CASA Guides:ATCA Advanced 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.
This CASA guide describes the loading, flagging, 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 and then try imaging the data following [this guide]. If you feel you are ready to tackle the full reduction job in CASA keep following this guide.
Obtaining the Data
To download the data needed for this tutorial you will need to use the [Australia Telescope Online Archive]. If you don't have an account already, you can request one [here]. Once logged in enter the project code C2728, click search and select the files 2012-10-25_0707.C2728, 2012-10-25_0903.C2728, 2012-10-25_1304.C2728 and 2012-10-25_1705.C2728 from the results. You can then use the download button to retrieve a tar file with the data, or get a file with the links to the data to download from another machine. (If that all seems like too much trouble, a ready made MS with the data is available for download [here](3.5GB download), you can extract that instead and continue in the section #The Observation.)
Once the download is complete, extract the files (within a working directory in which you will then run CASA):
# In a Terminal: tar xvf datafiles.tar
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 ATCA archive 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, importatca, lets us choose which of the simultaneously recorded frequencies to load. In this case we just want the continuum data, which we can select with spw=0. There are two other frequency settings in this data, a 33 channel continuum band and a 2048 channel spectral zoom band centered on the HI emission from NGC612. We might use the latter for a future spectral line tutorial. We specify the options 'birdie' to remove known bad channels and 'noac' to discard the autocorrelations.
# In CASA importatca(vis='ngc612.ms',files='*.C2728',spw=0,options='birdie,noac')
As the data loads a listing appears in the logger of the data encountered. The first part is reproduced here:
########################################## ##### Begin Task: importatca ##### importatca(files="*.C2728",vis="ngc612.ms.0",options="birdie,noac",spw=0,nscans=[0, 0], lowfreq="0.1GHz",highfreq="999GHz",fields=[''],edge=8) Expanded file names are : /data/ngc612/2012-10-25_0707.C2728 /data/ngc612/2012-10-25_0903.C2728 /data/ngc612/2012-10-25_1304.C2728 /data/ngc612/2012-10-25_1705.C2728 Checking header of file /data/ngc612/2012-10-25_0707.C2728 CABB data detected Reading file /data/ngc612/2012-10-25_0707.C2728 Scan # : 1 Object : 1934-638 Date : 2012/10/25/07:07:45 First data/header has NAnt=6, NChan=2049, NPol=4 Antenna : CA01 position:[-4.75168e+06, 2.79161e+06, -3.20048e+06] Antenna : CA02 position:[-4.75159e+06, 2.79176e+06, -3.20048e+06] Antenna : CA03 position:[-4.75156e+06, 2.79181e+06, -3.20048e+06] Antenna : CA04 position:[-4.75135e+06, 2.79217e+06, -3.20048e+06] Antenna : CA05 position:[-4.75129e+06, 2.79227e+06, -3.20048e+06] Antenna : CA06 position:[-4.74939e+06, 2.79549e+06, -3.20048e+06] IF 1 : Frequency = 2100 MHz, bandwidth = 2048MHz, #channels = 2049 : Polarizations XX - 9 , XY - 10 , YX - 11 , YY - 12 Scan 1 stored Scan # : 2 Object : secndry_cal Date : 2012/10/25/07:27:15 Scan 2 stored Scan # : 3 Object : east_lobe Date : 2012/10/25/07:31:15 Scan 3 stored Scan # : 4 Object : secndry_cal Date : 2012/10/25/07:32:25 Scan 4 stored Scan # : 5 Object : east_lobe Date : 2012/10/25/07:35:05 Scan 5 stored Scan # : 6 Object : west_lobe Date : 2012/10/25/07:40:45 Scan 6 stored Scan # : 7 Object : east_lobe Date : 2012/10/25/07:46:05 Scan 7 stored Scan # : 8 Object : west_lobe Date : 2012/10/25/07:51:25 Scan 8 