def plot_transit(self, fig=0, nbin=100):
from transitLightCurve.transitlightcurve import TransitLightcurve
from transitLightCurve.utilities import bin, fold
phase = fold(self.time, self.p, self.tc, shift=0.5)
flux = self.get_flux()
if nbin is not None:
phase, flux, fe = bin(phase, flux, nbin)
pl.figure(fig)
pl.plot(phase, flux, '.')
if self.fit is not None:
lc = TransitLightcurve(self.fit['parameterization'], ldpar=self.fit['ldc'], mode='phase')
phase = np.linspace(phase[0], phase[-1], 1000)
pl.plot(phase, lc(TWO_PI*(phase-0.5)))
def main():
##########################################################################################
##
## CONFIG AND OPTION PARSERS
## =========================
cp.read(opt.config_file)
##########################################################################################
##
## INITIALIZATION
## ==============
##
## General Options
## ---------------
basename = cp.get('General','basename')
method = cp.get('General','method')
targetid = CoRoT_targets[int(cp.get('General','name')[1:])]
maxpts = cp.getint('Target','max_pts') or None
fn_data = '{}_00_lc.pkl'.format(basename)
fn_initial = '{}_01_if.pkl'.format(basename)
fn_final = '{}_02_ff.pkl'.format(basename)
fn_mcmc = '{}_03_mc.pkl'.format(basename)
do_global_fit = not exists(fn_initial) or opt.do_global_fit
de_init_pars = {'npop':cp.getint('Initial DE','npop'),
'ngen':cp.getint('Initial DE','ngen'),
'C':cp.getfloat('Initial DE','C'),
'F':cp.getfloat('Initial DE','F')}
de_final_pars = {'npop':cp.getint('Final DE','npop'),
'ngen':cp.getint('Final DE','ngen'),
'C':cp.getfloat('Final DE','C'),
'F':cp.getfloat('Final DE','F')}
ds_pars = {'ftol':1e-4, 'disp':False}
combine_channels = cp.getboolean('General','combine_channels')
do_initial_fit = cp.getboolean('General','do_initial_fit') and opt.do_initial_fit
do_final_fit = cp.getboolean('General','do_final_fit') and opt.do_final_fit
do_mcmc = cp.getboolean('General','do_mcmc') and opt.do_mcmc
fit_pars = dict(cp.items('Fitting'))
for p in fit_pars.items():
if p[1].lower() == 'true': fit_pars[p[0]] = True
elif p[1].lower() == 'false': fit_pars[p[0]] = False
else:
try:
fit_pars[p[0]] = float(p[1])
except ValueError:
fit_pars[p[0]] = p[1]
fit_pars['n_threads'] = cp.getint('General','n_threads')
np.set_printoptions(precision=5)
np.random.seed(0)
INF = 1e8
##########################################################################################
##
## DEFINE HELPER FUNCTIONS
## =======================
##
def load_corot_data(targetid):
return import_as_MTLC(targetid, w_period, w_transit, maxpts=maxpts,
clean_pars=clean_pars,
ps_period=CoRoT.orbit_period,
combine_channels=combine_channels)
def fit_corot(targetid, data, parameterization, de_pars):
return fit_multitransit(data, parameterization,
de_pars=de_pars,
ds_pars=ds_pars,
method=method,
**fit_pars)
##########################################################################################
