FRBGalaxy Class

Module for galaxies related to FRBs

class frb.galaxies.frbgalaxy.FRBGalaxy(ra, dec, frb, cosmo=None)[source]

Bases: object

Parent class for galaxies in FRB fields

Simple object to hold key observable and derived quantities

Warning: Generating hundreds of these objects will likely be slow. Especially SkyCoord generation. A new class will be warranted for that

Parameters:

ra (float) – RA in deg
dec (float) – DEC in deg
frb (frb.FRB) – FRB object
cosmo (astropy.cosmology) – Cosmology, e.g. Planck18

redshift

Type:: dict

photom

Type:: dict

morphology

Type:: dict

neb_lines

Type:: dict

kinematics

Type:: dict

derived

Type:: dict

classmethod from_dict(frb, idict, override: bool = False, **kwargs)[source]

Instantiate from a dict

Parameters:

frb (frb.FRB)
idict (dict)
override (bool, optional) – Over-ride the cosmology error Not recommended unless you know what you are doing
**kwargs – Passed to the __init__ call

Returns:

classmethod from_json(frb, json_file, verbose: bool = True, **kwargs)[source]

Parameters:

frb (frb.FRB)
json_file
**kwargs

Returns:

FRBGalaxy or None

__init__(ra, dec, frb, cosmo=None)[source]

Parameters:

ra (float)
dec (float)
frb (frb.FRB)
cosmo (astropy.cosmology, optional)

property z

Return the redshift of the galaxy

Returns:: redshift or nadda
Return type:: float or None

property z_err

Return the redshift error of the galaxy

Returns:: redshift or nadda
Return type:: float or None

calc_nebular_lum(line)[source]

Calculate the line luminosity Applies dust extinction if self.derived[‘AV_nebular’] is filled

Mainly a wrapper to nebular.calc_lum()

Parameters:: line (str) – Name of the line

calc_nebular_AV(method='Ha/Hb', min_AV=None, **kwargs)[source]

Calculate an A_V extinction from a pair of Nebular lines

Mainly a wrapper to nebular.calc_dust_extinct

self.derived[‘AV_nebular’] is filled

Parameters:

method (str) – Method to use
min_AV (float) – Minimum A_V value allowed; might set 0. someday
**kwargs – Passed to nebular.calc_dust_extinct

Returns:

calc_nebular_SFR(method='Ha', **kwargs)[source]

Calculate a SFR from a nebular line

Mainly a wrapper to nebular.calc_SFR

self.derived[‘AV_nebular’] is filled with units SFR/yr

Parameters:

method (str) – Method to use, e.g. ‘Ha’ for Halpha
**kwargs – passed to nebular.calc_SFR

Returns:

calc_tot_uncert()[source]

Calculate total uncertainty in arcsec of FRB localization + Host localization in the reference frame of the FRB

Returns:: uncerta, uncertb [arcsec]
Return type:: tuple

parse_photom(phot_tbl, max_off=<Quantity 1. arcsec>, overwrite=True, EBV=None)[source]

Parse photometry from an input table

Fills the self.photom dict

Also fills fluxes in mJy

Parameters:

phot_tbl (astropy.table.Table) – ra, dec entires are required
max_off (Angle, optional)
overwrite (bool, optional)
EBV (float, optional) – Galactic reddening. If included, the photometry has been corrected for this. If not, who knows?! :)

Returns:

run_cigale(data_file='cigale_in.fits', config_file='pcigale.ini', wait_for_input=False, save_sed=True, plot=True, outdir='out', **kwargs)[source]

Generates the input data file for CIGALE given the photometric points and redshift of a galaxy

Parameters:

ID – str, optional An ID for the galaxy. If none, “GalaxyA” is assigned.
data_file (str, optional) – Root name for the photometry data file generated used as input to CIGALE
config_file (str, optional) – Root name for the file where CIGALE’s configuration is generated
wait_for_input (bool, optional) – If true, waits for the user to finish editing the auto-generated config file before running.
save_sed (bool, optional) – Saves the best fit SED if true
plot (bool, optional) – Plots the best fit SED if true
cores (int, optional) – Number of CPU cores to be used. Defaults to all cores on the system.
outdir (str, optional) – Path to the many outputs of CIGALE If not supplied, the outputs will appear in a folder named out/

kwargs: These are passed into gen_cigale_in() and _initialise()

sed_modules (list of ‘str’, optional):: A list of SED modules to be used in the PDF analysis. If this is being input, there should be a corresponding correct dict for sed_modules_params.
sed_module_params (dict, optional):: A dict containing parameter values for the input SED modules. Better not use this unless you know exactly what you’re doing.

