ATCA Continuum Polarization Tutorial NGC612-CASA4.7

This CASA Guide is for Version 4.6 of CASA. If you are using a later version of CASA and this is the most recent available guide, then you should be able to use most, if not all, of this casaguide, as we try to limit script breaking changes in CASA development.

Overview

This CASA guide describes the calibration and imaging of a two-pointing continuum data set taken with the Australia Telescope Compact Array (ATCA) of the nearby radio galaxy NGC612 NGC612. It has been adapted from the 3C391 Continuum Tutorial (CASA 4.6) for the VLA . The data were taken with 2048 MHz of bandwidth in 1 MHz channels, centered at 2.1 GHz, and recorded all polarizations. For ATCA data reduction there are two paths you can follow:

• If you are already familiar with the Miriad package, you can do the loading and optionally the flagging and calibration of the data in Miriad and then import the data into a CASA MeasurementSet with importmiriad.
• Alternatively, you can use importatca to load the ATCA archive files directly into CASA.

If this is your first attempt at using CASA for Compact Array data you are encouraged to start with a flagged and calibrated Miriad dataset which will be available here when this guide is complete and then try imaging the data. If you feel you are ready to tackle the full reduction job in CASA switch to [this guide]

Obtaining the Data

For the purposes of this tutorial, we have created a starting data set, upon which several initial processing steps have already been conducted. You may obtain the data set from here: available here when this guide is complete(dataset size: 2.0GB).

The steps taken to produce this dataset were:

• The archive data was loaded into Miriad
• Basic data flagging of the calibration source was applied. These data were taken in the 1-3 GHz band, which has a lot of interference, especially in the lower part of the band.
• Bandpass, polarization leakage and fluxscale calibration was done using an observation of 1934-638
• Phase calibration was solved for on a secondary calibrator
• All the calibration was applied to the target source observations
• Further automated flagging was applied to the target

Once the download is complete, unzip and unpack the file (within a working directory, which you will then run CASA):

# In a Terminal:
tar xzvf ngc612.tgz

How to Use This CASA Guide

Here are a number of possible ways to run CASA, described in more detail in Getting Started in CASA. In brief, there are at least three different ways to run CASA:

• Interactively examining task inputs. In this mode, one types taskname to load the task, inp to examine the inputs, and go once those inputs have been set to your satisfaction. Allowed inputs are shown in blue and bad inputs are colored red. The input parameters themselves are changed one by one, e.g., selectdata=T. Screenshots of the inputs to various tasks used in the data reduction below are provided, to illustrate which parameters need to be set. More detailed help can be obtained on any task by typing help taskname. Once a task is run, the set of inputs are stored and can be retrieved via tget taskname; subsequent runs will overwrite the previous tget file.

• Pseudo-interactively via task function calls. In this case, all of the desired inputs to a task are provided at once on the CASA command line. This tutorial is made up of such calls, which were developed by looking at the inputs for each task and deciding what needed to be changed from default values. For task function calls, only parameters that you want to be different from their defaults need to be set.

• Non-interactively via a script. A series of task function calls can be combined together into a script, and run from within CASA via execfile('scriptname.py'). This and other CASA Tutorial Guides have been designed to be extracted into a script via the script extractor by using the method described at the Extracting_scripts_from_these_tutorials page. Should you use the script generated by the script extractor for this CASA Guide, be aware that it will require some small amount of interaction related to the plotting, occasionally suggesting that you close the graphics window and hitting return in the terminal to proceed. It is in fact unnecessary to close the graphics windows (it is suggested that you do so purely to keep your desktop uncluttered).

If you are a relative novice or just new to CASA, it is strongly recommended to work through this tutorial by cutting and pasting the task function calls provided below after you have read all the associated explanations. Work at your own pace, look at the inputs to the tasks to see what other options exist, and read the help files. Later, when you are more comfortable, you might try to extract the script, modify it for your purposes, and begin to reduce other data.

Importing the Miriad data

Before beginning our data reduction, we must start CASA. If you have not used CASA before, some helpful tips are available on the Getting Started in CASA page.

