In [4]:
sources = utils.gather_source_list()
utils.plot_sky_map(uvd,dec_pad=55,ra_pad=55,clip=False,sources=sources)
import os
os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE'
import h5py
import hdf5plugin
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.ticker import FormatStrFormatter
import matplotlib.patches as mpatches
import matplotlib.gridspec as gridspec
import numpy as np
from pyuvdata import UVCal, UVData
import sys
import glob
import uvtools as uvt
from astropy.time import Time
from astropy.coordinates import EarthLocation, AltAz, Angle
from astropy.coordinates import SkyCoord as sc
import pandas
import warnings
import copy
from hera_notebook_templates import utils
import hera_qm
from hera_mc import cm_hookup
import importlib
from scipy import stats
from IPython.display import display, HTML
#warnings.filterwarnings('ignore')
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
display(HTML("<style>.container { width:100% !important; }</style>"))
#get data location
data_path = os.environ['DATA_PATH']
print(f'DATA_PATH = "{data_path}"')
statuses = os.environ['APRIORI_STATUSES']
print(f'APRIORI_STATUSES = {statuses}')
JD = os.environ['JULIANDATE']
print(f'JULIANDATE = {JD}')
utc = Time(JD, format='jd').datetime
print(f'Date = {utc.month}-{utc.day}-{utc.year}')
DATA_PATH = "/mnt/sn1/2460200" APRIORI_STATUSES = dish_maintenance,dish_ok,RF_maintenance,RF_ok,digital_ok,digital_maintenance,calibration_maintenance,calibration_triage,calibration_ok JULIANDATE = 2460200 Date = 9-12-2023
# Load in data
HHfiles, difffiles, HHautos, diffautos, uvdx, uvdy = utils.load_data(data_path,JD)
uvd = UVData()
unread = True
readInd=0
while unread and readInd<len(HHautos):
try:
uvd.read(HHautos[readInd])
unread = False
except:
readInd += 1
continue
use_ants = utils.get_use_ants(uvd,statuses,JD)
print(f'This day contains {len(use_ants)} antennas of the given status category.')
uvd.read(HHautos[::10], skip_bad_files=True, antenna_nums = use_ants)
lsts = uvd.lst_array
uvdx.select(antenna_nums=use_ants)
uvdy.select(antenna_nums=use_ants)
2534 sum files found between JDs 2460200.26372 and 2460200.92844 2534 diff files found between JDs 2460200.26372 and 2460200.92844 85 sum auto files found between JDs 2460200.76819 and 2460200.79613 85 diff auto files found between JDs 2460200.76819 and 2460200.79613 This day contains 196 antennas of the given status category.
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In [3], line 18 16 uvd.read(HHautos[::10], skip_bad_files=True, antenna_nums = use_ants) 17 lsts = uvd.lst_array ---> 18 uvdx.select(antenna_nums=use_ants) 19 uvdy.select(antenna_nums=use_ants) File ~/mambaforge/envs/RTP/lib/python3.10/site-packages/pyuvdata/uvdata/uvdata.py:8607, in UVData.select(self, antenna_nums, antenna_names, ant_str, bls, frequencies, freq_chans, times, time_range, lsts, lst_range, polarizations, blt_inds, phase_center_ids, catalog_names, inplace, keep_all_metadata, run_check, check_extra, run_check_acceptability, strict_uvw_antpos_check) 8599 uv_obj = self.copy() 8601 # Figure out which index positions we want to hold on to. 8602 ( 8603 blt_inds, 8604 freq_inds, 8605 pol_inds, 8606 history_update_string, -> 8607 ) = uv_obj._select_preprocess( 8608 antenna_nums, 8609 antenna_names, 8610 ant_str, 8611 bls, 8612 frequencies, 8613 freq_chans, 8614 times, 8615 time_range, 8616 lsts, 8617 lst_range, 8618 polarizations, 8619 blt_inds, 8620 phase_center_ids, 8621 catalog_names, 8622 ) 8624 # Call the low-level selection method. 8625 uv_obj._select_by_index( 8626 blt_inds, freq_inds, pol_inds, history_update_string, keep_all_metadata 8627 ) File ~/mambaforge/envs/RTP/lib/python3.10/site-packages/pyuvdata/uvdata/uvdata.py:7935, in UVData._select_preprocess(self, antenna_nums, antenna_names, ant_str, bls, frequencies, freq_chans, times, time_range, lsts, lst_range, polarizations, blt_inds, phase_center_ids, catalog_names) 7930 ant_check = np.logical_or( 7931 np.isin(antenna_nums, self.ant_1_array), 7932 np.isin(antenna_nums, self.ant_2_array), 7933 ) 7934 if not np.all(ant_check): -> 7935 raise ValueError( 7936 f"Antenna number {antenna_nums[~ant_check]} is not present in the " 7937 "ant_1_array or ant_2_array" 7938 ) 7939 ant_blt_inds = np.where( 7940 np.logical_and( 7941 np.isin(self.ant_1_array, antenna_nums), 7942 np.isin(self.ant_2_array, antenna_nums), 7943 ) 7944 )[0] 7945 else: ValueError: Antenna number [130 138 75 322 137 99 98 82 129 119 203 33 100 116 118 219 81 117 83] is not present in the ant_1_array or ant_2_array
Map of the sky (made using the Haslam 408MHz map). The RA/DEC range covered by this night of observation is shaded based on a 12 degree FWHM of the beam. Horizontal dashed lines represent the stripe that HERA can observe, while the shaded region is what was observed on this night. Vertical lines represent the beginning and ending LSTs of this observation. Selected sources are labelled, sources included are those in the GLEAM 4Jy catalog with a flux >10.9 Jy. Note that the map is clipped at the northern horizon.
