https://github.com/RadioAstronomySoftwareGroup/pyuvdata
Tip revision: 7ceb5993d263049feb8a5e214a11a6cd7f6d8190 authored by Paul La Plante on 10 August 2022, 05:35:54 UTC
Add basics for reading bitshuffle data
Add basics for reading bitshuffle data
Tip revision: 7ceb599
uvfits.py
# -*- mode: python; coding: utf-8 -*-
# Copyright (c) 2018 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""Class for reading and writing uvfits files."""
import copy
import os
import warnings
import numpy as np
from astropy import constants as const
from astropy.io import fits
from astropy.time import Time
from .. import utils as uvutils
from .uvdata import UVData
__all__ = ["UVFITS"]
class UVFITS(UVData):
"""
Defines a uvfits-specific subclass of UVData for reading and writing uvfits.
This class should not be interacted with directly, instead use the read_uvfits
and write_uvfits methods on the UVData class.
"""
def _get_parameter_data(
self,
vis_hdu,
run_check_acceptability,
background_lsts=True,
):
"""
Read just the random parameters portion of the uvfits file ("metadata").
Separated from full read so that header, metadata and data can be read
independently.
"""
# astropy.io fits reader scales date according to relevant PZER0 (?)
# uvfits standard is to have 2 DATE parameters, both floats:
# DATE (full day) and _DATE (fractional day)
# cotter uvfits files have one DATE that is a double
# using data.par('date') is general -- it will add them together if there are 2
self.time_array = vis_hdu.data.par("date")
self.Ntimes = len(np.unique(self.time_array))
# check if lst array is saved. It's not a standard metadata item in uvfits,
# but if the file was written with pyuvdata it may be present
# (depending on pyuvdata version)
proc = None
if "LST" in vis_hdu.data.parnames:
# angles in uvfits files are stored in degrees, so convert to radians
self.lst_array = np.deg2rad(vis_hdu.data.par("lst"))
if run_check_acceptability:
(
latitude,
longitude,
altitude,
) = self.telescope_location_lat_lon_alt_degrees
lst_array = uvutils.get_lst_for_time(
self.time_array, latitude, longitude, altitude
)
if not np.all(
np.isclose(
self.lst_array,
lst_array,
rtol=self._lst_array.tols[0],
atol=self._lst_array.tols[1],
)
):
warnings.warn(
"LST values stored in this file are not "
"self-consistent with time_array and telescope "
"location. Consider recomputing with "
"utils.get_lst_for_time."
)
else:
proc = self.set_lsts_from_time_array(background=background_lsts)
# if antenna arrays are present, use them. otherwise use baseline array
if "ANTENNA1" in vis_hdu.data.parnames and "ANTENNA2" in vis_hdu.data.parnames:
# Note: we no longer subtract 1 from the antenna arrays
# The antanna arrays are not indices but rather are numbers
# that correspond to particular antennas
self.ant_1_array = np.int32(vis_hdu.data.par("ANTENNA1"))
self.ant_2_array = np.int32(vis_hdu.data.par("ANTENNA2"))
# for instruments with a single subarray, the subarray should be set to 1s
subarray = np.int32(vis_hdu.data.par("SUBARRAY"))
# error on files with multiple subarrays
if len(set(subarray)) > 1:
raise ValueError(
"This file appears to have multiple subarray "
"values; only files with one subarray are "
"supported."
)
else:
# cannot set this to be the baseline array because it uses the
# 256 convention, not our 2048 convention
bl_input_array = np.int64(vis_hdu.data.par("BASELINE"))
# get antenna arrays based on uvfits baseline array
self.ant_1_array, self.ant_2_array = self.baseline_to_antnums(
bl_input_array
)
# check for multi source files. NOW SUPPORTED, W00T!
if "SOURCE" in vis_hdu.data.parnames:
# Preserve the source info just in case the AIPS SU table is missing, and
# we need to revert things back.
self._set_multi_phase_center(preserve_phase_center_info=True)
source = vis_hdu.data.par("SOURCE")
self.phase_center_id_array = source.astype(int)
# get self.baseline_array using our convention
self.baseline_array = self.antnums_to_baseline(
self.ant_1_array, self.ant_2_array
)
self.Nbls = len(np.unique(self.baseline_array))
# initialize internal variables based on the antenna lists
self.Nants_data = int(np.union1d(self.ant_1_array, self.ant_2_array).size)
# check for suffixes in the baseline coordinate names indicating the
# baseline coordinate system
if (
"UU" in vis_hdu.data.parnames
and "VV" in vis_hdu.data.parnames
and "WW" in vis_hdu.data.parnames
):
uvw_names = ["UU", "VV", "WW"]
elif (
"UU---SIN" in vis_hdu.data.parnames
and "VV---SIN" in vis_hdu.data.parnames
and "WW---SIN" in vis_hdu.data.parnames
):
uvw_names = ["UU---SIN", "VV---SIN", "WW---SIN"]
elif (
"UU---NCP" in vis_hdu.data.parnames
and "VV---NCP" in vis_hdu.data.parnames
and "WW---NCP" in vis_hdu.data.parnames
):
uvw_names = ["UU---NCP", "VV---NCP", "WW---NCP"]
warnings.warn(
"The baseline coordinates (uvws) in this file are specified in the "
"---NCP coordinate system, which is does not agree with our baseline "
"coordinate conventions. Rotating the uvws to match our convention "
"(Note that this rotation has not been widely tested)."
)
else:
raise ValueError(
"There is no consistent set of baseline coordinates in this file. "
"The UU, VV and WW coordinate must have no suffix or the '---SIN' or "
"'---NCP' suffix and the suffixes must match on all three baseline "
"coordinate parameters."
)
# read baseline vectors in units of seconds, return in meters
# FITS uvw direction convention is opposite ours and Miriad's.
# So conjugate the visibilities and flip the uvws:
self.uvw_array = (-1) * (
np.array(
np.stack(
(
vis_hdu.data.par(uvw_names[0]),
vis_hdu.data.par(uvw_names[1]),
vis_hdu.data.par(uvw_names[2]),
)
)
)
* const.c.to("m/s").value
).T
if "INTTIM" in vis_hdu.data.parnames:
self.integration_time = np.asarray(
vis_hdu.data.par("INTTIM"), dtype=np.float64
)
else:
if self.Ntimes > 1:
# assume that all integration times in the file are the same
int_time = self._calc_single_integration_time()
self.integration_time = (
np.ones_like(self.time_array, dtype=np.float64) * int_time
)
else:
warnings.warn(
"The integration time is not specified and only one time is "
"present so it cannot be calculated from the difference between "
"integration times. Setting to None which will cause the check to "
"error. Set `run_check` to False to read in the file without "
"checking. Then set the integration_time (to an array of length "
"Nblts) directly on the object to allow futher processing."
)
if proc is not None:
proc.join()
def _get_data(
self,
vis_hdu,
antenna_nums,
antenna_names,
ant_str,
bls,
frequencies,
freq_chans,
times,
time_range,
lsts,
lst_range,
polarizations,
blt_inds,
read_metadata,
keep_all_metadata,
run_check,
check_extra,
run_check_acceptability,
strict_uvw_antpos_check,
fix_old_proj,
fix_use_ant_pos,
check_autos,
fix_autos,
):
"""
Read just the visibility and flag data of the uvfits file.
Separated from full read so header and metadata can be read without data.
