Difference between revisions of "EVLA high frequency spectral line tutorial - IRC+10216 - calibration"

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'''This guide is under development.'''
+
'''This page is under development'''
  
=Getting the data=
+
This CASA Guide provides a simplified approach to the editing, calibration, and imaging of a galactic EVLA observation for use in NRAO Community Day Events.  For a complete description of the data reduction process see [[EVLA high frequency Spectral Line tutorial - IRC+10216 part1]] and [[EVLA high frequency Spectral Line tutorial - IRC+10216 part2]].
  
The data for this tutorial can be obtained by anonymous FTP from <tt>ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/</tt>.  Download all 4 files TAR in this directory.
+
[[Category:EVLA]][[Category:Calibration]][[Category:Spectral Line]]
 +
 
 +
== Overview ==
 +
[[Image:irc10216_dust.jpg|thumb|VLT V-band image of IRC+10216 showing dust rings out to a radius of 90" by Le&atilde;o et al. (2006, A&A, 455, 187).]]
 +
 
 +
This tutorial describes the data reduction for two spectral lines, HC3N and SiS, observed toward the AGB star IRC+10216 by the EVLA in D-configuration.
 +
 
 +
==Getting the data==
 +
 
 +
The data for this tutorial can be obtained by anonymous FTP from <tt>ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/</tt>.  Download all 4 TAR files.
  
 
For example,
 
For example,
Line 12: Line 21:
 
</source>
 
</source>
  
= Inspection and Flagging =
+
==Initial Inspection and Flagging==
 
 
== List observational parameters ==
 
  
{{listobs}} provides almost all relevant observational parameters such as correlator setup (frequencies, bandwidths, channel number and widths, polarization products), sources, scans, scan intents, and antenna locations.  The following command writes the listobs output to a file on disk.  You can review the output at any time using '''less''' from the casapy or UNIX command line.
+
GEt a summary listing of the data set using {{listobs}}.
  
 
<source lang="python">
 
<source lang="python">
 
# In CASA
 
# In CASA
vis='day2_TDEM0003_20s_full'
+
vis = 'day2_TDEM0003_20s_full'
listobs(vis=vis, verbose=True, listfile=vis+'.listobs.txt')
+
listobs(vis=vis, verbose=True)
 
</source>
 
</source>
  
Here is a subset of the listobs output.
+
Below we have cut and pasted the most relevant output from the logger.
  
<pre>
+
<pre style="background-color: #fffacd;">
 
Fields: 4
 
Fields: 4
 
   ID  Code Name                RA              Decl          Epoch  SrcId nVis
 
   ID  Code Name                RA              Decl          Epoch  SrcId nVis
Line 72: Line 79:
 
   18  ea28  N08      25.0 m  -107.37.07.5  +33.54.15.8
 
   18  ea28  N08      25.0 m  -107.37.07.5  +33.54.15.8
 
</pre>
 
</pre>
 
Note that the Rest Frequency and Systemic Velocity are wrong in the listobs log by a factor 10^6 and 1000, respectively, given the quoted units (MHz) and (km/s). This was due to a temporary error in the EVLA Observing Tool that has subsequently been fixed. Because the sky frequencies are correct, and we set the rest frequency explicitly later in the deconvolution stage, this does not present a problem for the data reductions.
 
  
 
We summarize the observing strategy in this table.
 
We summarize the observing strategy in this table.
Line 95: Line 100:
 
  |}
 
  |}
  
== Plot antenna positions ==
+
[[Image:Ant_locations.png|thumb|Antenna locations from running plotants ]]
  
We can use task {{plotants}} to generate a plot of the antenna positions.  This is useful for choosing a reference antenna.
+
Create a plot of antenna positions using {{plotants}}.
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
plotants(vis=vis,figfile=vis+'.plotants.png')
+
plotants(vis=vis)
 
</source>
 
</source>
  
We will use <tt>ea02</tt> as the reference antenna.
+
[[Image:plotallfields.png|thumb|Result of plotms]]
 +
[[Image:Zoom1_mark.png|thumb|Zooming in and marking region (hatched box)]]
  
== Flagging ==
+
Next, let's look at all the source amplitudes as a function of time using {{plotms}}.
  
Next, let's look at the elevation as a function of time for all sources. We will use {{plotms}} to plot the data.  It's not the case for these data, but if the elevation is very low (usually at start or end of track) you may want to flag. Also, how near in elevation your flux calibrator is to your target will impact your ultimate absolute flux calibration accuracy. Unfortunately, the target and flux calibrator are not particularly well-matched for this observation, as you can show by plotting the elevation for each source (each sources has a different colors).  Thus we are strongly dependent on the opacity and gaincurve corrections to get the flux scale right for these data. (This is something to keep in mind when planning observations!)
+
<source lang="python">
 
 
<source lang="Python">
 
# In CASA
 
plotms(vis=vis, xaxis='time',yaxis='elevation',correlation='RR,LL',
 
      avgchannel='64',spw='0:4~60', coloraxis='field')
 
</source>
 
 
 
Next, let's look at all the source amplitudes as a function of time.
 