sources = utils.gather_source_list()
utils.plot_sky_map(uvd,dec_pad=55,ra_pad=55,clip=False,sources=sources)
Shows the LSTs (in hours) and JDs for which data is collected. Green represents data, red means no data.
utils.plot_lst_coverage(uvd)
This plot shows autocorrelations for one timestamp of each antenna that is active and each polarization. For each node, antennas are ordered by SNAP number, and within that by SNAP input number. The antenna number label color corresponds to the a priori status of that antenna.
### plot autos
utils.plot_autos(uvdx, uvdy)
These plots show autocorrelation waterfalls of each antenna that is active and whose status qualifies for this notebook. For each node, antennas are ordered by SNAP number, and within that by SNAP input number. The antenna number label color corresponds to the a priori status of that antenna.
utils.plot_wfs(uvd, pol = 0)
utils.plot_wfs(uvd, pol = 1)
The first plot shows the correlation metric (described below) for a set of baseline types, as calculated at several times throughout the night. It is expected that longer baselines (darker color) will exhibit lower values than the short baselines.
The matrices show the phase correlation between antennas. Using the even and odd visibilities, each pixel is calculated as (even/abs(even)) * (conj(odd)/abs(odd)), and then averaged across time and frequency. If the phases are noise-like, this value will average down to zero. If the antennas are well correlated, the phases should not be noise-like, and this value should average to 1. The lines denoting node boundaries are intended to help confirm that inter-node correlations are functioning - if they aren't, this plot will appear block-diagonal.
This metric has shown to be LST locked - when comparing to other nights, be sure to compare for the same LST. It is expected that some LSTs will look much better or worse than others.
Note: Within each node, the order of antennas is determined by snap, and within that by snap input number.
badAnts = []
badAnts = utils.plotNodeAveragedSummary(uvd,HHfiles,JD,use_ants,mat_pols=['xx','yy','xy','yx'])
WARNING: unable to read /mnt/sn1/2460200/zen.2460200.29810.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.38138.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.42277.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.46460.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.50598.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.54759.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.58897.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.63058.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.67219.sum.uvh5 WARNING: unable to read /mnt/sn1/2460200/zen.2460200.71380.sum.uvh5
WARNING:matplotlib.legend:No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
Visibility amplitude spectra for a set of redundant baselines, labeled by inter vs. intranode baselines. The red and blue should exhibit the same bandpass shape - if the red are consistently different from the blue, this indicates an issue with internode correlations.
Note: antennas that were identified as bad by the correlation matrix have been removed from this plot.
utils.plotVisibilitySpectra(HHfiles[len(HHfiles)//2+1], JD, use_ants, badAnts=[])
<Figure size 640x480 with 0 Axes>
A waterfall showing the ratio between the even and odd visibilities. The purpose of this is to highlight xengine failures, which will cause this value to fall to zero or go to infinity. If things are working properly, this value should be stable at 1. The boundaries between different x-engines are shown by the vertical white lines.
