def input_thread(queuename, inqueue, bigqueue, checkpointqueue, blobsizes, opt,
input_num):
try:
import setproctitle
setproctitle.setproctitle('farm: input_%i' % input_num)
except:
pass
print('Input process', os.getpid(), 'starting')
import qdo
q = qdo.connect(queuename)
while True:
task = q.get(timeout=10)
if task is None:
#- no more tasks in queue so break
break
try:
brickname = task.task
debug('Brick', brickname)
# WORK
nblobs = queue_work(brickname, inqueue, bigqueue, checkpointqueue,
opt)
blobsizes.put((brickname, nblobs, task.id))
#
debug('Finished', brickname, 'with', nblobs, 'blobs')
except:
print('Oops')
import traceback
traceback.print_exc()
task.set_state(qdo.Task.FAILED, err=1)
def change_task_state(self,
task_ids,
to=None,
modify=False,
rm_files=False):
"""change qdo tasks state, for tasks with task_ids, to pending,failed, etc
Args:
to: change qdo state to this, pending,failed
rm_files: delete the output files for that task
modify: actually do the modifications (fail safe option)
"""
assert (to in ['pending', 'failed'])
q = qdo.connect(self.que_name)
for task_id in task_ids:
try:
task_obj = q.tasks(id=int(task_id))
if self.isCosmos():
brick, rs, do_skipids, do_more, subset = task_obj.task.split(
' ')
outdir = os.path.join(self.outdir, 'subset%s' % subset)
else:
brick, rs, do_skipids, do_more = task_obj.task.split(' ')
outdir = self.outdir
del_dirs = get_deldirs(outdir,
brick,
rs,
do_skipids=do_skipids,
do_more=do_more)
del_fns = [get_checkpoint_fn(outdir, brick, rs)]
if modify:
if to == 'pending':
# Stuck in pending b/c slurm job timed out
task_obj.set_state(qdo.Task.PENDING)
#print('id %s --> PENDING' % task_id)
elif to == 'failed':
# Manually force to failed, keep whatever outputs have
task_obj.set_state(qdo.Task.FAILED)
print('id %s --> FAILED' % task_id)
if rm_files:
for dr in del_dirs:
dobash('rm -r %s/*' % dr)
for fn in del_fns:
dobash('rm %s' % fn)
else:
print(
'set --modify to affect id=%d, which corresponds to taks_obj='
% task_id, task_obj)
print('set --rm_files to remove', del_dirs, del_fns)
except ValueError:
print('cant find task_id=%d' % task_id)
def get_tasks_logs(self):
"""get tasks and logs for the three types of qdo status"""
# Logs for all Failed tasks
tasks = {}
ids = {}
logs = defaultdict(list)
#err= defaultdict(lambda: [])
q = qdo.connect(self.que_name)
for res in QDO_RESULT:
if self.skip_succeed and res == 'succeeded':
continue
# List of "brick rs" for each QDO_RESULT
qdo_tasks = np.array(q.tasks(state=getattr(qdo.Task, res.upper())))
if self.rand_num:
qdo_tasks = qdo_tasks[np.random.randint(0,
len(qdo_tasks),
size=self.rand_num)]
elif not self.firstN is None:
qdo_tasks = qdo_tasks[:self.firstN]
if len(qdo_tasks) > 0:
ids[res], tasks[res] = zip(*[(a.id, a.task)
for a in qdo_tasks])
else:
ids[res], tasks[res] = [], []
# Corresponding log, slurm files
for task in tasks[res]:
# Logs
if self.isCosmos():
brick, rs, do_skipids, do_more, subset = task.split(' ')
outdir = os.path.join(self.outdir, 'subset%s' % subset)
else:
brick, rs, do_skipids, do_more = task.split(' ')
outdir = self.outdir
logfn = get_logfile(outdir,
brick,
rs,
do_skipids=do_skipids,
do_more=do_more)
logs[res].append(logfn)
return tasks, ids, logs
def __init__(self,
name,
previous_stage,
tasks_per_nodehr,
job_duration=2,
max_number_of_jobs=1000,
cores_per_worker=17,
arch='knl'):
"""name: name of the qdo queue; also used for calling the default
job scheudling script and for distinguishing jobs scheduled by
different stages
"""
self.cores_per_worker = cores_per_worker
self.job_duration = job_duration
self.max_number_of_jobs = max_number_of_jobs
self.arch = arch
try:
self.queue = qdo.connect(name)
except ValueError:
if self.auto_create_queue:
self.queue = qdo.create(name)
else:
raise
super().__init__(name, previous_stage, tasks_per_nodehr)
from astrometry.libkd.spherematch import *
parser = argparse.ArgumentParser()
parser.add_argument('--wrap', action='store_true',
help='Wrap RA at 180 degrees?')
parser.add_argument('args',nargs=argparse.REMAINDER)
opt = parser.parse_args()
args = opt.args
if len(args) < 1:
print('Need one+ arg: qdo queue name(s)')
sys.exit(-1)
state_radec = {}
for qname in args:
q = qdo.connect(qname, create_ok=False)
print('Connected to QDO queue', qname, q)
for state in qdo.Task.VALID_STATES:
print('State', state)
# Append jobs from all queues in this state into RA,Dec arrays
if state in state_radec:
ra,dec = state_radec[state]
else:
ra,dec = [],[]
state_radec[state] = (ra,dec)
tasks = q.tasks(state=state)
print(len(tasks), 'tasks with state', state)
parser.add_argument('bricks', nargs='*')
args = parser.parse_args()
plots = args.plots
bricks = args.bricks
kwargs = dict(get_depth_maps=args.depth_maps)
if args.margin is not None:
kwargs.update(margin=args.margin)
print('args:', bricks)
if len(bricks) == 1 and bricks[0] == 'qdo':
import qdo
#... find Queue...
