def test_write():
obs = '1061313128_99bl_1pol_half_time'
testfile = os.path.join(DATA_PATH, '%s.uvfits' % obs)
file_type = 'uvfits'
outfile = os.path.join(DATA_PATH, 'test_write.uvfits')
ss = SS()
ss.read(testfile)
custom = np.zeros_like(ss.data_array.mask)
custom[:ss.Nbls] = 1
# Flags the first time and no others
ss.apply_flags(flag_choice='custom', custom=custom)
# Write this out without combining flags
ss.write(outfile, 'uvfits', filename_in=testfile, combine=False)
# Check if the flags propagated correctly
UV = UVData()
UV.read(outfile)
assert np.all(
UV.flag_array[:2 * UV.Nbls]), "Not all expected flags were propagated"
assert not np.any(
UV.flag_array[2 * UV.Nbls:]), "More flags were made than expected"
os.remove(outfile)
def test_write():
obs = '1061313128_99bl_1pol_half_time'
testfile = os.path.join(DATA_PATH, f'{obs}.uvfits')
file_type = 'uvfits'
outfile = os.path.join(DATA_PATH, 'test_write.uvfits')
ss = SS()
ss.read(testfile, diff=True)
blt_inds = np.where(ss.time_array == np.unique(ss.time_array)[10])
custom = np.zeros_like(ss.data_array.mask)
custom[blt_inds, :, 64:128, :] = 1
# Flags the first time and no others
ss.apply_flags(flag_choice='custom', custom=custom)
# Write this out without combining flags, will issue a warning
with pytest.warns(
UserWarning,
match=
"Some nsamples are 0, which will result in failure to propagate flags. Setting nsample to default values where 0."
):
ss.write(outfile, 'uvfits', filename_in=testfile, combine=False)
# Check if the flags propagated correctly
UV = UVData()
UV.read(outfile)
blt_inds = np.isin(UV.time_array, np.unique(UV.time_array)[10:12])
assert np.all(
UV.flag_array[blt_inds, :,
64:128, :]), "Not all expected flags were propagated"
new_blt_inds = np.logical_not(
np.isin(UV.time_array,
np.unique(UV.time_array)[10:12]))
assert not np.any(
UV.flag_array[new_blt_inds, :,
64:128, :]), "More flags were made than expected"
os.remove(outfile)
# Test bad read.
bad_uv_filepath = os.path.join(DATA_PATH, '1061312640_mix.uvfits')
bad_uv = UVData()
bad_uv.read(bad_uv_filepath)
with pytest.raises(
ValueError,
match="UVData and SS objects were found to be incompatible."):
ss.write(outfile, 'uvfits', bad_uv)
time.strftime("%H:%M:%S"))
sys.stdout.write("Beginning flagging at %s" % time.strftime("%H:%M:%S"))
auto_bls = ss.UV.ant_1_array[:ss.UV.Nbls] == ss.UV.ant_2_array[:ss.UV.Nbls]
custom = np.copy(ss.UV.flag_array)
custom[:, auto_bls] = 1
custom[-4:-1] = 1
ss.apply_flags(choice='custom', custom=custom)
ss.MF_prepare(sig_thresh=5,
shape_dict={
'TV6': [1.74e8, 1.81e8],
'TV7': [1.81e8, 1.88e8],
'TV8': [1.88e8, 1.95e8],
'TV7_broad': [1.79e8, 1.9e8]
})
ss.MF.apply_match_test()
ss.apply_flags(choice='INS', INS=ss.INS)
sys.stdout.write("Done with flagging at %s" % time.strftime("%H:%M:%S"))
sys.stdout.write("Beginning writing at %s" % time.strftime("%H:%M:%S"))
ss.write('%s/%s.uvfits' % (args.outpath, args.obs),
'uvfits',
inpath=args.inpath,
nsample_default=8)
sys.stdout.write("Done with writing at %s" % time.strftime("%H:%M:%S"))
vmin=0,
vmax=0.03,
aspect=ss.UV.Nfreqs / ss.UV.Ntimes)
ss.INS.data[:, 0, :82] = np.ma.masked
ss.INS.data[:, 0, -21:] = np.ma.masked
ss.INS.data_ms = ss.INS.mean_subtract(order=1)
ss.MF_prepare(sig_thresh=5, N_thresh=20, shape_dict=shape_dict)
ss.MF.apply_match_test(apply_N_thresh=True, order=1)
ss.INS.data[ss.INS.data > 0.03] = np.ma.masked
ss.INS.data_ms = ss.INS.mean_subtract(order=0)
ss.INS.save()
cp.MF_plot(ss.MF,
ms_vmin=-5,
ms_vmax=5,
vmin=0,
vmax=0.03,
aspect=ss.UV.Nfreqs / ss.UV.Ntimes)
ss.apply_flags(choice='INS', INS=ss.INS)
ss.UV.data_array.mask[:, auto_bls] = True
ss.write('%s/%s.HH.uvfits' % (args.outdir, args.obs),
'uvfits',
UV=UV1 + UV2,
write_kwargs={
'force_phase': True,
'spoof_nonessential': True
})
UV.read(args.inpath, file_type='uvfits')
JD = np.unique(UV.time_array)[-2]
where = np.where(UV.time_array == JD)
UV.flag_array[where] = 1
auto_bl = np.where(UV.ant_1_array == UV.ant_2_array)
UV.flag_array[auto_bl] = 1
return (UV)
UV = UV_construct(args)
shape_dict = {
'TV6': [1.74e8, 1.81e8],
'TV7': [1.81e8, 1.88e8],
'TV8': [1.88e8, 1.95e8],
'broad6': [1.72e8, 1.83e8],
'broad7': [1.79e8, 1.9e8],
'broad8': [1.86e8, 1.97e8]
}
sky_sub = SS(obs=args.obs, UV=UV, outpath=args.outpath, flag_choice='original')
sky_sub.INS_prepare()
sky_sub.MF_prepare(sig_thresh=5, shape_dict=shape_dict, N_thresh=15)
sky_sub.MF.apply_match_test(apply_N_thresh=True)
sky_sub.apply_flags(choice='INS', INS=sky_sub.INS)
sky_sub.write('%s/%s.uvfits' % (args.outpath, args.obs),
'uvfits',
UV=UV_construct(args))
indir = args.infile[:args.infile.rfind('/')]
if indir == args.outdir:
raise ValueError("indir and outdir are the same")
ss = SS()
ss.read(args.infile, flag_choice='original')
ins = INS(ss)
ins.metric_array[-5:] = np.ma.masked
ins.metric_ms = ins.mean_subtract()
shape_dict = {
'TV4': [1.74e8, 1.81e8],
'TV5': [1.81e8, 1.88e8],
'TV6': [1.88e8, 1.95e8],
'broad6': [1.72e8, 1.83e8],
'broad7': [1.79e8, 1.9e8],
'broad8': [1.86e8, 1.98e8]
}
mf = MF(ins.freq_array, 5, shape_dict=shape_dict, N_samp_thresh=25)
mf.apply_match_test(ins, apply_samp_thresh=True)
cp.INS_plot(ins, '%s/%s' % (args.outdir, args.obsid))
ss.apply_flags(flag_choice='INS', INS=ins)
ss.write('%s/%s.uvfits' % (args.outdir, args.obsid),
'uvfits',
nsample_default=16)
