TWHydraBand7 Calibration for CASA 3.3
From CASA Guides
- This script assumes that you have downloaded RawDataAndTablesForReduction from TWHydraBand7#Getting_the_Data
- Details of the ALMA data are provided at TWHydraBand7
Observing Log and Priors
External info
# In CASA
data=['X3c1.ms','X5d8.ms','X7ef.ms']
for vis in data:
listobs(vis=vis,verbose=F)
Below we copy select parts of the listobs output reported in the CASA logger for reference.
X3c1.ms: Data records: 278352 Total integration time = 6109.06 seconds Observed from 22-Apr-2011/00:01:52.9 to 22-Apr-2011/01:43:42.0 (UTC) X5d8.ms: Data records: 278406 Total integration time = 5995.01 seconds Observed from 22-Apr-2011/01:48:05.8 to 22-Apr-2011/03:28:00.8 (UTC) X7ef.ms: Data records: 255717 Total integration time = 5407.49 seconds Observed from 22-Apr-2011/03:30:39.7 to 22-Apr-2011/05:00:47.2 (UTC) ID Code Name RA Decl Epoch SrcId 0 none 3c279 12:56:11.1666 -05.47.21.5247 J2000 0 1 none Titan 00:00:00.0000 +00.00.00.0000 J2000 1 2 none TW Hya 11:01:51.9063 -34.42.17.0212 J2000 2 3 none J1147-382=Q* 11:47:01.3815 -38.12.11.1179 J2000 3 4 none J1037-295=Q* 10:37:16.0899 -29.34.02.9888 J2000 4 SpwID Chans Frame Ch1(MHz) ChanWid(kHz)TotBW(kHz) Ref(MHz) Corrs 0 4 TOPO 184550 1500000 7500000 183300 I 1 128 TOPO 355740.062 15625 2000000 355732.25 XX YY 2 1 TOPO 356716.625 1796875 1796875 355732.25 XX YY 3 128 TOPO 356507.813 15625 2000000 356500 XX YY 4 1 TOPO 357484.375 1796875 1796875 356500 XX YY 5 128 TOPO 346792.187 15625 2000000 346800 XX YY 6 1 TOPO 345784.375 1796875 1796875 346800 XX YY 7 128 TOPO 345182.438 15625 2000000 345190.25 XX YY 8 1 TOPO 344174.625 1796875 1796875 345190.25 XX YY 9 128 TOPO 344386.763 15625 2000000 344394.575 XX YY 10 1 TOPO 343378.95 1796875 1796875 344394.575 XX YY 11 128 TOPO 346324.263 15625 2000000 346332.075 XX YY 12 1 TOPO 345316.45 1796875 1796875 346332.075 XX YY 13 128 TOPO 354402.388 15625 2000000 354394.575 XX YY 14 1 TOPO 355378.95 1796875 1796875 354394.575 XX YY 15 128 TOPO 356402.388 15625 2000000 356394.575 XX YY 16 1 TOPO 357378.95 1796875 1796875 356394.575 XX YY 17 3840 TOPO 356497.936 122.070312 468750 355732.25 XX YY 18 1 TOPO 356732.189 468750 468750 355732.25 XX YY 19 3840 TOPO 357734.314 122.070312 468750 356500 XX YY 20 1 TOPO 357499.939 468750 468750 356500 XX YY 21 3840 TOPO 346034.314 122.070312 468750 346800 XX YY 22 1 TOPO 345799.939 468750 468750 346800 XX YY 23 3840 TOPO 343955.936 122.070312 468750 345190.25 XX YY 24 1 TOPO 344190.189 468750 468750 345190.25 XX YY ID= 0-3: 'DV04'='J505', 'DV06'='T704', 'DV07'='J510', 'DV08'='T703', ID= 4-7: 'DV09'='N602', 'DV10'='N606', 'PM01'='T702', 'PM02'='T701', ID= 8-8: 'PM03'='J504'
Examine Tsys and WVR Tables, Apply, and Split
# In CASA
FDM=[17,19,21,23]
FDMtables=['X3c1.tsys.fdm','X5d8.tsys.fdm','X7ef.tsys.fdm']
plotrange=[0,0,50,500]
antennas='1,2,3,4,5,6,7,8]
for caltable in FDMtables:
for spw in FDM:
plotcal(caltable=caltable,xaxis='freq',yaxis='amp',
iteration='antenna',subplot=421,poln='',spw='%d'%spw,antenna=antennas,
showgui=F,figfile='FDM%d_%s.png'%(spw,caltable),fontsize=8.0,
plotrange=plotrange)
# In CASA
data=['X3c1.ms','X5d8.ms','X7ef.ms']
fdm='17,19,21,23'
sources=['0','1','2','4']
nocal='3' # This source had no Tsys measurements associated with it
For sources with Tsys measurements apply only to themselves
# In CASA
for vis in data:
for field in sources:
applycal(vis=vis,spw=fdm,field=field,gainfield=field,
gaintable=['%s.tsys.fdm'%(vis.split('.')[0]),'wvr_%s.cal'%(vis.split('.')[0])],
interp=['nearest','nearest'],flagbackup=F)
For sources without Tsys, couple them with best source with Tsys
# In CASA
for vis in data:
applycal(vis=vis,spw=fdm,field=nocal,
