def mkpsf_failures():
"""A simple script to loop over the standard tags for the mkpsf and
step1 processing steps. If exposure/ccd combo isn't marked as
'success' then report the failure.
This example uses the vos client directly.
"""
for expnum in storage.list_dbimages():
for ccd in range(36):
if not storage.get_status(MKPSF, "", expnum, "p", ccd):
# get_status returns FALSE if process didn't succeed,
# with return_message=True it returns the error message.
print expnum, ccd, storage.get_status(MKPSF, "", expnum, "p", ccd, return_message=True)
def mkpsf_failures():
"""A simple script to loop over the standard tags for the mkpsf and
step1 processing steps. If exposure/ccd combo isn't marked as
'success' then report the failure.
This example uses the vos client directly.
"""
for expnum in storage.list_dbimages():
for ccd in range(36):
if not storage.get_status(expnum, ccd, MKPSF):
# get_status returns FALSE if process didn't succeed,
# with return_message=True it returns the error message.
print expnum, ccd, storage.get_status(expnum,
ccd,
MKPSF,
return_message=True)
def detect_mbc(family_name, object_name, expnum, phot_table, test):
"""
Compare psf of asteroid with mean of stars to detect possible activity
"""
# read in asteroid identification values from the photometry output
asteroid_id = phot_table.query(
'{} == "{}" & {} == "{}"'.format(_OBJECT_HEADER, object_name, _EXPNUM_HEADER, expnum))
print asteroid_id
assert len(asteroid_id) == 1, 'No object or multiple objects identified'
# read in postage stamp header and data, do photometry to measure background (needed for saturation check)
header, exp_data, fits_file = fits_data(object_name, expnum, family_name)
# make sure that a mean star psf has been created form the OSSOS pipeline
if not storage.get_status(expnum.strip('p'), header[_CCD].split('d')[1], 'mkpsf'):
print '>> PSF does not exist'
ast_sky_psf = build_ast_profile(asteroid_id, exp_data, fwhm, family_name) # to build cutout of object
write_no_mkpsf(family_name, '{} {}'.format(expnum.strip('p'), header[_CCD].split('d')[1]))
return
# reject any object too bright that will definetly be saturated
mag = asteroid_id[_MAG_HEADER].values[0]
if mag < 18.5:
print '>> Object is too bright for accurate photometry'
ast_sky_psf = build_ast_profile(asteroid_id, exp_data, fwhm, family_name) # to build cutout of object
write_too_bright(family_name, asteroid_id)
return
# get fwhm from OSSOS VOSpace file
fwhm = storage.get_fwhm(expnum.strip('p'), header[_CCD].split('d')[1])
bkg, flux, fluxerr = sep_phot(exp_data, asteroid_id)
ast_sky_psf = build_ast_profile(asteroid_id, exp_data, fwhm, family_name)
ast_psf = np.subtract(ast_sky_psf, bkg)
try:
star_psf = build_star_profile(ast_psf, expnum, header, asteroid_id, fwhm, flux)
except Exception, e:
print 'Error calculating star psf: {}'.format(e)
return
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
def run(expnum,
ccd,
prefix='',
version='p',
sex_thresh=_SEX_THRESHOLD,
wave_thresh=_WAVE_THRESHOLD,
maxcount=_MAX_COUNT,
dry_run=False,
force=True):
"""run the actual step1jmp/matt codes.
expnum: the CFHT expousre to process
ccd: which ccd in the mosaic to process
fwhm: the image quality, FWHM, of the image. In pixels.
sex_thresh: the detection threhold to run sExtractor at
wave_thresh: the detection threshold for wavelet
maxcount: saturation level
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version, ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, version, ccd):
raise IOError(35, "Cannot start {} as {} not yet completed for {}{}{}{:02d}".format(
task, dependency, prefix, expnum, version, ccd))
logging.info("Retrieving imaging and input parameters from VOSpace")
storage.get_file(expnum, ccd, prefix=prefix, version=version, ext='mopheader')
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
fwhm = storage.get_fwhm(expnum, ccd, prefix=prefix, version=version)
basename = os.path.splitext(filename)[0]
_get_weight_map(filename, ccd)
logging.info("Launching step1jmp")
logging.info(util.exec_prog(['step1jmp',
'-f', basename,
'-t', str(wave_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
logging.info(util.exec_prog(['step1matt',
'-f', basename,
'-t', str(sex_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
if os.access('weight.fits', os.R_OK):
os.unlink('weight.fits')
if not dry_run:
for ext in ['obj.jmp', 'obj.matt']:
obj_uri = storage.get_uri(expnum, ccd, version=version, ext=ext,
prefix=prefix)
obj_filename = basename + "." + ext
count = 0
with open(obj_filename, 'r'):
while True:
try:
count += 1
logging.info("Attempt {} to copy {} -> {}".format(count, obj_filename, obj_uri))
storage.copy(obj_filename, obj_uri)
break
except Exception as ex:
if count > 10:
raise ex
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task, prefix, expnum, version, ccd, status=message)
if args.ccd is None:
ccdlist = range(0,36)
else:
ccdlist = [args.ccd]
if not args.no_sort:
args.expnums.sort()
prefix = ( args.fk and 'fk') or ''
for ccd in ccdlist:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnums[0], ccd, prefix+'step2', version=args.type):
raise IOError(35, "did step2 run on %s" % ( str(args.expnums)))
if storage.get_status(args.expnums[0], ccd, prefix+'step3', version=args.type) and not args.force:
logging.critical("step3 alread ran on expnum :%s, ccd: %d" % (
str(args.expnums), ccd))
continue
step3(args.expnums, ccd, version=args.type,
rate_min=args.rate_min,
rate_max=args.rate_max,
angle=args.angle,
width=args.width,
field=args.field,
prefix=prefix)
except Exception as e:
message = str(e)
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 run(expnum, ccd, version='p', prefix='', dry_run=False, force=False):
message = 'success'
if storage.get_status(task, prefix, expnum, version=version,
ccd=ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(
task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task=task,
prefix=prefix,
expnum=expnum,
ccd=ccd,
version=version,
dry_run=dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, "p",
ccd=ccd):
raise IOError("{} not yet run for {}".format(
dependency, expnum))
header = storage.get_astheader(expnum, ccd)
datasec = storage.datasec_to_list(
header.get('DATASEC', '[80:2080,30,4160]'))
try:
fwhm = "{:5.2f}".format(storage.get_fwhm(expnum, ccd))
except:
fwhm = 'unknown'
for keyword in del_keyword_list:
try:
del (header[keyword])
except:
pass
header['FWHM'] = (fwhm, 'FWHM in pixels')
header['EXTNAME'] = 'header'
primary_hdu = fits.PrimaryHDU(header=header)
hdu_list = fits.HDUList([
primary_hdu,
])
for ext in ['jmp', 'matt']:
extension = 'obj.' + ext
name = "{}p{:02d}.{}".format(expnum, ccd, extension)
try:
os.unlink(name)
os.unlink(name + ".fits")
except:
pass
logging.info("Retrieving {}".format(name))
obj_file = mop_file.Parser(expnum, ccd, extension)
obj_file.parse()
t = numpy.all([
datasec[0] < obj_file.data['X'],
obj_file.data['X'] < datasec[1],
datasec[2] < obj_file.data['Y'],
obj_file.data['Y'] < datasec[3]
],
axis=0)
logging.info(
"Source remaining after datasec cut: {} of {}".format(
len(obj_file.data[t]['X']), len(t)))
table_hdu = fits.table_to_hdu(obj_file.data[t])
table_hdu.header['CATALOG'] = name
table_hdu.header['EXTNAME'] = ext
hdu_list.append(table_hdu)
del table_hdu
del obj_file
os.unlink(name)
name = "{}p{:02d}.{}".format(expnum, ccd, 'obj.fits')
if os.access(name, os.F_OK):
os.unlink(name)
hdu_list.writeto(name)
uri = storage.dbimages_uri(expnum, ccd, 'p', ext=".obj.fits")
logging.info(name + " -> " + uri)
count = 0
with open(name):
while True:
count += 1
logging.info("Copy attempt {}".format(count))
try:
storage.copy(name, uri)
os.unlink(name)
break
except Exception as ex:
if count > 10:
raise ex
logging.info(message)
except Exception as e:
message = str(e)
logging.error(message)
if not dry_run:
storage.set_status(task,
prefix,
expnum,
version=version,
ccd=ccd,
status=message)
def run(expnum, ccd, version, dry_run=False, prefix="", force=False):
"""Run the OSSOS jmpmakepsf script.