qname = args.queue
q = qdo.connect(qname)
print('Connected to QDO queue', qname, q)
survey = LegacySurveyData()
while True:
task = q.get(timeout=10)
if task is None:
break
try:
print('Task:', task.task)
brickname = task.task
print('Checking for existing out file')
# shortcut
dirnm = os.path.join('depthcuts', brickname[:3])
def output_thread(queuename, outqueue, checkpointqueue, blobsizes,
finished_bricks, opt):
try:
import setproctitle
setproctitle.setproctitle('farm: output')
except:
pass
import qdo
q = qdo.connect(queuename)
allresults = {}
# Stored values from the 'blobsizes' queue.
# brick -> (nblobs, qdo_taskid)
brick_info = {}
# Local mapping of brickname -> [set of cancelled blob ids]
brick_cancelled = {}
def get_brick_nblobs(brick, defnblobs=None):
if not brick in brick_info:
try:
while True:
br, nb, tid = blobsizes.get(block=False)
brick_info[br] = (nb, tid)
except queue.Empty:
pass
return brick_info.get(brick, (defnblobs, None))
def check_brick_done(brick):
nblobs, taskid = get_brick_nblobs(brick)
if nblobs is None:
return
ncancelled = len(brick_cancelled.get(brick, []))
if len(allresults[brick]) + ncancelled < nblobs:
return
# Done this brick! Set qdo state=Succeeded
checkpoint_fn = opt.checkpoint % dict(brick=brick)
R = [
dict(brickname=brick, iblob=iblob, result=res)
for iblob, res in allresults[brick].items()
]
print('Writing final checkpoint', checkpoint_fn)
_write_checkpoint(R, checkpoint_fn)
print('Setting QDO task to Succeeded:', brick)
q.set_task_state(taskid, qdo.Task.SUCCEEDED)
del allresults[brick]
finished_bricks.put((brick, len(R)))
last_checkpoint = time.time()
last_checkpoint_size = {}
while True:
tnow = time.time()
dt = tnow - last_checkpoint
if dt > opt.checkpoint_period:
for brick, brickresults in allresults.items():
if brick in last_checkpoint_size:
if len(brickresults) == last_checkpoint_size[brick]:
#print('Brick', brick, 'has not changed since last checkpoint was written')
continue
checkpoint_fn = opt.checkpoint % dict(brick=brick)
R = [
dict(brickname=brick, iblob=iblob, result=res)
for iblob, res in brickresults.items()
]
last_checkpoint_size[brick] = len(brickresults)
nblobs, _ = get_brick_nblobs(brick, '(unknown)')
print('Writing interim checkpoint', checkpoint_fn, ':',
len(brickresults), 'of', nblobs, 'results')
_write_checkpoint(R, checkpoint_fn)
last_checkpoint = tnow
# Read any checkpointed results sent by the input thread
c = Counter()
while True:
try:
(brick, iblob, res) = checkpointqueue.get(block=False)
except:
break
if not brick in allresults:
allresults[brick] = {}
allresults[brick][iblob] = res
c[brick] += 1
#if len(c):
# print('Read checkpointed results:', c)
for brick, n in c.most_common():
nblobs, _ = get_brick_nblobs(brick, '(unknown)')
#print('Brick', brick, ': now', len(allresults[brick]), 'of', nblobs, 'done')
check_brick_done(brick)
try:
brick, iblob, msg = outqueue.get(timeout=60)
except:
# timeout
continue
if msg == 'cancel':
if not brick in brick_cancelled:
brick_cancelled[brick] = set()
brick_cancelled[brick].add(iblob)
debug('Output thread: got cancel for brick', brick, 'blob', iblob)
else:
if msg is None:
# short-cut empty work packet.
continue
# Worker sent a blob result
result = pickle.loads(msg)
if result is None:
### FIXME -- ???
continue
if not brick in allresults:
allresults[brick] = {}
allresults[brick][iblob] = result
check_brick_done(brick)
def main():
"""Main program.
"""
import argparse
parser = argparse.ArgumentParser(description="This script is used to produce lists of CCDs or bricks, for production purposes (building qdo queue, eg).")
parser.add_argument('--calibs', action='store_true',
help='Output CCDs that need to be calibrated.')
parser.add_argument('--nper', type=int, default=None,
help='Batch N calibs per line')
parser.add_argument('--forced', action='store_true',
help='Output forced-photometry commands')
parser.add_argument('--lsb', action='store_true',
help='Output Low-Surface-Brightness commands')
parser.add_argument('--touching', action='store_true',
help='Cut to only CCDs touching selected bricks')
parser.add_argument('--near', action='store_true',
help='Quick cut to only CCDs near selected bricks')
parser.add_argument('--check', action='store_true',
help='Check which calibrations actually need to run.')
parser.add_argument('--check-coadd', action='store_true',
help='Check which caoadds actually need to run.')
parser.add_argument('--out', help='Output filename for calibs, default %(default)s',
default='jobs')
parser.add_argument('--command', action='store_true',
help='Write out full command-line to run calib')
parser.add_argument('--opt', help='With --command, extra options to add')
parser.add_argument('--maxdec', type=float, help='Maximum Dec to run')
parser.add_argument('--mindec', type=float, help='Minimum Dec to run')
parser.add_argument('--region', help='Region to select')
parser.add_argument('--bricks', help='Set bricks.fits file to load')
parser.add_argument('--ccds', help='Set ccds.fits file to load')
parser.add_argument('--ignore_cuts', action='store_true',default=False,help='no photometric or blacklist cuts')
parser.add_argument('--save_to_fits', action='store_true',default=False,help='save cut brick,ccd to fits table')
parser.add_argument('--name', action='store',default='dr3',help='save with this suffix, e.g. refers to ccds table')
parser.add_argument('--delete-sky', action='store_true',
help='Delete any existing sky calibration files')
parser.add_argument('--delete-pvastrom', action='store_true',
help='Delete any existing PV WCS calibration files')
parser.add_argument('--write-ccds', help='Write CCDs list as FITS table?')
parser.add_argument('--brickq', type=int, default=None,
help='Queue only bricks with the given "brickq" value [0 to 3]')
parser.add_argument('--brickq-deps', action='store_true', default=False,
help='Queue bricks directly using qdo API, setting brickq dependencies')
parser.add_argument('--queue', default='bricks',
help='With --brickq-deps, the QDO queue name to use')
opt = parser.parse_args()
survey = LegacySurveyData()
if opt.bricks is not None:
B = fits_table(opt.bricks)
log('Read', len(B), 'from', opt.bricks)
else:
B = survey.get_bricks()
if opt.ccds is not None:
T = fits_table(opt.ccds)
log('Read', len(T), 'from', opt.ccds)
else:
T = survey.get_ccds()
log(len(T), 'CCDs')
T.index = np.arange(len(T))
if opt.ignore_cuts == False:
I = survey.photometric_ccds(T)
print(len(I), 'CCDs are photometric')
T.cut(I)
I = survey.apply_blacklist(T)
print(len(I), 'CCDs are not blacklisted')
T.cut(I)
print(len(T), 'CCDs remain')
# I,J,d,counts = match_radec(B.ra, B.dec, T.ra, T.dec, 0.2, nearest=True, count=True)
# plt.clf()
# plt.hist(counts, counts.max()+1)
# plt.savefig('bricks.png')
# B.cut(I[counts >= 9])
# plt.clf()
# plt.plot(B.ra, B.dec, 'b.')
# #plt.scatter(B.ra[I], B.dec[I], c=counts)
# plt.savefig('bricks2.png')
# DES Stripe82
#rlo,rhi = 350.,360.
