def add_depth_tag(decals, brick, outdir, overwrite=False):
outfn = os.path.join(outdir, 'tractor', brick[:3], 'tractor-%s.fits' % brick)
if os.path.exists(outfn) and not overwrite:
print 'Exists:', outfn
return
fn = decals.find_file('tractor', brick=brick)
if not os.path.exists(fn):
print 'Does not exist:', fn
return
T = fits_table(fn, lower=False)
primhdr = fitsio.read_header(fn)
hdr = fitsio.read_header(fn, ext=1)
print 'Read', len(T), 'from', fn
T.decam_depth = np.zeros((len(T), len(decals.allbands)), np.float32)
T.decam_galdepth = np.zeros((len(T), len(decals.allbands)), np.float32)
bands = 'grz'
ibands = [decals.index_of_band(b) for b in bands]
ix = np.clip(np.round(T.bx).astype(int), 0, 3599)
iy = np.clip(np.round(T.by).astype(int), 0, 3599)
for iband,band in zip(ibands, bands):
fn = decals.find_file('depth', brick=brick, band=band)
if os.path.exists(fn):
print 'Reading', fn
img = fitsio.read(fn)
T.decam_depth[:,iband] = img[iy, ix]
fn = decals.find_file('galdepth', brick=brick, band=band)
if os.path.exists(fn):
print 'Reading', fn
img = fitsio.read(fn)
T.decam_galdepth[:,iband] = img[iy, ix]
outfn = os.path.join(outdir, 'tractor', brick[:3], 'tractor-%s.fits' % brick)
trymakedirs(outfn, dir=True)
for s in [
'Data product of the DECam Legacy Survey (DECaLS)',
'Full documentation at http://legacysurvey.org',
]:
primhdr.add_record(dict(name='COMMENT', value=s, comment=s))
# print 'Header:', hdr
# T.writeto(outfn, header=hdr, primheader=primhdr)
# Yuck, all this to get the units right
tmpfn = outfn + '.tmp'
fits = fitsio.FITS(tmpfn, 'rw', clobber=True)
fits.write(None, header=primhdr)
cols = T.get_columns()
units = []
for i in range(1, len(cols)+1):
u = hdr.get('TUNIT%i' % i, '')
units.append(u)
# decam_depth units
fluxiv = '1/nanomaggy^2'
units[-2] = fluxiv
units[-1] = fluxiv
fits.write([T.get(c) for c in cols], names=cols, header=hdr, units=units)
fits.close()
os.rename(tmpfn, outfn)
print 'Wrote', outfn
def copy_files_to_cache(fns):
for fn in fns:
cachefn = fn.replace(survey.survey_dir, survey.cache_dir)
if not cachefn.startswith(survey.cache_dir):
print('Skipping', fn)
continue
outdir = os.path.dirname(cachefn)
trymakedirs(outdir)
print('Copy', fn)
print(' to', cachefn)
shutil.copyfile(fn, cachefn)
def merge_splinesky(survey, expnum, C, skyoutfn, opt):
skies = []
imobjs = []
Cgood = []
for ccd in C:
im = survey.get_image_object(ccd)
fn = im.skyfn
if not os.path.exists(fn):
print('File not found:', fn)
if opt.all_found:
return 0
continue
imobjs.append(im)
Cgood.append(ccd)
for ccd, im in zip(Cgood, imobjs):
fn = im.skyfn
print('Reading', fn)
T = None
try:
T = fits_table(fn)
except KeyboardInterrupt as e:
raise e
except:
print('Failed to read file', fn, ':', sys.exc_info()[1])
if T is not None:
skies.append(T)
if len(skies) == 0:
return
T = fits_table()
T.gridw = np.array([t.gridvals[0].shape[1] for t in skies])
T.gridh = np.array([t.gridvals[0].shape[0] for t in skies])
padded = pad_arrays([t.gridvals[0] for t in skies])
T.gridvals = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.xgrid[0] for t in skies])
T.xgrid = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.ygrid[0] for t in skies])
T.ygrid = np.concatenate([[p] for p in padded])
cols = skies[0].columns()
for c in ['gridvals', 'xgrid', 'ygrid', 'gridw', 'gridh']:
cols.remove(c)
T.add_columns_from(merge_tables(skies, columns=cols))
fn = skyoutfn
trymakedirs(fn, dir=True)
tmpfn = os.path.join(os.path.dirname(fn), 'tmp-' + os.path.basename(fn))
T.writeto(tmpfn)
os.rename(tmpfn, fn)
print('Wrote', fn)
return 1
def run_se(self, surveyname, imgfn, maskfn):
from astrometry.util.file import trymakedirs
# grab header values...
primhdr = self.read_image_primary_header()
try:
magzp = float(primhdr['MAGZERO'])
except:
magzp = 25.
seeing = self.pixscale * self.fwhm
print('FWHM', self.fwhm, 'pix')
print('pixscale', self.pixscale, 'arcsec/pix')
print('Seeing', seeing, 'arcsec')
print('magzp', magzp)
sedir = self.survey.get_se_dir()
trymakedirs(self.sefn, dir=True)
if surveyname != '90prime':
cmd = ' '.join([
'sex',
'-c',
os.path.join(sedir, surveyname + '.se'),
'-SEEING_FWHM %f' % seeing,
'-PARAMETERS_NAME',
os.path.join(sedir, surveyname + '.param'),
'-STARNNW_NAME',
os.path.join(sedir, 'default.nnw'),
'-PIXEL_SCALE 0',
# SE has a *bizarre* notion of "sigma"
'-DETECT_THRESH 1.0',
'-ANALYSIS_THRESH 1.0',
'-MAG_ZEROPOINT %f' % magzp,
'-FLAG_IMAGE %s' % maskfn,
'-FILTER_NAME %s' % os.path.join(sedir, 'gauss_5.0_9x9.conv'),
'-CATALOG_NAME %s %s' % (self.sefn, imgfn)
])
else:
cmd = ' '.join([
'sex', '-c',
os.path.join(sedir, surveyname + '.se'), '-PARAMETERS_NAME',
os.path.join(sedir, surveyname + '.param'), '-STARNNW_NAME',
os.path.join(sedir, 'default.nnw'),
'-FILTER_NAME %s' % os.path.join(sedir, surveyname + '.conv'),
'-PHOT_APERTURES 7.5,15.0,22.0',
'-CATALOG_NAME %s %s' % (self.sefn, imgfn)
])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
def merge_psfex(survey, expnum, C, psfoutfn, opt):
psfex = []
imobjs = []
Cgood = []
fns = []
for ccd in C:
im = survey.get_image_object(ccd)
for fn in [im.psffn, im.old_single_psffn]:
if os.path.exists(fn):
break
if not os.path.exists(fn):
print('File not found:', fn)
if opt.all_found:
return 0
continue
imobjs.append(im)
Cgood.append(ccd)
fns.append(fn)
for fn, ccd, im in zip(fns, Cgood, imobjs):
print('Reading', fn)
T = fits_table(fn)
cols = T.get_columns()
if not 'plver' in cols:
from legacypipe.image import psfex_single_to_merged
T = psfex_single_to_merged(fn, ccd.expnum, ccd.ccdname)
for k in ['plver', 'procdate', 'plprocid']:
T.set(k, np.array([getattr(ccd, k)]))
psfex.append(T)
if len(psfex) == 0:
return
padded = pad_arrays([p.psf_mask[0] for p in psfex])
cols = psfex[0].columns()
cols.remove('psf_mask')
T = merge_tables(psfex, columns=cols)
T.psf_mask = np.concatenate([[p] for p in padded])
fn = psfoutfn
trymakedirs(fn, dir=True)
tmpfn = os.path.join(os.path.dirname(fn), 'tmp-' + os.path.basename(fn))
T.writeto(tmpfn)
os.rename(tmpfn, fn)
print('Wrote', fn)
return 1
def run_se(self, imgfn, maskfn):
from astrometry.util.file import trymakedirs
sedir = self.survey.get_se_dir()
trymakedirs(self.sefn, dir=True)
# We write the SE catalog to a temp file then rename, to avoid
# partially-written outputs.
from legacypipe.survey import create_temp
import fitsio
tmpmaskfn = create_temp(suffix='.fits')
# # The test.mask file has 1 for good pix, 0 for bad... invert for SE
goodpix = fitsio.read(maskfn)
fitsio.write(tmpmaskfn, (1 - goodpix).astype(np.uint8), clobber=True)
#tmpmaskfn = maskfn
tmpfn = os.path.join(os.path.dirname(self.sefn),
'tmp-' + os.path.basename(self.sefn))
cmd = ' '.join([
'sex',
'-c',
os.path.join(sedir, self.camera + '.se'),
'-PARAMETERS_NAME',
os.path.join(sedir, self.camera + '.param'),
'-FILTER_NAME %s' % os.path.join(sedir, self.camera + '.conv'),
'-FLAG_IMAGE %s' % tmpmaskfn,
'-CATALOG_NAME %s' % tmpfn,
'-SEEING_FWHM %f' % 0.8,
'-FITS_UNSIGNED N',
#'-VERBOSE_TYPE FULL',
#'-PIXEL_SCALE 0.185',
#'-SATUR_LEVEL 100000',
imgfn
])
print(cmd)
rtn = os.system(cmd)
if rtn:
raise RuntimeError('Command failed: ' + cmd)
os.rename(tmpfn, self.sefn)
os.unlink(tmpmaskfn)
def run_psfex(self, surveyname):
from astrometry.util.file import trymakedirs
from legacypipe.survey import get_git_version
sedir = self.survey.get_se_dir()
trymakedirs(self.psffn, dir=True)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
verstr = get_git_version()
cmds = [
'psfex -c %s -PSF_DIR %s %s' %
(os.path.join(sedir, surveyname + '.psfex'),
os.path.dirname(self.psffn), self.sefn),
'modhead %s LEGPIPEV %s "legacypipe git version"' %
(self.psffn, verstr),
'modhead %s PLVER %s "CP ver of image file"' % (self.psffn, plver)
]
for cmd in cmds:
print(cmd)
rtn = os.system(cmd)
if rtn:
raise RuntimeError('Command failed: %s: return value: %i' %
(cmd, rtn))
def run_calibs(self,
pvastrom=True,
psfex=True,
sky=True,
se=False,
funpack=False,
fcopy=False,
use_mask=True,
force=False,
just_check=False,
git_version=None,
splinesky=False):
'''
Run calibration pre-processing steps.
Parameters
----------
just_check: boolean
If True, returns True if calibs need to be run.
'''
from .common import (create_temp, get_version_header, get_git_version)
#for fn in [self.pvwcsfn, self.sefn, self.psffn, self.skyfn, self.splineskyfn]:
# print('exists?', os.path.exists(fn), fn)
if psfex and os.path.exists(self.psffn) and (not force):
# Sometimes SourceExtractor gets interrupted or something and
# writes out 0 detections. Then PsfEx fails but in a way that
# an output file is still written. Try to detect & fix this
# case.
# Check the PsfEx output file for POLNAME1
hdr = fitsio.read_header(self.psffn, ext=1)
if hdr.get('POLNAME1', None) is None:
print('Did not find POLNAME1 in PsfEx header', self.psffn,
'-- deleting')
os.unlink(self.psffn)
else:
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
# Check SourceExtractor catalog for size = 0
fn = self.sefn
T = fits_table(fn, hdu=2)
print('Read', len(T), 'sources from SE catalog', fn)
if T is None or len(T) == 0:
print('SourceExtractor catalog', fn,
'has no sources -- deleting')
try:
os.unlink(fn)
except:
pass
if os.path.exists(self.sefn):
se = False
if se:
funpack = True
if pvastrom and os.path.exists(self.pvwcsfn) and (not force):
fn = self.pvwcsfn
if os.path.exists(fn):
try:
wcs = Sip(fn)
except:
print('Failed to read PV-SIP file', fn, '-- deleting')
os.unlink(fn)
if os.path.exists(fn):
pvastrom = False
if sky and (not force) and (
(os.path.exists(self.skyfn) and not splinesky) or
(os.path.exists(self.splineskyfn) and splinesky)):
fn = self.skyfn
if splinesky:
fn = self.splineskyfn
if os.path.exists(fn):
try:
hdr = fitsio.read_header(fn)
except:
print('Failed to read sky file', fn, '-- deleting')
os.unlink(fn)
if os.path.exists(fn):
print('File', fn, 'exists -- skipping')
sky = False
if just_check:
return (se or psfex or sky or pvastrom)
tmpimgfn = None
tmpmaskfn = None
# Unpacked image file
funimgfn = self.imgfn
funmaskfn = self.dqfn
if funpack:
# For FITS files that are not actually fpack'ed, funpack -E
# fails. Check whether actually fpacked.
hdr = fitsio.read_header(self.imgfn, ext=self.hdu)
if not ((hdr['XTENSION'] == 'BINTABLE')
and hdr.get('ZIMAGE', False)):
print(
'Image', self.imgfn, 'HDU', self.hdu,
'is not actually fpacked; not funpacking, just imcopying.')
fcopy = True
tmpimgfn = create_temp(suffix='.fits')
tmpmaskfn = create_temp(suffix='.fits')
if fcopy:
cmd = 'imcopy %s"+%i" %s' % (self.imgfn, self.hdu, tmpimgfn)
else:
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpimgfn,
self.imgfn)
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
funimgfn = tmpimgfn
if use_mask:
if fcopy:
cmd = 'imcopy %s"+%i" %s' % (self.dqfn, self.hdu,
tmpmaskfn)
else:
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpmaskfn,
self.dqfn)
print(cmd)
if os.system(cmd):
#raise RuntimeError('Command failed: ' + cmd)
print('Command failed: ' + cmd)
M, hdr = fitsio.read(self.dqfn, ext=self.hdu, header=True)
print('Read', M.dtype, M.shape)
fitsio.write(tmpmaskfn, M, header=hdr, clobber=True)
print('Wrote', tmpmaskfn, 'with fitsio')
funmaskfn = tmpmaskfn
if se:
# grab header values...
primhdr = self.read_image_primary_header()
magzp = primhdr['MAGZERO']
seeing = self.pixscale * self.fwhm
#print('FWHM', self.fwhm, 'pix')
#print('pixscale', self.pixscale, 'arcsec/pix')
#print('Seeing', seeing, 'arcsec')
if se:
maskstr = ''
if use_mask:
maskstr = '-FLAG_IMAGE ' + funmaskfn
sedir = self.decals.get_se_dir()
trymakedirs(self.sefn, dir=True)
cmd = ' '.join([
'sex',
'-c',
os.path.join(sedir, 'DECaLS.se'),
maskstr,
'-SEEING_FWHM %f' % seeing,
'-PARAMETERS_NAME',
os.path.join(sedir, 'DECaLS.param'),
'-FILTER_NAME',
os.path.join(sedir, 'gauss_5.0_9x9.conv'),
'-STARNNW_NAME',
os.path.join(sedir, 'default.nnw'),
'-PIXEL_SCALE 0',
# SE has a *bizarre* notion of "sigma"
'-DETECT_THRESH 1.0',
'-ANALYSIS_THRESH 1.0',
'-MAG_ZEROPOINT %f' % magzp,
'-CATALOG_NAME',
self.sefn,
funimgfn
])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if pvastrom:
# DECam images appear to have PV coefficients up to PVx_10,
# which are up to cubic terms in xi,eta,r. Overshoot what we
# need in SIP terms.
tmpwcsfn = create_temp(suffix='.wcs')
cmd = ('wcs-pv2sip -S -o 6 -e %i %s %s' %
(self.hdu, self.imgfn, tmpwcsfn))
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
# Read the resulting WCS header and add version info cards to it.
version_hdr = get_version_header(None,
self.decals.get_decals_dir(),
git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '').strip()
version_hdr.add_record(
dict(name='PLVER', value=plver,
comment='CP ver of image file'))
wcshdr = fitsio.read_header(tmpwcsfn)
os.unlink(tmpwcsfn)
for r in wcshdr.records():
version_hdr.add_record(r)
trymakedirs(self.pvwcsfn, dir=True)
fitsio.write(self.pvwcsfn, None, header=version_hdr, clobber=True)
print('Wrote', self.pvwcsfn)
if psfex:
sedir = self.decals.get_se_dir()
trymakedirs(self.psffn, dir=True)
# If we wrote *.psf instead of *.fits in a previous run...
oldfn = self.psffn.replace('.fits', '.psf')
if os.path.exists(oldfn):
print('Moving', oldfn, 'to', self.psffn)
os.rename(oldfn, self.psffn)
else:
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
verstr = get_git_version()
cmds = [
'psfex -c %s -PSF_DIR %s %s' %
(os.path.join(sedir, 'DECaLS.psfex'),
os.path.dirname(self.psffn), self.sefn),
'modhead %s LEGPIPEV %s "legacypipe git version"' %
(self.psffn, verstr),
'modhead %s PLVER %s "CP ver of image file"' %
(self.psffn, plver)
]
for cmd in cmds:
print(cmd)
rtn = os.system(cmd)
if rtn:
raise RuntimeError('Command failed: ' + cmd +
': return value: %i' % rtn)
if sky:
#print('Fitting sky for', self)
hdr = get_version_header(None,
self.decals.get_decals_dir(),
git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
hdr.delete('PROCTYPE')
hdr.add_record(
dict(name='PROCTYPE',
value='ccd',
comment='NOAO processing type'))
hdr.add_record(
dict(name='PRODTYPE',
value='skymodel',
comment='NOAO product type'))
hdr.add_record(
dict(name='PLVER', value=plver,
comment='CP ver of image file'))
slc = self.get_good_image_slice(None)
#print('Good image slice is', slc)
img = self.read_image(slice=slc)
wt = self.read_invvar(slice=slc)
if splinesky:
from tractor.splinesky import SplineSky
from scipy.ndimage.morphology import binary_dilation
# Start by subtracting the overall median
med = np.median(img[wt > 0])
# Compute initial model...
skyobj = SplineSky.BlantonMethod(img - med, wt > 0, 512)
skymod = np.zeros_like(img)
skyobj.addTo(skymod)
# Now mask bright objects in (image - initial sky model)
sig1 = 1. / np.sqrt(np.median(wt[wt > 0]))
masked = (img - med - skymod) > (5. * sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
# Now find the final sky model using that more extensive mask
skyobj = SplineSky.BlantonMethod(img - med,
np.logical_not(masked), 512)
# add the median back in
skyobj.offset(med)
if slc is not None:
sy, sx = slc
y0 = sy.start
x0 = sx.start
skyobj.shift(-x0, -y0)
trymakedirs(self.splineskyfn, dir=True)
skyobj.write_fits(self.splineskyfn, primhdr=hdr)
print('Wrote sky model', self.splineskyfn)
else:
img = img[wt > 0]
try:
skyval = estimate_mode(img, raiseOnWarn=True)
skymeth = 'mode'
except:
skyval = np.median(img)
skymeth = 'median'
tsky = ConstantSky(skyval)
hdr.add_record(
dict(name='SKYMETH',
value=skymeth,
comment='estimate_mode, or fallback to median?'))
trymakedirs(self.skyfn, dir=True)
tsky.write_fits(self.skyfn, hdr=hdr)
print('Wrote sky model', self.skyfn)
if tmpimgfn is not None:
os.unlink(tmpimgfn)
if tmpmaskfn is not None:
os.unlink(tmpmaskfn)
fns = glob(indir + '/*/*/*.fits')
# Test sets!
# fns = glob(indir + '/decam/00500/*.fits')
# fns = glob(indir + '/mosaic/00064/*.fits')
# fns = glob(indir + '/90prime/73380/*.fits')
# fns = (glob(indir + '/decam/00500/*.fits')[:10] +
# glob(indir + '/mosaic/00064/*.fits')[:10] +
# glob(indir + '/90prime/73380/*.fits')[:10])
fns.sort()
for ifn,fn in enumerate(fns):
print('Reading', ifn+1, 'of', len(fns), ':', fn)
outfn = fn.replace(indir, outdir)
dirname = os.path.dirname(outfn)
trymakedirs(dirname)
T = fits_table(fn)
hdr = T.get_header()
primhdr = fitsio.read_header(fn)
#print('Header:', hdr)
T.camera = T.camera.astype('S7') # '90prime'
T.ccdname = T.ccdname.astype('S4') # 'CCD4'
T.expnum = T.expnum.astype(np.int64)
T.ccd_cuts = T.ccd_cuts.astype(np.int64)
units = dict()
for i,c in enumerate(T.get_columns()):
u = hdr.get('TUNIT%i' % (i+1))
if u is None:
continue
def run_calibs(self, psfex=True, sky=True, funpack=False, git_version=None,
force=False,
**kwargs):
print('run_calibs for', self.name, ': sky=', sky, 'kwargs', kwargs)
se = False
if psfex and os.path.exists(self.psffn) and (not force):
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
se = False
if se:
sedir = self.survey.get_se_dir()
trymakedirs(self.sefn, dir=True)
####
trymakedirs('junk',dir=True) #need temp dir for mask-2 and invvar map
hdu=0
maskfn= self.imgfn.replace('_scie_','_mask_')
invvar= read_invvar(self.imgfn,maskfn,hdu) #note, all post processing on image,mask done in read_invvar
mask= read_dq(maskfn,hdu)
maskfn= os.path.join('junk',os.path.basename(maskfn))
invvarfn= maskfn.replace('_mask_','_invvar_')
fitsio.write(maskfn, mask)
fitsio.write(invvarfn, invvar)
print('wrote mask-2 to %s, invvar to %s' % (maskfn,invvarfn))
#run se
hdr=fitsio.read_header(self.imgfn,ext=hdu)
magzp = zeropoint_for_ptf(hdr)
seeing = hdr['PIXSCALE'] * hdr['MEDFWHM']
gain= hdr['GAIN']
cmd = ' '.join(['sex','-c', os.path.join(sedir,'ptf.se'),
'-WEIGHT_IMAGE %s' % invvarfn, '-WEIGHT_TYPE MAP_WEIGHT',
'-GAIN %f' % gain,
'-FLAG_IMAGE %s' % maskfn,
'-FLAG_TYPE OR',
'-SEEING_FWHM %f' % seeing,
'-DETECT_MINAREA 3',
'-PARAMETERS_NAME', os.path.join(sedir,'ptf.param'),
'-FILTER_NAME', os.path.join(sedir, 'ptf_gauss_3.0_5x5.conv'),
'-STARNNW_NAME', os.path.join(sedir, 'ptf_default.nnw'),
'-PIXEL_SCALE 0',
# SE has a *bizarre* notion of "sigma"
'-DETECT_THRESH 1.0',
'-ANALYSIS_THRESH 1.0',
'-MAG_ZEROPOINT %f' % magzp,
'-CATALOG_NAME', self.sefn,
self.imgfn])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if psfex:
sedir = self.survey.get_se_dir()
trymakedirs(self.psffn, dir=True)
# If we wrote *.psf instead of *.fits in a previous run...
oldfn = self.psffn.replace('.fits', '.psf')
if os.path.exists(oldfn):
print('Moving', oldfn, 'to', self.psffn)
os.rename(oldfn, self.psffn)
else:
cmd= ' '.join(['psfex',self.sefn,'-c', os.path.join(sedir,'ptf.psfex'),
'-PSF_DIR',os.path.dirname(self.psffn)])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
def run_calibs(self, psfex=True, sky=True, funpack=False, git_version=None,
force=False,
**kwargs):
from astrometry.util.file import trymakedirs
from legacypipe.common import (create_temp, get_version_header,
get_git_version)
print('run_calibs for', self.name, ': sky=', sky, 'kwargs', kwargs)
se = False
if psfex and os.path.exists(self.psffn) and (not force):
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
se = False
if se:
funpack = True
if sky and (not force) and os.path.exists(self.splineskyfn):
sky = False
tmpimgfn = None
tmpmaskfn = None
# Unpacked image file
funimgfn = self.imgfn
funmaskfn = self.dqfn
if funpack:
# For FITS files that are not actually fpack'ed, funpack -E
# fails. Check whether actually fpacked.
hdr = fitsio.read_header(self.imgfn, ext=self.hdu)
if not ((hdr['XTENSION'] == 'BINTABLE') and hdr.get('ZIMAGE', False)):
print('Image', self.imgfn, 'HDU', self.hdu, 'is not actually fpacked; not funpacking, just imcopying.')