 
 
<source lang="Python">
 
 
# In CASA
 
# In CASA
plotms(vis=vis, xaxis='time',yaxis='amp',correlation='RR,LL',
+
plotms(vis=vis, xaxis='time', yaxis='amp', correlation='RR,LL',
       avgchannel='64',spw='0:4~60', coloraxis='field')
+
       avgchannel='64', spw='0:4~60', coloraxis='field')
 
</source>
 
</source>
  
Now zoom in on the region very near zero amplitude for sources J0954+1743 and IRC+10216. To zoom, select the Zoom tool in lower left corner of the plotms GUI, then you can left click to draw a box. Look for the low values (you may want to zoom a few times to really see the suspect points clearly). Now use the Mark Region and Locate buttons (located along the bottom of the GUI) to see which antenna is causing problems. The output is be shown in the logger. Since all the "located" baselines include ea12, this is the responsible antenna.
+
Now zoom in on the region very near zero amplitude for sources J0954+1743 and IRC+10216. To zoom, select the  
 +
Zoom tool in lower left corner of the {{plotms}} GUI, then you can left click to draw a box.  
 +
Look for the low values (you may want to zoom a few times to really see the suspect points clearly). Now use the Mark Region and Locate buttons (located along the bottom of the GUI) to see which antenna is causing problems. The output will be shown in the logger. Since all the "located" baselines include ea12, this is the responsible antenna.
  
 
Now click the clear region button, and then go back to the zoom button to zoom in further to note exactly what the time range is: 03:41:00~04:10:00.
 
Now click the clear region button, and then go back to the zoom button to zoom in further to note exactly what the time range is: 03:41:00~04:10:00.
  
Check the other sideband by changing spw to 1:4~60. You will have to rezoom. If you have trouble, click on the Mark icon and then back to zoom. In spw=1, ea07 is bad from the beginning until after next pointing run: 03:21:40~04:10:00. To see this, compare the amplitudes when antenna is set to 'ea07' and when it is set to one of the other antennas, such as 'ea08'.
+
Check the other sideband by changing spw to 1:4~60. You will have to
 +
rezoom. If you have trouble, click on the Mark icon and then back to
 +
zoom. In spw=1, ea07 is bad from the beginning until after next
 +
pointing run: 03:21:40~04:10:00. To see this, compare the amplitudes when antenna is set to 'ea07' and when it is set to one of the other antennas, such as 'ea08'.
  
If you set antenna to 'ea12' and zoom in on this intial timerange, you can also see that ea12 is bad during the same time range as for spw 0. You can also see this by entering '!ea07' for antenna, which removes ea07 from the plot (in CASA selection, ! deselects).
+
If you set antenna to 'ea12' and zoom in on this intial timerange, you can also see that ea12 is bad during the same time range as for spw 0. You can also see this by entering '!ea07' for antenna, which removes ea07 from the plot (in CASA selection, ! deselects).  
  
We can set up a flagging command to get both bad antennas for the appropriate time and spw:
+
We can flag the bad data using {{flagdata}}.
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
flagdata(vis=vis, field=['2,3','2,3'], spw=['','1'], antenna=['ea12','ea07'],
+
flagdata(vis=vis,
 +
        field=['2,3','2,3'],
 +
        spw=['','1'],
 +
        antenna=['ea12','ea07'],
 
         timerange=['03:41:00~04:10:00','03:21:40~04:10:00'])
 
         timerange=['03:41:00~04:10:00','03:21:40~04:10:00'])
 
</source>
 
</source>
  
{{flagdata}} works by spanning up a matrix. The first entries in each list must be taken as one flagging command, as well as the second entries etc. Lists within lists are fine. In the above example, the first flagging command is issued for fields 2 and 3 for all spws and within the 03:41:00~04:10:00 timerange. A second command is again for the fields 2 and 3 but for spw 1 only and for the second timerange in the list '03:21:40~04:10:00'.
+
{{flagdata}} works by spanning up a matrix. The first entries in each list must be taken as one flagging command, as well as the second entries etc. Lists within lists are fine. In the above example, the first flagging command is issued for fields 2 and 3 for all spws and within the 03:41:00~04:10:00 timerange. A second command is again for the fields 2 and 3 but for spw 1 only and for the second timerange in the list '03:21:40~04:10:00'.  
  
Note that because the chosen timerange is limited to fields 2 and 3, the field parameter is not really needed; however, flagdata will run fastest if you put as many constraints as possible.
+
Note that because the chosen timerange is limited to fields 2 and 3, the field parameter is not really
 +
needed; however, flagdata will run fastest if you put as many constraints as possible.
  
