def merge_pulsar(src_pulsar_id, dest_pulsar_id, existdb=None):
"""Merge one pulsar entry into another.
Inputs:
src_pulsar_id: The ID of the pulsar entry that will
be merged.
NOTE: This entry will no longer exist following
the merge.
dest_pulsar_id: The ID of the pulsar entry that will
be merged into.
existdb: A (optional) existing database connection object.
(Default: Establish a db connection)
Outputs:
None
"""
notify.print_info("Merging pulsar '%s' (ID: %d) into '%s' (ID: %d)" %
(cache.get_pulsarname(src_pulsar_id), src_pulsar_id,
cache.get_pulsarname(dest_pulsar_id), dest_pulsar_id), 2)
# Connect to the database
db = existdb or database.Database()
db.connect()
trans = db.begin()
try:
# Update all relevant entries in the database
tables = [db.pulsar_aliases,
db.timfiles,
db.rawfiles,
db.templates,
db.parfiles,
db.master_parfiles,
db.master_templates,
db.toas]
values = {'pulsar_id': dest_pulsar_id}
for table in tables:
update = table.update().\
where(table.c.pulsar_id == src_pulsar_id)
results = db.execute(update, values)
results.close()
# Remove now unused entry in the pulsars table
delete = db.pulsars.delete().\
where(db.pulsars.c.pulsar_id == src_pulsar_id)
results = db.execute(delete)
results.close()
except:
trans.rollback()
raise
else:
trans.commit()
finally:
if existdb is None:
db.close()
def plot_cadence(toas):
"""Given a list of TOAs (as returned by create_timfile.get_toas(...)
make a plot of observing cadence.
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 = {}
for toa in toas:
psr = pulsars.setdefault(toa['pulsar_id'], [])
psr.append(toa['mjd'])
indices = []
labels = []
ax = plt.axes()
for ii, (psrid, mjds) in enumerate(pulsars.iteritems()):
indices.append(ii)
labels.append(cache.get_pulsarname(psrid))
ax.plot(mjds, ii*np.ones_like(mjds), 'k,')
ax.set_xlabel("MJD")
ax.yaxis.set_ticklabels(labels)
ax.yaxis.set_ticks(np.array(indices))
ax.set_ylim(-0.5, len(pulsars)-0.5)
return fig
def is_curator(user_id, pulsar_id, existdb=None):
"""Return whether user has curator privileges for the given
pulsar.
Inputs:
user_id: The ID of the user to check privileges for.
pulsar_id: The ID of the pulsar in question.
existdb: A (optional) existing database connection object.
(Default: Establish a db connection)
Output:
curator: True if the user has curator privileges.
False otherwise.
"""
# Check if user_id and pulsar_id are valid
# Exceptions will be raise if no matches are found
cache.get_userinfo(user_id)
cache.get_pulsarname(pulsar_id)
# Connect to the DB if necessary
db = existdb or database.Database()
db.connect()
select = db.select([db.curators.c.user_id], \
from_obj=[db.curators.\
outerjoin(db.users, \
onclause=db.curators.c.user_id == \
db.users.c.user_id)]).\
where((db.curators.c.pulsar_id == pulsar_id) & \
db.curators.c.user_id.in_((user_id,None)) & \
db.users.c.active)
result = db.execute(select)
rows = result.fetchall()
result.close()
curator = bool(rows)
return curator
def dump_pulsars(pulsar_ids=None):
"""Dump pulsar names and aliases to screen.
Input:
pulsar_ids: list of pulsar IDs to display.
(Default: dump all pulsars)
Outputs:
None
"""
# Grab the pulsar alias cache once rather than accessing it multiple times
pulsaralias_cache = cache.get_pulsaralias_cache()
if pulsar_ids is None:
pulsar_ids = sorted(pulsaralias_cache.keys())
for psrid in sorted(pulsar_ids):
psrname = cache.get_pulsarname(psrid)
print psrname
for alias in pulsaralias_cache[psrid]:
if alias == psrname:
continue
print alias
def show_procjobs(procjobs):
print "--" * 25
for procjob in procjobs:
print colour.cstring("Process Id:", underline=True, bold=True) + colour.cstring(
" %d" % procjob.process_id, bold=True
)
print "\nPulsar name: %s" % cache.get_pulsarname(procjob.pulsar_id)
print "Rawfile (ID=%d): %s" % (procjob.rawfile_id, procjob.rawfn)
if procjob.replacement_rawfile_id is not None:
colour.cprint("Rawfile has been superseded by rawfile_id=%d" % procjob.replacement_rawfile_id, "warning")
print "Manipulator: %s" % procjob.manipulator
print " Args: %s" % procjob.manipulator_args
print "Number of freq. chunks: %d" % procjob.nchan
print "Number of time chunks: %d" % procjob.nsub
print "Uploaded by: %s (%s)" % (procjob.real_name, procjob.email_address)
print "Date and time job completed: %s" % procjob.add_time.isoformat(" ")
if config.cfg.verbosity >= 1:
lines = ["Template (ID=%d): %s" % (procjob.template_id, procjob.tempfn)]
if procjob.parfile_id is not None:
lines.append("Parfile (ID=%d): %s" % (procjob.parfile_id, procjob.parfn))
else:
lines.append("No parfile installed during processing.")
notify.print_info("\n".join(lines), 1)
print "--" * 25
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