import wodenpy
from wodenpy.wodenpy_setup.git_helper import retrieve_gitdict
import numpy as np
import sys
import os
from astropy.io import fits
import warnings
[docs]
def get_parser():
"""
Runs the argument parser to get command line inputs - used by sphinx and
argparse extension to unpack the help below into the online readthedocs
documentation.
Returns
-------
parser : `argparse.ArgumentParser`
The populated argument parser used by `run_woden.py`
"""
import argparse
from argparse import RawTextHelpFormatter
class SmartFormatter(argparse.HelpFormatter):
"""Argparse by default ignores all \n and \t formatters. If you start
a help class with R| the formatters will be respected."""
def _split_lines(self, text, width):
if text.startswith('R|'):
return text[2:].splitlines()
# this is the RawTextHelpFormatter._split_lines
return argparse.HelpFormatter._split_lines(self, text, width)
parser = argparse.ArgumentParser(description="Run the WODEN simulator and profit. "
"WODEN is setup to simulate MWA-style observations, where the "
"full frequency bandwidth is split into 24 'coarse' bands, each "
"of which is split into fine channels. This naturally allows "
"any simulation to be split across multiple GPUs as separate "
"processes.", formatter_class=SmartFormatter)
freq_group = parser.add_argument_group('FREQUENCY OPTIONS')
freq_group.add_argument('--band_nums', default='all',
help='Defaults to running 24 coarse bands. Alternatively, enter required'
' numbers delineated by commas, e.g. --band_nums=1,7,9')
freq_group.add_argument('--lowest_channel_freq', default=False,
help='Set the frequency (Hz) of the lowest channel for band 1. '
'If using a metafits file, this will override the frequency in'
' the metafits')
freq_group.add_argument('--coarse_band_width', type=float, default=1.28e+6,
help='Set the width of each coarse band \
If using a metafits file, this will override the frequency in '
'the metafits')
freq_group.add_argument('--num_freq_channels', default='obs',
help='Number of fine frequency channels to simulate - defaults to '
'--coarse_band_width / --freq_res')
freq_group.add_argument('--freq_res', type=float, default=False,
help='Fine channel frequnecy resolution (Hz) - will default to what'
' is in the metafits')
time_group = parser.add_argument_group('TIME OPTIONS')
time_group.add_argument('--num_time_steps', default=False,
help='The number of time steps to simualte. Defaults to how many are in'
'the metafits if using metafits')
time_group.add_argument('--time_res', type=float,default=False,
help='Time resolution (s) - will default to what is in the metafits '
'if the metafits if using metafits')
obs_group = parser.add_argument_group('OBSERVATION OPTIONS')
obs_group.add_argument('--ra0', type=float, required=True,
help='RA of the desired phase centre (deg)')
obs_group.add_argument('--dec0', type=float, required=True,
help='Dec of the desired phase centre (deg)')
obs_group.add_argument('--date', default=False,
help='Initial UTC date of the observatio in format YYYY-MM-DDThh:mm:ss '
'This is used to set the LST and array precession. This is set '
'automatically when reading a metafits but including this will '
'override the date in the metafits')
obs_group.add_argument('--no_precession', default=False, action='store_true',
help='By default, WODEN rotates the array back to J2000 to match '
'the input sky catalogue. Add this to switch off precession')
tel_group = parser.add_argument_group('TELESCOPE OPTIONS')
tel_group.add_argument('--latitude', default=-26.703319405555554, type=float,
help='Latitude (deg) of the array - defaults to MWA at -26.703319405555554')
tel_group.add_argument('--longitude', default=116.67081523611111, type=float,
help='Longitude (deg) of the array - defaults to MWA at 116.67081523611111')
tel_group.add_argument('--array_height', default=377.827, type=float,
help='Height (m) of the array above sea level - defaults to MWA at 377.827')
tel_group.add_argument('--array_layout', default=False,
help='Instead of reading the array layout from the metafits file, read'
' from a text file. Store antenna positions as offset from array '
'centre, in east, north, height coords (metres)')
tel_group.add_argument('--primary_beam', default="none",
help="R|Which primary beam to use in the simulation.\nOptions are:\n"
"\t - MWA_FEE (MWA fully embedded element model)\n"
"\t - MWA_FEE_interp (MWA fully embedded element model that has had)\n"
"\t\t spherical harmonics interpolated over frequency\n"
"\t - Gaussian (Analytic symmetric Gaussian)\n"
"\t\t see --gauss_beam_FWHM and\n"
"\t\t and --gauss_beam_ref_freq for\nfine control)\n"
"\t - EDA2 (Analytic dipole with a ground mesh) \n"
"\t - MWA_analy (MWA analytic model)\n"
"\t - none (Don't use a primary beam at all)\n"
"Defaults to --primary_beam=none")
tel_group.add_argument('--gauss_beam_FWHM', default=20, type=float,
help='The FWHM of the Gaussian beam in deg - WODEN defaults to using'
' 20 deg if this is not set')
tel_group.add_argument('--gauss_beam_ref_freq', default=150e+6, type=float,
help='The frequency at which the gauss beam FWHM is set at. If not set,'
' WODEN will default to 150MHz.')
