def combine_all(infns, outfn, expected_nsubbands=None):
"""Given a list of ArchiveFile objects group them into sub-bands
then remove the edges of each sub-band to remove the artifacts
caused by aliasing. Finally, combine the sub-bands into a single
output file.
The combined sub-band files are not saved.
Inputs:
infns: A list of input ArchiveFile objects.
outfn: The output file's name.
expected_nsubbands: The expected number of subbands for each
subintegration.
Outputs:
combinedfns: A list of output (combined) files.
"""
if expected_nsubbands is None:
expected_nsubbands = config.cfg.expected_nsubbands
infns = check_files(infns, expected_nsubbands=expected_nsubbands)
groups = group_files(infns)
combinedfiles = []
# Combine files from the same sub-band in the time direction
for group in groups:
subbands = []
for ctr_freq, to_combine in utils.group_by_ctr_freq(group).iteritems():
utils.print_info("Combining %d subints at ctr freq %d MHz" % \
(len(to_combine), ctr_freq), 3)
# Combine sub-integrations for this sub-band
subfn = utils.get_outfn(outfn + ".%(freq)dMHz", to_combine[0])
if subfn in [f.fn for f in subbands]:
warnings.warn("'combined_all(...)' is overwritting files it " \
"previously created!")
subband = combine_subints(to_combine, subfn)
clean.trim_edge_channels(subband)
subbands.append(subband)
combinedfn = utils.get_outfn(outfn, subbands[0])
utils.print_info("Combining %d subbands into %s" % \
(len(subbands), combinedfn), 3)
if combinedfn in [f.fn for f in combinedfiles]:
warnings.warn("'combined_all(...)' is overwritting files it " \
"previously created!")
combinedfile = combine_subbands(subbands, combinedfn)
combinedfiles.append(combinedfile)
if not config.debug.INTERMEDIATE:
# Remove the temporary combined files
for sub in subbands:
os.remove(sub.fn)
return combinedfiles
def clean_archive(inarf, outfn, clean_re=None, *args, **kwargs):
import psrchive # Temporarily, because python bindings
# are not available on all computers
if clean_re is None:
clean_re = config.cfg.clean_strategy
try:
outfn = utils.get_outfn(outfn, inarf)
shutil.copy(inarf.fn, outfn)
outarf = utils.ArchiveFile(outfn)
trim_edge_channels(outarf)
prune_band(outarf)
remove_bad_channels(outarf)
remove_bad_subints(outarf)
matching_cleaners = [
clnr for clnr in cleaners
if clean_re and re.search(clean_re, clnr)
]
if len(matching_cleaners) == 1:
ar = psrchive.Archive_load(outarf.fn)
cleaner = eval(matching_cleaners[0])
utils.print_info(
"Cleaning using '%s(...)'." % matching_cleaners[0], 2)
cleaner(ar, *args, **kwargs)
ar.unload(outfn)
elif len(matching_cleaners) == 0:
utils.print_info("No cleaning strategy selected. Skipping...", 2)
else:
raise errors.CleanError("Bad cleaner selection. " \
"'%s' has %d matches." % \
(clean_re, len(matching_cleaners)))
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
return outarf
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
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