View source for NGC 5921: red-shifted HI emission 5.7.2

 Disclaimer: Due to continuous CASA software updates, GUI images may look different on more recent versions than those shown here.


[[Category: VLA]] [[Category: Calibration]] [[Category: Imaging]] [[Category: Spectral Line]]

== Overview ==

The technique used to calibrate and image continuum datasets generally applies to spectral line observations, except that an additional calibration step is required. '''Bandpass calibration''' flattens the spectral response of the observations, ensuring that spectral channel images are properly calibrated in amplitude and phase.

The following tutorial derives from an annotated script provided in the [http://casa.nrao.edu/ref_cookbook.shtml CASA Cookbook]. The script is largely reproduced and additionally annotated with figures and illustrations. It is assumed that this tutorial will be used interactively, and so interactive pauses in the original script have been removed.

<b>DATA</b>: The data are included with the CASA installation.



== Setting up the CASA Environment ==

Start up CASA in the directory you want to use. 

<source lang="bash">
# in bash
mkdir NGC5921
cd NGC5921
casa
</source>

<!--
Now, in CASA, set up paths and global variables to facilitate the data reduction. These operations can be performed on-the-fly if you are reducing data interactively, but it's better to have them prepared from the start in the scripting environment.

<source lang="python">
import os
scriptmode = True
prefix = 'ngc5921.demo' # The prefix to use for all output files
# Set up some useful variables (these will be altered later on)
msfile = prefix + '.ms'
btable = prefix + '.bcal'
gtable = prefix + '.gcal'
ftable = prefix + '.fluxscale'
splitms = prefix + '.src.split.ms'
imname = prefix + '.cleanimg'
</source>
-->

We'll use a python ''os'' command to get the appropriate CASA path for your installation in order to import the data. The use of '''os.environ.get''' is explained in [[#os.environ.get | the Appendix]].

<source lang="python">
# In CASA
%cpaste

# Press Enter or Return, then copy/paste the following:
import os
pathname=os.environ.get('CASAPATH').split()[0]
fitsdata=pathname+'/data/demo/NGC5921.fits'
--
</source>

Scripts are of course modified and repeated to the satisfaction of observer. To help clean up the bookkeeping and further avoid issues of write privileges, remove prior versions of the measurement set and calibration tables.

This can be done with the rmtables('table_name') command.

<!--
<div style="background-color: #dddddd;">
'''Tip:''' The first command in the following code block removes the measurement set. Depending on the size of the source data, refilling a measurement set can be time-consuming, and so you may want to consider editing a separate script that preserves the measurement set but skips the '''importuvfits''' command [[#Import the Data | given below]]. This NGC5921 dataset, however, is not large and refilling goes quickly.
</div>

<source lang="python">
rmtables(msfile)
rmtables(btable)
rmtables(gtable)
rmtables(ftable)
rmtables(ftable)
rmtables(splitms+'*')
rmtables(imname+'.*')
rmtables(prefix+'.moments*')
# Final clean up of auxiliary files
os.system('rm -rf '+prefix+'*')
</source>
-->

== Import the Data ==

The next step is to import the multisource UVFITS data to a CASA measurement set via the {{importuvfits}} filler. Note that you can set each parameter for any particular task one-by-one, or you could supply the task and input parameters with one command. Here we will set each parameter value first, save them, and run the import task. Throughout the remaining tutorial, we will call upon tasks with a single command. 

<!--
<source lang="python">
importuvfits(fitsfile=fitsdata, vis='ngc5921.demo.ms')
saveinputs('importuvfits', 'ngc5921.demo.importuvfits.saved')
</source>
-->

<source lang="python">
# Safest to start from task defaults
default('importuvfits')
# Use task importuvfits
fitsfile = fitsdata
vis='ngc5921.demo.ms'
saveinputs('importuvfits', 'ngc5921.demo.importuvfits.saved')
importuvfits()
</source>

[[saveinputs | Saveinputs]] saves the parameters of a given command to specified text file, handy to debug a script and see what actually was run. The parameters of {{importuvfits}} are saved to the file "ngc5921.demo.importuvfits.saved". A listing of this file follows. Notice that it is executable with '''execfile''' in CASA (remove the # commenting symbol before {{importuvfits}} to have the execfile run the command).

<pre>
CASA <71>: os.system('cat ngc5921.demo.importuvfits.saved')
taskname           = "importuvfits"
fitsfile           =  "/usr/lib64/casapy/30.0.9709test-001/data/demo/NGC5921.fits"
vis                =  "ngc5921.demo.ms"
antnamescheme      =  "old"
#importuvfits(fitsfile="/usr/lib64/casapy/30.0.9709test-001/data/demo/NGC5921.fits",vis="ngc5921.demo.ms",antnamescheme="old")

</pre>

== A Summary of the Data ==

We'll need to have a look at the observing tables to learn the calibrator and source names. The relevant command is {{listobs}}. 

[[File:n5921-01.png | thumb | Logger output of {{listobs}}.]]

<source lang="python">
listobs(vis='ngc5921.demo.ms', verbose=True)
</source>

The output goes to the logger window; see the screenshot at right.

<div style="background-color: #dddddd;">
'''Tip:''' You can control the text size of the logger window using <ctrl>-A (smaller font) and <ctrl>-L (larger font) in Linux (<Command>-A and <Command>-L on MacOS X).
</div>

A more complete listing of the {{listobs}} output follows.