Now remove the !ea07 from antenna and replot both spw, zooming in to be sure that all obviously low points are gone. Also zoom in and check 3C286 (J1229+0203 is already obvious because it is so bright!).
+
==Set Up the Model for the Flux Calibrator==
  
Lets look more closely at IRC+10216:
+
We set the model for the flux calibrator using {{setjy}}.  First, check the availability of calibration models.
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
plotms(vis=vis,field='3', xaxis='time',yaxis='amp',correlation='RR,LL',
+
setjy(vis=vis,listmodimages=T)
      avgchannel='64',spw='0~1:4~60', coloraxis='spw')
 
 
</source>
 
</source>
  
You can see a that there are some noisy high points. But now try
+
There is no Ka-band model of 3C286.  We will use the K-band model instead.
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
plotms(vis=vis, field='3', xaxis='uvdist', yaxis='amp', correlation='RR,LL',
+
setjy(vis=vis,field='7',spw='0~1',
      avgchannel='64', spw='0~1:4~60', coloraxis='spw')
+
      modimage='3C286_K.im')
 
</source>
 
</source>
  
Most of the high points on IRC+10216 are due to large scale emission on short baselines, but there is still some noisy stuff -- for a target like this with extended emission it's best to wait until later to decide what to do about it. We will not be able to get adequate calibration for antennas that are truly bad (even if they don't stand out here) so these will be obvious later.
+
{{setjy}} scales the total flux in the model image to that appropriate for your individual spectral window frequencies according to the calibrator's flux and reports this number to the logger.
 +
 
 +
<pre style="background-color: #fffacd;">
 +
The logger output for each spw is:
 +
J1331+3030 (fld ind 7) spw 0  [I=1.7762, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
 +
J1331+3030 (fld ind 7) spw 1  [I=1.7794, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
 +
</pre>
 +
 
 +
The absolute fluxes for the frequencies have now been determined and one can proceed to the bandpass and complex gain calibrations.
  
= Set the model for the flux calibrator =
+
==Bandpass Calibration==
  
Next, we set the model for the flux calibrator. Depending on your observing frequency and angular resolution you can do this several ways. In the past, one typically used a point source (constant flux) model for
+
Correct the phase variations with time before solving for the bandpass to
the flux calibrator, possibly with a uvrange cutoff if necessary. More recently for the VLA/EVLA,  model images for the most common flux calibrators have been made available for use in cases where the sources are somewhat resolved. This is most likely to be true at higher frequencies and at higher resolutions (more extended arrays).  
+
prevent decorrelation of the vector averaged bandpass
 +
solution.  
  
Currently, CASA contains models for the most common calibrators at the most common frequencies but not yet the new EVLA frequency bands S, Ku, and Ka. These will be added as soon as they become available. One may check the availability of calibration models in {{setjy}}:
+
[[Image:Prebp_phasecal2.png|thumb|Phase only calibration before bandpass. The 4 lines are both polarizations in both spw, unfortunately two of them get the same color green at the moment.]]
  
 
<source lang="python">
 
<source lang="python">
 
# In CASA
 
# In CASA
setjy(vis=vis,listmodimages=T)
+
gaincal(vis=vis, caltable='bpphase.gcal', field='5', spw='0~1:20~40',
 +
        refant='ea02', gaintype='G', calmode='p',solint='int',
 +
        gaincurve=T)
 
</source>
 
</source>
  
The terminal will now show the available models, e.g. 3C286_C.im, 3C48_K.im etc. (setjy will search in the working directory for images that may contain models, as well as in a CASA directory where known calibrator models are stored)
+
Plot the solutions using {{plotcal}}.
  
As mentioned above, the Ka band does not yet have a model.  We will use the K-band model instead.
+
<source lang="python">
 
 
<source lang="Python">
 
 
# In CASA
 
# In CASA
setjy(vis=vis, field='7', modimage='3C286_K.im')
+
plotcal(caltable='bpphase.gcal',xaxis='time',yaxis='phase',
 +
        iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
 
</source>
 
</source>
  
The logger output for each SPW is:
+
Next we can apply this phase solution on the fly while determining
 +
the bandpass solutions on the timescale of the bandpass calibrator scan (solint='inf').
  
<pre>
+
<source lang="python">
J1331+3030 (fld ind 7) spw 0  [I=1.7762, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
 
J1331+3030 (fld ind 7) spw 1  [I=1.7794, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
 
</pre>
 
 
 
The absolute fluxes for the frequencies have now been determined and we can proceed to the bandpass and complex gain calibrations.
 
 
 
= Bandpass Calibration =
 
 
 
Before determining the bandpass solution, we need to inspect phase and amplitude variations with time and frequency on the bandpass calibrator to decide how best to proceed. We limit the number of antennas to make the plot easier to see. We chose ea02 as it seems like a good candidate for the reference antenna.
 
