def run(self):
caltable = ""
for i in range(0, self.loops):
caltable = 'apcal_' + str(i)
self.caltables.append(caltable)
rmtables(caltable)
gaincal(vis=self.visfile, field=self.Imager.getField(), caltable=caltable, spw=self.Imager.getSpw(), gaintype=self.gaintype, refant=self.refant, calmode=self.calmode,
combine=self.combine, solint=self.solint[
i], minsnr=self.minsnr, minblperant=self.minblperant, gaintable=self.input_caltable, spwmap=self.spwmap,
solnorm=True)
self.plot_selfcal(caltable, xaxis="time", yaxis="amp", iteration="antenna",
subplot=421, plotrange=[0, 0, 0.2, 1.8], want_plot=self.want_plot)
versionname = 'before_apcal_' + str(i)
flagmanager(vis=self.visfile, mode='save',
versionname=versionname)
self.caltables_versions.append(versionname)
applycal(vis=self.visfile, spwmap=[self.spwmap, self.spwmap], field=self.Imager.getField(), gaintable=[
self.input_caltable, caltable], gainfield='', calwt=False, flagbackup=False, interp=self.interp, applymode=self.applymode)
imagename = self.imagename + '_ap' + str(i)
self.Imager.run(imagename)
if(self.flag_dataset_bool):
flag_dataset(mode=self.flag_mode)
self.psnr_history.append(self.Imager.getPSNR())
print("Solint: " + str(self.solint[i]) +
" - PSNR: " + str(self.psnr_history[i]))
print("Noise: " + str(self.Imager.getSTDV() * 1000.0) + " mJy/beam")
if(self.restore_PSNR):
if(i > 0):
if(self.psnr_history[i] < self.psnr_history[i - 1]):
self.restore_selfcal(
caltable_version=self.caltables_versions[i - 1])
self.psnr_history.pop()
self.caltables_versions.pop()
self.caltables.pop()
print(
"PSNR decreasing in this solution interval - restoring to last MS and exiting loop")
break
else:
if(self.selfcal_object):
if(self.psnr_history[i] < self.selfcal_object.getPSNRHistory()[-1]):
self.restore_selfcal(
caltable_version=self.selfcal_object.getCaltablesVersions()[-1])
self.psnr_history.pop()
self.caltables_versions.pop()
self.caltables.pop()
self.caltables = self.selfcal_object.getCaltables()
self.psnr_history = self.selfcal_object.getPSNRHistory()
self.caltables_versions = self.selfcal_object.getCaltablesVersions()
print(
"PSNR decreasing in this solution interval - restoring to last MS and exiting loop")
break
def run(self):
caltable = "before_selfcal"
flagmanager(vis=self.visfile, mode='save',
versionname=caltable)
self.caltables_versions.append(caltable)
imagename = self.imagename + '_original'
self.Imager.run(imagename)
print("Original: - PSNR: " + str(self.Imager.getPSNR()))
print("Noise: " + str(self.Imager.getSTDV() * 1000.0) + " mJy/beam")
self.psnr_history.append(self.Imager.getPSNR())
for i in range(0, self.loops):
caltable = 'pcal' + str(i)
self.caltables.append(caltable)
rmtables(caltable)
gaincal(vis=self.visfile, caltable=caltable, field=self.Imager.getField(), spw=self.Imager.getSpw(), gaintype=self.gaintype, refant=self.refant,
calmode=self.calmode, combine=self.combine, solint=self.solint[i], minsnr=self.minsnr, minblperant=self.minblperant)
self.plot_selfcal(caltable, xaxis="time", yaxis="phase", iteration="antenna",
subplot=421, plotrange=[0, 0, -180, 180], want_plot=self.want_plot)
versionname = 'before_phasecal_' + str(i)
flagmanager(vis=self.visfile, mode='save',
versionname=versionname)
self.caltables_versions.append(versionname)
applycal(vis=self.visfile, field=self.Imager.getField(), spwmap=self.spwmap, gaintable=[
caltable], gainfield='', calwt=False, flagbackup=False, interp=self.interp, applymode=self.applymode)
