uv.Nbls = 1
uv.Ntimes = Ntimes
uv.spw_array = [0]
uv.Nfreqs = Nfreqs
uv.freq_array = freqs[np.newaxis, :]
uv.Nblts = uv.Ntimes * uv.Nbls
uv.ant_1_array = np.zeros(uv.Nblts, dtype=int)
uv.ant_2_array = np.ones(uv.Nblts, dtype=int)
uv.baseline_array = uv.antnums_to_baseline(uv.ant_1_array, uv.ant_2_array)
uv.time_array = time_arr
uv.Npols = 1
uv.polarization_array=np.array([1])
uv.Nants_telescope = 2
uv.Nants_data = 2
uv.antenna_positions = uvutils.ECEF_from_ENU(np.stack([ant1_enu, ant2_enu]), latitude, longitude, altitude)
uv.Nspws = 1
uv.antenna_numbers = np.array([0,1])
uv.antenna_names = ['ant0', 'ant1']
#uv.channel_width = np.ones(uv.Nblts) * np.diff(freqs)[0]
uv.channel_width = np.diff(freqs)[0]
uv.integration_time = np.ones(uv.Nblts) * np.diff(time_arr)[0] * 24 * 3600. # Seconds
uv.uvw_array = np.tile(ant1_enu - ant2_enu, uv.Nblts).reshape(uv.Nblts, 3)
uv.history = 'Eorsky simulated'
uv.set_drift()
uv.telescope_name = 'Eorsky gaussian'
uv.instrument = 'simulator'
uv.object_name = 'zenith'
uv.vis_units = 'Jy'
uv.telescope_location_lat_lon_alt_degrees = (latitude, longitude, altitude)
uv.set_lsts_from_time_array()
uv.extra_keywords = {'bsq_int': beam_sq_int[0], 'skysig': sig, 'bm_fwhm' : fwhm, 'nside': Nside}
def apply_bda(
uv, max_decorr, pre_fs_int_time, corr_fov_angle, max_time, corr_int_time=None
):
"""Apply baseline dependent averaging to a UVData object.
For each baseline in the UVData object, the expected decorrelation from
averaging in time is computed. Baselines are averaged together in powers-
of-two until the specified level of decorrelation is reached (rounded down).
Parameters
----------
uv : UVData object
The UVData object to apply BDA to. No changes are made to this object,
and instead a copy is returned.
max_decorr : float
The maximum decorrelation fraction desired in the output object. Must
be between 0 and 1.
pre_fs_int_time : astropy Quantity
The pre-finge-stopping integration time inside of the correlator. The
quantity should be compatible with units of time.
corr_fov_angle : astropy Angle
The opening angle at which the maximum decorrelation is to be
calculated. Because a priori it is not known in which direction the
decorrelation will be largest, the expected decorrelation is computed in
all 4 cardinal directions at `corr_fov_angle` degrees off of zenith,
and the largest one is used. This is a "worst case scenario"
decorrelation.
max_time : astropy Quantity
The maximum amount of time that spectra from different times should be
combined for. The ultimate integration time for a given baseline will be
for max_time or the integration time that is smaller than the specified
decorrelation level, whichever is smaller. The quantity should be
compatible with units of time.
corr_int_time : astropy Quantity, optional
The output time of the correlator. If not specified, the smallest
integration_time in the UVData object is used. If specified, the
quantity should be compatible with units of time.
Returns
-------
uv2 : UVData object
The UVData object with BDA applied.
Raises
------
ValueError
This is raised if the input parameters are not the appropriate type or
in the appropriate range. It is also raised if the input UVData object
is not in drift mode (the BDA code does rephasing within an averaged
set of baselines).
AssertionError
This is raised if the baselines of the UVData object are not time-
ordered.
"""
if not isinstance(uv, UVData):
raise ValueError(
"apply_bda must be passed a UVData object as its first argument"
)
if not isinstance(corr_fov_angle, Angle):
raise ValueError(
"corr_fov_angle must be an Angle object from astropy.coordinates"
)
if not isinstance(pre_fs_int_time, units.Quantity):
raise ValueError("pre_fs_int_time must be an astropy.units.Quantity")
try:
pre_fs_int_time.to(units.s)
except UnitConversionError:
raise ValueError("pre_fs_int_time must be a Quantity with units of time")
if (
corr_fov_angle.to(units.deg).value < 0
or corr_fov_angle.to(units.deg).value > 90
):
raise ValueError("corr_fov_angle must be between 0 and 90 degrees")
if max_decorr < 0 or max_decorr > 1:
raise ValueError("max_decorr must be between 0 and 1")
if not isinstance(max_time, units.Quantity):
raise ValueError("max_time must be an astropy.units.Quantity")
try:
max_time.to(units.s)
except UnitConversionError:
raise ValueError("max_time must be a Quantity with units of time")
if corr_int_time is None:
# assume the correlator integration time is the smallest int_time of the
# UVData object
corr_int_time = np.unique(uv.integration_time)[0] * units.s
else:
if not isinstance(corr_int_time, units.Quantity):
raise ValueError("corr_int_time must be an astropy.units.Quantity")
try:
corr_int_time.to(units.s)
except UnitConversionError:
raise ValueError("corr_int_time must be a Quantity with units of time")
if uv.phase_type != "drift":
raise ValueError("UVData object must be in drift mode to apply BDA")
# get relevant bits of metadata
freq = np.amax(uv.freq_array[0, :]) * units.Hz
chan_width = uv.channel_width * units.Hz
antpos_enu, ants = uv.get_ENU_antpos()
lat, lon, alt = uv.telescope_location_lat_lon_alt
antpos_ecef = uvutils.ECEF_from_ENU(antpos_enu, lat, lon, alt)
telescope_location = EarthLocation.from_geocentric(
uv.telescope_location[0],
uv.telescope_location[1],
uv.telescope_location[2],
unit="m",
)
# make a new UVData object to put BDA baselines in
uv2 = UVData()
# copy over metadata
uv2.Nbls = uv.Nbls
uv2.Nfreqs = uv.Nfreqs
uv2.Npols = uv.Npols
uv2.vis_units = uv.vis_units
uv2.Nspws = uv.Nspws
uv2.spw_array = uv.spw_array
uv2.freq_array = uv.freq_array
uv2.polarization_array = uv.polarization_array
uv2.channel_width = uv.channel_width
uv2.object_name = uv.object_name
uv2.telescope_name = uv.telescope_name
uv2.instrument = uv.instrument
uv2.telescope_location = uv.telescope_location
history = uv.history + " Baseline dependent averaging applied."
