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'

# 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/sn1/2460400'
SUM_FILE = '/mnt/sn1/2460400/zen.2460400.43963.sum.uvh5'
OC_SKIP_OUTRIGGERS = 'True'

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: 3-30-2024

# 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 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 2234 csv files starting with /mnt/sn1/2460400/zen.2460400.18976.sum.ant_class.csv

# 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')

# 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()))

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)

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)

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()

# 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['RFI in Autos Class'] for t in tables]) == 'bad'
suspect_rfi = np.vstack([t['RFI in Autos Class'] for t in tables]) == 'suspect'

# 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]

# 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]

# 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]

# 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]

# find high power issues
high_power_strs = ap_strs[np.mean(bad_powers & (all_powers > median_power), axis=0) > high_power_thresh]

# 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]

# 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))]

# 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))]

# find antennas with excess RFI
excess_rfi_strs = ap_strs[np.mean(np.vstack([t['RFI in Autos 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))]

# 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))]

# 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]

# 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, anomolously high slopes, and extra channels identified as RFI.', 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 strucutre (identified as possible RFI) in their bandpassed relative to the ' + \
             'median antenna, 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.')]

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)

print_high_level_summary()

33 antpols (on 24 antennas) frequently flagged for Likely FEM Power Issue.
26 antpols (on 13 antennas) frequently flagged for All-Zeros.
21 antpols (on 14 antennas) frequently flagged for Other Low Power Issues.
19 antpols (on 16 antennas) frequently flagged for Low Correlation, But Not Low Power.
17 antpols (on 13 antennas) frequently flagged for High Power.
16 antpols (on 15 antennas) frequently flagged for Excess RFI.
9 antpols (on 9 antennas) frequently flagged for Bad Bandpass Shapes, But Not Bad Power.
5 antpols (on 5 antennas) frequently flagged for Excess Power in X-Engine Diffs.
2 antpols (on 1 antennas) frequently flagged for Cross-Polarized.
2 antpols (on 2 antennas) frequently flagged for Redcal chi^2.
0 antpols (on 0 antennas) frequently flagged for Excess Zeros in Either Even or Odd Spectra.

print_all_issue_summaries()

All Bad Antpols: 63e, 63n, 64e, 64n, 78e, 78n, 88e, 88n, 90e, 90n, 107e, 107n, 143e, 143n, 163e, 163n, 164e, 164n, 176e, 176n, 177e, 177n, 178e, 178n, 272e, 272n

Node 6:
	Antpols (6 total): 63e, 63n, 64e, 64n, 78e, 78n
	Whole Ants (3 total): 64, 78, 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 (6 total): 176e, 176n, 177e, 177n, 178e, 178n
	Whole Ants (3 total): 176, 177, 178
	Single Pols (0 total): 
Node 14:
	Antpols (6 total): 143e, 143n, 163e, 163n, 164e, 164n
	Whole Ants (3 total): 163, 164, 143
	Single Pols (0 total): 
Node 23:
	Antpols (2 total): 272e, 272n
	Whole Ants (1 total): 272
	Single Pols (0 total):

All Bad Antpols: 140e, 142n, 144n, 188n, 209n

Node 13:
	Antpols (2 total): 140e, 142n
	Whole Ants (0 total): 
	Single Pols (2 total): 140e, 142n

Node 14:
	Antpols (1 total): 144n
	Whole Ants (0 total): 
	Single Pols (1 total): 144n

Node 15:
	Antpols (1 total): 188n
	Whole Ants (0 total): 
	Single Pols (1 total): 188n

Node 20:
	Antpols (1 total): 209n
	Whole Ants (0 total): 
	Single Pols (1 total): 209n

All Bad Antpols: 93e, 93n

Node 10:
	Antpols (2 total): 93e, 93n
	Whole Ants (1 total): 93
	Single Pols (0 total):

All Bad Antpols: 3n, 21e, 21n, 34e, 68n, 86e, 86n, 93n, 99e, 104n, 109n, 112e, 115e, 117e, 117n, 118e, 118n, 119e, 138e, 138n, 170e, 194e, 194n, 196e, 196n, 200e, 208e, 217e, 269n, 332e, 332n, 333e, 333n

Node 1:
	Antpols (1 total): 3n
	Whole Ants (0 total): 
	Single Pols (1 total): 3n

Node 2:
	Antpols (2 total): 21e, 21n
	Whole Ants (1 total): 21
	Single Pols (0 total):

Node 3:
	Antpols (1 total): 68n
	Whole Ants (0 total): 
	Single Pols (1 total): 68n

Node 6:
	Antpols (1 total): 34e
	Whole Ants (0 total): 
	Single Pols (1 total): 34e

Antenna Classification Daily Summary¶

• 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 ¶

Settings¶

Load classifications and other metadata¶

Figure out and summarize per-antenna issues¶

Summary of Per-Antenna Issues¶

All-Zeros: (26 antpols across 13 antennas)

These antennas have visibilities that are more than half zeros.

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: (5 antpols across 5 antennas)

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

Cross-Polarized: (2 antpols across 1 antennas)

These antennas have their east and north cables swapped.

Likely FEM Power Issue: (33 antpols across 24 antennas)

These antennas have low power, anomolously high slopes, and extra channels identified as RFI.

High Power: (17 antpols across 13 antennas)

These antennas have high median power.

Other Low Power Issues: (21 antpols across 14 antennas)

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

Low Correlation, But Not Low Power: (19 antpols across 16 antennas)

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

Bad Bandpass Shapes, But Not Bad Power: (9 antpols across 9 antennas)

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

Excess RFI: (16 antpols across 15 antennas)

These antennas have excess strucutre (identified as possible RFI) in their bandpassed relative to the median antenna, but not low or high power or a bad bandpass.

Antenna Classification Daily Summary¶

• 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¶

Settings¶

Load classifications and other metadata¶

Figure out and summarize per-antenna issues¶

Summary of Per-Antenna Issues¶

All-Zeros: (26 antpols across 13 antennas)

These antennas have visibilities that are more than half zeros.

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: (5 antpols across 5 antennas)

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

Cross-Polarized: (2 antpols across 1 antennas)

These antennas have their east and north cables swapped.

Likely FEM Power Issue: (33 antpols across 24 antennas)

These antennas have low power, anomolously high slopes, and extra channels identified as RFI.

High Power: (17 antpols across 13 antennas)

These antennas have high median power.

Other Low Power Issues: (21 antpols across 14 antennas)

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

Low Correlation, But Not Low Power: (19 antpols across 16 antennas)

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

Bad Bandpass Shapes, But Not Bad Power: (9 antpols across 9 antennas)

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

Excess RFI: (16 antpols across 15 antennas)

These antennas have excess strucutre (identified as possible RFI) in their bandpassed relative to the median antenna, but not low or high power or a bad bandpass.

• 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 ¶