Single File Calibration

by Josh Dillon, Aaron Parsons, Tyler Cox, and Zachary Martinot, last updated December 15, 2025

This notebook is designed to infer as much information about the array from a single file, including pushing the calibration and RFI mitigation as far as possible. Calibration includes redundant-baseline calibration, RFI-based calibration of delay slopes, model-based calibration of overall amplitudes, and a full per-frequency phase gradient absolute calibration if abscal model files are available.

Here's a set of links to skip to particular figures and tables:

• Figure 1: RFI Flagging

• Figure 2: Plot of autocorrelations with classifications

• Figure 3: Summary of antenna classifications prior to calibration

• Figure 4: Redundant calibration of a single baseline group

• Figure 5: Absolute calibration of redcal degeneracies

• Figure 6: Relative Phase Calibration

• Figure 7: chi^2 per antenna across the array

• Figure 8: Summary of antenna classifications after redundant calibration

• Table 1: Complete summary of per antenna classifications

import time
tstart = time.time()
!hostname

bigmem2.rtp.pvt

import os
os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE'
import h5py
import hdf5plugin  # REQUIRED to have the compression plugins available
import numpy as np
from scipy import constants, interpolate
import copy
import glob
import re
import matplotlib
import matplotlib.pyplot as plt
import pandas as pd
pd.set_option('display.max_rows', 1000)
from uvtools.plot import plot_antpos, plot_antclass
from hera_qm import ant_metrics, ant_class, xrfi
from hera_cal import io, utils, redcal, apply_cal, datacontainer, abscal
from hera_filters import dspec
from hera_notebook_templates.data import DATA_PATH as HNBT_DATA
from IPython.display import display, HTML
import linsolve
display(HTML("<style>.container { width:100% !important; }</style>"))
_ = np.seterr(all='ignore')  # get rid of red warnings
%config InlineBackend.figure_format = 'retina'

# this enables better memory management on linux
import ctypes
def malloc_trim():
    try:
        ctypes.CDLL('libc.so.6').malloc_trim(0) 
    except OSError:
        pass

Parse inputs and outputs

To use this notebook interactively, you will have to provide a sum filename path if none exists as an environment variable. All other parameters have reasonable default values.

# figure out whether to save results
SAVE_RESULTS = os.environ.get("SAVE_RESULTS", "TRUE").upper() == "TRUE"
SAVE_OMNIVIS_FILE = os.environ.get("SAVE_OMNIVIS_FILE", "FALSE").upper() == "TRUE"

# get infile names
SUM_FILE = os.environ.get("SUM_FILE", None)
# SUM_FILE = '/lustre/aoc/projects/hera/h6c-analysis/IDR2/2459867/zen.2459867.46002.sum.uvh5' # If sum_file is not defined in the environment variables, define it here.
USE_DIFF = os.environ.get("USE_DIFF", "TRUE").upper() == "TRUE"
if USE_DIFF:
    DIFF_FILE = SUM_FILE.replace('sum', 'diff')
else:
    DIFF_FILE = None
    RTP_ANTCLASS = SUM_FILE.replace('.uvh5', '.rtp_ant_class.csv')
VALIDATION = os.environ.get("VALIDATION", "FALSE").upper() == "TRUE"

# get outfilenames
AM_FILE = (SUM_FILE.replace('.uvh5', '.ant_metrics.hdf5') if SAVE_RESULTS else None)
ANTCLASS_FILE = (SUM_FILE.replace('.uvh5', '.ant_class.csv') if SAVE_RESULTS else None)
OMNICAL_FILE = (SUM_FILE.replace('.uvh5', '.omni.calfits') if SAVE_RESULTS else None)
OMNIVIS_FILE = (SUM_FILE.replace('.uvh5', '.omni_vis.uvh5') if SAVE_RESULTS else None)

for fname in ['SUM_FILE', 'DIFF_FILE', 'AM_FILE', 'ANTCLASS_FILE', 'OMNICAL_FILE', 'OMNIVIS_FILE', 
              'SAVE_RESULTS', 'SAVE_OMNIVIS_FILE', 'USE_DIFF', 'VALIDATION']:
    print(f"{fname} = '{eval(fname)}'")

SUM_FILE = '/mnt/sn1/data2/2461076/zen.2461076.45955.sum.uvh5'
DIFF_FILE = '/mnt/sn1/data2/2461076/zen.2461076.45955.diff.uvh5'
AM_FILE = '/mnt/sn1/data2/2461076/zen.2461076.45955.sum.ant_metrics.hdf5'
ANTCLASS_FILE = '/mnt/sn1/data2/2461076/zen.2461076.45955.sum.ant_class.csv'
OMNICAL_FILE = '/mnt/sn1/data2/2461076/zen.2461076.45955.sum.omni.calfits'
OMNIVIS_FILE = '/mnt/sn1/data2/2461076/zen.2461076.45955.sum.omni_vis.uvh5'
SAVE_RESULTS = 'True'
SAVE_OMNIVIS_FILE = 'False'
USE_DIFF = 'True'
VALIDATION = 'False'

Parse settings

Load settings relating to the operation of the notebook, then print what was loaded (or default).

# parse plotting settings
PLOT = os.environ.get("PLOT", "TRUE").upper() == "TRUE"
if PLOT:
    %matplotlib inline

# parse omnical settings
OC_MAX_DIMS = int(os.environ.get("OC_MAX_DIMS", 4))
OC_MIN_DIM_SIZE = int(os.environ.get("OC_MIN_DIM_SIZE", 8))
OC_SKIP_OUTRIGGERS = os.environ.get("OC_SKIP_OUTRIGGERS", "TRUE").upper() == "TRUE"
OC_MIN_BL_LEN = float(os.environ.get("OC_MIN_BL_LEN", 1))
OC_MAX_BL_LEN = float(os.environ.get("OC_MAX_BL_LEN", 1e100))
OC_MAXITER = int(os.environ.get("OC_MAXITER", 50))
OC_MAX_RERUN = int(os.environ.get("OC_MAX_RERUN", 10))
OC_RERUN_MAXITER = int(os.environ.get("OC_RERUN_MAXITER", 250))
OC_MAX_CHISQ_FLAGGING_DYNAMIC_RANGE = float(os.environ.get("OC_MAX_CHISQ_FLAGGING_DYNAMIC_RANGE", 1.5))
OC_USE_PRIOR_SOL = os.environ.get("OC_USE_PRIOR_SOL", "FALSE").upper() == "TRUE"
OC_PRIOR_SOL_FLAG_THRESH = float(os.environ.get("OC_PRIOR_SOL_FLAG_THRESH", .95))
OC_RESTART_FROM_FC_EVERY_ITER = os.environ.get("OC_RESTART_FROM_FC_EVERY_ITER", "FALSE").upper() == "TRUE"
OC_USE_GPU = os.environ.get("OC_USE_GPU", "FALSE").upper() == "TRUE"

# parse RFI settings
RFI_DPSS_HALFWIDTH = float(os.environ.get("RFI_DPSS_HALFWIDTH", 300e-9))
RFI_NSIG = float(os.environ.get("RFI_NSIG", 4))

# parse abscal settings
ABSCAL_MODEL_FILES_GLOB = os.environ.get("ABSCAL_MODEL_FILES_GLOB", None)
ABSCAL_MIN_BL_LEN = float(os.environ.get("ABSCAL_MIN_BL_LEN", 1.0))
ABSCAL_MAX_BL_LEN = float(os.environ.get("ABSCAL_MAX_BL_LEN", 140.0))
CALIBRATE_CROSS_POLS = os.environ.get("CALIBRATE_CROSS_POLS", "TRUE").upper() == "TRUE"

# print settings
for setting in ['PLOT', 'OC_MAX_DIMS', 'OC_MIN_DIM_SIZE', 'OC_SKIP_OUTRIGGERS', 
                'OC_MIN_BL_LEN', 'OC_MAX_BL_LEN', 'OC_MAXITER', 'OC_MAX_RERUN', 'OC_RERUN_MAXITER', 
                'OC_MAX_CHISQ_FLAGGING_DYNAMIC_RANGE', 'OC_USE_PRIOR_SOL', 'OC_PRIOR_SOL_FLAG_THRESH', 
                'OC_USE_GPU', 'OC_RESTART_FROM_FC_EVERY_ITER', 'RFI_DPSS_HALFWIDTH', 'RFI_NSIG', 
                'ABSCAL_MODEL_FILES_GLOB', 'ABSCAL_MIN_BL_LEN', 'ABSCAL_MAX_BL_LEN', "CALIBRATE_CROSS_POLS"]:
    print(f'{setting} = {eval(setting)}')

PLOT = True
OC_MAX_DIMS = 4
OC_MIN_DIM_SIZE = 8
OC_SKIP_OUTRIGGERS = True
OC_MIN_BL_LEN = 1.0
OC_MAX_BL_LEN = 140.0
OC_MAXITER = 25
OC_MAX_RERUN = 10
OC_RERUN_MAXITER = 125
OC_MAX_CHISQ_FLAGGING_DYNAMIC_RANGE = 1.5
OC_USE_PRIOR_SOL = True
OC_PRIOR_SOL_FLAG_THRESH = 0.95
OC_USE_GPU = False
OC_RESTART_FROM_FC_EVERY_ITER = False
RFI_DPSS_HALFWIDTH = 3e-07
RFI_NSIG = 4.0
ABSCAL_MODEL_FILES_GLOB = None
ABSCAL_MIN_BL_LEN = 1.0
ABSCAL_MAX_BL_LEN = 140.0
CALIBRATE_CROSS_POLS = True

Parse bounds

Load settings related to classifying antennas as good, suspect, or bad, then print what was loaded (or default).

# ant_metrics bounds for low correlation / dead antennas
am_corr_bad = (0, float(os.environ.get("AM_CORR_BAD", 0.35)))
am_corr_suspect = (float(os.environ.get("AM_CORR_BAD", 0.35)), float(os.environ.get("AM_CORR_SUSPECT", 0.45)))

# ant_metrics bounds for cross-polarized antennas
am_xpol_bad = (-1, float(os.environ.get("AM_XPOL_BAD", -0.1)))
am_xpol_suspect = (float(os.environ.get("AM_XPOL_BAD", -0.1)), float(os.environ.get("AM_XPOL_SUSPECT", 0)))

# bounds on solar altitude (in degrees)
good_solar_altitude = (-90, float(os.environ.get("SUSPECT_SOLAR_ALTITUDE", 0)))
suspect_solar_altitude = (float(os.environ.get("SUSPECT_SOLAR_ALTITUDE", 0)), 90)

# bounds on zeros in spectra
good_zeros_per_eo_spectrum = (0, int(os.environ.get("MAX_ZEROS_PER_EO_SPEC_GOOD", 2)))
suspect_zeros_per_eo_spectrum = (0, int(os.environ.get("MAX_ZEROS_PER_EO_SPEC_SUSPECT", 8)))

# bounds on autocorrelation power
auto_power_good = (float(os.environ.get("AUTO_POWER_GOOD_LOW", 5)), float(os.environ.get("AUTO_POWER_GOOD_HIGH", 30)))
auto_power_suspect = (float(os.environ.get("AUTO_POWER_SUSPECT_LOW", 1)), float(os.environ.get("AUTO_POWER_SUSPECT_HIGH", 60)))

# bounds on autocorrelation slope
auto_slope_good = (float(os.environ.get("AUTO_SLOPE_GOOD_LOW", -0.4)), float(os.environ.get("AUTO_SLOPE_GOOD_HIGH", 0.4)))
auto_slope_suspect = (float(os.environ.get("AUTO_SLOPE_SUSPECT_LOW", -0.6)), float(os.environ.get("AUTO_SLOPE_SUSPECT_HIGH", 0.6)))

# bounds on autocorrelation RFI
auto_rfi_good = (0, float(os.environ.get("AUTO_RFI_GOOD", 1.5)))
auto_rfi_suspect = (0, float(os.environ.get("AUTO_RFI_SUSPECT", 2)))

# bounds on autocorrelation shape
auto_shape_good = (0, float(os.environ.get("AUTO_SHAPE_GOOD", 0.1)))
auto_shape_suspect = (0, float(os.environ.get("AUTO_SHAPE_SUSPECT", 0.2)))

# bound on per-xengine non-noiselike power in diff
bad_xengine_zcut = float(os.environ.get("BAD_XENGINE_ZCUT", 10.0))

# bounds on chi^2 per antenna in omnical
oc_cspa_good = (0, float(os.environ.get("OC_CSPA_GOOD", 2)))
oc_cspa_suspect = (0, float(os.environ.get("OC_CSPA_SUSPECT", 3)))

# print bounds
for bound in ['am_corr_bad', 'am_corr_suspect', 'am_xpol_bad', 'am_xpol_suspect', 
              'good_solar_altitude', 'suspect_solar_altitude',
              'good_zeros_per_eo_spectrum', 'suspect_zeros_per_eo_spectrum',
              'auto_power_good', 'auto_power_suspect', 'auto_slope_good', 'auto_slope_suspect',
              'auto_rfi_good', 'auto_rfi_suspect', 'auto_shape_good', 'auto_shape_suspect',
              'bad_xengine_zcut', 'oc_cspa_good', 'oc_cspa_suspect']:
    print(f'{bound} = {eval(bound)}')

am_corr_bad = (0, 0.35)
am_corr_suspect = (0.35, 0.45)
am_xpol_bad = (-1, -0.1)
am_xpol_suspect = (-0.1, 0.0)
good_solar_altitude = (-90, 0.0)
suspect_solar_altitude = (0.0, 90)
good_zeros_per_eo_spectrum = (0, 2)
suspect_zeros_per_eo_spectrum = (0, 8)
auto_power_good = (5.0, 30.0)
auto_power_suspect = (1.0, 60.0)
auto_slope_good = (-0.4, 0.4)
auto_slope_suspect = (-0.6, 0.6)
auto_rfi_good = (0, 1.5)
auto_rfi_suspect = (0, 2.0)
auto_shape_good = (0, 0.1)
auto_shape_suspect = (0, 0.2)
bad_xengine_zcut = 10.0
oc_cspa_good = (0, 2.0)
oc_cspa_suspect = (0, 3.0)

Load sum and diff data

read_start = time.time()
hd = io.HERADataFastReader(SUM_FILE)
data, _, _ = hd.read(read_flags=False, read_nsamples=False)
if USE_DIFF:
    hd_diff = io.HERADataFastReader(DIFF_FILE)
    diff_data, _, _ = hd_diff.read(read_flags=False, read_nsamples=False, dtype=np.complex64, fix_autos_func=np.real)
print(f'Finished loading data in {(time.time() - read_start) / 60:.2f} minutes.')

