def parkes_reader(line, get_telescope_id=True):
"""Parse line, assuming it is a TOA in parkes format.
Return a dictionary of information.
Input:
line: A single TOA line in parkes format.
get_telescope_id: Query the database to get the telescope
ID number. (Default: True)
Output:
toainfo: A dictionary of TOA information.
"""
parkes_toa_re = re.compile(r'^ *?(?P<bad>(#|(C ))(?P<comment1>.*?))?'
r' (?P<info>.{24})(?P<freq>.{9})(?P<imjd>.{7})(?P<fmjd>\..{12}) '
r'(?P<phaseoffset>.{8}) (?P<err>.{7})(?P<info2>.{7}) '
r'(?P<site>.)(?P<dmcorr>[^#]*)')
comment_re = re.compile(r'#(?P<comment>.*)$')
match = parkes_toa_re.search(line.rstrip())
if match is None:
toainfo = None
notify.print_debug("Line is not a Parkes-format TOA:\n %s" % line, 'toaparse')
else:
grp = match.groupdict()
toainfo = {}
toainfo['is_bad'] = (grp['bad'] is not None)
toainfo['freq'] = float(grp['freq'])
toainfo['imjd'] = int(grp['imjd'])
toainfo['fmjd'] = float(grp['fmjd'])
toainfo['toa_unc_us'] = float(grp['err'])
toainfo['telescope'] = grp['site']
if get_telescope_id:
toainfo['telescope_id'] = cache.get_telescope_info(grp['site'])['telescope_id']
toainfo['extras'] = {'phaseoffset': float(grp['phaseoffset']),
'infostr': grp['info'].strip() + ' -- ' + grp['info2'].strip()}
if grp['dmcorr']:
toainfo['extras']['dmcorr'] = float(grp['dmcorr'])
comments = []
if grp['comment1']:
comments.append(grp['comment1'].strip())
match2 = comment_re.search(line[match.end():])
if match2:
grp2 = match2.groupdict()
if grp2['comment']:
comments.append(grp2['comment'].strip())
toainfo['comment'] = " -- ".join(comments)
return toainfo
def tempo2_reader(line, get_telescope_id=True):
"""Parse line, assuming it is a TOA in tempo2 format.
Return a dictionary of information.
Input:
line: A single TOA line in Tempo2 format.
get_telescope_id: Query the database to get the telescope
ID number. (Default: True)
Output:
toainfo: A dictionary of TOA information.
"""
tempo2_toa_re = re.compile(r'^ *(?P<bad>(#|(C )|(c ))(?P<comment1>.*?))? *'
r'(?P<file>[^ ]+) +'
r'(?P<freq>\d+(\.\d+)?) +(?P<imjd>\d+)(?P<fmjd>\.\d+) +'
r'(?P<err>\d+(\.\d+)?) +(?P<site>[^ ]+)')
comment_re = re.compile(r'#(?P<comment>.*)$')
tempo2_flag_re = re.compile(r'-(?P<flagkey>[^ ]+) +(?P<flagval>[^ ]+)')
match = tempo2_toa_re.search(line)
if match is None:
toainfo = None
notify.print_debug("Line is not a Tempo2 TOA:\n %s" % line, 'toaparse')
else:
grp = match.groupdict()
toainfo = {}
toainfo['grp'] = grp
toainfo['is_bad'] = (line.strip().startswith('#') or line.strip().lower().startswith('c ')) #(grp['bad'] is not None)
toainfo['file'] = grp['file']
toainfo['freq'] = float(grp['freq'])
toainfo['imjd'] = int(grp['imjd'])
toainfo['fmjd'] = float(grp['fmjd'])
toainfo['toa_unc_us'] = float(grp['err'])
toainfo['telescope'] = grp['site']
toainfo['line'] = line
if get_telescope_id:
toainfo['telescope_id'] = cache.get_telescope_info(grp['site'])['telescope_id']
comments = []
if grp['comment1']:
comments.append(grp['comment1'].strip())
match2 = comment_re.search(line[match.end():])
if match2:
grp2 = match2.groupdict()
if grp2['comment']:
comments.append(grp2['comment'].strip())
toainfo['comment'] = " -- ".join(comments)
toainfo['extras'] = {}
for key, val in tempo2_flag_re.findall(line[match.end():]):
key = key.lower()
key = KNOWN_FLAG_ALIASES.get(key, key)
caster = KNOWN_FLAG_TYPES.get(key, str)
try:
toainfo['extras'][key] = caster(val.strip())
except:
notify.print_info("Couldn't cast %s:%s" % (key, val), 2)
notify.print_debug("TOA line: %s\nParsed info: %s" % (line, toainfo),
'toaparse')
return toainfo
def prep_file(fn):
"""Prepare file for archiving/loading.
