cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), [bandcube1])
a[cubespectrum1].setkey('pos', maxpos)
elif len(cslist) > 0:
cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), [bandcube1, cslist])
else:
#cubespectrum1 = a.addtask(CubeSpectrum_AT(), [bandcube1,csttab1])
cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), [bandcube1, csmom0])
csptab1 = (cubespectrum1, 0)
if stop == 'contsub': a.exit(1)
if usePV:
# PVSlice
if len(pvslice) == 4:
# hardcoded with a start,end
slice1 = a.addtask(admit.PVSlice_AT(slice=pvslice, width=pvwidth),
[bandcube1, csmom0])
elif len(pvslit) == 4:
# hardcoded with a center,len,pa
slice1 = a.addtask(admit.PVSlice_AT(slit=pvslit, width=pvwidth),
[bandcube1, csmom0])
else:
# use cubesum's map to generate the best slice
# the PPP method didn't seem to work so well yet, and is slow, so still commented out here
#slice1 = a.addtask(PVSlice_AT(width=5),[bandcube1,csttab1]) <-- BUG with summary needed a figure CSM style input makes
slice1 = a.addtask(admit.PVSlice_AT(width=pvwidth),
[bandcube1, csmom0])
a[slice1].setkey(
'clip',
2.0) # this is like a numsigma factor (sigma determined internally)
a[slice1].setkey('gamma', 1.0) # SB185 works better with gamma=4
# Master project.
p = admit.Project('all-cubes.admit', commit=False)
# Flow tasks.
t0 = p.addtask(admit.Ingest_AT(file='concat.spw17.image.fits'))
t1 = p.addtask(admit.CubeStats_AT(), [t0])
t2 = p.addtask(admit.CubeSum_AT(numsigma=5.0, sigma=1.0), [t0, t1])
t3 = p.addtask(admit.CubeSpectrum_AT(alias='spec11'), [t0, t2])
t4 = p.addtask(admit.LineSegment_AT(minchan=4, maxgap=4, numsigma=6.0),
[t1, t3])
t5 = p.addtask(admit.ContinuumSub_AT(fitorder=1, pad=40), [t0, t4])
t5a = p.addtask(admit.CubeStats_AT(), [t5])
t6 = p.addtask(admit.CubeSpectrum_AT(alias='spec12'), [t5, t2])
t7 = p.addtask(admit.Moment_AT(mom0clip=2.0, numsigma=[3.0]), [t5, t1])
t8 = p.addtask(admit.PVSlice_AT(clip=0.3, width=5), [t5, t2])
t9 = p.addtask(admit.PVCorr_AT(), [t8, t1])
t10 = p.addtask(
admit.LineID_AT(csub=[1, 1], minchan=3, maxgap=4, numsigma=6.0), [t5a, t6])
t11 = p.addtask(admit.LineCube_AT(pad=40), [t5, t10])
t12 = p.addtask(admit.Moment_AT(mom0clip=2.0, moments=[0, 1, 2]), [t11, t1])
t13 = p.addtask(admit.CubeSpectrum_AT(), [t11, t12])
p.run()
# Flow tasks.
t20 = p.addtask(admit.Ingest_AT(file='concat.spw19.image.fits'))
t21 = p.addtask(admit.CubeStats_AT(), [t20])
t22 = p.addtask(admit.CubeSum_AT(numsigma=4.0, sigma=1), [t20, t21])
t24 = p.addtask(admit.CubeSpectrum_AT(alias='spec13'), [t20, t22])
t26 = p.addtask(admit.LineSegment_AT(minchan=3, numsigma=4.0), [t21, t24])
# >0 force single cuberms sigma from cubestats; <0 would use rms(freq) table
a[moment1].setkey('sigma', 99.0)
csmom0 = (moment1, 0)
# CubeSpectrum
if len(maxpos) > 0:
cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), [bandcube1])
a[cubespectrum1].setkey('pos', maxpos)
else:
cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), [bandcube1, csmom0])
csptab1 = (cubespectrum1, 0)
# PVSlice
if len(pvslice) == 4:
# hardcoded with a start,end
slice1 = a.addtask(admit.PVSlice_AT(slice=pvslice, width=5),
[bandcube1, csmom0])
elif len(pvslit) == 4:
# hardcoded with a center,len,pa
slice1 = a.addtask(admit.PVSlice_AT(slit=pvslit, width=5),
[bandcube1, csmom0])
else:
# use cubesum's map to generate the best slice
slice1 = a.addtask(admit.PVSlice_AT(width=5), [bandcube1, csmom0])
a[slice1].setkey('clip', 0.3) # TODO: this is an absolute number for mom0
a[slice1].setkey('gamma', 1.0) # SB185 works better with gamma=4
a[slice1].setkey('smooth', pvSmooth) # smooth, in pixel numbers
pvslice1 = (slice1, 0)
corr1 = a.addtask(admit.PVCorr_AT(), [pvslice1, csttab1])
pvcorr1 = (corr1, 0)
else:
Tasks.append(
p.addtask(
admit.Ingest_AT(alias='incube',
file=cubefile,
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"],
#
# 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)))