def _prepare_demix_step(self, stepname, **kwargs):
"""
Prepare for a demixing step. This requires the setting of some
extra keys in the parset, as well as testing which A-team sources
must actually be demixed.
Parameters:
`stepname`: name of the demixing step in the parset.
`kwargs` : dict of extra arguments.
Returns: patch_dictionary that must be applied to the parset.
"""
# Add demix directory to sys.path before importing find_a_team module.
sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "demix"))
from find_a_team import getAteamList
patch_dictionary = {}
if kwargs['parmdb']:
patch_dictionary[stepname + '.instrumentmodel'] = kwargs['parmdb']
if kwargs['sourcedb']:
patch_dictionary[stepname + '.skymodel'] = kwargs['sourcedb']
demix_always = set(kwargs['demix_always'])
demix_if_needed = set(kwargs['demix_if_needed'])
# If the user specified a list of candidate A-team sources to remove,
# then determine the intersection of that list and the list of sources
# that need demixing according to the heuristics of getAteamList().
if demix_if_needed:
ateam_list = getAteamList(
kwargs['infile'],
outerDistance=2.e4,
elLimit=5.,
verbose=self.logger.isEnabledFor(logging.DEBUG)
)
self.logger.debug("getAteamList returned: %s" % ateam_list)
demix_if_needed.intersection_update(ateam_list)
# Determine the complete set of sources to be demixed.
demix_sources = list(demix_always.union(demix_if_needed))
self.logger.info("Removing %d target(s) from %s: %s" % (
len(demix_sources), kwargs['infile'], ', '.join(demix_sources)
)
)
patch_dictionary[stepname + '.subtractsources'] = demix_sources
# Return the patch dictionary.
return patch_dictionary
def _prepare_demix_step(self, stepname, **kwargs):
"""
Prepare for a demixing step. This requires the setting of some
extra keys in the parset, as well as testing which A-team sources
must actually be demixed.
Parameters:
`stepname`: name of the demixing step in the parset.
`kwargs` : dict of extra arguments.
Returns: patch_dictionary that must be applied to the parset.
"""
# Add demix directory to sys.path before importing find_a_team module.
sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "demix"))
from find_a_team import getAteamList
patch_dictionary = {}
if kwargs['parmdb']:
patch_dictionary[stepname + '.instrumentmodel'] = kwargs['parmdb']
if kwargs['sourcedb']:
patch_dictionary[stepname + '.skymodel'] = kwargs['sourcedb']
demix_always = set(kwargs['demix_always'])
demix_if_needed = set(kwargs['demix_if_needed'])
# If the user specified a list of candidate A-team sources to remove,
# then determine the intersection of that list and the list of sources
# that need demixing according to the heuristics of getAteamList().
if demix_if_needed:
ateam_list = getAteamList(
kwargs['infile'],
outerDistance=2.e4,
elLimit=5.,
verbose=self.logger.isEnabledFor(logging.DEBUG)
)
self.logger.debug("getAteamList returned: %s" % ateam_list)
demix_if_needed.intersection_update(ateam_list)
# Determine the complete set of sources to be demixed.
demix_sources = list(demix_always.union(demix_if_needed))
self.logger.info("Removing %d target(s) from %s: %s" % (
len(demix_sources), kwargs['infile'], ', '.join(demix_sources)
)
)
patch_dictionary[stepname + '.subtractsources'] = demix_sources
# Return the patch dictionary.
return patch_dictionary
def run(self, infile, working_dir, initscript, remove, target, clusterdesc,
timestep, freqstep, half_window, threshold, demixdir, skymodel,
db_host):
with log_time(self.logger):
if os.path.exists(infile):
self.logger.info("Started processing %s" % infile)
else:
self.logger.error("Dataset %s does not exist" % infile)
return 1
self.logger.debug("infile = %s", infile)
self.logger.debug("working_dir = %s", working_dir)
self.logger.debug("initscript = %s", initscript)
self.logger.debug("remove = %s", remove)
self.logger.debug("target = %s", target)
self.logger.debug("clusterdesc = %s", clusterdesc)
self.logger.debug("timestep = %d", timestep)
self.logger.debug("freqstep = %d", freqstep)
self.logger.debug("half_window = %d", half_window)
self.logger.debug("threshold = %f", threshold)
self.logger.debug("demixdir = %s", demixdir)
self.logger.debug("skymodel = %s", skymodel)
self.logger.debug("db_host= %s", db_host)
# Initialise environment
self.environment = read_initscript(self.logger, initscript)
