def generate_residual_IDR2_2(uvh5_file,
omni_vis,
omni_calfits,
abs_calfits,
outfile,
clobber=False):
# reading uvh5 data file
hd = HERAData(uvh5_file)
data, flags, nsamples = hd.read(polarizations=['ee', 'nn'])
# reading omnical model visibilities
hd_oc = HERAData(omni_vis)
omnivis, omnivis_flags, _ = hd_oc.read()
uvo = pyuvdata.UVData()
uvo.read_uvh5(omni_vis)
# reading calfits file
hc = HERACal(omni_calfits)
oc_gains, oc_flags, oc_quals, oc_total_quals = hc.read()
hc = HERACal(abs_calfits)
ac_gains, ac_flags, ac_quals, ac_total_quals = hc.read()
# calibrating the data
abscal_data, abscal_flags = copy.deepcopy(data), copy.deepcopy(flags)
calibrate_in_place(abscal_data,
ac_gains,
data_flags=abscal_flags,
cal_flags=ac_flags)
res_data, res_flags = copy.deepcopy(hd.data_array), copy.deepcopy(
hd.flag_array)
resdata, resflags = copy.deepcopy(abscal_data), copy.deepcopy(abscal_flags)
for i, p in enumerate(['ee', 'nn']):
# reading omnical model visibilities
hd_oc = HERAData(omni_vis)
omnivis, omnivis_flags, _ = hd_oc.read(polarizations=[p])
mod_bls = list(omnivis.keys())
red_bls = get_reds(hd.antpos, pols=p)
red = gr.RBL(red_bls)
for mbl in mod_bls:
bl_grp = red[tuple(mbl[0:2]) + ('J{}'.format(p), )]
for blp in bl_grp:
bl = (blp[0], blp[1], p)
inds = hd.antpair2ind(bl)
omnivis_scaled = omnivis[mbl] * oc_gains[(blp[0], 'J{}'.format(
p))] * np.conj(oc_gains[(blp[1], 'J{}'.format(p))])
omnivis_scaled /= (
ac_gains[(blp[0], 'J{}'.format(p))] *
np.conj(ac_gains[(blp[1], 'J{}'.format(p))]))
resdata[bl] = abscal_data[bl] - omnivis_scaled
resflags[bl] = abscal_flags[bl]
res_data[inds, 0, :, i] = resdata[bl]
res_flags[inds, 0, :, i] = resflags[bl]
# writing to file
hd.data_array = res_data
hd.flag_array = res_flags
hd.write_uvh5(outfile, clobber=clobber)
flag_file = flag_files[day]
bad_ant = bad_ants[day]
if not os.path.exists(f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}"):
os.mkdir(f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}")
flags = UVFlag(flag_file)
flags.select(frequencies = flags.freq_array[(flags.freq_array>=115*1e+6) & (flags.freq_array<175*1e+6)])
flags.select(times=flags.time_array[2600:2660])
hd_data = HERAData(data_file)
freqs = hd_data.freqs[(hd_data.freqs>=115*1e+6) & (hd_data.freqs<175*1e+6)]
data, flag, nsample = hd_data.read(polarizations=["ee"], frequencies=freqs)
for bl in data:
if (bl[0] == bad_ant).any() or (bl[1] == bad_ant).any():
flag[bl] = np.ones_like(flag[bl])
flag[bl] = flags.flag_array.squeeze()
hd_data.update(flags=flag)
hd_data.write_uvh5(f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}.uvh5", clobber=True)
del data, flag, nsample, hd_data
redcal.redcal_run(input_data=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}.uvh5", clobber=True, solar_horizon=90, verbose=True)
abscal.post_redcal_abscal_run(data_file=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}.uvh5", redcal_file=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}.omni.calfits", model_files=[data_file], clobber=True, data_solar_horizon=90, model_solar_horizon=90)
cs=smooth_cal.CalibrationSmoother(calfits_list=sorted(glob.glob(f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_*.abs.calfits")))
cs.time_freq_2D_filter(time_scale=21600)
cs.write_smoothed_cal(clobber=True, output_replace=(".abs.",".smooth_abs."))
apply_cal.apply_cal(data_infilename=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}.uvh5", data_outfilename=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}_smoothcal.uvh5", new_calibration=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}.smooth_abs.calfits", clobber=True)
vc = vis_clean.VisClean(f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}_smoothcal.uvh5")
vc.read()
vc.vis_clean(standoff=100, min_dly=600, mode="dpss_leastsq", skip_if_flag_within_edge_distance=1, flag_model_rms_outliers=True, max_contiguous_edge_flags=1)
vc.write_filtered_data(filled_outfilename=f"/users/kshahin/kshahin/HERA_Calibration/DayfxP_{day}/data_{day}_{chunk}_filtered.uvh5", clobber=True)