Antenna Classification Daily Summary¶

by Josh Dillon last updated June 19, 2023

This notebook parses and summarizes the output of the file_calibration notebook to produce a report on per-antenna malfunctions on a daily basis.

Quick links:

• Summary of Per Antenna Issues¶

• Figure 1: Per File Overall Antenna Classification Summary¶

• Figure 2: Per Classifier Antenna Flagging Summary¶

• Figure 3: Array Visualization of Overall Daily Classification¶

In [1]:
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 pandas as pd
import glob
import os
import matplotlib.pyplot as plt
from hera_cal import io, utils
from hera_qm import ant_class
from uvtools.plot import plot_antpos, plot_antclass
%matplotlib inline
from IPython.display import display, HTML
display(HTML("<style>.container { width:100% !important; }</style>"))
_ = np.seterr(all='ignore')  # get rid of red warnings
%config InlineBackend.figure_format = 'retina'

Settings¶

In [2]:
# Parse settings from environment
ANT_CLASS_FOLDER = os.environ.get("ANT_CLASS_FOLDER", "./")
SUM_FILE = os.environ.get("SUM_FILE", None)
# ANT_CLASS_FOLDER = "/mnt/sn1/2460330"
# SUM_FILE = "/mnt/sn1/2460330/zen.2460330.25463.sum.uvh5"
OC_SKIP_OUTRIGGERS = os.environ.get("OC_SKIP_OUTRIGGERS", "TRUE").upper() == "TRUE"

for param in ['ANT_CLASS_FOLDER', 'SUM_FILE', 'OC_SKIP_OUTRIGGERS']:
    print(f"{param} = '{eval(param)}'")

ANT_CLASS_FOLDER = '/mnt/sn1/data2/2460570'
SUM_FILE = '/mnt/sn1/data2/2460570/zen.2460570.47637.sum.uvh5'
OC_SKIP_OUTRIGGERS = 'True'
In [3]:
if SUM_FILE is not None:
    from astropy.time import Time, TimeDelta
    utc = Time(float(SUM_FILE.split('zen.')[-1].split('.sum.uvh5')[0]), format='jd').datetime
    print(f'Date: {utc.month}-{utc.day}-{utc.year}')

Date: 9-16-2024
In [4]:
# set thresholds for fraction of the day
overall_thresh = .1
all_zero_thresh = .1
eo_zeros_thresh = .1
xengine_diff_thresh = .1
cross_pol_thresh = .5
bad_fem_thresh = .1
high_power_thresh = .1
low_power_thresh = .1
low_corr_thresh = .1
bad_shape_thresh = .5
excess_rfi_thresh = .1
chisq_thresh = .25

Load classifications and other metadata¶

In [5]:
# Load csvs
csv_files = sorted(glob.glob(os.path.join(ANT_CLASS_FOLDER, '*.ant_class.csv')))
jds = [float(f.split('/')[-1].split('zen.')[-1].split('.sum')[0]) for f in csv_files]
tables = [pd.read_csv(f).dropna(axis=0, how='all') for f in csv_files]
table_cols = tables[0].columns[1::2]
class_cols = tables[0].columns[2::2]
print(f'Found {len(csv_files)} csv files starting with {csv_files[0]}')

Found 1882 csv files starting with /mnt/sn1/data2/2460570/zen.2460570.26632.sum.ant_class.csv
In [6]:
# parse ant_strings
ap_strs = np.array(tables[0]['Antenna'])
ants = sorted(set(int(a[:-1]) for a in ap_strs))
translator = ''.maketrans('e', 'n') | ''.maketrans('n', 'e')
In [7]:
# get node numbers
node_dict = {ant: 'Unknown' for ant in ants}
try:
    from hera_mc import cm_hookup
    hookup = cm_hookup.get_hookup('default')
    for ant_name in hookup:
        ant = int("".join(filter(str.isdigit, ant_name)))
        if ant in node_dict:
            if hookup[ant_name].get_part_from_type('node')['E<ground'] is not None:
                node_dict[ant] = int(hookup[ant_name].get_part_from_type('node')['E<ground'][1:])
except:
    pass
nodes = sorted(set(node_dict.values()))
In [8]:
def classification_array(col):
    class_array = np.vstack([t[col] for t in tables])
    class_array[class_array == 'good'] = 1.7
    class_array[class_array == 'suspect'] = 1
    class_array[class_array == 'bad'] = 0
    return class_array.astype(float)
In [9]:
if SUM_FILE is not None:
    hd = io.HERADataFastReader(SUM_FILE)
    ap_tuples = [(int(ap[:-1]), {'e': 'Jee', 'n': 'Jnn'}[ap[-1]]) for ap in ap_strs]
    bad_bools = np.mean(classification_array('Antenna Class') == 0, axis=0) > overall_thresh
    bad_aps = [ap_tuples[i] for i in np.arange(len(ap_tuples))[bad_bools]]
    suspect_bools = np.mean(classification_array('Antenna Class') == 1, axis=0) > overall_thresh
    suspect_aps = [ap_tuples[i] for i in np.arange(len(ap_tuples))[suspect_bools] if ap_tuples[i] not in bad_aps]
    good_aps = [ap for ap in ap_tuples if ap not in bad_aps and ap not in suspect_aps]
    overall_class = ant_class.AntennaClassification(bad=bad_aps, suspect=suspect_aps, good=good_aps)
    autos, _, _ = hd.read(bls=[bl for bl in hd.bls if utils.split_bl(bl)[0] == utils.split_bl(bl)[1]], read_flags=False, read_nsamples=False)
    avg_unflagged_auto = {}
    for pol in ['ee', 'nn']:
        unflagged_autos = [autos[bl] for bl in autos if bl[2] == pol and overall_class[utils.split_bl(bl)[0]] != 'bad']
        if len(unflagged_autos) > 0:
            avg_unflagged_auto[pol] = np.mean(unflagged_autos, axis=(0, 1))
        else:
            avg_unflagged_auto[pol] = np.zeros(len(hd.freqs), dtype=complex)

