def get_table_path(filename, datadir="data"):
"""
Parameters
----------
filename:
datadir:
Returns
-------
path: string
The path to the data file
"""
if filename in available_methods():
filename += ".hdf5"
if datadir == "data":
path = utils.get_path_to_file_from_here(filename, subdirs=["data"])
return path
def create(method,
output_dir='data',
filename=None,
zmin=0,
zmax=20,
num_samples=10000,
**kwargs):
"""
Creates an interpolated 1D redshift lookup table which can be read
in using :func:`~fruitbat.table.load`.
Parameters
----------
method : str
The DM-redshift relation to assume when creating the table.
output_dir : str, optional
The path of the output directory. If ``output_dir = 'data'``,
then created table will created in the same directory with
the builtin tables and will be found when using functions
such as :meth:`~fruitbat._frb.calc_redshift()`.
Default: 'data'
filename : str, optional
The output filename. If ``name=None`` then the filename will
become custom_method. Default: *None*
zmin : int or float, optional
The minimum redshift in the table. Default: 0
zmax : int or float, optional
The maximum redshift in the table. Default: 20
num_samples : int, optional
The number of sample dispersion measure and redshifts.
Default: 10000
Keyword Arguments
-----------------
cosmo : An instance of :obj:`astropy.cosmology`, optional
The cosmology to assume when calculating the outputs of the
table. Required when creating new tables of ``'Ioka2003'``,
``'Inoue2004'``, ``'Zhang2018'``.
free_elec : float or int, optional
The amount of free electrons per proton mass in the Universe.
This applies when using ``'Zhang2018'``. Must be between 0
and 1. Default: 0.875.
f_igm : float or int, optional
The fraction of baryons in the intergalactic medium. This
applies when using ``'Zhang2018'``. Must be between 0 and 1.
Default: 0.83
Generates
---------
A compressed file in .npz format containing the arrays ``'dm'``
and ``'z'``.
Example
-------
>>> def simple_dm(z):
dm = 1200 * z
return dm
>>> fruitbat.add_method("simple_dm", simple_dm)
>>> fruitbat.table.create("simple_dm")
>>> frb = fruitbat.Frb(1200)
>>> frb.calc_redshift(method="simple_dm")
<Quantity 1.>
"""
if method not in available_methods():
err_msg = ("{} is not a valid method."
"The currently defined methods "
"are: {}".format(method, available_methods()))
raise ValueError(err_msg)
else:
dm_function = method_functions()[method]
z_vals = np.linspace(zmin, zmax, num_samples)
dm_vals = np.array([dm_function(z, **kwargs) for z in z_vals])
if filename is not None:
output_name = filename
else:
output_name = "custom_{}".format(method)
if output_dir == 'data':
output_file = os.path.join(os.path.dirname(__file__), 'data',
output_name)
else:
output_file = os.path.join(output_dir, output_name)
np.savez(output_file, dm=dm_vals, z=z_vals)
import os
import pandas as pd
from e13tools import docstring_substitute
from fruitbat import Frb, methods, cosmologies
__all__ = ["create_analysis_catalogue", "create_methods_catalogue",
"read_frb_row"]
@docstring_substitute(meth=methods.available_methods(),
cosmo=cosmologies.available_cosmologies())
def create_analysis_catalogue(filename="fruitbat_analysis_catalogue",
dataset='default', method='Inoue2004',
cosmology='Planck18'):
"""
Analyses an FRB dataset and produces a CSV file containing the
estimated redshift, fluence, energy and luminosity for each FRB in
additional to its measured quantities.
Parameters
----------
filename: str, optional
The output file name. Default: 'fruitbat_analysis_catalogue'
dataset: str, optional
The path to the FRBCAT dataset. The dataset is required to have
the following columns: 'frb_name', 'utc', 'telescope',
'rop_raj', 'rop_decj', 'rop_gl', 'rop_gb', 'rop_bandwidth',
'rop_centre_frequency', 'rmp_dm', 'rmp_width', 'rmp_snr',
def test_reset_methods(self):
methods.reset_methods()
assert "new_method" not in methods.available_methods()
def test_add_method(self):
methods.add_method("new_method", self.new_method)
assert "new_method" in methods.available_methods()
def calc_redshift(self,
method='Batten2021',
cosmology="Planck18",
subtract_host=False,
lookup_table=None):
"""
Calculate the redshift of the FRB from its :attr:`dm`,
:attr:`dm_excess` or :attr:`dm_excess` - :attr:`dm_host_est`.
Parameters
----------
method : str, optional
The dispersion meausre -redshift relation to use when
calculating the redshift. Avaliable methods: %(meth)s.
Default: 'Inoue2004'
cosmology : str, optional
The cosmology to assume when calculating the redshift.
Avaliable cosmologies: %(cosmo)s. Default: 'Planck18'
subtract_host : bool, optional
Subtract :attr:`dm_host_est` from the :attr:`dm_excess`
before calculating the redshift. This is is used to account
for the dispersion measure that arises from the FRB host
galaxy. Default: False
lookup_table : str or None, optional
The path to the lookup table file. If ``lookup_table=None``
a table will attempted to be loaded from the data directory
based on the method name. Default: *None*
Returns
-------
float
The redshift of the FRB.
Notes
-----
The methods_ section in the documentation has a description for
each of the builtin methods.
The cosmology_ section in the documentation has a list of the
cosmological parameters for each cosmology
.. _cosmology: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#cosmology
.. _methods: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#methods
"""
utils.check_type("subtract_host", subtract_host, bool)
if subtract_host:
input_dm = self.dm_excess - self.dm_host_est
print(input_dm)
else:
input_dm = self.dm_excess
# If the user provides a table use that table for estimation.
if lookup_table is not None:
raise NotImplementedError("Not made yet!")
if method not in methods.available_methods():
err_msg = ("Method '{}' is not a valid method. "
"Valid methods are: {}".format(
method, methods.available_methods()))
raise ValueError(err_msg)
if method in methods.methods_hydrodynamic():
zvals, pdf, dz = self.calc_redshift_pdf(method=method)
z_median = utils.calc_median_from_pdf(zvals, pdf)
self.z = z_median
self.method = method
if method == "Batten2020":
self.cosmology = "EAGLE"
elif method in methods.methods_analytic():
if cosmology in cosmologies.available_cosmologies():
#if method in methods.builtin_method_functions().keys():
table_name = table.get_table_path(method)
self.z = table.get_z_from_table(input_dm, table_name,
cosmology)
self.cosmology = cosmology
self.method = method
else:
err_msg = ("Cosmology '{}' is not a valid cosmology. Valid "
"cosmologies are: {}".format(
cosmology, cosmologies.available_cosmologies()))
raise ValueError(err_msg)
else:
table_name = utils.get_path_to_file_from_here(
"{}.hdf5".format(method), subdirs=["data"])
self.z = table.get_z_from_table(input_dm, table_name)
self.cosmology = cosmology
self.method = method
return self.z
class Frb(object):
"""
Create a :class:`~Frb` object using the observered properties of a
FRB including dispersion measure (DM) and its sky coordinates. This
class utilises various DM-redshift relations as well as the YMW16
galactic DM model in the analysis.
A FRB can be defined simply with a single :attr:`dm` value. This
should be the observed DM prior to subtracting the Milky Way,
however if you do not provide any additional information, it is
asssumed that this value is also the :attr:`dm_excess` (DM -
Galactic DM). You can get the estimated redshift by using the
method :meth:`calc_redshift`.
To get a more accurate distance estimate you can account for the
contribution due to the Milky Way by supplying :attr:`dm_galaxy` or
by giving the coordinates of the FRB in ICRS (:attr:`raj`,
:attr:`decj`) or Galactic (:attr:`gl`, :attr:`gb`) coordinates and
calling the method :meth:`calc_dm_galaxy` before calling
:meth:`calc_redshift`.
Parameters
----------
dm : float
The observed dispersion measure of the FRB. This is without
Milky Way or host galaxy subtraction. Units: pc cm**-3
Keyword Arguments
-----------------
name : str or None, optional
The name of the frb object. Default: *None*
raj : str or None, optional
The right ascension in J2000 coordinates of the best estimate
of the FRB position. By default should be given in the ICRS
frame. An alternative frame can be specified by also including
the keyword ``frame``. e.g. ``frame='fk5'``. Default: *None*
decj : str or None, optional
The declination in J2000 coordinates of the best estimate of
the FRB position. By default should be given in the ICRS frame.
An alternative frame can be specified by also including the
keyword ``frame``. e.g. ``frame='fk5'``. Default: *None*
gl : str or None, optional
The Galactic longitude in degrees of the best estimate of the
FRB position. Default: *None*
gb : str or None, optional
The Galactic latitude in degrees of the best estimate of the
FRB position. Default: *None*
Other Parameters
----------------
dm_galaxy : float, optional
The modelled contribution to the FRB DM by electrons in the
Milky Way. This value is calculated using
:meth:`calc_dm_galaxy` Units: pc cm**-3 Default: 0.0
dm_excess : float or None, optional
The DM excess of the FRB over the estimated Galactic DM. If
:attr:`dm_excess` is *None*, then :attr:`dm_excess` is
calculated automatically with :meth:`calc_dm_excess`.
Units: pc cm**-3 Default: *None*
z_host : float or None, optional
The observed redshift of the localised FRB host galaxy.
Default: *None*
dm_host_est : float, optional
The estimated contribution to the measured FRB DM originating
from the FRB's host galaxy. This value is the amount of DM the
host galaxy contributes to the observed DM, *not* the DM of the
host galaxy. Setting this to a non-zero value and setting
``subtract_host=True`` when calling :meth:`calc_redshift`
accounts for the DM contribution due to the host galaxy.
Units: pc cm**-3 Default: 0.0
dm_host_loc : float, optional
The dispersion measure of a localised FRB host galaxy. This
value is *not* the contribution to the observed DM, but the DM
at the host galaxy. The observed DM is :attr:`dm_host_loc` but
attenuated by a factor of (1 + z). To use this, the redshift of
the host galaxy must be known. Units: pc cm**-3 Default: 0.0
dm_index : float or None, optional
The dispersion measure index of the burst :math:`\\alpha` such
that :math:`\\rm{DM} \\propto \\nu^{-\\alpha}` Default: *None*
scatt_index : float or None, optional
The scattering index (:math:`\\beta`) of the FRB pulse. The
scattering index describes how the width (:math:`\\rm{W}`) of
the FRB pulse evolves with frequency :math:`\\nu` such that
:math:`\\rm{W} \\propto \\nu^{-\\beta}`. Default: *None*
snr : float or None, optional
The signal-to-noise ratio of the burst.
