CARMA spectral line mosaic M99 3.1: Difference between revisions

From CASA Guides
Jump to navigationJump to search
← Older editNewer edit →
Cbrogan (talk | contribs)
operators
2,345 edits
Cbrogan (talk | contribs)
operators
2,345 edits
No edit summary
Line 1: Line 1:
== Overview ==
== Overview ==


Reducing a Spectral-Line mosaic (using CO J=1-0 in NGC4254 from CARMA STING, Rahman et al. 2010)


== Import fits files ==
== Import fits files ==
Line 21: Line 22:
</source>
</source>


Look at the logger output.  Notice that the CARMA data comes into
Look at the logger output.  Notice that the CARMA data comes into
CASA with antenna names that are numbers and that CASA also creates
CASA with antenna names that are numbers and that CASA also creates
an antenna id number for each antenna (it also creates id numbers
an antenna id number for each antenna (it also creates id numbers
for fields and spw). Both the antenna name and id can be used to
for fields and spw). Both the antenna name and id can be used to
identify an antenna, which is very confusing if both are numbers --
identify an antenna, which is very confusing if both are numbers --
but not the same number. The python commands below will append the
but not the same number. The python commands below will append the
antenna names with CA to more easily distinguish them from their
antenna names with CA to more easily distinguish them from their
ids. ALMA will already have antenna names that are strings, as does
ids. ALMA will already have antenna names that are strings, as does
the EVLA. This step is only needed for data that comes into CASA via
the EVLA. This step is only needed for data that comes into CASA via
importuvfits.
importuvfits.


<source lang="python">
<source lang="python">
Line 100: Line 101:


<pre style="background-color: E0FFFF;">
<pre style="background-color: E0FFFF;">
bandpass, gain, and flux cal 3c273 field id=1
bandpass, gain, and flux cal 3c273 field id=1
extra gain cal 3C274 field id=21
extra gain cal 3C274 field id=21
extra flux cal Mars field id=0
extra flux cal Mars field id=0


the target fields are 2~20
the target fields are 2~20


There is one wideband channel (spw=0) and two narrow band channels
There is one wideband channel (spw=0) and two narrow band channels
(spw=1,2)
(spw=1,2)
</pre>
</pre>


== Initial Inspection and Flagging ==
== Initial Inspection and Flagging ==


Flag edge channels  
Flag edge channels  


<source lang="python">
<source lang="python">
Line 122: Line 123:
</source>
</source>


First lets look at the wideband channel on all sources
First lets look at the wideband channel on all sources


[[Image:|thumb|]]
[[Image:|thumb|]]
Line 130: Line 131:
</source>
</source>


Click "Display" tab in the plotms gui and select colorize by field,
Click "Display" tab in the plotms gui and select colorize by field,
then click the plot button.
then click the plot button.


There are a few things to notice.
There are a few things to notice.


First there is some very noticably bad target data near the end of
First there is some very noticably bad target data near the end of
the observation. Use the zoom button to zoom in on the bad timerange and
the observation. Use the zoom button to zoom in on the bad timerange and
then use the Mark Region icon to put a box on a modest number of the
then use the Mark Region icon to put a box on a modest number of the
offending high points, and then press the Locate button. This will tell
offending high points, and then press the Locate button. This will tell
you that the offending telescope is antenna name=CA13 (id=12) and
you that the offending telescope is antenna name=CA13 (id=12) and
that the field-ids are 2~11. Looking at the plot the bad time range
that the field-ids are 2~11. Looking at the plot the bad time range
is 05:43:00~05:54:00.
is 05:43:00~05:54:00.


Click the "Clear Regions" button, and then the "house" button to
Click the "Clear Regions" button, and then the "house" button to
unzoom.
unzoom.


Next note that the first two scans on 3c273 and the last scan on
Next note that the first two scans on 3c273 and the last scan on
3c273 show some low points. Also the last scan on 3c274 shows low
3c273 show some low points. Also the last scan on 3c274 shows low
points.  Again use zoom, mark, and locate to see if you can see a
points.  Again use zoom, mark, and locate to see if you can see a
pattern.
pattern.


