def __init__(self, time, flux, airmass, tcenter, tduration, priors, nthr=4, tmodel=None, verbosity=0):
self.tmodel = tmodel or MandelAgol(nthr=nthr, lerp=False)
self.nldc = tmodel.nldc
self.time = asarray(time)
self.flux = atleast_2d(flux)
self.airmass = asarray(airmass)
self.npt = self.flux.shape[0]
self.npb = self.flux.shape[1]
self.mask_oot = (self.time < tcenter-0.55*tduration) | (self.time > tcenter+0.55*tduration)
self.ld = zeros(2*self.npb)
self.informative_limb_darkening = False
self.verbosity = verbosity
self.baseline = zeros_like(self.flux)
self.tmparr = zeros_like(self.flux)
elc = [f[self.mask_oot].std() for f in self.flux.T]
self.priors = [priors['transit_center'], ## 0 transit center, required
priors['period'], ## 1 period, required
priors['stellar_density'], ## 2 stellar density, required
priors.get('impact_parameter', UP(0.0, 0.99, 'b'))] ## 3 impact parameter
kmin, kmax = priors['radius_ratio'].limits()
for i in range(self.npb):
self.priors.append(UP(kmin**2, kmax**2, 'k2_{}'.format(i))) ## as + i squared radius ratios
for i in range(self.npb):
self.priors.append(UP(0.15*elc[i], 2*elc[i], 'el_{}'.format(i))) ## es + i point-to-point scatter
for i in range(self.npb):
for j in range(self.nldc):
ldc_label = 'ldc_{:d}_{:d}'.format(i,j)
if ldc_label in priors.keys():
if self.verbosity > 0:
print ('Using an informative prior on limb darkening: ' + ldc_label)
self.informative_limb_darkening = True
self.priors.append(priors.get(ldc_label, UP(-0.5, 1, ldc_label))) ## ls + 0 + nldc*i ldc coefficients
blmin, blmax = priors.get('baseline', UP(0.99,1.01)).limits()
for i in range(self.npb):
self.priors.extend([UP( blmin, blmax, 'bl_{}'.format(i)), ## bs + 0 + 2*i baseline level
UP( -0.020, 0.020, 'am_{}'.format(i))]) ## bs + 1 + 2*i airmass correction
self.ps = PriorSet(self.priors)
ks = self.k2_start = 4
es = self.err_start = ks+self.npb
ls = self.ldc_start = es+self.npb
bs = self.baseline_start = ls + self.nldc*self.npb
self.k2_slice = s_[ks:es]
self.err_slice = s_[es:ls]
self.ldc_slice = s_[ls:bs]
self.bsl_slices = [s_[bs+2*i:bs+2*(i+1)] for i in range(self.npb)]
def __init__(self, time, flux, airmass, tcenter, tduration, priors, nthr=4, tmodel=None):
self.tmodel = tmodel or MandelAgol(nthr=nthr, lerp=True)
self.time = asarray(time)
self.flux = asarray(flux)
self.airmass = asarray(airmass)
self.npb = self.flux.shape[1]
self.mask_oot = (self.time < tcenter-0.55*tduration) | (self.time > tcenter+0.55*tduration)
self.ld = zeros(2*self.npb)
self.baseline = zeros_like(self.flux)
self.tmparr = zeros_like(self.flux)
elc = [f[self.mask_oot].std() for f in self.flux.T]
self.priors = [priors['transit_center'], ## 0 transit center, required
priors['period'], ## 1 period, required
priors['stellar_density'], ## 2 stellar density, required
priors.get('impact_parameter', UP(0.0, 0.99, 'b'))] ## 3 impact parameter
kmin, kmax = priors['radius_ratio'].limits()
for i in range(self.npb):
self.priors.append(UP(kmin**2, kmax**2, 'k2_{}'.format(i))) ## as + i squared radius ratios
for i in range(self.npb):
self.priors.append(UP(0.15*elc[i], 2*elc[i], 'el_{}'.format(i))) ## es + i point-to-point scatter
for i in range(self.npb):
self.priors.extend([UP( 0.0001, 1, 'u_{}'.format(i)), ## ls + 0 + 2*i linear ldc
UP( 0.0001, 1, 'v_{}'.format(i))]) ## ls + 1 + 2*i quadratic ldc
blmin, blmax = priors.get('baseline', UP(0.99,1.01)).limits()