# Create working directory, if it does not yet exist.
if not os.path.exists(working_dir):
os.makedirs(working_dir)
# The output file names are based on the input filename, however
# they must be created in ``working_dir``.
filename = os.path.split(infile)[1]
outfile = os.path.join(working_dir, filename)
key = os.path.join(working_dir, 'key_' + filename)
mixingtable = os.path.join(working_dir, 'mixing_' + filename)
basename = outfile.replace('_uv.MS', '') + '_'
# If needed, run NDPPP to preflag input file out to demix.MS
t = pt.table(infile)
shp = t.getcell("DATA", 0).shape
t = 0
mstarget = outfile.replace('uv', target)
if os.system('rm -f -r ' + mstarget) != 0:
return 1
if (shp[0] == 64 or shp[0] == 128 or shp[0] == 256):
f = open(basename + 'NDPPP_dmx.parset', 'w')
f.write('msin = %s\n' % infile)
f.write('msin.autoweight = True\n')
f.write('msin.startchan = nchan/32\n')
f.write('msin.nchan = 30*nchan/32\n')
f.write('msout = %s\n' % mstarget)
f.write('steps=[preflag]\n')
f.write('preflag.type=preflagger\n')
f.write('preflag.corrtype=auto\n')
f.close()
self.logger.info("Starting NDPPP demix ...")
if not self._execute(['NDPPP', basename + 'NDPPP_dmx.parset']):
return 1
else:
if infile == mstarget:
self.logger.error("MS-file %s already exists" % mstarget)
return 1
else:
self.logger.info("Copying MS-file: %s --> %s" %
(infile, mstarget))
if os.system('cp -r ' + infile + ' ' + mstarget) != 0:
return 1
# Use heuristics to get a list of A-team sources that may need
# to be removed. If the user specified a list of candidate A-team
# sources to remove, then determine the intersection of both lists.
# Otherwise just use the list obtained from heuristics.
ateam_list = getAteamList(infile,
outerDistance=2.e4,
elLimit=5.,
verbose=self.logger.isEnabledFor(
logging.DEBUG))
self.logger.debug("getAteamList returned: %s" % ateam_list)
if remove:
remove = list(set(remove).intersection(ateam_list))
else:
remove = ateam_list
self.logger.info("Removing %d target(s) from %s: %s" %
(len(remove), mstarget, ', '.join(remove)))
spc.shiftphasecenter(mstarget, remove, freqstep, timestep)
# for each source to remove, and the target, do a freq/timesquash
# NDPPP
removeplustarget = numpy.append(remove, target)
avgoutnames = []
for rem in removeplustarget:
if os.system('rm -f ' + basename + 'dmx_avg.parset') != 0:
return 1
f = open(basename + 'dmx_avg.parset', 'w')
msin = outfile.replace('uv', rem)
f.write('msin = %s\n' % msin)
msout = msin.replace('.MS', '_avg.MS')
f.write('msout = %s\n' % msout)
f.write('steps=[avg]\n')
f.write('avg.type = averager\n')
f.write('avg.timestep = %d\n' % timestep)
f.write('avg.freqstep = %d\n' % freqstep)
f.close()
self.logger.debug("Squashing %s to %s" % (msin, msout))
if os.system('rm -f -r ' + msout) != 0:
return 1
if not self._execute(['NDPPP', basename + 'dmx_avg.parset']):
return 1
# Form avg output names.
msin = outfile.replace('uv', rem)
msout = msin.replace('.MS', '_avg.MS')
avgoutnames.append(msout)
msdem = msin.replace('.MS', '_avg_dem.MS')
if os.system('rm -f -r ' + msdem) != 0:
return 1
self.logger.info("Starting the demixing algorithm")
dmx.demixing(mstarget, mixingtable, avgoutnames, freqstep,
timestep, 4)
self.logger.info("Finished the demixing algorithm")
#
# run BBS on the demixed measurement sets
#
self.logger.info("Starting BBS run on demixed measurement sets")
for i in remove:
self.logger.info("Processing %s ..." % i)
msin = outfile.replace('uv', i)
msout = msin.replace('.MS', '_avg_dem.MS')
vds_file = basename + i + '.vds'
gds_file = basename + i + '.gds'
self.logger.info("Creating vds & gds files...")
