def mkpsf(expnum, ccd, version, dry_run=False, prefix=""):
"""Run the OSSOS jmpmakepsf script.
"""
## 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 file from VOSpace")
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
logging.info("Running mkpsf on %s %d" % (expnum, ccd))
## launch the makepsf script
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)
storage.copy(source, dest)
return
def mkpsf(expnum, ccd):
"""Run the OSSOS makepsf script.
"""
## get image from the vospace storage area
filename = storage.get_image(expnum, ccd, version='p')
logging.info("Running mkpsf on %s %d" % (expnum, ccd))
## launch the makepsf script
util.exec_prog(['jmpmakepsf.csh',
'./',
filename,
'no'])
## place the results into VOSpace
basename = os.path.splitext(filename)[0]
## confirm destination directory exists.
destdir = os.path.dirname(
storage.dbimages_uri(expnum, ccd, version='p',ext='fits'))
logging.info("Checking that destination direcoties exist")
storage.mkdir(destdir)
for ext in ('mopheader', 'psf.fits',
'zeropoint.used', 'apcor', 'fwhm', 'phot'):
dest = storage.dbimages_uri(expnum, ccd, version='p', ext=ext)
source = basename + "." + ext
storage.copy(source, dest)
return
def mkpsf(expnum, ccd, fversion):
"""Run the OSSOS makepsf script.
"""
## get image from the vospace storage area
filename = storage.get_image(expnum, ccd, version=fversion)
logging.info("Running mkpsf on %s %d" % (expnum, ccd))
## launch the makepsf script
util.exec_prog(['jmpmakepsf.csh',
'./',
filename,
'no'])
## place the results into VOSpace
basename = os.path.splitext(filename)[0]
## confirm destination directory exists.
destdir = os.path.dirname(
storage.dbimages_uri(expnum, ccd, version=fversion,ext='fits'))
logging.info("Checking that destination directories exist")
storage.mkdir(destdir)
for ext in ('mopheader', 'psf.fits',
'zeropoint.used', 'apcor', 'fwhm', 'phot'):
dest = storage.dbimages_uri(expnum, ccd, version=fversion, ext=ext)
source = basename + "." + ext
logging.info("Copying %s -> %s" % ( source, dest))
storage.remove(dest)
storage.copy(source, dest)
return
def mk_mopheader(expnum, ccd, version, dry_run=False, prefix=""):
"""Run the OSSOS mopheader script.
"""
## 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
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
logging.info("Running mopheader on %s %d" % (expnum, ccd))
## launch the mopheader script
## launch the makepsf script
expname = os.path.basename(filename).strip('.fits')
logging.info(util.exec_prog(['stepZjmp',
'-f',
expname]))
mopheader_filename = expname+".mopheader"
# mopheader_filename = mopheader.main(filename)
if dry_run:
return
destination = storage.dbimages_uri(expnum, ccd, prefix=prefix, version=version, ext='mopheader')
source = mopheader_filename
storage.copy(source, destination)
return
def build_source_reading(self, expnum, ccd, X, Y):
"""
Given the location of a source in the image, create a source reading.
"""
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=None,
version='p',
ext='.fits',
subdir=None)
logger.debug('Trying to access {}'.format(image_uri))
if not storage.exists(image_uri, force=False):
logger.warning('Image not in dbimages? Trying subdir.')
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p')
if not storage.exists(image_uri, force=False):
logger.warning("Image doesn't exist in ccd subdir. %s" % image_uri)
return None
slice_rows=config.read("CUTOUTS.SINGLETS.SLICE_ROWS")
slice_cols=config.read("CUTOUTS.SINGLETS.SLICE_COLS")
if X == -9999 or Y == -9999 :
logger.warning("Skipping {} as x/y not resolved.".format(image_uri))
return None
if not (-slice_cols/2. < X < 2048+slice_cols/2. and -slice_rows/2. < Y < 4600+slice_rows/2.0):
logger.warning("Central location ({},{}) off image cutout.".format(X,Y))
return None
mopheader_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p',
ext='.mopheader')
if not storage.exists(mopheader_uri, force=False):