Finished loading data in 0.58 minutes.

ants = sorted(set([ant for bl in hd.bls for ant in utils.split_bl(bl)]))
auto_bls = [bl for bl in data if (bl[0] == bl[1]) and (utils.split_pol(bl[2])[0] == utils.split_pol(bl[2])[1])]
antpols = sorted(set([ant[1] for ant in ants]))

# print basic information about the file
print(f'File: {SUM_FILE}')
print(f'JDs: {hd.times} ({np.median(np.diff(hd.times)) * 24 * 3600:.5f} s integrations)')
print(f'LSTS: {hd.lsts * 12 / np.pi } hours')
print(f'Frequencies: {len(hd.freqs)} {np.median(np.diff(hd.freqs)) / 1e6:.5f} MHz channels from {hd.freqs[0] / 1e6:.5f} to {hd.freqs[-1] / 1e6:.5f} MHz')
print(f'Antennas: {len(hd.data_ants)}')
print(f'Polarizations: {hd.pols}')

File: /mnt/sn1/data2/2461076/zen.2461076.45955.sum.uvh5
JDs: [2461076.45949503 2461076.45960688] (9.66368 s integrations)
LSTS: [9.46448141 9.46717312] hours
Frequencies: 1536 0.12207 MHz channels from 46.92078 to 234.29871 MHz
Antennas: 290
Polarizations: ['nn', 'ee', 'ne', 'en']

Classify good, suspect, and bad antpols

ALL_FLAGGED = False
def all_flagged():
    if ALL_FLAGGED:
        print('All antennas are flagged, so this cell is being skipped.')
    return ALL_FLAGGED

# initialize classes to None to help make Table 1 when everything is flagged
overall_class = None
am_totally_dead = None
am_corr = None
am_xpol = None
solar_class = None
zeros_class = None
auto_power_class = None
auto_slope_class = None
auto_rfi_class = None
auto_shape_class = None
xengine_diff_class = None
meta = None
redcal_class = None 

Load classifications that use diffs if diffs are not available

if not USE_DIFF:
    def read_antenna_classification(df, category):
        ac = ant_class.AntennaClassification()
        ac._data = {}
        for antname, class_data, antclass in zip(df['Antenna'], df[category], df[f'{category} Class']):
            try:        
                class_data = float(class_data)
            except:
                pass
            if isinstance(class_data, str) or np.isfinite(class_data):
                ant = (int(antname[:-1]), utils._comply_antpol(antname[-1]))
                ac[ant] = antclass
                ac._data[ant] = class_data
        return ac

    df = pd.read_csv(RTP_ANTCLASS)
    am_totally_dead = read_antenna_classification(df, 'Dead?')
    am_corr = read_antenna_classification(df, 'Low Correlation')
    am_xpol = read_antenna_classification(df, 'Cross-Polarized')
    zeros_class = read_antenna_classification(df, 'Even/Odd Zeros')
    xengine_diff_class = read_antenna_classification(df, 'Bad Diff X-Engines')

Run ant_metrics

This classifies antennas as cross-polarized, low-correlation, or dead. Such antennas are excluded from any calibration.

if USE_DIFF:
    am = ant_metrics.AntennaMetrics(SUM_FILE, DIFF_FILE, sum_data=data, diff_data=diff_data)
    am.iterative_antenna_metrics_and_flagging(crossCut=am_xpol_bad[1], deadCut=am_corr_bad[1])
    am.all_metrics = {}  # this saves time and disk by getting rid of per-iteration information we never use
    if SAVE_RESULTS:
        am.save_antenna_metrics(AM_FILE, overwrite=True)

if USE_DIFF:
    # Turn ant metrics into classifications
    totally_dead_ants = [ant for ant, i in am.xants.items() if i == -1]
    am_totally_dead = ant_class.AntennaClassification(good=[ant for ant in ants if ant not in totally_dead_ants], bad=totally_dead_ants)
    am_corr = ant_class.antenna_bounds_checker(am.final_metrics['corr'], bad=[am_corr_bad], suspect=[am_corr_suspect], good=[(0, 1)])
    am_xpol = ant_class.antenna_bounds_checker(am.final_metrics['corrXPol'], bad=[am_xpol_bad], suspect=[am_xpol_suspect], good=[(-1, 1)])
ant_metrics_class = am_totally_dead + am_corr + am_xpol
if np.all([ant_metrics_class[utils.split_bl(bl)[0]] == 'bad' for bl in auto_bls]):
    ALL_FLAGGED = True
    print('All antennas are flagged for ant_metrics.')

Mark sun-up (or high solar altitude) data as suspect

min_sun_alt = np.min(utils.get_sun_alt(hd.times))
solar_class = ant_class.antenna_bounds_checker({ant: min_sun_alt for ant in ants}, good=[good_solar_altitude], suspect=[suspect_solar_altitude])

Classify antennas responsible for 0s in visibilities as bad:

This classifier looks for X-engine failure or packet loss specific to an antenna which causes either the even visibilities (or the odd ones, or both) to be 0s.

if USE_DIFF:
    zeros_class = ant_class.even_odd_zeros_checker(data, diff_data, good=good_zeros_per_eo_spectrum, suspect=suspect_zeros_per_eo_spectrum)
if np.all([zeros_class[utils.split_bl(bl)[0]] == 'bad' for bl in auto_bls]):
    ALL_FLAGGED = True
    print('All antennas are flagged for too many even/odd zeros.')

All antennas are flagged for too many even/odd zeros.

Examine and classify autocorrelation power and slope

These classifiers look for antennas with too high or low power or to steep a slope.

auto_power_class = ant_class.auto_power_checker(data, good=auto_power_good, suspect=auto_power_suspect)
auto_slope_class = ant_class.auto_slope_checker(data, good=auto_slope_good, suspect=auto_slope_suspect, edge_cut=100, filt_size=17)
if np.all([(auto_power_class + auto_slope_class)[utils.split_bl(bl)[0]] == 'bad' for bl in auto_bls]):
    ALL_FLAGGED = True
    print('All antennas are flagged for bad autocorrelation power/slope.')
overall_class = auto_power_class + auto_slope_class + zeros_class + ant_metrics_class + solar_class

Find starting set of array flags

if not all_flagged():
    antenna_flags, array_flags = xrfi.flag_autos(data, flag_method="channel_diff_flagger", nsig=RFI_NSIG * 5, 
                                                 antenna_class=overall_class, flag_broadcast_thresh=.5)
    for key in antenna_flags:
        antenna_flags[key] = array_flags
    cache = {}
    _, array_flags = xrfi.flag_autos(data, freqs=data.freqs, flag_method="dpss_flagger",
                                     nsig=RFI_NSIG, antenna_class=overall_class,
                                     filter_centers=[0], filter_half_widths=[RFI_DPSS_HALFWIDTH],
                                     eigenval_cutoff=[1e-9], flags=antenna_flags, mode='dpss_matrix', 
                                     cache=cache, flag_broadcast_thresh=.5)

All antennas are flagged, so this cell is being skipped.

Classify antennas based on non-noiselike diffs

if not all_flagged():
    if USE_DIFF:
        xengine_diff_class = ant_class.non_noiselike_diff_by_xengine_checker(data, diff_data, flag_waterfall=array_flags, 
                                                                             antenna_class=overall_class, 
                                                                             xengine_chans=96, bad_xengine_zcut=bad_xengine_zcut)
        
        if np.all([overall_class[utils.split_bl(bl)[0]] == 'bad' for bl in auto_bls]):
            ALL_FLAGGED = True
            print('All antennas are flagged after flagging non-noiselike diffs.')
    overall_class += xengine_diff_class

All antennas are flagged, so this cell is being skipped.

Examine and classify autocorrelation excess RFI and shape, finding consensus RFI mask along the way

This classifier iteratively identifies antennas for excess RFI (characterized by RMS of DPSS-filtered autocorrelations after RFI flagging) and bad shape, as determined by a discrepancy with the mean good normalized autocorrelation's shape. Along the way, it iteratively discovers a conensus array-wide RFI mask.

def auto_bl_zscores(data, flag_array, cache={}):
    '''This function computes z-score arrays for each delay-filtered autocorrelation, normalized by the expected noise. 
    Flagged times/channels for the whole array are given 0 weight in filtering and are np.nan in the z-score.'''
    zscores = {}
    for bl in auto_bls:
        wgts = np.array(np.logical_not(flag_array), dtype=np.float64)
        model, _, _ = dspec.fourier_filter(hd.freqs, data[bl], wgts, filter_centers=[0], filter_half_widths=[RFI_DPSS_HALFWIDTH], mode='dpss_solve',
                                            suppression_factors=[1e-9], eigenval_cutoff=[1e-9], cache=cache)
        res = data[bl] - model
        int_time = 24 * 3600 * np.median(np.diff(data.times))
        chan_res = np.median(np.diff(data.freqs))
        int_count = int(int_time * chan_res)
        sigma = np.abs(model) / np.sqrt(int_count / 2)
        zscores[bl] = res / sigma    
        zscores[bl][flag_array] = np.nan

    return zscores

def rfi_from_avg_autos(data, auto_bls_to_use, prior_flags=None, nsig=RFI_NSIG):
    '''Average together all baselines in auto_bls_to_use, then find an RFI mask by looking for outliers after DPSS filtering.'''
    
    # If there are no good autos, return 100% flagged
    if len(auto_bls_to_use) == 0:
        return np.ones(data[next(iter(data))].shape, dtype=bool)
    
    # Compute int_count for all unflagged autocorrelations averaged together
    int_time = 24 * 3600 * np.median(np.diff(data.times_by_bl[auto_bls[0][0:2]]))
    chan_res = np.median(np.diff(data.freqs))
    int_count = int(int_time * chan_res) * len(auto_bls_to_use)
    avg_auto = {(-1, -1, 'ee'): np.mean([data[bl] for bl in auto_bls_to_use], axis=0)}
    
    # Flag RFI first with channel differences and then with DPSS
    antenna_flags, _ = xrfi.flag_autos(avg_auto, int_count=int_count, nsig=(nsig * 5))
    if prior_flags is not None:
        antenna_flags[(-1, -1, 'ee')] = prior_flags
    _, rfi_flags = xrfi.flag_autos(avg_auto, int_count=int_count, flag_method='dpss_flagger',
                                   flags=antenna_flags, freqs=data.freqs, filter_centers=[0],
                                   filter_half_widths=[RFI_DPSS_HALFWIDTH], eigenval_cutoff=[1e-9], nsig=nsig)

    return rfi_flags

# Iteratively develop RFI mask, excess RFI classification, and autocorrelation shape classification
if not all_flagged():
    stage = 1
    rfi_flags = np.array(array_flags)
    prior_end_states = set()
    while True:
        # compute DPSS-filtered z-scores with current array-wide RFI mask
        zscores = auto_bl_zscores(data, rfi_flags)
        rms = {bl: np.nanmean(zscores[bl]**2)**.5 if np.any(np.isfinite(zscores[bl])) else np.inf for bl in zscores}
        
        # figure out which autos to use for finding new set of flags
        candidate_autos = [bl for bl in auto_bls if overall_class[utils.split_bl(bl)[0]] != 'bad']
        if stage == 1:
            # use best half of the unflagged antennas
            med_rms = np.nanmedian([rms[bl] for bl in candidate_autos])
            autos_to_use = [bl for bl in candidate_autos if rms[bl] <= med_rms]
        elif stage == 2:
            # use all unflagged antennas which are auto RFI good, or the best half, whichever is larger
            med_rms = np.nanmedian([rms[bl] for bl in candidate_autos])
            best_half_autos = [bl for bl in candidate_autos if rms[bl] <= med_rms]
            good_autos = [bl for bl in candidate_autos if (overall_class[utils.split_bl(bl)[0]] != 'bad')
                          and (auto_rfi_class[utils.split_bl(bl)[0]] == 'good')]
            autos_to_use = (best_half_autos if len(best_half_autos) > len(good_autos) else good_autos)
        elif stage == 3:
            # use all unflagged antennas which are auto RFI good or suspect
            autos_to_use = [bl for bl in candidate_autos if (overall_class[utils.split_bl(bl)[0]] != 'bad')]
    
        # compute new RFI flags
        rfi_flags = rfi_from_avg_autos(data, autos_to_use)
    
        # perform auto shape and RFI classification
        overall_class = auto_power_class + auto_slope_class + zeros_class + ant_metrics_class + solar_class + xengine_diff_class
        auto_rfi_class = ant_class.antenna_bounds_checker(rms, good=auto_rfi_good, suspect=auto_rfi_suspect, bad=(0, np.inf))
        overall_class += auto_rfi_class
        auto_shape_class = ant_class.auto_shape_checker(data, good=auto_shape_good, suspect=auto_shape_suspect,
                                                        flag_spectrum=np.sum(rfi_flags, axis=0).astype(bool), 
                                                        antenna_class=overall_class)
        overall_class += auto_shape_class
        
        # check for convergence by seeing whether we've previously gotten to this number of flagged antennas and channels
        if stage == 3:
            if (len(overall_class.bad_ants), np.sum(rfi_flags)) in prior_end_states:
                break
            prior_end_states.add((len(overall_class.bad_ants), np.sum(rfi_flags)))
        else:
            stage += 1

All antennas are flagged, so this cell is being skipped.

auto_class = auto_power_class + auto_slope_class
if auto_rfi_class is not None:
    auto_class += auto_rfi_class
if auto_shape_class is not None:
    auto_class += auto_rfi_class
if np.all([overall_class[utils.split_bl(bl)[0]] == 'bad' for bl in auto_bls]):
    ALL_FLAGGED = True
    print('All antennas are flagged after flagging for bad autos power/slope/rfi/shape.')

All antennas are flagged after flagging for bad autos power/slope/rfi/shape.

if not all_flagged():
    def rfi_plot(cls, flags=rfi_flags):
        avg_auto = {(-1, -1, 'ee'): np.mean([data[bl] for bl in auto_bls if not cls[utils.split_bl(bl)[0]] == 'bad'], axis=0)}
        plt.figure(figsize=(12, 5), dpi=100)
        plt.semilogy(hd.freqs / 1e6, np.where(flags, np.nan, avg_auto[(-1, -1, 'ee')])[0], label = 'Average Good or Suspect Autocorrelation', zorder=100)
        plt.semilogy(hd.freqs / 1e6, np.where(False, np.nan, avg_auto[(-1, -1, 'ee')])[0], 'r', lw=.5, label=f'{np.sum(flags[0])} Channels Flagged for RFI')
        plt.legend()
        plt.xlabel('Frequency (MHz)')
        plt.ylabel('Uncalibrated Autocorrelation')
        plt.tight_layout()

All antennas are flagged, so this cell is being skipped.

