configuration.py 15 KB
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# -*- coding: utf-8 -*-
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# Copyright (C) 2012, 2013 Centre de données Astrophysiques de Marseille
# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
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# Author: Yannick Roehlly
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import pkgutil
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from collections import Iterable, OrderedDict
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import multiprocessing as mp
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from textwrap import wrap
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import configobj
from glob import glob  # To allow the use of glob() in "eval..."
import pkg_resources
import numpy as np

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from ..handlers.parameters_handler import ParametersHandler
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from ..data import Database
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from ..utils import read_table
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from .. import creation_modules
from .. import analysis_modules
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from ..warehouse import SedWarehouse

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# Limit the redshift to this number of decimals
REDSHIFT_DECIMALS = 2

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def list_modules(package_name):
    """Lists the modules available in a package

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    Parameters
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    ----------
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    package_name: string
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        Name of the package (e.g. pcigale.creation_modules).
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    Returns
    -------
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    module_name: array of strings
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        List of the available modules.

    """
    directory = pkg_resources.resource_filename(package_name, '')
    module_names = [name for _, name, _ in pkgutil.iter_modules([directory])]

    return module_names


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def evaluate_description(description):
    """Evaluate a description from the config file as a list.

    The description is read from the config file by configobj that transforms
    coma separated value in a list. From this description, this function try
    to evaluate the desired list of values:
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    - If the description is a string beginning with 'eval ', then its content
      (without 'eval ') is evaluated as Python code and its result returned.
      An array is expected.
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    - If the description is a string beginning by 'range', the start, step and
      stop values are then expected and the range is evaluated (stop included
      if reached.
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    - Then the function tries to evaluate the description as a Numpy array of
      float and returns the mere list if this fails.
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    Parameters
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    ----------
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    description: string or list
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        The description to be evaluated.

    Returns
    -------
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     results: list
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        The evaluated list of values.
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    """
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    results = description
    if type(description) == str:
        if description.startswith('eval '):
            results = eval(description[4:])
            # If the evaluation lead to a single value, we put it in a list.
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            if not isinstance(results, Iterable):
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                results = [results]
        elif description.startswith('range '):
            start, stop, step = [float(item) for item
                                 in description[5:].split()]
            results = np.arange(start, stop+step, step)
        else:
            # We need to return a list to combine the list of possible values
            # for each parameter.
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            results = [results]
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    # We prefer to evaluate the parameter as a numpy array of floats if
    # possible.
    try:
        results = np.array(results, float)
    except ValueError:
        pass
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    return results
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class Configuration(object):
    """This class manages the configuration of pcigale.
    """

    def __init__(self, filename="pcigale.ini"):
        """Initialise a pcigale configuration.

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        Parameters
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        ----------
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        filename: string
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            Name of the configuration file (pcigale.conf by default).

        """
        self.config = configobj.ConfigObj(filename,
                                          write_empty_values=True,
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                                          indent_type='  ',
                                          encoding='UTF8')
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    def create_blank_conf(self):
        """Create the initial configuration file

        Write the initial pcigale configuration file where the user can state
        which data file to use, which modules to use for the SED creation, as
        well as the method selected for statistical analysis.

        """

        self.config['data_file'] = ""
        self.config.comments['data_file'] = wrap(
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            "File containing the input data. The columns are 'id' (name of the"
            " object), 'redshift' (if 0 the distance is assumed to be 10 pc), "
            "the filter names for the fluxes, and the filter names with the "
            "'_err' suffix for the uncertainties. The fluxes and the "
            "uncertainties must be in mJy. This file is optional to generate "
            "the configuration file, in particular for the savefluxes module.")
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        self.config['creation_modules'] = []
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        self.config.comments['creation_modules'] = ([""] +
            ["Order of the modules use for SED creation. Available modules:"] +
            ["SFH: sfh2exp, sfhdelayed, sfhfromfile, sfhperiodic"] +
            ["SSP: bc03, m2005"] +
            ["Nebular emission: nebular"] +
            ["Dust attenuation: dustatt_calzleit, dustatt_powerlaw"] +
            ["Dust emission: casey2012, dale2014, dl2007, dl2014"] +
            ["AGN: dale2014, fritz2006"] +
            ["Radio: radio"] +
            ["Redshift: redshifting (mandatory!)"])
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        self.config['analysis_method'] = ""
        self.config.comments['analysis_method'] = [""] + wrap(
            "Method used for statistical analysis. Available methods: "
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            "pdf_analysis, savefluxes.")
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        self.config['cores'] = ""
        self.config.comments['cores'] = [""] + wrap(
            "Number of CPU cores available. This computer has {} cores."
            .format(mp.cpu_count()))

