def validateinput():
"""
Parse the input config file (command line argument) and validate that the
parameters look okay
"""
logger.info('This is version {0} of the pipeline'.format(processMeerKAT.__version__))
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool)
refant = va(taskvals, 'crosscal', 'refant', str)
fields = bookkeeping.get_field_ids(taskvals['fields'])
# Check if the reference antenna exists, and complain and quit if it doesn't
if not calcrefant:
refant = va(taskvals, 'crosscal', 'refant', str)
msmd.open(visname)
get_fields.check_refant(MS=visname, refant=refant, warn=False)
msmd.close()
msmd.done()
if not os.path.exists(visname):
raise IOError("Path to MS %s not found" % (visname))
def main():
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
fields = bookkeeping.get_field_ids(taskvals['fields'])
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool, default=False)
# Calculate reference antenna
if calcrefant:
if len(fields.fluxfield.split(',')) > 1:
field = fields.fluxfield.split(',')[0]
else:
field = fields.fluxfield
refant, badants = get_ref_ant(visname, field)
# Overwrite config file with new refant
config_parser.overwrite_config(args['config'],
conf_sec='crosscal',
conf_dict={'refant': refant})
config_parser.overwrite_config(args['config'],
conf_sec='crosscal',
conf_dict={'badants': badants})
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
spw = va(taskvals, 'crosscal', 'spw', str, default='')
specavg = va(taskvals, 'crosscal', 'width', int, default=1)
timeavg = va(taskvals, 'crosscal', 'timeavg', str, default='8s')
keepmms = va(taskvals, 'crosscal', 'keepmms', bool)
msmd.open(visname)
newvis = split_vis(visname, spw, fields, specavg, timeavg, keepmms)
config_parser.overwrite_config(args['config'],
conf_dict={'vis': "'{0}'".format(newvis)},
conf_sec='data')
config_parser.overwrite_config(
args['config'],
conf_dict={'crosscal_vis': "'{0}'".format(visname)},
conf_sec='run',
sec_comment='# Internal variables for pipeline execution')
msmd.done()
def main(args, taskvals):
visname = va(taskvals, 'run', 'crosscal_vis', str)
keepmms = va(taskvals, 'crosscal', 'keepmms', bool)
fields = bookkeeping.get_field_ids(taskvals['fields'])
run_tclean(visname, fields, keepmms)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool, default=False)
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
spw = va(taskvals, 'crosscal', 'spw', str, default='')
nspw = va(taskvals, 'crosscal', 'nspw', int, default='')
tasks = va(taskvals, 'slurm', 'ntasks_per_node', int)
preavg = va(taskvals, 'crosscal', 'chanbin', int, default=1)
include_crosshand = va(taskvals, 'run', 'dopol', bool, default=False)
createmms = va(taskvals, 'crosscal', 'createmms', bool, default=True)
# HPC Specific Configuration
known_hpc_path = os.path.dirname(SCRIPT_DIR) + "/known_hpc.cfg"
KNOWN_HPCS, HPC_CONFIG = config_parser.parse_config(known_hpc_path)
HPC_NAME = taskvals["run"]["hpc"]
HPC_NAME = HPC_NAME if HPC_NAME in KNOWN_HPCS.keys() else "unknown"
CPUS_PER_NODE_LIMIT = va(KNOWN_HPCS,
HPC_NAME,
"CPUS_PER_NODE_LIMIT".lower(),
dtype=int)
if nspw > 1:
casalog.setlogfile(
'logs/{SLURM_JOB_NAME}-{SLURM_ARRAY_JOB_ID}_{SLURM_ARRAY_TASK_ID}.casa'
.format(**os.environ))
else:
logfile = casalog.logfile()
casalog.setlogfile(
'logs/{SLURM_JOB_NAME}-{SLURM_JOB_ID}.casa'.format(**os.environ))
if ',' in spw:
low, high, unit, dirs = config_parser.parse_spw(args['config'])
spwname = '{0:.0f}~{1:.0f}MHz'.format(min(low), max(high))
else:
spwname = spw.replace('0:', '')
msmd.open(visname)
npol = msmd.ncorrforpol()[0]
if not include_crosshand and npol == 4:
npol = 2
CPUs = npol if tasks * npol <= CPUS_PER_NODE_LIMIT else 1 #hard-code for number of polarisations