The first two scans on 3c273 don't show a particular pattern -- no
The first two scans on 3c273 don't show a particular pattern -- no
particular antenna or individual time range appears to be
particular antenna or individual time range appears to be
responsible. This is usually a good indication that it cannot be
responsible. This is usually a good indication that it cannot be
calibrated out. Also note that it is unlikely that the target data
calibrated out. Also note that it is unlikely that the target data
in between is good, though this is not obvious because the target is
in between is good, though this is not obvious because the target is
weak. However, 3c274 does look ok, before the second 3c273 scan.
weak. However, 3c274 does look ok, before the second 3c273 scan.
Unfortunately, there is no way to calibrate the first target scans
Unfortunately, there is no way to calibrate the first target scans
even if they are good, with no calibrator scan to preceed them.  For
even if they are good, with no calibrator scan to preceed them.  For
now we will flag 3c273 scans and the target in that timerange.
now we will flag 3c273 scans and the target in that timerange.


Last scan on 3c273 appears to be antenna CA7, scan 272
Last scan on 3c273 appears to be antenna CA7, scan 272
Last scan on 3c274 appears to be antenna CA8, scan 255
Last scan on 3c274 appears to be antenna CA8, scan 255


Looking at the lowest points on all the 3c273 scans, baseline
Looking at the lowest points on all the 3c273 scans, baseline
CA2-CA8 appears low, we will also wait to see if this calibrates out.
CA2-CA8 appears low, we will also wait to see if this calibrates out.


We will flag the narrow band channels wherever we see problems in
We will flag the narrow band channels wherever we see problems in
wideband. You can either make separate plotting commands, or combine
wideband. You can either make separate plotting commands, or combine
as below. To demonstrate different possiblilites we use timerange to
as below. To demonstrate different possiblilites we use timerange to
identify some data, and scan number others.
identify some data, and scan number others.


<source lang="python">
<source lang="python">
Line 190: Line 191:
== Calibrate the Wideband Channel ==
== Calibrate the Wideband Channel ==


Lets start by looking at the bandpass calibrator's phase as a
Lets start by looking at the bandpass calibrator's phase as a
fuction of channel for the wideband data.
fuction of channel for the wideband data.


[[Image:|thumb|]]
[[Image:|thumb|]]
Line 200: Line 201:
</source>
</source>


Select colorize by antenna2, and select "custom" for unflagged
Select colorize by antenna2, and select "custom" for unflagged
points, and then raise the style to 3 and you will see that the
points, and then raise the style to 3 and you will see that the
phase does not change a great deal on individual baselines over
phase does not change a great deal on individual baselines over
the wide band channel (spw=0). This means that averaging over some  
the wide band channel (spw=0). This means that averaging over some  
channels will not introduce significant closure errors. Check
channels will not introduce significant closure errors. Check
other antennas if you like.
other antennas if you like.


Now look at the phase as a function of time. With avgtime a large
Now look at the phase as a function of time. With avgtime a large
number, but no avgscan=T, this command will show the average phase
number, but no avgscan=T, this command will show the average phase
per scan. Since the cache changes, the colorize option changes
per scan. Since the cache changes, the colorize option changes
too. You will have to select these again as above.
too. You will have to select these again as above.


[[Image:|thumb|]]
[[Image:|thumb|]]
Line 220: Line 221:
</source>
</source>


Here you see significant variation with time. This is not
Here you see significant variation with time. This is not
surprising as the bandpass calibrator was observed over a fairly
surprising as the bandpass calibrator was observed over a fairly
long period of time-- 6 hours, it is important to calibrate the
long period of time-- 6 hours, it is important to calibrate the
phase before solving for the bandpass. We choose a fairly narrow
phase before solving for the bandpass. We choose a fairly narrow
channel range since the bandpass phase as a function of frequency
channel range since the bandpass phase as a function of frequency
has not been taken out yet (though for these data it is quite well
has not been taken out yet (though for these data it is quite well
behaved).
behaved).