# rlo,rhi = 300., 10.
# dlo,dhi = -6., 4.
# TINY bit
#rlo,rhi = 350.,351.1
#dlo,dhi = 0., 1.1
# EDR+
# 860 bricks
# ~10,000 CCDs
#rlo,rhi = 239,246
#dlo,dhi = 5, 13
# DR1
#rlo,rhi = 0, 360
# part 1
#dlo,dhi = 25, 40
# part 2
#dlo,dhi = 20,25
# part 3
#dlo,dhi = 15,20
# part 4
#dlo,dhi = 10,15
# part 5
#dlo,dhi = 5,10
# the rest
#dlo,dhi = -11, 5
#dlo,dhi = 15,25.5
dlo,dhi = -25, 40
rlo,rhi = 0, 360
# Arjun says 3x3 coverage area is roughly
# RA=240-252 DEC=6-12 (but not completely rectangular)
# COSMOS
#rlo,rhi = 148.9, 151.2
#dlo,dhi = 0.9, 3.5
# A nice well-behaved region (EDR2/3)
# rlo,rhi = 243.6, 244.6
# dlo,dhi = 8.1, 8.6
# 56 bricks, ~725 CCDs
#B.cut((B.ra > 240) * (B.ra < 242) * (B.dec > 5) * (B.dec < 7))
# 240 bricks, ~3000 CCDs
#B.cut((B.ra > 240) * (B.ra < 244) * (B.dec > 5) * (B.dec < 9))
# 535 bricks, ~7000 CCDs
#B.cut((B.ra > 240) * (B.ra < 245) * (B.dec > 5) * (B.dec < 12))
if opt.region in ['test1', 'test2', 'test3', 'test4']:
nm = dict(test1='2446p115', # weird stuff around bright star
test2='1183p292', # faint sources around bright galaxy
test3='3503p005', # DES
test4='1163p277', # Pollux
)[opt.region]
B.cut(np.flatnonzero(np.array([s == nm for s in B.brickname])))
log('Cut to', len(B), 'bricks')
log(B.ra, B.dec)
dlo,dhi = -90,90
rlo,rhi = 0, 360
elif opt.region == 'edr':
# EDR:
# 535 bricks, ~7000 CCDs
rlo,rhi = 240,245
dlo,dhi = 5, 12
elif opt.region == 'edrplus':
rlo,rhi = 235,248
dlo,dhi = 5, 15
elif opt.region == 'edr-south':
rlo,rhi = 240,245
dlo,dhi = 5, 10
elif opt.region == 'cosmos1':
# 16 bricks in the core of the COSMOS field.
rlo,rhi = 149.75, 150.75
dlo,dhi = 1.6, 2.6
elif opt.region == 'pristine':
# Stream?
rlo,rhi = 240,250
dlo,dhi = 10,15
elif opt.region == 'des':
dlo, dhi = -6., 4.
rlo, rhi = 317., 7.
T.cut(np.flatnonzero(np.array(['CPDES82' in fn for fn in T.cpimage])))
log('Cut to', len(T), 'CCDs with "CPDES82" in filename')
elif opt.region == 'subdes':
rlo,rhi = 320., 360.
dlo,dhi = -1.25, 1.25
elif opt.region == 'northwest':
rlo,rhi = 240,360
dlo,dhi = 20,40
elif opt.region == 'north':
rlo,rhi = 120,240
dlo,dhi = 20,40
elif opt.region == 'northeast':
rlo,rhi = 0,120
dlo,dhi = 20,40
elif opt.region == 'southwest':
rlo,rhi = 240,360
dlo,dhi = -20,0
elif opt.region == 'south':
rlo,rhi = 120,240
dlo,dhi = -20,0
elif opt.region == 'southeast':
rlo,rhi = 0,120
dlo,dhi = -20,0
elif opt.region == 'southsoutheast':
rlo,rhi = 0,120
dlo,dhi = -20,-10
elif opt.region == 'midwest':
rlo,rhi = 240,360
dlo,dhi = 0,20
elif opt.region == 'middle':
rlo,rhi = 120,240
dlo,dhi = 0,20
elif opt.region == 'mideast':
rlo,rhi = 0,120
dlo,dhi = 0,20
elif opt.region == 'grz':
# Bricks with grz coverage.
# Be sure to use --bricks survey-bricks-in-dr1.fits
# which has_[grz] columns.
B.cut((B.has_g == 1) * (B.has_r == 1) * (B.has_z == 1))
log('Cut to', len(B), 'bricks with grz coverage')
elif opt.region == 'nogrz':
# Bricks without grz coverage.
# Be sure to use --bricks survey-bricks-in-dr1.fits
# which has_[grz] columns.
B.cut(np.logical_not((B.has_g == 1) * (B.has_r == 1) * (B.has_z == 1)))
log('Cut to', len(B), 'bricks withOUT grz coverage')
elif opt.region == 'deep2':
rlo,rhi = 250,260
dlo,dhi = 30,35
elif opt.region == 'deep2f3':
rlo,rhi = 351.25, 353.75
dlo,dhi = 0, 0.5
elif opt.region == 'virgo':
rlo,rhi = 185,190
dlo,dhi = 10, 15
elif opt.region == 'virgo2':
rlo,rhi = 182,192
dlo,dhi = 8, 18
elif opt.region == 'lsb':
rlo,rhi = 147.2, 147.8
dlo,dhi = -0.4, 0.4
elif opt.region == 'eboss-elg':
# RA -45 to +45
# Dec -5 to +7
rlo,rhi = 315., 45.
dlo,dhi = -5., 7.
elif opt.region == 'eboss-ngc':
# NGC ELGs
# RA 115 to 175
# Dec 15 to 30
rlo,rhi = 115., 175.
dlo,dhi = 15., 30.
elif opt.region == 'mzls':
dlo,dhi = 30., 90.
elif opt.region == 'dr4-bootes':
# https://desi.lbl.gov/trac/wiki/DecamLegacy/DR4sched
#dlo,dhi = 34., 35.