fcopy = True
tmpimgfn = create_temp(suffix='.fits')
tmpmaskfn = create_temp(suffix='.fits')
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpimgfn, self.imgfn)
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
funimgfn = tmpimgfn
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpmaskfn, self.dqfn)
print(cmd)
if os.system(cmd):
print('Command failed: ' + cmd)
M,hdr = self._read_fits(self.dqfn, ext=self.hdu, header=True)
print('Read', M.dtype, M.shape)
fitsio.write(tmpmaskfn, M, header=hdr, clobber=True)
print('Wrote', tmpmaskfn, 'with fitsio')
funmaskfn = tmpmaskfn
if se:
# grab header values...
primhdr = self.read_image_primary_header()
magzp = primhdr['MAGZERO']
seeing = self.pixscale * self.fwhm
print('FWHM', self.fwhm, 'pix')
print('pixscale', self.pixscale, 'arcsec/pix')
print('Seeing', seeing, 'arcsec')
if se:
maskstr = '-FLAG_IMAGE ' + funmaskfn
sedir = self.decals.get_se_dir()
trymakedirs(self.sefn, dir=True)
cmd = ' '.join([
'sex',
'-c', os.path.join(sedir, 'DECaLS.se'),
maskstr,
'-SEEING_FWHM %f' % seeing,
'-PARAMETERS_NAME', os.path.join(sedir, 'DECaLS.param'),
'-FILTER_NAME', os.path.join(sedir, 'gauss_5.0_9x9.conv'),
'-STARNNW_NAME', os.path.join(sedir, 'default.nnw'),
'-PIXEL_SCALE 0',
# SE has a *bizarre* notion of "sigma"
'-DETECT_THRESH 1.0',
'-ANALYSIS_THRESH 1.0',
'-MAG_ZEROPOINT %f' % magzp,
'-CATALOG_NAME', self.sefn,
funimgfn])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if psfex:
sedir = self.decals.get_se_dir()
trymakedirs(self.psffn, dir=True)
# If we wrote *.psf instead of *.fits in a previous run...
oldfn = self.psffn.replace('.fits', '.psf')
if os.path.exists(oldfn):
print('Moving', oldfn, 'to', self.psffn)
os.rename(oldfn, self.psffn)
else:
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
verstr = get_git_version()
cmds = ['psfex -c %s -PSF_DIR %s %s' %
(os.path.join(sedir, 'DECaLS.psfex'),
os.path.dirname(self.psffn), self.sefn),
'modhead %s LEGPIPEV %s "legacypipe git version"' %
(self.psffn, verstr),
'modhead %s PLVER %s "CP ver of image file"' %
(self.psffn, plver)]
for cmd in cmds:
print(cmd)
rtn = os.system(cmd)
if rtn:
raise RuntimeError('Command failed: ' + cmd + ': return value: %i' % rtn)
if sky:
#print('Fitting sky for', self)
hdr = get_version_header(None, self.decals.get_decals_dir(),
git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
hdr.delete('PROCTYPE')
hdr.add_record(dict(name='PROCTYPE', value='ccd',
comment='NOAO processing type'))
hdr.add_record(dict(name='PRODTYPE', value='skymodel',
comment='NOAO product type'))
hdr.add_record(dict(name='PLVER', value=plver,
comment='CP ver of image file'))
slc = self.get_good_image_slice(None)
#print('Good image slice is', slc)
img = self.read_image(slice=slc)
wt = self.read_invvar(slice=slc)
from tractor.splinesky import SplineSky
from scipy.ndimage.morphology import binary_dilation
# Start by subtracting the overall median
med = np.median(img[wt>0])
# Compute initial model...
skyobj = SplineSky.BlantonMethod(img - med, wt>0, 512)
skymod = np.zeros_like(img)
skyobj.addTo(skymod)
# Now mask bright objects in (image - initial sky model)
sig1 = 1./np.sqrt(np.median(wt[wt>0]))
masked = (img - med - skymod) > (5.*sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
# Now find the final sky model using that more extensive mask
skyobj = SplineSky.BlantonMethod(img - med, np.logical_not(masked), 512)
# add the median back in
skyobj.offset(med)
if slc is not None:
sy,sx = slc
y0 = sy.start
x0 = sx.start
skyobj.shift(-x0, -y0)
trymakedirs(self.splineskyfn, dir=True)
skyobj.write_fits(self.splineskyfn, primhdr=hdr)
print('Wrote sky model', self.splineskyfn)
if tmpimgfn is not None:
os.unlink(tmpimgfn)
if tmpmaskfn is not None:
os.unlink(tmpmaskfn)
def main(survey=None, opt=None, args=None):
'''Driver function for forced photometry of individual Legacy
Survey images.
'''
if args is None:
args = sys.argv[1:]
print('forced_photom.py', ' '.join(args))
if opt is None:
parser = get_parser()
opt = parser.parse_args(args)
import logging
if opt.verbose == 0:
lvl = logging.INFO
else:
lvl = logging.DEBUG
logging.basicConfig(level=lvl, format='%(message)s', stream=sys.stdout)
# tractor logging is *soooo* chatty
logging.getLogger('tractor.engine').setLevel(lvl + 10)
t0 = Time()
if survey is None:
survey = LegacySurveyData(survey_dir=opt.survey_dir,
cache_dir=opt.cache_dir,
output_dir=opt.out_dir)
if opt.skip:
if opt.out is not None:
outfn = opt.out
else:
outfn = survey.find_file('forced',
output=True,
camera=opt.camera,
expnum=opt.expnum)
if os.path.exists(outfn):
print('Ouput file exists:', outfn)
return 0
if opt.derivs and opt.agn:
print('Sorry, can\'t do --derivs AND --agn')
return -1
if opt.out is None and opt.out_dir is None:
print('Must supply either --out or --out-dir')
return -1
if opt.expnum is None and opt.out is None:
print('If no --expnum is given, must supply --out filename')
return -1
if not opt.forced:
opt.apphot = True
zoomslice = None
if opt.zoom is not None:
(x0, x1, y0, y1) = opt.zoom
zoomslice = (slice(y0, y1), slice(x0, x1))
ps = None
if opt.plots is not None:
from astrometry.util.plotutils import PlotSequence
ps = PlotSequence(opt.plots)
# Cache CCDs files before the find_ccds call...
# Copy required files into the cache?
if opt.pre_cache:
def copy_files_to_cache(fns):
for fn in fns:
cachefn = fn.replace(survey.survey_dir, survey.cache_dir)
if not cachefn.startswith(survey.cache_dir):
print('Skipping', fn)
continue
outdir = os.path.dirname(cachefn)
trymakedirs(outdir)
print('Copy', fn)
print(' to', cachefn)
shutil.copyfile(fn, cachefn)
assert (survey.cache_dir is not None)
fnset = set()
fn = survey.find_file('bricks')
fnset.add(fn)
fns = survey.find_file('ccd-kds')
fnset.update(fns)
copy_files_to_cache(fnset)
# Read metadata from survey-ccds.fits table
ccds = survey.find_ccds(camera=opt.camera,
expnum=opt.expnum,
ccdname=opt.ccdname)
print(len(ccds), 'with camera', opt.camera, 'and expnum', opt.expnum,
'and ccdname', opt.ccdname)
# sort CCDs
ccds.cut(np.lexsort((ccds.ccdname, ccds.expnum, ccds.camera)))
# If there is only one catalog survey_dir, we pass it to get_catalog_in_wcs
# as the northern survey.
catsurvey_north = survey
catsurvey_south = None
if opt.catalog_dir_north is not None:
assert (opt.catalog_dir_south is not None)
assert (opt.catalog_resolve_dec_ngc is not None)
catsurvey_north = LegacySurveyData(survey_dir=opt.catalog_dir_north)
catsurvey_south = LegacySurveyData(survey_dir=opt.catalog_dir_south)
elif opt.catalog_dir is not None:
catsurvey_north = LegacySurveyData(survey_dir=opt.catalog_dir)
# Copy required CCD & calib files into the cache?
if opt.pre_cache:
assert (survey.cache_dir is not None)
fnset = set()
for ccd in ccds:
im = survey.get_image_object(ccd)
for key in im.get_cacheable_filename_variables():
fn = getattr(im, key)
if fn is None or not (os.path.exists(fn)):
continue
fnset.add(fn)
copy_files_to_cache(fnset)
args = []
for ccd in ccds:
args.append((survey, catsurvey_north, catsurvey_south,
opt.catalog_resolve_dec_ngc, ccd, opt, zoomslice, ps))
if opt.threads:
from astrometry.util.multiproc import multiproc
from astrometry.util.timingpool import TimingPool, TimingPoolMeas
pool = TimingPool(opt.threads)
poolmeas = TimingPoolMeas(pool, pickleTraffic=False)
Time.add_measurement(poolmeas)
mp = multiproc(None, pool=pool)
tm = Time()
FF = mp.map(bounce_one_ccd, args)
print('Multi-processing forced-phot:', Time() - tm)
del mp
Time.measurements.remove(poolmeas)
del poolmeas
pool.close()
pool.join()
del pool
else:
FF = map(bounce_one_ccd, args)
FF = [F for F in FF if F is not None]
if len(FF) == 0:
print('No photometry results to write.')
return 0
# Keep only the first header
_, version_hdr, _, _ = FF[0]
# unpack results
outlier_masks = [m for _, _, m, _ in FF]
outlier_hdrs = [h for _, _, _, h in FF]
FF = [F for F, _, _, _ in FF]
F = merge_tables(FF)
if len(ccds):
version_hdr.delete('CPHDU')
version_hdr.delete('CCDNAME')
from legacypipe.utils import add_bits
from legacypipe.bits import DQ_BITS
add_bits(version_hdr, DQ_BITS, 'DQMASK', 'DQ', 'D')
from legacyzpts.psfzpt_cuts import CCD_CUT_BITS
add_bits(version_hdr, CCD_CUT_BITS, 'CCD_CUTS', 'CC', 'C')
for i, ap in enumerate(apertures_arcsec):
version_hdr.add_record(
dict(name='APRAD%i' % i,
value=ap,
comment='(optical) Aperture radius, in arcsec'))
unitmap = {
'exptime': 'sec',
'flux': 'nanomaggy',
'flux_ivar': '1/nanomaggy^2',
'apflux': 'nanomaggy',
'apflux_ivar': '1/nanomaggy^2',
'psfdepth': '1/nanomaggy^2',
'galdepth': '1/nanomaggy^2',
'sky': 'nanomaggy/arcsec^2',
'psfsize': 'arcsec',
'fwhm': 'pixels',
'ccdrarms': 'arcsec',
'ccddecrms': 'arcsec',
'ra': 'deg',
'dec': 'deg',
'skyrms': 'counts/sec',
'dra': 'arcsec',
'ddec': 'arcsec',
'dra_ivar': '1/arcsec^2',
'ddec_ivar': '1/arcsec^2'
}
columns = F.get_columns()
order = [
'release', 'brickid', 'brickname', 'objid', 'camera', 'expnum',
'ccdname', 'filter', 'mjd', 'exptime', 'psfsize', 'fwhm', 'ccd_cuts',
'airmass', 'sky', 'skyrms', 'psfdepth', 'galdepth', 'ccdzpt',
'ccdrarms', 'ccddecrms', 'ccdphrms', 'ra', 'dec', 'flux', 'flux_ivar',
'fracflux', 'rchisq', 'fracmasked', 'fracin', 'apflux', 'apflux_ivar',
'x', 'y', 'dqmask', 'dra', 'ddec', 'dra_ivar', 'ddec_ivar'
]
columns = [c for c in order if c in columns]
units = [unitmap.get(c, '') for c in columns]
if opt.out is not None:
outdir = os.path.dirname(opt.out)
if len(outdir):
trymakedirs(outdir)
tmpfn = os.path.join(outdir, 'tmp-' + os.path.basename(opt.out))
fitsio.write(tmpfn, None, header=version_hdr, clobber=True)
F.writeto(tmpfn, units=units, append=True, columns=columns)
os.rename(tmpfn, opt.out)
print('Wrote', opt.out)
else:
with survey.write_output('forced',
camera=opt.camera,
expnum=opt.expnum) as out:
F.writeto(None,
fits_object=out.fits,
primheader=version_hdr,
units=units,
columns=columns)
print('Wrote', out.real_fn)
if opt.outlier_mask is not None:
# Add outlier bit meanings to the primary header
version_hdr.add_record(
dict(name='COMMENT', value='Outlier mask bit meanings'))
version_hdr.add_record(
dict(name='OUTL_POS',
value=1,
comment='Outlier mask bit for Positive outlier'))
version_hdr.add_record(
dict(name='OUTL_NEG',
value=2,
comment='Outlier mask bit for Negative outlier'))
if opt.outlier_mask == 'default':
outdir = os.path.join(opt.out_dir, 'outlier-masks')
camexp = set(zip(ccds.camera, ccds.expnum))
for c, e in camexp:
I = np.flatnonzero((ccds.camera == c) * (ccds.expnum == e))
ccd = ccds[I[0]]
imfn = ccd.image_filename.strip()
outfn = os.path.join(outdir, imfn.replace('.fits',
'-outlier.fits'))
trymakedirs(outfn, dir=True)
tempfn = outfn.replace('.fits', '-tmp.fits')
with fitsio.FITS(tempfn, 'rw', clobber=True) as fits:
fits.write(None, header=version_hdr)
for i in I:
mask = outlier_masks[i]
_, _, _, meth, tile = survey.get_compression_args(
'outliers_mask', shape=mask.shape)
fits.write(mask,
header=outlier_hdrs[i],
extname=ccds.ccdname[i],
compress=meth,
tile_dims=tile)
os.rename(tempfn, outfn)
print('Wrote', outfn)
elif opt.outlier_mask is not None:
with fitsio.FITS(opt.outlier_mask, 'rw', clobber=True) as F:
F.write(None, header=version_hdr)
for i, (hdr, mask) in enumerate(zip(outlier_hdrs, outlier_masks)):
_, _, _, meth, tile = survey.get_compression_args(
'outliers_mask', shape=mask.shape)
F.write(mask,
header=hdr,
extname=ccds.ccdname[i],
compress=meth,
tile_dims=tile)
print('Wrote', opt.outlier_mask)
tnow = Time()
print('Total:', tnow - t0)
return 0
def main():
fn = '/global/cscratch1/sd/dstn/c4d_190730_024955_ori/c4d_190730_024955_ori.52.fits'
survey_dir = '/global/cscratch1/sd/dstn/subtractor-survey-dir'
imagedir = os.path.join(survey_dir, 'images')
trymakedirs(imagedir)
calibdir = os.path.join(survey_dir, 'calib')
psfexdir = os.path.join(calibdir, 'decam', 'psfex-merged')
trymakedirs(psfexdir)
skydir = os.path.join(calibdir, 'decam', 'splinesky-merged')
trymakedirs(skydir)
basename = os.path.basename(fn)
basename = basename.replace('.fits', '')
# Output filenames for legacyzpts calibration/zeropoint files
f, photfn = tempfile.mkstemp()
os.close(f)
surveyfn = os.path.join(survey_dir, 'survey-ccds-%s.fits.gz' % basename)
annfn = os.path.join(survey_dir, 'annotated-%s.fits' % basename)
mp = multiproc()
survey = LegacySurveyData(survey_dir)
# Use the subclass above to handle DECam images!
survey.image_typemap.update(decam=GoldsteinDecamImage)
# Grab the exposure number and CCD name
hdr = fitsio.read_header(fn)
expnum = hdr['EXPNUM']
ccdname = hdr['EXTNAME'].strip()
print('Exposure', expnum, 'CCD', ccdname)
import logging
lvl = logging.INFO
logging.basicConfig(level=lvl, format='%(message)s', stream=sys.stdout)
# tractor logging is *soooo* chatty
logging.getLogger('tractor.engine').setLevel(lvl + 10)
if not os.path.exists(surveyfn):
# Run calibrations and zeropoints
runit(fn,
photfn,
surveyfn,
annfn,
mp,
survey=survey,
camera='decam',
debug=False,
choose_ccd=ccdname,
splinesky=True,
calibdir=calibdir,
measureclass=GoldsteinDecamMeasurer)
# Find catalog sources touching this CCD
ccds = survey.find_ccds(expnum=expnum, ccdname=ccdname)
assert (len(ccds) == 1)
ccd = ccds[0]
print('Got CCD', ccd)
# Create Tractor image
im = survey.get_image_object(ccd)
print('Got image:', im)
# Look at this sub-image, or the whole chip?
#zoomslice=None
zoomslice = (slice(0, 1000), slice(0, 1000))
tim = im.get_tractor_image(slc=zoomslice,
pixPsf=True,
splinesky=True,
hybridPsf=True,
normalizePsf=True,
old_calibs_ok=True)
print('Got tim:', tim)
# Read catalog files touching this CCD
catsurvey = LegacySurveyData(
'/global/project/projectdirs/cosmo/work/legacysurvey/dr8/south')
T = get_catalog_in_wcs(tim.subwcs, catsurvey)
print('Got', len(T), 'DR8 catalog sources within CCD')
# Gaia stars: move RA,Dec to the epoch of this image.
I = np.flatnonzero(T.ref_epoch > 0)
if len(I):
from legacypipe.survey import radec_at_mjd
print('Moving', len(I), 'Gaia stars to MJD', tim.time.toMjd())
ra, dec = radec_at_mjd(T.ra[I], T.dec[I], T.ref_epoch[I].astype(float),
T.pmra[I], T.pmdec[I], T.parallax[I],
tim.time.toMjd())
T.ra[I] = ra
T.dec[I] = dec
# Create Tractor Source objects from the catalog
cat = read_fits_catalog(T, bands=tim.band)
print('Created', len(cat), 'source objects')
# Render model image!
tr = Tractor([tim], cat)
mod = tr.getModelImage(0)
# plots
ima = dict(interpolation='nearest',
origin='lower',
vmin=-2 * tim.sig1,
vmax=10 * tim.sig1,
cmap='gray')
plt.clf()
plt.imshow(tim.getImage(), **ima)
plt.title('Image')
plt.savefig('img.jpg')
plt.clf()
plt.imshow(mod, **ima)
plt.title('Model')
plt.savefig('mod.jpg')
plt.clf()
plt.imshow(tim.getImage() - mod, **ima)
plt.title('Residual')
plt.savefig('res.jpg')
def main(decals=None, opt=None):
'''Driver function for forced photometry of individual DECam images.
'''
if opt is None:
parser = get_parser()
opt = parser.parse_args()
Time.add_measurement(MemMeas)
t0 = Time()
if os.path.exists(opt.outfn):
print('Ouput file exists:', opt.outfn)
sys.exit(0)
if not opt.forced:
opt.apphot = True
zoomslice = None
if opt.zoom is not None:
(x0, x1, y0, y1) = opt.zoom
zoomslice = (slice(y0, y1), slice(x0, x1))
ps = None
if opt.plots is not None:
from astrometry.util.plotutils import PlotSequence
ps = PlotSequence(opt.plots)
# Try parsing filename as exposure number.
try:
expnum = int(opt.filename)
opt.filename = None
except:
# make this 'None' for decals.find_ccds()
expnum = None
# Try parsing HDU number
try:
opt.hdu = int(opt.hdu)
ccdname = None
except:
ccdname = opt.hdu
opt.hdu = -1
if decals is None:
decals = Decals()
if opt.filename is not None and opt.hdu >= 0:
# Read metadata from file
T = exposure_metadata([opt.filename], hdus=[opt.hdu])
print('Metadata:')
T.about()
else:
# Read metadata from decals-ccds.fits table
T = decals.find_ccds(expnum=expnum, ccdname=ccdname)
print(len(T), 'with expnum', expnum, 'and CCDname', ccdname)
if opt.hdu >= 0:
T.cut(T.image_hdu == opt.hdu)
print(len(T), 'with HDU', opt.hdu)
if opt.filename is not None:
T.cut(
np.array([f.strip() == opt.filename
for f in T.image_filename]))
print(len(T), 'with filename', opt.filename)
assert (len(T) == 1)
im = decals.get_image_object(T[0])
tim = im.get_tractor_image(slc=zoomslice, pixPsf=True, splinesky=True)
print('Got tim:', tim)
if opt.catfn in ['DR1', 'DR2']:
if opt.catalog_path is None:
opt.catalog_path = opt.catfn.lower()
margin = 20
TT = []
chipwcs = tim.subwcs
bricks = bricks_touching_wcs(chipwcs, decals=decals)
for b in bricks:
# there is some overlap with this brick... read the catalog.
fn = os.path.join(opt.catalog_path, 'tractor', b.brickname[:3],
'tractor-%s.fits' % b.brickname)
if not os.path.exists(fn):
print('WARNING: catalog', fn, 'does not exist. Skipping!')
continue
print('Reading', fn)
T = fits_table(fn)
ok, xx, yy = chipwcs.radec2pixelxy(T.ra, T.dec)
W, H = chipwcs.get_width(), chipwcs.get_height()
I = np.flatnonzero((xx >= -margin) * (xx <= (W + margin)) *
(yy >= -margin) * (yy <= (H + margin)))
T.cut(I)
print('Cut to', len(T), 'sources within image + margin')
# print('Brick_primary:', np.unique(T.brick_primary))
T.cut(T.brick_primary)
print('Cut to', len(T), 'on brick_primary')
T.cut((T.out_of_bounds == False) * (T.left_blob == False))
print('Cut to', len(T), 'on out_of_bounds and left_blob')
TT.append(T)
T = merge_tables(TT)
T._header = TT[0]._header
del TT
# Fix up various failure modes:
# FixedCompositeGalaxy(pos=RaDecPos[240.51147402832561, 10.385488075518923], brightness=NanoMaggies: g=(flux -2.87), r=(flux -5.26), z=(flux -7.65), fracDev=FracDev(0.60177207), shapeExp=re=3.78351e-44, e1=9.30367e-13, e2=1.24392e-16, shapeDev=re=inf, e1=-0, e2=-0)
# -> convert to EXP
I = np.flatnonzero(
np.array([((t.type == 'COMP') and (not np.isfinite(t.shapedev_r)))
for t in T]))
if len(I):
print('Converting', len(I), 'bogus COMP galaxies to EXP')
for i in I:
T.type[i] = 'EXP'
# Same thing with the exp component.
# -> convert to DEV
I = np.flatnonzero(
np.array([((t.type == 'COMP') and (not np.isfinite(t.shapeexp_r)))
for t in T]))
if len(I):
print('Converting', len(I), 'bogus COMP galaxies to DEV')
for i in I:
T.type[i] = 'DEV'
if opt.write_cat:
T.writeto(opt.write_cat)
print('Wrote catalog to', opt.write_cat)
else:
T = fits_table(opt.catfn)
T.shapeexp = np.vstack((T.shapeexp_r, T.shapeexp_e1, T.shapeexp_e2)).T
T.shapedev = np.vstack((T.shapedev_r, T.shapedev_e1, T.shapedev_e2)).T
cat = read_fits_catalog(T, ellipseClass=tractor.ellipses.EllipseE)
# print('Got cat:', cat)
print('Forced photom...')
opti = None
if opt.ceres:
from tractor.ceres_optimizer import CeresOptimizer
B = 8
opti = CeresOptimizer(BW=B, BH=B)
tr = Tractor([tim], cat, optimizer=opti)
tr.freezeParam('images')
for src in cat:
src.freezeAllBut('brightness')
src.getBrightness().freezeAllBut(tim.band)
F = fits_table()
F.brickid = T.brickid
F.brickname = T.brickname
F.objid = T.objid
F.filter = np.array([tim.band] * len(T))
F.mjd = np.array([tim.primhdr['MJD-OBS']] * len(T))
F.exptime = np.array([tim.primhdr['EXPTIME']] * len(T))
ok, x, y = tim.sip_wcs.radec2pixelxy(T.ra, T.dec)
F.x = (x - 1).astype(np.float32)
F.y = (y - 1).astype(np.float32)
if opt.apphot:
import photutils
img = tim.getImage()
ie = tim.getInvError()
with np.errstate(divide='ignore'):
imsigma = 1. / ie
imsigma[ie == 0] = 0.
apimg = []
apimgerr = []
# Aperture photometry locations
xxyy = np.vstack(
[tim.wcs.positionToPixel(src.getPosition()) for src in cat]).T
apxy = xxyy - 1.
apertures = apertures_arcsec / tim.wcs.pixel_scale()
print('Apertures:', apertures, 'pixels')
for rad in apertures:
aper = photutils.CircularAperture(apxy, rad)
p = photutils.aperture_photometry(img, aper, error=imsigma)
apimg.append(p.field('aperture_sum'))
apimgerr.append(p.field('aperture_sum_err'))
ap = np.vstack(apimg).T
ap[np.logical_not(np.isfinite(ap))] = 0.
