mangadap.proc.emissionlinetemplates module¶

Class that constructs a set of emission-line templates, primarily for use with mangadap.proc.sasuke.Sasuke.

License:

Copyright (c) 2017, SDSS-IV/MaNGA Pipeline Group: Licensed under BSD 3-clause license - see LICENSE.rst

Class usage examples:

To construct emission-line templates, you need a wavelength vector, the instrumental resolution at which to construct the templates, and an emission line database (see mangadap.par.emissionlinedb.EmissionLineDB). A simple construction would be:
# Imports
import numpy
from mangadap.par.emissionlinedb import EmissionLineDB
from mangadap.proc.emissionlinetemplates import EmissionLineTemplates

wave = numpy.logspace(*(numpy.log10([3600,10300]), 4563)
sigma_inst = 30                     # Instrumental resolution in km/s

tpl = EmissionLineTemplates(wave, sigma_inst, emldb=EmissionLineDB('ELPMILES'))

Revision history:: 08 Sep 2017: Originally pulled from mangadap.proc.sasuke by K. Westfall (KBW)

class mangadap.proc.emissionlinetemplates.EmissionLineTemplates(wave, sigma_inst, log=True, base=10, emldb=None, flux_density=True, loggers=None, quiet=False)[source]¶

Bases: object

Construct a set of emission-line templates based on an emission-line database, primarily for use in mangadap.proc.sasuke.Sasuke.

The templates are constructed based on the constraints provided by the emission-line database. See mangadap.par.emissionlinedb.EmissionLinePar for the structure of each row in the database and an explanation for each of its columns. The selected profile type for each line must have a parameters_from_moments method that returns the parameters of the line provided the first three moments (moments 0, 1, and 2).

Only lines with action=f are included in any template. The array tpli provides the index of the template that contains each line in the emission-line database. Lines that are not assigned to any template — either because they do not have action=f or their center lies outside the wavelength range in wave — are given an index of -1.

Only lines with mode=a (i.e., flux, velocity, and velocity dispersion are all tied) are included in the same template.

Lines with tied velocities are assigned the same velocity component (vgrp) and lines with the tied velocity dispersions are assigned the same sigma component (sgrp).

Warning

The construction of templates for use with Sasuke does not allow one to tie fluxes while leaving the velocities and/or velocity dispersions as independent.

Parameters:

wave (array-like) – A single wavelength vector with the wavelengths for the template spectra. The wavelengths are expected to be sample either linearly or geometrically (see log).
sigma_inst (float,array-like) – The single value or value as a function of wavelength for the instrumental dispersion (km/s) to use for the template construction.
log (bool) – (Optional) Flag that the wavelengths have been sampled geometrically.
base (float) – (Optional) Base for the geometric sampling.
( (emldb) – class:mangadap.par.emissionlinedb.EmissionLineDB’): (**Optional**) Emission-line database that is parsed to setup which lines to include in the same template because they are modeled as having the same velocity, velocity dispersion and flux ratio. If not provided, no templates are constructed in instantiation; to build the templates using an existing instantiation, use :func:`build_templates.
flux_density (bool) – (Optional) Return spectrum in units of flux density (flux per angstrom). Default is to return the spectrum in units of flux per pixel.
loggers (list) – (Optional) List of `logging.Logger`_ objects to log progress; ignored if quiet=True. Logging is done using mangadap.util.log.log_output(). Default is no logging. This can be reset in some methods.
quiet (bool) – (Optional) Suppress all terminal and logging output. Default is False.

wave¶

Array with the wavelength (angstroms) of each pixel for all the constructed templates. Shape is \(N_{\rm pix}\).

Type:	numpy.ndarray

sigma_inst¶

The object used to interpolate the instrumental dispersion (km/s) at the rest wavelength of each spectral line.

Type:	scipy.interpolate.interp1d

log¶

Flag that the spectrum is sampled geometrically.

Type:	bool

base¶

Base for the geometric sampling.

Type:	float

emldb¶

Database with the emission-line parameters. Shape is (\(N_{\rm pix}\),).

Type:	`mangadap.par.emissionlinedb.EmissionLineDB`

ntpl¶

Total number of templates.

Type:	int

flux¶

The template spectra. Shape is \((N_{\rm tpl},N_{\rm pix})\).

Type:	numpy.ndarray

tpli¶

The index of the template containing each emission line. Any emission-lines with tpli==-1 means that the emission line was not included in any template, which should only occur for lines with ``action==i` in the database. Shape is (\(N_{\rm eml}\),).

Type:	numpy.ndarray

comp¶

The component number assigned to each template. Templates with the same component number are forced to have the same velocity and velocity dispersion by pPXF. Shape is (\(N_{\rm tpl}\),).