get_metaspec(instr=None, return_all=False, specdb_file=None)[source]

Return the meta data and spectra for this FRBGalaxy from the specDB

If there is more than one spectrum, the code returns the first unless return_all=True

Parameters:

instr (str, optional) – Restrict to the input Instrument
return_all (bool, optional) – Return all of the meta, spectra
specdb_file (str, optional) – Path+name of the specDB file to use (over-ride the default)

Returns:

meta data, spectra

Return type:

astropy.table.Table, linetools.spectra.XSpectrum1D

parse_cigale(cigale_file, sfh_file=None, overwrite=True)[source]

Parse the output file from CIGALE

Read into self.derived

Parameters:

cigale_file (str) – Name of the CIGALE results file
sfh_file (str, optional) – Name of the best SFH model file.
overwrite (bool, optional) – Over-write any previous values

Returns:

parse_galfit(galfit_file, overwrite=True, twocomponent=False)[source]

Parse an output GALFIT file: or a gallight JSON file

Loaded into self.morphology

Parameters:

galfit_file (str) – processed ‘out.fits’ file produced by frb.galaxies.galfit.run. Contains a binary table with fit parameters. Or a JSON file from gallight
overwrite (bool, optional) – Need to overwrite the object’s attributes?
twocomponent (bool, optional) – Should the morphology attribute generated contain fit parameters of two components?

parse_ppxf(ppxf_file, overwrite=True, format='ascii.ecsv')[source]

Parse an output pPXF file generated by our custom run

Loaded into self.lines

Parameters:

ppxf_file (str) – pPXF results file
overwrite (bool, optional)
format (str, optional) – Format of the table

Returns:

set_z(z, origin, err=None)[source]

Set the redshift value(s) in self.redshift

Parameters:

z (float) – Redshift value
origin (str) – Origin ‘spec’ for spectroscopic ‘phot’ for photometric
err (float, optional) – Error in the redshift

Returns:

vet_one(attr)[source]

Vette one of the main_attr

Parameters:: attr (str)
Returns:: True = passed
Return type:: bool

vet_all()[source]

Vette all of the main dicts

Parameters:

dict
valid_defs

Returns:

True = passed

Return type:

bool

make_outfile()[source]

Auto-generate an output name for the class

Returns:: Output filename
Return type:: str

write_to_json(outfile=None, path='./', overwrite=True)[source]

Write key aspects of the class to disk in a JSON file

Parameters:

outfile (str, optional) – Output filename If not provided, one will be generated with make_outfile()
path (str, optional) – Path for the output file
overwrite (bool, optional) – Overwrite?

Returns:

class frb.galaxies.frbgalaxy.FRBHost(ra, dec, frb, z_frb=None, **kwargs)[source]

Bases: FRBGalaxy

Child of FRBGalaxy specific for an FRB host

Parameters:

ra (float) – RA in deg
dec (float) – DEC in deg
FRB (frb.FRB)

classmethod by_frb(frb, **kwargs)[source]

Parameters:

frb (frb.FRB) – FRB object
**kwargs

Return type:

FRBHost

__init__(ra, dec, frb, z_frb=None, **kwargs)[source]

Parameters:

ra (float)
dec (float)
frb (frb.FRB)
cosmo (astropy.cosmology, optional)

calc_dm_halo(**kwargs)[source]

Calculate the Halo contribution to the host DM given the host stellar mass in its derived properties dict and the FRB coordinates.

