def read_psf_model(self,
x0,
y0,
gaussPsf=False,
pixPsf=False,
const2psf=False,
psf_sigma=1.,
cx=0,
cy=0):
psffn = None
if gaussPsf:
from tractor.basics import GaussianMixturePSF
v = psf_sigma**2
psf = GaussianMixturePSF(1., 0., 0., v, v, 0.)
print('WARNING: using mock PSF:', psf)
psf.version = '0'
psf.plver = ''
elif pixPsf:
# spatially varying pixelized PsfEx
from tractor.psfex import PixelizedPsfEx
print('Reading PsfEx model from', self.psffn)
psf = PixelizedPsfEx(self.psffn)
psf.shift(x0, y0)
psffn = self.psffn
elif const2psf:
from tractor.psfex import PsfExModel
from tractor.basics import GaussianMixtureEllipsePSF
# 2-component constant MoG.
print('Reading PsfEx model from', self.psffn)
psffn = self.psffn
psfex = PsfExModel(self.psffn)
psfim = psfex.at(cx, cy)
psfim = psfim[5:-5, 5:-5]
print('Fitting PsfEx model as 2-component Gaussian...')
psf = GaussianMixtureEllipsePSF.fromStamp(psfim, N=2)
del psfim
del psfex
else:
assert (False)
print('Using PSF model', psf)
if psffn is not None:
hdr = fitsio.read_header(psffn)
psf.version = hdr.get('LEGSURV', None)
if psf.version is None:
psf.version = str(os.stat(psffn).st_mtime)
psf.plver = hdr.get('PLVER', '').strip()
return psf
def read_psf_model(self, x0, y0, gaussPsf=False, pixPsf=False,
const2psf=False, psf_sigma=1., cx=0, cy=0):
psffn = None
if gaussPsf:
from tractor.basics import GaussianMixturePSF
v = psf_sigma**2
psf = GaussianMixturePSF(1., 0., 0., v, v, 0.)
print('WARNING: using mock PSF:', psf)
psf.version = '0'
psf.plver = ''
elif pixPsf:
# spatially varying pixelized PsfEx
from tractor.psfex import PixelizedPsfEx
print('Reading PsfEx model from', self.psffn)
psf = PixelizedPsfEx(self.psffn)
psf.shift(x0, y0)
psffn = self.psffn
elif const2psf:
from tractor.psfex import PsfExModel
from tractor.basics import GaussianMixtureEllipsePSF
# 2-component constant MoG.
print('Reading PsfEx model from', self.psffn)
psffn = self.psffn
psfex = PsfExModel(self.psffn)
psfim = psfex.at(cx, cy)
psfim = psfim[5:-5, 5:-5]
print('Fitting PsfEx model as 2-component Gaussian...')
psf = GaussianMixtureEllipsePSF.fromStamp(psfim, N=2)
del psfim
del psfex
else:
assert(False)
print('Using PSF model', psf)
if psffn is not None:
hdr = fitsio.read_header(psffn)
psf.version = hdr.get('LEGSURV', None)
if psf.version is None:
psf.version = str(os.stat(psffn).st_mtime)
psf.plver = hdr.get('PLVER', '').strip()
return psf
def run_calibs(self,
ra,
dec,
pixscale,
W=2112,
H=4644,
se=True,
astrom=True,
psfex=True,
psfexfit=True):
'''
pixscale: in degrees/pixel
'''
for fn in [self.wcsfn, self.sefn, self.psffn, self.psffitfn]:
print('exists?', os.path.exists(fn), fn)
self.makedirs()
run_fcopy = False
run_se = False
run_astrom = False
run_psfex = False
run_psfexfit = False
sedir = 'NGVS-g-Single'
if not all([os.path.exists(fn) for fn in [self.sefn]]):
run_se = True
run_fcopy = True
if not all([
os.path.exists(fn)
for fn in [self.wcsfn, self.corrfn, self.sdssfn]
]):
run_astrom = True
if not os.path.exists(self.psffn):
run_psfex = True
if not os.path.exists(self.psffitfn):
run_psfexfit = True
if run_fcopy and (run_se and se):
tmpimgfn = create_temp(suffix='.fits')
cmd = 'imcopy %s"+%i" %s' % (self.imgfn, self.hdu, tmpimgfn)
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_astrom or run_se:
