View source for AntennaeBand7 Calibration 6.6.1

[[Category:ALMA]][[Category:Calibration]][[Category:Spectral Line]]

==Overview==

Details of these observations are provided at [[AntennaeBand7]]. This part of the CASA guide will step through the calibration of the visibility data. We will begin by flagging (marking as bad) data known to be useless before any inspection; for example, data where one telescope blocks the line of sight of another (shadowing). We will then apply telescope-generated calibration tables to partially correct for atmospheric effects. After inspecting the data, we will flag some additional data that exhibit pathologies. Using observations of the calibrators Titan and 3c279, it will be shown how to derive the phase and amplitude response of individual antennas as a function of time and frequency ("phase", "amplitude", and "bandpass" calibrations). We will apply these solutions to the data and then extract the calibrated source data into a file appropriate for imaging in the [[AntennaeBand7_Imaging]].

The general procedure in this guide follows other ALMA CASA guides: [[NGC3256Band3]] and [[TWHydraBand7]].

==Unpack the Data==

Download ''Antennae_Band7_UnCalibratedMSAndTablesForReduction.tgz'' from [[AntennaeBand7#Obtaining_the_Data]]. 

Unpack the file in a terminal (outside of CASA) using

<source lang="bash">
# in bash
tar -xvzf Antennae_Band7_UnCalibratedMSandTablesForReduction.tgz
</source>

then change directory to the new directory  

<source lang="bash">
# in bash
cd Antennae_Band7_UnCalibratedMSandTablesForReduction
</source>

You may wish to type

<source lang="bash">
# in bash
ls
</source>

to look at the files present. You should see a set of files with extension ".ms". These are CASA measurement set (MS) files. The data have already been converted to MS format from the native ALMA format using the CASA task {{importasdm_6.6.1}}. In addition to the data, we provide you with calibration tables containing system temperature (Tsys), water vapor radiometer (WVR), and antenna position information. For Early Science, these tables will either be pre-applied or supplied with the data.

To begin, start CASA by typing

<source lang="bash">
# in bash
casa

# on NRAO machines, specify a pre-installed version
casa -r 6.6.1-17-pipeline-2024.1.0.8

# if you wish to suppress the logger window and print output to terminal instead, you can add this to your startup command
--log2term --nologger
</source>

==Confirm your version of CASA==

This guide has been written for CASA release 6.6.1-17.  Please confirm your version before proceeding.
<source lang="python">
# In CASA
import casalith
version = casalith.version_string()
print("You are using {}".format(version))
if (version < '6.6.1'):
    print("YOUR VERSION OF CASA IS TOO OLD FOR THIS GUIDE.")
    print("PLEASE UPDATE IT BEFORE PROCEEDING.")
else:
    print("Your version of CASA is appropriate for this guide.")
</source>

==Initial Inspection==

First we will take stock of what we have. If you have not already done so, begin by reviewing the description of the observations here: [[AntennaeBand7]]. The 10 data sets each target either the Northern or the Southern Mosaic, as follows:

Northern Mosaic:
*uid___A002_X1ff7b0_Xb.ms
*uid___A002_X207fe4_X3a.ms
*uid___A002_X207fe4_X3b9.ms
*uid___A002_X2181fb_X49.ms

Southern Mosaic:
*uid___A002_X1ff7b0_X1c8.ms
*uid___A002_X207fe4_X1f7.ms
*uid___A002_X207fe4_X4d7.ms
*uid___A002_X215db8_X18.ms
*uid___A002_X215db8_X1d5.ms
*uid___A002_X215db8_X392.ms

The first step is to get basic information about the data: targets observed, time range, spectral setup, and so on. We do this using the task {{listobs_6.6.1}}, which will output a detailed summary of each dataset. Enter the following commands into CASA:

<source lang="python">
# In CASA

# Define a python list holding the names of all of our data sets
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

# Initialize user-input string.  (for Python testing)
user_input = ''

# Loop over each element in the list and create summary file using listobs
import os
for asdm in basename_all:
    os.system('rm '+asdm+'.listobs.txt')
    listobs(vis=asdm+'.ms', listfile=asdm+'.listobs.txt', verbose=True)
</source>

Note that after cutting and pasting a 'for' loop like this you often have to press return twice to execute. You may also want to take care to paste a line at a time if you are having trouble copy and pasting. Even better, you can use "cpaste" to paste blocks of code. To do so type "cpaste" at the CASA prompt, paste your commands, and then type "--" and hit return on the final (otherwise empty) line. This should look something like this:

<pre style="background-color: #fffacd;">

CASA <8>: cpaste
Pasting code; enter '--' alone on the line to stop.
:basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
:     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
:     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
:     "uid___A002_X215db8_X392"]
:
:for asdm in basename_all:
:    print(asdm)
:--
uid___A002_X1ff7b0_Xb
uid___A002_X207fe4_X3a
uid___A002_X207fe4_X3b9
uid___A002_X2181fb_X49
uid___A002_X1ff7b0_X1c8
uid___A002_X207fe4_X1f7
uid___A002_X207fe4_X4d7
uid___A002_X215db8_X18
uid___A002_X215db8_X1d5
uid___A002_X215db8_X392

CASA <9>: 

</pre>

cpaste should be ''much'' more robust than copying-and-pasting directly into the shell but if you have trouble, just carefully paste one line at a time directly into CASA and hit return until the desired command executes.

These commands define a python list called "basename_all", which contains the name of all 10 MS files. The "for" loop executes for each element in basename_all, calling listobs and directing the output to a file called, e.g., "uid___A002_X1ff7b0_Xb.listobs.txt" for the first measurement set. You can browse through the listobs output as you would normally look at a text file (use emacs, vi, or another editor). You can also send the output to the terminal from inside of CASA. To do so type:

<source lang="python">
# In CASA
os.system('cat uid___A002_X1ff7b0_Xb.listobs.txt')
</source>

or

<source lang="python">
# In CASA
os.system('more uid___A002_X1ff7b0_Xb.listobs.txt')
</source>

CASA knows a few basic shell commands like 'cat', 'ls', and 'rm' but for more complex commands you will need to run them inside 'os.system("command")'. For more information see [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/casa-fundamentals.html#Working-with-MS-Data Working with MS Data].

Here is an example of the (abridged) output from {{listobs_6.6.1}} for the first dataset in the list, uid___A002_X1ff7b0_Xb.ms, which targets the Northern Mosaic. You would see this if you had specified '''verbose''' to be False in the listobs call:

<pre style="background-color: #fffacd;">
================================================================================
           MeasurementSet Name:  /lustre/naasc/almauser/AntennaeBand7/uid___A002_X1ff7b0_Xb.ms      MS Version 2
================================================================================
   Observer: Unknown     Project: T.B.D.  
Observation: ALMA(11 antennas)
Data records: 181357       Total integration time = 4931.71 seconds
   Observed from   28-May-2011/01:25:27.6   to   28-May-2011/02:47:39.3 (UTC)

Fields: 26
  ID   Code Name                RA              Decl          Epoch   SrcId nRows  
  0    none 3c279               12:56:11.16657 -05.47.21.5247 J2000   0     39116  
  1    none Titan               12:42:43.94813 -01.43.38.3190 J2000   1     10626  
  2    none NGC4038 - Antennae *12:01:53.17008 -18.52.37.9200 J2000   2     4818   
  3    none NGC4038 - Antennae *12:01:51.90301 -18.51.49.9437 J2000   2     6435   
  4    none NGC4038 - Antennae *12:01:52.43086 -18.51.49.9437 J2000   2     6424   
  5    none NGC4038 - Antennae *12:01:52.95871 -18.51.49.9437 J2000   2     5478   
  6    none NGC4038 - Antennae *12:01:53.48656 -18.51.49.9436 J2000   2     6435   
  7    none NGC4038 - Antennae *12:01:54.01441 -18.51.49.9436 J2000   2     6446   
  8    none NGC4038 - Antennae *12:01:52.16693 -18.51.56.4319 J2000   2     6435   
  9    none NGC4038 - Antennae *12:01:52.69478 -18.51.56.4318 J2000   2     6424   
  10   none NGC4038 - Antennae *12:01:53.22263 -18.51.56.4318 J2000   2     6446   
  11   none NGC4038 - Antennae *12:01:53.75049 -18.51.56.4318 J2000   2     6446   
  12   none NGC4038 - Antennae *12:01:51.90301 -18.52.02.9201 J2000   2     6435   
  13   none NGC4038 - Antennae *12:01:52.43086 -18.52.02.9200 J2000   2     6424   
  14   none NGC4038 - Antennae *12:01:52.95871 -18.52.02.9200 J2000   2     4818   
  15   none NGC4038 - Antennae *12:01:53.48656 -18.52.02.9200 J2000   2     4829   
  16   none NGC4038 - Antennae *12:01:54.01441 -18.52.02.9199 J2000   2     4829   
  17   none NGC4038 - Antennae *12:01:52.16694 -18.52.09.4082 J2000   2     4829   
  18   none NGC4038 - Antennae *12:01:52.69479 -18.52.09.4082 J2000   2     4829   
  19   none NGC4038 - Antennae *12:01:53.22264 -18.52.09.4082 J2000   2     3872   
  20   none NGC4038 - Antennae *12:01:53.75049 -18.52.09.4081 J2000   2     4829   
  21   none NGC4038 - Antennae *12:01:51.90301 -18.52.15.8964 J2000   2     4829   
  22   none NGC4038 - Antennae *12:01:52.43087 -18.52.15.8964 J2000   2     4829   
  23   none NGC4038 - Antennae *12:01:52.95872 -18.52.15.8963 J2000   2     4818   
  24   none NGC4038 - Antennae *12:01:53.48657 -18.52.15.8963 J2000   2     4818   
  25   none NGC4038 - Antennae *12:01:54.01442 -18.52.15.8963 J2000   2     4840   
Spectral Windows:  (9 unique spectral windows and 2 unique polarization setups)
  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)  TotBW(kHz)  Corrs  
  0           4 TOPO  184550      1500000       7500000     I   
  1        3840 TOPO  344845.586  488.28125     1875000     XX  YY  
  2           1 TOPO  343908.086  1875000       1875000     XX  YY  
  3        3840 TOPO  354971.074  488.28125     1875000     XX  YY  
  4           1 TOPO  343908.086  1875000       1875000     XX  YY  
  5         128 TOPO  344900.518  15625         2000000     XX  YY  
  6           1 TOPO  343892.705  1796875       1796875     XX  YY  
  7         128 TOPO  354916.143  15625         2000000     XX  YY  
  8           1 TOPO  343892.705  1796875       1796875     XX  YY  
Antennas: 11 'name'='station' 
   ID=   0-3: 'DV02'='A015', 'DV04'='J505', 'DV06'='T704', 'DV07'='A004', 
   ID=   4-7: 'DV08'='A072', 'DV09'='A008', 'DV10'='A009', 'DV11'='A016', 
   ID=  8-10: 'PM01'='T702', 'PM02'='A017', 'PM03'='J504'
================================================================================

</pre>

And here is an extract from the full '''verbose''' {{listobs_6.6.1}} for uid___A002_X1ff7b0_X1c8.ms, which targets the Southern Mosaic (note that we have snipped out the record of individual scans):

<pre style="background-color: #fffacd;">

================================================================================
           MeasurementSet Name:  /lustre/naasc/almauser/AntennaeBand7/uid___A002_X1ff7b0_X1c8.ms      MS Version 2
================================================================================
   Observer: Unknown     Project: T.B.D.  
Observation: ALMA
Data records: 175615       Total integration time = 4927.1 seconds
   Observed from   28-May-2011/02:50:18.2   to   28-May-2011/04:12:25.3 (UTC)

