def queue():
if False:
survey = LegacySurveyData()
ccds = survey.get_ccds()
bricks = survey.get_bricks()
print(len(bricks), 'bricks')
print(len(ccds), 'CCDs')
bricks.cut((bricks.dec >= -30) * (bricks.dec <= 30))
print(len(bricks), 'in Dec [-30, +30]')
I = survey.photometric_ccds(ccds)
ccds.cut(I)
print(len(ccds), 'pass photometric cut')
I, J, d = match_radec(bricks.ra,
bricks.dec,
ccds.ra,
ccds.dec,
0.5,
nearest=True)
print(len(I), 'bricks with CCDs nearby')
bricks.cut(I)
bricknames = bricks.brickname
else:
# DR7: use Martin's list of bricks w/ CCD coverage
f = open('nccds.dat')
bricknames = []
for line in f.readlines():
words = line.strip().split(' ')
brick = words[0]
nccd = int(words[1])
if nccd > 0:
bricknames.append(brick)
# qdo
bb = bricknames
while len(bb):
print(' '.join(bb[:100]))
bb = bb[100:]
return
mp = multiproc(16)
N = len(bricks)
args = [(brick, i, N, plots, {}) for i, brick in enumerate(bricks)]
mp.map(run_one_brick, args)
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(
'--byexp',
action='store_true',
default=False,
help='Run one whole exposure per job (not one CCD per job)')
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('--stage', help='Stage image files to given directory')
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-coadd',
action='store_true',
help='Check which coadds 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('--maxra', type=float, help='Maximum RA to run')
parser.add_argument('--minra', type=float, help='Minimum RA to run')
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 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('--write-ccds', help='Write CCDs list as FITS table?')
parser.add_argument('--nccds',
action='store_true',
default=False,
help='Prints number of CCDs per brick')
parser.add_argument('--bands',
default='g,r,z',
help='Set bands to keep: comma-separated list.')
opt = parser.parse_args()
want_ccds = (opt.calibs or opt.forced or opt.lsb)
want_bricks = not want_ccds
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()
log('Bricks Dec range:', B.dec.min(), B.dec.max())
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:
log('Applying CCD cuts...')
if 'ccd_cuts' in T.columns():
T.cut(T.ccd_cuts == 0)
log(len(T), 'CCDs survive cuts')
bands = opt.bands.split(',')
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)
log('CCDs Dec range:', T.dec.min(), T.dec.max())
# 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 == 'dr8-decam':
rlo, rhi = 0, 360
dlo, dhi = -70, 40
log('DR8-DECam region')
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 == 'deep2f2':
rlo, rhi = 251.4, 254.4
dlo, dhi = 34.6, 35.3
elif opt.region == 'deep2f3':
rlo, rhi = 351.25, 353.75
dlo, dhi = 0, 0.5
elif opt.region == 'deep3':
rlo, rhi = 214, 216
dlo, dhi = 52.25, 53.25
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 == 'coma':
# van Dokkum et al Coma cluster ultra-diffuse galaxies: 3x3 field centered on Coma cluster
rc, dc = 195., 28.
dd = 1.5
cosdec = np.cos(np.deg2rad(dc))
rlo, rhi = rc - dd / cosdec, rc + dd / cosdec
dlo, dhi = dc - dd, dc + dd
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.
rlo, rhi = 126., 168.
dlo, dhi = 18., 33.
elif opt.region == 'mzls':
dlo, dhi = -10., 90. # -10: pull in Stripe 82 data too
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
elif opt.region == 'des-sn-x3':
#rlo,rhi = 36., 37.
#dlo,dhi = -5., -4.
rlo, rhi = 36., 36.5
dlo, dhi = -4.5, -4.