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        self.config.write()

    def generate_conf(self):
        """Generate the full configuration file

        Reads the user entries in the initial configuration file and add the
        configuration options of all selected modules as well as the filter
        selection based on the filters identified in the data table file.

        """

        # Getting the list of the filters available in pcigale database
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        with Database() as base:
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            filter_list = base.get_filter_names()
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        if self.config['data_file'] != '':
            obs_table = read_table(self.config['data_file'])

            # Check that the id and redshift columns are present in the input
            # file
            if 'id' not in obs_table.columns:
                raise Exception("Column id not present in input file")
            if 'redshift' not in obs_table.columns:
                raise Exception("Column redshift not present in input file")

            # Finding the known filters in the data table
            column_list = []
            for column in obs_table.columns:
                filter_name = column[:-4] if column.endswith('_err') else column
                if filter_name in filter_list:
                    column_list.append(column)

            # Check that we don't have an error column without the associated
            # flux
            for column in column_list:
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                if column.endswith('_err') and (column[:-4]
                                                not in column_list):
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                    raise Exception("The observation table as a {} column "
                                    "but no {} column.".format(column,
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                                                               column[:-4]))
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            self.config['column_list'] = column_list
        else:
            self.config['column_list'] = ''
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        self.config.comments['column_list'] = [""] + wrap(
            "List of the columns in the observation data file to use for "
            "the fitting.")

        # SED creation modules configurations. For each module, we generate
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        # the configuration section from its parameter list.
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        self.config['sed_creation_modules'] = {}
        self.config.comments['sed_creation_modules'] = ["", ""] + wrap(
            "Configuration of the SED creation modules.")

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        for module_name in self.config['creation_modules']:
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            self.config["sed_creation_modules"][module_name] = {}
            sub_config = self.config["sed_creation_modules"][module_name]

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            for name, (typ, description, default) in \
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                    creation_modules.get_module(
                        module_name,
                        blank=True).parameter_list.items():
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                if default is None:
                    default = ''
                sub_config[name] = default
                sub_config.comments[name] = wrap(description)

            self.config['sed_creation_modules'].comments[module_name] = [
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                creation_modules.get_module(module_name, blank=True).comments]
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        self.check_modules()

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        # Configuration for the analysis method
        self.config['analysis_configuration'] = {}
        self.config.comments['analysis_configuration'] = ["", ""] + wrap(
            "Configuration of the statistical analysis method.")
        module_name = self.config['analysis_method']
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        for name, (typ, desc, default) in \
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                analysis_modules.get_module(module_name).parameter_list.items():
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            if default is None:
                default = ''
            self.config['analysis_configuration'][name] = default
            self.config['analysis_configuration'].comments[name] = wrap(desc)

        self.config.write()
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    @property
    def configuration(self):
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        """Returns a dictionary for the session configuration.
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        Returns
        -------
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        configuration['data_file']: string
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            File containing the observations to fit.
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        configuration['column_list']: list of strings
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            List of the columns of data_file to use in the fitting.
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        configuration['creation_modules']: list of strings
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            List of the modules (in the right order) used to create the SEDs.
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        configuration['creation_modules_params']: list of dictionaries
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            Configuration parameters for each module. To each parameter, the
            dictionary associates a list of possible values (possibly only
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            one).
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        configuration['analysis_method']: string
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            Statistical analysis module used to fit the data.
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        configuration['analysis_method_params']: dictionary
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            Parameters for the statistical analysis module. To each parameter
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            is associated a list of possible values.
        """
        configuration = {}