# ELEVATE! we need to know to go off and reprocess/include this image.
logger.critical('Image exists but processing incomplete. Mopheader missing. {}'.format(image_uri))
return None
mopheader = get_mopheader(expnum, ccd)
# Build astrom.Observation
observation = astrom.Observation(expnum=str(expnum),
ftype='p',
ccdnum=str(ccd),
fk="")
observation.rawname = os.path.splitext(os.path.basename(image_uri))[0]+str(ccd).zfill(2)
observation.header = mopheader
return observation
def from_source_reference(expnum, ccd, X, Y):
"""
Given the location of a source in the image, create a source reading.
"""
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=None,
version='p',
ext='.fits',
subdir=None)
logger.debug('Trying to access {}'.format(image_uri))
if not storage.exists(image_uri, force=False):
logger.warning('Image not in dbimages? Trying subdir.')
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p')
if not storage.exists(image_uri, force=False):
logger.warning("Image doesn't exist in ccd subdir. %s" % image_uri)
return None
if X == -9999 or Y == -9999 :
logger.warning("Skipping {} as x/y not resolved.".format(image_uri))
return None
mopheader_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p',
ext='.mopheader')
if not storage.exists(mopheader_uri, force=False):
# ELEVATE! we need to know to go off and reprocess/include this image.
logger.critical('Image exists but processing incomplete. Mopheader missing. {}'.format(image_uri))
return None
mopheader = storage.get_mopheader(expnum, ccd)
# Build astrom.Observation
observation = Observation(expnum=str(expnum),
ftype='p',
ccdnum=str(ccd),
fk="")
observation.rawname = os.path.splitext(os.path.basename(image_uri))[0]+str(ccd).zfill(2)
observation.header = mopheader
return observation
def from_source_reference(expnum, ccd, x, y):
"""
Given the location of a source in the image, create a source reading.
"""
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=None,
version='p',
ext='.fits',
subdir=None)
logger.debug('Trying to access {}'.format(image_uri))
if not storage.exists(image_uri, force=False):
logger.warning('Image not in dbimages? Trying subdir.')
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p')
if not storage.exists(image_uri, force=False):
logger.warning("Image doesn't exist in ccd subdir. %s" % image_uri)
return None
if x == -9999 or y == -9999:
logger.warning(
"Skipping {} as x/y not resolved.".format(image_uri))
return None
mopheader_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p',
ext='.mopheader')
if not storage.exists(mopheader_uri, force=False):
# ELEVATE! we need to know to go off and reprocess/include this image.
logger.critical(
'Image exists but processing incomplete. Mopheader missing. {}'
.format(image_uri))
return None
# Build astrom.Observation
observation = Observation(expnum=str(expnum),
ftype='p',
ccdnum=str(ccd),
fk="")
observation.rawname = os.path.splitext(
os.path.basename(image_uri))[0] + str(ccd).zfill(2)
return observation
def main(expnum, ccd):
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
while True:
print("Copy attempt {}".format(count))
try:
storage.copy(name, uri)
os.unlink(name)
break
except Exception as ex:
if count > 10:
raise ex
count += 1
def compute_trans(expnums, ccd, version, prefix=None, default="WCS"):
"""
Pull the astrometric header for each image, compute an x/y transform and compare to trans.jmp
this one overides trans.jmp if they are very different.
