def __call__(self, parser, namespace, values, option_string):
colour.cprint("Available Cleaners:", \
bold=True, underline=True)
for name in sorted(cleaners.registered_cleaners):
cleaner = cleaners.load_cleaner(name)
print cleaner.get_help()
sys.exit(1)
def __call__(self, parser, namespace, values, option_string):
if values is None:
parser.print_help()
else:
cleaner = cleaners.load_cleaner(values)
print cleaner.get_help(full=True)
sys.exit(1)
def apply_bandwagon_cleaner(ar, badchantol=0.8, badsubtol=0.8):
print("Applying the bandwagon cleaner")
print("\t channel threshold = {0}".format(badchantol))
print("\t subint threshold = {0}".format(badsubtol))
bandwagon_cleaner = cleaners.load_cleaner('bandwagon')
bandwagon_parameters = "badchantol={0},badsubtol={1}".format(
badchantol, badsubtol)
bandwagon_cleaner.parse_config_string(bandwagon_parameters)
bandwagon_cleaner.run(ar)
def apply_surgical_cleaner(ar, tmp, cthresh=5.0, sthresh=5.0, plot=False):
print("Applying the surgical cleaner")
print("\t channel threshold = {0}".format(cthresh))
print("\t subint threshold = {0}".format(sthresh))
surgical_cleaner = cleaners.load_cleaner('surgical')
surgical_parameters = "chan_numpieces=1,subint_numpieces=1,chanthresh={1},subintthresh={2},template={0},plot={3}".format(
tmp, cthresh, sthresh, plot)
surgical_cleaner.parse_config_string(surgical_parameters)
surgical_cleaner.run(ar)
def clean_archive(archive,
template=None,
bandwagon=0.99,
channel_threshold=7,
subint_threshold=5,
output_directory=None):
"""
Cleans an archive using coast_guard
"""
# import necessary modules
import psrchive as ps
from coast_guard import cleaners
# Load the archive
archive = ps.Archive_load(str(archive))
archive_path, archive_name = os.path.split(archive.get_filename())
archive_name = archive_name.split('.')[0]
if output_directory is None:
output_directory = archive_path
# Clean the archive with surgical cleaner
print("Applying surgical cleaner")
surgical_cleaner = cleaners.load_cleaner('surgical')
surgical_parameters = 'chan_numpieces=1,subint_numpieces=1,\
chanthresh={},subintthresh={}'.format(
channel_threshold, subint_threshold)
surgical_cleaner.parse_config_string(surgical_parameters)
surgical_cleaner.run(archive)
# Apply bandwagon cleaner cleaner
print("Applying bandwagon cleaner")
bandwagon_cleaner = cleaners.load_cleaner('bandwagon')
bandwagon_parameters = 'badchantol={},badsubtol=1.0'.format(bandwagon)
bandwagon_cleaner.parse_config_string(bandwagon_parameters)
bandwagon_cleaner.run(archive)
# Unload cleaned archive
unload_path = os.path.join(output_directory, archive_name + ".clean")
print('Unloading cleaned archive as {0}'.format(unload_path))
archive.unload(unload_path)
return
def run_coastguard(calname, cal_dz):
#calname = sys.argv[1]
#cal_dz = sys.argv[2]
print calname
inarf = utils.ArchiveFile(calname)
config.cfg.load_configs_for_archive(inarf)
outfn = utils.get_outfn(cal_dz, inarf)
shutil.copy(inarf.fn, outfn)
outarf = utils.ArchiveFile(outfn)
ar = outarf.get_archive()
cleaner = cleaners.load_cleaner('preclean') # hard coded, need to be fixed
#for cfgstr in cfgstrs:
# cleaner.parse_config_string(cfgstr)
cleaner.run(ar)
cleaner = cleaners.load_cleaner('surgical') # hard coded, need to be fixed
cleaner.run(ar)
print(type(outfn))
ar.unload(str(outfn))
print "Cleaned archive: %s" % outfn
def main():
print ""
print " clean.py"
print " Patrick Lazarus"
print ""
file_list = args.files + args.from_glob
to_exclude = args.excluded_files + args.excluded_by_glob
to_clean = utils.exclude_files(file_list, to_exclude)
print "Number of input files: %d" % len(to_clean)
# Read configurations
for infn in to_clean:
inarf = utils.ArchiveFile(infn)
config.cfg.load_configs_for_archive(inarf)
outfn = utils.get_outfn(args.outfn, inarf)
shutil.copy(inarf.fn, outfn)
outarf = utils.ArchiveFile(outfn)
ar = outarf.get_archive()
try:
for name, cfgstrs in args.cleaner_queue:
# Set up the cleaner
cleaner = cleaners.load_cleaner(name)
for cfgstr in cfgstrs:
cleaner.parse_config_string(cfgstr)
cleaner.run(ar)
except:
# An error prevented cleaning from being successful
# Remove the output file because it may confuse the user
#if os.path.exists(outfn):
# os.remove(outfn)
raise
finally:
ar.unload(outfn)
print "Cleaned archive: %s" % outfn
print "nsubint Number of sub-integrations %s" % nSubint
print "type Observation type %s" % obsType
print "site Telescope name %s" % telescopeName
print "name Source name %s" % sourceName
print "coord Source coordinates %s%s" % (RA.getHMS(), Dec.getDMS())
print "freq Centre frequency (MHz) %s" % centreFrequency
print "bw Bandwidth (MHz) %s" % bandwidth
print "dm Dispersion measure (pc/cm^3) %s" % DM
print "rm Rotation measure (rad/m^2) %s" % RM
print "dmc Dispersion corrected %s" % isDedispersed
print "rmc Faraday Rotation corrected %s" % isFaradayRotated
print "polc Polarization calibrated %s" % isPolCalib
print "scale Data units %s" % dataUnits
print "state Data state %s" % dataState
print "length Observation duration (s) %s" % obsDuration
print "rcvr:name Receiver name %s" % receiverName
print "rcvr:basis Basis of receptors %s" % receptorBasis
print "be:name Name of the backend instrument %s" % backendName
cleanRFI = archive.clone()
cleaner = cleaners.load_cleaner("surgical")
cleaner.parse_config_string("chan_numpieces=1,subint_numpieces=1,chanthresh=3,subintthresh=3")
cleaner.run(cleanRFI)
name=os.path.splitext(file)[0]+'.clean'
print "Writing to %s" %name
cleanRFI.unload(name)