Second Round of Full Day RFI Flagging¶
by Josh Dillon, last updated October 13, 2024
This notebook is synthesizes information from individual delay_filtered_average_zscore notebooks to find low-level RFI and flag it. That notebook takes smooth_calibrated data, redundantly averages it, performs a high-pass delay filter, and then incoherently averages across baselines, creating a per-polarization z-score. This notebook then takes that whole night of z-scores and finds a new set of flags to both add to the smooth_cal files, which are updated in place, and to write down as new UVFlag waterfall-type .h5 files.
Here's a set of links to skip to particular figures and tables:
• Figure 1: Waterfall of Maximum z-Score of Either Polarization Before Round 2 Flagging¶
• Figure 2: Histogram of z-scores¶
• Figure 3: Waterfall of Maximum z-Score of Either Polarization After Round 2 Flagging¶
• Figure 4: Spectra of Time-Averaged z-Scores¶
• Figure 5: Summary of Flags Before and After Round 2 Flagging¶
In [1]:
import time
tstart = time.time()
In [2]:
import os
os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE'
import h5py
import hdf5plugin # REQUIRED to have the compression plugins available
import numpy as np
import glob
import matplotlib.pyplot as plt
import matplotlib
import copy
import warnings
from pyuvdata import UVFlag, UVCal
from hera_cal import utils
from hera_qm import xrfi
from hera_qm.time_series_metrics import true_stretches
from hera_filters import dspec
from IPython.display import display, HTML
%matplotlib inline
display(HTML("<style>.container { width:100% !important; }</style>"))
_ = np.seterr(all='ignore') # get rid of red warnings
%config InlineBackend.figure_format = 'retina'
In [3]:
# get input data file names
SUM_FILE = os.environ.get("SUM_FILE", None)
# SUM_FILE = '/lustre/aoc/projects/hera/h6c-analysis/IDR2/2459861/zen.2459861.25297.sum.uvh5'
SUM_SUFFIX = os.environ.get("SUM_SUFFIX", 'sum.uvh5')
# get input and output suffixes
SMOOTH_CAL_SUFFIX = os.environ.get("SMOOTH_CAL_SUFFIX", 'sum.smooth.calfits')
ZSCORE_SUFFIX = os.environ.get("ZSCORE_SUFFIX", 'sum.red_avg_zscore.h5')
FLAG_WATERFALL2_SUFFIX = os.environ.get("FLAG_WATERFALL2_SUFFIX", 'sum.flag_waterfall_round_2.h5')
OUT_YAML_SUFFIX = os.environ.get("OUT_YAML_SUFFIX", '_aposteriori_flags.yaml')
OUT_YAML_DIR = os.environ.get("OUT_YAML_DIR", None)
# build globs
sum_glob = '.'.join(SUM_FILE.split('.')[:-3]) + '.*.' + SUM_SUFFIX
cal_files_glob = sum_glob.replace(SUM_SUFFIX, SMOOTH_CAL_SUFFIX)
zscore_glob = sum_glob.replace(SUM_SUFFIX, ZSCORE_SUFFIX)
# build out yaml file
if OUT_YAML_DIR is None:
OUT_YAML_DIR = os.path.dirname(SUM_FILE)
out_yaml_file = os.path.join(OUT_YAML_DIR, SUM_FILE.split('.')[-4] + OUT_YAML_SUFFIX)
# get flagging parameters
Z_THRESH = float(os.environ.get("Z_THRESH", 4))
WS_Z_THRESH = float(os.environ.get("WS_Z_THRESH", 2))
AVG_Z_THRESH = float(os.environ.get("AVG_Z_THRESH", 1))
MAX_FREQ_FLAG_FRAC = float(os.environ.get("MAX_FREQ_FLAG_FRAC", .25))
MAX_TIME_FLAG_FRAC = float(os.environ.get("MAX_TIME_FLAG_FRAC", .1))
AVG_SPECTRUM_FILTER_DELAY = float(os.environ.get("AVG_SPECTRUM_FILTER_DELAY", 250)) # in ns
EIGENVAL_CUTOFF = float(os.environ.get("EIGENVAL_CUTOFF", 1e-12))
TIME_AVG_DELAY_FILT_SNR_THRESH = float(os.environ.get("TIME_AVG_DELAY_FILT_SNR_THRESH", 4.0))
TIME_AVG_DELAY_FILT_SNR_DYNAMIC_RANGE = float(os.environ.get("TIME_AVG_DELAY_FILT_SNR_DYNAMIC_RANGE", 1.5))
for setting in ['Z_THRESH', 'WS_Z_THRESH', 'AVG_Z_THRESH', 'MAX_FREQ_FLAG_FRAC', 'MAX_TIME_FLAG_FRAC', 'AVG_SPECTRUM_FILTER_DELAY',
'EIGENVAL_CUTOFF', 'TIME_AVG_DELAY_FILT_SNR_THRESH', 'TIME_AVG_DELAY_FILT_SNR_DYNAMIC_RANGE']:
print(f'{setting} = {eval(setting)}')
Z_THRESH = 4.0 WS_Z_THRESH = 2.0 AVG_Z_THRESH = 1.0 MAX_FREQ_FLAG_FRAC = 0.25 MAX_TIME_FLAG_FRAC = 0.1 AVG_SPECTRUM_FILTER_DELAY = 250.0 EIGENVAL_CUTOFF = 1e-12 TIME_AVG_DELAY_FILT_SNR_THRESH = 4.0 TIME_AVG_DELAY_FILT_SNR_DYNAMIC_RANGE = 1.5
Load z-scores¶
In [4]:
# load z-scores
zscore_files = sorted(glob.glob(zscore_glob))
print(f'Found {len(zscore_files)} *.{ZSCORE_SUFFIX} files starting with {zscore_files[0]}.')
uvf = UVFlag(zscore_files, use_future_array_shapes=True)
Found 1572 *.sum.red_avg_zscore.h5 files starting with /mnt/sn1/data2/2460774/zen.2460774.21069.sum.red_avg_zscore.h5.