uv2.history = history
uv2.Nants_data = uv.Nants_data
uv2.Nants_telescope = uv.Nants_telescope
uv2.antenna_names = uv.antenna_names
uv2.antenna_numbers = uv.antenna_numbers
uv2.x_orientation = uv.x_orientation
uv2.extra_keywords = uv.extra_keywords
uv2.antenna_positions = uv.antenna_positions
uv2.antenna_diameters = uv.antenna_diameters
uv2.gst0 = uv.gst0
uv2.rdate = uv.rdate
uv2.earth_omega = uv.earth_omega
uv2.dut1 = uv.dut1
uv2.timesys = uv.timesys
uv2.uvplane_reference_time = uv.uvplane_reference_time
# initialize place-keeping variables and Nblt-sized metadata
start_index = 0
uv2.Nblts = 0
uv2.uvw_array = np.zeros_like(uv.uvw_array)
uv2.time_array = np.zeros_like(uv.time_array)
uv2.lst_array = np.zeros_like(uv.lst_array)
uv2.ant_1_array = np.zeros_like(uv.ant_1_array)
uv2.ant_2_array = np.zeros_like(uv.ant_2_array)
uv2.baseline_array = np.zeros_like(uv.baseline_array)
uv2.integration_time = np.zeros_like(uv.integration_time)
uv2.data_array = np.zeros_like(uv.data_array)
uv2.flag_array = np.zeros_like(uv.flag_array)
uv2.nsample_array = np.zeros_like(uv.nsample_array)
# iterate over baselines
for key in uv.get_antpairs():
print("averaging baseline ", key)
ind1, ind2, indp = uv._key2inds(key)
if len(ind2) != 0:
raise AssertionError(
"ind2 from _key2inds() is not 0--exiting. This should not happen, "
"please contact the package maintainers."
)
data = uv._smart_slicing(
uv.data_array, ind1, ind2, indp, squeeze="none", force_copy=True
)
flags = uv._smart_slicing(
uv.flag_array, ind1, ind2, indp, squeeze="none", force_copy=True
)
nsamples = uv._smart_slicing(
uv.nsample_array, ind1, ind2, indp, squeeze="none", force_copy=True
)
# get lx and ly for baseline
ant1 = np.where(ants == key[0])[0][0]
ant2 = np.where(ants == key[1])[0][0]
x1, y1, z1 = antpos_ecef[ant1, :]
x2, y2, z2 = antpos_ecef[ant2, :]
lx = np.abs(x2 - x1) * units.m
ly = np.abs(y2 - y1) * units.m
# figure out how many time samples we can combine together
if key[0] == key[1]:
# autocorrelation--don't average
n_two_foldings = 0
else:
n_two_foldings = dc.bda_compression_factor(
max_decorr,
freq,
lx,
ly,
corr_fov_angle,
chan_width,
pre_fs_int_time,
corr_int_time,
)
# convert from max_time to max_samples
max_samples = (max_time / corr_int_time).to(units.dimensionless_unscaled)
max_two_foldings = int(np.floor(np.log2(max_samples)))
n_two_foldings = min(n_two_foldings, max_two_foldings)
n_int = 2 ** (n_two_foldings)
print("averaging {:d} time samples...".format(n_int))
# figure out how many output samples we're going to have
n_in = len(ind1)
n_out = n_in // n_int + min(1, n_in % n_int)
# get relevant metdata
uvw_array = uv.uvw_array[ind1, :]
times = uv.time_array[ind1]
if not np.all(times == np.sort(times)):
raise AssertionError(
"times of uvdata object are not monotonically increasing; "
"throwing our hands up"
)
lsts = uv.lst_array[ind1]
int_time = uv.integration_time[ind1]
# do the averaging
input_shape = data.shape
assert input_shape == (n_in, 1, uv.Nfreqs, uv.Npols)
output_shape = (n_out, 1, uv.Nfreqs, uv.Npols)
data_out = np.empty(output_shape, dtype=np.complex128)
flags_out = np.empty(output_shape, dtype=np.bool_)
nsamples_out = np.empty(output_shape, dtype=np.float32)
uvws_out = np.empty((n_out, 3), dtype=np.float64)
times_out = np.empty((n_out,), dtype=np.float64)
lst_out = np.empty((n_out,), dtype=np.float64)
int_time_out = np.empty((n_out,), dtype=np.float64)
if n_out == n_in:
# we don't need to average
current_index = start_index + n_out
uv2.data_array[start_index:current_index, :, :, :] = data
uv2.flag_array[start_index:current_index, :, :, :] = flags
uv2.nsample_array[start_index:current_index, :, :, :] = nsamples
uv2.uvw_array[start_index:current_index, :] = uvw_array
uv2.time_array[start_index:current_index] = times
uv2.lst_array[start_index:current_index] = lsts
uv2.integration_time[start_index:current_index] = int_time
uv2.ant_1_array[start_index:current_index] = key[0]
uv2.ant_2_array[start_index:current_index] = key[1]
uv2.baseline_array[start_index:current_index] = uvutils.antnums_to_baseline(
ant1, ant2, None
)
start_index = current_index
else:
# rats, we actually have to do work...
# phase up the data along each chunk of times
for i in range(n_out):
# compute zenith of the desired output time
i1 = i * n_int
i2 = min((i + 1) * n_int, n_in)
assert i2 - i1 > 0
t0 = Time((times[i1] + times[i2 - 1]) / 2, scale="utc", format="jd")
zenith_coord = SkyCoord(
alt=Angle(90 * units.deg),
az=Angle(0 * units.deg),
obstime=t0,
frame="altaz",
location=telescope_location,
)
obs_zenith_coord = zenith_coord.transform_to("icrs")
zenith_ra = obs_zenith_coord.ra
zenith_dec = obs_zenith_coord.dec
# get data, flags, and nsamples of slices
data_chunk = data[i1:i2, :, :, :]
flags_chunk = flags[i1:i2, :, :, :]
nsamples_chunk = nsamples[i1:i2, :, :, :]
# actually phase now
# compute new uvw coordinates
icrs_coord = SkyCoord(
ra=zenith_ra, dec=zenith_dec, unit="radian", frame="icrs"
)
uvws = np.float64(uvw_array[i1:i2, :])
itrs_telescope_location = SkyCoord(
x=uv.telescope_location[0] * units.m,
y=uv.telescope_location[1] * units.m,
z=uv.telescope_location[2] * units.m,
representation_type="cartesian",
frame="itrs",
obstime=t0,
)
itrs_lat_lon_alt = uv.telescope_location_lat_lon_alt
frame_telescope_location = itrs_telescope_location.transform_to("icrs")
frame_telescope_location.representation_type = "cartesian"
uvw_ecef = uvutils.ECEF_from_ENU(uvws, *itrs_lat_lon_alt)
itrs_uvw_coord = SkyCoord(
x=uvw_ecef[:, 0] * units.m,
y=uvw_ecef[:, 1] * units.m,
z=uvw_ecef[:, 2] * units.m,
representation_type="cartesian",
frame="itrs",
obstime=t0,
)
frame_uvw_coord = itrs_uvw_coord.transform_to("icrs")
frame_rel_uvw = (
frame_uvw_coord.cartesian.get_xyz().value.T
- frame_telescope_location.cartesian.get_xyz().value
)
new_uvws = uvutils.phase_uvw(
icrs_coord.ra.rad, icrs_coord.dec.rad, frame_rel_uvw
)
# average these uvws together to get the "average" position in
# the uv-plane
avg_uvws = np.average(new_uvws, axis=0)
# calculate and apply phasor
w_lambda = (
new_uvws[:, 2].reshape((i2 - i1), 1)
/ const.c.to("m/s").value
* uv.freq_array.reshape(1, uv.Nfreqs)
)
phs = np.exp(-1j * 2 * np.pi * w_lambda[:, None, :, None])
data_chunk *= phs
# sum data, propagate flag array, and adjusting nsample accordingly
data_slice = np.sum(data_chunk, axis=0)
flag_slice = np.sum(flags_chunk, axis=0)
nsamples_slice = np.sum(nsamples_chunk, axis=0) / (i2 - i1)
data_out[i, :, :, :] = data_slice
flags_out[i, :, :, :] = flag_slice
nsamples_out[i, :, :, :] = nsamples_slice
# update metadata
uvws_out[i, :] = avg_uvws
times_out[i] = (times[i1] + times[i2 - 1]) / 2
lst_out[i] = (lsts[i1] + lsts[i2 - 1]) / 2
int_time_out[i] = np.average(int_time[i1:i2]) * (i2 - i1)
# update data and metadata when we're done with this baseline
current_index = start_index + n_out
uv2.data_array[start_index:current_index, :, :, :] = data_out
uv2.flag_array[start_index:current_index, :, :, :] = flags_out
uv2.nsample_array[start_index:current_index, :, :, :] = nsamples_out
uv2.uvw_array[start_index:current_index, :] = uvws_out
uv2.time_array[start_index:current_index] = times_out
uv2.lst_array[start_index:current_index] = lst_out
uv2.integration_time[start_index:current_index] = int_time_out
uv2.ant_1_array[start_index:current_index] = key[0]
uv2.ant_2_array[start_index:current_index] = key[1]
uv2.baseline_array[start_index:current_index] = uvutils.antnums_to_baseline(
ant1, ant2, None
)
start_index = current_index
# clean up -- shorten all arrays to actually be size nblts
nblts = start_index
uv2.Nblts = nblts
uv2.data_array = uv2.data_array[:nblts, :, :, :]
uv2.flag_array = uv2.flag_array[:nblts, :, :, :]
uv2.nsample_array = uv2.nsample_array[:nblts, :, :, :]
uv2.uvw_array = uv2.uvw_array[:nblts, :]
uv2.time_array = uv2.time_array[:nblts]
uv2.lst_array = uv2.lst_array[:nblts]
uv2.integration_time = uv2.integration_time[:nblts]
uv2.ant_1_array = uv2.ant_1_array[:nblts]
uv2.ant_2_array = uv2.ant_2_array[:nblts]
uv2.baseline_array = uv2.baseline_array[:nblts]
uv2.Ntimes = len(np.unique(uv2.time_array))
# set phasing info
uv2.phase_type = "phased"
uv2.phase_center_ra = zenith_ra.rad
uv2.phase_center_dec = zenith_dec.rad
uv2.phase_center_frame = 2000.0
# fix up to correct old phasing method
uv2.phase(zenith_ra.rad, zenith_dec.rad, epoch="J2000", fix_old_proj=True)
# run a check
uv2.check()
return uv2
def initialize_uvdata(uvtask_list,
source_list_name,
uvdata_file=None,
obs_param_file=None,
telescope_config_file=None,
antenna_location_file=None):
"""
Initialize an empty uvdata object to fill with simulation.
Args:
uvtask_list: List of uvtasks to simulate.
source_list_name: Name of source list file or mock catalog.
uvdata_file: Name of input UVData file or None if initializing from
config files.
obs_param_file: Name of observation parameter config file or None if
initializing from a UVData file.
telescope_config_file: Name of telescope config file or None if
initializing from a UVData file.
antenna_location_file: Name of antenna location file or None if
initializing from a UVData file.
"""
if not isinstance(source_list_name, str):
raise ValueError('source_list_name must be a string')
if uvdata_file is not None:
if not isinstance(uvdata_file, str):
raise ValueError('uvdata_file must be a string')
if (obs_param_file is not None or telescope_config_file is not None
or antenna_location_file is not None):
raise ValueError('If initializing from a uvdata_file, none of '
'obs_param_file, telescope_config_file or '
'antenna_location_file can be set.')
elif (obs_param_file is None or telescope_config_file is None
or antenna_location_file is None):
if not isinstance(obs_param_file, str):
raise ValueError('obs_param_file must be a string')
if not isinstance(telescope_config_file, str):
raise ValueError('telescope_config_file must be a string')
if not isinstance(antenna_location_file, str):
raise ValueError('antenna_location_file must be a string')
raise ValueError('If not initializing from a uvdata_file, all of '
'obs_param_file, telescope_config_file or '
'antenna_location_file must be set.')