stored Scan # : 9 Object : east_lobe Date : 2012/10/25/07:56:55 Scan 9 stored Scan # : 10 Object : west_lobe Date : 2012/10/25/08:02:15 Scan 10 stored Scan # : 11 Object : east_lobe Date : 2012/10/25/08:07:45 Scan 11 stored Scan # : 12 Object : west_lobe Date : 2012/10/25/08:13:05 Scan 12 stored Scan # : 13 Object : east_lobe Date : 2012/10/25/08:18:25 Scan 13 stored Scan # : 14 Object : west_lobe Date : 2012/10/25/08:23:45 Scan 14 stored Scan # : 15 Object : secndry_cal Date : 2012/10/25/08:29:05 Scan 15 stored Scan # : 16 Object : secndry_cal Date : 2012/10/25/08:31:45 Scan 16 stored Scan # : 17 Object : east_lobe Date : 2012/10/25/08:34:05 Scan 17 stored Scan # : 18 Object : west_lobe Date : 2012/10/25/08:39:45 Scan 18 stored Scan # : 19 Object : secndry_cal Date : 2012/10/25/08:45:05 Scan 19 stored Scan # : 20 Object : east_lobe Date : 2012/10/25/08:47:45 Scan 20 skipped Scan # : 21 Object : 1934-638 Date : 2012/10/25/08:47:45 Scan 21 stored Scan # : 22 Object : 1934-638 Date : 2012/10/25/08:54:05 IF 2 : Frequency = 1891 MHz, bandwidth = 2048MHz, #channels = 33 : Polarizations XX - 9 , XY - 10 , YX - 11 , YY - 12 End of File Number of rows selected : 8910 Flagged : 5.1% Antenna off source : 5.1% ScanType (Point/Paddle): 0%
Scans that don't have valid or selected data will be marked 'skipped'. At the end a summary of the on-line flagging appears, we see about 5% of the data is flagged because antennas were not on source.
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. Since we've already seen the scans scroll past, we'll use verbose=False to get the summary:
# In CASA listobs(vis='ngc612.ms',verbose=False)
From the source listing we see there are 5 sources, the primary calibrator 1934-638, a secondary calibrator, and two target sources called east_lobe and west_lobe and some data on 0537-441. We also see the data has a 2048 MHz bandwidth, with 1 MHz channels, centered on 2.1 GHz with 4 linear polarizations.
##### Begin Task: listobs ##### listobs(vis="ngc612.ms.0",selectdata=True,spw="",field="",antenna="", uvrange="",timerange="",correlation="",scan="",intent="", feed="",array="",observation="",verbose=False,listfile="", listunfl=False,cachesize=50,overwrite=False) ================================================================================ MeasurementSet Name: /data/ngc612/casacal/ngc612.ms.0 MS Version 2 ================================================================================ Observer: obs Project: C2728 Observation: ATCA(6 antennas) Data records: 60465 Total elapsed time = 43730 seconds Observed from 25-Oct-2012/07:07:39.9 to 25-Oct-2012/19:16:29.9 (UTC) Compute subscan properties Fields: 5 ID Code Name RA Decl Epoch SrcId nRows 0 C 1934-638 19:39:25.025995 -188.8.131.52000 J2000 0 6645 1 secndry_cal 00:51:09.502006 -184.108.40.206294 J2000 1 5880 2 east_lobe 01:34:16.760003 -220.127.116.11004 J2000 2 23160 3 west_lobe 01:33:34.630993 -18.104.22.168998 J2000 3 22515 4 C 0537-441 05:38:50.362001 -44.05.08.93995 J2000 4 2265 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 2048000.0 2100.0000 XX XY YX YY Antennas: 6 'name'='station' ID= 0-3: 'CA01'='W98', 'CA02'='W109', 'CA03'='W113', 'CA04'='W140', ID= 4-5: 'CA05'='W148', 'CA06'='W392' ##### End Task: listobs ##### ##########################################
The antenna station names give away that this is a compact configuration, with CA01-CA05 close together and CA06 a long way away (multiply the station numbers by 15 to get distance in meters from station W0). It is actually a 750m array configuration, which means we would normally not include CA06 in the imaging. 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.