Figure 1: RFI Flagging

This figure shows RFI identified using the average of all autocorrelations---excluding bad antennas---for the first integration in the file.

if PLOT and not all_flagged(): rfi_plot(overall_class)

All antennas are flagged, so this cell is being skipped.

def autocorr_plot(cls):    
    fig, axes = plt.subplots(1, 2, figsize=(14, 5), dpi=100, sharey=True, gridspec_kw={'wspace': 0})
    labels = []
    colors = ['darkgreen', 'goldenrod', 'maroon']
    for ax, pol in zip(axes, antpols):
        for ant in cls.ants:
            if ant[1] == pol:
                color = colors[cls.quality_classes.index(cls[ant])]
                ax.semilogy(np.mean(data[utils.join_bl(ant, ant)], axis=0), color=color, lw=.5)
        ax.set_xlabel('Channel', fontsize=12)
        ax.set_title(f'{utils.join_pol(pol, pol)}-Polarized Autos')

    axes[0].set_ylabel('Raw Autocorrelation', fontsize=12)
    axes[1].legend([matplotlib.lines.Line2D([0], [0], color=color) for color in colors], 
                   [cl.capitalize() for cl in cls.quality_classes], ncol=1, fontsize=12, loc='upper right', framealpha=1)
    plt.tight_layout()

Figure 2: Plot of autocorrelations with classifications

This figure shows a plot of all autocorrelations in the array, split by polarization. Antennas are classified based on their autocorrelations into good, suspect, and bad, by examining power, slope, and RFI-occupancy.

if PLOT and not all_flagged(): autocorr_plot(auto_class)

All antennas are flagged, so this cell is being skipped.

Summarize antenna classification prior to redundant-baseline calibration

def array_class_plot(cls, extra_label=""):
    outriggers = [ant for ant in hd.data_ants if ant >= 320]

    if len(outriggers) > 0:
        fig, axes = plt.subplots(1, 2, figsize=(14, 6), dpi=100, gridspec_kw={'width_ratios': [2, 1]})
        plot_antclass(hd.antpos, cls, ax=axes[0], ants=[ant for ant in hd.data_ants if ant < 320], legend=False, title=f'HERA Core{extra_label}')
        plot_antclass(hd.antpos, cls, ax=axes[1], ants=outriggers, radius=50, title='Outriggers')
    else:
        fig, axes = plt.subplots(1, 1, figsize=(9, 6), dpi=100)
        plot_antclass(hd.antpos, cls, ax=axes, ants=[ant for ant in hd.data_ants if ant < 320], legend=False, title=f'HERA Core{extra_label}')

Figure 3: Summary of antenna classifications prior to calibration

This figure shows the location and classification of all antennas prior to calibration. Antennas are split along the diagonal, with ee-polarized antpols represented by the southeast half of each antenna and nn-polarized antpols represented by the northwest half. Outriggers are split from the core and shown at exaggerated size in the right-hand panel. This classification includes ant_metrics, a count of the zeros in the even or odd visibilities, and autocorrelation power, slope, and RFI occupancy. An antenna classified as bad in any classification will be considered bad. An antenna marked as suspect any in any classification will be considered suspect unless it is also classified as bad elsewhere.

if PLOT and not all_flagged(): array_class_plot(overall_class)

All antennas are flagged, so this cell is being skipped.

# delete diffs to save memory
if USE_DIFF:
    del diff_data, hd_diff
try:
    del cache
except NameError:
    pass
malloc_trim()

Perform redundant-baseline calibration

def classify_off_grid(reds, all_ants):
    '''Returns AntennaClassification of all_ants where good ants are in reds while bad ants are not.'''
    ants_in_reds = set([ant for red in reds for bl in red for ant in utils.split_bl(bl)])
    on_grid = [ant for ant in all_ants if ant in ants_in_reds]
    off_grid = [ant for ant in all_ants if ant not in ants_in_reds]
    return ant_class.AntennaClassification(good=on_grid, bad=off_grid)

def per_pol_filter_reds(reds, pols=['nn', 'ee'], **kwargs):
    '''Performs redcal filtering separately on polarizations (which might have different min_dim_size issues).'''
    return [red for pol in pols for red in redcal.filter_reds(copy.deepcopy(reds), pols=[pol], **kwargs)]

def check_if_whole_pol_flagged(redcal_class, pols=['Jee', 'Jnn'], thresh=.75):
    '''Checks if nearly an entire polarization is flagged (depending on thresh). 
    If it is, returns True and marks all antennas as bad in redcal_class.'''
    flag_fracs = np.array([np.mean([redcal_class[ant] == 'bad' for ant in redcal_class.ants if ant[1] == pol]) for pol in pols])
    if np.any(flag_fracs > thresh):
        for pol, frac in zip(pols, flag_fracs):
            if frac > thresh:
                print(f'Polarization {pol} is {frac:.3%} flagged > {thresh:.3%} threshold. Stopping redcal.')
        for ant in redcal_class:
            redcal_class[ant] = 'bad'
        return True
    return False

def recheck_chisq(cspa, sol, cutoff, avg_alg):
    '''Recompute chisq per ant without apparently bad antennas to see if any antennas get better.'''
    avg_cspa = {ant: avg_alg(np.where(rfi_flags, np.nan, cspa[ant])) for ant in cspa}
    sol2 = redcal.RedSol(sol.reds, gains={ant: sol[ant] for ant in avg_cspa if avg_cspa[ant] <= cutoff}, vis=sol.vis)
    new_chisq_per_ant = {ant: np.array(cspa[ant]) for ant in sol2.gains}
    if len(set([bl[2] for red in per_pol_filter_reds(sol2.reds, ants=sol2.gains.keys(), antpos=hd.data_antpos, **fr_settings) for bl in red])) >= 2:
        redcal.expand_omni_gains(sol2, sol2.reds, data, chisq_per_ant=new_chisq_per_ant)
    for ant in avg_cspa:
        if ant in new_chisq_per_ant:
            if np.any(np.isfinite(new_chisq_per_ant[ant])):
                if not np.all(np.isclose(new_chisq_per_ant[ant], 0)):
                    new_avg_cspa = avg_alg(np.where(rfi_flags, np.nan, cspa[ant]))
                    if new_avg_cspa > 0:
                        avg_cspa[ant] = np.min([avg_cspa[ant], new_avg_cspa])
    return avg_cspa

Perform iterative redcal

# figure out and filter reds and classify antennas based on whether or not they are on the main grid
if not all_flagged():
    fr_settings = {'max_dims': OC_MAX_DIMS, 'min_dim_size': OC_MIN_DIM_SIZE, 'min_bl_cut': OC_MIN_BL_LEN, 'max_bl_cut': OC_MAX_BL_LEN}
    reds = redcal.get_reds(hd.data_antpos, pols=['ee', 'nn'], pol_mode='2pol', bl_error_tol=2.0)
    reds = per_pol_filter_reds(reds, ex_ants=overall_class.bad_ants, antpos=hd.data_antpos, **fr_settings)
    if OC_SKIP_OUTRIGGERS:
        reds = redcal.filter_reds(reds, ex_ants=[ant for ant in ants if ant[0] >= 320])
    redcal_class = classify_off_grid(reds, ants)

All antennas are flagged, so this cell is being skipped.

if OC_USE_PRIOR_SOL and not all_flagged():
    # Find closest omnical file
    omnical_files = sorted(glob.glob('.'.join(OMNICAL_FILE.split('.')[:-5]) + '.*.' + '.'.join(OMNICAL_FILE.split('.')[-3:])))
    if len(omnical_files) == 0:
        OC_USE_PRIOR_SOL = False
    else:
        omnical_jds = np.array([float(re.findall("\d+\.\d+", ocf)[-1]) for ocf in omnical_files])
        closest_omnical = omnical_files[np.argmin(np.abs(omnical_jds - data.times[0]))]

        # Load closest omnical file and use it if the antenna flagging is not too dissimilar
        hc = io.HERACal(closest_omnical)
        prior_gains, prior_flags, _, _ = hc.read()
        not_bad_not_prior_flagged = [ant for ant in overall_class if not ant in redcal_class.bad_ants and not np.all(prior_flags[ant])]
        if (len(redcal_class.bad_ants) == len(redcal_class.ants)):
            OC_USE_PRIOR_SOL = False  # all antennas flagged
        elif (len(not_bad_not_prior_flagged) / (len(redcal_class.ants) - len(redcal_class.bad_ants))) < OC_PRIOR_SOL_FLAG_THRESH:
            OC_USE_PRIOR_SOL = False  # too many antennas unflaged that were flagged in the prior sol
        else:
            print(f'Using {closest_omnical} as a starting point for redcal.')

All antennas are flagged, so this cell is being skipped.

if not all_flagged():
    redcal_start = time.time()
    rc_settings = {'oc_conv_crit': 1e-10, 'gain': 0.4, 'run_logcal': False,
                   'oc_maxiter': OC_MAXITER, 'check_after': OC_MAXITER, 'use_gpu': OC_USE_GPU}
    
    if check_if_whole_pol_flagged(redcal_class):
        # skip redcal, initialize empty sol and meta 
        sol = redcal.RedSol(reds)
        meta = {'chisq': None, 'chisq_per_ant': None}
    else:    
        if OC_USE_PRIOR_SOL:
            # use prior unflagged gains and data to create starting point for next step
            sol = redcal.RedSol(reds=reds, gains={ant: prior_gains[ant] for ant in not_bad_not_prior_flagged})
            reds_to_update = [[bl for bl in red if (utils.split_bl(bl)[0] in sol.gains) and (utils.split_bl(bl)[1] in sol.gains)] for red in reds]
            reds_to_update = [red for red in reds_to_update if len(red) > 0]
            sol.update_vis_from_data(data, reds_to_update=reds_to_update)
            redcal.expand_omni_gains(sol, reds, data)
            sol.update_vis_from_data(data)
        else:
            sol = None
            
        malloc_trim()

All antennas are flagged, so this cell is being skipped.

if not all_flagged():
    all_high_chisq_found = False
    metric = 'median'
    
    # iteratively rerun redundant calibration
    for i in range(OC_MAX_RERUN + 1):
        # refilter reds and update classification to reflect new off-grid ants, if any
        reds = per_pol_filter_reds(reds, ex_ants=(overall_class + redcal_class).bad_ants, antpos=hd.data_antpos, **fr_settings)
        reds = sorted(reds, key=len, reverse=True)
        redcal_class = classify_off_grid(reds, ants)
        
        # check to see whether we're done because an entire pol is flagged
        if check_if_whole_pol_flagged(redcal_class):
            break
    
        # change settings for final run
        if all_high_chisq_found or (i == OC_MAX_RERUN):
            sol = None  # start from scratch
            rc_settings['oc_maxiter'] = rc_settings['check_after'] = OC_RERUN_MAXITER
        
        # optionally redo firstcal and start from there every iteration
        if OC_RESTART_FROM_FC_EVERY_ITER:
            sol = None

        # re-run redundant calibration using previous solution (if it's not the final run and if not OC_RESTART_FROM_FC_EVERY_ITER)
        meta, sol = redcal.redundantly_calibrate(data, reds, sol0=sol, max_dims=None, **rc_settings)
        malloc_trim()
        
        # recompute chi^2 for bad antennas without bad antennas to make sure they are actually bad
        avg_cspa = recheck_chisq(meta['chisq_per_ant'], sol, oc_cspa_suspect[1], (np.nanmean if metric == 'mean' else np.nanmedian))

        # flag bad antennas
        cspa_class = ant_class.antenna_bounds_checker(avg_cspa, good=oc_cspa_good, suspect=oc_cspa_suspect, bad=[(-np.inf, np.inf)])
        for ant in cspa_class.bad_ants:
            if avg_cspa[ant] < np.max(list(avg_cspa.values())) / OC_MAX_CHISQ_FLAGGING_DYNAMIC_RANGE:
                cspa_class[ant] = 'suspect'  # reclassify as suspect if they are much better than the worst antennas
        redcal_class += cspa_class

        if len(cspa_class.bad_ants) > 0:
            print(f'Removing {cspa_class.bad_ants} for high {metric} unflagged chi^2.')
            for ant in cspa_class.bad_ants:
                print(f'\t{ant}: {avg_cspa[ant]:.3f}')
    
        if check_if_whole_pol_flagged(redcal_class) or all_high_chisq_found or (i == OC_MAX_RERUN):
            break

        if len(cspa_class.bad_ants) == 0:
            if metric == 'median':
                metric = 'mean'  # switch to mean if no new median offenders found
            else:
                all_high_chisq_found = True  # no new antennas to flag, the next iteration will be the final one
    
    print(f'Finished redcal in {(time.time() - redcal_start) / 60:.2f} minutes.')
    overall_class += redcal_class

All antennas are flagged, so this cell is being skipped.

Expand solution to include calibratable baselines excluded from redcal (e.g. because they were too long)

if not all_flagged():
    expanded_reds = redcal.get_reds(hd.data_antpos, pols=['ee', 'nn'], pol_mode='2pol', bl_error_tol=2.0)
    expanded_reds = per_pol_filter_reds(expanded_reds, ex_ants=(ant_metrics_class + solar_class + zeros_class + auto_class + xengine_diff_class).bad_ants,
                                        max_dims=OC_MAX_DIMS, min_dim_size=OC_MIN_DIM_SIZE)
    if OC_SKIP_OUTRIGGERS:
        expanded_reds = redcal.filter_reds(expanded_reds, ex_ants=[ant for ant in ants if ant[0] >= 320])
    if len(sol.gains) > 0:
        redcal.expand_omni_vis(sol, expanded_reds, data, chisq=meta['chisq'], chisq_per_ant=meta['chisq_per_ant'])

All antennas are flagged, so this cell is being skipped.

if not all_flagged():
    # now figure out flags, nsamples etc.
    omni_flags = {ant: (~np.isfinite(g)) | (ant in overall_class.bad_ants) for ant, g in sol.gains.items()}
    vissol_flags = datacontainer.RedDataContainer({bl: ~np.isfinite(v) for bl, v in sol.vis.items()}, reds=sol.vis.reds)
    single_nsamples_array = np.ones((len(hd.times), len(hd.freqs)), dtype=float)
    nsamples = datacontainer.DataContainer({bl: single_nsamples_array for bl in data})
    vissol_nsamples = redcal.count_redundant_nsamples(nsamples, [red for red in expanded_reds if red[0] in vissol_flags], 
                                                      good_ants=[ant for ant in overall_class if ant not in overall_class.bad_ants])
    for bl in vissol_flags:
        vissol_flags[bl][vissol_nsamples[bl] == 0] = True
    sol.make_sol_finite()

All antennas are flagged, so this cell is being skipped.