In [5]:
# get calibration solution files
cal_files = sorted(glob.glob(cal_files_glob))
print(f'Found {len(cal_files)} *.{SMOOTH_CAL_SUFFIX} files starting with {cal_files[0]}.')
Found 1572 *.sum.smooth.calfits files starting with /mnt/sn1/data2/2460774/zen.2460774.21069.sum.smooth.calfits.
In [6]:
assert len(zscore_files) == len(cal_files)
In [7]:
# extract z-scores and correct by a single number per polarization to account for biases created by filtering
zscore = {pol: uvf.metric_array[:, :, np.argwhere(uvf.polarization_array == utils.polstr2num(pol, x_orientation=uvf.x_orientation))[0][0]] for pol in ['ee', 'nn']}
zscore = {pol: zscore[pol] - np.nanmedian(zscore[pol]) for pol in zscore}
In [8]:
freqs = uvf.freq_array
times = uvf.time_array
In [9]:
extent = [freqs[0] / 1e6, freqs[-1] / 1e6, times[-1] - int(times[0]), times[0] - int(times[0])]
In [10]:
def plot_max_z_score(zscore, flags=None, vmin=-5, vmax=5):
if flags is None:
flags = np.any(~np.isfinite(list(zscore.values())), axis=0)
plt.figure(figsize=(14,10), dpi=100)
plt.imshow(np.where(flags, np.nan, np.nanmax([zscore['ee'], zscore['nn']], axis=0)), aspect='auto',
cmap='coolwarm', interpolation='none', vmin=vmin, vmax=vmax, extent=extent)
plt.colorbar(location='top', label='Max z-score of either polarization', extend='both', aspect=40, pad=.02)
plt.xlabel('Frequency (MHz)')
plt.ylabel(f'JD - {int(times[0])}')
plt.tight_layout()
Figure 1: Waterfall of Maximum z-Score of Either Polarization Before Round 2 Flagging¶
Shows the worse of the two results from delay_filtered_average_zscore from either polarization. Dips near flagged channels are expected, due to overfitting of noise. Positive-going excursions are problematic and likely evidence of RFI.
In [11]:
plot_max_z_score(zscore)
All-NaN axis encountered
In [12]:
def plot_histogram():
plt.figure(figsize=(14,4), dpi=100)
bins = np.arange(-50, 100, .1)
hist_ee = plt.hist(np.ravel(zscore['ee']), bins=bins, density=True, label='ee-polarized z-scores', alpha=.5)
hist_nn = plt.hist(np.ravel(zscore['nn']), bins=bins, density=True, label='nn-polarized z-scores', alpha=.5)
plt.plot(bins, (2*np.pi)**-.5 * np.exp(-bins**2 / 2), 'k:', label='Gaussian approximate\nnoise-only distribution')
plt.axvline(WS_Z_THRESH, c='r', ls='--', label='Watershed z-score')
plt.axvline(Z_THRESH, c='r', ls='-', label='Threshold z-score')
plt.yscale('log')
all_densities = np.concatenate([hist_ee[0][hist_ee[0] > 0], hist_nn[0][hist_nn[0] > 0]])
plt.ylim(np.min(all_densities) / 2, np.max(all_densities) * 2)
plt.xlim([-50, 100])
plt.legend()
plt.xlabel('z-score')
plt.ylabel('Density')
plt.tight_layout()
Figure 2: Histogram of z-scores¶
Shows a comparison of the histogram of z-scores in this file (one per polarization) to a Gaussian approximation of what one might expect from thermal noise. Without filtering, the actual distribution is a weighted sum of Rayleigh distributions. Filtering further complicates this. To make the z-scores more reliable, a single per-polarization median is subtracted from each waterfall, which allows us to flag low-level outliers with more confidence. Any points beyond the solid red line are flagged. Any points neighboring a flag beyond the dashed red line are also flagged. Finally, flagging is performed for low-level outliers in whole times or channels.