if os.system('rm -f ' + vds_file + gds_file) != 0:
return 1
if not self._execute(['makevds', clusterdesc, msout, vds_file
]):
return 1
if not self._execute(['combinevds', gds_file, vds_file]):
return 1
self.logger.info("Starting first calibration run")
command = [
'calibrate', '-f', '--key', key, '--cluster-desc',
clusterdesc, '--db', db_host, '--db-user', 'postgres',
gds_file,
os.path.join(demixdir,
'bbs_' + i + '.parset'), skymodel, working_dir
]
if not self._execute(command):
return 1
self.logger.info("Generating smoothed instrument model")
input_parmdb = os.path.join(msout, 'instrument')
output_parmdb = os.path.join(msout, 'instrument_smoothed')
# smoothparmdb indirectly creates a subprocess, so we must
# make sure that the correct environment is set-up here.
env = os.environ
os.environ = self.environment
smdx.smoothparmdb(input_parmdb, output_parmdb, half_window,
threshold)
os.environ = env
self.logger.info("Starting second calibration run, "
"using smoothed instrument model")
command = [
'calibrate', '--clean', '--skip-sky-db',
'--skip-instrument-db', '--instrument-name',
'instrument_smoothed', '--key', key, '--cluster-desc',
clusterdesc, '--db', db_host, '--db-user', 'postgres',
gds_file,
os.path.join(demixdir, 'bbs_' + i + '_smoothcal.parset'),
skymodel, working_dir
]
if not self._execute(command):
return 1
# Form the list of input files and subtract.
self.logger.info("Subtracting removed sources from the data ...")
demfiles = [
outfile.replace('uv', rem + '_avg_dem') for rem in remove
]
sfa.subtract_from_averaged(mstarget.replace('.MS', '_avg.MS'),
mixingtable, demfiles,
mstarget.replace('.MS', '_sub.MS'))
# We're done.
return 0
def run(self, infile, working_dir, initscript, remove, target,
clusterdesc, timestep, freqstep, half_window, threshold,
demixdir, skymodel, db_host):
with log_time(self.logger):
if os.path.exists(infile):
self.logger.info("Started processing %s" % infile)
else:
self.logger.error("Dataset %s does not exist" % infile)
return 1
self.logger.debug("infile = %s", infile)
self.logger.debug("working_dir = %s", working_dir)
self.logger.debug("initscript = %s", initscript)
self.logger.debug("remove = %s", remove)
self.logger.debug("target = %s", target)
self.logger.debug("clusterdesc = %s", clusterdesc)
self.logger.debug("timestep = %d", timestep)
self.logger.debug("freqstep = %d", freqstep)
self.logger.debug("half_window = %d", half_window)
self.logger.debug("threshold = %f", threshold)
self.logger.debug("demixdir = %s", demixdir)
self.logger.debug("skymodel = %s", skymodel)
self.logger.debug("db_host= %s", db_host)
# Initialise environment
self.environment = read_initscript(self.logger, initscript)
# Create working directory, if it does not yet exist.
if not os.path.exists(working_dir):
os.makedirs(working_dir)
# The output file names are based on the input filename, however
# they must be created in ``working_dir``.
filename = os.path.split(infile)[1]
outfile = os.path.join(working_dir, filename)
key = os.path.join(working_dir, 'key_' + filename)
mixingtable = os.path.join(working_dir, 'mixing_' + filename)
basename = outfile.replace('_uv.MS', '') + '_'
# If needed, run NDPPP to preflag input file out to demix.MS
t = pt.table(infile)
shp = t.getcell("DATA", 0).shape
t = 0
mstarget = outfile.replace('uv',target)
if os.system ('rm -f -r ' + mstarget) != 0:
return 1
if (shp[0] == 64 or shp[0] == 128 or shp[0] == 256):
f=open(basename + 'NDPPP_dmx.parset','w')
f.write('msin = %s\n' % infile)
f.write('msin.autoweight = True\n')
f.write('msin.startchan = nchan/32\n')
f.write('msin.nchan = 30*nchan/32\n')
f.write('msout = %s\n' % mstarget)
f.write('steps=[preflag]\n')
f.write('preflag.type=preflagger\n')
f.write('preflag.corrtype=auto\n')
f.close()
self.logger.info("Starting NDPPP demix ...")