Fix the firstcal delay slope degeneracy using RFI transmitters

if not OC_USE_PRIOR_SOL and not all_flagged():
    # find channels clearly contaminated by RFI
    not_bad_ants = [ant for ant in overall_class.ants if (overall_class[ant] != 'bad') and (utils.join_bl(ant, ant) in data)]
    if len(not_bad_ants) > 0:
        chan_flags = np.mean([xrfi.detrend_medfilt(data[utils.join_bl(ant, ant)], Kf=8, Kt=2) for ant in not_bad_ants], axis=(0, 1)) > 5

        # hardcoded RFI transmitters and their headings
        # channel: frequency (Hz), heading (rad), chi^2
        phs_sol = {359: ( 90744018.5546875, 0.7853981, 23.3),
                   360: ( 90866088.8671875, 0.7853981, 10.8),
                   385: ( 93917846.6796875, 0.7853981, 27.3),
                   386: ( 94039916.9921875, 0.7853981, 18.1),
                   400: ( 95748901.3671875, 6.0632738, 24.0),
                   441: (100753784.1796875, 0.7853981, 21.7),
                   442: (100875854.4921875, 0.7853981, 19.4),
                   455: (102462768.5546875, 6.0632738, 18.8),
                   456: (102584838.8671875, 6.0632738,  8.8),
                   471: (104415893.5546875, 0.7853981, 13.3),
                   484: (106002807.6171875, 6.0632738, 21.2),
                   485: (106124877.9296875, 6.0632738,  4.0),
                  1181: (191085815.4296875, 0.7853981, 26.3),
                  1182: (191207885.7421875, 0.7853981, 27.0),
                  1183: (191329956.0546875, 0.7853981, 25.6),
                  1448: (223678588.8671875, 2.6075219, 25.7),
                  1449: (223800659.1796875, 2.6075219, 22.6),
                  1450: (223922729.4921875, 2.6075219, 11.6),
                  1451: (224044799.8046875, 2.6075219,  5.9),
                  1452: (224166870.1171875, 2.6075219, 22.6),
                  1510: (231246948.2421875, 0.1068141, 23.9)}

        if not np.isclose(hd.freqs[0], 46920776.3671875, atol=0.001) or len(hd.freqs) != 1536:
            # We have less frequencies than usual (maybe testing)
            phs_sol = {np.argmin(np.abs(hd.freqs - freq)): (freq, heading, chisq) for chan, (freq, heading, chisq) in phs_sol.items() if hd.freqs[0] <= freq <= hd.freqs[-1]}


        rfi_chans = [chan for chan in phs_sol if chan_flags[chan]]
        if len(rfi_chans) >= 2:
            print('Channels used for delay-slope calibration with RFI:', rfi_chans)
            rfi_angles = np.array([phs_sol[chan][1] for chan in rfi_chans])
            rfi_headings = np.array([np.cos(rfi_angles), np.sin(rfi_angles), np.zeros_like(rfi_angles)])
            rfi_chisqs = np.array([phs_sol[chan][2] for chan in rfi_chans])

            # resolve firstcal degeneracy with delay slopes set by RFI transmitters, update cal
            max_dly = np.max(np.abs(list(meta['fc_meta']['dlys'].values())))
            RFI_dly_slope_gains = abscal.RFI_delay_slope_cal([red for red in expanded_reds if red[0] in sol.vis], hd.antpos, sol.vis, hd.freqs, rfi_chans, rfi_headings, rfi_wgts=rfi_chisqs**-1,
                                                             min_tau=-max_dly, max_tau=max_dly, delta_tau=0.1e-9, return_gains=True, gain_ants=sol.gains.keys())
            sol.gains = {ant: g * RFI_dly_slope_gains[ant] for ant, g in sol.gains.items()}
            apply_cal.calibrate_in_place(sol.vis, RFI_dly_slope_gains)
            malloc_trim()
        else:
            print(f"Only {len(rfi_chans)} RFI channels with known headings were flagged for RFI, so RFI-firstcal is being skipped.")

Perform absolute amplitude calibration using a model of autocorrelations

# Load simulated and then downsampled model of autocorrelations that includes receiver noise, then interpolate to upsample
if VALIDATION:
    hd_auto_model = io.HERAData('/lustre/aoc/projects/hera/Validation/H6C_IDR2/sim_data/h6c_validation_autos_for_amp_abscal_with_Trx_100K.uvh5')
else:
    hd_auto_model = io.HERAData(f'{HNBT_DATA}/SSM_autocorrelations_downsampled_sum_pol_convention.uvh5')
if not all_flagged():
    model, _, _ = hd_auto_model.read()
    per_pol_interpolated_model = {}
    for bl in model:
        sorted_lsts, lst_indices = np.unique(model.lsts, return_index=True)
        periodic_model = np.vstack([model[bl][lst_indices, :], model[bl][lst_indices[0], :]])
        periodic_lsts = np.append(sorted_lsts, sorted_lsts[0] + 2 * np.pi)
        lst_interpolated = interpolate.CubicSpline(periodic_lsts, periodic_model, axis=0, bc_type='periodic')(data.lsts)
        per_pol_interpolated_model[bl[2]] = interpolate.CubicSpline(model.freqs, lst_interpolated, axis=1)(data.freqs)
    model = {bl: per_pol_interpolated_model[bl[2]] for bl in auto_bls if utils.split_bl(bl)[0] not in overall_class.bad_ants}

All antennas are flagged, so this cell is being skipped.

if not all_flagged():
    # Run abscal and update omnical gains with abscal gains
    if len(model) > 0:
        redcaled_autos = {bl: sol.calibrate_bl(bl, data[bl]) for bl in auto_bls if utils.split_bl(bl)[0] not in overall_class.bad_ants}
        g_abscal = abscal.abs_amp_logcal(model, redcaled_autos, verbose=False, return_gains=True, gain_ants=sol.gains)
        sol.gains = {ant: g * g_abscal[ant] for ant, g in sol.gains.items()}
        apply_cal.calibrate_in_place(sol.vis, g_abscal)
        del redcaled_autos, g_abscal

All antennas are flagged, so this cell is being skipped.

Full absolute calibration of phase gradients

If an ABSCAL_MODEL_FILES_GLOB is provided, try to perform a full absolute calibration of tip-tilt phase gradients across the array using that those model files. Specifically, this step calibrates omnical visbility solutions using unique baselines simulated with a model of the sky and HERA's beam.

if not all_flagged():
    if ABSCAL_MODEL_FILES_GLOB is not None:
        abscal_model_files = sorted(glob.glob(ABSCAL_MODEL_FILES_GLOB))
    elif VALIDATION:
        abscal_model_files = sorted(glob.glob('/lustre/aoc/projects/hera/Validation/H6C_IDR2/sim_data/foregrounds/zen.LST.*.foregrounds.uvh5'))
    else:
        # try to find files on site
        abscal_model_files = sorted(glob.glob('/mnt/sn1/data1/abscal_models/H6C/zen.2458894.?????.uvh5'))
        if len(abscal_model_files) == 0:
            # try to find files at NRAO
            abscal_model_files = sorted(glob.glob('/lustre/aoc/projects/hera/h6c-analysis/abscal_models/h6c_abscal_files_unique_baselines/zen.2458894.?????.uvh5'))
    print(f'Found {len(abscal_model_files)} abscal model files{" in " + os.path.dirname(abscal_model_files[0]) if len(abscal_model_files) > 0 else ""}.')

All antennas are flagged, so this cell is being skipped.

if not all_flagged():
    # Try to perform a full abscal of phase
    if len(abscal_model_files) == 0:
        DO_FULL_ABSCAL = False
        print('No model files found... not performing full absolute calibration of phase gradients.')
    elif np.all([ant in overall_class.bad_ants for ant in ants]):
        DO_FULL_ABSCAL = False
        print('All antennas classified as bad... skipping absolute calibration of phase gradients.')
    else:
        abscal_start = time.time()
        # figure out which model files match the LSTs of the data
        matched_model_files = sorted(set(abscal.match_times(SUM_FILE, abscal_model_files, filetype='uvh5')))
        if len(matched_model_files) == 0:
            DO_FULL_ABSCAL = False
            print(f'No model files found matching the LSTs of this file after searching for {(time.time() - abscal_start) / 60:.2f} minutes. '
                  'Not performing full absolute calibration of phase gradients.')
        else:
            DO_FULL_ABSCAL = True
            # figure out appropriate model times to load
            hdm = io.HERAData(matched_model_files)
            all_model_times, all_model_lsts = abscal.get_all_times_and_lsts(hdm, unwrap=True)
            d2m_time_map = abscal.get_d2m_time_map(data.times, np.unwrap(data.lsts), all_model_times, all_model_lsts, extrap_limit=.5)

All antennas are flagged, so this cell is being skipped.

if not all_flagged():
    if DO_FULL_ABSCAL:
        abscal_meta = {}
        for pol in ['ee', 'nn']:
            print(f'Performing absolute phase gradient calibration of {pol}-polarized visibility solutions...')
            
            # load matching times and baselines
            unflagged_data_bls = [bl for bl in vissol_flags if not np.all(vissol_flags[bl]) and bl[2] == pol]
            model_bls = copy.deepcopy(hdm.bls)
            model_antpos = hdm.data_antpos
            if len(matched_model_files) > 1:  # in this case, it's a dictionary
                model_bls = list(set([bl for bls in list(hdm.bls.values()) for bl in bls]))
                model_antpos = {ant: pos for antpos in hdm.data_antpos.values() for ant, pos in antpos.items()}
            data_bls, model_bls, data_to_model_bl_map = abscal.match_baselines(unflagged_data_bls, model_bls, data.antpos, model_antpos=model_antpos, 
                                                                             pols=[pol], data_is_redsol=True, model_is_redundant=True, tol=1.0,
                                                                             min_bl_cut=ABSCAL_MIN_BL_LEN, max_bl_cut=ABSCAL_MAX_BL_LEN, verbose=True)
            model, model_flags, _ = io.partial_time_io(hdm, np.unique([d2m_time_map[time] for time in data.times]), bls=model_bls)
            model_bls = [data_to_model_bl_map[bl] for bl in data_bls]
            
            # rephase model to match in lsts
            model_blvecs = {bl: model.antpos[bl[0]] - model.antpos[bl[1]] for bl in model.keys()}
            utils.lst_rephase(model, model_blvecs, model.freqs, data.lsts - model.lsts,
                              lat=hdm.telescope.location.lat.deg, inplace=True)
    
            # run abscal and apply 
            abscal_meta[pol], delta_gains = abscal.complex_phase_abscal(sol.vis, model, sol.reds, data_bls, model_bls)
            
            # apply gains
            sol.gains = {antpol : g * delta_gains.get(antpol, 1) for antpol, g in sol.gains.items()}
            apply_cal.calibrate_in_place(sol.vis, delta_gains)            
         
        del model, model_flags, delta_gains
        malloc_trim()    
        
        print(f'Finished absolute calibration of tip-tilt phase slopes in {(time.time() - abscal_start) / 60:.2f} minutes.')

All antennas are flagged, so this cell is being skipped.

if not all_flagged() and DO_FULL_ABSCAL and CALIBRATE_CROSS_POLS:
    cross_pol_cal_start = time.time()

    # Compute reds for good antennas 
    cross_reds = redcal.get_reds(hd.data_antpos, pols=['en', 'ne'], bl_error_tol=2.0)        
    cross_reds = redcal.filter_reds(cross_reds, ex_ants=overall_class.bad_ants, pols=['en', 'ne'], antpos=hd.antpos, **fr_settings)    
    unflagged_data_bls = [red[0] for red in cross_reds]

    # Get cross-polarized model visibilities
    model_bls = copy.deepcopy(hdm.bls)
    model_antpos = hdm.data_antpos
    if len(matched_model_files) > 1:  # in this case, it's a dictionary
        model_bls = list(set([bl for bls in list(hdm.bls.values()) for bl in bls]))
        model_antpos = {ant: pos for antpos in hdm.data_antpos.values() for ant, pos in antpos.items()}

    data_bls, model_bls, data_to_model_bl_map = abscal.match_baselines(unflagged_data_bls, model_bls, data.antpos, model_antpos=model_antpos, 
                                                                     pols=['en', 'ne'], data_is_redsol=False, model_is_redundant=True, tol=1.0,
                                                                     min_bl_cut=ABSCAL_MIN_BL_LEN, max_bl_cut=ABSCAL_MAX_BL_LEN, verbose=True)
    
    model, model_flags, _ = io.partial_time_io(hdm, np.unique([d2m_time_map[time] for time in data.times]), 
                                               bls=list(set([bl[0:2] for bl in model_bls])), polarizations=['en', 'ne'])
    model_bls = [data_to_model_bl_map[bl] for bl in data_bls]

    # rephase model to match in lsts
    model_blvecs = {bl: model.antpos[bl[0]] - model.antpos[bl[1]] for bl in model.keys()}
    utils.lst_rephase(model, model_blvecs, model.freqs, data.lsts - model.lsts, lat=hdm.telescope.location.lat.deg, inplace=True)

    wgts_here = {}
    data_here = {}
    
    for red in cross_reds:
        data_bl = red[0]
        if data_bl in data_to_model_bl_map:

            wgts_here[data_bl] = np.sum([
                np.logical_not(omni_flags[utils.split_bl(bl)[0]] | omni_flags[utils.split_bl(bl)[1]])
                for bl in red
            ], axis=0)
            data_here[data_bl] = np.nanmean([
                np.where(
                    omni_flags[utils.split_bl(bl)[0]] | omni_flags[utils.split_bl(bl)[1]],
                    np.nan, sol.calibrate_bl(bl, data[bl])
                ) 
                for bl in red
            ], axis=0)
    
    # Run cross-polarized phase calibration
    delta = abscal.cross_pol_phase_cal(
        model=model, data=data_here, wgts=wgts_here, data_bls=data_bls, model_bls=model_bls, return_gains=False, 
        refpol='Jee', gain_ants=sol.gains.keys()
    )
    delta_gains = {antpol: (np.ones_like(delta) if antpol[1] == 'Jee' else np.exp(1j * delta)) for antpol in sol.gains.keys()}
    
    # apply gains
    # \Delta = \phi_e - \phi_n, where V_{en}^{cal} = V_{en}^{uncal} * e^{i \Delta} 
    # and V_{ne}^{cal} = V_{ne}^{uncal} * e^{-i \Delta}
    sol.gains = {antpol: g * delta_gains[antpol] for antpol, g in sol.gains.items()}
    apply_cal.calibrate_in_place(sol.vis, delta_gains)
    del hdm, model, model_flags, delta_gains
    print(f'Finished relative polarized phase calibration in {(time.time() - cross_pol_cal_start) / 60:.2f} minutes.')

All antennas are flagged, so this cell is being skipped.

