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)
if stop == 'cubestats': a.exit(1)
# CubeSum
moment1 = a.addtask(admit.CubeSum_AT(), [bandcube1, csttab1])
a[moment1].setkey('numsigma', 4.0) # Nsigma clip in cube
a[moment1].setkey('sigma',
99.0) # >0 force single cuberms sigma from cubestats
#a[moment1].setkey('sigma',-1.0) # use rms(freq) table
a[moment1].setkey('pad', pad)
csmom0 = (moment1, 0)
if False:
# testing Export_AT()
fits000 = a.addtask(admit.Export_AT(basename="testCubeSum"), [csmom0])
if stop == 'cubesum': a.exit(1)
# SFind2D on CSM
if True:
# Create (or re-open) the ADMIT project.
# Our project directory is the input path with extension set to admit.
proj = admit.Project(os.path.splitext(ifile)[0] + '.admit', commit=False)
# Ingest the FITS cube.
proj.addtask(admit.Ingest_AT(file=ifile, alias='cube'))
# Cube manipulation template.
tmpl = proj.addtask(admit.Template_AT(imgslice=550, specpos=(183, 151)),
['cube'])
# Calculate some statistics on the FITS cube (including peak point plot).
cstats = proj.addtask(admit.CubeStats_AT(ppp=True), ['cube'])
# Calculate the moment-0 (integrated intensity) map for the entire cube.
csum = proj.addtask(admit.CubeSum_AT(numsigma=4., sigma=99.), ['cube', cstats])
# Calculate the source spectrum at (by default) the peak position in the cube.
cspect = proj.addtask(admit.CubeSpectrum_AT(), ['cube', csum])
# Identify lines in the cube.
lines = proj.addtask(admit.LineID_AT(numsigma=4.0, minchan=3),
[cspect, cstats])
# Cut input cube into line-specific sub-cubes (padding lines by 10 channels).
lcubes = proj.addtask(admit.LineCube_AT(pad=10), ['cube', lines])
# Finally, compute moment-0,1,2 maps and peak position spectrum for each line.
# Since lcubes is variadic, the following tasks will be replicated as needed.
mom = proj.addtask(admit.Moment_AT(moments=[0, 1, 2], mom0clip=2.0),
[lcubes, cstats])
#! /usr/bin/env casarun
#
# Example multi-file admit flow, hardcoded for a specific 4-spw case
#
# REMOVE existing project directory before running script for the first time!
#
import admit
# 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()
if pbcorfile == None:
Tasks.append(
p.addtask(
admit.Ingest_AT(alias='incube', file=cubefile,
box=KEYS["box"])))
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']))
# Default ADMIT plotting environment
a.plotparams(plotmode, plottype)
# Ingest
ingest1 = a.addtask(admit.Ingest_AT(file=file, alias=alias))
a[ingest1].setkey('mask', useMask)
bandcube1 = (ingest1, 0)
# 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)
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:
# list object for Tasks so we don't have to individually name them
Tasks = []
#
# 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:
import os
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()