@param expnums:
@param ccd:
@param version:
@param prefix:
@return: None
"""
wcs_dict = {}
for expnum in expnums:
try:
# TODO This assumes that the image is already N/E flipped.
# If compute_trans is called after the image is retrieved from archive then we get the disk version.
filename = storage.get_image(expnum, ccd, version, prefix=prefix)
this_wcs = wcs.WCS(fits.open(filename)[0].header)
except Exception as err:
logging.warning("WCS Trans compute failed. {}".format(str(err)))
return
wcs_dict[expnum] = this_wcs
x0 = wcs_dict[expnums[0]].header['NAXIS1'] / 2.0
y0 = wcs_dict[expnums[0]].header['NAXIS2'] / 2.0
(ra0, dec0) = wcs_dict[expnums[0]].xy2sky(x0, y0)
result = ""
for expnum in expnums:
filename = storage.get_file(expnum,
ccd,
version,
ext='.trans.jmp',
prefix=prefix)
jmp_trans = file(filename, 'r').readline().split()
(x, y) = wcs_dict[expnum].sky2xy(ra0, dec0)
x1 = float(
jmp_trans[0]) + float(jmp_trans[1]) * x + float(jmp_trans[2]) * y
y1 = float(
jmp_trans[3]) + float(jmp_trans[4]) * x + float(jmp_trans[5]) * y
dr = math.sqrt((x1 - x0)**2 + (y1 - y0)**2)
if dr > 0.5:
result += "WARNING: WCS-JMP transforms mis-matched {} reverting to using {}.\n".format(
expnum, default)
if default == "WCS":
uri = storage.dbimages_uri(expnum,
ccd,
version,
ext='.trans.jmp',
prefix=prefix)
filename = os.path.basename(uri)
trans = file(filename, 'w')
trans.write("{:5.2f} 1. 0. {:5.2f} 0. 1.\n".format(
x0 - x, y0 - y))
trans.close()
else:
result += "WCS-JMP transforms match {}\n".format(expnum)
return result
def mkpsf(expnum, ccd, version, dry_run=False, prefix=""):
"""Run the OSSOS jmpmakepsf script.
"""
## 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
filename = storage.get_image(expnum, ccd, version=version, prefix=prefix)
logging.info("Running mkpsf on %s %d" % (expnum, ccd))
## launch the makepsf script
logging.info(util.exec_prog(['jmpmakepsf.csh', './', filename, 'no']))
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)
storage.copy(source, dest)
return
def compute_trans(expnums, ccd, version, prefix=None, default="WCS"):
"""
Pull the astrometric header for each image, compute an x/y transform and compare to trans.jmp
this one overides trans.jmp if they are very different.
@param expnums:
@param ccd:
@param version:
@param prefix:
@return: None
"""
wcs_dict = {}
for expnum in expnums:
try:
# TODO This assumes that the image is already N/E flipped.
# If compute_trans is called after the image is retrieved from archive then we get the disk version.
filename = storage.get_image(expnum, ccd, version, prefix=prefix)
this_wcs = wcs.WCS(fits.open(filename)[0].header)
except Exception as err:
logging.warning("WCS Trans compute failed. {}".format(str(err)))
return
wcs_dict[expnum] = this_wcs
x0 = wcs_dict[expnums[0]].header['NAXIS1'] / 2.0
y0 = wcs_dict[expnums[0]].header['NAXIS2'] / 2.0
(ra0, dec0) = wcs_dict[expnums[0]].xy2sky(x0, y0)
result = ""
for expnum in expnums:
filename = storage.get_file(expnum, ccd, version, ext='.trans.jmp', prefix=prefix)
jmp_trans = file(filename, 'r').readline().split()
(x, y) = wcs_dict[expnum].sky2xy(ra0, dec0)
x1 = float(jmp_trans[0]) + float(jmp_trans[1]) * x + float(jmp_trans[2]) * y
y1 = float(jmp_trans[3]) + float(jmp_trans[4]) * x + float(jmp_trans[5]) * y
dr = math.sqrt((x1 - x0) ** 2 + (y1 - y0) ** 2)
if dr > 0.5:
result += "WARNING: WCS-JMP transforms mis-matched {} reverting to using {}.\n".format(expnum, default)
if default == "WCS":
uri = storage.dbimages_uri(expnum, ccd, version, ext='.trans.jmp', prefix=prefix)
filename = os.path.basename(uri)
trans = file(filename, 'w')
trans.write("{:5.2f} 1. 0. {:5.2f} 0. 1.\n".format(x0 - x, y0 - y))
trans.close()
else:
result += "WCS-JMP transforms match {}\n".format(expnum)
return result
def main(commands=['update_header', 'mkpsf', 'step1', 'step2', 'step3', 'combine'],
ccds=range(0,36),
launch=False, triplets_dir=TRIPLETS_NODE,
delete=False):