mvis = do_partition(visname, spw, preavg, CPUs, include_crosshand,
createmms, spwname)
mvis = "'{0}'".format(mvis)
vis = "'{0}'".format(visname)
config_parser.overwrite_config(args['config'],
conf_sec='data',
conf_dict={'vis': mvis})
config_parser.overwrite_config(
args['config'],
conf_sec='run',
sec_comment='# Internal variables for pipeline execution',
conf_dict={'orig_vis': vis})
msmd.done()
def main(args, taskvals):
visname = va(taskvals, 'run', 'crosscal_vis', str)
keepmms = va(taskvals, 'crosscal', 'keepmms', bool)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
msmd.open(visname)
if not os.path.exists(PLOT_DIR):
os.mkdir(PLOT_DIR)
# #Superseded by 'plotcal_spw.py'
# #Plot solutions for bandpass calibrator
# plotms(vis=calfiles.bpassfile, xaxis='Real', yaxis='Imag', coloraxis='corr', plotfile='{0}/bpass_real_imag.png'.format(PLOT_DIR),showgui=False)
# plotms(vis=calfiles.bpassfile, xaxis='freq', yaxis='Amp', coloraxis='antenna1', plotfile='{0}/bpass_freq_amp.png'.format(PLOT_DIR),showgui=False)
# plotms(vis=calfiles.bpassfile, xaxis='freq', yaxis='Phase', coloraxis='antenna1', plotfile='{0}/bpass_freq_phase.png'.format(PLOT_DIR),showgui=False)
#
# #Plot solutions for phase calibrator
# plotms(vis=calfiles.gainfile, xaxis='Real', yaxis='Imag', coloraxis='corr', plotfile='{0}/phasecal_real_imag.png'.format(PLOT_DIR),showgui=False)
# plotms(vis=calfiles.gainfile, xaxis='Time', yaxis='Amp', coloraxis='antenna1', plotfile='{0}/phasecal_time_amp.png'.format(PLOT_DIR),showgui=False)
# plotms(vis=calfiles.gainfile, xaxis='Time', yaxis='Phase', coloraxis='antenna1', plotfile='{0}/phasecal_time_phase.png'.format(PLOT_DIR),showgui=False)
#
# #Plot solutions for individual antennas of bandpass and phase calibrator in 3x2 panels
# plot_antennas('bpass',fields,calfiles,xaxis='freq',yaxis='amp')
# plot_antennas('bpass',fields,calfiles,xaxis='freq',yaxis='phase')
# plot_antennas('phasecal',fields,calfiles,xaxis='time',yaxis='amp')
# plot_antennas('phasecal',fields,calfiles,xaxis='time',yaxis='phase')
extn = 'mms' if keepmms else 'ms'
for field in fields:
if field != '':
for fname in field.split(','):
if fname.isdigit():
fname = msmd.namesforfields(int(fname))[0]
inname = '%s.%s.%s' % (os.path.splitext(visname)[0], fname,
extn)
if not os.path.exists('{0}/{1}_freq_amp.png'.format(
PLOT_DIR, fname)):
plotms(vis=inname,
xaxis='freq',
yaxis='Amp',
coloraxis='corr',
plotfile='{0}/{1}_freq_amp.png'.format(
PLOT_DIR, fname),
showgui=False)
plotms(vis=inname,
xaxis='Real',
yaxis='Imag',
coloraxis='corr',
plotfile='{0}/{1}_real_imag.png'.format(
PLOT_DIR, fname),
showgui=False)
msmd.done()
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
minbaselines = va(taskvals, 'crosscal', 'minbaselines', int, default=4)
do_parallel_cal_apply(visname, fields, calfiles)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool, default=False)
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
spw = va(taskvals, 'crosscal', 'spw', str, default='')
tasks = va(taskvals, 'slurm', 'ntasks_per_node', int)
preavg = va(taskvals, 'crosscal', 'chanbin', int, default=1)
include_crosshand = va(taskvals, 'run', 'dopol', bool, default=False)
createmms = va(taskvals, 'crosscal', 'createmms', bool, default=True)
msmd.open(visname)
npol = msmd.ncorrforpol()[0]
if not include_crosshand and npol == 4:
npol = 2
CPUs = npol if tasks * npol <= processMeerKAT.CPUS_PER_NODE_LIMIT else 1 #hard-code for number of polarisations
mvis = do_partition(visname, spw, preavg, CPUs, include_crosshand,
createmms)
mvis = "'{0}'".format(mvis)
vis = "'{0}'".format(visname)
config_parser.overwrite_config(args['config'],
conf_sec='data',
conf_dict={'vis': mvis})
config_parser.overwrite_config(
args['config'],