"""
# figure out what data to read in
blt_inds, freq_inds, pol_inds, history_update_string = self._select_preprocess(
antenna_nums,
antenna_names,
ant_str,
bls,
frequencies,
freq_chans,
times,
time_range,
lsts,
lst_range,
polarizations,
blt_inds,
)
if blt_inds is not None:
blt_frac = len(blt_inds) / float(self.Nblts)
else:
blt_frac = 1
if freq_inds is not None:
freq_frac = len(freq_inds) * float(self.Nspws) / float(self.Nfreqs)
else:
freq_frac = 1
if pol_inds is not None:
pol_frac = len(pol_inds) / float(self.Npols)
else:
pol_frac = 1
min_frac = np.min([blt_frac, freq_frac, pol_frac])
if min_frac == 1:
# no select, read in all the data
if vis_hdu.header["NAXIS"] == 7:
raw_data_array = vis_hdu.data.data[:, 0, 0, :, :, :, :]
assert self.Nspws == raw_data_array.shape[1]
else:
# in many uvfits files the spw axis is left out,
# here we put it back in so the dimensionality stays the same
raw_data_array = vis_hdu.data.data[:, 0, 0, :, :, :]
raw_data_array = raw_data_array[:, np.newaxis, :, :]
else:
# do select operations on everything except data_array, flag_array
# and nsample_array
self._select_by_index(
blt_inds, freq_inds, pol_inds, history_update_string, keep_all_metadata
)
# just read in the right portions of the data and flag arrays
if blt_frac == min_frac:
if vis_hdu.header["NAXIS"] == 7:
raw_data_array = vis_hdu.data.data[blt_inds, :, :, :, :, :, :]
raw_data_array = raw_data_array[:, 0, 0, :, :, :, :]
assert self.Nspws == raw_data_array.shape[1]
else:
# in many uvfits files the spw axis is left out,
# here we put it back in so the dimensionality stays the same
raw_data_array = vis_hdu.data.data[blt_inds, :, :, :, :, :]
raw_data_array = raw_data_array[:, 0, 0, :, :, :]
raw_data_array = raw_data_array[:, np.newaxis, :, :, :]
if freq_frac < 1:
raw_data_array = raw_data_array[:, :, freq_inds, :, :]
if pol_frac < 1:
raw_data_array = raw_data_array[:, :, :, pol_inds, :]
elif freq_frac == min_frac:
if vis_hdu.header["NAXIS"] == 7:
raw_data_array = vis_hdu.data.data[:, :, :, :, freq_inds, :, :]
raw_data_array = raw_data_array[:, 0, 0, :, :, :, :]
assert self.Nspws == raw_data_array.shape[1]
else:
# in many uvfits files the spw axis is left out,
# here we put it back in so the dimensionality stays the same
raw_data_array = vis_hdu.data.data[:, :, :, freq_inds, :, :]
raw_data_array = raw_data_array[:, 0, 0, :, :, :]
raw_data_array = raw_data_array[:, np.newaxis, :, :, :]
if blt_frac < 1:
raw_data_array = raw_data_array[blt_inds, :, :, :, :]
if pol_frac < 1:
raw_data_array = raw_data_array[:, :, :, pol_inds, :]
else:
if vis_hdu.header["NAXIS"] == 7:
raw_data_array = vis_hdu.data.data[:, :, :, :, :, pol_inds, :]
raw_data_array = raw_data_array[:, 0, 0, :, :, :, :]
assert self.Nspws == raw_data_array.shape[1]
else:
# in many uvfits files the spw axis is left out,
# here we put it back in so the dimensionality stays the same
raw_data_array = vis_hdu.data.data[:, :, :, :, pol_inds, :]
raw_data_array = raw_data_array[:, 0, 0, :, :, :]
raw_data_array = raw_data_array[:, np.newaxis, :, :, :]
if blt_frac < 1:
raw_data_array = raw_data_array[blt_inds, :, :, :, :]
if freq_frac < 1:
raw_data_array = raw_data_array[:, :, freq_inds, :, :]
assert len(raw_data_array.shape) == 5
# Reshape the data array to be the right size if we are working w/ multiple
# spectral windows to be 'flex_spw' compliant
if self.Nspws > 1:
raw_data_array = np.reshape(
raw_data_array,
(self.Nblts, 1, self.Nfreqs, self.Npols, raw_data_array.shape[4]),
)
# FITS uvw direction convention is opposite ours and Miriad's.
# So conjugate the visibilities and flip the uvws:
self.data_array = (
raw_data_array[:, :, :, :, 0] - 1j * raw_data_array[:, :, :, :, 1]
)
self.flag_array = raw_data_array[:, :, :, :, 2] <= 0
self.nsample_array = np.abs(raw_data_array[:, :, :, :, 2])
if fix_old_proj:
self.fix_phase(use_ant_pos=fix_use_ant_pos)
# check if object has all required UVParameters set
if run_check:
self.check(
check_extra=check_extra,
run_check_acceptability=run_check_acceptability,
strict_uvw_antpos_check=strict_uvw_antpos_check,
allow_flip_conj=True,
check_autos=check_autos,
fix_autos=fix_autos,
)
def read_uvfits(
self,
filename,
antenna_nums=None,
antenna_names=None,
ant_str=None,
bls=None,
frequencies=None,
freq_chans=None,
times=None,
time_range=None,
lsts=None,
lst_range=None,
polarizations=None,
blt_inds=None,
keep_all_metadata=True,
read_data=True,
background_lsts=True,
run_check=True,
check_extra=True,
run_check_acceptability=True,
strict_uvw_antpos_check=False,
fix_old_proj=False,
fix_use_ant_pos=True,
check_autos=True,
fix_autos=True,
):
"""
Read in header, metadata and data from a uvfits file.
Supports reading only selected portions of the data.
Parameters
----------
filename : str
The uvfits file to read from.
antenna_nums : array_like of int, optional
The antennas numbers to include when reading data into the object
(antenna positions and names for the removed antennas will be retained
unless `keep_all_metadata` is False). This cannot be provided if
`antenna_names` is also provided. Ignored if read_data is False.
antenna_names : array_like of str, optional
The antennas names to include when reading data into the object
(antenna positions and names for the removed antennas will be retained
unless `keep_all_metadata` is False). This cannot be provided if
`antenna_nums` is also provided. Ignored if read_data is False.
bls : list of tuple, optional
A list of antenna number tuples (e.g. [(0, 1), (3, 2)]) or a list of
baseline 3-tuples (e.g. [(0, 1, 'xx'), (2, 3, 'yy')]) specifying baselines
to include when reading data into the object. For length-2 tuples,
the ordering of the numbers within the tuple does not matter. For
length-3 tuples, the polarization string is in the order of the two
antennas. If length-3 tuples are provided, `polarizations` must be
None. Ignored if read_data is False.
ant_str : str, optional
A string containing information about what antenna numbers
and polarizations to include when reading data into the object.
Can be 'auto', 'cross', 'all', or combinations of antenna numbers
and polarizations (e.g. '1', '1_2', '1x_2y'). See tutorial for more
examples of valid strings and the behavior of different forms for ant_str.
If '1x_2y,2y_3y' is passed, both polarizations 'xy' and 'yy' will
be kept for both baselines (1, 2) and (2, 3) to return a valid
pyuvdata object.
