def get_tractor_sources_cas_dr9(table,
bandname='r',
bands=None,
extrabands=None,
nanomaggies=False):
'''
table: filename or astrometry.util.fits.fits_table() object
'''
from astrometry.sdss import band_names
from astrometry.util.fits import fits_table
if isinstance(table, basestring):
cas = fits_table(table)
else:
cas = table
# Make it look like a "photoObj" file.
cols = cas.get_columns()
N = len(cas)
T = tabledata()
T.ra = cas.ra
T.dec = cas.dec
# nchild
if not 'nchild' in cols:
T.nchild = np.zeros(N, int)
else:
T.nchild = cas.nchild
# rowc,colc -- shouldn't be necessary...
if not 'objc_flags' in cols:
T.objc_flags = np.zeros(N, int)
else:
T.objc_flags = cas.objc_flags
allbands = band_names()
nbands = len(allbands)
colmap = [
('phi_dev_deg', 'devphi'),
('phi_exp_deg', 'expphi'),
('theta_dev', 'devrad'),
('theta_exp', 'exprad'),
('ab_dev', 'devab'),
('ab_exp', 'expab'),
('psfflux', 'psfflux'),
('cmodelflux', 'cmodelflux'),
('devflux', 'devflux'),
('expflux', 'expflux'),
('fracdev', 'fracdev'),
('prob_psf', 'probpsf'),
]
for c1, c2 in colmap:
T.set(c1, np.zeros((N, nbands)))
for bi, b in enumerate(allbands):
for c1, c2 in colmap:
cname = '%s_%s' % (c2, b)
if cname in cols:
T.get(c1)[:, bi] = cas.get(cname)
return _get_sources(-1,
-1,
-1,
release='DR9',
objs=T,
sdss=DR9(),
bandname=bandname,
bands=bands,
nanomaggies=nanomaggies,
extrabands=extrabands)
def get_tractor_sources_cas_dr9(table, bandname='r', bands=None,
extrabands=None,
nanomaggies=False):
'''
table: filename or astrometry.util.fits.fits_table() object
'''
from astrometry.sdss import band_names
from astrometry.util.fits import fits_table
if isinstance(table, basestring):
cas = fits_table(table)
else:
cas = table
# Make it look like a "photoObj" file.
cols = cas.get_columns()
N = len(cas)
T = tabledata()
T.ra = cas.ra
T.dec = cas.dec
# nchild
if not 'nchild' in cols:
T.nchild = np.zeros(N,int)
else:
T.nchild = cas.nchild
# rowc,colc -- shouldn't be necessary...
if not 'objc_flags' in cols:
T.objc_flags = np.zeros(N,int)
else:
T.objc_flags = cas.objc_flags
allbands = band_names()
nbands = len(allbands)
colmap = [('phi_dev_deg', 'devphi'),
('phi_exp_deg', 'expphi'),
('theta_dev', 'devrad'),
('theta_exp', 'exprad'),
('ab_dev', 'devab'),
('ab_exp', 'expab'),
('psfflux', 'psfflux'),
('cmodelflux', 'cmodelflux'),
('devflux', 'devflux'),
('expflux', 'expflux'),
('fracdev', 'fracdev'),
('prob_psf', 'probpsf'),
]
for c1,c2 in colmap:
T.set(c1, np.zeros((N, nbands)))
for bi,b in enumerate(allbands):
for c1,c2 in colmap:
cname = '%s_%s' % (c2, b)
if cname in cols:
T.get(c1)[:,bi] = cas.get(cname)
return _get_sources(-1, -1, -1, release='DR9', objs=T, sdss=DR9(),
bandname=bandname, bands=bands, nanomaggies=nanomaggies,
extrabands=extrabands)
def _get_sources(run,
camcol,
field,
bandname='r',
sdss=None,
release='DR7',
objs=None,
retrieve=True,
checkFiles=True,
curl=False,
roi=None,
radecroi=None,
radecrad=None,
bands=None,
badmag=25,
nanomaggies=False,
getobjs=False,
getsourceobjs=False,
getobjinds=False,
extrabands=None,
fixedComposites=False,
forcePointSources=False,
useObjcType=False,
objCuts=True,
classmap={},
ellipse=GalaxyShape,
cutToPrimary=False):
'''
If set,
radecrad = (ra,dec,rad)
returns sources within "rad" degrees of the given RA,Dec (in degrees)
center.
