*****************
Getting the Data
******************
The complete package (4.1G) is available here:
https://bulk.cv.nrao.edu/almadata/public/working/sis14_twhya.tgz

tar -xvzf sis14_twhya.tar.gz

cd working
tar -xvf sis14_twhya_calibrated_flagged.ms.tar

******************
Starting CASA
******************

casa

******************
Using tasks, and getting oriented with the data
******************

listobs(vis='sis14_twhya_calibrated_flagged.ms')

******************
Inspecting the data
******************

plotms(vis='sis14_twhya_calibrated_flagged.ms', xaxis='u', yaxis='v', avgchannel='10000', avgspw=False, avgtime='1e9', avgscan=False, coloraxis="field", showgui=True)

*******************
First Look at TCLEAN
*******************

os.system('rm -rf phase_cal.*')

tclean(vis='sis14_twhya_calibrated_flagged.ms',
       imagename='phase_cal',
       field='3',
       spw='',
       specmode='mfs',
       deconvolver='hogbom',
       gridder='standard',
       imsize=[128,128],
       cell=['0.1arcsec'],
       weighting='briggs',
       threshold='0.0mJy',
       interactive=True)

os.system('rm -rf phase_cal.*')

tclean(vis='sis14_twhya_calibrated_flagged.ms',
       imagename='phase_cal',
       field='3',
       spw='',
       specmode='mfs',
       deconvolver='hogbom',
       gridder='standard',
       imsize=[128,128],
       cell=['0.1arcsec'],
       weighting='briggs',
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("phase_cal.image")

****************************
Experiment with TCLEAN
***************************

os.system('rm -rf phase_cal_robust.*')

tclean(vis='sis14_twhya_calibrated_flagged.ms',
       imagename='phase_cal_robust',
       field='3',
       spw='',
       specmode='mfs',
       gridder='standard',
       deconvolver='hogbom',
       imsize=[128,128],
       cell=['0.1arcsec'],
       weighting='briggs',
       robust=-1.0,
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("phase_cal_robust.image")

os.system('rm -rf amp_cal_robust.*')

tclean(vis='sis14_twhya_calibrated_flagged.ms',
       imagename='amp_cal_robust',
       field='2',
       spw='',
       specmode='mfs',
       gridder='standard',
       deconvolver='hogbom',
       imsize=[128,128],
       cell=['0.1arcsec'],
       weighting='briggs',
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("amp_cal_robust.image")

os.system('rm -rf amp_cal_bigpix.*')

tclean(vis='sis14_twhya_calibrated_flagged.ms',
       imagename='amp_cal_bigpix',
       field='2',
       spw='',
       specmode='mfs', 
       gridder='standard',
       deconvolver='hogbom',
       imsize=[32,32],
       cell=['0.5arcsec'],
       weighting='briggs',
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("amp_cal_bigpix.image")

*****************************
ASIDE: See the effects of calibration and flagging
*****************************

os.system("tar -xvf ../working/sis14_twhya_uncalibrated.ms.tar")
os.system("rm -rf sis14_twhya_uncalibrated.ms")
os.system("cp -r ../working/sis14_twhya_uncalibrated.ms .")

os.system('rm -rf phase_cal_uncalibrated.*')
tclean(vis='sis14_twhya_uncalibrated.ms',
       imagename='phase_cal_uncalibrated',
       field='3',
       spw='',
       specmode='mfs',
       gridder='standard',
       deconvolver='hogbom',
       imsize=[128,128],
       cell=['0.1arcsec'],
       weighting='natural',
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("phase_cal_uncalibrated.image")

os.system("tar -xvf ../working/sis14_twhya_calibrated.ms.tar")
os.system("rm -rf sis14_twhya_calibrated.ms")
os.system("cp -r ../working/sis14_twhya_calibrated.ms .")

os.system('rm -rf phase_cal_unflagged.*')

tclean(vis='sis14_twhya_calibrated.ms',
       imagename='phase_cal_unflagged',
       field='3',
       spw='',
       specmode='mfs',
       gridder='standard',
       deconvolver='hogbom',
       imsize=[128,128],
       cell=['0.1arcsec'],
       weighting='natural',
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("phase_cal_unflagged.image")

****************************
Image the science target
****************************

os.system('rm -rf twhya_smoothed.ms')

flagdata(vis='sis14_twhya_calibrated_flagged.ms',
         spw='0:244~244',action='apply', flagbackup=False)



split(vis='sis14_twhya_calibrated_flagged.ms', field='5', width='8', outputvis='twhya_smoothed.ms', datacolumn='data')

listobs('twhya_smoothed.ms')

os.system('rm -rf twhya_cont.*')

tclean(vis='twhya_smoothed.ms',
       imagename='twhya_cont',
       field='0',
       spw='',
       specmode='mfs',
       gridder='standard',
       deconvolver='hogbom',
       imsize=[250,250],
       cell=['0.08arcsec'],
       weighting='briggs',
       robust=0.5,
       threshold='0mJy',
       niter=5000,
       interactive=True)

imview("twhya_cont.image")

*****************************
Non-interactive clean
*****************************

os.system('rm -rf twhya_cont_auto.*')

tclean(vis='twhya_smoothed.ms',
       imagename='twhya_cont_auto',
       field='0',
       spw='',
       specmode='mfs',
       gridder='standard',
       deconvolver='hogbom',
       imsize=[250,250],
       cell=['0.08arcsec'],
       mask='box [ [ 100pix , 100pix] , [150pix, 150pix ] ]',
       weighting='briggs',
       robust=0.5,
       threshold='15mJy',
       niter=10000,
       interactive=False)

imview('twhya_cont_auto.image')

******************************
Primary beam correction
******************************

os.system('rm -rf twhya_cont.pbcor.image')

impbcor(imagename='twhya_cont.image',
        pbimage='twhya_cont.pb',
        outfile='twhya_cont.pbcor.image')

imview('twhya_cont.pbcor.image')