pvslice1 = (slice1, 0)
corr1 = a.addtask(admit.PVCorr_AT(), [pvslice1, csttab1])
pvcorr1 = (corr1, 0)
#----------- Workaround because ALMA data don't include VLSR in header -----------------
# Need to run now, since LineID_AT needs the vlsr
a.run()
a.write()
source = a.summaryData.get('object')[0].getValue()[0]
vlsr = get_vlsr(source, vlsr)
print "OBJECT = %s VLSR = ", (source, vlsr)
#---------------------------------------------------------------------------------------
# LineID uses integer segment=<STRING>: pick ASAP or ADMIT
lineid1 = a.addtask(admit.LineID_AT(vlsr=vlsr, segment="ADMIT"),
[csptab1, csttab1, pvcorr1])
lltab1 = (lineid1, 0)
# LineCube
linecube1 = a.addtask(admit.LineCube_AT(), [bandcube1, lltab1])
a[linecube1].setkey('grow', 10) # +growth
# RUN_1: now we need to run the flow, since we need to
# know the number of Lines found and produce the linecubes
# for the next for-loop.
a.run()
a.write()
nlines = len(a[linecube1])
print "Found %d lines during runtime" % nlines
pb=pbcorfile,
box=KEYS["box"])))
Tasks.append(p.addtask(admit.CubeStats_AT(alias='instats'), ['incube']))
Tasks.append(
p.addtask(admit.CubeSum_AT(sigma=1, numsigma=3.0, alias='insum'),
['incube', 'instats']))
Tasks.append(
p.addtask(admit.CubeSpectrum_AT(alias='spec1'), ['incube', 'insum']))
Tasks.append(
p.addtask(admit.PVSlice_AT(alias="cubepv", width=KEYS["width"]),
['incube', 'insum']))
Tasks.append(
p.addtask(
admit.LineID_AT(csub=[1, 1],
minchan=KEYS["minchan"],
numsigma=KEYS["numsigma"],
alias='lines'), ['instats', 'spec1']))
Tasks.append(
p.addtask(admit.LineCube_AT(alias='cutcubes', pad=KEYS["pad"]),
['incube', 'lines']))
Tasks.append(
p.addtask(
admit.Moment_AT(alias='linemom',
mom0clip=3.0,
numsigma=KEYS["cutoff"],
moments=[0, 1, 2]), ['cutcubes', 'instats']))
Tasks.append(
p.addtask(admit.CubeSpectrum_AT(alias='linespec'),
['cutcubes', 'linemom']))
# 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
a = admit.Project(projdir,
name='Testing LineID',
create=True,
loglevel=loglevel)
# Default ADMIT plotting environment
a.plotparams(plotmode, plottype)
for i in range(len(transitions)):
spec = a.addtask(
admit.GenerateSpectrum_AT(seed=seed[i],
nchan=nchan[i],
contin=contin[i],
delta=delta[i],
freq=freq[i],
transitions=transitions[i],
alias="test_%i" % (i)))
bdp_in = [(spec, 0)]
lineid1 = a.addtask(
admit.LineID_AT(vlsr=0.0, segment="ADMIT", csub=[1, 1]), bdp_in)
a[lineid1].setkey('numsigma', 2.0)
a[lineid1].setkey('minchan', 5)
a[lineid1].setkey('maxgap', 3) # 20 for the SB outflows
print "################## RUNNING TRANSITION %d ######################### " % i
# keep run() inside loop so that failures won't
# prevent us seeing output from previous tasks in the flow
a.run()