<snip>

Fields: 33
  ID   Code Name                RA              Decl          Epoch   SrcId nVis   
  0    none 3c279               12:56:11.16657 -05.47.21.5247 J2000   0     12232  
  1    none Titan               12:42:44.82765 -01.43.41.4224 J2000   1     10615  
  2    none 3c279               12:56:11.16600 -05.47.21.5250 J2000   2     27764  
  3    none Antennae            12:01:53.17008 -18.52.37.9200 J2000   3     4829   
  4    none Antennae            12:01:52.18699 -18.53.30.3952 J2000   3     3883   
  5    none Antennae            12:01:52.64413 -18.53.26.6494 J2000   3     3883   
  6    none Antennae            12:01:53.10127 -18.53.22.9035 J2000   3     3872   
  7    none Antennae            12:01:53.55841 -18.53.19.1577 J2000   3     4818   
  8    none Antennae            12:01:54.01554 -18.53.15.4119 J2000   3     4829   
  9    none Antennae            12:01:54.47268 -18.53.11.6661 J2000   3     4829   
  10   none Antennae            12:01:54.92982 -18.53.07.9203 J2000   3     3872   
  11   none Antennae            12:01:55.38696 -18.53.04.1744 J2000   3     3883   
  12   none Antennae            12:01:55.84409 -18.53.00.4286 J2000   3     4840   
  13   none Antennae            12:01:56.30123 -18.52.56.6828 J2000   3     4818   
  14   none Antennae            12:01:52.18700 -18.53.22.9033 J2000   3     4829   
  15   none Antennae            12:01:52.64414 -18.53.19.1575 J2000   3     4818   
  16   none Antennae            12:01:53.10128 -18.53.15.4116 J2000   3     4818   
  17   none Antennae            12:01:53.55842 -18.53.11.6658 J2000   3     4840   
  18   none Antennae            12:01:54.01555 -18.53.07.9200 J2000   3     3872   
  19   none Antennae            12:01:54.47269 -18.53.04.1742 J2000   3     4829   
  20   none Antennae            12:01:54.92983 -18.53.00.4284 J2000   3     4829   
  21   none Antennae            12:01:55.38697 -18.52.56.6825 J2000   3     4829   
  22   none Antennae            12:01:55.84410 -18.52.52.9367 J2000   3     4829   
  23   none Antennae            12:01:51.72988 -18.53.19.1572 J2000   3     4818   
  24   none Antennae            12:01:52.18702 -18.53.15.4114 J2000   3     4829   
  25   none Antennae            12:01:52.64415 -18.53.11.6656 J2000   3     4829   
  26   none Antennae            12:01:53.10129 -18.53.07.9197 J2000   3     2266   
  27   none Antennae            12:01:53.55843 -18.53.04.1739 J2000   3     2266   
  28   none Antennae            12:01:54.01557 -18.53.00.4281 J2000   3     3212   
  29   none Antennae            12:01:54.47270 -18.52.56.6823 J2000   3     3234   
  30   none Antennae            12:01:54.92984 -18.52.52.9365 J2000   3     3212   
  31   none Antennae            12:01:55.38698 -18.52.49.1906 J2000   3     2266   
  32   none Antennae            12:01:55.84411 -18.52.45.4448 J2000   3     3223   
   (nVis = Total number of time/baseline visibilities per field) 
Spectral Windows:  (9 unique spectral windows and 2 unique polarization setups)
  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)  TotBW(kHz)  Corrs  
  0           4 TOPO  184550      1500000       7500000     I   
  1        3840 TOPO  344845.586  488.28125     1875000     XX  YY  
  2           1 TOPO  343908.086  1875000       1875000     XX  YY  
  3        3840 TOPO  356845.586  488.28125     1875000     XX  YY  
  4           1 TOPO  343908.086  1875000       1875000     XX  YY  
  5         128 TOPO  344900.518  15625         2000000     XX  YY  
  6           1 TOPO  343892.705  1796875       1796875     XX  YY  
  7         128 TOPO  356900.518  15625         2000000     XX  YY  
  8           1 TOPO  343892.705  1796875       1796875     XX  YY  
Antennas: 11:
  ID   Name  Station   Diam.    Long.         Lat.         
  0    DV02  A015      12.0 m   -067.45.15.3  -22.53.26.0  
  1    DV04  J505      12.0 m   -067.45.18.0  -22.53.22.8  
  2    DV06  T704      12.0 m   -067.45.16.2  -22.53.22.1  
  3    DV07  A004      12.0 m   -067.45.15.9  -22.53.28.0  
  4    DV08  A072      12.0 m   -067.45.12.6  -22.53.24.0  
  5    DV09  A008      12.0 m   -067.45.15.4  -22.53.26.8  
  6    DV10  A009      12.0 m   -067.45.16.1  -22.53.26.1  
  7    DV11  A016      12.0 m   -067.45.16.4  -22.53.25.1  
  8    PM01  T702      12.0 m   -067.45.18.6  -22.53.24.1  
  9    PM02  A017      12.0 m   -067.45.15.9  -22.53.26.8  
  10   PM03  J504      12.0 m   -067.45.17.0  -22.53.23.0  
</pre>

This output shows that three sources were observed in each data set: 3c279, Titan, and the Antennae.

* The '''Antennae''' are our science target. Note that the source name changes between the Northern Mosaic, where it is "NGC4038 - Antennae", and the Southern Mosaic, where it is just "Antennae". Also note that the source corresponds to a number of individual fields (see the Field ID column). These are the individual mosaic pointings. There are 23 for the Northern Mosaic and 29 for the Southern Mosaic.
* '''Titan''' is observed once and will be used to set the absolute flux scale of the data.
* '''3c279''' plays two roles: it will serve as our bandpass calibrator, to characterize the frequency response of the antennas, and because it is fairly close on the sky to the Antennae (18.6 degrees away) it will serve as our secondary calibrator (also referred to as the "phase calibrator" or "complex gain calibrator"), to track changes in the phase and amplitude response of the telescopes over time. Observations of 3c279 are interleaved with observations of the Antennae.

The output also shows that the data contain many spectral windows. Using the labeling scheme in the listobs above these are:

* '''spw 0''' targets ~185 GHz and holds water vapor radiometer data
* '''spw 1''' and '''spw 3''' hold our science data. These are "Frequency Domain Mode" (FDM) data with small (0.49 MHz) channel width and wide (1.875 GHz) total bandwidth. As a result these have a lot of channels (3840). spw 1 holds the lower sideband (LSB) data and includes the CO(3-2) line. We will focus on these data. For the CO(3-2) line the channel width corresponds to 0.426 km/s and the bandwidth of spw 1 to 1634 km/s.
* '''spw 2''' and '''spw 4''' hold frequency-averaged versions of spw 1 and 3 ("Channel 0" for those familiar with AIPS). These are used for some quick automated inspection. We will not use them here but we will carry out an equivalent inspection using spw 1.
* '''spw 5''' and '''spw 7''' hold a lower resolution processing ("Time Domain Mode", TDM) of the data from the same part of the spectrum (baseband) as spws 1 and 3. These data have only 128 channels across 2 GHz bandwidth and so have a much coarser channel spacing than the FDM data. These were used to generate the calibration tables that we include in the tarball but will not otherwise appear in this guide.

The final column of the listobs output in the logger (not shown above) gives the scan intent. Later we will use this information to flag the pointing scans and the hot and ambient load calibration scans.

We'll now have a look at the configuration of the antennas used to take the data using the task {{plotants_6.6.1}} (see Figure 1).

[[File:Uid_A002_X1ff7b0_Xb.ANT_6.1.png|300px|thumb|right|'''Fig. 1.''' Position of antennas in dataset uid_A002_X1ff7b0_Xb obtained using task plotants. ]]

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    print("Antenna configuration for : "+asdm)
    plotants(vis=asdm+'.ms', figfile=asdm+'.plotants.png')
    clearstat()
    user_input = input("Hit <Enter> to see the antenna configuration for the next data set. Type 'stop'+<Enter> to break out: ")
    if user_input == "stop":
        break
</source> 

This will loop through all 10 data sets, show you the antenna position for each, and save that as a file named, e.g., "uid___A002_X1ff7b0_Xb.plotants.png" for the first data set. The "input" command asks CASA to wait for your input before proceeding. If you would prefer to just browse the .png files after the fact you can remove this. Notice that the antenna setup changes, but only slightly, over the course of the 10 data sets.

<br clear="all">

==How to Deal With 10 Measurement Sets==

It should already be clear from the initial inspection that dealing with 10 data sets at the same time can be a bit problematic. This is especially tricky in our case because the Antennae data contain two distinct sets of observations: the Northern and Southern Mosaics. The source name changes between these two scripts and there are different numbers of fields in the mosaic.

''As a general rule one would reduce each individual observation separately or at the very least only group data observed in a uniform way and very close in time.'' 

Unfortunately, a CASA Guide stepping through the reduction for each of 10 data sets would quickly become unwieldy. Therefore we will use a few tricks to reduce the Antennae data in a kind of batch mode. You have already seen the first trick: we can define a python list holding the names of each data set and then loop over this list to execute the same command on each data set. For example:

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    print(asdm)
</source>

<pre style="background-color: #E0FFFF;">
You only need to define your list of MS files once per CASA session. Then "basename_all" will be a variable in the casapy shell. You can check if it exists by typing "print(basename_all)". In the interests of allowing you to easily exit and restart CASA and pick this guide up at any point we will redefine "basename_all" in each section of the guide. Feel free to skip this step if you've already defined it in your session.
</pre>

This page will step you through the reduction of the whole Antennae Band 7 SV data set using these 'for' loops. We will not be able to show every diagnostic plot but we give an example of each and the syntax to generate the rest. Also please be aware that even on a very fast machine this whole process can take a while, as we are simply dealing with a lot of data.

<pre style="background-color: #E0FFFF;">
One potential "gotcha" is that the source name changes between the two data sets. Therefore at several points we will break apart our loop to iterate separately over the Northern and Southern Mosaics, where the source can be referred unambiguously. Another subtle point is that 3c279 appears with two distinct field IDs in the Southern Mosaic, but only one in the Northern Mosaic. We will largely avoid this by referring to the source by its name but if you tried to use field ID numbers and mingled the two data sets this could cause confusion.
</pre>

==''A Priori'' Flagging==

Even before we look in detail, we know that there are some data that we wish to exclude. We will start by flagging "shadowed" data where one antenna blocks the line of sight of another. We will also flag scans that were used to carry out pointing and atmospheric calibration, identified by their scan intent. Finally, we'll flag the autocorrelation data (the correlation of the signal from an antenna with itself) as we are only interested in cross-correlation data  to make an interferometric image.

Start by defining our list of MS files:

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]
</source>

You may want to reset the flagging if you have tried this step before and are starting over though this is not necessary on your first time through. Do so using {{flagdata_6.6.1}}:

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Resetting flags for "+asdm)
    flagdata(vis=asdm+'.ms', mode='unflag', flagbackup=False)
</source>

Then flag shadowed data using the command {{flagdata_6.6.1}}:

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Flagging shadowed data for "+asdm)
    flagdata(vis=asdm+'.ms', mode='shadow', flagbackup = False)
</source>

In the {{flagdata_6.6.1}} task we choose:

* '''vis''' = asdm+'.ms' : each measurement set
* '''mode''' = 'shadow': flag shadowed data
* '''flagbackup''' = False: Do not automatically back up the flag files. We will save all of the ''a priori'' flags together using {{flagmanager_6.6.1}} at the end of this subsection and save some space and time.

The relevant calibration information has already been extracted from the pointing and atmospheric scans and we will not need them moving forward. Flag the pointing scans using {{flagdata_6.6.1}} in 'manual' mode and selecting on 'intent':

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Flagging pointing scans for "+asdm)
    flagdata(vis=asdm+'.ms', mode='manual', intent='*POINTING*', flagbackup = False)
</source>

Note that because the atmospheric calibration scans contain only TDM spectral windows, which will be removed automatically when we separate out the FDM data below.

Now flag the autocorrelation data:

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Flagging autocorrelation data for "+asdm)
    flagdata(vis=asdm+'.ms', autocorr=True, flagbackup=False)
</source>

Finally store the current flags information using {{flagmanager_6.6.1}}: 

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Backing up 'a priori' flags for "+asdm)
    flagmanager(vis = asdm+'.ms', mode='save', versionname='Apriori')
</source>

Where '''versionname''' is just the name we assign to the current flagging state in the data. We can now roll back the flags to match the current version, called 'Apriori', whenever we want. There is no reason to do this now, but the syntax would be:

<source lang="python">
# In CASA - this section is commented out to avoid accidentally running this when unnecessary
'''
for asdm in basename_all:
    print("Restoring flag state to 'a priori' for "+asdm)
    flagmanager(vis=asdm+'.ms', mode='restore', versionname='Apriori')
'''
</source>


It would have been possible to set {{flagdata_6.6.1}} to '''flagbackup'''=True so that it stores the flags at each of the flagging step automatically, but this way it is a bit more efficient with regard to time and disk space. More important, lumping all the ''a priori'' flagging together gives us a natural point to roll back to if we get in trouble.


The flagmanager task will also allow you to view the saved flagging versions,
including those created by running flagdata with flagbackup=True.

For example try 

<source lang="python">
# In CASA
flagmanager(vis='uid___A002_X2181fb_X49.ms', mode='list')
</source>

The output in the logger should list the Apriori flagging that we have applied.
It will also indicate versions associated with any flagdata command where you
did not set flagbackup=False. Other tasks, for example applycal, will also create
flag version tables.

==Create and Apply Tsys, WVR, and Antenna Position Calibration Tables==

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]
</source>

===Tsys===

[[File:Xb.Tsys_vs_time.page1_6.5.4.png|300px|thumb|right|<caption>'''Fig. 2.''' Tsys vs. time plot for uid_A002_X1ff7b0_Xb (northern mosaic). First 8 antennas. Note the high y-axis values for DV04. The two different colors indicate the two polarizations (XX and YY).</caption>]]

[[File:Xb.Tsys_vs_time.page2_6.5.4.png|300px|thumb|right|<caption>'''Fig. 3.''' Tsys vs. time plot for uid_A002_X1ff7b0_Xb (northern mosaic). Remaining antennas.</caption>]]

The Tsys calibration gives a first-order correction for the atmospheric opacity as a function of time and frequency and associates weights with each visibility that persists through imaging.

Use gencal to create the Tsys calibration tables from the spectral windows with the CALIBRATE_ATMOSPHERE intent in listobs (i.e. the TDM spectral windows with 128 channels), which are spws 5 and 7.