tel_group.add_argument('--gauss_ra_point', default=False,
help='The initial RA (deg) to point the Gaussian beam at. This will be '
'used to calculate an hour angle at which the beam will remain '
'pointed at for the duration of the observation. Defaults to the '
'RA of the metafits if available, or the RA of the phase centre '
'if not')
tel_group.add_argument('--gauss_dec_point', default=False,
help='The initial Dec (deg) to point the Gaussian beam at. Defaults '
'to the Dec of the metafits if available, or the Dec of the phase centre'
' if not')
tel_group.add_argument('--hdf5_beam_path', default=False,
help='Location of the hdf5 file holding the FEE beam coefficients')
tel_group.add_argument('--MWA_FEE_delays', default=False,
help='R|A list of 16 delays to point the MWA FEE primary beam \n'
'model enter as as list like: \n'
'--MWA_FEE_delays=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]\n'
'for a zenith pointing. This is read directly from\n'
'the metafits if using a metafits file')
tel_group.add_argument('--telescope_name', default='MWA',
help='Name of telescope written out to the uvfits file, defaults to MWA')
tel_group.add_argument('--use_MWA_dipflags', default=False, action='store_true',
help='Apply the dipole flags stored in the metafits file. Only works'
' for the MWA FEE currently, not the MWA analytic model')
tel_group.add_argument('--use_MWA_dipamps', default=False, action='store_true',
help='Attempt to use bespoke MWA dipole amplitudes stored in the metafits'
' file. Must be stored under the `DipAmps` column. Only works'
' for the MWA FEE currently, not the MWA analytic model')
input_group = parser.add_argument_group('INPUT/OUTPUT OPTIONS')
input_group.add_argument('--IAU_order', default=False,
help='NEW IN WODEN versions >= 1.4.0. By default, the XX pol is now '
'from the East-West aligned dipoles. Add --IAU_order to define '
'the XX pol as North-South. Background: '
'the first polaristaion output in the uvfits is '
'called "XX". The IAU defines "XX" as aligned to North-South, '
'however typically it is assumed that "XX" in a uvfits is from '
'the East-West dipoles. Le sigh. For WODEN versions < 1.4.0, '
'XX was always the N-S dipoles. ')
input_group.add_argument('--cat_filename', required=True,
help='Path to WODEN style sky model')
input_group.add_argument('--metafits_filename',default=False,
help='MWA style metafits file to base the simulation on. Array layout,'
' frequency and time parameters are all set by this option, but '
'can be overridden using other arguments')
input_group.add_argument('--output_uvfits_prepend',default='output',
help='Prepend name for uvfits - will append band%%02d.uvfits %%band_num '
'at the end. Defaults to "output".')
input_group.add_argument('--sky_crop_components', default=True, action='store_true',
help='This option is deprecated, but held here for compatibility.')
input_group.add_argument('--sky_crop_sources', default=False, action='store_true',
help='WODEN will crop out sky model information that is below the '
'horizon for the given LST. By default, '
'WODEN will include any COMPONENT above the horizon, regardless '
'of which SOURCE it belongs to. If --sky_crop_source is included '
'for each SOURCE in the sky model, if any COMPONENT is below the ' 'horizon, the entire source will be flagged')
input_group.add_argument('--do_autos', default=False, action='store_true',
help='By default, WODEN only calculates cross-correlations. Add this'
' flag to include auto-correlations.')