Figure out and summarize per-antenna issues¶

In [10]:
def print_issue_summary(bad_ant_strs, title, notes='', plot=False):
    '''Print report for list of bad antenna polarizations strings'''
    unique_bad_antnums = [int(ap[:-1]) for ap in bad_ant_strs]
    display(HTML(f'<h2>{title}: ({len(bad_ant_strs)} antpols across {len(set([ba[:-1] for ba in bad_ant_strs]))} antennas)</h2>'))
    if len(notes) > 0:
        display(HTML(f'<h4>{notes}</h4>'))
    if len(bad_ant_strs) > 0:
        print(f'All Bad Antpols: {", ".join(bad_ant_strs)}\n')
    for node in nodes:
        if np.any([node == node_dict[a] for a in unique_bad_antnums]):
            aps = [ap for ap in bad_ant_strs if node_dict[int(ap[:-1])] == node]
            whole_ants = [str(wa) for wa in set([int(ap[:-1]) for ap in aps if ap.translate(translator) in bad_ant_strs])]
            single_pols =  [ap for ap in aps if ap.translate(translator) not in bad_ant_strs]
            print(f'Node {node}:')
            print(f'\tAntpols ({len(aps)} total): {", ".join(aps)}')
            print(f'\tWhole Ants ({len(whole_ants)} total): {", ".join(whole_ants)}')
            print(f'\tSingle Pols ({len(single_pols)} total): {", ".join(single_pols)}')
            if plot and SUM_FILE is not None:
                fig, axes = plt.subplots(1, 2, figsize=(12,4), dpi=70, sharey=True, gridspec_kw={'wspace': 0})
                for ax, pol in zip(axes, ['ee', 'nn']):                    
                    ax.semilogy(autos.freqs / 1e6, avg_unflagged_auto[pol], 'k--', label='Average\nUnflagged\nAuto')
                    for ap in aps:
                        ant = int(ap[:-1]), utils.comply_pol(ap[-1])
                        auto_bl = utils.join_bl(ant, ant)
                        if auto_bl[2] == pol:
                            ax.semilogy(autos.freqs / 1e6, np.mean(autos[auto_bl], axis=0), label=ap)
                    ax.legend()
                    ax.set_xlim([40, 299])
                    ax.set_title(f'{title} on Node {node} ({pol}-antennas)')
                    ax.set_xlabel('Frequency (MHz)')
                axes[0].set_ylabel('Single File Raw Autocorrelation')
                plt.tight_layout()
                plt.show()
In [11]:
# precompute various helpful quantities
all_slopes = np.vstack([t['Autocorr Slope'] for t in tables])
median_slope = np.median(all_slopes)
bad_slopes = np.vstack([t['Autocorr Slope Class'] for t in tables]) == 'bad'
suspect_slopes = np.vstack([t['Autocorr Slope Class'] for t in tables]) == 'suspect'
bad_shapes = np.vstack([t['Autocorr Shape Class'] for t in tables]) == 'bad'
suspect_shapes = np.vstack([t['Autocorr Shape Class'] for t in tables]) == 'suspect'
all_powers = np.vstack([t['Autocorr Power'] for t in tables])
median_power = np.median(all_powers)
bad_powers = np.vstack([t['Autocorr Power Class'] for t in tables]) == 'bad'
suspect_powers = np.vstack([t['Autocorr Power Class'] for t in tables]) == 'suspect'
bad_rfi = np.vstack([t['Auto RFI RMS Class'] for t in tables]) == 'bad'
suspect_rfi = np.vstack([t['Auto RFI RMS Class'] for t in tables]) == 'suspect'
In [12]:
# find all zeros
all_zeros_strs = ap_strs[np.mean(np.vstack([t['Dead? Class'] for t in tables]) == 'bad', axis=0) > all_zero_thresh]
In [13]:
# find even/odd zeros
eo_zeros_strs = ap_strs[np.mean(np.vstack([t['Even/Odd Zeros Class'] for t in tables]) == 'bad', axis=0) > eo_zeros_thresh]
eo_zeros_strs = [ap for ap in eo_zeros_strs if ap not in all_zeros_strs]
In [14]:
# find cross-polarized antennas
cross_pol_strs = ap_strs[np.mean(np.vstack([t['Cross-Polarized Class'] for t in tables]) == 'bad', axis=0) > cross_pol_thresh]
cross_pol_strs = [ap for ap in cross_pol_strs if ap not in all_zeros_strs]
In [15]:
# find FEM power issues: must be low power, high slope, and bad or suspect in power, slope, rfi, and shape
fem_off_prod = (bad_powers + .5 * suspect_powers) * (bad_slopes + .5 * suspect_slopes)
fem_off_prod *= (bad_rfi + .5 * suspect_rfi) * (bad_shapes + .5 * suspect_shapes)
fem_off_strs = ap_strs[np.mean(fem_off_prod * (all_powers < median_power) * (all_slopes > median_slope), axis=0) > .1]
In [16]:
# find high power issues
high_power_strs = ap_strs[np.mean(bad_powers & (all_powers > median_power), axis=0) > high_power_thresh]