<source lang="python">
# In CASA

#Removing existing Tsys tables that may be in your dir
os.system('rm -rf *tdm.tsys')

#Create Tsys tables
for asdm in basename_all:
    print("Creating TDM Tsys Table for "+asdm)
    gencal(vis=asdm+'.ms', caltable=asdm+'.tdm.tsys', spw='5,7', caltype='tsys')
</source>

Later in the applycal stage this TDM Tsys table will be interpolated to the FDM (3840 channels per spw) science spectral windows 1 and 3.

Next we inspect the Tsys tables for spw=5, channel=50 with {{plotms_6.6.1}}. In previous CASA versions, we used '''plotcal''' for this task, but most of '''plotcal''''s functionality is now included in {{plotms_6.6.1}}, and '''plotcal''' is deprecated. We want to check that Tsys data have reasonable values and identify any unexpected features as a function of either time or frequency. To get an idea of sensible Tsys under average atmospheric observations consult the [https://almascience.nrao.edu/proposing/sensitivity-calculator ALMA sensitivity calculator].

We start by plotting the Tsys for all the antennas and polarizations (XX and YY) as a function of time for each. <!--Here and throughout we focus on spw 1, which contains CO(3-2): -->

<pre style="background-color: #E0FFFF;">
Note that when iteraxis is set, plotms appends the axes being iterated over to the output filename specified in plotfile; this can make for rather unwieldy filenames (particularly when iteraxis='antenna'!) but is useful for the ALMA pipeline. 
</pre>

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Plotting Tsys vs. time for "+asdm)
    plotms(vis=asdm+'.tdm.tsys',
           xaxis='time', yaxis='tsys', coloraxis='corr',
           spw='5:50',
           gridrows=4, gridcols=2,
           antenna='0~7', iteraxis='antenna',
           plotfile=asdm+'.tsys_vs_time.page1.png', height=1000, width=1000, overwrite=True)
    # user_input = input("First eight antennas for "+asdm+" . Hit <Enter> to continue: ")
    plotms(vis=asdm+'.tdm.tsys',
           xaxis='time', yaxis='tsys', coloraxis='corr',
           spw='5:50',
           gridrows=4, gridcols=2,
           antenna='8~15', iteraxis='antenna',
           plotfile=asdm+'.tsys_vs_time.page2.png', height=1000, width=1000, overwrite=True)
    # user_input = input("Remaining antennas for "+asdm+" . Hit <Enter> to continue: ")
</source>

This sequence loops over all of our files and plots Tsys as a function of time for channel 50 in spectral window 5. In the call to {{plotms_6.6.1}}:

* '''gridrows'''=4 and '''gridcols'''=2 sets up a 4 x 2 panel grid. 
* '''iteraxis'''='antenna' tells {{plotms_6.6.1}} to make a separate plot for each antenna.
* '''spw'''='5:50' selects spw='5', channel='50'. This allows us to cleanly separate time variations from frequency variations.

Because 8 panels (2 panels for each antenna - LSB and USB) is not enough to show all antennas on one page, there are two {{plotms_6.6.1}} calls: one for the first 8 antennas ('''antenna'''='0~7'), and then for the remaining antennas ('''antenna'''='8~15').

The 'input' commands will wait for you to hit Enter before issuing the next plot command. In the example above these are commented out (the leading "#" means that CASA will ignore them). If you would like to interactively cycle through the plots, uncomment them by removing the "#". Otherwise, the '''plotfile''' parameter directs the output to .png files for later inspection. The easiest way to look at the 20 plots produced here is to simply inspect the .png files using your favorite viewer. As noted above, here {{plotms_6.6.1}} is adding the antenna information to the filenames because we set '''iteraxis''' = 'antenna', so check your directory for the impressively long filenames to view them.

The Tsys values in Figure 2 and Figure 3 look reliable, with typical values ~150 K except for some large values of Tsys at ~400 and 500 K for DV04. We will flag the data for that antenna later. 

<br clear="all">

We will also want to look at Tsys as a function of frequency. Make these plots using {{plotbandpass_6.6.1}}.

<source lang="python">
# In CASA
for asdm in basename_all:
    #rm existing Tsys plots
    os.system('rm -rf cal_plots/Tsys_plots/'+asdm+'.tdm.tsys*')
    #define fields list
    tsysfields=['3c279','Titan','*Antennae*']
    #create Tsys plots
    caltable=asdm+'.tdm.tsys'
    for field in tsysfields:
        plotbandpass(caltable=caltable, yaxis='amp', field=field, xaxis='freq',
                     showatm=True, overlay='time',
                     figfile='cal_plots/Tsys_plots/'+caltable+'.'+field,
                     buildpdf=False, interactive=False, chanrange='8~120', subplot=42)
</source>

You will see the following statement in the logger, but this is fine: 

<pre style="background-color: #fffacd;">
No ASDM_CALWVR, ASDM_CALATMOSPHERE, or CalWVR.xml table found.  Using PWV 1.0mm.
</pre>

Now have a look at the Tsys vs. frequency plots. You can see the effect of a close pair of atmospheric ozone absorption lines at about 343.2 GHz that makes Tsys larger near that frequency in all antennas. Applying the Tsys calibration tables will minimize the contribution of these atmospheric lines. Again DV04 stands out with its very high Tsys.  Although not present in the first data sets, Antenna DV12 exhibits periodic spikes in Tsys vs. frequency for one polarization (see Figure 7). It may or may not be possible to calibrate that behavior out.  We will make a note to look carefully at DV12 further on in the calibration process.

{| class="wikitable"
| [[File:uid___A002_X1ff7b0_Xb.tdm.tsys.*Antennae*.DV02.spw05_6.1.png|300px|thumb|'''Fig. 4.''' Tsys vs. frequency plot for uid_A002_X1ff7b0_Xb (northern mosaic). First 4 antennas. Note the high y-axis values for DV04 and the mesospheric line near 343.2 GHz.]]
| [[File:uid___A002_X1ff7b0_Xb.tdm.tsys.*Antennae*.DV08.spw05_6.1.png|300px|thumb|'''Fig. 5.''' Tsys vs. frequency plot for uid_A002_X1ff7b0_Xb (northern mosaic). Next 4 antennas.]]
| [[File:uid___A002_X1ff7b0_Xb.tdm.tsys.*Antennae*.PM01.spw05_6.1.png|300px|thumb|'''Fig. 6.''' Tsys vs. frequency plot for uid_A002_X1ff7b0_Xb (northern mosaic). Remaining antennas.]]
| [[File:uid___A002_X215db8_X392.tdm.tsys.3c279.PM01.spw05_6.1.png|300px|thumb|'''Fig. 7.''' Tsys vs. frequency plot for uid___A002_X215db8_X392, field 0 = 3c279. Note the pathological behavior for DV12.]]
|}

<br clear="all">

===WVR===
The WVR calibration uses observations of the wings of the 183 GHz atmospheric water line to correct for phase variations as a function of time. As noted in the tsys section, this run of {{wvrgcal_6.6.1}} will append to any existing WVR tables. To avoid this, pre-existing wvrgcal tables are removed. 
<source lang="python">
# In CASA
# Removing existing WVR information
os.system('rm -rf *.wvrgcal')
# Create new WVR tables
for asdm in basename_all:
    wvrgcal(vis=asdm+'.ms', caltable=asdm+'.wvrgcal', toffset=-1)
</source>

===Antenna Positions===

In general, the most appropriate antenna positions for the dataset will be determined and updated if needed during QA2. If the antenna positions need to be updated after QA2, we inform the PIs of the affected datasets and provide instructions on how to update the antenna positions. For the data in this guide, we do need to update the antenna positions. 

The antenna position table reflects refinements in the measured positions of the antennas from those stored in the data. {{gencal_6.6.1}} will now be used put antenna position data into each observation. Again, {{gencal_6.6.1}} will merely append to existing antenna position data, ruining any subsequent results. We start by removing any existing antenna position refinements, followed by defining the antenna names, then their refinements (both as arrays), finally running {{gencal_6.6.1}} to create the information CASA can refer to for antenna positions.

<source lang="python">
# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X1ff7b0_Xb.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:21]+'.antpos')
antenna='DV02,DV04,DV06,DV07,DV08,DV09,DV10,DV11,PM01,PM02,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00034, 0.00092, 0.00027, #PM02-A017 Before July 1
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X207fe4_X3a.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:22]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X207fe4_X3b9.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:23]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X2181fb_X49.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:22]+'.antpos')
antenna='DV01,DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,DV13,PM01,PM03'
parameter = [
-0.00004, 0.00026, 0.00019, #DV01-A137
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
 0.00009, 0.00033, 0.00023, #DV13-A075
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X1ff7b0_X1c8.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:23]+'.antpos')
antenna='DV02,DV04,DV06,DV07,DV08,DV09,DV10,DV11,PM01,PM02,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00034, 0.00092, 0.00027, #PM02-A017 Before July 1
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X207fe4_X1f7.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:23]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X207fe4_X4d7.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:23]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV11,DV12,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X215db8_X18.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:22]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,DV13,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
 0.00009, 0.00033, 0.00023, #DV13-A075
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X215db8_X1d5.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:23]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,DV13,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
 0.00009, 0.00033, 0.00023, #DV13-A075
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)

# In CASA
# The measurement set we are refining the antenna positions for
data='uid___A002_X215db8_X392.ms'
# Removing existing antenna refinements
os.system('rm -rf '+data[0:23]+'.antpos')
antenna='DV02,DV04,DV05,DV06,DV07,DV08,DV09,DV10,DV11,DV12,DV13,PM01,PM03'
parameter = [
 0.00000, 0.00000, 0.00000, #DV02-A015
-0.00004, 0.00059, 0.00024, #DV04-J505
-0.00019,-0.00003, 0.00035, #DV05-A067
-0.00027, 0.00033, 0.00022, #DV06-T704
 0.00006, 0.00057, 0.00032, #DV07-A004
-0.00027, 0.00025,-0.00003, #DV08-A072
-0.00037, 0.00025, 0.00003, #DV09-A008
-0.00056, 0.00028, 0.00026, #DV10-A009
-0.00028, 0.00024, 0.00011, #DV11-A016
-0.00018, 0.00010,-0.00014, #DV12-A011
 0.00009, 0.00033, 0.00023, #DV13-A075
-0.00017, 0.00013, 0.00030, #PM01-T702
-0.00007, 0.00034, -0.00004] #PM03-J504 
gencal(vis=data,caltable='%s.antpos'%(data.split('.')[0]),caltype='antpos',
       antenna=antenna,parameter=parameter)
</source>

===Applycal===

We are now ready to apply the Tsys and the WVR calibration tables to the data with {{applycal_6.6.1}}, which reads the specified gain calibration tables, applies them to the (raw) data column, and writes the calibrated results into the corrected column. Again, we loop through all the datasets. It is important to only apply Tsys and WVR corrections obtained close in time to the data being corrected, so in addition to looping over data sets we define the list of unique source names and loop over these. Then by setting '''gainfield''' and '''field''' to the same value we ensure that Tsys and WVR calibrations are only applied to the source for which they are measured. Because the source has a different name in the Northern Mosaic and the Southern Mosaic, we will carry out two loops. We will only correct '''spw''' 1 and 3, our science windows, because we will drop the other data in a moment.

The applycal task now has much more flexibility for interpolating and applying calibrations derived in one spectral window to another, even if they do not share the same spectral shape (number of channels and channel width). This new functionality is used below to interpolate the TDM (128 channel) Tsys measurements to the FDM (3840 channel) spectral windows. This is controlled through the spectral window mapping parameter '''spwmap'''. Because this can be a bit confusing, we've written a "helper" function that will tell you what you should put for the Tsys calibration table part of spwmap. We only need to run it on one of the datasets because they are all the same in this regard.

<source lang="python">
# In CASA
from casarecipes.almahelpers import tsysspwmap
tsysspwmap(vis='uid___A002_X207fe4_X3a.ms', tsystable='uid___A002_X207fe4_X3a.tdm.tsys')
</source>

This will print to your screen: [0, '''5''', 5, '''7''', 4, 5, 5, 7], which are the TDM Tsys spws to map to the respective FDM science spws [0, '''1''', 2, '''3''', 4, 5, 6, 7, <span style="color:red">8</span>]. This spwmap tells applycal to use the Tsys information in spw 5 for spw 1, and spw 7 for spw 3. Beyond that, it is only important that there are placeholders for the other spectral windows. Also note that you need not give placeholders for spw IDs larger than the largest spectral window you need to use, in this case 7, so our map does not have an index=8.

You also need to give '''spwmap''' placeholders for other tables that you give '''gaintable'''. If the Tsys table is second in '''gaintable''', then '''spwmap'''=[[],[0,5,5,7,4,5,5,7],[]].

Now run the {{applycal_6.6.1}} commands.