In [13]:
plot_histogram()
Perform flagging¶
In [14]:
def iteratively_flag_on_averaged_zscore(flags, zscore, avg_func=np.nanmean, avg_z_thresh=AVG_Z_THRESH, verbose=True):
'''Flag whole integrations or channels based on average z-score. This is done
iteratively to prevent bad times affecting channel averages or vice versa.'''
flagged_chan_count = 0
flagged_int_count = 0
while True:
zspec = avg_func(np.where(flags, np.nan, zscore), axis=0)
ztseries = avg_func(np.where(flags, np.nan, zscore), axis=1)
if (np.nanmax(zspec) < avg_z_thresh) and (np.nanmax(ztseries) < avg_z_thresh):
break
if np.nanmax(zspec) >= np.nanmax(ztseries):
flagged_chan_count += np.sum((zspec >= np.nanmax(ztseries)) & (zspec >= avg_z_thresh))
flags[:, (zspec >= np.nanmax(ztseries)) & (zspec >= avg_z_thresh)] = True
else:
flagged_int_count += np.sum((ztseries >= np.nanmax(zspec)) & (ztseries >= avg_z_thresh))
flags[(ztseries >= np.nanmax(zspec)) & (ztseries >= avg_z_thresh), :] = True
if verbose:
print(f'\tFlagging an additional {flagged_int_count} integrations and {flagged_chan_count} channels.')
def impose_max_chan_flag_frac(flags, max_flag_frac=MAX_FREQ_FLAG_FRAC, verbose=True):
'''Flag channels already flagged more than max_flag_frac (excluding completely flagged times).'''
unflagged_times = ~np.all(flags, axis=1)
frequently_flagged_chans = np.mean(flags[unflagged_times, :], axis=0) >= max_flag_frac
if verbose:
print(f'\tFlagging {np.sum(frequently_flagged_chans) - np.sum(np.all(flags, axis=0))} channels previously flagged {max_flag_frac:.2%} or more.')
flags[:, frequently_flagged_chans] = True
def impose_max_time_flag_frac(flags, max_flag_frac=MAX_TIME_FLAG_FRAC, verbose=True):
'''Flag times already flagged more than max_flag_frac (excluding completely flagged channels).'''
unflagged_chans = ~np.all(flags, axis=0)
frequently_flagged_times = np.mean(flags[:, unflagged_chans], axis=1) >= max_flag_frac
if verbose:
print(f'\tFlagging {np.sum(frequently_flagged_times) - np.sum(np.all(flags, axis=1))} times previously flagged {max_flag_frac:.2%} or more.')
flags[frequently_flagged_times, :] = True
def time_avg_zscore_dly_filt_SNRs(flags, filter_delay=AVG_SPECTRUM_FILTER_DELAY, eigenval_cutoff=EIGENVAL_CUTOFF):
"""Produces SNRs after time-averaging z-scores and delay filtering, accounting for flagging's effect on the filter."""
# figure out high and low band based on FM gap at 100 MHz
flagged_stretches = true_stretches(np.all(flags, axis=0))
FM_gap = [fs for fs in flagged_stretches if fs.start <= np.argmin(np.abs(freqs - 100e6)) < fs.stop][0]
low_band = slice((0 if flagged_stretches[0].start != 0 else flagged_stretches[0].stop), FM_gap.start)
high_band = slice(FM_gap.stop, (len(freqs) if flagged_stretches[-1].stop != len(freqs) else flagged_stretches[-1].start))
filt_SNR = {}
for pol in zscore:
# calculate timeavg_SNR and filter
noise_prediction = 1.0 / np.sum(~flags, axis=0)**.5
timeavg_SNR = np.nanmean(np.where(flags, np.nan, zscore[pol] / noise_prediction), axis=0)
wgts = np.where(np.isfinite(timeavg_SNR), 1, 0)
model = np.zeros_like(timeavg_SNR)
for band in [low_band, high_band]:
model[band], _, _ = dspec.fourier_filter(freqs[band], np.where(np.isfinite(timeavg_SNR[band]), timeavg_SNR[band], 0),
wgts[band], [0], [AVG_SPECTRUM_FILTER_DELAY / 1e9], mode="dpss_solve",
eigenval_cutoff=[EIGENVAL_CUTOFF], suppression_factors=[EIGENVAL_CUTOFF])
filt_SNR[pol] = timeavg_SNR - model
# correct for impact of filter
correction_factors = np.ones_like(wgts) * np.nan
for band in [low_band, high_band]:
X = dspec.dpss_operator(freqs[band], [0], filter_half_widths=[AVG_SPECTRUM_FILTER_DELAY / 1e9], eigenval_cutoff=[EIGENVAL_CUTOFF])[0]
W = wgts[band]
leverage = np.diag(X @ np.linalg.pinv(np.dot(X.T * W, X)) @ (X.T * W))
correction_factors[band] = np.where(leverage > 0, (1 - leverage)**.5, np.nan) # because the underlying data should be gaussian
filt_SNR[pol] /= correction_factors
return filt_SNR
def iteratively_flag_on_delay_filtered_time_avg_zscore(flags, thresh=TIME_AVG_DELAY_FILT_SNR_THRESH, dynamic_range=TIME_AVG_DELAY_FILT_SNR_DYNAMIC_RANGE,
filter_delay=AVG_SPECTRUM_FILTER_DELAY, eigenval_cutoff=EIGENVAL_CUTOFF):
"""Flag whole channels based on their outlierness after delay-filterd time-averaged zscores.