Also, perform some checks on the file to make sure we
won't run into problems later. Checks peformed:
- Existence of file.
- Read/write access for file (so it can be moved).
- Header contains all necessary values.
- Site/observing system is recognized.
Input:
fn: The name of the file to check.
Outputs:
params: A dictionary of info to be uploaded.
"""
# Check existence of file
verify_file_path(fn)
# Check file permissions allow for writing and reading
if not os.access(fn, os.R_OK):
raise errors.FileError("File (%s) is not readable!" % fn)
# Grab header info
hdritems = ["nbin", "nchan", "npol", "nsub", "type", "telescop",
"name", "dec", "ra", "freq", "bw", "dm", "rm",
# The names of these header params
# vary with psrchive version
# "dmc", "rm_c", "pol_c",
"scale", "state", "length",
"rcvr", "basis", "backend", "mjd"]
params = get_header_vals(fn, hdritems)
params['user_id'] = cache.get_userid()
# Normalise telescope name
tinfo = cache.get_telescope_info(params['telescop'])
params['telescop'] = tinfo['telescope_name']
params.update(tinfo)
# Check if obssystem_id, pulsar_id, user_id can be found
obssys_key = (params['telescop'].lower(), params['rcvr'].lower(),
params['backend'].lower())
obssys_ids = cache.get_obssystemid_cache()
if obssys_key not in obssys_ids:
t, r, b = obssys_key
raise errors.FileError("The observing system combination in the file "
"%s is not registered in the database. "
"(Telescope: %s, Receiver: %s; Backend: %s)." %
(fn, t, r, b))
else:
params['obssystem_id'] = obssys_ids[obssys_key]
obssysinfo = cache.get_obssysinfo(params['obssystem_id'])
params['band_descriptor'] = obssysinfo['band_descriptor']
params['obssys_name'] = obssysinfo['name']
# Check if pulsar_id is found
try:
psr_id = cache.get_pulsarid(params['name'])
except errors.UnrecognizedValueError:
if config.cfg.auto_add_pulsars:
notify.print_info("Automatically inserting pulsar with "
"name '%s'" % params['name'], 1)
# Add pulsar
psr_id = add_pulsar.add_pulsar(params['name'])
# Force an update of the pulsarid and pulsarname caches
cache.get_pulsarid_cache(update=True)
cache.get_pulsarname_cache(update=True)
else:
raise errors.FileError("The pulsar name %s (from file %s) is not "
"recognized." % (params['name'], fn))
# Normalise pulsar name
params['name'] = cache.get_prefname(params['name'])
params['pulsar_id'] = psr_id
return params
def plot_toa_histogram(toas):
"""Given a list of TOAs (as returned by create_timfile.get_toas(...)
make histogram plots.
Input:
toas: A list of TOAs.
Output:
fig: The newly created matplotlib Figure object.