Once you have CASA up and running in the directory containing the data, then start your data reduction by getting the data into a MeasurementSet. The task to do this importmiriad is very simple. If your observation has a large range of system temperature you may want to use tsys=True to use the Tsys for the visibility weights, this will improve the noise level but may increase the sidelobe level in the synthesized beam.

# In CASA
importmiriad(mirfile='ngc612.uv',vis='ngc612ms')

The Observation

Before diving into the imaging, lets have a look what we've got in our data. The task listobs can be used to get a listing of the individual scans comprising the observation, the frequency setup, source list, and antenna locations.

# In CASA
listobs(vis='ngc612.ms')

As you can see there are only two sources, called west_lobe and east_lobe. The galaxy ngc612 is quite large compared to the primary beam at 2 GHz, so two pointings were used to cover the emission with adequate sensitivity. The observation ran for close to 12 hours, this should give good uv coverage with the array in a short E-W configuration. From the antenna table we can see that antenna 1 to 5 are all within 750m and 6 is a long way off. We would generally not use antenna 6 for imaging in a 750m configuration unless we needed to get an accurate position for a point source or we were combining this observation with other configurations that fill in the large gap.

##########################################
##### Begin Task: listobs            #####
listobs(vis="ngc612.ms",selectdata=True,spw="",field="",antenna="",
        uvrange="",timerange="",correlation="",scan="",intent="",
        feed="",array="",observation="",verbose=True,listfile="",
        listunfl=False,cachesize=50,overwrite=False)
================================================================================
           MeasurementSet Name:  /Volumes/MacintoshHD2/data/ngc612/casatest/ngc612.ms      MS Version 2
================================================================================
   Observer: obs     Project: unknown  
Observation: ATCA
Data records: 45115       Total elapsed time = 42269.9 seconds
   Observed from   25-Oct-2012/07:32:00.0   to   25-Oct-2012/19:16:29.9 (UTC)
Compute subscan properties
   