Examining and Editing the Data
It is always a good idea to examine the data before jumping straight into calibration. Start by flagging data known to be bad from observing logs, then examine the data. At low frequencies there is a lot of RFI, some of it is very strong and persistent so lets get of rid of that first. Use plotms to make a plot of the XY and YX correlations on the secondary calibrator. These correlations should normally have little signal in them, certainly anything stronger than the calibrator flux will be interference. Specify axes of 'channel' and 'amp', zoom in and use the resulting plots to read off the worst channel ranges. To cut down on the amount of data we can use antenna selection "0&4", the longest baseline we're likely to use, if it is bad, the shorter ones will be worse. The following command flags the data in all the bad channel ranges we found, you may decide to excise a few more or fewer channel ranges. At the highest channel number (lowest frequencies) the RFI gets so bad, we've deleted large channel ranges. If you were desperate for spectral information in this range you could do a more careful job. Note that it is not necessary to be very accurate in this step, as we will do further flagging after this first pass.
By default flagdata will save a copy of the existing set of flags before entering any new flags. This is so that you can easily revert any flags you have applied using the flagmanager task. This comes in very handy for those occasions where you accidentally flag more than you intended.
# In CASA flagdata(vis=msname0,mode='manual',spw='0:243~247;548~551;631~634;895~899;1012~1025;1205~1234;1421~1439;1495~1599;1614~1625;1675~1676;1815~2048')
Next we will do some clipping on the cross correlations. To choose the clip level we checked the amplitudes on a XY and YX plot with all the data, to make sure we're not clipping any good data. After clipping we extend the flagged points using 'growaround=True' and also flag the corresponding parallel hand polarizations.
# In CASA flagdata(vis=msname0,mode='clip',clipminmax=[0,5],correlation='ABS,XY,YX') flagdata(vis=msname0,mode='extend',extendpols=True,growaround=True)
As a final step we'll use the 'tfcrop' algorithm to find further bad data. It automatically does a flag extend to the other polarizations. Read the help for flagdata for the details on how these flagging algorithms work.
# In CASA flagdata(vis=msname0,mode='tfcrop',usewindowstats='sum',correlation='ABS,XY,YX',halfwin=3)
After these steps the data is much improved but after replotting the secondary calibrator we notice one more flaw: there is a single integration with excess flux on the secondary calibrator.
# In CASA flagdata(vis=msname0,mode='manual',timerange='14:15:30~14:15:40')
After fixing that we inspect the rest of the data and it is looking pretty clean. We could do some more flagging but it is probably not warranted unless we notice problems later in the reduction.
Calibrating the Data
It is now time to begin calibrating the data. The general data reduction strategy is to derive a series of scaling factors or corrections from the calibrators, which are then collectively applied to the science data. For more discussion of the philosophy, strategy, and implementation of calibration of synthesis data within CASA, see Synthesis Calibration in the CASA Reference Manual.
The first thing we want to do is split the wide bandwidth up into 8 spectral windows so we can solve for the gains and polarisation leakages per spectral window. Make sure you are using CASA 4.7 or later for this step as earlier versions of mstransform had a bug that scrambled the baselines when used in this way.
# In CASA mstransform(vis=msname0,outputvis=msname,datacolumn='data',mode='channel', regridms=True,spw='0',nspw=8)
Next we set the flux scale for the primary calibrator 1934-638. We have a choice of standards: 'Perley-Butler 2010' works fine at frequencies below 11 GHz; 'Stevens-Reynolds 2016' first appeared in CASA 4.7 and has the same scale below 11 GHz but is more accurate above that frequency, make sure to use this for 15 or 7mm data.
# In CASA #set flux scale for primary calibrator setjy(vis=msname,field=pri,scalebychan=True,standard='Perley-Butler 2010')
The next thing we want to do is derive a bandpass solution for our data. Before we can do that though, we need to phase calibrate the data so we can integrate over a long solution interval to do the bandpass solution. We've chosen a central antenna as the reference. You may need to ensure it is not missing from the array too much. Because we're processing polarization data from an Az/El telescope we switch on parallactic angle rotation using parang=T.