<source lang="python">
<source lang="python">
Line 234: Line 235:
</source>
</source>


The use of solint='inf' here without setting combine will get one
The use of solint='inf' here without setting combine will get one
solution per scan.
solution per scan.


Look at the solutions
Look at the solutions


[[Image:|thumb|]]
[[Image:|thumb|]]
Line 246: Line 247:
</source>
</source>


Note the phase drift is > 100 degrees on some antennas -- this is
Note the phase drift is > 100 degrees on some antennas -- this is
why it would not have been appropriate to vector average these
why it would not have been appropriate to vector average these
data into one bp solution before taking out the phase. Use the
data into one bp solution before taking out the phase. Use the
"Next" button to page through all antennas.
"Next" button to page through all antennas.


Having done a preliminary phase solution we can now combine all the
Having done a preliminary phase solution we can now combine all the
3C273 scans into one bandpass solution, note the default combine
3C273 scans into one bandpass solution, note the default combine
parameter is combine='scan'.
parameter is combine='scan'.


<source lang="python">
<source lang="python">
Line 294: Line 295:
</source>
</source>


Note the significant phase variation within a single scan. If we
Note the significant phase variation within a single scan. If we
used an average phase in the next step to derive the amplitude
used an average phase in the next step to derive the amplitude
solutions, it would decorrelate the subsequent amplitude
solutions, it would decorrelate the subsequent amplitude
corrections.
corrections.


<source lang="python">
<source lang="python">
Line 313: Line 314:
</source>
</source>


Note the different gains for 3c273 scans and 3c274 scans, this
Note the different gains for 3c273 scans and 3c274 scans, this
just reflects that the two calibrators have different strengths.
just reflects that the two calibrators have different strengths.


Next plot the phase from the amplitude solutions -- this will be
Next plot the phase from the amplitude solutions -- this will be
the residual phase after taking out the integration-time based
the residual phase after taking out the integration-time based
solutions.  This gives a good idea of the residual phase
solutions.  This gives a good idea of the residual phase
noise. If this is more than a few degrees, the cause should be
noise. If this is more than a few degrees, the cause should be
investigated. Note that the scatter for 3c274 is larger than 3c273
investigated. Note that the scatter for 3c274 is larger than 3c273
-- this reflects that 3c273 is significantly weaker and thus has
-- this reflects that 3c273 is significantly weaker and thus has
less S/N.  
less S/N.  


[[Image:|thumb|]]
[[Image:|thumb|]]
Line 330: Line 331:
</source>
</source>


Here we re-run the phase only calibration but now getting one
Here we re-run the phase only calibration but now getting one
solution per scan to apply later to the target. An alternative
solution per scan to apply later to the target. An alternative
would be to smooth the intgration time phase calibration table,
would be to smooth the intgration time phase calibration table,
but this is a bit simpiler.
but this is a bit simpiler.


<source lang="python">
<source lang="python">
Line 348: Line 349:
         iteration='antenna',subplot=321,plotrange=[0,0,-180,180])
         iteration='antenna',subplot=321,plotrange=[0,0,-180,180])


This is a very important plot to look at carefully as these are
This is a very important plot to look at carefully as these are
the phase solutions that willl be applied to the target. Note that
the phase solutions that willl be applied to the target. Note that
the phases for 3c273 and 3c274 are very similar, but not exactly
the phases for 3c273 and 3c274 are very similar, but not exactly
the same. Unfortunately we can not color by field here to make it
the same. Unfortunately we can not color by field here to make it
easier to see.
easier to see.




== Calibrate the Narrow Band Bandpasses ==
== Calibrate the Narrow Band Bandpasses ==


Solve for narrow band bandpasses, applying wideband phase and
Solve for narrow band bandpasses, applying wideband phase and
amplitude corrections. Because there are 3 spw in the data, you must
amplitude corrections. Because there are 3 spw in the data, you must
set a placeholder for all three in spwmap, even though we are only
set a placeholder for all three in spwmap, even though we are only
solving for 2 of them.
solving for 2 of them.


