def main():
parser = argparse.ArgumentParser(
description='Run makepsf chunk of the OSSOS pipeline')
parser.add_argument('--ccd', '-c',
action='store',
type=int,
dest='ccd',
default=None,
help='which ccd to process, default is all')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument("--dry-run",
action="store_true",
help="DRY RUN, don't copy results to VOSpace, implies --force")
parser.add_argument("--fk", action="store_true", help="Run fk images")
parser.add_argument("--type", "-t", choices=['o', 'p', 's'],
help="which type of image: o-RAW, p-ELIXIR, s-SCRAMBLE", default='p')
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--force", default=False,
action="store_true")
parser.add_argument("--debug", "-d",
action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Started {}".format(cmd_line))
prefix = (args.fk and 'fk') or ''
storage.DBIMAGES = args.dbimages
exit_code = 0
for expnum in args.expnum:
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = range(0,36)
else:
# First exposrues with 40 CCD Megaprime
ccdlist = range(0, 40)
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
run(expnum, ccd, args.type, args.dry_run, prefix, args.force)
return exit_code
def main():
parser = argparse.ArgumentParser()
parser.add_argument('field')
parser.add_argument('ccd')
parser.add_argument(
'--expnum',
default=None,
help="Which exposure is the lead for this astrom file?")
parser.add_argument(
'--astrom-filename',
default=None,
help="Give the astrom file directly instead of looking-up "
"using the field/ccd naming scheme.")
parser.add_argument('--reals', action='store_true', default=False)
parser.add_argument('--type',
choices=['o', 'p', 's'],
help="Which type of image.",
default='s')
parser.add_argument('--measure3',
default='vos:OSSOS/measure3/2013B-L_redo/')
parser.add_argument('--dbimages', default=None)
parser.add_argument('--dry-run', action='store_true', default=False)
parser.add_argument('--force', action='store_true', default=False)
parser.add_argument("--fk",
action="store_true",
default=False,
help="Do fakes?")
parser.add_argument('--object-planted',
default=OBJECT_PLANTED,
help="Name of file contains list of planted objects.")
parser.add_argument(
'--bright-limit',
default=BRIGHT_LIMIT,
type=float,
help=
"Sources brighter than this limit {} are used to diagnose planting issues."
.format(BRIGHT_LIMIT))
parser.add_argument(
'--minimum-bright-detections',
default=MINIMUM_BRIGHT_DETECTIONS,
type=int,
help=
"required number of detections with mag brighter than bright-limit.")
parser.add_argument(
'--minimum-bright-fraction',
default=MINIMUM_BRIGHT_FRACTION,
type=float,
help=
"minimum fraction of objects above bright limit that should be found.")
parser.add_argument("--debug", action="store_true")
parser.add_argument("--verbose", "-v", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
prefix = (args.fk and "fk") or ""
version = args.type
ext = 'cands'
if args.reals:
ext = 'reals'
if args.dbimages is not None:
storage.DBIMAGES = args.dbimages
astrom.DATASET_ROOT = args.dbimages
storage.MEASURE3 = args.measure3
astrom_uri = storage.get_cands_uri(args.field,
ccd=args.ccd,
version=args.type,
prefix=prefix,
ext="measure3.{}.astrom".format(ext))
if args.astrom_filename is None:
astrom_filename = os.path.basename(astrom_uri)
else:
astrom_filename = args.astrom_filename
if not os.access(astrom_filename, os.F_OK):
astrom_filename = os.path.dirname(astrom_uri) + "/" + astrom_filename
# Load the list of astrometric observations that will be looked at.
fk_candidate_observations = astrom.parse(astrom_filename)
if args.expnum is None:
expnum = fk_candidate_observations.observations[0].expnum
else:
expnum = args.expnum
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version='',
ccd=args.ccd) and not args.force:
logging.info("{} completed successfully for {} {} {} {}".format(
task, prefix, expnum, '', args.ccd))
return
with storage.LoggingManager(task, prefix, expnum, args.ccd, version,
args.dry_run):
try:
match_filename = os.path.splitext(
os.path.basename(astrom_filename))[0] + '.match'
logging.info(f'Got back:{match_filename}')
match_uri = storage.get_cands_uri(
args.field,
ccd=args.ccd,
version=args.type,
prefix=prefix,
ext="measure3.{}.match".format(ext),
block=args.field)
try:
storage.copy(match_uri, match_filename)
except NotFoundException as ex:
logging.warning(
f'No match file found at {match_uri}, creating one.')
