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))
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 test_variflow(self):
p = admit.Project(self.outputDir)
p.setlogginglevel(50)
p.addtask(admit.File_AT(alias='root', file='root', touch=True))
p.addtask(admit.Flow11_AT(alias='flow1'), ['root'])
p.addtask(admit.Flow1N_AT(alias='flow1N', n=2, touch=True, exist=True),
['root'])
p.addtask(admit.Flow11_AT(alias='sub1Nf'), ['flow1N'])
p.addtask(admit.Flow11_AT(alias='sub1Nv'), [('flow1N', 1)])
p.addtask(admit.FlowMN_AT(alias='flowMN', n=2, touch=True, exist=True),
['flow1', 'root', ('flow1N', 1)])
p.addtask(admit.Flow11_AT(alias='subMNf'), ['flowMN'])
p.addtask(admit.FlowN1_AT(alias='subMNv', touch=True), [('flowMN', 0),
('flowMN', 2)])
p.addtask(admit.FlowN1_AT(alias='flowN1', touch=True),
['flow1N', ('flowMN', 1)])
p.addtask(admit.Flow11_AT(alias='subN1'), ['flowN1'])
p.show()
for n in [2, 3, 1, 2]:
if (p.fm.find(lambda at: at._alias == 'flow1N')):
p['flow1N'].setkey('n', n)
if (p.fm.find(lambda at: at._alias == 'flowMN')):
p['flowMN'].setkey('n', n + 1)
p.run()
p.show()
self.assertLessEqual(len(p), 20, "Incorrect task count")
def test_find_bdp(self):
project = admit.Project()
# add one task
task = admit.File_AT(touch=True)
name = "File.dat"
task.setkey("file", name)
project.addtask(task) # add task
# now add an output bdp
obdp = admit.File_BDP('Test')
task.addoutput(obdp)
self.p.addtask(task)
# find_bdp() will search Admit output data directory for *.bdp files
# should return an empty list since no *.bdp file created by this test
ret = self.p.find_bdp()
outdir = self.p.dir()
if (self.verbose):
if len(ret):
print "Found BDPs in", outdir
else:
print "No BDPs Found in", outdir
self.assertTrue(len(ret) == 0)
def _run(argv):
# Verify arguments are good
if (not admit.recipeutils._processargs(argv, REQARGS, OPTARGS, KEYS,
KEYDESC, __doc__)):
return
cubefile = argv[1]
projdir = os.path.splitext(argv[1])[0] + '.admit'
pbcorfile = None
if len(argv) == 3:
pbcorfile = argv[2]
#========================================================================
# Master project. Beginning for ADMIT Commands
#
p = admit.Project(projdir, commit=False)
# convert key values from string
try:
KEYS["minchan"] = int(KEYS["minchan"])
KEYS["numsigma"] = float(KEYS["numsigma"])
KEYS["pad"] = int(KEYS["pad"])
KEYS["width"] = int(KEYS["width"])
KEYS["cutoff"] = ast.literal_eval(str(KEYS["cutoff"]))
KEYS["box"] = ast.literal_eval(str(KEYS["box"]))
except Exception, e:
print("Exception converting keyword value to number:", e)
return
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 class
a = admit.Project(self.admitdir)
# instantiate hello world at
h = admit.HelloWorld_AT(yourname="Bob")
task1id = a.addtask(h)
# check the fm
a.fm.verify()
# run admit and save to disk
a.run()
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))
if (len(a.fm[atask]._bdp_in) != 0
and len(a2.fm[atask]._bdp_in) != 0):
self.assertEqual(a.fm[atask]._bdp_in[0]._taskid,
a2.fm[atask]._bdp_in[0]._taskid)
self.assertEqual(a.fm._connmap, a2.fm._connmap)
for at in a.fm:
for i in range(len(a.fm[at]._bdp_out)):
print "%d %d %d %s %s\n" % (i,
a.fm[at]._bdp_out[i]._taskid,
a2.fm[at]._bdp_out[i]._taskid,
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 setUp(self):
self.verbose = False
self.testName = "Admit Unit Test"
# sometimes CWD is set to self.outputDir that is deleted by
# tearDown() function, then we need to change back to the parent dir
try:
os.getcwd()
except OSError:
os.chdir('..')
