def run(s):
"""Function to create mirstr and run
Arguments:
s {tuple} -- Element one is the miriad task to execute and
the second is the working directory to execute in
"""
task = mu.mirstr(s[0])
task.run(cwd=s[1])
print(task)
"""
import mir_utils as mu
import shutil
import glob
import os
NFBIN = 4
IFSEL = 1
FREQ = '7700'
primary = f"{mu.primary}.{FREQ}"
secondary = f"{mu.secondary}.{FREQ}"
mosaic = f"{mu.science}.{FREQ}"
# Load in the data
atlod = mu.mirstr(f"atlod in=raw/*C3171 options=rfiflag,birdie,xycorr,noauto ifsel={IFSEL} out=data{IFSEL}.uv").run()
print(atlod)
# Flag the known bad channels out
mu.uvflag(atlod.attribute('out'), mu.flags_7)
# Split the data up
uvsplit = mu.mirstr(f"uvsplit vis={atlod.attribute('out')} options=mosaic").run()
print(uvsplit)
# Primary calibration
mfcal = mu.mirstr(f'mfcal vis={primary} interval=0.1').run()
gpcal = mu.mirstr(f'gpcal vis={primary} interval=0.1 nfbin={NFBIN} options=xyvary').run()
print(mfcal)
print(gpcal)
FREQ = '7700'
primary = f"{mu.primary}.{FREQ}"
secondary = f"{mu.secondary}.{FREQ}"
mosaic = f"{mu.science}.{FREQ}"
# Check for directories and files
if not os.path.exists('uv'):
print('Data uv files do not exist')
sys.exit(1)
# Load in the data
uv = 'uv/data1.uv'
# Split the data up
uvsplit = mu.mirstr(f"uvsplit vis={uv} options=mosaic").run()
print(uvsplit)
# Automated flagging
pgflag = mu.mirstr(f"pgflag vis={secondary} command='<b' stokes=i,q,u,v flagpar=8,5,5,3,6,3 options=nodisp").run()
print(pgflag)
pgflag = mu.mirstr(f"pgflag vis={secondary} command='<b' stokes=i,v,q,u flagpar=8,2,2,3,6,3 options=nodisp").run()
print(pgflag)
pgflag = mu.mirstr(f"pgflag vis={secondary} command='<b' stokes=i,v,u,q flagpar=8,2,2,3,6,3 options=nodisp").run()
print(pgflag)
sec_model = mu.model_secondary()