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version=version,
ccd=ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(
task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(
dependency, prefix, expnum, version, ccd=ccd):
raise IOError("{} not yet run for {}".format(
dependency, expnum))
# confirm destination directory exists.
destdir = os.path.dirname(
storage.dbimages_uri(expnum,
ccd,
prefix=prefix,
version=version,
ext='fits'))
if not dry_run:
storage.mkdir(destdir)
# get image from the vospace storage area
logging.info("Getting fits image from VOSpace")
filename = storage.get_image(expnum,
ccd,
version=version,
prefix=prefix)
# get mopheader from the vospace storage area
logging.info("Getting mopheader from VOSpace")
mopheader_filename = storage.get_file(expnum,
ccd,
version=version,
prefix=prefix,
ext='mopheader')
# run mkpsf process
logging.info("Running mkpsf on %s %d" % (expnum, ccd))
logging.info(
util.exec_prog(
['jmpmakepsf.csh', './', filename, 'yes', 'yes']))
if dry_run:
return
# place the results into VOSpace
basename = os.path.splitext(filename)[0]
for ext in ('mopheader', 'psf.fits', 'zeropoint.used', 'apcor',
'fwhm', 'phot'):
dest = storage.dbimages_uri(expnum,
ccd,
prefix=prefix,
version=version,
ext=ext)
source = basename + "." + str(ext)
count = 0
with open(source, 'r'):
while True:
count += 1
try:
logging.info("Attempt {} to copy {} -> {}".format(
count, source, dest))
storage.copy(source, dest)
break
except Exception as ex:
if count > 10:
raise ex
# set some data parameters associated with the image, determined in this step.
storage.set_status('fwhm',
prefix,
expnum,
version=version,
ccd=ccd,
status=str(
storage.get_fwhm(expnum,
ccd=ccd,
prefix=prefix,
version=version)))
storage.set_status('zeropoint',
prefix,
expnum,
version=version,
ccd=ccd,
status=str(
storage.get_zeropoint(expnum,
ccd=ccd,
prefix=prefix,
version=version)))
logging.info(message)
except Exception as e:
message = str(e)
logging.error(message)
storage.set_status(task,
prefix,
expnum,
version,
ccd=ccd,
status=message)
return
def run(expnum, ccd, version, dry_run=False, prefix="", force=False):
"""Run the OSSOS jmpmakepsf script.
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version=version, ccd=ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, "p", ccd=ccd):
raise IOError("{} not yet run for {}".format(dependency, expnum))
# confirm destination directory exists.
destdir = os.path.dirname(
storage.dbimages_uri(expnum, ccd, prefix=prefix, version=version, ext='fits'))
if not dry_run:
storage.mkdir(destdir)
# get image from the vospace storage area
logging.info("Getting fits image from VOSpace")
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
# get mopheader from the vospace storage area
logging.info("Getting mopheader from VOSpace")
mopheader_filename = storage.get_file(expnum, ccd, version=version, prefix=prefix, ext='mopheader')
# run mkpsf process
logging.info("Running mkpsf on %s %d" % (expnum, ccd))
logging.info(util.exec_prog(['jmpmakepsf.csh',
'./',
filename,
'yes', 'yes']))
if dry_run:
return
# place the results into VOSpace
basename = os.path.splitext(filename)[0]
for ext in ('mopheader', 'psf.fits',
'zeropoint.used', 'apcor', 'fwhm', 'phot'):
dest = storage.dbimages_uri(expnum, ccd, prefix=prefix, version=version, ext=ext)
source = basename + "." + str(ext)
count = 0
with open(source, 'r'):
while True:
count += 1
try:
logging.info("Attempt {} to copy {} -> {}".format(count, source, dest))
storage.copy(source, dest)
break
except Exception as ex:
if count > 10:
raise ex
# set some data parameters associated with the image, determined in this step.
storage.set_status('fwhm', prefix, expnum, version=version, ccd=ccd, status=str(storage.get_fwhm(
expnum, ccd=ccd, prefix=prefix, version=version)))
storage.set_status('zeropoint', prefix, expnum, version=version, ccd=ccd,
status=str(storage.get_zeropoint(
expnum, ccd=ccd, prefix=prefix, version=version)))
logging.info(message)
except Exception as e:
message = str(e)
logging.error(message)
storage.set_status(task, prefix, expnum, version, ccd=ccd, status=message)
return
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
storage._dbimages = args.dbimages
prefix = ( args.fk and 'fk' ) or ''
ccdlist = ( args.ccd is None and range(0,36) ) or [args.ccd]
for ccd in ccdlist:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnum, ccd, prefix+'step3'):
logging.error(storage.get_status(
args.expnum,
ccd,
'step3',
return_message=True))
raise IOError(35, "need to run step3 first")
if storage.get_status(args.expnum, ccd, prefix+'combine') and not args.force:
continue
message = combine(args.expnum,
ccd,
prefix=prefix,
type=args.type,
field=args.field,
measure3=args.measure3
)
def main():
"""Run the script."""
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="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')
args = parser.parse_args()
if args.dry_run:
args.force = True
storage.DBIMAGES = args.dbimages
## setup logging
level = logging.CRITICAL
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
logging.getLogger('vos').setLevel(level)
logging.getLogger('vos').addHandler(logging.StreamHandler())
if not args.nosort:
args.expnums.sort()
ccds = [args.ccd]
exit_status = 0
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
storage.set_logger(os.path.splitext(os.path.basename(sys.argv[0]))[0],
"", args.expnums[0], ccd, args.type, args.dry_run)
expnums = args.expnums
if storage.get_status(expnums[0], ccd,
'scramble', version='s') and not args.force:
continue
message = storage.SUCCESS
try:
scramble(expnums=expnums, ccd=ccd, version='p', dry_run=args.dry_run)
except Exception as e:
logging.error(e)
message = str(e)
exit_status = message
if not args.dry_run:
storage.set_status(expnums[0], ccd,
'scramble', version='s',
status=message)
return exit_status
level = logging.CRITICAL
if args.verbose:
level = logging.INFO
format = "%(message)s"
if args.debug:
level = logging.DEBUG
format = "%(module)s %(funcName)s %(lineno)s %(message)s"
logging.basicConfig(level=level, format=format)
message = storage.SUCCESS
try:
expnum=args.expnum
# skip if already succeeded and not in force mode
if storage.get_status(expnum, 36, 'update_header_p') and not args.force:
logging.info("Already updated, skipping")
sys.exit(0)
header = (args.header is not None and ((
os.access(args.header, os.W_OK) and args.header ) or (
storage.get_image(args.header, ext='head')))) or (
storage.get_image(args.expnum, ext='head'))
image = (os.access(args.expnum,os.W_OK) and args.expnum ) or (
storage.get_image(args.expnum) )
logging.info(
"Swapping header for %s for contents in %s \n" % (
image, header) )
def run(expnum, ccd, version='p', prefix='', dry_run=False, force=False):
message = 'success'
if storage.get_status(task, prefix, expnum, version=version, ccd=ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task=task, prefix=prefix, expnum=expnum, ccd=ccd, version=version, dry_run=dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, "p", ccd=ccd):
raise IOError("{} not yet run for {}".format(dependency, expnum))
header = storage.get_astheader(expnum, ccd)
datasec = storage.datasec_to_list(header.get('DATASEC', '[80:2080,30,4160]'))
try:
fwhm = "{:5.2f}".format(storage.get_fwhm(expnum, ccd))
except:
fwhm = 'unknown'
for keyword in del_keyword_list:
try:
del(header[keyword])
except:
pass
header['FWHM'] = (fwhm, 'FWHM in pixels')
header['EXTNAME'] = 'header'
primary_hdu = fits.PrimaryHDU(header=header)
hdu_list = fits.HDUList([primary_hdu, ])
for ext in ['jmp', 'matt']:
extension = 'obj.'+ext
name = "{}p{:02d}.{}".format(expnum, ccd, extension)
try:
os.unlink(name)
os.unlink(name+".fits")
except:
pass
logging.info("Retrieving {}".format(name))
obj_file = mop_file.Parser(expnum, ccd, extension)
obj_file.parse()
t = numpy.all([datasec[0] < obj_file.data['X'], obj_file.data['X'] < datasec[1],
datasec[2] < obj_file.data['Y'], obj_file.data['Y'] < datasec[3]], axis=0)
logging.info("Source remaining after datasec cut: {} of {}".format(len(obj_file.data[t]['X']), len(t)))
table_hdu = fits.table_to_hdu(obj_file.data[t])
table_hdu.header['CATALOG'] = name
table_hdu.header['EXTNAME'] = ext
hdu_list.append(table_hdu)
del table_hdu
del obj_file
os.unlink(name)
name = "{}p{:02d}.{}".format(expnum, ccd, 'obj.fits')
if os.access(name, os.F_OK):
os.unlink(name)
hdu_list.writeto(name)
uri = storage.dbimages_uri(expnum, ccd, 'p', ext=".obj.fits")
logging.info(name+" -> "+uri)
count = 0
with open(name):
while True:
count += 1
logging.info("Copy attempt {}".format(count))
try:
storage.copy(name, uri)
os.unlink(name)
break
except Exception as ex:
if count > 10:
raise ex
logging.info(message)
except Exception as e:
message = str(e)
logging.error(message)
if not dry_run:
storage.set_status(task, prefix, expnum, version=version, ccd=ccd, status=message)
elif args.verbose:
level = logging.INFO
if not args.no_sort:
args.expnums.sort()
logging.basicConfig(level=level, format="%(message)s")
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnums[0], ccd, 'scramble'):
raise IOError("scramble not yet run for %s ccd%s" %
(str(args.expnums), str(ccd).zfill(2)))
if storage.get_status(args.expnums[0], ccd,
'plant') and not args.force:
logging.info("plant done for %s[%s]" % (args.expnums[0], ccd))
continue
plant(args.expnums,
ccd,
args.rmin,
args.rmax,
args.ang,
args.width,
version=args.type)
except Exception as e:
message = str(e)
storage.DBIMAGES = args.dbimages
logging.basicConfig(level=level, format="%(message)s")
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
message = storage.SUCCESS
try:
storage.set_logger(
os.path.splitext(os.path.basename(sys.argv[0]))[0], "",
args.expnums[0], ccd, args.type, args.dry_run)
if not storage.get_status(
args.expnums[0], ccd, 'scramble', version=args.type):
raise IOError("scramble not yet run for %s ccd%s" %
(str(args.expnums), str(ccd).zfill(2)))
if storage.get_status(
args.expnums[0], ccd, 'plant',
version=args.type) and not args.force:
logging.info("plant done for %s[%s]" % (args.expnums[0], ccd))
continue
plant(args.expnums,
ccd,
args.rmin,
args.rmax,
args.ang,
args.width,
number=args.number,
version=args.type,
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")
args = parser.parse_args()
if args.dry_run:
args.force = True
if args.verbose:
logging.basicConfig(level=logging.INFO, format="%(message)s")
if args.debug:
logging.basicConfig(level=logging.DEBUG, format="%(message)s")
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccdlist = range(0, 36)
else:
ccdlist = [args.ccd]
if not args.no_sort:
args.expnums.sort()
prefix = (args.fk and 'fk') or ''
exit_status = 0
for ccd in ccdlist:
storage.set_logger(
os.path.splitext(os.path.basename(sys.argv[0]))[0], prefix,
args.expnums[0], ccd, args.type, args.dry_run)
message = storage.SUCCESS
try:
if not storage.get_status(
args.expnums[0], ccd, prefix + 'step2', version=args.type):
raise IOError(35, "did step2 run on %s" % str(args.expnums))
if storage.get_status(
args.expnums[0], ccd, prefix + 'step3',
version=args.type) and not args.force:
logging.critical("step3 alread ran on expnum :%s, ccd: %d" %
(str(args.expnums), ccd))
continue
step3(args.expnums,
ccd,
version=args.type,
rate_min=args.rate_min,
rate_max=args.rate_max,
angle=args.angle,
width=args.width,
field=args.field,
prefix=prefix,
dry_run=args.dry_run)
except Exception as e:
message = str(e)
exit_status = message
logging.error(message)
if not args.dry_run:
storage.set_status(args.expnums[0],
ccd,
prefix + 'step3',
version=args.type,
status=message)
return exit_status
obj = parsers.TNO(None, ast_filename=os.path.join(os.path.join(args.ast_dir, fn)))
discovery_frames = []
for original_observation in obj.orbit.observations:
if original_observation.discovery:
try:
discovery_frames.append(original_observation.comment.frame)
except Exception as ex:
print ex
try:
tracks_data = parser.parse(os.path.join(args.ast_dir, fn), print_summary=False)
except:
continue
new_observation_count = 0
new_observation_lines = ""
for obs in tracks_data.observations:
if obs.rawname not in discovery_frames: # are these new?