In [17]:
# find other low power issues
low_power_strs = ap_strs[np.mean(bad_powers & (all_powers < median_power), axis=0) > low_power_thresh]
low_power_strs = [ap for ap in low_power_strs if ap not in all_zeros_strs and ap not in fem_off_strs]
In [18]:
# find low correlation (but not low power)
low_corr_strs = ap_strs[np.mean(np.vstack([t['Low Correlation Class'] for t in tables]) == 'bad', axis=0) > low_corr_thresh]
low_corr_strs = [ap for ap in low_corr_strs if ap not in (set(low_power_strs) | set(all_zeros_strs) | set(fem_off_strs))]
In [19]:
# find bad bandpasses
bad_bandpass_strs = ap_strs[np.mean(bad_shapes, axis=0) > bad_shape_thresh]
bad_bandpass_strs = [ap for ap in bad_bandpass_strs if ap not in (set(low_power_strs) | set(all_zeros_strs) | set(high_power_strs) | set(fem_off_strs))]
In [20]:
# find antennas with excess RFI
excess_rfi_strs = ap_strs[np.mean(np.vstack([t['Auto RFI RMS Class'] for t in tables]) == 'bad', axis=0) > excess_rfi_thresh]
excess_rfi_strs = [ap for ap in excess_rfi_strs if ap not in (set(low_power_strs) | set(all_zeros_strs) |  set(fem_off_strs) |
                                                              set(bad_bandpass_strs) | set(high_power_strs))]
In [21]:
# find bad x-engine diffs
xengine_diff_strs = ap_strs[np.mean(np.vstack([t['Bad Diff X-Engines Class'] for t in tables]) == 'bad', axis=0) > xengine_diff_thresh]
xengine_diff_strs = [ap for ap in xengine_diff_strs if ap not in (set(bad_bandpass_strs) | set(low_power_strs) | set(excess_rfi_strs) | set(low_corr_strs) |
                                                                  set(all_zeros_strs) | set(high_power_strs) | set(fem_off_strs) | set(eo_zeros_strs))]
In [22]:
# find antennas with high redcal chi^2
chisq_strs = ap_strs[np.mean(np.vstack([t['Redcal chi^2 Class'] for t in tables]) == 'bad', axis=0) > chisq_thresh]
chisq_strs = [ap for ap in chisq_strs if ap not in (set(bad_bandpass_strs) | set(low_power_strs) | set(excess_rfi_strs) | set(low_corr_strs) |
                                                    set(all_zeros_strs) | set(high_power_strs) | set(fem_off_strs) | set(eo_zeros_strs) | set(xengine_diff_strs))]
if OC_SKIP_OUTRIGGERS:
    chisq_strs = [ap for ap in chisq_strs if int(ap[:-1]) < 320]
In [23]:
# collect all results
to_print = [(all_zeros_strs, 'All-Zeros', 'These antennas have visibilities that are more than half zeros.'),
            (eo_zeros_strs, 'Excess Zeros in Either Even or Odd Spectra', 
             'These antennas are showing evidence of packet loss or X-engine failure.', True),
            (xengine_diff_strs, 'Excess Power in X-Engine Diffs', 
             'These antennas are showing evidence of mis-written packets in either the evens or the odds.', True),            
            (cross_pol_strs, 'Cross-Polarized', 'These antennas have their east and north cables swapped.'),
            (fem_off_strs, 'Likely FEM Power Issue', 'These antennas have low power and anomolously high slopes.', True),
            (high_power_strs, 'High Power', 'These antennas have high median power.', True),
            (low_power_strs, 'Other Low Power Issues', 'These antennas have low power, but are not all-zeros and not FEM off.', True),
            (low_corr_strs, 'Low Correlation, But Not Low Power', 'These antennas are low correlation, but their autocorrelation power levels look OK.'),
            (bad_bandpass_strs, 'Bad Bandpass Shapes, But Not Bad Power', 
             'These antennas have unusual bandpass shapes, but are not all-zeros, high power, low power, or FEM off.', True),
            (excess_rfi_strs, 'Excess RFI', 'These antennas have excess RMS after DPSS filtering (likely RFI), but not low or high power or a bad bandpass.', True),
            (chisq_strs, 'Redcal chi^2', 'These antennas have been idenfied as not redundantly calibrating well, even after passing the above checks.')]
In [24]:
def print_high_level_summary():
    for tp in sorted(to_print, key=lambda x: len(x[0]), reverse=True):
        print(f'{len(tp[0])} antpols (on {len(set([ap[:-1] for ap in tp[0]]))} antennas) frequently flagged for {tp[1]}.')
        
