def plot_selfcal(self, caltable, xaxis="", yaxis="", timerange="", iteration="", antenna="", subplot=111, plotrange=[], want_plot=False, **kwargs):
figfile_name = caltable + ".png"
if want_plot:
plotcal(caltable=caltable, xaxis=xaxis, yaxis=yaxis, timerange=timerange,
iteration=iteration, subplot=subplot, antenna=antenna, plotrange=plotrange, figfile=figfile_name, showgui=True)
else:
plotcal(caltable=caltable, xaxis=xaxis, yaxis=yaxis, timerange=timerange,
iteration=iteration, subplot=subplot, antenna=antenna, plotrange=plotrange, figfile=figfile_name, showgui=False)
def selfcal(vis, spwn=6, doplots=True, INTERACTIVE=False, reclean=True, field='W51 Ku',
outdir_template="spw%i_selfcal_iter/", statsbox='170,50,229,97', ant1list=['ea14','ea05'],
ant2list=['ea16','ea07'], avgchannel_wide='128', avgchannel_narrow='8',
cleanboxes=cleanboxes, refant='ea27', solint='30s', niter=2,
multiscale=[0,5,10,15,25,50], imsize=512, robust=0.0 ):
"""
Docstring incomplete
"""
spw = int(spwn)
outdir = outdir_template % spwn
try:
os.mkdir(outdir)
except OSError:
pass
# you're supposed to pass in avg_data as input
avg_data = vis
mytb.open(vis+"/ANTENNA")
antnames = mytb.getcol("NAME")
# plot each antenna's ampl vs time for flagging purposes
for ant2 in ant2list:
for ant in ant1list:
plotms(vis=vis, spw=str(spwn), xaxis='time', yaxis='amp', avgchannel=avgchannel_wide,
avgscan=F, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
antenna=ant+"&"+ant2,
title='Amp vs Time before averaging for spw %i ant %s-%s' % (spwn,ant,ant2),
plotfile=outdir+'ampvstime_spw%i_ant%s-%s.png' % (spwn,ant,ant2),
field=field,
overwrite=True,
)
plotms(vis=vis, spw=str(spwn), xaxis='freq', yaxis='phase', avgtime='1e8',
avgscan=T, coloraxis='corr', iteraxis='baseline', xselfscale=T,
yselfscale=T,
antenna=ant+"&"+ant2,
title='Phase vs Freq with time averaging for spw %i ant %s-%s' % (spwn,ant,ant2),
plotfile=outdir+'phasevsfreq_spw%i_ant%s-%s.png' % (spwn,ant,ant2),
field=field,
overwrite=True,
)
plotms(vis=vis, spw=str(spwn), xaxis='amp', yaxis='phase', avgtime='1e8',
avgscan=T, coloraxis='corr', iteraxis='baseline', xselfscale=T,
yselfscale=T,
antenna=ant+"&"+ant2,
title='Phase vs Amp with time averaging for spw %i ant %s-%s' % (spwn,ant,ant2),
plotfile=outdir+'phasevsamp_spw%i_ant%s-%s.png' % (spwn,ant,ant2),
field=field,
overwrite=True,
)
# imagename = "noaverage_spw%i" % spwn
# os.system("rm -rf "+imagename+".image")
# os.system("rm -rf "+imagename+".model")
# os.system("rm -rf "+imagename+".flux")
# os.system("rm -rf "+imagename+".psf")
# os.system("rm -rf "+imagename+".residual")
# clean(vis=vis, field=field, imagename=imagename, mode='mfs',
# weighting='briggs', robust=robust, niter=500, imsize=512)
# viewer(imagename+".image",
# outfile=outdir+imagename+".image.png",
# outformat='png',
# gui=False)
# exportfits(imagename=imagename+".image", fitsimage=imagename+".fits", overwrite=True)
#width = 10 # for TW Hydra
# width = 4 # for NGC 3256
# (0) Using your split-off, calibrated data, plot the "model" in this MS using
# plotms. It should be unit-valued for all data. If not, run delmod to get
# rid of any model that might still be lurking in the header, and/or clearcal
# to set to 1 any MODEL data.
plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp',
avgchannel=avgchannel_wide, xdatacolumn='model', ydatacolumn='model', avgscan=F,
coloraxis='baseline', iteraxis='', xselfscale=T, yselfscale=T,
title='Model Amp vs Time after split for spw %i. Should be all 1s' % spwn,
plotfile=outdir+'ampvstime_model_shouldbe1.png', field=field,
overwrite=True,)
delmod(vis=avg_data)
plotms(vis=avg_data, spw='0', xaxis='phase', yaxis='amp',
avgchannel=avgchannel_wide, xdatacolumn='data', ydatacolumn='data', avgscan=F,
coloraxis='baseline', iteraxis='', xselfscale=T, yselfscale=T,
title='Corrected Phase vs Amp after split',
plotfile=outdir+'ampvsphase_corrected_avg_spw%i.png' % spwn, field=field,
overwrite=True,)
# (0.5) Run clean non-interactively with some set number of iterations, and be
# sure to keep the image around for comparison later. Run delmod to get rid of
# the model it saved to the MS header.
#if reclean:
# imagename="average_spw%i_shallowclean" % spwn
# for suffix in clean_output_suffixes:
# os.system("rm -rf "+imagename+suffix)
# clean(vis=avg_data, field=field, imagename=imagename, mode='mfs',
# weighting='briggs', robust=robust, niter=100, imsize=512)
# viewer(imagename+".image",
# outfile=outdir+imagename+".image.png",
# outformat='png',
# gui=False)
# exportfits(imagename=imagename+".image", fitsimage=imagename+".fits", overwrite=True)
# delmod(avg_data,scr=True)
# (1) Clean a single SPW *interactively*, boxing the brightest regions and not
# cleaning very deeply (maybe 100 iterations). Keep this model in the header
# -- it's what you'll use for the first round of self-calibration.
if reclean:
imagename="average_spw%i_shallowclean_masked" % spwn
for suffix in clean_output_suffixes:
os.system("rm -rf "+imagename+suffix)
clean(vis=avg_data, field=field, imagename=imagename, mode='mfs',
psfmode='hogbom',multiscale=multiscale,
weighting='briggs', robust=robust, niter=100, imsize=imsize,
mask=cleanboxes,
nterms=2,
usescratch=True)
viewer(imagename+".image.tt0",
outfile=outdir+imagename+".image.tt0.png",
outformat='png',
gui=False)
exportfits(imagename=imagename+".image.tt0", fitsimage=imagename+".fits", overwrite=True)
imrms = [imstat(imagename+".image.tt0",box=statsbox)['rms']]