# Version string to add to history
history = get_version_string()
history += ' Sources from source list: ' + source_list_name + '.'
if uvdata_file is not None:
history += ' Based on UVData file: ' + uvdata_file + '.'
else:
history += (' Based on config files: ' + obs_param_file + ', ' +
telescope_config_file + ', ' + antenna_location_file)
history += ' Npus = ' + str(Npus) + '.'
task_freqs = []
task_bls = []
task_times = []
task_antnames = []
task_antnums = []
task_antpos = []
task_uvw = []
ant_1_array = []
ant_2_array = []
telescope_name = uvtask_list[0].telescope.telescope_name
telescope_location = uvtask_list[0].telescope.telescope_location.geocentric
source_0 = uvtask_list[0].source
freq_0 = uvtask_list[0].freq
for task in uvtask_list:
if not task.source == source_0:
continue
task_freqs.append(task.freq)
if task.freq == freq_0:
task_bls.append(task.baseline)
task_times.append(task.time)
task_antnames.append(task.baseline.antenna1.name)
task_antnames.append(task.baseline.antenna2.name)
ant_1_array.append(task.baseline.antenna1.number)
ant_2_array.append(task.baseline.antenna2.number)
task_antnums.append(task.baseline.antenna1.number)
task_antnums.append(task.baseline.antenna2.number)
task_antpos.append(task.baseline.antenna1.pos_enu)
task_antpos.append(task.baseline.antenna2.pos_enu)
task_uvw.append(task.baseline.uvw)
antnames, ant_indices = np.unique(task_antnames, return_index=True)
task_antnums = np.array(task_antnums)
task_antpos = np.array(task_antpos)
antnums = task_antnums[ant_indices]
antpos = task_antpos[ant_indices]
freqs = np.unique(task_freqs)
uv_obj = UVData()
# add pyuvdata version info
history += uv_obj.pyuvdata_version_str
uv_obj.telescope_name = telescope_name
uv_obj.telescope_location = np.array(
[tl.to('m').value for tl in telescope_location])
uv_obj.instrument = telescope_name
uv_obj.Nfreqs = freqs.size
uv_obj.Ntimes = np.unique(task_times).size
uv_obj.Nants_data = antnames.size
uv_obj.Nants_telescope = uv_obj.Nants_data
uv_obj.Nblts = len(ant_1_array)
uv_obj.antenna_names = antnames.tolist()
uv_obj.antenna_numbers = antnums
antpos_ecef = uvutils.ECEF_from_ENU(
antpos, *
uv_obj.telescope_location_lat_lon_alt) - uv_obj.telescope_location
uv_obj.antenna_positions = antpos_ecef
uv_obj.ant_1_array = np.array(ant_1_array)
uv_obj.ant_2_array = np.array(ant_2_array)
uv_obj.time_array = np.array(task_times)
uv_obj.uvw_array = np.array(task_uvw)
uv_obj.baseline_array = uv_obj.antnums_to_baseline(ant_1_array,
ant_2_array)
uv_obj.Nbls = np.unique(uv_obj.baseline_array).size
if uv_obj.Nfreqs == 1:
uv_obj.channel_width = 1. # Hz
else:
uv_obj.channel_width = np.diff(freqs)[0]
if uv_obj.Ntimes == 1:
uv_obj.integration_time = np.ones_like(uv_obj.time_array,
dtype=np.float64) # Second
else:
# Note: currently only support a constant spacing of times
uv_obj.integration_time = (
np.ones_like(uv_obj.time_array, dtype=np.float64) *
np.diff(np.unique(task_times))[0])
uv_obj.set_lsts_from_time_array()
uv_obj.zenith_ra = uv_obj.lst_array
uv_obj.zenith_dec = np.repeat(uv_obj.telescope_location_lat_lon_alt[0],
uv_obj.Nblts) # Latitude
uv_obj.object_name = 'zenith'
uv_obj.set_drift()
uv_obj.vis_units = 'Jy'
uv_obj.polarization_array = np.array([-5, -6, -7, -8])
uv_obj.spw_array = np.array([0])
uv_obj.freq_array = np.array([freqs])
uv_obj.Nspws = uv_obj.spw_array.size
uv_obj.Npols = uv_obj.polarization_array.size
uv_obj.data_array = np.zeros(
(uv_obj.Nblts, uv_obj.Nspws, uv_obj.Nfreqs, uv_obj.Npols),
dtype=np.complex)
uv_obj.flag_array = np.zeros(
(uv_obj.Nblts, uv_obj.Nspws, uv_obj.Nfreqs, uv_obj.Npols), dtype=bool)
uv_obj.nsample_array = np.ones_like(uv_obj.data_array, dtype=float)
uv_obj.history = history
uv_obj.check()
return uv_obj
# Run simulation
# ---------------------------
print("Running simulation")
sys.stdout.flush()
visibs, time_array, baseline_inds = obs.make_visibilities(shell0, Nprocs=Nprocs)
uv_obj.time_array = time_array
uv_obj.set_lsts_from_time_array()
uv_obj.baseline_array = bl_array[baseline_inds]
uv_obj.ant_1_array, uv_obj.ant_2_array = uv_obj.baseline_to_antnums(uv_obj.baseline_array)
uv_obj.spw_array = np.array([0])
uv_obj.Npols = 1
uv_obj.polarization_array=np.array([1])
uv_obj.Nspws = 1
uv_obj.set_uvws_from_antenna_positions()
uv_obj.channel_width = np.diff(freqs)[0]
uv_obj.integration_time = np.ones(uv_obj.Nblts) * np.diff(time_arr)[0] * 24 * 3600. # Seconds
uv_obj.history = 'eorsky'
uv_obj.set_drift()
uv_obj.telescope_name = 'eorsky'
uv_obj.instrument = 'simulator'
uv_obj.object_name = 'zenith'
uv_obj.vis_units = 'Jy'
if sjob_id is None:
sjob_id = ''
if beam_type == 'gaussian':
fwhm = beam_attr['sigma'] * 2.355
uvfile = or_xx_files[0]
uvd = UVData()
uvd.read_miriad(uvfile)
# create uvdata object
uvd = UVData()
uvd.Nants_telescope = self.Nants
uvd.Nants_data = len(np.unique(bl_array))
uvd.Nbls = Nbls
uvd.Ntimes = Ntimes
uvd.Nblts = Nbls * Ntimes
uvd.Nfreqs = self.Nfreqs
uvd.Npols = self.Nxpols
uvd.Nspws = 1
uvd.antenna_numbers = self.ant_nums
uvd.antenna_names = np.array(self.ant_nums, dtype=str)
uvd.ant_1_array = np.concatenate(
[map(lambda x: x[0], bl_array) for i in range(Ntimes)])
uvd.ant_2_array = np.concatenate(
[map(lambda x: x[1], bl_array) for i in range(Ntimes)])
uvd.baseline_array = np.concatenate(
[np.arange(Nbls) for i in range(Ntimes)])
uvd.freq_array = (self.freqs * 1e6).reshape(1, -1)
uvd.time_array = np.repeat(np.array(JD_array)[:, np.newaxis], Nbls,
axis=1).ravel()
uvd.channel_width = (self.freqs * 1e6)[1] - (self.freqs * 1e6)[0]
uvd.data_array = self.vis_data.reshape(uvd.Nblts, 1, self.Nfreqs,
self.Nxpols)
uvd.flag_array = np.ones_like(uvd.data_array, dtype=np.bool)
def setup_uvdata(
array_layout=None,
telescope_location=None,
telescope_name=None,
Nfreqs=None,
start_freq=None,
bandwidth=None,
freq_array=None,
Ntimes=None,
time_cadence=None,
start_time=None,
time_array=None,
bls=None,
anchor_ant=None,
antenna_nums=None,
no_autos=True,
pols=["xx"],
make_full=False,
redundancy=None,
run_check=True,
):
"""
Setup a UVData object for simulating.