F.apflux = ap
ap = 1. / (np.vstack(apimgerr).T)**2
ap[np.logical_not(np.isfinite(ap))] = 0.
F.apflux_ivar = ap
if opt.forced:
kwa = {}
if opt.plots is None:
kwa.update(wantims=False)
R = tr.optimize_forced_photometry(variance=True,
fitstats=True,
shared_params=False,
**kwa)
if opt.plots:
(data, mod, ie, chi, roi) = R.ims1[0]
ima = tim.ima
imchi = dict(interpolation='nearest',
origin='lower',
vmin=-5,
vmax=5)
plt.clf()
plt.imshow(data, **ima)
plt.title('Data: %s' % tim.name)
ps.savefig()
plt.clf()
plt.imshow(mod, **ima)
plt.title('Model: %s' % tim.name)
ps.savefig()
plt.clf()
plt.imshow(chi, **imchi)
plt.title('Chi: %s' % tim.name)
ps.savefig()
F.flux = np.array([
src.getBrightness().getFlux(tim.band) for src in cat
]).astype(np.float32)
F.flux_ivar = R.IV.astype(np.float32)
F.fracflux = R.fitstats.profracflux.astype(np.float32)
F.rchi2 = R.fitstats.prochi2.astype(np.float32)
program_name = sys.argv[0]
version_hdr = get_version_header(program_name, decals.decals_dir)
# HACK -- print only two directory names + filename of CPFILE.
fname = os.path.basename(im.imgfn)
d = os.path.dirname(im.imgfn)
d1 = os.path.basename(d)
d = os.path.dirname(d)
d2 = os.path.basename(d)
fname = os.path.join(d2, d1, fname)
print('Trimmed filename to', fname)
#version_hdr.add_record(dict(name='CPFILE', value=im.imgfn, comment='DECam comm.pipeline file'))
version_hdr.add_record(
dict(name='CPFILE', value=fname, comment='DECam comm.pipeline file'))
version_hdr.add_record(
dict(name='CPHDU', value=im.hdu, comment='DECam comm.pipeline ext'))
version_hdr.add_record(
dict(name='CAMERA', value='DECam', comment='Dark Energy Camera'))
version_hdr.add_record(
dict(name='EXPNUM', value=im.expnum, comment='DECam exposure num'))
version_hdr.add_record(
dict(name='CCDNAME', value=im.ccdname, comment='DECam CCD name'))
version_hdr.add_record(
dict(name='FILTER', value=tim.band, comment='Bandpass of this image'))
version_hdr.add_record(
dict(name='EXPOSURE',
value='decam-%s-%s' % (im.expnum, im.ccdname),
comment='Name of this image'))
keys = [
'TELESCOP', 'OBSERVAT', 'OBS-LAT', 'OBS-LONG', 'OBS-ELEV', 'INSTRUME'
]
for key in keys:
if key in tim.primhdr:
version_hdr.add_record(dict(name=key, value=tim.primhdr[key]))
hdr = fitsio.FITSHDR()
units = {
'mjd': 'sec',
'exptime': 'sec',
'flux': 'nanomaggy',
'flux_ivar': '1/nanomaggy^2'
}
columns = F.get_columns()
for i, col in enumerate(columns):
if col in units:
hdr.add_record(dict(name='TUNIT%i' % (i + 1), value=units[col]))
outdir = os.path.dirname(opt.outfn)
if len(outdir):
trymakedirs(outdir)
fitsio.write(opt.outfn, None, header=version_hdr, clobber=True)
F.writeto(opt.outfn, header=hdr, append=True)
print('Wrote', opt.outfn)
print('Finished forced phot:', Time() - t0)
return 0
def merge_psfex(survey, expnum, C, psfoutfn, opt):
psfex = []
psfhdrvals = []
imobjs = []
Cgood = []
for ccd in C:
im = survey.get_image_object(ccd)
fn = im.psffn
if not os.path.exists(fn):
print('File not found:', fn)
if opt.all_found:
return
continue
imobjs.append(im)
Cgood.append(ccd)
for ccd, im in zip(Cgood, imobjs):
fn = im.psffn
print('Reading', fn)
T = fits_table(fn)
hdr = fitsio.read_header(fn, ext=1)
keys = [
'LOADED',
'ACCEPTED',
'CHI2',
'POLNAXIS',
'POLNGRP',
'PSF_FWHM',
'PSF_SAMP',
'PSFNAXIS',
'PSFAXIS1',
'PSFAXIS2',
'PSFAXIS3',
]
if hdr['POLNAXIS'] == 0:
# No polynomials. Fake it.
T.polgrp1 = np.array([0])
T.polgrp2 = np.array([0])
T.polname1 = np.array(['fake'])
T.polname2 = np.array(['fake'])
T.polzero1 = np.array([0])
T.polzero2 = np.array([0])
T.polscal1 = np.array([1])
T.polscal2 = np.array([1])
T.poldeg1 = np.array([0])
else:
keys.extend([
'POLGRP1', 'POLNAME1', 'POLZERO1', 'POLSCAL1', 'POLGRP2',
'POLNAME2', 'POLZERO2', 'POLSCAL2', 'POLDEG1'
])
for k in keys:
try:
v = hdr[k]
except:
print('Did not find key', k, 'in', fn)
sys.exit(-1)
T.set(k.lower(), np.array([hdr[k]]))
psfex.append(T)
#print(fn)
#T.about()
hdr = fitsio.read_header(fn)
psfhdrvals.append([hdr.get(k, '') for k in ['LEGPIPEV', 'PLVER']] +
[expnum, ccd.ccdname])
if len(psfex) == 0:
return
padded = pad_arrays([p.psf_mask[0] for p in psfex])
cols = psfex[0].columns()
cols.remove('psf_mask')
T = merge_tables(psfex, columns=cols)
T.psf_mask = np.concatenate([[p] for p in padded])
T.legpipev = np.array([h[0] for h in psfhdrvals])
T.plver = np.array([h[1] for h in psfhdrvals])
T.expnum = np.array([h[2] for h in psfhdrvals])
T.ccdname = np.array([h[3] for h in psfhdrvals])
fn = psfoutfn
trymakedirs(fn, dir=True)
T.writeto(fn)
print('Wrote', fn)
def main():
survey = LegacySurveyData()
ccds = survey.get_ccds()
print(len(ccds), 'CCDs')
expnums = np.unique(ccds.expnum)
print(len(expnums), 'unique exposures')
for expnum in expnums:
expnumstr = '%08i' % expnum
skyoutfn = os.path.join('splinesky', expnumstr[:5], 'decam-%s.fits' % expnumstr)
psfoutfn = os.path.join('psfex', expnumstr[:5], 'decam-%s.fits' % expnumstr)
if os.path.exists(skyoutfn) and os.path.exists(psfoutfn):
print('Exposure', expnum, 'is done already')
continue
C = ccds[ccds.expnum == expnum]
print(len(C), 'CCDs in expnum', expnum)
psfex = []
psfhdrvals = []
splinesky = []
skyhdrvals = []
for ccd in C:
im = survey.get_image_object(ccd)
fn = im.splineskyfn
if os.path.exists(fn):
T = fits_table(fn)
splinesky.append(T)
# print(fn)
# T.about()
hdr = fitsio.read_header(fn)
skyhdrvals.append([hdr[k] for k in [
'SKY', 'LEGPIPEV', 'PLVER']] + [expnum, ccd.ccdname])
else:
print('File not found:', fn)
fn = im.psffn
if os.path.exists(fn):
T = fits_table(fn)
hdr = fitsio.read_header(fn, ext=1)
keys = ['LOADED', 'ACCEPTED', 'CHI2', 'POLNAXIS',
'POLNGRP', 'PSF_FWHM', 'PSF_SAMP', 'PSFNAXIS',
'PSFAXIS1', 'PSFAXIS2', 'PSFAXIS3',]
if hdr['POLNAXIS'] == 0:
# No polynomials. Fake it.
T.polgrp1 = np.array([0])
T.polgrp2 = np.array([0])
T.polname1 = np.array(['fake'])
T.polname2 = np.array(['fake'])
T.polzero1 = np.array([0])
T.polzero2 = np.array([0])
T.polscal1 = np.array([1])
T.polscal2 = np.array([1])
T.poldeg1 = np.array([0])
T.poldeg2 = np.array([0])
else:
keys.extend([
'POLGRP1', 'POLNAME1', 'POLZERO1', 'POLSCAL1',
'POLGRP2', 'POLNAME2', 'POLZERO2', 'POLSCAL2',
'POLDEG1'])
for k in keys:
T.set(k.lower(), np.array([hdr[k]]))
psfex.append(T)
#print(fn)
#T.about()
hdr = fitsio.read_header(fn)
psfhdrvals.append([hdr.get(k,'') for k in [
'LEGPIPEV', 'PLVER']] + [expnum, ccd.ccdname])
else:
print('File not found:', fn)
if len(psfex):
padded = pad_arrays([p.psf_mask[0] for p in psfex])
cols = psfex[0].columns()
cols.remove('psf_mask')
T = merge_tables(psfex, columns=cols)
T.psf_mask = np.concatenate([[p] for p in padded])
T.legpipev = np.array([h[0] for h in psfhdrvals])
T.plver = np.array([h[1] for h in psfhdrvals])
T.expnum = np.array([h[2] for h in psfhdrvals])
T.ccdname = np.array([h[3] for h in psfhdrvals])
fn = psfoutfn
trymakedirs(fn, dir=True)
T.writeto(fn)
print('Wrote', fn)
if len(splinesky):
T = fits_table()
T.gridw = np.array([t.gridvals[0].shape[1] for t in splinesky])
T.gridh = np.array([t.gridvals[0].shape[0] for t in splinesky])
padded = pad_arrays([t.gridvals[0] for t in splinesky])
T.gridvals = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.xgrid[0] for t in splinesky])
T.xgrid = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.xgrid[0] for t in splinesky])
T.ygrid = np.concatenate([[p] for p in padded])
cols = splinesky[0].columns()
print('Columns:', cols)
for c in ['gridvals', 'xgrid', 'ygrid']:
cols.remove(c)
T.add_columns_from(merge_tables(splinesky, columns=cols))
T.skyclass = np.array([h[0] for h in skyhdrvals])
T.legpipev = np.array([h[1] for h in skyhdrvals])
T.plver = np.array([h[2] for h in skyhdrvals])
T.expnum = np.array([h[3] for h in skyhdrvals])
T.ccdname = np.array([h[4] for h in skyhdrvals])
fn = skyoutfn
trymakedirs(fn, dir=True)
T.writeto(fn)
print('Wrote', fn)
def run_calibs(
self,
pvastrom=True,
psfex=True,
sky=True,
se=False,
funpack=False,
fcopy=False,
use_mask=True,
force=False,
just_check=False,
git_version=None,
splinesky=False,
):
"""
Run calibration pre-processing steps.
Parameters
----------
just_check: boolean
If True, returns True if calibs need to be run.
"""
from .common import create_temp, get_version_header, get_git_version
# for fn in [self.pvwcsfn, self.sefn, self.psffn, self.skyfn, self.splineskyfn]:
# print('exists?', os.path.exists(fn), fn)
if psfex and os.path.exists(self.psffn) and (not force):
# Sometimes SourceExtractor gets interrupted or something and
# writes out 0 detections. Then PsfEx fails but in a way that
# an output file is still written. Try to detect & fix this
# case.
# Check the PsfEx output file for POLNAME1
hdr = fitsio.read_header(self.psffn, ext=1)
if hdr.get("POLNAME1", None) is None:
print("Did not find POLNAME1 in PsfEx header", self.psffn, "-- deleting")
os.unlink(self.psffn)
else:
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
# Check SourceExtractor catalog for size = 0
fn = self.sefn
T = fits_table(fn, hdu=2)
print("Read", len(T), "sources from SE catalog", fn)
if T is None or len(T) == 0:
print("SourceExtractor catalog", fn, "has no sources -- deleting")
try:
os.unlink(fn)
except:
pass
if os.path.exists(self.sefn):
se = False
if se:
funpack = True
if pvastrom and os.path.exists(self.pvwcsfn) and (not force):
fn = self.pvwcsfn
if os.path.exists(fn):
try:
wcs = Sip(fn)
except:
print("Failed to read PV-SIP file", fn, "-- deleting")
os.unlink(fn)
if os.path.exists(fn):
pvastrom = False
if (
sky
and (not force)
and ((os.path.exists(self.skyfn) and not splinesky) or (os.path.exists(self.splineskyfn) and splinesky))
):
fn = self.skyfn
if splinesky:
fn = self.splineskyfn
if os.path.exists(fn):
try:
hdr = fitsio.read_header(fn)
except:
print("Failed to read sky file", fn, "-- deleting")
os.unlink(fn)
if os.path.exists(fn):
print("File", fn, "exists -- skipping")
sky = False
if just_check:
return se or psfex or sky or pvastrom
tmpimgfn = None
tmpmaskfn = None
# Unpacked image file
funimgfn = self.imgfn
funmaskfn = self.dqfn
if funpack:
# For FITS files that are not actually fpack'ed, funpack -E
# fails. Check whether actually fpacked.
hdr = fitsio.read_header(self.imgfn, ext=self.hdu)
if not ((hdr["XTENSION"] == "BINTABLE") and hdr.get("ZIMAGE", False)):
print("Image", self.imgfn, "HDU", self.hdu, "is not actually fpacked; not funpacking, just imcopying.")
fcopy = True
tmpimgfn = create_temp(suffix=".fits")
tmpmaskfn = create_temp(suffix=".fits")
if fcopy:
cmd = 'imcopy %s"+%i" %s' % (self.imgfn, self.hdu, tmpimgfn)
else:
cmd = "funpack -E %i -O %s %s" % (self.hdu, tmpimgfn, self.imgfn)
print(cmd)
if os.system(cmd):
raise RuntimeError("Command failed: " + cmd)
funimgfn = tmpimgfn
if use_mask:
if fcopy:
cmd = 'imcopy %s"+%i" %s' % (self.dqfn, self.hdu, tmpmaskfn)
else:
cmd = "funpack -E %i -O %s %s" % (self.hdu, tmpmaskfn, self.dqfn)
print(cmd)
if os.system(cmd):
# raise RuntimeError('Command failed: ' + cmd)
print("Command failed: " + cmd)
M, hdr = fitsio.read(self.dqfn, ext=self.hdu, header=True)
print("Read", M.dtype, M.shape)
fitsio.write(tmpmaskfn, M, header=hdr, clobber=True)
print("Wrote", tmpmaskfn, "with fitsio")
funmaskfn = tmpmaskfn
if se:
# grab header values...
primhdr = self.read_image_primary_header()
magzp = primhdr["MAGZERO"]
seeing = self.pixscale * self.fwhm
# print('FWHM', self.fwhm, 'pix')
# print('pixscale', self.pixscale, 'arcsec/pix')
# print('Seeing', seeing, 'arcsec')
if se:
maskstr = ""
if use_mask:
maskstr = "-FLAG_IMAGE " + funmaskfn
sedir = self.decals.get_se_dir()
trymakedirs(self.sefn, dir=True)
cmd = " ".join(
[
"sex",
"-c",
os.path.join(sedir, "DECaLS.se"),
maskstr,
"-SEEING_FWHM %f" % seeing,
"-PARAMETERS_NAME",
os.path.join(sedir, "DECaLS.param"),
"-FILTER_NAME",
os.path.join(sedir, "gauss_5.0_9x9.conv"),
"-STARNNW_NAME",
os.path.join(sedir, "default.nnw"),
"-PIXEL_SCALE 0",
# SE has a *bizarre* notion of "sigma"
"-DETECT_THRESH 1.0",
"-ANALYSIS_THRESH 1.0",
"-MAG_ZEROPOINT %f" % magzp,
"-CATALOG_NAME",
self.sefn,
funimgfn,
]
)
print(cmd)
if os.system(cmd):
raise RuntimeError("Command failed: " + cmd)
if pvastrom:
# DECam images appear to have PV coefficients up to PVx_10,
# which are up to cubic terms in xi,eta,r. Overshoot what we
# need in SIP terms.
tmpwcsfn = create_temp(suffix=".wcs")
cmd = "wcs-pv2sip -S -o 6 -e %i %s %s" % (self.hdu, self.imgfn, tmpwcsfn)
print(cmd)
if os.system(cmd):
raise RuntimeError("Command failed: " + cmd)
# Read the resulting WCS header and add version info cards to it.
version_hdr = get_version_header(None, self.decals.get_decals_dir(), git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get("PLVER", "").strip()
version_hdr.add_record(dict(name="PLVER", value=plver, comment="CP ver of image file"))
wcshdr = fitsio.read_header(tmpwcsfn)
os.unlink(tmpwcsfn)
for r in wcshdr.records():
version_hdr.add_record(r)
trymakedirs(self.pvwcsfn, dir=True)
fitsio.write(self.pvwcsfn, None, header=version_hdr, clobber=True)
print("Wrote", self.pvwcsfn)
if psfex:
sedir = self.decals.get_se_dir()
trymakedirs(self.psffn, dir=True)
# If we wrote *.psf instead of *.fits in a previous run...
oldfn = self.psffn.replace(".fits", ".psf")
if os.path.exists(oldfn):
print("Moving", oldfn, "to", self.psffn)
os.rename(oldfn, self.psffn)
else:
primhdr = self.read_image_primary_header()
plver = primhdr.get("PLVER", "")
verstr = get_git_version()
cmds = [
"psfex -c %s -PSF_DIR %s %s"
% (os.path.join(sedir, "DECaLS.psfex"), os.path.dirname(self.psffn), self.sefn),
'modhead %s LEGPIPEV %s "legacypipe git version"' % (self.psffn, verstr),
'modhead %s PLVER %s "CP ver of image file"' % (self.psffn, plver),
]
for cmd in cmds:
print(cmd)
rtn = os.system(cmd)
if rtn:
raise RuntimeError("Command failed: " + cmd + ": return value: %i" % rtn)
if sky:
# print('Fitting sky for', self)
hdr = get_version_header(None, self.decals.get_decals_dir(), git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get("PLVER", "")
hdr.delete("PROCTYPE")
hdr.add_record(dict(name="PROCTYPE", value="ccd", comment="NOAO processing type"))
hdr.add_record(dict(name="PRODTYPE", value="skymodel", comment="NOAO product type"))
hdr.add_record(dict(name="PLVER", value=plver, comment="CP ver of image file"))
slc = self.get_good_image_slice(None)
# print('Good image slice is', slc)
img = self.read_image(slice=slc)
wt = self.read_invvar(slice=slc)
if splinesky:
from tractor.splinesky import SplineSky
from scipy.ndimage.morphology import binary_dilation
# Start by subtracting the overall median
med = np.median(img[wt > 0])
# Compute initial model...
skyobj = SplineSky.BlantonMethod(img - med, wt > 0, 512)
skymod = np.zeros_like(img)
skyobj.addTo(skymod)
# Now mask bright objects in (image - initial sky model)
sig1 = 1.0 / np.sqrt(np.median(wt[wt > 0]))
masked = (img - med - skymod) > (5.0 * sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
# Now find the final sky model using that more extensive mask
skyobj = SplineSky.BlantonMethod(img - med, np.logical_not(masked), 512)
# add the median back in
skyobj.offset(med)
if slc is not None:
sy, sx = slc
y0 = sy.start
x0 = sx.start
skyobj.shift(-x0, -y0)
trymakedirs(self.splineskyfn, dir=True)
skyobj.write_fits(self.splineskyfn, primhdr=hdr)
print("Wrote sky model", self.splineskyfn)
else:
img = img[wt > 0]
try:
skyval = estimate_mode(img, raiseOnWarn=True)
skymeth = "mode"
except:
skyval = np.median(img)
skymeth = "median"
tsky = ConstantSky(skyval)
hdr.add_record(dict(name="SKYMETH", value=skymeth, comment="estimate_mode, or fallback to median?"))
trymakedirs(self.skyfn, dir=True)
tsky.write_fits(self.skyfn, hdr=hdr)
print("Wrote sky model", self.skyfn)
if tmpimgfn is not None:
os.unlink(tmpimgfn)
if tmpmaskfn is not None:
os.unlink(tmpmaskfn)
for band in bands:
flux = [ [] for i in range(len(B)) ]
fluxiv = [ [] for i in range(len(B)) ]
mjd = [ [] for i in range(len(B)) ]
J = np.flatnonzero((T.brickname == brick) * (T.filter == band))
print(len(J), 'in brick', brick, 'band', band)
if len(J) == 0:
continue
for j in J:
i = tmap[T.srcid[j]]
flux[i].append(T.flux[j])
fluxiv[i].append(T.flux_ivar[j])
mjd[i].append(T.mjd[j])
nmax = max([len(lst) for lst in flux])
print('Band:', band, 'Nmax:', nmax)
if nmax == 0:
continue
for flist,col,dt in [(flux, 'forced_flux_%s' % band, np.float32),
(fluxiv, 'forced_flux_ivar_%s' % band, np.float32),
(mjd, 'forced_mjd_%s' % band, np.float64),]:
arr = np.zeros((len(B), nmax), dt)
for i,f in enumerate(flist):
arr[i,:len(f)] = f
B.set(col, arr)
outfn = os.path.join('fsweep', brick[:3], 'tractor-%s.fits' % brick)
trymakedirs(outfn, dir=True)
B.writeto(outfn)
def run_calibs(self, psfex=True, sky=True, se=False,
funpack=False, fcopy=False, use_mask=True,
force=False, just_check=False, git_version=None,
splinesky=False):
'''
Run calibration pre-processing steps.
Parameters
----------
just_check: boolean
If True, returns True if calibs need to be run.