Default: *None*
width : float or None, optional
The observed width of the pulse obtained by a pulse fitting
algorithm. Units: ms Default: *None*
peak_flux : float or None, optional
The observed peak flux density of the burst. Units: Jy
Default: *None*
fluence : float or None, optional
The observed fluence of the FRB. If :attr:`fluence` is *None*
and both :attr:`width` and :attr:`peak_flux` are not *None*
then :attr:`fluence` is automatically calculated with
:meth:`calc_fluence`. Units: Jy ms Default: *None*
obs_bandwidth : float or None, optional
The observing bandwidth. Units: MHz Default: *None*
obs_freq_central : float or None, optional
The central observing frequency, Units: MHz Deault: *None*
utc : str or None, optional
The UTC time of the FRB Burst. Format should be of the form
'1999-01-01T00:00:00.000'. Default: *None*
Example
-------
>>> import fruitbat
>>> FRB = fruitbat.Frb(879, gl="12:31:40.5", gb="3:41:10.0")
>>> FRB.calc_dm_galaxy()
>>> FRB.calc_redshift()
"""
def __init__(self,
dm,
name=None,
raj=None,
decj=None,
gl=None,
gb=None,
dm_galaxy=0.0,
dm_excess=None,
z_host=None,
dm_host_est=0.0,
dm_host_loc=0.0,
dm_index=None,
scatt_index=None,
snr=None,
width=None,
peak_flux=None,
fluence=None,
obs_bandwidth=None,
obs_freq_central=None,
utc=None,
**kwargs):
self.dm = dm
self.name = name
self.raj = raj
self.decj = decj
self.gl = gl
self.gb = gb
self.dm_galaxy = dm_galaxy
# Calculate dm_excess from existing parameters if it is not given.
if dm_excess is None:
self.calc_dm_excess()
else:
self.dm_excess = dm_excess
self.z_host = z_host
self.dm_host_est = dm_host_est
self.dm_host_loc = dm_host_loc
self.dm_index = dm_index
self.scatt_index = scatt_index
self.snr = snr
self.width = width
self.peak_flux = peak_flux
self.fluence = fluence
self.obs_bandwidth = obs_bandwidth
self.obs_freq_central = obs_freq_central
self.utc = utc
self.z = None
self.dm_igm = None
self.cosmology = None
self.method = None
self.dm_galaxy_model = None
self.z_conf_int_lower = None
self.z_conf_int_upper = None
self.tau_sc = None
# Calculate fluence if peak_flux and width are given
if ((self.fluence is None)
and (peak_flux is not None and width is not None)):
self.calc_fluence()
# Calculate the skycoords of the FRB from (raj, decj) or (gl, gb)
if (raj and decj) or (gl and gb):
if 'frame' in kwargs:
self.skycoords = self.calc_skycoords(frame=kwargs["frame"])
else:
self.skycoords = self.calc_skycoords()
self.raj = self.skycoords.transform_to('icrs').ra
self.decj = self.skycoords.transform_to('icrs').dec
self.gl = self.skycoords.transform_to('galactic').l
self.gb = self.skycoords.transform_to('galactic').b
else:
self.skycoords = None
def __repr__(self):
frb_repr = []
var_dict = vars(self)
for var in var_dict:
if var[1:] == "skycoords":
continue
var_name = var[1:]
if isinstance(var_dict[var], u.Quantity):
var_val = var_dict[var].value
else:
var_val = var_dict[var]
frb_repr.append("{}={}".format(var_name, var_val))
return "Frb({})".format(", ".join(map(str, frb_repr)))
@docstring_substitute(meth=methods.available_methods(),
cosmo=cosmologies.available_cosmologies())
def calc_redshift(self,
method='Batten2021',
cosmology="Planck18",
subtract_host=False,
lookup_table=None):
"""
Calculate the redshift of the FRB from its :attr:`dm`,
:attr:`dm_excess` or :attr:`dm_excess` - :attr:`dm_host_est`.
Parameters
----------
method : str, optional
The dispersion meausre -redshift relation to use when
calculating the redshift. Avaliable methods: %(meth)s.
Default: 'Inoue2004'
cosmology : str, optional
The cosmology to assume when calculating the redshift.
Avaliable cosmologies: %(cosmo)s. Default: 'Planck18'
subtract_host : bool, optional
Subtract :attr:`dm_host_est` from the :attr:`dm_excess`
before calculating the redshift. This is is used to account
for the dispersion measure that arises from the FRB host
galaxy. Default: False
lookup_table : str or None, optional
The path to the lookup table file. If ``lookup_table=None``
a table will attempted to be loaded from the data directory
based on the method name. Default: *None*
Returns
-------
float
The redshift of the FRB.
Notes
-----
The methods_ section in the documentation has a description for
each of the builtin methods.
The cosmology_ section in the documentation has a list of the
cosmological parameters for each cosmology
.. _cosmology: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#cosmology
.. _methods: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#methods
"""
utils.check_type("subtract_host", subtract_host, bool)
if subtract_host:
input_dm = self.dm_excess - self.dm_host_est
print(input_dm)
else:
input_dm = self.dm_excess
# If the user provides a table use that table for estimation.
if lookup_table is not None:
raise NotImplementedError("Not made yet!")
if method not in methods.available_methods():
err_msg = ("Method '{}' is not a valid method. "
"Valid methods are: {}".format(
method, methods.available_methods()))
raise ValueError(err_msg)
if method in methods.methods_hydrodynamic():
zvals, pdf, dz = self.calc_redshift_pdf(method=method)
z_median = utils.calc_median_from_pdf(zvals, pdf)
self.z = z_median
self.method = method
if method == "Batten2020":
self.cosmology = "EAGLE"
elif method in methods.methods_analytic():
if cosmology in cosmologies.available_cosmologies():
#if method in methods.builtin_method_functions().keys():
table_name = table.get_table_path(method)
self.z = table.get_z_from_table(input_dm, table_name,
cosmology)
self.cosmology = cosmology
self.method = method
else:
err_msg = ("Cosmology '{}' is not a valid cosmology. Valid "
"cosmologies are: {}".format(
cosmology, cosmologies.available_cosmologies()))
raise ValueError(err_msg)
else:
table_name = utils.get_path_to_file_from_here(
"{}.hdf5".format(method), subdirs=["data"])
self.z = table.get_z_from_table(input_dm, table_name)
self.cosmology = cosmology
self.method = method
return self.z
#@docstring_substitute(meth=methods.available_methods(),
# cosmo=cosmologies.available_cosmologies())
def calc_redshift_pdf(self,
method="Batten2021",
cosmology="Planck18",
prior="uniform",
subtract_host=False,
lookup_table=None):
"""
Calc
"""
if method == "Batten2021":
filename = utils.get_path_to_file_from_here("Batten2021.hdf5",
subdirs=["data"])
elif method in methods.methods_analytic():
filename = "{}.hdf5".format(method)
filename = utils.get_path_to_file_from_here(filename,
subdirs=["data"])
raise NotImplementedError(
"Getting PDFs from analytic moddels has not been implemented yet!"
)
else:
raise NotImplementedError("This has not been implemented yet!")
with h5py.File(filename, "r") as data:
DMzHist = data["DMz_hist"][:]
redshift_bin_widths = data["Redshift_Bin_Widths"][:]
redshifts = data["Redshifts_Bin_Edges"][1:]
DMBins = data["DM_Bin_Edges"][:]
max_bin_idx = np.where(self.dm_excess.value <= DMBins)[0][0]
prev_bin_idx = max_bin_idx - 1
hist_higher_dm = DMzHist[max_bin_idx]
hist_lower_dm = DMzHist[prev_bin_idx]
pdf2 = utils.normalise_to_pdf(hist_higher_dm,
bin_widths=redshift_bin_widths)
pdf1 = utils.normalise_to_pdf(hist_lower_dm,
bin_widths=redshift_bin_widths)
DMlower, DMhigher = DMBins[prev_bin_idx], DMBins[max_bin_idx]
lin_interp_pdf = utils.linear_interpolate_pdfs(
self.dm_excess.value, (DMlower, DMhigher), (pdf1, pdf2))
prior = utils.redshift_prior(redshifts, prior=prior)
z_pdf = lin_interp_pdf * prior
z_bins = redshifts
dz = redshift_bin_widths
self.z_bins = z_bins
self.z_pdf = z_pdf
self.dz = dz
return z_bins, z_pdf, dz
@docstring_copy(plot.redshift_pdf)
def plot_redshift_pdf(self, *args, **kwargs):
return plot.redshift_pdf(self, *args, **kwargs)
@docstring_substitute(meth=methods.available_methods(),
cosmo=cosmologies.available_cosmologies())
def calc_redshift_conf_int(self,
method="Batten2021",
sigma=1,
scatter_percentage=0,
**calc_redshift_kwargs):
#method='Batten2020', cosmology="Planck18", sigma=1,
# scatter_percentage=0, subtract_host=False, lookup_table=None):
"""
Calculates the mean redshift and the confidence interval of
an FRB from its :attr:`dm`, :attr:`dm_excess` or
:attr:`dm_excess` - :attr:`dm_host_est`.
Parameters
----------
method : str, optional
The dispersion meausre-redshift relation to use when
calculating the redshift. Avaliable methods: %(meth)s.
Default: 'Batten2020'
cosmology : str, optional
The cosmology to assume when calculating the redshift.
This value is overided if using a hydrodynamic method.
Avaliable cosmologies: %(cosmo)s. Default: 'Planck18'
sigma : int (1, 2, 3, 4, 5), optional
The width of the confidence interval in units of standard
deviation. `sigma=1` is the 68\% confidence interval.
scatter_percentage : float, optional
The amount of line of
Default: 0
subtract_host : bool, optional
Subtract :attr:`dm_host_est` from the :attr:`dm_excess`
before calculating the redshift. This is is used to account
for the dispersion measure that arises from the FRB host
galaxy. Default: False
lookup_table : str or None, optional
The path to the lookup table file. If ``lookup_table=None``
a table will attempted to be loaded from the data directory
based on the method name. Default: *None*
Returns
-------
float
The extimated redshift of the FRB.
float
The redshift confidence interval the FRB.
Notes
-----
The methods_ section in the documentation has a description for
each of the builtin methods.