# grab header values...
primhdr = self.read_image_primary_header()
hdr = self.read_image_header()
magzp = hdr['PHOT_C'] + 2.5 * np.log10(hdr['EXPTIME'])
seeing = self.seeing
print('Seeing', seeing, 'arcsec')
if run_se and se:
#'-SEEING_FWHM %f' % seeing,
#'-PIXEL_SCALE 0',
#'-PIXEL_SCALE %f' % (pixscale * 3600),
#'-MAG_ZEROPOINT %f' % magzp,
cmd = ' '.join([
'sex', '-c',
os.path.join(sedir, 'psfex.sex'), '-PARAMETERS_NAME',
os.path.join(sedir, 'psfex.param'), '-FILTER_NAME',
os.path.join(sedir, 'default.conv'), '-CATALOG_NAME',
self.sefn, tmpimgfn
])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_astrom and astrom:
cmd = ' '.join([
'solve-field --config', an_config, '-D . --temp-dir', tempdir,
'--ra %f --dec %f' % (ra, dec), '--radius 1',
'-L %f -H %f -u app' %
(0.9 * pixscale * 3600, 1.1 * pixscale * 3600),
'--continue --no-plots --no-remove-lines --uniformize 0',
'--no-fits2fits',
'-X x_image -Y y_image -s flux_auto --extension 2',
'--width %i --height %i' % (W, H), '--crpix-center',
'-N none -U none -S none -M none --rdls', self.sdssfn,
'--corr', self.corrfn, '--wcs', self.wcsfn, '--temp-axy',
'--tag-all', self.sefn
])
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_psfex and psfex:
cmd = ('psfex -c %s -PSF_DIR %s %s -NTHREADS 1' %
(os.path.join(sedir, 'gradmap.psfex'),
os.path.dirname(self.psffn), self.sefn))
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
dotpsf = self.psffn.replace('.fits', '.psf')
if os.path.exists(dotpsf) and not os.path.exists(self.psffn):
cmd = 'mv %s %s' % (dotpsf, self.psffn)
print(cmd)
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_psfexfit and psfexfit:
print('Fit PSF...')
from tractor.basics import GaussianMixtureEllipsePSF, GaussianMixturePSF
from tractor.psfex import PsfEx
iminfo = self.get_image_info()
#print 'img:', iminfo
H, W = iminfo['dims']
psfex = PsfEx(self.psffn,
W,
H,
ny=13,
nx=7,
psfClass=GaussianMixtureEllipsePSF)
psfex.savesplinedata = True
print('Fitting MoG model to PsfEx')
psfex._fitParamGrid(damp=1)
pp, XX, YY = psfex.splinedata
# Convert to GaussianMixturePSF
ppvar = np.zeros_like(pp)
for iy in range(psfex.ny):
for ix in range(psfex.nx):
psf = GaussianMixtureEllipsePSF(*pp[iy, ix, :])
mog = psf.toMog()
ppvar[iy, ix, :] = mog.getParams()
psfexvar = PsfEx(self.psffn,
W,
H,
ny=psfex.ny,
nx=psfex.nx,
psfClass=GaussianMixturePSF)
psfexvar.splinedata = (ppvar, XX, YY)
psfexvar.toFits(self.psffitfn, merge=True)
print('Wrote', self.psffitfn)
def run_calibs(self, ra, dec, pixscale, mock_psf,
W=2048, H=4096, se=True,
astrom=True, psfex=True, sky=True,
morph=False, se2=False, psfexfit=True,
funpack=True, fcopy=False, use_mask=True,
just_check=False):
'''
pixscale: in arcsec/pixel
just_check: if True, returns True if calibs need to be run.