'''
from .survey import (create_temp, get_version_header,
get_git_version)
if psfex and os.path.exists(self.psffn) and (not force):
if self.check_psf(self.psffn):
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
if self.check_se_cat(self.sefn):
se = False
if se:
funpack = True
if sky and (not force) and (
(os.path.exists(self.skyfn) and not splinesky) or
(os.path.exists(self.splineskyfn) and splinesky)):
fn = self.skyfn
if splinesky:
fn = self.splineskyfn
if os.path.exists(fn):
try:
hdr = fitsio.read_header(fn)
except:
print('Failed to read sky file', fn, '-- deleting')
os.unlink(fn)
if os.path.exists(fn):
print('File', fn, 'exists -- skipping')
sky = False
if just_check:
return (se or psfex or sky)
todelete = []
if funpack:
# The image & mask files to process (funpacked if necessary)
imgfn,maskfn = self.funpack_files(self.imgfn, self.dqfn, self.hdu, todelete)
else:
imgfn,maskfn = self.imgfn,self.dqfn
if se:
self.run_se('DECaLS', imgfn, maskfn)
if psfex:
self.run_psfex('DECaLS')
if sky:
#print('Fitting sky for', self)
hdr = get_version_header(None, self.survey.get_survey_dir(),
git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
hdr.delete('PROCTYPE')
hdr.add_record(dict(name='PROCTYPE', value='ccd',
comment='NOAO processing type'))
hdr.add_record(dict(name='PRODTYPE', value='skymodel',
comment='NOAO product type'))
hdr.add_record(dict(name='PLVER', value=plver,
comment='CP ver of image file'))
slc = self.get_good_image_slice(None)
#print('Good image slice is', slc)
img = self.read_image(slice=slc)
wt = self.read_invvar(slice=slc)
if splinesky:
from tractor.splinesky import SplineSky
from scipy.ndimage.morphology import binary_dilation
boxsize = DecamImage.splinesky_boxsize
# Start by subtracting the overall median
med = np.median(img[wt>0])
# Compute initial model...
skyobj = SplineSky.BlantonMethod(img - med, wt>0, boxsize)
skymod = np.zeros_like(img)
skyobj.addTo(skymod)
# Now mask bright objects in (image - initial sky model)
sig1 = 1./np.sqrt(np.median(wt[wt>0]))
masked = (img - med - skymod) > (5.*sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
sig1b = 1./np.sqrt(np.median(wt[masked == False]))
print('Sig1 vs sig1b:', sig1, sig1b)
# Now find the final sky model using that more extensive mask
skyobj = SplineSky.BlantonMethod(
img - med, np.logical_not(masked), boxsize)
# add the overall median back in
skyobj.offset(med)
if slc is not None:
sy,sx = slc
y0 = sy.start
x0 = sx.start
skyobj.shift(-x0, -y0)
hdr.add_record(dict(name='SIG1', value=sig1,
comment='Median stdev of unmasked pixels'))
hdr.add_record(dict(name='SIG1B', value=sig1,
comment='Median stdev of unmasked pixels+'))
trymakedirs(self.splineskyfn, dir=True)
skyobj.write_fits(self.splineskyfn, primhdr=hdr)
print('Wrote sky model', self.splineskyfn)
else:
try:
skyval = estimate_mode(img[wt > 0], raiseOnWarn=True)
skymeth = 'mode'
except:
skyval = np.median(img[wt > 0])
skymeth = 'median'
tsky = ConstantSky(skyval)
hdr.add_record(dict(name='SKYMETH', value=skymeth,
comment='estimate_mode, or fallback to median?'))
from scipy.ndimage.morphology import binary_dilation
sig1 = 1./np.sqrt(np.median(wt[wt>0]))
masked = (img - skyval) > (5.*sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
sig1b = 1./np.sqrt(np.median(wt[masked == False]))
print('Sig1 vs sig1b:', sig1, sig1b)
hdr.add_record(dict(name='SIG1', value=sig1,
comment='Median stdev of unmasked pixels'))
hdr.add_record(dict(name='SIG1B', value=sig1,
comment='Median stdev of unmasked pixels+'))
trymakedirs(self.skyfn, dir=True)
tsky.write_fits(self.skyfn, hdr=hdr)
print('Wrote sky model', self.skyfn)
for fn in todelete:
os.unlink(fn)
def render_fake_image(expnum, ccdname, survey_out_dir):
survey = LegacySurveyData()
ccds = survey.find_ccds(expnum=expnum,ccdname=ccdname)
ccd = ccds[0]
band = ccd.filter
im = survey.get_image_object(ccd)
print('Read', im)
tim = im.get_tractor_image(gaussPsf=True, nanomaggies=False, subsky=False)
tim.wcs = NullWCS()
H,W = im.shape
s0 = 4.
dsdy = 1./2000.
x0 = W/2.
y0 = H/2.
ny = 21
nx = 11
# Lay down a grid of point sources, where the PSF is varying in width as a
# function of Y position.
yy = np.linspace(0., H, ny+1)
xx = np.linspace(0., W, nx+1)
# center of cells
yy = yy[:-1] + (yy[1]-yy[0])/2.
xx = xx[:-1] + (xx[1]-xx[0])/2.
modimg = np.zeros_like(tim.getImage())
flux = NanoMaggies.magToNanomaggies(16.)
star = PointSource(PixPos(0.,0.), NanoMaggies(**{ band: flux }))
for y in yy:
for x in xx:
print('Rendering star at', x, y)
s = s0 + dsdy * (y - y0)
psf = NCircularGaussianPSF([s], [1.])
tim.psf = psf
star.pos.x = x
star.pos.y = y
mod = star.getModelPatch(tim)
mod.addTo(modimg)
np.random.seed(42)
noise = np.random.normal(size=modimg.shape)
ie = tim.getInvError()
noise /= ie
noise[ie == 0] = 0
modimg += noise
#
imagedir = os.path.join(survey_out_dir, 'images', 'decam')
trymakedirs(imagedir)
imagefn = os.path.join(imagedir, os.path.basename(ccd.image_filename.strip())).replace(
'.fits.fz', '.fits')
primhdr = im.read_image_primary_header()
hdr = im.read_image_header()
extname = hdr['EXTNAME']
import fitsio
fitsio.write(imagefn, None, header=primhdr, clobber=True)
fitsio.write(imagefn, modimg, header=hdr, extname=extname, clobber=False)
print('Wrote', imagefn)
dq = im.read_dq()
dqfn = imagefn.replace('_ooi_', '_ood_')
fitsio.write(dqfn, None, header=primhdr, clobber=True)
fitsio.write(dqfn, dq, header=hdr, clobber=False)
print('Wrote', dqfn)
iv = im.read_invvar()
wtfn = imagefn.replace('_ooi_', '_oow_')
fitsio.write(wtfn, None, header=primhdr, clobber=True)
fitsio.write(wtfn, iv, header=hdr, clobber=False)
print('Wrote', wtfn)
# cmd = 'ln -s %s %s' % (im.dqfn, dqfn)
# print cmd
# os.system(cmd)
#
# cmd = 'ln -s %s %s' % (im.wtfn, wtfn)
# print cmd
# os.system(cmd)
ccds.image_filename = np.array(['decam/' + os.path.basename(imagefn)])
ccds.image_hdu[0] = 1
ccdfn = os.path.join(survey_out_dir, 'survey-ccds.fits')
ccds.writeto(ccdfn)
print('Wrote', ccdfn)
cal = os.path.join(survey_out_dir, 'calib')
trymakedirs(cal)
for path in ['survey-bricks.fits', 'calib/se-config']:
pathnm = os.path.join(survey_out_dir, path)
if os.path.exists(pathnm):
continue
cmd = 'ln -s %s/%s %s' % (survey.get_survey_dir(), path, pathnm)
print(cmd)
os.system(cmd)
def main():
decals = Decals()
ccds = decals.get_ccds()
print(len(ccds), 'CCDs')
expnums = np.unique(ccds.expnum)
print(len(expnums), 'unique exposures')
for expnum in expnums:
expnumstr = '%08i' % expnum
skyoutfn = os.path.join('splinesky', expnumstr[:5],
'decam-%s.fits' % expnumstr)
psfoutfn = os.path.join('psfex', expnumstr[:5],
'decam-%s.fits' % expnumstr)
if os.path.exists(skyoutfn) and os.path.exists(psfoutfn):
print('Exposure', expnum, 'is done already')
continue
C = ccds[ccds.expnum == expnum]
print(len(C), 'CCDs in expnum', expnum)
psfex = []
psfhdrvals = []
splinesky = []
skyhdrvals = []
for ccd in C:
im = decals.get_image_object(ccd)
fn = im.splineskyfn
if os.path.exists(fn):
T = fits_table(fn)
splinesky.append(T)
# print(fn)
# T.about()
hdr = fitsio.read_header(fn)
skyhdrvals.append(
[hdr[k] for k in ['SKY', 'LEGPIPEV', 'PLVER']] +
[expnum, ccd.ccdname])
else:
print('File not found:', fn)
fn = im.psffn
if os.path.exists(fn):
T = fits_table(fn)
hdr = fitsio.read_header(fn, ext=1)
keys = [
'LOADED',
'ACCEPTED',
'CHI2',
'POLNAXIS',
'POLNGRP',
'PSF_FWHM',
'PSF_SAMP',
'PSFNAXIS',
'PSFAXIS1',
'PSFAXIS2',
'PSFAXIS3',
]
if hdr['POLNAXIS'] == 0:
# No polynomials. Fake it.
T.polgrp1 = np.array([0])
T.polgrp2 = np.array([0])
T.polname1 = np.array(['fake'])
T.polname2 = np.array(['fake'])
T.polzero1 = np.array([0])
T.polzero2 = np.array([0])
T.polscal1 = np.array([1])
T.polscal2 = np.array([1])
T.poldeg1 = np.array([0])
T.poldeg2 = np.array([0])
else:
keys.extend([
'POLGRP1', 'POLNAME1', 'POLZERO1', 'POLSCAL1',
'POLGRP2', 'POLNAME2', 'POLZERO2', 'POLSCAL2',
'POLDEG1'
])
for k in keys:
T.set(k.lower(), np.array([hdr[k]]))
psfex.append(T)
#print(fn)
#T.about()
hdr = fitsio.read_header(fn)
psfhdrvals.append(
[hdr.get(k, '')
for k in ['LEGPIPEV', 'PLVER']] + [expnum, ccd.ccdname])
else:
print('File not found:', fn)
if len(psfex):
padded = pad_arrays([p.psf_mask[0] for p in psfex])
cols = psfex[0].columns()
cols.remove('psf_mask')
T = merge_tables(psfex, columns=cols)
T.psf_mask = np.concatenate([[p] for p in padded])
T.legpipev = np.array([h[0] for h in psfhdrvals])
T.plver = np.array([h[1] for h in psfhdrvals])
T.expnum = np.array([h[2] for h in psfhdrvals])
T.ccdname = np.array([h[3] for h in psfhdrvals])
fn = psfoutfn
trymakedirs(fn, dir=True)
T.writeto(fn)
print('Wrote', fn)
if len(splinesky):
T = fits_table()
T.gridw = np.array([t.gridvals[0].shape[1] for t in splinesky])
T.gridh = np.array([t.gridvals[0].shape[0] for t in splinesky])
padded = pad_arrays([t.gridvals[0] for t in splinesky])
T.gridvals = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.xgrid[0] for t in splinesky])
T.xgrid = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.xgrid[0] for t in splinesky])
T.ygrid = np.concatenate([[p] for p in padded])
cols = splinesky[0].columns()
print('Columns:', cols)
for c in ['gridvals', 'xgrid', 'ygrid']:
cols.remove(c)
T.add_columns_from(merge_tables(splinesky, columns=cols))
T.skyclass = np.array([h[0] for h in skyhdrvals])
T.legpipev = np.array([h[1] for h in skyhdrvals])
T.plver = np.array([h[2] for h in skyhdrvals])
T.expnum = np.array([h[3] for h in skyhdrvals])
T.ccdname = np.array([h[4] for h in skyhdrvals])
fn = skyoutfn
trymakedirs(fn, dir=True)
T.writeto(fn)
print('Wrote', fn)
version_hdr.add_record(dict(name='CAMERA', value='DECam', comment='Dark Energy Camera'))
version_hdr.add_record(dict(name='EXPNUM', value=im.expnum, comment='DECam exposure num'))
version_hdr.add_record(dict(name='CCDNAME', value=im.ccdname, comment='DECam CCD name'))
version_hdr.add_record(dict(name='FILTER', value=tim.band, comment='Bandpass of this image'))
version_hdr.add_record(dict(name='EXPOSURE', value='decam-%s-%s' % (im.expnum, im.ccdname), comment='Name of this image'))
keys = ['TELESCOP','OBSERVAT','OBS-LAT','OBS-LONG','OBS-ELEV',
'INSTRUME']
for key in keys:
if key in tim.primhdr:
version_hdr.add_record(dict(name=key, value=tim.primhdr[key]))
hdr = fitsio.FITSHDR()
units = {'mjd':'sec', 'exptime':'sec', 'flux':'nanomaggy',
'flux_ivar':'1/nanomaggy^2'}
columns = F.get_columns()
for i,col in enumerate(columns):
if col in units:
hdr.add_record(dict(name='TUNIT%i' % (i+1), value=units[col]))
outdir = os.path.dirname(outfn)
if len(outdir):
trymakedirs(outdir)
fitsio.write(outfn, None, header=version_hdr, clobber=True)
F.writeto(outfn, header=hdr, append=True)
print 'Wrote', outfn
print 'Finished forced phot:', Time()-t0
def run_calibs(self,
psfex=True,
sky=True,
funpack=False,
git_version=None,
force=False,
**kwargs):
from astrometry.util.file import trymakedirs
from legacypipe.common import (create_temp, get_version_header,
get_git_version)
print('run_calibs for', self.name, ': sky=', sky, 'kwargs', kwargs)
se = False
if psfex and os.path.exists(self.psffn) and (not force):
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
se = False
if se:
funpack = True
if sky and (not force) and os.path.exists(self.splineskyfn):
sky = False
tmpimgfn = None
tmpmaskfn = None
# Unpacked image file
funimgfn = self.imgfn
funmaskfn = self.dqfn
if funpack:
# For FITS files that are not actually fpack'ed, funpack -E
# fails. Check whether actually fpacked.
hdr = fitsio.read_header(self.imgfn, ext=self.hdu)
if not ((hdr['XTENSION'] == 'BINTABLE')
and hdr.get('ZIMAGE', False)):
print(
'Image', self.imgfn, 'HDU', self.hdu,
'is not actually fpacked; not funpacking, just imcopying.')
fcopy = True
tmpimgfn = create_temp(suffix='.fits')
tmpmaskfn = create_temp(suffix='.fits')
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpimgfn, self.imgfn)
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
funimgfn = tmpimgfn
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpmaskfn, self.dqfn)
print(cmd)
if os.system(cmd):
print('Command failed: ' + cmd)
M, hdr = self._read_fits(self.dqfn, ext=self.hdu, header=True)
print('Read', M.dtype, M.shape)
fitsio.write(tmpmaskfn, M, header=hdr, clobber=True)
print('Wrote', tmpmaskfn, 'with fitsio')
funmaskfn = tmpmaskfn
if se:
# grab header values...
primhdr = self.read_image_primary_header()
magzp = primhdr['MAGZERO']
seeing = self.pixscale * self.fwhm
print('FWHM', self.fwhm, 'pix')
print('pixscale', self.pixscale, 'arcsec/pix')
print('Seeing', seeing, 'arcsec')
if se:
maskstr = '-FLAG_IMAGE ' + funmaskfn
sedir = self.decals.get_se_dir()
trymakedirs(self.sefn, dir=True)
cmd = ' '.join([
'sex',
'-c',
os.path.join(sedir, 'DECaLS.se'),
maskstr,
'-SEEING_FWHM %f' % seeing,
'-PARAMETERS_NAME',
os.path.join(sedir, 'DECaLS.param'),
'-FILTER_NAME',
os.path.join(sedir, 'gauss_5.0_9x9.conv'),
'-STARNNW_NAME',
os.path.join(sedir, 'default.nnw'),
'-PIXEL_SCALE 0',
# SE has a *bizarre* notion of "sigma"
'-DETECT_THRESH 1.0',
'-ANALYSIS_THRESH 1.0',
'-MAG_ZEROPOINT %f' % magzp,
'-CATALOG_NAME',
self.sefn,
funimgfn
])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if psfex:
sedir = self.decals.get_se_dir()
trymakedirs(self.psffn, dir=True)
# If we wrote *.psf instead of *.fits in a previous run...
oldfn = self.psffn.replace('.fits', '.psf')
if os.path.exists(oldfn):
print('Moving', oldfn, 'to', self.psffn)
os.rename(oldfn, self.psffn)
else:
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
verstr = get_git_version()
cmds = [
'psfex -c %s -PSF_DIR %s %s' %
(os.path.join(sedir, 'DECaLS.psfex'),
os.path.dirname(self.psffn), self.sefn),
'modhead %s LEGPIPEV %s "legacypipe git version"' %
(self.psffn, verstr),
'modhead %s PLVER %s "CP ver of image file"' %
(self.psffn, plver)
]
for cmd in cmds:
print(cmd)
rtn = os.system(cmd)
if rtn:
raise RuntimeError('Command failed: ' + cmd +
': return value: %i' % rtn)
if sky:
#print('Fitting sky for', self)
hdr = get_version_header(None,
self.decals.get_decals_dir(),
git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
hdr.delete('PROCTYPE')
hdr.add_record(
dict(name='PROCTYPE',
value='ccd',
comment='NOAO processing type'))
hdr.add_record(
dict(name='PRODTYPE',
value='skymodel',
comment='NOAO product type'))
hdr.add_record(
dict(name='PLVER', value=plver,
comment='CP ver of image file'))
slc = self.get_good_image_slice(None)
#print('Good image slice is', slc)
img = self.read_image(slice=slc)
wt = self.read_invvar(slice=slc)
from tractor.splinesky import SplineSky
from scipy.ndimage.morphology import binary_dilation
# Start by subtracting the overall median
med = np.median(img[wt > 0])
# Compute initial model...
skyobj = SplineSky.BlantonMethod(img - med, wt > 0, 512)
skymod = np.zeros_like(img)
skyobj.addTo(skymod)
# Now mask bright objects in (image - initial sky model)
sig1 = 1. / np.sqrt(np.median(wt[wt > 0]))
masked = (img - med - skymod) > (5. * sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
# Now find the final sky model using that more extensive mask
skyobj = SplineSky.BlantonMethod(img - med, np.logical_not(masked),
512)
# add the median back in
skyobj.offset(med)
if slc is not None:
sy, sx = slc
y0 = sy.start
x0 = sx.start
skyobj.shift(-x0, -y0)
trymakedirs(self.splineskyfn, dir=True)
skyobj.write_fits(self.splineskyfn, primhdr=hdr)
print('Wrote sky model', self.splineskyfn)
if tmpimgfn is not None:
os.unlink(tmpimgfn)
if tmpmaskfn is not None:
os.unlink(tmpmaskfn)
def add_depth_tag(decals, brick, outdir, overwrite=False):
outfn = os.path.join(outdir, 'tractor', brick[:3],
'tractor-%s.fits' % brick)
if os.path.exists(outfn) and not overwrite:
print 'Exists:', outfn
return
fn = decals.find_file('tractor', brick=brick)
if not os.path.exists(fn):
print 'Does not exist:', fn
return
T = fits_table(fn, lower=False)
primhdr = fitsio.read_header(fn)
hdr = fitsio.read_header(fn, ext=1)
print 'Read', len(T), 'from', fn
T.decam_depth = np.zeros((len(T), len(decals.allbands)), np.float32)
T.decam_galdepth = np.zeros((len(T), len(decals.allbands)), np.float32)
bands = 'grz'
ibands = [decals.index_of_band(b) for b in bands]
ix = np.clip(np.round(T.bx).astype(int), 0, 3599)
iy = np.clip(np.round(T.by).astype(int), 0, 3599)
for iband, band in zip(ibands, bands):
fn = decals.find_file('depth', brick=brick, band=band)
if os.path.exists(fn):
print 'Reading', fn
img = fitsio.read(fn)
T.decam_depth[:, iband] = img[iy, ix]
fn = decals.find_file('galdepth', brick=brick, band=band)
if os.path.exists(fn):
print 'Reading', fn
img = fitsio.read(fn)
T.decam_galdepth[:, iband] = img[iy, ix]
outfn = os.path.join(outdir, 'tractor', brick[:3],
'tractor-%s.fits' % brick)
trymakedirs(outfn, dir=True)
for s in [
'Data product of the DECam Legacy Survey (DECaLS)',
'Full documentation at http://legacysurvey.org',
]:
primhdr.add_record(dict(name='COMMENT', value=s, comment=s))
# print 'Header:', hdr
# T.writeto(outfn, header=hdr, primheader=primhdr)
# Yuck, all this to get the units right
tmpfn = outfn + '.tmp'
fits = fitsio.FITS(tmpfn, 'rw', clobber=True)
fits.write(None, header=primhdr)
cols = T.get_columns()
units = []
for i in range(1, len(cols) + 1):
u = hdr.get('TUNIT%i' % i, '')
units.append(u)
# decam_depth units
fluxiv = '1/nanomaggy^2'
units[-2] = fluxiv
units[-1] = fluxiv
fits.write([T.get(c) for c in cols], names=cols, header=hdr, units=units)
fits.close()
os.rename(tmpfn, outfn)
print 'Wrote', outfn
def merge_splinesky(survey, expnum, C, skyoutfn, opt):
splinesky = []
skyhdrvals = []
imobjs = []
Cgood = []
for ccd in C:
im = survey.get_image_object(ccd)
fn = im.splineskyfn
if not os.path.exists(fn):
print('File not found:', fn)
if opt.all_found:
return
continue
imobjs.append(im)
Cgood.append(ccd)
for ccd, im in zip(Cgood, imobjs):
fn = im.splineskyfn
print('Reading', fn)
T = None
try:
T = fits_table(fn)
except KeyboardInterrupt:
raise
except:
print('Failed to read file', fn, ':', sys.exc_info()[1])
if T is not None:
splinesky.append(T)
# print(fn)
# T.about()
hdr = fitsio.read_header(fn)
skyhdrvals.append(
[hdr[k] for k in ['SKY', 'LEGPIPEV', 'PLVER', 'SIG1']] +
[expnum, ccd.ccdname])
if len(splinesky) == 0:
return
T = fits_table()
T.gridw = np.array([t.gridvals[0].shape[1] for t in splinesky])
T.gridh = np.array([t.gridvals[0].shape[0] for t in splinesky])
padded = pad_arrays([t.gridvals[0] for t in splinesky])
T.gridvals = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.xgrid[0] for t in splinesky])
T.xgrid = np.concatenate([[p] for p in padded])
padded = pad_arrays([t.ygrid[0] for t in splinesky])
T.ygrid = np.concatenate([[p] for p in padded])
cols = splinesky[0].columns()
#print('Columns:', cols)
for c in ['gridvals', 'xgrid', 'ygrid']:
cols.remove(c)
T.add_columns_from(merge_tables(splinesky, columns=cols))
T.skyclass = np.array([h[0] for h in skyhdrvals])
T.legpipev = np.array([h[1] for h in skyhdrvals])
T.plver = np.array([h[2] for h in skyhdrvals])
T.sig1 = np.array([h[3] for h in skyhdrvals])
T.expnum = np.array([h[4] for h in skyhdrvals])
T.ccdname = np.array([h[5] for h in skyhdrvals])
fn = skyoutfn
trymakedirs(fn, dir=True)
T.writeto(fn)
print('Wrote', fn)
def main():
import argparse
parser = argparse.ArgumentParser(
description='This script creates small self-contained data sets that '
'are useful for test cases of the pipeline codes.')