def print_all_issue_summaries():
    for tp in to_print:
        print_issue_summary(*tp)

Summary of Per-Antenna Issues¶

In [25]:
print_high_level_summary()

90 antpols (on 45 antennas) frequently flagged for All-Zeros.
36 antpols (on 34 antennas) frequently flagged for Excess RFI.
14 antpols (on 13 antennas) frequently flagged for Likely FEM Power Issue.
13 antpols (on 11 antennas) frequently flagged for Low Correlation, But Not Low Power.
12 antpols (on 11 antennas) frequently flagged for Bad Bandpass Shapes, But Not Bad Power.
9 antpols (on 8 antennas) frequently flagged for Redcal chi^2.
8 antpols (on 7 antennas) frequently flagged for Excess Power in X-Engine Diffs.
8 antpols (on 6 antennas) frequently flagged for High Power.
6 antpols (on 3 antennas) frequently flagged for Cross-Polarized.
6 antpols (on 6 antennas) frequently flagged for Other Low Power Issues.
0 antpols (on 0 antennas) frequently flagged for Excess Zeros in Either Even or Odd Spectra.
In [26]:
print_all_issue_summaries()

All-Zeros: (90 antpols across 45 antennas)

These antennas have visibilities that are more than half zeros.

All Bad Antpols: 22e, 22n, 34e, 34n, 35e, 35n, 40e, 40n, 47e, 47n, 48e, 48n, 49e, 49n, 56e, 56n, 61e, 61n, 62e, 62n, 63e, 63n, 64e, 64n, 69e, 69n, 77e, 77n, 78e, 78n, 88e, 88n, 90e, 90n, 107e, 107n, 152e, 152n, 153e, 153n, 154e, 154n, 176e, 176n, 177e, 177n, 178e, 178n, 179e, 179n, 185e, 185n, 186e, 186n, 187e, 187n, 199e, 199n, 207e, 207n, 211e, 211n, 220e, 220n, 221e, 221n, 222e, 222n, 223e, 223n, 224e, 224n, 235e, 235n, 241e, 241n, 242e, 242n, 243e, 243n, 244e, 244n, 245e, 245n, 285e, 285n, 329e, 329n, 333e, 333n