'''
print 'run_calibs:', str(self), 'near RA,Dec', ra,dec, 'with pixscale', pixscale, 'arcsec/pix'
for fn in [self.wcsfn, self.sefn, self.psffn, self.psffitfn, self.skyfn]:
print 'exists?', os.path.exists(fn), fn
self.makedirs()
if mock_psf:
psfex = False
psfexfit = False
run_funpack = False
run_se = False
run_se2 = False
run_astrom = False
run_psfex = False
run_psfexfit = False
run_morph = False
run_sky = False
if se and not all([os.path.exists(fn) for fn in [self.sefn]]):
run_se = True
run_funpack = True
if se2 and not all([os.path.exists(fn) for fn in [self.se2fn]]):
run_se2 = True
run_funpack = True
#if not all([os.path.exists(fn) for fn in [self.wcsfn,self.corrfn,self.sdssfn]]):
if astrom and not os.path.exists(self.wcsfn):
run_astrom = True
if psfex and not os.path.exists(self.psffn):
run_psfex = True
if psfexfit and not (os.path.exists(self.psffitfn) and os.path.exists(self.psffitellfn)):
run_psfexfit = True
if morph and not os.path.exists(self.morphfn):
run_morph = True
run_funpack = True
if sky and not os.path.exists(self.skyfn):
run_sky = True
if just_check:
return (run_se or run_se2 or run_astrom or run_psfex or run_psfexfit
or run_morph or run_sky)
if run_funpack and (funpack or fcopy):
tmpimgfn = create_temp(suffix='.fits')
tmpmaskfn = create_temp(suffix='.fits')
if funpack:
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpimgfn, self.imgfn)
else:
cmd = 'imcopy %s"+%i" %s' % (self.imgfn, self.hdu, tmpimgfn)
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if use_mask:
cmd = 'funpack -E %i -O %s %s' % (self.hdu, tmpmaskfn, self.dqfn)
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_astrom or run_morph or run_se or run_se2:
# grab header values...
primhdr = self.read_image_primary_header()
hdr = self.read_image_header()
magzp = primhdr['MAGZERO']
fwhm = hdr['FWHM']
seeing = pixscale * fwhm
print 'FWHM', fwhm, 'pix'
print 'pixscale', pixscale, 'arcsec/pix'
print 'Seeing', seeing, 'arcsec'
if run_se:
maskstr = ''
if use_mask:
maskstr = '-FLAG_IMAGE ' + tmpmaskfn
cmd = ' '.join([
'sex',
'-c', os.path.join(sedir, 'DECaLS-v2.sex'),
maskstr, '-SEEING_FWHM %f' % seeing,
'-PIXEL_SCALE 0',
#'-PIXEL_SCALE %f' % (pixscale),
'-MAG_ZEROPOINT %f' % magzp, '-CATALOG_NAME', self.sefn,
tmpimgfn])
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_se2:
cmd = ' '.join([
'sex',
'-c', os.path.join(sedir, 'DECaLS-v2-2.sex'),
'-FLAG_IMAGE', tmpmaskfn, '-SEEING_FWHM %f' % seeing,
'-PIXEL_SCALE %f' % (pixscale),
'-MAG_ZEROPOINT %f' % magzp, '-CATALOG_NAME', self.se2fn,
tmpimgfn])
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_astrom:
cmd = ' '.join([
'solve-field --config', an_config, '-D . --temp-dir', tempdir,
'--ra %f --dec %f' % (ra,dec), '--radius 1',
'-L %f -H %f -u app' % (0.9 * pixscale, 1.1 * pixscale),
'--continue --no-plots --no-remove-lines --uniformize 0',
'--no-fits2fits',
'-X x_image -Y y_image -s flux_auto --extension 2',
'--width %i --height %i' % (W,H),
'--crpix-center',
'-N none -U none -S none -M none',
#'--rdls', self.sdssfn,
#'--corr', self.corrfn,
'--rdls none --corr none',
'--wcs', self.wcsfn,
'--temp-axy', '--tag-all', self.sefn])
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if not os.path.exists(self.wcsfn):
