configuration.py 11.9 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
# Author: Yannick Roehlly <yannick.roehlly@oamp.fr>
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import atpy
import configobj
import pkg_resources
import pkgutil
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import collections
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import itertools
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import numpy as np
from textwrap import wrap
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from .tools import param_dict_combine
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from ..data import Database
from ..sed.modules import common as modules
from ..stats import common as analysis


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

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    Parameters
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    ----------
    package_name : string
        Name of the package (e.g. pcigale.sed.modules).

    Returns
    -------
    module_name : array of strings
        List of the available modules.

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

    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 list beginning by 'range', the start, step and
      stop values are then expected and the range is evaluated.
    - 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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    if not type(description) == list:
        description = [description]
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    if description[0].startswith('eval '):
        results = eval(description[0][4:])
        # If the evaluation lead to a single value, we put it in a list.
        if not isinstance(results, collections.Iterable):
            results = [results]
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    elif description[0] == 'range':
        start = float(description[1])
        step = float(description[2])
        stop = float(description[3])
        results = np.arange(start, stop, step, float)
    else:
        try:
            results = np.array(description, float)
        except ValueError:
            results = description
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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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        ----------
        filename : string
            Name of the configuration file (pcigale.conf by default).

        """
        self.config = configobj.ConfigObj(filename,
                                          write_empty_values=True,
                                          indent_type='  ')

    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(
            "File containing the observation data to be fitted. Each flux "
            "column must have the name of the corresponding filter, the "
            "error columns are suffixed with '_err'. The values must be "
            "in mJy.")

        self.config['sed_modules'] = []
        self.config.comments['sed_modules'] = [""] + wrap(
            "Order of the modules use for SED creation. Available modules : "
            + ', '.join(list_modules('pcigale.sed.modules')) + ".")

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        self.config['redshift_module'] = ""
        self.config.comments['redshift_module'] = [""] + wrap(
            "Module used to redshift the SED before the integration in the "
            "filters. This is a SED creation module that accepts a 'redshift' "
            "parameter (see the documentation).")

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        self.config['analysis_method'] = ""
        self.config.comments['analysis_method'] = [""] + wrap(
            "Method used for statistical analysis. Available methods: "
            + ', '.join(list_modules('pcigale.stats')) + ".")

        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
        base = Database()
        filter_list = base.get_filter_list()[0]
        base.close()

        # Finding the known filters in the data table
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        obs_table = atpy.Table(self.config['data_file'], verbose=False)
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        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:
            if column.endswith('_err') and (column[:-4] not in column_list):
                raise StandardError("The observation table as a {} column "
                                    "but no {} column.".format(column,
                                                               column[:-4]))

        self.config['column_list'] = column_list
        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.")

        for module_name in self.config['sed_modules']:
            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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                    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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                modules.get_module(module_name, blank=True).comments]
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        # Configuration for the redshift module
        self.config['redshift_configuration'] = {}
        self.config.comments['redshift_configuration'] = ["", ""] + wrap(
            "Set the 'redshift' parameter to None (or delete the line). If "
            "there are other parameters, you must give only one value for "
            "each.")
        module_name = self.config['redshift_module']
        for name, (typ, desc, default) in \
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                modules.get_module(module_name,
                                   blank=True).parameter_list.items():
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            if default is None:
                default = ''
            self.config['redshift_configuration'][name] = default
            self.config['redshift_configuration'].comments[name] = wrap(desc)

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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.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
        -------
        configuration['data_file'] : string
            File containing the observations to fit.
        configuration['column_list'] : list of strings
            List of the columns of data_file to use in the fitting.
        configuration['sed_modules'] : list of strings
            List of the modules (in the right order) used to create the SEDs.
        configuration['sed_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['redshift_module'] : string
        configuration['redshift_configuration'] : dictionary
            Parameters for the redshift module.
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        configuration['analysis_method'] : string
            Statistical analysis module used to fit the data.
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        configuration['analysis_method_params'] : dictionary
            Parameters for the statistical analysis module. To each parameter
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            is associated a list of possible values.
        """
        configuration = {}

        for section in ['data_file', 'column_list', 'sed_modules',
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                        'redshift_module', 'analysis_method']:
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            configuration[section] = self.config[section]

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        # Parsing the SED modules parameters
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        configuration['sed_modules_params'] = []
        for module in self.config['sed_modules']:
            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)
            configuration['sed_modules_params'].append(module_params)
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        # Parsing the redshift module parameters
        configuration['redshift_configuration'] = {}
        for key, value in self.config['redshift_configuration'].items():
            configuration['redshift_configuration'][key] = \
                evaluate_description(value)
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        # Parsing the statistical analysis parameters
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        configuration['analysis_method_params'] = {}
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        for key, value in self.config['analysis_configuration'].items():
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            configuration['analysis_method_params'][key] = \
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                evaluate_description(value)

        return configuration
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    @property
    def sed_modules_conf_array(self):
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        """Return the array of all the possible parameter sets from the
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        SED creation modules.

        TODO: Maybe it would be more optimal to create an iterator that would
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              iterate over the whole parameter combinations instead of
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              creating the array.

        Returns
        -------
        result : array of arrays of dictionaries
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            The inner arrays contains the various parameter dictionaries
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            for the modules listed in configuration['sed_modules'].

        """

        # First, for each module, we transform the dictionary containing all
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        # the possible value for each parameter in a list of dictionaries
        # containing one value for each parameter. We put this list in a list
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        # corresponding to the SED modules one.
        tmp_list = [param_dict_combine(dictionary) for dictionary in
                    self.configuration['sed_modules_params']]

        # The we use itertools to create an array of all possible
        # combinations.
        return [x for x in itertools.product(*tmp_list)]