# -*- mode: python; coding: utf-8 -*
# Copyright (c) 2019 Radio Astronomy Software Group
# Licensed under the 3-clause BSD License
"""Utility methods."""
import os
import astropy.units as units
import erfa
import numpy as np
from astropy.coordinates import Angle
from astropy.coordinates.builtin_frames.utils import get_jd12
from astropy.time import Time
from astropy.units import Quantity
from pyradiosky.data import DATA_PATH as SKY_DATA_PATH
# The frame radio astronomers call the apparent or current epoch is the
# "true equator & equinox" frame, notated E_upsilon in the USNO circular
# astropy doesn't have this frame but it's pretty easy to adapt the CIRS frame
# by modifying the ra to reflect the difference between
# GAST (Grenwich Apparent Sidereal Time) and the earth rotation angle (theta)
def _tee_to_cirs_ra(tee_ra, time):
"""
Convert from the true equator & equinox frame to the CIRS frame.
The frame radio astronomers call the apparent or current epoch is the
"true equator & equinox" frame, notated E_upsilon in the USNO circular
astropy doesn't have this frame but it's pretty easy to adapt the CIRS frame
by modifying the ra to reflect the difference between
GAST (Grenwich Apparent Sidereal Time) and the earth rotation angle (theta)
Parameters
----------
tee_ra : :class:`astropy.Angle`
Current epoch RA (RA in the true equator and equinox frame).
time : :class:`astropy.Time`
Time object for the epoch of the `tee_ra`.
"""
era = erfa.era00(*get_jd12(time, "ut1"))
theta_earth = Angle(era, unit="rad")
assert isinstance(time, Time)
assert isinstance(tee_ra, Angle)
gast = time.sidereal_time("apparent", longitude=0)
cirs_ra = tee_ra - (gast - theta_earth)
return cirs_ra
def _cirs_to_tee_ra(cirs_ra, time):
"""
Convert from CIRS frame to the true equator & equinox frame.
The frame radio astronomers call the apparent or current epoch is the
"true equator & equinox" frame, notated E_upsilon in the USNO circular
astropy doesn't have this frame but it's pretty easy to adapt the CIRS frame
by modifying the ra to reflect the difference between
GAST (Grenwich Apparent Sidereal Time) and the earth rotation angle (theta)
Parameters
----------
cirs_ra : :class:`astropy.Angle`
CIRS RA.
time : :class:`astropy.Time`
Time object for time to convert to the "true equator & equinox" frame.
"""
era = erfa.era00(*get_jd12(time, "ut1"))
theta_earth = Angle(era, unit="rad")
assert isinstance(time, Time)
assert isinstance(cirs_ra, Angle)
gast = time.sidereal_time("apparent", longitude=0)
tee_ra = cirs_ra + (gast - theta_earth)
return tee_ra
[docs]def stokes_to_coherency(stokes_arr):
"""
Convert Stokes array to coherency matrix.
Parameters
----------
stokes_arr : Quantity
Array of stokes parameters in order [I, Q, U, V], shape(4,) or (4, Nfreqs, Ncomponents).
Returns
-------
coherency matrix : array of float
Array of coherencies, shape (2, 2) or (2, 2, Nfreqs, Ncomponents)
"""
if not isinstance(stokes_arr, Quantity):
raise ValueError("stokes_arr must be an astropy Quantity.")
initial_shape = stokes_arr.shape
if initial_shape[0] != 4:
raise ValueError("First dimension of stokes_vector must be length 4.")
if stokes_arr.size == 4 and len(initial_shape) == 1:
stokes_arr = stokes_arr[:, np.newaxis, np.newaxis]
coherency = (
0.5
* np.array(
[
[
stokes_arr[0, :, :] + stokes_arr[1, :, :],
stokes_arr[2, :, :] - 1j * stokes_arr[3, :, :],
],
[
stokes_arr[2, :, :] + 1j * stokes_arr[3, :, :],
stokes_arr[0, :, :] - stokes_arr[1, :, :],
],
]
)
* stokes_arr.unit
)
if stokes_arr.size == 4 and len(initial_shape) == 1:
coherency = coherency.squeeze()
return coherency
[docs]def coherency_to_stokes(coherency_matrix):
"""
Convert coherency matrix to vector of 4 Stokes parameter in order [I, Q, U, V].