<pre>
2018-09-12 20:19:48 INFO listobs	##########################################
2018-09-12 20:19:48 INFO listobs	##### Begin Task: listobs            #####
2018-09-12 20:19:48 INFO listobs	listobs(vis="ngc5921.demo.ms",selectdata=True,spw="",field="",antenna="",
2018-09-12 20:19:48 INFO listobs	        uvrange="",timerange="",correlation="",scan="",intent="",
2018-09-12 20:19:48 INFO listobs	        feed="",array="",observation="",verbose=True,listfile="",
2018-09-12 20:19:48 INFO listobs	        listunfl=False,cachesize=50,overwrite=False)
2018-09-12 20:19:49 INFO listobs	================================================================================
2018-09-12 20:19:49 INFO listobs	           MeasurementSet Name:  /lustre/aoc/sciops/akapinsk/oldVLA/ngc5921/ngc5921.demo.ms      MS Version 2
2018-09-12 20:19:49 INFO listobs	================================================================================
2018-09-12 20:19:49 INFO listobs	   Observer: TEST     Project:   
2018-09-12 20:19:49 INFO listobs	Observation: VLA
2018-09-12 20:19:49 INFO listobs	Computing scan and subscan properties...
2018-09-12 20:19:49 INFO listobs	Data records: 22653       Total elapsed time = 5310 seconds
2018-09-12 20:19:49 INFO listobs	   Observed from   13-Apr-1995/09:18:45.0   to   13-Apr-1995/10:47:15.0 (TAI)
2018-09-12 20:19:49 INFO listobs	   
2018-09-12 20:19:49 INFO listobs	   ObservationID = 0         ArrayID = 0
2018-09-12 20:19:49 INFO listobs	  Date        Timerange (TAI)          Scan  FldId FieldName             nRows     SpwIds   Average Interval(s)    ScanIntent
2018-09-12 20:19:49 INFO listobs	  13-Apr-1995/09:18:45.0 - 09:24:45.0     1      0 1331+30500002_0           4509  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	              09:27:15.0 - 09:29:45.0     2      1 1445+09900002_0           1890  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	              09:32:45.0 - 09:48:15.0     3      2 N5921_2                   6048  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	              09:50:15.0 - 09:51:15.0     4      1 1445+09900002_0            756  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	              10:21:45.0 - 10:23:15.0     5      1 1445+09900002_0           1134  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	              10:25:45.0 - 10:43:15.0     6      2 N5921_2                   6804  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	              10:45:15.0 - 10:47:15.0     7      1 1445+09900002_0           1512  [0]  [30] 
2018-09-12 20:19:49 INFO listobs	           (nRows = Total number of rows per scan) 
2018-09-12 20:19:49 INFO listobs	Fields: 3
2018-09-12 20:19:49 INFO listobs	  ID   Code Name                RA               Decl           Epoch   SrcId      nRows
2018-09-12 20:19:49 INFO listobs	  0         1331+30500002_0     13:31:08.287300 +30.30.32.95900 J2000   0           4509
2018-09-12 20:19:49 INFO listobs	  1         1445+09900002_0     14:45:16.465600 +09.58.36.07300 J2000   1           5292
2018-09-12 20:19:49 INFO listobs	  2         N5921_2             15:22:00.000000 +05.04.00.00000 J2000   2          12852
2018-09-12 20:19:49 INFO listobs	Spectral Windows:  (1 unique spectral windows and 1 unique polarization setups)
2018-09-12 20:19:49 INFO listobs	  SpwID  Name   #Chans   Frame   Ch0(MHz)  ChanWid(kHz)  TotBW(kHz) CtrFreq(MHz)  Corrs  
2018-09-12 20:19:49 INFO listobs	  0      none      63   LSRK    1412.665        24.414      1550.2   1413.4219   RR  LL
2018-09-12 20:19:49 INFO listobs	Sources: 3
2018-09-12 20:19:49 INFO listobs	  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
2018-09-12 20:19:49 INFO listobs	  0    1331+30500002_0     0     1420.405752    0            
2018-09-12 20:19:49 INFO listobs	  1    1445+09900002_0     0     1420.405752    0            
2018-09-12 20:19:49 INFO listobs	  2    N5921_2             0     1420.405752    0            
2018-09-12 20:19:49 INFO listobs	Antennas: 27:
2018-09-12 20:19:49 INFO listobs	  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
2018-09-12 20:19:49 INFO listobs	                                                                     East         North     Elevation               x               y               z
2018-09-12 20:19:49 INFO listobs	  0    1     VLA:N7    25.0 m   -107.37.07.2  +33.54.12.9        -30.2623      345.7477       -0.8872 -1601155.613187 -5041783.882304  3555162.343090
2018-09-12 20:19:49 INFO listobs	  1    2     VLA:W1    25.0 m   -107.37.05.9  +33.54.00.5          3.5004      -39.7725        0.9883 -1601188.991307 -5042000.530918  3554843.409670
2018-09-12 20:19:49 INFO listobs	  2    3     VLA:W2    25.0 m   -107.37.07.4  +33.54.00.9        -37.1358      -25.0262        1.0383 -1601225.244615 -5041980.431775  3554855.677111
2018-09-12 20:19:49 INFO listobs	  3    4     VLA:E1    25.0 m   -107.37.05.7  +33.53.59.2          6.9833      -79.6414        1.1565 -1601192.444530 -5042022.911771  3554810.411780
2018-09-12 20:19:49 INFO listobs	  4    5     VLA:E3    25.0 m   -107.37.02.8  +33.54.00.5         81.5188      -37.9632        1.0246 -1601114.335629 -5042023.211477  3554844.931655
2018-09-12 20:19:49 INFO listobs	  5    6     VLA:E9    25.0 m   -107.36.45.1  +33.53.53.6        536.8977     -250.3175        0.1183 -1600715.915813 -5042273.186780  3554668.167811
2018-09-12 20:19:49 INFO listobs	  6    7     VLA:E6    25.0 m   -107.36.55.6  +33.53.57.7        267.7566     -124.8145        1.2815 -1600951.554888 -5042125.947753  3554772.987072
2018-09-12 20:19:49 INFO listobs	  7    8     VLA:W8    25.0 m   -107.37.21.6  +33.53.53.0       -401.2640     -270.6305        2.2293 -1601614.059494 -5042001.699973  3554652.484758
2018-09-12 20:19:49 INFO listobs	  8    9     VLA:N5    25.0 m   -107.37.06.7  +33.54.08.0        -16.9948      194.1215       -0.1368 -1601168.756077 -5041869.099542  3555036.914367
2018-09-12 20:19:49 INFO listobs	  9    10    VLA:W3    25.0 m   -107.37.08.9  +33.54.00.1        -74.4964      -50.1921        1.1608 -1601265.132224 -5041982.597979  3554834.857504
2018-09-12 20:19:49 INFO listobs	  10   11    VLA:N4    25.0 m   -107.37.06.5  +33.54.06.1        -11.7487      134.3686        0.1774 -1601173.922897 -5041902.701204  3554987.495105
2018-09-12 20:19:49 INFO listobs	  11   12    VLA:W5    25.0 m   -107.37.13.0  +33.53.57.8       -179.2554     -120.8635        1.4872 -1601376.990711 -5041988.712764  3554776.381187
2018-09-12 20:19:49 INFO listobs	  12   13    VLA:N3    25.0 m   -107.37.06.3  +33.54.04.8         -8.2438       94.5297        0.3947 -1601177.362708 -5041925.112425  3554954.550128
2018-09-12 20:19:49 INFO listobs	  13   14    VLA:N1    25.0 m   -107.37.06.0  +33.54.01.8         -0.0030        0.0445        0.8773 -1601185.580779 -5041978.216463  3554876.396287
2018-09-12 20:19:49 INFO listobs	  14   15    VLA:N2    25.0 m   -107.37.06.2  +33.54.03.5         -4.7904       54.7090        0.5774 -1601180.839839 -5041947.470902  3554921.600805
2018-09-12 20:19:49 INFO listobs	  15   16    VLA:E7    25.0 m   -107.36.52.4  +33.53.56.5        348.8969     -162.6653        1.0336 -1600880.544215 -5042170.427468  3554741.431900
2018-09-12 20:19:49 INFO listobs	  16   17    VLA:E8    25.0 m   -107.36.48.9  +33.53.55.1        438.6654     -204.5038        0.5027 -1600801.910482 -5042219.412805  3554706.408864
2018-09-12 20:19:49 INFO listobs	  17   18    VLA:W4    25.0 m   -107.37.10.8  +33.53.59.1       -122.0163      -82.2819        1.2624 -1601315.866196 -5041985.352573  3554808.279150
2018-09-12 20:19:49 INFO listobs	  18   19    VLA:E5    25.0 m   -107.36.58.4  +33.53.58.8        195.8349      -91.2758        1.2155 -1601014.427180 -5042086.300814  3554800.787928
2018-09-12 20:19:49 INFO listobs	  19   20    VLA:W9    25.0 m   -107.37.25.1  +33.53.51.0       -491.1000     -331.2429        2.5539 -1601709.998072 -5042006.975455  3554602.355417
2018-09-12 20:19:49 INFO listobs	  20   21    VLA:W6    25.0 m   -107.37.15.6  +33.53.56.4       -244.9704     -165.2178        1.6861 -1601447.161927 -5041992.554228  3554739.677219
2018-09-12 20:19:49 INFO listobs	  21   22    VLA:E4    25.0 m   -107.37.00.8  +33.53.59.7        133.6478      -62.2829        1.0919 -1601068.773396 -5042051.970054  3554824.783566
2018-09-12 20:19:49 INFO listobs	  23   24    VLA:E2    25.0 m   -107.37.04.4  +33.54.01.1         40.6649      -18.9151        0.9550 -1601150.040469 -5042000.665669  3554860.702914
2018-09-12 20:19:49 INFO listobs	  24   25    VLA:N6    25.0 m   -107.37.06.9  +33.54.10.3        -23.2197      265.3902       -0.4819 -1601162.569974 -5041829.054708  3555095.873969
2018-09-12 20:19:49 INFO listobs	  25   26    VLA:N9    25.0 m   -107.37.07.8  +33.54.19.0        -46.5533      532.1581       -1.8550 -1601139.422904 -5041679.082136  3555316.518142
2018-09-12 20:19:49 INFO listobs	  26   27    VLA:N8    25.0 m   -107.37.07.5  +33.54.15.8        -38.0437      434.7201       -1.3387 -1601147.894127 -5041733.868915  3555235.935926
2018-09-12 20:19:49 INFO listobs	  27   28    VLA:W7    25.0 m   -107.37.18.4  +33.53.54.8       -319.1171     -215.2368        1.9407 -1601526.340031 -5041996.897001  3554698.302182
2018-09-12 20:19:49 INFO listobs	##### End Task: listobs              #####
2018-09-12 20:19:49 INFO listobs	##########################################
</pre>