# FAILS!!!!
#plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp',
# avgchannel='128', xdatacolumn='model', ydatacolumn='model', avgscan=F,
# coloraxis='baseline', iteraxis='', xselfscale=T, yselfscale=T,
# title='Model Amp vs Time after shallow clean for spw %i.' % spwn,
# plotfile=outdir+'ampvstime_model_shallowclean_spw%i.png' % spwn, field=field,
# overwrite=True,)
for calnum in xrange(niter):
# for Ku D W51 Ku spw 2
if reclean:
first_image = 'spw%i_C_C_firstim_selfcal%i' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+first_image+suffix)
clean(vis=avg_data,imagename=first_image,field=field, mode='mfs',
psfmode='hogbom',multiscale=multiscale,
weighting='briggs', robust=robust, niter=100, imsize=imsize,
mask=cleanboxes,
nterms=2,
usescratch=True)
exportfits(imagename=first_image+".image.tt0", fitsimage=first_image+".fits", overwrite=True)
viewer(first_image+".image.tt0",
outfile=outdir+first_image+".image.tt0.png",
outformat='png',
gui=False)
# this fails?
#plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp',
# avgchannel='128', xdatacolumn='model', ydatacolumn='model', avgscan=F,
# coloraxis='baseline', iteraxis='', xselfscale=T, yselfscale=T,
# title='Model Amp vs Time after shallow clean for spw %i iter %i.' % (spwn,calnum),
# plotfile=outdir+'ampvstime_model_shallowclean_spw%i_iter%i.png' % (spwn,calnum), field=field,
# overwrite=True,)
# DONE avg/split ing
caltable = 'selfcal%i_%s_spw%i.gcal' % (calnum,field.replace(" ",""),spwn)
if reclean:
os.system('rm -rf '+caltable)
gaincal(vis=avg_data,
field='',
caltable=caltable,
spw='',
# gaintype = 'T' could reduce failed fit errors by averaging pols...
gaintype='G', # 'G' from http://casaguides.nrao.edu/index.php?title=EVLA_Advanced_Topics_3C391
solint=solint,
refant=refant,
calmode='p',
combine='scan',
minblperant=4)
#
# Watch out for failed solutions noted in the terminal during this
# solution. If you see a large fraction (really more than 1 or 2) of
# your antennas failing to converge in many time intervals then you
# may need to lengthen the solution interval.
#
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
# INSPECT THE CALIBRATION
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
#
# After you have run the gaincal, you want to inspect the
# solution. Use PLOTCAL to look at the solution (here broken into
# panels by SPW with individual antennas mapped to colors). Look at
# the overall magnitude of the correction to get an idea of how
# important the selfcal is and at how quickly it changes with time to
# get an idea of how stable the instrument and atmosphere were.
#
if doplots:
for ant2 in ant2list:
for ant in ant1list:
# (4) Have a look at the gain solutions by antenna. Which antennas
# have the largest phase corrections? Before applying the
# calibration, use plotms to display the corrected phase vs. amp
# for these antennas, to compare with *after* the correction is
# applied.
plotcal(caltable=caltable,
xaxis='time', yaxis='phase',
showgui=False,
antenna=ant+'&'+ant2,
figfile=outdir+'selfcal%i_spw%i_phasevstime_ant%s-%s.png' % (calnum,spwn,ant,ant2),
iteration='')#, subplot = 221)
#plotcal(caltable=caltable, xaxis='amp', yaxis='phase',
# showgui=False,
# antenna=ant,
# figfile=outdir+'selfcal%i_spw%i_phasevsamp_ant%s.png' % (calnum,spwn,ant),
# iteration='')#, subplot = 221)
if calnum == 0:
datacol='data'
else:
datacol='corrected'
plotms(vis=avg_data, xaxis='time', yaxis='phase',
xdatacolumn=datacol, ydatacolumn=datacol,
avgtime='15s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s. datacol=%s' % (calnum,spwn,ant,ant2,datacol),
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phasetime.png' % (calnum,spwn,ant,ant2),)
plotms(vis=avg_data, xaxis='time', yaxis='amp',
xdatacolumn=datacol, ydatacolumn=datacol,
avgtime='15s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s. datacol=%s' % (calnum,spwn,ant,ant2,datacol),
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_amptime.png' % (calnum,spwn,ant,ant2),)
plotms(vis=avg_data, xaxis='phase', yaxis='amp',
xdatacolumn=datacol, ydatacolumn=datacol,
avgtime='60s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s. datacol=%s' % (calnum,spwn,ant,ant2,datacol),
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phaseamp.png' % (calnum,spwn,ant,ant2),)
plotcal(caltable=caltable,
xaxis='time', yaxis='phase',
plotrange=[0,0,-180,180],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_phasevstime.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
plotcal(caltable=caltable,
xaxis='antenna', yaxis='phase',
showgui=INTERACTIVE,
figfile=outdir+'selfcal%i_spw%i_phasevsantenna.png' % (calnum,spwn),
iteration='')
plotcal(caltable=caltable,
xaxis='time', yaxis='amp',
plotrange=[0,0,0.5,1.5],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvstime.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
#plotcal(caltable=caltable,
# xaxis='phase', yaxis='amp',
# plotrange=[-50,50,0.5,1.5],
# showgui=INTERACTIVE,
# figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvsphase.png' % (calnum,spwn),
# iteration='spw' if INTERACTIVE else '')#, subplot = 221)
# THERE WILL BE WEIRD "LUSTRE" ERRORS GENERATED BY THE FILE SYSTEM. DO
# NOT FREAK OUT. These are just a feature of our fast file
# system. Plotcal will still work.
# It can be useful useful to plot the X-Y solutions (i.e., differences
# between polarizations) as an indicator of the noise in the
# solutions.
plotcal(caltable=caltable,
xaxis='time',
yaxis='phase',
plotrange=[0,0,-25, 25],
poln = '/',
showgui=INTERACTIVE,
iteration='spw,antenna' if INTERACTIVE else '',
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_poldiff.png' % (calnum,spwn),
subplot = 221 if INTERACTIVE else 111)
plotms(vis=avg_data,
xaxis='uvdist',
yaxis='amp',
xdatacolumn='corrected',
ydatacolumn='corrected',
avgtime='1e8s',
avgchannel=avgchannel_narrow,
coloraxis='baseline',
overwrite=True,
title='Iteration %i for spw %i' % (calnum,spw),
plotfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_uvdistamp.png' % (calnum,spwn),
)
#plotms(vis=avg_data,
# xaxis='phase',
# yaxis='amp',
# xdatacolumn='corrected',
# ydatacolumn='corrected',
# avgtime='60s',
# avgchannel=avgchannel_narrow,
# coloraxis='corr',
# overwrite=True,
# title='Iteration %i for spw %i' % (calnum,spw),
# plotfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_phaseamp.png' % (calnum,spwn),
# )
plotms(vis=avg_data,
xaxis='time',
yaxis='amp',
xdatacolumn='corrected',
ydatacolumn='corrected',
avgtime='10s',
avgchannel=avgchannel_narrow,
coloraxis='baseline',
overwrite=True,
title='Iteration %i for spw %i' % (calnum,spw),
plotfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_amptime.png' % (calnum,spwn),
)