An ant_str cannot be passed in addition to any of `antenna_nums`,
`antenna_names`, `bls` args or the `polarizations` parameters,
if it is a ValueError will be raised. Ignored if read_data is False.
frequencies : array_like of float, optional
The frequencies to include when reading data into the object, each
value passed here should exist in the freq_array. Ignored if
read_data is False.
freq_chans : array_like of int, optional
The frequency channel numbers to include when reading data into the
object. Ignored if read_data is False.
times : array_like of float, optional
The times to include when reading data into the object, each value
passed here should exist in the time_array.
time_range : array_like of float, optional
The time range in Julian Date to keep in the object, must be
length 2. Some of the times in the object should fall between the
first and last elements. Cannot be used with `times`.
lsts : array_like of float, optional
The local sidereal times (LSTs) to keep in the object, each value
passed here should exist in the lst_array. Cannot be used with
`times`, `time_range`, or `lst_range`.
lst_range : array_like of float, optional
The local sidereal time (LST) range in radians to keep in the
object, must be of length 2. Some of the LSTs in the object should
fall between the first and last elements. If the second value is
smaller than the first, the LSTs are treated as having phase-wrapped
around LST = 2*pi = 0, and the LSTs kept on the object will run from
the larger value, through 0, and end at the smaller value.
polarizations : array_like of int, optional
The polarizations numbers to include when reading data into the
object, each value passed here should exist in the polarization_array.
Ignored if read_data is False.
blt_inds : array_like of int, optional
The baseline-time indices to include when reading data into the
object. This is not commonly used. Ignored if read_data is False.
keep_all_metadata : bool
Option to keep all the metadata associated with antennas, even those
that do not have data associated with them after the select option.
read_data : bool
Read in the visibility, nsample and flag data. If set to False, only
the metadata will be read in. Setting read_data to False results in
a metadata only object.
background_lsts : bool
When set to True, the lst_array is calculated in a background thread.
run_check : bool
Option to check for the existence and proper shapes of parameters
after after reading in the file (the default is True,
meaning the check will be run). Ignored if read_data is False.
check_extra : bool
Option to check optional parameters as well as required ones (the
default is True, meaning the optional parameters will be checked).
Ignored if read_data is False.
run_check_acceptability : bool
Option to check acceptable range of the values of parameters after
reading in the file (the default is True, meaning the acceptable
range check will be done). Ignored if read_data is False.
strict_uvw_antpos_check : bool
Option to raise an error rather than a warning if the check that
uvws match antenna positions does not pass.
fix_old_proj : bool
Applies a fix to uvw-coordinates and phasing, assuming that the old `phase`
method was used prior to writing the data, which had errors of the order of
one part in 1e4 - 1e5. See the phasing memo for more details. Default is
False.
fix_use_ant_pos : bool
If setting `fix_old_proj` to True, use the antenna positions to derive the
correct uvw-coordinates rather than using the baseline vectors. Default is
True.
check_autos : bool
Check whether any auto-correlations have non-zero imaginary values in
data_array (which should not mathematically exist). Default is True.
fix_autos : bool
If auto-correlations with imaginary values are found, fix those values so
that they are real-only in data_array. Default is True.
Raises
------
IOError
If filename doesn't exist.
ValueError
If incompatible select keywords are set (e.g. `ant_str` with other
antenna selectors, `times` and `time_range`) or select keywords
exclude all data or if keywords are set to the wrong type.
If the data have multi spw with different channel widths.
If the metadata are not internally consistent or missing.
"""
# update filename attribute
basename = os.path.basename(filename)
self.filename = [basename]
self._filename.form = (1,)
with fits.open(filename, memmap=True) as hdu_list:
vis_hdu = hdu_list[0] # assumes the visibilities are in the primary hdu
vis_hdr = vis_hdu.header.copy()
hdunames = uvutils._fits_indexhdus(hdu_list) # find the rest of the tables
# First get everything we can out of the header.
self._set_phased()
# check if we have an spw dimension
if vis_hdr["NAXIS"] == 7:
self.Nspws = vis_hdr.pop("NAXIS5")
self.spw_array = (
uvutils._fits_gethduaxis(vis_hdu, 5).astype(np.int64) - 1
)
# the axis number for phase center depends on if the spw exists
self.phase_center_ra_degrees = float(vis_hdr.pop("CRVAL6"))
self.phase_center_dec_degrees = float(vis_hdr.pop("CRVAL7"))
else:
self.Nspws = 1
self.spw_array = np.array([np.int64(0)])
# the axis number for phase center depends on if the spw exists
self.phase_center_ra_degrees = float(vis_hdr.pop("CRVAL5"))
self.phase_center_dec_degrees = float(vis_hdr.pop("CRVAL6"))
# get shapes
self.Npols = vis_hdr.pop("NAXIS3")
self.Nblts = vis_hdr.pop("GCOUNT")
if self.Nspws > 1:
# If this is multi-spw, use the 'flexible' spectral window setup
self._set_flex_spw()
uvfits_nchan = vis_hdr.pop("NAXIS4")
self.Nfreqs = uvfits_nchan * self.Nspws
self.flex_spw_id_array = np.transpose(
np.tile(np.arange(self.Nspws), (uvfits_nchan, 1))
).flatten()
fq_hdu = hdu_list[hdunames["AIPS FQ"]]
assert self.Nspws == fq_hdu.header["NO_IF"]
# TODO: This is fine for now, although I (karto) think that this
# is relative to the ref_freq, which can be specified as part of
# the AIPS SU table.
# Get rest freq value
ref_freq = uvutils._fits_gethduaxis(vis_hdu, 4)[0]
self.channel_width = np.transpose(
np.tile(abs(fq_hdu.data["CH WIDTH"]), (uvfits_nchan, 1))
).flatten()
self.freq_array = np.reshape(
np.transpose(
(
ref_freq
+ fq_hdu.data["IF FREQ"]
+ np.outer(np.arange(uvfits_nchan), fq_hdu.data["CH WIDTH"])
)
),
(1, -1),
)
else:
self.Nfreqs = vis_hdr.pop("NAXIS4")
self.freq_array = uvutils._fits_gethduaxis(vis_hdu, 4)
# TODO: Spw axis to be collapsed in future release
self.freq_array.shape = (1,) + self.freq_array.shape
self.channel_width = vis_hdr.pop("CDELT4")
self.polarization_array = np.int32(uvutils._fits_gethduaxis(vis_hdu, 3))
# other info -- not required but frequently used
self.object_name = vis_hdr.pop("OBJECT", None)
self.telescope_name = vis_hdr.pop("TELESCOP", None)
self.instrument = vis_hdr.pop("INSTRUME", None)
latitude_degrees = vis_hdr.pop("LAT", None)
longitude_degrees = vis_hdr.pop("LON", None)
altitude = vis_hdr.pop("ALT", None)
self.x_orientation = vis_hdr.pop("XORIENT", None)
blt_order_str = vis_hdr.pop("BLTORDER", None)
if blt_order_str is not None:
self.blt_order = tuple(blt_order_str.split(", "))
if self.blt_order == ("bda",):
self._blt_order.form = (1,)
self.history = str(vis_hdr.get("HISTORY", ""))
if not uvutils._check_history_version(
self.history, self.pyuvdata_version_str
):
self.history += self.pyuvdata_version_str
self.vis_units = vis_hdr.pop("BUNIT", "uncalib")
