def _run(argv):
# Verify arguments are good
if ( not admit.recipeutils._processargs(argv,REQARGS,OPTARGS,KEYS,KEYDESC,__doc__)): return
bdpname = argv[1]
cubefile = argv[2]
projdir = os.path.splitext(argv[2])[0] + '.admit'
pbcorfile = None
if len(argv) == 4:
pbcorfile = argv[3]
#========================================================================
# Master project. Beginning for ADMIT Commands
#
p = admit.Project(projdir,commit=False)
#
# 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.
#
Task0 = p.addtask(admit.BDPIngest_AT( alias='bdptable', file=bdpname
))
if pbcorfile == None:
Task1 = p.addtask(admit.Ingest_AT(alias='incube', file=cubefile ))
else:
Task1 = p.addtask(admit.Ingest_AT(alias='incube', file=cubefile, pb=pbcorfile))
Task2 = p.addtask(admit.CubeSpectrum_AT(alias='cubespec',xaxis=KEYS["xaxis"]), ['incube', 'bdptable'])
#
# Execute ADMIT flow
#
p.run()
# 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])
csp = proj.addtask(admit.CubeSpectrum_AT(alias='lcs'), [lcubes, mom])
# Run project and save to disk. (Open project index.html to view summary.)
#!/usr/bin/env casarun
import admit
NUM_SIGMA = 2
MIN_CHAN = 2
MAX_CHAN = 10
FITS_CUBE = "/media/haotian/documents-local/ASTR4998/data/products/SerpS_TC_spw5.pbcor_cutout_180_180_100_line.fits"
VLSR = 8.0
if __name__ == "__main__":
p = admit.Project("{}.admit_BDP".format(FITS_CUBE), dataserver=True)
t0 = p.addtask(admit.Ingest_AT(file=FITS_CUBE))
t1 = p.addtask(admit.CubeStats_AT(ppp=True), [t0])
t2 = p.addtask(admit.Moment_AT(mom0clip=2.0, numsigma=[NUM_SIGMA]),
[t0, t1])
t3 = p.addtask(admit.CubeSpectrum_AT(), [t0, t2])
t5 = p.addtask(
admit.LineSegment_AT(maxgap=MAX_CHAN,
minchan=MIN_CHAN,
numsigma=NUM_SIGMA,
csub=[0, 0]), [t1, t3])
t6 = p.addtask(admit.ContinuumSub_AT(), [t0, t5])
t7 = p.addtask(admit.CubeStats_AT(ppp=True), [t6])
t8 = p.addtask(admit.Moment_AT(mom0clip=2.0, numsigma=[NUM_SIGMA]),
[t6, t7])
t9 = p.addtask(admit.CubeSpectrum_AT(), [t6, t8])
t10 = p.addtask(
admit.LineID_AT(allowexotics=True,
maxgap=MAX_CHAN,
minchan=MIN_CHAN,
numsigma=NUM_SIGMA,
try:
sfind1 = a.addtask(admit.SFind2D_AT(alias='csm'), [csmom0])
a[sfind1].setkey('numsigma', numsigma)
a.run()
ncs = len(a[sfind1][0])
print "N sources in CSM:", ncs
if ncs > 0:
cslist = (sfind1, 0)
except:
print "SFind2D failed on the CSM map... Continuing on"
# PJT testing
# a.exit(1)
# CubeSpectrum
if len(maxpos) > 0:
cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), [bandcube1])
a[cubespectrum1].setkey('pos', maxpos)
else:
bdp_in = [bandcube1]
if cspbdp[0] and len(csttab1) > 0: bdp_in.append(csttab1)
if cspbdp[1] and len(csmom0) > 0: bdp_in.append(csmom0)
if cspbdp[2] and len(cslist) > 0:
bdp_in.append(cslist) # could be CONT or CSM
#print "CSP: using %d bpd's" % (len(bdp_in))
#print "BDP_IN",bdp_in
cubespectrum1 = a.addtask(admit.CubeSpectrum_AT(), bdp_in)
a[cubespectrum1].setkey('sources', sources)
csptab1 = (cubespectrum1, 0)
if stop == 'cubespectrum': a.exit(1)
#! /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()
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']))
Tasks.append(
p.addtask(
admit.Moment_AT(alias='linemom',
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(file=cubefile, alias='incube'))
else:
Task0 = p.addtask(
admit.Ingest_AT(file=cubefile, pb=pbcorfile, alias='incube'))
Task1 = p.addtask(admit.CubeStats_AT(alias='instats'), ['incube'])
Task2 = p.addtask(admit.CubeSum_AT(sigma=1, numsigma=3.0, alias='insum'),
['incube', 'instats'])
Task3 = p.addtask(admit.CubeSpectrum_AT(alias='spec1'),
['incube', 'insum'])
Task4 = p.addtask(
admit.LineID_AT(csub=[1, 1],
minchan=KEYS["minchan"],
numsigma=KEYS["numsigma"],
alias='lines'), ['instats', 'spec1'])
Task5 = p.addtask(admit.LineCube_AT(alias='cutcubes', pad=KEYS["pad"]),
['incube', 'lines'])
Task6 = p.addtask(
admit.Moment_AT(mom0clip=3.0,
numsigma=KEYS["cutoff"],
moments=[0, 1, 2],
alias='linemom'), ['cutcubes', 'instats'])
Task7 = p.addtask(admit.CubeSpectrum_AT(alias='linespec'),
['cutcubes', 'linemom'])
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:
if KEYS["contpb"] == None:
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}")