 
 
<source lang="Python">
 
 
# In CASA
 
# In CASA
plotms(vis=vis, field='5', xaxis='channel', yaxis='phase', correlation='RR',
+
bandpass(vis=vis, caltable='bandpass.bcal', field='5', refant='ea02',
      avgtime='1e8', spw='0:4~60', antenna='ea02', antenna='ea02&ea23')
+
        solint='inf', solnorm=T, gaintable='bpphase.gcal',
 +
        gaincurve=T)
 
</source>
 
</source>
  
The phase variation is modest ~10 degrees. Now expand to all baselines that include ea02, then hit the "Plot" button.
+
Plot the solutions, amplitude and phase:
 +
[[Image:Bandpass_amp.png|thumb|Amplitude Bandpass solutions]]
 +
[[Image:Bandpass_phase1.png|thumb|Phase Bandpass solutions]]
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
plotms(vis=vis,field='5', xaxis='channel', yaxis='phase', correlation='RR',
+
plotcal(caltable='bandpass.bcal',xaxis='chan',yaxis='amp',
      avgtime='1e8', spw='0:4~60', antenna='ea02', coloraxis='antenna2')
+
        iteration='antenna',subplot=331)
 
</source>
 
</source>
  
From this you can see that the phase variation across the bandpass is modest. Next check LL, and spw=1, both correlations. Also check other antennas if you like.
 
  
Now look at the phase as a function of time.
+
<source lang="python">
 
 
<source lang="Python">
 
 
# In CASA
 
# In CASA
plotms(vis=vis, field='5', xaxis='time', yaxis='phase', correlation='RR',
+
plotcal(caltable='bandpass.bcal',xaxis='chan',yaxis='phase',
      avgchannel='64', spw='0:4~60', antenna='ea02&ea23')
+
        iteration='antenna',subplot=331)
 
</source>
 
</source>
  
Expand to all antennas with ea02
+
==Remaining Calibration==
  
<source lang="Python">
+
In this Community Day Event guide, we will skip over the remaining calibration steps.  However, you can refer to [[EVLA high frequency Spectral Line tutorial - IRC+10216 part1]] for full details.  To summarize the missing steps, you bootstrap the flux densities of the secondary calibrators by
# In CASA
 
plotms(vis=vis, field='5', xaxis='time', yaxis='phase', correlation='RR',
 
      avgchannel='64', spw='0:4~60', antenna='ea02', coloraxis='antenna2')
 
</source>
 
  
You may want to select "Custom" under "unflagged points symbol" and then change Style from "2" to "3" under the "Display" tab, "Unflagged Points Symbol" .
+
# doing a phase only calibration on all calibrators using {{gaincal}},
 +
# doing amplitude only calibration on all calibrators while applying the phase-only solutions, and
 +
# deriving the flux density of the secondary calibrators while applying the previously obtained solutions.
  
You can see that the phase variations are smooth, but do vary significantly over the 5 minutes of observation -- in most cases by a few 10s of degrees. Zoom in to see this better if you want.
+
Then, you can calibrate the target source using the phase and amplitude solutions you have obtained.  Apply the target source calibration solutions using {{applycal}}.  Use {{plotms}} to examine the calibrated data.  If more flagging is required, redo all calibration steps.  When the data look good, {{split}} the target source into a separate measurement set.  Subtract the continuum flux using {{uvcontsub}}. Make Doppler corrections using {{cvel}}, or let {{clean}} do the Doppler corrections on the fly.
  
The conclusion from this investigation is that you need to correct the phase variations with time before solving for the bandpass to prevent decorrelation of the vector averaged bandpass solution. Since the phase variation as a function of channel is modest, you can average over several channels to increase the signal to noise of the phase vs. time solution. If the phase variation as a function of channel is larger you may need to use only a few channels to prevent introducing delay-based closure errors as can happen from averaging over non-bandpass corrected channels with large phase variations.  
+
This tutorial picks up where [[ EVLA high frequency spectral line tutorial - IRC+10216 - calibration]] leaves off.  
  
Since the bandpass calibrator is quite strong we do the phase-only solution on the integration time of 20 seconds (solint='int').
+
==Imaging==
  
<source lang="Python">
+
[[Image:irc10216_uvspec.png|thumb|UV-plot of the spectral line signal in both spw for IRC+10216.]]
# In CASA
 
bpphase = vis + '.bpphase.gcal'
 
gaincal(vis=vis, caltable=bpphase, field='5', spw='0~1:20~40',
 
        solint='int', refant='ea02', gaintype='G', calmode='p', gaincurve=True)
 
</source>
 
  
Plot the solutions.
+
The continuum-subtracted spectral line data is contained in <tt>IRC10216_spls.ms</tt>.  Use {{plotms}} to plot the lines.
  