# Added here as a fix since some previous versions of UVData allowed for
# all caps versions of UNCALIB.
if self.vis_units == "UNCALIB":
self.vis_units = "uncalib"
self.phase_center_epoch = vis_hdr.pop("EPOCH", None)
# PHSFRAME is not a standard UVFITS keyword, but was used by older
# versions of pyuvdata. To ensure backwards compatibility, we look
# for it first to determine the coordinate frame for the data
self.phase_center_frame = vis_hdr.pop("PHSFRAME", None)
# If we don't find the special keyword PHSFRAME, try for the more
# FITS-standard RADESYS
if self.phase_center_frame is None:
self.phase_center_frame = vis_hdr.pop("RADESYS", None)
# If we still don't find anything, try the two 'special' variant names
# for the coordinate frame that seem to have been documented
if self.phase_center_frame is None:
self.phase_center_frame = vis_hdr.pop("RADESYSA", None)
if self.phase_center_frame is None:
self.phase_center_frame = vis_hdr.pop("RADESYSa", None)
# If we _still_ can't find anything, take a guess based on the value
# listed in the EPOCH. The behavior listed here is based off of the
# AIPS task REGRD (http://www.aips.nrao.edu/cgi-bin/ZXHLP2.PL?REGRD)
if self.phase_center_frame is None:
if self.phase_center_epoch is None:
self.phase_center_frame = "icrs"
else:
frame = "fk4" if (self.phase_center_epoch == 1950.0) else "fk5"
self.phase_center_frame = frame
self.extra_keywords = uvutils._get_fits_extra_keywords(
vis_hdr, keywords_to_skip=["DATE-OBS"]
)
# Next read the antenna table
ant_hdu = hdu_list[hdunames["AIPS AN"]]
# stuff in the header
if self.telescope_name is None:
self.telescope_name = ant_hdu.header["ARRNAM"]
self.gst0 = ant_hdu.header["GSTIA0"]
self.rdate = ant_hdu.header["RDATE"]
self.earth_omega = ant_hdu.header["DEGPDY"]
self.dut1 = ant_hdu.header["UT1UTC"]
if "TIMESYS" in ant_hdu.header.keys():
self.timesys = ant_hdu.header["TIMESYS"]
else:
# CASA misspells this one
self.timesys = ant_hdu.header["TIMSYS"]
if "FRAME" in ant_hdu.header.keys():
xyz_telescope_frame = ant_hdu.header["FRAME"]
else:
warnings.warn(
"Required Antenna keyword 'FRAME' not set; "
"Assuming frame is 'ITRF'."
)
xyz_telescope_frame = "ITRF"
# get telescope location and antenna positions.
# VLA incorrectly sets ARRAYX/ARRAYY/ARRAYZ to 0, and puts array center
# in the antenna positions themselves
if (
np.isclose(ant_hdu.header["ARRAYX"], 0)
and np.isclose(ant_hdu.header["ARRAYY"], 0)
and np.isclose(ant_hdu.header["ARRAYZ"], 0)
):
x_telescope = np.mean(ant_hdu.data["STABXYZ"][:, 0])
y_telescope = np.mean(ant_hdu.data["STABXYZ"][:, 1])
z_telescope = np.mean(ant_hdu.data["STABXYZ"][:, 2])
self.antenna_positions = ant_hdu.data.field("STABXYZ") - np.array(
[x_telescope, y_telescope, z_telescope]
)
else:
x_telescope = ant_hdu.header["ARRAYX"]
y_telescope = ant_hdu.header["ARRAYY"]
z_telescope = ant_hdu.header["ARRAYZ"]
# AIPS memo #117 says that antenna_positions should be relative to
# the array center, but in a rotated ECEF frame so that the x-axis
# goes through the local meridian.
rot_ecef_positions = ant_hdu.data.field("STABXYZ")
latitude, longitude, altitude = uvutils.LatLonAlt_from_XYZ(
np.array([x_telescope, y_telescope, z_telescope]),
check_acceptability=run_check_acceptability,
)
self.antenna_positions = uvutils.ECEF_from_rotECEF(
rot_ecef_positions, longitude
)
if xyz_telescope_frame == "ITRF":
self.telescope_location = np.array(
[x_telescope, y_telescope, z_telescope]
)
else:
if (
latitude_degrees is not None
and longitude_degrees is not None
and altitude is not None
):
self.telescope_location_lat_lon_alt_degrees = (
latitude_degrees,
longitude_degrees,
altitude,
)
# stuff in columns
ant_names = ant_hdu.data.field("ANNAME").tolist()
self.antenna_names = []
for name in ant_names:
# Sometimes CASA writes antnames as bytes not strings.
# If the ant name is shorter than 8 characters, the trailing
# characters may be non-ascii.
# This is technically a FITS violation as FITS requires ascii.
# So we just ignore any non-ascii bytes in the decode.
if isinstance(name, bytes):
ant_name_str = str(name.decode("utf-8", "ignore"))
else:
ant_name_str = name
# remove non-printing ascii characters and exclamation points
ant_name_str = (
ant_name_str.replace("\x00", "")
.replace("\x07", "")
.replace("!", "")
)
self.antenna_names.append(ant_name_str)
# Note: we no longer subtract one to get to 0-indexed values
# rather than 1-indexed values. Antenna numbers are not indices
# but are unique to each antenna.
self.antenna_numbers = ant_hdu.data.field("NOSTA")
self.Nants_telescope = len(self.antenna_numbers)
if "DIAMETER" in ant_hdu.columns.names:
self.antenna_diameters = ant_hdu.data.field("DIAMETER")
try:
self.set_telescope_params()
except ValueError as ve:
warnings.warn(str(ve))
# Now read in the random parameter info
self._get_parameter_data(
vis_hdu,
run_check_acceptability,
background_lsts=background_lsts,
)
# If we find the source attribute in the FITS random paramter list,
# the multi_phase_center attribute will be set to True, and we should also
# expect that there must be an AIPS SU table.
if self.multi_phase_center and "AIPS SU" not in hdunames.keys():
warnings.warn(
"UVFITS file is missing AIPS SU table, which is required when "
"SOURCE is one of the `random paramters` in the main binary "
"table. Bypassing for now, but note that this file _may_ not "
"work correctly in UVFITS-based programs (e.g., AIPS, CASA)."
)
cat_id = list(self.phase_center_catalog)[0]
self.object_name = self.phase_center_catalog[cat_id]["cat_name"]
self.phase_center_ra = self.phase_center_catalog[cat_id]["cat_lon"]
self.phase_center_dec = self.phase_center_catalog[cat_id]["cat_lat"]
self.phase_center_frame = self.phase_center_catalog[cat_id]["cat_frame"]
self.phase_center_epoch = self.phase_center_catalog[cat_id]["cat_epoch"]
self.multi_phase_center = False
self._phase_center_id_array.required = False
self._Nphase.required = False
self._phase_center_catalog.required = False
self.Nphase = None
self.phase_center_catalog = None
self.phase_center_id_array = None
elif self.multi_phase_center:
su_hdu = hdu_list[hdunames["AIPS SU"]]
# We should have as many entries in the AIPS SU header as we have
# unique entries in the SOURCES random paramter (checked in the call
# to get_parameter_data above)
if len(su_hdu.data) != len(np.unique(self.phase_center_id_array)):
raise RuntimeError(
"The UVFITS file has a malformed AIPS SU table - number of "
"sources do not match the number of unique source IDs in the "
"primary data header."