<!-- previous version for CASA 5.1
2011-04-25 19:52:17 INFO listobs	##########################################
2011-04-25 19:52:17 INFO listobs	##### Begin Task: listobs            #####
2011-04-25 19:52:17 INFO  	listobs::::casa
2011-04-25 19:52:17 INFO listobs	================================================================================
2011-04-25 19:52:17 INFO listobs	           MeasurementSet Name:  /Science/VLA_tutorial_check/NGC_5921_red-shifted_HI/ngc5921.demo.ms      MS Version 2
2011-04-25 19:52:17 INFO listobs	================================================================================
2011-04-25 19:52:17 INFO listobs	   Observer: TEST     Project:   
2011-04-25 19:52:17 INFO listobs	Observation: VLA
2011-04-25 19:52:17 INFO listobs	Data records: 22653       Total integration time = 5280 seconds
2011-04-25 19:52:17 INFO listobs	   Observed from   13-Apr-1995/09:19:00.0   to   13-Apr-1995/10:47:00.0 (TAI)
2011-04-25 19:52:17 INFO  	listobs::ms::summary
2011-04-25 19:52:17 INFO listobs	   ObservationID = 0         ArrayID = 0
2011-04-25 19:52:17 INFO listobs	  Date        Timerange (TAI)          Scan  FldId FieldName nVis   Int(s)   SpwIds      ScanIntent
2011-04-25 19:52:17 INFO listobs	  13-Apr-1995/09:19:00.0 - 09:24:30.0     1      0 1331+305000* 4509   30       [0]                         
2011-04-25 19:52:17 INFO listobs	              09:27:30.0 - 09:29:30.0     2      1 1445+099000* 1890   30       [0]                         
2011-04-25 19:52:17 INFO listobs	              09:33:00.0 - 09:48:00.0     3      2 N5921_2      6048   30       [0]                         
2011-04-25 19:52:17 INFO listobs	              09:50:30.0 - 09:51:00.0     4      1 1445+099000* 756    30       [0]                         
2011-04-25 19:52:17 INFO listobs	              10:22:00.0 - 10:23:00.0     5      1 1445+099000* 1134   30       [0]                         
2011-04-25 19:52:17 INFO listobs	              10:26:00.0 - 10:43:00.0     6      2 N5921_2      6804   30       [0]                         
2011-04-25 19:52:17 INFO listobs	              10:45:30.0 - 10:47:00.0     7      1 1445+099000* 1512   30       [0]                         
2011-04-25 19:52:17 INFO listobs	           (nVis = Total number of time/baseline visibilities per scan) 
2011-04-25 19:52:17 INFO listobs	Fields: 3
2011-04-25 19:52:17 INFO listobs	  ID   Code Name         RA            Decl           Epoch   SrcId nVis   
2011-04-25 19:52:17 INFO listobs	  0    C    1331+305000* 13:31:08.2873 +30.30.32.9590 J2000   0     4509   
2011-04-25 19:52:17 INFO listobs	  1    A    1445+099000* 14:45:16.4656 +09.58.36.0730 J2000   1     5292   
2011-04-25 19:52:17 INFO listobs	  2         N5921_2      15:22:00.0000 +05.04.00.0000 J2000   2     12852  
2011-04-25 19:52:17 INFO listobs	   (nVis = Total number of time/baseline visibilities per field) 
2011-04-25 19:52:17 INFO listobs	Spectral Windows:  (1 unique spectral windows and 1 unique polarization setups)
2011-04-25 19:52:17 INFO listobs	  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)TotBW(kHz)  Ref(MHz)    Corrs   
2011-04-25 19:52:17 INFO listobs	  0          63 LSRK  1412.66507  24.4140625  1550.19688  1413.42801  RR  LL  
2011-04-25 19:52:17 INFO listobs	Sources: 3
2011-04-25 19:52:17 INFO listobs	  ID   Name         SpwId RestFreq(MHz)  SysVel(km/s) 
2011-04-25 19:52:17 INFO listobs	  0    1331+305000* 0     1420.405752    0            
2011-04-25 19:52:17 INFO listobs	  1    1445+099000* 0     1420.405752    0            
2011-04-25 19:52:17 INFO listobs	  2    N5921_2      0     1420.405752    0            
2011-04-25 19:52:17 INFO listobs	Antennas: 27:
2011-04-25 19:52:17 INFO listobs	  ID   Name  Station   Diam.    Long.         Lat.         
2011-04-25 19:52:17 INFO listobs	  0    1     VLA:N7    25.0 m   -107.37.07.2  +33.54.12.9  
2011-04-25 19:52:17 INFO listobs	  1    2     VLA:W1    25.0 m   -107.37.05.9  +33.54.00.5  
2011-04-25 19:52:17 INFO listobs	  2    3     VLA:W2    25.0 m   -107.37.07.4  +33.54.00.9  
2011-04-25 19:52:17 INFO listobs	  3    4     VLA:E1    25.0 m   -107.37.05.7  +33.53.59.2  
2011-04-25 19:52:17 INFO listobs	  4    5     VLA:E3    25.0 m   -107.37.02.8  +33.54.00.5  
2011-04-25 19:52:17 INFO listobs	  5    6     VLA:E9    25.0 m   -107.36.45.1  +33.53.53.6  
2011-04-25 19:52:17 INFO listobs	  6    7     VLA:E6    25.0 m   -107.36.55.6  +33.53.57.7  
2011-04-25 19:52:17 INFO listobs	  7    8     VLA:W8    25.0 m   -107.37.21.6  +33.53.53.0  
2011-04-25 19:52:17 INFO listobs	  8    9     VLA:N5    25.0 m   -107.37.06.7  +33.54.08.0  
2011-04-25 19:52:17 INFO listobs	  9    10    VLA:W3    25.0 m   -107.37.08.9  +33.54.00.1  
2011-04-25 19:52:17 INFO listobs	  10   11    VLA:N4    25.0 m   -107.37.06.5  +33.54.06.1  
2011-04-25 19:52:17 INFO listobs	  11   12    VLA:W5    25.0 m   -107.37.13.0  +33.53.57.8  
2011-04-25 19:52:17 INFO listobs	  12   13    VLA:N3    25.0 m   -107.37.06.3  +33.54.04.8  
2011-04-25 19:52:17 INFO listobs	  13   14    VLA:N1    25.0 m   -107.37.06.0  +33.54.01.8  
2011-04-25 19:52:17 INFO listobs	  14   15    VLA:N2    25.0 m   -107.37.06.2  +33.54.03.5  
2011-04-25 19:52:17 INFO listobs	  15   16    VLA:E7    25.0 m   -107.36.52.4  +33.53.56.5  
2011-04-25 19:52:17 INFO listobs	  16   17    VLA:E8    25.0 m   -107.36.48.9  +33.53.55.1  
2011-04-25 19:52:17 INFO listobs	  17   18    VLA:W4    25.0 m   -107.37.10.8  +33.53.59.1  
2011-04-25 19:52:17 INFO listobs	  18   19    VLA:E5    25.0 m   -107.36.58.4  +33.53.58.8  
2011-04-25 19:52:17 INFO listobs	  19   20    VLA:W9    25.0 m   -107.37.25.1  +33.53.51.0  
2011-04-25 19:52:17 INFO listobs	  20   21    VLA:W6    25.0 m   -107.37.15.6  +33.53.56.4  
2011-04-25 19:52:17 INFO listobs	  21   22    VLA:E4    25.0 m   -107.37.00.8  +33.53.59.7  
2011-04-25 19:52:17 INFO listobs	  23   24    VLA:E2    25.0 m   -107.37.04.4  +33.54.01.1  
2011-04-25 19:52:17 INFO listobs	  24   25    VLA:N6    25.0 m   -107.37.06.9  +33.54.10.3  
2011-04-25 19:52:17 INFO listobs	  25   26    VLA:N9    25.0 m   -107.37.07.8  +33.54.19.0  
2011-04-25 19:52:17 INFO listobs	  26   27    VLA:N8    25.0 m   -107.37.07.5  +33.54.15.8  
2011-04-25 19:52:17 INFO listobs	  27   28    VLA:W7    25.0 m   -107.37.18.4  +33.53.54.8  
2011-04-25 19:52:17 INFO  	listobs::::casa
2011-04-25 19:52:17 INFO listobs	##### End Task: listobs              #####
2011-04-25 19:52:17 INFO listobs	##########################################
-->


=== Key Information from {{listobs | Listobs}} ===

Certainly the output of {{listobs}} is dense with information, but there are some particularly vital data that we'll need for the calibration.

* The calibrators are '''1331+305*''' (3C286, the flux and bandpass calibrator) and '''1445+099*''' (the phase calibrator). We can use wild-cards '''1331*''' and '''1445*''' since they uniquely identify the sources.
* The calibrator field indices are field='0' (1331+305) and field='1' (1445+099).
* The name of the source in the observations list is '''N5921_2''', or field = '2'.
* The data were taken in a single IF (a single spectral window, SpwID = 0), divided into 63 channels.
* Only RR and LL correlations are present; cross-pols are absent.

== Flagging ==

=== Flag the autocorrelations ===

We don't need the autocorrelation data, and we can use {{flagdata}} to get rid of them. You shouldn't have to specify the measurement set, because the variable ''vis'' is already set, but it never hurts to be cautious.

<source lang="python">
flagdata(vis="ngc5921.demo.ms", autocorr=True)
</source>

=== Interactive Flagging ===

[[file:spectrum-flagging.png|thumb|Plotms settings for flagging spectral line data. Click to enlarge.]]


{{plotms | Plotms}} is a good tool for flagging spectral line data. Check out the [[Data flagging with casaplotms | tutorial]] that describes editing VLA continuum data. Spectral line data of course require some consideration of channels and channel averaging. 

<source lang="python">
plotms()
</source>


The figure at right highlights the settings needed for effective editing of a spectral line data set. The key settings are as follows.

* Specify the measurement set in '''File'''; the '''Browse''' button allows you to hunt down the measurement set.
* It's better to edit one source at a time. In the illustrated example, the flux / bandpass calibrator 1331+305* is displayed.
* Average the channels. First, specify the central channels to remove band edge effects. Channels 6~56 in the first spectral window (IF) are appropriate (see [[#Inspect the Bandpass Response Curve]], below). In plotms() specify: spw=0:06~56. In the '''Channel Averaging''' box, enter 51 channels to average over all channels in the given range.
* Ideally you want the channels to have the same (''u'', ''v'') coverage (projected baseline spacings as viewed from the source); otherwise, the beam (point spread function) will be different for each channel. Therefore, if you flag data from a given channel it's usually a good idea to flag those data from all channels. Under the '''Flagging''' tab, specify '''Extend flags''' to '''Channel.'''


With these settings, interactive flagging proceeds as for [[Data flagging with plotms | continuum data]]. When you're satisfied with the edits, '''File &rarr; Quit''' to return to the CASA prompt.