##
## LOAD DATA
## =========
##
clean_pars = {'top':3, 'bottom':10}
w_period = cp.getfloat('General','w_period')
w_transit = cp.getfloat('General','w_transit')
phase_lim = cp.getfloat('General','phase_lim')
if not opt.load_lcdata:
data = load_corot_data(targetid) if is_root else None
if opt.save_lcdata and is_root:
f = open(fn_data, 'w')
cPickle.dump(data, f)
f.close()
elif is_root:
f = open(fn_data, 'r')
data = cPickle.load(f)
f.close()
if with_mpi:
data = mpi_comm.bcast(data)
##########################################################################################
##
## DEFINE PARAMETERS
## =================
parameter_defs = {}
for p in cp.items('MCMC Parameters'):
parameter_defs[p[0]] = eval(p[1])
def addpar(name, pdef):
if name not in parameter_defs.keys():
parameter_defs[name] = pdef
for ch in range(len(data)):
if 'error {}'.format(ch) not in parameter_defs.keys():
std = data[ch].get_std().mean()
parameter_defs['error {}'.format(ch)] = {"sigma":1e-4, 'free':True, 'value':std, 'use':'om', "prior":UniformPrior(1e-1*std, 1e1*std), 'description':'Error {}'.format(ch), 'units':'-'}
addpar('zp {}'.format(ch), {"sigma":1e-4, 'free':True, 'value':1., 'use':'om', "prior":UniformPrior(0.995, 1.005), 'description':'Zeropoint', 'units':'-'})
addpar('b', {"sigma":1e-2, 'free':True, 'value':0.5, 'use':'om', "prior":UniformPrior(0.0, 1.0), 'description':'Impact parameter', 'units':'-'})
addpar('tc', {"sigma":1e-4, 'free':True, 'value':targetid.tc, 'use':'om', "prior":UniformPrior(targetid.tc-2e-1, targetid.tc+2e-1), 'description':'Transit center', 'units':'d'})
addpar('p', {"sigma":1e-4, 'free':True, 'value':targetid.p, 'use':'om', "prior":UniformPrior(targetid.p-1e-1, targetid.p+1e-1), 'description':'Period', 'units':'d'})
mcmc_pars = {'n_steps':cp.getint('MCMC','nsteps'),
'n_chains':cp.getint('MCMC','nchains'),
'seed':cp.getint('MCMC','seed'),
'thinning':cp.getint('MCMC','thinning'),
'autotune_length':cp.getint('MCMC','autotune_length'),
'autotune_interval':cp.getint('MCMC','autotune_interval'),
'monitor_interval':cp.getint('MCMC','monitor_interval'),
'autosave_interval':cp.getint('MCMC','autosave_interval'),
'autosave_filename':cp.get('MCMC','autosave_filename'),
'use_curses':opt.use_curses}
##########################################################################################
##
## MINIMIZATION
## ============
##
parameterization = MTFitParameterization(parameter_defs, len(data), data[0].n_transits,
mode='o', **fit_pars)
## Initial fit
## ===========
if do_global_fit:
mres = fit_corot(targetid, data, parameterization, de_init_pars)
if is_root: mres.save(fn_initial)
if with_mpi: mres = mpi_comm.bcast(mres)
else:
mres = load_MTFitResult(fn_initial)
## Clean the data using the initial fit
## ====================================
if is_root:
if opt.plot_transits: plot_transits(500, data, targetid, '%s_initial_transits.pdf'%targetid.basename)
#tp = TransitParameterization('physical', mres.ephemeris)
#for i, d in enumerate(data):