# The rms noise is about 4 to 8 deg, depending on antenna, but the
# phase changes are considerably larger. This indicates that the
# application of this solution will improve the image.
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
# APPLY THE CALIBRATION
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
#
# If you are satisfied with your solution, you can now apply it to the
# data to generate a new corrected data column, which you can then
# image. Be sure to save the previous flags before you do so because
# applycal will flag data without good solutions. The commented
# command after the applycal will roll back to the saved solution in
# case you get in trouble.
#
# flagmanager(vis=avg_data,
# mode='save',
# versionname='before_selfcal_apply')
# 2013-03-04 19:53:37 SEVERE agentflagger:: (file /opt/casa/stable-2013-02/gcwrap/tools/flagging/agentflagger_cmpt.cc, line 37) Exception Reported: Invalid Table operation: ArrayColumn::setShape; shape cannot be changed for row 0 column FLAG
# *** Error *** Invalid Table operation: ArrayColumn::setShape; shape cannot be changed for row 0 column FLAG
if reclean:
applycal(vis=avg_data,
gaintable=caltable,
interp='linear',
flagbackup=True) # was False when flagmanager was used
# (6) Plot corrected phase vs. amp for the antennas you picked out in (4),
# to check that in fact the corrections have been applied as expected.
for ant2 in ant2list:
for ant in ant1list:
plotms(vis=avg_data, xaxis='time', yaxis='phase',
xdatacolumn='corrected', ydatacolumn='corrected',
avgtime='15s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s' % (calnum,spwn,ant,ant2),
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phasetime_applied.png' % (calnum,spwn,ant,ant2),)
plotms(vis=avg_data, xaxis='time', yaxis='amp',
xdatacolumn='corrected', ydatacolumn='corrected',
avgtime='60s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s' % (calnum,spwn,ant,ant2),
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_amptime_applied.png' % (calnum,spwn,ant,ant2),)
plotms(vis=avg_data, xaxis='phase', yaxis='amp',
xdatacolumn='corrected', ydatacolumn='corrected',
avgtime='60s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s' % (calnum,spwn,ant,ant2),
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phaseamp_applied.png' % (calnum,spwn,ant,ant2),)
plotms(vis=vis, spw='0', xaxis='freq', yaxis='phase', avgtime='1e8',
avgscan=T, coloraxis='corr', iteraxis='baseline', xselfscale=T,
yselfscale=T,
antenna=ant+'&'+ant2,
title='Phase vs Freq with time averaging for spw %i ant %s-%s iter %i' % (spwn,ant,ant2,calnum),
plotfile=outdir+'phasevsfreq_spw%i_ant%s-%s_selfcal%i.png' % (spwn,ant,ant2,calnum),
field=field,
overwrite=True,
)
# Use this command to roll back to the previous flags in the event of
# an unfortunate applycal.
#flagmanager(vis=avg_data,
# mode='restore',
# versionname='before_selfcal_apply')
if reclean:
selfcal_image = 'spw%i_C_C_selfcal%i' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=avg_data,imagename=selfcal_image,field=field, mode='mfs',
psfmode='hogbom',multiscale=multiscale,
weighting='briggs', robust=robust, niter=1000, imsize=imsize,
nterms=2,
mask=cleanboxes,
usescratch=True)
exportfits(imagename=selfcal_image+".image.tt0", fitsimage=selfcal_image+".fits", overwrite=True)
plotms(vis=avg_data, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after CSCLEAN iter %i' % calnum,
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after CSCLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after CSCLEAN iter %i' % (calnum) ,
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist.png' % (calnum,spwn),
field=field,
overwrite=True,
)
imrms.append(imstat(selfcal_image+".image.tt0",box=statsbox)['rms'])
viewer(selfcal_image+".image.tt0",
outfile=outdir+selfcal_image+".image.tt0.png",
outformat='png',
gui=False)
print "FINISHED ITERATION %i" % calnum
print "FINISHED ITERATING!!! YAY!"
# final phase + gain cal:
# http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey#One_Last_Iteration:_Amplitude_.26_Phase_Self_Calibration
aptable = 'selfcal_ap_%s_spw%i.gcal' % (field.replace(" ",""),spwn)
gaincal(vis=avg_data, field='', caltable=aptable, gaintable=caltable, spw='',
solint='inf', refant=refant, calmode='ap', combine='', minblperant=4)
plotcal(caltable=aptable,
xaxis='phase', yaxis='amp',
plotrange=[-50,50,0.5,1.5],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvsphase_final.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
applycal(vis=avg_data,
gaintable=[aptable,caltable],
interp='linear',
flagbackup=True) # was False when flagmanager was used
selfcal_image = 'spw%i_C_C_selfcal%i_final' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=avg_data,imagename=selfcal_image,field=field, mode='mfs', mask=cleanboxes,
weighting='briggs', robust=robust, niter=10000, imsize=imsize,
nterms=2,
usescratch=True)
exportfits(imagename=selfcal_image+".image.tt0", fitsimage=selfcal_image+".fits", overwrite=True)
plotms(vis=avg_data, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after CSCLEAN iter %i' % calnum,
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after CSCLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after CSCLEAN iter %i' % (calnum) ,
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist.png' % (calnum,spwn),
field=field,
overwrite=True,
)
selfcal_image = 'spw%i_C_C_selfcal%i_final_multiscale' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=avg_data,imagename=selfcal_image,field=field, mode='mfs', imagermode='csclean',# mask=cleanboxes,
multiscale=multiscale, psfmode='hogbom',
nterms=2,
weighting='briggs', robust=robust, niter=10000, imsize=imsize,
usescratch=True)
exportfits(imagename=selfcal_image+".image.tt0", fitsimage=selfcal_image+".fits", overwrite=True)
plotms(vis=avg_data, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
return imrms
def split_and_cal(rootvis, rootprefix, spwn, fluxcal, phasecal, target,
anttable=[], fieldpre=[], fresh_clean=False):