== Calibration ==

Calibration of spectral line data broadly follows the approach for [[Calibrating a VLA 5 GHz continuum survey | continuum data]], except that the amplitude and phase corrections are a function of frequency and so must be corrected by '''bandpass calibration.''' The basic calibration steps follow.
* [[#Setting the Flux Scale | Set the flux scale]] of the primary calibrator, here, 1331+305 = 3C 286.
* [[#Bandpass Calibration | Determine bandpass corrections]] based on the primary calibrator. In the script that follows, the bandpass calibration will be stored in ''ngc5921.demo.bcal''.
* [[#Inspect the Bandpass Response Curve | Inspect the bandpass correction]] to determine viable channels for averaging and imaging. We want to toss out end channels where the response is poor.
* [[#Gain Calibration | Determine the gain calibrations]] on the bandpass-corrected and channel-averaged data. In this step, we effectively turn the spectral line data into a single-channel continuum data set and calibrate accordingly. The calibration is first stored in ''ngc5921.demo.gcal''. In the second part of this step we correct the fluxscale of the .gcal table, and store the final calibration solutions with correct fluxes in ''ngc5921.demo.fluxscale'' (this is the table that needs to be applied later to the data, not the .gcal version).
* [[#Inspect the Calibration Solutions | Inspect the gain calibration solutions]] to look for any aberrant solutions that hint at bad calibrator data.
* [[#Apply the Solutions | Apply the calibration solutions]] to the source (N5921_2). This action literally adds a new column of data to the measurement set. This new column contains the data with the gain calibration and bandpass calibration applied, but it does not overwrite the raw data in case the calibration needs revision.



=== Setting the Flux Scale ===

{{setjy | Setjy}} generates a source model for the primary calibrator, 1331+305 = 3C286. From CASA 5.3+ the default standard is Perley-Butler 2017, and includes resolved structure of the calibrators. This is 1.4GHz D-config and 1331+305 is sufficiently unresolved that, in principle, we don't need a model image; however, here we proceed with applying the detailed model, as a good practise.

{{setjy | Setjy}} also looks up the radio SED for common flux calibrators and automatically assigns the total flux density.

<source lang="python">
# 1331+305 = 3C286 is our primary calibrator. Use the wildcard on the end of the source name
setjy(vis='ngc5921.demo.ms', field='1331+305*', model='3C286_L.im')
</source>


A summary of the operation is sent to the logger window. Here's a listing of the output.

<pre>
2018-09-12 20:43:38 INFO setjy	##########################################
2018-09-12 20:43:38 INFO setjy	##### Begin Task: setjy              #####
2018-09-12 20:43:38 INFO setjy	setjy(vis="ngc5921.demo.ms",field="1331+305*",spw="",selectdata=False,timerange="",
2018-09-12 20:43:38 INFO setjy	        scan="",intent="",observation="",scalebychan=True,standard="Perley-Butler 2017",
2018-09-12 20:43:38 INFO setjy	        model="3C286_L.im",modimage="",listmodels=False,fluxdensity=-1,spix=0.0,
2018-09-12 20:43:38 INFO setjy	        reffreq="1GHz",polindex=[],polangle=[],rotmeas=0.0,fluxdict={},
2018-09-12 20:43:38 INFO setjy	        useephemdir=False,interpolation="nearest",usescratch=False,ismms=False)
2018-09-12 20:43:38 INFO setjy	{'field': '1331+305*'}
2018-09-12 20:43:38 INFO Imager	Opening MeasurementSet [...]
2018-09-12 20:43:38 INFO setjy	Using /home/casa/data/distro/nrao/VLA/CalModels/3C286_L.im for modimage.
2018-09-12 20:43:38 INFO setjy	CASA Version 5.3.0-143  
2018-09-12 20:43:38 INFO setjy	   
2018-09-12 20:43:39 INFO imager	Using channel dependent flux densities
2018-09-12 20:43:39 INFO imager	Selected 4509 out of 22653 rows.
2018-09-12 20:43:39 INFO imager	1331+30500002_0 (fld ind 0) spw 0  [I=15.016, Q=0, U=0, V=0] Jy @ 1.4127e+09Hz, (Perley-Butler 2017)
2018-09-12 20:43:40 INFO imager	Using model image /home/casa/data/distro/nrao/VLA/CalModels/3C286_L.im
2018-09-12 20:43:40 INFO imager	Scaling spw(s) [0]'s model image by channel to  I = 15.0159, 15.0118, 15.0077 Jy @(1.41265e+09, 1.41343e+09, 1.41419e+09)Hz (LSRK) for visibility prediction (a few representative values are shown).
2018-09-12 20:43:40 INFO imager	The model image's reference pixel is 0.00904522 arcsec from 1331+30500002_0's phase center.
2018-09-12 20:43:40 INFO imager	Will clear any existing model with matching field=1331+30500002_0 and spw=*
2018-09-12 20:43:40 INFO  	Clearing model records in MS header for selected fields.
2018-09-12 20:43:40 INFO  	 1331+30500002_0 (id = 0) deleted.
2018-09-12 20:43:40 INFO imager	Selected 4509 out of 22653 rows.
2018-09-12 20:43:40 INFO setjy	##### End Task: setjy                #####
2018-09-12 20:43:40 INFO setjy	##########################################
</pre>



<!-- PREVIOUS VERSION, FOR CASA 5.1.0

{{setjy | Setjy}} generates a point source model for the primary calibrator, 1331+305 = 3C286. These data are of low angular resolution, and so the point source model is adequate for our purposes. For observations with higher angular resolution (longer baseline configurations), you can specify a model of the calibrator using the ''modimage'' parameter (see the tutorial [[Calibrating a VLA 5 GHz continuum survey#Set the Flux Scale]] for an example of how to use ''modimage''). 

{{setjy | Setjy}} also looks up the radio SED for common flux calibrators and automatically assigns the total flux density.

<source lang="python">
# 1331+305 = 3C286 is our primary calibrator. Use the wildcard on the end of the source name
# This is 1.4GHz D-config and 1331+305 is sufficiently unresolved that we dont need a model image.  
# For higher frequencies (particularly in A and B config) you would want to use one.
setjy(vis='ngc5921.demo.ms', field='1331+305*', modimage='')
</source>

<!--
<source lang="python">
default('setjy')
vis = msfile
#
# 1331+305 = 3C286 is our primary calibrator
# Use the wildcard on the end of the source name
# since the field names in the MS have inherited the
# AIPS qualifiers
field = '1331+305*'
# This is 1.4GHz D-config and 1331+305 is sufficiently unresolved
# that we dont need a model image.  For higher frequencies
# (particularly in A and B config) you would want to use one.
modimage = ''
# Setjy knows about this source so we dont need anything more
saveinputs('setjy',prefix+'.setjy.saved')
setjy()
</source>
-->

<!-- PREVIOUS VERSION, FOR CASA 5.1.0

<pre>
2011-04-25 19:50:53 INFO setjy	##########################################
2011-04-25 19:50:53 INFO setjy	##### Begin Task: setjy              #####
2011-04-25 19:50:53 INFO  	setjy::::casa
2011-04-25 19:50:53 INFO setjy	Adding MODEL_DATA and CORRECTED_DATA columns
2011-04-25 19:50:53 INFO setjy	Initializing MODEL_DATA (to unity) and CORRECTED_DATA (to DATA)
2011-04-25 19:50:54 INFO setjy	Initialized 22653 rows.
2011-04-25 19:50:54 INFO setjy	1331+30500002_0  spwid=  0  [I=14.79, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
2011-04-25 19:50:54 INFO setjy	Selecting data
2011-04-25 19:50:54 INFO setjy	Selected 4509 out of 22653 visibilities.
2011-04-25 19:50:54 INFO setjy	Selecting 63 channels, starting at 0, stepped by 1, for spw 0
2011-04-25 19:50:54 INFO setjy	Fourier transforming: replacing MODEL_DATA column
2011-04-25 19:50:54 INFO setjy	Processing after subtracting componentlist .setjy_1331+30500002_0_1.41342GHz49820d.cl
2011-04-25 19:50:54 INFO setjy	Performing interferometric gridding...
2011-04-25 19:50:55 INFO  	setjy::::casa
2011-04-25 19:50:55 INFO setjy	##### End Task: setjy                #####
2011-04-25 19:50:55 INFO setjy	##########################################
</pre>
-->



=== Bandpass Calibration ===

The flux calibrator 1331+305 = 3C 286 now has a model assigned to it. Since the bandwidth of our observations is only 1.55 MHz, the model doesn't change over this narrow range of frequencies, so we can use it to determine amplitude and phase (gain) corrections for each channel independently. The result is the bandpass calibration.

As for any antenna-based calibration scheme, we have to pick an antenna to act as the reference point for the calibration. Any antenna will do, but it's better to pick one near the center of the array. For the remainder of the calibration, we will use '''refant = '15''''.