conf_sec='run',
sec_comment='# Internal variables for pipeline execution',
conf_dict={'orig_vis': vis})
msmd.done()
def main(args,taskvals):
visname = va(taskvals, "data", "vis", str)
if os.path.exists(os.path.join(os.getcwd(), "caltables")):
shutil.rmtree(os.path.join(os.getcwd(), "caltables"))
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals["fields"])
spw = va(taskvals, "crosscal", "spw", str, default="")
standard = va(taskvals, "crosscal", "standard", str, default="Stevens-Reynolds 2016")
dopol = va(taskvals, 'run', 'dopol', bool, default=False)
createmms = va(taskvals, 'crosscal', 'createmms', bool, default=True)
do_setjy(visname, spw, fields, standard, dopol, createmms)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
do_cross_cal_apply(visname, fields, calfiles, caldir)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
do_pre_flag_2(visname, fields)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
minbaselines = va(taskvals, 'crosscal', 'minbaselines', int, default=4)
standard = va(taskvals,
'crosscal',
'standard',
str,
default='Stevens-Reynolds 2016')
refant = va(taskvals, 'crosscal', 'refant', str, default='m059')
do_parallel_cal(visname, fields, calfiles, refant, caldir, minbaselines,
standard)
def main():
config = config_parser.parse_args()['config']
# Parse config file
taskvals, config = config_parser.parse_config(config)
visname = va(taskvals, 'data', 'vis', str)
keepmms = va(taskvals, 'crosscal', 'keepmms', bool)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
msmd.open(visname)
if not os.path.exists(PLOT_DIR):
os.mkdir(PLOT_DIR)
#Plot solutions for bandpass calibrator
plotms(vis=calfiles.bpassfile, xaxis='Real', yaxis='Imag', coloraxis='corr', plotfile='{0}/bpass_real_imag.png'.format(PLOT_DIR),showgui=False)
plotms(vis=calfiles.bpassfile, xaxis='freq', yaxis='Amp', coloraxis='antenna1', plotfile='{0}/bpass_freq_amp.png'.format(PLOT_DIR),showgui=False)
plotms(vis=calfiles.bpassfile, xaxis='freq', yaxis='Phase', coloraxis='antenna1', plotfile='{0}/bpass_freq_phase.png'.format(PLOT_DIR),showgui=False)
#Plot solutions for phase calibrator
plotms(vis=calfiles.gainfile, xaxis='Real', yaxis='Imag', coloraxis='corr', plotfile='{0}/phasecal_real_imag.png'.format(PLOT_DIR),showgui=False)
plotms(vis=calfiles.gainfile, xaxis='Time', yaxis='Amp', coloraxis='antenna1', plotfile='{0}/phasecal_time_amp.png'.format(PLOT_DIR),showgui=False)
plotms(vis=calfiles.gainfile, xaxis='Time', yaxis='Phase', coloraxis='antenna1', plotfile='{0}/phasecal_time_phase.png'.format(PLOT_DIR),showgui=False)
#Plot solutions for individual antennas of bandpass and phase calibrator in 3x2 panels
plot_antennas('bpass',fields,calfiles,xaxis='freq',yaxis='amp')
plot_antennas('bpass',fields,calfiles,xaxis='freq',yaxis='phase')
plot_antennas('phasecal',fields,calfiles,xaxis='time',yaxis='amp')
plot_antennas('phasecal',fields,calfiles,xaxis='time',yaxis='phase')
extn = 'mms' if keepmms else 'ms'
for field in fields:
for subf in field.split(','):
fname = msmd.namesforfields(int(subf))[0]
inname = '%s.%s.%s' % (os.path.splitext(visname)[0], fname, extn)
if not os.path.exists('{0}/{1}_freq_amp.png'.format(PLOT_DIR,fname)):
plotms(vis=inname, xaxis='freq', yaxis='Amp', coloraxis='corr', plotfile='{0}/{1}_freq_amp.png'.format(PLOT_DIR,fname),showgui=False)
plotms(vis=inname, xaxis='Real', yaxis='Imag', coloraxis='corr', plotfile='{0}/{1}_real_imag.png'.format(PLOT_DIR,fname),showgui=False)
msmd.close()
msmd.done()
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
minbaselines = va(taskvals, 'crosscal', 'minbaselines', int, default=4)
standard = va(taskvals,
'crosscal',
'standard',
str,
default='Perley-Butler 2010')
do_cross_cal(visname, fields, calfiles, refant, caldir, minbaselines,