print "Beginning calibration and mapping of spw ", spwn
prefix = rootprefix+"_spw"+spwn
# hopefully this decreases read/write times...
vis = outvis = prefix+".ms"
split(vis=rootvis, outputvis=outvis, spw=spwn, datacolumn='all')
listobs(outvis)
plotants(vis=vis,figfile=prefix+'plotants_'+vis+".png")
#plotms(vis=vis, xaxis='', yaxis='', averagedata=False, transform=False, extendflag=False,
# plotfile='FirstPlot_AmpVsTime.png',selectdata=True,field='')
plotms(vis=vis, spw='0', averagedata=True, avgchannel='64', avgtime='5', xaxis='uvdist', yaxis='amp', field=phasecal, plotfile=prefix+"phasecal_%s_AmpVsUVdist_spw%s.png" % (phasecal,spwn),overwrite=True)
plotms(vis=vis, spw='0', averagedata=True, avgchannel='64', avgtime='5', xaxis='uvdist', yaxis='amp', field=fluxcal, plotfile=prefix+"fluxcal_%s_AmpVsUVdist_spw%s.png" % (fluxcal,spwn),overwrite=True)
plotms(vis=vis, spw='0', averagedata=True, avgchannel='64', avgtime='5', xaxis='uvdist', yaxis='amp', field=target, plotfile=prefix+"target_%s_AmpVsUVdist_spw%s.png" % (target,spwn),overwrite=True)
plotms(vis=vis, field='',correlation='RR,LL',timerange='',antenna='ea01',spw='0',
xaxis='time',yaxis='antenna2',coloraxis='field',plotfile=prefix+'antenna2vsantenna1vstime_spw%s.png' % spwn,overwrite=True)
#gencal(vis=vis,caltable=prefix+".antpos",caltype="antpos")
# this apparently doubles the data size... clearcal(vis=vis,field='',spw='')
#setjy(vis=vis, listmodels=T)
gaincal(vis=vis, caltable=prefix+'.G0all',
field='0,1', refant='ea21', spw='0:32~96',
gaintype='G',calmode='p', solint='int',
minsnr=5, gaintable=anttable)
#didn't work
plotcal(caltable=prefix+'.G0all',xaxis='time',yaxis='phase',
spw='0',
poln='R',plotrange=[-1,-1,-180,180],
figfile=prefix+'.G0all.png')
gaincal(vis=vis, caltable=prefix+'.G0',
field=fluxcal, refant='ea21', spw='0:20~100', calmode='p', solint='int',
minsnr=5, gaintable=anttable)
plotcal(caltable=prefix+'.G0',xaxis='time',yaxis='phase',
spw='0',
poln='R',plotrange=[-1,-1,-180,180],
figfile=prefix+'.G0.png')
gaincal(vis=vis,caltable=prefix+'.K0',
field=fluxcal,refant='ea21',spw='0:5~123',gaintype='K',
solint='inf',combine='scan',minsnr=5,
gaintable=anttable+[
prefix+'.G0'])
plotcal(caltable=prefix+'.K0',xaxis='antenna',yaxis='delay',
spw='0',
figfile=prefix+'.K0_delayvsant_spw'+spwn+'.png')
bandpass(vis=vis,caltable=prefix+'.B0',
field=fluxcal,spw='0',refant='ea21',solnorm=True,combine='scan',
solint='inf',bandtype='B',
gaintable=anttable+[
prefix+'.G0',
prefix+'.K0'])
# In CASA
plotcal(caltable= prefix+'.B0',poln='R',
spw='0',
xaxis='chan',yaxis='amp',field=fluxcal,subplot=221,
figfile=prefix+'plotcal_fluxcal-B0-R-amp_spw'+spwn+'.png')
#
plotcal(caltable= prefix+'.B0',poln='L',
spw='0',
xaxis='chan',yaxis='amp',field=fluxcal,subplot=221,
figfile=prefix+'plotcal_fluxcal-B0-L-amp_spw'+spwn+'.png')
#
plotcal(caltable= prefix+'.B0',poln='R',
spw='0',
xaxis='chan',yaxis='phase',field=fluxcal,subplot=221,
plotrange=[-1,-1,-180,180],
figfile=prefix+'plotcal_fluxcal-B0-R-phase_spw'+spwn+'.png')
#
plotcal(caltable= prefix+'.B0',poln='L',
spw='0',
xaxis='chan',yaxis='phase',field=fluxcal,subplot=221,
plotrange=[-1,-1,-180,180],
figfile=prefix+'plotcal_fluxcal-B0-L-phase_spw'+spwn+'.png')
gaincal(vis=vis,caltable=prefix+'.G1',
field=fluxcal,spw='0:5~123',
solint='inf',refant='ea21',gaintype='G',calmode='ap',solnorm=F,
gaintable=anttable+[
prefix+'.K0',
prefix+'.B0'])
gaincal(vis=vis,caltable=prefix+'.G1',
field=phasecal,
spw='0:5~123',solint='inf',refant='ea21',gaintype='G',calmode='ap',
gaintable=anttable+[
prefix+'.K0',
prefix+'.B0'],
append=True)
plotcal(caltable=prefix+'.G1',xaxis='time',yaxis='phase',
spw='0',
poln='R',plotrange=[-1,-1,-180,180],figfile=prefix+'plotcal_fluxcal-G1-phase-R_spw'+spwn+'.png')
plotcal(caltable=prefix+'.G1',xaxis='time',yaxis='phase',
spw='0',
poln='L',plotrange=[-1,-1,-180,180],figfile=prefix+'plotcal_fluxcal-G1-phase-L_spw'+spwn+'.png')
plotcal(caltable=prefix+'.G1',xaxis='time',yaxis='amp',
spw='0',
poln='R',figfile=prefix+'plotcal_fluxcal-G1-amp-R_spw'+spwn+'.png')
plotcal(caltable=prefix+'.G1',xaxis='time',yaxis='amp',
spw='0',
poln='L',figfile=prefix+'plotcal_fluxcal-G1-amp-L_spw'+spwn+'.png')
myscale = fluxscale(vis=vis,
caltable=prefix+'.G1',
fluxtable=prefix+'.fluxscale1',
reference=[fluxcal],
transfer=[phasecal])
applycal(vis=vis,
field=fluxcal,
spw='0',
gaintable=anttable+[
prefix+'.fluxscale1',
prefix+'.K0',
prefix+'.B0',
],
gainfield=fieldpre+[fluxcal,'',''],
interp=fieldpre+['nearest','',''],
calwt=F)
applycal(vis=vis,
field=phasecal,
spw='0',
gaintable=anttable+[
prefix+'.fluxscale1',
prefix+'.K0',
prefix+'.B0',
],
gainfield=fieldpre+[phasecal,'',''],
interp=fieldpre+['nearest','',''],
calwt=F)
applycal(vis=vis,
field=target,
spw='0',
gaintable=anttable+[
prefix+'.fluxscale1',
prefix+'.K0',
