def lnlike_rv():
if len(all_rv_instruments) == 1:
model = rv_model.pl_rv_array(xrv,parameters['mu']['object'].value,parameters['K']['object'].value,\
parameters['omega']['object'].value*np.pi/180.,parameters['ecc']['object'].value,\
parameters['t0']['object'].value,parameters['P']['object'].value)
residuals = (yrv - model)
taus = 1.0 / ((yerrrv)**2 +
(parameters['sigma_w_rv']['object'].value)**2)
log_like = -0.5 * (
n_data_rvs[0] * log2pi +
np.sum(np.log(1. / taus) + taus * (residuals**2)))
return log_like
else:
log_like = 0.0
for i in range(len(all_rv_instruments)):
model = rv_model.pl_rv_array(xrv[all_rv_instruments_idxs[i]],parameters['mu_'+all_rv_instruments[i]]['object'].value,\
parameters['K']['object'].value, parameters['omega']['object'].value*np.pi/180.,parameters['ecc']['object'].value,\
parameters['t0']['object'].value,parameters['P']['object'].value)
residuals = (yrv[all_rv_instruments_idxs[i]] - model)
taus = 1.0 / (
(yerrrv[all_rv_instruments_idxs[i]])**2 +
(parameters['sigma_w_rv_' +
all_rv_instruments[i]]['object'].value)**2)
log_like = log_like - 0.5 * (n_data_rvs[i] * log2pi + np.sum(
np.log(1. / taus) + taus * (residuals**2)))
return log_like
def lnlike_rv():
if len(all_rv_instruments) == 1:
model = rv_model.pl_rv_array(xrv,parameters['mu']['object'].value,parameters['K']['object'].value,\
parameters['omega']['object'].value*np.pi/180.,parameters['ecc']['object'].value,\
parameters['t0']['object'].value,parameters['P']['object'].value)
residuals = (yrv-model)
taus = 1.0/((yerrrv)**2 + (parameters['sigma_w_rv']['object'].value)**2)
log_like = -0.5*(n_data_rvs[0]*log2pi+np.sum(np.log(1./taus)+taus*(residuals**2)))
return log_like
else:
log_like = 0.0
for i in range(len(all_rv_instruments)):
model = rv_model.pl_rv_array(xrv[all_rv_instruments_idxs[i]],parameters['mu_'+all_rv_instruments[i]]['object'].value,\
parameters['K']['object'].value, parameters['omega']['object'].value*np.pi/180.,parameters['ecc']['object'].value,\
parameters['t0']['object'].value,parameters['P']['object'].value)
residuals = (yrv[all_rv_instruments_idxs[i]]-model)
taus = 1.0/((yerrrv[all_rv_instruments_idxs[i]])**2 + (parameters['sigma_w_rv_'+all_rv_instruments[i]]['object'].value)**2)
log_like = log_like -0.5*(n_data_rvs[i]*log2pi+np.sum(np.log(1./taus)+taus*(residuals**2)))
return log_like
def plot_transit_and_rv(t,f,trv,rv,rv_err,parameters,ld_law,rv_jitter,transit_instruments,rv_instruments,\
resampling = False, phase_max = 0.025, texp = 0.01881944, N_resampling = 5):
# Extract parameters:
P = parameters['P']['object'].value
inc = parameters['inc']['object'].value
a = parameters['a']['object'].value
p = parameters['p']['object'].value
t0 = parameters['t0']['object'].value
q1 = parameters['q1']['object'].value
q2 = parameters['q2']['object'].value
K = parameters['K']['object'].value
ecc = parameters['ecc']['object'].value
omega = parameters['omega']['object'].value
all_rv_instruments,all_rv_instruments_idxs,n_data_rvs = count_instruments(rv_instruments)
if len(all_rv_instruments)>1:
mu = {}
for instrument in all_rv_instruments:
mu[instrument] = parameters['mu_'+instrument]['object'].value
else:
mu = parameters['mu']['object'].value
# Get data phases:
phases = get_phases(t,P,t0)
# Generate model times by super-sampling the times:
model_t = np.linspace(np.min(t),np.max(t),len(t)*2)
model_phase = get_phases(model_t,P,t0)
# Initialize the parameters of the transit model,
# and prepare resampling data if resampling is True:
if resampling:
idx_resampling = np.where((model_phase>-phase_max)&(model_phase<phase_max))[0]
t_resampling = np.array([])
for i in range(len(idx_resampling)):
tij = np.zeros(N_resampling)
for j in range(1,N_resampling+1):
# Eq (35) in Kipping (2010)
tij[j-1] = model_t[idx_resampling[i]] + ((j - ((N_resampling+1)/2.))*(texp/np.double(N_resampling)))
t_resampling = np.append(t_resampling, np.copy(tij))
idx_resampling_pred = np.where((phases>-phase_max)&(phases<phase_max))[0]
t_resampling_pred = np.array([])
for i in range(len(idx_resampling_pred)):
tij = np.zeros(N_resampling)
for j in range(1,N_resampling+1):
tij[j-1] = t[idx_resampling_pred[i]] + ((j - ((N_resampling+1)/2.))*(texp/np.double(N_resampling)))
t_resampling_pred = np.append(t_resampling_pred, np.copy(tij))
params,m = init_batman(t_resampling, law=ld_law)
params2,m2 = init_batman(t_resampling_pred, law=ld_law)
transit_flat = np.ones(len(model_t))
transit_flat[idx_resampling] = np.zeros(len(idx_resampling))
transit_flat_pred = np.ones(len(t))
transit_flat_pred[idx_resampling_pred] = np.zeros(len(idx_resampling_pred))
else:
params,m = init_batman(model_t,law=ld_law)
params2,m2 = init_batman(t,law=ld_law)
coeff1,coeff2 = reverse_ld_coeffs(ld_law, q1, q2)
params.t0 = t0
params.per = P
params.rp = p
params.a = a
params.inc = inc
params.ecc = ecc
params.omega = omega
params.u = [coeff1,coeff2]
# Generate model and predicted lightcurves:
if resampling:
model = m.light_curve(params)
for i in range(len(idx_resampling)):
transit_flat[idx_resampling[i]] = np.mean(model[i*N_resampling:N_resampling*(i+1)])
model_lc = transit_flat
model = m2.light_curve(params)
for i in range(len(idx_resampling_pred)):
transit_flat_pred[idx_resampling_pred[i]] = np.mean(model[i*N_resampling:N_resampling*(i+1)])
model_pred = transit_flat_pred
else:
model_lc = m.light_curve(params)
model_pred = m2.light_curve(params)
# Now plot:
plt.style.use('ggplot')
plt.subplot(211)
#plt.xlabel('Phase')
plt.title('exonailer final fit + data')
plt.ylabel('Relative flux')
idx = np.argsort(model_phase)
plt.plot(phases,f,'.',color='black',alpha=0.4)
plt.plot(model_phase[idx],model_lc[idx])
plt.plot(phases,f-model_pred+(1-1.8*(p**2)),'.',color='black',alpha=0.4)
plt.subplot(212)
plt.ylabel('Radial velocity (m/s)')
plt.xlabel('Phase')
model_rv = rv_model.pl_rv_array(model_t,0.0,K,omega*np.pi/180.,ecc,t0,P)
if len(all_rv_instruments)>1:
for i in range(len(all_rv_instruments)):
rv_phases = get_phases(trv[all_rv_instruments_idxs[i]],P,t0)
plt.errorbar(rv_phases,(rv[all_rv_instruments_idxs[i]]-mu[all_rv_instruments[i]])*1e3,yerr=rv_err[all_rv_instruments_idxs[i]]*1e3,fmt='o',label='RVs from '+all_rv_instruments[i])
plt.legend()
else:
rv_phases = get_phases(trv,P,t0)
plt.errorbar(rv_phases,(rv-mu)*1e3,yerr=rv_err*1e3,fmt='o')
plt.plot(model_phase[idx],(model_rv[idx])*1e3)
plt.show()
opt = raw_input('\t Save lightcurve and RV data and models? (y/n)')
if opt == 'y':
fname = raw_input('\t Output filename (without extension): ')
fout = open('results/'+fname+'_lc_data.dat','w')
fout.write('# Time Phase Normalized flux \n')
for i in range(len(phases)):
fout.write(str(t[i])+' '+str(phases[i])+' '+str(f[i])+'\n')
fout.close()
fout = open('results/'+fname+'_lc_model.dat','w')
fout.write('# Phase Normalized flux \n')
for i in range(len(model_phase[idx])):
fout.write(str(model_phase[idx][i])+' '+str(model_lc[idx][i])+'\n')
fout.close()
fout = open('results/'+fname+'_rvs_data.dat','w')
fout.write('# Phase RV (m/s) Error (m/s) Instrument\n')