   ObservationID = 0         ArrayID = 0
  Date        Timerange (UTC)          Scan  FldId FieldName             nRows     SpwIds   Average Interval(s)    ScanIntent
  25-Oct-2012/07:32:00.0 - 07:40:49.9     0      0 east_lobe                  495  [0]  [9.86] 
              07:41:10.0 - 07:46:09.9     1      1 west_lobe                  450  [0]  [9.86] 
              07:46:30.0 - 07:51:29.9     2      0 east_lobe                  450  [0]  [9.86] 
              07:52:00.0 - 07:56:59.9     3      1 west_lobe                  450  [0]  [9.86] 
              07:57:20.0 - 08:02:19.9     4      0 east_lobe                  450  [0]  [9.86] 
              08:02:40.0 - 08:07:49.9     5      1 west_lobe                  460  [0]  [9.86] 
              08:08:10.0 - 08:13:09.9     6      0 east_lobe                  450  [0]  [9.86] 
              08:13:30.0 - 08:18:29.9     7      1 west_lobe                  450  [0]  [9.86] 
              08:18:50.0 - 08:23:49.9     8      0 east_lobe                  450  [0]  [9.86] 
              08:24:10.0 - 08:29:09.9     9      1 west_lobe                  434  [0]  [9.86] 
              08:34:50.0 - 08:39:49.9    10      0 east_lobe                  450  [0]  [9.86] 
              08:40:10.0 - 08:45:09.9    11      1 west_lobe                  450  [0]  [9.86] 
              09:23:00.0 - 09:27:59.9    12      0 east_lobe                  450  [0]  [9.86] 
              09:28:20.0 - 09:33:19.9    13      1 west_lobe                  450  [0]  [9.86] 
              09:33:40.0 - 09:38:39.9    14      0 east_lobe                  450  [0]  [9.86] 
              09:39:00.0 - 09:43:59.9    15      1 west_lobe                  450  [0]  [9.86] 
              09:44:20.0 - 09:49:19.9    16      0 east_lobe                  436  [0]  [9.86] 
              09:49:40.0 - 09:54:39.9    17      1 west_lobe                  450  [0]  [9.86] 
              09:55:00.0 - 09:59:59.9    18      0 east_lobe                  450  [0]  [9.86] 
              10:00:20.0 - 10:05:19.9    19      1 west_lobe                  450  [0]  [9.86] 
              10:05:40.0 - 10:10:39.9    20      0 east_lobe                  437  [0]  [9.86] 
              10:11:00.0 - 10:15:59.9    21      1 west_lobe                  449  [0]  [9.86] 
              10:21:40.0 - 10:26:39.9    22      0 east_lobe                  450  [0]  [9.86] 
              10:27:00.0 - 10:31:59.9    23      1 west_lobe                  450  [0]  [9.86] 
              10:32:20.0 - 10:37:19.9    24      0 east_lobe                  450  [0]  [9.86] 
              10:37:40.0 - 10:42:39.9    25      1 west_lobe                  449  [0]  [9.86] 
              10:43:00.0 - 10:47:59.9    26      0 east_lobe                  450  [0]  [9.86] 
              10:48:20.0 - 10:53:19.9    27      1 west_lobe                  450  [0]  [9.86] 
              10:53:40.0 - 10:58:39.9    28      0 east_lobe                  450  [0]  [9.86] 
              10:59:00.0 - 11:03:59.9    29      1 west_lobe                  450  [0]  [9.86] 
              11:04:20.0 - 11:09:19.9    30      0 east_lobe                  450  [0]  [9.86] 
              11:09:40.0 - 11:14:39.9    31      1 west_lobe                  450  [0]  [9.86] 
              11:20:40.0 - 11:25:39.9    32      0 east_lobe                  450  [0]  [9.86] 
              11:26:00.0 - 11:30:59.9    33      1 west_lobe                  450  [0]  [9.86] 
              11:31:20.0 - 11:36:19.9    34      0 east_lobe                  450  [0]  [9.86] 
              11:36:40.0 - 11:41:39.9    35      1 west_lobe                  450  [0]  [9.86] 
              11:42:00.0 - 11:46:59.9    36      0 east_lobe                  450  [0]  [9.86] 
              11:47:20.0 - 11:52:19.9    37      1 west_lobe                  450  [0]  [9.86] 
              12:19:50.0 - 12:24:49.9    38      0 east_lobe                  450  [0]  [9.86] 
              12:25:10.0 - 12:30:09.9    39      1 west_lobe                  450  [0]  [9.86] 
              12:30:30.0 - 12:35:29.9    40      0 east_lobe                  450  [0]  [9.86] 
              12:35:50.0 - 12:40:49.9    41      1 west_lobe                  450  [0]  [9.86] 
              12:41:10.0 - 12:46:09.9    42      0 east_lobe                  450  [0]  [9.86] 
              12:46:30.0 - 12:51:29.9    43      1 west_lobe                  450  [0]  [9.86] 
              12:51:50.0 - 12:56:49.9    44      0 east_lobe                  450  [0]  [9.86] 
              12:57:10.0 - 13:02:09.9    45      1 west_lobe                  450  [0]  [9.86] 
              13:02:30.0 - 13:07:29.9    46      0 east_lobe                  450  [0]  [9.86] 
              13:07:50.0 - 13:12:49.9    47      1 west_lobe                  450  [0]  [9.86] 
              13:19:30.0 - 13:24:29.9    48      0 east_lobe                  450  [0]  [9.86] 
              13:24:50.0 - 13:29:49.9    49      1 west_lobe                  450  [0]  [9.86] 
              13:30:10.0 - 13:35:09.9    50      0 east_lobe                  450  [0]  [9.86] 
              13:35:30.0 - 13:40:29.9    51      1 west_lobe                  450  [0]  [9.86] 
              13:40:50.0 - 13:45:49.9    52      0 east_lobe                  450  [0]  [9.86] 
              13:46:10.0 - 13:51:09.9    53      1 west_lobe                  450  [0]  [9.86] 
              13:51:30.0 - 13:56:29.9    54      0 east_lobe                  450  [0]  [9.86] 
              13:56:50.0 - 14:01:49.9    55      1 west_lobe                  450  [0]  [9.86] 
              14:02:10.0 - 14:07:09.9    56      0 east_lobe                  450  [0]  [9.86] 
              14:07:30.0 - 14:12:29.9    57      1 west_lobe                  450  [0]  [9.86] 
              14:18:10.0 - 14:23:09.9    58      0 east_lobe                  450  [0]  [9.86] 
              14:23:30.0 - 14:28:29.9    59      1 west_lobe                  450  [0]  [9.86] 