) # pragma: no cover
# Reset the catalog, since it has some dummy information stored within
# it (that was pulled off the primary table)
self._remove_phase_center(list(self.phase_center_catalog)[0])
# Set up these arrays so we can assign values to them
self.phase_center_app_ra = np.zeros(self.Nblts)
self.phase_center_app_dec = np.zeros(self.Nblts)
self.phase_center_app_pa = np.zeros(self.Nblts)
# Alright, we are off to the races!
for idx in range(len(su_hdu.data)):
# Grab the indv source entry
sou_info = su_hdu.data[idx]
sou_id = sou_info["ID. NO."]
sou_name = sou_info["SOURCE"]
sou_ra = sou_info["RAEPO"] * (np.pi / 180.0)
sou_dec = sou_info["DECEPO"] * (np.pi / 180.0)
sou_epoch = sou_info["EPOCH"]
sou_frame = "fk5"
self._add_phase_center(
sou_name,
cat_id=sou_id,
cat_type="sidereal",
cat_lon=sou_ra,
cat_lat=sou_dec,
cat_frame=sou_frame,
cat_epoch=sou_epoch,
info_source="uvfits file",
)
# Calculate the apparent coordinate values
self._set_app_coords_helper()
# fix up the uvws if in the NCP baseline coordinate frame.
# Must be done here because it requires the phase_center_app_dec
if "UU---NCP" in vis_hdu.data.parnames:
self.uvw_array = uvutils._rotate_one_axis(
self.uvw_array[:, :, None], self.phase_center_app_dec - np.pi / 2, 0
)[:, :, 0]
if not read_data:
# don't read in the data. This means the object is a metadata
# only object but that may not matter for many purposes.
return
# Now read in the data
self._get_data(
vis_hdu,
antenna_nums,
antenna_names,
ant_str,
bls,
frequencies,
freq_chans,
times,
time_range,
lsts,
lst_range,
polarizations,
blt_inds,
False,
keep_all_metadata,
run_check,
check_extra,
run_check_acceptability,
strict_uvw_antpos_check,
fix_old_proj,
fix_use_ant_pos,
check_autos,
fix_autos,
)
def write_uvfits(
self,
filename,
spoof_nonessential=False,
write_lst=True,
force_phase=False,
run_check=True,
check_extra=True,
run_check_acceptability=True,
strict_uvw_antpos_check=False,
check_autos=True,
fix_autos=False,
):
"""
Write the data to a uvfits file.
If using this method to write out a data set for import into CASA, users should
be aware that the `importuvifts` task does not currently support reading in
data sets where the number of antennas is > 255. If writing out such a data set
for use in CASA, we suggest using the measurement set writer (`UVData.write_ms`)
instead.
Parameters
----------
filename : str
The uvfits file to write to.
spoof_nonessential : bool
Option to spoof the values of optional UVParameters that are not set
but are required for uvfits files. This keyword is now deprecated, as values
are automatically set to their best known values if not previously set.
write_lst : bool
Option to write the LSTs to the metadata (random group parameters).
force_phase : bool
Option to automatically phase drift scan data to zenith of the first
timestamp.
run_check : bool
Option to check for the existence and proper shapes of parameters
before writing the file.
check_extra : bool
Option to check optional parameters as well as required ones.
run_check_acceptability : bool
Option to check acceptable range of the values of parameters before
writing the file.
strict_uvw_antpos_check : bool
Option to raise an error rather than a warning if the check that
uvws match antenna positions does not pass.
check_autos : bool
Check whether any auto-correlations have non-zero imaginary values in
data_array (which should not mathematically exist). Default is True.
fix_autos : bool
If auto-correlations with imaginary values are found, fix those values so
that they are real-only in data_array. Default is False.
Raises
------
ValueError
The `phase_type` of the object is "drift" and the `force_phase`
keyword is not set.
If the frequencies are not evenly spaced or are separated by more
than their channel width.
The polarization values are not evenly spaced.
If the `timesys` parameter is set to anything other than "UTC" or None.
TypeError
If any entry in extra_keywords is not a single string or number.
"""
if run_check:
self.check(
check_extra=check_extra,
run_check_acceptability=run_check_acceptability,
check_freq_spacing=True,
strict_uvw_antpos_check=strict_uvw_antpos_check,
check_autos=check_autos,
fix_autos=fix_autos,
)
if spoof_nonessential:
warnings.warn(
(
"UVFITS-required metadata are now set automatically to their "
'best known values, and no longer need to be "spoofed". As such, '
"the spoof_nonessential parameter is deprecated, and will be "
"removed in a future release."
),
DeprecationWarning,
)
if self.phase_type == "phased":
pass
elif self.phase_type == "drift":
if force_phase:
print(
"The data are in drift mode and do not have a "
"defined phase center. Phasing to zenith of the first "
"timestamp."
)
phase_time = Time(self.time_array[0], format="jd")
self.phase_to_time(phase_time)
else:
raise ValueError(
"The data are in drift mode. "
"Set force_phase to true to phase the data "
"to zenith of the first timestamp before "
"writing a uvfits file."
)
if self.flex_spw:
# If we have a 'flexible' spectral window, we will need to evaluate the
# frequency axis slightly differently.
if self.future_array_shapes:
freq_array_use = self.freq_array
else:
freq_array_use = self.freq_array[0, :]
nchan_list = []
start_freq_array = []
delta_freq_array = []
for idx in self.spw_array:
chan_mask = self.flex_spw_id_array == idx
nchan_list += [np.sum(chan_mask)]
start_freq_array += [freq_array_use[chan_mask][0]]
# Need the array direction here since channel_width is always supposed
# to be > 0, but channels can be in decending freq order
freq_dir = np.sign(np.median(np.diff(freq_array_use[chan_mask])))
delta_freq_array += [
np.median(self.channel_width[chan_mask]) * freq_dir
]
start_freq_array = np.reshape(np.array(start_freq_array), (1, -1)).astype(
np.float64
)
delta_freq_array = np.reshape(np.array(delta_freq_array), (1, -1)).astype(
np.float64
)
# We've constructed a couple of lists with relevant values, now time to
# check them to make sure that the data will write correctly
# Make sure that all the windows are of the same size
if len(np.unique(nchan_list)) != 1:
raise IndexError(
"UVFITS format cannot handle spectral windows of different sizes!"
)
# Make sure freq values are greater zero. Note that I think _technically
# one could write negative frequencies into the dataset, but I am pretty
# sure that reduction packages may balk hard.
if np.any(start_freq_array <= 0):
raise ValueError("Frequency values must be > 0 for UVFITS!")
# Make sure the delta values are non-zero
if np.any(delta_freq_array == 0):
raise ValueError("Something is wrong, frequency values not unique!")
# If we passed all the above checks, then it's time to fill some extra
# array values. Note that 'ref_freq' is something of a placeholder for
# other exciting things...
ref_freq = start_freq_array[0, 0]
else:
if self.future_array_shapes:
ref_freq = self.freq_array[0]
# we've already run the check_freq_spacing, so channel widths are the
# same to our tolerances
delta_freq_array = np.array([[np.median(self.channel_width)]]).astype(
np.float64
)
else:
ref_freq = self.freq_array[0, 0]
delta_freq_array = np.array([[self.channel_width]]).astype(np.float64)
if self.Npols > 1:
pol_indexing = np.argsort(np.abs(self.polarization_array))
polarization_array = self.polarization_array[pol_indexing]
if not uvutils._test_array_constant_spacing(polarization_array):
raise ValueError(
"The polarization values are not evenly spaced (probably "
"because of a select operation). The uvfits format "
"does not support unevenly spaced polarizations."
