import re
import glob 

finalvis= '../semipass/calibrated_X1d0.ms'


# Use plotms to identify line and continuum spectral windows.
#>>> If you have a project with multiple fields, you will want to run
#>>> the following plotms command separately for each source. If the
#>>> spectra for each field are significantly different from each other,
#>>> it may be necessary to make separate average continuum  and
#>>> continuum-subtracted measurement sets for each field.

#plotms(vis=finalvis, xaxis='channel', yaxis='amplitude',
#       ydatacolumn='data',
#       avgtime='1e8', avgscan=True, avgchannel='1', 
#       iteraxis='spw' )

# Set spws to be used to form continuum
contspws = '17,19,21,23'

# Flag the "line channels"
flagchannels='19:63~72' # only applicable to Tune147 data

#for thisvis in finalvisall:
#    flagmanager(vis=thisvis,mode='save',
#                versionname='before_cont_flags')
#    initweights(vis=thisvis,wtmode='weight',dowtsp=True)
#    if (thisvis != '../minimosaic/calibrated_X164.ms' and thisvis != '../minimosaic/calibrated_X184.ms'):
#        flagdata(vis=thisvis,mode='manual',
#                 spw=flagchannels,flagbackup=False)
#    else:
#        print 'hi'

#for thisvis in ['../minimosaic/calibrated_X164.ms','../minimosaic/calibrated_X184.ms']:
#    flagmanager(vis=thisvis,mode='restore',
#                versionname='before_cont_flags')

flagmanager(vis=finalvis,mode='save',
            versionname='before_cont_flags')
initweights(vis=finalvis,wtmode='weight',dowtsp=True)
flagdata(vis=finalvis,mode='manual',
         spw=flagchannels,flagbackup=False)


#>>> In CASA 4.4 and higher, the behavior of the avgchannel parameter
#>>> has changed. Now when you plot binned channels, plotms displays
#>>> the "bin" number rather than the average channel number of each
#>>> bin. A ticket has been filed to revert this back to the previous
#>>> (more sensible) behavior, but this behavior hasn't been fixed as of CASA 5.1.

#>>> If you don't see any obvious lines in the above plot, you may to try
#>>> to set avgbaseline=True with uvrange (e.g., <100m). Limiting the
#>>> uvrange to the short baselines greatly improves the visibility of
#>>> lines with extended emission.

#>>> If you have multiple sources, the line channel ranges may be
#>>> different for different sources. Thus you would need to repeat the
#>>> process below for each source.



# If you have complex line emission and no dedicated continuum
# windows, you will need to flag the line channels prior to averaging.


#flagdata(vis=finalvis,mode='manual',
#          spw=flagchannels,flagbackup=False)

# check that flags are as expected, NOTE must check reload on plotms
# gui if its still open.

#contvis='calibrated_minimosaic_final_cont.ms'
#rmtables(contvis)
#os.system('rm -rf ' + contvis + '.flagversions')

contvis= 'calibrated_X1d0_cont_CORR.ms'
conttimevis='calibrated_X1d0_conttime_CORR.ms'
#>>> Note that to mitigate bandwidth smearing, please keep the width
#>>> of averaged channels less than 125MHz in Band 3, 4, and 6, and 250MHz
#>>> in Band 7 for both TDM and FDM modes. For example, for a 2GHz TDM window
#>>> with 15.625 MHz channels, this means that the maximum width parameter
#>>> should be 8 channels for Bands 3, 4, and 6 and 16 channels for Band 7.
#>>> This is especially important for any long baseline data. These limits
#>>> have been designed to have minimize the reduction of the peak flux to
#>>> 95%. See the "for continuum" header for more information on the imaging
#>>> wiki for more infomration.

#>>> Note that in CASA 5.1, split2 is now split. Previously split2 was
#>>> needed to deal correctly with channelized weights.
split(vis=finalvis,
      spw=contspws,
      outputvis=contvis,
      width=[8,8,8,8],
#      timebin='10s',
      datacolumn='data')

split(vis=finalvis,
      spw=contspws,
      outputvis=conttimevis,
      width=[8,8,8,8],
      timebin='10s',
      datacolumn='data')


# Check the weights. You will need to change antenna and field to
# appropriate values
plotms(vis=contvis, yaxis='wtsp',xaxis='freq',spw='',antenna='DA43',field='0')

## If you flagged any line channels, restore the previous flags
#for thisvis in finalvisall:
flagmanager(vis=finalvis,mode='restore',
            versionname='before_cont_flags')

# Inspect continuum for any problems
#plotms(vis=contvis,xaxis='uvdist',yaxis='amp',coloraxis='spw')