<source lang="python">
# In CASA

# A new list of file names that contain only data from the Northern Mosaic
basename_north = ["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9","uid___A002_X2181fb_X49"]
field_names_north = ['Titan','3c279','NGC*']

for asdm in basename_north:
    print("Apply Tsys, WVR, and Antenna Position calibrations to "+asdm)
    for field in field_names_north:
        applycal(vis=asdm+".ms", spw='1,3', 
            field=field, gainfield=['',field,field],
            interp=['','linear,spline','nearest'], 
            gaintable=[asdm+'.antpos',asdm+'.tdm.tsys',asdm+'.wvrgcal'],
            spwmap=[[],[0, 5, 5, 7, 4, 5, 5, 7],[]],
            flagbackup=False, calwt=True)

# A new list of file names that contain only data from the Southern Mosaic
basename_south=["uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7","uid___A002_X207fe4_X4d7",
                           "uid___A002_X215db8_X18","uid___A002_X215db8_X1d5","uid___A002_X215db8_X392"]
field_names_south = ['Titan','3c279','Ant*']

for asdm in basename_south:
    print("Apply Tsys, WVR, and Antenna Position calibrations to "+asdm)
    for field in field_names_south:
        applycal(vis=asdm+".ms", spw='1,3', 
            field=field, gainfield=['',field,field],
            interp=['','linear,spline','nearest'],
            gaintable=[asdm+'.antpos',asdm+'.tdm.tsys',asdm+'.wvrgcal'],
            spwmap=[[],[0, 5, 5, 7, 4, 5, 5, 7],[]],  
            flagbackup=False, calwt=True)
</source>

where:

*'''field''': the field ''to'' which we will apply the calibration, 
*'''gainfield''': the field ''from'' which we wish to take the calibration table
*'''interp''' = 'nearest' : apply the nearest solution from the calibration table rather than interpolating.

As you browse through the whole data set, you will probably note some problems along the same lines as the DV04 issue we saw above. We'll apply these as additional data flagging in just a moment.

==Inspect Data==
We are not quite done with the original ".ms" data sets yet. Before going further it will be useful to use {{plotms_6.6.1}} to show the effects of applying the calibration. In the process we'll take a quick look at each antenna and search for pathologies in the data.

For this basic inspection, we want to compare the phase and amplitude as a function of frequency and time in the DATA and CORRECTED columns of each measurement set. The CORRECTED column has had the Tsys and WVR calibrations applied and so we expect lower phase scatter and flatter amplitude response as a function of time and frequency. We are looking for antenna-based issues, so cycling through a set of baselines that includes each antenna once will be a good start. We'll focus these plots on the phase+bandpass calibrator, 3c279, and on baselines that include antenna DV11, which we will make our reference antenna in just a bit.
<!-- The DATA column holds the current raw data, though using split as we just did we can change the definition of
"raw" data. -->

<div style="background-color: #E0FFFF; padding: 10px; font-family: 'Consolas', monospace;>
Each CASA Measurement Set has up to three "columns" of data: DATA, CORRECTED, and MODEL (though it is possible
for a MS to hold only a DATA column if it has not been processed at all).
A column entry exists for each data point (baseline, frequency, time).
* The CORRECTED column holds the result of applying one or more calibration tables (e.g., via {{applycal_6.6.1}}) to the DATA column and so represents a corrected version of the DATA column. 
* The MODEL column is set for example by {{setjy_6.6.1}} '''usescratch'''=True or {{tclean_6.6.1}} '''savemodel'''='modelcolumn').
To get an intuitive feel for the columns you may wish to explore using {{plotms_6.6.1}} (which can plot different data 
columns, as seen below) or the {{browsetable_6.6.1}} task - [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/data_examination.html#Browse-MS/Calibration-Tables see examples here].
</div>

[[File:Uid_A002_X1ff7b0_Xb_ampfreq_DV11_data_6.5.4.png|300px|thumb|right|<caption>'''Fig. 8.''' Example of Amplitude vs. Frequency before correction for 3c279: DATA column.</caption>]]
[[File:Uid_A002_X1ff7b0_Xb_ampfreq_DV11_corrected_6.5.4.png|300px|thumb|right|<caption>'''Fig. 9.''' Same baseline as Figure 8 but now after correction using WVR and Tsys calibrations: CORRECTED column.</caption>]]

First, we plot amplitude as a function of frequency for 3c279. We start by plotting the DATA column, set color to indicate the two correlations (i.e., the XX and YY polarizations), and ask plotms to iterate over baseline. By setting '''antenna''' to 'DV11&*' we select only baselines that include DV11 (see [https://casadocs.readthedocs.io/en/v6.6.1/notebooks/visibility_data_selection.html#The-antenna-Parameter Visibility Data Selection - '''antenna''' parameter]). We ask plotms to average all data over a very long timescale, '''avgtime'''=1e8 seconds ~ 3 years, much longer than the time spanned by the whole data set. By setting '''avgscan'''=True we allow {{plotms_6.6.1}} to average across scan boundaries. The result is a plot of average amplitude per channel vs. frequency. Try first with just one MS.

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

asdm=basename_all[0]

plotms(vis=asdm+'.ms', 
       field='3c279',
       xaxis='frequency', yaxis='amp',
       selectdata=True, spw='1', 
       avgtime='1e8', avgscan=True,
       coloraxis='corr',
       iteraxis='baseline',
       antenna='DV11&*',
       ydatacolumn='data', 
       showgui=True)
</source>

Notice the green arrows along the bottom of the {{plotms_6.6.1}} window. We asked {{plotms_6.6.1}} to iterate over baseline. As you click the arrows, the plot will rotate from baseline to baseline, always with DV11 so that each antenna shows up once. To see the effect of the calibration, go to the "Axes" tab along the left of the {{plotms_6.6.1}} window and pull down the Data Column menu under the Y Axis. Set this from DATA to CORRECTED and you should see the effects of the calibration. You may need to ensure that the "Force Reload" box is checked before clicking "Plot" (both buttons lie at the bottom of the panel). For the most part things get better (flatter), but as we noted before DV04 is problematic.

You can now make analogous calls to examine the phase vs. frequency, amplitude vs. time, and phase vs. time.

<source lang="python">
# In CASA
plotms(vis=asdm+'.ms', 
       field='3c279',
       xaxis='frequency', yaxis='phase',
       selectdata=True, spw='1', 
       avgtime='1e8', avgscan=True,
       coloraxis='corr',
       iteraxis='baseline',
       antenna='DV11&*',
       ydatacolumn='data', 
       showgui=True)

plotms(vis=asdm+'.ms', 
       field='3c279',
       xaxis='time', yaxis='amp',
       selectdata=True, spw='1:1200~1299', 
       avgchannel='100', avgscan=False,
       coloraxis='corr',
       iteraxis='baseline',
       antenna='DV11&*',
       ydatacolumn='data', 
       showgui=True)

plotms(vis=asdm+'.ms', 
       field='3c279',
       xaxis='time', yaxis='phase',
       selectdata=True, spw='1:1200~1299', 
       avgchannel='100', avgscan=False,
       coloraxis='corr',
       iteraxis='baseline',
       antenna='DV11&*',
       ydatacolumn='data', 
       showgui=True)
</source>

Where:

* '''spw''' is set to cover only channels 1200~1300 for the time plots in order to isolate time dependent variations from frequency-dependent behavior. Those 101 channels represent only a small part of the total spw 1 bandpass.
* '''avgchannel''' set to a large number causes the plots of phase and amplitude vs. time to average data at all frequencies into a single point for each measurement.
* '''coloraxis''' corr sets the colors to correspond to the two polarizations of the data.

In each case, you will want to examine each baseline, alternating between the DATA and CORRECTED columns.

This is a lot of data inspection and that's only for one of 10 data sets! You can iterate across the data by hand, updating "asdm" to refer to each data set in order and cycling between baselines and DATA/CORRECTED. It is also possible to script CASA to show you the key plots in succession (see the next block down). However you approach the infrastructure, you are looking for:

* Improved scatter and lower variability in phase and amplitude vs. frequency and time. This indicates that the WVR and Tsys calibrations helped. 
* Sudden jumps in phase or amplitude as a function of either time or frequency. These may indicate problems with the antenna during that observation.
* Large gradients, especially full wraps, in phase as a function of frequency. This may indicate a problem in the delays, the signal path length to the telescopes.
* Unusual magnitude, scatter, or patterns in any plot - though this may be better explored using plots that show all data together, which we'll make in a moment.
* Missing data. For example, if the phase calibrator drops out for a period of time we will not be able to calibrate and will need to flag the data.

As you look through, note individual potentially problematic antennas. If ''all'' antennas in a data set appear problematic it may be that your "reference" antenna, DV11 in the example above, is the source of the problem. In this case swap this reference antenna for another and see whether the problem is isolated to your original reference antenna.

<pre style="background-color: #E0FFFF;">

A brief aside on structure:

This section (Data Inspection) and the next (Apply Flags) are closely linked. We will present them as two
separate steps. The idea here is that you look through your data, note problems, and then write commands to
flag problematic data. This mimics one approach to writing data reduction scripts for CASA, where you will
group all flagging together into one convenient place. Other CASA guides take a different approach, interleaving 
flagging and plotting. There is no "right" answer here. Find an approach to data inspection that works for you.

</pre>

If you do wish to semi-automate the plot generation, the following sequence will cycle between data and corrected plots for each data set in turn. Type "stop" at any input call to break out.
<!--
'''Note:''' In loops like this involving {{plotms_6.6.1}}, hitting enter before the last dataset completes loading may cause {{plotms_6.6.1}} to stop refreshing the plot window at each step, or cause the window to disappear altogether. This will be fixed in an upcoming CASA release. Right now, you may need to exit CASA and restart to bring up the {{plotms_6.6.1}} window again, but you should be able to continue in the script where you left off.
-->

<source lang="python">
# In CASA

user_input = ""
for asdm in basename_all:
    # check if a stop has been requested
    if user_input == "stop":
        break
    # Extract antenna list for this data set.
    tb.open(asdm+'.ms/ANTENNA', nomodify=True)
    ants = tb.getcol('NAME')
    tb.close
    # Define the reference antenna to make baselines with
    ref_ant = 'DV11'
    # Loop over antennas
    for ant in ants:
        # Check if the user wants to stop
        if user_input == "stop":
            break
        # Skip correlation of reference antenna with itself (autocorrelations are flagged anyhow)        
        if ant == ref_ant:
            continue
        # Define the baseline with the reference antenna for current antenna
        ant_str = ref_ant+'&'+ant
        print("Showing baseline "+ant_str+" for data set "+asdm)
        print("Use this to inspect effect of applying wvrcal and Tsys calibrations: ")
        # Loop over phase and amplitude as axes
        for y_axis in ["amp", "phase"]:
            # Make 'before' plot for frequency x-axis
            print("... "+y_axis+" vs. frequency for DATA:")    
            plotms(vis=asdm+'.ms', spw='1', field='3c279',
               antenna=ant_str, xaxis="frequency", yaxis=y_axis,
               avgtime="1e8", avgscan=True, coloraxis="corr",
               ydatacolumn="data", showgui=True)
            user_input = input("Hit <ENTER> to see CORRECTED data [type 'stop'+<Enter> to break out]: ")
            if user_input == "stop":
                break
            # Make 'after' plot for frequency x-axis
            print("... "+y_axis+" vs. frequency for CORRECTED:")
            plotms(vis=asdm+'.ms', spw='1', field='3c279',
               antenna=ant_str, xaxis="frequency", yaxis=y_axis,
               avgtime="1e8", avgscan=True, coloraxis="corr",
               ydatacolumn="corrected", showgui=True)
            user_input = input("Hit <ENTER> to proceed to next plot [type 'stop'+<Enter> to break out]: ")
            if user_input == "stop":
                break
            # Make 'before' plot for time x-axis
            print("... "+y_axis+" vs. time for DATA:")    
            plotms(vis=asdm+'.ms', spw='1:1200~1299', field='3c279',
               antenna=ant_str, xaxis="time", yaxis=y_axis,
               avgchannel="100", coloraxis="corr",
               ydatacolumn="data", showgui=True)
            user_input = input("Hit <ENTER> to see CORRECTED data [type 'stop'+<Enter> to break out]: ")
            if user_input == "stop":
                break
            # Make 'after' plot for time y-axis
            print("... "+y_axis+" vs. time for CORRECTED:")
            plotms(vis=asdm+'.ms', spw='1:1200~1299', field='3c279',
               antenna=ant_str, xaxis="time", yaxis=y_axis,
               avgchannel="100", coloraxis="corr",
               ydatacolumn="corrected", showgui=True)
            user_input = input("Hit <ENTER> to proceed to next plot [type 'stop'+<Enter> to break out]: ")
            if user_input == "stop":
                break
</source>

A detailed explanation of the procedure is a bit outside the scope of this guide (for more on python see http://www.python.org/ and for more on the CASA toolkit see http://casa.nrao.edu/), but the basic process is to loop over each data set, baseline with the reference antenna (here DV11), and y-axis of interest (phase or amplitude) then plot the effect of the calibration vs. frequency and time for each combination. Running this to step through the data will give you about 200 "before and after" plots from which you could note a subset of problematic cases to be followed up by hand. Many other strategies to inspect the data are also viable.

With the Tsys and WVR calibrations applied successfully and the ''a priori'' flagging taken care of we will now {{split_6.6.1}} out the corrected data. We will keep only the corrected data, specified via '''datacolumn''', and only spectral window 1, which contains the FDM (high spectral resolution) observations of the CO(3-2) line. Setting '''keepflags'''=False tells {{split_6.6.1}} not to carry over any fully flagged rows from the original data set to the new MS. We give the new MS files the extension ".wvrtsys.ms" to indicate that they have been corrected for WVR and Tsys effects. Because split will not overwrite existing files, we remove any previous versions of the new MS before beginning.