cmd_order={'LEAD': ['update_header', 'mkpsf', 'step1', 'step2', 'step3', 'combine'],
'OTHER': ['update_header', 'mkpsf', 'step1' ] }
existance = {'mkpsf': ['psf.fits', ],
'step1': ['obj.jmp', 'obj.matt'],
'step2': ['unid.jmp', 'unid.matt'],
'step3': ['cands.jmp', 'cands.matt']}
for line in get_triplets(triplets_dir):
for command in commands:
exp_type = 'LEAD'
for expnum in line[0:3]:
tags = storage.get_tags(expnum)
if command not in cmd_order[exp_type]:
continue
for ccd in ccds:
tag = storage.tag_uri(storage.get_process_tag(command, ccd))
print line[3], command, expnum, ccd, tags.get(tag,None)
if tags.get(tag,None) != storage.SUCCESS:
if launch:
submit(command, expnum, ccd)
if delete:
success=True
for ext in existance[command]:
uri = storage.dbimages_uri(expnum, ccd, version='p', ext=ext)
if not storage.exists(uri):
success=False
print expnum, ccd, success
#for next_command in cmd_order[exp_type][commands.index(command)+1:]:
# storage.set_status(expnum, ccd, next_command, command+" FAILED")
if success:
storage.set_status(expnum, ccd, command, version='p', status='success')
exp_type='OTHER'
def step2(expnums, ccd, version, prefix=None):
'''run the actual step2 on the given exp/ccd combo'''
jmp_args = ['step2jmp']
matt_args = ['step2matt_jmp']
idx = 0
for expnum in expnums:
jmp_args.append(
storage.get_image(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_image(expnum,
ccd=ccd,
version=version,
ext='obj.matt',
prefix=prefix
)[0:-9]
)
util.exec_prog(jmp_args)
util.exec_prog(matt_args)
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)
return
def step2(expnums, ccd, version, prefix=None):
'''run the actual step2 on the given exp/ccd combo'''
jmp_args = ['step2jmp']
matt_args = ['step2matt_jmp']
idx = 0
for expnum in expnums:
jmp_args.append(
storage.get_image(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_image(expnum,
ccd=ccd,
version=version,
ext='obj.matt',
prefix=prefix)[0:-9])
util.exec_prog(jmp_args)
util.exec_prog(matt_args)
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)
return
def get_image_uri(self):
return storage.dbimages_uri(self.expnum,
ccd=self.ccdnum,
version=self.ftype,
prefix=self.fk,
ext='.fits')
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(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
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)
print("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")
print(name+" -> "+uri)
count = 0
while count < 10:
print("Copy attempt {}".format(count))
try:
storage.copy(name, uri)
os.unlink(name)
break
except Exception as ex:
print(ex)
count += 1
continue
except Exception as ex:
print(ex)
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 get_zmag_uri(self):
return storage.dbimages_uri(self.expnum,
ccd=self.ccdnum,
version=self.ftype,
prefix=self.fk,
ext=storage.ZEROPOINT_USED_EXT)
def get_apcor_uri(self):
return storage.dbimages_uri(self.expnum,
ccd=self.ccdnum,
version=self.ftype,
prefix=self.fk,
ext=storage.APCOR_EXT)
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
def main(expnum, ccd):
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
while True:
print(("Copy attempt {}".format(count)))
try:
storage.copy(name, uri)
os.unlink(name)
break
except Exception as ex:
if count > 10:
raise ex
count += 1
logging.basicConfig(level=logging.INFO, format="%(message)s")
message = storage.SUCCESS
try:
image = (os.access(args.expnum, os.W_OK)
and args.expnum) or (storage.get_image(args.expnum))
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'))
logging.info("Swapping header for %s for contents in %s \n" %
(image, header))
run_update_header(image, header)
if args.replace:
expnum = args.expnum or fits.open(image)[0].header['EXPNUM']
dest = storage.dbimages_uri(expnum)
storage.copy(image, dest)
storage.set_status(args.expnum, 36, 'update_header', message)
sys.exit(0)
except Exception as e:
logging.error("Error replacing header for %s" % (args.expnum))
logging.error(str(e))