# note: explicit call to a.updateHTML() is not needed -- a.run() already calls it.
# 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.
#
# Add spectral line processing to flow
if KEYS["specpb"] == None:
Tasks.append(p.addtask(admit.Ingest_AT(file=cubefile, alias='incube')))
else:
Tasks.append(p.addtask(admit.Ingest_AT(file=cubefile, alias='incube', pb=KEYS["specpb"])))
Tasks.append(p.addtask(admit.CubeStats_AT (alias='instats'), ['incube']))
Tasks.append(p.addtask(admit.CubeSum_AT (alias='insum', sigma=1, numsigma=3.0), ['incube', 'instats']))
Tasks.append(p.addtask(admit.CubeSpectrum_AT (alias='spec1'), ['incube', 'insum']))
Tasks.append(p.addtask(admit.PVSlice_AT ( width=KEYS["width"]), ['incube', 'insum']))
Tasks.append(p.addtask(admit.LineID_AT (alias='lines', csub=[0,0], minchan=KEYS["minchan"], numsigma=KEYS["numsigma"]), ['instats','spec1']))
Tasks.append(p.addtask(admit.LineCube_AT (alias='cutcubes', pad=KEYS["pad"]), ['incube', 'lines']))
Tasks.append(p.addtask(admit.Moment_AT (alias='linemom', mom0clip=2.0, numsigma=KEYS["cutoff"], moments=[0, 1, 2]), ['cutcubes', 'instats']))
Tasks.append(p.addtask(admit.CubeSpectrum_AT (alias='linespec'), ['cutcubes', 'linemom']))
# 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:
pvcorr1 = (corr1, 0)
if stop == 'pvcorr': a.exit(1)
a.run()
source = a.summaryData.get('object')[0].getValue()[0]
print "OBJECT = ", source
# lineID
bdp_in = []
if linebdp[0]: bdp_in.append(csptab1)
if linebdp[1]: bdp_in.append(csttab1)
if linebdp[2]: bdp_in.append(pvcorr1)
if vlsr == None:
# let vlsr be inherited by the Summary
lineid1 = a.addtask(admit.LineID_AT(), bdp_in)
else:
# @todo problem: vlsr is also in the Summary, and can be different from this vlsr
lineid1 = a.addtask(admit.LineID_AT(vlsr=vlsr), bdp_in)
# hidden!!
#a[lineid1].boxcar = False
#
if lineUID:
a[lineid1].setkey('identifylines', False)
#a[lineid1].setkey('recomblevel','OFF')
#a[lineid1].setkey('recomblevel','DEEP')
if len(linepar) > 0:
a[lineid1].setkey('numsigma', linepar[0]) # 5.0
a[lineid1].setkey('minchan', linepar[1]) # 4
a[lineid1].setkey('maxgap', linepar[2]) # 3
# LineSegment
ls1 = a.addtask(admit.LineSegment_AT(),[gstab1])
if len(linepar) > 0:
a[ls1].setkey('numsigma',linepar[0])
a[ls1].setkey('minchan', linepar[1])
a[ls1].setkey('maxgap', linepar[2])
a[ls1].setkey('csub',[0,csub])
a[ls1].setkey('iterate',iterate)
a[ls1].setkey('smooth',llsmooth)
lstab1 = (ls1,0)
if stop == 'segment': a.exit(1)
# LineID
ll1 = a.addtask(admit.LineID_AT(),[gstab1])
if len(linepar) > 0:
a[ll1].setkey('numsigma',linepar[0])
a[ll1].setkey('minchan', linepar[1])
a[ll1].setkey('maxgap', linepar[2])
if lineUID:
a[ll1].setkey('identifylines',False)
a[ll1].setkey('csub',[0,csub])
a[ll1].setkey('iterate',iterate)
a[ll1].setkey('smooth',llsmooth)
a[ll1].setkey('vlsr',vlsr)
a[ll1].setkey('references',reflist)
a[ll1].setkey('online',online)
a[ll1].setkey('tier1width',tier1width)
lltab1 = (ll1,0)
project = os.getenv('PROJECT')
if project is None:
raise ValueError
else:
print(f"Project -> {project}")
basefn = os.path.basename(project).replace(".image", "")
print(f"basefn = {basefn}")
p = admit.Project(f'{basefn}.admit', dataserver=True)
# Flow tasks.
t0 = p.addtask(admit.Ingest_AT(file=basefn + '.image'))
t1 = p.addtask(admit.CubeStats_AT(ppp=True), [t0])
t2 = p.addtask(admit.CubeSum_AT(numsigma=5.0, sigma=99.0), [t0, t1])
t3 = p.addtask(admit.CubeSpectrum_AT(), [t0, t2])
t4 = p.addtask(
admit.LineSegment_AT(csub=[0, 0], minchan=4, maxgap=6, numsigma=5.0),
[t1, t3])
t5 = p.addtask(admit.ContinuumSub_AT(fitorder=1, pad=60), [t0, t4])
t6 = p.addtask(admit.CubeStats_AT(ppp=True), [t5])
t7 = p.addtask(admit.CubeSpectrum_AT(), [t5, t6])
t8 = p.addtask(admit.Moment_AT(mom0clip=2.0, numsigma=[3.0]), [t5, t6])
t9 = p.addtask(admit.LineID_AT(csub=[0, 0], minchan=4, maxgap=6, numsigma=5.0),
[t6, t7])
t10 = p.addtask(admit.LineCube_AT(pad=40), [t5, t9])
t11 = p.addtask(admit.Moment_AT(mom0clip=2.0, moments=[0, 1, 2]), [t10, t6])
t11 = p.addtask(admit.CubeSpectrum_AT(), [t10, t11])
p.run()
print(f"Done running ADMIT for {basefn} <-> {project}")