# lc = TransitLightcurve(tp, ldpar=mres.ldc[i], method='fortran', mode='time')
# d.clean_with_lc(lc, top=5., bottom=12.)
#if opt.plot_transits: plot_transits(600, data, targetid, '%s_cleaned_transits.pdf'%targetid.basename, lc)
#if with_mpi:
# data = mpi_comm.bcast(data)
## Final fit
## ==========
#if do_final_fit:
# mres = fit_corot(targetid, data, parameterization, de_final_pars)
# if is_root: mres.save(fn_final)
# if with_mpi: mres = mpi_comm.bcast(mres)
#else:
# mres = load_MTFitResult(fn_final)
##########################################################################################
##
## MCMC
## ====
##
if do_mcmc:
parameterization = parameterization.mcmc_from_opt(mres.pv)
mcmc = MultiTransitMCMC(data, parameterization, mcmc_pars, **fit_pars)
mcmcres = mcmc()
mcmcres.save(cp.get('MCMC','file'))
# pl.figure(1)
# for i in range(2):
# pl.subplot(3,1,i+1)
# pl.plot(np.sqrt(mcmcres.steps[0,::3,i]))
# pl.subplot(3,1,3)
# pl.plot(mcmcres.steps[0,::3,2])
# pl.figure(2)
# for i in range(2):
# pl.subplot(2,1,i+1)
# pl.hist(np.sqrt(mcmcres.steps[0,::3,i]))
# pl.figure(3)
# for i in range(2):
# pl.subplot(2,1,i+1)
# pl.plot(np.sqrt(mcmcres.steps[0,::20,i]))
# pl.figure(4)
# for i in range(2):
# pl.subplot(2,1,i+1)
# pl.hist(np.sqrt(mcmcres.steps[0,::20,i]))
# pl.figure(5)
# for i in range(2):
# pl.subplot(2,1,i+1)
# d = np.sqrt(mcmcres.steps[0,:,i])
# pl.acorr(d-d.mean(), maxlags=100)
# print mcmcres.get_acceptance()
# pl.show()
# sys.exit()
##########################################################################################
##
## WRITE REPORT
## ============
##
pp = PdfPages('%s_initial.pdf'%targetid.basename)
figi = 10
slices = [t.get_transit_slices() for t in data]
tnumbs = []
for i, ch in enumerate(data):
tnumbs.append(np.zeros(ch.get_time().size))
for sl, tn in zip(slices[i], [t.number for t in ch.transits]):
tnumbs[i][sl] = tn
ttv_a = mres.parameterization.parameter_view.get('ttv a', None)
ttv_p = mres.parameterization.parameter_view.get('ttv p', None)
tp = TransitParameterization('physical', mres.ephemeris)
if ttv_a is None:
p = [fold(d.get_time(), tp.pv[2], origo=tp.pv[1], shift=0.5)-0.5 for d in data]
else:
p = [fold(d.get_time() + ttv_a*np.sin(TWO_PI*ttv_p * tp.pv[2]*tnumbs[i]), tp.pv[2], origo=tp.pv[1],
shift=0.5)-0.5 for i,d in enumerate(data)]
pm = [np.abs(tmp)<phase_lim for tmp in p]
f = [d.get_flux() for d in data]
p = [tmp[mask] for mask,tmp in zip(pm,p)]
f = [tmp[mask] for mask,tmp in zip(pm,f)]
fmin = min([tmp.min() for tmp in f])
fmax = max([tmp.max() for tmp in f])
pmin = min([tmp.min() for tmp in p])
pmax = max([tmp.max() for tmp in p])
pb = []; fb = []; eb = []
for i in range(len(data)):
pbt, fbt, ebt = bin(p[i],f[i],50)
pb.append(pbt)
fb.append(fbt)
eb.append(ebt)
fbmin = min([tmp.min() for tmp in fb])
fbmax = max([tmp.max() for tmp in fb])
fbmrg = (fbmax - fbmin)*0.05
for i, d in enumerate(data):
pl.figure(figi)
lc = TransitLightcurve(tp, ldpar=mres.ldc[i], method=method, mode='phase')
p2 = np.linspace(p[i].min(),p[i].max(), 2000)
pl.plot(p[i], f[i]/mres.zp[i],',', c='0')
pl.plot(p2, lc(p2*2.*np.pi), lw=3, c='0')
pl.plot(p2, lc(p2*2.*np.pi), lw=1, c='0.9')
pl.ylim(fmin, fmax)
pl.xlim(pmin, pmax)
pp.savefig()
figi+=1
for i, d in enumerate(data):
pl.figure(figi)
lc = TransitLightcurve(tp, ldpar=mres.ldc[i], method=method, mode='phase')
p2 = np.linspace(pb[i].min(),pb[i].max(), 2000)
pl.errorbar(pb[i], fb[i]/mres.zp[i], eb[i], fmt='.', c='0')
pl.plot(p2, lc(p2*2.*np.pi), lw=1.5, c='0')
pl.plot(p2, lc(p2*2.*np.pi), lw=0.5, c='0.9')
#pl.ylim(fbmin-fbmrg, fbmax+fbmrg)
#pl.ylim(0.9992, 1.0004)
pl.xlim(pmin, pmax)
pp.savefig()
figi+=1
pp.close()