The cosmology_ section in the documentation has a list of the
cosmological parameters for each cosmology
.. _cosmology: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#cosmology
.. _methods: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#methods
"""
redshift = self.calc_redshift(**calc_redshift_kwargs)
if method in methods.methods_hydrodynamic():
if method == "Batten2021":
zvals, pdf, dz = self.calc_redshift_pdf(method="Batten2021")
conf_lower_lim, conf_upper_lim = utils.sigma_to_pdf_percentiles(
sigma=sigma)
conf_int_lower = utils.calc_z_from_pdf_percentile(
zvals, pdf, percentile=conf_lower_lim)
conf_int_upper = utils.calc_z_from_pdf_percentile(
zvals, pdf, percentile=conf_upper_lim)
self.z_conf_int_lower = conf_int_lower
self.z_conf_int_upper = conf_int_upper
return self.z, (self.z_conf_int_lower, self.z_conf_int_upper)
def calc_skycoords(self, frame=None):
"""
Calculates the skycoord position on the sky of the FRB from
(:attr:`raj`, :attr:`decj`) or (:attr:`gl`, :attr:`gb`). If
both (:attr:`raj`, :attr:`decj`) and (:attr:`gl`, :attr:`gb`)
are given, preference is given to (:attr:`raj`, :attr:`decj`).
Parameters
----------
frame: str or None, optional
The type of coordinate frame. If ``frame = None`` then
:meth:`calc_skycoords` will use a default frame based on
the coordinates given. If :attr:`raj` and :attr:`decj` are
given the default frame is 'icrs'. If :attr:`gl` and
:attr:`gb` are given the default frame is 'galactic'.
Default: *None*
Returns
-------
:obj:`astropy.coordinates.SkyCoord`
The sky coordinates of the FRB.
"""
if self.raj is not None and self.decj is not None:
if frame is None:
frame = "icrs"
skycoords = SkyCoord(ra=self.raj,
dec=self.decj,
frame=frame,
unit=(u.hourangle, u.deg))
elif self.gl is not None and self.gb is not None:
if frame is None:
frame = "galactic"
skycoords = SkyCoord(self.gl, self.gb, frame=frame, unit=u.deg)
else:
raise ValueError("To calculate skycoords either (raj and decj)"
"or (gl, gb) must be provided")
return skycoords
def calc_dm_excess(self):
"""
Calculates the dispersion measure excess of the FRB by
subtracting the DM contribution from the Milky Way.
Returns
-------
:obj:`astropy.units.Quantity`
The dispersion measure excess.
Notes
-----
:math:`\\rm{DM_{excess}}` is calculated as follows:
.. math::
\\rm{DM_{excess} = DM - DM_{galaxy}}
"""
dm_excess = self.dm.value - self.dm_galaxy.value
if dm_excess < 0:
print("dm_excess < 0: This implies that the DM estimate "
"from the Milky Way is higher than the observed DM. "
"Setting dm_excess = 0")
self.dm_excess = 0
else:
self.dm_excess = dm_excess
return dm_excess
def calc_dm_galaxy(self,
model='ymw16',
include_halo=False,
return_tau_sc=False):
"""
Calculates the dispersion measure contribution of the Milky Way
from either (:attr:`raj`, :attr:`decj`) or (:attr:`gl`,
:attr:`gb`). Uses the YMW16 model of the Milky Way free
electron column density.
Parameters
----------
model : 'ymw16' or 'ne2001', optional
The Milky Way dispersion measure model. To use 'ne2001' you
will need to install the python port. See
https://fruitbat.readthedocs.io/en/latest/user_guide/ne2001_installation.html
Default: 'ymw16'
include_halo : bool, optional
Include the DM of the galactic halo which isn't included
in NE2001 or YMW16. This used the YT2020 halo model. Default: False
return_tau_sc : bool, optional
Return the scattering timescale in addition to the DM.
Default: False
Returns
-------
dm_galaxy: :obj:`astropy.units.Quantity`
The dispersion measure contribution from the Milky Way of
the FRB.
tau_sc: :obj:`astropy.units.Quantity`, optional
The scattering timescale at 1 GHz (s). Only returns if
:attr:`return_tau_sc` is `True`.
"""
YMW16_options = ["ymw16", "YMW16"]
NE2001_options = ["ne2001", "NE2001"]
if model in YMW16_options:
model = 'YMW16'
elif model in NE2001_options:
model = 'NE2001'
else:
raise ValueError(
"'{}' is not a valid galactic DM model".format(model))
# Check to make sure some of the keyword are not None
coord_list = [self.skycoords, self.raj, self.decj, self.gl, self.gb]
if all(val is None for val in coord_list):
raise ValueError("""Can not calculate dm_galaxy since coordinates
for FRB burst were not provided. Please provide
(raj, decj) or (gl, gb) coordinates.""")
# Calculate skycoords position if it
elif (self.skycoords is None and
(self.raj is not None and self.decj is not None)
or (self.gl is not None and self.gb is not None)):
self._skycoords = self.calc_skycoords()
dm_galaxy, tau_sc = pygedm.dist_to_dm(gl=self._skycoords.galactic.l,
gb=self._skycoords.galactic.b,
dist=25000.0,
method=model)
if include_halo:
self.galaxy_halo = pygedm.calculate_halo_dm(
gl=self._skycoords.galactic.l,
gb=self._skycoords.galactic.b,
method='yt2020')
else:
self.galaxy_halo = 0 * u.pc * u.cm**(-3)
self.dm_galaxy_model = model
self.dm_galaxy = dm_galaxy.value + self.galaxy_halo.value
self.tau_sc = tau_sc.value
self.calc_dm_excess()
if return_tau_sc:
return self.dm_galaxy, self.tau_sc
else:
return self.dm_galaxy
def calc_dm_igm(self):
"""
Calculates the dispersion measure of the intergalactic medium
along the line-of-sight of the FRB. This can only be done if
the redshift and dispersion measure contribution of the FRB
host galaxy is known.
Returns
-------
:obj:`astropy.units.Quantity`
The dispersion measure contribution of the IGM.
Notes
-----
:math:`\\rm{DM_{IGM}}` is calculated as follows:
.. math::
\\rm{DM_{IGM}} = \\rm{DM_{excess}} -
\\frac{\\rm{DM_{host, loc}}}{1 + z}
"""
if self.z_host is None:
err_msg = ("z_host is None. Provide a non zero value for the "
"FRB host redshift")
raise ValueError(err_msg)
if self.dm_host_loc == 0.0:
err_msg = ("dm_host_loc = 0. The dm_igm will be the same as "
"dm_excess. Provide a non-zero value for dm_host_loc")
raise ValueError(err_msg)
dm_igm = self.dm_excess - (self.dm_host_loc / (1 + self.z_host))
self.dm_igm = dm_igm.value
return self.dm_igm
def calc_fluence(self):
"""
Calculates the observed fluence of the FRB. This requires
:attr:`width` and :attr:`peak_flux` to not be *None*.
Returns
-------
:obj:`astropy.units.Quantity` or None:
The fluence of the FRB.
Notes
-----
The fluence (:math:`\\rm{F_{obs}}`) is calculated as follows:
.. math::
F_{obs} = W_{obs} S_{\\nu, p}
Where :math:`W_{obs}` is the with of the FRB pulse and
:math:`S_{\\nu, p}` is the specific peak flux.
"""
if (self.width is None) or (self.peak_flux is None):
err_msg = ("calc_fluence requires both width and peak_flux "
"to not be None")
raise ValueError(err_msg)
fluence = self.width * self.peak_flux
self.fluence = fluence.value
return fluence
def calc_luminosity_distance(self):
"""
Calculates the luminosity distance to the FRB based on its
redshift. To calculate a luminosity distance either call
:meth:`calc_redshift` first to determine a redshift estimate
or provide a value for :attr:`dm_host`.
Returns
-------
:obj:`astropy.units.Quantity`
The luminosity distance to the FRB.
"""
if self.z is None:
raise ValueError(
""" Can not calculate luminosity distance without a redshift.
Use calc_redshift() to calculate the FRB redshift or provide
a value for z_host.
""")
cosmo = cosmologies.cosmology_functions()[self.cosmology]
return cosmo.luminosity_distance(self.z)
def calc_comoving_distance(self):
"""
Calculates the comoving distance to the FRB based on its
redshift. To calculate a comoving distance either call
:meth:`calc_redshift` first to determine a redshift estimate
or provide a value for :attr:`dm_host`.
Returns
-------
:obj:`astropy.units.Quantity`
The comoving distance to the FRB.
"""
if self.z is not None:
z_sample = self.z
elif self.z_host is not None:
z_sample = self.z_host
else:
raise ValueError(
""" Can not calculate comoving distance without a redshift.
Use calc_redshift() to calculate the FRB redshift or provide
a value for z_host.
""")
cosmo = cosmologies.cosmology_functions()[self.cosmology]
return cosmo.comoving_distance(z_sample)
def calc_luminosity(self, use_bandwidth=False):
"""
Calculates the isotropic peak luminosity of the FRB. This is
the upper limit to the the true peak luminosity since the
luminosity distance required is also an upper limit to the true
luminosity distance.
Parameters
----------
use_bandwidth: bool, optional
The default method of calculating the luminosity of a FRB
uses :attr:`obs_freq_central` as described in Zhang 2018.
However some estimates of the FRB luminosity instead use
:attr:`obs_bandwidth` (see Law et al. 2017). Set to
``True`` to use :attr:`obs_bandwidth` instead of
:attr:`obs_freq_central`. Default: False
Returns
-------
:obj:`astropy.units.Quantity`
The estimated isotropic peak luminosity of the FRB in units
of ergs/s.
Notes
-----
The luminosity of a FRB is calculated following that in
Zhang 2018.
.. math::
L_{FRB} \\simeq 4 \\pi D_{\\rm{L}}^2 S_{\\nu, p} \\nu_c
Where :math:`S_{\\nu, p}` is the specific peak flux of the FRB,
:math:`\\nu_c` is the central observing frequency,
:math:`D_{\\rm{L}}` is the luminosity distance.
In Law et al. 2017, the bandwidth (:math:`B`) is used instead
of :math:`\\nu_c` to estimate luminosity.
"""
D = self.calc_luminosity_distance()
if self.peak_flux is None:
err_msg = ("Can not calculate energy without peak_flux. Provide "
"peak_flux before calculating luminosity.")
raise ValueError(err_msg)
else:
S = self.peak_flux
if use_bandwidth:
if self.obs_bandwidth is None:
err_msg = ("Can not calculate energy without observing "
"bandwidth. Provide obs_bandwidth before "
"calculating energy.")
raise ValueError(err_msg)
B = self.obs_bandwidth
lum = 4 * np.pi * D**2 * S * B
else:
if self.obs_freq_central is None:
err_msg = ("Can not calculate energy without observing "
"frequency. Provide obs_freq_central before "
"calculating energy.")
raise ValueError(err_msg)
nu = self.obs_freq_central
lum = 4 * np.pi * D**2 * S * nu
return lum.to('erg s**-1')
def calc_energy(self, use_bandwidth=False):
"""
Calculates the isotropic energy of the FRB. This is the upper
limit to the the true energy since the luminosity distance
required is also an upper limit to the true luminosity
distance.
Parameters
----------
use_bandwidth: bool, optional
The default method of calculating the energy of a FRB uses
:attr:`obs_freq_central` as described in Zhang 2018.
