def test_dist_to_dm():
""" Test that astropy units / angles work with dist_to_dm """
a = pygedm.dist_to_dm(204, -6.5, 200, method='ne2001')
b = pygedm.dist_to_dm(Angle(204, unit='degree'), Angle(-6.5, unit='degree'), 200, method='ne2001')
c = pygedm.dist_to_dm(204, -6.5, 200 * Unit('pc'), method='ne2001')
assert a[0] == b[0] == c[0]
assert a[1] == b[1] == c[1]
def test_tau_sc_nu():
""" Test that tau_sc changes with nu """
dm, tau_sc = pygedm.dist_to_dm(0, 0, 100, method='ymw16', nu=1)
dm_, tau_sc_ = pygedm.dist_to_dm(0, 0, 100, method='ymw16', nu=1000*u.MHz)
assert dm == dm_
assert tau_sc == tau_sc_
dm, tau_sc = pygedm.dist_to_dm(0, 0, 100, method='ne2001', nu=1)
dm_, tau_sc_ = pygedm.dist_to_dm(0, 0, 100, method='ne2001', nu=1000*u.MHz)
assert dm == dm_
assert tau_sc == tau_sc_
dist, tau_sc = pygedm.dist_to_dm(0, 0, 100, method='ymw16', nu=1)
dist_, tau_sc_ = pygedm.dist_to_dm(0, 0, 100, method='ymw16', nu=1000*u.MHz)
assert dist == dist_
assert tau_sc == tau_sc_
dist, tau_sc = pygedm.dist_to_dm(0, 0, 100, method='ne2001', nu=1)
dist_, tau_sc_ = pygedm.dist_to_dm(0, 0, 100, method='ne2001', nu=1000*u.MHz)
assert dist == dist_
assert tau_sc == tau_sc_
dm, tau_sc_1GHz = pygedm.dm_to_dist(0, 0, 1000, method='ymw16', nu=1.0)
dm, tau_sc_100MHz = pygedm.dm_to_dist(0, 0, 1000, method='ymw16', nu=0.1)
assert np.isclose(tau_sc_1GHz.value, 0.31681767)
assert np.isclose(tau_sc_100MHz.value, 3168.17671061)
assert np.isclose((0.1/1.0)**(-4) * tau_sc_1GHz.value, tau_sc_100MHz.value)
dm, tau_sc_1GHz = pygedm.dm_to_dist(0, 0, 1000, method='ne2001', nu=1.0)
dm, tau_sc_100MHz = pygedm.dm_to_dist(0, 0, 1000, method='ne2001', nu=0.1)
assert np.isclose(tau_sc_1GHz.value, 198.57881596)
assert np.isclose(tau_sc_100MHz.value, 4988074.33385041)
def test_raises():
""" Test that IGM mode FAILS as expected """
with pytest.raises(RuntimeError):
pygedm.dm_to_dist(100, 10, 100, method='ymw1066')
with pytest.raises(RuntimeError):
pygedm.dist_to_dm(100, 10, 100, method='ne2020')
with pytest.raises(RuntimeError):
pygedm.calculate_electron_density_xyz(100, 10, 100, method='tc93')
with pytest.raises(RuntimeError):
pygedm.calculate_electron_density_lbr(100,
10,
100,
method='ymwPaleolithic')
with pytest.raises(RuntimeError):
pygedm.dist_to_dm(100, 10, 100, mode='igm', method='ne2001')
with pytest.raises(RuntimeError):
pygedm.convert_lbr_to_xyz(0, 0, 0, method='chicken')
def test_igm():
""" Test that IGM mode works as expected
Note: tested against YMW16 code with:
# CMD: ./ ymw16 -d data -v IGM 204 -6.5 2000 100 1
# OUTPUT: DM_Gal: 252.05 DM_MC: 0.00 DM_IGM: 1647.95 DM_Host: 100.00
# z: 2.311 Dist: 5336.4 log(tau_sc): -2.218
"""
dist, tau = pygedm.dm_to_dist(204, -6.5, 2000, dm_host=100, mode='igm')
assert np.isclose(dist.value, 5336.4, rtol=0.1)
assert np.isclose(np.log10(tau.value), -2.218, rtol=0.1)
dm, tau = pygedm.dist_to_dm(204, -6.5, 5336.4, mode='igm')
dm_total = dm.value + 252.05 + 100 # Add galactic and host contribution
assert np.isclose(dm_total, 2000, rtol=0.1)
dm, tau = pygedm.dist_to_dm(204, -6.5, 5336.4 * u.Mpc, mode='igm')
dm_total = dm.value + 252.05 + 100 # Add galactic and host contribution
assert np.isclose(dm_total, 2000, rtol=0.1)
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", "ne2001"]
if model.lower() in YMW16_options:
# Since the GEDMs only give a dispersion measure out to a
# distance within the galaxy, to get the entire DM contribution of the
# galaxy we need to integrate across the full Galaxy
max_galaxy_dist = 30 * u.kpc # 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 = pygedm.dist_to_dm(self._skycoords.galactic.l,
self._skycoords.galactic.b,