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        # Before building the configuration dictionary, we ensure that all the
        # fields are filled
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        self.complete_redshifts()
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        for section in ['data_file', 'column_list', 'creation_modules',
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                        'analysis_method']:
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            configuration[section] = self.config[section]
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        configuration['cores'] = int(self.config['cores'])
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        # Parsing the SED modules parameters
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        configuration['creation_modules_params'] = []
        for module in self.config['creation_modules']:
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            module_params = {}
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            for key, value in \
                    self.config['sed_creation_modules'][module].items():
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                module_params[key] = evaluate_description(value)
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            configuration['creation_modules_params'].append(module_params)
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        if (self.config['analysis_method'] == 'savefluxes' and
            not self.config['analysis_configuration']['variables']):
            warehouse = SedWarehouse()
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            params = ParametersHandler(configuration)
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            sed = warehouse.get_sed(configuration['creation_modules'],
                                    params.from_index(0))
            info = list(sed.info.keys())
            info.sort()
            self.config['analysis_configuration']['variables'] = info
        elif (self.config['analysis_method'] == 'pdf_analysis' and
              not self.config['analysis_configuration']['analysed_variables']):
            warehouse = SedWarehouse()
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            params = ParametersHandler(configuration)
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            sed = warehouse.get_sed(configuration['creation_modules'],
                                    params.from_index(0))
            info = list(sed.info.keys())
            info.sort()
            self.config['analysis_configuration']['analysed_variables'] = info
        else:
            raise Exception("Cannot determine which physical variables are to"
                            "be computed with the {} module.").format(
                            configuration['analysis_method'])

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        # Analysis method parameters
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        configuration['analysis_method_params'] = \
            self.config['analysis_configuration']
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        return configuration
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    def check_modules(self):
        """Make a basic check to ensure that some required modules are present.
        Otherwise we emit a warning so the user knows their list of modules is
        suspicious. We do not emit an exception as they may be using an
        unofficial module that is not in our list
        """

        modules = OrderedDict((('SFH', ['sfh2exp', 'sfhdelayed', 'sfhfromfile',
                                        'sfhperiodic']),
                               ('SSP', ['bc03', 'm2005']),
                               ('nebular', ['nebular']),
                               ('dust attenuation', ['dustatt_calzleit',
                                                     'dustatt_powerlaw']),
                               ('dust emission', ['casey2012', 'dale2014',
                                                  'dl2007', 'dl2014']),
                               ('AGN', ['dale2014', 'fritz2006']),
                               ('radio', ['radio']),
                               ('redshift', ['redshifting'])))

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        comments = {'SFH': "ERROR! Choosing one SFH module is mandatory.",
                    'SSP': "ERROR! Choosing one SSP module is mandatory.",
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                    'nebular': "WARNING! Choosing the nebular module is "
                               "recommended. Without it the Lyman continuum "
                               "is left untouched.",
                    'dust attenuation': "No dust attenuation module found.",
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                    'dust emission': "No dust emission module found.",
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                    'AGN': "No AGN module found.",
                    'radio': "No radio module found.",
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                    'redshift': "ERROR! No redshifting module found."}
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        for module in modules:
            if all([user_module not in modules[module] for user_module in
                    self.config['creation_modules']]):
                print("{} Options are: {}.".
                      format(comments[module], ', '.join(modules[module])))
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    def complete_redshifts(self):
        """Complete the configuration when the redshifts are missing from the
        configuration file and must be extracted from the input flux file.
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        """

        z_mod = self.config['sed_creation_modules']['redshifting']['redshift']
        if type(z_mod) is str and not z_mod:
            if self.config['data_file']:
                obs_table = read_table(self.config['data_file'])
                z = np.unique(np.around(obs_table['redshift'],
                                        decimals=REDSHIFT_DECIMALS))
                self.config['sed_creation_modules']['redshifting']['redshift'] = z
            else:
                raise Exception("No flux file and no redshift indicated. "
                                "The spectra cannot be computed. Aborting.")