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))
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,
recomblevel='deep',
tier1width=10.0,
vlsr=VLSR,
csub=[0, None]), [t7, t9])
t11 = p.addtask(admit.LineCube_AT(), [t6, t10])
t12 = p.addtask(admit.Moment_AT(mom0clip=2.0, moments=[0, 1, 2]),
[t11, t7])
t13 = p.addtask(admit.CubeSpectrum_AT(), [t11, t12])
p.run()
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()
a.run()
if stop == 'lineid': a.exit(1)
nlines = len(a[lltab1[0]][0])
print "Found %d lines in LineID" % nlines
# special case, exit here if you don't want any linecubes
if maxlines == 0:
print "maxlines=0; no linecube's will be produced - end of admit1"
a.exit(1)
#
if len(bandcube1_orig) > 0 and not useSmooth: bandcube1 = bandcube1_orig
# LineCube
linecube1 = a.addtask(admit.LineCube_AT(), [bandcube1, lltab1])
a[linecube1].setkey('pad', pad) # +growth on either side
#a.exit(1)
# RUN_1: now we need to run the flow, since we need to
# know the number of Lines found and produce the linecubes
# for the next for-loop.
a.run()
nlines = len(a[linecube1])
print "Found %d lines in LineCube" % nlines
if stop == 'linecube': a.exit(1)
x = range(nlines) # place holder to contain mol/line
# 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])
t26 = p.addtask(admit.LineSegment_AT(minchan=3, numsigma=4.0), [t21, t24])
t26a = p.addtask(admit.ContinuumSub_AT(fitorder=1, pad=60), [t20, t26])
t26b = p.addtask(admit.CubeSpectrum_AT(alias='spec14'), [t26a, t21])
t23 = p.addtask(admit.Moment_AT(mom0clip=2.0, numsigma=[3.0]), [t26a, t21])
t25 = p.addtask(admit.PVSlice_AT(clip=0.3, width=5), [t26a, t22])
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',
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(
# 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:
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}")