logging.debug(f'{ex}')
pass
logging.info(
("Comparing planted and measured magnitudes "
"for sources in {} and {}\n".format(args.object_planted,
astrom_filename)))
result = match_planted(
fk_candidate_observations,
match_filename=match_filename,
object_planted=args.object_planted,
bright_limit=args.bright_limit,
minimum_bright_detections=args.minimum_bright_detections,
bright_fraction=args.minimum_bright_fraction)
if not args.dry_run:
storage.copy(match_filename, match_uri)
uri = os.path.dirname(astrom_uri)
keys = [storage.tag_uri(os.path.basename(astrom_uri))]
values = [result]
storage.set_tags_on_uri(uri, keys, values)
logger.info(message)
except Exception as err:
import traceback
traceback.print_exc()
message = str(err)
logging.error(message)
if not args.dry_run:
storage.set_status(task,
prefix,
expnum,
version='',
ccd=args.ccd,
status=message)
return
def main():
parser = argparse.ArgumentParser(
description='Run makepsf chunk of the OSSOS pipeline')
parser.add_argument('--ccd',
'-c',
action='store',
type=int,
dest='ccd',
default=None,
help='which ccd to process, default is all')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument(
"--dry-run",
action="store_true",
help="DRY RUN, don't copy results to VOSpace, implies --force")
parser.add_argument("--fk", action="store_true", help="Run fk images")
parser.add_argument(
"--type",
"-t",
choices=['o', 'p', 's'],
help="which type of image: o-RAW, p-ELIXIR, s-SCRAMBLE",
default='p')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--force", default=False, action="store_true")
parser.add_argument("--debug", "-d", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Started {}".format(cmd_line))
prefix = (args.fk and 'fk') or ''
storage.DBIMAGES = args.dbimages
exit_code = 0
for expnum in args.expnum:
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
run(expnum, ccd, args.type, args.dry_run, prefix, args.force)
return exit_code
def main():
# Must be running as a script
parser = argparse.ArgumentParser(
description='Run step3jmp and step3matt on a given triple.')
parser.add_argument("--ccd",
"-c",
action="store",
default=None,
type=int,
dest="ccd")
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnums",
type=int,
nargs=3,
help="3 expnums to process")
parser.add_argument("--version", action='version', version='%(prog)s 1.0')
parser.add_argument('-t',
'--type',
help='which type of image to process',
choices=['s', 'p', 'o'],
default='p')
parser.add_argument('--fk',
help='Do fakes?',
default=False,
action='store_true')
parser.add_argument(
'--field',
help='a string that identifies which field is being searched',
nargs='?')
parser.add_argument('--no-sort',
help='preserve input exposure order',
action='store_true')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--debug", action="store_true")
parser.add_argument("--rate_min",
default=_RATE_MIN,
help='minimum rate to accept',
type=float)
parser.add_argument('--rate_max',
default=_RATE_MAX,
help='maximum rate to accept',
type=float)
parser.add_argument('--angle',
default=_ANGLE_CENTRE,
help='angle of x/y motion, West is 0, North 90',
type=float)
parser.add_argument('--width',
default=_ANGLE_WIDTH,
help='openning angle of search cone',
type=float)
parser.add_argument("--dry-run",
action="store_true",
help="do not copy to VOSpace, implies --force")
parser.add_argument("--force", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = (args.fk and 'fk') or ''
expnums = args.expnums
version = args.type
if args.ccd is None:
expnum = min(expnums)
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
if not args.no_sort:
args.expnums.sort()
for ccd in ccdlist:
run(expnums,
ccd,
version=version,
rate_min=args.rate_min,
rate_max=args.rate_max,
angle=args.angle,
width=args.width,
field=args.field,
prefix=prefix,
force=args.force,
dry_run=args.dry_run)
def main():
parser = argparse.ArgumentParser(
description='Run step1jmp and step1matt on a given exposure.')