Parameters
----------
coherency matrix : Quantity
Array of coherencies, shape (2, 2) or (2, 2, Ncomponents)
Returns
-------
stokes_arr : array of float
Array of stokes parameters, shape(4,) or (4, Ncomponents)
"""
if not isinstance(coherency_matrix, Quantity):
raise ValueError("coherency_matrix must be an astropy Quantity.")
initial_shape = coherency_matrix.shape
if len(initial_shape) < 2 or initial_shape[0] != 2 or initial_shape[1] != 2:
raise ValueError("First two dimensions of coherency_matrix must be length 2.")
if coherency_matrix.size == 4 and len(initial_shape) == 2:
coherency_matrix = coherency_matrix[:, :, np.newaxis]
stokes = (
np.array(
[
coherency_matrix[0, 0, :] + coherency_matrix[1, 1, :],
coherency_matrix[0, 0, :] - coherency_matrix[1, 1, :],
coherency_matrix[0, 1, :] + coherency_matrix[1, 0, :],
-(coherency_matrix[0, 1, :] - coherency_matrix[1, 0, :]).imag,
]
).real
* coherency_matrix.unit
)
if coherency_matrix.size == 4 and len(initial_shape) == 2:
stokes = stokes.squeeze()
return stokes
[docs]def jy_to_ksr(freqs):
"""
Calculate multiplicative factors to convert [Jy] to [K sr].
Parameters
----------
freqs : :class:`astropy.Quantity` or array_like of float (Deprecated)
Frequencies, assumed to be in Hz if not a Quantity.
Returns
-------
Quantity
Conversion factor(s) to go from [Jy] to [K sr]. Shape equal to shape of freqs.
"""
freqs = np.atleast_1d(freqs)
if not isinstance(freqs, Quantity):
freqs = freqs * units.Hz
equiv = units.brightness_temperature(freqs, beam_area=1 * units.sr)
conv_factor = (1 * units.Jy).to(units.K, equivalencies=equiv) * units.sr / units.Jy
return conv_factor
[docs]def download_gleam(
path=".", filename="gleam.vot", overwrite=False, row_limit=None, for_testing=False
):
"""
Download the GLEAM vot table from Vizier.
Parameters
----------
path : str
Folder location to save catalog to.
filename : str
Filename to save catalog to.
overwrite : bool
Option to download the file even if it already exists.
row_limit : int, optional
Max number of rows (sources) to download, default is None meaning download all rows.
for_testing : bool
Download a file to use for unit tests. If True, some additional columns are
included, the rows are limited to 50, the path and filename are set to put
the file in the correct location and the overwrite keyword is set to True.
"""
try:
from astroquery.vizier import Vizier
except ImportError as e:
raise ImportError(
"The astroquery module is required to use the download_gleam function."
) from e
if for_testing: # pragma: no cover
path = SKY_DATA_PATH
filename = "gleam_50srcs.vot"
overwrite = True
row_limit = 50
# We have frequent CI failures with messages like
# "Failed to resolve 'vizier.u-strasbg.fr'"
# Try using a US mirror to see if we have fewer errors
Vizier.VIZIER_SERVER = "vizier.cfa.harvard.edu"
opath = os.path.join(path, filename)
if os.path.exists(opath) and not overwrite:
print(
f"GLEAM already downloaded to {opath}. Set overwrite=True to re-download it."
)
return
# full download is too slow for unit tests
if row_limit is None: # pragma: no cover
Vizier.ROW_LIMIT = -1
else:
Vizier.ROW_LIMIT = row_limit
desired_columns = [
"GLEAM",
"RAJ2000",
"DEJ2000",
"Fintwide",
"e_Fintwide",
"alpha",
"e_alpha",
"chi2",
"Fintfit200",
"e_Fintfit200",
"Fint076",
"Fint084",
"Fint092",
"Fint099",
"Fint107",
"Fint115",
"Fint122",
"Fint130",
"Fint143",
"Fint151",
"Fint158",
"Fint166",
"Fint174",
"Fint181",
"Fint189",
"Fint197",
"Fint204",
"Fint212",
"Fint220",
"Fint227",
"e_Fint076",
"e_Fint084",
"e_Fint092",
"e_Fint099",
"e_Fint107",
"e_Fint115",
"e_Fint122",
"e_Fint130",
"e_Fint143",
"e_Fint151",
"e_Fint158",
"e_Fint166",
"e_Fint174",
"e_Fint181",
"e_Fint189",
"e_Fint197",
"e_Fint204",
"e_Fint212",
"e_Fint220",
"e_Fint227",
]
if for_testing: # pragma: no cover
desired_columns.extend(["Fpwide", "e_Fp076"])
# There is a bug that causes astroquery to only download the first 14-16 specified
# columns if you pass it a long list of columns.
# The workaround is to download all columns and then remove the ones we don't need.
# This is not ideal because it substantially increases the download time, but seems
# to be required for now.
Vizier.columns = ["all"]
catname = "VIII/100/gleamegc"
table = Vizier.get_catalogs(catname)[0]
for col in desired_columns:
assert col in table.colnames, f"column {col} not in downloaded table."
columns_to_remove = list(set(table.colnames) - set(desired_columns))
table.remove_columns(columns_to_remove)
table.write(opath, format="votable", overwrite=overwrite)
print("GLEAM catalog downloaded and saved to " + opath)