              14:28:50.0 - 14:33:49.9    60      0 east_lobe                  450  [0]  [9.86] 
              14:34:10.0 - 14:39:09.9    61      1 west_lobe                  450  [0]  [9.86] 
              14:39:30.0 - 14:44:29.9    62      0 east_lobe                  450  [0]  [9.86] 
              14:44:50.0 - 14:49:49.9    63      1 west_lobe                  450  [0]  [9.86] 
              15:20:50.0 - 15:25:49.9    64      0 east_lobe                  450  [0]  [9.86] 
              15:26:10.0 - 15:31:09.9    65      1 west_lobe                  450  [0]  [9.86] 
              15:31:30.0 - 15:36:29.9    66      0 east_lobe                  450  [0]  [9.86] 
              15:36:50.0 - 15:41:49.9    67      1 west_lobe                  450  [0]  [9.86] 
              15:42:10.0 - 15:47:09.9    68      0 east_lobe                  450  [0]  [9.86] 
              15:47:30.0 - 15:52:29.9    69      1 west_lobe                  450  [0]  [9.86] 
              15:52:50.0 - 15:57:49.9    70      0 east_lobe                  450  [0]  [9.86] 
              15:58:10.0 - 16:03:09.9    71      1 west_lobe                  450  [0]  [9.86] 
              16:03:30.0 - 16:08:29.9    72      0 east_lobe                  450  [0]  [9.86] 
              16:08:50.0 - 16:13:49.9    73      1 west_lobe                  450  [0]  [9.86] 
              16:19:30.0 - 16:24:29.9    74      0 east_lobe                  450  [0]  [9.86] 
              16:24:50.0 - 16:29:49.9    75      1 west_lobe                  450  [0]  [9.86] 
              16:30:10.0 - 16:35:09.9    76      0 east_lobe                  450  [0]  [9.86] 
              16:35:30.0 - 16:40:29.9    77      1 west_lobe                  450  [0]  [9.86] 
              16:40:50.0 - 16:45:49.9    78      0 east_lobe                  450  [0]  [9.86] 
              16:46:10.0 - 16:51:09.9    79      1 west_lobe                  450  [0]  [9.86] 
              16:51:30.0 - 16:56:29.9    80      0 east_lobe                  450  [0]  [9.86] 
              16:56:50.0 - 17:01:49.9    81      1 west_lobe                  450  [0]  [9.86] 
              17:02:10.0 - 17:07:09.9    82      0 east_lobe                  450  [0]  [9.86] 
              17:07:30.0 - 17:12:29.9    83      1 west_lobe                  450  [0]  [9.86] 
              17:17:50.0 - 17:22:49.9    84      0 east_lobe                  450  [0]  [9.86] 
              17:23:10.0 - 17:28:09.9    85      1 west_lobe                  450  [0]  [9.86] 
              17:28:30.0 - 17:33:29.9    86      0 east_lobe                  450  [0]  [9.86] 
              17:33:50.0 - 17:38:49.9    87      1 west_lobe                  450  [0]  [9.86] 
              17:39:10.0 - 17:44:09.9    88      0 east_lobe                  450  [0]  [9.86] 
              17:44:30.0 - 17:49:29.9    89      1 west_lobe                  450  [0]  [9.86] 
              18:17:00.0 - 18:21:59.9    90      0 east_lobe                  450  [0]  [9.86] 
              18:22:20.0 - 18:27:19.9    91      1 west_lobe                  450  [0]  [9.86] 
              18:27:40.0 - 18:32:39.9    92      0 east_lobe                  450  [0]  [9.86] 
              18:33:00.0 - 18:37:59.9    93      1 west_lobe                  450  [0]  [9.86] 
              18:38:20.0 - 18:43:19.9    94      0 east_lobe                  450  [0]  [9.86] 
              18:43:40.0 - 18:48:39.9    95      1 west_lobe                  450  [0]  [9.86] 
              18:49:00.0 - 18:53:59.9    96      0 east_lobe                  450  [0]  [9.86] 
              18:54:20.0 - 18:59:19.9    97      1 west_lobe                  450  [0]  [9.86] 
              18:59:40.0 - 19:04:39.9    98      0 east_lobe                  450  [0]  [9.86] 
              19:05:00.0 - 19:09:59.9    99      1 west_lobe                  450  [0]  [9.86] 
              19:15:20.0 - 19:16:29.9   100      0 east_lobe                  105  [0]  [9.86] 
           (nRows = Total number of rows per scan) 
Fields: 2
  ID   Code Name                RA               Decl           Epoch   SrcId      nRows
  0         east_lobe           01:34:16.760003 -36.30.13.52004 J2000   0          22623
  1         west_lobe           01:33:34.630993 -36.29.21.54998 J2000   1          22492
Spectral Windows:  (1 unique spectral windows and 1 unique polarization setups)
  SpwID  Name   #Chans   Frame   Ch0(MHz)  ChanWid(kHz)  TotBW(kHz) CtrFreq(MHz)  Corrs          
  0              2049   TOPO    3124.000      1000.000   2048999.9   2099.9999   XX  XY  YX  YY
Sources: 2
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
  0    east_lobe           any   0              0            
  1    west_lobe           any   0              0            
Antennas: 6:
  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
                                                                     East         North     Elevation               x               y               z
  0    CA01  ANT1      22.0 m   +149.33.56.6  -30.08.43.7       1499.9964        0.7791       -1.6154 -4751674.968380  2791612.462760 -3200482.261996
  1    CA02  ANT2      22.0 m   +149.33.50.3  -30.08.43.7       1331.6268        0.6976       -1.7776 -4751589.522380  2791757.539760 -3200482.250996
  2    CA03  ANT3      22.0 m   +149.33.48.0  -30.08.43.7       1270.4080        0.6519       -1.8365 -4751558.446380  2791810.284760 -3200482.260996
  3    CA04  ANT4      22.0 m   +149.33.32.6  -30.08.43.7        857.1507        0.4408       -2.2258 -4751348.701380  2792166.358760 -3200482.247996
  4    CA05  ANT5      22.0 m   +149.33.28.0  -30.08.43.7        734.6981        0.3677       -2.3339 -4751286.547380  2792271.864760 -3200482.256996
  5    CA06  ANT6      22.0 m   +149.31.08.2  -30.08.43.8      -2999.9964       -0.8846       -4.6136 -4749390.961380  2795489.734760 -3200482.194996
##### End Task: listobs              #####
##########################################

