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()
def runTest(self):
try:
# instantiate the Admit class
a = admit.Project(self.admitdir)
# set up to write out figure files
a.plotparams(admit.PlotControl.BATCH, admit.PlotControl.PNG)
fitsin = admit.Ingest_AT(file=self.inputFile)
task0id = a.addtask(fitsin)
# instantiate a moment AT and set some moment parameters
m = admit.Smooth_AT()
m.setkey('bmaj', {'value': 10.0, 'unit': 'arcsec'})
m.setkey('bmin', {'value': 10.0, 'unit': 'arcsec'})
m.setkey('velres', {'value': 205, 'unit': 'km/s'})
m.setkey('bpa', 0.0)
task1id = a.addtask(m, [(task0id, 0)])
# check the fm
a.fm.verify()
# run admit
a.run()
# save it out to disk.
a.write()
a2 = admit.Project(
self.admitdir) # read in the admit.xml and bdp files
self.assertEqual(len(a.fm), len(a2.fm))
for atask in a.fm:
self.assertEqual(len(a.fm[atask]._bdp_out),
len(a2.fm[atask]._bdp_out))
# Note: we don't check bdp_in because they are connected
# "just in time" so will be set None up read-in.
self.assertEqual(a.fm._connmap, a2.fm._connmap)
for at in a.fm:
for i in range(len(a.fm[at]._bdp_out)):
self.assertEqual(a.fm[at]._bdp_out[i]._taskid,
a2.fm[at]._bdp_out[i]._taskid)
self.assertEqual(a.fm[at]._bdp_out[i].xmlFile,
a2.fm[at]._bdp_out[i].xmlFile)
self.success = "OK"
except Exception, e:
m = "exception=%s, file=%s, lineno=%s" % (
sys.exc_info()[0].__name__,
os.path.basename(
sys.exc_info()[2].tb_frame.f_code.co_filename),
sys.exc_info()[2].tb_lineno)
self.success = "FAILED"
traceback.print_exc()
self.fail("%s failed with: %s" % (self.__class__.__name__, m))
def runTest(self):
try:
# instantiate the class
a = admit.Project(self.admitDir)
a.plotparams(admit.PlotControl.BATCH,admit.PlotControl.PNG)
fitsin = admit.Ingest_AT(file=self.inputFile)
task0id = a.addtask(fitsin)
l = admit.LineID_AT()
task2id = a.addtask(l)
l._needToSave = True
ll = admit.LineList_BDP()
# ll.addRow([115.271,"CO","CO-115.271","Carbon Monoxide","1-0",0.0,0.0,3.2,0.01,1.3,0.0,5.0,15,20,5.2])
# ll.addRow([115.832,"U", "U-115.832", "", "",0.0,0.0,0.0,0.0,0.0,0.0,0.0,25,35,2.4])
# keys (column names of LineList_BDP)
# "frequency", "uid", "formula", "name", "transition", "velocity",
# "El", "Eu", "linestrength", "peakintensity", "peakoffset", "fwhm",
# "startchan", "endchan", "peakrms", "blend"
keys = {"frequency":115.271, "uid":"CO","formula":"CO-115.271",
"name":"Carbon Monoxide", "transition":"1-0",
"velocity":0.0,
"linestrength":0.01, "peakintensity":1.3,
"peakoffset":0.0, "fwhm":5.0,
"peakrms":5.2, "blend":0}
data = admit.LineData()
data.setkey(name=keys)
ll.addRow(data)
keys = {"frequency":115.832, "uid":"U","formula":"U-115.832",
"name":"", "transition":"",
"velocity":0.0,
"linestrength":0.0, "peakintensity":0.0,
"peakoffset":0.0, "fwhm":0.0,
"peakrms":2.4, "blend":0}
data.setkey(name=keys)
ll.addRow(data)
l.addoutput(ll)
l.markUpToDate()
# instantiate a linecube_AT
lcube = admit.LineCube_AT()
task1id = a.addtask(lcube,[(task0id,0),(task2id,0)])
# check the fm
a.fm.verify()
# run admit
a.run()
a.write()
# read in the admit.xml and bdp files
a2 = admit.Project(self.admitDir)
self.assertEqual(len(a.fm),len(a2.fm))
for atask in a.fm:
self.assertEqual(len(a.fm[atask]._bdp_out),
len(a2.fm[atask]._bdp_out))
self.assertEqual(a.fm._connmap,a2.fm._connmap)
for at in a.fm:
for i in range(len(a.fm[at]._bdp_out)) :
self.assertEqual( a.fm[at]._bdp_out[i]._taskid,
a2.fm[at]._bdp_out[i]._taskid)
self.assertEqual( a.fm[at]._bdp_out[i].xmlFile,
a2.fm[at]._bdp_out[i].xmlFile)
self.success = "OK"
except Exception, e:
m = "exception=%s, file=%s, lineno=%s" % ( sys.exc_info()[0].__name__, os.path.basename(sys.exc_info()[2].tb_frame.f_code.co_filename), sys.exc_info()[2].tb_lineno)
self.success = "FAILED"
traceback.print_exc()
self.fail("%s failed with: %s" % (self.__class__.__name__ , m))