<source lang="python">
# In CASA
for asdm in basename_all:
    os.system('rm -rf '+asdm+'.wvrtsys.ms')
    print("Splitting out corrected data for "+asdm)
    split(vis=asdm+'.ms', outputvis=asdm+'.wvrtsys.ms', 
          datacolumn='corrected', spw='1', keepflags=False)
</source>

Be patient, {{split_6.6.1}} may take awhile. The WVR and Tsys-corrected data now sit in the DATA column of the new measurement sets, which have only one spectral window (now labeled spectral window 0 though it was spectral window 1 in the original data). You may wish to run {{listobs_6.6.1}} to illustrate the changes:

<source lang="python">
# In CASA
for asdm in basename_all:
    os.system('rm '+asdm+'.wvrtsys.listobs.txt')
    listobs(vis=asdm+'.wvrtsys.ms', listfile=asdm+'.wvrtsys.listobs.txt', verbose=True)
</source>

Note the new spectral window information:

<pre style="background-color: #fffacd;">

2011-08-05 01:07:08 INFO listobs	Spectral Windows:  (1 unique spectral windows and 1 unique polarization setups)
2011-08-05 01:07:08 INFO listobs	  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)TotBW(kHz)  Ref(MHz)    Corrs   
2011-08-05 01:07:08 INFO listobs	  0        3840 TOPO  344845.586  488.28125   1875000     344908.33   XX  YY  

</pre>

[[File:plotms_amp_vs_time_north_6.1.png|300px|thumb|right|<caption>'''Fig. 10.''' Example of Amplitude vs. Time for a Northern mosaic data set.</caption>]]
[[File:plotms_amp_vs_time_south_6.1.png|300px|thumb|right|<caption>'''Fig. 11.''' Example of Amplitude vs. Time for a Southern mosaic data set.</caption>]]
[[File:Uid_A002_X1ff7b0_Xb.wvrtsys_3c279_ampuvdist_6.5.4.png|300px|thumb|right|<caption>'''Fig. 12.''' Example of Amplitude vs. UV-distance for 3c279 in the first Northern mosaic data set.</caption>]]

Next we will do a bit more inspection using {{plotms_6.6.1}} to look at whole data sets. This will help us identify missing data or look for egregious outliers.

First we plot amplitude versus time (see Fig. 10 and Fig. 11), averaging over all channels. We colorize by field so that scans on Titan are red, the bandpass and phase calibrator 3c279 is black (and orange in the Southern Mosaic where it has two field IDs), and the Antennae mosaic appears as a range of colors (one per pointing).

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    plotms(vis=asdm+'.wvrtsys.ms', 
           xaxis='time', yaxis='amp', 
           avgchannel='3840', coloraxis='field', showgui=True)
    user_input = input("Examining amplitude vs. time for "+asdm+" . Hit <Enter> to proceed.[type 'stop'+<Enter> to break out]: ")
    if user_input == "stop":
        break
</source>

Here look for:

* Missing data. Science target scans need to be bracketed by phase calibrator scans - if those are missing for any reason we need to flag the appropriate target scan.
* Dramatic outliers. Does the source suddenly get very bright or the otherwise bright calibrator appear anomalously faint for a brief time? This likely indicates problematic data that should be identified and flagged. You can use the "mark regions" (box with green plus along the bottom row in plotms) and "locate" (magnifying glass) buttons in {{plotms_6.6.1}} to isolate and identify problem data (it will print to the log). Write this to a {{flagdata_6.6.1}} call later - flagging with the GUI is not recommended since it is difficult to keep a record and reproduce results.
* Smooth variation with time. A sudden jump may indicate a problem and often the safest approach is to flag data near a discontinuity.

Look through the amplitudes vs. time for each data set (remember that we've already examined the phases vs. time and amplitude vs. time for individual baselines above).

There are two other very useful "averaging" plots worth making. First, we plot amplitude as a function of u-v distance (projected antenna separation). Discontinuities and spikes in this plot are often from non-astrophysical sources. In Phase vs UVdist, the effects of atmospheric decorrelation can be assessed from increased scatter at longer u-v distances. While using Titan as our flux calibrator, we may want to watch for flaring amplitudes at short u-v distances. These may indicate that Saturn is contaminating our beam. For a perfect, bright point source, we expect flat amplitudes as a function of u-v distance at the source amplitudes. Figure 12 shows an example of this plot, generated via:

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    plotms(vis=asdm+'.wvrtsys.ms', 
           field='3c279',
           xaxis='uvdist', yaxis='amp', 
           avgchannel='3840', coloraxis='corr', showgui=True)
    user_input = input("Examining amplitude vs. UV Distance for 3c279 for "+asdm+" . Hit <Enter> to proceed. Type 'stop'+<Enter> to break out: ")
    if user_input == "stop":
        break
    plotms(vis=asdm+'.wvrtsys.ms', 
        field='Titan',
        xaxis='uvdist', yaxis='amp', 
        avgchannel='3840', coloraxis='corr', showgui=True)
    user_input = input("Examining amplitude vs. UV Distance for Titan for "+asdm+" . Hit <Enter> to proceed [type 'stop'+<Enter> to break out]: ")
    if user_input == "stop":
        break
</source>

It can also be useful to examine the average amplitude as a function of frequency for each target. This allows one to check for lingering atmospheric effects, unexpected line emission or absorption in the calibrators, or decreased sensitivity due to "roll-off" of the telescope sensitivity at the band edges. These plots are created by the sequence of commands below, where we have broken up the script to loop separately over the Northern and Southern Mosaics to reflect the different source names.

<source lang="python">
# In CASA

basename_north=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9","uid___A002_X2181fb_X49"]
field_names = ["3c279","Titan","NGC*"]

user_input=""
for asdm in basename_north:
    if user_input == "stop":
        break
    for field in field_names:
        plotms(vis=asdm+'.wvrtsys.ms', 
               field=field,
               xaxis='frequency', yaxis='amp', 
               avgtime='1e8', avgscan=True, coloraxis='corr', showgui=True)
        user_input = input("Examining amplitude vs. frequency for "+field+" in "+asdm+". Hit <Enter> to proceed. Type 'stop'+<Enter> to break out: ")
        if user_input == "stop":
            break
 
basename_south=["uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7","uid___A002_X207fe4_X4d7",
                           "uid___A002_X215db8_X18","uid___A002_X215db8_X1d5","uid___A002_X215db8_X392"]
field_names = ["3c279","Titan","Ant*"]

user_input=""
for asdm in basename_south:
    if user_input == "stop":
        break
    for field in field_names:
        plotms(vis=asdm+'.wvrtsys.ms', 
               field=field,
               xaxis='frequency', yaxis='amp', 
               avgtime='1e8', avgscan=True, coloraxis='corr', showgui=True)
        user_input = input("Examining amplitude vs. frequency for "+field+" in "+asdm+". Hit <Enter> to proceed. Type 'stop'+<Enter> to break out: ")
        if user_input == "stop":
            break
</source>

{| class="wikitable"
| [[File:Uid_A002_X207fe4_X3a.wvrtsys_3c279_ampfreq_6.5.4.png|300px|thumb|'''Fig. 13.''' Amplitude vs. Frequency for 3c279 in the second Northern mosaic data set.]]
| [[File:Uid_A002_X207fe4_X3a.wvrtsys_Titan_ampfreq_6.5.4.png|300px|thumb|'''Fig. 14.''' Amplitude vs. Frequency for Titan in the second Northern mosaic data set. Note the strong line (this is CO 3-2)!]]
| [[File:Uid_A002_X207fe4_X3a.wvrtsys_NGC_ampfreq_6.5.4.png|300px|thumb|'''Fig. 15.''' Amplitude vs. Frequency for the Antennae in the second Northern mosaic data set. The CO(3-2) line is visible.]]
|}

For this command notice that we can see the CO(3-2) line in the Antennae even before calibration (see Figure 15) and that Titan also shows evidence of a strong line (see Figure 14)! This will need to be flagged before we can use Titan to calibrate the flux scale of our data.

This suite of plots (along with the earlier inspection of the Tsys tables) gives us the tools we need to identify problematic data through the data sets. We use this to generate a set of inspection-driven {{flagdata_6.6.1}} commands for each data set. We apply these before the bandpass and gain calibration.

==Apply Flagging==
Based on this inspection and the other plots we have made, we now flag problematic portions of the data. We break up the flags by reason for flagging in order to illustrate the process. As you reduce your own data it may be more efficient to group flags by data set and make use of {{flagcmd_6.6.1}} which takes batches of {{flagdata_6.6.1}} commands. Except for the "post-calibration" flagging, the inspection plots that we just looked through have already revealed all of the problems that we flag. We structure the guide so that the flagging is grouped in one place.

As before, we may wish to reset our flags before beginning (particularly if one iterates this process) via:

<source lang="python">
# In CASA

basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
    "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
    "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
    "uid___A002_X215db8_X392"]
for asdm in basename_all:
    flagdata(vis=asdm+'.wvrtsys.ms', mode='unflag', flagbackup=False)
</source>

Remember that we dropped the flagged data when splitting out after the WVR and Tsys calibration, so this should not undo your "A Priori" flagging of shadowed data, autocorrelations, etc.. In any case this unflagging step is not necessary during the first iteration.

* '''Edge Channels'''

[[File:amp_vs_channel_example.png|200px|thumb|right|<caption>'''Fig. 16.''' Amplitude vs. Channel for one uncalibrated antenna pair. This kind of plot can be inspected to get an idea of the presence or magnitude of any roll-off in sensitivity near the edges of the spectral window.</caption>]]

ALMA's sensitivity decreases near the edge of the baseband and it is often useful to check for a 'roll-off' in sensitivity near the edge of the band. This will appear as a downturn in amplitude as a function of channel near the edge of the window in the uncalibrated data, or as a flaring due to increased noise at the spw edges in the calibrated data. It will also be visible in the amplitude part of the bandpass calibration table. Because our FDM spw does not cover the full baseband, we do not see a strong roll off in our data (see Figure 16). There is a hint of a roll-off at the high end only, but we do flag a few channels at both edges to be safe.

<source lang="python">
# In CASA

for asdm in basename_all:
    flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', spw='0:0~7;3831~3839', flagbackup=False)
</source>

<br clear="all">

* '''ATM line'''

Flag a small channel range affected by an atmospheric line, which we will see later in bandpass calibration plots.
<source lang="python">
# In CASA

for asdm in basename_all:
    flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', spw='0:3260~3320', flagbackup=False)
</source>

Note that in more recent operations, it is typical to not flag ATM lines, since they can often be handled through calibration.

<br clear="all">

* '''Problematic Tsys measurements'''

Above we noted issues with the Tsys measurements for both DV04 and DV12, so we flag the affected data. Each of these issues should be visible in the Tsys plots you made (e.g., Figures 4 and 5).

<source lang="python">
# In CASA

asdm_list=["uid___A002_X1ff7b0_Xb","uid___A002_X1ff7b0_X1c8"]
for asdm in asdm_list:
    flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='DV04', flagbackup=False)

asdm_list=["uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9","uid___A002_X2181fb_X49",
    "uid___A002_X207fe4_X1f7","uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18",
    "uid___A002_X215db8_X1d5","uid___A002_X215db8_X392"]
for asdm in asdm_list:
    flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='DV12', correlation='YY', flagbackup=False)
</source>

<br clear="all">

* '''Unreliable Short-Spacing Measurements on Titan'''

[[File:amp_vs_uv_titan_obs.png|200px|thumb|right|<caption>'''Fig. 17.''' Amplitude vs. UV-distance for observations of Titan in the first data set. Note the scatter for low projected antenna separations. We will flag these short-spacing data, which may reflect contamination by Saturn, and use only the more extended baselines for flux calibration.</caption>]]

Saturn may contaminate the short u-v spacings from Titan. In any case these often show significant scatter (Figure 17), so we flag them. There are still enough baselines to determine a good amplitude calibration for each antenna.

<source lang="python">
# In CASA

asdm="uid___A002_X1ff7b0_Xb"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~50', flagbackup=False)

asdm="uid___A002_X207fe4_X3a"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~40', flagbackup=False)

asdm="uid___A002_X207fe4_X3b9"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~50', flagbackup=False)

asdm="uid___A002_X2181fb_X49"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~30', flagbackup=False)

asdm="uid___A002_X1ff7b0_X1c8"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~50', flagbackup=False)

asdm="uid___A002_X207fe4_X1f7" 
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~30', flagbackup=False)

asdm="uid___A002_X207fe4_X4d7" 
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', field='Titan', uvrange='0~30', flagbackup=False)
</source>

<br clear="all">

* '''Delay Issues'''

[[File:phase_vs_freq_DV13.png|200px|thumb|right|<caption>'''Fig. 18.''' Phase vs. Frequency for DV13 in a data set where this antenna shows evidence of imperfect delay calibration.</caption>]]

DV13 and a few other antennas show signatures of an imperfect delay calibration. This is most easily identified via strong "wrapping" of phase as a function of frequency (see Figure 18). Such effects can be calibrated out with mild delay issues largely accounted for by the bandpass solution. The phase wrapping in DV13 seems weak enough that we will trust the calibrations to remove it. For a more extreme example see the CASA guide describing the calibration of [[NGC3256Band3]].