parser.add_argument('ccds', help='CCDs table describing region to grab')
parser.add_argument('outdir', help='Output directory name')
parser.add_argument('brick', help='Brick containing these images')
parser.add_argument('--wise', help='For WISE outputs, give the path to a WCS file describing the sub-brick region of interest, eg, a coadd image')
parser.add_argument('--fpack', action='store_true', default=False)
parser.add_argument('--pad', action='store_true', default=False,
help='Keep original image size, but zero out pixels outside ROI')
args = parser.parse_args()
C = fits_table(args.ccds)
print(len(C), 'CCDs in', args.ccds)
C.camera = np.array([c.strip() for c in C.camera])
survey = LegacySurveyData()
bricks = survey.get_bricks_readonly()
outbricks = bricks[np.array([n == args.brick for n in bricks.brickname])]
assert(len(outbricks) == 1)
outsurvey = LegacySurveyData(survey_dir = args.outdir)
trymakedirs(args.outdir)
outbricks.writeto(os.path.join(args.outdir, 'survey-bricks.fits.gz'))
targetwcs = wcs_for_brick(outbricks[0])
H,W = targetwcs.shape
tycho = fits_table(os.path.join(survey.get_survey_dir(), 'tycho2.fits.gz'))
print('Read', len(tycho), 'Tycho-2 stars')
ok,tx,ty = targetwcs.radec2pixelxy(tycho.ra, tycho.dec)
margin = 100
tycho.cut(ok * (tx > -margin) * (tx < W+margin) *
(ty > -margin) * (ty < H+margin))
print('Cut to', len(tycho), 'Tycho-2 stars within brick')
del ok,tx,ty
tycho.writeto(os.path.join(args.outdir, 'tycho2.fits.gz'))
outccds = C.copy()
for c in ['ccd_x0', 'ccd_x1', 'ccd_y0', 'ccd_y1',
'brick_x0', 'brick_x1', 'brick_y0', 'brick_y1',
'plver', 'skyver', 'wcsver', 'psfver', 'skyplver', 'wcsplver',
'psfplver' ]:
outccds.delete_column(c)
outccds.image_hdu[:] = 1
# Convert to list to avoid truncating filenames
outccds.image_filename = [fn for fn in outccds.image_filename]
for iccd,ccd in enumerate(C):
decam = (ccd.camera.strip() == 'decam')
bok = (ccd.camera.strip() == '90prime')
im = survey.get_image_object(ccd)
print('Got', im)
slc = (slice(ccd.ccd_y0, ccd.ccd_y1), slice(ccd.ccd_x0, ccd.ccd_x1))
tim = im.get_tractor_image(slc, pixPsf=True, splinesky=True,
subsky=False, nanomaggies=False)
print('Tim:', tim.shape)
psf = tim.getPsf()
print('PSF:', psf)
psfex = psf.psfex
print('PsfEx:', psfex)
outim = outsurvey.get_image_object(ccd)
print('Output image:', outim)
print('Image filename:', outim.imgfn)
trymakedirs(outim.imgfn, dir=True)
imgdata = tim.getImage()
dqdata = tim.dq
if decam:
# DECam-specific code remaps the DQ codes... re-read raw
print('Reading data quality from', im.dqfn, 'hdu', im.hdu)
dqdata = im._read_fits(im.dqfn, im.hdu, slice=tim.slice)
ivdata = tim.getInvvar()
if args.pad:
# Create zero image of full size, copy in data.
fullsize = np.zeros((ccd.height, ccd.width), imgdata.dtype)
fullsize[slc] = imgdata
imgdata = fullsize
fullsize = np.zeros((ccd.height, ccd.width), dqdata.dtype)
fullsize[slc] = dqdata
dqdata = fullsize
fullsize = np.zeros((ccd.height, ccd.width), ivdata.dtype)
fullsize[slc] = ivdata
ivdata = fullsize
else:
# Adjust the header WCS by x0,y0
crpix1 = tim.hdr['CRPIX1']
crpix2 = tim.hdr['CRPIX2']
tim.hdr['CRPIX1'] = crpix1 - ccd.ccd_x0
tim.hdr['CRPIX2'] = crpix2 - ccd.ccd_y0
# Add image extension to filename
# fitsio doesn't compress .fz by default, so drop .fz suffix
outim.imgfn = outim.imgfn.replace('.fits', '-%s.fits' % im.ccdname)
if not args.fpack:
outim.imgfn = outim.imgfn.replace('.fits.fz', '.fits')
# if bok:
# outim.whtfn = outim.whtfn .replace('.wht.fits', '-%s.wht.fits' % im.ccdname)
# if not args.fpack:
# outim.whtfn = outim.whtfn .replace('.fits.fz', '.fits')
# else:
if True:
outim.wtfn = outim.wtfn .replace('.fits', '-%s.fits' % im.ccdname)
if not args.fpack:
outim.wtfn = outim.wtfn .replace('.fits.fz', '.fits')
if outim.dqfn is not None:
outim.dqfn = outim.dqfn .replace('.fits', '-%s.fits' % im.ccdname)
if not args.fpack:
outim.dqfn = outim.dqfn .replace('.fits.fz', '.fits')
if bok:
outim.psffn = outim.psffn.replace('.psf', '-%s.psf' % im.ccdname)
ccdfn = outim.imgfn
ccdfn = ccdfn.replace(outsurvey.get_image_dir(),'')
if ccdfn.startswith('/'):
ccdfn = ccdfn[1:]
outccds.image_filename[iccd] = ccdfn
print('Changed output filenames to:')
print(outim.imgfn)
print(outim.dqfn)
ofn = outim.imgfn
if args.fpack:
f,ofn = tempfile.mkstemp(suffix='.fits')
os.close(f)
fitsio.write(ofn, None, header=tim.primhdr, clobber=True)
fitsio.write(ofn, imgdata, header=tim.hdr, extname=ccd.ccdname)
if args.fpack:
cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, outim.imgfn, ofn)
print('Running:', cmd)
rtn = os.system(cmd)
assert(rtn == 0)
h,w = tim.shape
if not args.pad:
outccds.width[iccd] = w
outccds.height[iccd] = h
outccds.crpix1[iccd] = crpix1 - ccd.ccd_x0
outccds.crpix2[iccd] = crpix2 - ccd.ccd_y0
wcs = Tan(*[float(x) for x in
[ccd.crval1, ccd.crval2, ccd.crpix1, ccd.crpix2,
ccd.cd1_1, ccd.cd1_2, ccd.cd2_1, ccd.cd2_2, ccd.width, ccd.height]])
if args.pad:
subwcs = wcs
else:
subwcs = wcs.get_subimage(ccd.ccd_x0, ccd.ccd_y0, w, h)
outccds.ra[iccd],outccds.dec[iccd] = subwcs.radec_center()
#if not bok:
if True:
print('Weight filename:', outim.wtfn)
wfn = outim.wtfn
# else:
# print('Weight filename:', outim.whtfn)
# wfn = outim.whtfn
trymakedirs(wfn, dir=True)
ofn = wfn
if args.fpack:
f,ofn = tempfile.mkstemp(suffix='.fits')
os.close(f)
fitsio.write(ofn, None, header=tim.primhdr, clobber=True)
fitsio.write(ofn, ivdata, header=tim.hdr, extname=ccd.ccdname)
if args.fpack:
cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, wfn, ofn)
print('Running:', cmd)
rtn = os.system(cmd)
assert(rtn == 0)
if outim.dqfn is not None:
print('DQ filename', outim.dqfn)
trymakedirs(outim.dqfn, dir=True)
ofn = outim.dqfn
if args.fpack:
f,ofn = tempfile.mkstemp(suffix='.fits')
os.close(f)
fitsio.write(ofn, None, header=tim.primhdr, clobber=True)
fitsio.write(ofn, dqdata, header=tim.hdr, extname=ccd.ccdname)
if args.fpack:
cmd = 'fpack -g -q 0 -S %s > %s && rm %s' % (ofn, outim.dqfn, ofn)
print('Running:', cmd)
rtn = os.system(cmd)
assert(rtn == 0)
print('PSF filename:', outim.psffn)
trymakedirs(outim.psffn, dir=True)
psfex.writeto(outim.psffn)
if not bok:
print('Sky filename:', outim.splineskyfn)
sky = tim.getSky()
print('Sky:', sky)
trymakedirs(outim.splineskyfn, dir=True)
sky.write_fits(outim.splineskyfn)
outccds.writeto(os.path.join(args.outdir, 'survey-ccds-1.fits.gz'))
# WISE
if args.wise is not None:
from wise.forcedphot import unwise_tiles_touching_wcs
from wise.unwise import (unwise_tile_wcs, unwise_tiles_touching_wcs,
get_unwise_tractor_image, get_unwise_tile_dir)
# Read WCS...
print('Reading TAN wcs header from', args.wise)
targetwcs = Tan(args.wise)
tiles = unwise_tiles_touching_wcs(targetwcs)
print('Cut to', len(tiles), 'unWISE tiles')
H,W = targetwcs.shape
r,d = targetwcs.pixelxy2radec(np.array([1, W, W/2, W/2]),
np.array([H/2, H/2, 1, H ]))
roiradec = [r[0], r[1], d[2], d[3]]
unwise_dir = os.environ['UNWISE_COADDS_DIR']
wise_out = os.path.join(args.outdir, 'images', 'unwise')
print('Will write WISE outputs to', wise_out)
unwise_tr_dir = os.environ['UNWISE_COADDS_TIMERESOLVED_DIR']
wise_tr_out = os.path.join(args.outdir, 'images', 'unwise-tr')
print('Will write WISE time-resolved outputs to', wise_tr_out)
W = fits_table(os.path.join(unwise_tr_dir, 'time_resolved_neo1-atlas.fits'))
print('Read', len(W), 'time-resolved WISE coadd tiles')
W.cut(np.array([t in tiles.coadd_id for t in W.coadd_id]))
print('Cut to', len(W), 'time-resolved vs', len(tiles), 'full-depth')
# Write the time-resolved index subset.
W.writeto(os.path.join(wise_tr_out, 'time_resolved_neo1-atlas.fits'))
# this ought to be enough for anyone =)
Nepochs = 5
wisedata = []
# full depth
for band in [1,2,3,4]:
wisedata.append((unwise_dir, wise_out, tiles.coadd_id, band))
# time-resolved
for band in [1,2]:
# W1 is bit 0 (value 0x1), W2 is bit 1 (value 0x2)
bitmask = (1 << (band-1))
for e in range(Nepochs):
# Which tiles have images for this epoch?
I = np.flatnonzero(W.epoch_bitmask[:,e] & bitmask)
if len(I) == 0:
continue
print('Epoch %i: %i tiles:' % (e, len(I)), W.coadd_id[I])
edir = os.path.join(unwise_tr_dir, 'e%03i' % e)
eoutdir = os.path.join(wise_tr_out, 'e%03i' % e)
wisedata.append((edir, eoutdir, tiles.coadd_id[I], band))
wrote_masks = set()
for indir, outdir, tiles, band in wisedata:
for tile in tiles:
wanyband = 'w'
tim = get_unwise_tractor_image(indir, tile, band,
bandname=wanyband, roiradecbox=roiradec)
print('Got unWISE tim', tim)
print(tim.shape)
thisdir = get_unwise_tile_dir(outdir, tile)
print('Directory for this WISE tile:', thisdir)
base = os.path.join(thisdir, 'unwise-%s-w%i-' % (tile, band))
print('Base filename:', base)
masked = True
mu = 'm' if masked else 'u'
imfn = base + 'img-%s.fits' % mu
ivfn = base + 'invvar-%s.fits.gz' % mu
nifn = base + 'n-%s.fits.gz' % mu
nufn = base + 'n-u.fits.gz'
#print('WISE image header:', tim.hdr)
# Adjust the header WCS by x0,y0
wcs = tim.wcs.wcs
tim.hdr['CRPIX1'] = wcs.crpix[0]
tim.hdr['CRPIX2'] = wcs.crpix[1]
H,W = tim.shape
tim.hdr['IMAGEW'] = W
tim.hdr['IMAGEH'] = H
print('WCS:', wcs)
print('Header CRPIX', tim.hdr['CRPIX1'], tim.hdr['CRPIX2'])
trymakedirs(imfn, dir=True)
fitsio.write(imfn, tim.getImage(), header=tim.hdr, clobber=True)
print('Wrote', imfn)
fitsio.write(ivfn, tim.getInvvar(), header=tim.hdr, clobber=True)
print('Wrote', ivfn)
fitsio.write(nifn, tim.nims, header=tim.hdr, clobber=True)
print('Wrote', nifn)
fitsio.write(nufn, tim.nuims, header=tim.hdr, clobber=True)
print('Wrote', nufn)
if not (indir,tile) in wrote_masks:
print('Looking for mask file for', indir, tile)
# record that we tried this dir/tile combo
wrote_masks.add((indir,tile))
for idir in indir.split(':'):
tdir = get_unwise_tile_dir(idir, tile)
maskfn = 'unwise-%s-msk.fits.gz' % tile
fn = os.path.join(tdir, maskfn)
print('Mask file:', fn)
if os.path.exists(fn):
print('Reading', fn)
(x0,x1,y0,y1) = tim.roi
roislice = (slice(y0,y1), slice(x0,x1))
F = fitsio.FITS(fn)[0]
hdr = F.read_header()
M = F[roislice]
outfn = os.path.join(thisdir, maskfn)
fitsio.write(outfn, M, header=tim.hdr, clobber=True)
print('Wrote', outfn)
break
outC = outsurvey.get_ccds_readonly()
for iccd,ccd in enumerate(outC):
outim = outsurvey.get_image_object(ccd)
print('Got output image:', outim)
otim = outim.get_tractor_image(pixPsf=True, splinesky=True)
print('Got output tim:', otim)
def main(survey=None, opt=None):
'''Driver function for forced photometry of individual Legacy
Survey images.
'''
if opt is None:
parser = get_parser()
opt = parser.parse_args()
Time.add_measurement(MemMeas)
t0 = Time()
if os.path.exists(opt.outfn):
print('Ouput file exists:', opt.outfn)
sys.exit(0)
if opt.derivs and opt.agn:
print('Sorry, can\'t do --derivs AND --agn')
sys.exit(0)
if not opt.forced:
opt.apphot = True
zoomslice = None
if opt.zoom is not None:
(x0, x1, y0, y1) = opt.zoom
zoomslice = (slice(y0, y1), slice(x0, x1))
ps = None
if opt.plots is not None:
import pylab as plt
from astrometry.util.plotutils import PlotSequence
ps = PlotSequence(opt.plots)
# Try parsing filename as exposure number.
try:
expnum = int(opt.expnum)
filename = None
except:
# make this 'None' for survey.find_ccds()
expnum = None
filename = opt.expnum
# Try parsing HDU number
try:
hdu = int(opt.ccdname)
ccdname = None
except:
hdu = -1
ccdname = opt.ccdname
if survey is None:
survey = LegacySurveyData()
catsurvey = survey
if opt.catalog_dir is not None:
catsurvey = LegacySurveyData(survey_dir=opt.catalog_dir)
if filename is not None and hdu >= 0:
# FIXME -- try looking up in CCDs file?
# Read metadata from file
print('Warning: faking metadata from file contents')
T = exposure_metadata([filename], hdus=[hdu])
print('Metadata:')
T.about()
if not 'ccdzpt' in T.columns():
phdr = fitsio.read_header(filename)
T.ccdzpt = np.array([phdr['MAGZERO']])
print('WARNING: using header MAGZERO')
T.ccdraoff = np.array([0.])
T.ccddecoff = np.array([0.])
print('WARNING: setting CCDRAOFF, CCDDECOFF to zero.')
else:
# Read metadata from survey-ccds.fits table
T = survey.find_ccds(expnum=expnum, ccdname=ccdname)
print(len(T), 'with expnum', expnum, 'and CCDname', ccdname)
if hdu >= 0:
T.cut(T.image_hdu == hdu)
print(len(T), 'with HDU', hdu)
if filename is not None:
T.cut(np.array([f.strip() == filename for f in T.image_filename]))
print(len(T), 'with filename', filename)
if opt.camera is not None:
T.cut(T.camera == opt.camera)
print(len(T), 'with camera', opt.camera)
assert (len(T) == 1)
ccd = T[0]
im = survey.get_image_object(ccd)
if opt.do_calib:
#from legacypipe.survey import run_calibs
#kwa = dict(splinesky=True)
#run_calibs((im, kwa))
im.run_calibs(splinesky=True)
tim = im.get_tractor_image(slc=zoomslice,
pixPsf=True,
splinesky=True,
constant_invvar=opt.constant_invvar,
hybridPsf=opt.hybrid_psf,
normalizePsf=opt.normalize_psf)
print('Got tim:', tim)
print('Read image:', Time() - t0)
if opt.catfn in ['DR1', 'DR2', 'DR3', 'DR5', 'DR']:
margin = 20
TT = []
chipwcs = tim.subwcs
bricks = bricks_touching_wcs(chipwcs, survey=catsurvey)
for b in bricks:
# there is some overlap with this brick... read the catalog.
fn = catsurvey.find_file('tractor', brick=b.brickname)
if not os.path.exists(fn):
print('WARNING: catalog', fn, 'does not exist. Skipping!')
continue
print('Reading', fn)
T = fits_table(fn)
ok, xx, yy = chipwcs.radec2pixelxy(T.ra, T.dec)
W, H = chipwcs.get_width(), chipwcs.get_height()
I = np.flatnonzero((xx >= -margin) * (xx <= (W + margin)) *
(yy >= -margin) * (yy <= (H + margin)))
T.cut(I)
print('Cut to', len(T), 'sources within image + margin')
# print('Brick_primary:', np.unique(T.brick_primary))
T.cut(T.brick_primary)
print('Cut to', len(T), 'on brick_primary')
for col in ['out_of_bounds', 'left_blob']:
if col in T.get_columns():
T.cut(T.get(col) == False)
print('Cut to', len(T), 'on', col)
if len(T):
TT.append(T)
if len(TT) == 0:
print('No sources to photometer.')
return 0
T = merge_tables(TT, columns='fillzero')
T._header = TT[0]._header
del TT
print('Total of', len(T), 'catalog sources')
# Fix up various failure modes:
# FixedCompositeGalaxy(pos=RaDecPos[240.51147402832561, 10.385488075518923], brightness=NanoMaggies: g=(flux -2.87), r=(flux -5.26), z=(flux -7.65), fracDev=FracDev(0.60177207), shapeExp=re=3.78351e-44, e1=9.30367e-13, e2=1.24392e-16, shapeDev=re=inf, e1=-0, e2=-0)
# -> convert to EXP
I = np.flatnonzero(
np.array([((t.type == 'COMP') and (not np.isfinite(t.shapedev_r)))
for t in T]))
if len(I):
print('Converting', len(I), 'bogus COMP galaxies to EXP')
for i in I:
T.type[i] = 'EXP'
# Same thing with the exp component.
# -> convert to DEV
I = np.flatnonzero(
np.array([((t.type == 'COMP') and (not np.isfinite(t.shapeexp_r)))
for t in T]))
if len(I):
print('Converting', len(I), 'bogus COMP galaxies to DEV')
for i in I:
T.type[i] = 'DEV'
if opt.write_cat:
T.writeto(opt.write_cat)
print('Wrote catalog to', opt.write_cat)
else:
T = fits_table(opt.catfn)
surveydir = survey.get_survey_dir()
del survey
kwargs = {}
cols = T.get_columns()
if 'flux_r' in cols and not 'decam_flux_r' in cols:
kwargs.update(fluxPrefix='')
cat = read_fits_catalog(T, **kwargs)
# Replace the brightness (which will be a NanoMaggies with g,r,z)
# with a NanoMaggies with this image's band only.
for src in cat:
src.brightness = NanoMaggies(**{tim.band: 1.})
print('Read catalog:', Time() - t0)
print('Forced photom...')
F = run_forced_phot(cat,
tim,
ceres=opt.ceres,
derivs=opt.derivs,
fixed_also=True,
agn=opt.agn,
do_forced=opt.forced,
do_apphot=opt.apphot,
ps=ps)
t0 = Time()
F.release = T.release
F.brickid = T.brickid
F.brickname = T.brickname
F.objid = T.objid
F.camera = np.array([ccd.camera] * len(F))
F.expnum = np.array([im.expnum] * len(F)).astype(np.int32)
F.ccdname = np.array([im.ccdname] * len(F))
# "Denormalizing"
F.filter = np.array([tim.band] * len(T))
F.mjd = np.array([tim.primhdr['MJD-OBS']] * len(T))
F.exptime = np.array([tim.primhdr['EXPTIME']] * len(T)).astype(np.float32)
F.ra = T.ra
F.dec = T.dec
ok, x, y = tim.sip_wcs.radec2pixelxy(T.ra, T.dec)
F.x = (x - 1).astype(np.float32)
F.y = (y - 1).astype(np.float32)
h, w = tim.shape
F.mask = tim.dq[np.clip(np.round(F.y).astype(int), 0, h - 1),
np.clip(np.round(F.x).astype(int), 0, w - 1)]
program_name = sys.argv[0]
version_hdr = get_version_header(program_name, surveydir)
filename = getattr(ccd, 'image_filename')
if filename is None:
# HACK -- print only two directory names + filename of CPFILE.
fname = os.path.basename(im.imgfn)
d = os.path.dirname(im.imgfn)
d1 = os.path.basename(d)
d = os.path.dirname(d)
d2 = os.path.basename(d)
filename = os.path.join(d2, d1, fname)
print('Trimmed filename to', filename)
version_hdr.add_record(
dict(name='CPFILE', value=filename, comment='CP file'))
version_hdr.add_record(dict(name='CPHDU', value=im.hdu, comment='CP ext'))
version_hdr.add_record(
dict(name='CAMERA', value=ccd.camera, comment='Camera'))
version_hdr.add_record(
dict(name='EXPNUM', value=im.expnum, comment='Exposure num'))
version_hdr.add_record(
dict(name='CCDNAME', value=im.ccdname, comment='CCD name'))
version_hdr.add_record(
dict(name='FILTER', value=tim.band, comment='Bandpass of this image'))
version_hdr.add_record(
dict(name='EXPOSURE',
value='%s-%s-%s' % (ccd.camera, im.expnum, im.ccdname),
comment='Name of this image'))
keys = [
'TELESCOP', 'OBSERVAT', 'OBS-LAT', 'OBS-LONG', 'OBS-ELEV', 'INSTRUME'
]
for key in keys:
if key in tim.primhdr:
version_hdr.add_record(dict(name=key, value=tim.primhdr[key]))
hdr = fitsio.FITSHDR()
units = {
'exptime': 'sec',
'flux': 'nanomaggy',
'flux_ivar': '1/nanomaggy^2'
}
columns = F.get_columns()
for i, col in enumerate(columns):
if col in units:
hdr.add_record(dict(name='TUNIT%i' % (i + 1), value=units[col]))
outdir = os.path.dirname(opt.outfn)
if len(outdir):
trymakedirs(outdir)
fitsio.write(opt.outfn, None, header=version_hdr, clobber=True)
F.writeto(opt.outfn, header=hdr, append=True)
print('Wrote', opt.outfn)
if opt.save_model or opt.save_data:
hdr = fitsio.FITSHDR()
tim.getWcs().wcs.add_to_header(hdr)
if opt.save_model:
print('Getting model image...')