WARNING, this method alters the "objs" argument, if given.
Consider calling objs.copy() before calling.
-"bandname" is the SDSS band used to cut on position, select
star/gal/exp/dev, and set galaxy shapes.
-"bands" are the bands to include in the returned Source objects;
they will be initialized from the SDSS bands.
-"extrabands" are also included in the returned Source objects;
they will be initialized to the SDSS flux for either the first of
"bands", if given, or "bandname".
'''
from astrometry.sdss import (DR7, DR8, DR9, band_names, band_index,
photo_flags1_map)
# brightPointSourceThreshold=0.):
if sdss is None:
dr = dict(DR7=DR7, DR8=DR8, DR9=DR9)[release]
sdss = dr(curl=curl)
drnum = sdss.getDRNumber()
isdr7 = (drnum == 7)
if bands is None:
bands = band_names()
bandnum = band_index(bandname)
bandnums = np.array([band_index(b) for b in bands])
bandnames = bands
if extrabands is None:
extrabands = []
if objs is None:
from astrometry.util.fits import fits_table
if isdr7:
# FIXME
rerun = 0
if checkFiles:
_check_sdss_files(sdss,
run,
camcol,
field,
bandnum, ['tsObj', 'tsField'],
retrieve=retrieve,
tryopen=True)
tsf = sdss.readTsField(run, camcol, field, rerun)
objfn = sdss.getPath('tsObj',
run,
camcol,
field,
bandname,
rerun=rerun)
else:
if checkFiles:
_check_sdss_files(sdss,
run,
camcol,
field,
bandnum, ['photoObj'],
retrieve=retrieve,
tryopen=True)
objfn = sdss.getPath('photoObj', run, camcol, field)
objs = fits_table(objfn)
if objs is None:
print('No sources in SDSS file', objfn)
return []
objs.index = np.arange(len(objs))
if getobjs:
allobjs = objs.copy()
if roi is not None:
x0, x1, y0, y1 = roi
# FIXME -- we keep only the sources whose centers are within
# the ROI box. Should instead do some ellipse-overlaps
# geometry.
x = objs.colc[:, bandnum]
y = objs.rowc[:, bandnum]
objs.cut((x >= x0) * (x < x1) * (y >= y0) * (y < y1))
if radecroi is not None:
r0, r1, d0, d1 = radecroi
objs.cut((objs.ra >= r0) * (objs.ra <= r1) * (objs.dec >= d0) *
(objs.dec <= d1))
if radecrad is not None:
from astrometry.libkd.spherematch import match_radec
(ra, dec, rad) = radecrad
I, J, d = match_radec(ra, dec, objs.ra, objs.dec, rad)
objs.cut(J)
del I
del d
if objCuts:
# Only deblended children;
# No BRIGHT sources
bright = photo_flags1_map.get('BRIGHT')
objs.cut((objs.nchild == 0) * ((objs.objc_flags & bright) == 0))
if cutToPrimary:
objs.cut((objs.resolve_status & 256) > 0)
if len(objs) == 0:
sources = []
if not (getobjs or getobjinds or getsourceobjs):
return sources
rtn = [sources]
if getobjs:
rtn.append(None)
if getobjinds:
rtn.append(None)
if getsourceobjs:
rtn.append(None)
return rtn
if isdr7:
objs.rename('phi_dev', 'phi_dev_deg')
objs.rename('phi_exp', 'phi_exp_deg')
objs.rename('r_dev', 'theta_dev')
objs.rename('r_exp', 'theta_exp')
# SDSS and Tractor have different opinions on which way this rotation goes
objs.phi_dev_deg *= -1.
objs.phi_exp_deg *= -1.