sim_group = parser.add_argument_group('SIMULATOR OPTIONS')
sim_group.add_argument('--precision', default='double',
help='What precision to run WODEN at. Options are "double" or "float". '
'Defaults to "double"')
sim_group.add_argument('--remove_phase_tracking', default=False, action='store_true',
help='By adding this flag, remove the phase tracking of the '
'visibilities - use this to feed uvfits into the RTS')
sim_group.add_argument('--no_tidy', default=False, action='store_true',
help='Defaults to deleting output binary files from woden and json '
'files. Add this flag to not delete those files')
sim_group.add_argument('--chunking_size', type=float, default=1e10,
help='The chunk size to break up the point sources into for processing '
'- defaults to 1e10')
sim_group.add_argument('--dry_run', default=False, action='store_true',
help='Add this to NOT call the WODEN executable - this will just write '
'out the .json file and do nothing else')
##Add a number of hidden arguments. This means we can add attributes to
##the args object to conveniently pass things into functions, but without
##them showing up in --help
parser.add_argument('--east', help=argparse.SUPPRESS)
parser.add_argument('--north', help=argparse.SUPPRESS)
parser.add_argument('--height', help=argparse.SUPPRESS)
parser.add_argument('--num_antennas', help=argparse.SUPPRESS)
parser.add_argument('--array_layout_name', help=argparse.SUPPRESS)
parser.add_argument('--dipamps', help=argparse.SUPPRESS)
parser.add_argument('--dipflags', help=argparse.SUPPRESS)
return parser
[docs]
def select_argument_and_check(parser_arg, parser_value,
metafits_arg, parser_string,
do_exit=True):
"""Some arguments taken from the argparse.parser should override settings
from the metafits if present. If the parser argument `parser_arg` is
defined (i.e. not False), update it to equal `parser_value`. If not defined,
update `parser_arg` to `metafits_arg`, which is the value read in from
the metafits file. If both `parser_arg` and `metafits_arg` are False,
WODEN will fail, so exit with a message. Use `parser_string` to define
which parser arguement has failed; this will be included in the error
message.
Parameters
----------
parser_arg : attribute of `argparse.Namespace`
The option in `args` to update
parser_value : Expected type for `parser_arg`
The value to set `parser_arg` to (e.g. float(parser_arg))
metafits_arg : Expected type for `parser_arg`
The value read in from the metafits if using metafits; False if not
parser_string : string
The parser option under test to be written out in the error message,
e.g. "--MWA_FEE_delays"
do_exit : Boolean
Whether to call `sys.exit` upon both `parser_arg` and `metafits_arg`
being False. Defaults to True
Returns
-------
parser_arg : attribute of `argparse.Namespace`
The update option in `args`
"""
##If a parser arg is there, reset it to the parser_value give
if parser_arg:
parser_arg = parser_value
##If not there, check if a metafits equivalent has been found
else:
if metafits_arg:
parser_arg = metafits_arg
else:
error_message = ("ARGS ERROR: args.{:s} has not been set. \n"
"Either specify using --{:s} or get from a metafits using "
"--metafits_filename\nExiting now as WODEN cannot run").format(parser_string, parser_string)
if do_exit:
sys.exit(error_message)
return parser_arg
[docs]
def select_correct_enh(args):
"""Depending on whether we are reading the array layout from the metafits
file or a text file, read in the correct amount of east,north,height coords.
Sets `args.east`, `args.north`, `args.height`, `args.num_antennas`, and
`args.array_layout_name`.