parser.add_argument("--ccd", "-c",
action="store",
default=None,
type=int,
dest="ccd")
parser.add_argument("--fk", help="add the fk prefix on processing?",
default=False,
action='store_true')
parser.add_argument("--dbimages",
action="store",
default=storage.DBIMAGES,
help='vospace dbimages containerNode')
parser.add_argument("--field",
action="store",
default=None,
help="Name of the field being combined")
parser.add_argument("expnum",
type=int,
help="expnum to process")
parser.add_argument("--measure3",
action="store",
help="VOSpace location for measure3 files",
default=storage.MEASURE3)
parser.add_argument('--type', default='p', choices=['o', 'p', 's'],
help="which type of image")
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--debug", '-d',
action='store_true')
parser.add_argument("--force", '-f', action='store_true')
parser.add_argument("--dry-run", action="store_true",
help="Don't push back to VOSpace, implies --force")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
storage.MEASURE3 = args.measure3
expnum = args.expnum
version = args.type
prefix = (args.fk and 'fk') or ''
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccd_list = list(range(0, 36))
else:
# First exposures with 40 CCD Megaprime
ccd_list = list(range(0, 40))
else:
ccd_list = [args.ccd]
for ccd in ccd_list:
run(args.expnum,
ccd,
prefix=prefix,
version=version,
field=args.field,
measure3_dir=args.measure3,
dry_run=args.dry_run,
force=args.force)
def main():
parser = argparse.ArgumentParser(
description='Run mopheader chunk of the OSSOS pipeline')
parser.add_argument('--ccd', '-c',
action='store',
type=int,
dest='ccd',
default=None,
help='which ccd to process, default is all')
parser.add_argument('--ignore-update-headers', action='store_true', dest='ignore_update_headers')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument("--dry-run",
action="store_true",
help="DRY RUN, don't copy results to VOSpace, implies --force")
parser.add_argument("--fk", action="store_true", help="Run fk images")
parser.add_argument("--type", "-t", choices=['o', 'p', 's'],
help="which type of image: o-RAW, p-ELIXIR, s-SCRAMBLE", default='p')
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--force", default=False,
action="store_true")
parser.add_argument("--debug", "-d",
action="store_true")
args = parser.parse_args()
util.set_logger(args)
logging.info("started")
prefix = (args.fk and 'fk') or ''
task = util.task()
dependency = 'update_header'
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccdlist = range(0, 36)
else:
ccdlist = [args.ccd]
exit_code = 0
for expnum in args.expnum:
for ccd in ccdlist:
logging.info("Attempting to get status on header for {} {}".format(expnum, ccd))
storage.set_logger(task,
prefix, expnum, ccd, args.type, args.dry_run)
if storage.get_status(task, prefix, expnum, version=args.type, ccd=ccd) and not args.force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, args.type, ccd))
continue
message = 'success'
try:
logging.info("Building a header ")
if not storage.get_status(dependency, prefix, expnum, "p", 36) and not args.ignore_update_headers:
raise IOError("{} not yet run for {}".format(dependency, expnum))
mk_mopheader(expnum, ccd, args.type, args.dry_run, prefix=prefix)
except CalledProcessError as cpe:
message = str(cpe.output)
exit_code = message
except Exception as e:
message = str(e)
logging.info(message)
logging.error(message)
if not args.dry_run:
storage.set_status(task, prefix, expnum, version=args.type, ccd=ccd, status=message)
return exit_code
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--ccd',
action='store',
type=int,
default=None,
help='which ccd to process')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnums",
type=int,
nargs=3,
help="expnum(s) to process")
parser.add_argument("--type",
action='store',
default='s',
choices=['s', 'p', 'o'],
help='which type of image')
parser.add_argument('--no-sort',
action='store_true',
default=False,
help='no sorting exposure before processing')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--debug", '-d', action='store_true')
parser.add_argument("--number",
"-n",
type=int,
help="Number of KBOs to plant into images.",
default=10)
parser.add_argument("--mmin",
type=float,
help="Minimum magnitude value to add source with.",
default=21.0)
parser.add_argument("--mmax",
type=float,
help="Maximum magnitude value to add source with.",
default=25.5)
parser.add_argument("--rmin",
default=0.5,
type=float,
help="minimum motion rate")
parser.add_argument("--rmax",
default=15,
type=float,
help="maximum motion rate")
parser.add_argument("--width",
default=30,
type=float,
help="angle opening")
parser.add_argument("--ang",
default=20,
type=float,
help="angle of motion, 0 is West")
parser.add_argument("--force", action="store_true")
parser.add_argument("--dry-run", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
expnums = args.expnums
version = args.type
if args.ccd is None:
expnum = min(expnums)
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
if not args.no_sort:
args.expnums.sort()
for ccd in ccdlist:
plant(args.expnums,
ccd,
args.rmin,
args.rmax,
args.ang,
args.width,
number=args.number,
mmin=args.mmin,
mmax=args.mmax,
version=version,
dry_run=args.dry_run)
parser.add_argument("--fk", action="store_true", help="Run fk images")
parser.add_argument("--type", "-t", choices=['o', 'p', 's'],
help="which type of image: o-RAW, p-ELIXIR, s-SCRAMBLE", default='p')
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--force", default=False,
action="store_true")
parser.add_argument("--debug", "-d",
action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Started {}".format(cmd_line))
prefix = (args.fk and 'fk') or ''
storage.DBIMAGES = args.dbimages
for expnum in args.expnum:
if args.ccd is None:
ccdlist = storage.get_ccdlist(expnum)
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
run(expnum, ccd)
def main():
# Must be running as a script
parser = argparse.ArgumentParser(
description='Run step2jmp and step2matt on a given exposure.')
