Commit 9c316ef7 authored by Yannick Roehlly's avatar Yannick Roehlly
Browse files

Add analysis module to save fluxes

parent 80be02a4
# -*- 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 <>
This module was developed to use pcigale (in fact the *pcigale* script) to
generate a table with the fluxes of all the generated SED in a given set of
filters, without doing any statistical analysis.
The data file is used only to get the list of fluxes to be computed.
import os
from itertools import product
from datetime import datetime
from astropy.table import Table
from progressbar import ProgressBar
from . import common
from ..warehouse import SedWarehouse
from import Database
class Module(common.AnalysisModule):
This module saves a table containing all the parameters and desired fluxes
for all the computed models.
parameter_list = {
"output_file": (
"Name of the output file.",
"output_format": (
"Format of the output file. Any format supported by astropy.table "
"e.g. votable or ascii.",
"storage_type": (
"Type of storage used to cache the generate SED.",
def process(self, data_file, column_list, sed_modules,
sed_modules_params, redshift_module,
redshift_configuration, parameters):
"""Process with the savedfluxes analysis.
All the possible theoretical SED are created and the fluxes in the
filters from the column_list are computed and saved to a table,
alongside the parameter values.
data_file: string
Name of the file containing the observations to fit.
column_list: list of strings
Name of the columns from the data file to use for the analysis.
sed_modules: list of strings
List of the module names (in the right order) to use for creating
the SEDs.
sed_modules_params: list of dictionaries
List of the parameter dictionaries for each module.
redshift_module_name : string
Name of the module used to redshift the SED.
redshift_configuration : dictionary
Configuration dictionary for the module used to redshift the SED.
parameters: dictionary
Dictionary containing the parameters.
out_file = parameters["output_file"][0]
out_format = parameters["output_format"][0]
# If the output file already exists make a copy.
if os.path.isfile(out_file):
new_name ="%Y%m%d%H%M") + "_" + out_file
os.rename(out_file, new_name)
# Get the filters in the database
filter_names = [name for name in column_list
if not name.endswith('_err')]
base = Database()
filter_list = [base.get_filter(name) for name in filter_names]
# Columns of the output table
out_columns = []
for module_param_list in zip(sed_modules, sed_modules_params[0]):
for module_param in product([module_param_list[0]],
out_columns += filter_names
# Content of the output table
out_rows = []
# Open the warehouse
sed_warehouse = SedWarehouse(
# We loop over all the possible theoretical SEDs
progress_bar = ProgressBar(maxval=len(sed_modules_params)).start()
for model_index, parameters in enumerate(sed_modules_params):
sed = sed_warehouse.get_sed(sed_modules, parameters)
row = []
# Add the parameter values to the row. Some parameters are array
# so we must join their content.
for module_param in parameters:
for value in module_param.values():
if type(value) == list:
value = ".".join(value)
# Add the flux in each filter to the row
row += [sed.compute_fnu(filter.trans_table,
for filter in filter_list]
progress_bar.update(model_index + 1)
# The zip call is to convert the list of rows to a list of columns.
out_table = Table(zip(*out_rows), names=out_columns)
out_table.write(out_file, format=out_format)
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