Source code for pyuvdata.uvdata.uvfits

# -*- 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 os
import copy
import warnings

import numpy as np
from astropy import constants as const
from astropy.time import Time
from astropy.io import fits

from .uvdata import UVData
from .. import utils as uvutils

__all__ = ["UVFITS"]


[docs]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. Attributes ---------- uvfits_required_extra : list of str Names of optional UVParameters that are required for uvfits. """ uvfits_required_extra = [ "antenna_positions", "gst0", "rdate", "earth_omega", "dut1", "timesys", ] 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: uvfits antennas are 1 indexed, # need to subtract one to get to 0-indexed self.ant_1_array = np.int32(vis_hdu.data.par("ANTENNA1")) - 1 self.ant_2_array = np.int32(vis_hdu.data.par("ANTENNA2")) - 1 subarray = np.int32(vis_hdu.data.par("SUBARRAY")) - 1 # 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) # 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("UU"), vis_hdu.data.par("VV"), vis_hdu.data.par("WW"), ) ) ) * 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, ): """ 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_metadata( 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, )
[docs] 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, ): """ 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. 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 ant_ind, name in enumerate(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) # subtract one to get to 0-indexed values rather than 1-indexed values self.antenna_numbers = ant_hdu.data.field("NOSTA") - 1 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)." ) name = list(self.phase_center_catalog.keys())[0] self.phase_center_ra = self.phase_center_catalog[name]["cat_lon"] self.phase_center_dec = self.phase_center_catalog[name]["cat_lat"] self.phase_center_frame = self.phase_center_catalog[name]["cat_frame"] self.phase_center_epoch = self.phase_center_catalog[name]["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.object_name = name 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.keys())[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() 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, )
[docs] 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, ): """ Write the data to a uvfits file. 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. 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. 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. Any of ['antenna_positions', 'gst0', 'rdate', 'earth_omega', 'dut1', 'timesys'] are not set on the object and `spoof_nonessential` is False. If the `timesys` parameter is not set to "UTC". 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, ) 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_spacing = np.diff(self.polarization_array) pol_indexing = np.argsort(np.abs(self.polarization_array)) polarization_array = self.polarization_array[pol_indexing] pol_spacing = np.diff(polarization_array) if np.min(pol_spacing) < np.max(pol_spacing): 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 = pol_spacing[0] else: pol_indexing = np.asarray([0]) polarization_array = self.polarization_array pol_spacing = 1 for p in self.extra(): param = getattr(self, p) if param.name in self.uvfits_required_extra: if param.value is None: if spoof_nonessential: param.apply_spoof() setattr(self, p, param) else: raise ValueError( "Required attribute {attribute} " "for uvfits not defined. Define or " "set spoof_nonessential to True to " "spoof this attribute.".format(attribute=p) ) # 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 # Note that uvfits antenna arrays are 1-indexed so we add 1 # to our 0-indexed arrays 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 + 1, "ANTENNA2": self.ant_2_array + 1, "SUBARRAY": np.ones_like(self.ant_1_array), "INTTIM ": int_time_array, } if self.multi_phase_center: id_offset = np.any( [ temp_dict["cat_id"] == 0 for temp_dict in self.phase_center_catalog.values() ] ) 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") 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) # convert to 1-indexed from 0-indexed indicies col4 = fits.Column(name="NOSTA", format="1J", array=self.antenna_numbers + 1) 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" ant_hdu.header["GSTIA0"] = self.gst0 # 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] ant_hdu.header["RDATE"] = self.rdate ant_hdu.header["UT1UTC"] = self.dut1 ant_hdu.header["TIMESYS"] = self.timesys if 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["ARRNAM"] = self.telescope_name ant_hdu.header["NO_IF"] = self.Nspws ant_hdu.header["DEGPDY"] = 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(list(self.phase_center_catalog.keys())) 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, name in enumerate(name_arr): phase_dict = self.phase_center_catalog[name] # This is a stub for something smarter in the future sou_ids[idx] = self.phase_center_catalog[name]["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 ) cat_id = self.phase_center_catalog[name]["cat_id"] 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()