parser.add_argument("--ccd",
"-c",
action="store",
default=None,
type=int,
dest="ccd")
parser.add_argument("--fk",
action="store_true",
default=False,
help="Do fakes?")
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnums",
type=int,
nargs=3,
help="3 expnums to process")
parser.add_argument("--version", action='version', version='%(prog)s 1.0')
parser.add_argument('-t',
'--type',
help='which type of image to process',
choices=['s', 'p', 'o'],
default='p')
parser.add_argument('--no-sort',
help='preserve input exposure order',
action='store_true')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--default",
default="WCS",
choices=['WCS', 'JMP'],
help="Which shift should be used if they dis-agree?")
parser.add_argument("--debug", action="store_true")
parser.add_argument(
"--dry-run",
action="store_true",
help="run without pushing back to VOSpace, implies --force")
parser.add_argument("--force", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = (args.fk and "fk") or ""
expnums = args.expnums
version = args.type
if args.ccd is None:
expnum = min(expnums)
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
if not args.no_sort:
args.expnums.sort()
for ccd in ccdlist:
run(args.expnums,
ccd,
version=version,
prefix=prefix,
dry_run=args.dry_run,
default=args.default,
force=args.force)
def main():
### Must be running as a script
parser = argparse.ArgumentParser(
description='Run step1jmp and step1matt on a given exposure.')
parser.add_argument("--ccd", "-c",
action="store",
default=None,
type=int,
dest="ccd")
parser.add_argument("--ignore", help="Try to run even in previous step failed.",
default=False,
action="store_true")
parser.add_argument("--fk", help="add the fk prefix on processing?",
default=False,
action='store_true')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("--sex_thresh",
action="store",
type=float,
default=_SEX_THRESHOLD,
help="sExtractor detection threhold")
parser.add_argument("--wavelet_thresh",
type=float,
default=_WAVE_THRESHOLD,
help="Wavelet detection threhold")
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument("--version",
action='version',
version='%(prog)s 1.0')
parser.add_argument('--type', default='p',
choices=['o', 'p', 's'], help="which type of image")
parser.add_argument('--log', default=None, help="Write standard out to this file")
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--debug", '-d',
action='store_true')
parser.add_argument("--force", action="store_true")
parser.add_argument("--dry-run", action="store_true", help="Do a dry run, not changes to vospce, implies --force")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = (args.fk and 'fk') or ''
version = args.type
exit_code = 0
for expnum in args.expnum:
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = range(0,36)
else:
# First exposrues with 40 CCD Megaprime
ccdlist = range(0, 40)
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
run(expnum,
ccd,
prefix=prefix,
version=version,
sex_thresh=args.sex_thresh,
wave_thresh=args.wavelet_thresh,
dry_run=args.dry_run,
force=args.force)
parser.add_argument("--fk", action="store_true", help="Run fk images")
parser.add_argument(
"--type",
"-t",
choices=['o', 'p', 's'],
help="which type of image: o-RAW, p-ELIXIR, s-SCRAMBLE",
default='p')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--force", default=False, action="store_true")
parser.add_argument("--debug", "-d", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Started {}".format(cmd_line))
prefix = (args.fk and 'fk') or ''
storage.DBIMAGES = args.dbimages
for expnum in args.expnum:
if args.ccd is None:
ccdlist = storage.get_ccdlist(expnum)
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
run(expnum, ccd)
def main(task='step1'):
### Must be running as a script
parser = argparse.ArgumentParser(
description='Run step1jmp and step1matt on a given exposure.')
