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')
fnames = msmd.namesforfields()
config_parser.overwrite_config(
args['config'],
conf_dict={'fieldnames': "{0}".format(fnames)},
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)
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)
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(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# #Superseded by 'plotcal_spw.py'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:
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.done()
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'])
do_cross_cal_apply(visname, fields, calfiles, caldir)
def main(args, taskvals):
visname = va(taskvals, 'data', 'vis', str)
name = visname.split('/')[-1].replace('.ms', '')
listobs(vis=visname, listfile=name + "_listobs.txt")
return
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')
SPWs = 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
CPUs = int(sys.argv[-1])
for spw in SPWs.split(','):
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)
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):
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(args,taskvals):
spw = sys.argv[-1]
visname = va(taskvals, "data", "vis", str)
visname = visname.split('/')[-1]
mmsfile = visname.replace('ms',spw+'.mms')
mmsfile = "'{0}'".format(mmsfile)
config_parser.overwrite_config(args['config'], conf_sec='data', conf_dict={'vis':mmsfile})
logger.info('Updated (vis) in [data] section written to "{0}".'.format(args['config']))
spw = '0:'+spw
spw = "'{0}'".format(spw)
config_parser.overwrite_config(args['config'], conf_sec='crosscal', conf_dict={'spw':spw})
config_parser.overwrite_config(args['config'], conf_sec='crosscal', conf_dict={'nspw':1})
logger.info('Updated (spw,nspw) in [crosscal] section written to "{0}".'.format(args['config']))
return
def main(args, taskvals):
visname = va(taskvals, "data", "vis", str)
fields = read_fields(visname)
if len(fields) > 0:
config_parser.overwrite_config(args['config'],
conf_dict=fields,
conf_sec='fields')
logger.info(
'[fields] section written to "{0}". Edit this section if you need to change field IDs (comma-separated string for multiple IDs, not supported for calibrators).'
.format(args['config']))
else:
logger.info(
'No updated [fields] section written to "{0}". Edit this section manually (comma-separated string for multiple IDs, not supported for calibrators).'
.format(args['config']))
return
def do_concat(visname, fields, dirs='*MHz'):
#msmd.open(visname)
fieldnames = va(taskvals, 'run', 'fieldnames', str)
newvis = visname
logger.info('Beginning {0}.'.format(sys.argv[0]))
basename, ext = os.path.splitext(visname)
filebase = os.path.split(basename)[1]
for field in [fields.targetfield, fields.gainfields, fields.extrafields]:
if field != '':
for target in field.split(','):
#fname = msmd.namesforfields(int(target))[0]
fname = fieldnames[int(target)]
#Concat tt0 images (into continuum cube)
suffix = 'images/*{0}*image.tt0'.format(fname)
files, pattern = get_infiles(dirs, suffix)
out = '{0}.{1}.contcube'.format(filebase, fname)
images = check_output(fname,
files,
pattern,
out,
job='imageconcat',
filetype='image')
if images is not None:
images.sort(key=sortbySPW)
logger.info(
'Creating continuum cube with following command:')
logger.info(
'ia.imageconcat(infiles={0}, outfile={1}, axis=-1, relax=True)'
.format(images, out))
ia.imageconcat(infiles=images,
outfile=out,
axis=-1,
relax=True)
if os.path.exists(out):
if not os.path.exists(out + '.fits'):
exportfits(imagename=out, fitsimage=out + '.fits')
else:
logger.error(
"Output image '{0}' attempted to write but was not written."
.format(out))
#Concat images (into continuum cube)
suffix = 'images/*{0}*image'.format(fname)
files, pattern = get_infiles(dirs, suffix)
out = '{0}.{1}.contcube'.format(filebase, fname)
images = check_output(fname,
files,
pattern,
out,
job='imageconcat',
filetype='image')
if images is not None:
images.sort(key=sortbySPW)
logger.info(
'Creating continuum cube with following command:')
logger.info(
'ia.imageconcat(infiles={0}, outfile={1}, axis=-1, relax=True)'
.format(images, out))
ia.imageconcat(infiles=images,
outfile=out,
axis=-1,
relax=True)
if os.path.exists(out):
if not os.path.exists(out + '.fits'):
exportfits(imagename=out, fitsimage=out + '.fits')
else:
logger.error(
"Output image '{0}' attempted to write but was not written."
.format(out))
#Concat MSs
suffix = '*{0}*.ms'.format(fname)
files, pattern = get_infiles(dirs, suffix)
out = '{0}.{1}.ms'.format(filebase, fname)
MSs = check_output(fname,
files,
pattern,
out,
job='concat',
filetype='MS')
if MSs is not None:
MSs.sort(key=sortbySPW)
logger.info('Concatenating MSs with following command:')
logger.info('concat(vis={0}, concatvis={1})'.format(
MSs, out))
concat(vis=MSs, concatvis=out)
if target == fields.targetfield.split(',')[0]:
newvis = out
if not os.path.exists(out):
logger.error(
"Output MS '{0}' attempted to write but was not written."
.format(out))
#Concat MMSs
suffix = '*{0}*.mms'.format(fname)
files, pattern = get_infiles(dirs, suffix)
out = '{0}.{1}.mms'.format(filebase, fname)
MMSs = check_output(fname,
files,
pattern,
out,
job='virtualconcat',
filetype='MMS')
if MMSs is not None:
MMSs.sort(key=sortbySPW)
logger.info('Concatenating MMSs with following command:')
logger.info('virtualconcat(vis={0}, concatvis={1})'.format(
MMSs, out))
virtualconcat(vis=MMSs, concatvis=out)
if target == fields.targetfield.split(',')[0]:
newvis = out
if not os.path.exists(out):
logger.error(
"Output MMS '{0}' attempted to write but was not written."
.format(out))
#msmd.done()
logger.info('Completed {0}.'.format(sys.argv[0]))
return newvis