gaintable=['%s.tsys.fdm'%(vis.split('.')[0]),'wvr_%s.cal'%(vis.split('.')[0])],
gainfield=['4',nocal],interp=['nearest','nearest'],flagbackup=F)
Check Tsys application
# In CASA
plotms(vis='X5d8.ms',spw='17,19,21,23',xaxis='frequency',yaxis='amp',field='0,1',
avgtime='1e8',avgscan=T,coloraxis='field',ydatacolumn='data')
spw 19 with atmospheric absorption gets a strange upward hitch probably from the interpolation from TDM
# In CASA
for vis in data:
split(vis=vis,outputvis='%s_wvrtsys.ms'%(vis.split('.')[0]),datacolumn='corrected',spw=fdm)
Initial Inspection and Flagging
# In CASA
data=['X3c1_wvrtsys.ms','X5d8_wvrtsys.ms','X7ef_wvrtsys.ms']
for vis in data:
flagdata(vis=vis,autocorr=True, flagbackup=T)
flagdata(vis=vis,mode='shadow',diameter=12.0, flagbackup=F)
flagdata(vis=vis,antenna='DV04', flagbackup=F)
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='',xaxis='time',yaxis='amp',field='',avgchannel='3840',
coloraxis='field',iteraxis='spw')
# In CASA
plotms(vis='X5d8_wvrtsys.ms',spw='',xaxis='time',yaxis='amp',field='',avgchannel='3840',
coloraxis='field',iteraxis='spw')
# In CASA
plotms(vis='X7ef_wvrtsys.ms',spw='',xaxis='time',yaxis='amp',field='',avgchannel='3840',
coloraxis='field',iteraxis='spw')
In spw2 there are some low points. Locate suggests YY and PM03. Switch to coloraxis='corr'
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='2',xaxis='time',yaxis='amp',field='',avgchannel='3840',
coloraxis='corr')
To further check remove PM03 from the plot.
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='2',xaxis='time',yaxis='amp',field='',avgchannel='3840',
coloraxis='corr',antenna='!PM03')
Unzoom does not work, but flip to next page and back does.
# In CASA
data=['X3c1_wvrtsys.ms','X5d8_wvrtsys.ms','X7ef_wvrtsys.ms']
for vis in data:
flagdata(vis=vis, flagbackup=T,
spw=['2'],
antenna=['PM03'],
correlation=['YY'])
Check phase / delay
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='',xaxis='frequency',yaxis='phase',field='0',antenna='DV06',
avgtime='1e8',avgscan=T,coloraxis='baseline',iteraxis='spw',xselfscale=T)
# In CASA
plotms(vis='X5d8_wvrtsys.ms',spw='',xaxis='frequency',yaxis='phase',field='0',antenna='DV06',
avgtime='1e8',avgscan=T,coloraxis='baseline',iteraxis='spw',xselfscale=T)
# In CASA
plotms(vis='X7ef_wvrtsys.ms',spw='',xaxis='frequency',yaxis='phase',field='0',antenna='DV06',
avgtime='1e8',avgscan=T,coloraxis='baseline',iteraxis='spw',xselfscale=T)
Now look for birdies
Titan and 3C279
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='',xaxis='frequency',yaxis='amp',field='0,1',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',xselfscale=T)
TW Hydra and Phase cals
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='',xaxis='frequency',yaxis='amp',field='2,3,4',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',xselfscale=T,yselfscale=T)
Quick check that other two datasets are the same
Titan and 3C279
# In CASA
plotms(vis='X5d8_wvrtsys.ms',spw='',xaxis='frequency',yaxis='amp',field='0,1',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',xselfscale=T)
# In CASA
plotms(vis='X7ef_wvrtsys.ms',spw='',xaxis='frequency',yaxis='amp',field='0,1',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',xselfscale=T)
TW Hydra and Phase cals
# In CASA
plotms(vis='X5d8_wvrtsys.ms',spw='',xaxis='frequency',yaxis='amp',field='2,3,4',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',xselfscale=T,yselfscale=T)
birdies seem weaker, some gone
# In CASA
plotms(vis='X7ef_wvrtsys.ms',spw='',xaxis='frequency',yaxis='amp',field='2,3,4',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',xselfscale=T,yselfscale=T)
Change to channel space to get channels for flagging