This is done iteratively since the delay filter can be unduly influenced by large outliers."""
filt_SNR = time_avg_zscore_dly_filt_SNRs(flags, filter_delay=AVG_SPECTRUM_FILTER_DELAY, eigenval_cutoff=EIGENVAL_CUTOFF)
while True:
largest_SNR = np.nanmax(list(filt_SNR.values()))
if largest_SNR < thresh:
break
#
cut = np.max([thresh, largest_SNR / dynamic_range])
for pol in filt_SNR:
flags[:, filt_SNR[pol] > cut] = True
filt_SNR = time_avg_zscore_dly_filt_SNRs(flags, filter_delay=AVG_SPECTRUM_FILTER_DELAY, eigenval_cutoff=EIGENVAL_CUTOFF)
In [15]:
flags = np.any(~np.isfinite(list(zscore.values())), axis=0)
print(f'{np.mean(flags):.3%} of waterfall flagged to start.')
# flag whole integrations or channels using outliers in median
while True:
nflags = np.sum(flags)
for pol in ['ee', 'nn']:
iteratively_flag_on_averaged_zscore(flags, zscore[pol], avg_func=np.nanmedian, avg_z_thresh=AVG_Z_THRESH, verbose=True)
impose_max_chan_flag_frac(flags, max_flag_frac=MAX_FREQ_FLAG_FRAC, verbose=True)
impose_max_time_flag_frac(flags, max_flag_frac=MAX_TIME_FLAG_FRAC, verbose=True)
if np.sum(flags) == nflags:
break
print(f'{np.mean(flags):.3%} of waterfall flagged after flagging whole times and channels with median z > {AVG_Z_THRESH}.')
# flag largest outliers
for pol in ['ee', 'nn']:
flags |= (zscore[pol] > Z_THRESH)
print(f'{np.mean(flags):.3%} of waterfall flagged after flagging z > {Z_THRESH} outliers.')
# watershed flagging
while True:
nflags = np.sum(flags)
for pol in ['ee', 'nn']:
flags |= xrfi._ws_flag_waterfall(zscore[pol], flags, WS_Z_THRESH)
if np.sum(flags) == nflags:
break
print(f'{np.mean(flags):.3%} of waterfall flagged after watershed flagging on z > {WS_Z_THRESH} neighbors of prior flags.')
# flag whole integrations or channels using outliers in mean
while True:
nflags = np.sum(flags)
for pol in ['ee', 'nn']:
iteratively_flag_on_averaged_zscore(flags, zscore[pol], avg_func=np.nanmean, avg_z_thresh=AVG_Z_THRESH, verbose=True)
impose_max_chan_flag_frac(flags, max_flag_frac=MAX_FREQ_FLAG_FRAC, verbose=True)
impose_max_time_flag_frac(flags, max_flag_frac=MAX_TIME_FLAG_FRAC, verbose=True)
if np.sum(flags) == nflags:
break
print(f'{np.mean(flags):.3%} of waterfall flagged after flagging whole times and channels with average z > {AVG_Z_THRESH}.')
# flag channels based on delay filter
iteratively_flag_on_delay_filtered_time_avg_zscore(flags, thresh=TIME_AVG_DELAY_FILT_SNR_THRESH, dynamic_range=TIME_AVG_DELAY_FILT_SNR_DYNAMIC_RANGE,
filter_delay=AVG_SPECTRUM_FILTER_DELAY, eigenval_cutoff=EIGENVAL_CUTOFF)
print(f'{np.mean(flags):.3%} of flagging channels that are {TIME_AVG_DELAY_FILT_SNR_THRESH}σ outliers after delay filtering the time average.')
# watershed flagging again
while True:
nflags = np.sum(flags)
for pol in ['ee', 'nn']:
flags |= xrfi._ws_flag_waterfall(zscore[pol], flags, WS_Z_THRESH)
if np.sum(flags) == nflags:
break
print(f'{np.mean(flags):.3%} of waterfall flagged after another round of watershed flagging on z > {WS_Z_THRESH} neighbors of prior flags.')
37.601% of waterfall flagged to start.
All-NaN slice encountered
Flagging an additional 0 integrations and 10 channels. Flagging 0 channels previously flagged 25.00% or more. Flagging 0 times previously flagged 10.00% or more.
Flagging an additional 0 integrations and 6 channels. Flagging 0 channels previously flagged 25.00% or more. Flagging 0 times previously flagged 10.00% or more.
Flagging an additional 0 integrations and 0 channels. Flagging 0 channels previously flagged 25.00% or more. Flagging 0 times previously flagged 10.00% or more.
Flagging an additional 0 integrations and 0 channels. Flagging 0 channels previously flagged 25.00% or more. Flagging 0 times previously flagged 10.00% or more. 38.320% of waterfall flagged after flagging whole times and channels with median z > 1.0. 38.807% of waterfall flagged after flagging z > 4.0 outliers.
40.375% of waterfall flagged after watershed flagging on z > 2.0 neighbors of prior flags. Flagging an additional 0 integrations and 0 channels. Flagging 22 channels previously flagged 25.00% or more. Flagging 190 times previously flagged 10.00% or more.
Mean of empty slice Mean of empty slice
Flagging an additional 0 integrations and 0 channels. Flagging 0 channels previously flagged 25.00% or more. Flagging 0 times previously flagged 10.00% or more. Flagging an additional 0 integrations and 0 channels.
Flagging 0 channels previously flagged 25.00% or more. Flagging 0 times previously flagged 10.00% or more. Flagging an additional 0 integrations and 0 channels. Flagging 0 channels previously flagged 25.00% or more.