prefix+'.B0',
],
gainfield=fieldpre+[phasecal,'',''],
interp=fieldpre+['linear','',''],
calwt=F)
plotms(vis=prefix+'.ms',field=fluxcal,correlation='',
spw='0',
antenna='',avgtime='60s',
xaxis='channel',yaxis='amp',ydatacolumn='corrected',
plotfile=prefix+'_fluxcal-corrected-amp_spw'+spwn+'.png',overwrite=True)
#
plotms(vis=prefix+'.ms',field=fluxcal,correlation='',
spw='0',
antenna='',avgtime='60s',
xaxis='channel',yaxis='phase',ydatacolumn='corrected',
plotrange=[-1,-1,-180,180],coloraxis='corr',
plotfile=prefix+'_fluxcal-corrected-phase_spw'+spwn+'.png',overwrite=True)
#
plotms(vis=prefix+'.ms',field=phasecal,correlation='RR,LL',
spw='0',
timerange='',antenna='',avgtime='60s',
xaxis='channel',yaxis='amp',ydatacolumn='corrected',
plotfile=prefix+'_phasecal-corrected-amp_spw'+spwn+'.png',overwrite=True)
#
plotms(vis=prefix+'.ms',field=phasecal,correlation='RR,LL',
spw='0',
timerange='',antenna='',avgtime='60s',
xaxis='channel',yaxis='phase',ydatacolumn='corrected',
plotrange=[-1,-1,-180,180],coloraxis='corr',
plotfile=prefix+'_phasecal-corrected-phase_spw'+spwn+'.png',overwrite=True)
plotms(vis=prefix+'.ms',field=phasecal,correlation='RR,LL',
spw='0',
timerange='',antenna='',avgtime='60s',
xaxis='phase',xdatacolumn='corrected',yaxis='amp',ydatacolumn='corrected',
plotrange=[-180,180,0,3],coloraxis='corr',
plotfile=prefix+'_phasecal-corrected-ampvsphase_spw'+spwn+'.png',overwrite=True)
plotms(vis=vis,xaxis='uvwave',yaxis='amp',
spw='0',
field=fluxcal,avgtime='30s',correlation='RR',
plotfile=prefix+'_fluxcal-mosaic0-uvwave_spw'+spwn+'.png',overwrite=True)
plotms(vis=vis,xaxis='uvwave',yaxis='amp',
spw='0',
field=target,avgtime='30s',correlation='RR',
plotfile=prefix+'_target-mosaic0-uvwave_spw'+spwn+'.png',overwrite=True)
for antenna in xrange(28):
plotms(vis=vis, xaxis='time', yaxis='amp', spw='0',
field='', avgchannel='64', coloraxis='corr',
avgtime='5s',
antenna='%i' % antenna,
plotfile=prefix+"_antenna%02i_ampVStime.png" % antenna,
overwrite=True)
imagename = prefix+"_mfs"
if fresh_clean:
shutil.rmtree(imagename+".model")
shutil.rmtree(imagename+".image")
shutil.rmtree(imagename+".psf")
shutil.rmtree(imagename+".flux")
shutil.rmtree(imagename+".residual")
clean(vis=outvis,
imagename=imagename,
field=target,spw='',
mode='mfs', # use channel to get cubes
nterms=1, # no linear polynomial
niter=5000,
gain=0.1, threshold='1.0mJy',
psfmode='clark',
multiscale=[0],
interactive=False,
imsize=[2560,2560],
cell=['0.1arcsec','0.1arcsec'],
stokes='I',
weighting='uniform',
allowchunk=True,
usescratch=True)
exportfits(imagename=imagename+".image", fitsimage=imagename+".fits", overwrite=True)
print "Finished spw ",spwn
def selfcal(vis, spwn=6, doplots=True, INTERACTIVE=False, reclean=True, field='W51 Ku',
outdir_template="spw%i_selfcal_iter/", statsbox='170,50,229,97', ant1list=['ea14','ea05'],
ant2list=['ea16','ea07'], avgchannel_wide='128', avgchannel_narrow='8',
cleanboxes=cleanboxes, refant='ea27', solint='30s', niter=2,
multiscale=[0,5,10,15,25,50], imsize=512, ):
"""
Docstring incomplete
"""
spw = int(spwn)
outdir = outdir_template % spwn
try:
os.mkdir(outdir)
except OSError:
pass
# you're supposed to pass in avg_data as input
avg_data = vis
mytb.open(vis+"/ANTENNA")
antnames = mytb.getcol("NAME")
# (1) Clean a single SPW *interactively*, boxing the brightest regions and not
# cleaning very deeply (maybe 100 iterations). Keep this model in the header
# -- it's what you'll use for the first round of self-calibration.
if reclean:
imagename="average_spw%i_shallowclean_masked" % spwn
for suffix in clean_output_suffixes:
os.system("rm -rf "+imagename+suffix)
clean(vis=avg_data, field=field, imagename=imagename, mode='mfs',
psfmode='hogbom',multiscale=multiscale,
weighting='briggs', robust=0.0, niter=100, imsize=imsize,
mask=cleanboxes,
nterms=2,
usescratch=True)
viewer(imagename+".image.tt0",
outfile=outdir+imagename+".image.tt0.png",
outformat='png',
gui=False)
exportfits(imagename=imagename+".image.tt0", fitsimage=imagename+".fits", overwrite=True)
imrms = [imstat(imagename+".image.tt0",box=statsbox)['rms']]
for calnum in xrange(niter):
# for Ku D W51 Ku spw 2
if reclean:
first_image = 'spw%i_ku_d_firstim_selfcal%i' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+first_image+suffix)
clean(vis=avg_data,imagename=first_image,field=field, mode='mfs',
psfmode='hogbom',multiscale=multiscale,
weighting='briggs', robust=0.0, niter=100, imsize=imsize,
mask=cleanboxes,
nterms=2,
usescratch=True)
exportfits(imagename=first_image+".image.tt0", fitsimage=first_image+".fits", overwrite=True)
viewer(first_image+".image.tt0",
outfile=outdir+first_image+".image.tt0.png",
outformat='png',
gui=False)
caltable = 'selfcal%i_%s_spw%i.pcal' % (calnum,field.replace(" ",""),spwn)
if reclean:
os.system('rm -rf '+caltable)