Parameters
----------
args : `argparse.Namespace`
The populated arguments `args = parser.parse_args()`` as returned from
the parser given by :func:`~run_woden.get_parser`
"""
if args.array_layout == "from_the_metafits":
##Using metafits for array layout. Have previously read in e,n,h
##In the metafits it lists XX,YY for each antenna so we select every second one
selection = np.arange(0,len(args.east),2)
args.num_antennas = int(len(selection))
args.east = args.east[selection]
args.north = args.north[selection]
args.height = args.height[selection]
args.ant_names = args.ant_names[selection]
else:
try:
array_layout = np.loadtxt(args.array_layout)
args.num_antennas,_ = array_layout.shape
args.east = array_layout[:,0]
args.north = array_layout[:,1]
args.height = array_layout[:,2]
args.ant_names = np.array(["%05d" %ant for ant in range(1,args.num_antennas + 1)])
except:
exit("Could not read array layout file:\n"
"\t{:s}\nExiting before woe beings".format(args.array_layout))
[docs]
def check_args(args):
"""Check that the combination of arguments parsed will work with the
WODEN executable. Attempts to grab information from a metafits file if
possible. Should error with helpful messages if a combination that won't
work is attempted by the user
Parameters
----------
args : `argparse.Namespace`
The populated arguments `args = parser.parse_args()`` as returned from
the parser given by :func:`~run_woden.get_parser`
Returns
-------
args : `argparse.Namespacer`
The populated arguments which will now have been checked and had
information from metafits incorporated if requested
"""
if args.primary_beam not in ['MWA_FEE', 'Gaussian', 'EDA2', 'none', 'None',
'MWA_FEE_interp', 'MWA_analy']:
exit('Primary beam option --primary_beam must be one of:\n'
'\t MWA_FEE, MWA_FEE_interp, Gaussian, EDA2, none\n'
'User has entered --primary_beam={:s}\n'
'Please fix and try again. Exiting now'.format(args.primary_beam))
##Be a little flexible in how people specify 'none'
if args.primary_beam in ['None', 'none']:
args.primary_beam = 'none'
##If we're using the MWA FEE beam, make sure we can find the stored
##spherical harmonics file
if args.primary_beam == 'MWA_FEE':
if args.hdf5_beam_path:
if not os.path.isfile(args.hdf5_beam_path):
exit('Could not open hdf5 MWA FEE path as specified by user as:\n'
'\t--hdf5_beam_path={:s}.\n'
'This will cause WODEN to fail, exiting now'.format(args.hdf5_beam_path))
else:
try:
MWA_FEE_HDF5 = os.environ['MWA_FEE_HDF5']
args.hdf5_beam_path = MWA_FEE_HDF5
if not os.path.isfile(args.hdf5_beam_path):
exit('Could not open hdf5 MWA FEE path as specified by user as:\n'
'\t--environ["MWA_FEE_HDF5"]={:s}.\n'
'This will cause WODEN to fail, exiting now'.format(args.hdf5_beam_path))
except KeyError:
exit('To use MWA FEE beam, either --hdf5_beam_path or environment\n'
'variable MWA_FEE_HDF5 must point towards the file\n'
'mwa_full_embedded_element_pattern.h5. Exiting now as WODEN will fail.')
##If we're using the MWA FEE beam, make sure we can find the stored
##spherical harmonics file
elif args.primary_beam == 'MWA_FEE_interp':
if args.hdf5_beam_path:
if not os.path.isfile(args.hdf5_beam_path):
exit('Could not open hdf5 MWA FEE path as specified by user as:\n'
'\t--hdf5_beam_path={:s}.\n'
'This will cause WODEN to fail, exiting now'.format(args.hdf5_beam_path))
else:
try:
MWA_FEE_HDF5_INTERP = os.environ['MWA_FEE_HDF5_INTERP']
args.hdf5_beam_path = MWA_FEE_HDF5_INTERP
if not os.path.isfile(args.hdf5_beam_path):
exit('Could not open hdf5 MWA FEE path as specified by user as:\n'
'\t--environ["MWA_FEE_HDF5_INTERP"]={:s}.\n'
'This will cause WODEN to fail, exiting now'.format(args.hdf5_beam_path))
except KeyError:
exit('To use MWA FEE intrep beam, either --hdf5_beam_path or environment\n'
'variable MWA_FEE_HDF5_INTERP must point towards the file\n'
'MWA_embedded_element_pattern_rev2_interp_167_197MHz.h5. Exiting now as WODEN will fail.')