Parameters:: **kwargs – Passed to dm_host.dm_host_halo
Returns:: Halo contribution to the DM in pc/cm^3
Return type:: DM_halo (float)

make_outfile()[source]

Overloads the parent method for Host specific naming

Naming is FRBXXXXXX_host.json with XXXXXXX supplied by self.frb

Returns:: Name of the default outfile
Return type:: str

set_z(z, origin, err=None)[source]

Partially overload the main method

The main change is that the input z also sets z_FRB

self.redshift is modified in place

Parameters:

z (float) – Redshift value
origin (str) – Origin ‘spec’ for spectroscopic ‘phot’ for photometric
err (float, optional) – Error in the redshift

Returns:

class frb.galaxies.frbgalaxy.FGGalaxy(ra, dec, frb, **kwargs)[source]

Bases: FRBGalaxy

Foreground galaxy class (child of FRBGalaxy)

__init__(ra, dec, frb, **kwargs)[source]

Parameters:

ra (float)
dec (float)
frb (frb.FRB)
cosmo (astropy.cosmology, optional)

Overview

This module provides the core functionality for handling galaxies related to Fast Radio Bursts (FRBs). It contains the main FRBGalaxy class which serves as a parent class for galaxies in FRB fields, providing a simple object to hold key observable and derived quantities.

Classes

FRBGalaxy

class frb.galaxies.frbgalaxy.FRBGalaxy(ra, dec, frb, cosmo=None)[source]

Bases: object

Parent class for galaxies in FRB fields

Simple object to hold key observable and derived quantities

Warning: Generating hundreds of these objects will likely be slow. Especially SkyCoord generation. A new class will be warranted for that

Parameters:

ra (float) – RA in deg
dec (float) – DEC in deg
frb (frb.FRB) – FRB object
cosmo (astropy.cosmology) – Cosmology, e.g. Planck18

redshift

Type:: dict

photom

Type:: dict

morphology

Type:: dict

neb_lines

Type:: dict

kinematics

Type:: dict

derived

Type:: dict

The FRBGalaxy class is designed to hold key observable and derived quantities for galaxies associated with FRB events.

Key Attributes:

redshift (dict): Redshift measurements and estimates
photom (dict): Photometric data across multiple bands
morphology (dict): Morphological properties
neb_lines (dict): Nebular emission line measurements
kinematics (dict): Kinematic measurements
derived (dict): Derived physical quantities
offsets (dict): Positional offsets from FRB coordinates
positional_error (dict): Astrometric and source position errors

Warning

Generating hundreds of these objects will likely be slow, especially due to SkyCoord generation. A new class will be warranted for that use case.

classmethod from_dict(frb, idict, override: bool = False, **kwargs)[source]

Instantiate from a dict

Parameters:

frb (frb.FRB)
idict (dict)
override (bool, optional) – Over-ride the cosmology error Not recommended unless you know what you are doing
**kwargs – Passed to the __init__ call

Returns:

classmethod from_json(frb, json_file, verbose: bool = True, **kwargs)[source]

Parameters:

frb (frb.FRB)
json_file
**kwargs

Returns:

FRBGalaxy or None

__init__(ra, dec, frb, cosmo=None)[source]

Parameters:

ra (float)
dec (float)
frb (frb.FRB)
cosmo (astropy.cosmology, optional)

property z

Return the redshift of the galaxy

Returns:: redshift or nadda
Return type:: float or None

property z_err

Return the redshift error of the galaxy

Returns:: redshift or nadda
Return type:: float or None

calc_nebular_lum(line)[source]

Calculate the line luminosity Applies dust extinction if self.derived[‘AV_nebular’] is filled

Mainly a wrapper to nebular.calc_lum()

Parameters:: line (str) – Name of the line

calc_nebular_AV(method='Ha/Hb', min_AV=None, **kwargs)[source]

Calculate an A_V extinction from a pair of Nebular lines

Mainly a wrapper to nebular.calc_dust_extinct

self.derived[‘AV_nebular’] is filled

Parameters:

method (str) – Method to use
min_AV (float) – Minimum A_V value allowed; might set 0. someday
**kwargs – Passed to nebular.calc_dust_extinct

Returns:

calc_nebular_SFR(method='Ha', **kwargs)[source]

Calculate a SFR from a nebular line

Mainly a wrapper to nebular.calc_SFR

self.derived[‘AV_nebular’] is filled with units SFR/yr

Parameters:

method (str) – Method to use, e.g. ‘Ha’ for Halpha
**kwargs – passed to nebular.calc_SFR

Returns:

calc_tot_uncert()[source]

Calculate total uncertainty in arcsec of FRB localization + Host localization in the reference frame of the FRB

Returns:: uncerta, uncertb [arcsec]
Return type:: tuple

parse_photom(phot_tbl, max_off=<Quantity 1. arcsec>, overwrite=True, EBV=None)[source]