<source lang="python">
# We can first do the bandpass on the single 5min scan on 1331+305. At 1.4GHz phase stablility should be sufficient to do this without
# a first (rough) gain calibration. This will give us the relative antenna gain as a function of frequency.
bandpass(vis='ngc5921.demo.ms', caltable='ngc5921.demo.bcal', field='0', selectdata=False, bandtype='B', solint='inf', combine='scan', refant='15')
</source>

* field='0' : Use the flux calibrator 1331+305 = 3C286 (FIELD_ID 0) as bandpass calibrator.
* bandtype='B' : Choose bandpass solution type. Pick standard time-binned B (rather than BPOLY).
* solint='inf' and combine='scan' : Set solution interval arbitrarily long (get single bandpass).
* refant = '15' : Reference antenna Name 15 (15=VLA:N2) (Id 14)

<!--
default('bandpass')
# We can first do the bandpass on the single 5min scan on 1331+305
# At 1.4GHz phase stablility should be sufficient to do this without
# a first (rough) gain calibration.  This will give us the relative
# antenna gain as a function of frequency.
vis = msfile
# set the name for the output bandpass caltable
btable = prefix + '.bcal'
caltable = btable
# No gain tables yet
gaintable = ''
gainfield = ''
interp = ''
# Use flux calibrator 1331+305 = 3C286 (FIELD_ID 0) as bandpass calibrator
field = '0'
# all channels
spw = ''
# No other selection
selectdata = False
# In this band we do not need a-priori corrections for
# antenna gain-elevation curve or atmospheric opacity
# (at 8GHz and above you would want these)
opacity = 0.0
# Choose bandpass solution type
# Pick standard time-binned B (rather than BPOLY)
bandtype = 'B'
# set solution interval arbitrarily long (get single bpass)
solint = 'inf'
combine = 'scan'
# reference antenna Name 15 (15=VLA:N2) (Id 14)
refant = '15'
saveinputs('bandpass',prefix+'.bandpass.saved')
bandpass()
-->



=== Inspect the Bandpass Response Curve ===

[[File:ngc5921-bandpass.png | thumb | Bandpass response curves generated by {{plotcal}}. The solutions for different antennas are indicated by differently colored plotting symbols. Plots for individual antennas can be generated by setting '''iteration = 'antenna'''' for {{plotcal}}.]]

In the [[#Gain Calibration | gain calibration]] to follow, we will effectively convert the spectral line data into a continuum data set. Before proceeding, we need to inspect the bandpass calibration to make sure that it contains no bad values and also to inspect which channels to average to produce the continuum data. {{plotcal | Plotcal}} is the standard tool for plotting calibration solutions. The following commands produce the figure at right. 

<source lang="python">
# Set up 2x1 panels - upper panel amp vs. channel
plotcal(caltable='ngc5921.demo.bcal', field='0', subplot=211, yaxis='amp', showgui=True)
</source>

<source lang="python">
# Set up 2x1 panels - lower panel phase vs. channel
plotcal(caltable='ngc5921.demo.bcal', field='0', subplot=212, yaxis='phase', showgui=True)
</source>

By inspection, the amplitude response curve is flat over channels 6~56; that channel range will be used to generate the continuum data for gain calibration. If you want to further inspect the plots interactively and iterate over antenna, set iteration = 'antenna'

Notice that {{plotcal}} is run twice: once to display gain amplitudes as a function of channel (frequency), and again to plot gain phases as a function of channel.

<!--
If the '''scriptmode''' is set to '''False''', the plot is saved to ngc5921.demo.plotcal.png.
-->

<!--
default('plotcal')
caltable = btable
field = '0'
# Set up 2x1 panels - upper panel amp vs. channel
subplot = 211
yaxis = 'amp'
saveinputs('plotcal',prefix+'.plotcal.b.amp.saved')
showgui = True
plotcal()
#
# Set up 2x1 panels - lower panel phase vs. channel
subplot = 212
yaxis = 'phase'
saveinputs('plotcal',prefix+'.plotcal.b.phase.saved')
#
# Note the rolloff in the start and end channels.  Looks like
# channels 6-56 (out of 0-62) are the best
# If you want to do this interactively and iterate over antenna, set
# iteration = 'antenna'
plotcal()
-->



=== Gain Calibration ===

From [[#Inspect the Bandpass Response Curve  | inspection of the bandpass response curve]], we can average channels 6~56 to produce continuum data for the calibrators. For VLA data, this averaging is specified through the '''spw''' (spectral window) parameter, which takes the form IF:Channel-range, as follows.

<source lang="python">
spw = '0:6~56'
</source>

That is, there is only one spectral window (IF), '''spw = 0''', and we want to average channels '''6~56''' within that spectral window.

Gain calibrations are otherwise determined as for [[Calibrating a VLA 5 GHz continuum survey#Calibration | continuum data]]. 
* {{gaincal}}() is run only on the calibrators, 1331+305 (flux calibrator) and 1445+099 (phase calibrator).
* The default model for gain calibrations is a 1 Jy point-source. The flux scale is overridden by {{setjy}}, which has been performed for the flux calibrator. We need to transfer that flux scale to the phase calibrator using {{fluxscale}}().  
* Note that fluxscale() determines the flux density of the phase calibrator and accordingly adjusts its model and calibration solutions. A report of the results are sent to the logger window.

<source lang="python">
# Armed with the bandpass, we now solve for the time-dependent antenna gains using our previously determined bandpass.
# Note this will automatically be applied to all sources not just the one used to determine the bandpass

gaincal(vis='ngc5921.demo.ms', caltable='ngc5921.demo.gcal', gaintable=['ngc5921.demo.bcal'], interp=['nearest'], field='0,1', spw='0:6~56', gaintype='G', solint='inf', calmode='ap', refant='15')
</source>

<!-- gaincal(vis='ngc5921.demo.ms', caltable='ngc5921.demo.gcal', gaintable='ngc5921.demo.bcal', interp='nearest', field='0,1', 
        spw='0:6~56', gaintype='G', solint='inf', calmode='ap', refant='15', minsnr=1.0)-->

<source lang="python">
# Now we will transfer the flux scale to the phase calibrator. 
# We will be using 1331+305 (the source we did setjy on) as our flux standard reference.
# Note its extended name as in the FIELD table summary above (it has a VLA seq number appended)

fluxscale(vis='ngc5921.demo.ms', fluxtable='ngc5921.demo.fluxscale', caltable='ngc5921.demo.gcal', reference='1331*', transfer='1445*')
</source>


<!--
<source lang="python">
default('gaincal')

vis = msfile
# set the name for the output gain caltable
gtable = prefix + '.gcal'
caltable = gtable
# Use our previously determined bandpass
# Note this will automatically be applied to all sources
# not just the one used to determine the bandpass
gaintable = btable
gainfield = ''
# Use nearest (there is only one bandpass entry)
interp = 'nearest'
# Gain calibrators are 1331+305 and 1445+099 (FIELD_ID 0 and 1)
field = '0,1'
# We have only a single spectral window (SPW 0)
# Choose 51 channels 6-56 out of the 63
# to avoid end effects.
# Channel selection is done inside spw
spw = '0:6~56'
# No other selection
selectdata = False
# In this band we do not need a-priori corrections for
# antenna gain-elevation curve or atmospheric opacity
# (at 8GHz and above you would want these)
opacity = 0.0
# scan-based G solutions for both amplitude and phase
gaintype = 'G'
solint = 'inf'
combine = ''
calmode = 'ap'
# minimum SNR allowed
minsnr = 1.0
# reference antenna 15 (15=VLA:N2)
refant = '15'
saveinputs('gaincal',prefix+'.gaincal.saved')
gaincal()
#=====================================================================
#
# Bootstrap flux scale
#
print '--Fluxscale--'
default('fluxscale')
vis = msfile
# set the name for the output rescaled caltable
ftable = prefix + '.fluxscale'
fluxtable = ftable
# point to our first gain cal table
caltable = gtable
# we will be using 1331+305 (the source we did setjy on) as
# our flux standard reference - note its extended name as in
# the FIELD table summary above (it has a VLA seq number appended)
reference = '1331*'
# we want to transfer the flux to our other gain cal source 1445+099
transfer = '1445*'
saveinputs('fluxscale',prefix+'.fluxscale.saved')
fluxscale()
</source>
-->

The output from {{fluxscale}} follows. A relatively large uncertainty for the phase calibrator is a sign that something went wrong, perhaps bad solutions in {{gaincal}}. Here, the phase calibrator scaled to 2.486 &plusmn; 0.001 Jy, which looks reasonable.

<pre>
2018-09-12 22:38:05 INFO fluxscale	##########################################
2018-09-12 22:38:05 INFO fluxscale	##### Begin Task: fluxscale          #####
2018-09-12 22:38:05 INFO fluxscale	fluxscale(vis="ngc5921.demo.ms",caltable="ngc5921.demo.gcal",fluxtable="ngc5921.demo.fluxscale",reference="1331*",transfer="1445*",
2018-09-12 22:38:05 INFO fluxscale	        listfile="",append=False,refspwmap=[-1],gainthreshold=-1.0,antenna="",
2018-09-12 22:38:05 INFO fluxscale	        timerange="",scan="",incremental=False,fitorder=1,display=False)
2018-09-12 22:38:05 INFO fluxscale	****Using NEW VI2-driven calibrater tool****
2018-09-12 22:38:05 INFO fluxscale	Opening MS: ngc5921.demo.ms for calibration.
2018-09-12 22:38:05 INFO fluxscale	Initializing nominal selection to the whole MS.
2018-09-12 22:38:05 INFO fluxscale	Beginning fluxscale--(MSSelection version)-------
2018-09-12 22:38:05 INFO fluxscale	 Found reference field(s): 1331+30500002_0
2018-09-12 22:38:05 INFO fluxscale	 Found transfer field(s):  1445+09900002_0
2018-09-12 22:38:05 INFO fluxscale	 Flux density for 1445+09900002_0 in SpW=0 (freq=1.41342e+09 Hz) is: 2.52609 +/- 0.00218206 (SNR = 1157.67, N = 54)
2018-09-12 22:38:05 INFO fluxscale	Storing result in ngc5921.demo.fluxscale
2018-09-12 22:38:05 INFO fluxscale	Writing solutions to table: ngc5921.demo.fluxscale
2018-09-12 22:38:06 INFO fluxscale	CASA Version 5.3.0-143  
2018-09-12 22:38:06 INFO fluxscale	   
2018-09-12 22:38:07 INFO fluxscale	##### End Task: fluxscale            #####
2018-09-12 22:38:07 INFO fluxscale	##########################################