new_observation_count += 1
new_observation_lines += '{} {}\n'.format(obs.rawname, Time(obs.mjd, format='mjd', scale='utc').mpc)
# Any processing-related reason why this image hasn't been measured yet? If so we need to process.
# assert storage.get_status('update_header', '', obs.expnum, "p", 36)
if args.check_mkpsf and not (storage.get_status('mkpsf', '', obs.expnum, "p", obs.ccdnum) or \
storage.get_status('mk_mopheader', '', obs.expnum, "p",
obs.ccdnum)):
with open('mkpsf_inputs_{}.txt'.format(args.block), 'a') as mkpsf_input:
mkpsf_input.write('{} {}\n'.format(obs.expnum, obs.ccdnum))
print('{} unmeasured observations!\n'.format(new_observation_count))
ofile.write('{} unmeasured observations!\n'.format(new_observation_count))
ofile.write(new_observation_lines)
ofile.flush()
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('--object-planted', default=OBJECT_PLANTED,
help="Name of file contains list of planted objects.")
parser.add_argument('--bright-limit', default=BRIGHT_LIMIT,
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,
help="required number of detections with mag brighter than bright-limit.")
parser.add_argument('--minimum-bright-fraction', default=MINIMUM_BRIGHT_FRACTION,
help="minimum fraction of objects above bright limit that should be found.")
args = parser.parse_args()
logging.basicConfig(level=logging.CRITICAL)
prefix = 'fk'
ext = args.reals and 'reals' or 'cands'
task = util.task()
storage.MEASURE3 = args.measure3
if args.dbimages is not None:
storage.DBIMAGES = args.dbimages
astrom.DATASET_ROOT = args.dbimages
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
storage.set_logger(os.path.splitext(os.path.basename(sys.argv[0]))[0], prefix, expnum, "", ext, args.dry_run)
match_filename = os.path.splitext(os.path.basename(astrom_filename))[0] + '.match'
exit_status = 0
status = storage.SUCCESS
try:
if (not storage.get_status(task, prefix, expnum=expnum, version='', ccd=args.ccd)) or args.force:
logging.info(("Comparing planted and measured magnitudes "
"for sources in {} and {}\n".format(args.object_planted, astrom_filename)))
message = 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)
match_uri = storage.get_cands_uri(args.field,
ccd=args.ccd,
version=args.type,
prefix=prefix,
ext="measure3.{}.match".format(ext), block=args.field)
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 = [message]
storage.set_tags_on_uri(uri, keys, values)
except Exception as err:
sys.stderr.write(str(err))
status = str(err)
exit_status = err.message
if not args.dry_run:
storage.set_status(task, prefix, expnum, version='', ccd=args.ccd, status=status)
return exit_status
def plant(expnums,
ccd,
rmin,
rmax,
ang,
width,
number=10,
mmin=21.0,
mmax=25.5,
version='s',
dry_run=False,
force=True):
"""Plant artificial sources into the list of images provided.
@param dry_run: don't push results to VOSpace.
@param width: The +/- range of angles of motion
@param ang: The mean angle of motion to add sources
@param rmax: The maximum rate of motion to add sources at (''/hour)
@param rmin: The minimum rate of motion to add sources at (''/hour)
@param expnums: list of MegaPrime exposure numbers to add artificial KBOs to
@param ccd: which ccd to work on.
@param mmax: Maximum magnitude to plant sources at
@param version: Add sources to the 'o', 'p' or 's' images
@param mmin: Minimum magnitude to plant sources at
@param number: number of sources to plant.
@param force: Run, even if we already succeeded at making a fk image.
"""
message = storage.SUCCESS
if storage.get_status(task, "", expnums[0], version, ccd) and not force:
logging.info("{} completed successfully for {}{}{}{:02d}".format(
task, "", expnums[0], version, ccd))
return
with storage.LoggingManager(task, "", expnums[0], ccd, version, dry_run):
try:
# Construct a list of artificial KBOs with positions in the image
# and rates of motion within the bounds given by the caller.
filename = storage.get_image(expnums[0], ccd=ccd, version=version)
header = fits.open(filename)[0].header
bounds = util.get_pixel_bounds_from_datasec_keyword(
header.get('DATASEC', '[33:2080,1:4612]'))
# generate a set of artificial KBOs to add to the image.
kbos = KBOGenerator.get_kbos(n=number,
rate=(rmin, rmax),
angle=(ang - width, ang + width),
mag=(mmin, mmax),
x=(bounds[0][0], bounds[0][1]),
y=(bounds[1][0], bounds[1][1]),
filename='Object.planted')
for expnum in expnums:
filename = storage.get_image(expnum, ccd, version)
psf = storage.get_file(expnum, ccd, version, ext='psf.fits')
plant_kbos(filename, psf, kbos,
get_shifts(expnum, ccd, version), "fk")
if dry_run:
return
uri = storage.get_uri('Object',
ext='planted',
version='',
subdir=f"{expnums[0]}/ccd{int(ccd):02d}")
storage.copy('Object.planted', uri)
for expnum in expnums:
uri = storage.get_uri(expnum,
ccd=ccd,
version=version,
ext='fits',
prefix='fk')
filename = os.path.basename(uri)
storage.copy(filename, uri)
except Exception as ex:
message = str(ex)
logging.error(message)
storage.set_status(task, "", expnums[0], version, ccd, status=message)
return
logging.basicConfig(level=logging.INFO,
format='%(message)s')
if args.debug:
logging.basicConfig(level=logging.DEBUG)
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccdlist = range(0,36)
else:
ccdlist = [args.ccd]
for expnum in args.expnum:
for ccd in ccdlist:
if storage.get_status(expnum, ccd, 'mkpsf') and not args.force:
logging.info("Already did %s %s, skipping" %( str(expnum),
str(ccd)))
continue
try:
message = 'success'
mkpsf(expnum, ccd)
storage.set_status(expnum,
ccd,
'fwhm',
str(storage.get_fwhm(
expnum, ccd)))
storage.set_status(expnum,
ccd,
'zeropoint',
str(storage.get_zeropoint(
storage._dbimages = args.dbimages
## setup logging
level = logging.CRITICAL
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
if not args.nosort:
args.expnums.sort()
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
expnums = args.expnums
if storage.get_status(expnums[0], ccd, 'scramble') and not args.force:
continue
message = storage.SUCCESS
try:
scramble(expnums=expnums, ccd=ccd, version=args.type)
except Exception as e:
logging.error(e)
message = str(e)
storage.set_status(expnums[0], ccd, 'scramble', message)
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")
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO, format="%(message)s")
if args.debug:
logging.basicConfig(level=logging.DEBUG, format="%(message)s")
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccd_list = range(0, 36)
else:
ccd_list = [args.ccd]
prefix = (args.fk and "fk") or ""
if not args.no_sort:
args.expnums.sort()
task = util.task()
dependency = "step1"
expnums = args.expnums
version = args.type
exit_status = 0
for ccd in ccd_list:
storage.set_logger(os.path.splitext(os.path.basename(sys.argv[0]))[0],
prefix, args.expnums[0], ccd, args.type, args.dry_run)
try:
message = storage.SUCCESS
# Check if dependent task has finished for each of the input exposure ids.
for expnum in expnums:
if not storage.get_status(dependency, prefix, expnum, version=version, ccd=ccd):
raise IOError(35, "Cannot start {} as {} not yet completed for {}{}{}{:02d}".format(
task, dependency, prefix, expnum, args.type, ccd))
# Check if we need to run this step on the current frame.
if not (args.force or args.dry_run) and storage.get_status(task, prefix, args.expnums[0], version=version,
ccd=ccd):
logging.info("{} completed successfully for {}{}{}{:02d}".format(
task, prefix, expnums[0], version, ccd))
continue
logging.info("Executing {} on {} {} {} {}".format(
task, prefix, args.expnums, args.type, ccd))
step2(args.expnums, ccd, version=version, prefix=prefix, dry_run=args.dry_run, default=args.default)
logging.info(message)
except CalledProcessError as cpe:
message = str(cpe)
logging.error(message)
exit_status = message
except Exception as e:
message = str(e)
logging.error(message)
exit_status = message
if not args.dry_run:
storage.set_status(task, prefix, args.expnums[0], version=version, ccd=ccd, status=message)
return exit_status
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('--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()
if args.dry_run:
args.force = True
if args.debug:
logging.basicConfig(level=logging.DEBUG)
elif args.verbose:
logging.basicConfig(level=logging.INFO)
prefix = (args.fk and 'fk') or ''
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:
storage.set_logger(
os.path.splitext(os.path.basename(sys.argv[0]))[0], prefix,
expnum, ccd, args.type, args.dry_run)
if storage.get_status(
expnum, ccd, prefix + task,
version=args.type) and not args.force:
logging.info(
"{} completed successfully for {} {} {} {}".format(
task, prefix, expnum, args.type, ccd))
continue
message = 'success'
try:
if not storage.get_status(
expnum, 36,
'update_header') and not args.ignore_update_headers:
raise IOError(
"update_header not yet run for {}".format(expnum))
mkpsf(expnum, ccd, args.type, args.dry_run, prefix=prefix)
if args.dry_run:
continue
storage.set_status(expnum,
ccd,
prefix + 'fwhm',
version=args.type,
status=str(
storage.get_fwhm(expnum,
ccd,
version=args.type)))
storage.set_status(expnum,
ccd,
prefix + 'zeropoint',
version=args.type,
status=str(
storage.get_zeropoint(
expnum, ccd, version=args.type)))
except CalledProcessError as cpe:
message = str(cpe.output)
exit_code = message
except Exception as e:
message = str(e)
logging.error(message)
if not args.dry_run:
storage.set_status(expnum,
ccd,
prefix + 'mkpsf',
version=args.type,
status=message)
return exit_code
files = working_context.get_listing('ast')
files = [f for f in files if f.startswith(args.block)]
with open(outfile, 'a') as ofile:
ofile.write('Examining {} object files.\n'.format(len(files)))
for fn in files:
with open(outfile, 'a') as ofile:
ofile.write('{}\n'.format(fn))
parser = ssos.TracksParser(skip_previous=True)
tracks_data = parser.parse(parameters.REAL_KBO_AST_DIR + fn)
if len(tracks_data.observations) > 1: # it is set to always return the discovery image
with open(outfile, 'a') as ofile:
ofile.write('{} unmeasured observations!\n'.format(len(tracks_data.observations) - 1))
obj = parsers.TNO(mpc.MPCReader(parameters.REAL_KBO_AST_DIR + fn))
for obs in tracks_data.observations:
discovery_frame = obj.discovery.comment.frame.split('p')[0].strip(' ')
if obs.expnum != discovery_frame: # are these new?
with open(outfile, 'a') as ofile:
ofile.write('{}\n'.format(obs.get_mpc_date()))
# Any processing-related reason why this image hasn't been measured yet? If so we need to process.
# assert storage.get_status('update_header', '', obs.expnum, "p", 36)
if not storage.get_status('mkpsf', '', obs.expnum, "p", obs.ccdnum) or \
storage.get_status('mk_mopheader', '', obs.expnum, "p", obs.ccdnum):
with open(outfile, 'a') as ofile:
ofile.write('{}\n'.format(obs.expnum))
if args.ccd is None:
ccdlist = range(0,36)
else:
ccdlist = [args.ccd]
if not args.no_sort:
args.expnums.sort()
prefix = ( args.fk and 'fk') or ''
for ccd in ccdlist:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnums[0], ccd, prefix+'step2'):
raise IOError(35, "did step2 run on %s" % ( str(args.expnums)))
if storage.get_status(args.expnums[0], ccd, prefix+'step3') and not args.force:
logging.critical("step3 alread ran on expnum :%s, ccd: %d" % (
str(args.expnums), ccd))
continue
step3(args.expnums, ccd, version=args.type,
rate_min=args.rate_min,
rate_max=args.rate_max,
angle=args.angle,
width=args.width,
field=args.field,
prefix=prefix)
except Exception as e:
message = str(e)
def main():
"""Do the script."""
parser = argparse.ArgumentParser(
description='replace image header')
parser.add_argument('--extname',
help='name of extension to in header')
parser.add_argument('expnum', type=str,
help='exposure to update')
parser.add_argument('-r', '--replace',
action='store_true',
help='store modified image back to VOSpace?')
parser.add_argument('-v', '--verbose', action='store_true')
parser.add_argument('--debug', action='store_true')
parser.add_argument('--force', action='store_true', help="Re-run even if previous success recorded")
parser.add_argument('--dbimages', help="VOSpace DATA storage area.", default="vos:OSSOS/dbimages")
args = parser.parse_args()
task = util.task()
dependency = 'preproc'
prefix = ""
storage.DBIMAGES = args.dbimages
level = logging.CRITICAL
message_format = "%(message)s"
if args.verbose:
level = logging.INFO
if args.debug:
level = logging.DEBUG
message_format = "%(module)s %(funcName)s %(lineno)s %(message)s"
logging.basicConfig(level=level, format=message_format)
storage.set_logger(task, prefix, args.expnum, None, None, False)
message = storage.SUCCESS
expnum = args.expnum
exit_status = 0
try:
# skip if already succeeded and not in force mode
if storage.get_status(task, prefix, expnum, "p", 36) and not args.force:
logging.info("Already updated, skipping")
sys.exit(0)
image_hdulist = storage.get_image(args.expnum, return_file=False)
ast_hdulist = storage.get_astheader(expnum, ccd=None)
run_update_header(image_hdulist, ast_hdulist)
image_filename = os.path.basename(storage.get_uri(expnum))
image_hdulist.writeto(image_filename)
if args.replace:
dest = storage.dbimages_uri(expnum)
storage.copy(image_filename, dest)
storage.set_status('update_header', "", expnum, 'p', 36, message)
except Exception as e:
message = str(e)
if args.replace:
storage.set_status(task, prefix, expnum, 'p', 36, message)
exit_status = message
logging.error(message)
return exit_status
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="vos:OSSOS/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=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")
args = parser.parse_args()
if args.dry_run:
args.force = True
level = logging.CRITICAL
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
storage.DBIMAGES = args.dbimages
storage.MEASURE3 = args.measure3
prefix = (args.fk and 'fk') or ''
ccd_list = (args.ccd is None and range(0, 36)) or [args.ccd]
exit_code = 0
for ccd in ccd_list:
storage.set_logger(
os.path.splitext(os.path.basename(sys.argv[0]))[0], prefix,
args.expnum, ccd, args.type, args.dry_run)
if not storage.get_status(
args.expnum, ccd, prefix + 'step3',
version=args.type) and not args.dry_run:
logging.error(
storage.get_status(args.expnum,
ccd,
'step3',
return_message=True))
raise IOError(35, "need to run step3 first")
if storage.get_status(
args.expnum, ccd, prefix + 'combine',
version=args.type) and not args.force:
continue
try:
message = combine(args.expnum,
ccd,
prefix=prefix,
file_type=args.type,
field=args.field,
measure3=args.measure3,
dry_run=args.dry_run)
except CalledProcessError as cpe:
message = str(cpe)
exit_code = message
except Exception as e:
message = str(e)
exit_code = message
logging.info(message)
if not args.dry_run:
storage.set_status(args.expnum,
ccd,
prefix + 'combine',
version=args.type,
status=message)
return exit_code
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="vos:OSSOS/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=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")
args = parser.parse_args()
level = logging.CRITICAL
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
storage.DBIMAGES = args.dbimages
storage.MEASURE3 = args.measure3
prefix = (args.fk and 'fk') or ''
task = util.task()
dependency = 'step3'
ccd_list = (args.ccd is None and range(0, 36)) or [args.ccd]
exit_code = 0
for ccd in ccd_list:
storage.set_logger(task, prefix, args.expnum, ccd, args.type, args.dry_run)
try:
if not storage.get_status(dependency, prefix, args.expnum, version=args.type, ccd=ccd) and not args.dry_run:
message = storage.get_status(dependency, prefix, args.expnum, "p", ccd, return_message=True)
raise IOError(35, message)
if storage.get_status(task, prefix, args.expnum, version=args.type, ccd=ccd) and not args.force:
continue
message = combine(args.expnum,
ccd,
prefix=prefix,
file_type=args.type,
field=args.field,