##variables that will be filled by metafits if reading a metafits
##set them as False here for testing later on
MWA_FEE_delays = False
time_res = False
freq_res = False
freqcent = False
lowest_channel_freq = False
num_time_steps = False
date = False
array_layout = False
##read in args from the metafits if requested
if args.metafits_filename:
if not os.path.isfile(args.metafits_filename):
exit('Could not open metafits specified by user as:\n'
'\t--metafits_filename={:s}.\n'
'Cannot get required observation settings, exiting now'.format(args.metafits_filename))
with fits.open(args.metafits_filename) as f:
date = f[0].header['DATE-OBS']
##Need to order the antennas via the Tile column to be consistent
## with hyperdrive
tilenames = f[1].data['Tile']
##The same tile name is repeated for X and Y dipoles. Doing an
##argsort on this sometimes returns the X first, sometimes the Y.
##This is bad as we use this to re-order dipole amplitude and flags
##later on; so only select one of the pols, do an argsort, and
##expand back to both pols
tilenames = tilenames[np.arange(0, len(tilenames), 2)]
order = np.argsort(tilenames)
antenna_order = np.empty(2*len(order), dtype=int)
antenna_order[np.arange(0, 2*len(order), 2)] = 2*order
antenna_order[np.arange(1, 2*len(order), 2)] = 2*order + 1
##Get the east, north, height antenna positions from the metafits
east = f[1].data['East'][antenna_order]
north = f[1].data['North'][antenna_order]
height = f[1].data['Height'][antenna_order]
tilenames = f[1].data['Tilename'][antenna_order]
args.east = east
args.north = north
args.height = height
args.ant_names = tilenames
##Use this to signal that reading in array layout from metafits
##was successful
array_layout = "from_the_metafits"
##Read observation parameters from the metafits file
time_res = float(f[0].header['INTTIME'])
freq_res = float(f[0].header['FINECHAN'])*1e+3
freqcent = float(f[0].header['FREQCENT'])*1e+6
b_width = float(f[0].header['BANDWDTH'])*1e+6
lowest_channel_freq = freqcent - (b_width/2) - (freq_res/2)
num_time_steps = int(f[0].header['NSCANS'])
delays = np.array(f[0].header['DELAYS'].split(','),dtype=int)
delays[np.where(delays == 32)] = 0
MWA_FEE_delays = str(list(delays))
##If user hasn't specified a pointing for a Gaussian beam,
##fill in using the metafits file
if not args.gauss_ra_point:
args.gauss_ra_point = float(f[0].header['RA'])
if not args.gauss_dec_point:
args.gauss_dec_point = float(f[0].header['DEC'])
f.close()
##Override metafits and/or load arguments
args.lowest_channel_freq = select_argument_and_check(args.lowest_channel_freq,
float(args.lowest_channel_freq),
lowest_channel_freq, "lowest_channel_freq")
args.num_time_steps = select_argument_and_check(args.num_time_steps,
int(args.num_time_steps),
num_time_steps, "num_time_steps")
args.freq_res = select_argument_and_check(args.freq_res, args.freq_res,
freq_res, "freq_res")
args.time_res = select_argument_and_check(args.time_res, args.time_res,
time_res, "time_res")
args.date = select_argument_and_check(args.date, args.date,
date, "date")
args.array_layout = select_argument_and_check(args.array_layout, args.array_layout,
array_layout, "array_layout")
##TODO change this from MWA_FEE_delays to MWA_delays (or allow both via
##some argparse magic)
##If the user has manually specified some MWA FEE delays, ensure they
##can be made into an array of 16 floats
if args.MWA_FEE_delays:
message = ("ERROR - failed to convert --MWA_FEE_delays into a list"
" of 16 floats correctly. You have entered:\n"
" --MWA_FEE_delays={:s}\n"
"Exiting now.".format(args.MWA_FEE_delays))
try:
test_list = list(np.array(args.MWA_FEE_delays.strip('[]').split(','),dtype=float))
if len(test_list) != 16:
exit(message)
except:
exit(message)
##Do the test on MWA_FEE_delays only if this is an MWA_FEE simulation
if args.primary_beam == 'MWA_FEE' or args.primary_beam == 'MWA_FEE_interp' or args.primary_beam == 'MWA_analy':
args.MWA_FEE_delays = select_argument_and_check(args.MWA_FEE_delays,
args.MWA_FEE_delays,
MWA_FEE_delays, "MWA_FEE_delays")
##Set the band numbers we are simulating in this run
if args.num_freq_channels == 'obs':
args.num_freq_channels = int(np.floor(args.coarse_band_width / args.freq_res))
else:
args.num_freq_channels = int(args.num_freq_channels)
if args.band_nums == 'all':
args.band_nums = range(1,25)
else:
try:
args.band_nums = list(np.array(args.band_nums.split(','),dtype=int))
except:
message = ("ERROR - failed to convert --band_nums into a list of ints"
" correctly. You entered:\n"
f" --band_nums={args.band_nums}\n"
"Exiting now.")