TW Hydra and Phase cals
# In CASA
plotms(vis='X3c1_wvrtsys.ms',spw='',xaxis='channel',yaxis='amp',field='2,3,4',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw')
# In CASA
data=['X3c1_wvrtsys.ms','X5d8_wvrtsys.ms','X7ef_wvrtsys.ms']
for vis in data:
flagdata(vis=vis, flagbackup=T,
spw=['0:1067~1068;1279~1280;2367~2368;3775~3776',
'1:1279~1280;2367~2368;3775~3776',
'2:1279~1280;3775~3776',
'3:831~832;1535~1536;2367~2368;3775~3776;3839~3839'])
Force reload and check that flagging has been done as anticipated.
Concatenate the Data
Here we will concatenate the three datasets for convience. WARNING: it is not always safe to do this [explain].
# In CASA
data=['X3c1_wvrtsys.ms','X5d8_wvrtsys.ms','X7ef_wvrtsys.ms']
concat(vis=data,concatvis='Band7multi_april22.ms')
# In CASA
listobs(vis='Band7multi_april22.ms',verbose=F)
SpwID #Chans Frame Ch1(MHz) ChanWid(kHz)TotBW(kHz) Ref(MHz) Corrs 0 3840 TOPO 356497.936 122.070312 468750 355732.25 XX YY 1 3840 TOPO 357734.314 122.070312 468750 356500 XX YY 2 3840 TOPO 346034.314 122.070312 468750 346800 XX YY 3 3840 TOPO 343955.936 122.070312 468750 345190.25 XX YY
Fix Titan Coordinates
Note that in the near future this step will be unnecessary.
It is temporarily necessary to correct the positions of ephemeris objects observed by ALMA, as they are currently erroneously written to the data with coordinates of 00:00:00.0000 +00.00.00.0000 J2000 (see listobs output in TWHydraBand7_Calibration#Observing_Log_and_Priors). For this data we need to correct Titan which we observed as the absolute flux calibrator. It is important to apply the fix after concatenation of the data, or Titan will be at slightly different positions in all three datasets.
For Linux OS initialize CASA script with
# In CASA
execfile(os.getenv("CASAPATH").split(' ')[0]+"/lib/python2.6/recipes/fixplanets.py")
For Mac OSX initialize CASA script with
# In CASA
execfile(os.getenv("CASAPATH").split(' ')[0]+"/Resources/python/recipes/fixplanets.py")
Now fix the position of Titan
# In CASA
fixplanets('Band7multi_april22.ms', 'Titan', True)
Check the header information again to see that the information for Titan has changed.
# In CASA
listobs(vis='Band7multi_april22.ms',verbose=F)
2011-05-23 17:23:52 INFO listobs ID Code Name RA Decl Epoch SrcId 2011-05-23 17:23:52 INFO listobs 0 none 3c279 12:56:11.1666 -05.47.21.5247 J2000 0 2011-05-23 17:23:52 INFO listobs 1 none Titan 12:49:26.5120 -02.22.10.8190 J2000 1 2011-05-23 17:23:52 INFO listobs 2 none TW Hya 11:01:51.9063 -34.42.17.0212 J2000 2 2011-05-23 17:23:52 INFO listobs 3 none J1147-382=Q* 11:47:01.3815 -38.12.11.1179 J2000 3 2011-05-23 17:23:52 INFO listobs 4 none J1037-295=Q* 10:37:16.0899 -29.34.02.9888 J2000 4
Flag Calibrator Spectral Features
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='channel',yaxis='amp',field='0',
avgtime='1e8',coloraxis='field',iteraxis='spw')
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='channel',yaxis='amp',field='1',
avgtime='1e8',coloraxis='field',iteraxis='spw')
Flag strong spectral features in the calibrators being careful about backing up flag tables so flagged regions can be restored later
# In CASA
flagmanager(vis='Band7multi_april22.ms',mode='save',versionname='before_calspectralflags')
Flag absorption features
# In CASA
flagdata(vis='Band7multi_april22.ms',
spw=['1:2000~3840','2:1945~1960'])
# In CASA
flagmanager(vis='Band7multi_april22.ms',mode='save',versionname='before_emissionflags')
Flag emission features
<source lang="python">
# In CASA
flagdata(vis='Band7multi_april22.ms',
field=['1','1'],
spw=['2:300~3660','3:1000~3000'])
Check if you like that the right things have been flagged.