<source lang="Python">
+
<source lang="python">
# In CASA
+
plotms(vis='IRC10216_spls.ms', xaxis='channel', yaxis='amp',
plotcal(caltable=bpphase, xaxis='time',yaxis='phase',
+
      avgtime='1e8', avgscan=T, coloraxis='spw')
        iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
 
 
</source>
 
</source>
  
These solutions will appear in the CASA plotter gui. If you closed it after plotting the antennas above, it should reopen. If it is still open from before, the new plots should just appear. After you are done looking at the first set of plots, push the "Next" button on the GUI to see the next set of antennas.  
+
Now it is time to image the visibility data using {{clean}}. For illustration, we will clean channel 22 of the SiS line.
  
Next we can apply this phase solution on the fly while determining the bandpass solutions on the timescale of the bandpass calibrator scan ('''solint='inf' ''').
+
<source lang="python">
 
 
<source lang="Python">
 
 
# In CASA
 
# In CASA
bpass = vis + '.bandpass.bcal'
+
os.system('rm -rf ch22.*') # remove previously generated image, if it exists
bandpass( vis=vis, caltable=bpass, field='5', solint='inf',
+
clean(vis='IRC10216_spls.ms', imagename='ch22', spw='1:22~22',
          refant='ea02', solnorm=True, gaintable=bpphase,
+
      mode='channel', nchan=1, start='', width=1, niter=100000,  
          gaincurve=True )
+
      gain=0.1, threshold='3.0mJy', psfmode='clark', imagermode='csclean',
 +
      interactive=T, npercycle=100, imsize=300, cell=['0.4arcsec', '0.4arcsec'],
 +
      stokes='I', weighting='briggs', robust=0.5)  
 
</source>
 
</source>
  
Plot the solutions, amplitude and phase.
+
After running the above command, make a region in the CASA viewer.  Double-click inside the region and clean by clicking the green circular arrow.  After each cycle, click the green circular arrow again if the flux inside the region is brighter than the flux peaks outside the region.  When you are finished cleaning, click the red 'STOP' button.  
  
<source lang="Python">
+
Open the resulting image using the {{viewer}}.
# In CASA
 
plotcal(caltable=bpass, xaxis='chan', yaxis='amp',
 
        iteration='antenna', subplot=331)
 
</source>
 
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
plotcal(caltable=bpass, xaxis='chan', yaxis='phase',
+
viewer("ch22.image")
        iteration='antenna', subplot=331)
 
 
</source>
 
</source>
  
Note that phases on ea12 look noiser than on other antennas. This jitter could indicate bad pointing; note that ea12 had just come back in the array.  
+
In the viewer, make a region and click inside it to get statistics about the portion of the image in the region.
  
= Gain Calibration =
+
==Analyze the Image Cubes==
  
Now that we have a bandpass solution to apply we can solve for the antenna-based phase and amplitude gain calibration. Since the phase changes on a much shorter timescale than the amplitude, we will solve for them separately. In particular, if the phase changes significantly over a scan time, the amplitude would be decorrelated, if the un-corrected phase were averaged over this timescale. Note that we re-solve for the gain solutions of the bandpass calibrator, so we can derive new solutions that are corrected for the bandpass shape. Since the bandpass calibrator will not be used again, this is not strictly necessary, but is useful to check its calibrated flux density for example. We use a minimum signal-to-noise of 2 here as it seems to be a good compromise for using good data without rejecting too many solutions (minsnr=2).  
+
Open the HC3N image cube in the {{viewer}}.
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
gaincal(vis=vis, caltable=intphase, field='2,5,7', spw='0~1:4~60',
+
viewer("IRC10216_HC3N.image")
        refant='ea02', calmode='p', solint='int', minsnr=2.0,
 
        gaintable=bpass, gaincurve=T)
 
 
</source>
 
</source>
  
Here solint='int' coupled with calmode='p' will derive a single phase solution for each 20 second integration. Note that the bandpass table is applied on-the-fly before solving for the phase solutions, however the bandpass is NOT applied to the data permanently until applycal is run later on.  
+
Click the 'Play' button to view all channels in the cube.  Select '''Tool --> Spectral profile...''' from the pull down menu.  Create a region on the image to view the spectrum within the region.
  
Note that quite a few solutions are rejected due to SNR<2 (printed to terminal). For the most part it is only one or two solutions out of >30 so this isn't too worrying. Take note if you see large numbers of rejected solutions per integration. This is likely an indication that solint is too short for the S/N of the data.  
+
Open the SiS image cube in the viewer.
  
Now look at the phase solution, and note the obvious scatter within a scan time.
+
<source lang="python">
 
 
<source lang="Python">
 
 
# In CASA
 
# In CASA
plotcal(caltable=intphase, xaxis='time',yaxis='phase',
+
viewer("IRC10216_SiS.image")
        iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
 
 
</source>
 
</source>
  
Although solint='int' (i.e. the integration time of 10 seconds) is the best choice to apply before for solving for the amplitude solutions, it is not a good idea to use this to apply to the target. This is because the phase-scatter within a scan can dominate the interpolation between calibrator scans. Instead, we also solve for the phase on the scan time, solint='inf' (but combine=' ', since we want one solution per scan) for application to the target later on. Unlike the bandpass task, for gaincal, the default of the combine parameter is combine=' '.  
+
Determine what channels in the cube have emission. Then make moment maps using {{immoments}}.
  