#rlo,rhi = 209.5, 210.5
dlo,dhi = 33., 36.
rlo,rhi = 216.5, 219.5
if opt.mindec is not None:
dlo = opt.mindec
if opt.maxdec is not None:
dhi = opt.maxdec
if rlo < rhi:
B.cut((B.ra >= rlo) * (B.ra <= rhi) *
(B.dec >= dlo) * (B.dec <= dhi))
else: # RA wrap
B.cut(np.logical_or(B.ra >= rlo, B.ra <= rhi) *
(B.dec >= dlo) * (B.dec <= dhi))
log(len(B), 'bricks in range')
for name in B.get('brickname'):
print(name)
B.writeto('bricks-cut.fits')
I,J,d = match_radec(B.ra, B.dec, T.ra, T.dec, survey.bricksize)
keep = np.zeros(len(B), bool)
for i in I:
keep[i] = True
B.cut(keep)
log('Cut to', len(B), 'bricks near CCDs')
plt.clf()
plt.plot(B.ra, B.dec, 'b.')
plt.title('DR3 bricks')
plt.axis([360, 0, np.min(B.dec)-1, np.max(B.dec)+1])
plt.savefig('bricks.png')
if opt.brickq is not None:
B.cut(B.brickq == opt.brickq)
log('Cut to', len(B), 'with brickq =', opt.brickq)
if opt.touching:
keep = np.zeros(len(T), bool)
for j in J:
keep[j] = True
T.cut(keep)
log('Cut to', len(T), 'CCDs near bricks')
# Aside -- how many near DR1=1 CCDs?
if False:
T2 = D.get_ccds()
log(len(T2), 'CCDs')
T2.cut(T2.dr1 == 1)
log(len(T2), 'CCDs marked DR1=1')
log(len(B), 'bricks in range')
I,J,d = match_radec(B.ra, B.dec, T2.ra, T2.dec, survey.bricksize)
keep = np.zeros(len(B), bool)
for i in I:
keep[i] = True
B2 = B[keep]
log('Total of', len(B2), 'bricks near CCDs with DR1=1')
for band in 'grz':
Tb = T2[T2.filter == band]
log(len(Tb), 'in filter', band)
I,J,d = match_radec(B2.ra, B2.dec, Tb.ra, Tb.dec, survey.bricksize)
good = np.zeros(len(B2), np.uint8)
for i in I:
good[i] = 1
B2.set('has_' + band, good)
B2.writeto('survey-bricks-in-dr1.fits')
sys.exit(0)
# sort by dec decreasing
#B.cut(np.argsort(-B.dec))
# RA increasing
B.cut(np.argsort(B.ra))
for b in B:
if opt.check:
fn = 'dr1n/tractor/%s/tractor-%s.fits' % (b.brickname[:3], b.brickname)
if os.path.exists(fn):
print('Exists:', fn, file=sys.stderr)
continue
if opt.check_coadd:
fn = 'dr1b/coadd/%s/%s/decals-%s-image.jpg' % (b.brickname[:3], b.brickname, b.brickname)
if os.path.exists(fn):
print('Exists:', fn, file=sys.stderr)
continue
print(b.brickname)
if opt.save_to_fits:
assert(opt.touching)
# Write cut tables to file
for tab,typ in zip([B,T],['bricks','ccds']):
fn='%s-%s-cut.fits' % (typ,opt.name)
if os.path.exists(fn):
os.remove(fn)
tab.writeto(fn)
print('Wrote %s' % fn)
# Write text files listing ccd and filename names
nm1,nm2= 'ccds-%s.txt'% opt.name,'filenames-%s.txt' % opt.name
if os.path.exists(nm1):
os.remove(nm1)
if os.path.exists(nm2):
os.remove(nm2)
f1,f2=open(nm1,'w'),open(nm2,'w')
fns= list(set(T.get('image_filename')))
for fn in fns:
f2.write('%s\n' % fn.strip())
for ti in T:
f1.write('%s\n' % ti.get('image_filename').strip())
f1.close()
f2.close()
print('Wrote *-names.txt')
if opt.brickq_deps:
import qdo
from legacypipe.survey import on_bricks_dependencies
#... find Queue...
q = qdo.connect(opt.queue, create_ok=True)
print('Connected to QDO queue', opt.queue, q)
brick_to_task = dict()
I = survey.photometric_ccds(T)
print(len(I), 'CCDs are photometric')
T.cut(I)
I = survey.apply_blacklist(T)
print(len(I), 'CCDs are not blacklisted')
T.cut(I)
print(len(T), 'CCDs remaining')
T.wra = T.ra + (T.ra > 180) * -360
wra = rlo - 360
plt.clf()
plt.plot(T.wra, T.dec, 'b.')
ax = [wra, rhi, dlo, dhi]
plt.axis(ax)
plt.title('CCDs')
plt.savefig('q-ccds.png')
B.wra = B.ra + (B.ra > 180) * -360
# this slight overestimate (for DECam images) is fine
radius = 0.3
Iccds = match_radec(B.ra, B.dec, T.ra, T.dec, radius,
indexlist=True)
ikeep = []
for ib,(b,Iccd) in enumerate(zip(B, Iccds)):
if Iccd is None or len(Iccd) == 0:
print('No matched CCDs to brick', b.brickname)
continue
wcs = wcs_for_brick(b)
cI = ccds_touching_wcs(wcs, T[np.array(Iccd)])
print(len(cI), 'CCDs touching brick', b.brickname)
if len(cI) == 0:
continue
ikeep.append(ib)
B.cut(np.array(ikeep))
print('Cut to', len(B), 'bricks touched by CCDs')
for brickq in range(4):
I = np.flatnonzero(B.brickq == brickq)
print(len(I), 'bricks with brickq =', brickq)
J = np.flatnonzero(B.brickq < brickq)
preB = B[J]
reqs = []
if brickq > 0:
for b in B[I]:
# find brick dependencies
brickdeps = on_bricks_dependencies(b, survey, bricks=preB)
# convert to task ids
taskdeps = [brick_to_task.get(b.brickname,None) for b in brickdeps]
# If we dropped a dependency brick from a previous brickq because
# of no overlapping CCDs, it won't appear in the brick_to_task map.
taskdeps = [t for t in taskdeps if t is not None]
reqs.append(taskdeps)
plt.clf()
plt.plot(B.wra, B.dec, '.', color='0.5')
plt.plot(B.wra[I], B.dec[I], 'b.')
plt.axis(ax)
plt.title('Bricks: brickq=%i' % brickq)
plt.savefig('q-bricks-%i.png' % brickq)
# submit to qdo queue
print('Queuing', len(B[I]), 'bricks')
if brickq == 0:
reqs = None
else:
assert(len(I) == len(reqs))
taskids = q.add_multiple(B.brickname[I], requires=reqs)
assert(len(taskids) == len(I))
print('Queued', len(taskids), 'bricks')
brick_to_task.update(dict(zip(B.brickname[I], taskids)))
if not (opt.calibs or opt.forced or opt.lsb):
sys.exit(0)
bands = 'grz'
log('Filters:', np.unique(T.filter))
T.cut(np.flatnonzero(np.array([f in bands for f in T.filter])))
log('Cut to', len(T), 'CCDs in filters', bands)
if opt.touching:
allI = set()
for b in B:
wcs = wcs_for_brick(b)
I = ccds_touching_wcs(wcs, T)
log(len(I), 'CCDs for brick', b.brickid, 'RA,Dec (%.2f, %.2f)' % (b.ra, b.dec))
if len(I) == 0:
continue
allI.update(I)
allI = list(allI)
allI.sort()
elif opt.near:
# Roughly brick radius + DECam image radius
radius = 0.35
allI,nil,nil = match_radec(T.ra, T.dec, B.ra, B.dec, radius, nearest=True)
else:
allI = np.arange(len(T))
if opt.write_ccds:
T[allI].writeto(opt.write_ccds)
log('Wrote', opt.write_ccds)