measure3=args.measure3,
dry_run=args.dry_run)
except CalledProcessError as cpe:
message = str(cpe)
exit_code = message
except Exception as e:
message = str(e)
exit_code = message
logging.info(message)
if not args.dry_run:
storage.set_status(task, prefix, args.expnum, version=args.type, ccd=ccd, status=message)
return exit_code
storage.DBIMAGES = args.dbimages
prefix = ""
task = util.task()
dependency = "step1"
logging.basicConfig(level=level, format="%(message)s")
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
message = storage.SUCCESS
try:
storage.set_logger(task, prefix, args.expnums[0], ccd, args.type, args.dry_run)
if not storage.get_status(dependency, prefix, args.expnums[0], version=args.type, ccd=ccd):
raise IOError("mkpsf not yet run for %s ccd%s, can't run align" % (
str(args.expnums), str(ccd).zfill(2)))
if storage.get_status(task, prefix, args.expnums[0], version=args.type, ccd=ccd) and not args.force:
logging.info("align done for %s[%s]" % (args.expnums[0], ccd))
continue
align(args.expnums, ccd, version=args.type, dry_run=args.dry_run)
except CalledProcessError as cpe:
message = str(cpe)
exit_code = message
logging.error("ERROR: {}".format(str(cpe)))
except Exception as e:
logging.error("Exception: {}".format(str(e)))
message = str(e)
logging.critical(message)
def main(argv):
"""
@param argv: an array of arguments to be parsed, normally sys.argv
@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('--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("--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")
args = parser.parse_args(argv)
# # setup logging
level = logging.CRITICAL
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
if not args.no_sort:
args.expnums.sort()
storage.DBIMAGES = args.dbimages
logging.basicConfig(level=level, format="%(message)s")
task = util.task()
prefix = ""
dependency = 'mkpsf'
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
exit_code = 0
for ccd in ccds:
message = storage.SUCCESS
try:
storage.set_logger(task, prefix, args.expnums[0], ccd, args.type, args.dry_run)
if not storage.get_status(dependency, prefix, args.expnums[0], version='s', ccd=ccd):
raise IOError("{} not yet run for {} {} {}".format(dependency, args.expnums, args.type, ccd))
if storage.get_status(task, prefix, args.expnums[0], version=args.type, ccd=ccd) and not args.force:
logging.info("{} previously completed successfully for {}{}{:02d}".format(task,
args.expnums[0],
args.type,
ccd))
continue
plant(args.expnums,
ccd,
args.rmin, args.rmax, args.ang, args.width,
number=args.number, mmin=args.mmin, mmax=args.mmax,
version=args.type,
dry_run=args.dry_run)
except CalledProcessError as cpe:
message = str(cpe)
exit_code = message
except Exception as e:
message = str(e)
logging.critical(message)
if not args.dry_run:
storage.set_status(task, prefix, args.expnums[0], version=args.type, ccd=ccd, status=message)
return exit_code
storage.DBIMAGES = args.dbimages
logging.basicConfig(level=level, format="%(message)s")
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
message = storage.SUCCESS
try:
storage.set_logger(
os.path.splitext(os.path.basename(sys.argv[0]))[0], "",
args.expnums[0], ccd, args.type, args.dry_run)
if not storage.get_status(
args.expnums[0], ccd, 'step2', version=args.type):
raise IOError("scramble not yet run for %s ccd%s" %
(str(args.expnums), str(ccd).zfill(2)))
if storage.get_status(
args.expnums[0], ccd, 'align',
version=args.type) and not args.force:
logging.info("align done for %s[%s]" % (args.expnums[0], ccd))
continue
align(args.expnums, ccd, version=args.type, dry_run=args.dry_run)
except CalledProcessError as cpe:
message = str(cpe)
exit_code = message
except Exception as e:
message = str(e)
logging.critical(message)
if args.ccd is None:
ccdlist = range(0, 36)
else:
ccdlist = [args.ccd]
prefix = (args.fk and "fk") or ""
if not args.no_sort:
args.expnums.sort()
for ccd in ccdlist:
try:
message = storage.SUCCESS
for expnum in args.expnums:
if not storage.get_status(expnum, ccd, prefix + 'step1'):
raise IOError(35, "missing step1 for %s" % (expnum))
if storage.get_status(args.expnums[0], ccd,
prefix + 'step2') and not args.force:
logging.info("Already did %s %s, skipping" %
(str(expnum), str(ccd)))
continue
logging.info("step2 on expnums :%s, ccd: %d" %
(str(args.expnums), ccd))
step2(args.expnums, ccd, version=args.type, prefix=prefix)
except Exception as e:
message = str(e)
logging.error(message)
storage.set_status(args.expnums[0], ccd, prefix + 'step2', message)
logging.basicConfig(level=logging.INFO,
format='%(message)s')
if args.debug:
logging.basicConfig(level=logging.DEBUG)
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccdlist = range(0,36)
else:
ccdlist = [args.ccd]
for expnum in args.expnum:
for ccd in ccdlist:
if storage.get_status(expnum, ccd, 'mkpsf', version=args.type) and not args.force:
logging.info("Already did %s %s, skipping" %( str(expnum),
str(ccd)))
continue
try:
message = 'success'
mkpsf(expnum, ccd, args.type)
storage.set_status(expnum,
ccd,
'fwhm',
version=args.type,
status=str(storage.get_fwhm(
expnum, ccd, version=args.type)))
storage.set_status(expnum,
ccd,
'zeropoint',
def scramble(expnums, ccd, version='p', dry_run=False, force=False, prefix=''):
"""
run the plant script on this combination of exposures
@param expnums: list of exposure numbers to scramble the time on
@param ccd: which CCD in (assumes this is a CFHT MegaCam MEF)
@param version: should we scramble the 'p' or 'o' images?
@param dry_run: if dry run then don't save back to VOSpace.
@param force: if true then create scramble set, even if already exists.
@param prefix: a string that will be pre-pended to the EXPNUM to get the filename, sometimes 'fk'.
@return: None
"""
# Get a list of the MJD values and then write a re-ordering of those into files with 's'
# as their type instead of 'p' or 'o'
mjds = []
fobjs = []
message = storage.SUCCESS
if not (force or dry_run) and storage.get_status(
task, prefix, expnums[0], version='s', ccd=ccd):
logging.info("{} recorded as complete for {} ccd {}".format(
task, expnums, ccd))
return
with storage.LoggingManager(task, prefix, expnums[0], ccd, version):
try:
for expnum in expnums:
filename = storage.get_image(expnum, ccd=ccd, version=version)
fobjs.append(fits.open(filename))
# Pull out values to replace in headers.. must pull them
# as otherwise we get pointers...
mjds.append(fobjs[-1][0].header['MJD-OBS'])
order = [0, 2, 1]
for idx in range(len(fobjs)):
logging.info(
"Flipping %d to %d" %
(fobjs[idx][0].header['EXPNUM'], expnums[order[idx]]))
fobjs[idx][0].header['EXPNUM'] = expnums[order[idx]]
fobjs[idx][0].header['MJD-OBS'] = mjds[order[idx]]
uri = storage.get_uri(expnums[order[idx]],
ccd=ccd,
version='s',
ext='fits')
scramble_file_name = os.path.basename(uri)
if os.access(scramble_file_name, os.F_OK):
os.unlink(scramble_file_name)
fobjs[idx].writeto(scramble_file_name)
if not dry_run:
storage.copy(scramble_file_name, uri)
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task,
prefix,
expnum,
version,
ccd,
status=message)
return
def run(expnums,
ccd,
version,
prefix=None,
dry_run=False,
default="WCS",
force=False):
"""run the actual step2 on the given exp/ccd combo"""
jmp_trans = ['step2ajmp']
jmp_args = ['step2bjmp']
matt_args = ['step2matt_jmp']
if storage.get_status(task, prefix, expnums[0], version,
ccd) and not force:
logging.info("{} completed successfully for {}{}{}{:02d}".format(
task, prefix, expnums[0], version, ccd))
return
with storage.LoggingManager(task, prefix, expnums[0], ccd, version,
dry_run):
try:
for expnum in expnums:
if not storage.get_status(
dependency, prefix, expnum, version=version, ccd=ccd):
raise IOError(
35,
"Cannot start {} as {} not yet completed for {}{}{}{:02d}"
.format(task, dependency, prefix, expnum, version,
ccd))
message = storage.SUCCESS
idx = 0
logging.info("Retrieving catalog files to do matching.")
for expnum in expnums:
jmp_args.append(
storage.get_file(expnum,
ccd=ccd,
version=version,
ext='obj.jmp',
prefix=prefix)[0:-8])
jmp_trans.append(
storage.get_file(expnum,
ccd=ccd,
version=version,
ext='obj.jmp',
prefix=prefix)[0:-8])
idx += 1
matt_args.append('-f%d' % idx)
matt_args.append(
storage.get_file(expnum,
ccd=ccd,
version=version,
ext='obj.matt',
prefix=prefix)[0:-9])
logging.info(
"Computing the catalog alignment using sources in catalogs.")
try:
logging.info(util.exec_prog(jmp_trans))
if default == "WCS":
logging.info("Comparing computed transform to WCS values")
logging.info(
compute_trans(expnums,
ccd,
version,
prefix,
default=default))
except Exception as ex:
logging.info("JMP Trans failed: {}".format(ex))
logging.info(
compute_trans(expnums, ccd, version, prefix,
default="WCS"))
logging.info("Using transform to match catalogs for three images.")
logging.info(util.exec_prog(jmp_args))
logging.info(util.exec_prog(matt_args))
# check that the shifts from step2 are rational by matching the bright star lists.
logging.info(
"Uisng checktrans to ensure that transforms were reasonable.")