However some estimates of the FRB energy instead use
:attr:`obs_bandwidth` (see Law et al. 2017). Set to
``True`` to use :attr:`obs_bandwidth` instead of
:attr:`obs_freq_central`. Default: False
Returns
-------
:obj:`astropy.units.Quantity`
The estimated isotropic energy of the FRB, in units of
ergs.
Notes
-----
The energy of a FRB is calculated following that in Zhang 2018.
.. math::
E_{FRB} \\simeq \\frac{4 \\pi}{1 + z} D_{\\rm{L}}^2 F_{obs} \\nu_c
Where :math:`F_{obs}` is the fluence of the FRB, :math:`\\nu_c`
is the central observing frequency, :math:`D_{\\rm{L}}` is the
luminosity distance and :math:`z` is the estimated redshift.
In Law et al. 2017, the bandwidth (:math:`B`) is used instead
of :math:`\\nu_c` to estimate energy.
"""
D = self.calc_luminosity_distance()
if self.fluence is None:
err_msg = ("Can not calculate energy without fluence. Provide "
"fluence or peak_flux and width before calculating "
"energy.")
raise ValueError(err_msg)
else:
fluence = self.fluence
if use_bandwidth:
if self.obs_bandwidth is None:
err_msg = ("Can not calculate energy without observing "
"bandwidth. Provide obs_bandwidth before "
"calculating energy.")
raise ValueError(err_msg)
else:
bandwidth = self.obs_bandwidth
energy = fluence * bandwidth * 4 * np.pi * D**2 * (1 + self.z)**-1
else:
if self.obs_freq_central is None:
err_msg = ("Can not calculate energy without observing "
"frequency. Provide obs_freq_central before "
"calculating energy.")
raise ValueError(err_msg)
else:
nu = self.obs_freq_central
energy = fluence * nu * 4 * np.pi * D**2 * (1 + self.z)**-1
return energy.to("erg")
def _set_value_units(self, value, unit=None, non_negative=False):
"""
Converts ``value`` into a :obj:`~astropy.unit.Quantity` with
units. Also checks if ``value`` has existing units and the
units are convertable with ``unit``. If ``value`` is a
:obj:`~astropy.unit.Quantity` with convertable units then
``value`` is returned unchanged.
Parameters
----------
value: float, int, or :obj:`~astropy.unit.Quantity`
The input value.
unit: :obj:`astropy.unit` or None
The unit to set for ``value``. If ``unit = None`` then
``value`` will become a dimensionless quantity.
non_negative: bool, optional
Raise an error if the value is negative. This is used to
verify values that can only be positive are correctly
specified. Default: *False*
Return
------
var : :obj:`~astropy.unit.Quantity` or None
The output quantity with units. If ``value=None``
returns *None*
"""
# Check if the value already has units
if not isinstance(value, u.Quantity):
if value is None:
var = None
elif non_negative and value < 0.0:
raise ValueError("Value must be greater than zero.")
elif unit is None:
var = value * u.dimensionless_unscaled
else:
var = value * unit
else:
# If passed units check that they are the correct units by checking
# that they are equivalent
if value.unit.is_equivalent(unit):
var = value
else:
err_msg = ("Quantity expected to have units of {} instead was "
"passed units {} which is not convertable".format(
unit, value.unit))
raise ValueError(err_msg)
return var
@property
def name(self):
"""
name: str
The name of the FRB object.
"""
return self._name
@name.setter
def name(self, value):
if isinstance(value, str):
self._name = value
elif value is None:
self._name = None
else:
self._name = str(value)
@property
def dm(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed dispersion measure of the FRB. This is without
Milky Way or host galaxy subtraction.
"""
return self._dm
@dm.setter
def dm(self, value):
utils.check_type("dm", value, str, desire=False)
self._dm = self._set_value_units(value,
unit=u.pc * u.cm**-3,
non_negative=True)
@property
def dm_galaxy(self):
"""
:obj:`astropy.units.Quantity` or None:
The galactic component of the dispersion measure. This is
quantity is calculated using :meth:`calc_dm_galaxy`.
"""
return self._dm_galaxy
@dm_galaxy.setter
def dm_galaxy(self, value):
self._dm_galaxy = self._set_value_units(value,
unit=u.pc * u.cm**-3,
non_negative=True)
@property
def dm_excess(self):
"""
:obj:`astropy.units.Quantity` or None:
The dispersion measure with the Milky Way component
subtracted. This value approximates the dispersion measure
of the intergalatic medium by assuming that the host galaxy
contributes zero to the observed dispersion measure. This
quantity is calculated using :meth:`calc_dm_excess`.
"""
return self._dm_excess
@dm_excess.setter
def dm_excess(self, value):
self._dm_excess = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def dm_host_est(self):
"""
:obj:`astropy.units.Quantity` or None:
The estimated dispersion measure from the FRB host galaxy.
"""
return self._dm_host_est
@dm_host_est.setter
def dm_host_est(self, value):
self._dm_host_est = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def dm_host_loc(self):
"""
:obj:`astropy.units.Quantity` or None:
The dispersion measure from a localised FRB host galaxy.
"""
return u.Quantity(self._dm_host_loc, u.pc * u.cm**-3)
@dm_host_loc.setter
def dm_host_loc(self, value):
self._dm_host_loc = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def dm_index(self):
"""
:obj:`astropy.units.Quantity` or None:
The dispersion measure index of the burst.
"""
return self._dm_index
@dm_index.setter
def dm_index(self, value):
self._dm_index = self._set_value_units(value)
@property
def z(self):
"""
:obj:`astropy.units.Quantity` or None:
The estimated redshift of the burst. By default this
assumes that the entire :attr:`dm_excess` arrives from the
IGM and the host galaxy of the FRB and any surrounding
material contribute nothing to the total DM. This should be
taken as an upper limit to the bursts true redshift. To
provide an estimate of the DM contribution due to he host
galaxy, set :attr:`dm_host_est` to a non-zero value and use
``subract_host=True`` when calling :meth:`calc_redshift()`.
"""
return self._z
@z.setter
def z(self, value):
self._z = self._set_value_units(value, non_negative=True)
@property
def z_conf_int_lower(self):
"""
:obj:`astropy.units.Quantity` or None:
The lower bound of the redshift confidence interval.
"""
return self._z_conf_int_lower
@z_conf_int_lower.setter
def z_conf_int_lower(self, value):
self._z_conf_int_lower = self._set_value_units(value,
non_negative=True)
@property
def z_conf_int_upper(self):
"""
:obj:`astropy.units.Quantity` or None:
The upper bound of the redshift confidence interval.
"""
return self._z_conf_int_upper
@z_conf_int_upper.setter
def z_conf_int_upper(self, value):
self._z_conf_int_upper = self._set_value_units(value,
non_negative=True)
@property
def z_host(self):
"""
:obj:`astropy.units.Quantity` or None:
The redshift of the localised FRB host galaxy. Note that
this an observed quantity, not the estimated redshift
:attr:`z` calculated with :meth:`calc_redshift()`.
"""
return self._z_host
@z_host.setter
def z_host(self, value):
self._z_host = self._set_value_units(value)
@property
def scatt_index(self):
"""
:obj:`astropy.units.Quantity` or None:
The scattering index of the burst.
"""
return self._scatt_index
@scatt_index.setter
def scatt_index(self, value):
self._scatt_index = self._set_value_units(value)
@property
def width(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed width of the pulse.
"""
return self._width
@width.setter
def width(self, value):
self._width = self._set_value_units(value, u.ms, non_negative=True)
@property
def peak_flux(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed peak flux density of the FRB.
"""
return self._peak_flux
@peak_flux.setter
def peak_flux(self, value):
self._peak_flux = self._set_value_units(value, u.Jy, non_negative=True)
@property
def fluence(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed fluence of the FRB. This is calculated from
:meth:`calc_fluence`.
"""
return self._fluence
@fluence.setter
def fluence(self, value):
self._fluence = self._set_value_units(value,
u.Jy * u.ms,
non_negative=True)
@property
def obs_bandwidth(self):
"""
:obj:`astropy.units.Quantity` or None:
The observing bandwidth of the FRB.
"""
return self._obs_bandwidth
@obs_bandwidth.setter
def obs_bandwidth(self, value):
self._obs_bandwidth = self._set_value_units(value,
u.MHz,
non_negative=True)
@property
def obs_freq_central(self):
"""
:obj:`astropy.units.Quantity` or None:
The central observing frequency of the FRB.
"""
return self._obs_freq_central
@obs_freq_central.setter
def obs_freq_central(self, value):
self._obs_freq_central = self._set_value_units(value,
u.MHz,
non_negative=True)
@property
def raj(self):
"""
:obj:`astropy.coordinates.Longitude` or None:
The right accension in J2000 coordinates of the best
estimate of the FRB position. This is given in the IRCS
frame.
"""
return self._raj
@raj.setter
def raj(self, value):
if value is None:
self._raj = None
else:
self._raj = coord.angles.Longitude(value, u.hourangle)
@property
def decj(self):
"""
:obj:`astropy.coordinates.Latitude` or None:
The declination in J2000 coordinates of the best estimate
of the FRB position. This is given in the IRCS frame.
"""
return self._decj
@decj.setter
def decj(self, value):
if value is None:
self._decj = None
else:
self._decj = coord.angles.Latitude(value, u.deg)
@property
def gl(self):
"""
:obj:`astropy.coordinates.Longitude` or None:
The longitude in galactic coordinates of the best estimate
of the FRB position.
"""
return self._gl
@gl.setter
def gl(self, value):
if value is None:
self._gl = None
else:
self._gl = coord.angles.Longitude(value, u.deg)
@property
def gb(self):
"""
:obj:`astropy.coordinates.Latitude` or None:
The latitude in galactic coordinates of the best estimate
of the FRB position.
"""
return self._gb
@gb.setter
def gb(self, value):
if value is None:
self._gb = None
else:
self._gb = coord.angles.Latitude(value, u.deg)
@property
def skycoords(self):
"""
:obj:`astropy.coordinates.SkyCoord` or None:
The skycoords of the FRB. This is calculated from either
(:attr:`raj`, :attr:`decj`) or (:attr:`gl`, :attr:`gb`)
using :meth:`calc_skycoords`.
"""
return self._skycoords
@skycoords.setter
def skycoords(self, value):
if value is None:
self._skycoords = None
else:
self._skycoords = SkyCoord(value)
@property
def dm_igm(self):
"""
:obj:`astropy.units.Quantity` or None:
The estimated disperison measure from the IGM. This can be
calculated for a FRB for which the redshift of its host
galaxy is known. This value is determined using
:meth:`calc_dm_igm`.