gaincal(vis=avg_data,
field='',
caltable=caltable,
spw='',
# gaintype = 'T' could reduce failed fit errors by averaging pols...
gaintype='G', # 'G' from http://casaguides.nrao.edu/index.php?title=EVLA_Advanced_Topics_3C391
solint=solint,
refant=refant,
calmode='p',
combine='scan',
minblperant=4)
if reclean:
applycal(vis=avg_data,
gaintable=caltable,
interp='linear',
flagbackup=True) # was False when flagmanager was used
if reclean:
selfcal_image = 'spw%i_ku_d_selfcal%i' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=avg_data,imagename=selfcal_image,field=field, mode='mfs',
psfmode='hogbom',multiscale=multiscale,
weighting='briggs', robust=0.5, niter=1000, imsize=imsize,
nterms=2,
mask=cleanboxes,
usescratch=True)
exportfits(imagename=selfcal_image+".image.tt0", fitsimage=selfcal_image+".fits", overwrite=True)
imrms.append(imstat(selfcal_image+".image.tt0",box=statsbox)['rms'])
viewer(selfcal_image+".image.tt0",
outfile=outdir+selfcal_image+".image.tt0.png",
outformat='png',
gui=False)
print "FINISHED ITERATION %i" % calnum
print "FINISHED ITERATING!!! YAY!"
# final phase + gain cal:
# http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey#One_Last_Iteration:_Amplitude_.26_Phase_Self_Calibration
aptable = 'selfcal_ap_%s_spw%i.gcal' % (field.replace(" ",""),spwn)
gaincal(vis=avg_data, field='', caltable=aptable, gaintable=caltable, spw='',
solint='inf', refant=refant, calmode='ap', combine='', minblperant=4)
plotcal(caltable=aptable,
xaxis='phase', yaxis='amp',
plotrange=[-50,50,0.5,1.5],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvsphase_final.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
applycal(vis=avg_data,
gaintable=[aptable,caltable],
interp='linear',
flagbackup=True) # was False when flagmanager was used
selfcal_image = 'spw%i_ku_d_selfcal%i_final' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=avg_data,imagename=selfcal_image,field=field, mode='mfs', mask=cleanboxes,
weighting='briggs', robust=0.5, niter=10000, imsize=imsize,
nterms=2,
usescratch=True)
exportfits(imagename=selfcal_image+".image.tt0", fitsimage=selfcal_image+".fits", overwrite=True)
plotms(vis=avg_data, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after CSCLEAN iter %i' % calnum,
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after CSCLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after CSCLEAN iter %i' % (calnum) ,
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist.png' % (calnum,spwn),
field=field,
overwrite=True,
)
selfcal_image = 'spw%i_ku_d_selfcal%i_final_multiscale' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=avg_data,imagename=selfcal_image,field=field, mode='mfs', imagermode='csclean',# mask=cleanboxes,
multiscale=multiscale, psfmode='hogbom',
nterms=2,
weighting='briggs', robust=0.5, niter=10000, imsize=imsize,
usescratch=True)
exportfits(imagename=selfcal_image+".image.tt0", fitsimage=selfcal_image+".fits", overwrite=True)
plotms(vis=avg_data, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=avg_data, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
return imrms
def selfcal(vis, spw='6', doplots=True, INTERACTIVE=False, reclean=True,
field='W51 Ku', outdir_template="spw%i_selfcal_iter/",
statsbox='170,50,229,97', ant1list=['ea14','ea05'],
ant2list=['ea16','ea07'], avgchannel_wide='128',
avgchannel_narrow='8', cleanboxes="", refant='ea27', solint='30s',
niter=2, multiscale=[0,3,6,12,24,48,96], imsize=512,
cell='0.1arcsec', weighting='uniform', robust=0.0,
minsnr=3, psfmode='clark', openviewer=False,
shallowniter=100,
midniter=1000,
deepniter=1e4,
minblperant=4,
gaintype='G'):
"""
Docstring incomplete
"""
# Jan 2016: the fact that I have to make these declarations indicates that
# this code never actually worked.
spwn = int(spw)
split(vis=vis, outputvis="selfcal_copy_{0}".format(vis))
vis_for_selfcal = "selfcal_copy_{0}".format(vis)
outdir = outdir_template % spwn
if not os.path.exists(outdir):
os.mkdir(outdir)
shallowniter = int(shallowniter)
midniter = int(midniter)
deepniter = int(deepniter)
fieldstr = field.replace(" ","")
# (1) Clean a single SPW *interactively*, boxing the brightest regions and not
# cleaning very deeply (maybe 100 iterations). Keep this model in the header
# -- it's what you'll use for the first round of self-calibration.
#
# Those are the official directions. They are nonsense when dealing with
# the extended emission of W51.
if reclean:
imagename="selfcal_spw%i_shallowclean_iter0" % int(spw)
for suffix in clean_output_suffixes:
os.system("rm -rf "+imagename+suffix)
clean(vis=vis_for_selfcal, field=field, imagename=imagename, mode='mfs',
psfmode=psfmode, multiscale=multiscale,
weighting=weighting, robust=robust, niter=shallowniter,
imsize=imsize, cell=cell,
mask=cleanboxes,
nterms=1,
interactive=INTERACTIVE,
usescratch=True)
exportfits(imagename=imagename+".image", fitsimage=imagename+".fits",
overwrite=True, dropdeg=True)
imrms = [imstat(imagename+".image",box=statsbox)['rms']]
for calnum in xrange(niter):
if reclean:
first_image = 'selfcal_{0}_{1}_firstim_selfcal{2}'.format(fieldstr,
spw,
calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+first_image+suffix)
clean(vis=vis_for_selfcal,imagename=first_image,field=field,
mode='mfs', psfmode=psfmode, multiscale=multiscale,
weighting=weighting, robust=robust, niter=shallowniter,
imsize=imsize, mask=cleanboxes, cell=cell, nterms=1,
usescratch=True)
exportfits(imagename=first_image+".image",
fitsimage=first_image+".fits", overwrite=True,
dropdeg=True)
caltable = 'selfcal%i_%s_spw%i.pcal' % (calnum,fieldstr,spwn)
if reclean:
os.system('rm -rf '+caltable)
gaincal(vis=vis_for_selfcal,
field='',
caltable=caltable,
spw='',
# gaintype = 'T' could reduce failed fit errors by averaging pols...
gaintype=gaintype, # 'G' from http://casaguides.nrao.edu/index.php?title=EVLA_Advanced_Topics_3C391
solint=solint,
refant=refant,
calmode='p',
combine='scan',
minsnr=minsnr,
minblperant=minblperant)