<source lang="python">
<source lang="python">
Line 390: Line 391:
</source>
</source>


Flux density for 3C274 in SpW=0 is: 3.11626 +/- 0.0146614 (SNR = 212.549, nAnt= 15)
Flux density for 3C274 in SpW=0 is: 3.11626 +/- 0.0146614 (SNR = 212.549, nAnt= 15)


== Applycal and Inspect ==
== Applycal and Inspect ==
Line 454: Line 455:
</source>
</source>


in plotms in the "trans" tab set the CO rest frequency (115271.2
in plotms in the "trans" tab set the CO rest frequency (115271.2
MHz) in order to see the velocity range of the narrow band
MHz) in order to see the velocity range of the narrow band
channels. Unfortunately the individual pointings are a bit too
channels. Unfortunately the individual pointings are a bit too
weak to see the UV vector averaged CO signal but you can at least
weak to see the UV vector averaged CO signal but you can at least
see the observed velocity range.
see the observed velocity range.




Go to display tab and chose colorize by spw. Notice that the edge
Go to display tab and chose colorize by spw. Notice that the edge
channels are a bit noisy -- especially a concern in the overlap
channels are a bit noisy -- especially a concern in the overlap
region. We will exclude these below.
region. We will exclude these below.


<source lang="python">
<source lang="python">

Revision as of 16:55, 13 May 2010

Overview

Reducing a Spectral-Line mosaic (using CO J=1-0 in NGC4254 from CARMA STING, Rahman et al. 2010)

Import fits files

myfiles = []
for i in range(4,7):
        msfile = "c0104I"+str(i)+".ms"
        importuvfits(fitsfile="fits/c0104I."+str(i)+".fits",
                     vis=msfile)
        myfiles.append(msfile)

concat(vis=myfiles,concatvis='c0104I',timesort=True)

listobs(vis='c0104I')

Look at the logger output. Notice that the CARMA data comes into CASA with antenna names that are numbers and that CASA also creates an antenna id number for each antenna (it also creates id numbers for fields and spw). Both the antenna name and id can be used to identify an antenna, which is very confusing if both are numbers -- but not the same number. The python commands below will append the antenna names with CA to more easily distinguish them from their ids. ALMA will already have antenna names that are strings, as does the EVLA. This step is only needed for data that comes into CASA via importuvfits. 

tb.open("c0104I/ANTENNA",nomodify=False)
namelist=tb.getcol("NAME").tolist()
for i in range(len(namelist)):
	name = 'CA'+namelist[i]
	print ' Changing '+namelist[i]+' to '+name
	namelist[i]=name

tb.putcol("NAME",namelist)
tb.close()

listobs(vis='c0104I')