# Run a second phase...
an_config_2 = os.path.join(decals_dir, 'calib', 'an-config', 'cfg2')
cmd = ' '.join([
'solve-field --config', an_config_2, '-D . --temp-dir', tempdir,
'--ra %f --dec %f' % (ra,dec), '--radius 1',
'-L %f -H %f -u app' % (0.9 * pixscale, 1.1 * pixscale),
'--continue --no-plots --uniformize 0',
'--no-fits2fits',
'-X x_image -Y y_image -s flux_auto --extension 2',
'--width %i --height %i' % (W,H),
'--crpix-center',
'-N none -U none -S none -M none',
'--rdls none --corr none',
'--wcs', self.wcsfn,
'--temp-axy', '--tag-all', self.sefn])
#--no-remove-lines
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_psfex:
cmd = ('psfex -c %s -PSF_DIR %s %s' %
(os.path.join(sedir, 'DECaLS-v2.psfex'),
os.path.dirname(self.psffn), self.sefn))
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_psfexfit:
print 'Fit PSF...'
from tractor.basics import GaussianMixtureEllipsePSF, GaussianMixturePSF
from tractor.psfex import PsfEx
iminfo = self.get_image_info()
#print 'img:', iminfo
H,W = iminfo['dims']
psfex = PsfEx(self.psffn, W, H, ny=13, nx=7,
psfClass=GaussianMixtureEllipsePSF)
psfex.savesplinedata = True
print 'Fitting MoG model to PsfEx'
psfex._fitParamGrid(damp=1)
pp,XX,YY = psfex.splinedata
psfex.toFits(self.psffitellfn, merge=True)
print 'Wrote', self.psffitellfn
# Convert to GaussianMixturePSF
ppvar = np.zeros_like(pp)
for iy in range(psfex.ny):
for ix in range(psfex.nx):
psf = GaussianMixtureEllipsePSF(*pp[iy, ix, :])
mog = psf.toMog()
ppvar[iy,ix,:] = mog.getParams()
psfexvar = PsfEx(self.psffn, W, H, ny=psfex.ny, nx=psfex.nx,
psfClass=GaussianMixturePSF)
psfexvar.splinedata = (ppvar, XX, YY)
psfexvar.toFits(self.psffitfn, merge=True)
print 'Wrote', self.psffitfn
if run_morph:
cmd = ' '.join(['sex -c', os.path.join(sedir, 'CS82_MF.sex'),
'-FLAG_IMAGE', tmpmaskfn,
'-SEEING_FWHM %f' % seeing,
'-MAG_ZEROPOINT %f' % magzp,
'-PSF_NAME', self.psffn,
'-CATALOG_NAME', self.morphfn,
tmpimgfn])
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_sky:
img = self.read_image()
wt = self.read_invvar()
img = img[wt > 0]
try:
skyval = estimate_mode(img, raiseOnWarn=True)
except:
skyval = np.median(img)
sky = ConstantSky(skyval)
tt = type(sky)
sky_type = '%s.%s' % (tt.__module__, tt.__name__)
hdr = fitsio.FITSHDR()
hdr.add_record(dict(name='SKY', value=sky_type, comment='Sky class'))
sky.toFitsHeader(hdr, prefix='SKY_')
fits = fitsio.FITS(self.skyfn, 'rw', clobber=True)
fits.write(None, header=hdr)
def run_calibs(self, ra, dec, pixscale, W=2112, H=4644, se=True,
astrom=True, psfex=True, psfexfit=True):
'''
pixscale: in degrees/pixel
'''
for fn in [self.wcsfn,self.sefn,self.psffn,self.psffitfn]:
print 'exists?', os.path.exists(fn), fn
self.makedirs()
run_fcopy = False
run_se = False
run_astrom = False
run_psfex = False
run_psfexfit = False
sedir = 'NGVS-g-Single'
if not all([os.path.exists(fn) for fn in [self.sefn]]):
run_se = True
run_fcopy = True
if not all([os.path.exists(fn) for fn in [self.wcsfn,self.corrfn,self.sdssfn]]):
run_astrom = True
if not os.path.exists(self.psffn):
run_psfex = True
if not os.path.exists(self.psffitfn):
run_psfexfit = True
if run_fcopy and (run_se and se):
tmpimgfn = create_temp(suffix='.fits')
cmd = 'imcopy %s"+%i" %s' % (self.imgfn, self.hdu, tmpimgfn)
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_astrom or run_se:
# grab header values...
primhdr = self.read_image_primary_header()
hdr = self.read_image_header()
magzp = hdr['PHOT_C'] + 2.5 * np.log10(hdr['EXPTIME'])
seeing = self.seeing
print 'Seeing', seeing, 'arcsec'
if run_se and se:
#'-SEEING_FWHM %f' % seeing,
#'-PIXEL_SCALE 0',
#'-PIXEL_SCALE %f' % (pixscale * 3600),
#'-MAG_ZEROPOINT %f' % magzp,
cmd = ' '.join([
'sex',
'-c', os.path.join(sedir, 'psfex.sex'),
'-PARAMETERS_NAME', os.path.join(sedir, 'psfex.param'),
'-FILTER_NAME', os.path.join(sedir, 'default.conv'),
'-CATALOG_NAME', self.sefn,
tmpimgfn])
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_astrom and astrom:
cmd = ' '.join([
'solve-field --config', an_config, '-D . --temp-dir', tempdir,
'--ra %f --dec %f' % (ra,dec), '--radius 1',
'-L %f -H %f -u app' % (0.9 * pixscale * 3600, 1.1 * pixscale * 3600),
'--continue --no-plots --no-remove-lines --uniformize 0',
'--no-fits2fits',
'-X x_image -Y y_image -s flux_auto --extension 2',
'--width %i --height %i' % (W,H),
'--crpix-center',
'-N none -U none -S none -M none --rdls', self.sdssfn,
'--corr', self.corrfn, '--wcs', self.wcsfn,
'--temp-axy', '--tag-all', self.sefn])
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_psfex and psfex:
cmd = ('psfex -c %s -PSF_DIR %s %s -NTHREADS 1' %
(os.path.join(sedir, 'gradmap.psfex'),
os.path.dirname(self.psffn), self.sefn))
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
dotpsf = self.psffn.replace('.fits', '.psf')
if os.path.exists(dotpsf) and not os.path.exists(self.psffn):
cmd = 'mv %s %s' % (dotpsf, self.psffn)
print cmd
if os.system(cmd):
raise RuntimeError('Command failed: ' + cmd)
if run_psfexfit and psfexfit:
print 'Fit PSF...'
from tractor.basics import GaussianMixtureEllipsePSF, GaussianMixturePSF
from tractor.psfex import PsfEx
iminfo = self.get_image_info()
#print 'img:', iminfo
H,W = iminfo['dims']
psfex = PsfEx(self.psffn, W, H, ny=13, nx=7,
psfClass=GaussianMixtureEllipsePSF)
psfex.savesplinedata = True
print 'Fitting MoG model to PsfEx'
psfex._fitParamGrid(damp=1)
pp,XX,YY = psfex.splinedata
# Convert to GaussianMixturePSF
ppvar = np.zeros_like(pp)
for iy in range(psfex.ny):
for ix in range(psfex.nx):
psf = GaussianMixtureEllipsePSF(*pp[iy, ix, :])
mog = psf.toMog()
ppvar[iy,ix,:] = mog.getParams()
psfexvar = PsfEx(self.psffn, W, H, ny=psfex.ny, nx=psfex.nx,
psfClass=GaussianMixturePSF)
psfexvar.splinedata = (ppvar, XX, YY)
psfexvar.toFits(self.psffitfn, merge=True)
print 'Wrote', self.psffitfn