"""
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(10, 6))
# Summarize TOA info
pulsars = {}
telescopes = set()
bands = set()
psrnames = set()
for toa in toas:
psr = pulsars.setdefault(toa['pulsar_id'], {})
obssysid = toa['obssystem_id']
obssysinfo = cache.get_obssysinfo(obssysid)
telid = obssysinfo['telescope_id']
telname = cache.get_telescope_info(telid)['telescope_name']
band = toa['band_descriptor']
bands.add(band)
telescopes.add(telname)
psr[telname] = psr.get(telname, 0)+1
psr[band] = psr.get(band, 0)+1
band_colours = dict(zip(sorted(bands), ['r', 'b', 'g', 'c']))
telescope_colours = {'Effelsberg': '#FFCE00',
'Jodrell': '#CE1124',
'Nancay': '#0055A4',
'WSRT': '#FF7F00',
'Sardinia': '#007FFF',
'Parkes': '#EDC9AF',
'GBT': '#22BB22',
'Arecibo': '#00BFFF'}
indices = []
labels = []
telleg = {}
bandleg = {}
telax = plt.axes((0.15, 0.1, 0.39, 0.8))
bandax = plt.axes((0.56, 0.1, 0.39, 0.8), sharey=telax)
for ii, (psrid, info) in enumerate(pulsars.iteritems()):
indices.append(ii)
labels.append(cache.get_pulsarname(psrid))
total = 0
for telname in sorted(telescopes):
if telname in info:
count = info[telname]
bb = telax.barh(ii, count, height=1, left=total,
color=telescope_colours[telname])
telleg[telname] = bb
total += count
total = 0
for band in ['P-band', 'L-band', 'S-band']:
if band in info:
count = info[band]
bb = bandax.barh(ii, count, height=1, left=total,
color=band_colours[band])
bandleg[band] = bb
total += count
telax.yaxis.set_ticks(np.array(indices)+0.5)
telax.yaxis.set_ticklabels(labels)
telax.set_ylim(-0.5, len(pulsars)+2.5)
plt.setp((telax.get_xticklabels(),
bandax.get_xticklabels()),
rotation=30, ha='right')
telax.set_xlabel("Number of TOAs")
bandax.set_xlabel("Number of TOAs")
telax.set_title("By telescope")
bandax.set_title("By observing band")
labels, handles = zip(*sorted(telleg.items()))
telax.legend(handles, labels, prop=dict(size='small'))
handles, labels = zip(*bandleg.items())
bandax.legend(labels, handles, prop=dict(size='small'))
plt.setp(bandax.yaxis.get_ticklabels(), visible=False)
return fig
def main(args):
# Connect to the database
db = database.Database()
db.connect()
try:
if args.from_file is not None:
# Re-create parser, so we can read arguments from file
parser = utils.DefaultArguments()
add_arguments(parser)
if args.from_file == '-':
obssyslist = sys.stdin
else:
if not os.path.exists(args.from_file):
raise errors.FileError("The obssystem list (%s) does " \
"not appear to exist." % args.from_file)
obssyslist = open(args.from_file, 'r')
numfails = 0
numadded = 0
for line in obssyslist:
# Strip comments
line = line.partition('#')[0].strip()
if not line:
# Skip empty line
continue
try:
customargs = copy.deepcopy(args)
arglist = shlex.split(line.strip())
parser.parse_args(arglist, namespace=customargs)
if customargs.telescope is None or customargs.backend is None or \
customargs.frontend is None or customargs.band is None or \
customargs.clock is None:
raise errors.BadInputError("Observing systems " \
"must have a telescope, backend, frontend, " \
"band descriptor, and clock file! At least " \
"one of these is missing.")
tinfo = cache.get_telescope_info(customargs.telescope)
telescope_id = tinfo['telescope_id']
if customargs.name is None:
customargs.name = "%s_%s_%s" % \
(tinfo['telescope_abbrev'].upper(), \
customargs.backend.upper(), \
customargs.frontend.upper())
obssystem_id = add_obssystem(db, customargs.name, telescope_id, \
customargs.frontend, customargs.backend, \
customargs.band, customargs.clock)
print "Successfully inserted new observing system. " \
"Returned obssystem_id: %d" % obssystem_id
numadded += 1
except errors.ToasterError:
numfails += 1
traceback.print_exc()
if args.from_file != '-':
obssyslist.close()
if numadded:
notify.print_success("\n\n===================================\n" \
"%d obssystems successfully added\n" \
"===================================\n" % numadded)
if numfails:
raise errors.ToasterError(\
"\n\n===================================\n" \
"The adding of %d obssystems failed!\n" \
"Please review error output.\n" \
"===================================\n" % numfails)
else:
if args.telescope is None or args.backend is None or \
args.frontend is None or args.band is None or \
args.clock is None:
raise errors.BadInputError("Observing systems " \
"must have a telescope, backend, frontend, " \
"band descriptor, and clock file! At least " \
"one of these is missing.")
tinfo = cache.get_telescope_info(args.telescope)
telescope_id = tinfo['telescope_id']
if args.name is None:
args.name = "%s_%s_%s" % \
(tinfo['telescope_abbrev'].upper(), \
args.backend.upper(), \
args.frontend.upper())
obssystem_id = add_obssystem(db, args.name, telescope_id, \
args.frontend, args.backend, args.band, args.clock)
print "Successfully inserted new observing system. " \
"Returned obssystem_id: %d" % obssystem_id
finally:
db.close()