message = str(e)
storage.set_status(args.expnum, 36, 'update_header', message)
sys.exit(2)
def step2(expnums, ccd, version, prefix=None, dry_run=False, default="WCS"):
"""run the actual step2 on the given exp/ccd combo"""
jmp_trans = ['step2ajmp']
jmp_args = ['step2bjmp']
matt_args = ['step2matt_jmp']
idx = 0
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(util.exec_prog(jmp_trans))
if default == "WCS":
logging.info(
compute_trans(expnums, ccd, version, prefix, default=default))
logging.info(util.exec_prog(jmp_args))
logging.info(util.exec_prog(matt_args))
## check that the shifts from step2 are rational
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 ValueError(errno.EBADEXEC, '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)
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, 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
axis=0)
print(("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")
print((name + " -> " + uri))
count = 0
while count < 10:
print(("Copy attempt {}".format(count)))
try:
storage.copy(name, uri)
os.unlink(name)
break
except Exception as ex:
print(ex)
count += 1
continue
except Exception as ex:
print(ex)
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 parse(self, ssos_result_filename_or_lines):
"""
given the result table create 'source' objects.
:type ssos_result_table: Table
:param ssos_result_table:
"""
table_reader = ascii.get_reader(Reader=ascii.Basic)
table_reader.inconsistent_handler = self._skip_missing_data
table_reader.header.splitter.delimiter = '\t'
table_reader.data.splitter.delimiter = '\t'
table = table_reader.read(ssos_result_filename_or_lines)
sources = []
observations = []
source_readings = []
ref_pvwcs = None
downloader = Downloader()
warnings.filterwarnings('ignore')
for row in table:
# check if a dbimages object exists
ccd = int(row['Ext']) - 1
expnum = row['Image'].rstrip('p')
# ADDING THIS TEMPORARILY TO GET THE NON-OSSOS DATA OUT OF THE WAY WHILE DEBUGGING
if (row['Telescope_Insturment'] != 'CFHT/MegaCam') or (row['Filter'] != 'r.MP9601'):
continue
# it's fine for OSSOS, go get the image
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=None,
version='p',
ext='.fits',
subdir=None)
logger.info('Trying to access %s\n%s' % (row.data, image_uri))
if not storage.exists(image_uri, force=False):
logger.warning('Image not in dbimages? Trying subdir.')
image_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p')
if not storage.exists(image_uri, force=False):
logger.warning("Image doesn't exist in ccd subdir. %s" % image_uri)
continue
if row['X'] == -9999 or row['Y'] == -9999 :
logger.warning("Skipping %s as x/y not resolved." % ( row['Image']))
continue
mopheader_uri = storage.dbimages_uri(expnum=expnum,
ccd=ccd,
version='p',
ext='.mopheader')
if not mopheader_uri in mopheaders:
if not storage.exists(mopheader_uri, force=False):
logger.warning('mopheader missing, but images exists')
continue
# raise flag if no MOPHEADER
mopheader_fpt = cStringIO.StringIO(storage.open_vos_or_local(mopheader_uri).read())
mopheader = fits.open(mopheader_fpt)
mopheaders[mopheader_uri] = mopheader
mopheader = mopheaders[mopheader_uri]
# Build astrom.Observation
observation = astrom.Observation(expnum=str(expnum),
ftype='p',
ccdnum=str(ccd),
fk="")
observation.rawname = os.path.splitext(os.path.basename(image_uri))[0]+str(ccd).zfill(2)
observation.header = mopheader[0].header
MJD_OBS_CENTER = mpc.Time(observation.header['MJD-OBSC'],
format='mjd',
scale='utc', precision=5 ).replicate(format='mpc')
observation.header['MJD_OBS_CENTER'] = str(MJD_OBS_CENTER)
observation.header['MAXCOUNT'] = MAXCOUNT
observation.header['SCALE'] = observation.header['PIXSCALE']
#observation.header['CHIP'] = str(observation.header['CHIPNUM']).zfill(2)
observation.header['NAX1'] = observation.header['NAXIS1']
observation.header['NAX2'] = observation.header['NAXIS2']
observation.header['MOPversion'] = observation.header['MOP_VER']