#
# =============================================================================
# Used Python and ADMIT functionality.
import os
import admit
# 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.
#!/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,
else:
print "All done, we just read an existing admit.xml and it should do nothing"
print "Use admit0.py to re-run inside of your admit directory"
#
a.fm.diagram(a.dir() + 'admit.dot')
a.show()
a.showsetkey()
sys.exit(
0
) # doesn't work properly in IPython, leaves the user with a confusing mess
# Default ADMIT plotting environment
a.plotparams(plotmode, plottype)
# ingest
ingest1 = a.addtask(admit.Ingest_AT(file=file, basename=basename))
a[ingest1].setkey('mask', useMask)
a[ingest1].setkey('pb', pb)
a[ingest1].setkey('smooth', insmooth)
if vlsr != None:
a[ingest1].setkey('vlsr', vlsr)
if restfreq != None:
a[ingest1].setkey('restfreq', restfreq)
if len(inbox) > 0:
a[ingest1].setkey('box', inbox)
if len(inedge) > 0:
a[ingest1].setkey('edge', inedge)
bandcube1 = (ingest1, 0)
if False:
# test File_AT:
#! /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()
KEYS["box"] = ast.literal_eval(str(KEYS["box"]))
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.
#
# 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(
if a.new:
# copy the script into the admit directory
print "Starting a new ADMIT using ", argv[0]
os.system('cp -a %s %s' % (argv[0], adir))
else:
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)
# convert key values from string
try:
KEYS["minchan"] = int(KEYS["minchan"])
KEYS["numsigma"] = float(KEYS["numsigma"])
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'])
#========================================================================
# Master project. Beginning for ADMIT Commands
#
p = admit.Project(projdir,commit=False,loglevel=loglevel)
# 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.
print "Starting a new ADMIT using ", argv[0]
os.system('cp -a %s %s' % (argv[0], adir))
else:
print "All done, we just read an existing admit.xml and it should do nothing"
print "Use admit0.py to re-run inside of your admit directory"
#
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)
a[ingest1].setkey('smooth', insmooth)
if len(inbox) > 0:
a[ingest1].setkey('box', inbox)
if len(inedge) > 0:
a[ingest1].setkey('edge', inedge)
bandcube1 = (ingest1, 0)
if len(smooth) > 0:
smooth1 = a.addtask(admit.Smooth_AT(), [bandcube1])
a[smooth1].setkey('bmaj', {'value': smooth[0], 'unit': 'pixel'})
a[smooth1].setkey('bmin', {'value': smooth[1], 'unit': 'pixel'})
a[smooth1].setkey('bpa', 0.0)
if len(smooth) > 2:
a[smooth1].setkey('velres', {'value': smooth[2], 'unit': 'pixel'})
for line in lines:
exec(line.strip())
else:
print "All done, we just read an existing admit.xml and it should do nothing"
print "Use admit0.py to re-run inside of your admit directory"
#
a.fm.diagram(a.dir()+'admit.dot')
a.show()
a.showsetkey()
sys.exit(0) # doesn't work in IPython!
# Default ADMIT plotting environment
a.plotparams(plotmode,plottype)
# Ingest
ingest1 = a.addtask(admit.Ingest_AT(file=file,basename=basename))
a[ingest1].setkey('mask',useMask)
a[ingest1].setkey('smooth',insmooth)
a[ingest1].setkey('pb',pb)
if len(inbox) > 0:
a[ingest1].setkey('box',inbox)
bandcube1 = (ingest1,0)
pbmap1 = (ingest1,1)
if stop == 'ingest': a.exit(1)
if len(smooth) > 0:
smooth1 = a.addtask(admit.Smooth_AT(), [bandcube1])
a[smooth1].setkey('bmaj',{'value':smooth[0], 'unit':'pixel'}) # yuck, i'd like the default not to have to mention it here
a[smooth1].setkey('bmin',{'value':smooth[1], 'unit':'pixel'})
a[smooth1].setkey('bpa',0.0)
p = admit.Project(projdir,commit=False)
# convert key values from string
try:
KEYS["numsigma"] = float(KEYS["numsigma"])
KEYS["snmax"] = float(KEYS["snmax"])
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(alias='inimage',file=imagefile))
else:
Task0 = p.addtask(admit.Ingest_AT( alias='inimage', file=imagefile, pb=pbcorfile ))
Task1 = p.addtask(admit.CubeStats_AT(alias='instats'), ['inimage'])
Task2 = p.addtask(admit.SFind2D_AT(alias='srcfind',numsigma=KEYS["numsigma"], snmax=KEYS["snmax"]), ['inimage', 'instats'])
#
# Execute ADMIT flow
#
p.run()
if __name__ == "__main__":
# Command line processing to pick-up file name and define
# ADMIT directory that you will be creating
argv = admit.utils.casa_argv(sys.argv)
# set up admit in the casa environment
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])