)
pol_spacing = polarization_array[1] - polarization_array[0]
else:
pol_indexing = np.asarray([0])
polarization_array = self.polarization_array
pol_spacing = 1
# check for unflagged data with nsample = 0. Warn if any found
wh_nsample0 = np.where(self.nsample_array == 0)
if np.any(~self.flag_array[wh_nsample0]):
warnings.warn(
"Some unflagged data has nsample = 0. Flags and "
"nsamples are combined in uvfits files such that "
"these data will appear to be flagged."
)
uvfits_data_shape = (
self.Nblts,
1,
1,
self.Nspws,
self.Nfreqs // self.Nspws,
self.Npols,
1,
)
# Reshape the arrays so that they match the uvfits conventions
# FITS uvw direction convention is opposite ours and Miriad's.
# So conjugate the visibilities and flip the uvws:
data_array = np.reshape(np.conj(self.data_array), uvfits_data_shape)
weights_array = np.reshape(
self.nsample_array * np.where(self.flag_array, -1, 1),
uvfits_data_shape,
)
data_array = data_array[:, :, :, :, :, pol_indexing, :]
weights_array = weights_array[:, :, :, :, :, pol_indexing, :]
uvfits_array_data = np.concatenate(
[data_array.real, data_array.imag, weights_array], axis=6
)
# FITS uvw direction convention is opposite ours and Miriad's.
# So conjugate the visibilities and flip the uvws:
uvw_array_sec = -1 * self.uvw_array / const.c.to("m/s").value
# uvfits convention is that there are two float32 time_arrays and the
# float64 sum of them + relevant PZERO = actual JD
# a common practice is to set the PZERO to the JD at midnight of the first time
jd_midnight = np.floor(self.time_array[0] - 0.5) + 0.5
time_array1 = np.float32(self.time_array - jd_midnight)
time_array2 = np.float32(
self.time_array - jd_midnight - np.float64(time_array1)
)
int_time_array = self.integration_time
baselines_use = self.antnums_to_baseline(
self.ant_1_array, self.ant_2_array, attempt256=True
)
# Set up dictionaries for populating hdu
# Antenna arrays are populated with actual antenna numbers,
# that is, numbers that are unique to each antenna.
# We no longer add 1 to the arrays as the arrays are not indices.
group_parameter_dict = {
"UU ": uvw_array_sec[:, 0],
"VV ": uvw_array_sec[:, 1],
"WW ": uvw_array_sec[:, 2],
"DATE ": time_array1,
"DATE2 ": time_array2,
"BASELINE": baselines_use,
"SOURCE ": None,
"FREQSEL ": np.ones_like(self.time_array, dtype=np.float32),
"ANTENNA1": self.ant_1_array,
"ANTENNA2": self.ant_2_array,
"SUBARRAY": np.ones_like(self.ant_1_array),
"INTTIM ": int_time_array,
}
if self.multi_phase_center:
id_offset = int(0 in self.phase_center_catalog)
group_parameter_dict["SOURCE "] = self.phase_center_id_array + id_offset
pscal_dict = {
"UU ": 1.0,
"VV ": 1.0,
"WW ": 1.0,
"DATE ": 1.0,
"DATE2 ": 1.0,
"BASELINE": 1.0,
"SOURCE ": 1.0,
"FREQSEL ": 1.0,
"ANTENNA1": 1.0,
"ANTENNA2": 1.0,
"SUBARRAY": 1.0,
"INTTIM ": 1.0,
}
pzero_dict = {
"UU ": 0.0,
"VV ": 0.0,
"WW ": 0.0,
"DATE ": jd_midnight,
"DATE2 ": 0.0,
"BASELINE": 0.0,
"SOURCE ": 0.0,
"FREQSEL ": 0.0,
"ANTENNA1": 0.0,
"ANTENNA2": 0.0,
"SUBARRAY": 0.0,
"INTTIM ": 0.0,
}
if write_lst:
# lst is a non-standard entry (it's not in the AIPS memo)
# but storing it can be useful (e.g. can avoid recalculating it on read)
# need to store it in 2 parts to get enough accuracy
# angles in uvfits files are stored in degrees, so first convert to degrees
lst_array_deg = np.rad2deg(self.lst_array)
lst_array_1 = np.float32(lst_array_deg)
lst_array_2 = np.float32(lst_array_deg - np.float64(lst_array_1))
group_parameter_dict["LST "] = lst_array_1
pscal_dict["LST "] = 1.0
pzero_dict["LST "] = 0.0
# list contains arrays of [u,v,w,date,baseline];
# each array has shape (Nblts)
parnames_use = ["UU ", "VV ", "WW ", "DATE ", "DATE2 "]
if np.max(self.ant_1_array) < 255 and np.max(self.ant_2_array) < 255:
# if the number of antennas is less than 256 then include both the
# baseline array and the antenna arrays in the group parameters.
# Otherwise just use the antenna arrays
parnames_use.append("BASELINE")
else:
warnings.warn(
"Found antenna numbers > 255 in this data set. This is permitted by "
"UVFITS standards, but may cause the `importuvfits` utility within "
"CASA to crash. If attempting to use this data set in CASA, consider "
"using the measurement set writer method (`write_ms`) instead."
)
if self.multi_phase_center:
parnames_use.append("SOURCE ")
parnames_use += ["ANTENNA1", "ANTENNA2", "SUBARRAY", "INTTIM "]
if write_lst:
parnames_use.append("LST ")
group_parameter_list = [
group_parameter_dict[parname] for parname in parnames_use
]
if write_lst:
# add second LST array part
parnames_use.append("LST ")
group_parameter_list.append(lst_array_2)
parnames_use_datefix = copy.deepcopy(parnames_use)
parnames_use_datefix[parnames_use_datefix.index("DATE2 ")] = "DATE "
hdu = fits.GroupData(
uvfits_array_data,
parnames=parnames_use_datefix,
pardata=group_parameter_list,
bitpix=-32,
)
hdu = fits.GroupsHDU(hdu)
for i, key in enumerate(parnames_use):
hdu.header["PSCAL" + str(i + 1) + " "] = pscal_dict[key]
hdu.header["PZERO" + str(i + 1) + " "] = pzero_dict[key]
# ISO string of first time in self.time_array
hdu.header["DATE-OBS"] = Time(self.time_array[0], scale="utc", format="jd").isot
hdu.header["CTYPE2 "] = "COMPLEX "