for i in range(self.npb):
self.priors.extend([UP( blmin, blmax, 'bl_{}'.format(i)), ## bs + 0 + 2*i baseline level
UP( 0.000, 0.020, 'am_{}'.format(i))]) ## bs + 1 + 2*i airmass correction
self.ps = PriorSet(self.priors)
ks = self.k2_start = 4
es = self.err_start = ks+self.npb
ls = self.ldc_start = es+self.npb
bs = self.baseline_start = ls + 2*self.npb
self.k2_slice = s_[ks:es]
self.err_slice = s_[es:ls]
self.ldc_slice = s_[ls:bs]
self.bsl_slices = [s_[bs+2*i:bs+2*(i+1)] for i in range(self.npb)]
class SingleTransitMultiColorLPF(object):
def __init__(self, time, flux, airmass, tcenter, tduration, priors, nthr=4, tmodel=None, verbosity=0):
self.tmodel = tmodel or MandelAgol(nthr=nthr, lerp=False)
self.nldc = tmodel.nldc
self.time = asarray(time)
self.flux = atleast_2d(flux)
self.airmass = asarray(airmass)
self.npt = self.flux.shape[0]
self.npb = self.flux.shape[1]
self.mask_oot = (self.time < tcenter-0.55*tduration) | (self.time > tcenter+0.55*tduration)
self.ld = zeros(2*self.npb)
self.informative_limb_darkening = False
self.verbosity = verbosity
self.baseline = zeros_like(self.flux)
self.tmparr = zeros_like(self.flux)
elc = [f[self.mask_oot].std() for f in self.flux.T]
self.priors = [priors['transit_center'], ## 0 transit center, required
priors['period'], ## 1 period, required
priors['stellar_density'], ## 2 stellar density, required
priors.get('impact_parameter', UP(0.0, 0.99, 'b'))] ## 3 impact parameter
kmin, kmax = priors['radius_ratio'].limits()
for i in range(self.npb):
self.priors.append(UP(kmin**2, kmax**2, 'k2_{}'.format(i))) ## as + i squared radius ratios
for i in range(self.npb):
self.priors.append(UP(0.15*elc[i], 2*elc[i], 'el_{}'.format(i))) ## es + i point-to-point scatter
for i in range(self.npb):
for j in range(self.nldc):
ldc_label = 'ldc_{:d}_{:d}'.format(i,j)
if ldc_label in priors.keys():
if self.verbosity > 0:
print ('Using an informative prior on limb darkening: ' + ldc_label)
self.informative_limb_darkening = True
self.priors.append(priors.get(ldc_label, UP(-0.5, 1, ldc_label))) ## ls + 0 + nldc*i ldc coefficients
blmin, blmax = priors.get('baseline', UP(0.99,1.01)).limits()
for i in range(self.npb):
self.priors.extend([UP( blmin, blmax, 'bl_{}'.format(i)), ## bs + 0 + 2*i baseline level
UP( -0.020, 0.020, 'am_{}'.format(i))]) ## bs + 1 + 2*i airmass correction
self.ps = PriorSet(self.priors)
ks = self.k2_start = 4
es = self.err_start = ks+self.npb
ls = self.ldc_start = es+self.npb
bs = self.baseline_start = ls + self.nldc*self.npb
self.k2_slice = s_[ks:es]
self.err_slice = s_[es:ls]
self.ldc_slice = s_[ls:bs]
self.bsl_slices = [s_[bs+2*i:bs+2*(i+1)] for i in range(self.npb)]
def create_initial_population(self, npop):
pv0 = self.ps.generate_pv_population(npop)
if not self.informative_limb_darkening:
pv0[:, self.ldc_slice] = uniform(0.0, 1./self.nldc, size=(npop, self.nldc*self.npb))
return pv0
def compute_lc_model(self, pv):
_tc, _p, _b = pv[0], pv[1], pv[3]
_ld = pv[self.ldc_slice]
_a = as_from_rhop(pv[2], pv[1])
_i = m.acos(_b/_a)
k = np.sqrt(pv[self.k2_slice])
_k = k.mean()
kf = (k/_k)**2
z = of.z_circular(self.time, _tc, _p, _a, _i, 4)
flux = self.tmodel(z, _k, pv[self.ldc_slice])
return (kf*(flux-1.)+1.).reshape((self.npt,self.npb))
def compute_baseline(self, pv):
for i in range(self.npb):
bpv = pv[self.bsl_slices[i]]
self.baseline[:,i] = bpv[0]/np.exp(bpv[1]*self.airmass)
return self.baseline