Flagging 0 times previously flagged 10.00% or more. 45.343% of waterfall flagged after flagging whole times and channels with average z > 1.0.
Mean of empty slice Casting complex values to real discards the imaginary part Casting complex values to real discards the imaginary part
48.675% of flagging channels that are 4.0σ outliers after delay filtering the time average.
48.989% of waterfall flagged after another round of watershed flagging on z > 2.0 neighbors of prior flags.
Show results of flagging¶
Figure 3: Waterfall of Maximum z-Score of Either Polarization After Round 2 Flagging¶
The same as Figure 1, but after the flagging performed in this notebook.
In [16]:
plot_max_z_score(zscore, flags=flags)
All-NaN axis encountered
In [17]:
def zscore_spectra(ylim=[-3, 3], flags=flags):
fig, axes = plt.subplots(2, 1, figsize=(14,6), dpi=100, sharex=True, sharey=True, gridspec_kw={'hspace': 0})
for ax, pol in zip(axes, ['ee', 'nn']):
ax.plot(freqs / 1e6, np.nanmean(zscore[pol], axis=0),'r', label=f'{pol}-Polarization Before Round 2 Flagging', lw=.5)
ax.plot(freqs / 1e6, np.nanmean(np.where(flags, np.nan, zscore[pol]), axis=0), label=f'{pol}-Polarization After Round 2 Flagging')
ax.legend(loc='lower right')
ax.set_ylabel('Time-Averged Z-Score\n(Excluding Flags)')
ax.set_ylim(ylim)
axes[1].set_xlabel('Frequency (MHz)')
plt.tight_layout()
Figure 4: Spectra of Time-Averaged z-Scores¶
The average along the time axis of Figures 1 and 3 (though now separated per-polarization). This plot is useful for showing channels with repeated low-level RFI.
In [18]:
zscore_spectra()
Mean of empty slice Mean of empty slice
In [19]:
def summarize_flagging(flags=flags):
plt.figure(figsize=(14,10), dpi=100)
cmap = matplotlib.colors.ListedColormap(((0, 0, 0),) + matplotlib.cm.get_cmap("Set2").colors[0:2])
plt.imshow(np.where(np.any(~np.isfinite(list(zscore.values())), axis=0), 1, np.where(flags, 2, 0)),
aspect='auto', cmap=cmap, interpolation='none', extent=extent)
plt.clim([-.5, 2.5])
cbar = plt.colorbar(location='top', aspect=40, pad=.02)
cbar.set_ticks([0, 1, 2])
cbar.set_ticklabels(['Unflagged', 'Previously Flagged', 'Flagged Here Using Delayed Filtered z-Scores'])
plt.xlabel('Frequency (MHz)')
plt.ylabel(f'JD - {int(times[0])}')
plt.tight_layout()
Figure 5: Summary of Flags Before and After Round 2 Flagging¶
This plot shows which times and frequencies were flagged before and after this notebook. It is directly comparable to Figure 5 of the first round full_day_rfi notebook.
In [20]:
summarize_flagging()
The get_cmap function was deprecated in Matplotlib 3.7 and will be removed in 3.11. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap()`` or ``pyplot.get_cmap()`` instead.
Save results¶
In [21]:
add_to_history = 'by full_day_rfi_round_2 notebook with the following environment:\n' + '=' * 65 + '\n' + os.popen('conda env export').read() + '=' * 65
In [22]:
tind = 0
always_flagged_ants = set()
ever_unflagged_ants = set()
for cal_file in cal_files:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# update cal_file
uvc = UVCal()
uvc.read(cal_file, use_future_array_shapes=True)
uvc.flag_array |= (flags[tind:tind + len(uvc.time_array), :].T)[None, :, :, None]
uvc.history += 'Modified ' + add_to_history
uvc.write_calfits(cal_file, clobber=True)
# keep track of flagged antennas
for antnum in uvc.ant_array:
for antpol in ['Jee', 'Jnn']:
if np.all(uvc.get_flags(antnum, antpol)):
if (antnum, antpol) not in ever_unflagged_ants:
always_flagged_ants.add((antnum, antpol))
else:
ever_unflagged_ants.add((antnum, antpol))
always_flagged_ants.discard((antnum, antpol))
# Create new flag object
uvf_out = UVFlag(uvc, waterfall=True, mode='flag')
uvf_out.flag_array |= flags[tind:tind + len(uvc.time_array), :, None]
uvf_out.history += 'Produced ' + add_to_history
uvf_out.write(cal_file.replace(SMOOTH_CAL_SUFFIX, FLAG_WATERFALL2_SUFFIX), clobber=True)
# increment time index
tind += len(uvc.time_array)
print(f'Saved {len(cal_files)} *.{FLAG_WATERFALL2_SUFFIX} files starting with {cal_files[0].replace(SMOOTH_CAL_SUFFIX, FLAG_WATERFALL2_SUFFIX)}.')
Saved 1572 *.sum.flag_waterfall_round_2.h5 files starting with /mnt/sn1/data2/2460774/zen.2460774.21069.sum.flag_waterfall_round_2.h5.
