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(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 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(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