</pre>

<!--
2011-04-25 19:54:25 INFO fluxscale	##########################################
2011-04-25 19:54:25 INFO fluxscale	##### Begin Task: fluxscale          #####
2011-04-25 19:54:25 INFO  	fluxscale::::casa
2011-04-25 19:54:25 INFO fluxscale	Opening MS: ngc5921.demo.ms for calibration.
2011-04-25 19:54:25 INFO fluxscale	Initializing nominal selection to the whole MS.
2011-04-25 19:54:26 INFO fluxscale	Beginning fluxscale--(MSSelection version)-------
2011-04-25 19:54:26 INFO fluxscale	 Found reference field(s): 1331+30500002_0
2011-04-25 19:54:26 INFO fluxscale	 Found transfer field(s):  1445+09900002_0
2011-04-25 19:54:26 INFO fluxscale	 Flux density for 1445+09900002_0 in SpW=0 (freq=1.41342e+09 Hz) is: 2.53882 +/- 0.00218946 (SNR = 1159.57, N = 54)
2011-04-25 19:54:26 INFO fluxscale	Storing result in ngc5921.demo.fluxscale
2011-04-25 19:54:26 INFO fluxscale	Writing solutions to table: ngc5921.demo.fluxscale
2011-04-25 19:54:26 INFO  	fluxscale::::casa
2011-04-25 19:54:26 INFO fluxscale	##### End Task: fluxscale            #####
2011-04-25 19:54:26 INFO fluxscale	##########################################
</pre>
-->



=== Inspect the Calibration Solutions ===

[[File:ngc5921-gaincal.png|thumb|Gain calibration solutions from {{gaincal}} and {{fluxscale}}.]]

Now inspect the results of {{gaincal}}. The setup is identical to that used to plot the [[#Inspect the Bandpass Response Curve | bandpass response curve]]. The only change is that we are plotting the gaintable ngc5921.demo.gcal, and we're looking at solutions for both of the calibrator sources. The results are shown at right.

<source lang="python">
# Set up 2x1 panels - upper panel amp vs. time
plotcal(caltable='ngc5921.demo.fluxscale', field='0,1', subplot=211, yaxis='amp', showgui=True)
</source>

<source lang="python">
# Set up 2x1 panels - lower panel phase vs. time
plotcal(caltable='ngc5921.demo.fluxscale', field='0,1', subplot=212, yaxis='phase', showgui=True)
</source>

The amp and phase coherence looks good. If you want to do this interactively and iterate over antenna, set iteration = 'antenna'.

<!--
default('plotcal')
caltable = ftable
field = '0,1'
# Set up 2x1 panels - upper panel amp vs. time
subplot = 211
yaxis = 'amp'
# No output file yet (wait to plot next panel)
saveinputs('plotcal',prefix+'.plotcal.gscaled.amp.saved')
showgui = True
plotcal()
#
# Set up 2x1 panels - lower panel phase vs. time
subplot = 212
yaxis = 'phase'
saveinputs('plotcal',prefix+'.plotcal.gscaled.phase.saved')
#
# The amp and phase coherence looks good
# Pause script if you are running in scriptmode
# If you want to do this interactively and iterate over antenna, set
#iteration = 'antenna'
plotcal()
-->



=== Apply the Solutions ===

Next, apply the calibration solutions to the calibrators themselves, and finally transfer the calibration solutions by interpolation (or nearest-neighbor sampling) to the source. The relevant task is {{applycal}}, which fills out a new column (CORRECTED_DATA) of calibrated data in the measurement set without wiping out the raw data column. The application is identical to that used for [[Calibrating a VLA 5 GHz continuum survey|continuum data]], except that the bandpass table is also included in the calibration. To apply multiple calibrations at once, provide the '''gaintable''' parameter with a list of calibration tables, as follows.

<source lang="python">
gaintable = ['ngc5921.demo.fluxscale', 'ngc5921.demo.bcal']
</source>

We want to correct the calibrators using themselves and transfer from 1445+099 to itself and the target N5921. Start with the fluxscale/gain and bandpass tables. We will pick the 1445+099 out of the gain table for transfer and use all of the bandpass table. Also, note that the table .fluxscale has the .gcal solutions with the correct flux scale applied, and so there is no need to invoke the .gcal again in the applycal() command below.

<source lang="python">
applycal(vis='ngc5921.demo.ms', field='1,2', gaintable=['ngc5921.demo.fluxscale','ngc5921.demo.bcal'], gainfield=['1','*'], 
         interp=['linear','nearest'], spwmap=[], selectdata=False)
</source>

Now for completeness apply 1331+305 to itself. 

<source lang="python">
applycal(vis='ngc5921.demo.ms', field='0', gaintable=['ngc5921.demo.fluxscale','ngc5921.demo.bcal'], gainfield=['0','*'], 
         interp=['linear','nearest'], spwmap=[], selectdata=False)
</source>

<!---
In the script snippet below, the python global variables ''ftable'' and ''btable'' replace the full table names.

default('applycal')
vis = msfile
# We want to correct the calibrators using themselves
# and transfer from 1445+099 to itself and the target N5921
# Start with the fluxscale/gain and bandpass tables
gaintable = [ftable,btable]
# pick the 1445+099 out of the gain table for transfer
# use all of the bandpass table
gainfield = ['1','*']
# interpolation using linear for gain, nearest for bandpass
interp = ['linear','nearest']
# only one spw, do not need mapping
spwmap = []
# all channels
spw = ''
selectdata = False
# as before
opacity = 0.0
# select the fields for 1445+099 and N5921
field = '1,2'
applycal()
# Now for completeness apply 1331+305 to itself
field = '0'
gainfield = ['0','*']
# The CORRECTED_DATA column now contains the calibrated visibilities
saveinputs('applycal',prefix+'.applycal.saved')
applycal()

-->

== Plot the Spectrum ==

[[File:spectrum-plotting.png|thumb|{{plotms|Plotms}} settings to produce the integrated spectrum from the calibrated visibilities data.]]

Before we attempt to image the 21 cm cube of the source, we need to subtract off the underlying continuum, which means we need to plot the integrated spectrum of the source to determine the continuum channels.

We can do this in {{plotms}}.

<source lang="python">
plotms(vis='ngc5921.demo.ms', selectdata=True, field='N5921*', spw='0:6~56', averagedata=True, avgtime='3600', avgscan=True, 
       avgbaseline=True, xaxis='channel', yaxis='amp', ydatacolumn='corrected')
</source>

Note that we have entered all the relevent parameters via the task interface, as an alternative to entering each option into the GUI.  If the symbols appear too small,  the size may be increased via the Display tab: change the Unflagged Points Symbol to 'Custom' and increase the number of pixels for the plotting symbol.  The resulting plot is illustrated in the figure at right. Briefly, we want to average both in time and over baselines to get the signal-to-noise necessary to reveal the 21 cm profile (see [[Averaging data in plotms]] for more details on averaging options). If you wish to enter the values directly into the GUI, you can follow the (Tab)'''Command''' convention of the [[Data flagging with casaplotms|flagging tutorial]] with the following settings :
* (Data)'''field''' = N5921*
* (Data)'''spw''' = 0:6~56
* (Data)'''Averaging &rarr; Time''' = 3600 (average over some long time window)
* (Data)'''Averaging &rarr; Scan''' = True (checkmark; average in time across scan boundaries)
* (Data)'''Averaging &rarr; All Baselines''' = True (checkmark)
* (Axes)'''X Axis''' = Channel
* (Axes)'''Y Axis''' = Amp

From inspection of this plot, it looks like channels 4~6 and 50~59 contain line-free channels, suitable to use for continuum subtraction.

== Continuum Subtraction ==

The next step is to split off the NGC 5921 data from the multisource measurement set and subtract the continuum. Splitting uses the {{split}} command, as follows.

<source lang="python">
split(vis='ngc5921.demo.ms', outputvis='ngc5921.demo.src.split.ms', field='N5921*', spw='', datacolumn='corrected')
</source>

<!--
default('split')
vis = msfile
splitms = prefix + '.src.split.ms'
outputvis = splitms
field = 'N5921*'
spw = ''
datacolumn = 'corrected'
saveinputs('split',prefix+'.split.n5921.saved')
split()
print "Created "+splitms
-->

This action generated a new measurement set called ''ngc5921.demo.src.split.ms'' and copied the ''calibrated'' source data (datacolumn = 'corrected') into it.

{{uvcontsub|Uvcontsub}} subtracts the continuum from the data in the visibility (''u'', ''v'') plane. We will be using channels 4-6 and 50-59 for continuum.

<source lang="python">
uvcontsub(vis='ngc5921.demo.src.split.ms', field='N5921*', fitspw='0:4~6;50~59', spw='0', solint=0.0, fitorder=0, want_cont=True)
</source>

<!--
default('uvcontsub')
vis = splitms
field = 'N5921*'
# Use channels 4-6 and 50-59 for continuum
fitspw='0:4~6;50~59'
# Output all of spw 0
spw = '0'
# Averaging time (none)
solint = 0.0
# Fit only a mean level
fitorder = 0
# Do the uv-plane subtraction
fitmode = 'subtract'
# Let it split out the data automatically for us
splitdata = True
saveinputs('uvcontsub',prefix+'.uvcontsub.saved')
uvcontsub()
</source>
-->

Notice that {{uvcontsub}} splits two new measurement sets, 'ngc5921.demo.ms.cont', which contains an average of the continuum channels, and 'ngc5921.demo.ms.contsub', which contains the continuum-subtracted spectral line data.

