Example #1
0
    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)))
Example #2
0
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()