def runTest(self):
try:
# instantiate the class
a = admit.Project(self.admitdir)
#use a GenerateSpectrum_AT that reads in a spectrum
gs1 = a.addtask(
admit.GenerateSpectrum_AT(file=self.specfile,
freq=124.470,
seed=-1))
gstab1 = (gs1, 0)
# instantiate a LineSegment AT and set parameters
l = admit.LineSegment_AT()
task1id = a.addtask(l, [gstab1])
a.fm.verify()
a.run()
# read in the admit.xml and bdp files
a2 = admit.Project(self.admitdir)
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))
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,
recomblevel='deep',
tier1width=10.0,
vlsr=VLSR,
csub=[0, None]), [t7, t9])
def runTest(self):
print "#### %s ####" % self.testName
try:
for i in range(len(self.transitions)):
spec = self.a.addtask(
admit.GenerateSpectrum_AT(seed=self.seed[i],
nchan=self.nchan[i],
contin=self.contin[i],
delta=self.delta[i],
freq=self.freq[i],
transitions=self.transitions[i],
alias="test_%i" % (i)))
bdp_in = [(spec, 0)]
csub = [1, 1]
segment = "ADMIT"
numsigma = 2.0
minchan = 5
maxgap = 3
vlsr = 0.0
linesegment1 = self.a.addtask(
admit.LineSegment_AT(segment=segment, csub=csub), bdp_in)
self.a[linesegment1].setkey('numsigma', numsigma)
self.a[linesegment1].setkey('minchan', minchan)
self.a[linesegment1].setkey('maxgap', maxgap)
lineid1 = self.a.addtask(
admit.LineID_AT(vlsr=vlsr, segment=segment, csub=csub),
bdp_in)
self.a[lineid1].setkey('numsigma', numsigma)
self.a[lineid1].setkey('minchan', minchan)
self.a[lineid1].setkey('maxgap', maxgap)
self.a[lineid1].setkey('identifylines', False)
print "################## RUNNING TRANSITION %d: %s ######################### " % (
i, self.transitions[i][0][0])
self.a.run()
segtable = self.a.fm[linesegment1]._bdp_out[0].table
linetable = self.a.fm[lineid1]._bdp_out[0].table
number_of_segments = len(segtable)
number_of_lines = len(linetable)
self.assertEqual(
number_of_segments,
number_of_lines,
msg=
"Number of Line Segments doesn't match number of LineIDs")
for rowindex in range(min(number_of_segments,
number_of_lines)):
rowS = segtable.getRowAsDict(rowindex)
rowL = linetable.getRowAsDict(rowindex)
self.assertEqual(
rowS, rowL,
"Values for row %d of segment table and line table do not match"
% rowindex)
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))
#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)
# Find line segments from cubestats and/or cubespect
# For SD maps cubestats should not be used, since there is a false (negative) continuum
if lineSEG:
bdp_in = []
if contbdp[0]: bdp_in.append(csptab1) # CubeSpectrum
if contbdp[1]: bdp_in.append(csttab1) # CubeStats
segment1 = a.addtask(admit.LineSegment_AT(), bdp_in)
if len(linepar) > 0:
a[segment1].setkey('numsigma', linepar[0])
a[segment1].setkey('minchan', linepar[1])
a[segment1].setkey('maxgap', linepar[2])
else:
a[segment1].setkey('numsigma', 5.0)
a[segment1].setkey('minchan', 4)
a[segment1].setkey('maxgap', 3)
#a[segment1].setkey('csub',[1,1])
a[segment1].setkey('csub', [0, 0])
a[segment1].setkey('smooth', llsmooth)
a[segment1].setkey('iterate', iterate)
lstab1 = (segment1, 0)
a.run()
#
# 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()
a.showsetkey()
sys.exit(0) # doesn't work in IPython!
# Default ADMIT plotting environment
a.plotparams(plotmode,plottype)
# GenerateSpectrum
# here we use a little backdoor in GenerateSpectrum_AT that reads in
# a spectrum
gs1 = a.addtask(admit.GenerateSpectrum_AT(file=file,seed=-1,alias=alias))
gstab1 = (gs1,0)
if stop == 'generate': a.exit(1)
# LineSegment
ls1 = a.addtask(admit.LineSegment_AT(),[gstab1])
if len(linepar) > 0:
a[ls1].setkey('numsigma',linepar[0])
a[ls1].setkey('minchan', linepar[1])
a[ls1].setkey('maxgap', linepar[2])
a[ls1].setkey('csub',[0,csub])
a[ls1].setkey('iterate',iterate)
a[ls1].setkey('smooth',llsmooth)
lstab1 = (ls1,0)
if stop == 'segment': a.exit(1)
# LineID
ll1 = a.addtask(admit.LineID_AT(),[gstab1])
if len(linepar) > 0:
a[ll1].setkey('numsigma',linepar[0])
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}")