tr = Tractor([tim], cat)
mod = tr.getModelImage(tim)
fitsio.write(opt.save_model, mod, header=hdr, clobber=True)
print('Wrote', opt.save_model)
if opt.save_data:
fitsio.write(opt.save_data, tim.getImage(), header=hdr, clobber=True)
print('Wrote', opt.save_data)
print('Finished forced phot:', Time() - t0)
return 0
def rbmain():
from legacypipe.catalog import read_fits_catalog
from legacypipe.survey import LegacySurveyData, wcs_for_brick
from tractor.galaxy import DevGalaxy
from tractor import PointSource, Catalog
from tractor import GaussianMixturePSF
from legacypipe.survey import BrickDuck
from legacypipe.forced_photom import main as forced_main
from astrometry.util.file import trymakedirs
import shutil
ceres = 'ceres' in sys.argv
psfex = 'psfex' in sys.argv
for v in [
'UNWISE_COADDS_TIMERESOLVED_DIR', 'SKY_TEMPLATE_DIR',
'LARGEGALAXIES_CAT', 'GAIA_CAT_DIR', 'TYCHO2_KD_DIR'
]:
if v in os.environ:
del os.environ[v]
oldargs = sys.argv
sys.argv = [sys.argv[0]]
main()
sys.argv = oldargs
# Test create_kdtree and (reading CCD kd-tree)!
indir = os.path.join(os.path.dirname(__file__), 'testcase6')
with tempfile.TemporaryDirectory() as surveydir:
files = [
'calib', 'gaia', 'images', 'survey-bricks.fits.gz',
'tycho2.kd.fits'
]
for fn in files:
src = os.path.join(indir, fn)
dst = os.path.join(surveydir, fn)
#trymakedirs(dst, dir=True)
print('Copy', src, dst)
if os.path.isfile(src):
shutil.copy(src, dst)
else:
shutil.copytree(src, dst)
from legacypipe.create_kdtrees import create_kdtree
infn = os.path.join(indir, 'survey-ccds-1.fits.gz')
outfn = os.path.join(surveydir, 'survey-ccds-1.kd.fits')
create_kdtree(infn, outfn, False)
os.environ['TYCHO2_KD_DIR'] = surveydir
outdir = 'out-testcase6-kd'
main(args=[
'--brick', '1102p240', '--zoom', '500', '600', '650', '750',
'--force-all', '--no-write', '--no-wise', '--no-gaia',
'--survey-dir', surveydir, '--outdir', outdir
])
fn = os.path.join(outdir, 'tractor', '110', 'tractor-1102p240.fits')
assert (os.path.exists(fn))
T = fits_table(fn)
assert (len(T) == 2)
# Since there is a Tycho-2 star in the blob, forced to be PSF.
assert (T.type[0].strip() == 'PSF')
assert (T.type[1].strip() == 'PSF')
# There is a Tycho-2 star in the blob.
I = np.flatnonzero(T.ref_cat == 'T2')
assert (len(I) == 1)
assert (T.ref_id[I][0] == 1909016711)
cat = read_fits_catalog(T)
assert (len(cat) == 2)
assert (isinstance(cat[0], PointSource))
assert (isinstance(cat[1], PointSource))
cat, ivs = read_fits_catalog(T, invvars=True)
assert (len(cat) == 2)
assert (isinstance(cat[0], PointSource))
assert (isinstance(cat[1], PointSource))
cat2 = Catalog(*cat)
assert (len(ivs) == len(cat2.getParams()))
# test --fit-on-coadds
outdir = 'out-testcase6-coadds'
main(args=[
'--brick', '1102p240', '--zoom', '500', '600', '650', '750',
'--force-all', '--no-write', '--no-wise', '--no-gaia',
'--survey-dir', surveydir, '--fit-on-coadds', '--outdir', outdir
])
fn = os.path.join(outdir, 'tractor', '110', 'tractor-1102p240.fits')
assert (os.path.exists(fn))
T = fits_table(fn)
assert (len(T) == 2)
# Since there is a Tycho-2 star in the blob, forced to be PSF.
assert (T.type[0].strip() == 'PSF')
assert (T.type[1].strip() == 'PSF')
# There is a Tycho-2 star in the blob.
I = np.flatnonzero(T.ref_cat == 'T2')
assert (len(I) == 1)
assert (T.ref_id[I][0] == 1909016711)
del os.environ['TYCHO2_KD_DIR']
# test --skip-coadds
r = main(args=[
'--brick', '1102p240', '--zoom', '500', '600', '650', '750',
'--force-all', '--no-write', '--no-wise', '--no-gaia',
'--survey-dir', surveydir, '--outdir', outdir, '--skip-coadd'
])
assert (r == 0)
# test --skip
r = main(args=[
'--brick', '1102p240', '--zoom', '500', '600', '650', '750',
'--force-all', '--no-write', '--no-wise', '--no-gaia',
'--survey-dir', surveydir, '--outdir', outdir, '--skip'
])
assert (r == 0)
# NothingToDoError (neighbouring brick)
r = main(args=[
'--brick', '1102p240', '--zoom', '0', '100', '0', '100',
'--force-all', '--no-write', '--no-wise', '--no-gaia',
'--survey-dir', surveydir, '--outdir', outdir
])
assert (r == 0)
surveydir = os.path.join(os.path.dirname(__file__), 'testcase9')
# Test for some get_tractor_image kwargs
survey = LegacySurveyData(surveydir)
fakebrick = BrickDuck(9.1228, 3.3975, 'quack')
wcs = wcs_for_brick(fakebrick, W=100, H=100)
ccds = survey.ccds_touching_wcs(wcs)
ccd = ccds[0]
im = survey.get_image_object(ccd)
H, W = wcs.shape
targetrd = np.array([
wcs.pixelxy2radec(x, y)
for x, y in [(1, 1), (W, 1), (W, H), (1, H), (1, 1)]
])
tim = im.get_tractor_image(radecpoly=targetrd)
assert (tim.getImage() is not None)
assert (tim.getInvError() is not None)
assert (tim.dq is not None)
tim2 = im.get_tractor_image(radecpoly=targetrd, pixels=False)
assert (np.all(tim2.getImage() == 0.))
tim4 = im.get_tractor_image(radecpoly=targetrd, invvar=False)
u = np.unique(tim4.inverr)
assert (len(u) == 1)
u = u[0]
target = tim4.zpscale / tim4.sig1
assert (np.abs(u / target - 1.) < 0.001)
tim3 = im.get_tractor_image(radecpoly=targetrd, invvar=False, dq=False)
assert (not hasattr(tim3, 'dq'))
tim5 = im.get_tractor_image(radecpoly=targetrd, gaussPsf=True)
print(tim5.getPsf())
assert (isinstance(tim5.getPsf(), GaussianMixturePSF))
surveydir = os.path.join(os.path.dirname(__file__), 'testcase12')
os.environ['TYCHO2_KD_DIR'] = surveydir
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
os.environ['UNWISE_MODEL_SKY_DIR'] = os.path.join(surveydir, 'images',
'unwise-mod')
#python legacypipe/runbrick.py --radec --width 100 --height 100 --outdir dup5b --survey-dir test/testcase12 --force-all --no-wise
unwdir = os.path.join(surveydir, 'images', 'unwise')
main(args=[
'--radec', '346.684', '12.791', '--width', '100', '--height', '100',
'--no-wise-ceres', '--unwise-dir', unwdir, '--survey-dir', surveydir,
'--outdir', 'out-testcase12', '--skip-coadd', '--force-all'
])
# --plots for stage_wise_forced
main(args=[
'--radec', '346.684', '12.791', '--width', '100', '--height', '100',
'--no-wise-ceres', '--unwise-dir', unwdir, '--survey-dir', surveydir,
'--outdir', 'out-testcase12', '--stage', 'wise_forced', '--plots'
])
del os.environ['GAIA_CAT_DIR']
del os.environ['GAIA_CAT_VER']
del os.environ['TYCHO2_KD_DIR']
del os.environ['UNWISE_MODEL_SKY_DIR']
M = fitsio.read(
'out-testcase12/coadd/cus/custom-346684p12791/legacysurvey-custom-346684p12791-maskbits.fits.fz'
)
# Count masked & unmasked bits (the cluster splits this 100x100 field)
from collections import Counter
c = Counter(M.ravel())
from legacypipe.bits import MASKBITS
assert (c[0] >= 4000)
assert (c[MASKBITS['CLUSTER']] >= 4000)
surveydir = os.path.join(os.path.dirname(__file__), 'testcase9')
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
os.environ['LARGEGALAXIES_CAT'] = os.path.join(surveydir,
'sga-sub.kd.fits')
main(args=[
'--radec', '9.1228', '3.3975', '--width', '100', '--height', '100',
'--old-calibs-ok', '--no-wise-ceres', '--no-wise', '--survey-dir',
surveydir, '--outdir', 'out-testcase9', '--skip', '--force-all',
'--ps', 'tc9-ps.fits', '--ps-t0',
str(int(time.time()))
])
# (omit --force-all --no-write... reading from pickles below!)
# Test with --apodize
main(args=[
'--radec', '9.1228', '3.3975', '--width', '100', '--height', '100',
'--old-calibs-ok', '--no-wise', '--force-all', '--no-write',
'--survey-dir', surveydir, '--outdir', 'out-testcase9-ap', '--apodize'
])
main(args=[
'--radec', '9.1228', '3.3975', '--width', '100', '--height', '100',
'--old-calibs-ok', '--no-wise-ceres', '--no-wise', '--survey-dir',
surveydir, '--outdir', 'out-testcase9', '--plots', '--stage', 'halos'
])
main(args=[
'--radec', '9.1228', '3.3975', '--width', '100', '--height', '100',
'--old-calibs-ok', '--no-wise-ceres', '--no-wise', '--survey-dir',
surveydir, '--outdir', 'out-testcase9-coadds', '--stage',
'image_coadds', '--blob-image'
])
T = fits_table(
'out-testcase9/tractor/cus/tractor-custom-009122p03397.fits')
assert (len(T) == 4)
# Gaia star becomes a DUP!
assert (np.sum([t == 'DUP' for t in T.type]) == 1)
# LSLGA galaxy exists!
Igal = np.flatnonzero([r == 'L3' for r in T.ref_cat])
assert (len(Igal) == 1)
assert (np.all(T.ref_id[Igal] > 0))
assert (T.type[Igal[0]] == 'SER')
# --brick and --zoom rather than --radec --width --height
main(args=[
'--survey-dir', surveydir, '--outdir', 'out-testcase9b', '--zoom',
'1950', '2050', '340', '440', '--brick', '0091p035', '--force-all'
])
# test forced phot??
shutil.copy('test/testcase9/survey-bricks.fits.gz', 'out-testcase9b')
forced_main(args=[
'--survey-dir', surveydir, '--no-ceres', '--catalog-dir',
'out-testcase9b', '372546', 'N26', 'forced1.fits'
])
assert (os.path.exists('forced1.fits'))
_ = fits_table('forced1.fits')
# ... more tests...!
forced_main(args=[
'--survey-dir', surveydir, '--no-ceres', '--catalog-dir',
'out-testcase9b', '--derivs', '--threads', '2', '--apphot', '372547',
'N26', 'forced2.fits'
])
assert (os.path.exists('forced2.fits'))
_ = fits_table('forced2.fits')
forced_main(args=[
'--survey-dir', surveydir, '--no-ceres', '--catalog-dir',
'out-testcase9b', '--agn', '257266', 'S21', 'forced3.fits'
])
assert (os.path.exists('forced3.fits'))
_ = fits_table('forced3.fits')
if ceres:
forced_main(args=[
'--survey-dir', surveydir, '--catalog-dir', 'out-testcase9b',
'--derivs', '--threads', '2', '--apphot', '372546', 'N26',
'forced4.fits'
])
assert (os.path.exists('forced4.fits'))
_ = fits_table('forced4.fits')
# Test cache_dir
with tempfile.TemporaryDirectory() as cachedir, \
tempfile.TemporaryDirectory() as tempsurveydir:
files = []
for dirpath, _, filenames in os.walk(surveydir):
for fn in filenames:
path = os.path.join(dirpath, fn)
relpath = os.path.relpath(path, surveydir)
files.append(relpath)
# cache or no?
files.sort()
files_cache = files[::2]
files_nocache = files[1::2]
# Survey-ccds *must* be in nocache.
fn = 'survey-ccds-1.kd.fits'
if fn in files_cache:
files_cache.remove(fn)
files_nocache.append(fn)
for fn in files_cache:
src = os.path.join(surveydir, fn)
dst = os.path.join(cachedir, fn)
trymakedirs(dst, dir=True)
print('Copy', src, dst)
shutil.copy(src, dst)
for fn in files_nocache:
src = os.path.join(surveydir, fn)
dst = os.path.join(tempsurveydir, fn)
trymakedirs(dst, dir=True)
print('Copy', src, dst)
shutil.copy(src, dst)
main(args=[
'--radec', '9.1228', '3.3975', '--width', '100', '--height', '100',
'--no-wise', '--survey-dir', tempsurveydir, '--cache-dir',
cachedir, '--outdir', 'out-testcase9cache', '--force-all'
])
del os.environ['GAIA_CAT_DIR']
del os.environ['GAIA_CAT_VER']
del os.environ['LARGEGALAXIES_CAT']
# if ceres:
# surveydir = os.path.join(os.path.dirname(__file__), 'testcase3')
# main(args=['--brick', '2447p120', '--zoom', '1020', '1070', '2775', '2815',
# '--no-wise', '--force-all', '--no-write', '--ceres',
# '--survey-dir', surveydir,
# '--outdir', 'out-testcase3-ceres',
# '--no-depth-cut'])
# MzLS + BASS data
# python legacypipe/runbrick.py --run north --brick 1773p595 --zoom 1300 1500 700 900 --survey-dir dr9-north -s coadds
# fitscopy coadd/177/1773p595/legacysurvey-1773p595-ccds.fits"[#row<3 || #row==12]" cx.fits
# python legacyanalysis/create_testcase.py cx.fits test/mzlsbass2 1773p595 --survey-dir dr9-north/ --fpack
surveydir2 = os.path.join(os.path.dirname(__file__), 'mzlsbass2')
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir2, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
main(args=[
'--brick', '1773p595', '--zoom', '1300', '1500', '700', '900',
'--no-wise', '--force-all', '--no-write', '--survey-dir', surveydir2,
'--outdir', 'out-mzlsbass2'
])
T = fits_table('out-mzlsbass2/tractor/177/tractor-1773p595.fits')
assert (np.sum(T.ref_cat == 'G2') == 3)
assert (np.sum(T.ref_id > 0) == 3)
# Test --max-blobsize, --checkpoint, --bail-out
outdir = 'out-mzlsbass2b'
chk = 'checkpoint-mzb2b.p'
if os.path.exists(chk):
os.unlink(chk)
main(args=[
'--brick', '1773p595', '--zoom', '1300', '1500', '700', '900',
'--no-wise', '--force-all', '--stage', 'fitblobs', '--write-stage',
'srcs', '--survey-dir', surveydir2, '--outdir', outdir, '--checkpoint',
chk, '--nblobs', '3'
])
# err... --max-blobsize does not result in bailed-out blobs masked,
# because it treats large blobs as *completed*...
#'--max-blobsize', '3000',
outdir = 'out-mzlsbass2c'
main(args=[
'--brick', '1773p595', '--zoom', '1300', '1500', '700', '900',
'--no-wise', '--force-all', '--survey-dir', surveydir2, '--outdir',
outdir, '--bail-out', '--checkpoint', chk, '--no-write'
])
del os.environ['GAIA_CAT_DIR']
del os.environ['GAIA_CAT_VER']
M = fitsio.read(
os.path.join(outdir, 'coadd', '177', '1773p595',
'legacysurvey-1773p595-maskbits.fits.fz'))
assert (np.sum((M & MASKBITS['BAILOUT']) > 0) >= 1000)
# Test RexGalaxy
surveydir = os.path.join(os.path.dirname(__file__), 'testcase6')
outdir = 'out-testcase6-rex'
the_args = [
'--brick',
'1102p240',
'--zoom',
'500',
'600',
'650',
'750',
'--force-all',
'--no-write',
'--no-wise',
'--skip-calibs',
#'--rex', #'--plots',
'--survey-dir',
surveydir,
'--outdir',
outdir
]
print('python legacypipe/runbrick.py', ' '.join(the_args))
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
main(args=the_args)
fn = os.path.join(outdir, 'tractor', '110', 'tractor-1102p240.fits')
assert (os.path.exists(fn))
T = fits_table(fn)
assert (len(T) == 2)
print('Types:', T.type)
# Since there is a Tycho-2 star in the blob, forced to be PSF.
assert (T.type[0].strip() == 'PSF')
cmd = (
'(cd %s && sha256sum -c %s)' %
(outdir, os.path.join('tractor', '110', 'brick-1102p240.sha256sum')))
print(cmd)
rtn = os.system(cmd)
assert (rtn == 0)
# Test with a Tycho-2 star in the blob.
surveydir = os.path.join(os.path.dirname(__file__), 'testcase6')
outdir = 'out-testcase6'
main(args=[
'--brick', '1102p240', '--zoom', '500', '600', '650', '750',
'--force-all', '--no-write', '--no-wise', '--survey-dir', surveydir,
'--outdir', outdir
])
fn = os.path.join(outdir, 'tractor', '110', 'tractor-1102p240.fits')
assert (os.path.exists(fn))
T = fits_table(fn)
assert (len(T) == 2)
print('Types:', T.type)
# Since there is a Tycho-2 star in the blob, forced to be PSF.
assert (T.type[0].strip() == 'PSF')
del os.environ['GAIA_CAT_DIR']
del os.environ['GAIA_CAT_VER']
# Test that we can run splinesky calib if required...
from legacypipe.decam import DecamImage
DecamImage.splinesky_boxsize = 128
surveydir = os.path.join(os.path.dirname(__file__), 'testcase4')
survey = LegacySurveyData(surveydir)
# get brick by id
brickid = 473357
brick = survey.get_brick(brickid)
assert (brick.brickname == '1867p255')
assert (brick.brickid == brickid)
outdir = 'out-testcase4'
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
fn = os.path.join(surveydir, 'calib', 'sky-single', 'decam', 'CP',
'V4.8.2', 'CP20170315', 'c4d_170316_062107_ooi_z_ls9',
'c4d_170316_062107_ooi_z_ls9-N2-splinesky.fits')
if os.path.exists(fn):
os.unlink(fn)
main(args=[
'--brick', '1867p255', '--zoom', '2050', '2300', '1150', '1400',
'--force-all', '--no-write', '--coadd-bw', '--unwise-dir',
os.path.join(surveydir, 'images', 'unwise'), '--unwise-tr-dir',
os.path.join(surveydir, 'images',
'unwise-tr'), '--blob-image', '--no-hybrid-psf',
'--survey-dir', surveydir, '--outdir', outdir, '-v', '--no-wise-ceres'
])
print('Checking for calib file', fn)
assert (os.path.exists(fn))
# Test with blob-masking when creating sky calib.
os.unlink(fn)
main(args=[
'--brick', '1867p255', '--zoom', '2050', '2300', '1150', '1400',
'--force-all', '--no-write', '--coadd-bw', '--blob-mask-dir',
surveydir, '--survey-dir', surveydir, '--stage', 'image_coadds',
'--outdir', 'out-testcase4b', '--plots'
])
print('Checking for calib file', fn)
assert (os.path.exists(fn))
if ceres:
main(args=[
'--brick', '1867p255', '--zoom', '2050', '2300', '1150', '1400',
'--force-all', '--no-write', '--coadd-bw', '--unwise-dir',
os.path.join(surveydir, 'images', 'unwise'), '--unwise-tr-dir',
os.path.join(surveydir, 'images', 'unwise-tr'), '--survey-dir',
surveydir, '--outdir', outdir
])
if psfex:
# Check that we can regenerate PsfEx files if necessary.
fn = os.path.join(surveydir, 'calib', 'psfex', 'decam', 'CP', 'V4.8.2',
'CP20170315',
'c4d_170316_062107_ooi_z_ls9-psfex.fits')
if os.path.exists(fn):
os.unlink(fn)
main(args=[
'--brick', '1867p255', '--zoom', '2050', '2300', '1150', '1400',
'--force-all', '--no-write', '--coadd-bw', '--unwise-dir',
os.path.join(surveydir, 'images', 'unwise'), '--unwise-tr-dir',
os.path.join(surveydir, 'images', 'unwise-tr'), '--blob-image',
'--survey-dir', surveydir, '--outdir', outdir, '-v'
])
print('After generating PsfEx calib:')
os.system('find %s' % (os.path.join(surveydir, 'calib')))
# Wrap-around, hybrid PSF
surveydir = os.path.join(os.path.dirname(__file__), 'testcase8')
outdir = 'out-testcase8'
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
main(args=[
'--brick',
'1209p050',
'--zoom',
'720',
'1095',
'3220',
'3500',
'--force-all',
'--no-write',
'--no-wise', #'--plots',
'--survey-dir',
surveydir,
'--outdir',
outdir
])
# Test with a Tycho-2 star + another saturated star in the blob.
surveydir = os.path.join(os.path.dirname(__file__), 'testcase7')
outdir = 'out-testcase7'
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
main(args=[
'--brick',
'1102p240',
'--zoom',
'250',
'350',
'1550',
'1650',
'--force-all',
'--no-write',
'--no-wise', #'--plots',
'--survey-dir',
surveydir,
'--outdir',
outdir
])
del os.environ['GAIA_CAT_DIR']
del os.environ['GAIA_CAT_VER']
fn = os.path.join(outdir, 'tractor', '110', 'tractor-1102p240.fits')
assert (os.path.exists(fn))
T = fits_table(fn)
assert (len(T) == 4)
# Check skipping blobs outside the brick's unique area.
# (this now doesn't detect any sources at all, reasonably)
# surveydir = os.path.join(os.path.dirname(__file__), 'testcase5')
# outdir = 'out-testcase5'
#
# fn = os.path.join(outdir, 'tractor', '186', 'tractor-1867p255.fits')
# if os.path.exists(fn):
# os.unlink(fn)
#
# main(args=['--brick', '1867p255', '--zoom', '0', '150', '0', '150',
# '--force-all', '--no-write', '--coadd-bw',
# '--survey-dir', surveydir,
# '--early-coadds',
# '--outdir', outdir] + extra_args)
#
# assert(os.path.exists(fn))
# T = fits_table(fn)
# assert(len(T) == 1)
# Custom RA,Dec; blob ra,dec.
surveydir = os.path.join(os.path.dirname(__file__), 'testcase4')
outdir = 'out-testcase4b'
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
# Catalog written with one entry (--blobradec)
fn = os.path.join(outdir, 'tractor', 'cus',
'tractor-custom-186743p25461.fits')
if os.path.exists(fn):
os.unlink(fn)
main(args=[
'--radec', '186.743965', '25.461788', '--width', '250', '--height',
'250', '--force-all', '--no-write', '--no-wise', '--blobradec',
'186.740369', '25.453855', '--survey-dir', surveydir, '--outdir',
outdir
])
assert (os.path.exists(fn))
T = fits_table(fn)
assert (len(T) == 1)
surveydir = os.path.join(os.path.dirname(__file__), 'testcase3')
outdir = 'out-testcase3'
os.environ['GAIA_CAT_DIR'] = os.path.join(surveydir, 'gaia')
os.environ['GAIA_CAT_VER'] = '2'
checkpoint_fn = os.path.join(outdir, 'checkpoint.pickle')
if os.path.exists(checkpoint_fn):
os.unlink(checkpoint_fn)
main(args=[
'--brick', '2447p120', '--zoom', '1020', '1070', '2775', '2815',
'--no-wise', '--force-all', '--no-write', '--survey-dir', surveydir,
'--outdir', outdir, '--checkpoint', checkpoint_fn,
'--checkpoint-period', '1', '--threads', '2'
])
# Read catalog into Tractor sources to test read_fits_catalog
survey = LegacySurveyData(survey_dir=outdir)
fn = survey.find_file('tractor', brick='2447p120')
print('Checking', fn)
T = fits_table(fn)
cat = read_fits_catalog(T)
print('Read catalog:', cat)
assert (len(cat) == 2)
src = cat[1]
print('Source0', src)
from tractor.sersic import SersicGalaxy
assert (type(src) in [DevGalaxy, SersicGalaxy])
assert (np.abs(src.pos.ra - 244.77973) < 0.00001)
assert (np.abs(src.pos.dec - 12.07234) < 0.00002)
src = cat[0]
print('Source1', src)
assert (type(src) == PointSource)
assert (np.abs(src.pos.ra - 244.77828) < 0.00001)
assert (np.abs(src.pos.dec - 12.07250) < 0.00001)
# Check that we can run again, using that checkpoint file.
main(args=[
'--brick', '2447p120', '--zoom', '1020', '1070', '2775', '2815',
'--no-wise', '--force-all', '--no-write', '--survey-dir', surveydir,
'--outdir', outdir, '--checkpoint', checkpoint_fn,
'--checkpoint-period', '1', '--threads', '2'
])
# Assert...... something?
# Test --checkpoint without --threads
main(args=[
'--brick', '2447p120', '--zoom', '1020', '1070', '2775', '2815',
'--no-wise', '--force-all', '--no-write', '--survey-dir', surveydir,
'--outdir', outdir, '--checkpoint', checkpoint_fn,
'--checkpoint-period', '1'
])
# From Kaylan's Bootes pre-DR4 run
# surveydir2 = os.path.join(os.path.dirname(__file__), 'mzlsbass3')
# main(args=['--brick', '2173p350', '--zoom', '100', '200', '100', '200',
# '--no-wise', '--force-all', '--no-write',
# '--survey-dir', surveydir2,
# '--outdir', 'out-mzlsbass3'] + extra_args)
# With plots!
main(args=[
'--brick', '2447p120', '--zoom', '1020', '1070', '2775', '2815',
'--no-wise', '--force-all', '--no-write', '--survey-dir', surveydir,
'--outdir', 'out-testcase3', '--plots', '--nblobs', '1'
])
def main(decals=None, opt=None):
'''Driver function for forced photometry of individual DECam images.