parser.add_argument("--ccd", "-c",
action="store",
default=None,
type=int,
dest="ccd")
parser.add_argument("--ignore", help="Try to run even in previous step failed.",
default=False,
action="store_true")
parser.add_argument("--fk", help="add the fk prefix on processing?",
default=False,
action='store_true')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("--sex_thresh",
action="store",
type=float,
default=_SEX_THRESHOLD,
help="sExtractor detection threhold")
parser.add_argument("--wavelet_thresh",
type=float,
default=_WAVE_THRESHOLD,
help="Wavelet detection threhold")
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument("--version",
action='version',
version='%(prog)s 1.0')
parser.add_argument('--type', default='p',
choices=['o', 'p', 's'], help="which type of image")
parser.add_argument('--log', default=None, help="Write standard out to this file")
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--debug", '-d',
action='store_true')
parser.add_argument("--force", action="store_true")
parser.add_argument("--dry-run", action="store_true", help="Do a dry run, not changes to vospce, implies --force")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = (args.fk and 'fk') or ''
task = util.task()
dependency = "mkpsf"
version = args.type
exit_code = 0
for expnum in args.expnum:
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = range(0,36)
else:
# First exposrues with 40 CCD Megaprime
ccdlist = range(0, 40)
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
try:
message = storage.SUCCESS
if not (args.force or args.dry_run) and storage.get_status(task, prefix, expnum, version, ccd):
logging.critical("{} completed successfully for {}{}{}{:02d}".format(
task, prefix, expnum, version, ccd))
continue
if not storage.get_status(dependency, prefix, expnum, version, ccd) and not args.ignore:
raise IOError(35, "Cannot start {} as {} not yet completed for {}{}{}{:02d}".format(
task, dependency, prefix, expnum, version, ccd))
storage.set_logger(task, prefix, expnum, ccd, args.type, args.dry_run)
step1(expnum, ccd, prefix=prefix, version=version, dry_run=args.dry_run)
except Exception as ex:
message = str(ex)
logging.error(message)
if not args.dry_run:
storage.set_status(task, prefix, expnum, version, ccd, status=message)
logging.info(message)
return exit_code
def main():
"""
Run the align process.
@return: None
"""
parser = argparse.ArgumentParser()
parser.add_argument('--ccd',
action='store',
type=int,
default=None,
help='which ccd to process')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnums",
type=int,
nargs=3,
help="expnum(s) to process")
parser.add_argument("--type",
action='store',
default='s',
choices=['s', 'p', 'o'],
help='which type of image')
parser.add_argument("--fk",
help="add the fk prefix on processing?",
default=False,
action='store_true')
parser.add_argument(
'--no-sort',
action='store_true',
default=False,
help='do not sort exposure list by expnum before processing')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--debug", '-d', action='store_true')
parser.add_argument("--force", action="store_true")
parser.add_argument("--dry-run", action="store_true")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = (args.fk and 'fk') or ''
version = args.type
if not args.no_sort:
args.expnums.sort()
if args.ccd is None:
if int(args.expnums[0]) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
align(args.expnums,
ccd,
version=version,
prefix=prefix,
dry_run=args.dry_run)
def main():
# Must be running as a script
parser = argparse.ArgumentParser(
description='Run step1jmp and step1matt on a given exposure.')
parser.add_argument("--ccd", "-c",
action="store",
default=None,
type=int,
dest="ccd")
parser.add_argument("--ignore", help="Try to run even in previous step failed.",
default=False,
action="store_true")
parser.add_argument("--fk", help="add the fk prefix on processing?",
default=False,
action='store_true')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("--sex_thresh",
action="store",
type=float,
default=_SEX_THRESHOLD,
help="sExtractor detection threhold")
parser.add_argument("--wavelet_thresh",
type=float,
default=_WAVE_THRESHOLD,
help="Wavelet detection threhold")
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument("--version",
action='version',
version='%(prog)s 1.0')
parser.add_argument('--type', default='p',
choices=['o', 'p', 's'], help="which type of image")
parser.add_argument('--log', default=None, help="Write standard out to this file")
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--debug", '-d',
action='store_true')
parser.add_argument("--force", action="store_true")
parser.add_argument("--dry-run", action="store_true", help="Do a dry run, not changes to vospce, implies --force")
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info("Starting {}".format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = (args.fk and 'fk') or ''
version = args.type
for expnum in args.expnum:
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
run(expnum,
ccd,
prefix=prefix,
version=version,
sex_thresh=args.sex_thresh,
wave_thresh=args.wavelet_thresh,
dry_run=args.dry_run,
force=args.force,
ignore=args.ignore)
def main():
"""Run the script."""
parser = argparse.ArgumentParser(
description='time scramble the input images by tweaking their headers.'