Args:
array_layout : str
Filepath to array layout in ENU coordinates [meters]
telescope_location : len-3 tuple
Telescope location on Earth in LatLonAlt coordinates [deg, deg, meters]
telescope_name : str
Name of telescope
Nfreqs : int
Number of frequency channels
start_freq : float
Starting frequency [Hz]
bandwidth : float
Total frequency bandwidth of spectral window [Hz]
freq_array : ndarray
frequency array [Hz], cannot be specified if start_freq, Nfreqs or bandwidth is specified
Ntimes : int
Number of integration bins
time_cadence : float
Cadence of time bins [seconds]
start_time : float
Time of the first integration bin [Julian Date]
time_array : ndarray
time array [Julian Date], cannot be specified if start_time, Ntimes and time_cadence is specified
bls : list
List of antenna-pair tuples for baseline selection
anchor_ant: int
Selects baselines such that one of the pair is a specified antenna number
redundancy: float
Redundant baseline selection tolerance for selection
antenna_nums : list
List of antenna numbers to keep in array
make_full : Generate the full UVData object, includes arrays of length Nblts.
Default behavior creates an invalid UVData object, where baseline_array has length Nbls, etc.
This is to avoid excessive memory usage up front when it's not necessary.
Returns:
UVData object with zeroed data_array
"""
# get antenna information
tele_dict = parse_telescope_params(
dict(
array_layout=array_layout,
telescope_location=telescope_location,
telescope_name=telescope_name,
))
lat, lon, alt = uvutils.LatLonAlt_from_XYZ(tele_dict["telescope_location"])
antpos = tele_dict["antenna_positions"]
enu = uvutils.ENU_from_ECEF(
tele_dict["antenna_positions"] + tele_dict["telescope_location"], lat,
lon, alt)
anums = tele_dict["antenna_numbers"]
antnames = tele_dict["antenna_names"]
Nants = tele_dict["Nants_data"]
# setup object and fill in basic info
uv_obj = UVData()
uv_obj.telescope_location = tele_dict["telescope_location"]
uv_obj.telescope_location_lat_lon_alt = (lat, lon, alt)
uv_obj.telescope_location_lat_lon_alt_degrees = (
np.degrees(lat),
np.degrees(lon),
alt,
)
uv_obj.antenna_numbers = anums
uv_obj.antenna_names = antnames
uv_obj.antenna_positions = antpos
uv_obj.Nants_telescope = Nants
# fill in frequency and time info: wait to fill in len-Nblts arrays until later
if freq_array is not None:
if Nfreqs is not None or start_freq is not None or bandwidth is not None:
raise ValueError(
"Cannot specify freq_array as well as Nfreqs, start_freq or bandwidth"
)
if freq_array.ndim == 1:
freq_array = freq_array.reshape(1, -1)
Nfreqs = freq_array.size
else:
freq_dict = parse_frequency_params(
dict(Nfreqs=Nfreqs, start_freq=start_freq, bandwidth=bandwidth))
freq_array = freq_dict["freq_array"]
if time_array is not None:
if Ntimes is not None or start_time is not None or time_cadence is not None:
raise ValueError(
"Cannot specify time_array as well as Ntimes, start_time or time_cadence"
)
Ntimes = time_array.size
else:
time_dict = parse_time_params(
dict(Ntimes=Ntimes,
start_time=start_time,
time_cadence=time_cadence))
time_array = time_dict["time_array"]
uv_obj.freq_array = freq_array
uv_obj.Nfreqs = Nfreqs
uv_obj.Ntimes = Ntimes
# fill in other attributes
uv_obj.spw_array = np.array([0], dtype=int)
uv_obj.Nspws = 1
uv_obj.polarization_array = np.array(
[uvutils.polstr2num(pol) for pol in pols], dtype=int)
uv_obj.Npols = uv_obj.polarization_array.size
if uv_obj.Nfreqs > 1:
uv_obj.channel_width = np.diff(uv_obj.freq_array[0])[0]
else:
uv_obj.channel_width = 1.0
uv_obj._set_drift()
uv_obj.telescope_name = tele_dict["telescope_name"]
uv_obj.instrument = "simulator"
uv_obj.object_name = "zenith"
uv_obj.vis_units = "Jy"
uv_obj.history = ""
if redundancy is not None:
red_tol = redundancy
reds, vec_bin_centers, lengths = uvutils.get_antenna_redundancies(
anums, enu, tol=red_tol, include_autos=not bool(no_autos))
bls = [r[0] for r in reds]
bls = [uvutils.baseline_to_antnums(bl_ind, Nants) for bl_ind in bls]