# In CASA gaincal(vis=msname,caltable=prefix+'.G0',field=pri,refant='CA03',gaintype='G',calmode='p',parang=T,solint='60s'); bandpass(vis=msname,caltable=prefix+'.B0',field=pri,spw='',refant='CA03',solnorm=True,solint='inf',bandtype='B',gaintable=[prefix+'.G0'],parang=T);
After the bandpass solution we're ready to calibrate the gains using the phase calibrator. We're using a 60s solution interval and apply the bandpass table we've just created.
# In CASA gaincal(vis=msname,caltable=prefix+'.G1',field=pri+','+sec,refant='CA03',spw='*',gaintype='G',calmode='ap',parang=T,solint='60s',gaintable=[prefix+'.B0'])
The remaining calibration to solve for is the polarization leakage or D-terms. For the ATCA we can often use the unpolarized primary calibrator 1934-638 for this, but you can also use the secondary calibrator. In both cases we need to determine the polarization of the secondary so we can correct the gains for source polarization. Here we use polcal with the primary calibrator and apply the previously determined bandpass and gain calibration. We then use the qufromgain routine to extract the source model for the secondary. Since we don't know the flux of the secondary yet, it is assumed to be 1 by gaincal and our source model is relative to this. The qufromgain routine has a paoffset parameter that we need to set to 45 degrees for ATCA except for 7mm observations (in that case use 135 degrees, if you have analyzed polarized 7mm data let us know if you think this advice is incorrect.)
# In CASA polcal(vis=msname,caltable=prefix+'.D0',field=pri,refant='CA03',gaintable=[prefix+'.B0',prefix+'.G1'],poltype='D',solint='inf') # Get Q/U from gains, X feed is at 45 degrees (unless 7mm -> 135 deg) qu = qufromgain(prefix+'.G1',fieldids=,paoffset=45.) smodel=[1,qu,qu,0]
Now we redo the whole calibration using our best estimates for gains, leakages and secondary polarization.
# In CASA # Redo gaincal bandpass(vis=msname,caltable=prefix+'.B1',field=pri,spw='',refant='CA03',solnorm=True, solint='inf',bandtype='B',gaintable=[prefix+'.G1',prefix+'.D0'],parang=T); gaincal(vis=msname,caltable=prefix+'.G2',field=pri,refant='CA03',spw='*', gaintype='G',calmode='ap',parang=T,solint='int',gaintable=[prefix+'.B1',prefix+'.D0']) gaincal(vis=msname,caltable=prefix+'.G2',field=sec,refant='CA03',spw='*', gaintype='G',calmode='ap',parang=T,solint='int',gaintable=[prefix+'.B1',prefix+'.D0'],smodel=smodel,append=True) polcal(vis=msname,caltable=prefix+'.D1',field=pri,refant='CA03',gaintable=[prefix+'.B1',prefix+'.G2'],poltype='Dlls',solint='inf')
All that remains now is to correct the flux scale using comparison between the primary and secondary calibrator and then apply all the corrections.
# In CASA # flux cal fluxscale(vis=msname,caltable=prefix+'.G2',fluxtable=prefix+'.F0',reference='1934-638'); # Apply calibration applycal(vis=msname,gaintable=[prefix+'.B1',prefix+'.D1',prefix+'.F0'],gainfield=[pri,pri,sec],parang=T)
At this point we've got a fully calibrated dataset ready for imaging. The imaging proceeds exactly as in the ATCA tutorial that started with a calibrated dataset.
# In CASA # make first image os.system('rm -rf tmp-ngc612*') clean(vis='ngc612.ms',imagename='tmp-ngc612',spw='0,1,2:0~170',imagermode='mosaic',multiscale=[0,10,30],imsize=500,cell='5.0arcsec',stokes='IV',weighting='briggs',robust=0.5,antenna='!5',field='*_lobe') # use viewer to create cleanbox file # clean deeper image #!rm -rf ngc612h.* clean(vis='ngc612.ms',imagename='ngc612h1',spw='0,1,2:0~170',imagermode='mosaic',multiscale=[0,8,24],imsize=500,cell='5.0arcsec',stokes='IQUV',weighting='briggs',robust=0.5,niter=5000,threshold='0.5mJy',antenna='!5',mask='box [[01:34:28.51334, -036.32.55.9841], [01:33:14.14565, -036.25.15.8659]]',field='*_lobe')