<br clear="all">

* '''Missing Phase Calibrator Observations'''

[[File:amp_vs_time_missing_scans.png|200px|thumb|right|<caption>'''Fig. 19.''' Amplitude vs. Time colored by field for a data set where the final visit to the phase calibrator is missing. We will flag the last set of target data to ensure that each visit to the target is flanked in time by visits to the phase calibrator.</caption>]]

As a general rule, we want to be sure that observations of the phase calibrator (3c279) bracket each source observation. Two of the data sets do not include a final phase calibrator observation (see Figure 19) and for those two cases we flag the affected source observations.

<source lang="python">
# In CASA

asdm="uid___A002_X207fe4_X3b9"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', timerange='00:53:47~01:08:00', flagbackup=False)

asdm="uid___A002_X215db8_X18"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='DV10', timerange='19:46:20~20:34:40', flagbackup=False)
</source>

<br clear="all">

* '''Unexpected Scatter or Discontinuity in the Data'''

[[File:phase_vs_time_DV09.png|200px|thumb|right|<caption>'''Fig. 20.''' Phase vs. Time for DV09 on a problematic day. It may prove problematic to calibrate the data near this discontinuity so we flag data near this time.</caption>]]

For several antennas we find sudden jumps in the phase of the phase calibrator as a function of time. These are visible in the plots of uncalibrated phase vs. time for single baselines above, and we show an example in Figure 20. It will not be possible to effectively interpolate the phase between measurements when we see these discontinuities. The safest approach is to flag the source data across these jumps. We do so here (though note that the last two flaggings are borderline cases).

<source lang="python">
# In CASA

asdm="uid___A002_X207fe4_X3a"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='DV09', timerange='21:24:09~21:35:35', flagbackup=False)

asdm="uid___A002_X207fe4_X1f7" 
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='DV09', timerange='23:30:52~24:10:00', flagbackup=False)
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='PM01', timerange='23:16:50~24:10:00', flagbackup=False)
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='PM03', timerange='23:16:50~24:10:00', flagbackup=False)
</source>

<br clear="all">

* '''Outliers Visible After Calibration'''

[[File:amp_vs_uvdist_outliers.png|200px|thumb|right|<caption>'''Fig. 21.''' Amplitude vs. UV-distance ''after'' calibration. Note the outlying data. We track these down using the select (box with green "+") and locate (magnifying glass) features inside plotms and identify several problematic baselines across our data. ''Note that you cannot make this plot at this point in the guide, these pathologies become evident after calibration, requiring an iterative approach to reduction.''</caption>]]

Often issues with the data may become evident after calibration (i.e., after the next few steps that we apply). See Figure 21. These data can appear as outliers in diagnostic plots for the calibrated data or even show up in the imaging stages. Once these are identified, best practice is to apply this new flagging then redo the calibration (if the issue is very minor, then re-calibrating may not be necessary).

<source lang="python">
# In CASA
asdm="uid___A002_X207fe4_X3a"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', timerange='21:18:00~21:22:15', flagbackup=False)

asdm="uid___A002_X2181fb_X49"
flagdata(vis=asdm+'.wvrtsys.ms', mode='manual', antenna='DV01&DV04', flagbackup=False)
</source>

<br clear="all">

Now that we've applied our flagging, back up the flags as version "User" using {{flagmanager_6.6.1}}:

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    flagmanager(vis=asdm+'.wvrtsys.ms', mode='save', versionname='User')
</source>

Applying this flagging will remove the most egregious pathologies from the data. We are now ready to calibrate the data.

<br clear="all">

==Bandpass Calibration==

[[File:plotms_phase_vs_freq_example_6.1.png|300px|thumb|right|<caption>'''Fig. 22.''' Phase vs. frequency for the bandpass calibrator, 3c279 in the first data set. We plot all baselines with DV02, averaged over time, and show only the 'XX' correlation.</caption>]]

We begin by calibrating the phase and amplitude response of each antenna as a function of frequency, called "bandpass calibration." We have already seen that the data contain smooth but systematic variations in both phase and amplitude as a function of frequency. We can see this again in a more compact form by plotting phase as a function of frequency for all baselines associated with each antenna (Figure 22).

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    plotms(vis= asdm+'.wvrtsys.ms', 
            xaxis='freq', yaxis='phase', 
            selectdata=True, field='3c279', correlation='XX',
            avgtime='1e8', avgscan=True, antenna='*&*',
            coloraxis='baseline', iteraxis='antenna', showgui=True)
    user_input = input("Plotting phase vs. frequency for "+asdm+". Hit <Enter> for next data set or cycle through antennas [type 'stop'+<Enter> to break out]: ")
    if user_input == "stop":
        break
</source>

Each plot shows phase as a function of frequency for all baselines with one antenna for 3c279. We plot only the 'XX' correlation, colorizing by baseline. With '''iteraxis''' set to antenna the green arrows at the bottom of {{plotms_6.6.1}} will cycle through antennas. By using '''avgscan''' and a large '''avgtime''' we average  all scans and integrations. 

[[File:Uid_A002_X1ff7b0_Xb-phasecont_6.1.png|300px|thumb|right|<caption>'''Fig. 23.''' Phase vs. time for the bandpass calibrator, 3c279. Averaged over channel. Only baselines with antenna DV02, and corr='XX'</caption>]]

The phase (and amplitude) also varies as a function of time, as we saw before. Here are the similar plots for phase vs. time (see Figure 23).

<source lang="python">
# In CASA
for asdm in basename_all:
    plotms(vis= asdm+'.wvrtsys.ms', 
           xaxis='time', yaxis='phase', 
           selectdata=True, field='3c279', 
           spw='0:1200~1299', antenna='*&*', correlation='XX',
           avgchannel='100',  avgscan=True, 
           coloraxis='baseline', iteraxis='antenna', showgui=True)
    user_input = input("Plotting phase vs. time for "+asdm+". Hit <Enter> for next data set or cycle through antennas [type 'stop'+<Enter> to break out]: ")
    if user_input == "stop":
        break
</source>

Figure 23 shows that the phase varies with time. We need to take this temporal variation into account when we solve for the frequency variations. Therefore we carry out the bandpass calibration in two steps. First, we use {{gaincal_6.6.1}} to solve for the variation of phase as a function of time for 3c279 on very short timescales. We set {{gaincal_6.6.1}} to derive a separate phase solution for each antenna every integration by setting '''solint''' to 'int'. We solve, averaging together only a small fraction of the total bandpass (channels 1100-1300) to avoid the effects of the phase vs. frequency behavior ({{gaincal_6.6.1}} will by default use gaintype='G' which averages the specified channels per-spw). We will then apply this solution to remove time-dependent behavior when we solve for the frequency response of the antennas with {{bandpass_6.6.1}}.

<pre style="background-color: #E0FFFF;">
The integration time "T_int" is the smallest time quantum of observation in the data, usually a few seconds. 
You can check the integration length for each scan (per-spw) in listobs, where it is referred to as "Average Interval."
</pre>

[[File:uid___A002_X215db8_X392.bpphase.6.5.4.png|300px|thumb|right|<caption>'''Fig. 24.''' Short interval phase vs. time solution for uid___A002_X215db8_X392, which will be applied on-the-fly before bandpass calibration, colorized by antenna. This solution removes any systematic variations in phase vs. time.</caption>]]

[[File:Uid___A002_X1ff7b0_X1c8.bandpass.DV02.spw0.t1_6.1.png|300px|thumb|right|<caption>'''Fig. 25.''' Bandpass amplitude and phase solutions for the first set of antennas and the first data set.</caption>]]

<!--
This is old and included in Fig 25.
[[File:uid___A002_X1ff7b0_Xb.bcal_phase.page1.png|300px|thumb|right|<caption>'''Fig. 26.''' Phase vs. frequency calibration from the bandpass calibration for the first set of antennas and the first data set.</caption>]]
-->

<source lang="python">
# In CASA

for asdm in basename_all:
    print("Running a short solution interval phase calibration for "+asdm)
    os.system('rm -rf '+asdm+'.bpphase.gcal')
    gaincal(vis=asdm+'.wvrtsys.ms',
            selectdata=True, field='3c279', spw='0:1100~1300',
            caltable=asdm+'.bpphase.gcal',
            solint='int', refant='DV11', calmode='p')
</source>

Here is an example {{plotms_6.6.1}} command to examine these tables:
<source lang="python">
# In CASA
plotms(vis='uid___A002_X215db8_X392.bpphase.gcal', xaxis='time', yaxis='phase', coloraxis='antenna1', clearplots=True,
       title='bpphase.gcal', plotfile='uid_A002_X215db8_X392.bpphase.gcal.png', overwrite=True)
</source>

Now we use {{bandpass_6.6.1}} to solve for the frequency response of each antenna. To do this, we average all data in time by setting '''solint''' to 'inf' (that is, 'infinite'). We allow combination across scans and the different field IDs found for 3c279 by setting '''combine''' to "scan,field" (note that since our command below loops through each asdm, we are still deriving solutions per-EB, not creating a combined solution. This is a precaution in the event a single EB has multiple field IDs or scans for the BP calibrator). We apply the phase vs. time calibration that we just derived on-the-fly using the parameter "gaintable".

<source lang="python">
# In CASA
for asdm in basename_all:
    print("Running a bandpass calibration for "+asdm)
    os.system('rm -rf '+asdm+'.bandpass.bcal')
    bandpass(vis=asdm+'.wvrtsys.ms',
             field='3c279',
             gaintable=asdm+'.bpphase.gcal',
             caltable=asdm+'.bandpass.bcal',
             bandtype='B',
             solint='inf', combine='scan,field', solnorm=True, refant='DV11',
             minblperant=3, minsnr=2, fillgaps=62)
</source>

in these calls:

*'''caltable''' specifies the output calibration table
*'''gaintable''' specifies any calibration tables to be applied "on the fly" to the data before solving.
*'''solint''' sets the time interval for which solutions are derived for each antenna.
*'''refant''' set the reference antenna, here DV11, which is defined to have zero correction by construction.
*'''calmode''' 'p' sets {{gaincal_6.6.1}} to calibrate the phase only, other options are 'a'mplitude or 'ap' - amplitude and phase.
*'''minblperant''' sets the minimum baselines required per antenna for a successful solution.
*'''minsnr''' sets the minimum signal-to-noise ratio required for a successful solution.
*'''bandtype''' here 'B' tells {{bandpass_6.6.1}} to solve for the phase and frequency response of each antenna in each channel, averaging data in time across the solution interval.
*'''fillgaps''' tells {{bandpass_6.6.1}} to interpolate across channel gaps 1 channel wide.
*'''solnorm''' tells {{bandpass_6.6.1}} to normalize the bandpass amplitude and phase corrections to have magnitude unity. The absolute scale of the calibration will come from our later {{gaincal_6.6.1}} solutions.

Do not worry about the message "Insufficient unflagged antennas" when running the {{bandpass_6.6.1}} task. This indicates that {{bandpass_6.6.1}} is failing on the flagged edge channels, which is expected.

It is now a good idea to plot both sets of solutions to look for irregularities, especially:

* discontinuities in the gaincal solution
* rapid wrapping of phase in either gaincal or bandpass solution
* large roll-off in the amplitude response near the band edge in the bandpass solution
* large scatter in any solution

We loop through generating .png files of each bandpass calibration using {{plotbandpass_6.6.1}}. '''yaxis'''='both' will make amp and phase plots.
<!--
Again this warning:
No ASDM_CALWVR, ASDM_CALATMOSPHERE, or CalWVR.xml table found.  Using PWV 1.0mm.
-->

<source lang="python">
# In CASA

os.system('rm -rf cal_plots/*bandpass*.png')
for asdm in basename_all:
    plotbandpass(caltable=asdm+'.bandpass.bcal',
                 field='', xaxis='freq', yaxis='both',
                 figfile='cal_plots/'+asdm+'.bandpass.png',
                 showatm=True, interactive=False, subplot=42)
</source>

==Absolute Flux Calibration of Titan==

The bandpass calibration will account for the phase and amplitude response of our antennas as a function of frequency. We now solve for the absolute flux scale of the data by referencing to Titan. In the next section we will calibrate the phase and amplitude behavior of the antennas as a function of time.