if len(HHautos) == len(diffautos):
uvd_diff = UVData()
uvd_diff.read(diffautos[::10], skip_bad_files=True, antenna_nums=use_ants)
rat = utils.plotEvenOddWaterfalls(uvd,uvd_diff)
else:
uvd_diff = UVData()
use_diffs = [f for f in diffautos if '%s/zen.%s.%s.sum.autos.uvh5' % (data_path,f.split('.')[1],f.split('.')[2]) in HHautos[::10]]
uvd_diff.read(use_diffs, skip_bad_files=True, antenna_nums = use_ants)
uvd_sum = uvd.select(times=np.unique(uvd_diff.time_array),inplace=False)
rat = utils.plotEvenOddWaterfalls(uvd_sum,uvd_diff)
These are differences between different panels of the correlation matrices shown above (see panel titles for specifics). Antennas showing as consistently blue are ones which are correlating stronger in the cross pols than in the auto pols, indicating that the antenna polarizations are likely crossed.
crossedAnts = utils.plotNodeAveragedSummary(uvd,HHfiles,JD,use_ants,mat_pols=['xx','yy','xy','yx'],plotRatios=True,
plotSummary=False)
WARNING: unable to read /mnt/sn1/2460200/zen.2460200.29810.sum.uvh5
Antennas outlined in black here have been identified by the correlation matrix as bad antennas. Antennas with a colorful outline correspond to their status as identified by ant_metrics (see above plot). Faded antennas are those not meeting the apriori status requirement for this notebook run. Gold stars are node box locations.
uvd1 = UVData()
uvd1.read(HHfiles[readInd], skip_bad_files=True)
utils.plot_antenna_positions(uvd1, badAnts=badAnts,use_ants=use_ants)
Antennas of status digital_OK or better that are flagged as bad by any of the above metrics are plotted here so observers can inspect their failures in more detail. Additionally, a 'good' template has been used to identify outliers. The upper line plots are averages over the whole observation, and the lower line plots are slices of a single time in the middle of the observation. These plots are recommended diagnostics for demoting antennas to lower statuses or reporting issues. If the plots below look OK, check other plots in notebook to hunt why the antenna was flagged. NOTE: The colorbar/power scales in these plots are NOT locked between antennas OR polarizations so that the detail will be visible on all plots. Be sure to check for reasonable power levels, as this may be the reason the antenna was flagged for inspection.
d, tempAnts = utils.flag_by_template(uvd,HHautos,JD,use_ants=use_ants,pols=['XX','YY'],plotMap=False)
inspectAnts = utils.plot_inspect_ants(uvd,JD,badAnts=badAnts,use_ants=use_ants,
tempAnts=tempAnts,crossedAnts=crossedAnts)
Antennas that require further inspection are: [ 3 5 7 9 10 15 17 19 20 21 27 28 30 31 37 38 40 41 42 44 45 51 53 56 62 65 66 67 68 69 70 71 72 84 85 86 88 91 98 99 100 101 103 105 106 107 112 116 118 121 122 123 128 129 130 140 141 142 144 145 146 147 148 149 150 151 152 153 154 157 158 161 162 163 164 165 167 168 169 170 171 172 173 176 177 178 181 183 186 187 189 190 191 192 193 202 205 206 221 222 223 226 227 237 238 239 241 242 243 320 325]
######################################### Data for antenna 44 is entirely zeros #########################################
######################################### Data for antenna 62 is entirely zeros #########################################
######################################### Data for antenna 98 is entirely zeros ######################################### ######################################### Data for antenna 99 is entirely zeros #########################################
######################################### Data for antenna 116 is entirely zeros #########################################
######################################### Data for antenna 129 is entirely zeros ######################################### ######################################### Data for antenna 130 is entirely zeros #########################################
######################################### Data for antenna 157 is entirely zeros ######################################### ######################################### Data for antenna 158 is entirely zeros #########################################
######################################### Data for antenna 202 is entirely zeros ######################################### ######################################### Data for antenna 205 is entirely zeros ######################################### ######################################### Data for antenna 206 is entirely zeros ######################################### ######################################### Data for antenna 221 is entirely zeros ######################################### ######################################### Data for antenna 222 is entirely zeros ######################################### ######################################### Data for antenna 223 is entirely zeros ######################################### ######################################### Data for antenna 226 is entirely zeros #########################################
######################################### Data for antenna 237 is entirely zeros ######################################### ######################################### Data for antenna 238 is entirely zeros ######################################### ######################################### Data for antenna 239 is entirely zeros ######################################### ######################################### Data for antenna 241 is entirely zeros ######################################### ######################################### Data for antenna 242 is entirely zeros ######################################### ######################################### Data for antenna 243 is entirely zeros #########################################
Here the mean value in each frequency bin has been subtracted out. This effectively subtracts out the bandpass shape, making time variations more visible.
utils.plot_wfs(uvd,0,mean_sub=True,jd=JD)
utils.plot_wfs(uvd,1,mean_sub=True,jd=JD)