## Be careful here -- T has been cut; we want to write out T.index.
## 'allI' contains indices into T.
if opt.forced:
log('Writing forced-photometry commands to', opt.out)
f = open(opt.out,'w')
log('Total of', len(allI), 'CCDs')
for j,i in enumerate(allI):
expstr = '%08i' % T.expnum[i]
outfn = os.path.join('forced', expstr[:5], expstr,
'decam-%s-%s-forced.fits' %
(expstr, T.ccdname[i]))
imgfn = os.path.join(survey.survey_dir, 'images',
T.image_filename[i].strip())
if (not os.path.exists(imgfn) and
imgfn.endswith('.fz') and
os.path.exists(imgfn[:-3])):
imgfn = imgfn[:-3]
#f.write('python legacypipe/forced_photom_decam.py %s %i DR3 %s\n' %
# (imgfn, T.image_hdu[i], outfn))
f.write('python legacypipe/forced_photom_decam.py --apphot --constant-invvar %i %s DR3 %s\n' %
(T.expnum[i], T.ccdname[i], outfn))
f.close()
log('Wrote', opt.out)
sys.exit(0)
if opt.lsb:
log('Writing LSB commands to', opt.out)
f = open(opt.out,'w')
log('Total of', len(allI), 'CCDs')
for j,i in enumerate(allI):
exp = T.expnum[i]
ext = T.ccdname[i].strip()
outfn = 'lsb/lsb-%s-%s.fits' % (exp, ext)
f.write('python projects/desi/lsb.py --expnum %i --extname %s --out %s -F -n > lsb/lsb-%s-%s.log 2>&1\n' % (exp, ext, outfn, exp, ext))
f.close()
log('Wrote', opt.out)
sys.exit(0)
log('Writing calibs to', opt.out)
f = open(opt.out,'w')
log('Total of', len(allI), 'CCDs')
batch = []
def write_batch(f, batch, cmd):
if cmd is None:
cmd = ''
f.write(cmd + ' '.join(batch) + '\n')
cmd = None
if opt.command:
cmd = 'python legacypipe/run-calib.py '
if opt.opt is not None:
cmd += opt.opt + ' '
for j,i in enumerate(allI):
if opt.delete_sky or opt.delete_pvastrom:
log(j+1, 'of', len(allI))
im = survey.get_image_object(T[i])
if opt.delete_sky and os.path.exists(im.skyfn):
log(' deleting:', im.skyfn)
os.unlink(im.skyfn)
if opt.delete_pvastrom and os.path.exists(im.pvwcsfn):
log(' deleting:', im.pvwcsfn)
os.unlink(im.pvwcsfn)
if opt.check:
log(j+1, 'of', len(allI))
im = survey.get_image_object(T[i])
if not im.run_calibs(im, just_check=True):
log('Calibs for', im.expnum, im.ccdname, im.calname, 'already done')
continue
if opt.command:
s = '%i-%s' % (T.expnum[i], T.ccdname[i])
prefix = 'python legacypipe/run-calib.py ' + opt.opt
#('python legacypipe/run-calib.py --expnum %i --ccdname %s' %
# (T.expnum[i], T.ccdname[i]))
else:
s = '%i' % T.index[i]
prefix = ''
if j < 10:
print('Index', T.index[i], 'expnum', T.expnum[i], 'ccdname', T.ccdname[i],
'filename', T.image_filename[i])
if not opt.nper:
f.write(prefix + s + '\n')
else:
batch.append(s)
if len(batch) >= opt.nper:
write_batch(f, batch, cmd)
batch = []
if opt.check:
f.flush()
if len(batch):
write_batch(f, batch, cmd)
f.close()
log('Wrote', opt.out)
return 0
August 2017 Martin Landriau LBNL
"""
import os
import qdo
import glob
from hashlib import sha256
import sys
nstart = int(sys.argv[1])
nend = int(sys.argv[2])
outdir = "/global/projecta/projectdirs/cosmo/work/legacysurvey/dr6/"
ncoaddall = 0
notractor = []
q = qdo.connect('dr6')
a = q.tasks(state=qdo.Task.SUCCEEDED)
n = len(a)
for i in range(nstart, nend):
brick = a[i].task
subdir = brick[0:3]
fullpath = outdir + "tractor/" + subdir + "/"
filename0 = "brick-" + brick + ".sha256sum"
ncoadd = 0
if (not os.path.isfile(fullpath + filename0)):
notractor.append(filename0)
else:
f = open(outdir + "tractor/" + subdir + "/brick-" + brick +
".sha256sum")
filelist = f.readlines()
for line in filelist:
"""Load bricks from file to the Prefarm qdo queue
"""
from settings import PREFARM_QNAME
import sys, qdo
if len(sys.argv) != 2:
print('Usage python load_queue.py <inputfile>')
exit(1)
with open(sys.argv[1], 'r') as f:
try:
q = qdo.connect(PREFARM_QNAME)
except ValueError:
q = qdo.create(PREFARM_QNAME)
tasks = set(t.task for t in q.tasks())
count = 0
for l in f:
task = l.strip()
if task not in tasks:
q.add(task)
tasks.add(task)
count += 1
print('Added', count, 'tasks to', PREFARM_QNAME)
def main():
"""Main program.
"""
import argparse
parser = argparse.ArgumentParser(
description=
"This script is used to produce lists of CCDs or bricks, for production purposes (building qdo queue, eg)."
)
parser.add_argument('--calibs',
action='store_true',
help='Output CCDs that need to be calibrated.')
parser.add_argument('--nper',
type=int,
default=None,
help='Batch N calibs per line')
parser.add_argument('--forced',
action='store_true',
help='Output forced-photometry commands')
parser.add_argument('--lsb',
action='store_true',
help='Output Low-Surface-Brightness commands')
parser.add_argument('--touching',
action='store_true',
help='Cut to only CCDs touching selected bricks')
parser.add_argument('--near',
action='store_true',
help='Quick cut to only CCDs near selected bricks')
parser.add_argument('--check',
action='store_true',
help='Check which calibrations actually need to run.')
parser.add_argument('--check-coadd',
action='store_true',
help='Check which caoadds actually need to run.')