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='channel',yaxis='amp',field='0,1',
avgtime='1e8',coloraxis='field',iteraxis='spw')
Set Up the Flux Calibrator Model
# In CASA
setjy(vis='Band7multi_april22.ms',field='1',
standard='Butler-JPL-Horizons 2010',scalebychan=F)
Bandpass
# In CASA
gaincal(vis='Band7multi_april22.ms',caltable='bpphase.gcal',
field='0',spw='0~3:900~1100',refant='DV06',
calmode='p',solint='int',minsnr=2.0,minblperant=4)
# In CASA
bandpass(vis='Band7multi_april22.ms',caltable='bandpass.bcal',
field='0',spw='',combine='',refant='DV06',
solint='inf',solnorm=T,minblperant=4,fillgaps=17,
gaintable=['bpphase.gcal'])
# In CASA
plotcal(caltable='bpphase.gcal',xaxis='time',yaxis='phase',spw='',antenna=ants,
iteration='antenna',subplot=321,plotrange=[0,0,-180,180],poln='X')
# In CASA
plotcal(caltable='bandpass.bcal',xaxis='freq',yaxis='amp',antenna=ants,
iteration='antenna',subplot=321,spw='0')
# In CASA
plotcal(caltable='bandpass.bcal',xaxis='freq',yaxis='phase',antenna=ants,
iteration='antenna',subplot=321,spw='0')
Gain Calibration
# In CASA
gaincal(vis='Band7multi_april22.ms',caltable='intphase.gcal',
field='0,1,3,4',spw='0~3:40~3800',refant='DV06',
calmode='p',solint='int',minsnr=2.0,minblperant=4,
gaintable=['bandpass.bcal'])
# In CASA
gaincal(vis='Band7multi_april22.ms',caltable='scanphase.gcal',
field='0,1,3,4',spw='0~3:40~3800',refant='DV06',
calmode='p',solint='inf',minsnr=2.0,minblperant=4,
gaintable=['bandpass.bcal'])
# In CASA
gaincal(vis='Band7multi_april22.ms',caltable='amp.gcal',
field='0,1,3,4',spw='0~3:40~3800',refant='DV06',
calmode='ap',solint='inf',minsnr=2.0,minblperant=4,
gaintable=['bandpass.bcal','intphase.gcal'])
# In CASA
fluxscale(vis='Band7multi_april22.ms',caltable='amp.gcal',
fluxtable='flux.cal',reference='1',refspwmap=[0,1,3,3])
# In CASA
plotcal(caltable='intphase.gcal',xaxis='time',yaxis='phase',antenna=ants,
spw='',field='0,1,3,4',
iteration='antenna',subplot=221,plotrange=[0,0,-180,180])
# In CASA
plotcal(caltable='scanphase.gcal',xaxis='time',yaxis='phase',
spw='',field='0,1,3,4',antenna=ants, poln='X',
iteration='antenna',subplot=221,plotrange=[0,0,-180,180])
# In CASA
plotcal(caltable='scanphase.gcal',xaxis='time',yaxis='phase',
spw='',field='0,1,3,4',antenna=ants, poln='Y',
iteration='antenna',subplot=221,plotrange=[0,0,-180,180])
# In CASA
plotcal(caltable='amp.gcal',xaxis='time',yaxis='phase',antenna=ants,
spw='0',field='0,1,3,4',
iteration='antenna',subplot=221)
# In CASA
plotcal(caltable='amp.gcal',xaxis='time',yaxis='amp',field='3,4',antenna=ants,
iteration='antenna',subplot=221,spw='',poln='X',plotrange=[0,0,0.0,0.3])
# In CASA
plotcal(caltable='amp.gcal',xaxis='time',yaxis='amp',field='3,4',antenna=ants,
iteration='antenna',subplot=221,spw='',poln='Y')
Applycal and Inspect
# In CASA
flagmanager(vis='Band7multi_april22.ms',mode='restore',versionname='before_calspectralflags')
# In CASA
applycal(vis='Band7multi_april22.ms',field='0',
gaintable=['bandpass.bcal','intphase.gcal','flux.cal'],
interp=['nearest','nearest','nearest'],
gainfield=['0','0','0'],flagbackup=T)