# MAGIC -- minimum size of galaxy.
objs.theta_dev = np.maximum(objs.theta_dev, 1. / 30.)
objs.theta_exp = np.maximum(objs.theta_exp, 1. / 30.)
if forcePointSources:
Lstar = np.ones(len(objs), float)
Lgal = np.zeros(len(objs), float)
Ldev = Lexp = Lgal
else:
if useObjcType:
objs.cut(np.logical_or(objs.objc_type == 6, objs.objc_type == 3))
Lstar = (objs.objc_type == 6)
Lgal = (objs.objc_type == 3)
else:
Lstar = (objs.prob_psf[:, bandnum] == 1) * 1.0
Lgal = (objs.prob_psf[:, bandnum] == 0) * 1.0
if isdr7:
fracdev = objs.fracpsf[:, bandnum]
else:
fracdev = objs.fracdev[:, bandnum]
Ldev = Lgal * fracdev
Lexp = Lgal * (1. - fracdev)
if isdr7:
from .sdss_dr7 import _dr7_getBrightness
if nanomaggies:
raise RuntimeError('Nanomaggies not supported for DR7 (yet)')
def lup2bright(lups):
counts = [
tsf.luptitude_to_counts(lup, j) for j, lup in enumerate(lups)
]
counts = np.array(counts)
bright = _dr7_getBrightness(counts, tsf, bandnames, extrabands)
return bright
flux2bright = lup2bright
starflux = objs.psfcounts
compflux = objs.counts_model
devflux = objs.counts_dev
expflux = objs.counts_exp
def comp2bright(lups, Ldev, Lexp):
counts = [
tsf.luptitude_to_counts(lup, j) for j, lup in enumerate(lups)
]
counts = np.array(counts)
dcounts = counts * Ldev
ecounts = counts * Lexp
dbright = _dr7_getBrightness(dcounts, tsf, bands, extrabands)
ebright = _dr7_getBrightness(ecounts, tsf, bands, extrabands)
return dbright, ebright
else:
def nmgy2bright(flux):
if len(bandnums):
flux = flux[bandnums]
else:
flux = flux[np.array([bandnum])]
bb = bandnames + extrabands
if nanomaggies:
if len(extrabands):
if len(bandnums) == 0:
# Only "extrabands", no SDSS bands.
flux = np.zeros(len(extrabands)) + flux[0]
else:
flux = np.append(flux, np.zeros(len(extrabands)))
bright = NanoMaggies(order=bb, **dict(zip(bb, flux)))
else:
I = (flux > 0)
mag = np.zeros_like(flux) + badmag
mag[I] = sdss.nmgy_to_mag(flux[I])
if len(extrabands):
mag = np.append(mag, np.zeros(len(extrabands)) + badmag)
bright = Mags(order=bb, **dict(zip(bb, mag)))
return bright
def comp2bright(flux, Ldev, Lexp):
dflux = flux * Ldev
eflux = flux * Lexp
dbright = nmgy2bright(dflux)
ebright = nmgy2bright(eflux)
return dbright, ebright
flux2bright = nmgy2bright
starflux = objs.psfflux
compflux = objs.cmodelflux
devflux = objs.devflux
expflux = objs.expflux
sources = []
nstars, ndev, nexp, ncomp = 0, 0, 0, 0
isources = []
ptsrcclass = classmap.get(PointSource, PointSource)
for i in range(len(objs)):
if Lstar[i]:
pos = RaDecPos(objs.ra[i], objs.dec[i])
flux = starflux[i, :]
bright = flux2bright(flux)