# Setup array and implement antenna/baseline selections.
bl_array = []
_bls = [(a1, a2) for a1 in anums for a2 in anums if a1 <= a2]
if bls is not None:
if isinstance(bls, str):
bls = ast.literal_eval(bls)
bls = [bl for bl in _bls if bl in bls]
else:
bls = _bls
if anchor_ant is not None:
bls = [bl for bl in bls if anchor_ant in bl]
if bool(no_autos):
bls = [bl for bl in bls if bl[0] != bl[1]]
if antenna_nums is not None:
if isinstance(antenna_nums, str):
antenna_nums = ast.literal_eval(antenna_nums)
if isinstance(antenna_nums, int):
antenna_nums = [antenna_nums]
bls = [(a1, a2) for (a1, a2) in bls
if a1 in antenna_nums or a2 in antenna_nums]
bls = sorted(bls)
for (a1, a2) in bls:
bl_array.append(uvutils.antnums_to_baseline(a1, a2, 1))
bl_array = np.asarray(bl_array)
print("Nbls: {}".format(bl_array.size))
if bl_array.size == 0:
raise ValueError("No baselines selected.")
uv_obj.time_array = time_array # Keep length Ntimes
uv_obj.baseline_array = bl_array # Length Nbls
if make_full:
uv_obj = complete_uvdata(uv_obj, run_check=run_check)
return uv_obj
def fake_data_generator():
"""Generate a fake dataset as a module-level fixture."""
# generate a fake data file for testing BDA application
uvd = UVData()
t0 = 2459000.0
dt = (2 * units.s).to(units.day)
t1 = t0 + dt.value
t2 = t0 + 2 * dt.value
# define baseline-time spacing
uvd.ant_1_array = np.asarray([0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=np.int_)
uvd.ant_2_array = np.asarray([0, 1, 2, 0, 1, 2, 0, 1, 2], dtype=np.int_)
uvd.time_array = np.asarray([t0, t0, t0, t1, t1, t1, t2, t2, t2],
dtype=np.float64)
uvd.Ntimes = 3
uvd.Nbls = 3
uvd.Nblts = uvd.Ntimes * uvd.Nbls
# define frequency array
nfreqs = 1024
freq_array = np.linspace(50e6, 250e6, num=nfreqs)
uvd.freq_array = freq_array[np.newaxis, :]
uvd.spw_array = [0]
uvd.Nfreqs = nfreqs
uvd.Nspws = 1
# define polarization array
uvd.polarization_array = [-5]
uvd.Npols = 1
# make random data for data array
data_shape = (uvd.Nblts, 1, uvd.Nfreqs, uvd.Npols)
uvd.data_array = np.zeros(data_shape, dtype=np.complex128)
rng = default_rng()
uvd.data_array += rng.standard_normal(data_shape)
uvd.data_array += 1j * rng.standard_normal(data_shape)
uvd.flag_array = np.zeros_like(uvd.data_array, dtype=np.bool_)
uvd.nsample_array = np.ones_like(uvd.data_array, dtype=np.float32)
# set telescope and antenna positions
hera_telescope = pyuvdata.telescopes.get_telescope("HERA")
uvd.telescope_location_lat_lon_alt = hera_telescope.telescope_location_lat_lon_alt
antpos0 = np.asarray([0, 0, 0], dtype=np.float64)
antpos1 = np.asarray([14, 0, 0], dtype=np.float64)
antpos2 = np.asarray([28, 0, 0], dtype=np.float64)
antpos_enu = np.vstack((antpos0, antpos1, antpos2))
antpos_xyz = uvutils.ECEF_from_ENU(antpos_enu,
*uvd.telescope_location_lat_lon_alt)
uvd.antenna_positions = antpos_xyz - uvd.telescope_location
uvw_array = np.zeros((uvd.Nblts, 3), dtype=np.float64)
uvw_array[::3, :] = antpos0 - antpos0
uvw_array[1::3, :] = antpos1 - antpos0
uvw_array[2::3, :] = antpos2 - antpos0
uvd.uvw_array = uvw_array
uvd.antenna_numbers = np.asarray([0, 1, 2], dtype=np.int_)
uvd.antenna_names = np.asarray(["H0", "H1", "H2"], dtype=np.str_)
uvd.Nants_data = 3
uvd.Nants_telescope = 3
# set other metadata
uvd.vis_units = "uncalib"
uvd.channel_width = 5e4 # 50 kHz
uvd.phase_type = "drift"
uvd.baseline_array = uvd.antnums_to_baseline(uvd.ant_1_array,
uvd.ant_2_array)
uvd.history = "BDA test file"
uvd.instrument = "HERA"
uvd.telescope_name = "HERA"
uvd.object_name = "zenith"
uvd.integration_time = 2 * np.ones_like(uvd.baseline_array,
dtype=np.float64)
uvd.set_lsts_from_time_array()
# run a check
uvd.check()
yield uvd
# clean up when done
del uvd
return
def uvdata_from_sim_data(
array_lat,
array_lon,
array_height,
jd_axis,
nu_axis,
r_axis,
ant_pairs,
V_sim,
integration_time="derived",
channel_width="derived",
antenna_numbers="derived",
antenna_names="derived",
instrument="left blank by user",
telescope_name="left blank by user",
history="left blank by user",
object_name="left blank by user",
):
HERA_LAT = array_lat
HERA_LON = array_lon
HERA_HEIGHT = array_height
HERA_LAT_LON_ALT = (HERA_LAT, HERA_LON, HERA_HEIGHT)
HERA_LOC = coord.EarthLocation(
lat=HERA_LAT * units.rad,
lon=HERA_LON * units.rad,
height=HERA_HEIGHT * units.meter,
)
jd_obj = Time(jd_axis, format="jd", location=HERA_LOC)
lst_axis = jd_obj.sidereal_time("apparent").radian
if integration_time == "derived":
del_jd = jd_obj[1] - jd_obj[0]
integration_time = del_jd.sec
uvd = UVData()
uvd.telescope_location = HERA_LOC.value
uvd.telescope_location_lat_lon_alt = HERA_LAT_LON_ALT
if antenna_numbers == "derived":