'''
if opt is None:
parser = get_parser()
opt = parser.parse_args()
Time.add_measurement(MemMeas)
t0 = Time()
if os.path.exists(opt.outfn):
print('Ouput file exists:', opt.outfn)
sys.exit(0)
if not opt.forced:
opt.apphot = True
zoomslice = None
if opt.zoom is not None:
(x0,x1,y0,y1) = opt.zoom
zoomslice = (slice(y0,y1), slice(x0,x1))
ps = None
if opt.plots is not None:
from astrometry.util.plotutils import PlotSequence
ps = PlotSequence(opt.plots)
# Try parsing filename as exposure number.
try:
expnum = int(opt.filename)
opt.filename = None
except:
# make this 'None' for decals.find_ccds()
expnum = None
# Try parsing HDU number
try:
opt.hdu = int(opt.hdu)
ccdname = None
except:
ccdname = opt.hdu
opt.hdu = -1
if decals is None:
decals = Decals()
if opt.filename is not None and opt.hdu >= 0:
# Read metadata from file
T = exposure_metadata([opt.filename], hdus=[opt.hdu])
print('Metadata:')
T.about()
else:
# Read metadata from decals-ccds.fits table
T = decals.find_ccds(expnum=expnum, ccdname=ccdname)
print(len(T), 'with expnum', expnum, 'and CCDname', ccdname)
if opt.hdu >= 0:
T.cut(T.image_hdu == opt.hdu)
print(len(T), 'with HDU', opt.hdu)
if opt.filename is not None:
T.cut(np.array([f.strip() == opt.filename for f in T.image_filename]))
print(len(T), 'with filename', opt.filename)
assert(len(T) == 1)
im = decals.get_image_object(T[0])
tim = im.get_tractor_image(slc=zoomslice, pixPsf=True, splinesky=True)
print('Got tim:', tim)
if opt.catfn in ['DR1', 'DR2']:
if opt.catalog_path is None:
opt.catalog_path = opt.catfn.lower()
margin = 20
TT = []
chipwcs = tim.subwcs
bricks = bricks_touching_wcs(chipwcs, decals=decals)
for b in bricks:
# there is some overlap with this brick... read the catalog.
fn = os.path.join(opt.catalog_path, 'tractor', b.brickname[:3],
'tractor-%s.fits' % b.brickname)
if not os.path.exists(fn):
print('WARNING: catalog', fn, 'does not exist. Skipping!')
continue
print('Reading', fn)
T = fits_table(fn)
ok,xx,yy = chipwcs.radec2pixelxy(T.ra, T.dec)
W,H = chipwcs.get_width(), chipwcs.get_height()
I = np.flatnonzero((xx >= -margin) * (xx <= (W+margin)) *
(yy >= -margin) * (yy <= (H+margin)))
T.cut(I)
print('Cut to', len(T), 'sources within image + margin')
# print('Brick_primary:', np.unique(T.brick_primary))
T.cut(T.brick_primary)
print('Cut to', len(T), 'on brick_primary')
T.cut((T.out_of_bounds == False) * (T.left_blob == False))
print('Cut to', len(T), 'on out_of_bounds and left_blob')
TT.append(T)
T = merge_tables(TT)
T._header = TT[0]._header
del TT
# Fix up various failure modes:
# FixedCompositeGalaxy(pos=RaDecPos[240.51147402832561, 10.385488075518923], brightness=NanoMaggies: g=(flux -2.87), r=(flux -5.26), z=(flux -7.65), fracDev=FracDev(0.60177207), shapeExp=re=3.78351e-44, e1=9.30367e-13, e2=1.24392e-16, shapeDev=re=inf, e1=-0, e2=-0)
# -> convert to EXP
I = np.flatnonzero(np.array([((t.type == 'COMP') and
(not np.isfinite(t.shapedev_r)))
for t in T]))
if len(I):
print('Converting', len(I), 'bogus COMP galaxies to EXP')
for i in I:
T.type[i] = 'EXP'
# Same thing with the exp component.
# -> convert to DEV
I = np.flatnonzero(np.array([((t.type == 'COMP') and
(not np.isfinite(t.shapeexp_r)))
for t in T]))
if len(I):
print('Converting', len(I), 'bogus COMP galaxies to DEV')
for i in I:
T.type[i] = 'DEV'
if opt.write_cat:
T.writeto(opt.write_cat)
print('Wrote catalog to', opt.write_cat)
else:
T = fits_table(opt.catfn)
T.shapeexp = np.vstack((T.shapeexp_r, T.shapeexp_e1, T.shapeexp_e2)).T
T.shapedev = np.vstack((T.shapedev_r, T.shapedev_e1, T.shapedev_e2)).T
cat = read_fits_catalog(T, ellipseClass=tractor.ellipses.EllipseE)
# print('Got cat:', cat)
print('Forced photom...')
opti = None
if opt.ceres:
from tractor.ceres_optimizer import CeresOptimizer
B = 8
opti = CeresOptimizer(BW=B, BH=B)
tr = Tractor([tim], cat, optimizer=opti)
tr.freezeParam('images')
for src in cat:
src.freezeAllBut('brightness')
src.getBrightness().freezeAllBut(tim.band)
F = fits_table()
F.brickid = T.brickid
F.brickname = T.brickname
F.objid = T.objid
F.filter = np.array([tim.band] * len(T))
F.mjd = np.array([tim.primhdr['MJD-OBS']] * len(T))
F.exptime = np.array([tim.primhdr['EXPTIME']] * len(T))
ok,x,y = tim.sip_wcs.radec2pixelxy(T.ra, T.dec)
F.x = (x-1).astype(np.float32)
F.y = (y-1).astype(np.float32)
if opt.apphot:
import photutils
img = tim.getImage()
ie = tim.getInvError()
with np.errstate(divide='ignore'):
imsigma = 1. / ie
imsigma[ie == 0] = 0.
apimg = []
apimgerr = []
# Aperture photometry locations
xxyy = np.vstack([tim.wcs.positionToPixel(src.getPosition()) for src in cat]).T
apxy = xxyy - 1.
apertures = apertures_arcsec / tim.wcs.pixel_scale()
print('Apertures:', apertures, 'pixels')
for rad in apertures:
aper = photutils.CircularAperture(apxy, rad)
p = photutils.aperture_photometry(img, aper, error=imsigma)
apimg.append(p.field('aperture_sum'))
apimgerr.append(p.field('aperture_sum_err'))
ap = np.vstack(apimg).T
ap[np.logical_not(np.isfinite(ap))] = 0.
F.apflux = ap
ap = 1./(np.vstack(apimgerr).T)**2
ap[np.logical_not(np.isfinite(ap))] = 0.
F.apflux_ivar = ap
if opt.forced:
kwa = {}
if opt.plots is None:
kwa.update(wantims=False)
R = tr.optimize_forced_photometry(variance=True, fitstats=True,
shared_params=False, **kwa)
if opt.plots:
(data,mod,ie,chi,roi) = R.ims1[0]
ima = tim.ima
imchi = dict(interpolation='nearest', origin='lower', vmin=-5, vmax=5)
plt.clf()
plt.imshow(data, **ima)
plt.title('Data: %s' % tim.name)
ps.savefig()
plt.clf()
plt.imshow(mod, **ima)
plt.title('Model: %s' % tim.name)
ps.savefig()
plt.clf()
plt.imshow(chi, **imchi)
plt.title('Chi: %s' % tim.name)
ps.savefig()
F.flux = np.array([src.getBrightness().getFlux(tim.band)
for src in cat]).astype(np.float32)
F.flux_ivar = R.IV.astype(np.float32)
F.fracflux = R.fitstats.profracflux.astype(np.float32)
F.rchi2 = R.fitstats.prochi2 .astype(np.float32)
program_name = sys.argv[0]
version_hdr = get_version_header(program_name, decals.decals_dir)
# HACK -- print only two directory names + filename of CPFILE.
fname = os.path.basename(im.imgfn)
d = os.path.dirname(im.imgfn)
d1 = os.path.basename(d)
d = os.path.dirname(d)
d2 = os.path.basename(d)
fname = os.path.join(d2, d1, fname)
print('Trimmed filename to', fname)
#version_hdr.add_record(dict(name='CPFILE', value=im.imgfn, comment='DECam comm.pipeline file'))
version_hdr.add_record(dict(name='CPFILE', value=fname, comment='DECam comm.pipeline file'))
version_hdr.add_record(dict(name='CPHDU', value=im.hdu, comment='DECam comm.pipeline ext'))
version_hdr.add_record(dict(name='CAMERA', value='DECam', comment='Dark Energy Camera'))
version_hdr.add_record(dict(name='EXPNUM', value=im.expnum, comment='DECam exposure num'))
version_hdr.add_record(dict(name='CCDNAME', value=im.ccdname, comment='DECam CCD name'))
version_hdr.add_record(dict(name='FILTER', value=tim.band, comment='Bandpass of this image'))
version_hdr.add_record(dict(name='EXPOSURE', value='decam-%s-%s' % (im.expnum, im.ccdname), comment='Name of this image'))
keys = ['TELESCOP','OBSERVAT','OBS-LAT','OBS-LONG','OBS-ELEV',
'INSTRUME']
for key in keys:
if key in tim.primhdr:
version_hdr.add_record(dict(name=key, value=tim.primhdr[key]))
hdr = fitsio.FITSHDR()
units = {'mjd':'sec', 'exptime':'sec', 'flux':'nanomaggy',
'flux_ivar':'1/nanomaggy^2'}
columns = F.get_columns()
for i,col in enumerate(columns):
if col in units:
hdr.add_record(dict(name='TUNIT%i' % (i+1), value=units[col]))
outdir = os.path.dirname(opt.outfn)
if len(outdir):
trymakedirs(outdir)
fitsio.write(opt.outfn, None, header=version_hdr, clobber=True)
F.writeto(opt.outfn, header=hdr, append=True)
print('Wrote', opt.outfn)
print('Finished forced phot:', Time()-t0)
return 0
fluxiv = [[] for i in range(len(B))]
mjd = [[] for i in range(len(B))]
J = np.flatnonzero((T.brickname == brick) * (T.filter == band))
print(len(J), 'in brick', brick, 'band', band)
if len(J) == 0:
continue
for j in J:
i = tmap[T.srcid[j]]
flux[i].append(T.flux[j])
fluxiv[i].append(T.flux_ivar[j])
mjd[i].append(T.mjd[j])
nmax = max([len(lst) for lst in flux])
print('Band:', band, 'Nmax:', nmax)
if nmax == 0:
continue
for flist, col, dt in [
(flux, 'forced_flux_%s' % band, np.float32),
(fluxiv, 'forced_flux_ivar_%s' % band, np.float32),
(mjd, 'forced_mjd_%s' % band, np.float64),
]:
arr = np.zeros((len(B), nmax), dt)
for i, f in enumerate(flist):
arr[i, :len(f)] = f
B.set(col, arr)
outfn = os.path.join('fsweep', brick[:3], 'tractor-%s.fits' % brick)
trymakedirs(outfn, dir=True)
B.writeto(outfn)
def main(survey=None, opt=None):
print(' '.join(sys.argv))
'''Driver function for forced photometry of individual Legacy
Survey images.
'''
if opt is None:
parser = get_parser()
opt = parser.parse_args()
Time.add_measurement(MemMeas)
t0 = tlast = Time()
if opt.skip and os.path.exists(opt.outfn):
print('Ouput file exists:', opt.outfn)
sys.exit(0)
if opt.derivs and opt.agn:
print('Sorry, can\'t do --derivs AND --agn')
sys.exit(0)
if not opt.forced:
opt.apphot = True
zoomslice = None
if opt.zoom is not None:
(x0, x1, y0, y1) = opt.zoom
zoomslice = (slice(y0, y1), slice(x0, x1))
ps = None
if opt.plots is not None:
from astrometry.util.plotutils import PlotSequence
ps = PlotSequence(opt.plots)
# Try parsing first arg as exposure number (otherwise, it's a filename)
try:
expnum = int(opt.expnum)
filename = None
except:
# make this 'None' for survey.find_ccds()
expnum = None
filename = opt.expnum
# Try parsing HDU: "all" or HDU name or HDU number.
all_hdus = (opt.ccdname == 'all')
hdu = -1
ccdname = None
if not all_hdus:
try:
hdu = int(opt.ccdname)
except:
ccdname = opt.ccdname
if survey is None:
survey = LegacySurveyData(survey_dir=opt.survey_dir)
catsurvey_north = survey
catsurvey_south = None
if opt.catalog_dir_north is not None:
assert (opt.catalog_dir_south is not None)
assert (opt.catalog_resolve_dec_ngc is not None)
catsurvey_north = LegacySurveyData(survey_dir=opt.catalog_dir_north)
catsurvey_south = LegacySurveyData(survey_dir=opt.catalog_dir_south)
if opt.catalog_dir is not None:
catsurvey_north = LegacySurveyData(survey_dir=opt.catalog_dir)
if filename is not None and hdu >= 0:
# FIXME -- try looking up in CCDs file?
# Read metadata from file
print('Warning: faking metadata from file contents')
T = exposure_metadata([filename], hdus=[hdu])
print('Metadata:')
T.about()
if not 'ccdzpt' in T.columns():
phdr = fitsio.read_header(filename)
T.ccdzpt = np.array([phdr['MAGZERO']])
print('WARNING: using header MAGZERO')
T.ccdraoff = np.array([0.])
T.ccddecoff = np.array([0.])
print('WARNING: setting CCDRAOFF, CCDDECOFF to zero.')
else:
# Read metadata from survey-ccds.fits table
T = survey.find_ccds(expnum=expnum, ccdname=ccdname)
print(len(T), 'with expnum', expnum, 'and ccdname', ccdname)
if hdu >= 0:
T.cut(T.image_hdu == hdu)
print(len(T), 'with HDU', hdu)
if filename is not None:
T.cut(np.array([f.strip() == filename for f in T.image_filename]))
print(len(T), 'with filename', filename)
if opt.camera is not None:
T.cut(T.camera == opt.camera)
print(len(T), 'with camera', opt.camera)
if not all_hdus:
assert (len(T) == 1)
args = []
for ccd in T:
args.append((survey, catsurvey_north, catsurvey_south,
opt.catalog_resolve_dec_ngc, ccd, opt, zoomslice, ps))
if opt.threads:
from astrometry.util.multiproc import multiproc
from astrometry.util.timingpool import TimingPool, TimingPoolMeas
pool = TimingPool(opt.threads)
poolmeas = TimingPoolMeas(pool, pickleTraffic=False)
Time.add_measurement(poolmeas)
mp = multiproc(None, pool=pool)
tm = Time()
FF = mp.map(bounce_one_ccd, args)
print('Multi-processing forced-phot:', Time() - tm)
else:
FF = map(bounce_one_ccd, args)
FF = [F for F in FF if F is not None]
if len(FF) == 0:
print('No photometry results to write.')
return 0
# Keep only the first header
_, version_hdr = FF[0]
FF = [F for F, hdr in FF]
F = merge_tables(FF)
if all_hdus:
version_hdr.delete('CPHDU')
version_hdr.delete('CCDNAME')
units = {
'exptime': 'sec',
'flux': 'nanomaggy',
'flux_ivar': '1/nanomaggy^2',
'apflux': 'nanomaggy',
'apflux_ivar': '1/nanomaggy^2',
'psfdepth': '1/nanomaggy^2',
'galdepth': '1/nanomaggy^2',
'sky': 'nanomaggy/arcsec^2',
'psfsize': 'arcsec'
}
if opt.derivs:
units.update({
'dra': 'arcsec',
'ddec': 'arcsec',
'dra_ivar': '1/arcsec^2',
'ddec_ivar': '1/arcsec^2'
})
columns = F.get_columns()
order = [
'release', 'brickid', 'brickname', 'objid', 'camera', 'expnum',
'ccdname', 'filter', 'mjd', 'exptime', 'psfsize', 'ccd_cuts',
'airmass', 'sky', 'psfdepth', 'galdepth', 'ra', 'dec', 'flux',
'flux_ivar', 'fracflux', 'rchisq', 'fracmasked', 'apflux',
'apflux_ivar', 'x', 'y', 'dqmask', 'dra', 'ddec', 'dra_ivar',
'ddec_ivar'
]
columns = [c for c in order if c in columns]
# Set units headers (must happen after column ordering is set!)
hdr = fitsio.FITSHDR()
for i, col in enumerate(columns):
if col in units:
hdr.add_record(dict(name='TUNIT%i' % (i + 1), value=units[col]))
outdir = os.path.dirname(opt.outfn)
if len(outdir):
trymakedirs(outdir)
tmpfn = os.path.join(outdir, 'tmp-' + os.path.basename(opt.outfn))
fitsio.write(tmpfn, None, header=version_hdr, clobber=True)
F.writeto(tmpfn, header=hdr, append=True, columns=columns)
os.rename(tmpfn, opt.outfn)
print('Wrote', opt.outfn)
tnow = Time()
print('Total:', tnow - t0)
return 0
def render_fake_image(expnum, ccdname, decals_out_dir):
decals = Decals()
ccds = decals.find_ccds(expnum=expnum, ccdname=ccdname)
ccd = ccds[0]
band = ccd.filter
im = decals.get_image_object(ccd)
print('Read', im)
tim = im.get_tractor_image(gaussPsf=True, nanomaggies=False, subsky=False)
tim.wcs = NullWCS()
H, W = im.shape
s0 = 4.
dsdy = 1. / 2000.
x0 = W / 2.
y0 = H / 2.
ny = 21
nx = 11
# Lay down a grid of point sources, where the PSF is varying in width as a
# function of Y position.
yy = np.linspace(0., H, ny + 1)
xx = np.linspace(0., W, nx + 1)
# center of cells
yy = yy[:-1] + (yy[1] - yy[0]) / 2.
xx = xx[:-1] + (xx[1] - xx[0]) / 2.
modimg = np.zeros_like(tim.getImage())
flux = NanoMaggies.magToNanomaggies(16.)
star = PointSource(PixPos(0., 0.), NanoMaggies(**{band: flux}))
for y in yy:
for x in xx:
print('Rendering star at', x, y)
s = s0 + dsdy * (y - y0)
psf = NCircularGaussianPSF([s], [1.])
tim.psf = psf
star.pos.x = x
star.pos.y = y
mod = star.getModelPatch(tim)
mod.addTo(modimg)
np.random.seed(42)
noise = np.random.normal(size=modimg.shape)
ie = tim.getInvError()
noise /= ie
noise[ie == 0] = 0
modimg += noise
#
imagedir = os.path.join(decals_out_dir, 'images', 'decam')
trymakedirs(imagedir)
imagefn = os.path.join(imagedir,
os.path.basename(
ccd.image_filename.strip())).replace(
'.fits.fz', '.fits')
primhdr = im.read_image_primary_header()
hdr = im.read_image_header()
extname = hdr['EXTNAME']
import fitsio
fitsio.write(imagefn, None, header=primhdr, clobber=True)
fitsio.write(imagefn, modimg, header=hdr, extname=extname, clobber=False)
print('Wrote', imagefn)
dq = im.read_dq()
dqfn = imagefn.replace('_ooi_', '_ood_')
fitsio.write(dqfn, None, header=primhdr, clobber=True)
fitsio.write(dqfn, dq, header=hdr, clobber=False)
print('Wrote', dqfn)
iv = im.read_invvar()
wtfn = imagefn.replace('_ooi_', '_oow_')
fitsio.write(wtfn, None, header=primhdr, clobber=True)
fitsio.write(wtfn, iv, header=hdr, clobber=False)
print('Wrote', wtfn)
# cmd = 'ln -s %s %s' % (im.dqfn, dqfn)
# print cmd
# os.system(cmd)
#
# cmd = 'ln -s %s %s' % (im.wtfn, wtfn)
# print cmd
# os.system(cmd)
ccds.image_filename = np.array(['decam/' + os.path.basename(imagefn)])
ccds.image_hdu[0] = 1
ccdfn = os.path.join(decals_out_dir, 'decals-ccds.fits')
ccds.writeto(ccdfn)
print('Wrote', ccdfn)
cal = os.path.join(decals_out_dir, 'calib')
trymakedirs(cal)
for path in ['decals-bricks.fits', 'calib/se-config']:
pathnm = os.path.join(decals_out_dir, path)
if os.path.exists(pathnm):
continue
cmd = 'ln -s %s/%s %s' % (decals.get_decals_dir(), path, pathnm)
print(cmd)
os.system(cmd)
def main():
import argparse
parser = argparse.ArgumentParser(
description='This script creates small self-contained data sets that '
'are useful for test cases of the pipeline codes.')
parser.add_argument('ccds', help='CCDs table describing region to grab')
parser.add_argument('outdir', help='Output directory name')
parser.add_argument('brick', help='Brick containing these images')
parser.add_argument('--survey-dir', type=str, default=None)
parser.add_argument('--cache-dir', type=str, default=None,
help='Directory to search for cached files')
parser.add_argument('--wise', help='For WISE outputs, give the path to a WCS file describing the sub-brick region of interest, eg, a coadd image')
parser.add_argument('--wise-wcs-hdu', help='For WISE outputs, the HDU to read the WCS from in the file given by --wise.', type=int, default=0)
parser.add_argument('--fpack', action='store_true', default=False)
parser.add_argument('--gzip', action='store_true', default=False)
parser.add_argument('--pad', action='store_true', default=False,
help='Keep original image size, but zero out pixels outside ROI')
args = parser.parse_args()
v = 'SKY_TEMPLATE_DIR'
if v in os.environ:
del os.environ[v]
C = fits_table(args.ccds)
print(len(C), 'CCDs in', args.ccds)
C.camera = np.array([c.strip() for c in C.camera])
survey = LegacySurveyData(cache_dir=args.cache_dir, survey_dir=args.survey_dir)
if ',' in args.brick:
ra,dec = args.brick.split(',')
ra = float(ra)
dec = float(dec)
fakebricks = fits_table()
fakebricks.brickname = np.array([('custom-%06i%s%05i' %
(int(1000*ra), 'm' if dec < 0 else 'p',
int(1000*np.abs(dec))))])
fakebricks.ra = np.array([ra])
fakebricks.dec = np.array([dec])
bricks = fakebricks
outbricks = bricks
else:
bricks = survey.get_bricks_readonly()
outbricks = bricks[np.array([n == args.brick for n in bricks.brickname])]
assert(len(outbricks) == 1)
outsurvey = LegacySurveyData(survey_dir = args.outdir)
trymakedirs(args.outdir)
outbricks.writeto(os.path.join(args.outdir, 'survey-bricks.fits.gz'))
targetwcs = wcs_for_brick(outbricks[0])
H,W = targetwcs.shape
tycho2fn = survey.find_file('tycho2')
kd = tree_open(tycho2fn, 'stars')
radius = 1.
rc,dc = targetwcs.radec_center()
I = tree_search_radec(kd, rc, dc, radius)
print(len(I), 'Tycho-2 stars within', radius, 'deg of RA,Dec (%.3f, %.3f)' % (rc,dc))
# Read only the rows within range.
tycho = fits_table(tycho2fn, rows=I)
del kd
print('Read', len(tycho), 'Tycho-2 stars')
ok,tx,ty = targetwcs.radec2pixelxy(tycho.ra, tycho.dec)
#margin = 100
#tycho.cut(ok * (tx > -margin) * (tx < W+margin) *
# (ty > -margin) * (ty < H+margin))
print('Cut to', len(tycho), 'Tycho-2 stars within brick')
del ok,tx,ty
#tycho.writeto(os.path.join(args.outdir, 'tycho2.fits.gz'))
f,tfn = tempfile.mkstemp(suffix='.fits')
os.close(f)
tycho.writeto(tfn)
outfn = os.path.join(args.outdir, 'tycho2.kd.fits')
cmd = 'startree -i %s -o %s -P -k -n stars -T' % (tfn, outfn)
print(cmd)
rtn = os.system(cmd)
assert(rtn == 0)
os.unlink(tfn)
from legacypipe.gaiacat import GaiaCatalog
gcat = GaiaCatalog()
# from ps1cat.py:
wcs = targetwcs
step=100.
margin=10.