<source lang="Python">
+
<source lang="python">
 
# In CASA
 
# In CASA
scanphase = vis + '.scanphase.gcal'
+
os.system('rm -rf IRC10216_Sis.mom0') # remove previously generated map, if it exists
gaincal(vis=vis, caltable=scanphase, field='2,5,7',spw='0~1:4~60',
+
immoments(imagename="IRC10216_SiS.image", moments=[0], axis="spectral",
        refant='ea02',calmode='p',solint='inf',minsnr=2.0,
+
          chans="12~40", outfile="IRC10216_Sis.mom0")  
        gaincurve=T)
 
 
</source>
 
</source>
  
<source lang="Python">
+
Open the moment map in the viewer.
 +
 
 +
<source lang="python">
 
# In CASA
 
# In CASA
plotcal(caltable=scanphase,xaxis='time',yaxis='phase',
+
viewer("IRC10216_Sis.mom0")
        iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
 
 
</source>
 
</source>
  
Note that there are no failed solutions here because of the added S/N afforded by the longer solint. Alternatively, instead of making a separate phase solution for application to the target, one can also run {{smoothcal}} to smooth the solutions derived on the integration time.  
+
Overlay contours by selecting '''Data --> Open''' from the pull down menu, selecting the moment-0 map, and clicking 'contour map'.
  
Next we apply the bandpass and solint='int' phase-only calibration solutions on-the-fly to derive amplitude solutions. Here the use of solint='inf', but combine=' ' will result in one solution per scan interval.
+
[[Main Page | &#8629; '''CASAguides''']]
  
<source lang="Python">
+
{{Checked 3.3.0}}
# In CASA
 
amp_gcal = vis + '.amp.gcal'
 
gaincal(vis=vis, caltable=amp_gcal,
 
        field='2,5,7',spw='0~1:4~60',
 
        refant='ea02',calmode='ap',solint='inf',minsnr=2.0,
 
        gaintable=[bpass, intphase], gaincurve=T)
 
</source>
 

Latest revision as of 16:57, 6 January 2012

This page is under development

This CASA Guide provides a simplified approach to the editing, calibration, and imaging of a galactic EVLA observation for use in NRAO Community Day Events. For a complete description of the data reduction process see EVLA high frequency Spectral Line tutorial - IRC+10216 part1 and EVLA high frequency Spectral Line tutorial - IRC+10216 part2.

Overview

VLT V-band image of IRC+10216 showing dust rings out to a radius of 90" by Leão et al. (2006, A&A, 455, 187).

This tutorial describes the data reduction for two spectral lines, HC3N and SiS, observed toward the AGB star IRC+10216 by the EVLA in D-configuration.

Getting the data

The data for this tutorial can be obtained by anonymous FTP from ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/. Download all 4 TAR files.

For example,

# In UNIX
wget 'ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/*'

Initial Inspection and Flagging

GEt a summary listing of the data set using listobs.

# In CASA
vis = 'day2_TDEM0003_20s_full'
listobs(vis=vis, verbose=True)

Below we have cut and pasted the most relevant output from the logger.