max_galaxy_dist,
method=model)
self.dm_galaxy = dm_galaxy.value
self.calc_dm_excess()
return self.dm_galaxy
def test_magellanic_cloud():
""" Test that MC mode agrees with YMW16
Note: tested against YMW16 code with:
CMD: ./ymw16 -d data -v MC 280.46 -32.88 50000 2
OUTPUT: MC: gl= 280.460 gb= -32.880 Dist= 50000.0
dtest=50000.000000, nstep=10000.000000, dstep=5.000000
DM_Gal: 58.03 DM_MC: 78.87 DM: 136.90 log(tau_sc): -5.399
"""
dm, tau = pygedm.dist_to_dm(280.46, -32.88, 50000, mode='mc')
assert np.isclose(dm.value, 136.90)
assert np.isclose(np.log10(tau.value), -5.399, rtol=0.1)
def test_basic():
""" Basic tests of YMW16 model
Note: tested against online NE2001 interface
https://www.nrl.navy.mil/rsd/RORF/ne2001/
"""
# No access to actual model via web interface
#a = pygedm.calculate_electron_density_xyz(1, 2, 3)
#assert np.isclose(a.value, 5.220655, atol=0.0001)
# FRB180301 value
dm, tau = pygedm.dist_to_dm(204, -6.5, 25*u.kpc, method='ne2001')
assert np.isclose(dm.value, 150.80, atol=0.01)
# Loop through distances and check round trip
for dist in (10.*u.pc, 100.*u.pc, 1000.*u.pc):
dm, tau = pygedm.dist_to_dm(0, 0, dist, method='ne2001')
dist_out, tau = pygedm.dm_to_dist(0, 0, dm, method='ne2001')
print(dist, dm, dist_out)
assert np.isclose(dist_out.to('pc').value, dist.to('pc').value, rtol=0.1)
def test_basic():
""" Basic tests of YMW16 model
Note: tested against online YMW16 interface
http://www.atnf.csiro.au/research/pulsar/ymw16/index.php
"""
a = pygedm.calculate_electron_density_xyz(1, 2, 3)
assert np.isclose(a.value, 5.220655, atol=0.0001)
a = pygedm.calculate_electron_density_lbr(0, 0, 4000)
assert np.isclose(a.value, 0.388407, atol=0.0001)
# FRB180301 value
dm, tau = pygedm.dist_to_dm(204, -6.5, 25000)
assert np.isclose(dm.value, 252.0501, atol=0.01)
# Loop through distances and check round trip
for dist in (10., 100., 1000.):
dm, tau = pygedm.dist_to_dm(0, 0, dist)
dist_out, tau = pygedm.dm_to_dist(0, 0, dm.value)
assert np.isclose(dist_out.value, dist, rtol=0.1)
def test_frb_calc_dm_galaxy(self):
dm_galaxy = self.frb_raj_decj.calc_dm_galaxy()
dm_pymw16, t_sc_pymw16 = pygedm.dist_to_dm(
self.frb_raj_decj.skycoords.galactic.l,
self.frb_raj_decj.skycoords.galactic.b, 30 * u.kpc)
assert np.isclose(dm_galaxy.value, dm_pymw16.value)
dm_galaxy = self.frb_raj_decj.calc_dm_galaxy(model='ne2001')
dm_ne2001, t_sc_ne2001 = pygedm.dist_to_dm(
self.frb_raj_decj.skycoords.galactic.l,
self.frb_raj_decj.skycoords.galactic.b,
30 * u.kpc,
method='ne2001')
assert np.isclose(dm_galaxy.value, dm_ne2001.value)
dm_galaxy = self.frb_raj_decj.calc_dm_galaxy(model='ymw16')
dm_pymw16, t_sc_pymw16 = pygedm.dist_to_dm(
self.frb_raj_decj.skycoords.galactic.l,
self.frb_raj_decj.skycoords.galactic.b,
30 * u.kpc,
method='ymw16')
assert np.isclose(dm_galaxy.value, dm_pymw16.value)
import pygedm
print("\n--- DM to dist ---")
print("YMW16:", pygedm.dm_to_dist(100, 0, 250, dm_host=0, method='ymw16'))
print("NE2001:", pygedm.dm_to_dist(100, 0, 250, dm_host=0, method='ne2001'))
print("\n--- dist to DM ---")
print("YMW16:", pygedm.dist_to_dm(100, 0, 250, method='ymw16'))
print("NE2001:", pygedm.dist_to_dm(100, 0, 250, method='ne2001'))
print("\n--- Electron density ---")
print("YMW16:", pygedm.calculate_electron_density_xyz(0, 0, 0, method='ymw16'))
print("NE2001:", pygedm.calculate_electron_density_xyz(0, 0, 0, method='ne2001'))
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 find_delta_dm(transient_type,
transient_data,
ism_model,
b_val,
mc_deg=5,
save_df=True):
"""
Find pulsar/FRB DMs corrected for by the MW ISM DM and remove observations in complex DM regions.