observation.header['FWHM'] = 4
# a download pixel 1,1 of this data to due offsets with.
x_cen = int(min(max(1,row['X']),observation.header['NAX1']))
y_cen = int(min(max(1,row['Y']),observation.header['NAX2']))
if image_uri not in astheaders:
hdulist = downloader.download_hdulist(
uri=image_uri,
view='cutout',
cutout='[{}][{}:{},{}:{}]'.format(ccd+1, x_cen, x_cen, y_cen, y_cen))
astheaders[image_uri] = hdulist
hdulist = astheaders[image_uri]
pvwcs = wcs.WCS(hdulist[0].header)
(ra,dec) = pvwcs.xy2sky(x_cen, y_cen)
if ref_pvwcs is None:
ref_pvwcs = pvwcs
xref = row['X']
yref = row['Y']
(x0, y0) = ref_pvwcs.sky2xy(ra,dec)
x0 += row['X'] - x_cen
y0 += row['Y'] - y_cen
# Build astrom.SourceReading
observations.append(observation)
from_input_file = observation.rawname in self.input_rawnames
null_observation = observation.rawname in self.null_observations
print observation.rawname, observation.header['MJD_OBS_CENTER'], null_observation, from_input_file
source_reading = astrom.SourceReading(x=row['X'], y=row['Y'],
xref=xref, yref=yref,
x0=x0, y0=y0,
ra=row['Object_RA'], dec=row['Object_Dec'],
obs=observation,
ssos=True,
from_input_file=from_input_file,
null_observation=null_observation)
#if observation.rawname in self.input_rawnames:
# source_readings.insert(0, source_reading)
#else:
source_readings.append(source_reading)
# build our array of SourceReading objects
sources.append(source_readings)
warnings.filterwarnings('once')
return SSOSData(observations, sources, self.provisional_name)
def step2(expnums, ccd, version, prefix=None, dry_run=False, default="WCS"):
"""run the actual step2 on the given exp/ccd combo"""
jmp_trans = ['step2ajmp']
jmp_args = ['step2bjmp']
matt_args = ['step2matt_jmp']
idx = 0
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(util.exec_prog(jmp_trans))
if default == "WCS":
logging.info(compute_trans(expnums, ccd, version, prefix, default=default))
logging.info(util.exec_prog(jmp_args))
logging.info(util.exec_prog(matt_args))
## check that the shifts from step2 are rational
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)
return
message = storage.SUCCESS
try:
image = (os.access(args.expnum,os.W_OK) and args.expnum ) or (
storage.get_image(args.expnum) )
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'))
logging.info(
"Swapping header for %s for contents in %s \n" % (
image, header) )
run_update_header(image, header)
if args.replace:
expnum = args.expnum or fits.open(image)[0].header['EXPNUM']
dest = storage.dbimages_uri(expnum)
storage.copy(image, dest)
storage.set_status(args.expnum, 36, 'update_header', message)
sys.exit(0)
except Exception as e:
logging.error("Error replacing header for %s" % ( args.expnum))
logging.error(str(e))
message = str(e)
storage.set_status(args.expnum, 36, 'update_header', message)
sys.exit(2)
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