== Imaging ==
[[File:spectrum-uvplot.png|thumb|Plot of amplitude vs. projected baseline length (in units of the observing wavelength) produced by casaplotms. The maximum baseline is just below 5 kilo-lambda.]]


Now we can generate the primary science product, a {{clean}} data cube (ra, dec, velocity) from the continuum-subtracted (''u'', ''v'', channel) measurement set, ''ngc5921.demo.ms.contsub''. Things to consider in using {{clean}}:
* To ensure channels aren't averaged prior to imaging, choose '''mode='channel''''.
* Specify the channels to image using '''start = 5''', '''width = 1''' (no averaging over channels), '''nchan = 46'''; only channels 5~51 will be imaged.
* The maximum baseline is just under 5 kilolambda (see the figure at right), and so the expected synthetic beam is roughly 1.22 &times; 206265 / 5000 = 50 arcseconds (subject to the details of ''u'', ''v'' weighting). Pixels should sample the beam better than 3 times, so 15 arcseconds is a good choice of pixel size ('''cell = ['15.0arcsec','15.0arcsec']''').
* We only want to {{clean}} down to the noise, which is easily determined by trial-and-error imaging of a single channel (choosing '''nchan=1''' and '''start''' appropriately). Here, {{clean}} stops when the maximum residual on the channel is below '''threshold='8.0mJy''''. 

<source lang="python">
# Image the continuum subtracted measurement set
clean(vis='ngc5921.demo.src.split.ms.contsub', imagename='ngc5921.demo.cleanimg', field='0', mode='channel', nchan=46, start=5, width=1,
      spw='', gain=0.1, imsize=[256,256], psfmode='clark', imagermode='', cell=['15.0arcsec','15.0arcsec'], niter=6000,
      threshold='8.0mJy', weighting='briggs', robust=0.5, mask = [108,108,148,148], interactive=False)
</source>

<!--
srcsplitms = splitms + '.contsub'
#=====================================================================
#
# Now clean an image cube of N5921
#
default('clean')
# Pick up our split source continuum-subtracted data
vis = srcsplitms
# Make an image root file name
imname = prefix + '.cleanimg'
imagename = imname
# Set up the output image cube
mode = 'channel'
nchan = 46
start = 5
width = 1
# This is a single-source MS with one spw
field = '0'
spw = ''
# Standard gain factor 0.1
gain = 0.1
# Set the output image size and cell size (arcsec)
imsize = [256,256]
# Do a simple Clark clean
psfmode = 'clark'
# No Cotton-Schwab iterations
csclean = False
# Pixel size 15 arcsec for this data (1/3 of 45" beam)
# VLA D-config L-band
cell = ['15.0arcsec','15.0arcsec']
# Fix maximum number of iterations
niter = 6000
# Also set flux residual threshold (in mJy)
threshold='8.0mJy'
# Set up the weighting
# Use Briggs weighting (a moderate value, on the uniform side)
weighting = 'briggs'
robust = 0.5
# Set a cleanbox +/-20 pixels around the center 128,128
mask = [108,108,148,148]
# If you want interactive clean set to True
#interactive=True
interactive=False
saveinputs('clean',prefix+'.clean.saved')
clean()
-->

Use {{imhead}} to look at the cube header:

<source lang="python">
imhead(imagename='ngc5921.demo.cleanimg.image', mode='summary')
</source>

<!--
clnimage = imname+'.image' # store the clean image in a python global for future use
default('imhead')
imagename = clnimage
mode = 'summary'
imhead()
-->

The output, as follows, appears in the logger window.

<pre>
2011-04-25 20:10:29 INFO imhead	##########################################
2011-04-25 20:10:29 INFO imhead	##### Begin Task: imhead             #####
2011-04-25 20:10:29 INFO  	imhead::::casa
2011-04-25 20:10:29 INFO  	ImageAnalysis::summary
2011-04-25 20:10:29 INFO ImageAnalysis	Image name       : ngc5921.demo.cleanimg.image
2011-04-25 20:10:29 INFO ImageAnalysis	Object name      : N5921_2
2011-04-25 20:10:29 INFO ImageAnalysis	Image type       : PagedImage
2011-04-25 20:10:29 INFO ImageAnalysis	Image quantity   : Intensity
2011-04-25 20:10:29 INFO ImageAnalysis	Pixel mask(s)    : None
2011-04-25 20:10:29 INFO ImageAnalysis	Region(s)        : None
2011-04-25 20:10:29 INFO ImageAnalysis	Image units      : Jy/beam
2011-04-25 20:10:29 INFO ImageAnalysis	Restoring Beam   : 51.7693 arcsec, 47.2192 arcsec, -170.658 deg
2011-04-25 20:10:29 INFO  	ImageAnalysis::summary
2011-04-25 20:10:29 INFO ImageAnalysis	Direction reference : J2000
2011-04-25 20:10:29 INFO ImageAnalysis	Spectral  reference : LSRK
2011-04-25 20:10:29 INFO ImageAnalysis	Velocity  type      : RADIO
2011-04-25 20:10:29 INFO ImageAnalysis	Rest frequency      : 1.42041e+09 Hz
2011-04-25 20:10:29 INFO ImageAnalysis	Pointing center     :  15:22:00.000000  +05.04.00.000000
2011-04-25 20:10:29 INFO ImageAnalysis	Telescope           : VLA
2011-04-25 20:10:29 INFO ImageAnalysis	Observer            : TEST
2011-04-25 20:10:29 INFO ImageAnalysis	Date observation    : 1995/04/13/09:33:00
2011-04-25 20:10:29 INFO ImageAnalysis	Telescope position: [-1.60119e+06m, -5.04198e+06m, 3.55488e+06m] (ITRF)
2011-04-25 20:10:29 INFO  	ImageAnalysis::summary+
2011-04-25 20:10:29 INFO ImageAnalysis	Axis Coord Type      Name             Proj Shape Tile   Coord value at pixel    Coord incr Units
2011-04-25 20:10:29 INFO ImageAnalysis	------------------------------------------------------------------------------------------------ 
2011-04-25 20:10:29 INFO ImageAnalysis	0    0     Direction Right Ascension   SIN   256   64  15:22:00.000   128.00 -1.500000e+01 arcsec
2011-04-25 20:10:29 INFO ImageAnalysis	1    0     Direction Declination       SIN   256   64 +05.04.00.000   128.00  1.500000e+01 arcsec
2011-04-25 20:10:29 INFO ImageAnalysis	2    1     Stokes    Stokes                    1    1             I
2011-04-25 20:10:29 INFO ImageAnalysis	3    2     Spectral  Frequency                46    8   1.41279e+09     0.00 2.4414062e+04 Hz
2011-04-25 20:10:29 INFO ImageAnalysis	                     Velocity                               1607.99     0.00 -5.152860e+00 km/s
2011-04-25 20:10:29 INFO  	imhead::::casa
2011-04-25 20:10:29 INFO imhead	##### End Task: imhead               #####
2011-04-25 20:10:29 INFO imhead	##########################################
</pre>

== Additional Science Products ==

If things went well, you should now have a spectral line cube (''ngc5921.demo.cleanimg.image'') as a primary science product. The demo script illustrates further how to generate cube statistics (using {{imstat}}), an integrated spectrum, and moment maps. 

=== Cube Statistics ===

{{imstat|Imstat}} is the tool for displaying statistics of images and cubes. The following example displays the statistics for the whole cube.

<source lang="python">
cubestat=imstat(imagename='ngc5921.demo.cleanimg.image', box='')
</source>

<!--
default('imstat')
imagename = clnimage # or imagename = "ngc5921.demo.cleanimg.img"
# Do whole image
box = ''
# or you could stick to the cleanbox
#box = '108,108,148,148'
cubestats = imstat()
-->

The output goes to the logger window.