Plotting

def redundant_group_plot():
    if np.all([ant in overall_class.bad_ants for ant in ants]):
        print('All antennas classified as bad. Nothing to plot.')
        return
    
    fig, axes = plt.subplots(2, 2, figsize=(14, 6), dpi=100, sharex='col', sharey='row', gridspec_kw={'hspace': 0, 'wspace': 0})
    for i, pol in enumerate(['ee', 'nn']):
        reds_here = redcal.get_reds(hd.data_antpos, pols=[pol], pol_mode='1pol', bl_error_tol=2.0)
        red = sorted(redcal.filter_reds(reds_here, ex_ants=overall_class.bad_ants), key=len, reverse=True)[0]
        rc_data = {bl: sol.calibrate_bl(bl, data[bl]) for bl in red}
        for bl in red:
            axes[0, i].plot(hd.freqs/1e6, np.angle(rc_data[bl][0]), alpha=.5, lw=.5)
            axes[1, i].semilogy(hd.freqs/1e6, np.abs(rc_data[bl][0]), alpha=.5, lw=.5)
        axes[0, i].plot(hd.freqs / 1e6, np.angle(sol.vis[red[0]][0]), lw=1, c='k')
        axes[1, i].semilogy(hd.freqs / 1e6, np.abs(sol.vis[red[0]][0]), lw=1, c='k', label=f'Baseline Group:\n{(int(red[0][0]), int(red[0][1]), red[0][2])}')
        axes[1, i].set_xlabel('Frequency (MHz)')
        axes[1, i].legend(loc='upper right')
    axes[0, 0].set_ylabel('Visibility Phase (radians)')
    axes[1, 0].set_ylabel('Visibility Amplitude (Jy)')
    plt.tight_layout()

def abscal_degen_plot():
    if DO_FULL_ABSCAL:
        fig, axes = plt.subplots(3, 1, figsize=(14, 6), dpi=100, sharex=True, gridspec_kw={'hspace': .05})

        for ax, pol in zip(axes[:2], ['ee', 'nn']):
            for kk in range(abscal_meta[pol]['Lambda_sol'].shape[-1]):
                ax.plot(hd.freqs[~rfi_flags[0]] * 1e-6, abscal_meta[pol]['Lambda_sol'][0, ~rfi_flags[0], kk], '.', ms=1, label=f"Component {kk}")

            ax.set_ylim(-np.pi-0.5, np.pi+0.5)
            ax.set_xlabel('Frequency (MHz)')
            ax.set_ylabel('Phase Gradient\nVector Component')
            ax.legend(markerscale=20, title=f'{pol}-polarization', loc='lower right')
            ax.grid()
            
        for pol, color in zip(['ee', 'nn'], ['b', 'r']):
            axes[2].plot(hd.freqs[~rfi_flags[0]]*1e-6, abscal_meta[pol]['Z_sol'].real[0, ~rfi_flags[0]], '.', ms=1, label=pol, color=color)
        axes[2].set_ylim(-.25, 1.05)
        axes[2].set_ylabel('Re[Z($\\nu$)]')
        axes[2].legend(markerscale=20, loc='lower right')
        axes[2].grid()            
        plt.tight_layout()

def polarized_gain_phase_plot():
    if CALIBRATE_CROSS_POLS and DO_FULL_ABSCAL:
        plt.figure(figsize=(14, 4), dpi=100)
        for i, time in enumerate(data.times):
            plt.plot(data.freqs / 1e6, np.where(rfi_flags[i], np.nan, delta[i, :]), '.', ms=1.5, label=f'{time:.6f}')
        plt.ylim(-np.pi-0.5, np.pi+0.5)
        plt.xlabel('Frequency (MHz)')
        plt.ylabel('Relative Phase $\Delta \ (\phi_{ee} - \phi_{nn})$')
        plt.grid()
        plt.legend()

Figure 4: Redundant calibration of a single baseline group

The results of a redundant-baseline calibration of a single integration and a single group, the one with the highest redundancy in each polarization after antenna classification and excision based on the above, plus the removal of antennas with high chi^2 per antenna. The black line is the redundant visibility solution. Each thin colored line is a different baseline group. Phases are shown in the top row, amplitudes in the bottom, ee-polarized visibilities in the left column, and nn-polarized visibilities in the right.

if PLOT and not all_flagged(): redundant_group_plot()

All antennas are flagged, so this cell is being skipped.

Figure 5: Absolute calibration of redcal degeneracies

This figure shows the per-frequency phase gradient solutions across the array for both polarizations and all components of the degenerate subspace of redundant-baseline calibraton. While full HERA only has two such tip-tilt degeneracies, a subset of HERA can have up to OC_MAX_DIMS (depending on antenna flagging). In addition to the absolute amplitude, this is the full set of the calibration degrees of freedom not constrainted by redcal. This figure also includes a plot of $Re[Z(\nu)]$, the complex objective function which varies from -1 to 1 and indicates how well the data and the absolute calibration model have been made to agree. Perfect agreement is 1.0 and good agreement is anything above $\sim$0.5 Decorrelation yields values closer to 0, where anything below $\sim$0.3 is suspect.

if PLOT and not all_flagged(): abscal_degen_plot()

All antennas are flagged, so this cell is being skipped.

Figure 6: Relative Phase Calibration

This figure shows the relative phase calibration between the ee vs. nn polarizations.

if PLOT and not all_flagged(): polarized_gain_phase_plot()

All antennas are flagged, so this cell is being skipped.

Attempt to calibrate some flagged antennas

This attempts to calibrate bad antennas using information from good or suspect antennas without allowing bad antennas to affect their calibration. However, introducing 0s in gains or infs/nans in gains or visibilities can create problems down the line, so those are removed.

if not all_flagged():
    expand_start = time.time()
    expanded_reds = redcal.get_reds(hd.data_antpos, pols=['ee', 'nn'], pol_mode='2pol', bl_error_tol=2.0)
    sol.vis.build_red_keys(expanded_reds)
    redcal.expand_omni_gains(sol, expanded_reds, data, chisq_per_ant=meta['chisq_per_ant'])
    if not np.all([ant in overall_class.bad_ants for ant in ants]):
        redcal.expand_omni_vis(sol, expanded_reds, data)
    
    # Replace near-zeros in gains and infs/nans in gains/sols
    for ant in sol.gains:
        zeros_in_gains = np.isclose(sol.gains[ant], 0)
        if ant in omni_flags:
            omni_flags[ant][zeros_in_gains] = True
        sol.gains[ant][zeros_in_gains] = 1.0 + 0.0j
    sol.make_sol_finite()
    malloc_trim()
    print(f'Finished expanding gain solution in {(time.time() - expand_start) / 60:.2f} minutes.')

All antennas are flagged, so this cell is being skipped.

def array_chisq_plot(include_outriggers=True):
    if np.all([ant in overall_class.bad_ants for ant in ants]):
        print('All antennas classified as bad. Nothing to plot.')
        return    
    
    def _chisq_subplot(ants, size=250):
        fig, axes = plt.subplots(1, 2, figsize=(14, 5), dpi=100)
        for ax, pol in zip(axes, ['ee', 'nn']):
            ants_to_plot = set([ant for ant in meta['chisq_per_ant'] if utils.join_pol(ant[1], ant[1]) == pol and (ant[0] in ants)])
            cspas = np.array([np.nanmean(np.where(rfi_flags, np.nan, meta['chisq_per_ant'][ant])) for ant in ants_to_plot])
            xpos = [hd.antpos[ant[0]][0] for ant in ants_to_plot]
            ypos = [hd.antpos[ant[0]][1] for ant in ants_to_plot]
            scatter = ax.scatter(xpos, ypos, s=size, c=cspas, lw=.25, edgecolors=np.where(np.isfinite(cspas) & (cspas > 0), 'none', 'k'), 
                                 norm=matplotlib.colors.LogNorm(vmin=1, vmax=oc_cspa_suspect[1]))
            for ant in ants_to_plot:
                ax.text(hd.antpos[ant[0]][0], hd.antpos[ant[0]][1], ant[0], va='center', ha='center', fontsize=8,
                        c=('r' if ant in overall_class.bad_ants else 'w'))
            plt.colorbar(scatter, ax=ax, extend='both')
            ax.axis('equal')
            ax.set_xlabel('East-West Position (meters)')
            ax.set_ylabel('North-South Position (meters)')
            ax.set_title(f'{pol}-pol $\\chi^2$ / Antenna (Red is Flagged)')
        plt.tight_layout()    
    
    _chisq_subplot([ant for ant in hd.data_ants if ant < 320])
    outriggers = [ant for ant in hd.data_ants if ant >= 320]    
    if include_outriggers & (len(outriggers) > 0):
        _chisq_subplot([ant for ant in hd.data_ants if ant >= 320], size=400)

Figure 7: chi^2 per antenna across the array

This plot shows median (taken over time and frequency) of the normalized chi^2 per antenna. The expectation value for this quantity when the array is perfectly redundant is 1.0. Antennas that are classified as bad for any reason have their numbers shown in red. Some of those antennas were classified as bad during redundant calibration for high chi^2. Some of those antennas were originally excluded from redundant calibration because they were classified as bad earlier for some reason. See here for more details. Note that the color scale saturates at below 1 and above 10.

if PLOT and not all_flagged(): array_chisq_plot(include_outriggers=(not OC_SKIP_OUTRIGGERS))

All antennas are flagged, so this cell is being skipped.

Figure 8: Summary of antenna classifications after redundant calibration

This figure is the same as Figure 2, except that it now includes additional suspect or bad antennas based on redundant calibration. This can include antennas with high chi^2, but it can also include antennas classified as "bad" because they would add extra degeneracies to calibration.

if PLOT and not all_flagged(): array_class_plot(overall_class, extra_label=", Post-Redcal")

All antennas are flagged, so this cell is being skipped.

to_show = {'Antenna': [f'{ant[0]}{ant[1][-1]}' for ant in ants]}
classes = {'Antenna': [overall_class[ant] if ant in overall_class else '-' for ant in ants]}
to_show['Dead?'] = [{'good': 'No', 'bad': 'Yes'}[am_totally_dead[ant]] if (ant in am_totally_dead) else '' for ant in ants]
classes['Dead?'] = [am_totally_dead[ant] if (ant in am_totally_dead) else '' for ant in ants]
for title, ac in [('Low Correlation', am_corr),
                  ('Cross-Polarized', am_xpol),
                  ('Solar Alt', solar_class),
                  ('Even/Odd Zeros', zeros_class),
                  ('Autocorr Power', auto_power_class),
                  ('Autocorr Slope', auto_slope_class),
                  ('Auto RFI RMS', auto_rfi_class),
                  ('Autocorr Shape', auto_shape_class),
                  ('Bad Diff X-Engines', xengine_diff_class)]:
    to_show[title] = [f'{ac._data[ant]:.2G}' if (ac is not None and ant in ac._data) else '' for ant in ants]
    classes[title] = [ac[ant] if (ac is not None and ant in ac) else 'bad' for ant in ants]
    
to_show['Redcal chi^2'] = [f'{np.nanmean(np.where(rfi_flags, np.nan, meta["chisq_per_ant"][ant])):.3G}' \
                           if (meta is not None and meta['chisq_per_ant'] is not None and ant in meta['chisq_per_ant']) else '' for ant in ants]
classes['Redcal chi^2'] = [redcal_class[ant] if redcal_class is not None and ant in redcal_class else 'bad' for ant in ants]

df = pd.DataFrame(to_show)
df_classes = pd.DataFrame(classes)
colors = {'good': 'darkgreen', 'suspect': 'goldenrod', 'bad': 'maroon'}
df_colors = df_classes.applymap(lambda x: f'background-color: {colors.get(x, None)}')

table = df.style.hide() \
                .apply(lambda x: pd.DataFrame(df_colors.values, columns=x.columns), axis=None) \
                .set_properties(subset=['Antenna'], **{'font-weight': 'bold', 'border-right': "3pt solid black"}) \
                .set_properties(subset=df.columns[1:], **{'border-left': "1pt solid black"}) \
                .set_properties(**{'text-align': 'center', 'color': 'white'})

Table 1: Complete summary of per-antenna classifications

This table summarizes the results of the various classifications schemes detailed above. As before, green is good, yellow is suspect, and red is bad. The color for each antenna (first column) is the final summary of all other classifications. Antennas missing from redcal $\chi^2$ were excluded redundant-baseline calibration, either because they were flagged by ant_metrics or the even/odd zeros check, or because they would add unwanted extra degeneracies.

HTML(table.to_html())