self.outputDir = "AdmitUnitTest"
self.p = admit.Project(self.outputDir)
def test_multiflow(self):
# Parent projects.
p1 = admit.Project(self.outputDir + "/p1")
p2 = admit.Project(self.outputDir + "/p2")
for p in [p1, p2]:
task = admit.File_AT(touch=True)
task.setkey("file", "File.dat")
tid1 = p.addtask(task)
task = admit.Flow11_AT(alias="at" + p.baseDir[-2]) # at1 or at2
task.setkey("file", "Flow11.dat")
tid2 = p.addtask(task, [(tid1, 0)])
p.run()
# Multiflow project.
mflow = admit.Project(self.outputDir + "/mflow")
# Add parent projects to the multiflow.
# Note they must be completely up-to-date for this to succeed.
pid1 = mflow.pm.addProject(self.outputDir + "/p1")
pid2 = mflow.pm.addProject(self.outputDir + "/p2")
print "Parent project p1 ID = ", pid1
print "Parent project p2 ID = ", pid2
# Find some ATs to link into the multiflow.
# Here searching is done by alias name.
stuples = []
for pid in [pid1, pid2]:
alias = "at" + mflow.pm[pid].baseDir[-2]
print "Looking for alias", alias, "..."
ats = mflow.pm.findTaskAlias(pid, alias)
print "Result:", ats
self.assertEqual(len(ats), 1, "Found wrong number of matches")
self.assertEqual(ats[0]._alias, alias, "Alias mismatch")
self.assertNotEqual(ats[0].getProject(), 0, "Null project ID")
print alias, "belongs to project ", \
mflow.pm.getProjectDir(ats[0].getProject())
# Add task to the multiflow (must be a root task---no stuples).
tid = mflow.addtask(ats[0])
print "tid=%d stale=%s" % (tid, mflow[tid].isstale())
self.assertNotEqual(tid, -1, "mflow.addtask(" + alias + ") failed")
stuples.append((tid, 0))
# Combine output from the two newly linked tasks.
print "stuples =", stuples
tid = mflow.addtask(admit.FlowN1_AT(file="FlowN1.dat", touch=True),
stuples)
self.assertNotEqual(tid, -1, "mflow.addtask(FlowN1) failed")
mflow.show()
# Run the multiflow.
mflow.run()
# Make at2 out of date, then re-run the multiflow to update everything.
at2 = mflow.findtask(lambda at: at._alias == "at2")
self.assertEqual(len(at2), 1, "Found wrong number of matches for at2")
self.assertEqual(at2[0]._alias, "at2", "Alias mismatch for at2")
at2[0].setkey("file", "Flow11-at2.dat")
mflow.show()
mflow.run()
# for individual spectral lines.
#
# Usage: admit-example0.py input.fits
#
# =============================================================================
# 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.
#!/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,
# announce version
print 'ADMIT3: Version ', version
# do the work in a proper ".admit" directory
adir = admit_dir(file)
# dirty method, it really should check if adir is an admit directory
if clean and adir != file:
print "Removing previous results from ", adir
os.system('rm -rf %s' % adir)
create = True
else:
create = False
a = admit.Project(adir,
name='Testing ADMIT3 style pipeline - version %s' % version,
create=create,
loglevel=loglevel)
if a.new:
print "Starting a new ADMIT using ", argv[0]
os.system('cp -a %s %s' % (argv[0], adir))
a.set(admit_dir=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 in IPython!