standard)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
fields = bookkeeping.get_field_ids(taskvals['fields'])
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool)
spw = va(taskvals, 'crosscal', 'spw', str)
nspw = va(taskvals, 'crosscal', 'nspw', int)
# Calculate reference antenna
if calcrefant:
if len(fields.fluxfield.split(',')) > 1:
field = fields.fluxfield.split(',')[0]
else:
field = fields.fluxfield
refant, badants = get_ref_ant(visname, field)
# Overwrite config file with new refant
config_parser.overwrite_config(
args['config'],
conf_sec='crosscal',
conf_dict={'refant': "'{0}'".format(refant)})
config_parser.overwrite_config(args['config'],
conf_sec='crosscal',
conf_dict={'badants': badants})
#Replace reference antenna in each SPW config
if nspw > 1:
for SPW in spw.split(','):
spw_config = '{0}/{1}'.format(SPW.replace('0:', ''),
args['config'])
# Overwrite config file with new refant
config_parser.overwrite_config(
spw_config,
conf_sec='crosscal',
conf_dict={'refant': "'{0}'".format(refant)})
config_parser.overwrite_config(spw_config,
conf_sec='crosscal',
conf_dict={'badants': badants})
config_parser.overwrite_config(spw_config,
conf_sec='crosscal',
conf_dict={'calcrefant': False})
else:
logger.info(
"Skipping calculation of reference antenna, as 'calcrefant=False' in '{0}'."
.format(args['config']))
def main(args,taskvals):
visname = va(taskvals, 'data', 'vis', str)
badfreqranges = taskvals['crosscal'].pop('badfreqranges', ['935~947MHz', '1160~1310MHz', '1476~1611MHz', '1670~1700MHz'])
badants = taskvals['crosscal'].pop('badants')
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
do_pre_flag(visname, fields, badfreqranges, badants)
def main(args, taskvals):
"""
Parse the input config file (command line argument) and validate that the
parameters look okay
"""
logger.info('This is version {0} of the pipeline'.format(
processMeerKAT.__version__))
visname = va(taskvals, 'data', 'vis', str)
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool)
refant = taskvals['crosscal']['refant']
if type(refant) is str and 'm' in refant:
refant = va(taskvals, 'crosscal', 'refant', str)
else:
refant = va(taskvals, 'crosscal', 'refant', int)
nspw = va(taskvals, 'crosscal', 'nspw', int)
fields = bookkeeping.get_field_ids(taskvals['fields'])
# Check if the reference antenna exists, and complain and quit if it doesn't
if not calcrefant:
refant = va(taskvals, 'crosscal', 'refant', str)
msmd.open(visname)
read_ms.check_refant(MS=visname,
refant=refant,
config=args['config'],
warn=False)
msmd.done()
if not os.path.exists(visname):
raise IOError("Path to MS %s not found" % (visname))
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
spw = va(taskvals, 'crosscal', 'spw', str, default='')
nspw = va(taskvals, 'crosscal', 'nspw', int, default='')
fields = bookkeeping.get_field_ids(taskvals['fields'])
dirs = config_parser.parse_spw(args['config'])[3]
if ',' in spw:
newvis = do_concat(visname, fields, dirs)
config_parser.overwrite_config(
args['config'],
conf_dict={'vis': "'{0}'".format(newvis)},
conf_sec='data')
config_parser.overwrite_config(
args['config'],
conf_dict={'crosscal_vis': "'{0}'".format(visname)},
conf_sec='run',
sec_comment='# Internal variables for pipeline execution')
else:
logger.error(
"Only found one SPW in '{0}', so will skip concat.".format(
args['config']))
def main():
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
calcrefant = va(taskvals, 'crosscal', 'calcrefant', bool, default=False)
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
spw = va(taskvals, 'crosscal', 'spw', str, default='')
mvis = do_partition(visname, spw)
mvis = "'{0}'".format(mvis)
vis = "'{0}'".format(visname)