parser.add_argument('--out',
help='Output filename for calibs, default %(default)s',
default='jobs')
parser.add_argument('--command',
action='store_true',
help='Write out full command-line to run calib')
parser.add_argument('--opt', help='With --command, extra options to add')
parser.add_argument('--maxdec', type=float, help='Maximum Dec to run')
parser.add_argument('--mindec', type=float, help='Minimum Dec to run')
parser.add_argument('--region', help='Region to select')
parser.add_argument('--bricks', help='Set bricks.fits file to load')
parser.add_argument('--ccds', help='Set ccds.fits file to load')
parser.add_argument('--ignore_cuts',
action='store_true',
default=False,
help='no photometric or blacklist cuts')
parser.add_argument('--save_to_fits',
action='store_true',
default=False,
help='save cut brick,ccd to fits table')
parser.add_argument(
'--name',
action='store',
default='dr3',
help='save with this suffix, e.g. refers to ccds table')
parser.add_argument('--delete-sky',
action='store_true',
help='Delete any existing sky calibration files')
parser.add_argument('--delete-pvastrom',
action='store_true',
help='Delete any existing PV WCS calibration files')
parser.add_argument('--write-ccds', help='Write CCDs list as FITS table?')
parser.add_argument(
'--brickq',
type=int,
default=None,
help='Queue only bricks with the given "brickq" value [0 to 3]')
parser.add_argument(
'--brickq-deps',
action='store_true',
default=False,
help='Queue bricks directly using qdo API, setting brickq dependencies'
)
parser.add_argument('--queue',
default='bricks',
help='With --brickq-deps, the QDO queue name to use')
opt = parser.parse_args()
survey = LegacySurveyData()
if opt.bricks is not None:
B = fits_table(opt.bricks)
log('Read', len(B), 'from', opt.bricks)
else:
B = survey.get_bricks()
if opt.ccds is not None:
T = fits_table(opt.ccds)
log('Read', len(T), 'from', opt.ccds)
else:
T = survey.get_ccds()
log(len(T), 'CCDs')
T.index = np.arange(len(T))
if opt.ignore_cuts == False:
I = survey.photometric_ccds(T)
print(len(I), 'CCDs are photometric')
T.cut(I)
I = survey.apply_blacklist(T)
print(len(I), 'CCDs are not blacklisted')
T.cut(I)
print(len(T), 'CCDs remain')
# I,J,d,counts = match_radec(B.ra, B.dec, T.ra, T.dec, 0.2, nearest=True, count=True)
# plt.clf()
# plt.hist(counts, counts.max()+1)
# plt.savefig('bricks.png')
# B.cut(I[counts >= 9])
# plt.clf()
# plt.plot(B.ra, B.dec, 'b.')
# #plt.scatter(B.ra[I], B.dec[I], c=counts)
# plt.savefig('bricks2.png')
# DES Stripe82
#rlo,rhi = 350.,360.
# rlo,rhi = 300., 10.
# dlo,dhi = -6., 4.
# TINY bit
#rlo,rhi = 350.,351.1
#dlo,dhi = 0., 1.1
# EDR+
# 860 bricks
# ~10,000 CCDs
#rlo,rhi = 239,246
#dlo,dhi = 5, 13
# DR1
#rlo,rhi = 0, 360
# part 1
#dlo,dhi = 25, 40
# part 2
#dlo,dhi = 20,25
# part 3
#dlo,dhi = 15,20
# part 4
#dlo,dhi = 10,15
# part 5
#dlo,dhi = 5,10
# the rest
#dlo,dhi = -11, 5
#dlo,dhi = 15,25.5
dlo, dhi = -25, 40
rlo, rhi = 0, 360
# Arjun says 3x3 coverage area is roughly
# RA=240-252 DEC=6-12 (but not completely rectangular)
# COSMOS
#rlo,rhi = 148.9, 151.2
#dlo,dhi = 0.9, 3.5
# A nice well-behaved region (EDR2/3)
# rlo,rhi = 243.6, 244.6
# dlo,dhi = 8.1, 8.6
# 56 bricks, ~725 CCDs
#B.cut((B.ra > 240) * (B.ra < 242) * (B.dec > 5) * (B.dec < 7))
# 240 bricks, ~3000 CCDs
#B.cut((B.ra > 240) * (B.ra < 244) * (B.dec > 5) * (B.dec < 9))
# 535 bricks, ~7000 CCDs
#B.cut((B.ra > 240) * (B.ra < 245) * (B.dec > 5) * (B.dec < 12))
if opt.region in ['test1', 'test2', 'test3', 'test4']:
nm = dict(
test1='2446p115', # weird stuff around bright star
test2='1183p292', # faint sources around bright galaxy
test3='3503p005', # DES
test4='1163p277', # Pollux
)[opt.region]
B.cut(np.flatnonzero(np.array([s == nm for s in B.brickname])))
log('Cut to', len(B), 'bricks')
log(B.ra, B.dec)
dlo, dhi = -90, 90
rlo, rhi = 0, 360
elif opt.region == 'edr':
# EDR:
# 535 bricks, ~7000 CCDs
rlo, rhi = 240, 245
dlo, dhi = 5, 12
elif opt.region == 'edrplus':
rlo, rhi = 235, 248
dlo, dhi = 5, 15
elif opt.region == 'edr-south':
rlo, rhi = 240, 245
dlo, dhi = 5, 10
elif opt.region == 'cosmos1':
# 16 bricks in the core of the COSMOS field.
rlo, rhi = 149.75, 150.75
dlo, dhi = 1.6, 2.6
elif opt.region == 'pristine':
# Stream?
rlo, rhi = 240, 250
dlo, dhi = 10, 15
elif opt.region == 'des':
dlo, dhi = -6., 4.
rlo, rhi = 317., 7.
T.cut(np.flatnonzero(np.array(['CPDES82' in fn for fn in T.cpimage])))
log('Cut to', len(T), 'CCDs with "CPDES82" in filename')
elif opt.region == 'subdes':
rlo, rhi = 320., 360.
dlo, dhi = -1.25, 1.25
elif opt.region == 'northwest':
rlo, rhi = 240, 360
dlo, dhi = 20, 40
elif opt.region == 'north':
rlo, rhi = 120, 240
dlo, dhi = 20, 40
elif opt.region == 'northeast':
rlo, rhi = 0, 120
dlo, dhi = 20, 40
elif opt.region == 'southwest':
rlo, rhi = 240, 360
dlo, dhi = -20, 0
elif opt.region == 'south':
rlo, rhi = 120, 240
dlo, dhi = -20, 0
elif opt.region == 'southeast':
rlo, rhi = 0, 120
dlo, dhi = -20, 0
elif opt.region == 'southsoutheast':
rlo, rhi = 0, 120
dlo, dhi = -20, -10
elif opt.region == 'midwest':
rlo, rhi = 240, 360
dlo, dhi = 0, 20
elif opt.region == 'middle':
rlo, rhi = 120, 240
dlo, dhi = 0, 20
elif opt.region == 'mideast':
rlo, rhi = 0, 120
dlo, dhi = 0, 20
elif opt.region == 'grz':