Before using Titan to set the flux, there is an important systematic to account for. When we looked at the integrated spectra of our targets above, remember that Titan showed a whopping spectral line, in fact the same CO(3-2) line that we wish to observe in the Antennae. We will set the flux of Titan (and by extension, the other fields as well) by referencing to a model of Titan in CASA that does not account for this line. Therefore we need to flag the part of the Titan observations contaminated by the line before we calibrate. We run the following additional flagging step:

[[File:Antennae-TitanLine_6.1.png|300px|thumb|right|<caption>'''Fig. 27.''' Uncalibrated amplitude vs. channel plot for the flux calibrator, Titan (uid___A002_X1ff7b0_Xb dataset). Averaged over time, corr='XX', and colorized by baseline. The emission line has been flagged.</caption>]]

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    print("Flagging CO(3-2) in Titan for "+asdm)
    flagdata(vis=asdm+'.wvrtsys.ms', flagbackup=False, 
             field='Titan', spw='0:1100~1700')

for asdm in basename_all:
    flagmanager(vis=asdm+'.wvrtsys.ms', mode='save', versionname='Calibration')
</source>

Next, we will use the {{setjy_6.6.1}} task to read the predicted complex visibilities for Titan into the MODEL column of each data set. '''''usescratch''' should be explicitly set to True.'' <!-- especially for ephemeris calibrators -->

<source lang="python">
# In CASA
# make sure usescratch=True
for asdm in basename_all:
    print("Reading model for Titan into "+asdm)
    setjy(vis=asdm+'.wvrtsys.ms', field='Titan',
          usescratch=True, scalebychan=True,
          standard='Butler-JPL-Horizons 2012')
</source>

{{setjy_6.6.1}} will output the flux of Titan to the CASA logger and it is worth recording this information. The flux of Titan at these frequencies is about 3.3 Jy. For example, for dataset uid___A002_X1ff7b0_Xb.wvrtsys.ms:

<pre style="background-color: #fffacd;">
Titan: spw0 Flux:[I=3.2637,Q=0.0,U=0.0,V=0.0] +/- [I=0.0,Q=0.0,U=0.0,V=0.0] Jy @ 344.85GHz
</pre>

[[File:2012_titan_model_6.1.png|thumb|right|300px|<caption>'''Fig. 28.''' Titan model produced by 'Butler-JPL-Horizons 2012'.</caption>]]

Now we are going to take a look at the Titan model for one dataset:

<source lang="python">
# In CASA
plotms(vis='uid___A002_X1ff7b0_X1c8.wvrtsys.ms', xaxis='uvdist', yaxis='amp',
       ydatacolumn='model', field='Titan', avgtime='1e8', avgchannel='',
       avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)

plotms(vis='uid___A002_X1ff7b0_X1c8.wvrtsys.ms', xaxis='uvdist', yaxis='phase',
       ydatacolumn='model', field='Titan', avgtime='1e8', avgchannel='',
       avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
</source>

Note the model phase is a flat 0 deg across UVdist.

<!--
<div style="background-color: #E0FFFF;">
The setjy invocation made in this section uses the flux density standard '''standard='Butler-JPL-Horizons 2012' '''.  Previous versions of this guide used an older flux density standard '''standard='Butler-JPL-Horizons 2010' '''. Figures 28 and 29 show the differences in the Titan models produced using these two standards. 
</div>
[[File:2010_titan_model.png|thumb|right|300px|<caption>'''Fig. 29.''' Titan model produced by 'Butler-JPL-Horizons 2010'.</caption>]]
-->
<br clear="all">

==Gain Calibration of Titan and 3c279==

With the flux now properly scaled for Titan, we will calibrate the phase and amplitude behavior of the antennas as a function of time.

First we derive a long timescale phase solution from the calibrators that will be used to apply phase corrections from adjacent calibrator scans to the science target scans in between them. We set '''solint''' to "inf", but not allowing scan combination. This calibration has higher signal to noise due to combining more data. It doesn't hurt to include Titan here, but note that its solution in this table is not used; in the next section, our {{applycal_6.6.1}} commands for the science target apply gaintable=asdm+'.scanphase.gcal' corresponding to gainfield='3c279' only. <!-- it is just as precise as the short timescale solution. -->

<source lang="python">
# In CASA

for asdm in basename_all:
    print("Carrying out longer timescale phase solution for "+asdm)
    os.system('rm -rf '+asdm+'.scanphase.gcal')
    gaincal(vis=asdm+'.wvrtsys.ms',
            gaintable=asdm+'.bandpass.bcal', 
            caltable=asdm+'.scanphase.gcal',
            calmode='p',
            field='Titan,3c279',
            spw='0:40~3800',
            refant='DV11', solint='inf', minsnr=2.0, minblperant=4)
</source>

The next three steps build toward an amp/flux calibration table that will be applied to both calibrators and the science target. First we use a short-solution interval {{gaincal_6.6.1}} to solve for phase variation on short timescales during observations of our two calibrators, with '''solint''' set to "int". This calibrates between the many integrations within a scan. By applying this on-the-fly, we can remove any decorrelation in the data due to phase scatter when we solve for the amplitude calibration. This table will also be used to apply phase solutions derived from the calibrators to themselves (in a sense, this is "self-calibration" of the calibrators). <!-- However, there is no benefit to using this short-timescale solution to calibrate the science target because we only have information on the gain during calibrator visits (though see the Imaging portion of this guide). -->

<source lang="python">
# In CASA
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

for asdm in basename_all:
    print("Carrying out short timescale phase solution for "+asdm)
    os.system('rm -rf '+asdm+'.intphase.gcal')
    gaincal(vis=asdm+'.wvrtsys.ms',
            gaintable=asdm+'.bandpass.bcal', 
            caltable=asdm+'.intphase.gcal',
            calmode='p',
            field='Titan,3c279',
            spw='0:40~3800',
            refant='DV11', solint='int', minsnr=2.0, minblperant=4)
</source>

Both phase solutions above are reminiscent of the phase-only correction from the previous Bandpass step (bpphase.gcal), with a key difference: here we correct the frequency response on-the-fly with *bandpass.bcal, so we can use nearly the full channel range for these solutions.

Now we apply the short-timescale phase solution and carry out a scan length ('''solint''' set to "inf") amp+phase calibration of the data using '''calmode'''='ap'. Since the short phase solutions are being applied, this is mostly an amplitude calibration per scan - however, the amplitude calibration is better when we allow minor phase adjustments. Think of "scanphase.gcal" and "intphase.gcal" as phase vs time only - they have no amplitude information. Think of "amp.cal" and "flux.cal" (below) primarily as amp vs time corrections, with some minor phase vs time corrections as well. All four are averaged in frequency.

<source lang="python">
# In CASA

for asdm in basename_all:
    print("Solving for longer (scan) interval amplitude solution for "+asdm)
    os.system('rm -rf '+asdm+'.amp.cal')
    gaincal(vis=asdm+'.wvrtsys.ms',
            gaintable=[asdm+'.bandpass.bcal',asdm+'.intphase.gcal'],
            caltable=asdm+'.amp.cal',
            calmode='ap',
            field='Titan,3c279',
            spw='0:40~3800',
            refant='DV11', solint='inf', minblperant=4)
</source>

This "amp.cal" solution gives us the amplitude variations as a function of time, but they are not yet bootstrapped to a realistic scale except in the case of Titan, where we have solved using the model input by {{setjy_6.6.1}}. We will set the flux of our secondary calibrator 3c279 with reference to Titan using {{fluxscale_6.6.1}}.

<source lang="python">
# In CASA

for asdm in basename_all:
    print("Bootstrapping flux scale (absolute amplitude calibration) from Titan to 3c279 for "+asdm)
    os.system('rm -rf '+asdm+'.flux.cal')
    fluxscale(vis=asdm+'.wvrtsys.ms',
              caltable=asdm+'.amp.cal',
              fluxtable=asdm+'.flux.cal',
              reference='Titan',
              transfer='3c279')
</source>

This new correctly-scaled flux table ".flux.cal" replaces the previous ".amp.cal" table as the correct amplitude calibration table to apply to the data, i.e., ".flux.cal" contains both the time variability of the amplitude solved for in ".amp.cal" and the correct flux scaling set with {{fluxscale_6.6.1}}. Fluxscale only adjusts the amplitudes from "amp.cal" - the minor phase corrections in "amp.cal" carry over unchanged to "flux.cal".

Fluxscale will output the derived flux for 3c279 to the CASA logger. This information is worth noting. We find that the flux of 3c279 is 10.79 Jy by averaging the fluxes obtained from the ten available datasets. If we check this value against reported flux measurements in the [http://sma1.sma.hawaii.edu/callist/callist.html SMA calibrator list], we find that a flux of 10.79 Jy agrees within a few per cent of a linear interpolation between the two 0.85 mm measurements closest in time to the ALMA observations: (23 May 2011, SMA 11.644 ± 0.583; 01 July 2011, 9.748 ± 0.488).

<!--
<div class="noprint" style="float:none; border:0px solid blue;background-color:#F6CEF5;padding:2px;">
If you used the older, Butler-JPL-Horizons 2010, flux density standard when you ran {{setjy_6.6.1}} earlier in this tutorial, the derived flux values for 3c279 will be slightly lower.  The flux of 3c279, when averaged over all 10 measurement sets, will be 10.41 Jy.
</div>
-->

Now we plot the final phase and amplitude calibration tables that will be applied to the target for each data set. A well-behaved calibration table will show smooth variations as a function of time. Sudden jumps or wild variations among the antenna amplitude gains should prompt further investigation and possibly additional flagging.

[[File:uid___A002_X215db8_X392_all_tables_6.5.4.png|500px|thumb|right|<caption>'''Fig. 27.''' For one execution, plot all six bandpass and gain calibration tables on a vertical grid to visualize the differences.</caption>]]

<source lang="python">
# In CASA

for asdm in basename_all:
    print("Plotting solutions for "+asdm)
    plotms(vis=asdm+'.scanphase.gcal',
          xaxis='time', yaxis='phase', coloraxis='corr',
          iteraxis='antenna', antenna='0~7', plotrange=[0,0,-180,180],
          gridrows=4, gridcols=1, showgui=False,
          plotfile=asdm+'.scanphase.page1.png')
    # user_input = input("Hit <Enter> to see next plot: ")
    plotms(vis=asdm+'.scanphase.gcal',
          xaxis='time', yaxis='phase', coloraxis='corr',
          iteraxis='antenna', antenna='8~15', plotrange=[0,0,-180,180],
          showgui=False, gridrows=4, gridcols=1, 
          plotfile=asdm+'.scanphase.page2.png')
    # user_input = input("Hit <Enter> to see next plot: ")
    plotms(vis=asdm+'.flux.cal', 
          xaxis='time', yaxis='amp', coloraxis='corr',
          iteraxis='antenna', antenna='0~7', plotrange=[0,0,0,0],
          showgui=False, gridrows=4, gridcols=1, 
          plotfile=asdm+'.flux.page1.png')
    # user_input = input("Hit <Enter> to see next plot: ")
    plotms(vis=asdm+'.flux.cal', 
          xaxis='time', yaxis='amp', coloraxis='corr',
          iteraxis='antenna', antenna='8~15', plotrange=[0,0,0,0],
          showgui=False, gridrows=4, gridcols=1, 
          plotfile=asdm+'.flux.page2.png')
    # user_input = input("Hit <Enter> to see next plot: ")
</source>

A fun way to visualize all the progress we've made is to make a plot grid. Choosing one execution, we can plot all six of our bandpass and gain calibration tables, choosing the most import axes for each. Feel free to change the axes and colorizations of any plot interactively. This is a good way to get a feel for the purpose of each table.

<source lang="python">
# In CASA

plotms(vis='uid___A002_X215db8_X392.bpphase.gcal', xaxis='time', yaxis='phase', coloraxis='antenna1', clearplots=True, gridrows=6, plotindex=0, rowindex=0, title='bpphase.gcal')
plotms(vis='uid___A002_X215db8_X392.bandpass.bcal', xaxis='freq', yaxis='amp', coloraxis='antenna1', clearplots=False, gridrows=6, plotindex=1, rowindex=1, title='bandpass.bcal')
plotms(vis='uid___A002_X215db8_X392.scanphase.gcal', xaxis='time', yaxis='phase', coloraxis='antenna1', clearplots=False, gridrows=6, plotindex=2, rowindex=2, title='scanphase.gcal')
plotms(vis='uid___A002_X215db8_X392.intphase.gcal', xaxis='time', yaxis='phase', coloraxis='antenna1', clearplots=False, gridrows=6, plotindex=3, rowindex=3, title='intphase.gcal')
plotms(vis='uid___A002_X215db8_X392.amp.cal', xaxis='time', yaxis='amp', coloraxis='antenna1', clearplots=False, gridrows=6, plotindex=4, rowindex=4, title='amp.cal')
plotms(vis='uid___A002_X215db8_X392.flux.cal', xaxis='time', yaxis='amp', coloraxis='antenna1', clearplots=False, gridrows=6, plotindex=5, rowindex=5, title='flux.cal')
</source>

==Apply Calibrations to the Science Target==
Now we will use {{applycal_6.6.1}} to apply the bandpass, phase, and amplitude (flux) calibration tables that we generated in the previous sections to the data. We apply the solutions separately to the bandpass+gain calibrator (3c279), the flux calibrator (Titan), and the target source (NGC*/Ant*). In most data sets, the bandpass and gain calibrator will not be the same and this step would include one additional {{applycal_6.6.1}}.