"""
return self._dm_igm
@dm_igm.setter
def dm_igm(self, value):
self._dm_igm = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def utc(self):
"""
:obj:`astropy.time.Time` or None
The UTC time of the burst.
"""
return self._utc
@utc.setter
def utc(self, value):
if value is None:
self._utc = None
else:
self._utc = Time(value, format='isot', scale='utc')
@property
def snr(self):
"""
:obj:`astropy.units.Quantity`:
The signal-to-noise ratio of the burst.
"""
return self._snr
@snr.setter
def snr(self, value):
self._snr = self._set_value_units(value, non_negative=True)
@property
def cosmology(self):
"""
str or None:
The cosmology used to calculate redshift.
"""
return self._cosmology
@cosmology.setter
def cosmology(self, value):
if isinstance(value, str):
self._cosmology = value
else:
self._cosmology = str(value)
@property
def method(self):
"""
str or None:
The method used to calculate redshift.
"""
return self._method
@method.setter
def method(self, value):
if isinstance(value, str):
self._method = value
else:
self._method = str(value)
@property
def dm_galaxy_model(self):
"""
str or None:
The method used to calculate redshift.
"""
return self._dm_galaxy_model
@dm_galaxy_model.setter
def dm_galaxy_model(self, value):
if isinstance(value, str):
self._dm_galaxy_model = value
else:
self._dm_galaxy_model = str(value)
def calc_redshift(self,
method='Inoue2004',
cosmology="Planck18",
subtract_host=False,
lookup_table=None):
"""
Calculate the redshift of the FRB from its :attr:`dm`,
:attr:`dm_excess` or :attr:`dm_excess` - :attr:`dm_host_est`.
Parameters
----------
method : str, optional
The dispersion meausre -redshift relation to use when
calculating the redshift. Avaliable methods: %(meth)s.
Default: 'Inoue2004'
cosmology : str, optional
The cosmology to assume when calculating the redshift.
Avaliable cosmologies: %(cosmo)s. Default: 'Planck18'
subtract_host : bool, optional
Subtract :attr:`dm_host_est` from the :attr:`dm_excess`
before calculating the redshift. This is is used to account
for the dispersion measure that arises from the FRB host
galaxy. Default: False
lookup_table : str or None, optional
The path to the lookup table file. If ``lookup_table=None``
a table will attempted to be loaded from the data directory
based on the method name. Default: *None*
Returns
-------
float
The redshift of the FRB.
Notes
-----
The methods_ section in the documentation has a description for
each of the builtin methods.
The cosmology_ section in the documentation has a list of the
cosmological parameters for each cosmology
.. _cosmology: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#cosmology
.. _methods: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#methods
"""
if not isinstance(subtract_host, bool):
raise ValueError("subtract_host must be of type bool.")
if subtract_host:
input_dm = self.dm_excess - self.dm_host_est
else:
input_dm = self.dm_excess
if method not in methods.available_methods():
err_msg = ("Method '{}' is not a valid method. "
"Valid methods are: {}".format(
method, methods.available_methods()))
raise ValueError(err_msg)
if cosmology not in cosmologies.available_cosmologies():
err_msg = ("Cosmology '{}' is not a valid cosmology. Valid "
"cosmologies are: {}".format(
cosmology, cosmologies.available_cosmologies()))
raise ValueError(err_msg)
# If the user provides a table use that table for estimation.
if lookup_table is not None:
lookup_table = table.load(lookup_table)
else:
if method in methods.builtin_method_functions().keys():
table_name = "".join(["_".join([method, cosmology]), ".npz"])
else:
table_name = "".join(["custom_", method, ".npz"])
lookup_table = table.load(table_name)
self.z = table.get_z_from_table(input_dm, lookup_table)
lookup_table.close()
self.cosmology = cosmology
self.method = method
return self.z
class Frb(object):
"""
Create a :class:`~Frb` object using the observered properties of a
FRB including dispersion measure (DM) and its sky coordinates. This
class utilises various DM-redshift relations as well as the YMW16
galactic DM model in the analysis.
A FRB can be defined simply with a single :attr:`dm` value. This
should be the observed DM prior to subtracting the Milky Way,
however if you do not provide any additional information, it is
asssumed that this value is also the :attr:`dm_excess` (DM -
Galactic DM). You can get the estimated redshift by using the
method :meth:`calc_redshift`.
To get a more accurate distance estimate you can account for the
contribution due to the Milky Way by supplying :attr:`dm_galaxy` or
by giving the coordinates of the FRB in ICRS (:attr:`raj`,
:attr:`decj`) or Galactic (:attr:`gl`, :attr:`gb`) coordinates and
calling the method :meth:`calc_dm_galaxy` before calling
:meth:`calc_redshift`.
Parameters
----------
dm : float
The observed dispersion measure of the FRB. This is without
Milky Way or host galaxy subtraction. Units: pc cm**-3
Keyword Arguments
-----------------
name : str or None, optional
The name of the frb object. Default: *None*
raj : str or None, optional
The right ascension in J2000 coordinates of the best estimate
of the FRB position. By default should be given in the ICRS
frame. An alternative frame can be specified by also including
the keyword ``frame``. e.g. ``frame='fk5'``. Default: *None*
decj : str or None, optional
The declination in J2000 coordinates of the best estimate of
the FRB position. By default should be given in the ICRS frame.
An alternative frame can be specified by also including the
keyword ``frame``. e.g. ``frame='fk5'``. Default: *None*
gl : str or None, optional
The Galactic longitude in degrees of the best estimate of the
FRB position. Default: *None*
gb : str or None, optional
The Galactic latitude in degrees of the best estimate of the
FRB position. Default: *None*
Other Parameters
----------------
dm_galaxy : float, optional
The modelled contribution to the FRB DM by electrons in the
Milky Way. This value is calculated using
:meth:`calc_dm_galaxy` Units: pc cm**-3 Default: 0.0
dm_excess : float or None, optional
The DM excess of the FRB over the estimated Galactic DM. If
:attr:`dm_excess` is *None*, then :attr:`dm_excess` is
calculated automatically with :meth:`calc_dm_excess`.
Units: pc cm**-3 Default: *None*
z_host : float or None, optional
The observed redshift of the localised FRB host galaxy.
Default: *None*
dm_host_est : float, optional
The estimated contribution to the measured FRB DM originating
from the FRB's host galaxy. This value is the amount of DM the
host galaxy contributes to the observed DM, *not* the DM of the
host galaxy. Setting this to a non-zero value and setting
``subtract_host=True`` when calling :meth:`calc_redshift`
accounts for the DM contribution due to the host galaxy.
Units: pc cm**-3 Default: 0.0
dm_host_loc : float, optional
The dispersion measure of a localised FRB host galaxy. This
value is *not* the contribution to the observed DM, but the DM
at the host galaxy. The observed DM is :attr:`dm_host_loc` but
attenuated by a factor of (1 + z). To use this, the redshift of
the host galaxy must be known. Units: pc cm**-3 Default: 0.0
dm_index : float or None, optional
The dispersion measure index of the burst :math:`\\alpha` such
that :math:`\\rm{DM} \\propto \\nu^{-\\alpha}` Default: *None*
scatt_index : float or None, optional
The scattering index (:math:`\\beta`) of the FRB pulse. The
scattering index describes how the width (:math:`\\rm{W}`) of
the FRB pulse evolves with frequency :math:`\\nu` such that
:math:`\\rm{W} \\propto \\nu^{-\\beta}`. Default: *None*
snr : float or None, optional
The signal-to-noise ratio of the burst.
Default: *None*
width : float or None, optional
The observed width of the pulse obtained by a pulse fitting
algorithm. Units: ms Default: *None*
peak_flux : float or None, optional
The observed peak flux density of the burst. Units: Jy
Default: *None*
fluence : float or None, optional
The observed fluence of the FRB. If :attr:`fluence` is *None*
and both :attr:`width` and :attr:`peak_flux` are not *None*
then :attr:`fluence` is automatically calculated with
:meth:`calc_fluence`. Units: Jy ms Default: *None*
obs_bandwidth : float or None, optional
The observing bandwidth. Units: MHz Default: *None*
obs_freq_central : float or None, optional
The central observing frequency, Units: MHz Deault: *None*
utc : str or None, optional
The UTC time of the FRB Burst. Format should be of the form
'1999-01-01T00:00:00.000'. Default: *None*
Example
-------
>>> import fruitbat
>>> FRB = fruitbat.Frb(879, gl="12:31:40.5", gb="3:41:10.0")
>>> FRB.calc_dm_galaxy()
>>> FRB.calc_redshift()
"""
def __init__(self,
dm,
name=None,
raj=None,
decj=None,
gl=None,
gb=None,
dm_galaxy=0.0,
dm_excess=None,
z_host=None,
dm_host_est=0.0,
dm_host_loc=0.0,
dm_index=None,
scatt_index=None,
snr=None,
width=None,
peak_flux=None,
fluence=None,
obs_bandwidth=None,
obs_freq_central=None,
utc=None,
**kwargs):
self.dm = dm
self.name = name
self.raj = raj
self.decj = decj
self.gl = gl
self.gb = gb
self.dm_galaxy = dm_galaxy
# Calculate dm_excess from existing parameters if it is not given.
if dm_excess is None:
self.calc_dm_excess()
else:
self.dm_excess = dm_excess
self.z_host = z_host
self.dm_host_est = dm_host_est
self.dm_host_loc = dm_host_loc
self.dm_index = dm_index
self.scatt_index = scatt_index
self.snr = snr
self.width = width
self.peak_flux = peak_flux
self.fluence = fluence
self.obs_bandwidth = obs_bandwidth
self.obs_freq_central = obs_freq_central
self.utc = utc
self.z = None
self.dm_igm = None
self.cosmology = None
self.method = None
# Calculate fluence if peak_flux and width are given
if ((self.fluence is None)
and (peak_flux is not None and width is not None)):
self.calc_fluence()
# Calculate the skycoords of the FRB from (raj, decj) or (gl, gb)
if (raj and decj) or (gl and gb):
if 'frame' in kwargs:
self.skycoords = self.calc_skycoords(frame=kwargs["frame"])
else:
self.skycoords = self.calc_skycoords()
self.raj = self.skycoords.transform_to('icrs').ra
self.decj = self.skycoords.transform_to('icrs').dec
self.gl = self.skycoords.transform_to('galactic').l
self.gb = self.skycoords.transform_to('galactic').b
else:
self.skycoords = None
def __repr__(self):
frb_repr = []
var_dict = vars(self)
for var in var_dict:
if var[1:] == "skycoords":
continue
var_name = var[1:]
if isinstance(var_dict[var], u.Quantity):
var_val = var_dict[var].value
else:
var_val = var_dict[var]
frb_repr.append("{}={}".format(var_name, var_val))
return "Frb({})".format(", ".join(map(str, frb_repr)))
@docstring_substitute(meth=methods.available_methods(),
cosmo=cosmologies.available_cosmologies())
def calc_redshift(self,
method='Inoue2004',
cosmology="Planck18",
subtract_host=False,
lookup_table=None):
"""
Calculate the redshift of the FRB from its :attr:`dm`,
:attr:`dm_excess` or :attr:`dm_excess` - :attr:`dm_host_est`.