In [23]:
# write summary of entirely flagged times/freqs/ants to yaml
all_flagged_times = np.all(flags, axis=1)
all_flagged_freqs = np.all(flags, axis=0)
all_flagged_ants = [(int(ant[0]), ant[1]) for ant in sorted(always_flagged_ants)]
dt = np.median(np.diff(times))
out_yml_str = 'JD_flags: ' + str([[float(times[flag_stretch][0] - dt / 2), float(times[flag_stretch][-1] + dt / 2)]
for flag_stretch in true_stretches(all_flagged_times)])
df = np.median(np.diff(freqs))
out_yml_str += '\n\nfreq_flags: ' + str([[float(freqs[flag_stretch][0] - df / 2), float(freqs[flag_stretch][-1] + df / 2)]
for flag_stretch in true_stretches(all_flagged_freqs)])
out_yml_str += '\n\nex_ants: ' + str(all_flagged_ants).replace("'", "").replace('(', '[').replace(')', ']')
print(f'Writing the following to {out_yaml_file}\n' + '-' * (25 + len(out_yaml_file)))
print(out_yml_str)
with open(out_yaml_file, 'w') as outfile:
outfile.writelines(out_yml_str)
Writing the following to /mnt/sn1/data2/2460774/2460774_aposteriori_flags.yaml ------------------------------------------------------------------------------ JD_flags: [[2460774.2105749557, 2460774.2678411864], [2460774.2679530345, 2460774.271644022], [2460774.27175587, 2460774.2749994653], [2460774.275223161, 2460774.2755587054], [2460774.2756705536, 2460774.2764534904], [2460774.2765653385, 2460774.276900883], [2460774.2773482753, 2460774.2777956678], [2460774.2783549083, 2460774.2786904527], [2460774.278802301, 2460774.2792496933], [2460774.2794733895, 2460774.284394706], [2460774.285177643, 2460774.2857368835], [2460774.2859605798, 2460774.286296124], [2460774.286631668, 2460774.287526453], [2460774.287750149, 2460774.2880856935], [2460774.288756782, 2460774.289651567], [2460774.2899871115, 2460774.2912174407], [2460774.291329289, 2460774.2917766813], [2460774.2918885294, 2460774.2932307064], [2460774.2933425545, 2460774.295579517], [2460774.295691365, 2460774.295915061], [2460774.2960269093, 2460774.296921694], [2460774.2971453904, 2460774.2978164786], [2460774.298263871, 2460774.299158656], [2460774.2993823523, 2460774.2997178966], [2460774.299941593, 2460774.3003889853], [2460774.3006126815, 2460774.301060074], [2460774.301171922, 2460774.301954859], [2460774.3027377957, 2460774.302961492], [2460774.305533998, 2460774.3057576944], [2460774.3058695425, 2460774.3059813906], [2460774.306316935, 2460774.306540631], [2460774.307435416, 2460774.3076591124], [2460774.3079946567, 2460774.308442049], [2460774.3085538973, 2460774.3086657454], [2460774.3087775935, 2460774.3091131374], [2460774.3093368337, 2460774.309672378], [2460774.3100079224, 2460774.3101197705], [2460774.3103434667, 2460774.310679011], [2460774.3109027073, 2460774.3110145554], [2460774.311573796, 2460774.311685644], [2460774.3122448847, 2460774.312356733], [2460774.3131396696, 2460774.3132515177], [2460774.31369891, 2460774.3139226064], [2460774.3141463026, 2460774.3153766314], [2460774.3154884796, 2460774.3156003277], [2460774.315824024, 2460774.31604772], [2460774.3164951126, 2460774.316718809], [2460774.317054353, 2460774.3172780494], [2460774.3173898975, 2460774.318060986], [2460774.3182846825, 2460774.3183965306], [2460774.3192913155, 2460774.3194031636], [2460774.3195150117, 2460774.319738708], [2460774.319850556, 2460774.319962404], [2460774.3200742523, 2460774.320409796], [2460774.3205216443, 2460774.3206334924], [2460774.3208571887, 2460774.321192733], [2460774.322087518, 2460774.322311214], [2460774.3224230623, 2460774.3225349104], [2460774.3228704548, 2460774.322982303], [2460774.323317847, 2460774.323877088], [2460774.323988936, 2460774.3246600246], [2460774.324995569, 2460774.3255548095], [2460774.3256666576, 2460774.325890354], [2460774.3268969865, 2460774.3271206827], [2460774.327344379, 2460774.3276799233], [2460774.3280154676, 2460774.328239164], [2460774.328351012, 2460774.32846286], [2460774.329469493, 2460774.3295813412], [2460774.33025243, 2460774.3308116705], [2460774.331147215, 2460774.331370911], [2460774.3314827587, 2460774.331706455], [2460774.332713088, 2460774.332824936], [2460774.3329367843, 2460774.3331604805], [2460774.3340552654, 2460774.3343908098], [2460774.3352855947, 2460774.335397443], [2460774.3358448353, 2460774.3359566834], [2460774.337187012, 2460774.3372988603], [2460774.3375225565, 2460774.3376344047], [2460774.337969949, 