<source lang="python">
# In CASA
basename_north=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9","uid___A002_X2181fb_X49"]
 
for asdm in basename_north: 
    print("Applying calibrations for "+asdm)
    # apply BP, short phase, and flux calibrations derived from BP/gain cal to itself
    applycal(vis=asdm+'.wvrtsys.ms', field='3c279',
            gaintable=[asdm+'.bandpass.bcal',asdm+'.intphase.gcal',asdm+'.flux.cal'],
            interp=['nearest','nearest','nearest'],
            gainfield=['3c279','3c279','3c279'], flagbackup=False, calwt=False)
    # apply BP calibration derived from BP/gain cal to the flux cal, then apply short phase and flux calibrations derived from flux cal to itself
    applycal(vis=asdm+'.wvrtsys.ms', field='Titan',
            gaintable=[asdm+'.bandpass.bcal',asdm+'.intphase.gcal',asdm+'.flux.cal'],
            interp=['nearest','nearest','nearest'],
            gainfield=['3c279','Titan','Titan'], flagbackup=False, calwt=False)
    # apply BP, long phase, and flux calibrations derived from BP/gain cal to the science target
    applycal(vis=asdm+'.wvrtsys.ms', field='NGC*',
            interp=['nearest','linear','linear'],
            gaintable=[asdm+'.bandpass.bcal',asdm+'.scanphase.gcal',asdm+'.flux.cal'],
            gainfield=['3c279','3c279','3c279'], flagbackup=False, calwt=False)

basename_south=["uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7","uid___A002_X207fe4_X4d7",
                           "uid___A002_X215db8_X18","uid___A002_X215db8_X1d5","uid___A002_X215db8_X392"]
 
for asdm in basename_south: 
    print("Applying calibrations for "+asdm)
    # apply BP, short phase, and flux calibrations derived from BP/gain cal to itself
    applycal(vis=asdm+'.wvrtsys.ms', field='3c279',
            gaintable=[asdm+'.bandpass.bcal',asdm+'.intphase.gcal',asdm+'.flux.cal'],
            interp=['nearest','nearest','nearest'],
            gainfield=['3c279','3c279','3c279'], flagbackup=False, calwt=False)
    # apply BP calibration derived from BP/gain cal to the flux cal, then apply short phase and flux calibrations derived from flux cal to itself
    applycal(vis=asdm+'.wvrtsys.ms', field='Titan',
            gaintable=[asdm+'.bandpass.bcal',asdm+'.intphase.gcal',asdm+'.flux.cal'],
            interp=['nearest','nearest','nearest'],
            gainfield=['3c279','Titan','Titan'], flagbackup=False, calwt=False)
    # apply BP, long phase, and flux calibrations derived from BP/gain cal to the science target
    applycal(vis=asdm+'.wvrtsys.ms', field='Ant*',
            interp=['nearest','linear','linear'],
            gaintable=[asdm+'.bandpass.bcal',asdm+'.scanphase.gcal',asdm+'.flux.cal'],
            gainfield=['3c279','3c279','3c279'], flagbackup=False, calwt=False)
</source>

Here:
* '''vis''' and '''field''' specify the measurement set and field to calibrate.
* '''gaintable''' specifies the tables to apply to the data. There may be several tables applied all at once, here we apply the bandpass, phase, and flux calibrations.
* '''interp''' specifies the type of interpolation used to match calibration tables to the data. If there are several gaintables then interp may be either a single value (e.g., "linear" or "nearest") or a list of values with size equal to the list of gaintables. In the case where interp is a list, applycal will match each element to the corresponding gaintable (e.g., first gaintable with first interp parameter).
* '''gainfield''' specifies field from which to draw the calibration. As with interp, this can be a list of size matched to gaintable, so that the first element of gainfield will be the field used for the first table. For example, in the above commands the bandpass calibration (the first table) will always be applied from '3c279' (the first gainfield).
* '''calwt''' indicates that the weights, which were derived from the Tsys measurements, should also be calibrated. Note that '''calwt''' is True by default.

Once calibrations are applied, it is important to go back and inspect the calibrated data. New problematic antennas or baselines may be visible after calibration. Repeat the steps above, focusing on the CORRECTED data column. Bear in mind that for any point source calibrators we now expect to find phase scattering around zero and to find flat amplitudes as a function of u-v distance. Look for outliers and other signatures of problematic data. As a general rule, you will want to incorporate these data into your overall flagging script then rerun the whole calibration process, so that reduction is iterative. If the data only represent a minor problem, however, it may not be terribly harmful to flag them after the fact so that they do not interfere with imaging but trust that the calibrations are mostly unaffected.

<pre style="background-color: #E0FFFF;">
The purpose of applying calibration tables derived from calibrator sources to those sources themselves is to make diagnostic plots of the calibrators and assess calibration quality. Calibration imperfections will be easy to identify in the corrected data of the calibrator sources, and should be fixed before applying those calibrations to the science target and splitting it out for imaging.
</pre>

As an example of this inspection, we cycle through the corrected amplitudes and phases of 3c279 and Titan as a function u-v distance, frequency and time. Amp and Phase vs time should be near constant in all cases. For point sources, corrected phase should be near zero, and amp vs uvdist should near be constant.

[[File:Xb_3c279_corrected_amp_freq_6.5.4.png|300px|thumb|right|<caption>'''Fig. 30.''' Calibrated Amp vs. Freq plot for 3c279 (uid___A002_X1ff7b0_Xb dataset). </caption>]]
[[File:Xb_3c279_corrected_phase_time_6.5.4.png|300px|thumb|right|<caption>'''Fig. 31.''' Calibrated Phase vs. Time plot for 3c279 (uid___A002_X1ff7b0_Xb dataset). </caption>]]

<source lang="python">
# In CASA

basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]

# 3c279
for asdm in basename_all:
    print("Examining calibrated data for "+asdm)
    # amp vs uvdist
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='uvdist', yaxis='amp',
          ydatacolumn='corrected', field='3c279',
          averagedata=True, avgchannel='3840', avgtime='',
          avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # amp vs time
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='time', yaxis='amp',
          ydatacolumn='corrected', field='3c279',
          averagedata=True, avgchannel='3840', avgtime='',
          avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # amp vs freq
    plotms(vis = asdm+'.wvrtsys.ms', xaxis='freq', yaxis='amp',
          ydatacolumn='corrected', field='3c279', avgtime='1e8',
          avgchannel='', avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # phase vs time
    plotms(vis = asdm+'.wvrtsys.ms', xaxis='time', yaxis='phase',
          ydatacolumn='corrected', field='3c279',
          avgchannel='3840', avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot [type 'stop'+<Enter> to break out]: ")
    # check if a stop has been requested
    if user_input == "stop":
        break

# Titan
for asdm in basename_all:
    print("Examining calibrated data for "+asdm)
    # amp vs uvdist
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='uvdist', yaxis='amp',
          ydatacolumn='corrected', field='Titan',
          averagedata=True, avgchannel='3840', avgtime='',
          avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # phase vs uvdist
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='uvdist', yaxis='phase',
          ydatacolumn='corrected', field='Titan',
          averagedata=True, avgchannel='3840', avgtime='',
          avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # amp vs freq
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='freq', yaxis='amp',
          ydatacolumn='corrected', field='Titan', avgtime='1e8',
          avgchannel='', avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot [type 'stop'+<Enter> to break out]: ")
    # check if a stop has been requested
    if user_input == "stop":
        break
</source>

In Figure 30 and Figure 31 we plot amp vs. freq and phase vs. time for 3c279 for the uid___A002_X1ff7b0_Xb dataset. 

[[File:Xb_NGC_corrected_amp_uvdist_6.5.4.png|300px|thumb|right|<caption>'''Fig. 32.''' Calibrated Amp vs. UVdist for NGC* in Northern mosaic (_Xb dataset). </caption>]]
[[File:Xb_NGC_corrected_amp_freq_6.5.4.png|300px|thumb|right|<caption>'''Fig. 33.''' Calibrated Amp vs. Freq for NGC* in Northern mosaic 3c279 (_Xb dataset). </caption>]]

Finally we can use {{plotms_6.6.1}} to examine the corrected amplitude of the Antennae galaxies as a function of freq and uv-distance (Fig 32 and 33). Pay special attention to the averaging used in each case to better understand the plots.

<source lang="python">
# In CASA

# northern mosaic
for asdm in basename_north:
    print("Examining calibrated data for "+asdm)
    # amp vs uvdist
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='uvdist', yaxis='amp',
          ydatacolumn='corrected', field='NGC*',
          averagedata=True, avgchannel='3840', avgtime='',
          avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # amp vs freq
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='freq', yaxis='amp',
          ydatacolumn='corrected', field='NGC*',
          avgtime='1e8', avgscan=True, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot [type 'stop'+<Enter> to break out]: ")
    if user_input == "stop":
        break

# southern mosaic
for asdm in basename_south:
    print("Examining calibrated data for "+asdm)
    # amp vs uvdist
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='uvdist', yaxis='amp',
          ydatacolumn='corrected', field='Ant*',
          averagedata=True, avgchannel='3840', avgtime='',
          avgscan=False, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot: ")
    # amp vs freq
    plotms(vis=asdm+'.wvrtsys.ms', xaxis='freq', yaxis='amp',
          ydatacolumn='corrected', field='Ant*',
          avgtime='1e8', avgscan=True, avgbaseline=False, coloraxis='corr', showgui=True)
    user_input = input("Hit <Enter> for next plot [type 'stop'+<Enter> to break out]: ")
    if user_input == "stop":
        break
</source>

==Split and Concatenate Data for Northern and Southern Mosaics==
The individual data sets are now calibrated. We can safely split out the calibrated data for our science target and drop the calibrators. As we do so, we will smooth the data in frequency, averaging together groups of 23 channels by setting '''width'''=23 in {{split_6.6.1}}. The new data will have a channel width corresponding to about ~10 km/s, very similar to the SMA data being verified. The factor of >20 drop in data volume will also make the imaging steps ''much'' more tractable. We also make a new {{listobs_6.6.1}} for the new target-only data sets.

<source lang="python">
# In CASA

basename_north=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9","uid___A002_X2181fb_X49"]

basename_south=["uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7","uid___A002_X207fe4_X4d7",
                           "uid___A002_X215db8_X18","uid___A002_X215db8_X1d5","uid___A002_X215db8_X392"]

for asdm in basename_north:
    os.system('rm -rf '+asdm+'.cal.ms')
    split(vis=asdm+'.wvrtsys.ms', outputvis=asdm+'.cal.ms',
          field='NGC*', spw='0', width=23, keepflags=False)
    os.system('rm -rf '+asdm+'.cal.listobs.txt')
    listobs(asdm+'.cal.ms', listfile=asdm+'.cal.listobs.txt')

for asdm in basename_south:
    os.system('rm -rf '+asdm+'.cal.ms')
    split(vis=asdm+'.wvrtsys.ms', outputvis=asdm+'.cal.ms',
          field='Ant*', spw='0', width=23, keepflags=False)
    os.system('rm -rf '+asdm+'.cal.listobs.txt')
    listobs(asdm+'.cal.ms', listfile=asdm+'.cal.listobs.txt')
</source>

Note: you will see a warning that the last output channel in the new spw 0 will be dropped, as it has less than 23 channels over which to average.

<pre style="background-color: #fffacd;">
INFO MSTransformDataHandler	The last output channel of spw 0 has only 22 input channels.
WARN MSTransformManager	        Not enough input channels to populate output channel n# 166 from SPW 0.
WARN MSTransformManager	        The channel will be dropped in order to have an uniform grid.
</pre>

In this case we can remove pointing information from the calibrated data. Normally, the pointing information would apply important corrections to be used while imaging the data. However, some aspects of this are still under development and the pointing information in these data interacts poorly with CASA. We will remove the pointing information using the CASA {{toolkit_6.6.1}} Table tool (tb). ''This kind of operation is dangerous and should not be a regular feature of your CASA reduction.''

<source lang="python">
# In CASA
 
basename_all=["uid___A002_X1ff7b0_Xb","uid___A002_X207fe4_X3a","uid___A002_X207fe4_X3b9",
     "uid___A002_X2181fb_X49","uid___A002_X1ff7b0_X1c8","uid___A002_X207fe4_X1f7",
     "uid___A002_X207fe4_X4d7","uid___A002_X215db8_X18","uid___A002_X215db8_X1d5",
     "uid___A002_X215db8_X392"]
 
for asdm in basename_all:
    print("Manually removing pointing table from "+asdm+".cal.ms ... Please be careful!")
    tb.open(asdm+'.cal.ms/POINTING', nomodify=False)
    a=tb.rownumbers()
    tb.removerows(a)
    tb.close()
</source>

For convenience we concatenate all data for the Northern Mosaic into a single MS and place all data for the Southern Mosaic into a second MS using {{concat_6.6.1}}. The syntax used to construct the 'cal_north_vis' list adds '.cal.ms' to each member of 'basename_north'. Finally, run {{listobs_6.6.1}} one last time on your two final MS.

<source lang="python">
# In CASA

cal_north_vis = [vis+'.cal.ms' for vis in basename_north]
cal_south_vis = [vis+'.cal.ms' for vis in basename_south]

print(cal_north_vis)
print(cal_south_vis)

os.system('rm -rf Antennae_North.cal.ms')
concat(vis=cal_north_vis, concatvis='Antennae_North.cal.ms', timesort=True)

os.system('rm -rf Antennae_South.cal.ms')
concat(vis=cal_south_vis, concatvis='Antennae_South.cal.ms', timesort=True)

listobs('Antennae_North.cal.ms', listfile='Antennae_North.cal.listobs.txt')
listobs('Antennae_South.cal.ms', listfile='Antennae_South.cal.listobs.txt')
</source>

Now you have fully reduced the target data, and can continue on to [[AntennaeBand7_Imaging]]!

{{Checked_6.6.1}}