def setUp(self):
self.root = admit.utils.admit_root()
self.testoutput = self.root + "/INTEGTESTRESULT"
self.success = "FAILED"
self.testName = "Test LineSegment_AT vs. LineID_AT identifylines=False"
self.transitions = [
[["13COv=0", [110.15, 110.25], 6.0, 30.0,
5.0]], # 0 single 13CO line
[["CH3CNv=0", [110.21, 110.5], 8.5, 15.0,
0.0]], # 2 Methyl cyanide cluster
[["N2H+v=0", [93.1, 93.2], 15.5, 0.25,
0.0]], # 4 narrow, blended hyperfines
[
["COv=0", [115.2, 115.3], 5.5, 20.0,
-30.0], # 6 galactic emission type spectrum
["COv=0", [115.2, 115.3], 5.0, 20.0, 30.0]
],
[
["COv=0", [115.2, 115.3], 5.5, 20.0,
-30.0], # 8 P-cygni type profile
["COv=0", [115.2, 115.3], -5.0, 20.0, 30.0]
],
[
["(CH3)2COv=0", [240.0, 242.0], 10.0, 5.0,
0.0], # 10 complex molecules
["CH3OCHOv=0", [240.0, 242.0], 15.0, 3.0, 1.0],
["CH3CH2CNv=0", [240.0, 242.0], 20.0, 5.0, 0.0],
["CH3OCH3", [240.0, 242.0], 5.0, 5.0, 0.0],
["CH3OHvt=0", [240.0, 242.0], 20.0, 5.0, 0.0],
["CH3OHvt=1", [240.0, 242.0], 5.0, 5.0, 0.0]
],
[
["COv=0", [115.2, 115.3], 3.0, 30.0,
-40.0], # 12 outflow type spectrum
["COv=0", [115.2, 115.3], 3.0, 30.0, 40.0],
["COv=0", [115.2, 115.3], 6.0, 8.0, 15.0],
["COv=0", [115.2, 115.3], 5.5, 8.0, -15.0],
["COv=0", [115.2, 115.3], -3.5, 8.0, 0.0]
],
[["CH3CH2CNv=0", [93.65, 93.7], 8.0, 2.0, 0.0],
["CH3OCH3", [93.65, 93.7], 6.5, 2.0,
0.0]], # 14 blended lines from different molecules
[["Hα", [99.02, 99.025], 4.0, 55.0, -10.0],
["CH3CHOvt=1", [99.02, 99.025], 4.0, 5.0,
0.0]], # 16 wide and narrow blended lines
[["N2H+v=0", [93.1, 93.2], -15.5, 0.25,
0.0]], # 18 pure absorption
[["NH2CHO", [102.2, 102.25], 5.5, 17.0, -40.0],
["NH2CHO", [102.2, 102.25], 5.0, 17.0, 40.0],
["CH3CCHv=0", [102.5, 102.55], 30.0, 17.0, -39.0],
["CH3CCHv=0", [102.5, 102.55], 25.0, 17.0, 39.0],
["H2CS", [103.0, 103.1], 6.5, 17.0, -40.0],
["H2CS", [103.0, 103.1], 5.7, 17.0, 40.0],
["DNCO", [101.9, 102.1], 3.5, 10.0,
39.5]], # 20 glactic emission with multiple non-tier 1 molecules
[["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 0.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 4.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, -4.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, -8.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 8.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, -12.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 12.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 16.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, -16.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 20.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, -20.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0, 24.0],
["CH3CCHv=0", [102.547, 102.55], 6.5, 6.0,
-24.0]], # 22 wide plateau like line
[["NH2CHO", [102.2, 102.25], 3.5, 8.0, 1.0],
["CH3CCHv=0", [102.5, 102.55], 2.2, 4.0, -1.5],
["H2CS", [103.0, 103.1], 4.5, 5.2, 0.0],
["DNCO", [101.9, 102.1], 3.0, 3.5, 0.5]], # 24 few weak lines
[["CH3OCH3", [90.935, 90.94], 12.0, 0.5,
0.1]] # 26 pure triplet of lines
]
self.delta = [
0.5, 0.5, 0.005, 0.5, 0.5, 0.5, 0.1, 0.1, 0.2, 0.005, 0.4, 0.2,
0.5, 0.025
] #MHz
self.contin = [
0.5, 1.3, 0.1, 3.0, 1.2, 0.5, 0.1, 1.2, 2.0, 1.0, 10.0, 3.0, 0.0,
1.5, 2.5
] #SNR
self.seed = [10, 25, 15, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80]
self.freq = [
110.25, 110.3, 93.175, 115.271, 115.3, 241.0, 115.26, 93.68, 99.0,
93.175, 102.5, 102.52, 102.55, 90.94
] #GHz
self.nchan = [
1000, 500, 2000, 1000, 1000, 4000, 1000, 1000, 1000, 2100, 4000,
800, 4000, 1000
]
today = dt.date.today()
date = "%i-%02i-%02i" % (today.year, today.month, today.day)
plotmode = admit.PlotControl.BATCH # NOPLOT, BATCH, INTERACTIVE, SHOW_AT_END
plottype = admit.PlotControl.PNG # PNG, JPG, etc.