uvd.antenna_numbers = np.arange(r_axis.shape[0], dtype=np.int64)
ant_num_pairs = ant_pairs
else:
uvd.antenna_numbers = antenna_numbers
ant_num_pairs = np.array([(antenna_numbers[ap[0]],
antenna_numbers[ap[1]])
for ap in ant_pairs])
if antenna_names == "derived":
uvd.antenna_names = [str(ant_ind) for ant_ind in uvd.antenna_numbers]
else:
uvd.antenna_names = antenna_names
ant_pos_ECEF = pyuvdata.utils.ECEF_from_ENU(r_axis, HERA_LOC.lat.rad,
HERA_LOC.lon.rad,
HERA_LOC.height.value)
uvd.antenna_positions = ant_pos_ECEF - uvd.telescope_location
bls = [
uvd.antnums_to_baseline(ant_num_pair[0], ant_num_pair[1])
for ant_num_pair in ant_num_pairs
]
uvd.freq_array = nu_axis.reshape((1, nu_axis.size))
pols = ["xx", "yy", "xy", "yx"]
uvd.polarization_array = np.array(
[polstr2num(pol_str) for pol_str in pols])
uvd.x_orientation = "east"
if channel_width == "derived":
uvd.channel_width = nu_axis[1] - nu_axis[0]
else:
uvd.channel_width = channel_width
uvd.Nfreqs = nu_axis.size
uvd.Nspws = 1
uvd.Npols = len(pols)
bl_arr, lst_arr = np.meshgrid(np.array(bls), lst_axis)
uvd.baseline_array = bl_arr.flatten()
uvd.lst_array = lst_arr.flatten()
_, time_arr = np.meshgrid(np.array(bls), jd_axis)
uvd.time_array = time_arr.flatten()
ant1_arr, _ = np.meshgrid(ant_num_pairs[:, 0], lst_axis)
ant2_arr, _ = np.meshgrid(ant_num_pairs[:, 1], lst_axis)
uvd.ant_1_array = ant1_arr.flatten()
uvd.ant_2_array = ant2_arr.flatten()
# Nants_data might be less than r_axis.shape[0] for redundant arrays
uvd.Nants_data = len(
np.unique(np.r_[ant1_arr.flatten(),
ant2_arr.flatten()]))
uvd.Nants_telescope = r_axis.shape[0]
uvd.set_uvws_from_antenna_positions()
uvd.Nbls = len(bls)
uvd.Ntimes = lst_axis.size
uvd.Nblts = bl_arr.size
uvd.data_array = np.zeros((uvd.Nblts, uvd.Nspws, uvd.Nfreqs, uvd.Npols),
dtype=np.complex128)
uvd.flag_array = np.zeros_like(uvd.data_array, dtype=np.bool)
uvd.nsample_array = np.ones((uvd.Nblts, uvd.Nspws, uvd.Nfreqs, uvd.Npols),
dtype=np.float64)
uvd.spw_array = np.ones(1, dtype=np.int64)
uvd.integration_time = integration_time * np.ones(uvd.Nblts)
uvd.phase_type = "drift"
# (0,0) <-> 'xx' <-> East-East, etc.
# matches order of uvd.polarization_array
pol_map = {(0, 0): 0, (1, 1): 1, (0, 1): 2, (1, 0): 3}
for i_a in range(2):
for i_b in range(2):
i_p = pol_map[(i_a, i_b)]
for k in range(ant_num_pairs.shape[0]):
a_i, a_j = ant_num_pairs[k]
bl_num = uvd.antnums_to_baseline(a_i, a_j)
bl_ind = np.where(uvd.baseline_array == bl_num)[0]
uvd.data_array[bl_ind, 0, :, i_p] = np.copy(V_sim[:, :, k, i_a,
i_b])
uvd.vis_units = "Jy"
uvd.instrument = instrument
uvd.telescope_name = telescope_name
uvd.history = history
uvd.object_name = object_name
uvd.check()
return uvd
logger.info('Getting baseline pair: (%d, %d)..' % (a1, a2))
times.append(time.time())
if a1 == a2:
bram.imag = 0
bram.real = bram.real / float(
feng.corr.acc_len * feng.corr.spec_per_acc)
else:
bram = bram / float(
feng.corr.acc_len * feng.corr.spec_per_acc)
c.append(bram)
poco.append(np.transpose(c))
# Write output to pyuvdata file
data = UVData()
data.Nfreqs = len(fqs)
data.Nspws = 1
data.Npols = 1
data.Nbls = len(bls)
data.Ntimes = len(times)
data.Nblts = data.Ntimes
# Init flag array with no flags
data.flag_array = np.empty(
(data.Nblts, data.Nspws, data.Nfreqs, data.Npols), dtype=bool)
data.flag_array[:] = False
# Init nsamples array with unity weights
data.nsample_array = np.ones(
(data.Nblts, data.Nspws, data.Nfreqs, data.Npols), dtype=float)
# Create frequency array
def sim_obs(self,
bl_array,
JD_array,
pool=None,
write_miriad=False,
fname=None,
clobber=False,
one_beam_model=True,
interp=True,
Tnoise=None,
fast_noise=False):
"""
Simulate a visibility observation of the sky
Input:
------
bl_array : list, shape=(Nbls, 2), entry_format=tuple(int, int)
list of baselines (antenna pairs)
in (ant1, ant2) with type(ant1) == int
JD_array : list, shape=(Ntimes,), dtype=float
list of Julian Dates for observations
"""
# get array info
Nbls = len(bl_array)
str_bls = [(str(x[0]), str(x[1])) for x in bl_array]
Ntimes = len(JD_array)
rel_ants = np.unique(np.concatenate(bl_array)) # relevant antennas
rel_ant2ind = OrderedDict(
zip(np.array(rel_ants, str), np.arange(len(rel_ants))))
# get antenna indices
ant_inds = map(lambda x: self.ant2ind[str(x)], rel_ants)
# get antenna positions for each baseline
ant1_pos = np.array(map(lambda x: self.ant_pos[x[0]], str_bls))
ant2_pos = np.array(map(lambda x: self.ant_pos[x[1]], str_bls))
# get vector in u-v plane
wavelengths = 2.9979e8 / (self.freqs * 1e6)
self.uv_vecs = (ant2_pos - ant1_pos).reshape(Nbls, 3, -1) / wavelengths
# Get direction unit vector, s-hat
x, y, z = hp.pix2vec(self.beam_nside, np.arange(self.beam_npix))