exit(message)
##If pointing for Gaussian beam is not set, point it at the phase centre
if args.primary_beam == 'Gaussian':
##Explicitly test if False here as it could point at 0.0 deg, which
##get interpreted as False in a simple if statement doh
if args.gauss_ra_point is False:
args.gauss_ra_point = args.ra0
else:
args.gauss_ra_point = float(args.gauss_ra_point)
if args.gauss_dec_point is False:
args.gauss_dec_point = args.dec0
else:
args.gauss_dec_point = float(args.gauss_dec_point)
if args.gauss_beam_ref_freq: args.gauss_beam_ref_freq = float(args.gauss_beam_ref_freq)
if args.gauss_beam_FWHM: args.gauss_beam_FWHM = float(args.gauss_beam_FWHM)
if args.precision not in ['double', 'float']:
print(f"Arg --precision={args.precision} is not valid. Should be either"
"'double' or 'float'. Setting to 'double'")
args.precision='double'
##Either read the array layout from a file or use what was in the metafits
select_correct_enh(args)
##If user asks to crop by source, change cropping by component to False
if args.sky_crop_sources:
args.sky_crop_components = False
##Now read in dipole flags/amplitudes if using requested
##Do this after reading in the array layout as we need to know how many
##antennas there are to check the shapes of the dipole flags/amplitudes
##Do dipole flags first
args.dipflags = np.ones(2*args.num_antennas*16)
if args.use_MWA_dipflags:
if args.primary_beam != 'MWA_FEE' and args.primary_beam != 'MWA_FEE_interp':
exit('ERROR: --use_MWA_dipflags can only be used with the MWA FEE beam'
' so must be used with --primary_beam=MWA_FEE or --primary_beam=MWA_FEE_interp.')
if not args.metafits_filename:
exit('ERROR: --use_MWA_dipflags can only be used with the MWA FEE beam'
' so must be used with a metafits file. Exiting now.')
##We read in the Delays array, which has 16 delays per tile per pol
##If that delay is 32, its flagged
with fits.open(args.metafits_filename) as f:
try:
dip_delays = f[1].data['Delays']
##This should never happen as Delays should always be in an MWA metafits
##but if people make something bespoke you never know
except KeyError:
exit('ERROR: --use_MWA_dipflags was specified but no `Delays` column'
' was found in the metafits file. Exiting now.')
f.close()
# print(dip_flags.shape, dip_flags.size)
# print(dip_flags[0])
if dip_delays.shape[0] != 2*args.num_antennas or dip_delays.shape[1] != 16:
exit('ERROR: --use_MWA_dipflags was specified. The shape of the `DipoleFlags`'
f' in the metafits file was {dip_delays.shape}. This shape should be'
f' (2*num_tiles, 16). Twice number of tiles as we need both X,Y dipoles.'
' The number of tiles is set to be {args.num_antennas}.'
' Either check your metafits file or if you have --array_layout set,'
' check how may tiles are in that file. Exiting now.')
##make sure ordering is consistent with hyperdrive
dip_delays = dip_delays[antenna_order, :]
flag_indexes = np.where(dip_delays == 32)
if len(flag_indexes[0]) == 0:
warnings.warn('No dipoles were flagged at all in the metafits file.'