Antenna	Dead?	Low Correlation	Cross-Polarized	Solar Alt	Even/Odd Zeros	Autocorr Power	Autocorr Slope	Auto RFI RMS	Autocorr Shape	Bad Diff X-Engines	Redcal chi^2
3e	No	0.52	0.31	-43	1.9E+02	12	-0.0079
3n	No	0.52	0.31	-43	1.9E+02	17	-0.095
4e	No	0.36	0.17	-43	1.9E+02	13	0.075
4n	No	0.34	0.17	-43	1.9E+02	15	0.25
5e	No	0.57	0.35	-43	1.9E+02	15	-0.11
5n	No	0.56	0.35	-43	1.9E+02	19	-0.17
7e	No	0.55	0.33	-43	1.9E+02	20	-0.052
7n	No	0.55	0.33	-43	1.9E+02	22	-0.13
8e	No	0.56	0.34	-43	1.9E+02	24	-0.075
8n	No	0.54	0.34	-43	1.9E+02	11	0.063
9e	No	0.56	0.34	-43	1.9E+02	19	-0.054
9n	No	0.55	0.34	-43	1.9E+02	19	-0.11
10e	No	0.55	0.35	-43	1.9E+02	25	-0.048
10n	No	0.55	0.35	-43	1.9E+02	13	-0.034
15e	No	0.56	0.34	-43	1.9E+02	28	-0.081
15n	No	0.56	0.34	-43	1.9E+02	31	-0.17
16e	No	0.58	0.35	-43	1.9E+02	18	-0.05
16n	No	0.57	0.35	-43	1.9E+02	16	-0.016
17e	No	0.58	0.34	-43	1.9E+02	17	-0.079
17n	No	0.57	0.34	-43	1.9E+02	20	-0.081
18e	No	0.029	0.0062	-43	1.9E+02	0.64	0.33
18n	No	0.034	0.0062	-43	1.9E+02	0.57	0.39
19e	No	0.58	0.35	-43	1.9E+02	19	-0.081
19n	No	0.56	0.35	-43	1.9E+02	19	-0.092
20e	No	0.56	0.34	-43	1.9E+02	17	0.0016
20n	No	0.56	0.34	-43	1.9E+02	21	-0.099
21e	No	0.55	0.33	-43	1.9E+02	7.9	-0.021
21n	No	0.54	0.33	-43	1.9E+02	8	0.05
27e	No	0.15	-0.021	-43	1.9E+02	11	0.19
27n	No	0.1	-0.021	-43	1.9E+02	7	0.38
28e	No	0.12	0.037	-43	1.9E+02	6	0.52
28n	No	0.21	0.037	-43	1.9E+02	2.4	0.078
29e	No	0.58	0.33	-43	1.9E+02	21	-0.045
29n	No	0.5	0.33	-43	1.9E+02	17	0.64
30e	No	0.57	0.34	-43	1.9E+02	15	-0.04
30n	No	0.52	0.34	-43	1.9E+02	2.5	-0.04
31e	No	0.59	0.34	-43	1.9E+02	17	-0.1
31n	No	0.57	0.34	-43	1.9E+02	17	-0.1
32e	No	0.53	0.31	-43	1.9E+02	3.1	0.04
32n	No	0.43	0.31	-43	1.9E+02	3.6	0.83
33e	No	0.57	0.39	-43	1.9E+02	17	-0.049
33n	No	0.36	0.39	-43	1.9E+02	16	-0.061
36e	No	0.55	0.33	-43	1.9E+02	25	-0.38
36n	No	0.53	0.33	-43	1.9E+02	20	-0.42
37e	No	0.57	0.35	-43	1.9E+02	12	-0.018
37n	No	0.56	0.35	-43	1.9E+02	25	-0.13
38e	No	0.57	0.34	-43	1.9E+02	22	-0.04
38n	No	0.56	0.34	-43	1.9E+02	32	-0.12
40e	No	0.58	0.35	-43	1.9E+02	13	-0.049
40n	No	0.53	0.35	-43	1.9E+02	3.4	-0.023
41e	No	0.59	0.34	-43	1.9E+02	19	-0.14
41n	No	0.58	0.34	-43	1.9E+02	29	-0.16
42e	No	0.59	0.36	-43	1.9E+02	11	-0.062
42n	No	0.51	0.36	-43	1.9E+02	1.7	-0.023
43e	No	0.59	0.34	-43	1.9E+02	20	-0.086
43n	No	0.57	0.34	-43	1.9E+02	17	-0.039
44e	No	0.04	0.005	-43	1.9E+02	0.62	0.3
44n	No	0.031	0.005	-43	1.9E+02	0.55	0.36
45e	No	0.58	0.33	-43	1.9E+02	19	-0.086
45n	No	0.56	0.33	-43	1.9E+02	20	-0.076
46e	No	0.56	0.34	-43	1.9E+02	17	1.2
46n	No	0.57	0.34	-43	1.9E+02	18	-0.14
50e	No	0.58	0.36	-43	1.9E+02	17	-0.057
50n	No	0.56	0.36	-43	1.9E+02	18	-0.16
51e	No	0.58	0.35	-43	1.9E+02	18	-0.032
51n	No	0.57	0.35	-43	1.9E+02	17	-0.16
52e	No	0.58	0.34	-43	1.9E+02	21	-0.33
52n	No	0.57	0.34	-43	1.9E+02	18	-0.34
53e	No	0.59	0.34	-43	1.9E+02	15	-0.12
53n	No	0.58	0.34	-43	1.9E+02	22	-0.24
54e	No	0.58	0.33	-43	1.9E+02	16	-0.0098
54n	No	0.58	0.33	-43	1.9E+02	19	-0.075
55e	No	0.58	0.33	-43	1.9E+02	15	-0.044
55n	No	0.57	0.33	-43	1.9E+02	14	-0.13
56e	No	0.6	0.34	-43	1.9E+02	24	-0.1
56n	No	0.58	0.34	-43	1.9E+02	23	-0.088
57e	No	0.59	0.45	-43	1.9E+02	10	-0.074
57n	No	0.043	0.45	-43	1.9E+02	0.55	0.4
58e	No	0.6	0.34	-43	1.9E+02	15	0.022
58n	No	0.58	0.34	-43	1.9E+02	16	-0.031
59e	No	0.59	0.33	-43	1.9E+02	26	-0.049
59n	No	0.58	0.33	-43	1.9E+02	18	-0.034
60e	No	0.59	0.34	-43	1.9E+02	14	0.024
60n	No	0.56	0.34	-43	1.9E+02	5.8	0.012
65e	No	0.58	0.36	-43	1.9E+02	19	-0.08
65n	No	0.57	0.36	-43	1.9E+02	18	-0.13
66e	No	0.59	0.36	-43	1.9E+02	20	-0.1
66n	No	0.58	0.36	-43	1.9E+02	23	-0.14
67e	No	0.6	0.35	-43	1.9E+02	21	-0.094
67n	No	0.58	0.35	-43	1.9E+02	27	-0.11
68e	No	0.6	0.34	-43	1.9E+02	18	-0.093
68n	No	0.59	0.34	-43	1.9E+02	17	-0.17
69e	No	0.59	0.33	-43	1.9E+02	18	-0.054
69n	No	0.58	0.33	-43	1.9E+02	21	-0.033
70e	No	0.6	0.34	-43	1.9E+02	16	-0.056
70n	No	0.57	0.34	-43	1.9E+02	23	-0.011
71e	No	0.59	0.33	-43	1.9E+02	14	-0.086
71n	No	0.58	0.33	-43	1.9E+02	9.4	-0.11
72e	No	0.6	0.34	-43	1.9E+02	18	0.068
72n	No	0.58	0.34	-43	1.9E+02	11	-0.15
73e	No	0.59	0.33	-43	1.9E+02	19	0.027
73n	No	0.58	0.33	-43	1.9E+02	15	-0.065
74e	No	0.59	0.33	-43	1.9E+02	13	-0.052
74n	No	0.59	0.33	-43	1.9E+02	13	-0.12
75e	No	0.24	-0.17	-43	1.9E+02	2.8	0.059
75n	No	0.17	-0.17	-43	1.9E+02	0.84	0.19
76e	No	0.033	0.0017	-43	1.9E+02	2.9	0.34
76n	No	0.032	0.0017	-43	1.9E+02	2.6	0.35
79e	No	0.55	0.33	-43	1.9E+02	18	0.06
79n	No	0.55	0.33	-43	1.9E+02	26	-0.035
80e	No	0.5	0.29	-43	1.9E+02	12	0.13
80n	No	0.5	0.29	-43	1.9E+02	13	0.23
81e	No	0.51	0.36	-43	1.9E+02	0.68	-0.37
81n	No	0.56	0.36	-43	1.9E+02	2.9	-0.51
82e	No	0.58	0.34	-43	1.9E+02	15	0.088
82n	No	0.56	0.34	-43	1.9E+02	14	0.011
83e	No	0.57	0.33	-43	1.9E+02	5.7	0.0041
83n	No	0.55	0.33	-43	1.9E+02	17	0.22
84e	No	0.59	0.33	-43	1.9E+02	17	0.0036
84n	No	0.58	0.33	-43	1.9E+02	18	-0.039
85e	No	0.6	0.34	-43	1.9E+02	18	-0.15
85n	No	0.59	0.34	-43	1.9E+02	20	-0.18
86e	No	0.27	-0.3	-43	1.9E+02	24	-0.03
86n	No	0.27	-0.3	-43	1.9E+02	29	-0.17
87e	No	0.61	0.34	-43	1.9E+02	22	-0.1
87n	No	0.59	0.34	-43	1.9E+02	22	-0.16
88e	Yes			-43	1.5E+03	0	0
88n	Yes			-43	1.5E+03	0	0
89e	No	0.045	0.0028	-43	1.9E+02	0.92	0.32
89n	No	0.043	0.0028	-43	1.9E+02	0.87	0.35
90e	Yes			-43	1.5E+03	0	0
90n	Yes			-43	1.5E+03	0	0
91e	No	0.6	0.34	-43	1.9E+02	18	-0.11
91n	No	0.58	0.34	-43	1.9E+02	12	-0.11
92e	No	0.59	0.34	-43	1.9E+02	14	-0.022
92n	No	0.57	0.34	-43	1.9E+02	15	-0.066
93e	No	0.54	0.35	-43	1.9E+02	2.6	0.025
93n	No	0.58	0.35	-43	1.9E+02	16	-0.1
94e	No	0.57	0.32	-43	1.9E+02	25	-0.057
94n	No	0.56	0.32	-43	1.9E+02	30	-0.1
95e	No	0.55	0.33	-43	1.9E+02	18	0.097
95n	No	0.56	0.33	-43	1.9E+02	27	-0.046
96e	No	0.54	0.32	-43	1.9E+02	15	0.086
96n	No	0.54	0.32	-43	1.9E+02	15	0.022
97e	No	0.54	0.34	-43	1.9E+02	17	-0.018
97n	No	0.51	0.34	-43	1.9E+02	10	0.11
98e	No	0.57	0.34	-43	1.9E+02	13	-0.064
98n	No	0.56	0.34	-43	1.9E+02	12	-0.35
99e	No	0.16	0.4	-43	1.9E+02	1	0.39
99n	No	0.56	0.4	-43	1.9E+02	60	-0.18
100e	No	0.6	0.34	-43	1.9E+02	22	-0.043
100n	No	0.59	0.34	-43	1.9E+02	20	-0.049
101e	No	0.6	0.34	-43	1.9E+02	18	-0.13
101n	No	0.59	0.34	-43	1.9E+02	15	-0.17
102e	No	0.61	0.34	-43	1.9E+02	21	-0.092
102n	No	0.59	0.34	-43	1.9E+02	22	-0.038
103e	No	0.57	0.33	-43	1.9E+02	4.5	0.038
103n	No	0.59	0.33	-43	1.9E+02	21	-0.073
104e	No	0.6	0.45	-43	1.9E+02	16	0.016
104n	No	0.025	0.45	-43	1.9E+02	0.044	0.13
105e	No	0.6	0.33	-43	1.9E+02	14	-0.074
105n	No	0.59	0.33	-43	1.9E+02	16	-0.15
106e	No	0.6	0.33	-43	1.9E+02	19	-0.17
106n	No	0.59	0.33	-43	1.9E+02	15	-0.28
107e	Yes			-43	1.5E+03	0	0
107n	Yes			-43	1.5E+03	0	0
108e	No	0.6	0.34	-43	1.9E+02	16	0.04
108n	No	0.58	0.34	-43	1.9E+02	13	0.036
109e	No	0.59	0.33	-43	1.9E+02	15	-0.011
109n	No	0.58	0.33	-43	1.9E+02	16	-0.063
110e	No	0.59	0.33	-43	1.9E+02	14	0.035
110n	No	0.58	0.33	-43	1.9E+02	17	-0.032
111e	No	0.58	0.33	-43	1.9E+02	9.9	-0.054
111n	No	0.58	0.33	-43	1.9E+02	17	-0.081
112e	No	0.6	0.35	-43	1.9E+02	24	-0.072
112n	No	0.58	0.35	-43	1.9E+02	16	-0.15
113e	No	0.56	0.33	-43	1.9E+02	22	0.02
113n	No	0.56	0.33	-43	1.9E+02	21	0.024
114e	No	0.024	0.0016	-43	1.9E+02	0.28	-0.28
114n	No	0.027	0.0016	-43	1.9E+02	0.4	-0.26
115e	No	0.53	0.33	-43	1.9E+02	20	-0.033
115n	No	0.52	0.33	-43	1.9E+02	13	0.038
116e	No	0.55	0.33	-43	1.9E+02	11	0.031
116n	No	0.55	0.33	-43	1.9E+02	14	-0.022
117e	No	0.58	0.34	-43	1.9E+02	16	0.048
117n	No	0.58	0.34	-43	1.9E+02	17	-0.077
118e	No	0.59	0.34	-43	1.9E+02	21	-0.03
118n	No	0.58	0.34	-43	1.9E+02	41	-0.14
119e	No	0.6	0.34	-43	1.9E+02	26	-0.14
119n	No	0.59	0.34	-43	1.9E+02	26	-0.12
120e	No	0.61	0.34	-43	1.9E+02	28	-0.16
120n	No	0.58	0.34	-43	1.9E+02	48	-0.16
121e	No	0.6	0.33	-43	1.9E+02	16	-0.028
121n	No	0.6	0.33	-43	1.9E+02	17	-0.19
122e	No	0.6	0.33	-43	1.9E+02	18	-0.074
122n	No	0.6	0.33	-43	1.9E+02	16	-0.13
123e	No	0.61	0.33	-43	1.9E+02	16	-0.15
123n	No	0.6	0.33	-43	1.9E+02	17	-0.19
124e	No	0.61	0.33	-43	1.9E+02	14	-0.075
124n	No	0.59	0.33	-43	1.9E+02	16	-0.023
125e	No	0.6	0.34	-43	1.9E+02	18	-0.12
125n	No	0.58	0.34	-43	1.9E+02	16	-0.12
126e	No	0.6	0.33	-43	1.9E+02	19	-0.13
126n	No	0.59	0.33	-43	1.9E+02	16	-0.21
127e	No	0.59	0.33	-43	1.9E+02	13	-0.058
127n	No	0.58	0.33	-43	1.9E+02	13	-0.094
128e	No	0.61	0.34	-43	1.9E+02	21	-0.08
128n	No	0.58	0.34	-43	1.9E+02	9.4	-0.0049
129e	No	0.6	0.34	-43	1.9E+02	18	-0.051
129n	No	0.59	0.34	-43	1.9E+02	17	-0.12
130e	No	0.59	0.34	-43	1.9E+02	23	-0.083
130n	No	0.58	0.34	-43	1.9E+02	17	-0.038
131e	No	0.56	0.33	-43	1.9E+02	14	0.043
131n	No	0.55	0.33	-43	1.9E+02	13	0.039
132e	No	0.56	0.33	-43	1.9E+02	21	-0.011
132n	No	0.55	0.33	-43	1.9E+02	17	-0.0037
133e	No	0.55	0.33	-43	1.9E+02	18	-0.017
133n	No	0.54	0.33	-43	1.9E+02	18	-0.02
134e	No	0.54	0.34	-43	1.9E+02	30	-0.087
134n	No	0.53	0.34	-43	1.9E+02	18	0.031
135e	No	0.047	0.4	-43	1.9E+02	6.9	2.1
135n	No	0.56	0.4	-43	1.9E+02	17	-0.079
136e	No	0.58	0.35	-43	1.9E+02	19	-0.12
136n	No	0.56	0.35	-43	1.9E+02	16	0.15
137e	No	0.57	0.33	-43	1.9E+02	16	-0.01
137n	No	0.57	0.33	-43	1.9E+02	32	-0.12
138e	No	0.59	0.33	-43	1.9E+02	20	-0.086
138n	No	0.58	0.33	-43	1.9E+02	17	-0.057
139e	No	0.52	0.29	-43	4.8E+02	32	0.44
139n	No	0.52	0.29	-43	4.8E+02	26	0.43
140e	No	0.6	0.33	-43	1.9E+02	17	-0.1
140n	No	0.58	0.33	-43	1.9E+02	18	0.21
141e	No	0.61	0.33	-43	1.9E+02	17	-0.088
141n	No	0.6	0.33	-43	1.9E+02	18	-0.12
142e	No	0.6	0.34	-43	1.9E+02	19	0.008
142n	No	0.56	0.34	-43	1.9E+02	13	1.4
143e	No	0.61	0.34	-43	1.9E+02	24	-0.077
143n	No	0.6	0.34	-43	1.9E+02	27	-0.098
144e	No	0.61	0.34	-43	1.9E+02	16	-0.09
144n	No	0.6	0.34	-43	1.9E+02	23	-0.13
145e	No	0.62	0.34	-43	1.9E+02	17	-0.13
145n	No	0.6	0.34	-43	1.9E+02	23	-0.098
146e	No	0.51	0.2	-43	1.9E+02	35	0.46
146n	No	0.55	0.2	-43	1.9E+02	19	-0.22
147e	No	0.6	0.34	-43	1.9E+02	21	-0.06
147n	No	0.6	0.34	-43	1.9E+02	18	-0.098
148e	No	0.58	0.32	-43	1.9E+02	21	0.026
148n	No	0.58	0.32	-43	1.9E+02	18	-0.081
149e	No	0.6	0.34	-43	1.9E+02	18	-0.036
149n	No	0.59	0.34	-43	1.9E+02	18	-0.099
150e	No	0.6	0.35	-43	1.9E+02	22	-0.12
150n	No	0.59	0.35	-43	1.9E+02	17	-0.093
151e	Yes			-43	1.5E+03	0	0
151n	Yes			-43	1.5E+03	0	0
152e	No	0.54	0.31	-43	1.9E+02	17	0.02
152n	No	0.54	0.31	-43	1.9E+02	18	-0.025
153e	No	0.54	0.32	-43	1.9E+02	17	0.0068
153n	No	0.54	0.32	-43	1.9E+02	18	0.054
154e	No	0.52	0.33	-43	1.9E+02	18	0.0037
154n	No	0.53	0.33	-43	1.9E+02	18	-0.0039
155e	No	0.56	0.35	-43	1.9E+02	17	-0.06
155n	No	0.56	0.35	-43	1.9E+02	19	-0.092
156e	No	0.31	0.11	-43	1.9E+02	18	-0.2
156n	No	0.3	0.11	-43	1.9E+02	15	-0.22
157e	No	0.57	0.33	-43	1.9E+02	16	-0.1
157n	No	0.57	0.33	-43	1.9E+02	17	-0.077
158e	No	0.59	0.34	-43	1.9E+02	15	0.025
158n	No	0.59	0.34	-43	1.9E+02	17	-0.043
159e	No	0.53	0.31	-43	1.9E+02	16	0.12
159n	No	0.54	0.31	-43	1.9E+02	19	-0.0057
160e	No	0.6	0.33	-43	1.9E+02	17	-0.11
160n	No	0.59	0.33	-43	1.9E+02	17	-0.079
161e	No	0.6	0.32	-43	1.9E+02	19	0.043
161n	No	0.44	0.32	-43	1.9E+02	11	0.87
162e	No	0.6	0.33	-43	1.9E+02	18	0.012
162n	No	0.59	0.33	-43	1.9E+02	10	-0.023
163e	No	0.61	0.34	-43	1.9E+02	16	-0.098
163n	No	0.6	0.34	-43	1.9E+02	17	-0.18
164e	No	0.61	0.34	-43	1.9E+02	12	-0.021
164n	No	0.6	0.34	-43	1.9E+02	12	-0.12
165e	No	0.6	0.34	-43	1.9E+02	13	-0.14
165n	No	0.58	0.34	-43	1.9E+02	8.9	-0.069
166e	No	0.58	0.32	-43	1.9E+02	24	0.023
166n	No	0.59	0.32	-43	1.9E+02	31	-0.16
167e	No	0.61	0.34	-43	1.9E+02	16	-0.064
167n	No	0.6	0.34	-43	1.9E+02	42	-0.13
168e	No	0.6	0.34	-43	1.9E+02	23	-0.068
168n	No	0.59	0.34	-43	1.9E+02	19	-0.079
169e	No	0.6	0.33	-43	1.9E+02	12	-0.05
169n	No	0.59	0.33	-43	1.9E+02	15	-0.099
170e	No	0.045	0.36	-43	1.9E+02	0.58	0.34