# Watch out for failed solutions noted in the terminal during this
# solution. If you see a large fraction (really more than 1 or 2) of
# your antennas failing to converge in many time intervals then you
# may need to lengthen the solution interval.
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
# INSPECT THE CALIBRATION
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
# After you have run the gaincal, you want to inspect the
# solution. Use PLOTCAL to look at the solution (here broken into
# panels by SPW with individual antennas mapped to colors). Look at
# the overall magnitude of the correction to get an idea of how
# important the selfcal is and at how quickly it changes with time to
# get an idea of how stable the instrument and atmosphere were.
#
if doplots:
for ant2 in ant2list:
for ant in ant1list:
# (4) Have a look at the gain solutions by antenna. Which antennas
# have the largest phase corrections? Before applying the
# calibration, use plotms to display the corrected phase vs. amp
# for these antennas, to compare with *after* the correction is
# applied.
plotcal(caltable=caltable,
xaxis='time', yaxis='phase',
showgui=INTERACTIVE,
antenna=ant+'&'+ant2,
figfile=outdir+'selfcal%i_spw%i_phasevstime_ant%s-%s.png' % (calnum,spwn,ant,ant2),
iteration='')#, subplot = 221)
#plotcal(caltable=caltable, xaxis='amp', yaxis='phase',
# showgui=INTERACTIVE,
# antenna=ant,
# figfile=outdir+'selfcal%i_spw%i_phasevsamp_ant%s.png' % (calnum,spwn,ant),
# iteration='')#, subplot = 221)
if calnum == 0:
datacol='data'
else:
datacol='corrected'
plotms(vis=vis_for_selfcal, xaxis='time', yaxis='phase',
xdatacolumn=datacol, ydatacolumn=datacol,
avgtime='15s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s. datacol=%s' % (calnum,spwn,ant,ant2,datacol),
showgui=INTERACTIVE,
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phasetime.png' % (calnum,spwn,ant,ant2),)
plotms(vis=vis_for_selfcal, xaxis='time', yaxis='amp',
xdatacolumn=datacol, ydatacolumn=datacol,
avgtime='15s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s. datacol=%s' % (calnum,spwn,ant,ant2,datacol),
showgui=INTERACTIVE,
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_amptime.png' % (calnum,spwn,ant,ant2),)
plotms(vis=vis_for_selfcal, xaxis='phase', yaxis='amp',
xdatacolumn=datacol, ydatacolumn=datacol,
avgtime='60s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s. datacol=%s' % (calnum,spwn,ant,ant2,datacol),
showgui=INTERACTIVE,
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phaseamp.png' % (calnum,spwn,ant,ant2),)
plotcal(caltable=caltable,
xaxis='time', yaxis='phase',
plotrange=[0,0,-180,180],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_phasevstime.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
plotcal(caltable=caltable,
xaxis='antenna', yaxis='phase',
showgui=INTERACTIVE,
figfile=outdir+'selfcal%i_spw%i_phasevsantenna.png' % (calnum,spwn),
iteration='')
plotcal(caltable=caltable,
xaxis='time', yaxis='amp',
plotrange=[0,0,0.5,1.5],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvstime.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
#plotcal(caltable=caltable,
# xaxis='phase', yaxis='amp',
# plotrange=[-50,50,0.5,1.5],
# showgui=INTERACTIVE,
# figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvsphase.png' % (calnum,spwn),
# iteration='spw' if INTERACTIVE else '')#, subplot = 221)
# THERE WILL BE WEIRD "LUSTRE" ERRORS GENERATED BY THE FILE SYSTEM. DO
# NOT FREAK OUT. These are just a feature of our fast file
# system. Plotcal will still work.
# It can be useful useful to plot the X-Y solutions (i.e., differences
# between polarizations) as an indicator of the noise in the
# solutions.
plotcal(caltable=caltable,
xaxis='time',
yaxis='phase',
plotrange=[0,0,-25, 25],
poln = '/',
showgui=INTERACTIVE,
iteration='spw,antenna' if INTERACTIVE else '',
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_poldiff.png' % (calnum,spwn),
subplot = 221 if INTERACTIVE else 111)
plotms(vis=vis_for_selfcal,
xaxis='uvdist',
yaxis='amp',
xdatacolumn='corrected',
ydatacolumn='corrected',
avgtime='1e8s',
avgchannel=avgchannel_narrow,
coloraxis='baseline',
overwrite=True,
showgui=INTERACTIVE,
title='Iteration %i for spw %i' % (calnum,spwn),
plotfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_uvdistamp.png' % (calnum,spwn),
)
#plotms(vis=vis_for_selfcal,
# xaxis='phase',
# yaxis='amp',
# xdatacolumn='corrected',
# ydatacolumn='corrected',
# avgtime='60s',
# avgchannel=avgchannel_narrow,
# coloraxis='corr',
# overwrite=True,
# title='Iteration %i for spw %i' % (calnum,spw),
# plotfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_phaseamp.png' % (calnum,spwn),
# )
plotms(vis=vis_for_selfcal,
xaxis='time',
yaxis='amp',
xdatacolumn='corrected',
ydatacolumn='corrected',
avgtime='10s',
avgchannel=avgchannel_narrow,
coloraxis='baseline',
overwrite=True,
showgui=INTERACTIVE,
title='Iteration %i for spw %i' % (calnum,spwn),
plotfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_amptime.png' % (calnum,spwn),
)
# The rms noise is about 4 to 8 deg, depending on antenna, but the
# phase changes are considerably larger. This indicates that the
# application of this solution will improve the image.
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
# APPLY THE CALIBRATION
# =%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%=%
#
# If you are satisfied with your solution, you can now apply it to the
# data to generate a new corrected data column, which you can then
# image. Be sure to save the previous flags before you do so because
# applycal will flag data without good solutions. The commented
# command after the applycal will roll back to the saved solution in
# case you get in trouble.
#
# flagmanager(vis=vis_for_selfcal,
# mode='save',
# versionname='before_selfcal_apply')
# 2013-03-04 19:53:37 SEVERE agentflagger:: (file /opt/casa/stable-2013-02/gcwrap/tools/flagging/agentflagger_cmpt.cc, line 37) Exception Reported: Invalid Table operation: ArrayColumn::setShape; shape cannot be changed for row 0 column FLAG
# *** Error *** Invalid Table operation: ArrayColumn::setShape; shape cannot be changed for row 0 column FLAG
if reclean:
flagmanager(vis=vis_for_selfcal, mode='backup', versionname='pre_applycal1')
applycal(vis=vis_for_selfcal,
gaintable=caltable,
interp='linear',
flagbackup=False) # no need when using flagmanager
flagmanager(vis=vis_for_selfcal, mode='restore', versionname='pre_applycal_1')