check_args = ['checktrans']
if os.access('proc-these-files', os.R_OK):
os.unlink('proc-these-files')
ptf = open('proc-these-files', 'w')
ptf.write(
"# A dummy file that is created so checktrans could run.\n")
ptf.write("# Frame FWHM PSF?\n")
for expnum in expnums:
filename = os.path.splitext(
storage.get_image(expnum,
ccd,
version=version,
prefix=prefix))[0]
if not os.access(filename + ".bright.psf", os.R_OK):
os.link(filename + ".bright.jmp", filename + ".bright.psf")
if not os.access(filename + ".obj.psf", os.R_OK):
os.link(filename + ".obj.jmp", filename + ".obj.psf")
ptf.write("{:>19s}{:>10.1f}{:>5s}\n".format(
filename, _FWHM, "NO"))
ptf.close()
if os.access('BAD_TRANS', os.F_OK):
os.unlink('BAD_TRANS')
logging.info(util.exec_prog(check_args))
if os.access('BAD_TRANS', os.F_OK):
raise OSError(errno.EBADMSG, 'BAD_TRANS')
if os.access('proc-these-files', os.F_OK):
os.unlink('proc-these-files')
if dry_run:
return
for expnum in expnums:
for ext in ['unid.jmp', 'unid.matt', 'trans.jmp']:
uri = storage.dbimages_uri(expnum,
ccd=ccd,
version=version,
ext=ext,
prefix=prefix)
filename = os.path.basename(uri)
storage.copy(filename, uri)
except Exception as ex:
message = str(ex)
logging.error(message)
storage.set_status(task,
prefix,
expnums[0],
version,
ccd,
status=message)
return
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
if not args.no_sort:
args.expnums.sort()
storage.DBIMAGES = args.dbimages
logging.basicConfig(level=level, format="%(message)s")
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnums[0], ccd, "scramble", version=args.type):
raise IOError("scramble not yet run for %s ccd%s" % (str(args.expnums), str(ccd).zfill(2)))
if storage.get_status(args.expnums[0], ccd, "plant", version=args.type) and not args.force:
logging.info("plant done for %s[%s]" % (args.expnums[0], ccd))
continue
plant(args.expnums, ccd, args.rmin, args.rmax, args.ang, args.width, version=args.type)
except Exception as e:
message = str(e)
logging.error(str(e))
storage.set_status(args.expnums[0], ccd, "plant", version=args.type, status=message)
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
logging.getLogger('vos').setLevel(level)
logging.getLogger('vos').addHandler(logging.StreamHandler())
if not args.nosort:
args.expnums.sort()
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0,36)
for ccd in ccds:
expnums = args.expnums
if storage.get_status(expnums[0], ccd,
'scramble', version='s') and not args.force:
continue
message = storage.SUCCESS
try:
scramble(expnums=expnums, ccd=ccd, version='p')
except Exception as e:
logging.error(e)
message = str(e)
storage.set_status(expnums[0], ccd,
'scramble', version='s',
status=message)
if not args.no_sort:
args.expnums.sort()
logging.basicConfig(level=level, format="%(message)s")
ccds = [args.ccd]
if args.ccd is None:
ccds = range(0,36)
for ccd in ccds:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnums[0], ccd,
'scramble'):
raise IOError("scramble not yet run for %s ccd%s" % (
str(args.expnums), str(ccd).zfill(2)))
if storage.get_status(args.expnums[0], ccd,
'plant') and not args.force:
logging.info("plant done for %s[%s]" % ( args.expnums[0], ccd))
continue
plant(args.expnums,
ccd,
args.rmin, args.rmax, args.ang, args.width,
version=args.type)
except Exception as e:
message = str(e)
logging.error(str(e))
storage.set_status(args.expnums[0],
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('--object-planted', default=OBJECT_PLANTED,
help="Name of file contains list of planted objects.")
parser.add_argument('--bright-limit', default=BRIGHT_LIMIT,
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,
help="required number of detections with mag brighter than bright-limit.")
parser.add_argument('--minimum-bright-fraction', default=MINIMUM_BRIGHT_FRACTION,
help="minimum fraction of objects above bright limit that should be found.")
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
prefix = 'fk'
ext = args.reals and 'reals' or 'cands'
storage.MEASURE3 = args.measure3
if args.dbimages is not None:
storage.DBIMAGES = args.dbimages
astrom.DATASET_ROOT = args.dbimages
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
storage.set_logger(os.path.splitext(os.path.basename(sys.argv[0]))[0], prefix, expnum, "", ext, args.dry_run)
match_filename = os.path.splitext(os.path.basename(astrom_filename))[0] + '.match'
exit_status = 0
status = storage.SUCCESS
try:
if (not storage.get_status(expnum, ccd=args.ccd, program='astrom_mag_check', version='')) or args.force:
message = 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)
match_uri = storage.get_cands_uri(args.field,
ccd=args.ccd,
version=args.type,
prefix=prefix,
ext="measure3.{}.match".format(ext))
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 = [message]
storage.set_tags_on_uri(uri, keys, values)
except Exception as err:
sys.stderr.write(str(err))
status = str(err)
exit_status = err.message
if not args.dry_run:
storage.set_status(expnum, args.ccd, 'astrom_mag_check', version='', status=status)
return exit_status
def run(expnum,
ccd,
prefix='',
version='p',
sex_thresh=_SEX_THRESHOLD,
wave_thresh=_WAVE_THRESHOLD,
maxcount=_MAX_COUNT,
dry_run=False,
force=True, ignore=False):
"""run the actual step1jmp/matt codes.
expnum: the CFHT expousre to process
ccd: which ccd in the mosaic to process
fwhm: the image quality, FWHM, of the image. In pixels.
sex_thresh: the detection threhold to run sExtractor at
wave_thresh: the detection threshold for wavelet
maxcount: saturation level
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version, ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(task, prefix, expnum, version, ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, version, ccd) and not ignore:
raise IOError(35, "Cannot start {} as {} not yet completed for {}{}{}{:02d}".format(
task, dependency, prefix, expnum, version, ccd))
logging.info("Retrieving imaging and input parameters from VOSpace")
storage.get_file(expnum, ccd, prefix=prefix, version=version, ext='mopheader')
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
fwhm = storage.get_fwhm(expnum, ccd, prefix=prefix, version=version, default=3.5)
basename = os.path.splitext(filename)[0]
_get_weight_map(filename, ccd)
logging.info("Launching step1jmp")
logging.info(util.exec_prog(['step1jmp',
'-f', basename,
'-t', str(wave_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
logging.info(util.exec_prog(['step1matt',
'-f', basename,
'-t', str(sex_thresh),
'-w', str(fwhm),
'-m', str(maxcount)]))
if os.access('weight.fits', os.R_OK):
os.unlink('weight.fits')
if not dry_run:
for ext in ['obj.jmp', 'obj.matt']:
obj_uri = storage.get_uri(expnum, ccd, version=version, ext=ext,
prefix=prefix)
obj_filename = basename + "." + ext
count = 0
with open(obj_filename, 'r'):
while True:
try:
count += 1
logging.info("Attempt {} to copy {} -> {}".format(count, obj_filename, obj_uri))
storage.copy(obj_filename, obj_uri)
break
except Exception as ex:
if count > 10:
raise ex
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task, prefix, expnum, version, ccd, status=message)
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
storage._dbimages = args.dbimages
if args.ccd is None:
ccdlist = range(0,36)
else:
ccdlist = [args.ccd]
prefix = ( args.fk and 'fk') or ''
for expnum in args.expnum:
for ccd in ccdlist:
try:
message = storage.SUCCESS
if not storage.get_status(expnum, ccd, 'mkpsf'):
raise IOError(35, "mkpsf hasn't run?")
if storage.get_status(expnum, ccd, prefix+'step1') and not args.force:
logging.critical(
"Already did %s %s, skipping" %(prefix+str(expnum),
str(ccd)))
continue
logging.info("step1 on expnum: %s, ccd: %s" % (
prefix+str(expnum), str(ccd)))
step1(expnum, ccd, prefix=prefix, version=args.type)
except Exception as e:
message = str(e)
logging.error("Error running step1: %s " %(message))
storage.set_status(expnum,
ccd,
logging.basicConfig(level=level, format="%(message)s")
storage._dbimages = args.dbimages
if args.ccd is None:
ccdlist = range(0, 36)
else:
ccdlist = [args.ccd]
prefix = (args.fk and 'fk') or ''
for expnum in args.expnum:
for ccd in ccdlist:
try:
message = storage.SUCCESS
if not storage.get_status(expnum, ccd, 'mkpsf'):
raise IOError(35, "mkpsf hasn't run?")
if storage.get_status(expnum, ccd,
prefix + 'step1') and not args.force:
logging.critical("Already did %s %s, skipping" %
(prefix + str(expnum), str(ccd)))
continue
logging.info("step1 on expnum: %s, ccd: %s" %
(prefix + str(expnum), str(ccd)))
step1(expnum, ccd, prefix=prefix, version=args.type)
except Exception as e:
message = str(e)
logging.error("Error running step1: %s " % (message))
storage.set_status(expnum, ccd, prefix + 'step1', message)
def main():
"""Run the script."""