# Grid the CCD in pixel space
W,H = wcs.get_width(), wcs.get_height()
xx,yy = np.meshgrid(
np.linspace(1-margin, W+margin, 2+int((W+2*margin)/step)),
np.linspace(1-margin, H+margin, 2+int((H+2*margin)/step)))
# Convert to RA,Dec and then to unique healpixes
ra,dec = wcs.pixelxy2radec(xx.ravel(), yy.ravel())
healpixes = set()
for r,d in zip(ra,dec):
healpixes.add(gcat.healpix_for_radec(r, d))
for hp in healpixes:
hpcat = gcat.get_healpix_catalog(hp)
ok,xx,yy = wcs.radec2pixelxy(hpcat.ra, hpcat.dec)
onccd = np.flatnonzero((xx >= 1.-margin) * (xx <= W+margin) *
(yy >= 1.-margin) * (yy <= H+margin))
hpcat.cut(onccd)
if len(hpcat):
outfn = os.path.join(args.outdir, 'gaia', 'chunk-%05d.fits' % hp)
trymakedirs(os.path.join(args.outdir, 'gaia'))
hpcat.writeto(outfn)
outccds = C.copy()
cols = outccds.get_columns()
for c in ['ccd_x0', 'ccd_x1', 'ccd_y0', 'ccd_y1',
'brick_x0', 'brick_x1', 'brick_y0', 'brick_y1',
'skyver', 'wcsver', 'psfver', 'skyplver', 'wcsplver',
'psfplver' ]:
if c in cols:
outccds.delete_column(c)
outccds.image_hdu[:] = 1
# Convert to list to avoid truncating filenames
outccds.image_filename = [fn for fn in outccds.image_filename]
for iccd,ccd in enumerate(C):
decam = (ccd.camera.strip() == 'decam')
bok = (ccd.camera.strip() == '90prime')
im = survey.get_image_object(ccd)
print('Got', im)
if survey.cache_dir is not None:
im.check_for_cached_files(survey)
slc = (slice(ccd.ccd_y0, ccd.ccd_y1), slice(ccd.ccd_x0, ccd.ccd_x1))
psfkwargs = dict(pixPsf=True, gaussPsf=False, hybridPsf=False,
normalizePsf=False)
tim = im.get_tractor_image(slc, pixPsf=True,
subsky=False, nanomaggies=False,
no_remap_invvar=True, old_calibs_ok=True)
print('Tim:', tim.shape)
psfrow = psfhdr = None
if args.pad:
psf = im.read_psf_model(0, 0, w=im.width, h=im.height, **psfkwargs)
psfex = psf.psfex
else:
psf = tim.getPsf()
psfex = psf.psfex
# Did the PSF model come from a merged file?
for fn in [im.merged_psffn, im.psffn] + im.old_merged_psffns:
if not os.path.exists(fn):
continue
T = fits_table(fn)
I, = np.nonzero((T.expnum == im.expnum) *
np.array([c.strip() == im.ccdname for c in T.ccdname]))
if len(I) != 1:
continue
psfrow = T[I]
x0 = ccd.ccd_x0
y0 = ccd.ccd_y0
psfrow.polzero1[0] -= x0
psfrow.polzero2[0] -= y0
#psfhdr = fitsio.read_header(im.merged_psffn)
break
psfex.fwhm = tim.psf_fwhm
#### HACK
#psfrow = None
assert(psfrow is not None)
if psfrow is not None:
print('PSF row:', psfrow)
#else:
# print('PSF:', psf)
# print('PsfEx:', psfex)
skyrow = skyhdr = None
if args.pad:
primhdr = fitsio.read_header(im.imgfn)
imghdr = fitsio.read_header(im.imgfn, hdu=im.hdu)
sky = im.read_sky_model(splinesky=True, primhdr=primhdr, imghdr=imghdr)
#skyhdr = fitsio.read_header(im.splineskyfn)
#msky = im.read_merged_splinesky_model(slc=slc, old_calibs_ok=True)
else:
sky = tim.getSky()
# Did the sky model come from a merged file?
#msky = im.read_merged_splinesky_model(slc=slc, old_calibs_ok=True)
print('merged skyfn:', im.merged_skyfn)
print('single skyfn:', im.skyfn)
print('old merged skyfns:', im.old_merged_skyfns)
for fn in [im.merged_skyfn, im.skyfn] + im.old_merged_skyfns:
if not os.path.exists(fn):
continue
T = fits_table(fn)
I, = np.nonzero((T.expnum == im.expnum) *
np.array([c.strip() == im.ccdname for c in T.ccdname]))
skyrow = T[I]
skyrow.x0[0] = ccd.ccd_x0
skyrow.y0[0] = ccd.ccd_y0
# s_med = skyrow.sky_med[0]
# s_john = skyrow.sky_john[0]
# skyhdr = fitsio.read_header(fn)
assert(skyrow is not None)
### HACK
#skyrow = None
if skyrow is not None:
print('Sky row:', skyrow)
else:
print('Sky:', sky)
# Output filename format:
fn = ccd.image_filename.strip()
ccd.image_filename = os.path.join(os.path.dirname(fn),
'%s.%s.fits' % (os.path.basename(fn).split('.')[0], ccd.ccdname.strip()))
outim = outsurvey.get_image_object(ccd)
print('Output image:', outim)
print('Image filename:', outim.imgfn)
trymakedirs(outim.imgfn, dir=True)
imgdata = tim.getImage()
ivdata = tim.getInvvar()
# Since we remap DQ codes (always with Mosaic and Bok, sometimes with DECam),
# re-read from the FITS file rather than using tim.dq.
print('Reading data quality from', im.dqfn, 'hdu', im.hdu)
dqdata = im._read_fits(im.dqfn, im.hdu, slice=tim.slice)
print('Tim shape:', tim.shape, 'Slice', tim.slice)
print('image shape:', imgdata.shape, 'iv', ivdata.shape, 'DQ', dqdata.shape)
from collections import Counter
dqvals = Counter(dqdata.ravel())
print('DQ pixel counts:')
for k,n in dqvals.most_common():
print(' 0x%x' % k, ':', n)
if args.pad:
# Create zero image of full size, copy in data.
fullsize = np.zeros((ccd.height, ccd.width), imgdata.dtype)
fullsize[slc] = imgdata
imgdata = fullsize
fullsize = np.zeros((ccd.height, ccd.width), dqdata.dtype)
fullsize[slc] = dqdata
dqdata = fullsize
fullsize = np.zeros((ccd.height, ccd.width), ivdata.dtype)
fullsize[slc] = ivdata
ivdata = fullsize
else:
# Adjust the header WCS by x0,y0
crpix1 = tim.hdr['CRPIX1']
crpix2 = tim.hdr['CRPIX2']
tim.hdr['CRPIX1'] = crpix1 - ccd.ccd_x0
tim.hdr['CRPIX2'] = crpix2 - ccd.ccd_y0
# Add image extension to filename
# fitsio doesn't compress .fz by default, so drop .fz suffix
#outim.imgfn = outim.imgfn.replace('.fits', '-%s.fits' % im.ccdname)
if not args.fpack:
outim.imgfn = outim.imgfn.replace('.fits.fz', '.fits')
if args.gzip:
outim.imgfn = outim.imgfn.replace('.fits', '.fits.gz')
#outim.wtfn = outim.wtfn.replace('.fits', '-%s.fits' % im.ccdname)
if not args.fpack:
outim.wtfn = outim.wtfn.replace('.fits.fz', '.fits')
if args.gzip:
outim.wtfn = outim.wtfn.replace('.fits', '.fits.gz')
if outim.dqfn is not None:
#outim.dqfn = outim.dqfn.replace('.fits', '-%s.fits' % im.ccdname)
if not args.fpack:
outim.dqfn = outim.dqfn.replace('.fits.fz', '.fits')
if args.gzip:
outim.dqfn = outim.dqfn.replace('.fits', '.fits.gz')
if bok:
outim.psffn = outim.psffn.replace('.psf', '-%s.psf' % im.ccdname)
ccdfn = outim.imgfn
ccdfn = ccdfn.replace(outsurvey.get_image_dir(), '')
if ccdfn.startswith('/'):
ccdfn = ccdfn[1:]
outccds.image_filename[iccd] = ccdfn
print('Changed output filenames to:')
print(outim.imgfn)
print(outim.dqfn)
ofn = outim.imgfn
if args.fpack:
f,ofn = tempfile.mkstemp(suffix='.fits')
os.close(f)
fits = fitsio.FITS(ofn, 'rw', clobber=True)
fits.write(None, header=tim.primhdr)
fits.write(imgdata, header=tim.hdr, extname=ccd.ccdname)
fits.close()
if args.fpack:
cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, outim.imgfn, ofn)
print('Running:', cmd)
rtn = os.system(cmd)
assert(rtn == 0)
h,w = tim.shape
if not args.pad:
outccds.width[iccd] = w
outccds.height[iccd] = h
outccds.crpix1[iccd] = crpix1 - ccd.ccd_x0
outccds.crpix2[iccd] = crpix2 - ccd.ccd_y0
wcs = Tan(*[float(x) for x in
[ccd.crval1, ccd.crval2, ccd.crpix1, ccd.crpix2,
ccd.cd1_1, ccd.cd1_2, ccd.cd2_1, ccd.cd2_2, ccd.width, ccd.height]])
if args.pad:
subwcs = wcs
else:
subwcs = wcs.get_subimage(ccd.ccd_x0, ccd.ccd_y0, w, h)
outccds.ra[iccd],outccds.dec[iccd] = subwcs.radec_center()
print('Weight filename:', outim.wtfn)
wfn = outim.wtfn
trymakedirs(wfn, dir=True)
ofn = wfn
if args.fpack:
f,ofn = tempfile.mkstemp(suffix='.fits')
os.close(f)
fits = fitsio.FITS(ofn, 'rw', clobber=True)
fits.write(None, header=tim.primhdr)
fits.write(ivdata, header=tim.hdr, extname=ccd.ccdname)
fits.close()
if args.fpack:
cmd = 'fpack -qz 8 -S %s > %s && rm %s' % (ofn, wfn, ofn)
print('Running:', cmd)
rtn = os.system(cmd)
assert(rtn == 0)
if outim.dqfn is not None:
print('DQ filename', outim.dqfn)
trymakedirs(outim.dqfn, dir=True)
ofn = outim.dqfn
if args.fpack:
f,ofn = tempfile.mkstemp(suffix='.fits')
os.close(f)
fits = fitsio.FITS(ofn, 'rw', clobber=True)
fits.write(None, header=tim.primhdr)
fits.write(dqdata, header=tim.hdr, extname=ccd.ccdname)
fits.close()
if args.fpack:
cmd = 'fpack -g -q 0 -S %s > %s && rm %s' % (ofn, outim.dqfn, ofn)
print('Running:', cmd)
rtn = os.system(cmd)
assert(rtn == 0)
psfout = outim.psffn
#if psfrow:
# psfout = outim.merged_psffn
print('PSF output filename:', psfout)
trymakedirs(psfout, dir=True)
if psfrow:
psfrow.writeto(psfout, primhdr=psfhdr)
else:
print('Writing PsfEx:', psfout)
psfex.writeto(psfout)
# update header
F = fitsio.FITS(psfout, 'rw')
F[0].write_keys([dict(name='EXPNUM', value=ccd.expnum),
dict(name='PLVER', value=psf.plver),
dict(name='PROCDATE', value=psf.procdate),
dict(name='PLPROCID', value=psf.plprocid),])
F.close()
skyout = outim.skyfn
#if skyrow:
# skyout = outim.merged_splineskyfn
print('Sky output filename:', skyout)
trymakedirs(skyout, dir=True)
if skyrow is not None:
skyrow.writeto(skyout, primhdr=skyhdr)
else:
primhdr = fitsio.FITSHDR()
primhdr['PLVER'] = sky.plver
primhdr['PLPROCID'] = sky.plprocid
primhdr['PROCDATE'] = sky.procdate
primhdr['EXPNUM'] = ccd.expnum
primhdr['IMGDSUM'] = sky.datasum
primhdr['S_MED'] = s_med
primhdr['S_JOHN'] = s_john
sky.write_fits(skyout, primhdr=primhdr)
# HACK -- check result immediately.
outccds.writeto(os.path.join(args.outdir, 'survey-ccds-1.fits.gz'))
outsurvey.ccds = None
outC = outsurvey.get_ccds_readonly()
occd = outC[iccd]
outim = outsurvey.get_image_object(occd)
print('Got output image:', outim)
otim = outim.get_tractor_image(pixPsf=True,
hybridPsf=True, old_calibs_ok=True)
print('Got output tim:', otim)
outccds.writeto(os.path.join(args.outdir, 'survey-ccds-1.fits.gz'))
# WISE
if args.wise is not None:
from wise.forcedphot import unwise_tiles_touching_wcs
from wise.unwise import (unwise_tile_wcs, unwise_tiles_touching_wcs,
get_unwise_tractor_image, get_unwise_tile_dir)
# Read WCS...
print('Reading TAN wcs header from', args.wise, 'HDU', args.wise_wcs_hdu)
targetwcs = Tan(args.wise, args.wise_wcs_hdu)
tiles = unwise_tiles_touching_wcs(targetwcs)
print('Cut to', len(tiles), 'unWISE tiles')
H,W = targetwcs.shape
r,d = targetwcs.pixelxy2radec(np.array([1, W, W/2, W/2]),
np.array([H/2, H/2, 1, H ]))
roiradec = [r[0], r[1], d[2], d[3]]
unwise_dir = os.environ['UNWISE_COADDS_DIR']
wise_out = os.path.join(args.outdir, 'images', 'unwise')
print('Will write WISE outputs to', wise_out)
unwise_tr_dir = os.environ['UNWISE_COADDS_TIMERESOLVED_DIR']
wise_tr_out = os.path.join(args.outdir, 'images', 'unwise-tr')
print('Will write WISE time-resolved outputs to', wise_tr_out)
trymakedirs(wise_tr_out)
W = fits_table(os.path.join(unwise_tr_dir, 'time_resolved_atlas.fits'))
print('Read', len(W), 'time-resolved WISE coadd tiles')
W.cut(np.array([t in tiles.coadd_id for t in W.coadd_id]))
print('Cut to', len(W), 'time-resolved vs', len(tiles), 'full-depth')
# Write the time-resolved index subset.
W.writeto(os.path.join(wise_tr_out, 'time_resolved_atlas.fits'))
# this ought to be enough for anyone =)
_,Nepochs = W.epoch_bitmask.shape
print('N epochs in time-resolved atlas:', Nepochs)
wisedata = []
# full depth
for band in [1,2,3,4]:
wisedata.append((unwise_dir, wise_out, tiles.coadd_id, band, True))
# time-resolved
for band in [1,2]:
# W1 is bit 0 (value 0x1), W2 is bit 1 (value 0x2)
bitmask = (1 << (band-1))
for e in range(Nepochs):
# Which tiles have images for this epoch?
I = np.flatnonzero(W.epoch_bitmask[:,e] & bitmask)
if len(I) == 0:
continue
print('Epoch %i: %i tiles:' % (e, len(I)), W.coadd_id[I])
edir = os.path.join(unwise_tr_dir, 'e%03i' % e)
eoutdir = os.path.join(wise_tr_out, 'e%03i' % e)
wisedata.append((edir, eoutdir, tiles.coadd_id[I], band, False))
wrote_masks = set()
model_dir = os.environ.get('UNWISE_MODEL_SKY_DIR')
if model_dir is not None:
model_dir_out = os.path.join(args.outdir, 'images', 'unwise-mod')
trymakedirs(model_dir_out)
for indir, outdir, tiles, band, fulldepth in wisedata:
for tile in tiles:
wanyband = 'w'
tim = get_unwise_tractor_image(indir, tile, band,
bandname=wanyband, roiradecbox=roiradec)
print('Got unWISE tim', tim)
print(tim.shape)
if model_dir is not None and fulldepth and band in [1,2]:
print('ROI', tim.roi)
#0387p575.1.mod.fits
fn = '%s.%i.mod.fits' % (tile, band)
print('Filename', fn)
F = fitsio.FITS(os.path.join(model_dir, fn))
x0,x1,y0,y1 = tim.roi
slc = slice(y0,y1),slice(x0,x1)
phdr = F[0].read_header()
outfn = os.path.join(model_dir_out, fn)
for e,extname in [(1,'MODEL'), (2,'SKY')]:
pix = F[e][slc]
hdr = F[e].read_header()
crpix1 = hdr['CRPIX1']
crpix2 = hdr['CRPIX2']
hdr['CRPIX1'] -= x0
hdr['CRPIX2'] -= y0
#print('mod', mod)
#print('Model', mod.shape)
if e == 1:
fitsio.write(outfn, None, clobber=True, header=phdr)
fitsio.write(outfn, pix, header=hdr, extname=extname)
print('Wrote', outfn)
thisdir = get_unwise_tile_dir(outdir, tile)
print('Directory for this WISE tile:', thisdir)
base = os.path.join(thisdir, 'unwise-%s-w%i-' % (tile, band))
print('Base filename:', base)
masked = True
mu = 'm' if masked else 'u'
imfn = base + 'img-%s.fits' % mu
ivfn = base + 'invvar-%s.fits.gz' % mu
nifn = base + 'n-%s.fits.gz' % mu
nufn = base + 'n-u.fits.gz'
#print('WISE image header:', tim.hdr)
# Adjust the header WCS by x0,y0
wcs = tim.wcs.wcs
tim.hdr['CRPIX1'] = wcs.crpix[0]
tim.hdr['CRPIX2'] = wcs.crpix[1]
H,W = tim.shape
tim.hdr['IMAGEW'] = W
tim.hdr['IMAGEH'] = H
print('WCS:', wcs)
print('Header CRPIX', tim.hdr['CRPIX1'], tim.hdr['CRPIX2'])
trymakedirs(imfn, dir=True)
fitsio.write(imfn, tim.getImage(), header=tim.hdr, clobber=True)
print('Wrote', imfn)
fitsio.write(ivfn, tim.getInvvar(), header=tim.hdr, clobber=True)
print('Wrote', ivfn)
fitsio.write(nifn, tim.nims, header=tim.hdr, clobber=True)
print('Wrote', nifn)
fitsio.write(nufn, tim.nuims, header=tim.hdr, clobber=True)
print('Wrote', nufn)
if not (indir,tile) in wrote_masks:
print('Looking for mask file for', indir, tile)
# record that we tried this dir/tile combo
wrote_masks.add((indir,tile))
for idir in indir.split(':'):
tdir = get_unwise_tile_dir(idir, tile)
maskfn = 'unwise-%s-msk.fits.gz' % tile
fn = os.path.join(tdir, maskfn)
print('Mask file:', fn)
if os.path.exists(fn):
print('Reading', fn)
(x0,x1,y0,y1) = tim.roi
roislice = (slice(y0,y1), slice(x0,x1))
F = fitsio.FITS(fn)[0]
hdr = F.read_header()
M = F[roislice]
outfn = os.path.join(thisdir, maskfn)
fitsio.write(outfn, M, header=tim.hdr, clobber=True)
print('Wrote', outfn)
break
outC = outsurvey.get_ccds_readonly()
for iccd,ccd in enumerate(outC):
outim = outsurvey.get_image_object(ccd)
print('Got output image:', outim)
otim = outim.get_tractor_image(pixPsf=True,
hybridPsf=True, old_calibs_ok=True)
print('Got output tim:', otim)
def run_calibs(self, psfex=True, sky=True, se=False,
funpack=False, fcopy=False, use_mask=True,
force=False, just_check=False, git_version=None,
splinesky=False):
'''
Run calibration pre-processing steps.
Parameters
----------
just_check: boolean
If True, returns True if calibs need to be run.
'''
from .survey import (create_temp, get_version_header,
get_git_version)
if psfex and os.path.exists(self.psffn) and (not force):
if self.check_psf(self.psffn):
psfex = False
if psfex:
se = True
if se and os.path.exists(self.sefn) and (not force):
if self.check_se_cat(self.sefn):
se = False
if se:
funpack = True
if sky and (not force) and (
(os.path.exists(self.skyfn) and not splinesky) or
(os.path.exists(self.splineskyfn) and splinesky)):
fn = self.skyfn
if splinesky:
fn = self.splineskyfn
if os.path.exists(fn):
try:
hdr = fitsio.read_header(fn)
except:
print('Failed to read sky file', fn, '-- deleting')
os.unlink(fn)
if os.path.exists(fn):
print('File', fn, 'exists -- skipping')
sky = False
if just_check:
return (se or psfex or sky)
todelete = []
if funpack:
# The image & mask files to process (funpacked if necessary)
imgfn,maskfn = self.funpack_files(self.imgfn, self.dqfn, self.hdu, todelete)
else:
imgfn,maskfn = self.imgfn,self.dqfn
if se:
self.run_se('DECaLS', imgfn, maskfn)
if psfex:
self.run_psfex('DECaLS')
if sky:
#print('Fitting sky for', self)
hdr = get_version_header(None, self.survey.get_survey_dir(),
git_version=git_version)
primhdr = self.read_image_primary_header()
plver = primhdr.get('PLVER', '')
hdr.delete('PROCTYPE')
hdr.add_record(dict(name='PROCTYPE', value='ccd',
comment='NOAO processing type'))
hdr.add_record(dict(name='PRODTYPE', value='skymodel',
comment='NOAO product type'))
hdr.add_record(dict(name='PLVER', value=plver,
comment='CP ver of image file'))
slc = self.get_good_image_slice(None)
#print('Good image slice is', slc)
img = self.read_image(slice=slc)
wt = self.read_invvar(slice=slc)
if splinesky:
from tractor.splinesky import SplineSky
from scipy.ndimage.morphology import binary_dilation
boxsize = DecamImage.splinesky_boxsize
# Start by subtracting the overall median
med = np.median(img[wt>0])
# Compute initial model...
skyobj = SplineSky.BlantonMethod(img - med, wt>0, boxsize)
skymod = np.zeros_like(img)
skyobj.addTo(skymod)
# Now mask bright objects in (image - initial sky model)
sig1 = 1./np.sqrt(np.median(wt[wt>0]))
masked = (img - med - skymod) > (5.*sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
sig1b = 1./np.sqrt(np.median(wt[masked == False]))
print('Sig1 vs sig1b:', sig1, sig1b)
# Now find the final sky model using that more extensive mask
skyobj = SplineSky.BlantonMethod(
img - med, np.logical_not(masked), boxsize)
# add the overall median back in
skyobj.offset(med)
if slc is not None:
sy,sx = slc
y0 = sy.start
x0 = sx.start
skyobj.shift(-x0, -y0)
hdr.add_record(dict(name='SIG1', value=sig1,
comment='Median stdev of unmasked pixels'))
hdr.add_record(dict(name='SIG1B', value=sig1,
comment='Median stdev of unmasked pixels+'))
trymakedirs(self.splineskyfn, dir=True)
skyobj.write_fits(self.splineskyfn, primhdr=hdr)
print('Wrote sky model', self.splineskyfn)
else:
try:
skyval = estimate_mode(img[wt > 0], raiseOnWarn=True)
skymeth = 'mode'
except:
skyval = np.median(img[wt > 0])
skymeth = 'median'
tsky = ConstantSky(skyval)
hdr.add_record(dict(name='SKYMETH', value=skymeth,
comment='estimate_mode, or fallback to median?'))
from scipy.ndimage.morphology import binary_dilation
sig1 = 1./np.sqrt(np.median(wt[wt>0]))
masked = (img - skyval) > (5.*sig1)
masked = binary_dilation(masked, iterations=3)
masked[wt == 0] = True
sig1b = 1./np.sqrt(np.median(wt[masked == False]))
print('Sig1 vs sig1b:', sig1, sig1b)
hdr.add_record(dict(name='SIG1', value=sig1,
comment='Median stdev of unmasked pixels'))
hdr.add_record(dict(name='SIG1B', value=sig1,
comment='Median stdev of unmasked pixels+'))
trymakedirs(self.skyfn, dir=True)
tsky.write_fits(self.skyfn, hdr=hdr)
print('Wrote sky model', self.skyfn)
for fn in todelete:
os.unlink(fn)