imagename = self.imagename + '_ph' + str(i)
self.Imager.run(imagename)
if(self.flag_dataset_bool):
flag_dataset(mode=self.flag_mode)
self.psnr_history.append(self.Imager.getPSNR())
print("Solint: " + str(self.solint[i]) +
" - PSNR: " + str(self.psnr_history[-1]))
print("Noise: " + str(self.Imager.getSTDV() * 1000.0) + " mJy/beam")
if(self.restore_PSNR):
print(self.psnr_history)
print(self.caltables_versions)
print(self.caltables)
if(self.psnr_history[-1] < self.psnr_history[-2]):
self.restore_selfcal(
caltable_version=self.caltables_versions[i])
self.psnr_history.pop()
self.caltables_versions.pop()
self.caltables.pop()
print(
"PSNR decreasing in this solution interval - restoring to last MS and exiting loop")
break
def applySolutions3(self, gainfield=[], applymode="calflagstrict"):
gaintable=[self.kcrosstable, self.leakagetable]
firstspw=self.spw_ids[0]
lastspw=self.spw_ids[-1]
spw = str(firstspw)+'~'+str(lastspw)
self.logger.info("Spw: "+ spw)
self.casalog.post("Spw: "+ spw, "INFO")
spwmap0 = [self.mapped_spw] * self.nspw
interp = [''] * len(gaintable)
calwt = [False] * len(gaintable)
if(gainfield == []): gainfield = ['']
applycal(vis=self.vis, field='', spw=spw, gaintable=gaintable, spwmap=[spwmap0], calwt=calwt, applymode=applymode, interp=interp, gainfield=gainfield, antenna='*&*', parang=True, flagbackup=True)
def _fillweight(vis):
if not os.path.exists(vis):
return
casalog.post('fill WEIGHT and SIGMA columns for %s ...' % (vis))
# work with private cb tool
with sdutil.cbmanager(vis, compress=False, addcorr=False,
addmodel=False) as cb:
status = cb.initweights()
if status:
# cb.initweights() succeeded so try to apply Tsys to
# weight column
# procedure:
# 1. generate temporary Tsys caltable
# 2. apply temporary Tsys caltable to vis
# 3. remove temporary Tsys caltable
import time
from gencal import gencal
from applycal import applycal
caltable = 'temporary_caltable%s.tsys' % (str(time.time()).replace(
'.', ''))
casalog.post('tempolary caltable name: %s' % (caltable))
try:
gencal(vis=vis, caltable=caltable, caltype='tsys')
# add 0.5*INTERVAL to the TIME values in caltable to make them time of
# integration midpoint, because gencal currently sets (TIME_VIS -
# INTERVAL_VIS/2), namely start time, into TIME in its output based on
# ALMA's conventions...(2014/6/17 WK)
with sdutil.tbmanager(caltable, nomodify=False) as tbcal:
with sdutil.tbmanager(vis) as tbvis:
interval = tbvis.getcol('INTERVAL')[0]
tbcal.putcol('TIME', tbcal.getcol('TIME') + 0.5 * interval)
applycal(vis=vis,
docallib=False,
gaintable=[caltable],
applymode='calonly')
except Exception, e:
# Tsys application failed so that reset WEIGHT and SIGMA to 1.0
_resetweight(vis)
raise e
finally:
def applySolutions(self, spwmap=[], gaintable=[], gainfield=[], applymode="calflagstrict", antenna='*&*', flagbackup=True):
#leakagegain.append(fluxtable)
if(gaintable == []):
if(self.kcrosstable == ""):
gaintable=[self.leakagetable, self.polangletable]
else:
gaintable=[self.kcrosstable, self.leakagetable, self.polangletable]
self.logger.info("Applying solutions")
self.casalog.post("Applying solutions", "INFO")
print("Gain tables: ", gaintable)
firstspw=self.spw_ids[0]
lastspw=self.spw_ids[-1]
interp = [''] * len(gaintable)
spw = str(firstspw)+'~'+str(lastspw)
spwmap0 = [self.mapped_spw] * self.nspw
if(spwmap == []):
if(len(gaintable)-1 > 0):