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="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')
args = parser.parse_args()
prefix = ""
task = util.task()
dependency = "update_header"
storage.DBIMAGES = args.dbimages
## setup logging
level = logging.CRITICAL
if args.debug:
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
logging.getLogger('vos').setLevel(level)
logging.getLogger('vos').addHandler(logging.StreamHandler())
if not args.nosort:
args.expnums.sort()
ccds = [args.ccd]
exit_status = 0
if args.ccd is None:
ccds = range(0, 36)
for ccd in ccds:
storage.set_logger(task, prefix, args.expnums[0], ccd, args.type, args.dry_run)
expnums = args.expnums
if not (args.force or args.dry_run) and storage.get_status(task, prefix, expnums[0], version='s', ccd=ccd):
continue
message = storage.SUCCESS
try:
scramble(expnums=expnums, ccd=ccd, version='p', dry_run=args.dry_run)
except Exception as e:
logging.error(e)
message = str(e)
exit_status = message
if not args.dry_run:
storage.set_status(task, prefix, expnums[0], version='s', ccd=ccd, status=message)
return exit_status
print(ex)
try:
tracks_data = parser.parse(os.path.join(args.ast_dir, fn),
print_summary=False)
except:
continue
new_observation_count = 0
new_observation_lines = ""
for obs in tracks_data.observations:
if obs.rawname not in discovery_frames: # are these new?
new_observation_count += 1
new_observation_lines += '{} {}\n'.format(
obs.rawname,
Time(obs.mjd, format='mjd', scale='utc').mpc)
# Any processing-related reason why this image hasn't been measured yet? If so we need to process.
# assert storage.get_status('update_header', '', obs.expnum, "p", 36)
if args.check_mkpsf and not (storage.get_status('mkpsf', '', obs.expnum, "p", obs.ccdnum) or \
storage.get_status('mk_mopheader', '', obs.expnum, "p",
obs.ccdnum)):
with open('mkpsf_inputs_{}.txt'.format(args.block),
'a') as mkpsf_input:
mkpsf_input.write('{} {}\n'.format(
obs.expnum, obs.ccdnum))
print((
'{} unmeasured observations!\n'.format(new_observation_count)))
ofile.write(
'{} unmeasured observations!\n'.format(new_observation_count))
ofile.write(new_observation_lines)
ofile.flush()
def align(expnums, ccd, version='s', prefix='', dry_run=False, force=True):
"""Create a 'shifts' file that transforms the space/flux/time scale of all
images to the first image.
This function relies on the .fwhm, .trans.jmp, .phot and .zeropoint.used files for inputs.
The scaling we are computing here is for use in planting sources into the image at the same sky/flux locations
while accounting for motions of sources with time.
:param expnums: list of MegaPrime exposure numbers to add artificial KBOs to,
the first frame in the list is the reference.
:param ccd: which ccd to work on.
:param prefix: put this string in front of expnum when looking for exposure, normally '' or 'fk'
:param force: When true run task even if this task is recorded as having succeeded
:param version: Add sources to the 'o', 'p' or 's' images
:param dry_run: don't push results to VOSpace.
"""
message = storage.SUCCESS
if storage.get_status(task, prefix, expnums[0], version,
ccd) and not force:
logging.info("{} completed successfully for {} {} {} {}".format(
task, prefix, expnums[0], version, ccd))
return
# Get the images and supporting files that we need from the VOSpace area
# get_image and get_file check if the image/file is already on disk.
# re-computed fluxes from the PSF stars and then recompute x/y/flux scaling.
# some dictionaries to hold the various scale
pos = {}
apcor = {}
mags = {}
zmag = {}
mjdates = {}
with storage.LoggingManager(task, prefix, expnums[0], ccd, version,
dry_run):
try:
for expnum in expnums:
filename = storage.get_image(expnum, ccd=ccd, version=version)
zmag[expnum] = storage.get_zeropoint(expnum,
ccd,
prefix=None,
version=version)
mjdates[expnum] = float(
fits.open(filename)[0].header.get('MJD-OBS'))
apcor[expnum] = [
float(x) for x in open(
storage.get_file(
expnum,
ccd=ccd,
version=version,
ext=storage.APCOR_EXT)).read().split()
]
keys = ['crval1', 'cd1_1', 'cd1_2', 'crval2', 'cd2_1', 'cd2_2']
# load the .trans.jmp values into a 'wcs' like dictionary.
# .trans.jmp maps current frame to reference frame in pixel coordinates.
# the reference frame of all the frames supplied must be the same.
shifts = dict(
list(
zip(keys, [
float(x) for x in open(
storage.get_file(
expnum,
ccd=ccd,
version=version,
ext='trans.jmp')).read().split()
])))
shifts['crpix1'] = 0.0
shifts['crpix2'] = 0.0
# now create a wcs object based on those transforms, this wcs links the current frame's
# pixel coordinates to the reference frame's pixel coordinates.
w = get_wcs(shifts)
# get the PHOT file that was produced by the mkpsf routine
logging.debug("Reading .phot file {}".format(expnum))
phot = ascii.read(storage.get_file(expnum,
ccd=ccd,
version=version,
ext='phot'),
format='daophot')
# compute the small-aperture magnitudes of the stars used in the PSF
logging.debug("Running phot on {}".format(filename))
mags[expnum] = daophot.phot(filename,
phot['XCENTER'],
phot['YCENTER'],
aperture=apcor[expnum][0],
sky=apcor[expnum][1] + 1,
swidth=apcor[expnum][0],
zmag=zmag[expnum])
# covert the x/y positions to positions in Frame 1 based on the trans.jmp values.
logging.debug(
"Doing the XY translation to refrence frame: {}".format(w))
(x, y) = w.wcs_pix2world(mags[expnum]["XCENTER"],
mags[expnum]["YCENTER"], 1)
pos[expnum] = numpy.transpose([x, y])
# match this exposures PSF stars position against those in the first image of the set.
logging.debug("Matching lists")
idx1, idx2 = util.match_lists(pos[expnums[0]], pos[expnum])
# compute the magnitdue offset between the current frame and the reference.
dmags = numpy.ma.array(
mags[expnums[0]]["MAG"] - apcor[expnums[0]][2] -
(mags[expnum]["MAG"][idx1] - apcor[expnum][2]),
mask=idx1.mask)
dmags.sort()
# logging.debug("Computed dmags between input and reference: {}".format(dmags))
error_count = 0
error_count += 1
logging.debug("{}".format(error_count))
# compute the median and determine if that shift is small compared to the scatter.
try:
midx = int(
numpy.sum(numpy.any([~dmags.mask], axis=0)) / 2.0)
dmag = float(dmags[midx])
logging.debug("Computed a mag delta of: {}".format(dmag))
except Exception as e:
logging.error(str(e))
logging.error(
"Failed to compute mag offset between plant and found using: {}"
.format(dmags))
dmag = 99.99
error_count += 1
logging.debug("{}".format(error_count))
try:
if math.fabs(dmag) > 3 * (dmags.std() + 0.01):
logging.warning(
"Magnitude shift {} between {} and {} is large: {}"
.format(dmag, expnums[0], expnum, shifts))
except Exception as e:
logging.error(str(e))
error_count += 1
logging.debug("{}".format(error_count))
shifts['dmag'] = dmag
shifts['emag'] = dmags.std()
shifts['nmag'] = len(dmags.mask) - dmags.mask.sum()
shifts['dmjd'] = mjdates[expnums[0]] - mjdates[expnum]
shift_file = os.path.basename(
storage.get_uri(expnum, ccd, version, '.shifts'))
error_count += 1
logging.debug("{}".format(error_count))
try:
fh = open(shift_file, 'w')
fh.write(
json.dumps(shifts,
sort_keys=True,
indent=4,
separators=(',', ': '),
cls=NpEncoder))
fh.write('\n')
fh.close()
except Exception as e:
logging.error(
"Creation of SHIFTS file failed while trying to write: {}"
.format(shifts))
raise e
error_count += 1
logging.debug("{}".format(error_count))
if not dry_run:
storage.copy(
shift_file,
storage.get_uri(expnum, ccd, version, '.shifts'))
logging.info(message)
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task,
prefix,
expnum,
version,
ccd,
status=message)
def run(expnum, ccd, prefix=None, version='p', field=None,
measure3_dir=storage.MEASURE3, dry_run=False, force=False):
message = storage.SUCCESS
if storage.get_status(task, prefix, expnum, version, ccd) and not force:
logging.info(
"{} completed successfully for {} {} {} {}".format(task, prefix,
expnum, version,
ccd))
return
with storage.LoggingManager(task, prefix, expnum, ccd, version, dry_run):
try:
if not storage.get_status(dependency, prefix, expnum, version, ccd):
raise IOError(35, "Cannot start {} as {} not yet completed "
"for {}{}{}{:02d}".format(task, dependency,
prefix, expnum,
version, ccd))
if field is None:
field = str(expnum)
if prefix is not None and len(prefix) > 0:
field = "%s_%s" % (prefix, field)
field += "_%s%s" % (str(version), str(ccd))
logging.info("Doing combine on field {}".format(field))
for ext in ['moving.matt', 'moving.jmp']:
storage.get_file(expnum, ccd=ccd, version=version, ext=ext,
prefix=prefix)
# Get the list of objects planted into the field if prefix='fk'
if prefix == 'fk':
storage.get_file('Object',
version='',
ext='planted',
subdir=str(expnum) + "/ccd%s" % (
str(ccd).zfill(2)))
else:
prefix = ''
cmd_args = ['comb-list',
prefix + str(expnum) + version + str(ccd).zfill(2)]
logging.info(str(cmd_args))
logging.info(util.exec_prog(cmd_args))
