slope of the power law.",
"NAME_FILTER": "Attenuation in the FILTER filter.",
}
))
])
out_parameter_list = OrderedDict([
("E_BVs_young", "E(B-V)*, the colour excess of the stellar continuum "
"light for the young population."),
("E_BVs_old", "E(B-V)*, the colour excess of the stellar "
"continuum light for the old population."),
("attenuation_young", "Amount of luminosity attenuated from the "
"young population in W."),
("E_BVs_old_factor", "Ratio of the old population E(B-V)* to the "
"young one."),
("attenuation_old", "Amount of luminosity attenuated from the "
"old population in W."),
("attenuation", "Total amount of luminosity attenuated in W."),
("uv_bump_wavelength", "Central wavelength of UV bump in nm."),
("uv_bump_width", "Width of the UV bump in nm."),
("uv_bump_amplitude", "Amplitude of the UV bump in nm."),
("powerlaw_slope", "Slope of the power law."),
("FILTER", "Attenuation in the FILTER filter.")
])
def _init_code(self):
"""Get the filters from the database"""
......
pcigale/sed/modules/dustatt_powerlaw.py
View file @ 4fcb6311
......@@ -10,6 +10,7 @@ in Charlot and Fall (2000) with a UV bump added.
"""
import numpy as np
from collections import OrderedDict
from . import common
from ...data import Database
......@@ -94,75 +95,75 @@ class Module(common.SEDCreationModule):
"""Add CCM dust attenuation based on Charlot and Fall (2000) power law.
"""
parameter_list = {
"Av_young": (
parameter_list = OrderedDict([
("Av_young", (
"float",
"V-band attenuation of the young population.",
None
),
"Av_old_factor": (
)),
("Av_old_factor", (
"float",
"Reduction factor for the V-band attenuation of the old "
"population compared to the young one (<1).",
None
),
"young_contribution_name": (
)),
("young_contribution_name", (
"string",
"Name of the contribution containing the spectrum of the "
"young population.",
"m2005_young"
),
"old_contribution_name": (
)),
("old_contribution_name", (
"string",
"Name of the contribution containing the spectrum of the "
"old population. If it is set to 'None', only one population "
"is considered.",
"m2005_old"
),
"uv_bump_wavelength": (
)),
("uv_bump_wavelength", (
"float",
"Central wavelength of the UV bump in nm.",
217.5
),
"uv_bump_width": (
)),
("uv_bump_width", (
"float",
"Width (FWHM) of the UV bump in nm.",
None
),
"uv_bump_amplitude": (
)),
("uv_bump_amplitude", (
"float",
"Amplitude of the UV bump in nm.",
None
),
"powerlaw_slope": (
)),
("powerlaw_slope", (
"float",
"Slope delta of the power law continuum.",
-0.7
),
"filters": (
)),
("filters", (
"list of strings",
"List of the filters for which the attenuation will be computed.",
['V_B90', 'FUV']
)
}
out_parameter_list = {
"NAME_Av_young": "V-band attenuation of the young population.",
"NAME_Av_old": "V-band attenuation of the old population.",
"NAME_attenuation_young": "Amount of luminosity attenuated from the "
"young population in W.",
"NAME_Av_old_factor": "Reduction factor for the V-band attenuation "
"of the old population compared to the young "
"one (<1).",
"NAME_attenuation_old": "Amount of luminosity attenuated from the "
"old population in W.",
"NAME_attenuation": "Total amount of luminosity attenuated in W.",
"NAME_uv_bump_wavelength": "Central wavelength of UV bump in nm.",
"NAME_uv_bump_width": "Width of the UV bump in nm.",
"NAME_uv_bump_amplitude": "Amplitude of the UV bump in nm.",
"NAME_powerlaw_slope": "Slope of the power law.",
"NAME_FILTER": "Attenuation in the FILTER filter.",
}
))
])