 Fields: 22
   ID   Code Name         RA            Decl           Epoch   nVis   
   0         MARS         09:15:50.0585 +17.21.03.8918 J2000   9450   
   1         3C273        12:29:06.7000 +02.03.08.5980 J2000   60480  
   2         NGC4254      12:18:47.8090 +14.24.13.9342 J2000   24570  
   3         NGC4254      12:18:49.6000 +14.24.13.9342 J2000   24570  
   4         NGC4254      12:18:51.3910 +14.24.13.9342 J2000   24570  
   5         NGC4254      12:18:52.2865 +14.24.36.4672 J2000   24570  
   6         NGC4254      12:18:50.4955 +14.24.36.4672 J2000   24570  
   7         NGC4254      12:18:48.7045 +14.24.36.4672 J2000   24570  
   8         NGC4254      12:18:46.9135 +14.24.36.4672 J2000   24570  
   9         NGC4254      12:18:46.0179 +14.24.59.0000 J2000   24570  
   10        NGC4254      12:18:47.8090 +14.24.59.0000 J2000   24570  
   11        NGC4254      12:18:49.6000 +14.24.59.0000 J2000   24570  
   12        NGC4254      12:18:51.3910 +14.24.59.0000 J2000   24570  
   13        NGC4254      12:18:53.1821 +14.24.59.0000 J2000   24570  
   14        NGC4254      12:18:52.2865 +14.25.21.5328 J2000   24570  
   15        NGC4254      12:18:50.4955 +14.25.21.5328 J2000   24570  
   16        NGC4254      12:18:48.7045 +14.25.21.5328 J2000   24570  
   17        NGC4254      12:18:46.9135 +14.25.21.5328 J2000   22680  
   18        NGC4254      12:18:47.8090 +14.25.44.0658 J2000   22680  
   19        NGC4254      12:18:49.6000 +14.25.44.0658 J2000   22680  
   20        NGC4254      12:18:51.3910 +14.25.44.0658 J2000   22680  
   21        3C274        12:30:49.4230 +12.23.28.0440 J2000   45360  
    (nVis = Total number of time/baseline visibilities per field) 
 Spectral Windows:  (3 unique spectral windows and 1 unique polarization setups)
   SpwID  Chans Frame Ch1(MHz)    ChanWid(kHz)TotBW(kHz)  Ref(MHz)    Corrs
   0          15 LSRK  113978.067  31250       468750      113978.067  RR  
   1          63 LSRK  114289.671  976.5625    61523.4375  114289.671  RR  
   2          63 LSRK  114341.036  976.5625    61523.4375  114341.036  RR  
 The SOURCE table is empty: see the FIELD table
 Antennas: 15:
   ID   Name  Station   Diam.    Long.         Lat.         
   0    CA1     ANT1      10.4 m   -116.45.01.0  +37.13.43.4  
   1    CA2     ANT2      10.4 m   -116.59.48.3  +37.52.00.3  
   2    CA3     ANT3      10.4 m   -120.06.43.6  +37.35.02.8  
   3    CA4     ANT4      10.4 m   -119.38.33.8  +38.26.22.2  
   4    CA5     ANT5      10.4 m   -119.13.25.0  +35.03.23.4  
   5    CA6     ANT6      10.4 m   -119.06.39.2  +38.54.24.4  
   6    CA7     ANT7      6.1  m   -119.30.34.9  +36.58.55.6  
   7    CA8     ANT8      6.1  m   -118.08.34.0  +37.16.45.8  
   8    CA9     ANT9      6.1  m   -118.46.59.9  +36.48.41.4  
   9    CA10    ANT10     6.1  m   -118.29.04.6  +36.03.45.6  
   10   CA11    ANT11     6.1  m   -118.48.40.9  +37.15.57.8  
   11   CA12    ANT12     6.1  m   -119.33.27.5  +36.06.46.1  
   12   CA13    ANT13     6.1  m   -118.31.43.5  +37.05.19.4  
   13   CA14    ANT14     6.1  m   -118.13.18.7  +36.50.34.6  
   14   CA15    ANT15     6.1  m   -117.23.50.2  +36.25.48.2  

bandpass, gain, and flux cal 3c273 field id=1
extra gain cal 3C274 field id=21
extra flux cal Mars field id=0

the target fields are 2~20

There is one wideband channel (spw=0) and two narrow band channels
(spw=1,2)

Initial Inspection and Flagging

Flag edge channels 

flagdata(vis='c0104I',mode='manualflag',selectdata=True,spw='0:0~1;13~14')

flagdata(vis='c0104I',mode='manualflag',selectdata=True,spw='1~2:0~1;61~62')

First lets look at the wideband channel on all sources

[[Image:|thumb|]] 

plotms(vis='c0104I',xaxis='time',yaxis='amp',field='1~21', spw='0',
      avgchannel='15')

Click "Display" tab in the plotms gui and select colorize by field, then click the plot button.

There are a few things to notice.

First there is some very noticably bad target data near the end of the observation. Use the zoom button to zoom in on the bad timerange and then use the Mark Region icon to put a box on a modest number of the offending high points, and then press the Locate button. This will tell you that the offending telescope is antenna name=CA13 (id=12) and that the field-ids are 2~11. Looking at the plot the bad time range is 05:43:00~05:54:00.