if not self._execute(['NDPPP', basename + 'NDPPP_dmx.parset']):
return 1
else:
if infile == mstarget:
self.logger.error("MS-file %s already exists" % mstarget)
return 1
else:
self.logger.info(
"Copying MS-file: %s --> %s" % (infile, mstarget)
)
if os.system ('cp -r ' + infile + ' ' + mstarget) != 0:
return 1
# Use heuristics to get a list of A-team sources that may need
# to be removed. If the user specified a list of candidate A-team
# sources to remove, then determine the intersection of both lists.
# Otherwise just use the list obtained from heuristics.
ateam_list = getAteamList(
infile,
outerDistance=2.e4,
elLimit=5.,
verbose=self.logger.isEnabledFor(logging.DEBUG)
)
self.logger.debug("getAteamList returned: %s" % ateam_list)
if remove:
remove = list(set(remove).intersection(ateam_list))
else:
remove = ateam_list
self.logger.info("Removing %d target(s) from %s: %s" %
(len(remove), mstarget, ', '.join(remove)))
spc.shiftphasecenter (mstarget, remove, freqstep, timestep)
# for each source to remove, and the target, do a freq/timesquash
# NDPPP
removeplustarget = numpy.append (remove, target)
avgoutnames = []
for rem in removeplustarget:
if os.system ('rm -f ' + basename + 'dmx_avg.parset') != 0:
return 1
f=open(basename + 'dmx_avg.parset','w')
msin = outfile.replace('uv',rem)
f.write('msin = %s\n' % msin)
msout = msin.replace ('.MS','_avg.MS')
f.write('msout = %s\n' % msout)
f.write('steps=[avg]\n')
f.write('avg.type = averager\n')
f.write('avg.timestep = %d\n' % timestep)
f.write('avg.freqstep = %d\n' % freqstep)
f.close()
self.logger.debug("Squashing %s to %s" % (msin, msout))
if os.system ('rm -f -r '+msout) != 0:
return 1
if not self._execute(['NDPPP', basename + 'dmx_avg.parset']):
return 1
# Form avg output names.
msin = outfile.replace('uv',rem)
msout = msin.replace ('.MS','_avg.MS')
avgoutnames.append (msout)
msdem = msin.replace ('.MS','_avg_dem.MS')
if os.system ('rm -f -r '+msdem) != 0:
return 1
self.logger.info("Starting the demixing algorithm")
dmx.demixing (mstarget, mixingtable, avgoutnames,
freqstep, timestep, 4)
self.logger.info("Finished the demixing algorithm")
#
# run BBS on the demixed measurement sets
#
self.logger.info("Starting BBS run on demixed measurement sets")
for i in remove:
self.logger.info("Processing %s ..." % i)
msin = outfile.replace('uv', i)
msout = msin.replace ('.MS','_avg_dem.MS')
vds_file = basename + i +'.vds'
gds_file = basename + i +'.gds'
self.logger.info("Creating vds & gds files...")
if os.system ('rm -f '+ vds_file + gds_file) != 0:
return 1
if not self._execute(['makevds', clusterdesc, msout, vds_file]):
return 1
if not self._execute(['combinevds', gds_file, vds_file]):
return 1
self.logger.info("Starting first calibration run")
command=['calibrate',
'-f',
'--key', key,
'--cluster-desc', clusterdesc,
'--db', db_host,
'--db-user', 'postgres',
gds_file,
os.path.join(demixdir, 'bbs_'+i+'.parset'),
skymodel,
working_dir]
if not self._execute(command):
return 1
self.logger.info("Generating smoothed instrument model")
input_parmdb = os.path.join(msout, 'instrument')
output_parmdb= os.path.join(msout, 'instrument_smoothed')
# smoothparmdb indirectly creates a subprocess, so we must
# make sure that the correct environment is set-up here.
env = os.environ
os.environ = self.environment
smdx.smoothparmdb(input_parmdb, output_parmdb,
half_window, threshold)
os.environ = env
self.logger.info("Starting second calibration run, "
"using smoothed instrument model")
command=['calibrate',
'--clean',
'--skip-sky-db',
'--skip-instrument-db',
'--instrument-name', 'instrument_smoothed',
'--key', key,
'--cluster-desc', clusterdesc,
'--db', db_host,
'--db-user', 'postgres',
gds_file,
os.path.join(demixdir, 'bbs_'+i+'_smoothcal.parset'),
skymodel,
working_dir]
if not self._execute(command):
return 1
# Form the list of input files and subtract.
self.logger.info("Subtracting removed sources from the data ...")
demfiles = [outfile.replace('uv',rem+'_avg_dem') for rem in remove]
sfa.subtract_from_averaged (mstarget.replace('.MS','_avg.MS'),
mixingtable,
demfiles,
mstarget.replace('.MS','_sub.MS'))
# We're done.
return 0