spwmap_empty = [[]] * (len(gaintable)-1) #subtract kcrosstable
spwmap_empty.insert(0, spwmap0)
spwmap = spwmap_empty
else:
spwmap=[spwmap0]
calwt = [False] * len(gaintable)
selectdata=True
if(self.old_VLA):
interp = 'nearest'
spwmap = []
spw = ''
calwt = [False]
selectdata=False
antenna=''
self.logger.info("Spw: "+ spw)
self.casalog.post("Spw: "+ spw, "INFO")
print("Spwmap: ", spwmap)
if(gainfield == []): gainfield = [''] * len(gaintable)
applycal(vis=self.vis, field='', spw=spw, gaintable=gaintable, selectdata=selectdata, spwmap=spwmap, calwt=calwt, applymode=applymode, interp=interp, gainfield=gainfield, antenna=antenna, parang=True, flagbackup=flagbackup)
def _fillweight(vis):
if not os.path.exists(vis):
return
casalog.post('fill WEIGHT and SIGMA columns for %s ...'%(vis))
# work with private cb tool
with sdutil.cbmanager(vis, compress=False, addcorr=False, addmodel=False) as cb:
status = cb.initweights()
if status:
# cb.initweights() succeeded so try to apply Tsys to
# weight column
# procedure:
# 1. generate temporary Tsys caltable
# 2. apply temporary Tsys caltable to vis
# 3. remove temporary Tsys caltable
import time
from gencal import gencal
from applycal import applycal
caltable = 'temporary_caltable%s.tsys'%(str(time.time()).replace('.',''))
casalog.post('tempolary caltable name: %s'%(caltable))
try:
gencal(vis=vis, caltable=caltable, caltype='tsys')
# add 0.5*INTERVAL to the TIME values in caltable to make them time of
# integration midpoint, because gencal currently sets (TIME_VIS -
# INTERVAL_VIS/2), namely start time, into TIME in its output based on
# ALMA's conventions...(2014/6/17 WK)
with sdutil.tbmanager(caltable, nomodify=False) as tbcal:
with sdutil.tbmanager(vis) as tbvis:
interval = tbvis.getcol('INTERVAL')[0]
tbcal.putcol('TIME', tbcal.getcol('TIME') + 0.5*interval)
applycal(vis=vis, docallib=False, gaintable=[caltable], applymode='calonly')
except Exception, e:
# Tsys application failed so that reset WEIGHT and SIGMA to 1.0
_resetweight(vis)
raise e
finally:
"IncrementalSelfcalScript")
casalog.post(
"caltables set to {0}, calinfo set to {1}".format(
caltables, calinfo), "INFO", "IncrementalSelfcalScript")
print("Skipping {0}".format(imagename))
continue
if len(caltables) > 0:
print("Applying caltables {0}".format(caltables))
casalog.post("Applying caltables {0}".format(caltables), "INFO",
"IncrementalSelfcalScript")
applycal(
vis=selfcal_vis,
field=field,
gaintable=caltables,
spwmap=[[0] * nspws if calinfo[ii]['combine'] == 'spw' else []
for ii in range(len(caltables))],
interp=
'linear,linear', #['linearperobs,linear' if combine=='spw' else 'linearperobs,linear']*len(caltables),
applymode='calonly',
calwt=True)
for ttsuffix in ('.tt0', '.tt1', '.tt2'):
for suffix in (
'pb{tt}',
'weight',
'sumwt{tt}',
'psf{tt}',
'model{tt}',
'mask',
'image{tt}',
'residual{tt}',
def applySingleSolution(self, field='', spw='', gaintable=[], gainfield=[], selectdata=True, spwmap=[], calwt=[False], applymode="calflagstrict", interp='linear', antenna='', flagbackup=True):
applycal(vis=self.vis, field='', spw=spw, gaintable=gaintable, gainfield=gainfield, selectdata=selectdata, spwmap=spwmap, calwt=calwt, applymode=applymode, interp=interp, antenna=antenna, parang=True, flagbackup=flagbackup)
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 apply_calibration(vis, caltables, **kwargs):
print 'Applying Calibrations to the Visibility'
applycal(vis, gaintable=caltables)