2460774.3381936452], [2460774.3386410377, 2460774.338752886], [2460774.3392002783, 2460774.3393121264], [2460774.339759519, 2460774.339983215], [2460774.3402069113, 2460774.3403187594], [2460774.3404306076, 2460774.3405424557], [2460774.340766152, 2460774.340878], [2460774.3411016962, 2460774.3413253925], [2460774.3414372406, 2460774.341660937], [2460774.3424438736, 2460774.3425557218], [2460774.344121595, 2460774.344345291], [2460774.345128228, 2460774.3454637723], [2460774.3464704053, 2460774.3466941016], [2460774.347141494, 2460774.3474770384], [2460774.3478125827, 2460774.348148127], [2460774.3488192153, 2460774.3489310634], [2460774.349378456, 2460774.349490304], [2460774.350496937, 2460774.3507206333], [2460774.351279874, 2460774.351615418], [2460774.3527338994, 2460774.3528457475], [2460774.3529575956, 2460774.3530694437], [2460774.3550827093, 2460774.3553064056], [2460774.3562011905, 2460774.3564248867], [2460774.3573196717, 2460774.357543368], [2460774.3604514184, 2460774.3606751147], [2460774.378570812, 2460774.378794508], [2460774.3820381034, 2460774.382261799], [2460774.3833802803, 2460774.3836039766], [2460774.38516985, 2460774.3852816983], [2460774.386847572, 2460774.38695942], [2460774.3909859518, 2460774.391209648], [2460774.4108949145, 2460774.411342307], [2460774.414250358, 2460774.414362206], [2460774.4189479784, 2460774.4190598265], [2460774.4214086365, 2460774.4215204846], [2460774.4216323327, 2460774.421744181], [2460774.421967877, 2460774.422079725], [2460774.4254351687, 2460774.425547017], [2460774.4338237764, 2460774.4340474727], [2460774.436284435, 2460774.436396283], [2460774.441429448, 2460774.441653144], [2460774.44780479, 2460774.447916638], [2460774.452055018, 2460774.452278714], [2460774.4560815496, 2460774.456305246], [2460774.458206664, 2460774.45843036], [2460774.471963981, 2460774.4720758293], [2460774.488964893, 2460774.489188589], [2460774.493774362, 2460774.49388621], [2460774.4945572987, 2460774.4947809945], [2460774.5011563366, 2460774.5012681847], [2460774.513795173, 2460774.514018869], [2460774.5252036797, 2460774.525539224], [2460774.5260984646, 2460774.5262103127], [2460774.529789452, 2460774.530013148], [2460774.530907933, 2460774.5311316294], [2460774.53403968, 2460774.534263376], [2460774.540191326, 2460774.540415022], [2460774.5429875287, 2460774.543099377], [2460774.54410601, 2460774.544217858], [2460774.544329706, 2460774.544441554], [2460774.545671883, 2460774.5458955793], [2460774.558198871, 2460774.558310719], [2460774.5614424665, 2460774.561778011]] freq_flags: [[49911499.0234375, 50033569.3359375], [62240600.5859375, 62728881.8359375], [69931030.2734375, 70053100.5859375], [77621459.9609375, 77987670.8984375], [87265014.6484375, 108261108.3984375], [109603881.8359375, 109725952.1484375], [109970092.7734375, 110092163.0859375], [112533569.3359375, 113388061.5234375], [113632202.1484375, 113754272.4609375], [116073608.3984375, 116195678.7109375], [116439819.3359375, 116561889.6484375], [116683959.9609375, 116806030.2734375], [124862670.8984375, 125228881.8359375], [126205444.3359375, 126327514.6484375], [127548217.7734375, 127670288.0859375], [129989624.0234375, 130111694.3359375], [136337280.2734375, 136459350.5859375], [136825561.5234375, 138290405.2734375], [138656616.2109375, 138778686.5234375], [141464233.3984375, 141586303.7109375], [141708374.0234375, 141830444.3359375], [142074584.9609375, 142318725.5859375], [142562866.2109375, 143539428.7109375], [143783569.3359375, 144027709.9609375], [144882202.1484375, 145004272.4609375], [145492553.7109375, 145736694.3359375], [146224975.5859375, 146347045.8984375], [147445678.7109375, 147567749.0234375], [149154663.0859375, 149276733.3984375], [149887084.9609375, 150009155.2734375], [153060913.0859375, 153182983.3984375], [154159545.8984375, 154403686.5234375], [155014038.0859375, 155136108.3984375], [155258178.7109375, 155380249.0234375], [155868530.2734375, 156112670.8984375], [157577514.6484375, 157699584.9609375], [158187866.2109375, 158309936.5234375], [158432006.8359375, 158554077.1484375], [158676147.4609375, 158798217.7734375], [159164428.7109375, 159286499.0234375], [160140991.2109375, 160385131.8359375], [161361694.3359375, 161483764.6484375], [169906616.2109375, 170150756.8359375], [170272827.1484375, 