Applying Parallactic Angle Calibration

The first thing we need to do when dealing with ATCA linear polarization data is correct for the parallactic angle rotation of the feeds with respect to the sky. Since the antennas have an Alt-Az mount and the receptors are linearly polarized, the X and Y receptors rotate on the sky. The calibration term 'P', for parallactic angle, corrects for this rotation. Without it the Stokes Q and U images will come out quite wrong. Since the 'P' calibration can be calculated exactly, all we need to do is run Template:Applyca with the parang parameter set to True.

# In CASA
applycal(vis='ngc612.ms',parang=True)

Multi-scale Polarization Clean

To image this source we need to use mosaicing, and because the source is quite extended, we will also use the multiscale option. Because the lower part of the band has a lot of interference and the full 1.1-3.1 GHz band is too wide to image properly in one go (even with MFS) we will restrict the imaging to the top 1/3 of the band, which corresponds to the bottom 680 channels. To specify this selection we need to use 'spw='0:0~680', indicating channel 0 to 680 from spectral window 0. We will make a test image to see what the field looks like.

# In CASA
clean(vis='ngc612.ms',imagename='t-ngc612',spw='0:0~680',imagermode='mosaic',multiscale=[0,3,10],imsize=512,cell='5.0arcsec',stokes='I',weighting='briggs',robust=0.5)

Constructing Polarization Intensity and Angle Images

Questions about this tutorial? Please contact the NRAO Helpdesk.

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Last checked on CASA Version 4.6.0