def extract_from_file(fname, n_pixels, threshold, fwhmfilt, isolation_radius,
aperture_radius,
region_filename=None):
logger.info('Extracting catalogue from %s', fname)
with open_fits(fname) as infile:
header = infile[0].header
ref_image_id = header['image_id']
source_table = source_detect(fname,
n_pixels=n_pixels,
threshold=threshold,
fwhmfilt=fwhmfilt,
aperture_radius=aperture_radius)
logger.info('Found %s sources', len(source_table))
filtered_source_table = filter_source_table(source_table,
radius=isolation_radius)
logger.info('Keeping %s sources', len(filtered_source_table))
if region_filename is not None:
with RegionFile(region_filename,
aperture_radius=aperture_radius) as rfile:
rfile.add_regions(filtered_source_table, colour='green')
rfile.add_regions(source_table, colour='red')
inc_prescan = image_has_prescan(fname)
logger.debug('Image has prescan: %s', inc_prescan)
for row in filtered_source_table:
yield TransmissionCatalogueEntry(
aperture_radius=aperture_radius,
ref_image_id=int(ref_image_id),
x_coordinate=float(row['X_coordinate']),
y_coordinate=float(row['Y_coordinate']),
inc_prescan=inc_prescan,
flux_adu=float(row['Aper_flux_3']))
def add_regions(self, catalogue, colour):
logger.debug('Adding %s regions', colour)
for row in catalogue:
self.fptr.write(
self.circle(
row['X_coordinate'], row['Y_coordinate'],
colour=colour))
def time_context(message=None):
start = time.time()
yield
end = time.time()
if message is None:
logger.debug("Time taken: %s seconds", end - start)
else:
logger.debug(message, end - start)
def upload_to_database(self, cursor):
keys = self._fields
values = [getattr(self, key) for key in keys]
query = '''insert into transmission_log ({keys})
values ({placeholder})'''.format(
keys=', '.join(keys),
placeholder=', '.join(['%s'] * len(keys)))
logger.debug('Executing query: `%s` : [%s]', query,
', '.join(map(str, values)))
cursor.execute(query, values)
def main(args):
if args.verbose:
logger.setLevel("DEBUG")
logger.debug(args)
with connect_to_database_from_args(args) as cursor:
entry = TransmissionEntry.from_file(
args.filename, cursor, sky_radius_inner=args.radius_inner, sky_radius_outer=args.radius_outer
)
entry.upload_to_database(cursor)
def source_detect(fname, n_pixels, threshold, fwhmfilt, aperture_radius):
logger.info('Running source detect')
logger.debug('n_pixels: %s, threshold: %s', n_pixels, threshold)
with tempfile.NamedTemporaryFile(suffix='.fits') as tfile:
cmd = ['imcore', fname, 'noconf', tfile.name, n_pixels, threshold,
'--noell', '--filtfwhm', fwhmfilt, '--rcore', aperture_radius]
str_cmd = list(map(str, cmd))
logger.debug('Running command [%s]', ' '.join(str_cmd))
sp.check_call(str_cmd)
tfile.seek(0)
with open_fits(tfile.name) as infile:
return infile[1].data
def upload_info(extracted_data, cursor):
query = '''insert into transmission_sources ({fields})
values ({placeholders})'''
def format_query(query_str):
return ' '.join([line.strip() for line in query_str.split('\n')])
for row in extracted_data:
full_query = query.format(
fields=','.join(row._fields),
placeholders=','.join(['%s'] * len(row._fields)))
logger.debug('Inserting %s: %s', format_query(full_query), list(row))
cursor.execute(full_query, args=row)
def get_refcat_id(filename):
logger.debug("Extracting reference image id from {filename}".format(filename=filename))
with open_fits(filename) as infile:
header = infile[0].header
try:
return header["agrefimg"]
except KeyError:
logger.exception(
"""No autoguider reference image found in file %s.
Assuming this is ok and continuing.""",
filename,
)
raise NoAutoguider
def photometry_local(data, x, y, aperture_radius, sky_radius_inner,
sky_radius_outer):
logger.debug('Sky annulus radii: %s -> %s', sky_radius_inner,
sky_radius_outer)
apertures = ph.CircularAperture((x, y), r=aperture_radius)
annulus_apertures = ph.CircularAnnulus((x, y),
r_in=sky_radius_inner,
r_out=sky_radius_outer)
rawflux_table = ph.aperture_photometry(data, apertures)
bkgflux_table = ph.aperture_photometry(data, annulus_apertures)
bkg_mean = bkgflux_table['aperture_sum'] / annulus_apertures.area()
bkg_sum = bkg_mean * apertures.area()
final_sum = rawflux_table['aperture_sum'] - bkg_sum
return np.array(final_sum)
def main(args):
if args.verbose:
logger.setLevel('DEBUG')
logger.debug(args)
build_catalogue(
refimage=args.refimage,
region_filename=args.refimage + '.reg',
n_pixels=args.npix,
threshold=args.threshold,
fwhmfilt=args.fwhmfilt,
isolation_radius=args.isolation_radius,
aperture_radius=args.aperture_radius,
db_host=args.db_host,
db_user=args.db_user,
db_name=args.db_name,
db_socket=args.db_socket,
fits_out=args.fits_out,)
def main(args):
if args.verbose:
logger.setLevel('DEBUG')
logger.debug(args)
schema = database_schema()
tables = {}
for table_name in schema:
query = raw_create_table(table_name, schema)
tables[table_name] = query
with connect_to_database_from_args(args) as cursor:
for table_name, query in tables.items():
cursor.execute('drop table if exists {table_name}'.format(
table_name=table_name))
logger.debug('Executing query `%s`', query)
cursor.execute(query)
def connect_to_database(user, host, db, unix_socket):
if host is not None:
with pymysql.connect(user=user, host=host, db=db) as cursor:
logger.debug('Connected to database')
yield cursor
logger.debug('Closing database connection')
else:
with pymysql.connect(user=user,
unix_socket=unix_socket,
db=db) as cursor:
logger.debug('Connected to database')
yield cursor
logger.debug('Closing database connection')
def watcher(connection):
logger.info("Starting watcher")
logger.debug("Connecting to central hub")
hub = Pyro4.Proxy("PYRONAME:central.hub")
try:
hub.startThread("Transparency")
except Exception as err:
logger.exception("Cannot connect to pyro hub")
raise
while True:
try:
logger.debug("Pinging hub")
hub.update_transp(time.time())
except Exception as err:
logger.exception("Failure communicating with hub process")
raise
with time_context():
watcher_loop_step(connection)
logger.debug("Sleeping for %s seconds", SLEEP_TIME)
time.sleep(SLEEP_TIME)
def transaction(connection):
with connection as cursor:
yield cursor
logger.debug('Committing')