Node 4:
	Antpols (6 total): 40e, 40n, 56e, 56n, 69e, 69n
	Whole Ants (3 total): 40, 56, 69
	Single Pols (0 total): 
Node 6:
	Antpols (24 total): 22e, 22n, 34e, 34n, 35e, 35n, 47e, 47n, 48e, 48n, 49e, 49n, 61e, 61n, 62e, 62n, 63e, 63n, 64e, 64n, 77e, 77n, 78e, 78n
	Whole Ants (12 total): 64, 34, 35, 77, 78, 47, 48, 49, 22, 61, 62, 63
	Single Pols (0 total): 
Node 9:
	Antpols (6 total): 88e, 88n, 90e, 90n, 107e, 107n
	Whole Ants (3 total): 88, 90, 107
	Single Pols (0 total): 
Node 12:
	Antpols (12 total): 176e, 176n, 177e, 177n, 178e, 178n, 179e, 179n, 329e, 329n, 333e, 333n
	Whole Ants (6 total): 329, 333, 176, 177, 178, 179
	Single Pols (0 total): 
Node 14:
	Antpols (6 total): 185e, 185n, 186e, 186n, 187e, 187n
	Whole Ants (3 total): 185, 186, 187
	Single Pols (0 total): 
Node 16:
	Antpols (6 total): 152e, 152n, 153e, 153n, 154e, 154n
	Whole Ants (3 total): 152, 153, 154
	Single Pols (0 total): 
Node 17:
	Antpols (4 total): 199e, 199n, 235e, 235n
	Whole Ants (2 total): 235, 199
	Single Pols (0 total): 
Node 18:
	Antpols (6 total): 220e, 220n, 221e, 221n, 222e, 222n
	Whole Ants (3 total): 220, 221, 222
	Single Pols (0 total): 
Node 19:
	Antpols (12 total): 207e, 207n, 223e, 223n, 224e, 224n, 241e, 241n, 242e, 242n, 243e, 243n
	Whole Ants (6 total): 224, 207, 241, 242, 243, 223
	Single Pols (0 total): 
Node 20:
	Antpols (6 total): 211e, 211n, 244e, 244n, 245e, 245n
	Whole Ants (3 total): 211, 244, 245
	Single Pols (0 total): 
Node 23:
	Antpols (2 total): 285e, 285n
	Whole Ants (1 total): 285
	Single Pols (0 total):

Excess Zeros in Either Even or Odd Spectra: (0 antpols across 0 antennas)

These antennas are showing evidence of packet loss or X-engine failure.

Excess Power in X-Engine Diffs: (8 antpols across 7 antennas)

These antennas are showing evidence of mis-written packets in either the evens or the odds.

All Bad Antpols: 28n, 32n, 136n, 188n, 209n, 266e, 340e, 340n

Node 1:
	Antpols (1 total): 28n
	Whole Ants (0 total): 
	Single Pols (1 total): 28n
No description has been provided for this image 
Node 2:
	Antpols (1 total): 32n
	Whole Ants (0 total): 
	Single Pols (1 total): 32n
No description has been provided for this image 
Node 12:
	Antpols (1 total): 136n
	Whole Ants (0 total): 
	Single Pols (1 total): 136n
No description has been provided for this image 
Node 15:
	Antpols (1 total): 188n
	Whole Ants (0 total): 
	Single Pols (1 total): 188n
No description has been provided for this image 
Node 20:
	Antpols (1 total): 209n
	Whole Ants (0 total): 
	Single Pols (1 total): 209n
No description has been provided for this image 
Node 21:
	Antpols (2 total): 340e, 340n
	Whole Ants (1 total): 340
	Single Pols (0 total):
No description has been provided for this image 
Node 22:
	Antpols (1 total): 266e
	Whole Ants (0 total): 
	Single Pols (1 total): 266e
No description has been provided for this image

Cross-Polarized: (6 antpols across 3 antennas)

These antennas have their east and north cables swapped.

All Bad Antpols: 86e, 86n, 136e, 136n, 256e, 256n

Node 8:
	Antpols (2 total): 86e, 86n
	Whole Ants (1 total): 86
	Single Pols (0 total): 
Node 12:
	Antpols (2 total): 136e, 136n
	Whole Ants (1 total): 136
	Single Pols (0 total): 
Node 23:
	Antpols (2 total): 256e, 256n
	Whole Ants (1 total): 256
	Single Pols (0 total):

Likely FEM Power Issue: (14 antpols across 13 antennas)

These antennas have low power and anomolously high slopes.

All Bad Antpols: 15n, 57e, 86n, 96e, 104n, 109n, 120e, 170e, 182e, 200e, 272e, 326e, 332e, 332n

Node 1:
	Antpols (1 total): 15n
	Whole Ants (0 total): 
	Single Pols (1 total): 15n
No description has been provided for this image 
Node 4:
	Antpols (1 total): 57e
	Whole Ants (0 total): 
	Single Pols (1 total): 57e
No description has been provided for this image 
Node 8:
	Antpols (3 total): 86n, 104n, 120e
	Whole Ants (0 total): 
	Single Pols (3 total): 86n, 104n, 120e
No description has been provided for this image 
Node 10:
	Antpols (1 total): 109n
	Whole Ants (0 total): 
	Single Pols (1 total): 109n
No description has been provided for this image 
Node 11:
	Antpols (1 total): 96e
	Whole Ants (0 total): 
	Single Pols (1 total): 96e
No description has been provided for this image 
Node 13:
	Antpols (1 total): 182e
	Whole Ants (0 total): 
	Single Pols (1 total): 182e
No description has been provided for this image 
Node 15:
	Antpols (1 total): 170e
	Whole Ants (0 total): 
	Single Pols (1 total): 170e
No description has been provided for this image 
Node 18:
	Antpols (1 total): 200e
	Whole Ants (0 total): 
	Single Pols (1 total): 200e
No description has been provided for this image 
Node 21:
	Antpols (3 total): 326e, 332e, 332n
	Whole Ants (1 total): 332
	Single Pols (1 total): 326e
No description has been provided for this image 
Node 23:
	Antpols (1 total): 272e
	Whole Ants (0 total): 
	Single Pols (1 total): 272e
No description has been provided for this image

High Power: (8 antpols across 6 antennas)

These antennas have high median power.