Returns array of DMs
FRB data is available as a csv in the FRBs/FRB/frb/data/FRBs repo (FRB catalogue [Petroff et al. 2017])
Pulsar data is avaiable as a csv in the FRBs/pulsars/pulsars/data/atnf_cat repo (v1.61 ATNF pulsar catalogue [Manchester et al. 2005])
Arguments:
transient_type (str):
Accepts 'frb' or 'pulsar'.
transient_data (str):
Path to data (in .csv format).
ism_model (str):
Model used to calculated the MW halo DM.
Accepts 'ymw16' [Yao et al. 2017] or 'ne2001' [Cordes & Lazio 2003].
b_val (int):
Galactic latitude considered (b>b_val, b<-b_val).
mc_deg (int):
Number of degrees from Magellanic clouds within which transients are removed.
save_df (str, optional):
Save transient DMs and coords to csv.
Outputs:
"""
# Sort data and get coords
if transient_type == 'frb':
transcat_df = pd.read_csv(transient_data,
skiprows=1,
usecols=[0, 5, 6, 7],
names=['Name', 'l', 'b', 'dm'])
transcat_df['dm'] = transcat_df['dm'].str.split('&').str[0].astype(
float).values
coords = SkyCoord(l=transcat_df['l'],
b=transcat_df['b'],
unit=(u.degree),
frame=Galactic)
elif transient_type == 'pulsar':
transcat_df = pd.read_csv(
transient_data,
skiprows=2,
usecols=[1, 2, 3, 9, 10],
names=['Name', 'Pref', 'dm', 'RAJD', 'DECJD'])
transcat_df = transcat_df[~transcat_df['dm'].str.
contains('*', regex=False)].reset_index(
drop=True)
transcat_df['dm'] = transcat_df['dm'].astype(float)
c_icrs = SkyCoord(ra=transcat_df['RAJD'],
dec=transcat_df['DECJD'],
unit=(u.degree),
frame='icrs')
transcat_df['l'] = pd.DataFrame(c_icrs.galactic.l.value)
transcat_df['b'] = pd.DataFrame(c_icrs.galactic.b.value)
coords = SkyCoord(l=transcat_df['l'],
b=transcat_df['b'],
unit=(u.degree),
frame=Galactic)
# Find transients in line of sight of MCs
logging.info('Removing transients near Magellanic clouds...')
# LMC
lmc_distance = 50 * u.kpc
lmc_coord = SkyCoord('J052334.6-694522',
unit=(u.hourangle, u.deg),
distance=lmc_distance)
close_to_lmc = lmc_coord.separation(coords) < mc_deg * u.deg
lmc_trans = list(transcat_df[close_to_lmc]['Name'])
# SMC
smc_distance = 61 * u.kpc
smc_coord = SkyCoord('J005238.0-724801',
unit=(u.hourangle, u.deg),
distance=smc_distance)
close_to_smc = smc_coord.separation(coords) < mc_deg * u.deg
smc_trans = list(transcat_df[close_to_smc]['Name'])
transcat_df = transcat_df[~transcat_df['Name'].
isin(lmc_trans)].reset_index(drop=True)
transcat_df = transcat_df[~transcat_df['Name'].
isin(smc_trans)].reset_index(drop=True)
if transient_type == 'pulsar':
transcat_df = transcat_df[~transcat_df['Pref'].str.
contains('mfl+06', regex=False)].reset_index(
drop=True)
elif transient_type == 'frb':
pass
# Remove transients with low Galactic lattitudes
logging.info('Removing transients with low Galactic lattitudes...')
transcat_df = pd.concat([
transcat_df[transcat_df.b > b_val], transcat_df[transcat_df.b < -b_val]
],
ignore_index=True)
# ISM model
logging.info('Correcting transient DMs for ISM...')
trans_ism = []
if ism_model == 'ymw16':
for i in range(len(transcat_df['dm'])):
trans_ism_ = pygedm.dist_to_dm(transcat_df['l'].iloc[i],
transcat_df['b'].iloc[i],
100000)[0].value
trans_ism = np.append(trans_ism, trans_ism_)
elif ism_model == 'ne2001':
for i in range(len(transcat_df['dm'])):
trans_ism_ = ne.DM(transcat_df['l'].iloc[i],
transcat_df['b'].iloc[i], 100.).value
trans_ism = np.append(trans_ism, trans_ism_)
transcat_df['trans_ism'] = pd.DataFrame(trans_ism)
transcat_df['deltaDM'] = pd.DataFrame(transcat_df['dm'] -
transcat_df['trans_ism'])
if save_df == True:
transcat_df.to_csv('transient_data/' + transient_type + 'cat_df_' +
ism_model + '_' + str(int(b_val)) + '.csv')
logging.info('Transient data saved to csv.')
else:
pass
return np.array(transcat_df['deltaDM'])