elif opt.region == 'ngc2632':
# open cluster
rlo, rhi = 129.0, 131.0
dlo, dhi = 19.0, 20.5
elif opt.region == 'dr8sky':
rlo, rhi = 35.0, 37.0
dlo, dhi = -3.0, -1.0
# ADM DR8 test regions, see, e.g.:
# https://desi.lbl.gov/trac/wiki/DecamLegacy/DR8#Testregions
elif opt.region == 'dr8-test-s82':
rlo, rhi = 0, 45
dlo, dhi = -1.25, 1.25
elif opt.region == 'dr8-test-hsc-sgc':
rlo, rhi = 30, 40
dlo, dhi = -6.5, -1.25
elif opt.region == 'dr8-test-hsc-ngc':
rlo, rhi = 177.5, 182.5
dlo, dhi = -1, 1
elif opt.region == 'dr8-test-edr':
rlo, rhi = 240, 245
dlo, dhi = 5, 12
elif opt.region == 'dr8-test-hsc-north':
rlo, rhi = 240, 250
dlo, dhi = 42, 45
elif opt.region == 'dr8-test-deep2-egs':
rlo, rhi = 213, 216.5
dlo, dhi = 52, 54
elif opt.region == 'dr8-test-overlap':
rlo, rhi = 132, 140.5
dlo, dhi = 31.5, 35
if opt.mindec is not None:
dlo = opt.mindec
if opt.maxdec is not None:
dhi = opt.maxdec
if opt.minra is not None:
rlo = opt.minra
if opt.maxra is not None:
rhi = opt.maxra
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; cut Dec range', B.dec.min(), B.dec.max())
#for name in B.get('brickname'):
# print(name)
#B.writeto('bricks-cut.fits')
bricksize = 0.25
# A bit more than 0.25-degree brick radius + Bok image radius ~ 0.57
search_radius = 1.05 * np.sqrt(2.) * (bricksize +
(0.455 * 4096 / 3600.)) / 2.
log(len(T), 'CCDs')
log(len(B), 'Bricks')
I, J, d = match_radec(B.ra,
B.dec,
T.ra,
T.dec,
search_radius,
nearest=True)
B.cut(I)
log('Cut to', len(B), 'bricks near CCDs')
log('Bricks Dec range:', B.dec.min(), B.dec.max())
# 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.touching:
I, J, d = match_radec(T.ra,
T.dec,
B.ra,
B.dec,
search_radius,
nearest=True)
# list the ones that will be cut
# drop = np.ones(len(T))
# drop[I] = False
# for i in np.flatnonzero(drop):
# from astrometry.util.starutil_numpy import degrees_between
# dists = degrees_between(B.ra, B.dec, T.ra[i], T.dec[i])
# mindist = min(dists)
# print('Dropping:', T.ra[i], T.dec[i], 'min dist', mindist, 'search_radius', search_radius)
T.cut(I)
log('Cut to', len(T), 'CCDs near bricks')
# sort by RA increasing
B.cut(np.argsort(B.ra))
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)
log('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()
# log('Wrote *-names.txt')
if opt.touching:
if want_bricks:
# Shortcut the list of bricks that are definitely touching CCDs --
# a brick-ccd pair within this radius must be touching.
closest_radius = 0.95 * (bricksize + 0.262 * 2048 / 3600.) / 2.
J1, nil, nil = match_radec(B.ra,
B.dec,
T.ra,
T.dec,
closest_radius,
nearest=True)
log(len(J1), 'of', len(B), 'bricks definitely touch CCDs')
tocheck = np.ones(len(B), bool)
tocheck[J1] = False
J2 = []
for j in np.flatnonzero(tocheck):
b = B[j]
wcs = wcs_for_brick(b)
I = ccds_touching_wcs(wcs, T)
log(len(I), 'CCDs for brick', b.brickname)
if len(I) == 0:
continue
J2.append(j)
J = np.hstack((J1, J2))
J = np.sort(J).astype(int)
B.cut(J)
log('Cut to', len(B), 'bricks touching CCDs')
else:
J = []
allI = set()
for j, b in enumerate(B):
wcs = wcs_for_brick(b)
I = ccds_touching_wcs(wcs, T)
log(len(I), 'CCDs for brick', b.brickname)
if len(I) == 0:
continue
allI.update(I)
J.append(j)
allI = list(allI)
allI.sort()
B.cut(np.array(J))
log('Cut to', len(B), 'bricks touching CCDs')
elif opt.near:
# Find CCDs near bricks
allI, nil, nil = match_radec(T.ra,
T.dec,
B.ra,
B.dec,
search_radius,
nearest=True)
# Find bricks near CCDs
J, nil, nil = match_radec(B.ra,
B.dec,
T.ra,
T.dec,
search_radius,
nearest=True)
B.cut(J)
log('Cut to', len(B), 'bricks near CCDs')
else:
allI = np.arange(len(T))
if opt.byexp:
nil, eI = np.unique(T.expnum[allI], return_index=True)
allI = allI[eI]
print('Cut to', len(allI), 'expnums')
if opt.nccds:
from queue import Queue
from threading import Thread
log('Checking number of CCDs per brick')
def worker():
while True:
i = q.get()
if i is None:
break
b = B[i]
wcs = wcs_for_brick(b)
I = ccds_touching_wcs(wcs, T)
log(b.brickname, len(I))
q.task_done()
q = Queue()
num_threads = 24
threads = []
for i in range(num_threads):
t = Thread(target=worker)
t.start()
threads.append(t)
for i in range(len(B)):
q.put(i)
q.join()
for i in range(num_threads):
q.put(None)
for t in threads:
t.join()
if opt.write_ccds:
T[allI].writeto(opt.write_ccds)
log('Wrote', opt.write_ccds)
if want_bricks:
# Print the list of bricks and exit.
for b in B:
print(b.brickname)
if opt.save_to_fits:
B.writeto('bricks-%s-touching.fits' % opt.region)
if not want_ccds:
sys.exit(0)
## Be careful here -- T has been cut; we want to write out T.index.
## 'allI' contains indices into T.
if opt.stage is not None:
cmd_pat = 'rsync -LRarv %s %s'
fns = set()
for iccd in allI:
im = survey.get_image_object(T[iccd])
fns.update([
im.imgfn, im.wtfn, im.dqfn, im.psffn, im.merged_psffn,
im.merged_splineskyfn, im.splineskyfn
])
for i, fn in enumerate(fns):
print('File', i + 1, 'of', len(fns), ':', fn)
if not os.path.exists(fn):
print('No such file:', fn)
continue
base = survey.get_survey_dir()
if base.endswith('/'):
base = base[:-1]
rel = os.path.relpath(fn, base)
dest = os.path.join(opt.stage, rel)
print('Dest:', dest)
if os.path.exists(dest):
print('Exists:', dest)
continue
cmd = cmd_pat % ('%s/./%s' % (base, rel), opt.stage)
print(cmd)
rtn = os.system(cmd)
assert (rtn == 0)
sys.exit(0)
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]
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]
outfn = os.path.join(
expstr[:5], expstr, 'forced-%s-%s-%s.fits' %
(T.camera[i].strip(), expstr, T.ccdname[i]))
f.write(
'python legacypipe/forced_photom.py --apphot --derivs --catalog-dir /project/projectdirs/cosmo/data/legacysurvey/dr7/ %i %s forced/%s\n'
% (T.expnum[i], T.ccdname[i], outfn))
f.close()
log('Wrote', opt.out)
fn = 'forced-ccds.fits'
T[allI].writeto(fn)
print('Wrote', fn)
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 legacyanalysis/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:
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.command:
if opt.byexp:
s = '--expnum %i' % (T.expnum[i])
else:
s = '%i-%s' % (T.expnum[i], T.ccdname[i])
prefix = 'python legacypipe/run-calib.py '
if opt.opt is not None:
prefix = prefix + 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 len(batch):
write_batch(f, batch, cmd)
f.close()
log('Wrote', opt.out)
return 0
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
def make_pickle_file(pfn, derivs=False, agn=False):
survey = LegacySurveyData()
ccds = survey.get_ccds()
brickname = '0364m042'
bricks = survey.get_bricks()
brick = bricks[bricks.brickname == brickname][0]
print('Brick', brick)
catfn = survey.find_file('tractor', brick=brickname)
print('Reading catalog from', catfn)
cat = fits_table(catfn)
print(len(cat), 'catalog entries')
cat.cut(cat.brick_primary)
print(len(cat), 'brick primary')
'''
BRICKNAM BRICKID BRICKQ BRICKROW BRICKCOL RA DEC
0364m042 306043 3 343 145 36.4255910987483 -4.25000000000000
RA1 RA2 DEC1 DEC2
36.3004172461752 36.5507649513213 -4.37500000000000 -4.12500000000000
'''
rlo, rhi = brick.ra1, brick.ra2
dlo, dhi = brick.dec1, brick.dec2
#rlo,rhi = 36.4, 36.5
#dlo,dhi = -4.4, -4.3
ra, dec = (rlo + rhi) / 2., (dlo + dhi) / 2.