170n	No	0.53	0.36	-43	1.9E+02	30	-0.066
171e	Yes			-43	1.5E+03	0	0
171n	Yes			-43	1.5E+03	0	0
172e	Yes			-43	1.5E+03	0	0
172n	No	1		-43	1.5E+03	0	0
173e	No	0.54	0.32	-43	1.9E+02	17	0.029
173n	No	0.54	0.32	-43	1.9E+02	18	-0.018
174e	No	0.53	0.32	-43	1.9E+02	20	0.011
174n	No	0.54	0.32	-43	1.9E+02	31	-0.11
175e	No	0.5	0.33	-43	1.9E+02	16	0.068
175n	No	0.52	0.33	-43	1.9E+02	25	-0.044
176e	No	0.56	0.34	-43	1.9E+02	49	-0.17
176n	No	0.56	0.34	-43	1.9E+02	18	-0.14
177e	No	0.58	0.34	-43	1.9E+02	12	-0.096
177n	No	0.58	0.34	-43	1.9E+02	16	-0.12
178e	No	0.57	0.33	-43	1.9E+02	20	-0.025
178n	No	0.58	0.33	-43	1.9E+02	24	-0.15
179e	No	0.59	0.34	-43	1.9E+02	17	0.0098
179n	No	0.59	0.34	-43	1.9E+02	18	-0.04
180e	No	0.6	0.33	-43	1.9E+02	18	0.0016
180n	No	0.44	0.33	-43	1.9E+02	13	0.77
181e	No	0.6	0.33	-43	1.9E+02	20	-0.081
181n	No	0.58	0.33	-43	1.9E+02	19	-0.0057
182e	No	0.56	0.32	-43	3.8E+02	10	0.048
182n	No	0.57	0.32	-43	3.8E+02	15	-0.11
183e	No	0.53	0.3	-43	1.9E+02	26	-0.11
183n	No	0.53	0.3	-43	1.9E+02	35	-0.16
184e	No	0.59	0.33	-43	1.9E+02	9.4	0.16
184n	No	0.6	0.33	-43	1.9E+02	17	-0.03
185e	No	0.6	0.33	-43	1.9E+02	12	0.078
185n	No	0.6	0.33	-43	1.9E+02	14	-0.022
186e	No	0.59	0.33	-43	1.9E+02	31	-0.1
186n	No	0.58	0.33	-43	1.9E+02	22	-0.077
187e	No	0.6	0.34	-43	1.9E+02	22	-0.058
187n	No	0.58	0.34	-43	1.9E+02	6.1	-0.0095
188e	No	0.59	0.34	-43	1.9E+02	19	-0.042
188n	No	0.59	0.34	-43	1.9E+02	36	-0.11
189e	No	0.58	0.33	-43	1.9E+02	18	-0.035
189n	No	0.58	0.33	-43	1.9E+02	20	-0.12
190e	No	0.6	0.34	-43	1.9E+02	18	-0.009
190n	No	0.59	0.34	-43	1.9E+02	17	-0.035
191e	No	0.6	0.35	-43	1.9E+02	20	-0.07
191n	No	0.59	0.35	-43	1.9E+02	30	-0.01
192e	No	0.57	0.33	-43	3.2E+02	21	0.0014
192n	No	0.56	0.33	-43	3.2E+02	26	-0.011
193e	No	0.55	0.32	-43	3.8E+02	17	0.09
193n	No	0.54	0.32	-43	3.8E+02	15	0.012
194e	No	0.53	0.31	-43	1.9E+02	33	-0.095
194n	No	0.53	0.31	-43	1.9E+02	27	-0.1
195e	No	0.54	0.33	-43	1.9E+02	23	-0.041
195n	No	0.53	0.33	-43	1.9E+02	24	-0.025
196e	No	0.039	0.4	-43	1.9E+02	3	0.3
196n	No	0.54	0.4	-43	1.9E+02	20	-0.05
197e	No	0.54	0.31	-43	1.9E+02	16	0.088
197n	No	0.54	0.31	-43	1.9E+02	19	-0.049
198e	No	0.57	0.33	-43	1.9E+02	28	-0.081
198n	No	0.57	0.33	-43	1.9E+02	33	-0.14
200e	No	0.045	0.44	-43	1.9E+02	2.8	0.36
200n	No	0.57	0.44	-43	1.9E+02	26	-0.064
201e	No	0.56	0.33	-43	1.9E+02	53	0.00074
201n	No	0.58	0.33	-43	1.9E+02	43	-0.14
202e	No	0.6	0.34	-43	1.9E+02	33	-0.045
202n	No	0.58	0.34	-43	1.9E+02	19	0.023
203e	No	0.58	0.32	-43	1.9E+02	21	-0.042
203n	No	0.57	0.32	-43	1.9E+02	17	-0.12
204e	No	0.6	0.33	-43	1.9E+02	15	-0.31
204n	No	0.57	0.33	-43	1.9E+02	17	-0.25
205e	No	0.58	0.32	-43	1.9E+02	23	-0.049
205n	No	0.58	0.32	-43	1.9E+02	22	-0.086
206e	No	0.59	0.34	-43	1.9E+02	32	-0.064
206n	No	0.58	0.34	-43	1.9E+02	21	-0.061
207e	No	0.58	0.43	-43	1.9E+02	24	0.00033
207n	No	0.044	0.43	-43	1.9E+02	2.7	0.39
208e	No	0.57	0.33	-43	1.9E+02	31	-0.09
208n	No	0.56	0.33	-43	1.9E+02	42	-0.055
209e	No	0.56	0.32	-43	1.9E+02	26	-0.042
209n	No	0.4	0.32	-43	1.9E+02	20	0.66
210e	No	0.59	0.34	-43	1.9E+02	22	-0.37
210n	No	0.58	0.34	-43	1.9E+02	14	-0.33
211e	No	0.57	0.34	-43	1.9E+02	28	-0.028
211n	No	0.56	0.34	-43	1.9E+02	21	-0.032
212e	No	0.55	0.33	-43	1.9E+02	25	-0.016
212n	No	0.51	0.33	-43	1.9E+02	12	0.029
213e	No	0.52	0.33	-43	1.9E+02	17	0.083
213n	No	0.54	0.33	-43	1.9E+02	19	-0.043
214e	No	0.55	0.35	-43	1.9E+02	21	-0.0052
214n	No	0.54	0.35	-43	1.9E+02	19	0.0045
215e	No	0.56	0.34	-43	1.9E+02	36	-0.089
215n	No	0.53	0.34	-43	1.9E+02	16	0.13
216e	No	0.56	0.33	-43	1.9E+02	20	0.017
216n	No	0.53	0.33	-43	1.9E+02	13	0.085
217e	No	0.57	0.33	-43	1.9E+02	27	0.018
217n	No	0.55	0.33	-43	1.9E+02	18	0.053
218e	No	0.56	0.41	-43	1.9E+02	28	-0.055
218n	No	0.19	0.41	-43	1.9E+02	0.63	0.13
219e	No	0.57	0.33	-43	1.9E+02	22	-0.064
219n	No	0.56	0.33	-43	1.9E+02	18	-0.029
220e	No	0.57	0.32	-43	1.9E+02	20	0.03
220n	No	0.57	0.32	-43	1.9E+02	18	-0.041
221e	No	0.57	0.32	-43	1.9E+02	17	0.079
221n	No	0.57	0.32	-43	1.9E+02	17	0.03
222e	No	0.57	0.33	-43	1.9E+02	17	0.084
222n	No	0.58	0.33	-43	1.9E+02	27	-0.059
223e	No	0.56	0.31	-43	1.9E+02	17	-0.013
223n	No	0.56	0.31	-43	1.9E+02	18	-0.064
224e	No	0.56	0.32	-43	1.9E+02	22	0.12
224n	No	0.57	0.32	-43	1.9E+02	22	-0.035
225e	No	0.58	0.33	-43	1.9E+02	24	-0.0084
225n	No	0.57	0.33	-43	1.9E+02	21	-0.049
226e	No	0.58	0.33	-43	1.9E+02	24	-0.084
226n	No	0.53	0.33	-43	1.9E+02	32	0.23
227e	No	0.56	0.32	-43	1.9E+02	19	0.021
227n	No	0.55	0.32	-43	1.9E+02	14	0.019
228e	No	0.55	0.31	-43	1.9E+02	19	0.053
228n	No	0.55	0.31	-43	1.9E+02	18	0.0069
229e	No	0.55	0.33	-43	1.9E+02	17	0.049
229n	No	0.55	0.33	-43	1.9E+02	17	-0.047
231e	No	0.54	0.33	-43	1.9E+02	38	-0.06
231n	No	0.55	0.33	-43	1.9E+02	30	-0.15
232e	No	0.54	0.34	-43	1.9E+02	48	-0.14
232n	No	0.52	0.34	-43	1.9E+02	15	0.0028
233e	No	0.54	0.32	-43	1.9E+02	19	-0.034
233n	No	0.44	0.32	-43	1.9E+02	29	0.56
234e	No	0.55	0.33	-43	1.9E+02	28	-0.00082
234n	No	0.51	0.33	-43	1.9E+02	11	0.089
237e	No	0.55	0.31	-43	1.9E+02	18	0.039
237n	No	0.56	0.31	-43	1.9E+02	20	0.004
238e	No	0.2	0.4	-43	1.9E+02	3.1	0.34
238n	No	0.57	0.4	-43	1.9E+02	18	0.017
239e	No	0.58	0.33	-43	1.9E+02	20	-0.021
239n	No	0.57	0.33	-43	1.9E+02	25	-0.069
240e	No	0.54	0.32	-43	1.9E+02	12	0.11
240n	No	0.56	0.32	-43	1.9E+02	19	0.026
241e	No	0.57	0.33	-43	1.9E+02	19	-0.031
241n	No	0.56	0.33	-43	1.9E+02	17	0.023
242e	No	0.57	0.34	-43	1.9E+02	25	-0.049
242n	No	0.51	0.34	-43	1.9E+02	8.6	0.066
243e	No	0.57	0.34	-43	1.9E+02	35	-0.035
243n	No	0.56	0.34	-43	1.9E+02	18	-0.039
244e	No	0.56	0.33	-43	1.9E+02	17	-0.041
244n	No	0.56	0.33	-43	1.9E+02	17	0.012
245e	No	0.57	0.34	-43	1.9E+02	28	-0.027
245n	No	0.53	0.34	-43	1.9E+02	20	0.29
246e	No	0.56	0.33	-43	1.9E+02	18	0.072
246n	No	0.55	0.33	-43	1.9E+02	26	-0.00044
250e	No	0.54	0.32	-43	1.9E+02	22	0.064
250n	No	0.53	0.32	-43	1.9E+02	20	-0.012
251e	No	0.067	0.099	-43	2.9E+02	5	0.46
251n	No	0.22	0.099	-43	2.9E+02	23	-0.031
252e	No	0.55	0.33	-43	1.9E+02	17	0.028
252n	No	0.54	0.33	-43	1.9E+02	18	-0.042
253e	No	0.54	0.32	-43	1.9E+02	16	0.042
253n	No	0.52	0.32	-43	1.9E+02	11	0.08
254e	No	0.57	0.33	-43	1.9E+02	34	-0.051
254n	No	0.57	0.33	-43	1.9E+02	26	0.015
255e	No	0.54	0.32	-43	1.9E+02	13	0.13
255n	No	0.56	0.32	-43	1.9E+02	20	0.0064
256e	No	0.54	0.31	-43	1.9E+02	24	0.17
256n	No	0.53	0.31	-43	1.9E+02	11	0.053
257e	No	0.57	0.33	-43	1.9E+02	38	-0.045
257n	No	0.57	0.33	-43	1.9E+02	27	-0.13
261e	No	0.54	0.32	-43	1.9E+02	11	0.051
261n	No	0.5	0.32	-43	1.9E+02	9.2	0.18
262e	No	0.58	0.34	-43	1.9E+02	13	-0.28
262n	No	0.56	0.34	-43	1.9E+02	19	-0.33
266e	No	0.56	0.34	-43	1.9E+02	10	-0.32
266n	No	0.56	0.34	-43	1.9E+02	14	-0.47
267e	No	0.55	0.33	-43	1.9E+02	18	-0.064
267n	No	0.54	0.33	-43	1.9E+02	15	-0.074
268e	No	0.52	0.34	-43	1.9E+02	10	0.084
268n	No	0.55	0.34	-43	1.9E+02	20	-0.036
269e	No	0.55	0.33	-43	1.9E+02	21	-0.033
269n	No	0.55	0.33	-43	1.9E+02	21	-0.051
270e	No	0.56	0.33	-43	1.9E+02	25	-0.022
270n	No	0.56	0.33	-43	1.9E+02	30	-0.055
271e	No	0.043	0.46	-43	1.9E+02	3	0.35
271n	No	0.55	0.46	-43	1.9E+02	19	-0.055
272e	No	0.53	0.31	-43	1.9E+02	18	0.17
272n	No	0.54	0.31	-43	1.9E+02	26	-0.024
273e	No	0.27	0.19	-43	1.9E+02	75	-0.031
273n	No	0.048	0.19	-43	1.9E+02	2.5	0.38
277e	No	0.43	0.34	-43	1.9E+02	14	0.65
277n	No	0.56	0.34	-43	1.9E+02	25	-0.035
278e	No	0.28	0.34	-43	1.9E+02	4.2	0.32
278n	No	0.48	0.34	-43	1.9E+02	7.6	0.12
281e	No	0.53	0.32	-43	1.9E+02	18	0.13
281n	No	0.53	0.32	-43	1.9E+02	16	-0.016
282e	No	0.55	0.33	-43	1.9E+02	18	0.011
282n	No	0.54	0.33	-43	1.9E+02	34	-0.053
283e	No	0.56	0.34	-43	1.9E+02	22	-0.076
283n	No	0.54	0.34	-43	1.9E+02	18	-0.055
284e	No	0.56	0.34	-43	1.9E+02	30	-0.029
284n	No	0.56	0.34	-43	1.9E+02	34	-0.11
285e	No	0.048	0.0033	-43	1.9E+02	2.9	0.37
285n	No	0.052	0.0033	-43	1.9E+02	2.6	0.41
286e	No	0.23	-0.31	-43	1.9E+02	32	-0.041
286n	No	0.22	-0.31	-43	1.9E+02	77	-0.2
287e	No	0.56	0.31	-43	1.9E+02	40	-0.084
287n	No	0.24	0.31	-43	1.9E+02	28	-0.17
290e	No	0.5	0.29	-43	1.9E+02	74	-0.16
290n	No	0.5	0.29	-43	47	73	-0.18
291e	No	0.53	0.44	-43	1.9E+02	70	-0.18
291n	No	0.063	0.44	-43	1.9E+02	0.67	-0.24
292e	No	0.54	0.35	-43	1.9E+02	17	0.13
292n	No	0.56	0.35	-43	1.9E+02	36	-0.089
293e	No	0.42	0.33	-43	1.9E+02	22	0.66
293n	No	0.54	0.33	-43	1.9E+02	16	-0.022
294e	No	0.47	0.34	-43	1.9E+02	22	0.39
294n	No	0.54	0.34	-43	1.9E+02	22	-0.1
295e	No	0.55	0.44	-43	2.9E+02	4.8	-0.41
295n	No	0.04	0.44	-43	2.9E+02	0.72	-0.15
299e	No	0.54	0.34	-43	1.9E+02	24	0.013
299n	No	0.53	0.34	-43	1.9E+02	16	-0.027
300e	No	0.55	0.34	-43	1.9E+02	26	-0.1
300n	No	0.42	0.34	-43	1.9E+02	21	0.74
301e	No	0.55	0.35	-43	1.9E+02	31	-0.078
301n	No	0.51	0.35	-43	1.9E+02	13	-0.0092
302e	No	0.41	0.38	-43	1.9E+02	5	0.21
302n	No	0.54	0.38	-43	1.9E+02	21	-0.038
306e	No	0.52	0.32	-43	1.9E+02	13	0.019
306n	No	0.42	0.32	-43	1.9E+02	17	0.67
307e	No	0.4	0.33	-43	1.9E+02	16	0.69
307n	No	0.52	0.33	-43	1.9E+02	18	-0.078
311e	No	0.52	0.36	-43	1.9E+02	16	0.043
311n	No	0.26	0.36	-43	1.9E+02	4	0.57
312e	No	0.21	-0.28	-43	1.9E+02	23	0.027
312n	No	0.19	-0.28	-43	1.9E+02	7.6	0.089
313e	No	0.39	0.34	-43	1.9E+02	9.4	0.69
313n	No	0.55	0.34	-43	1.9E+02	41	-0.12
314e	No	0.55	0.35	-43	1.9E+02	39	-0.071
314n	No	0.54	0.35	-43	1.9E+02	33	-0.067
315e	No	0.54	0.34	-43	1.9E+02	20	-0.042
315n	No	0.51	0.34	-43	1.9E+02	16	0.06
316e	No	0.53	0.35	-43	1.9E+02	14	0.039
316n	No	0.54	0.35	-43	1.9E+02	23	-0.089
317e	No	0.55	0.36	-43	1.9E+02	30	-0.12
317n	No	0.52	0.36	-43	1.9E+02	14	-0.017
318e	No	0.53	0.36	-43	1.9E+02	64	-0.21
318n	No	0.51	0.36	-43	1.9E+02	78	-0.22
319e	No	0.55	0.36	-43	1.9E+02	22	-0.054
319n	No	0.55	0.36	-43	1.9E+02	28	-0.085
320e	No	0.054	0.0024	-43	1.9E+02	1.5	0.44
320n	No	0.05	0.0024	-43	1.9E+02	1.4	0.36
321e	No	0.42	0.32	-43	1.9E+02	8.2	-0.091
321n	No	0.46	0.32	-43	1.9E+02	12	-0.23
322e	No	0.039	0.0036	-43	1.9E+02	3.1	0.34
322n	No	0.034	0.0036	-43	1.9E+02	2.8	0.38
323e	No	0.041	-0.00024	-43	1.9E+02	2.8	0.39
323n	No	0.038	-0.00024	-43	1.9E+02	2.8	0.39
324e	No	0.46	0.31	-43	1.9E+02	30	-0.073
324n	No	0.46	0.31	-43	1.9E+02	33	-0.13
325e	No	0.49	0.33	-43	1.9E+02	27	-0.06
325n	No	0.49	0.33	-43	1.9E+02	21	-0.057
326e	No	0.043	0.0014	-43	1.9E+02	3.1	0.35
326n	No	0.046	0.0014	-43	1.9E+02	2.9	0.36
327e	No	0.47	0.3	-43	1.9E+02	28	-0.03
327n	No	0.47	0.3	-43	1.9E+02	31	-0.092
328e	No	0.05	0.36	-43	1.9E+02	3.1	0.34
328n	No	0.47	0.36	-43	1.9E+02	22	-0.096
329e	No	0.35	0.33	-43	1.9E+02	13	0.74
329n	No	0.49	0.33	-43	1.9E+02	22	-0.16
331e	No	0.36	0.22	-43	1.9E+02	23	0.73
331n	No	0.39	0.22	-43	1.9E+02	18	0.72
332e	No	0.47	0.33	-43	1.9E+02	28	-0.036
332n	No	0.46	0.33	-43	1.9E+02	14	-0.0055
333e	No	0.41	0.31	-43	1.9E+02	8.5	-0.0077
333n	No	0.45	0.31	-43	1.9E+02	13	-0.15
336e	No	0.15	-0.27	-43	1.9E+02	50	-0.12
336n	No	0.15	-0.27	-43	1.9E+02	22	-0.035
339e	No	0.74		-43	1.5E+03	0	0
339n	Yes			-43	1.5E+03	0	0
340e	No	0.47	0.32	-43	1.9E+02	26	-0.21
340n	No	0.47	0.32	-43	1.9E+02	19	-0.23
342e	No	0.02	0.0049	-43	1.9E+02	0.071	-0.31
342n	No	0.026	0.0049	-43	1.9E+02	0.36	-0.28
343e	No	0.053	0.4	-43	1.9E+02	3	0.37
343n	No	0.49	0.4	-43	1.9E+02	71	-0.18
344e	No	0.036	0.002	-43	1.9E+02	2.8	0.37
344n	No	0.038	0.002	-43	1.9E+02	2.5	0.38
345e	No	0.35	2.8E-05	-43	1.5E+03	0	0
345n	No	1	2.8E-05	-43	1.5E+03	0	0
346e	No	0.31	0.22	-43	1.9E+02	4.8	0.24
346n	No	0.15	0.22	-43	1.9E+02	2.7	0.34
347e	No	0.034	-0.00013	-43	1.9E+02	2.9	0.33
347n	No	0.033	-0.00013	-43	1.9E+02	2.5	0.36
348e	No	0.041	0.095	-43	1.9E+02	3.1	0.4
348n	No	0.15	0.095	-43	1.9E+02	2.9	0.36
349e	No	0.46	0.33	-43	1.9E+02	57	-0.18
349n	No	0.45	0.33	-43	1.9E+02	73	-0.22