170394897.4609375], [170516967.7734375, 170639038.0859375], [170883178.7109375, 171005249.0234375], [174789428.7109375, 175765991.2109375], [176132202.1484375, 176254272.4609375], [179672241.2109375, 179794311.5234375], [180892944.3359375, 181747436.5234375], [183212280.2734375, 183334350.5859375], [186386108.3984375, 186508178.7109375], [187362670.8984375, 187606811.5234375], [189682006.8359375, 189804077.1484375], [189926147.4609375, 190048217.7734375], [190658569.3359375, 191757202.1484375], [193222045.8984375, 193344116.2109375], [195297241.2109375, 195541381.8359375], [195663452.1484375, 195785522.4609375], [195907592.7734375, 196151733.3984375], [196395874.0234375, 196517944.3359375], [196884155.2734375, 197372436.5234375], [197860717.7734375, 198715209.9609375], [199203491.2109375, 199325561.5234375], [200057983.3984375, 200180053.7109375], [201400756.8359375, 202011108.3984375], [203231811.5234375, 203353881.8359375], [204940795.8984375, 205062866.2109375], [205184936.5234375, 205429077.1484375], [206893920.8984375, 207015991.2109375], [207138061.5234375, 207382202.1484375], [208480834.9609375, 208724975.5859375], [209945678.7109375, 210067749.0234375], [210433959.9609375, 210556030.2734375], [212142944.3359375, 212265014.6484375], [215194702.1484375, 215316772.4609375], [215682983.3984375, 215805053.7109375], [220565795.8984375, 220809936.5234375], [221176147.4609375, 221298217.7734375], [221664428.7109375, 221786499.0234375], [222030639.6484375, 222274780.2734375], [222396850.5859375, 222518920.8984375], [222640991.2109375, 223739624.0234375], [223861694.3359375, 223983764.6484375], [224349975.5859375, 224472045.8984375], [225692749.0234375, 225814819.3359375], [227401733.3984375, 227767944.3359375], [227890014.6484375, 228134155.2734375], [229110717.7734375, 229598999.0234375], [229965209.9609375, 230087280.2734375], [231063842.7734375, 231185913.0859375], [232528686.5234375, 232650756.8359375], [232894897.4609375, 233016967.7734375], [233383178.7109375, 233627319.3359375], [233871459.9609375, 234359741.2109375]] ex_ants: [[4, Jee], [8, Jee], [8, Jnn], [10, Jee], [10, Jnn], [15, Jnn], [18, Jee], [18, Jnn], [20, Jee], [20, Jnn], [21, Jee], [27, Jee], [27, Jnn], [28, Jee], [28, Jnn], [29, Jnn], [30, Jee], [32, Jnn], [33, Jnn], [34, Jee], [35, Jnn], [37, Jnn], [40, Jnn], [42, Jee], [42, Jnn], [44, Jee], [45, Jee], [46, Jee], [49, Jnn], [51, Jee], [51, Jnn], [60, Jnn], [64, Jnn], [67, Jnn], [71, Jnn], [72, Jnn], [75, Jnn], [76, Jee], [76, Jnn], [77, Jnn], [78, Jee], [80, Jnn], [81, Jnn], [82, Jnn], [86, Jnn], [87, Jee], [90, Jee], [92, Jee], [97, Jnn], [99, Jnn], [103, Jee], [104, Jnn], [105, Jee], [106, Jee], [107, Jee], [108, Jnn], [109, Jnn], [112, Jee], [113, Jnn], [115, Jee], [115, Jnn], [117, Jee], [120, Jee], [120, Jnn], [121, Jee], [128, Jee], [130, Jee], [130, Jnn], [131, Jnn], [134, Jnn], [135, Jee], [148, Jee], [149, Jee], [153, Jnn], [154, Jnn], [155, Jnn], [161, Jnn], [169, Jee], [170, Jee], [171, Jee], [171, Jnn], [172, Jnn], [175, Jnn], [176, Jnn], [180, Jee], [180, Jnn], [197, Jnn], [199, Jnn], [200, Jee], [200, Jnn], [202, Jnn], [204, Jnn], [206, Jnn], [209, Jnn], [212, Jnn], [213, Jee], [214, Jee], [214, Jnn], [215, Jnn], [216, Jee], [216, Jnn], [218, Jnn], [227, Jee], [227, Jnn], [231, Jnn], [232, Jee], [233, Jnn], [238, Jnn], [239, Jee], [240, Jnn], [244, Jee], [246, Jee], [250, Jee], [251, Jee], [253, Jnn], [255, Jee], [255, Jnn], [262, Jee], [262, Jnn], [266, Jee], [266, Jnn], [268, Jee], [268, Jnn], [320, Jee], [320, Jnn], [321, Jee], [321, Jnn], [322, Jee], [322, Jnn], [323, Jee], [323, Jnn], [324, Jee], [324, Jnn], [325, Jee], [325, Jnn], [326, Jee], [326, Jnn], [327, Jee], [327, Jnn], [328, Jee], [328, Jnn], [329, Jee], [329, Jnn], [331, Jee], [331, Jnn], [332, Jee], [332, Jnn], [333, Jee], [333, Jnn], [336, Jee], [336, Jnn], [340, Jee], [340, Jnn]]
Metadata¶
In [24]:
for repo in ['hera_cal', 'hera_qm', 'hera_filters', 'hera_notebook_templates', 'pyuvdata']:
exec(f'from {repo} import __version__')
print(f'{repo}: {__version__}')
hera_cal: 3.7.1.dev45+g4a0c6f1 hera_qm: 2.2.1.dev2+ga535e9e hera_filters: 0.1.6.dev9+gf165ec1
hera_notebook_templates: 0.1.dev989+gee0995d pyuvdata: 3.1.3
In [25]:
print(f'Finished execution in {(time.time() - tstart) / 60:.2f} minutes.')
Finished execution in 29.36 minutes.