Click the "Clear Regions" button, and then the "house" button to unzoom.

Next note that the first two scans on 3c273 and the last scan on 3c273 show some low points. Also the last scan on 3c274 shows low points. Again use zoom, mark, and locate to see if you can see a pattern.

The first two scans on 3c273 don't show a particular pattern -- no particular antenna or individual time range appears to be responsible. This is usually a good indication that it cannot be calibrated out. Also note that it is unlikely that the target data in between is good, though this is not obvious because the target is weak. However, 3c274 does look ok, before the second 3c273 scan. Unfortunately, there is no way to calibrate the first target scans even if they are good, with no calibrator scan to preceed them. For now we will flag 3c273 scans and the target in that timerange.

Last scan on 3c273 appears to be antenna CA7, scan 272 Last scan on 3c274 appears to be antenna CA8, scan 255

Looking at the lowest points on all the 3c273 scans, baseline CA2-CA8 appears low, we will also wait to see if this calibrates out.

We will flag the narrow band channels wherever we see problems in wideband. You can either make separate plotting commands, or combine as below. To demonstrate different possiblilites we use timerange to identify some data, and scan number others. 

flagdata(vis='c0104I',spw='0~2',
	 antenna=['CA13','','CA7','CA8'],
	 field=['2~11','1~20','1','21'],
	 scan=['','','272','255'],
	 timerange=['05:43:00~05:54:00','00:25:00~00:55:00','',''])

Set the Absolute Flux Scale

The flux of 3C273 is inserted from CARMA flux monitoring

setjy(vis='c0104I', field='3C273',fluxdensity=[17.8,0.,0.,0.], spw='0~2')

Calibrate the Wideband Channel

Lets start by looking at the bandpass calibrator's phase as a fuction of channel for the wideband data.

[[Image:|thumb|]] 

plotms(vis='c0104I',xaxis='channel',yaxis='phase',
       field='1',spw='0',antenna='CA1',
       avgtime='1e8',avgscan=T)

Select colorize by antenna2, and select "custom" for unflagged points, and then raise the style to 3 and you will see that the phase does not change a great deal on individual baselines over the wide band channel (spw=0). This means that averaging over some channels will not introduce significant closure errors. Check other antennas if you like.

Now look at the phase as a function of time. With avgtime a large number, but no avgscan=T, this command will show the average phase per scan. Since the cache changes, the colorize option changes too. You will have to select these again as above.

[[Image:|thumb|]] 

plotms(vis='c0104I',xaxis='time',yaxis='phase',
       field='1',spw='0',
       antenna='CA1',
       avgchannel='15',avgtime='1e8')

Here you see significant variation with time. This is not surprising as the bandpass calibrator was observed over a fairly long period of time-- 6 hours, it is important to calibrate the phase before solving for the bandpass. We choose a fairly narrow channel range since the bandpass phase as a function of frequency has not been taken out yet (though for these data it is quite well behaved). 

gaincal(vis='c0104I',caltable='c0104I.bpphase_widecal',
        field='1',spw='0:5~9',
        refant='CA9',calmode='p',solint='inf',minsnr=2.0)

The use of solint='inf' here without setting combine will get one solution per scan.

Look at the solutions

[[Image:|thumb|]] 

plotcal(caltable='c0104I.bpphase_widecal',
        xaxis='time',yaxis='phase',
        iteration='antenna',subplot=321)

Note the phase drift is > 100 degrees on some antennas -- this is why it would not have been appropriate to vector average these data into one bp solution before taking out the phase. Use the "Next" button to page through all antennas.