# Save antenna classification table as a csv
if SAVE_RESULTS:
    for ind, col in zip(np.arange(len(df.columns), 0, -1), df_classes.columns[::-1]):
        df.insert(int(ind), col + ' Class', df_classes[col])
    df.to_csv(ANTCLASS_FILE)    

print('Final Ant-Pol Classification:\n\n', overall_class)

Final Ant-Pol Classification:

 Jee:
----------
bad (290 antpols):
3, 4, 5, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 231, 232, 233, 234, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 250, 251, 252, 253, 254, 255, 256, 257, 261, 262, 266, 267, 268, 269, 270, 271, 272, 273, 277, 278, 281, 282, 283, 284, 285, 286, 287, 290, 291, 292, 293, 294, 295, 299, 300, 301, 302, 306, 307, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 331, 332, 333, 336, 339, 340, 342, 343, 344, 345, 346, 347, 348, 349


Jnn:
----------
bad (290 antpols):
3, 4, 5, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 231, 232, 233, 234, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 250, 251, 252, 253, 254, 255, 256, 257, 261, 262, 266, 267, 268, 269, 270, 271, 272, 273, 277, 278, 281, 282, 283, 284, 285, 286, 287, 290, 291, 292, 293, 294, 295, 299, 300, 301, 302, 306, 307, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 331, 332, 333, 336, 339, 340, 342, 343, 344, 345, 346, 347, 348, 349

Save calibration solutions

if not all_flagged():
    # update flags in omnical gains and visibility solutions
    for ant in omni_flags:
        omni_flags[ant] |= rfi_flags
    for bl in vissol_flags:
        vissol_flags[bl] |= rfi_flags

All antennas are flagged, so this cell is being skipped.

if SAVE_RESULTS:
    add_to_history = 'Produced by file_calibration notebook with the following environment:\n' + '=' * 65 + '\n' + os.popen('conda env export').read() + '=' * 65    
    
    if not all_flagged():
        hd_vissol = io.HERAData(SUM_FILE)
        hc_omni = hd_vissol.init_HERACal(gain_convention='divide', cal_style='redundant')
        hc_omni.pol_convention = hd_auto_model.pol_convention
        hc_omni.gain_scale = hd_auto_model.vis_units
        hc_omni.update(gains=sol.gains, flags=omni_flags, quals=meta['chisq_per_ant'], total_qual=meta['chisq'])
        hc_omni.history += add_to_history
        hc_omni.write_calfits(OMNICAL_FILE, clobber=True)
        del hc_omni
        malloc_trim()
        
        if SAVE_OMNIVIS_FILE:
            # output results, harmonizing keys over polarizations
            all_reds = redcal.get_reds(hd.data_antpos, pols=['ee', 'nn', 'en', 'ne'], pol_mode='4pol', bl_error_tol=2.0)
            bl_to_red_map = {bl: red[0] for red in all_reds for bl in red}
            hd_vissol.read(bls=[bl_to_red_map[bl] for bl in sol.vis], return_data=False)
            hd_vissol.empty_arrays()
            hd_vissol.history += add_to_history
            hd_vissol.update(data={bl_to_red_map[bl]: sol.vis[bl] for bl in sol.vis}, 
                             flags={bl_to_red_map[bl]: vissol_flags[bl] for bl in vissol_flags}, 
                             nsamples={bl_to_red_map[bl]: vissol_nsamples[bl] for bl in vissol_nsamples})
            hd_vissol.pol_convention = hd_auto_model.pol_convention
            hd_vissol.vis_units = hd_auto_model.vis_units
            hd_vissol.write_uvh5(OMNIVIS_FILE, clobber=True)
    
        del hd_vissol
        malloc_trim()        

All antennas are flagged, so this cell is being skipped.

Output fully flagged calibration file if OMNICAL_FILE is not written

if SAVE_RESULTS and not os.path.exists(OMNICAL_FILE):
    print(f'WARNING: No calibration file produced at {OMNICAL_FILE}. Creating a fully-flagged placeholder calibration file.')
    hd_writer = io.HERAData(SUM_FILE)
    # create fully flagged unit gains with chi^2 = 0
    hc_omni = hd_writer.init_HERACal(gain_convention='divide', cal_style='redundant')
    hc_omni.history += add_to_history
    hc_omni.pol_convention = hd_auto_model.pol_convention
    hc_omni.gain_scale = hd_auto_model.vis_units
    hc_omni.write_calfits(OMNICAL_FILE, clobber=True)
    del hc_omni

WARNING: No calibration file produced at /mnt/sn1/data2/2461076/zen.2461076.45955.sum.omni.calfits. Creating a fully-flagged placeholder calibration file.

Output empty visibility file if OMNIVIS_FILE is not written

if SAVE_RESULTS and SAVE_OMNIVIS_FILE and not os.path.exists(OMNIVIS_FILE):
    print(f'WARNING: No omnivis file produced at {OMNIVIS_FILE}. Creating an empty visibility solution file.')
    hd_writer = io.HERAData(SUM_FILE)
    hd_writer.initialize_uvh5_file(OMNIVIS_FILE, clobber=True)

Metadata

for repo in ['pyuvdata', 'hera_cal', 'hera_filters', 'hera_qm', 'hera_notebook_templates']:
    exec(f'from {repo} import __version__')
    print(f'{repo}: {__version__}')

pyuvdata: 3.2.5.dev1+g5a985ae31
hera_cal: 3.7.7.dev97+gc2668d3f7
hera_filters: 0.1.7
hera_qm: 2.2.1.dev4+gf6d02113b
hera_notebook_templates: 0.0.1.dev1313+g92178a09c

print(f'Finished execution in {(time.time() - tstart) / 60:.2f} minutes.')

Finished execution in 1.93 minutes.