hdu.header["CRVAL2 "] = 1.0
hdu.header["CRPIX2 "] = 1.0
hdu.header["CDELT2 "] = 1.0
# Note: This axis is called STOKES to comply with the AIPS memo 117
# However, this confusing because it is NOT a true Stokes axis,
# it is really the polarization axis.
hdu.header["CTYPE3 "] = "STOKES "
hdu.header["CRVAL3 "] = float(polarization_array[0])
hdu.header["CRPIX3 "] = 1.0
hdu.header["CDELT3 "] = float(pol_spacing)
hdu.header["CTYPE4 "] = "FREQ "
hdu.header["CRVAL4 "] = ref_freq
hdu.header["CRPIX4 "] = 1.0
hdu.header["CDELT4 "] = delta_freq_array[0, 0]
hdu.header["CTYPE5 "] = "IF "
hdu.header["CRVAL5 "] = 1.0
hdu.header["CRPIX5 "] = 1.0
hdu.header["CDELT5 "] = 1.0
hdu.header["CTYPE6 "] = "RA"
hdu.header["CRVAL6 "] = self.phase_center_ra_degrees
hdu.header["CTYPE7 "] = "DEC"
hdu.header["CRVAL7 "] = self.phase_center_dec_degrees
hdu.header["BUNIT "] = self.vis_units
hdu.header["BSCALE "] = 1.0
hdu.header["BZERO "] = 0.0
name = "MULTI" if self.multi_phase_center else self.object_name
hdu.header["OBJECT "] = name
hdu.header["TELESCOP"] = self.telescope_name
hdu.header["LAT "] = self.telescope_location_lat_lon_alt_degrees[0]
hdu.header["LON "] = self.telescope_location_lat_lon_alt_degrees[1]
hdu.header["ALT "] = self.telescope_location_lat_lon_alt[2]
hdu.header["INSTRUME"] = self.instrument
if self.phase_center_epoch is not None:
hdu.header["EPOCH "] = float(self.phase_center_epoch)
# TODO: This is a keyword that should at some point get added for velocity
# reference stuff, although for right now pyuvdata doesn't do any sort of
# handling of this, so stub this out for now.
# hdu.header["SPECSYS "] = "TOPOCENT"
if self.phase_center_frame is not None:
# Previous versions of pyuvdata wrote this header as PHSFRAME
hdu.header["RADESYS"] = self.phase_center_frame
if self.x_orientation is not None:
hdu.header["XORIENT"] = self.x_orientation
if self.blt_order is not None:
blt_order_str = ", ".join(self.blt_order)
hdu.header["BLTORDER"] = blt_order_str
for line in self.history.splitlines():
hdu.header.add_history(line)
# end standard keywords; begin user-defined keywords
for key, value in self.extra_keywords.items():
# header keywords have to be 8 characters or less
if len(str(key)) > 8:
warnings.warn(
"key {key} in extra_keywords is longer than 8 "
"characters. It will be truncated to 8 as required "
"by the uvfits file format.".format(key=key)
)
keyword = key[:8].upper()
if isinstance(value, (dict, list, np.ndarray)):
raise TypeError(
"Extra keyword {keyword} is of {keytype}. "
"Only strings and numbers are "
"supported in uvfits.".format(keyword=key, keytype=type(value))
)
if keyword == "COMMENT":
for line in value.splitlines():
hdu.header.add_comment(line)
else:
hdu.header[keyword] = value
# ADD the ANTENNA table
staxof = np.zeros(self.Nants_telescope)
# 0 specifies alt-az, 6 would specify a phased array
mntsta = np.zeros(self.Nants_telescope)
# beware, X can mean just about anything
poltya = np.full((self.Nants_telescope), "X", dtype=np.object_)
polaa = [90.0] + np.zeros(self.Nants_telescope)
poltyb = np.full((self.Nants_telescope), "Y", dtype=np.object_)
polab = [0.0] + np.zeros(self.Nants_telescope)
col1 = fits.Column(name="ANNAME", format="8A", array=self.antenna_names)
# AIPS memo #117 says that antenna_positions should be relative to
# the array center, but in a rotated ECEF frame so that the x-axis
# goes through the local meridian.
longitude = self.telescope_location_lat_lon_alt[1]
rot_ecef_positions = uvutils.rotECEF_from_ECEF(
self.antenna_positions, longitude
)
col2 = fits.Column(name="STABXYZ", format="3D", array=rot_ecef_positions)
# col3 = fits.Column(name="ORBPARAM", format="0D", array=Norb)
col4 = fits.Column(name="NOSTA", format="1J", array=self.antenna_numbers)
col5 = fits.Column(name="MNTSTA", format="1J", array=mntsta)
col6 = fits.Column(name="STAXOF", format="1E", array=staxof)
col7 = fits.Column(name="POLTYA", format="1A", array=poltya)
col8 = fits.Column(name="POLAA", format="1E", array=polaa)
# col9 = fits.Column(name='POLCALA', format='0E', array=Npcal, Nspws)
col10 = fits.Column(name="POLTYB", format="1A", array=poltyb)
col11 = fits.Column(name="POLAB", format="1E", array=polab)
# col12 = fits.Column(name='POLCALB', format='0E', array=Npcal, Nspws)
col_list = [col1, col2, col4, col5, col6, col7, col8, col10, col11]
# The commented out entires are up above to help check for consistency with the
# UVFITS format. ORBPARAM, POLCALA, and POLCALB are all technically required,
# but are all of zero length. Added here to help with debugging.
if self.antenna_diameters is not None:
col12 = fits.Column(
name="DIAMETER", format="1E", array=self.antenna_diameters
)
col_list.append(col12)
cols = fits.ColDefs(col_list)
ant_hdu = fits.BinTableHDU.from_columns(cols)
ant_hdu.header["EXTNAME"] = "AIPS AN"
ant_hdu.header["EXTVER"] = 1
# write XYZ coordinates
ant_hdu.header["ARRAYX"] = self.telescope_location[0]
ant_hdu.header["ARRAYY"] = self.telescope_location[1]
ant_hdu.header["ARRAYZ"] = self.telescope_location[2]
ant_hdu.header["FRAME"] = "ITRF"
# TODO Karto: Do this more intelligently in the future
if self.future_array_shapes:
ant_hdu.header["FREQ"] = self.freq_array[0]
else:
ant_hdu.header["FREQ"] = self.freq_array[0, 0]
if (self.rdate is None) or (self.rdate == ""):
rdate_obj = Time(np.floor(self.time_array[0]), format="jd", scale="utc")
else:
try:
rdate_obj = Time(self.rdate, scale="utc")
except ValueError:
rdate_obj = Time(np.floor(self.time_array[0]), format="jd", scale="utc")
if self.rdate is None:
ant_hdu.header["RDATE"] = rdate_obj.strftime("%Y-%m-%d")
else:
ant_hdu.header["RDATE"] = self.rdate
if self.gst0 is None:
ant_hdu.header["GSTIA0"] = rdate_obj.sidereal_time("apparent", "tio").deg
else:
ant_hdu.header["GSTIA0"] = self.gst0
if self.dut1 is None:
ant_hdu.header["UT1UTC"] = float(rdate_obj.delta_ut1_utc)
else:
ant_hdu.header["UT1UTC"] = self.dut1
if not (self.timesys is None or self.timesys == "UTC"):
raise ValueError(
"This file has a time system {tsys}. Only "
'"UTC" time system files are supported'.format(tsys=self.timesys)
)
ant_hdu.header["TIMESYS"] = "UTC"
ant_hdu.header["ARRNAM"] = self.telescope_name
ant_hdu.header["NO_IF"] = self.Nspws
# Note the value below is basically 360 deg x num of sidereal days in a year /
# num of soalr days in a year.
ant_hdu.header["DEGPDY"] = (
360.9856438593 if self.earth_omega is None else self.earth_omega
)
# This is just a statically defined value
ant_hdu.header["IATUTC"] = 37.0
# set mandatory parameters which are not supported by this object
# (or that we just don't understand)
ant_hdu.header["NUMORB"] = 0
# note: Bart had this set to 3. We've set it 0 after aips 117. -jph
ant_hdu.header["NOPCAL"] = 0
ant_hdu.header["POLTYPE"] = "X-Y LIN"