Parameters
----------
method : str, optional
The dispersion meausre -redshift relation to use when
calculating the redshift. Avaliable methods: %(meth)s.
Default: 'Inoue2004'
cosmology : str, optional
The cosmology to assume when calculating the redshift.
Avaliable cosmologies: %(cosmo)s. Default: 'Planck18'
subtract_host : bool, optional
Subtract :attr:`dm_host_est` from the :attr:`dm_excess`
before calculating the redshift. This is is used to account
for the dispersion measure that arises from the FRB host
galaxy. Default: False
lookup_table : str or None, optional
The path to the lookup table file. If ``lookup_table=None``
a table will attempted to be loaded from the data directory
based on the method name. Default: *None*
Returns
-------
float
The redshift of the FRB.
Notes
-----
The methods_ section in the documentation has a description for
each of the builtin methods.
The cosmology_ section in the documentation has a list of the
cosmological parameters for each cosmology
.. _cosmology: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#cosmology
.. _methods: https://fruitbat.readthedocs.io/en/latest/user_guide/method_and_cosmology.html#methods
"""
if not isinstance(subtract_host, bool):
raise ValueError("subtract_host must be of type bool.")
if subtract_host:
input_dm = self.dm_excess - self.dm_host_est
else:
input_dm = self.dm_excess
if method not in methods.available_methods():
err_msg = ("Method '{}' is not a valid method. "
"Valid methods are: {}".format(
method, methods.available_methods()))
raise ValueError(err_msg)
if cosmology not in cosmologies.available_cosmologies():
err_msg = ("Cosmology '{}' is not a valid cosmology. Valid "
"cosmologies are: {}".format(
cosmology, cosmologies.available_cosmologies()))
raise ValueError(err_msg)
# If the user provides a table use that table for estimation.
if lookup_table is not None:
lookup_table = table.load(lookup_table)
else:
if method in methods.builtin_method_functions().keys():
table_name = "".join(["_".join([method, cosmology]), ".npz"])
else:
table_name = "".join(["custom_", method, ".npz"])
lookup_table = table.load(table_name)
self.z = table.get_z_from_table(input_dm, lookup_table)
lookup_table.close()
self.cosmology = cosmology
self.method = method
return self.z
def calc_skycoords(self, frame=None):
"""
Calculates the skycoord position on the sky of the FRB from
(:attr:`raj`, :attr:`decj`) or (:attr:`gl`, :attr:`gb`). If
both (:attr:`raj`, :attr:`decj`) and (:attr:`gl`, :attr:`gb`)
are given, preference is given to (:attr:`raj`, :attr:`decj`).
Parameters
----------
frame: str or None, optional
The type of coordinate frame. If ``frame = None`` then
:meth:`calc_skycoords` will use a default frame based on
the coordinates given. If :attr:`raj` and :attr:`decj` are
given the default frame is 'icrs'. If :attr:`gl` and
:attr:`gb` are given the default frame is 'galactic'.
Default: *None*
Returns
-------
:obj:`astropy.coordinates.SkyCoord`
The sky coordinates of the FRB.
"""
if self.raj is not None and self.decj is not None:
if frame is None:
frame = "icrs"
skycoords = SkyCoord(ra=self.raj,
dec=self.decj,
frame=frame,
unit=(u.hourangle, u.deg))
elif self.gl is not None and self.gb is not None:
if frame is None:
frame = "galactic"
skycoords = SkyCoord(self.gl, self.gb, frame=frame, unit=u.deg)
else:
raise ValueError("To calculate skycoords either (raj and decj)"
"or (gl, gb) must be provided")
return skycoords
def calc_dm_excess(self):
"""
Calculates the dispersion measure excess of the FRB by
subtracting the DM contribution from the Milky Way.
Returns
-------
:obj:`astropy.units.Quantity`
The dispersion measure excess.
Notes
-----
:math:`\\rm{DM_{excess}}` is calculated as follows:
.. math::
\\rm{DM_{excess} = DM - DM_{galaxy}}
"""
dm_excess = self.dm.value - self.dm_galaxy.value
if dm_excess < 0:
print("dm_excess < 0: This implies that the DM estimate "
"from the Milky Way is higher than the observed DM. "
"Setting dm_excess = 0")
self.dm_excess = 0
else:
self.dm_excess = dm_excess
return dm_excess
def calc_dm_galaxy(self, model='ymw16'):
"""
Calculates the dispersion measure contribution of the Milky Way
from either (:attr:`raj`, :attr:`decj`) or (:attr:`gl`,
:attr:`gb`). Uses the YMW16 model of the Milky Way free
electron column density.
Parameters
----------
model : 'ymw16' or 'ne2001', optional
The Milky Way dispersion measure model. To use 'ne2001' you
will need to install the python port. See
https://fruitbat.readthedocs.io/en/latest/user_guide/ne2001_installation.html
Default: 'ymw16'
Returns
-------
:obj:`astropy.units.Quantity`
The dispersion measure contribution from the Milky Way of
the FRB.
"""
YMW16_options = ["ymw16", "YMW16"]
NE2001_options = ["ne2001", "NE2001"]
if model in YMW16_options:
# Since the YMW16 model only gives you a dispersion measure out to a
# distance within the galaxy, to get the entire DM contribution of the
# galaxy we need to specify the furthest distance in the YMW16 model.
max_galaxy_dist = 25000 # units: pc
# Check to make sure some of the keyword are not None
coord_list = [
self.skycoords, self.raj, self.decj, self.gl, self.gb
]
if all(val is None for val in coord_list):
raise ValueError(
"""Can not calculate dm_galaxy since coordinates
for FRB burst were not provided. Please provide
(raj, decj) or (gl, gb) coordinates.""")
# Calculate skycoords position if it
elif (self.skycoords is None and
(self.raj is not None and self.decj is not None)
or (self.gl is not None and self.gb is not None)):
self._skycoords = self.calc_skycoords()
dm_galaxy, tau_sc = ymw16.dist_to_dm(self._skycoords.galactic.l,
self._skycoords.galactic.b,
max_galaxy_dist)
elif model in NE2001_options:
try:
from ne2001 import density
except ModuleNotFoundError:
msg = ("""
By default only the YMW16 Milky Way electron density model
is installed with Fruitbat. However Fruitbat due support using
the NE2001 model via a python port from JXP and Ben Baror.
To install the ne2001 model compatible with Fruitbat download
and install it from github:
>>> git clone https://github.com/FRBs/ne2001
>>> cd ne2001
>>> pip install .
Once you have installed it you should be able to use Fruitbat
in exactly the same way by passing 'ne2001' instead of 'ymw16'.
""")
raise ModuleNotFoundError(msg)
# This is the same max distanc e that we used for the YMW16 model
# However the NE2001 model specifies distance in kpc not pc.
max_galaxy_dist = 25 # units kpc
# NE2001 models needs gl and gb in floats
gl = float(self._skycoords.galactic.l.value)
gb = float(self._skycoords.galactic.b.value)
ne = density.ElectronDensity()
dm_galaxy = ne.DM(gl, gb, max_galaxy_dist)
self.dm_galaxy = dm_galaxy.value
self.calc_dm_excess()
return self.dm_galaxy
def calc_dm_igm(self):
"""
Calculates the dispersion measure of the intergalactic medium
along the line-of-sight of the FRB. This can only be done if
the redshift and dispersion measure contribution of the FRB
host galaxy is known.
Returns
-------
:obj:`astropy.units.Quantity`
The dispersion measure contribution of the IGM.
Notes
-----
:math:`\\rm{DM_{IGM}}` is calculated as follows:
.. math::
\\rm{DM_{IGM}} = \\rm{DM_{excess}} -
\\frac{\\rm{DM_{host, loc}}}{1 + z}
"""
if self.z_host is None:
err_msg = ("z_host is None. Provide a non zero value for the "
"FRB host redshift")
raise ValueError(err_msg)
if self.dm_host_loc == 0.0:
err_msg = ("dm_host_loc = 0. The dm_igm will be the same as "
"dm_excess. Provide a non-zero value for dm_host_loc")
raise ValueError(err_msg)
dm_igm = self.dm_excess - (self.dm_host_loc / (1 + self.z_host))
self.dm_igm = dm_igm.value
return self.dm_igm
def calc_fluence(self):
"""
Calculates the observed fluence of the FRB. This requires
:attr:`width` and :attr:`peak_flux` to not be *None*.
Returns
-------
:obj:`astropy.units.Quantity` or None:
The fluence of the FRB.
Notes
-----
The fluence (:math:`\\rm{F_{obs}}`) is calculated as follows:
.. math::
F_{obs} = W_{obs} S_{\\nu, p}
Where :math:`W_{obs}` is the with of the FRB pulse and
:math:`S_{\\nu, p}` is the specific peak flux.
"""
if (self.width is None) or (self.peak_flux is None):
err_msg = ("calc_fluence requires both width and peak_flux "
"to not be None")
raise ValueError(err_msg)
fluence = self.width * self.peak_flux
self.fluence = fluence.value
return fluence
def calc_luminosity_distance(self):
"""
Calculates the luminosity distance to the FRB based on its
redshift. To calculate a luminosity distance either call
:meth:`calc_redshift` first to determine a redshift estimate
or provide a value for :attr:`dm_host`.
Returns
-------
:obj:`astropy.units.Quantity`
The luminosity distance to the FRB.
"""
if self.z is None:
raise ValueError(
""" Can not calculate luminosity distance without a redshift.
Use calc_redshift() to calculate the FRB redshift or provide
a value for z_host.
""")
cosmo = cosmologies.cosmology_functions()[self.cosmology]
return cosmo.luminosity_distance(self.z)
def calc_comoving_distance(self):
"""
Calculates the comoving distance to the FRB based on its
redshift. To calculate a comoving distance either call
:meth:`calc_redshift` first to determine a redshift estimate
or provide a value for :attr:`dm_host`.
Returns
-------
:obj:`astropy.units.Quantity`
The comoving distance to the FRB.
"""
if self.z is not None:
z_sample = self.z
elif self.z_host is not None:
z_sample = self.z_host
else:
raise ValueError(
""" Can not calculate comoving distance without a redshift.
Use calc_redshift() to calculate the FRB redshift or provide
a value for z_host.
