
%matplotlib inline


import os


# Import the CASA tasks and programs we'll need:

from casatasks import (listobs, clearcal, flagmanager, flagdata,
                       setjy, bandpass, gaincal, applycal, blcal, fluxscale)
from casaplotms import plotms

You appear to be importing analysisUtils into python (not CASA). version =  3.8.12
CASAPATH is not defined, so I am skipping a lot of imports


myvis = '230424_09:18:48_bin8.ms'


out = listobs(myvis)


# variable names for the sources are case sensitive
flux = 'Ceres'

bpcal= '3c279'

# Gain calibrators
# NOTE: SMA observations often have 2 gain calibrators. If you only have one, comment out `pcal2' and remove its
# use in `bothpcal`. Similarly, you *could* have more than two, in which case add a `pcal3` and add to `bothpcal`
#  ppropriate!
pcal1 = '1743-038'
pcal2= '1733-130'
# A variable to use both gain cals
bothpcal = f"{pcal1},{pcal2}"

# A variable with all the calibrator names for convenience later
calfields= ",".join([bpcal, bothpcal, flux])

# If you have more than 1 science field, separate the source names by a comma in the string.
science_fields = 'HD163296'


flagmanager(vis=myvis, mode='save', versionname='original')

2023-05-11 18:06:47	WARN	flagmanager::::casa	Version name 'original' already exist. Will rename it to original.old.1683828406


plotms(vis=myvis, xaxis='channel',
       yaxis='amp',field=bpcal, avgtime='1e8', avgscan=False,
       coloraxis='ant1',iteraxis='spw', ydatacolumn='data',
       gridrows=4, gridcols=3, yselfscale=True)


flagdata(vis=myvis, mode='manual', spw='1:127', flagbackup=False) # We'll save a flag version after all manual flagging is done
flagdata(vis=myvis, mode='manual', spw='1:143', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='1:151', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='1:134~136', flagbackup=False) # Flag a range from 134 to 136

{}


flagdata(vis=myvis, mode='manual', spw='1:127,10:127', flagbackup=False) # We'll save a flag version after all manual flagging is done
flagdata(vis=myvis, mode='manual', spw='1:143,10:143', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='1:151,10:151', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='1:134~136,10:134~136', flagbackup=False) # Flag a range from 134 to 136

{}


flagdata(vis=myvis, mode='manual', spw='2:117,9:117', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='2:124~125,9:124~125', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='2:141,9:141', flagbackup=False)

{}


# Chunk 5 in the lower sideband (LSB) and upper sideband (USB)
flagdata(vis=myvis, mode='manual', spw='13:127,22:127', flagbackup=False) # We'll save a flag version after all manual flagging is done
flagdata(vis=myvis, mode='manual', spw='13:143,22:143', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='13:151,22:151', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='13:134~136,22:134~136', flagbackup=False) # Flag a range from 134 to 136

# Chunk 4 in the lower sideband (LSB) and upper sideband (USB)
flagdata(vis=myvis, mode='manual', spw='14:125,21:125', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='14:141,21:141', flagbackup=False)

# Chunk 2 in the lower sideband (LSB) and upper sideband (USB)
flagdata(vis=myvis, mode='manual', spw='16:1536,19:1536', flagbackup=False)
flagdata(vis=myvis, mode='manual', spw='16:1731,19:1731', flagbackup=False)

### Back up a version of the flags we've just added! ####
flagmanager(vis=myvis, mode='save', versionname='manual_flagging_initial')


# Factor the data have been downsampled by:
rechunk = 8

# Original number of channels is 16384. Divide that by how many we have rechunked.
chan_num = int(16384 / rechunk)

# Set the fraction of channels to flag at each edge.
edgechan_frac = 0.025

# Range of channels to flag at the lower edge
edge_chan_low = int(np.floor(chan_num * edgechan_frac))
# Range of channels to flag at the upper edge
edge_chan_high = int(np.floor(chan_num * (1. - edgechan_frac)))