# In CASA
applycal(vis='Band7multi_april22.ms',field='1',
gaintable=['bandpass.bcal','intphase.gcal','flux.cal'],
interp=['nearest','nearest','nearest'],
gainfield=['0','1','1'],flagbackup=T)
- Secondary Phase cal
# In CASA
applycal(vis='Band7multi_april22.ms',field='3',
gaintable=['bandpass.bcal','scanphase.gcal','flux.cal'],
interp=['nearest','nearest','nearest'],
gainfield=['0','4','4'],flagbackup=T)
- Primary Phase cal
# In CASA
applycal(vis='Band7multi_april22.ms',field='4',
gaintable=['bandpass.bcal','intphase.gcal','flux.cal'],
interp=['nearest','nearest','nearest'],
gainfield=['0','4','4'],flagbackup=T)
# In CASA
applycal(vis='Band7multi_april22.ms',field='2',
interp=['nearest','linear','linear'],
gaintable=['bandpass.bcal','scanphase.gcal','flux.cal'],
gainfield=['0','3,4','3,4'],flagbackup=T)
Check results
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='time',yaxis='amp',field='',avgchannel='3840',
coloraxis='field',iteraxis='spw',ydatacolumn='corrected')
Pretty good but some high points at end of 1st SB. Look at only phase cals to simplify plot
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='time',yaxis='phase',field='3,4',avgchannel='3840',
coloraxis='field',iteraxis='spw',ydatacolumn='corrected')
# In CASA
applycal(vis='Band7multi_april22.ms',field='3',
gaintable=['bandpass.bcal','intphase.gcal','flux.cal'],
interp=['nearest','nearest','nearest'],
gainfield=['0','3','3'],flagbackup=T)
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='time',yaxis='phase',field='3,4',avgchannel='3840',
coloraxis='field',iteraxis='spw',ydatacolumn='corrected')
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='time',yaxis='amp',field='3,4',avgchannel='3840',
coloraxis='field',iteraxis='spw',ydatacolumn='corrected')
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='uvdist',yaxis='amp',field='2',avgchannel='3840',
coloraxis='field',iteraxis='spw',ydatacolumn='corrected')
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='frequency',yaxis='amp',field='2',
avgtime='1e8',avgscan=T,coloraxis='field',iteraxis='spw',
ydatacolumn='corrected',xselfscale=T)
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='frequency',yaxis='amp',field='0',
avgtime='1e8',avgscan=T,coloraxis='field',ydatacolumn='corrected',
iteraxis='spw',xselfscale=T)
# In CASA
plotms(vis='Band7multi_april22.ms',spw='2,3',xaxis='frequency',yaxis='amp',field='0,1',
avgtime='1e8',avgscan=T,coloraxis='field',ydatacolumn='corrected')
# In CASA
plotms(vis='Band7multi_april22.ms',spw='',xaxis='frequency',yaxis='amp',field='3,4',
avgtime='1e8',avgscan=T,coloraxis='field',ydatacolumn='corrected')
Check velocity of TWHydra should be around 2.88 km/s
- CO 3-2 rest freq 345.79599 GHz
- HCO+ 4-3 rest freq 356.7342 GHz
# In CASA
plotms(vis='Band7multi_april22.ms',spw='2',xaxis='velocity',yaxis='amp',field='2',
avgtime='1e8',avgscan=T,transform=T,freqframe='LSRK',restfreq='345.79599GHz')
# In CASA
plotms(vis='Band7multi_april22.ms',spw='0',xaxis='velocity',yaxis='amp',field='2',
avgtime='1e8',avgscan=T,transform=T,freqframe='LSRK',restfreq='356.7342GHz')