<pre>
2011-04-25 20:12:13 INFO imstat	##########################################
2011-04-25 20:12:13 INFO imstat	##### Begin Task: imstat             #####
2011-04-25 20:12:13 INFO  	imstat::::casa
2011-04-25 20:12:13 INFO imstat	No region specified. Using full positional plane.
2011-04-25 20:12:13 INFO imstat	Using all spectral channels.
2011-04-25 20:12:13 INFO imstat	Using polarizations I
2011-04-25 20:12:13 INFO imstat	Determining stats for image ngc5921.demo.cleanimg.image
2011-04-25 20:12:13 INFO imstat	Selected bounding box : 
2011-04-25 20:12:13 INFO imstat	    [0, 0, 0, 0] to [255, 255, 0, 45]  (15:24:08.404, +04.31.59.181, I, 1.41279e+09Hz to 15:19:52.390, +05.35.44.246, I, 1.41389e+09Hz)
2011-04-25 20:12:13 INFO imstat	Regions --- 
2011-04-25 20:12:13 INFO imstat	         -- bottom-left corner (pixel) [blc]:  [0, 0, 0, 0]
2011-04-25 20:12:13 INFO imstat	         -- top-right corner (pixel) [trc]:    [255, 255, 0, 45]
2011-04-25 20:12:13 INFO imstat	         -- bottom-left corner (world) [blcf]: 15:24:08.404, +04.31.59.181, I, 1.41279e+09Hz
2011-04-25 20:12:13 INFO imstat	         -- top-right corner (world) [trcf]:   15:19:52.390, +05.35.44.246, I, 1.41389e+09Hz
2011-04-25 20:12:13 INFO imstat	Values --- 
2011-04-25 20:12:13 INFO imstat	         -- flux density [flux]:     4.14845 Jy
2011-04-25 20:12:13 INFO imstat	         -- number of points [npts]:                3.01466e+06
2011-04-25 20:12:13 INFO imstat	         -- maximum value [max]:                    0.0555024 Jy/beam
2011-04-25 20:12:13 INFO imstat	         -- minimum value [min]:                    -0.0107881 Jy/beam
2011-04-25 20:12:13 INFO imstat	         -- position of max value (pixel) [maxpos]: [134, 134, 0, 38]
2011-04-25 20:12:13 INFO imstat	         -- position of min value (pixel) [minpos]: [230, 0, 0, 15]
2011-04-25 20:12:13 INFO imstat	         -- position of max value (world) [maxposf]: 15:21:53.976, +05.05.29.998, I, 1.41371e+09Hz
2011-04-25 20:12:13 INFO imstat	         -- position of min value (world) [maxposf]: 15:20:17.679, +04.31.59.470, I, 1.41315e+09Hz
2011-04-25 20:12:13 INFO imstat	         -- Sum of pixel values [sum]:               51.0692 Jy/beam
2011-04-25 20:12:13 INFO imstat	         -- Sum of squared pixel values [sumsq]:     12.2781 Jy/beam.Jy/beam
2011-04-25 20:12:13 INFO  	imstat::::
2011-04-25 20:12:13 INFO imstat	Statistics --- 
2011-04-25 20:12:13 INFO imstat	        -- Mean of the pixel values [mean]:         1.69403e-05 Jy/beam
2011-04-25 20:12:13 INFO imstat	        -- Variance of the pixel values :           4.07252e-06 Jy/beam
2011-04-25 20:12:13 INFO imstat	        -- Standard deviation of the Mean [sigma]:  0.00201805 Jy/beam
2011-04-25 20:12:13 INFO imstat	        -- Root mean square [rms]:                  0.00201812 Jy/beam
2011-04-25 20:12:13 INFO imstat	        -- Median of the pixel values [median]:     -1.18009e-05 Jy/beam
2011-04-25 20:12:13 INFO imstat	        -- Median of the deviations [medabsdevmed]: 0.00126199 Jy/beam
2011-04-25 20:12:13 INFO imstat	        -- Quartile [quartile]:                     0.00252393 Jy/beam
2011-04-25 20:12:13 INFO  	imstat::::casa
2011-04-25 20:12:13 INFO imstat	##### End Task: imstat               #####
2011-04-25 20:12:13 INFO imstat	##########################################
</pre>

=== The Integrated Spectrum ===

[[File:spectrum-integrated.png|thumb|Example of the {{viewer}} rectangle selection tool on one channel of the NGC&nbsp;5921 21&nbsp;cm data cube. The spectral profile window is shown at right.]]


We saw earlier [[#Plot the Spectrum|how to generate an integrated spectrum]] from the (''u'', ''v'') measurement set. Here's how to produce the integrated spectrum from the spectral line cube. First, load the cube into {{viewer}}.

<source lang="python">
viewer(infile='ngc5921.demo.cleanimg.image')
</source>

<!--
# Store the name of the clean image into a python global
clnimage = imname+'.image'
viewer(clnimage)
-->

To generate the integrated spectrum, perform the following tasks.
* Use the player controls [[File:vcrNext.png]] to inspect the cube one channel at a time.
* From the {{viewer}} Tools menu, select '''Spectral Profile'''. A new graphics window should appear.
* By default, the rectangle selection tool [[File:drawingSelector.png]] is assigned to the right mouse button, and you can just right-click and drag a box over the region where you want to (spatially) integrate the spectrum. See the figure at upper right. 
* Alternatively, you can assign one of the other selection tools by right-clicking on the appropriate button.
* The spectrum now appears in the graphics window; see the figure at right.

You can save the integrated spectrum to a text file by clicking the [[File:save-as-text-file.png]] button on the graphics window. There are also buttons to print the figure or save the figure to disk.

=== Cube Moments ===

[[File:spectrum-momzero.png|thumb|The moment 0 (integrated intensity) 21&nbsp;cm image of NGC&nbsp;5921, produced using {{immoments}}]]

Cube moments are maps of weighted sums along the velocity axis. In CASA, they are generated by the task {{immoments}}. The zeroth moment (moments = 0) is a sum of intensities along the velocity axis (the integrated intensity map); the first moment (moment = 1) is the sum of velocities weighted by intensity (the ''velocity field''); the second moment (moment = 2) is a map of the velocity dispersion; see the {{immoments|helpfile}} for additional options.

The following example produces maps of the zeroth and first moments, or the integrated intensity and velocity field. The respective measurement sets are the moment zero image ''ngc5921.demo.moments.integrated'' and moment one image''ngc5921.demo.moments.weighted_coord''.

We will do the zeroth and first moments and mask out noisy pixels using hard global limits. We will also collapse along the spectral (channel) axis and include all planes.

<source lang="python">
immoments(imagename='ngc5921.demo.cleanimg.image', moments=[0,1], excludepix=[-100, 0.009], axis='spectral', chans='', outfile='ngc5921.demo.moments')
</source>

* moments = [0,1] : Do zeroth and first moments
* excludepix = [-100,0.009] : Mask out noisy pixels using hard global limits
* axis  = 'spectral' : Collapse along the spectral (channel) axis
* chans = '' :Include all planes

<!--
default('immoments')
imagename = clnimage
# Do zeroth and first moments
moments = [0,1]
# Need to mask out noisy pixels, currently done
# using hard global limits
excludepix = [-100,0.009]
# Collapse along the spectral (channel) axis
axis  = 'spectral'
# Include all planes
chans = ''
# Output root name
momfile = prefix + '.moments'
outfile = momfile
saveinputs('immoments',prefix+'.immoments.saved')
immoments()
momzeroimage = momfile + '.integrated'
momoneimage = momfile + '.weighted_coord'
-->

To examine the moment images, use {{viewer}}; the resulting moment zero image is displayed at right.

Note that you may have to play with the color map (Data Display Options button in viewer) in order to replicate the image in this tutorial.

<source lang="python">
viewer(infile='ngc5921.demo.moments.integrated')
</source>

== Export the Data ==

To export the (''u'', ''v'') data and image cube as FITS files, use {{exportuvfits}} and {{exportfits}}, respectively.

Here's how to export the continuum-subtracted (''u'', ''v'') data.

<source lang="python">
exportuvfits(vis='ngc5921.demo.src.split.ms.contsub', fitsfile='ngc5921.demo.contsub.uvfits', datacolumn='corrected', multisource=True)
</source>

<!--
default('exportuvfits')
srcuvfits = prefix + '.contsub.uvfits' # recall: prefix = 'ngc5921.demo'
vis = splitms + '.contsub'
fitsfile = srcuvfits
datacolumn = 'corrected'
multisource = True
async = True
myhandle = exportuvfits()
-->

And now, the FITS cube.
<source lang="python">
exportfits(imagename='ngc5921.demo.cleanimg.image', fitsimage='ngc5921.demo.cleanimg.fits')
</source>

<!--
default('exportfits')
clnfits = prefix + '.cleanimg.fits'
imagename = clnimage
fitsimage = clnfits
async = True
saveinputs('exportfits',prefix+'.exportfits.saved')
myhandle2 = exportfits()
-->

The moment maps (or any CASA images) can be similarly exported using {{exportfits}}.

== Appendix: Python Notes ==

=== os.system ===

'''os.system''' allows you to run shell commands from within python / CASA. For example:

<pre>
import os
os.system('ls -sF')
</pre>

will give an OS-level listing of the current directory's contents.

=== os.environ.get ===
It's worth having a look at the output of the '''os.environ.get''' command to understand the python syntax (alternative: '''os.getenv'''). You can think of '''os.environ''' as a list of operating system environment variables, and '''get''' is a method that extracts information about the requested environment variable, here, CASAPATH. '''Get''' returns a string of whitespace separated information, and '''.split()''' turns that string into a list. The array index '''[0]''' extracts the first element of that list, which contains the path. 

To illustrate, here is some example python I/O in CASA.

<pre>
CASA <12>: print os.environ.get('CASAPATH')
/usr/lib64/casapy/30.0.9709test-001 linux local el5bld64b

CASA <13>: print os.environ.get('CASAPATH').split()
['/usr/lib64/casapy/30.0.9709test-001', 'linux', 'local', 'el5bld64b']

CASA <14>: print os.environ.get('CASAPATH').split()[0]
/usr/lib64/casapy/30.0.9709test-001
</pre>

[[Pre-upgrade VLA Tutorials | &#8629; '''Pre-upgrade VLA Tutorials''']]

{{Checked 5.1.1}}