# Combine into the format that CASA's flagdata will interpret
# To select all SPWs, we use the "*" wildcard.
# Also note that channel counting starts at "0", so we set the upper limit to be `chan_num-1`
edgechan = "*:0~{0};{1}~{2}".format(edge_chan_low,
                                    edge_chan_high, chan_num-1)

print(edgechan)

*:0~51;1996~2047


flagdata(vis=myvis, mode='manual', spw=edgechan, flagbackup=False)
flagmanager(vis=myvis, mode='save', versionname='edge_flagging')


plotms(vis=myvis, xaxis='channel',
       yaxis='amp',field=flux, avgtime='1e8', avgscan=False,
       coloraxis='ant1',iteraxis='spw', ydatacolumn='data',
       gridrows=4, gridcols=3, yselfscale=True)


# This is an individual channel outlier that only appear in 1 channel, not in both sidebands.
# Based on the color of the points, these outliers are all coming from the same antenna: Ant4
flagdata(vis=myvis, mode='manual', field=flux, spw="10:732", antenna='Ant4', flagbackup=False)

flagdata(vis=myvis, mode='manual', field=flux, spw="13:732,22:732", antenna='Ant4', flagbackup=False)
flagdata(vis=myvis, mode='manual', field=flux, spw="13:1329,22:1329", antenna='Ant4', flagbackup=False)

flagdata(vis=myvis, mode='manual', field=flux, spw="14:124,21:124", antenna='Ant4', flagbackup=False)
flagdata(vis=myvis, mode='manual', field=flux, spw="14:133,21:133", antenna='Ant4', flagbackup=False)
flagdata(vis=myvis, mode='manual', field=flux, spw="14:230,21:230", antenna='Ant4', flagbackup=False)

{}


plotms(vis=myvis, xaxis='time',
       yaxis='amp',field=flux, avgchannel='1e8',
       coloraxis='ant1',iteraxis='spw', ydatacolumn='data',
       gridrows=4, gridcols=3, yselfscale=True)

2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 0 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 0
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 1 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 1
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 2 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 2
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 3 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 3
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 4 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 4
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 5 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 5
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 6 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 6
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 7 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 7
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 8 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 8
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 9 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 9
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 10 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 10
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 11 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 11
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 12 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 12
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 13 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 13
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 14 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 14
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 15 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 15
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 16 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 16
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 17 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 17
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 18 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 18
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 19 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 19
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 20 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 20
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 21 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 21
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 22 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 22
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams	Number of selected channels 2048 for SPW 23 is smaller than specified chanbin 100000000
2023-05-11 13:27:28	WARN	MSTransformManager::initDataSelectionParams+	Setting chanbin to 2048 for SPW 23
2023-05-11 13:27:29	INFO	MeasIERS::fillMeas(MeasIERS::Files, Double) 	Requested JD 60058.4 is outside the range of the IERS (Earth axis data) table.
2023-05-11 13:27:29	INFO	MeasIERS::fillMeas(MeasIERS::Files, Double) +	Calculations will proceed with less precision
2023-05-11 13:27:29	SEVERE	MeasTable::dUTC(Double) (file casa-source/casatools/casacore/measures/Measures/MeasTable.cc, line 4290)	Leap second table TAI_UTC seems out-of-date.
2023-05-11 13:27:29	SEVERE	MeasTable::dUTC(Double) (file casa-source/casatools/casacore/measures/Measures/MeasTable.cc, line 4290)+	Until the table is updated (see the CASA documentation or your system admin),
2023-05-11 13:27:29	SEVERE	MeasTable::dUTC(Double) (file casa-source/casatools/casacore/measures/Measures/MeasTable.cc, line 4290)+	times and coordinates derived from UTC could be wrong by 1s or more.

Tutorial for SMA Data Calibration in CASA¶

Purpose¶

Using this tutorial with CASA¶

Installing CASA¶

Review the observing log¶

Initial Steps: converting the MIR format to a CASA Measurement Set¶

CASA Data Calibration¶

What's in the data?¶

Visually inspecting the data, and intro to manual flagging¶

Flagging edge channels¶

More manual flagging: Visualizing and flagging for our whole calibrator suite¶