All Bad Antpols: 8e, 8n, 73n, 201n, 232e, 270e, 270n, 272n

Node 2:
	Antpols (2 total): 8e, 8n
	Whole Ants (1 total): 8
	Single Pols (0 total):
No description has been provided for this image 
Node 5:
	Antpols (1 total): 73n
	Whole Ants (0 total): 
	Single Pols (1 total): 73n
No description has been provided for this image 
Node 18:
	Antpols (1 total): 201n
	Whole Ants (0 total): 
	Single Pols (1 total): 201n
No description has been provided for this image 
Node 21:
	Antpols (1 total): 232e
	Whole Ants (0 total): 
	Single Pols (1 total): 232e
No description has been provided for this image 
Node 23:
	Antpols (3 total): 270e, 270n, 272n
	Whole Ants (1 total): 270
	Single Pols (1 total): 272n
No description has been provided for this image

Other Low Power Issues: (6 antpols across 6 antennas)

These antennas have low power, but are not all-zeros and not FEM off.

All Bad Antpols: 82n, 100n, 137e, 218n, 251e, 262n

Node 7:
	Antpols (3 total): 82n, 100n, 137e
	Whole Ants (0 total): 
	Single Pols (3 total): 82n, 100n, 137e
No description has been provided for this image 
Node 17:
	Antpols (1 total): 218n
	Whole Ants (0 total): 
	Single Pols (1 total): 218n
No description has been provided for this image 
Node 20:
	Antpols (1 total): 262n
	Whole Ants (0 total): 
	Single Pols (1 total): 262n
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Node 22:
	Antpols (1 total): 251e
	Whole Ants (0 total): 
	Single Pols (1 total): 251e
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Low Correlation, But Not Low Power: (13 antpols across 11 antennas)

These antennas are low correlation, but their autocorrelation power levels look OK.

All Bad Antpols: 27e, 28e, 86e, 136e, 171n, 255n, 256e, 256n, 281e, 326n, 328e, 328n, 331e

Node 1:
	Antpols (2 total): 27e, 28e
	Whole Ants (0 total): 
	Single Pols (2 total): 27e, 28e
Node 8:
	Antpols (1 total): 86e
	Whole Ants (0 total): 
	Single Pols (1 total): 86e
Node 10:
	Antpols (2 total): 328e, 328n
	Whole Ants (1 total): 328
	Single Pols (0 total): 
Node 12:
	Antpols (1 total): 136e
	Whole Ants (0 total): 
	Single Pols (1 total): 136e
Node 16:
	Antpols (1 total): 171n
	Whole Ants (0 total): 
	Single Pols (1 total): 171n
Node 21:
	Antpols (2 total): 326n, 331e
	Whole Ants (0 total): 
	Single Pols (2 total): 326n, 331e
Node 22:
	Antpols (1 total): 281e
	Whole Ants (0 total): 
	Single Pols (1 total): 281e
Node 23:
	Antpols (3 total): 255n, 256e, 256n
	Whole Ants (1 total): 256
	Single Pols (1 total): 255n

Bad Bandpass Shapes, But Not Bad Power: (12 antpols across 11 antennas)

These antennas have unusual bandpass shapes, but are not all-zeros, high power, low power, or FEM off.

All Bad Antpols: 18e, 27e, 28e, 33n, 87e, 98n, 130e, 130n, 142n, 161n, 180n, 184e

Node 1:
	Antpols (3 total): 18e, 27e, 28e
	Whole Ants (0 total): 
	Single Pols (3 total): 18e, 27e, 28e
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Node 2:
	Antpols (1 total): 33n
	Whole Ants (0 total): 
	Single Pols (1 total): 33n
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Node 7:
	Antpols (1 total): 98n
	Whole Ants (0 total): 
	Single Pols (1 total): 98n
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Node 8:
	Antpols (1 total): 87e
	Whole Ants (0 total): 
	Single Pols (1 total): 87e
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Node 10:
	Antpols (2 total): 130e, 130n
	Whole Ants (1 total): 130
	Single Pols (0 total):
No description has been provided for this image 
Node 13:
	Antpols (3 total): 142n, 161n, 180n
	Whole Ants (0 total): 
	Single Pols (3 total): 142n, 161n, 180n
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Node 14:
	Antpols (1 total): 184e
	Whole Ants (0 total): 
	Single Pols (1 total): 184e
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Excess RFI: (36 antpols across 34 antennas)

These antennas have excess RMS after DPSS filtering (likely RFI), but not low or high power or a bad bandpass.