self.s_hat = np.array([y, x, z])
# get phase map in topocentric frame (sqrt of full phase term)
self.phase = np.exp(-1j * np.pi *
np.einsum('ijk,jl->ikl', self.uv_vecs, self.s_hat))
# build beams for each antenna in topocentric coordinates
self.build_beams(ant_inds=ant_inds, one_beam_model=one_beam_model)
# create phase and beam product maps (Npol, Nbl, Nfreqs, Npix)
self.beam_phs = self.ant_beam_models.reshape(
self.Npols, -1, self.Nfreqs, self.beam_npix) * self.phase
# loop over JDs
self.vis_data = []
for jd in JD_array:
# map through each antenna and project polarized, multi-frequency beam model onto sky
if one_beam_model == True:
self.proj_beam_phs = self.project_beams(
jd,
self.sky_theta,
self.sky_phi,
beam_models=self.beam_phs,
output=True,
interp=interp)
else:
#proj_ant_beam_models = self.project_beams(JD, self.sky_theta, self.sky_phi,
#beam_models=np.array(map(lambda x: self.ant_beam_models[str(x)], self.ant_nums)), output=True)
self.proj_beam_phs = self.project_beams(
jd,
self.sky_theta,
self.sky_phi,
beam_models=self.beam_phs,
output=True,
interp=interp)
# calculate visibility
if pool is None:
M = map
else:
M = pool.map
# add noise
if Tnoise is None or fast_noise is True:
sky_models = self.sky_models
else:
sky_models = self.sky_models + self.generate_noise_map(
Tnoise, self.sky_models.shape)
if one_beam_model is True:
if self.onepol is True:
vis = np.einsum("ijkl, ikl -> ijk", self.proj_beam_phs**2,
sky_models)
else:
vis = np.einsum("ijkl, imkl, mjkl -> imjk",
self.proj_beam_phs, sky_models,
self.proj_beam_phs)
else:
vis = np.array(
map(
lambda x: np.einsum(
"ijk, jk, ljk -> ilj", self.proj_beam_phs[
rel_ant2ind[x[1][0]]], sky_models, self.
proj_beam_phs[rel_ant2ind[x[1][1]]]),
enumerate(str_bls)))
self.vis_data.append(vis)
if self.onepol is True:
self.vis_data = np.moveaxis(np.array(self.vis_data), 0, 2)
else:
self.vis_data = np.moveaxis(np.array(self.vis_data), 0, 3)
# normalize by the effective-beam solid angle
if one_beam_model == True:
self.ant_beam_sa = np.repeat(
np.einsum('ijk,ijk->ij', self.ant_beam_models,
self.ant_beam_models)[:, np.newaxis, :], Nbls, 1)
else:
self.ant_beam_sa = np.array(
map(
lambda x: np.einsum(
'ijk,ljk->ilj', self.proj_ant_beam_models[rel_ant2ind[
x[1][0]]], self.proj_ant_beam_models[rel_ant2ind[x[
1][1]]]), enumerate(str_bls)))
if self.onepol is True:
self.vis_data /= self.ant_beam_sa[:, :, np.newaxis, :]
self.vis_data_shape = "(1, Nbls, Ntimes, Nfreqs)"
else:
self.vis_data /= self.ant_beam_sa[:, :, :, np.newaxis, :]
self.vis_data_shape = "(2, 2, Nbls, Ntimes, Nfreqs)"
if fast_noise is True and Tnoise is not None:
self.vis_data += self.generate_vis_noise(
Tnoise,
self.freqs * 1e6,
self.ant_beam_sa.squeeze(),
self.vis_data.shape,
bandwidth=self.bandwidth * 1e6,
int_time=10.7)
# write to file
if write_miriad == True:
# create uvdata object
uvd = UVData()
uvd.Nants_telescope = self.Nants
uvd.Nants_data = len(np.unique(bl_array))
uvd.Nbls = Nbls
uvd.Ntimes = Ntimes
uvd.Nblts = Nbls * Ntimes
uvd.Nfreqs = self.Nfreqs
uvd.Npols = self.Nxpols
uvd.Nspws = 1
uvd.antenna_numbers = self.ant_nums
uvd.antenna_names = np.array(self.ant_nums, dtype=str)
uvd.ant_1_array = np.concatenate(
[map(lambda x: x[0], bl_array) for i in range(Ntimes)])
uvd.ant_2_array = np.concatenate(
[map(lambda x: x[1], bl_array) for i in range(Ntimes)])
uvd.baseline_array = np.concatenate(
[np.arange(Nbls) for i in range(Ntimes)])
uvd.freq_array = (self.freqs * 1e6).reshape(1, -1)
uvd.time_array = np.repeat(np.array(JD_array)[:, np.newaxis],
Nbls,
axis=1).ravel()
uvd.channel_width = (self.freqs * 1e6)[1] - (self.freqs * 1e6)[0]
uvd.data_array = self.vis_data.reshape(uvd.Nblts, 1, self.Nfreqs,
self.Nxpols)
uvd.flag_array = np.ones_like(uvd.data_array, dtype=np.bool)
uvd.history = " "
uvd.instrument = " "
uvd.integration_time = 10.7
uvd.lst_array = np.repeat(np.array(
map(lambda x: self.JD2LST(self.loc, x), JD_array))[:,
np.newaxis],
Nbls,
axis=1).ravel()
uvd.nsample_array = np.ones_like(uvd.data_array, dtype=np.float)
uvd.object_name = ""
uvd.phase_type = "drift"
uvd.polarization_array = np.array(
map(lambda x: {
"XX": -5,
"YY": -6,
"XY": -7,
"YX": -8
}[x], self.xpols))
uvd.spw_array = np.array([0])
uvd.telescope_location = np.array([
6378137. * np.cos(self.loc.lon) * np.cos(self.loc.lat),
6378137. * np.sin(self.loc.lon) * np.cos(self.loc.lat),
6378137. * np.sin(self.loc.lat)
])
uvd.telescope_name = " "
uvd.uvw_array = np.ones((uvd.Nblts, 3))
uvd.vis_units = "Jy"
zen_dec, zen_ra = self.loc.radec_of(0, np.pi / 2)
uvd.zenith_dec = np.ones(uvd.Nblts) * zen_dec
uvd.zenith_ra = np.ones(uvd.Nblts) * zen_ra
uvd.write_miriad(fname, clobber=clobber)