loglevel = 50 # 10=DEBUG, 15=TIMING 20=INFO 30=WARNING 40=ERROR 50=FATAL
self.outdir = tempfile.mkdtemp()
self.admitdir = "%s/%s" % (self.outdir, date)
print "################## %s Project directory = %s ################" % (
self.__class__.__name__, self.admitdir)
admit.util.utils.rmdir(self.outdir)
self.a = admit.Project(self.admitdir,
name='LineSegment vs. LineID',
create=True,
loglevel=loglevel)
# Default ADMIT plotting environment
self.a.plotparams(plotmode, plottype)
#! /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()
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))
freq = [
110.25, 110.3, 93.175, 115.271, 115.3, 241.0, 115.26, 93.68, 99.0, 93.175,
102.5, 102.52, 102.55, 90.94
] #GHz
nchan = [
1000, 500, 2000, 1000, 1000, 4000, 1000, 1000, 1000, 2100, 4000, 800, 4000,
1000
]
projdir = "%s/%s" % (args['dir'][0], date)
print "################## PROJECTDIR = %s ################" % projdir
admit.util.utils.rmdir(projdir)
a = admit.Project(projdir,
name='Testing LineID',
create=True,
loglevel=loglevel)
# Default ADMIT plotting environment
a.plotparams(plotmode, plottype)
for i in range(len(transitions)):
spec = a.addtask(
admit.GenerateSpectrum_AT(seed=seed[i],
nchan=nchan[i],
contin=contin[i],
delta=delta[i],
freq=freq[i],
transitions=transitions[i],
alias="test_%i" % (i)))
bdp_in = [(spec, 0)]
# convert key values from string
try:
KEYS["minchan"] = int(KEYS["minchan"])
KEYS["numsigma"] = float(KEYS["numsigma"])
KEYS["pad"] = int(KEYS["pad"])
KEYS["width"] = int(KEYS["width"])
KEYS["cutoff"] = ast.literal_eval(str(KEYS["cutoff"]))
except Exception, e:
print("Exception converting keyword value to number:",e)
return
#========================================================================
# 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"])))
#!/usr/bin/env python
#
# Hello multiworld (type 1) test script.
#
# Run unittest_multiflow1.py first to create projects p1, p2;
# otherwise no tasks will be found and the script will fail.
#
import admit
import admit.at as at
# Create multiflow project.
mflow = admit.Project("mflow")
pm = mflow.getManager()
# Add projects with tasks to link.
proj1 = pm.addProject("p1")
proj2 = pm.addProject("p2")
# Find some tasks and link them into the multiflow.
stuples = []
#
ats = pm.findTaskAlias(proj1, "at1")
tid = mflow.addtask(ats[0])
stuples.append((tid, 0))
ats = pm.findTaskAlias(proj2, "at2")
tid = mflow.addtask(ats[0])
stuples.append((tid, 0))
# Combine outputs from the linked tasks into a new task.
tid = mflow.addtask(at.FlowN1(file="FlowN1.dat", touch=True), stuples)
def setUp(self):
self.verbose = False
self.testName = "AT Base Class Unit Test"
self.project = admit.Project("UnitTest")
# 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])