All Bad Antpols: 9e, 18n, 21e, 27n, 31n, 36e, 37e, 37n, 42n, 45e, 46e, 51e, 72n, 73e, 92e, 97n, 108n, 117e, 120n, 121e, 180e, 202n, 206e, 212n, 213e, 215n, 240e, 240n, 246e, 250e, 253n, 268n, 281n, 321e, 324e, 336e

Node 1:
	Antpols (2 total): 18n, 27n
	Whole Ants (0 total): 
	Single Pols (2 total): 18n, 27n
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Node 2:
	Antpols (4 total): 9e, 21e, 31n, 321e
	Whole Ants (0 total): 
	Single Pols (4 total): 9e, 21e, 31n, 321e
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Node 3:
	Antpols (4 total): 36e, 37e, 37n, 51e
	Whole Ants (1 total): 37
	Single Pols (2 total): 36e, 51e
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Node 4:
	Antpols (3 total): 42n, 72n, 324e
	Whole Ants (0 total): 
	Single Pols (3 total): 42n, 72n, 324e
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Node 5:
	Antpols (3 total): 45e, 46e, 73e
	Whole Ants (0 total): 
	Single Pols (3 total): 45e, 46e, 73e
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Node 7:
	Antpols (1 total): 117e
	Whole Ants (0 total): 
	Single Pols (1 total): 117e
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Node 8:
	Antpols (2 total): 120n, 121e
	Whole Ants (0 total): 
	Single Pols (2 total): 120n, 121e
No description has been provided for this image 
Node 9:
	Antpols (1 total): 108n
	Whole Ants (0 total): 
	Single Pols (1 total): 108n
No description has been provided for this image 
Node 10:
	Antpols (1 total): 92e
	Whole Ants (0 total): 
	Single Pols (1 total): 92e
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Node 11:
	Antpols (1 total): 97n
	Whole Ants (0 total): 
	Single Pols (1 total): 97n
No description has been provided for this image 
Node 13:
	Antpols (1 total): 180e
	Whole Ants (0 total): 
	Single Pols (1 total): 180e
No description has been provided for this image 
Node 16:
	Antpols (1 total): 213e
	Whole Ants (0 total): 
	Single Pols (1 total): 213e
No description has been provided for this image 
Node 17:
	Antpols (1 total): 215n
	Whole Ants (0 total): 
	Single Pols (1 total): 215n
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Node 18:
	Antpols (1 total): 202n
	Whole Ants (0 total): 
	Single Pols (1 total): 202n
No description has been provided for this image 
Node 19:
	Antpols (3 total): 206e, 240e, 240n
	Whole Ants (1 total): 240
	Single Pols (1 total): 206e
No description has been provided for this image 
Node 20:
	Antpols (1 total): 246e
	Whole Ants (0 total): 
	Single Pols (1 total): 246e
No description has been provided for this image 
Node 21:
	Antpols (2 total): 212n, 336e
	Whole Ants (0 total): 
	Single Pols (2 total): 212n, 336e
No description has been provided for this image 
Node 22:
	Antpols (4 total): 250e, 253n, 268n, 281n
	Whole Ants (0 total): 
	Single Pols (4 total): 250e, 253n, 268n, 281n
No description has been provided for this image

Redcal chi^2: (9 antpols across 8 antennas)

These antennas have been idenfied as not redundantly calibrating well, even after passing the above checks.

All Bad Antpols: 83n, 131e, 155e, 188e, 193e, 200n, 215e, 231e, 231n

Node 7:
	Antpols (1 total): 83n
	Whole Ants (0 total): 
	Single Pols (1 total): 83n
Node 11:
	Antpols (1 total): 131e
	Whole Ants (0 total): 
	Single Pols (1 total): 131e
Node 12:
	Antpols (1 total): 155e
	Whole Ants (0 total): 
	Single Pols (1 total): 155e
Node 15:
	Antpols (1 total): 188e
	Whole Ants (0 total): 
	Single Pols (1 total): 188e
Node 16:
	Antpols (1 total): 193e
	Whole Ants (0 total): 
	Single Pols (1 total): 193e
Node 17:
	Antpols (1 total): 215e
	Whole Ants (0 total): 
	Single Pols (1 total): 215e
Node 18:
	Antpols (1 total): 200n
	Whole Ants (0 total): 
	Single Pols (1 total): 200n
Node 21:
	Antpols (2 total): 231e, 231n
	Whole Ants (1 total): 231
	Single Pols (0 total):