# things to copy back to VOSpace, if this is an 'fk' image
# then we have missed and found files too.
ext_list = ['cands.comb']
if prefix == 'fk':
ext_list.extend(['jmp.missed', 'matt.missed',
'jmp.found', 'matt.found',
'comb.missed', 'comb.found'])
for ext in ext_list:
uri = storage.get_uri(expnum,
ccd=ccd,
prefix=prefix,
version=version,
ext=ext)
filename = os.path.basename(uri)
if not os.access(filename, os.R_OK):
logging.critical("No %s file" % filename)
continue
vospace_name = "%s.%s" % (field, ext)
if not dry_run:
logging.info("%s -> %s" % (
filename, os.path.join(measure3_dir, vospace_name)))
storage.copy(filename, os.path.join(measure3_dir, vospace_name))
base_name = prefix + str(expnum) + version + str(ccd).zfill(2)
cands_file = base_name + '.cands.comb'
if not os.access(cands_file, os.R_OK):
no_cands_file = (prefix +
str(expnum) +
version +
str(ccd).zfill(2) +
'.no_candidates')
open(no_cands_file, 'w').close()
if not dry_run:
vospace_name = "%s.no_candidates" % field
storage.copy(no_cands_file,
os.path.join(measure3_dir, vospace_name))
else:
measure3.run(base_name, storage.DBIMAGES)
if not dry_run:
filename = base_name + ".measure3.cands.astrom"
vospace_filename = "%s.measure3.cands.astrom" % field
storage.copy(filename, os.path.join(measure3_dir, vospace_filename))
except Exception as ex:
message = str(ex)
logging.error(message)
if not dry_run:
storage.set_status(task, prefix, expnum, version, ccd,
status=message)
def main():
"""Do the script."""
parser = argparse.ArgumentParser(description='replace image header')
parser.add_argument('--extname', help='name of extension to in header')
parser.add_argument('expnum', type=str, help='exposure to update')
parser.add_argument('-r',
'--replace',
action='store_true',
help='store modified image back to VOSpace?')
parser.add_argument('-v', '--verbose', action='store_true')
parser.add_argument('--debug', action='store_true')
parser.add_argument('--force',
action='store_true',
help="Re-run even if previous success recorded")
parser.add_argument('--dbimages',
help="VOSpace DATA storage area.",
default="vos:OSSOS/dbimages")
args = parser.parse_args()
task = util.task()
dependency = 'preproc'
prefix = ""
storage.DBIMAGES = args.dbimages
level = logging.CRITICAL
message_format = "%(message)s"
if args.verbose:
level = logging.INFO
if args.debug:
level = logging.DEBUG
message_format = "%(module)s %(funcName)s %(lineno)s %(message)s"
logging.basicConfig(level=level, format=message_format)
storage.set_logger(task, prefix, args.expnum, None, None, False)
message = storage.SUCCESS
expnum = args.expnum
exit_status = 0
try:
# skip if already succeeded and not in force mode
if storage.get_status(task, prefix, expnum, "p",
36) and not args.force:
logging.info("Already updated, skipping")
sys.exit(0)
image_hdulist = storage.get_image(args.expnum, return_file=False)
ast_hdulist = storage.get_astheader(expnum, ccd=None)
run_update_header(image_hdulist, ast_hdulist)
image_filename = os.path.basename(storage.get_uri(expnum))
image_hdulist.writeto(image_filename)
if args.replace:
dest = storage.dbimages_uri(expnum)
storage.copy(image_filename, dest)
storage.set_status('update_header', "", expnum, 'p', 36, message)
except Exception as e:
message = str(e)
if args.replace:
storage.set_status(task, prefix, expnum, 'p', 36, message)
exit_status = message
logging.error(message)
return exit_status
def run(expnums,
ccd,
version,
rate_min,
rate_max,
angle,
width,
field=None,
prefix=None,
dry_run=False,
force=False):
"""run the actual step2 on the given exp/ccd combo"""
jmp_args = ['step3jmp']
matt_args = ['step3matt']
if storage.get_status(task, prefix, expnums[0], version=version,
ccd=ccd) and not force:
logging.info("{} completed successfully for {}{}{}{:02d}".format(
task, prefix, expnums[0], version, ccd))
return
with storage.LoggingManager(task, prefix, expnums[0], ccd, version,
dry_run):
try:
if not storage.get_status(
dependency, prefix, expnums[0], version=version, ccd=ccd):
raise IOError(
35, "Cannot start {} as {} not yet completed {}{}{}{:02d}".
format(task, dependency, prefix, expnums[0], version, ccd))
# Default message is success, message gets overwritten with failure messages.
message = storage.SUCCESS
idx = 0
cmd_args = []
for expnum in expnums:
idx += 1
for ext in ['unid.jmp', 'unid.matt', 'trans.jmp']:
storage.get_file(expnum,
ccd=ccd,
version=version,
ext=ext,
prefix=prefix)
image = os.path.splitext(
os.path.basename(
storage.get_uri(expnum,
ccd,
version=version,
prefix=prefix)))[0]
cmd_args.append('-f%d' % idx)
cmd_args.append(image)
cmd_args.extend([
'-rn',
str(rate_min), '-rx',
str(rate_max), '-a',
str(angle), '-w',
str(width)
])
jmp_args.extend(cmd_args)
matt_args.extend(cmd_args)
logging.info(util.exec_prog(jmp_args))
logging.info(util.exec_prog(matt_args))
if dry_run:
return
if field is None:
field = str(expnums[0])
# Make sure a dbimages destination exists for this file.
storage.mkdir(
os.path.dirname(
storage.get_uri(field,
ccd=ccd,
version=version,
prefix=prefix)))
for ext in ['moving.jmp', 'moving.matt']:
uri = storage.get_uri(field,
ccd=ccd,
version=version,
ext=ext,
prefix=prefix)
filename = '%s%d%s%s.%s' % (prefix, expnums[0], version,
str(ccd).zfill(2), ext)
storage.copy(filename, uri)
except Exception as ex:
message = str(ex)
logging.error(message)
storage.set_status(task,
prefix,
expnums[0],
version=version,
ccd=ccd,
status=message)
return
level = logging.DEBUG
elif args.verbose:
level = logging.INFO
logging.basicConfig(level=level, format="%(message)s")
storage._dbimages = args.dbimages
prefix = (args.fk and 'fk') or ''
ccdlist = (args.ccd is None and range(0, 36)) or [args.ccd]
for ccd in ccdlist:
message = storage.SUCCESS
try:
if not storage.get_status(args.expnum, ccd, prefix + 'step3'):
logging.error(
storage.get_status(args.expnum,
ccd,
'step3',
return_message=True))
raise IOError(35, "need to run step3 first")
if storage.get_status(args.expnum, ccd,
prefix + 'combine') and not args.force:
continue
message = combine(args.expnum, ccd, prefix=prefix, type=args.type)
except Exception as e:
message = str(e)
storage.set_status(args.expnum, ccd, prefix + 'combine', message)
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccdlist = range(0,36)
else:
ccdlist = [args.ccd]
prefix = ( args.fk and 'fk') or ''
for expnum in args.expnum:
for ccd in ccdlist:
try:
message = storage.SUCCESS
if not storage.get_status(expnum, ccd, 'mkpsf', version=args.type):
raise IOError(35, "mkpsf hasn't run?")
if storage.get_status(expnum, ccd, prefix+'step1', version=args.type) and not args.force:
logging.critical(
"Step1 completed for %s%s, skipping" %(prefix+str(expnum),
str(args.type)+str(ccd)))
continue
logging.info("step1_p on expnum: %s, ccd: %s" % (
prefix+str(expnum), str(ccd)))
step1(expnum, ccd, prefix=prefix, version=args.type)
except Exception as e:
message = str(e)
logging.error("Error running step1_p: %s " %(message))
storage.set_status(expnum,
ccd,
storage.DBIMAGES = args.dbimages
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:
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))
main(expnum, ccd) # , args.type, args.dry_run, prefix=prefix)
except Exception as e:
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():
### 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")
args = parser.parse_args()
if args.dry_run:
args.force = True
if args.verbose:
logging.basicConfig(level=logging.INFO, format="%(message)s")
if args.debug:
logging.basicConfig(level=logging.DEBUG, format="%(message)s")
storage.DBIMAGES = args.dbimages
if args.ccd is None:
ccd_list = range(0, 36)
else:
ccd_list = [args.ccd]
prefix = (args.fk and "fk") or ""
if not args.no_sort:
args.expnums.sort()
exit_status = 0
for ccd in ccd_list:
storage.set_logger(
os.path.splitext(os.path.basename(sys.argv[0]))[0], prefix,
args.expnums[0], ccd, args.type, args.dry_run)
try:
message = storage.SUCCESS
for expnum in args.expnums:
if not storage.get_status(
expnum, ccd, prefix + 'step1', version=args.type):
raise IOError(35, "missing step1 for %s" % expnum)
if storage.get_status(
args.expnums[0], ccd, prefix + 'step2',
version=args.type) and not args.force:
logging.info("Already did %s %s, skipping" %
(str(args.expnums[0]), str(ccd)))
continue
logging.info("step2 on expnums :%s, ccd: %d" %
(str(args.expnums), ccd))
step2(args.expnums,
ccd,
version=args.type,
prefix=prefix,
dry_run=args.dry_run,
default=args.default)
logging.info(message)
except CalledProcessError as cpe:
message = str(cpe)
logging.error(message)
exit_status = message
except Exception as e:
message = str(e)
logging.error(message)
exit_status = message
if not args.dry_run:
storage.set_status(args.expnums[0],
ccd,
prefix + 'step2',
version=args.type,
status=message)
return exit_status