Type:	numpy.ndarray

vgrp¶

The velocity group assigned to each template. Templates in the same velocity group have their velocity parameters tied in pPXF, but the velocity dispersion parameters are independent. Shape is (\(N_{\rm tpl}\),).

Type:	numpy.ndarray

sgrp¶

The velocity disperison (sigma) group assigned to each template. Templates in the same sigma group have their velocity dispersion parameters tied in pPXF, but the velocity parameters are independent. Shape is (\(N_{\rm tpl}\),).

Type:	numpy.ndarray

eml_sigma_inst¶

The instrumental dispersion (km/s) at the rest wavelength of each emission line. This is mostly used to aid the velocity dispersion corrections determined by Sasuke. Shape is (\(N_{\rm eml}\),).

Type:	numpy.ndarray

loggers¶

List of `logging.Logger`_ objects to log progress; ignored if quiet=True. Logging is done using mangadap.util.log.log_output().

Type:	list

quiet¶

Suppress all terminal and logging output.

Type:	bool

_parse_emission_line_database()[source]¶

Parse the input emission-line database; see mangadap.par.emissionlinedb.EmissionLinePar.

Only lines with action=f are included in any template. The array tpli provides the index of the template that contains each line in the emission-line database. Lines that are not assigned to any template — either because they do not have action=f or their center lies outside the wavelength range in wave — are given an index of -1.

Only lines with mode=a (i.e., tie flux, velocity, and velocity dispersion) are included in the same template.

Lines with tied velocities are assigned the same velocity component (vgrp) and lines with the tied velocity dispersions are assigned the same sigma component (sgrp).

Warning

The construction of templates for use with Sasuke does not allow one to tie fluxes while leaving the velocities and/or velocity dispersions as independent.

This is an entirely internal procedure, taking no arguments and only assigning results to self.

Raises:	`ValueError` – Raised if the parsing of the database leaves some templates without an assigned component, velocity group, and/or sigma group. This implies an error in the construction of the emission-line database, not the code itself.

_tied_index(i, primary=False)[source]¶

Return the index of the line to which this one is tied.

The result may be that this line is tied to one that is also tied to a second line. If that’s the case, the primary keyword can be use to trace the parameter tying back to the independent line.

Arg:: i (int): The index of the line in the database. primary (bool): (Optional) Trace the line tying all the

way back to the independent (primary) line.

Returns:	The index of the line to which this one is tied.
Return type:	int
Raises:	`ValueError` – Raised if the primary option is selected and the line does not trace back to a primary line. This represents a poorly constructed emission-line database and should be avoided!

build_templates(emldb, flux_density=True, loggers=None, quiet=False)[source]¶

Build the set of templates for a given emission-line database. The function uses the current values in wave and sigma_inst. Any existing templates from a previous call to build_templates() or from the object instantiation will be overwritten using the provided emission-line database.

See check_database() for the requirements of the provided emission-line database, and see _parse_emission_line_database() for how the database is interpretted when constructing the templates.

The function constructs and returns the following attributes: flux, comp, vgrp, and sgrp

Todo

Warn the user if any line is undersampled; i.e., the FWHM of the line is less than 2.1 or sigma < 0.9.
Warn the user if any line grouped in the same template falls outside the spectral range.

Parameters:	( (emldb) – class:`mangadap.par.emissionlinedb.EmissionLineDB’): Emission-line database. flux_density (bool) – (Optional) Return spectrum in units of flux density (flux per angstrom). Default is to return the spectrum in units of flux per pixel. loggers (list) – (Optional) List of `logging.Logger`_ objects to log progress; ignored if quiet=True. Logging is done using `mangadap.util.log.log_output()`. quiet (bool) – (Optional) Suppress all terminal and logging output.
Returns:	Returns 4 arrays: (1) the set of templates with shape \(N_{\rm tpl}\times N_{\rm wave}\), (2) the kinematic component assignement for each template, (3) the velocity group associated with each template, and (4) the sigma group assocated with each template.
Return type:	numpy.ndarray

check_database(emldb)[source]¶

Check that the provided emission-line database can be used with the EmissionLineTemplates class. Most checks are performed by mangadap.proc.spectralfitting.EmissionLineFit.check_emission_line_database().

Additional checks specific to EmissionLineTemplates are:

Any lines with mode w is treated as f and a warning is provided.

The EmissionLineTemplates object cannot be used with mode x; any lines with this mode will cause a ValueError to be raised..

This function does not check if the initial parameters provided by the database are consistent with other elements in the database because they are not used to construct the templates.

Parameters:	( (emldb) – class:`mangadap.par.emissionlinedb.EmissionLineDB’): Emission-line database.
Raises:	`TypeError` – Raised if the provided object is not an instance of `mangadap.par.emissionlinedb.EmissionLineDB`. `ValueError` – Raised if any line has a mode of x or if the database does not provide a valid definition for any templates. `NameError` – Raised if a defined profile type is not known.