## optional
cat.cut(
(cat.ra > rlo) * (cat.ra < rhi) * (cat.dec > dlo) * (cat.dec < dhi))
print('Cut to', len(cat), 'catalog objects in RA,Dec box')
lightcurves = dict([((brickname, oid), []) for oid in cat.objid])
# close enough to equator to ignore cos(dec)
dra = 4096 / 2. * 0.262 / 3600.
ddec = 2048 / 2. * 0.262 / 3600.
ccds.cut((np.abs(ccds.ra - ra) <
(rhi - rlo) / 2. + dra) * (np.abs(ccds.dec - dec) <
(dhi - dlo) / 2. + ddec))
print('Cut to', len(ccds), 'CCDs overlapping brick')
### HACK
#ccds = ccds[:50]
for i, (expnum, ccdname) in enumerate(zip(ccds.expnum, ccds.ccdname)):
ee = '%08i' % expnum
flavor = 'vanilla'
cols = [
'brickname', 'objid', 'camera', 'expnum', 'ccdname', 'mjd',
'filter', 'flux', 'flux_ivar'
]
if derivs:
flavor = 'derivs'
cols.extend(
['flux_dra', 'flux_ddec', 'flux_dra_ivar', 'flux_ddec_ivar'])
if agn:
flavor = 'agn'
cols.extend(['flux_agn', 'flux_agn_ivar'])
fn = 'forced/%s/%s/%s/forced-decam-%s-%s.fits' % (flavor, ee[:5], ee,
ee, ccdname)
if not os.path.exists(fn):
print('WARNING: missing:', fn)
continue
T = fits_table(fn)
print(i + 1, 'of', len(ccds), ':', len(T), 'in', fn)
T.cut(T.brickname == brickname)
print(len(T), 'in brick', brickname)
found = 0
for t in T: #oid,expnum,ccdname,mjd,filter,flux,fluxiv in zip(T.objid, T.expnum, T.ccdname, T.mjd, T.filter, T.flux, T.flux_ivar):
lc = lightcurves.get((t.brickname, t.objid), None)
if lc is None:
continue
found += 1
#lc.append((expnum, ccdname, mjd, filter, flux, fluxiv))
lc.append([t.get(c) for c in cols])
print('Matched', found, 'sources to light curves')
#pickle_to_file(lightcurves, pfn)
ll = {}
for k, v in lightcurves.items():
if len(v) == 0:
continue
T = fits_table()
# T.expnum = np.array([vv[0] for vv in v])
# T.ccdname= np.array([vv[1] for vv in v])
# T.mjd = np.array([vv[2] for vv in v])
# T.filter = np.array([vv[3] for vv in v])
# T.flux = np.array([vv[4] for vv in v])
# T.fluxiv = np.array([vv[5] for vv in v])
for i, c in enumerate(cols):
T.set(c, np.array([vv[i] for vv in v]))
ll[k] = T
pickle_to_file(ll, pfn)
'--outdir',
help='Set output base directory',
default='tractor2')
parser.add_argument('--north',
help='Set Dec limits for Northern Cap surveys',
action='store_true')
parser.add_argument(
'--overwrite',
action='store_true',
default=False,
help='Overwrite existing output files? Default is to skip them.')
opt = parser.parse_args()
survey = LegacySurveyData(survey_dir=opt.survey_dir, output_dir=opt.outdir)
bricks = survey.get_bricks()
if opt.north:
bricks.cut(bricks.dec > 30)
else:
bricks.cut(bricks.dec > -25)
bricks.cut(bricks.dec < 40)
## HACK -- cut to COSMOS
#bricks.cut((np.abs(bricks.ra - 150) < 2) *
# (np.abs(bricks.dec - 2.2) < 2))
#print('Cut to', len(bricks), 'bricks near COSMOS')
# Note to self: don't bother multiprocessing this; I/O bound
for brick in bricks.brickname:
add_depth_tag(survey, brick, overwrite=opt.overwrite)
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
parser = argparse.ArgumentParser()
parser.add_argument('--survey-dir', type=str, default=None,
help='Override the $LEGACY_SURVEY_DIR environment variable')
parser.add_argument('-d', '--outdir', help='Set output base directory',
default='tractor2')
parser.add_argument('--north', help='Set Dec limits for Northern Cap surveys',
action='store_true')
parser.add_argument('--overwrite', action='store_true', default=False,
help='Overwrite existing output files? Default is to skip them.')
opt = parser.parse_args()
survey = LegacySurveyData(survey_dir=opt.survey_dir,
output_dir=opt.outdir)
bricks = survey.get_bricks()
if opt.north:
bricks.cut(bricks.dec > 30)
else:
bricks.cut(bricks.dec > -25)
bricks.cut(bricks.dec < 40)
## HACK -- cut to COSMOS
#bricks.cut((np.abs(bricks.ra - 150) < 2) *
# (np.abs(bricks.dec - 2.2) < 2))
#print('Cut to', len(bricks), 'bricks near COSMOS')
# Note to self: don't bother multiprocessing this; I/O bound
for brick in bricks.brickname:
add_depth_tag(survey, brick, overwrite=opt.overwrite)