config_parser.overwrite_config(args['config'],
conf_sec='data',
conf_dict={'vis': mvis})
config_parser.overwrite_config(args['config'],
conf_sec='data',
conf_dict={'orig_vis': vis})
def main():
config = config_parser.parse_args()['config']
# Parse config file
taskvals, config = config_parser.parse_config(config)
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
#Plot solutions for bandpass calibrator
fastplot(calfiles.bpassfile,
col='CPARAM',
xaxis='Real',
yaxis='Imag',
fname='bpass_real_imag.png')
fastplot(calfiles.bpassfile,
col='CPARAM',
xaxis='chan',
yaxis='Amp',
logy=True,
fname='bpass_chan_amp.png')
fastplot(calfiles.bpassfile,
col='CPARAM',
xaxis='chan',
yaxis='Phase',
fname='bpass_chan_phase.png')
#Plot solutions for phase calibrator
fastplot(calfiles.gainfile,
col='CPARAM',
xaxis='Amp',
yaxis='Time',
fname='phasecal_time_amp.png',
markersize=2,
extent=1e-8)
fastplot(calfiles.gainfile,
col='CPARAM',
xaxis='Phase',
yaxis='Time',
fname='phasecal_time_phase.png',
markersize=2,
extent=1e-8)
def main(args,taskvals):
try:
if not os.path.exists(PLOT_DIR):
os.makedirs(PLOT_DIR)
fields = bookkeeping.get_field_ids(taskvals['fields'])
visname = va(taskvals, 'run', 'crosscal_vis', str)
polfield = bookkeeping.polfield_name(visname)
msmd.open(visname)
caldir = 'caltables'
spwdir = config_parser.parse_spw(args['config'])[3]
if type(spwdir) is str:
spwdir = glob.glob(spwdir)
for ff in fields.gainfields.split(','):
plotstr='phase,time'
table_ext = 'gcal'
title='Gain Phase'
outname = '{}/field_{}_gain_phase'.format(PLOT_DIR,ff)
plotcal(plotstr, int(msmd.fieldsforname(ff)[0]), spwdir, caldir, table_ext, title, outname)
plotstr='amp,time'
table_ext = 'gcal'
title='Gain Amp'
outname = '{}/field_{}_gain_amp'.format(PLOT_DIR,ff)
plotcal(plotstr, int(msmd.fieldsforname(ff)[0]), spwdir, caldir, table_ext, title, outname)
#print("k")
#plotstr='delay,freq'
#table_ext = 'kcal'
#title='Delay'
#outname = '{}/field_{}_delay'.format(PLOT_DIR,fields.fluxfield)
#plotcal(plotstr, int(msmd.fieldsforname(fields.fluxfield)[0]), spwdir, caldir, table_ext, title, outname)
#print("kcross")
#plotstr='delay,freq'
#table_ext = 'xdel'
#title='Crosshand Delay'
#outname = '{}/field_{}_crosshanddelay'.format(PLOT_DIR,fields.fluxfield)
#plotcal(plotstr, int(msmd.fieldsforname(fields.fluxfield)[0]), spwdir, caldir, table_ext, title, outname)
plotstr='amp,freq'
table_ext = 'bcal'
title='Bandpass Amp'
outname = '{}/field_{}_bandpass_amp'.format(PLOT_DIR,fields.fluxfield)
plotcal(plotstr, int(msmd.fieldsforname(fields.fluxfield)[0]), spwdir, caldir, table_ext, title, outname)
plotstr='phase,freq'
table_ext = 'bcal'
title='Bandpass Phase'
outname = '{}/field_{}_bandpass_phase'.format(PLOT_DIR,fields.fluxfield)
plotcal(plotstr, int(msmd.fieldsforname(fields.fluxfield)[0]), spwdir, caldir, table_ext, title, outname)
plotstr='amp,freq'
table_ext = 'pcal'
title='Leakage Amp'
outname = '{}/field_{}_leakage_amp'.format(PLOT_DIR,fields.bpassfield)
plotcal(plotstr, int(msmd.fieldsforname(fields.dpolfield)[0]), spwdir, caldir, table_ext, title, outname, None, [0, 0.1])
plotstr='phase,freq'
table_ext = 'pcal'
title='Leakage Phase'
outname = '{}/field_{}_leakage_phase'.format(PLOT_DIR,fields.bpassfield)
plotcal(plotstr, int(msmd.fieldsforname(fields.dpolfield)[0]), spwdir, caldir, table_ext, title, outname)
plotstr='phase,freq'
table_ext = 'xyambcal'
title='XY Phase'
outname = '{}/field_{}_xyamb_phase'.format(PLOT_DIR,polfield)
plotcal(plotstr, int(msmd.fieldsforname(polfield)[0]), spwdir, caldir, table_ext, title, outname)
plotstr='phase,freq'
table_ext = 'xycal'
title='XY Phase (amb resolved)'
outname = '{}/field_{}_xy_phase'.format(PLOT_DIR,polfield)