Fields: 4
  ID   Code Name                RA              Decl          Epoch   SrcId nVis
  2    D    J0954+1743          09:54:56.82363 +17.43.31.2224 J2000   2     32726
  3    NONE IRC+10216           09:47:57.38200 +13.16.40.6600 J2000   3     99540
  5    F    J1229+0203          12:29:06.69973 +02.03.08.5982 J2000   5     5436
  7    E    J1331+3030          13:31:08.28798 +30.30.32.9589 J2000   7     2736
   (nVis = Total number of time/baseline visibilities per field)
Spectral Windows:  (2 unique spectral windows and 1 unique polarization setups)
  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)  TotBW(kHz)  Corrs
  0          64 TOPO  36387.2295  125           8000        RR  RL  LR  LL
  1          64 TOPO  36304.542   125           8000        RR  RL  LR  LL
Sources: 10
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s)
  0    J1008+0730          0     0.03639232     -0.026
  0    J1008+0730          1     0.03639232     -0.026
  2    J0954+1743          0     0.03639232     -0.026
  2    J0954+1743          1     0.03639232     -0.026
  3    IRC+10216           0     0.03639232     -0.026
  3    IRC+10216           1     0.03639232     -0.026
  5    J1229+0203          0     0.03639232     -0.026
  5    J1229+0203          1     0.03639232     -0.026
  7    J1331+3030          0     0.03639232     -0.026
  7    J1331+3030          1     0.03639232     -0.026
Antennas: 19:
  ID   Name  Station   Diam.    Long.         Lat.
  0    ea01  W09       25.0 m   -107.37.25.2  +33.53.51.0
  1    ea02  E02       25.0 m   -107.37.04.4  +33.54.01.1
  2    ea03  E09       25.0 m   -107.36.45.1  +33.53.53.6
  3    ea04  W01       25.0 m   -107.37.05.9  +33.54.00.5
  4    ea05  W08       25.0 m   -107.37.21.6  +33.53.53.0
  5    ea07  N06       25.0 m   -107.37.06.9  +33.54.10.3
  6    ea08  N01       25.0 m   -107.37.06.0  +33.54.01.8
  7    ea09  E06       25.0 m   -107.36.55.6  +33.53.57.7
  8    ea12  E08       25.0 m   -107.36.48.9  +33.53.55.1
  9    ea15  W06       25.0 m   -107.37.15.6  +33.53.56.4
  10   ea19  W04       25.0 m   -107.37.10.8  +33.53.59.1
  11   ea20  N05       25.0 m   -107.37.06.7  +33.54.08.0
  12   ea21  E01       25.0 m   -107.37.05.7  +33.53.59.2
  13   ea22  N04       25.0 m   -107.37.06.5  +33.54.06.1
  14   ea23  E07       25.0 m   -107.36.52.4  +33.53.56.5
  15   ea24  W05       25.0 m   -107.37.13.0  +33.53.57.8
  16   ea25  N02       25.0 m   -107.37.06.2  +33.54.03.5
  17   ea27  E03       25.0 m   -107.37.02.8  +33.54.00.5
  18   ea28  N08       25.0 m   -107.37.07.5  +33.54.15.8

We summarize the observing strategy in this table.

Gain calibrator J0954+1743 field id = 2
Bandpass calibrator J1229+0203 field id = 5
Flux calibrator J1331+3030 (3C286) field id = 7
Science target IRC+10216 field id = 3
Antenna locations from running plotants

Create a plot of antenna positions using plotants.

# In CASA
plotants(vis=vis)
Result of plotms
Zooming in and marking region (hatched box)

Next, let's look at all the source amplitudes as a function of time using plotms.

# In CASA
plotms(vis=vis, xaxis='time', yaxis='amp', correlation='RR,LL',
       avgchannel='64', spw='0:4~60', coloraxis='field')

Now zoom in on the region very near zero amplitude for sources J0954+1743 and IRC+10216. To zoom, select the Zoom tool in lower left corner of the plotms GUI, then you can left click to draw a box. Look for the low values (you may want to zoom a few times to really see the suspect points clearly). Now use the Mark Region and Locate buttons (located along the bottom of the GUI) to see which antenna is causing problems. The output will be shown in the logger. Since all the "located" baselines include ea12, this is the responsible antenna.

Now click the clear region button, and then go back to the zoom button to zoom in further to note exactly what the time range is: 03:41:00~04:10:00.

Check the other sideband by changing spw to 1:4~60. You will have to rezoom. If you have trouble, click on the Mark icon and then back to zoom. In spw=1, ea07 is bad from the beginning until after next pointing run: 03:21:40~04:10:00. To see this, compare the amplitudes when antenna is set to 'ea07' and when it is set to one of the other antennas, such as 'ea08'.

If you set antenna to 'ea12' and zoom in on this intial timerange, you can also see that ea12 is bad during the same time range as for spw 0. You can also see this by entering '!ea07' for antenna, which removes ea07 from the plot (in CASA selection, ! deselects).

We can flag the bad data using flagdata.

# In CASA
flagdata(vis=vis,
         field=['2,3','2,3'],
         spw=['','1'],
         antenna=['ea12','ea07'],
         timerange=['03:41:00~04:10:00','03:21:40~04:10:00'])

flagdata works by spanning up a matrix. The first entries in each list must be taken as one flagging command, as well as the second entries etc. Lists within lists are fine. In the above example, the first flagging command is issued for fields 2 and 3 for all spws and within the 03:41:00~04:10:00 timerange. A second command is again for the fields 2 and 3 but for spw 1 only and for the second timerange in the list '03:21:40~04:10:00'.

Note that because the chosen timerange is limited to fields 2 and 3, the field parameter is not really needed; however, flagdata will run fastest if you put as many constraints as possible.

Set Up the Model for the Flux Calibrator

We set the model for the flux calibrator using setjy. First, check the availability of calibration models.

# In CASA
setjy(vis=vis,listmodimages=T)

There is no Ka-band model of 3C286. We will use the K-band model instead.

# In CASA
setjy(vis=vis,field='7',spw='0~1',
      modimage='3C286_K.im')

setjy scales the total flux in the model image to that appropriate for your individual spectral window frequencies according to the calibrator's flux and reports this number to the logger.