Parse photometry from an input table

Fills the self.photom dict

Also fills fluxes in mJy

Parameters:

phot_tbl (astropy.table.Table) – ra, dec entires are required
max_off (Angle, optional)
overwrite (bool, optional)
EBV (float, optional) – Galactic reddening. If included, the photometry has been corrected for this. If not, who knows?! :)

Returns:

run_cigale(data_file='cigale_in.fits', config_file='pcigale.ini', wait_for_input=False, save_sed=True, plot=True, outdir='out', **kwargs)[source]

Generates the input data file for CIGALE given the photometric points and redshift of a galaxy

Parameters:

ID – str, optional An ID for the galaxy. If none, “GalaxyA” is assigned.
data_file (str, optional) – Root name for the photometry data file generated used as input to CIGALE
config_file (str, optional) – Root name for the file where CIGALE’s configuration is generated
wait_for_input (bool, optional) – If true, waits for the user to finish editing the auto-generated config file before running.
save_sed (bool, optional) – Saves the best fit SED if true
plot (bool, optional) – Plots the best fit SED if true
cores (int, optional) – Number of CPU cores to be used. Defaults to all cores on the system.
outdir (str, optional) – Path to the many outputs of CIGALE If not supplied, the outputs will appear in a folder named out/

kwargs: These are passed into gen_cigale_in() and _initialise()

sed_modules (list of ‘str’, optional):: A list of SED modules to be used in the PDF analysis. If this is being input, there should be a corresponding correct dict for sed_modules_params.
sed_module_params (dict, optional):: A dict containing parameter values for the input SED modules. Better not use this unless you know exactly what you’re doing.

get_metaspec(instr=None, return_all=False, specdb_file=None)[source]

Return the meta data and spectra for this FRBGalaxy from the specDB

If there is more than one spectrum, the code returns the first unless return_all=True

Parameters:

instr (str, optional) – Restrict to the input Instrument
return_all (bool, optional) – Return all of the meta, spectra
specdb_file (str, optional) – Path+name of the specDB file to use (over-ride the default)

Returns:

meta data, spectra

Return type:

astropy.table.Table, linetools.spectra.XSpectrum1D

parse_cigale(cigale_file, sfh_file=None, overwrite=True)[source]

Parse the output file from CIGALE

Read into self.derived

Parameters:

cigale_file (str) – Name of the CIGALE results file
sfh_file (str, optional) – Name of the best SFH model file.
overwrite (bool, optional) – Over-write any previous values

Returns:

parse_galfit(galfit_file, overwrite=True, twocomponent=False)[source]

Parse an output GALFIT file: or a gallight JSON file

Loaded into self.morphology

Parameters:

galfit_file (str) – processed ‘out.fits’ file produced by frb.galaxies.galfit.run. Contains a binary table with fit parameters. Or a JSON file from gallight
overwrite (bool, optional) – Need to overwrite the object’s attributes?
twocomponent (bool, optional) – Should the morphology attribute generated contain fit parameters of two components?

parse_ppxf(ppxf_file, overwrite=True, format='ascii.ecsv')[source]

Parse an output pPXF file generated by our custom run

Loaded into self.lines

Parameters:

ppxf_file (str) – pPXF results file
overwrite (bool, optional)
format (str, optional) – Format of the table

Returns:

set_z(z, origin, err=None)[source]

Set the redshift value(s) in self.redshift

Parameters:

z (float) – Redshift value
origin (str) – Origin ‘spec’ for spectroscopic ‘phot’ for photometric
err (float, optional) – Error in the redshift

Returns:

vet_one(attr)[source]

Vette one of the main_attr

Parameters:: attr (str)
Returns:: True = passed
Return type:: bool

vet_all()[source]

Vette all of the main dicts

Parameters:

dict
valid_defs

Returns:

True = passed

Return type:

bool

make_outfile()[source]

Auto-generate an output name for the class

Returns:: Output filename
Return type:: str

write_to_json(outfile=None, path='./', overwrite=True)[source]

Write key aspects of the class to disk in a JSON file

Parameters:

outfile (str, optional) – Output filename If not provided, one will be generated with make_outfile()
path (str, optional) – Path for the output file
overwrite (bool, optional) – Overwrite?

