# ingest-cont: only used for source finding for CubeSpectrum, this map is not used
# to subtract the continuum, since there is no guarentee about the
# resolution ('cont' maps usually mismatch, 'mfs' maps are ok but not
# part of the ALMA pipeline
if cont != '':
# @todo note we don't have an option here to do pb?
ingest2 = a.addtask(
admit.Ingest_AT(file=cont, basename=basename, alias='sfcont'))
contmap = (ingest2, 0)
a.run()
#
cubestats2 = a.addtask(admit.CubeStats_AT(), [contmap])
#a[cubestats1].setkey('robust',robust)
csttab2 = (cubestats2, 0)
sfind2 = a.addtask(admit.SFind2D_AT(), [contmap, csttab2])
cslist = (sfind2, 0)
a.run()
ncs = len(a[cslist[0]][0])
print "N Cont sources in ingested contmap :", ncs
if ncs == 0:
cslist = ()
else:
cslist = ()
# cubestats
cubestats1 = a.addtask(admit.CubeStats_AT(), [bandcube1])
a[cubestats1].setkey('robust', robust)
a[cubestats1].setkey('ppp', usePPP)
a[cubestats1].setkey('psample', psample)
csttab1 = (cubestats1, 0)
# While 'linemom' produces 3 moment image BDPs, the default input is taken
# here, which is the first BDP which is the zeroth moment. This relies on
# Moment_AT's default behavior of putting the zeroth moment in the
# BDP index 0.
Tasks.append(p.addtask(admit.PVSlice_AT ( width=KEYS["width"]), ['cutcubes', 'linemom']))
# If given, add continuum map processing to flow
if contfile != None:
if KEYS["contpb"] == None:
Tasks.append(p.addtask(admit.Ingest_AT (alias='incont', file=contfile)))
else:
Tasks.append(p.addtask(admit.Ingest_AT (alias='incont', file=contfile, pb=KEYS["contpb"])))
Tasks.append(p.addtask(admit.CubeStats_AT (alias='contstats'), ['incont']))
Tasks.append(p.addtask(admit.SFind2D_AT (alias='contsfind'), ['incont','contstats']))
# Only add this CubeSpectrum_at to flow if SFind2D found at least one source.
# This can only be known by running up the flow to now.
p.run()
if p['contsfind'][0] != None and len(p['contsfind'][0]) > 0:
Tasks.append(p.addtask(admit.CubeSpectrum_AT (alias='contspec'), ['cutcubes','contsfind']))
#
# Execute ADMIT flow
#
p.run()
if __name__ == "__main__":
# or do LineID with bandcube2, but make linecube's from bandcube1
bandcube1 = bandcube2
if stop == 'smooth': a.exit(1)
# CubeStats - will also do log(Noise),log(Peak) plot
cubestats1 = a.addtask(admit.CubeStats_AT(), [bandcube1])
a[cubestats1].setkey('robust',robust)
a[cubestats1].setkey('ppp',False)
csttab1 = (cubestats1,0)
if stop == 'cubestats': a.exit(1)
#sfind1 = a.addtask(admit.SFind2D_AT(), [bandcube1])
#NEW:
sfind1 = a.addtask(admit.SFind2D_AT(), [bandcube1,pbmap1,csttab1])
#OLD
#sfind1 = a.addtask(admit.SFind2D_AT(), [bandcube1,csttab1])
#a[sfind1].setkey('numsigma',6.0)
#a[sfind1].setkey('sigma',-1.0)
#a[sfind1].setkey('robust',())
#a[sfind1].setkey('robust',('classic','auto'))
#a[sfind1].setkey('robust',('hin',1.5))
#a[sfind1].setkey('robust',('chau',-1.0))
#a[sfind1].setkey('robust',('fit-half','zero')) # bug
#a[sfind1].setkey('snmax',40.0)
# finish off !
a.run()
a.showsetkey(adir+'/admit.apar')
# in this model, it would be better to use insmooth= for Ingest_AT, it doesn't
# need the extra space to hold bandcube1
#
# Another model could be to have two flows in this script, up to LineID,
# one with each (or more) smoothing factor and decide which one to continue with
# or do LineID with bandcube2, but make linecube's from bandcube1
bandcube1 = bandcube2
# If a continuum image was given, set up to ingest it and run
# source-find on it.
if cont != '':
ingest2 = a.addtask(admit.Ingest_AT(file=cont, alias=alias + '-cont'))
contmap = (ingest2, 0)
cubestats2 = a.addtask(admit.CubeStats_AT(), [contmap])
csttab2 = (cubestats2, 0)
sfind2 = a.addtask(admit.SFind2D_AT(), [contmap, csttab2])
cslist = (sfind2, 0)
else:
cslist = ()
# CubeStats - will also do log(Noise),log(Peak) plot
cubestats1 = a.addtask(admit.CubeStats_AT(), [bandcube1])
a[cubestats1].setkey('robust', robust)
a[cubestats1].setkey('ppp', usePPP)
csttab1 = (cubestats1, 0)
# CubeSum
moment1 = a.addtask(admit.CubeSum_AT(), [bandcube1, csttab1])
a[moment1].setkey('numsigma', 4.0) # Nsigma clip in cube
# >0 force single cuberms sigma from cubestats; <0 would use rms(freq) table
a[moment1].setkey('sigma', 99.0)
try:
KEYS["numsigma"] = float(KEYS["numsigma"])
KEYS["snmax"] = float(KEYS["snmax"])
except Exception, e:
print("Exception converting keyword value to number:",e)
return
#
# Set-up all ADMIT Flow tasks for execution including their aliases and connections
# The aliases allow you to refer to a task's input by the alias name of the (previous)
# task providing that input.
#
if pbcorfile == None:
Task0 = p.addtask(admit.Ingest_AT(alias='inimage',file=imagefile))
else:
Task0 = p.addtask(admit.Ingest_AT( alias='inimage', file=imagefile, pb=pbcorfile ))
Task1 = p.addtask(admit.CubeStats_AT(alias='instats'), ['inimage'])
Task2 = p.addtask(admit.SFind2D_AT(alias='srcfind',numsigma=KEYS["numsigma"], snmax=KEYS["snmax"]), ['inimage', 'instats'])
#
# Execute ADMIT flow
#
p.run()
if __name__ == "__main__":
# Command line processing to pick-up file name and define
# ADMIT directory that you will be creating
argv = admit.utils.casa_argv(sys.argv)
# now do the work
_run(argv)