def normalize_flux(self, pv):
return self.flux/self.compute_baseline(pv)
def log_posterior(self, pv):
if any(pv < self.ps.pmins) or any(pv>self.ps.pmaxs): return -1e18
#if not (0. < pv[self.ldc_slice].sum() < 1.): return -1e18
o = self.normalize_flux(pv)
m = self.compute_lc_model(pv)
self.tmparr[:] = ((o-m)/pv[self.err_slice])**2
chi_sqr = self.tmparr.sum()
log_p = self.ps.c_log_prior(pv)
log_l = - 0.5*self.time.size*np.log(2*pi) - (self.time.shape[0]*np.log(pv[self.err_slice])).sum() - 0.5*chi_sqr
return log_p + log_l
class SingleTransitMultiColorQuadraticLPF(object):
def __init__(self, time, flux, airmass, tcenter, tduration, priors, nthr=4, tmodel=None):
self.tmodel = tmodel or MandelAgol(nthr=nthr, lerp=True)
self.time = asarray(time)
self.flux = asarray(flux)
self.airmass = asarray(airmass)
self.npb = self.flux.shape[1]
self.mask_oot = (self.time < tcenter-0.55*tduration) | (self.time > tcenter+0.55*tduration)
self.ld = zeros(2*self.npb)
self.baseline = zeros_like(self.flux)
self.tmparr = zeros_like(self.flux)
elc = [f[self.mask_oot].std() for f in self.flux.T]
self.priors = [priors['transit_center'], ## 0 transit center, required
priors['period'], ## 1 period, required
priors['stellar_density'], ## 2 stellar density, required
priors.get('impact_parameter', UP(0.0, 0.99, 'b'))] ## 3 impact parameter
kmin, kmax = priors['radius_ratio'].limits()
for i in range(self.npb):
self.priors.append(UP(kmin**2, kmax**2, 'k2_{}'.format(i))) ## as + i squared radius ratios
for i in range(self.npb):
self.priors.append(UP(0.15*elc[i], 2*elc[i], 'el_{}'.format(i))) ## es + i point-to-point scatter
for i in range(self.npb):
self.priors.extend([UP( 0.0001, 1, 'u_{}'.format(i)), ## ls + 0 + 2*i linear ldc
UP( 0.0001, 1, 'v_{}'.format(i))]) ## ls + 1 + 2*i quadratic ldc
blmin, blmax = priors.get('baseline', UP(0.99,1.01)).limits()
for i in range(self.npb):
self.priors.extend([UP( blmin, blmax, 'bl_{}'.format(i)), ## bs + 0 + 2*i baseline level
UP( 0.000, 0.020, 'am_{}'.format(i))]) ## bs + 1 + 2*i airmass correction
self.ps = PriorSet(self.priors)
ks = self.k2_start = 4
es = self.err_start = ks+self.npb
ls = self.ldc_start = es+self.npb
bs = self.baseline_start = ls + 2*self.npb
self.k2_slice = s_[ks:es]
self.err_slice = s_[es:ls]
self.ldc_slice = s_[ls:bs]
self.bsl_slices = [s_[bs+2*i:bs+2*(i+1)] for i in range(self.npb)]
def compute_lc_model(self, pv):
_tc, _p, _b = pv[0], pv[1], pv[3]
_ld = pv[self.ldc_slice]
_a = as_from_rhop(pv[2], pv[1])
_i = m.acos(_b/_a)
self.ld[0::2] = 2.*np.sqrt(_ld[0::2])*_ld[1::2]
self.ld[1::2] = np.sqrt(_ld[0::2])*(1.-2.*_ld[1::2])
k = np.sqrt(pv[self.k2_slice])
_k = k.mean()
kf = (k/_k)**2
z = of.z_circular(self.time, _tc, _p, _a, _i, 4)
flux = self.tmodel(z, _k, self.ld)
return kf*(flux-1.)+1.
def compute_baseline(self, pv):
for i in range(self.npb):
bpv = pv[self.bsl_slices[i]]
self.baseline[:,i] = bpv[0]/np.exp(bpv[1]*self.airmass)
return self.baseline
def normalize_flux(self, pv):
return self.flux/self.compute_baseline(pv)
def log_posterior(self, pv):
if any(pv < self.ps.pmins) or any(pv>self.ps.pmaxs): return -1e18
o = self.normalize_flux(pv)
m = self.compute_lc_model(pv)
self.tmparr[:] = ((o-m)/pv[self.err_slice])**2
chi_sqr = self.tmparr.sum()
log_p = self.ps.c_log_prior(pv)
log_l = - 0.5*self.time.size*np.log(2*pi) - (self.time.shape[0]*np.log(pv[self.err_slice])).sum() - 0.5*chi_sqr
return log_p + log_l