# Bricks with grz coverage.
# Be sure to use --bricks survey-bricks-in-dr1.fits
# which has_[grz] columns.
B.cut((B.has_g == 1) * (B.has_r == 1) * (B.has_z == 1))
log('Cut to', len(B), 'bricks with grz coverage')
elif opt.region == 'nogrz':
# Bricks without grz coverage.
# Be sure to use --bricks survey-bricks-in-dr1.fits
# which has_[grz] columns.
B.cut(np.logical_not((B.has_g == 1) * (B.has_r == 1) * (B.has_z == 1)))
log('Cut to', len(B), 'bricks withOUT grz coverage')
elif opt.region == 'deep2':
rlo, rhi = 250, 260
dlo, dhi = 30, 35
elif opt.region == 'deep2f3':
rlo, rhi = 351.25, 353.75
dlo, dhi = 0, 0.5
elif opt.region == 'virgo':
rlo, rhi = 185, 190
dlo, dhi = 10, 15
elif opt.region == 'virgo2':
rlo, rhi = 182, 192
dlo, dhi = 8, 18
elif opt.region == 'lsb':
rlo, rhi = 147.2, 147.8
dlo, dhi = -0.4, 0.4
elif opt.region == 'eboss-sgc':
# generous boundaries to make sure get all relevant images
# RA -45 to +45
# Dec -5 to +7
rlo, rhi = 310., 50.
dlo, dhi = -6., 6.
elif opt.region == 'eboss-ngc':
# generous boundaries to make sure get all relevant images
# NGC ELGs
# RA 115 to 175
# Dec 15 to 30
rlo, rhi = 122., 177.
dlo, dhi = 12., 32.
elif opt.region == 'mzls':
dlo, dhi = 30., 90.
elif opt.region == 'dr4-bootes':
# https://desi.lbl.gov/trac/wiki/DecamLegacy/DR4sched
#dlo,dhi = 34., 35.
#rlo,rhi = 209.5, 210.5
dlo, dhi = 33., 36.
rlo, rhi = 216.5, 219.5
if opt.mindec is not None:
dlo = opt.mindec
if opt.maxdec is not None:
dhi = opt.maxdec
if rlo < rhi:
B.cut((B.ra >= rlo) * (B.ra <= rhi) * (B.dec >= dlo) * (B.dec <= dhi))
else: # RA wrap
B.cut(
np.logical_or(B.ra >= rlo, B.ra <= rhi) * (B.dec >= dlo) *
(B.dec <= dhi))
log(len(B), 'bricks in range')
#for name in B.get('brickname'):
#print(name)
B.writeto('bricks-cut.fits')
I, J, d = match_radec(B.ra, B.dec, T.ra, T.dec, survey.bricksize)
keep = np.zeros(len(B), bool)
for i in I:
keep[i] = True
B.cut(keep)
log('Cut to', len(B), 'bricks near CCDs')
plt.clf()
plt.plot(B.ra, B.dec, 'b.')
plt.title('DR3 bricks')
plt.axis([360, 0, np.min(B.dec) - 1, np.max(B.dec) + 1])
plt.savefig('bricks.png')
if opt.brickq is not None:
B.cut(B.brickq == opt.brickq)
log('Cut to', len(B), 'with brickq =', opt.brickq)
if opt.touching:
keep = np.zeros(len(T), bool)
for j in J:
keep[j] = True
T.cut(keep)
log('Cut to', len(T), 'CCDs near bricks')
# Aside -- how many near DR1=1 CCDs?
if False:
T2 = D.get_ccds()
log(len(T2), 'CCDs')
T2.cut(T2.dr1 == 1)
log(len(T2), 'CCDs marked DR1=1')
log(len(B), 'bricks in range')
I, J, d = match_radec(B.ra, B.dec, T2.ra, T2.dec, survey.bricksize)
keep = np.zeros(len(B), bool)
for i in I:
keep[i] = True
B2 = B[keep]
log('Total of', len(B2), 'bricks near CCDs with DR1=1')
for band in 'grz':
Tb = T2[T2.filter == band]
log(len(Tb), 'in filter', band)
I, J, d = match_radec(B2.ra, B2.dec, Tb.ra, Tb.dec,
survey.bricksize)
good = np.zeros(len(B2), np.uint8)
for i in I:
good[i] = 1
B2.set('has_' + band, good)
B2.writeto('survey-bricks-in-dr1.fits')
sys.exit(0)
# sort by dec decreasing
#B.cut(np.argsort(-B.dec))
# RA increasing
B.cut(np.argsort(B.ra))
for b in B:
if opt.check:
fn = 'dr1n/tractor/%s/tractor-%s.fits' % (b.brickname[:3],
b.brickname)
if os.path.exists(fn):
print('Exists:', fn, file=sys.stderr)
continue
if opt.check_coadd:
fn = 'dr1b/coadd/%s/%s/decals-%s-image.jpg' % (
b.brickname[:3], b.brickname, b.brickname)
if os.path.exists(fn):
print('Exists:', fn, file=sys.stderr)
continue
#print(b.brickname)
if opt.save_to_fits:
assert (opt.touching)
# Write cut tables to file
for tab, typ in zip([B, T], ['bricks', 'ccds']):
fn = '%s-%s-cut.fits' % (typ, opt.region)
if os.path.exists(fn):
os.remove(fn)
tab.writeto(fn)
print('Wrote %s' % fn)
# Write text files listing ccd and filename names
nm1, nm2 = 'ccds-%s.txt' % opt.region, 'filenames-%s.txt' % opt.region
if os.path.exists(nm1):
os.remove(nm1)
if os.path.exists(nm2):
os.remove(nm2)
f1, f2 = open(nm1, 'w'), open(nm2, 'w')
fns = list(set(T.get('image_filename')))
for fn in fns:
f2.write('%s\n' % fn.strip())
for ti in T:
f1.write('%s\n' % ti.get('image_filename').strip())
f1.close()
f2.close()
print('Wrote *-names.txt')
if opt.brickq_deps:
import qdo
from legacypipe.survey import on_bricks_dependencies
#... find Queue...
q = qdo.connect(opt.queue, create_ok=True)
print('Connected to QDO queue', opt.queue, q)
brick_to_task = dict()
I = survey.photometric_ccds(T)
print(len(I), 'CCDs are photometric')
T.cut(I)
I = survey.apply_blacklist(T)
print(len(I), 'CCDs are not blacklisted')
T.cut(I)
print(len(T), 'CCDs remaining')
T.wra = T.ra + (T.ra > 180) * -360
wra = rlo - 360
plt.clf()
plt.plot(T.wra, T.dec, 'b.')