Full-Day Visualizations¶

In [27]:
def classification_plot(col):
    class_array = classification_array(col)
    plt.figure(figsize=(12, len(ants) / 10), dpi=100)
    plt.imshow(class_array.T, aspect='auto', interpolation='none', cmap='RdYlGn', vmin=0, vmax=2,
               extent=[jds[0] - np.floor(jds[0]), jds[-1] - np.floor(jds[0]), len(ants), 0])
    plt.xlabel(f'JD - {int(jds[0])}')
    plt.yticks(ticks=np.arange(.5, len(ants)+.5), labels=[ant for ant in ants], fontsize=6)
    plt.ylabel('Antenna Number (East First, Then North)')
    plt.gca().tick_params(right=True, top=True, labelright=True, labeltop=True)
    plt.tight_layout()
    plt.title(f'{col}: Green is "good", Yellow is "suspect", Red is "bad"')

Figure 1: Per-File Overall Antenna Classification Summary¶

This "big green board" shows the overall (i.e. after redundant calibration) classification of antennas on a per-file basis. This is useful for looking at time-dependent effects across the array. While only antenna numbers are labeled, both polarizations are shown, first East then North going down, above and below the antenna's tick mark.

In [28]:
classification_plot('Antenna Class')
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In [29]:
# compute flag fractions for all classifiers and antennas
frac_flagged = []
for col in class_cols[1:]:
    class_array = np.vstack([t[col] for t in tables])
    class_array[class_array == 'good'] = False
    class_array[class_array == 'suspect'] = False
    class_array[class_array == 'bad'] = True
    frac_flagged.append(np.sum(class_array, axis=0))
In [30]:
def plot_flag_frac_all_classifiers():
    ticks = []
    for i, col in enumerate(list(class_cols[1:])):
        ticks.append(f'{col} ({np.nanmean(np.array(frac_flagged).astype(float)[i]) / len(csv_files):.2%})')
    plt.figure(figsize=(8, len(ants) / 10), dpi=100)
    plt.imshow(np.array(frac_flagged).astype(float).T, aspect='auto', interpolation='none', cmap='viridis')
    plt.xticks(ticks=np.arange(len(list(class_cols[1:]))), labels=ticks, rotation=-45, ha='left')
    plt.yticks(ticks=np.arange(.5, len(ap_strs)+.5, 2), labels=[ant for ant in ants], fontsize=6)
    plt.ylabel('Antenna Number (East First, Then North)')
    plt.gca().tick_params(right=True, labelright=True,)
    ax2 = plt.gca().twiny()
    ax2.set_xticks(ticks=np.arange(len(list(class_cols[1:]))), labels=ticks, rotation=45, ha='left')
    plt.colorbar(ax=plt.gca(), label=f'Number of Files Flagged Out of {len(csv_files)}', aspect=50)
    plt.tight_layout()

Figure 2: Per-Classifier Antenna Flagging Summary¶

This plot shows the fraction of files flagged for each reason for each antenna. It's useful for seeing which problems are transitory and which ones are more common. Note that not all flags are independent and in particular redcal chi^2 takes an OR of other classifications as an input. Also note that only antenna numbers are labeled, both polarizations are shown, first East then North going down, above and below the antenna's tick mark.

In [31]:
plot_flag_frac_all_classifiers()
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In [32]:
def array_class_plot():
    fig, axes = plt.subplots(1, 2, figsize=(14, 6), dpi=100, gridspec_kw={'width_ratios': [2, 1]})
    plot_antclass(hd.antpos, overall_class, ax=axes[0], ants=[ant for ant in hd.data_ants if ant < 320], legend=False, 
                  title=f'HERA Core: Overall Flagging Based on {overall_thresh:.1%} Daily Threshold')
    plot_antclass(hd.antpos, overall_class, ax=axes[1], ants=[ant for ant in hd.data_ants if ant >= 320], radius=50, title='Outriggers')

Figure 3: Array Visualization of Overall Daily Classification¶

Overall classification of antenna-polarizations shown on the array layout. If any antenna is marked bad for any reason more than the threshold (default 10%), it is marked bad here. Likewise, if any antenna is marked suspect for more than 10% of the night (but not bad), it's suspect here.

In [33]:
if SUM_FILE is not None: array_class_plot()
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In [34]:
for repo in ['pyuvdata', 'hera_cal', 'hera_qm', 'hera_notebook_templates']:
    exec(f'from {repo} import __version__')
    print(f'{repo}: {__version__}')

pyuvdata: 3.0.1.dev70+g283dda3
hera_cal: 3.6.2.dev110+g0529798
hera_qm: 2.2.0

hera_notebook_templates: 0.1.dev936+gdc93cad