)
parser.add_argument('--ccd',
action='store',
type=int,
default=None,
help='which ccd to process')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnums",
type=int,
nargs=3,
help="expnums to scramble")
parser.add_argument("--nosort",
action='store_true',
default=False,
help="do not sort before processing")
parser.add_argument("--type",
action='store',
default='p',
choices=['p', 'o'],
help='which type of image')
parser.add_argument("--verbose", "-v", action="store_true")
parser.add_argument("--debug", '-d', action='store_true')
parser.add_argument("--dry-run",
action="store_true",
help="Do not copy back to VOSpace, implies --force")
parser.add_argument("--force", action='store_true')
cmd_line = " ".join(sys.argv)
args = parser.parse_args()
util.set_logger(args)
logging.info('Starting {}'.format(cmd_line))
storage.DBIMAGES = args.dbimages
prefix = ''
version = args.type
if not args.nosort:
args.expnums.sort()
expnums = args.expnums
if args.ccd is None:
if int(expnums[0]) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = list(range(0, 36))
else:
# First exposrues with 40 CCD Megaprime
ccdlist = list(range(0, 40))
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
# check if scramble image alraedy made for this ccd
scramble(expnums=expnums,
ccd=ccd,
version=version,
dry_run=args.dry_run,
prefix=prefix)
def main(task='mkpsf'):
parser = argparse.ArgumentParser(
description='Run makepsf chunk of the OSSOS pipeline')
parser.add_argument('--ccd', '-c',
action='store',
type=int,
dest='ccd',
default=None,
help='which ccd to process, default is all')
parser.add_argument("--dbimages",
action="store",
default="vos:OSSOS/dbimages",
help='vospace dbimages containerNode')
parser.add_argument("expnum",
type=int,
nargs='+',
help="expnum(s) to process")
parser.add_argument("--dry-run",
action="store_true",
help="DRY RUN, don't copy results to VOSpace, implies --force")
parser.add_argument("--fk", action="store_true", help="Run fk images")
parser.add_argument("--type", "-t", choices=['o', 'p', 's'],
help="which type of image: o-RAW, p-ELIXIR, s-SCRAMBLE", default='p')
parser.add_argument("--verbose", "-v",
action="store_true")
parser.add_argument("--force", default=False,
action="store_true")
parser.add_argument("--debug", "-d",
action="store_true")
args = parser.parse_args()
util.set_logger(args)
prefix = (args.fk and 'fk') or ''
task = util.task()
dependency = 'mk_mopheader'
storage.DBIMAGES = args.dbimages
exit_code = 0
for expnum in args.expnum:
if args.ccd is None:
if int(expnum) < 1785619:
# Last exposures with 36 CCD Megaprime
ccdlist = range(0,36)
else:
# First exposrues with 40 CCD Megaprime
ccdlist = range(0, 40)
else:
ccdlist = [args.ccd]
for ccd in ccdlist:
if storage.get_status(task, prefix, expnum, version=args.type, ccd=ccd) and not args.force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, args.type, ccd))
continue
storage.set_logger(task,
prefix, expnum, ccd, args.type, args.dry_run)
message = 'success'
try:
if not storage.get_status(dependency, prefix, expnum, "p", ccd=ccd):
raise IOError("{} not yet run for {}".format(dependency, expnum))
mkpsf(expnum, ccd, args.type, args.dry_run, prefix=prefix)
if args.dry_run:
continue
storage.set_status('fwhm', prefix, expnum, version=args.type, ccd=ccd, status=str(storage.get_fwhm(
expnum, ccd, version=args.type)))
storage.set_status('zeropoint', prefix, expnum, version=args.type, ccd=ccd,
status=str(storage.get_zeropoint(
expnum, ccd, version=args.type)))
except Exception as e:
message = str(e)
logging.error(message)
if not args.dry_run:
storage.set_status(task, prefix, expnum, version=args.type, ccd=ccd, status=message)
return exit_code