ax = [wra, rhi, dlo, dhi]
plt.axis(ax)
plt.title('CCDs')
plt.savefig('q-ccds.png')
B.wra = B.ra + (B.ra > 180) * -360
# this slight overestimate (for DECam images) is fine
radius = 0.3
Iccds = match_radec(B.ra, B.dec, T.ra, T.dec, radius, indexlist=True)
ikeep = []
for ib, (b, Iccd) in enumerate(zip(B, Iccds)):
if Iccd is None or len(Iccd) == 0:
print('No matched CCDs to brick', b.brickname)
continue
wcs = wcs_for_brick(b)
cI = ccds_touching_wcs(wcs, T[np.array(Iccd)])
print(len(cI), 'CCDs touching brick', b.brickname)
if len(cI) == 0:
continue
ikeep.append(ib)
B.cut(np.array(ikeep))
print('Cut to', len(B), 'bricks touched by CCDs')
for brickq in range(4):
I = np.flatnonzero(B.brickq == brickq)
print(len(I), 'bricks with brickq =', brickq)
J = np.flatnonzero(B.brickq < brickq)
preB = B[J]
reqs = []
if brickq > 0:
for b in B[I]:
# find brick dependencies
brickdeps = on_bricks_dependencies(b, survey, bricks=preB)
# convert to task ids
taskdeps = [
brick_to_task.get(b.brickname, None) for b in brickdeps
]
# If we dropped a dependency brick from a previous brickq because
# of no overlapping CCDs, it won't appear in the brick_to_task map.
taskdeps = [t for t in taskdeps if t is not None]
reqs.append(taskdeps)
plt.clf()
plt.plot(B.wra, B.dec, '.', color='0.5')
plt.plot(B.wra[I], B.dec[I], 'b.')
plt.axis(ax)
plt.title('Bricks: brickq=%i' % brickq)
plt.savefig('q-bricks-%i.png' % brickq)
# submit to qdo queue
print('Queuing', len(B[I]), 'bricks')
if brickq == 0:
reqs = None
else:
assert (len(I) == len(reqs))
taskids = q.add_multiple(B.brickname[I], requires=reqs)
assert (len(taskids) == len(I))
print('Queued', len(taskids), 'bricks')
brick_to_task.update(dict(zip(B.brickname[I], taskids)))
if not (opt.calibs or opt.forced or opt.lsb):
sys.exit(0)
bands = 'grz'
log('Filters:', np.unique(T.filter))
T.cut(np.flatnonzero(np.array([f in bands for f in T.filter])))
log('Cut to', len(T), 'CCDs in filters', bands)
if opt.touching:
allI = set()
for b in B:
wcs = wcs_for_brick(b)
I = ccds_touching_wcs(wcs, T)
log(len(I), 'CCDs for brick', b.brickid,
'RA,Dec (%.2f, %.2f)' % (b.ra, b.dec))
if len(I) == 0:
continue
allI.update(I)
allI = list(allI)
allI.sort()
elif opt.near:
# Roughly brick radius + DECam image radius
radius = 0.35
allI, nil, nil = match_radec(T.ra,
T.dec,
B.ra,
B.dec,
radius,
nearest=True)
else:
allI = np.arange(len(T))
if opt.write_ccds:
T[allI].writeto(opt.write_ccds)
log('Wrote', opt.write_ccds)
## Be careful here -- T has been cut; we want to write out T.index.
## 'allI' contains indices into T.
if opt.forced:
log('Writing forced-photometry commands to', opt.out)
f = open(opt.out, 'w')
log('Total of', len(allI), 'CCDs')
for j, i in enumerate(allI):
expstr = '%08i' % T.expnum[i]
outfn = os.path.join(
'forced', expstr[:5], expstr,
'decam-%s-%s-forced.fits' % (expstr, T.ccdname[i]))
imgfn = os.path.join(survey.survey_dir, 'images',
T.image_filename[i].strip())
if (not os.path.exists(imgfn) and imgfn.endswith('.fz')
and os.path.exists(imgfn[:-3])):
imgfn = imgfn[:-3]
#f.write('python legacypipe/forced_photom_decam.py %s %i DR3 %s\n' %
# (imgfn, T.image_hdu[i], outfn))
f.write(
'python legacypipe/forced_photom_decam.py --apphot --constant-invvar %i %s DR3 %s\n'
% (T.expnum[i], T.ccdname[i], outfn))
f.close()
log('Wrote', opt.out)
sys.exit(0)
if opt.lsb:
log('Writing LSB commands to', opt.out)
f = open(opt.out, 'w')
log('Total of', len(allI), 'CCDs')
for j, i in enumerate(allI):
exp = T.expnum[i]
ext = T.ccdname[i].strip()
outfn = 'lsb/lsb-%s-%s.fits' % (exp, ext)
f.write(
'python projects/desi/lsb.py --expnum %i --extname %s --out %s -F -n > lsb/lsb-%s-%s.log 2>&1\n'
% (exp, ext, outfn, exp, ext))
f.close()
log('Wrote', opt.out)
sys.exit(0)
log('Writing calibs to', opt.out)
f = open(opt.out, 'w')
log('Total of', len(allI), 'CCDs')
batch = []
def write_batch(f, batch, cmd):
if cmd is None:
cmd = ''
f.write(cmd + ' '.join(batch) + '\n')
cmd = None
if opt.command:
cmd = 'python legacypipe/run-calib.py '
if opt.opt is not None:
cmd += opt.opt + ' '
for j, i in enumerate(allI):
if opt.delete_sky or opt.delete_pvastrom:
log(j + 1, 'of', len(allI))
im = survey.get_image_object(T[i])
if opt.delete_sky and os.path.exists(im.skyfn):
log(' deleting:', im.skyfn)
os.unlink(im.skyfn)
if opt.delete_pvastrom and os.path.exists(im.pvwcsfn):
log(' deleting:', im.pvwcsfn)
os.unlink(im.pvwcsfn)
if opt.check:
log(j + 1, 'of', len(allI))
im = survey.get_image_object(T[i])
if not im.run_calibs(im, just_check=True):
log('Calibs for', im.expnum, im.ccdname, im.calname,
'already done')
continue
if opt.command:
s = '%i-%s' % (T.expnum[i], T.ccdname[i])
prefix = 'python legacypipe/run-calib.py ' + opt.opt
#('python legacypipe/run-calib.py --expnum %i --ccdname %s' %
# (T.expnum[i], T.ccdname[i]))
else:
s = '%i' % T.index[i]
prefix = ''
if j < 10:
print('Index', T.index[i], 'expnum', T.expnum[i], 'ccdname',
T.ccdname[i], 'filename', T.image_filename[i])
if not opt.nper:
f.write(prefix + s + '\n')
else:
batch.append(s)
if len(batch) >= opt.nper:
write_batch(f, batch, cmd)
batch = []
if opt.check:
f.flush()
if len(batch):
write_batch(f, batch, cmd)
f.close()
log('Wrote', opt.out)
return 0