# note: we do not support the concept of "frequency setups"
# -- lists of spws given in a SU table.
# Karto: Here might be a place to address freq setup?
ant_hdu.header["FREQID"] = 1
# if there are offsets in images, this could be the culprit
ant_hdu.header["POLARX"] = 0.0
ant_hdu.header["POLARY"] = 0.0
ant_hdu.header["DATUTC"] = 0 # ONLY UTC SUPPORTED
# we always output right handed coordinates
ant_hdu.header["XYZHAND"] = "RIGHT"
# At some point, we can fill these in more completely using astropy IERS
# utilities, since CASA/AIPS doesn't want to be told what the apparent coords
# are, but rather wants to calculate them itself.
# ant_hdu.header["RDATE"] = '2020-07-24T16:35:39.144087'
# ant_hdu.header["POLARX"] = 0.0
# ant_hdu.header["POLARY"] = 0.0
fits_tables = [hdu, ant_hdu]
# If needed, add the FQ table
if self.Nspws > 1:
fmt_d = "%iD" % self.Nspws
fmt_e = "%iE" % self.Nspws
fmt_j = "%iJ" % self.Nspws
# TODO Karto: Temp implementation until we fix some other things in UVData
if_freq = start_freq_array - ref_freq
ch_width = delta_freq_array
tot_bw = (self.Nfreqs // self.Nspws) * np.abs(delta_freq_array)
sideband = np.sign(delta_freq_array) * np.ones((1, self.Nspws))
# FRQSEL is hardcoded at the moment, could think about doing this
# at least somewhat more intelligently...
col_list = [
fits.Column(name="FRQSEL", format="1J", array=[1]),
fits.Column(name="IF FREQ", unit="HZ", format=fmt_d, array=if_freq),
fits.Column(name="CH WIDTH", unit="HZ", format=fmt_e, array=ch_width),
fits.Column(
name="TOTAL BANDWIDTH", unit="HZ", format=fmt_e, array=tot_bw
),
fits.Column(name="SIDEBAND", format=fmt_j, array=sideband),
]
fq_hdu = fits.BinTableHDU.from_columns(fits.ColDefs(col_list))
fq_hdu.header["EXTNAME"] = "AIPS FQ"
fq_hdu.header["NO_IF"] = self.Nspws
fits_tables.append(fq_hdu)
# If needed, add the SU table
if self.multi_phase_center:
fmt_d = "%iD" % self.Nspws
fmt_e = "%iE" % self.Nspws
fmt_j = "%iJ" % self.Nspws
int_zeros = np.zeros(self.Nphase, dtype=int)
flt_zeros = np.zeros(self.Nphase, dtype=np.float64)
zero_arr = np.zeros((self.Nphase, self.Nspws))
sou_ids = np.zeros(self.Nphase)
name_arr = np.array(
[ps_dict["cat_name"] for ps_dict in self.phase_center_catalog.values()]
)
cal_code = [" "] * self.Nphase
# These are things we need to flip through on a source-by-source basis
ra_arr = np.zeros(self.Nphase, dtype=np.float64)
app_ra = np.zeros(self.Nphase, dtype=np.float64)
dec_arr = np.zeros(self.Nphase, dtype=np.float64)
app_dec = np.zeros(self.Nphase, dtype=np.float64)
epo_arr = np.zeros(self.Nphase, dtype=np.float64)
pm_ra = np.zeros(self.Nphase, dtype=np.float64)
pm_dec = np.zeros(self.Nphase, dtype=np.float64)
rest_freq = np.zeros((self.Nphase, self.Nspws), dtype=np.float64)
for idx, cat_id in enumerate(self.phase_center_catalog):
phase_dict = self.phase_center_catalog[cat_id]
# This is a stub for something smarter in the future
sou_ids[idx] = cat_id + id_offset
rest_freq[idx][:] = np.mean(self.freq_array)
pm_ra[idx] = 0.0
pm_dec[idx] = 0.0
if phase_dict["cat_type"] == "sidereal":
# So here's the deal -- we need all the objects to be in the same
# coordinate frame, although nothing in phase_center_catalog forces
# objects to share the same frame. So we want to make sure that
# everything lines up with the coordinate frame listed.
ra_arr[idx], dec_arr[idx] = uvutils.transform_sidereal_coords(
phase_dict["cat_lon"],
phase_dict["cat_lat"],
phase_dict["cat_frame"],
"fk5",
in_coord_epoch=phase_dict.get("cat_epoch"),
out_coord_epoch=phase_dict.get("cat_epoch"),
time_array=np.mean(self.time_array),
)
epo_arr[idx] = (
phase_dict["cat_epoch"]
if "cat_epoch" in (phase_dict.keys())
else 2000.0
)
app_ra[idx] = np.median(
self.phase_center_app_ra[self.phase_center_id_array == cat_id]
)
app_dec[idx] = np.median(
self.phase_center_app_dec[self.phase_center_id_array == cat_id]
)
ra_arr *= 180.0 / np.pi
dec_arr *= 180.0 / np.pi
app_ra *= 180.0 / np.pi
app_dec *= 180.0 / np.pi
col_list = [
fits.Column(name="ID. NO.", format="1J", array=sou_ids),
fits.Column(name="SOURCE", format="20A", array=name_arr),
fits.Column(name="QUAL", format="1J", array=int_zeros),
fits.Column(name="CALCODE", format="4A", array=cal_code),
fits.Column(name="IFLUX", format=fmt_e, unit="JY", array=zero_arr),
fits.Column(name="QFLUX", format=fmt_e, unit="JY", array=zero_arr),
fits.Column(name="UFLUX", format=fmt_e, unit="JY", array=zero_arr),
fits.Column(name="VFLUX", format=fmt_e, unit="JY", array=zero_arr),
fits.Column(name="FREQOFF", format=fmt_d, unit="HZ", array=zero_arr),
fits.Column(name="BANDWIDTH", format="1D", unit="HZ", array=flt_zeros),
fits.Column(name="RAEPO", format="1D", unit="DEGREES", array=ra_arr),
fits.Column(name="DECEPO", format="1D", unit="DEGREES", array=dec_arr),
fits.Column(name="EPOCH", format="1D", unit="YEARS", array=epo_arr),
fits.Column(name="RAAPP", format="1D", unit="DEGREES", array=app_ra),
fits.Column(name="DECAPP", format="1D", unit="DEGREES", array=app_dec),
fits.Column(name="LSRVEL", format=fmt_d, unit="M/SEC", array=zero_arr),
fits.Column(name="RESTFREQ", format=fmt_d, unit="HZ", array=rest_freq),
fits.Column(name="PMRA", format="1D", unit="DEG/DAY", array=pm_ra),
fits.Column(name="PMDEC", format="1D", unit="DEG/DAY", array=pm_dec),
]
su_hdu = fits.BinTableHDU.from_columns(fits.ColDefs(col_list))
su_hdu.header["EXTNAME"] = "AIPS SU"
su_hdu.header["NO_IF"] = self.Nspws
su_hdu.header["FREQID"] = 1
su_hdu.header["VELDEF"] = "RADIO"
# TODO: Eventually we want to not have this hardcoded, but pyuvdata at
# present does not carry around any velocity information. As per usual,
# I (Karto) am tipping my hand on what I might be working on next...
su_hdu.header["VELTYP"] = "LSR"
fits_tables.append(su_hdu)
# write the file
hdulist = fits.HDUList(hdus=fits_tables)
hdulist.writeto(filename, overwrite=True)
hdulist.close()