# (6) Plot corrected phase vs. amp for the antennas you picked out in (4),
# to check that in fact the corrections have been applied as expected.
if doplots:
for ant2 in ant2list:
for ant in ant1list:
plotms(vis=vis_for_selfcal, xaxis='time', yaxis='phase',
xdatacolumn='corrected', ydatacolumn='corrected',
avgtime='15s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s' % (calnum,spwn,ant,ant2),
showgui=INTERACTIVE,
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phasetime_applied.png' % (calnum,spwn,ant,ant2),)
plotms(vis=vis_for_selfcal, xaxis='time', yaxis='amp',
xdatacolumn='corrected', ydatacolumn='corrected',
avgtime='60s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s' % (calnum,spwn,ant,ant2),
showgui=INTERACTIVE,
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_amptime_applied.png' % (calnum,spwn,ant,ant2),)
plotms(vis=vis_for_selfcal, xaxis='phase', yaxis='amp',
xdatacolumn='corrected', ydatacolumn='corrected',
avgtime='60s', avgchannel=avgchannel_narrow, coloraxis='corr',
antenna=ant+'&'+ant2,
overwrite=True, title='Iteration %i for spw %i and ant %s-%s' % (calnum,spwn,ant,ant2),
showgui=INTERACTIVE,
plotfile=outdir+'selfcal%i_spw%i_ant%s-%s_phaseamp_applied.png' % (calnum,spwn,ant,ant2),)
plotms(vis=vis, spw='0', xaxis='freq', yaxis='phase', avgtime='1e8',
avgscan=T, coloraxis='corr', iteraxis='baseline', xselfscale=T,
yselfscale=T,
antenna=ant+'&'+ant2,
title='Phase vs Freq with time averaging for spw %i ant %s-%s iter %i' % (spwn,ant,ant2,calnum),
plotfile=outdir+'phasevsfreq_spw%i_ant%s-%s_selfcal%i.png' % (spwn,ant,ant2,calnum),
field=field,
overwrite=True,
showgui=INTERACTIVE,
)
# Use this command to roll back to the previous flags in the event of
# an unfortunate applycal.
#flagmanager(vis=vis_for_selfcal,
# mode='restore',
# versionname='before_selfcal_apply')
if reclean:
selfcal_image = 'selfcal_{0} {1}_selfcal{2}'.format(fieldstr,spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=vis_for_selfcal, imagename=selfcal_image, field=field,
mode='mfs', psfmode=psfmode, multiscale=multiscale,
weighting=weighting, robust=robust, niter=midniter,
imsize=imsize, cell=cell, nterms=1, mask=cleanboxes,
psfmode=psfmode,
usescratch=True)
exportfits(imagename=selfcal_image+".image", fitsimage=selfcal_image+".fits", overwrite=True)
if doplots:
plotms(vis=vis_for_selfcal, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after CSCLEAN iter %i' % calnum,
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline.png' % (calnum,spwn),
field=field,
overwrite=True,
showgui=INTERACTIVE,
)
plotms(vis=vis_for_selfcal, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after CSCLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime.png' % (calnum,spwn),
field=field,
overwrite=True,
showgui=INTERACTIVE,
)
plotms(vis=vis_for_selfcal, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after CSCLEAN iter %i' % (calnum) ,
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist.png' % (calnum,spwn),
field=field,
overwrite=True,
showgui=INTERACTIVE,
)
imrms.append(imstat(selfcal_image+".image",box=statsbox)['rms'])
print "FINISHED ITERATION %i" % calnum
print "FINISHED ITERATING!!! YAY!"
# final phase + gain cal:
# http://casaguides.nrao.edu/index.php?title=Calibrating_a_VLA_5_GHz_continuum_survey#One_Last_Iteration:_Amplitude_.26_Phase_Self_Calibration
aptable = 'selfcal_ap_%s_spw%i.gcal' % (field.replace(" ",""),spwn)
gaincal(vis=vis_for_selfcal, field='', caltable=aptable, gaintable=caltable, spw='',
solint='inf', refant=refant, calmode='ap', combine='', minblperant=4,
gaintype=gaintype, minsnr=minsnr)
if doplots:
plotcal(caltable=aptable,
xaxis='phase', yaxis='amp',
plotrange=[-50,50,0.5,1.5],
showgui=INTERACTIVE,
figfile='' if INTERACTIVE else outdir+'selfcal%i_spw%i_ampvsphase_final.png' % (calnum,spwn),
iteration='spw' if INTERACTIVE else '')#, subplot = 221)
applycal(vis=vis_for_selfcal,
gaintable=[aptable,caltable],
interp='linear',
flagbackup=True) # was False when flagmanager was used
flagmanager(vis=vis_for_selfcal, mode='restore', versionname='applycal_1')
selfcal_image = 'spw%i_ku_d_selfcal%i_final' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=vis_for_selfcal,imagename=selfcal_image,field=field, mode='mfs',
mask=cleanboxes, weighting=weighting, robust=robust, niter=deepniter,
psfmode=psfmode, imsize=imsize, cell=cell, nterms=1, usescratch=True)
exportfits(imagename=selfcal_image+".image", fitsimage=selfcal_image+".fits", overwrite=True)
if doplots:
plotms(vis=vis_for_selfcal, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after CSCLEAN iter %i' % calnum,
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=vis_for_selfcal, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after CSCLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=vis_for_selfcal, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after CSCLEAN iter %i' % (calnum) ,
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist.png' % (calnum,spwn),
field=field,
overwrite=True,
)
selfcal_image = 'spw%i_ku_d_selfcal%i_final_multiscale' % (spwn,calnum)
for suffix in clean_output_suffixes:
os.system("rm -rf "+selfcal_image+suffix)
clean(vis=vis_for_selfcal,imagename=selfcal_image,field=field, mode='mfs',
psfmode=psfmode, nterms=1, weighting=weighting, robust=robust,
niter=deepniter, imsize=imsize, cell=cell, usescratch=True)
exportfits(imagename=selfcal_image+".image", fitsimage=selfcal_image+".fits", overwrite=True)
if doplots:
plotms(vis=vis_for_selfcal, spw='0', xaxis='baseline', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Baseline after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVSbaseline_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=vis_for_selfcal, spw='0', xaxis='time', yaxis='amp', avgtime='5s',
ydatacolumn='corrected-model',
coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. Time after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVStime_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
plotms(vis=vis_for_selfcal, spw='0', xaxis='uvdist', yaxis='amp', avgtime='1e8',
ydatacolumn='corrected-model',
avgscan=T, coloraxis='baseline', iteraxis='', xselfscale=T,
yselfscale=T,
title='Residual vs. UVDIST after multiscale CLEAN iter %i' % (calnum),
plotfile=outdir+'post_selfcal%i_spw%i_residVSuvdist_multiscale.png' % (calnum,spwn),
field=field,
overwrite=True,
)
return imrms