plotcal(plotstr, int(msmd.fieldsforname(polfield)[0]), spwdir, caldir, table_ext, title, outname)
msmd.done()
except Exception as err:
logger.error('Exception found in the pipeline of type {0}: {1}'.format(type(err),err))
logger.error(traceback.format_exc())
msmd.done()
specmode='mfs',
deconvolver=deconvolver,
nterms=terms,
scales=[],
savemodel='none',
gridder='standard',
restoration=True,
pblimit=0,
parallel=parallel)
exportfits(imagename=secimname + '.image' + suffix,
fitsimage=secimname + '.fits')
msmd.close()
msmd.done()
if __name__ == '__main__':
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
keepmms = va(taskvals, 'crosscal', 'keepmms', bool)
fields = bookkeeping.get_field_ids(taskvals['fields'])
run_tclean(visname, fields, keepmms)
parang=True)
logger.info(" applying calibration -> target calibrator")
applycal(vis=visname,
field=fields.targetfield,
selectdata=False,
calwt=False,
gaintable=[calfiles.kcorrfile, calfiles.bpassfile, fluxfile],
gainfield=[
fields.kcorrfield, fields.bpassfield, fields.secondaryfield
],
parang=True)
if __name__ == '__main__':
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
minbaselines = va(taskvals, 'crosscal', 'minbaselines', int, default=4)
do_parallel_cal_apply(visname, fields, calfiles)
reference=fields.fluxfield,
transfer='',
fluxtable=calfiles.fluxfile,
listfile=os.path.join(caldir, 'fluxscale_xy_yx.txt'),
append=False,
display=False)
if __name__ == '__main__':
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
refant = va(taskvals, 'crosscal', 'refant', str, default='m005')
minbaselines = va(taskvals, 'crosscal', 'minbaselines', int, default=4)
standard = va(taskvals,
'crosscal',
'standard',
str,
default='Perley-Butler 2010')
do_cross_cal(visname,
fields,
calfiles,
overwrite=True, writeflags=True)
# now flag using 'rflag' option
flagdata(vis=visname, mode="rflag", datacolumn="corrected",
field=fields.targetfield, timecutoff=5.0, freqcutoff=5.0, timefit="poly",
freqfit="poly", flagdimension="freqtime", extendflags=False,
timedevscale=5.0, freqdevscale=5.0, spectralmax=500.0,
extendpols=False, growaround=False, flagneartime=False,
flagnearfreq=False, action="apply", flagbackup=True, overwrite=True,
writeflags=True)
# Now summary
flagdata(vis=visname, mode="summary", datacolumn="corrected",
extendflags=True, name=visname + 'summary.split', action="apply",
flagbackup=True, overwrite=True, writeflags=True)
if __name__ == '__main__':
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
do_pre_flag_2(visname, fields)
field=fname,
spw=spw,
keepflags=False,
createmms=keepmms,
chanaverage=chanaverage,
chanbin=specavg,
timeaverage=True,
timebin=timeavg,
usewtspectrum=True)
if __name__ == '__main__':
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
spw = va(taskvals, 'crosscal', 'spw', str, default='')
specavg = va(taskvals, 'crosscal', 'specavg', int, default=1)
timeavg = va(taskvals, 'crosscal', 'timeavg', str, default='8s')
keepmms = va(taskvals, 'crosscal', 'keepmms', bool)
split_vis(visname, spw, fields, specavg, timeavg, keepmms)
else:
setjy(vis=visname,
field=setjyname,
spw=spw,
scalebychan=True,
standard=standard)
if __name__ == '__main__':
# Get the name of the config file
args = config_parser.parse_args()
# Parse config file
taskvals, config = config_parser.parse_config(args['config'])
visname = va(taskvals, 'data', 'vis', str)
if os.path.exists(os.path.join(os.getcwd(), 'caltables')):
shutil.rmtree(os.path.join(os.getcwd(), 'caltables'))
calfiles, caldir = bookkeeping.bookkeeping(visname)
fields = bookkeeping.get_field_ids(taskvals['fields'])
spw = va(taskvals, 'crosscal', 'spw', str, default='')
standard = va(taskvals,
'crosscal',
'standard',
str,
default='Perley-Butler 2010')
do_setjy(visname, spw, fields, standard)