""")
cosmo = cosmologies.cosmology_functions()[self.cosmology]
return cosmo.comoving_distance(z_sample)
def calc_luminosity(self, use_bandwidth=False):
"""
Calculates the isotropic peak luminosity of the FRB. This is
the upper limit to the the true peak luminosity since the
luminosity distance required is also an upper limit to the true
luminosity distance.
Parameters
----------
use_bandwidth: bool, optional
The default method of calculating the luminosity of a FRB
uses :attr:`obs_freq_central` as described in Zhang 2018.
However some estimates of the FRB luminosity instead use
:attr:`obs_bandwidth` (see Law et al. 2017). Set to
``True`` to use :attr:`obs_bandwidth` instead of
:attr:`obs_freq_central`. Default: False
Returns
-------
:obj:`astropy.units.Quantity`
The estimated isotropic peak luminosity of the FRB in units
of ergs/s.
Notes
-----
The luminosity of a FRB is calculated following that in
Zhang 2018.
.. math::
L_{FRB} \\simeq 4 \\pi D_{\\rm{L}}^2 S_{\\nu, p} \\nu_c
Where :math:`S_{\\nu, p}` is the specific peak flux of the FRB,
:math:`\\nu_c` is the central observing frequency,
:math:`D_{\\rm{L}}` is the luminosity distance.
In Law et al. 2017, the bandwidth (:math:`B`) is used instead
of :math:`\\nu_c` to estimate luminosity.
"""
D = self.calc_luminosity_distance()
if self.peak_flux is None:
err_msg = ("Can not calculate energy without peak_flux. Provide "
"peak_flux before calculating luminosity.")
raise ValueError(err_msg)
else:
S = self.peak_flux
if use_bandwidth:
if self.obs_bandwidth is None:
err_msg = ("Can not calculate energy without observing "
"bandwidth. Provide obs_bandwidth before "
"calculating energy.")
raise ValueError(err_msg)
B = self.obs_bandwidth
lum = 4 * np.pi * D**2 * S * B
else:
if self.obs_freq_central is None:
err_msg = ("Can not calculate energy without observing "
"frequency. Provide obs_freq_central before "
"calculating energy.")
raise ValueError(err_msg)
nu = self.obs_freq_central
lum = 4 * np.pi * D**2 * S * nu
return lum.to('erg s**-1')
def calc_energy(self, use_bandwidth=False):
"""
Calculates the isotropic energy of the FRB. This is the upper
limit to the the true energy since the luminosity distance
required is also an upper limit to the true luminosity
distance.
Parameters
----------
use_bandwidth: bool, optional
The default method of calculating the energy of a FRB uses
:attr:`obs_freq_central` as described in Zhang 2018.
However some estimates of the FRB energy instead use
:attr:`obs_bandwidth` (see Law et al. 2017). Set to
``True`` to use :attr:`obs_bandwidth` instead of
:attr:`obs_freq_central`. Default: False
Returns
-------
:obj:`astropy.units.Quantity`
The estimated isotropic energy of the FRB, in units of
ergs.
Notes
-----
The energy of a FRB is calculated following that in Zhang 2018.
.. math::
E_{FRB} \\simeq \\frac{4 \\pi}{1 + z} D_{\\rm{L}}^2 F_{obs} \\nu_c
Where :math:`F_{obs}` is the fluence of the FRB, :math:`\\nu_c`
is the central observing frequency, :math:`D_{\\rm{L}}` is the
luminosity distance and :math:`z` is the estimated redshift.
In Law et al. 2017, the bandwidth (:math:`B`) is used instead
of :math:`\\nu_c` to estimate energy.
"""
D = self.calc_luminosity_distance()
if self.fluence is None:
err_msg = ("Can not calculate energy without fluence. Provide "
"fluence or peak_flux and width before calculating "
"energy.")
raise ValueError(err_msg)
else:
F = self.fluence
if use_bandwidth:
if self.obs_bandwidth is None:
err_msg = ("Can not calculate energy without observing "
"bandwidth. Provide obs_bandwidth before "
"calculating energy.")
raise ValueError(err_msg)
else:
B = self.obs_bandwidth
energy = F * B * 4 * np.pi * D**2 * (1 + self.z)**-1
else:
if self.obs_freq_central is None:
err_msg = ("Can not calculate energy without observing "
"frequency. Provide obs_freq_central before "
"calculating energy.")
raise ValueError(err_msg)
else:
nu = self.obs_freq_central
energy = F * nu * 4 * np.pi * D**2 * (1 + self.z)**-1
return energy.to("erg")
def _set_value_units(self, value, unit=None, non_negative=False):
"""
Converts ``value`` into a :obj:`~astropy.unit.Quantity` with
units. Also checks if ``value`` has existing units and the
units are convertable with ``unit``. If ``value`` is a
:obj:`~astropy.unit.Quantity` with convertable units then
``value`` is returned unchanged.
Parameters
----------
value: float, int, or :obj:`~astropy.unit.Quantity`
The input value.
unit: :obj:`astropy.unit` or None
The unit to set for ``value``. If ``unit = None`` then
``value`` will become a dimensionless quantity.
non_negative: bool, optional
Raise an error if the value is negative. This is used to
verify values that can only be positive are correctly
specified. Default: *False*
Return
------
var : :obj:`~astropy.unit.Quantity` or None
The output quantity with units. If ``value=None``
returns *None*
"""
# Check if the value already has units
if not isinstance(value, u.Quantity):
if value is None:
var = None
elif non_negative and value < 0.0:
raise ValueError("Value must be greater than zero.")
elif unit is None:
var = value * u.dimensionless_unscaled
else:
var = value * unit
else:
# If passed units check that they are the correct units by checking
# that they are equivalent
if value.unit.is_equivalent(unit):
var = value
else:
err_msg = ("Quantity expected to have units of {} instead was "
"passed units {} which is not convertable".format(
unit, value.unit))
raise ValueError(err_msg)
return var
@property
def name(self):
"""
name: str
The name of the FRB object.
"""
return self._name
@name.setter
def name(self, value):
if isinstance(value, str):
self._name = value
else:
self._name = str(value)
@property
def dm(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed dispersion measure of the FRB. This is without
Milky Way or host galaxy subtraction.
"""
return self._dm
@dm.setter
def dm(self, value):
self._dm = self._set_value_units(value,
unit=u.pc * u.cm**-3,
non_negative=True)
@property
def dm_galaxy(self):
"""
:obj:`astropy.units.Quantity` or None:
The galactic component of the dispersion measure. This is
quantity is calculated using :meth:`calc_dm_galaxy`.
"""
return self._dm_galaxy
@dm_galaxy.setter
def dm_galaxy(self, value):
self._dm_galaxy = self._set_value_units(value,
unit=u.pc * u.cm**-3,
non_negative=True)
@property
def dm_excess(self):
"""
:obj:`astropy.units.Quantity` or None:
The dispersion measure with the Milky Way component
subtracted. This value approximates the dispersion measure
of the intergalatic medium by assuming that the host galaxy
contributes zero to the observed dispersion measure. This
quantity is calculated using :meth:`calc_dm_excess`.
"""
return self._dm_excess
@dm_excess.setter
def dm_excess(self, value):
self._dm_excess = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def dm_host_est(self):
"""
:obj:`astropy.units.Quantity` or None:
The estimated dispersion measure from the FRB host galaxy.
"""
return self._dm_host_est
@dm_host_est.setter
def dm_host_est(self, value):
self._dm_host_est = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def dm_host_loc(self):
"""
:obj:`astropy.units.Quantity` or None:
The dispersion measure from a localised FRB host galaxy.
"""
return u.Quantity(self._dm_host_loc, u.pc * u.cm**-3)
@dm_host_loc.setter
def dm_host_loc(self, value):
self._dm_host_loc = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def dm_index(self):
"""
:obj:`astropy.units.Quantity` or None:
The dispersion measure index of the burst.
"""
return self._dm_index
@dm_index.setter
def dm_index(self, value):
self._dm_index = self._set_value_units(value)
@property
def z(self):
"""
:obj:`astropy.units.Quantity` or None:
The estimated redshift of the burst. By default this
assumes that the entire :attr:`dm_excess` arrives from the
IGM and the host galaxy of the FRB and any surrounding
material contribute nothing to the total DM. This should be
taken as an upper limit to the bursts true redshift. To
provide an estimate of the DM contribution due to he host
galaxy, set :attr:`dm_host_est` to a non-zero value and use
``subract_host=True`` when calling :meth:`calc_redshift()`.
"""
return self._z
@z.setter
def z(self, value):
self._z = self._set_value_units(value)
@property
def z_host(self):
"""
:obj:`astropy.units.Quantity` or None:
The redshift of the localised FRB host galaxy. Note that
this an observed quantity, not the estimated redshift
:attr:`z` calculated with :meth:`calc_redshift()`.
"""
return self._z_host
@z_host.setter
def z_host(self, value):
self._z_host = self._set_value_units(value)
@property
def scatt_index(self):
"""
:obj:`astropy.units.Quantity` or None:
The scattering index of the burst.
"""
return self._scatt_index
@scatt_index.setter
def scatt_index(self, value):
self._scatt_index = self._set_value_units(value)
@property
def width(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed width of the pulse.
"""
return self._width
@width.setter
def width(self, value):
self._width = self._set_value_units(value, u.ms, non_negative=True)
@property
def peak_flux(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed peak flux density of the FRB.
"""
return self._peak_flux
@peak_flux.setter
def peak_flux(self, value):
self._peak_flux = self._set_value_units(value, u.Jy, non_negative=True)
@property
def fluence(self):
"""
:obj:`astropy.units.Quantity` or None:
The observed fluence of the FRB. This is calculated from
:meth:`calc_fluence`.
"""
return self._fluence
@fluence.setter
def fluence(self, value):
self._fluence = self._set_value_units(value,
u.Jy * u.ms,
non_negative=True)
@property
def obs_bandwidth(self):
"""
:obj:`astropy.units.Quantity` or None:
The observing bandwidth of the FRB.
"""
return self._obs_bandwidth
@obs_bandwidth.setter
def obs_bandwidth(self, value):
self._obs_bandwidth = self._set_value_units(value,
u.MHz,
non_negative=True)
@property
def obs_freq_central(self):
"""
:obj:`astropy.units.Quantity` or None:
The central observing frequency of the FRB.
"""
return self._obs_freq_central
@obs_freq_central.setter
def obs_freq_central(self, value):
self._obs_freq_central = self._set_value_units(value,
u.MHz,
non_negative=True)
@property
def raj(self):
"""
:obj:`astropy.coordinates.Longitude` or None:
The right accension in J2000 coordinates of the best
estimate of the FRB position. This is given in the IRCS
frame.
