#!/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,
# Retrieve FITS file name, respecting CASA options.
ifile = admit.utils.casa_argv(sys.argv)[1]
# 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.
#! /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 stop == 'smooth': a.exit(1)
else:
bandcube1_orig = ()
# 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)
# list object for Tasks so we don't have to individually name them
Tasks = []
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(
print "All done, we just read an existing admit.xml and it should do nothing"
a.fm.diagram(a.dir() + 'admit.dot')
a.show()
a.showsetkey()
sys.exit(0) # doesn't work properly in IPython!
# 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)
KEYS["pad"] = int(KEYS["pad"])
KEYS["cutoff"] = ast.literal_eval(str(KEYS["cutoff"]))
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(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],
bandcube2 = (smooth1, 0)
# Forget about the original, so we can continue the flow with the smoothed cube
# 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
import admit
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()