# This should work, I just don't feel like testing it now...
# if brightPointSourceThreshold:
# ps = SdssPointSource(pos, bright, thresh=brightPointSourceThreshold)
# else:
# ps = PointSource(pos, bright)
sources.append(ptsrcclass(pos, bright))
nstars += 1
isources.append(i)
continue
hasdev = (Ldev[i] > 0)
hasexp = (Lexp[i] > 0)
iscomp = (hasdev and hasexp)
pos = RaDecPos(objs.ra[i], objs.dec[i])
if iscomp:
flux = compflux[i, :]
elif hasdev:
flux = devflux[i, :]
elif hasexp:
flux = expflux[i, :]
else:
print(
'Skipping object with Lstar = %g, Ldev = %g, Lexp = %g (fracdev=%g)'
% (Lstar[i], Ldev[i], Lexp[i], fracdev[i]))
continue
isources.append(i)
if iscomp:
if fixedComposites:
bright = flux2bright(flux)
fdev = (Ldev[i] / (Ldev[i] + Lexp[i]))
else:
dbright, ebright = comp2bright(flux, Ldev[i], Lexp[i])
else:
bright = flux2bright(flux)
if hasdev:
re = objs.theta_dev[i, bandnum]
ab = objs.ab_dev[i, bandnum]
phi = objs.phi_dev_deg[i, bandnum]
dshape = ellipse(re, ab, phi)
if hasexp:
re = objs.theta_exp[i, bandnum]
ab = objs.ab_exp[i, bandnum]
phi = objs.phi_exp_deg[i, bandnum]
eshape = ellipse(re, ab, phi)
if iscomp:
if fixedComposites:
gal = FixedCompositeGalaxy(pos, bright, fdev, eshape, dshape)
else:
gal = CompositeGalaxy(pos, ebright, eshape, dbright, dshape)
ncomp += 1
elif hasdev:
gal = DevGalaxy(pos, bright, dshape)
ndev += 1
elif hasexp:
gal = ExpGalaxy(pos, bright, eshape)
nexp += 1
sources.append(gal)
print(
'Created',
ndev,
'deV,',
nexp,
'exp,',
ncomp,
'composite',
)
print('(total %i) galaxies and %i stars' % (ndev + nexp + ncomp, nstars))
if not (getobjs or getobjinds or getsourceobjs):
return sources
if nstars + ndev + nexp + ncomp < len(objs):
objs = objs[np.array(isources)]
rtn = [sources]
if getobjs:
rtn.append(allobjs)
if getobjinds:
rtn.append(objs.index if len(objs) else np.array([]))
if getsourceobjs:
rtn.append(objs)
return rtn
def _get_sources(run, camcol, field, bandname='r', sdss=None, release='DR7',
objs=None,
retrieve=True, curl=False, roi=None,
radecroi=None,
radecrad=None,
bands=None,
badmag=25, nanomaggies=False,
getobjs=False, getsourceobjs=False, getobjinds=False,
extrabands=None,
fixedComposites=False,
forcePointSources=False,
useObjcType=False,
objCuts=True,
classmap={},
ellipse=GalaxyShape,
cutToPrimary=False):
'''
If set,
radecrad = (ra,dec,rad)
returns sources within "rad" degrees of the given RA,Dec (in degrees)
center.
WARNING, this method alters the "objs" argument, if given.
Consider calling objs.copy() before calling.
-"bandname" is the SDSS band used to cut on position, select
star/gal/exp/dev, and set galaxy shapes.
-"bands" are the bands to include in the returned Source objects;
they will be initialized from the SDSS bands.
-"extrabands" are also included in the returned Source objects;
they will be initialized to the SDSS flux for either the first of
"bands", if given, or "bandname".
'''
from astrometry.sdss import (DR7, DR8, DR9, band_names, band_index,
photo_flags1_map)
# brightPointSourceThreshold=0.):
if sdss is None:
dr = dict(DR7=DR7, DR8=DR8, DR9=DR9)[release]
sdss = dr(curl=curl)
drnum = sdss.getDRNumber()
isdr7 = (drnum == 7)
if bands is None:
bands = band_names()
bandnum = band_index(bandname)
bandnums = np.array([band_index(b) for b in bands])
bandnames = bands
if extrabands is None:
extrabands = []
if objs is None:
from astrometry.util.fits import fits_table
if isdr7:
# FIXME
rerun = 0
_check_sdss_files(sdss, run, camcol, field, bandnum,
['tsObj', 'tsField'],
retrieve=retrieve, tryopen=True)
tsf = sdss.readTsField(run, camcol, field, rerun)
objfn = sdss.getPath('tsObj', run, camcol, field,
bandname, rerun=rerun)
else:
_check_sdss_files(sdss, run, camcol, field, bandnum, ['photoObj'],
tryopen=True, retrieve=retrieve)
objfn = sdss.getPath('photoObj', run, camcol, field)
objs = fits_table(objfn)
if objs is None:
print('No sources in SDSS file', objfn)
return []
objs.index = np.arange(len(objs))
if getobjs:
allobjs = objs.copy()
if roi is not None:
x0,x1,y0,y1 = roi
# FIXME -- we keep only the sources whose centers are within
# the ROI box. Should instead do some ellipse-overlaps
# geometry.
x = objs.colc[:,bandnum]
y = objs.rowc[:,bandnum]
objs.cut((x >= x0) * (x < x1) * (y >= y0) * (y < y1))
if radecroi is not None:
r0,r1,d0,d1 = radecroi
objs.cut((objs.ra >= r0) * (objs.ra <= r1) *
(objs.dec >= d0) * (objs.dec <= d1))
if radecrad is not None:
from astrometry.libkd.spherematch import match_radec
(ra,dec,rad) = radecrad
I,J,d = match_radec(ra, dec, objs.ra, objs.dec, rad)
objs.cut(J)
del I
del d
if objCuts:
# Only deblended children;
# No BRIGHT sources
bright = photo_flags1_map.get('BRIGHT')
objs.cut((objs.nchild == 0) * ((objs.objc_flags & bright) == 0))
if cutToPrimary:
objs.cut((objs.resolve_status & 256) > 0)
if isdr7:
objs.rename('phi_dev', 'phi_dev_deg')
objs.rename('phi_exp', 'phi_exp_deg')
objs.rename('r_dev', 'theta_dev')
objs.rename('r_exp', 'theta_exp')
# SDSS and Tractor have different opinions on which way this rotation goes
objs.phi_dev_deg *= -1.
objs.phi_exp_deg *= -1.
# MAGIC -- minimum size of galaxy.
objs.theta_dev = np.maximum(objs.theta_dev, 1./30.)
objs.theta_exp = np.maximum(objs.theta_exp, 1./30.)
if forcePointSources:
Lstar = np.ones(len(objs), float)
Lgal = np.zeros(len(objs), float)
Ldev = Lexp = Lgal
else:
if useObjcType:
objs.cut(np.logical_or(objs.objc_type == 6,
objs.objc_type == 3))
Lstar = (objs.objc_type == 6)
Lgal = (objs.objc_type == 3)
else:
Lstar = (objs.prob_psf[:,bandnum] == 1) * 1.0
Lgal = (objs.prob_psf[:,bandnum] == 0)
if isdr7:
fracdev = objs.fracpsf[:,bandnum]
else:
fracdev = objs.fracdev[:,bandnum]
Ldev = Lgal * fracdev
Lexp = Lgal * (1. - fracdev)
if isdr7:
if nanomaggies:
raise RuntimeError('Nanomaggies not supported for DR7 (yet)')
def lup2bright(lups):
counts = [tsf.luptitude_to_counts(lup,j)
for j,lup in enumerate(lups)]
counts = np.array(counts)
bright = _getBrightness(counts, tsf, bandnames, extrabands)
return bright
flux2bright = lup2bright
starflux = objs.psfcounts
compflux = objs.counts_model
devflux = objs.counts_dev
expflux = objs.counts_exp
def comp2bright(lups, Ldev, Lexp):
counts = [tsf.luptitude_to_counts(lup,j)
for j,lup in enumerate(lups)]
counts = np.array(counts)
dcounts = counts * Ldev
ecounts = counts * Lexp
dbright = _getBrightness(dcounts, tsf, bands, extrabands)
ebright = _getBrightness(ecounts, tsf, bands, extrabands)
return dbright, ebright
else:
def nmgy2bright(flux):
if len(bandnums):
flux = flux[bandnums]
else:
flux = flux[np.array([bandnum])]
bb = bandnames + extrabands
if nanomaggies:
if len(extrabands):
if len(bandnums) == 0:
# Only "extrabands", no SDSS bands.
flux = np.zeros(len(extrabands)) + flux[0]
else:
flux = np.append(flux, np.zeros(len(extrabands)))
bright = NanoMaggies(order=bb, **dict(zip(bb, flux)))
else:
I = (flux > 0)
mag = np.zeros_like(flux) + badmag
mag[I] = sdss.nmgy_to_mag(flux[I])
if len(extrabands):
mag = np.append(mag, np.zeros(len(extrabands)) + badmag)
bright = Mags(order=bb, **dict(zip(bb,mag)))
return bright
def comp2bright(flux, Ldev, Lexp):
dflux = flux * Ldev
eflux = flux * Lexp
dbright = nmgy2bright(dflux)
ebright = nmgy2bright(eflux)
return dbright, ebright
flux2bright = nmgy2bright
starflux = objs.psfflux
compflux = objs.cmodelflux
devflux = objs.devflux
expflux = objs.expflux
sources = []
nstars, ndev, nexp, ncomp = 0, 0, 0, 0
isources = []
ptsrcclass = classmap.get(PointSource, PointSource)
for i in range(len(objs)):
if Lstar[i]:
pos = RaDecPos(objs.ra[i], objs.dec[i])
flux = starflux[i,:]
bright = flux2bright(flux)
# This should work, I just don't feel like testing it now...
# if brightPointSourceThreshold:
# ps = SdssPointSource(pos, bright, thresh=brightPointSourceThreshold)
# else:
# ps = PointSource(pos, bright)
sources.append(ptsrcclass(pos, bright))
nstars += 1
isources.append(i)
continue
hasdev = (Ldev[i] > 0)
hasexp = (Lexp[i] > 0)
iscomp = (hasdev and hasexp)
pos = RaDecPos(objs.ra[i], objs.dec[i])
if iscomp:
flux = compflux[i,:]
elif hasdev:
flux = devflux[i,:]
elif hasexp:
flux = expflux[i,:]
else:
print('Skipping object with Lstar = %g, Ldev = %g, Lexp = %g (fracdev=%g)'
% (Lstar[i], Ldev[i], Lexp[i], fracdev[i]))
continue
isources.append(i)
if iscomp:
if fixedComposites:
bright = flux2bright(flux)
fdev = (Ldev[i] / (Ldev[i] + Lexp[i]))
else:
dbright,ebright = comp2bright(flux, Ldev[i], Lexp[i])
else:
bright = flux2bright(flux)
if hasdev:
re = objs.theta_dev [i,bandnum]
ab = objs.ab_dev [i,bandnum]
phi = objs.phi_dev_deg[i,bandnum]
dshape = ellipse(re, ab, phi)
if hasexp:
re = objs.theta_exp [i,bandnum]
ab = objs.ab_exp [i,bandnum]
phi = objs.phi_exp_deg[i,bandnum]
eshape = ellipse(re, ab, phi)
if iscomp:
if fixedComposites:
gal = FixedCompositeGalaxy(pos, bright, fdev, eshape, dshape)
else:
gal = CompositeGalaxy(pos, ebright, eshape, dbright, dshape)
ncomp += 1
elif hasdev:
gal = DevGalaxy(pos, bright, dshape)
ndev += 1
elif hasexp:
gal = ExpGalaxy(pos, bright, eshape)
nexp += 1
sources.append(gal)
print('Created', ndev, 'deV,', nexp, 'exp,', ncomp, 'composite',)
print('(total %i) galaxies and %i stars' % (ndev+nexp+ncomp, nstars))
if not (getobjs or getobjinds or getsourceobjs):
return sources
if nstars + ndev + nexp + ncomp < len(objs):
objs = objs[np.array(isources)]
rtn = [sources]
if getobjs:
rtn.append(allobjs)
if getobjinds:
rtn.append(objs.index if len(objs) else np.array([]))
if getsourceobjs:
rtn.append(objs)
return rtn