The logger output for each spw is:
J1331+3030 (fld ind 7) spw 0  [I=1.7762, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
J1331+3030 (fld ind 7) spw 1  [I=1.7794, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)

The absolute fluxes for the frequencies have now been determined and one can proceed to the bandpass and complex gain calibrations.

Bandpass Calibration

Correct the phase variations with time before solving for the bandpass to prevent decorrelation of the vector averaged bandpass solution.

Phase only calibration before bandpass. The 4 lines are both polarizations in both spw, unfortunately two of them get the same color green at the moment.
# In CASA
gaincal(vis=vis, caltable='bpphase.gcal', field='5', spw='0~1:20~40',
        refant='ea02', gaintype='G', calmode='p',solint='int',
        gaincurve=T)

Plot the solutions using plotcal.

# In CASA
plotcal(caltable='bpphase.gcal',xaxis='time',yaxis='phase',
        iteration='antenna',subplot=331,plotrange=[0,0,-180,180])

Next we can apply this phase solution on the fly while determining the bandpass solutions on the timescale of the bandpass calibrator scan (solint='inf').

# In CASA
bandpass(vis=vis, caltable='bandpass.bcal', field='5', refant='ea02',
         solint='inf', solnorm=T, gaintable='bpphase.gcal',
         gaincurve=T)

Plot the solutions, amplitude and phase:

Amplitude Bandpass solutions
Phase Bandpass solutions
# In CASA
plotcal(caltable='bandpass.bcal',xaxis='chan',yaxis='amp',
        iteration='antenna',subplot=331)


# In CASA
plotcal(caltable='bandpass.bcal',xaxis='chan',yaxis='phase',
        iteration='antenna',subplot=331)

Remaining Calibration

In this Community Day Event guide, we will skip over the remaining calibration steps. However, you can refer to EVLA high frequency Spectral Line tutorial - IRC+10216 part1 for full details. To summarize the missing steps, you bootstrap the flux densities of the secondary calibrators by

  1. doing a phase only calibration on all calibrators using gaincal,
  2. doing amplitude only calibration on all calibrators while applying the phase-only solutions, and
  3. deriving the flux density of the secondary calibrators while applying the previously obtained solutions.

Then, you can calibrate the target source using the phase and amplitude solutions you have obtained. Apply the target source calibration solutions using applycal. Use plotms to examine the calibrated data. If more flagging is required, redo all calibration steps. When the data look good, split the target source into a separate measurement set. Subtract the continuum flux using uvcontsub. Make Doppler corrections using cvel, or let clean do the Doppler corrections on the fly.

This tutorial picks up where EVLA high frequency spectral line tutorial - IRC+10216 - calibration leaves off.

Imaging

UV-plot of the spectral line signal in both spw for IRC+10216.

The continuum-subtracted spectral line data is contained in IRC10216_spls.ms. Use plotms to plot the lines.

plotms(vis='IRC10216_spls.ms', xaxis='channel', yaxis='amp',
       avgtime='1e8', avgscan=T, coloraxis='spw')

Now it is time to image the visibility data using clean. For illustration, we will clean channel 22 of the SiS line.

# In CASA
os.system('rm -rf ch22.*') # remove previously generated image, if it exists
clean(vis='IRC10216_spls.ms', imagename='ch22', spw='1:22~22',
      mode='channel', nchan=1, start='', width=1, niter=100000, 
      gain=0.1, threshold='3.0mJy', psfmode='clark', imagermode='csclean',
      interactive=T, npercycle=100, imsize=300, cell=['0.4arcsec', '0.4arcsec'],
      stokes='I', weighting='briggs', robust=0.5)

After running the above command, make a region in the CASA viewer. Double-click inside the region and clean by clicking the green circular arrow. After each cycle, click the green circular arrow again if the flux inside the region is brighter than the flux peaks outside the region. When you are finished cleaning, click the red 'STOP' button.

Open the resulting image using the viewer.

# In CASA
viewer("ch22.image")

In the viewer, make a region and click inside it to get statistics about the portion of the image in the region.

Analyze the Image Cubes

Open the HC3N image cube in the viewer.

# In CASA
viewer("IRC10216_HC3N.image")

Click the 'Play' button to view all channels in the cube. Select Tool --> Spectral profile... from the pull down menu. Create a region on the image to view the spectrum within the region.

Open the SiS image cube in the viewer.

# In CASA
viewer("IRC10216_SiS.image")

Determine what channels in the cube have emission. Then make moment maps using immoments.

# In CASA
os.system('rm -rf IRC10216_Sis.mom0') # remove previously generated map, if it exists
immoments(imagename="IRC10216_SiS.image", moments=[0], axis="spectral",
          chans="12~40", outfile="IRC10216_Sis.mom0")

Open the moment map in the viewer.

# In CASA
viewer("IRC10216_Sis.mom0")

Overlay contours by selecting Data --> Open from the pull down menu, selecting the moment-0 map, and clicking 'contour map'.

CASAguides

Last checked on CASA Version 3.3.0.