def get_standard(arf, base_standards_dir=None, analytic=None):
"""Given an archive file name return the name of the
standard profile to use for TOA fitting.
Input:
arf: An ArchiveFile object for which we want to get a standard.
base_stddir: The base directory containing standard profiles.
(Default: Use value from configuration file.)
analytic: True if an analytic profile should be returned.
(Default: Use value from configuration file.)
Output:
std: The name of the standard profile.
"""
if base_standards_dir is None:
base_standards_dir = config.cfg.base_standards_dir
if analytic is None:
analytic = config.cfg.analytic
if analytic:
fn = utils.get_outfn("%(name)s_%(telescop)s_%(rcvr)s_%(backend)s.m",
arf)
else:
fn = utils.get_outfn("%(name)s_%(telescop)s_%(rcvr)s_%(backend)s.std",
arf)
fn = fn.capitalize() # J/B should be capitalized, all the rest lower case
path = os.path.join(base_standards_dir, arf['telescop'].lower(), \
arf['rcvr'].lower(), arf['backend'].lower())
fn = os.path.join(path, fn)
return fn
def __init__(self, infns, outfn, is_asterix=False, maketoas=True):
"""Given a list of PSRCHIVE file names create a
ReductionJob object.
Input:
infns: A list of input PSRCHIVE archive file names.
outfn: The name of the reduced archive output.
is_asterix: If the data is from Effelsberg's Asterix backend.
If True, the header information will be corrected.
(Default: False)
maketoas: Whether or not TOAs should be made.
(Default: True)
Output:
job: The Reduction job object.
"""
self.infns = infns
self.outfn = outfn
self.basenm = os.path.splitext(self.outfn)[0]
self.is_asterix = is_asterix # Hopefully only temporary
self.maketoas = maketoas
logfn = utils.get_outfn(self.basenm+'.log', infns[0])
self.log = ReductionLog(infns, logfn)
def main():
print ""
print " toas.py"
print " Patrick Lazarus"
print ""
file_list = args + options.from_glob
to_exclude = options.excluded_files + options.excluded_by_glob
to_time = utils.exclude_files(file_list, to_exclude)
print "Number of input files: %d" % len(to_time)
to_time = [utils.ArchiveFile(fn) for fn in to_time]
# Read configurations
for arf in to_time:
config.cfg.load_configs_for_archive(arf)
stdfn = get_standard(arf)
if not os.path.isfile(stdfn):
raise errors.StandardProfileError("The standard profile (%s) " \
"cannot be found!" % stdfn)
toastrs = get_toas(arf, stdfn)
for toastr in toastrs:
flagstrs = [
utils.get_outfn(flag, arf) for flag in config.cfg.flags
]
if flagstrs:
toastr = toastr + " " + " ".join(flagstrs)
print toastr
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
#!/usr/bin/env python
import sys
import os.path
import utils
if "-h" in sys.argv or "--help" in sys.argv or len(sys.argv) < 3:
sys.stderr.write("Usage: %s OUTNAME INFILE\n" % \
os.path.split(sys.argv[0])[-1])
sys.exit(1)
arf = utils.ArchiveFile(sys.argv[2])
print utils.get_outfn(sys.argv[1], arf)