def _pipeline_sparx(self, Xmol, src, pop, img, cnv, tmb, genimg=True):
"""
Pipeline for generating SPARX solutions
"""
# Calculate excitation
if not exists(pop):
#tasks.task_amc(source=src, molec='o-h2o_2lev', out=pop)
utils.call("mpirun -np %d sparx --parallel run task_amc source='%s' molec='%s' out='%s' fixiter=10 lte=%s trace=%s nrays=%d snr=%.0f tolerance=%.2e maxiter=%d"%(NPROC, src, self.mol.name, pop, FROMLTE, TRACE, NRAYS, SNR, TOLERANCE, MAXITER))
#utils.call("sparx run task_amc source='%s' molec='o-h2o_2lev' out='%s'"%(src, pop))
if genimg:
# Generate synthesized map
if not exists(img):
tasks.task_lineobs(
source=pop,
chan="[%d,'%gkms^-1']"%(self.chan_n, self.chan_width),
dist="%gpc"%(self.dist / Unit.pc),
line=0,
out=img,
npix="[256,256]",
cell="['0.5asec','0.5asec']",
unit="JY/PIXEL")
# To avoid mysterious 'invalid argument' bug in miriad
from time import sleep
sleep(0.5)
# Convolve with beam
if not exists(cnv):
miriad.convol(img, cnv, self.fwhm)
# To avoid mysterious 'invalid argument' bug in miriad
from time import sleep
sleep(0.5)
# Convert to brightness temperature
if not exists(tmb):
miriad.convert_flux_to_tb(cnv, tmb, self.freq, self.fwhm)
return
src3d = "%s.%s.src3d"%(name, molec)
out3d = "%s.%s.xyv3d"%(name, molec)
tau3d = "%s.%s.tau3d"%(name, molec)
# Reset inputs (safer)
inputs.reset_inputs()
# Calculate analytical solution
Tb_est, tau_est = Estimate(molec)
# Generate model
tasks.task_valline1d(out=src1d, molec=molec, xmol=1e-10)
tasks.task_valline3d(out=src3d, molec=molec, xmol=1e-10)
# Generate synthetic dust observations
tasks.task_lineobs(source=src1d, out=out1d, tau=tau1d, line="0", cell="['0.5asec', '0.5asec']", unit='K', chan="[32, '0.2kms^-1']")
tasks.task_lineobs(source=src3d, out=out3d, tau=tau3d, line="0", cell="['0.5asec', '0.5asec']", unit='K', chan="[32, '0.2kms^-1']")
from subprocess import Popen, PIPE
# Get brightness temperature
p = Popen("imspec in=%s options=eformat,nohead region='rel,box(0,0,0,0)' plot=sum | head -n 18 | tail -n 1 | awk '{print $3}'"%out1d, shell=True, stdout=PIPE, stderr=PIPE)
Tb_s1d = float(p.communicate()[0])
p = Popen("imspec in=%s options=eformat,nohead region='rel,box(0,0,0,0)' plot=sum | head -n 18 | tail -n 1 | awk '{print $3}'"%out3d, shell=True, stdout=PIPE, stderr=PIPE)
Tb_s3d = float(p.communicate()[0])
# Get peak tau
p = Popen("imspec in=%s options=eformat,nohead region='rel,box(0,0,0,0)' plot=sum | head -n 18 | tail -n 1 | awk '{print $3}'"%tau1d, shell=True, stdout=PIPE, stderr=PIPE)
tau_s1d = float(p.communicate()[0])
p = Popen("imspec in=%s options=eformat,nohead region='rel,box(0,0,0,0)' plot=sum | head -n 18 | tail -n 1 | awk '{print $3}'"%tau3d, shell=True, stdout=PIPE, stderr=PIPE)
tau_s3d = float(p.communicate()[0])