def prepare_subints(subdirs,
subints,
baseoutdir,
trimpcnt=6.25,
effix=False,
backend=None):
"""Prepare subints by
- Copying them to the temporary working directory
- De-weighting a percentage from each sub-band edge
- Converting archive format to PSRFITS
Inputs:
subdirs: List of sub-band directories containing
sub-ints to combine
subints: List of subint files to be combined.
(NOTE: These are the file name only (i.e. no path)
Each file listed should appear in each of the
subdirs.)
baseoutdir: Directory containing the sub-directories
of preprared files.
trimpcnt: Percentage (ie between 0-100) of subband
to trim from _each_ edge of the band.
(Default: 6.25%)
effix: Change observation site to eff_psrix to correct
for asterix clock offsets. (Default: False)
backend: Name of the backend. (Default: leave as is)
Outputs:
prepsubdirs: The sub-directories containing prepared files.
"""
devnull = open(os.devnull)
tmpsubdirs = []
for subdir in utils.show_progress(subdirs, width=50):
freqdir = os.path.split(os.path.abspath(subdir))[-1]
freqdir = os.path.join(baseoutdir, freqdir)
try:
os.makedirs(freqdir)
except OSError:
# Directory already exists
pass
fns = [os.path.join(subdir, fn) for fn in subints]
preproc = 'convert psrfits'
if effix:
preproc += ',edit site=eff_psrix'
if backend:
if ("," in backend) or ("=" in backend) or (' ' in backend):
raise errors.UnrecognizedValueError("Backend value (%s) is "
"invalid. It cannot "
"contain ',' or '=' or "
"' '" % backend)
preproc += ',edit be:name=%s' % backend
utils.execute(
['paz', '-j', preproc, '-E',
'%f' % trimpcnt, '-O', freqdir] + fns,
stderr=devnull)
tmpsubdirs.append(freqdir)
utils.print_info(
"Prepared %d subint fragments in %d freq sub-dirs" %
(len(subints), len(subdirs)), 3)
return tmpsubdirs
def set_file_as_bad(self, reason='rfi'):
if self.file_id:
note = "File failed quality control."
if reason == 'rfi':
note += " RFI has rendered the observation unsalvageable!"
elif reason == 'nondetect':
note += " The observation is a non-detection."
else:
raise errors.UnrecognizedValueError("The reason for "
"setting the file as "
"bad is not "
"recognized: %s" %
reason)
with self.db.transaction() as conn:
now = datetime.datetime.now()
update = self.db.files.update().\
where(self.db.files.c.file_id == self.file_id).\
values(qcpassed=False,
status='failed',
note=note,
last_modified=now)
conn.execute(update)
insert = self.db.qctrl.insert().\
values(file_id=self.file_id,
obs_id=self.fileinfo['obs_id'],
user=os.getlogin(),
qcpassed=False,
note=note,
added=now,
last_modified=now)
conn.execute(insert)
if self.fileinfo['stage'] == 'calibrated':
# Mark former cleaned file to be loaded
ancestors = reduce_data.get_all_ancestors(self.file_id, self.db)
for ancestor in ancestors:
if ancestor['stage'] == 'cleaned':
ancestor_file_id = ancestor['file_id']
break
update = self.db.files.update().\
where((self.db.files.c.file_id == ancestor_file_id)).\
values(status='toload',
note="Derived calibrated file failed quality control.",
last_modified=datetime.datetime.now())
conn.execute(update)
# Update observation's current file
update = self.db.obs.update().\
where((self.db.obs.c.obs_id == self.fileinfo['obs_id'])).\
values(current_file_id=ancestor_file_id,
last_modified=datetime.datetime.now())
conn.execute(update)
self.advance_file()
def load_cleaner(cleaner_name):
"""Import a cleaner class and return an instance.
Input:
cleaner_name: The name of the cleaner.
Output:
clean: A cleaner instance.
"""
if cleaner_name not in registered_cleaners:
raise errors.UnrecognizedValueError('The cleaner, %s, ' \
'is not a registered cleaner. The following ' \
're registered: %s' % \
(cleaner_name, "', '".join(registered_cleaners)))
mod = __import__(cleaner_name, globals())
return mod.Cleaner()
def load_cleaner(cleaner_name):
"""Import a cleaner class and return an instance.
Input:
cleaner_name: The name of the cleaner.
Output:
clean: A cleaner instance.
"""
if cleaner_name not in registered_cleaners:
raise errors.UnrecognizedValueError('The cleaner, %s, ' \
'is not a registered cleaner. The following ' \
're registered: %s' % \
(cleaner_name, "', '".join(registered_cleaners)))
mod = importlib.import_module('.'+cleaner_name, 'coast_guard.cleaners')
return mod.Cleaner()
def load_cleaner(cleaner_name):
"""Import a cleaner class and return an instance.
Input:
cleaner_name: The name of the cleaner.
Output:
clean: A cleaner instance.
"""
if cleaner_name not in registered_cleaners:
raise errors.UnrecognizedValueError('The cleaner, %s, ' \
'is not a registered cleaner. The following ' \
're registered: %s' % \
(cleaner_name, "', '".join(registered_cleaners)))
mod = __import__("coast_guard.cleaners.{0}".format(cleaner_name),
fromlist=["None"])
return mod.Cleaner()