Having done a preliminary phase solution we can now combine all the 3C273 scans into one bandpass solution, note the default combine parameter is combine='scan'. 

bandpass(vis='c0104I',caltable='c0104I.bp_widecal',
         interp='',field='1',spw='0',
         bandtype='B',solint='inf',
         refant='CA9',solnorm=F,
         gaintable=['c0104I.bpphase_widecal'],
         spwmap=[[]])

[[Image:|thumb|]] 

plotcal(caltable='c0104I.bp_widecal',xaxis='chan',yaxis='amp',
        iteration='antenna',subplot=321)

[[Image:|thumb|]] 

plotcal(caltable='c0104I.bp_widecal',xaxis='chan',yaxis='phase',
        iteration='antenna',subplot=321)

Now resolve for phase and also amplitude while applying the
bandpass solutions, for both calibrators 3c273 and 3c274. We will
not use the first gain solution again.

gaincal(vis='c0104I',caltable='c0104I.phase_widecal',
        field='1,21',spw='0',
        refant='CA9',calmode='p',solint='int',minsnr=2.0,
        gaintable=['c0104I.bp_widecal'],
        spwmap=[[]])

[[Image:|thumb|]] 

plotcal(caltable='c0104I.phase_widecal',xaxis='time',yaxis='phase',
        iteration='antenna',subplot=321,plotrange=[0,0,-180,180])

Note the significant phase variation within a single scan. If we used an average phase in the next step to derive the amplitude solutions, it would decorrelate the subsequent amplitude corrections. 

gaincal(vis='c0104I',caltable='c0104I.amp_widecal',
        field='1,21',spw='0',
        refant='CA9',calmode='ap',solint='inf',minsnr=2.0,
        gaintable=['c0104I.bp_widecal','c0104I.phase_widecal'],
        spwmap=[[]])

[[Image:|thumb|]] 

plotcal(caltable='c0104I.amp_widecal',xaxis='time',yaxis='amp',
        iteration='antenna',subplot=321)

Note the different gains for 3c273 scans and 3c274 scans, this just reflects that the two calibrators have different strengths.

Next plot the phase from the amplitude solutions -- this will be the residual phase after taking out the integration-time based solutions. This gives a good idea of the residual phase noise. If this is more than a few degrees, the cause should be investigated. Note that the scatter for 3c274 is larger than 3c273 -- this reflects that 3c273 is significantly weaker and thus has less S/N.

[[Image:|thumb|]] 

plotcal(caltable='c0104I.amp_widecal',xaxis='time',yaxis='phase',
        iteration='antenna',subplot=321)

Here we re-run the phase only calibration but now getting one solution per scan to apply later to the target. An alternative would be to smooth the intgration time phase calibration table, but this is a bit simpiler. 

gaincal(vis='c0104I',caltable='c0104I.phase_wide_inf_cal',
        field='1,21',spw='0',
        refant='CA9',calmode='p',solint='inf',minsnr=2.0,
        gaintable=['c0104I.bp_widecal'],
        spwmap=[[]])

[[Image:|thumb|]] 

plotcal(caltable='c0104I.phase_wide_inf_cal',xaxis='time',yaxis='phase',
        iteration='antenna',subplot=321,plotrange=[0,0,-180,180])

This is a very important plot to look at carefully as these are
the phase solutions that willl be applied to the target. Note that
the phases for 3c273 and 3c274 are very similar, but not exactly
the same. Unfortunately we can not color by field here to make it
easier to see.


== Calibrate the Narrow Band Bandpasses ==

Solve for narrow band bandpasses, applying wideband phase and
amplitude corrections. Because there are 3 spw in the data, you must
set a placeholder for all three in spwmap, even though we are only
solving for 2 of them.

<source lang="python">
bandpass(vis='c0104I',caltable='c0104I.bp_narrowcal',
         interp='',field='1',spw='1,2',
         bandtype='B',solint='inf',
         refant='CA9',solnorm=F,
         gaintable=['c0104I.phase_widecal','c0104I.amp_widecal'],
         spwmap=[[0,0,0],[0,0,0]])

[[Image:|thumb|]] 

plotcal(caltable='c0104I.bp_narrowcal',xaxis='chan',yaxis='amp',
        iteration='antenna',subplot=331)

[[Image:|thumb|]] 

plotcal(caltable='c0104I.bp_narrowcal',xaxis='chan',yaxis='phase',
        iteration='antenna',subplot=331)