' Switchng off --use_MWA_dipflags. If you do not have'
' --use_MWA_dipamps set, you will use the same primary'
' beam for all antennas. This is way faster hooray')
args.use_MWA_dipflags = False
##Apply flags and flatten
args.dipflags = np.ones(dip_delays.shape)
args.dipflags[flag_indexes] = 0
dipflags = np.empty_like(args.dipflags)
num_y_flags = 0
num_x_flags = 0
num_tiles = 0
for ant in range(int(len(antenna_order)/2)):
add_tile = 0
slice = args.dipflags[2*ant, :]
flag_len = len(np.where(slice == 0)[0])
if flag_len > 0:
# print('Y dip', flag_len, len(slice))
num_y_flags += 1
add_tile = 1
slice = args.dipflags[2*ant+1, :]
flag_len = len(np.where(slice == 0)[0])
if flag_len > 0:
# print('X dip', flag_len, len(slice))
num_x_flags += 1
add_tile = 1
##Flip things compared to metafits as meta goes E-W, N-S.
##WODEN likes things IAU style which is N-S,E-W
dipflags[2*ant+1, :] = args.dipflags[2*ant, :]
dipflags[2*ant, :] = args.dipflags[2*ant+1, :]
num_tiles += add_tile
# print(f"Num tiles N-S flags: {num_x_flags}")
# print(f"Num tiles E-W flags: {num_y_flags}")
print(f"Num tiles with dipole flags: {num_tiles}")
args.dipflags = dipflags.flatten()
##Now do dipole amplitudes
args.dipamps = np.ones(2*args.num_antennas*16)
if args.use_MWA_dipamps:
if args.primary_beam != 'MWA_FEE' and args.primary_beam != 'MWA_FEE_interp':
exit('ERROR: --use_MWA_dipamps can only be used with the MWA FEE beam'
' so must be used with --primary_beam=MWA_FEE or --primary_beam=MWA_FEE_interp.')
if not args.metafits_filename:
exit('ERROR: --use_MWA_dipamps can only be used with the MWA FEE beam'
' so must be used with a metafits file. Exiting now.')
with fits.open(args.metafits_filename) as f:
try:
dip_amps = f[1].data['DipAmps']
except KeyError:
exit('ERROR: --use_MWA_dipamps was specified but no `DipAmps` column'
' was found in the metafits file. Exiting now.')
f.close()
if dip_amps.shape[0] != 2*args.num_antennas or dip_amps.shape[1] != 16:
exit('ERROR: --use_MWA_dipamps was specified. The shape of the `DipAmps`'
f' in the metafits file was {dip_amps.shape}. This shape should be'
f' (2*num_tiles, 16). Twice number of tiles as we need both X,Y dipoles.'
' The number of tiles is set to be {args.num_antennas}.'
' Either check your metafits file or if you have --array_layout set,'
' check how may tiles are in that file. Exiting now.')
##Things are stored in the metafits as e-w first, n-s second. WODEN
##works internally to IAU def which is n-s first, e-w second. So need
##to reverse the order of the amplitudes here
args.dipamps = dip_amps[antenna_order, :]
dipamps = np.empty_like(args.dipamps)
for ant in range(int(len(args.dipamps)/2)):
dipamps[2*ant+1, :] = args.dipamps[2*ant, :]
dipamps[2*ant, :] = args.dipamps[2*ant+1, :]
args.dipamps = dipamps.flatten()
##Combine the dipole amplitudes and flags into a single array
##One or the other might be array of ones so this can always be done
##args.dipamps only is carried into the C/CUDA code, so always turn on
##the use_MWA_diamps flag
if args.use_MWA_dipflags or args.use_MWA_dipamps:
args.dipamps = args.dipflags*args.dipamps
args.use_MWA_dipamps = True
return args
[docs]
def get_code_version():
"""
Returns either the git hash if installed via a git repo, or the __version__
if installed from a release
Returns
-------
version : string
Either the git commit or release version
"""
git_dict = retrieve_gitdict()
if git_dict:
version = git_dict['describe']
else:
##If doing testing with pip install -e, __version__ will not exists
try:
version = wodenpy.__version__
except AttributeError:
version = "No git describe nor __version__ avaible"
print(f"You are using WODEN commit: {version}")
return version