"""
return self._raj
@raj.setter
def raj(self, value):
if value is None:
self._raj = None
else:
self._raj = coord.angles.Longitude(value, u.hourangle)
@property
def decj(self):
"""
:obj:`astropy.coordinates.Latitude` or None:
The declination in J2000 coordinates of the best estimate
of the FRB position. This is given in the IRCS frame.
"""
return self._decj
@decj.setter
def decj(self, value):
if value is None:
self._decj = None
else:
self._decj = coord.angles.Latitude(value, u.deg)
@property
def gl(self):
"""
:obj:`astropy.coordinates.Longitude` or None:
The longitude in galactic coordinates of the best estimate
of the FRB position.
"""
return self._gl
@gl.setter
def gl(self, value):
if value is None:
self._gl = None
else:
self._gl = coord.angles.Longitude(value, u.deg)
@property
def gb(self):
"""
:obj:`astropy.coordinates.Latitude` or None:
The latitude in galactic coordinates of the best estimate
of the FRB position.
"""
return self._gb
@gb.setter
def gb(self, value):
if value is None:
self._gb = None
else:
self._gb = coord.angles.Latitude(value, u.deg)
@property
def skycoords(self):
"""
:obj:`astropy.coordinates.SkyCoord` or None:
The skycoords of the FRB. This is calculated from either
(:attr:`raj`, :attr:`decj`) or (:attr:`gl`, :attr:`gb`)
using :meth:`calc_skycoords`.
"""
return self._skycoords
@skycoords.setter
def skycoords(self, value):
if value is None:
self._skycoords = None
else:
self._skycoords = SkyCoord(value)
@property
def dm_igm(self):
"""
:obj:`astropy.units.Quantity` or None:
The estimated disperison measure from the IGM. This can be
calculated for a FRB for which the redshift of its host
galaxy is known. This value is determined using
:meth:`calc_dm_igm`.
"""
return self._dm_igm
@dm_igm.setter
def dm_igm(self, value):
self._dm_igm = self._set_value_units(value,
u.pc * u.cm**-3,
non_negative=True)
@property
def utc(self):
"""
:obj:`astropy.time.Time` or None
The UTC time of the burst.
"""
return self._utc
@utc.setter
def utc(self, value):
if value is None:
self._utc = None
else:
self._utc = Time(value, format='isot', scale='utc')
@property
def snr(self):
"""
:obj:`astropy.units.Quantity`:
The signal-to-noise ratio of the burst.
"""
return self._snr
@snr.setter
def snr(self, value):
self._snr = self._set_value_units(value, non_negative=True)
@property
def cosmology(self):
"""
str or None:
The cosmology used to calculate redshift.
"""
return self._cosmology
@cosmology.setter
def cosmology(self, value):
if isinstance(value, str):
self._cosmology = value
else:
self._cosmology = str(value)
@property
def method(self):
"""
str or None:
The method used to calculate redshift.
"""
return self._method
@method.setter
def method(self, value):
if isinstance(value, str):
self._method = value
else:
self._method = str(value)
fig, ax = plt.subplots(1, 1, constrained_layout=True)
extents = [0, 3, 5, -1]
im = ax.imshow(data["arr_0"].T,
aspect=3 / 5,
cmap="magma",
interpolation='none',
extent=extents)
ax.set_ylim(1, 4)
ax.set_xlim(0, 3)
ax.set_xlabel(r"Redshift")
ax.set_ylabel(r"$\rm{log\left(DM\right)}\ \left[pc\ cm^{-3}\right]$")
dm_vals = 10**np.linspace(1, 4, 1000)
method_list = methods.available_methods()
colours = ["#66c2a5", "#e7298a", "#8da0cb"]
label = [r"$\rm{Ioka\ 2003}$", r"$\rm{Inoue\ 2004}$", r"$\rm{Zhang\ 2018}$"]
lstyle = ["-", "--", "-."]
for j, method in enumerate(method_list):
z_vals = np.zeros(len(dm_vals))
cosmology = 'Planck18'
table_name = "".join(["_".join([method, cosmology]), ".npz"])
lookup_table = table.load(table_name)
for i, dm in enumerate(dm_vals):
z_vals[i] = table.get_z_from_table(dm, lookup_table)
ax.plot(z_vals,
def create(method, output_dir='data', filename=None, zmin=0, zmax=20,
num_samples=10000, **method_kwargs):
"""
Creates lookup table
which can be read
in using :func:`~fruitbat.table.load`.
Parameters
----------
method : str
The DM-redshift relation to assume when creating the table.
output_dir : str, optional
The path of the output directory. If ``output_dir = 'data'``,
then created table will created in the same directory with
the builtin tables and will be found when using functions
such as :meth:`~fruitbat._frb.calc_redshift()`.
Default: 'data'
filename : str, optional
The output filename. If ``name=None`` then the filename will
become custom_method. Default: *None*
zmin : int or float, optional
The minimum redshift in the table. Default: 0
zmax : int or float, optional
The maximum redshift in the table. Default: 20
num_samples : int, optional
The number of sample dispersion measure and redshifts.
Default: 10000
Keyword Arguments
-----------------
cosmo : An instance of :obj:`astropy.cosmology`, optional
The cosmology to assume when calculating the outputs of the
table. Required when creating new tables of ``'Ioka2003'``,
``'Inoue2004'``, ``'Zhang2018'``.
free_elec : float or int, optional
The amount of free electrons per proton mass in the Universe.
This applies when using ``'Zhang2018'``. Must be between 0
and 1. Default: 0.875.
f_igm : float or int, optional
The fraction of baryons in the intergalactic medium. This
applies when using ``'Zhang2018'``. Must be between 0 and 1.
Default: 0.83
Returns
-------
string
The path to the generated hdf5 file containing the table data.
Generates
---------
A hdf5 file containing datasets for `'DM'` and 'z'`.
Example
-------
>>> def simple_dm(z):
dm = 1200 * z
return dm
>>> fruitbat.add_method("simple_dm", simple_dm)
>>> fruitbat.table.create("simple_dm")
>>> frb = fruitbat.Frb(1200)
>>> frb.calc_redshift(method="simple_dm")
<Quantity 1.>
"""
if method not in available_methods():
err_msg = ("{} is not a valid method."
"The currently defined methods "
"are: {}".format(method, available_methods()))
raise ValueError(err_msg)
# The filename that the user provides can not be one of these as it would
# over write the built in datasets.
restricted_filenames = set([
utils.get_path_to_file_from_here("Ioka2003.hdf5", subdirs=["data"]),
utils.get_path_to_file_from_here("Inoue2004.hdf5", subdirs=["data"]),
utils.get_path_to_file_from_here("Zhang2018.hdf5", subdirs=["data"]),
utils.get_path_to_file_from_here("Batten2020.hdf5", subdirs=["data"]),
])
# Generate the output filename.
if (filename is not None) and (filename not in restricted_filenames):
filename = "{}.hdf5".format(filename)
else:
filename = "{}.hdf5".format(method)
# Generate the DM and z values for the method
dm_function = method_functions()[method]
z_vals = np.linspace(zmin, zmax, num_samples)
dm_vals = np.array([dm_function(z, **method_kwargs) for z in z_vals])
if output_dir == "data":
output_file = utils.get_path_to_file_from_here(filename, subdirs=["data"])
else:
output_file = os.path.join(output_dir, filename)
with h5py.File(output_file, "w") as new_table:
new_table.create_group("Header")
if "cosmo" in method_kwargs:
cosmo = method_kwargs["cosmo"]
add_cosmo_params_to_dataset_attrs = True
# Use a default cosmology name if the prodived one doesnt have a name
if not cosmo.name:
cosmo.name = "cosmology"
dataset_group_name = cosmo.name
else:
add_cosmo_params_to_dataset_attrs = False
dataset_group_name = method
new_table.create_group(dataset_group_name)
new_table[dataset_group_name].create_dataset("DM", data=dm_vals, dtype=np.float)
new_table[dataset_group_name]["DM"].attrs["Units"] = "pc cm**-3"
new_table[dataset_group_name]["DM"].attrs["VarDesc"] = "Dispersion Measure"
new_table[dataset_group_name].create_dataset("z", data=z_vals, dtype=np.float)
new_table[dataset_group_name]["z"].attrs["Units"] = "Dimensionless"
new_table[dataset_group_name]["z"].attrs["VarDesc"] = "Redshift"
if add_cosmo_params_to_dataset_attrs:
new_table[dataset_group_name].attrs["Flat"] = True
new_table[dataset_group_name].attrs["H0"] = cosmo.H0.value
new_table[dataset_group_name].attrs["OmegaBaryon0"] = cosmo.Ob0
new_table[dataset_group_name].attrs["OmegaLambda0"] = cosmo.Ode0
new_table[dataset_group_name].attrs["OmegaMatter0"] = cosmo.Om0
new_table[dataset_group_name].attrs["t0"] = cosmo.age(0).value
return output_file
def method_comparison(filename=None, extension="png", usetex=False,
passed_ax=None, **kwargs):
"""
Create a plot comparing how estimated redshift changes as a
function of dispersion measure for each DM-z relation.
Parameters
----------
filename: string or None, optional
The filename of the saved figure. Default: *None*
extension: string, optional
The format to save the figure. e.g "png", "pdf", "eps", etc...
Default: "png"
usetex: bool, optional
Use LaTeX for for fonts.
passed_ax: or None, optional
Generates
---------
A figure displaying how estimated redshift changes as a function of
dispersion measure for each of the different cosmologies.
"""
set_rc_params(usetex)
if passed_ax:
ax = passed_ax
else:
fig = plt.figure(figsize=(8, 8), constrained_layout=True)
ax = fig.add_subplot(111)
method_list = methods.available_methods()
dm_vals = np.linspace(0, 3000, 1000)
colours = ["#1b9e77", "#d95f02", "#7570b3"]
label = [r"$\rm{Ioka 2003}$", r"$\rm{Inoue 2004}$", r"$\rm{Zhang 2018}$"]
for j, method in enumerate(method_list):
z_vals = np.zeros(len(dm_vals))
if 'cosmology' in kwargs:
cosmology = kwargs['cosmology']
else:
cosmology = 'Planck18'
table_name = "".join(["_".join([method, cosmology]), ".npz"])
lookup_table = table.load(table_name)
for i, dm in enumerate(dm_vals):
z_vals[i] = table.get_z_from_table(dm, lookup_table)
ax.plot(dm_vals, z_vals, colours[j], label=label[j], **kwargs)
if not passed_ax:
ax.set_ylabel(r"$\rm{Redshift}$")
ax.set_xlabel(r"$\rm{DM\ \left[pc \ cm^{-3}\right]}$")
ax.legend(loc='lower right', frameon=False)
if filename is not None:
plt.savefig(".".join([filename, extension]))
if passed_ax:
return ax
else:
return fig