Calibrate Absolute Flux

fluxscale(vis='c0104I',caltable='c0104I.amp_widecal',
          fluxtable='c0104I.fluxcal',reference='1')

Flux density for 3C274 in SpW=0 is: 3.11626 +/- 0.0146614 (SNR = 212.549, nAnt= 15)

Applycal and Inspect

applycal(vis='c0104I',field='1',spw='0',
        gaintable=['c0104I.bp_widecal','c0104I.phase_widecal','c0104I.fluxcal'],
        spwmap=[[],[],[]],gainfield=['1','1','1'])

applycal(vis='c0104I',field='1',spw='1,2',
        gaintable=['c0104I.bp_narrowcal','c0104I.phase_widecal','c0104I.fluxcal'],
        spwmap=[[],[0,0,0],[0,0,0]],gainfield=['1','1','1'])

applycal(vis='c0104I',field='21',spw='0',
        gaintable=['c0104I.bp_widecal','c0104I.phase_widecal','c0104I.fluxcal'],
        spwmap=[[],[],[]],gainfield=['1','21','21'])



applycal(vis='c0104I',field='21',spw='1,2',
        gaintable=['c0104I.bp_narrowcal','c0104I.phase_widecal','c0104I.fluxcal'],
        spwmap=[[],[0,0,0],[0,0,0]],gainfield=['1','21','21'])

For the target we will use both calibrators, so which ever is
closest in time will be applied to the target.

applycal(vis='c0104I',field='2~20',spw='0',
        gaintable=['c0104I.bp_widecal','c0104I.phase_wide_inf_cal','c0104I.fluxcal'],
        spwmap=[[],[],[]],gainfield=['1','1,21','1,21'])

applycal(vis='c0104I',field='2~20',spw='1,2',
        gaintable=['c0104I.bp_narrowcal','c0104I.phase_wide_inf_cal','c0104I.fluxcal'],
        spwmap=[[],[0,0,0],[0,0,0]],gainfield=['1','1,21','1,21'])

plotms(vis='c0104I',xaxis='frequency',ydatacolumn='corrected',
       field='1',avgtime='1e8')

[[Image:|thumb|]] 

plotms(vis='c0104I',xaxis='time',yaxis='amp',ydatacolumn='corrected',
       field='1~21',spw='0',
       avgchannel='15',avgtime='1e8')

Deconvolution and Imaging

[[Image:|thumb|]] 

plotms(vis='c0104I',xaxis='velocity',yaxis='amp',ydatacolumn='corrected',
       field='2',spw='1~2',avgtime='1e8')

in plotms in the "trans" tab set the CO rest frequency (115271.2 MHz) in order to see the velocity range of the narrow band channels. Unfortunately the individual pointings are a bit too weak to see the UV vector averaged CO signal but you can at least see the observed velocity range.


Go to display tab and chose colorize by spw. Notice that the edge channels are a bit noisy -- especially a concern in the overlap region. We will exclude these below. 

clean(vis='c0104I',imagename='M99_cube_nearest',spw='1~2:3~59',field='2~20',
      phasecenter='11',
      cell='1.0arcsec',imsize=500,
      mode='velocity',start='2268km/s',width='10.0km/s',
      interpolation='nearest',
      imagermode='mosaic',cyclefactor=2,
      restfreq='115.2712GHz',interactive=F,
      mask='../M99_cube.mask',
      minpb=0.1,pbcor=F,
      niter=5000,threshold='40mJy')


Image Analysis

immoments(imagename='M99_cube_nearest.image',moments=[0],axis='spectral',
          excludepix=[-100,0.075],outfile='M99_cube.moment0')

immoments(imagename='M99_cube_nearest.image',moments=[1],axis='spectral',
          excludepix=[-100,0.125],outfile='M99_cube.moment1')
Retrieved from "https://casaguides.nrao.edu/index.php?title=CARMA_spectral_line_mosaic_M99_3.1&oldid=2929"