Returns:

Key Methods

Class Methods

classmethod FRBGalaxy.from_dict(frb, idict, override: bool = False, **kwargs)[source]

Instantiate from a dict

Parameters:

frb (frb.FRB)
idict (dict)
override (bool, optional) – Over-ride the cosmology error Not recommended unless you know what you are doing
**kwargs – Passed to the __init__ call

Returns:

Instantiate an FRBGalaxy object from a dictionary containing galaxy parameters.

classmethod FRBGalaxy.from_json(frb, json_file, verbose: bool = True, **kwargs)[source]

Parameters:

frb (frb.FRB)
json_file
**kwargs

Returns:

FRBGalaxy or None

Load an FRBGalaxy object from a JSON file.

Instance Methods

FRBGalaxy.set_z(z, origin, err=None)[source]

Set the redshift value(s) in self.redshift

Parameters:

z (float) – Redshift value
origin (str) – Origin ‘spec’ for spectroscopic ‘phot’ for photometric
err (float, optional) – Error in the redshift

Returns:

Set the redshift value(s) with specified origin (spectroscopic or photometric).

FRBGalaxy.calc_nebular_lum(line)[source]

Calculate the line luminosity Applies dust extinction if self.derived[‘AV_nebular’] is filled

Mainly a wrapper to nebular.calc_lum()

Parameters:: line (str) – Name of the line

Calculate line luminosity with optional dust extinction correction.

FRBGalaxy.run_cigale(data_file='cigale_in.fits', config_file='pcigale.ini', wait_for_input=False, save_sed=True, plot=True, outdir='out', **kwargs)[source]

Generates the input data file for CIGALE given the photometric points and redshift of a galaxy

Parameters:

ID – str, optional An ID for the galaxy. If none, “GalaxyA” is assigned.
data_file (str, optional) – Root name for the photometry data file generated used as input to CIGALE
config_file (str, optional) – Root name for the file where CIGALE’s configuration is generated
wait_for_input (bool, optional) – If true, waits for the user to finish editing the auto-generated config file before running.
save_sed (bool, optional) – Saves the best fit SED if true
plot (bool, optional) – Plots the best fit SED if true
cores (int, optional) – Number of CPU cores to be used. Defaults to all cores on the system.
outdir (str, optional) – Path to the many outputs of CIGALE If not supplied, the outputs will appear in a folder named out/

kwargs: These are passed into gen_cigale_in() and _initialise()

sed_modules (list of ‘str’, optional):: A list of SED modules to be used in the PDF analysis. If this is being input, there should be a corresponding correct dict for sed_modules_params.
sed_module_params (dict, optional):: A dict containing parameter values for the input SED modules. Better not use this unless you know exactly what you’re doing.

Run CIGALE SED fitting analysis on the galaxy’s photometry.

FRBGalaxy.parse_photom(phot_tbl, max_off=<Quantity 1. arcsec>, overwrite=True, EBV=None)[source]

Parse photometry from an input table

Fills the self.photom dict

Also fills fluxes in mJy

Parameters:

phot_tbl (astropy.table.Table) – ra, dec entires are required
max_off (Angle, optional)
overwrite (bool, optional)
EBV (float, optional) – Galactic reddening. If included, the photometry has been corrected for this. If not, who knows?! :)

Returns:

Parse photometry from an input table and populate the photom dictionary.

FRBGalaxy.vet_one(attr)[source]

Vette one of the main_attr

Parameters:: attr (str)
Returns:: True = passed
Return type:: bool

Validate one of the main attribute dictionaries against allowed values.

Properties

property FRBGalaxy.z

Return the redshift of the galaxy

Returns:: redshift or nadda
Return type:: float or None

Return the preferred redshift of the galaxy.

property FRBGalaxy.z_err

Return the redshift error of the galaxy

Returns:: redshift or nadda
Return type:: float or None

Return the error in the preferred redshift.

Examples

Creating an FRBGalaxy instance:

from frb.frb import FRB
from frb.galaxies.frbgalaxy import FRBGalaxy

# Create FRB object
frb = FRB.by_name('FRB180924')

# Create galaxy object
galaxy = FRBGalaxy(ra=349.24, dec=-40.9, frb=frb)

# Set redshift
galaxy.set_z(0.3214, 'spec', err=0.0001)

Loading from dictionary:

# Load from dictionary
galaxy_dict = {
    'ra': 349.24,
    'dec': -40.9,
    'cosmo': 'Planck18'
}
galaxy = FRBGalaxy.from_dict(frb, galaxy_dict)