#!/usr/bin/env

"""

split, clean, and self-cal continuum and line data
  
NOTE: this is intended to be an interactive, iterative process
      so this is more a log that should be run by cutting and
      pasting into casa rather than as an executable script

      search "CHANGEME" for variables to be changed
      
10/9/15 MCA

"""



# ======================== Setup ===========================


# III_109
# 16:10:01.320 -39:06:44.899

field = 4                                     # CHANGEME 

file_ms = '../science_calibrated.ms'
contspw   = '2,3,4'
contspw_w = [128,3840,1920] 

robust     = 0.5
imsize     = [640,640]
cell       = '0.03arcsec'
imagermode = 'csclean'
refant     = 'DA52'                            # CHANGEME

xc         = 320                               # CHANGEME
yc         = 320                               # CHANGEME
in_a       = 80
out_a      = 120
aper       = 0.5                               # CHANGEME

boxwidth = 300.
box = rg.box([xc-boxwidth,yc-boxwidth],[xc+boxwidth,yc+boxwidth])



# ================ Split Off Continuum/Lines ===============

# split off field from full ms
split(vis = file_ms,
      outputvis = 'f'+str(field)+'.vis',
      field = field,
      datacolumn = 'data')

# split off continuum (take the large bw spw and average
split(vis = 'f'+str(field)+'.vis',
      outputvis = 'f'+str(field)+'_cont.vis',
      spw = contspw,
      width = contspw_w,
      datacolumn = 'data')

# plot uv-distance vs. amplitude (not resolved)
plotms(vis='f'+str(field)+'_cont.vis', xaxis='uvdist',yaxis='amp', coloraxis='spw',
        plotfile='f'+str(field)+'_ampuv_orig.png', showgui=False, highres=True, overwrite=True)

# find antenna close to center of configuration
# check pipeline log that this ant is OK
plotants(vis='f'+str(field)+'_cont.vis')          #, figfile='f'+str(field)+'_ants.png')



                        

                        
# ================== Clean continuum before selfcal ===================

# light clean (100 iterations) to set the mask around the main peaks
# os.system('rm -rf f'+str(field)+'_cont_best*')
clean(vis = 'f'+str(field)+'_cont.vis',
      imagename = 'f'+str(field)+'_cont_best',
      mode = 'mfs',
      psfmode = 'clark',
      niter = 100,
      threshold = '0.0mJy',
      interactive = False,
      mask = '',
      cell = cell,
      imsize = imsize,
      weighting = 'briggs',
      robust = robust,
      imagermode = imagermode)
# source not seen
# cleaned in automated mode without mask


im_max = imstat(imagename = 'f'+str(field)+'_cont_best.image')['max'][0]
im_rms = imstat(imagename = 'f'+str(field)+'_cont_best.image',
                region='annulus[['+str(xc)+'pix,'+str(yc)+'pix],['+str(in_a)+'pix,'+str(out_a)+'pix]]')['rms'][0]
bmaj = imhead(imagename = 'f'+str(field)+'_cont_best.image', mode="get", hdkey="beammajor")
bmin = imhead(imagename = 'f'+str(field)+'_cont_best.image', mode="get", hdkey="beamminor")
print 'Peak = {0:.2f} mJy, rms = {1:.2f} mJy, S/N = {2:.1f}'.format(1000*im_max, 1000*im_rms, im_max/im_rms)
print 'Beam = {0:.2f} x {1:.2f} arcsec'.format(bmaj.get('value'),bmin.get('value'))

# robust = 0.5
# Peak = 1.28 mJy, rms = 0.31 mJy, S/N = 4.1
# Beam = 0.33 x 0.30 arcsec

# save this to a fits file
exportfits(imagename='f'+str(field)+'_cont_best.image', fitsimage='f'+str(field)+'_cont.fits')

# measure flux
im_rms = imstat(imagename = 'f'+str(field)+'_cont_best.image',
                region='annulus[['+str(xc)+'pix,'+str(yc)+'pix],['+str(in_a)+'pix,'+str(out_a)+'pix]]')['rms'][0]
im_flux = imstat(imagename = 'f'+str(field)+'_cont_best.image',
                 region='circle[['+str(xc)+'pix,'+str(yc)+'pix],'+str(aper)+'arcsec]')['flux'][0]
print 'Flux = {0:.2f} mJy, rms = {1:.2f} mJy, S/N = {2:.1f}'.format(1000*im_flux, 1000*im_rms, im_flux/im_rms)
# Flux = 0.99 mJy, rms = 0.30 mJy, S/N = 3.3


# re-center image on source and use get_flux.py to get COG flux
ia.fromimage(outfile = 'f'+str(field)+'_cont_cropped.image',
             infile  = 'f'+str(field)+'_cont.fits',
             region  = box )
ia.close() 
exportfits(imagename = 'f'+str(field)+'_cont_cropped.image',
           fitsimage = 'f'+str(field)+'_cont_cropped.fits')



# ======================== Measure flux with UVMODELFIT ==================

# calculate offset from phase center in arcsec
pixscale = 0.03             # must match 'cell'                 
dx = pixscale*(320.0-xc)    # offset to east (left)
dy = pixscale*(yc-320.0)    # offset to north (up)


# measure flux as point source
uvmodelfit(vis       = 'f'+str(field)+'_cont.vis',
           comptype  = 'P',
           sourcepar = [im_flux,dx,dy],
           varypar   = [T,F,F],
           niter     = 10)
'''

reduced chi2=1.3947
I = 0.000326575 +/- 0.000246813
x = 0 +/- 0 arcsec
y = 0 +/- 0 arcsec

consistent with aperture method
non-detection so won't try gaussian

'''