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.Moment_AT()
m.setkey('moments', [0, 1, 2])
m.setkey('sigma', 0.005)
m.setkey('numsigma', [3.0])
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))
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.)
proj.run()
#!/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,
#
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)
pm = a.getManager() # get ProjectManager
bdps = []
for ap in argv[2:]: # loop over projects
_p = pm.addProject(ap)
# Search for Moment_AT tasks in the projects
ats = pm.findTask(_p, lambda at: type(at) == type(admit.Moment_AT()))
print "Found %d Moment_AT's in %s" % (len(ats), ap)
for at in ats:
tid = a.addtask(at) # add the AT to the
bdps.append((tid, 0)) # for now, assume '0' was the mom0
print "Moment_AT ", ap, tid, 0
print "ADIR:", argv[2:]
print "Found %d BDP's" % len(bdps)
print "BDPs:", bdps
pca = a.addtask(admit.PrincipalComponent_AT(), bdps)
# Run the flow, write the outputs, update the web page.
a.run()
a.write()
if stop == 'linecube': a.exit(1)
x = range(nlines) # place holder to contain mol/line
m = {} # task id for moment on this mol/line
sp = {} # task id for cubespectrum on this mol/line
st = {} # task id for cubestats
# loop over all lines
# produce moments and spectra from the linecubes just created
for i in range(nlines):
x[i] = a[linecube1][i].getimagefile()
print "LineDir:", i, x[i]
# Moment maps from the LineCube
linecubei = (linecube1, i)
m[x[i]] = a.addtask(admit.Moment_AT(), [linecubei, csttab1])
print "MOMENT_AT:", m[x[i]]
a[m[x[i]]].setkey('moments', [0, 1, 2])
#a[m[x[i]]].setkey('moments',[0])
#a[m[x[i]]].setkey('cutoff',[2.0,3.0,3.0])
a[m[x[i]]].setkey('numsigma', [2.0])
a[m[x[i]]].setkey('mom0clip', 2.0)
if usePeak:
if useCSM:
momenti0 = csmom0 # CubeSum mom0
else:
momenti0 = (m[x[i]], 0) # this linecube mom0
# CubeSpectrum through the line cube where the mom0 map has peak
sp[x[i]] = a.addtask(admit.CubeSpectrum_AT(), [linecubei, momenti0])
elif len(maxpos) > 0:
# CubeSpectrum through the line cube at given point,
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()
# 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])
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"],
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(alias="linepv", width=KEYS["width"]),
['cutcubes', 'linemom']))
#
# Execute ADMIT flow
#
p.run()
# 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)))
else:
Tasks.append(p.addtask(admit.Ingest_AT (alias='incont', file=contfile, pb=KEYS["contpb"])))
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}")