for i in range(len(all_rv_instruments)):
rv_phases = get_phases(trv[all_rv_instruments_idxs[i]],P,t0)
for j in range(len(rv_phases)):
fout.write(str(rv_phases[j])+' '+str(((rv[all_rv_instruments_idxs[i]]-mu[all_rv_instruments[i]])*1e3)[j])+\
' '+str(((rv_err[all_rv_instruments_idxs[i]])*1e3)[j])+\
' '+all_rv_instruments[i]+'\n')
fout.close()
fout = open('results/'+fname+'_rvs_model.dat','w')
fout.write('# Phase RV (m/s) \n')
for i in range(len(model_phase[idx])):
fout.write(str(model_phase[idx][i])+' '+str(((model_rv[idx])*1e3)[i])+'\n')
fout.close()
t = np.append(t,np.mean(tsampling))
f = np.append(f,np.mean(fsampling))
if tcurrent >= tend:
break
f = f + np.random.normal(0,sigma_w[i]*1e-6,len(t))
else:
tstart = t0 + (tr_ncycle[i]-tr_phases[i])*P
tend = t0 + (tr_ncycle[i]+tr_ncycles[i]+tr_phases[i])*P
t = np.arange(tstart,tend,texp[i])
fsampling = get_transit_model(t,\
t0,P,p[i],a[i],inc,q1[i],q2[i],ld_law)
f = fsampling + np.random.normal(0,sigma_w[i]*1e-6,len(t))
for ii in range(len(t)):
fout_lc.write('{0:.10f} {1:.10f} {2:.10f} '.format(t[ii],f[ii],sigma_w[i]*1e-6)+tr_instrument_names[i]+'\n')
fout_lc.close()
fout_rv = open(fname_rv,'w')
# Now RV data:
for i in range(len(rv_ncycle)):
tstart = t0 + (rv_ncycle[i])*P
tend = t0 + (rv_ncycle[i]+rv_ncycles[i])*P
t = np.arange(tstart,tend,rv_texp[i])
t = t + np.random.uniform(-0.25,0.25,len(t))
rvs = rv_model.pl_rv_array(t,rv_mu[i],K,\
omega*np.pi/180.,ecc,\
t0,P)
rvs = rvs + np.random.normal(0,sigma_w_rv[i],len(t))
for ii in range(len(t)):
fout_rv.write('{0:.10f} {1:.10f} {2:.10f} '.format(t[ii],rvs[ii],sigma_w_rv[i])+rv_instrument_names[i]+'\n')
fout_rv.close()
import ajplanet
from numpy import pi,arange
t = 2 * 30.433 * arange(10)/999
v0 = 0
K = 968.6
w = 189.1 * pi / 180.
e = 0.5170
t0 = 0.0
P = 5.633
K=1000.0
w=0
e=0
t0=0
P=1
t=arange(11)/10.
print t
for i in range(10):
y = ajplanet.pl_rv(t[i], v0, K, w, e, t0, P)
print y
res = ajplanet.pl_rv_array(t,v0, K, w, e, t0, P)
print res
def main():
"""Main."""
star = "HD30501"
obsnum = "1"
chip = 1
obs_name = select_observation(star, obsnum, chip)
# Load observation
observed_spectra = load_spectrum(obs_name)
if chip == 4:
# Ignore first 40 pixels
observed_spectra.wav_select(observed_spectra.xaxis[40], observed_spectra.xaxis[-1])
# Load models
host_spectrum_model, companion_spectrum_model = load_PHOENIX_hd30501(limits=[2100, 2200], normalize=True)
obs_resolution = crires_resolution(observed_spectra.header)
# Convolve models to resolution of instrument
host_spectrum_model, companion_spectrum_model = convolve_models((host_spectrum_model, companion_spectrum_model),
obs_resolution, chip_limits=None)
plot_obs_with_model(observed_spectra, host_spectrum_model, companion_spectrum_model,
show=False, title="Before BERV Correction")
# Berv Correct
# Calculate the star RV relative to synthetic spectum
# [mean_val, K1, omega, e, Tau, Period, starmass (Msun), msini(Mjup), i]
parameters = {"HD30501": [23.710, 1703.1, 70.4, 0.741, 53851.5, 2073.6, 0.81, 90],
"HD211847": [6.689, 291.4, 159.2, 0.685, 62030.1, 7929.4, 0.94, 19.2, 7]}
try:
host_params = parameters[star]
except ValueError:
print("Parameters for {} are not in parameters list. Improve this.".format(star))
raise
host_params[1] = host_params[1] / 1000 # Convert K! to km/s
host_params[2] = np.deg2rad(host_params[2]) # Omega needs to be in radians for ajplanet
obs_time = observed_spectra.header["DATE-OBS"]
print(obs_time, isinstance(obs_time, str))
print(obs_time.replace("T", " ").split("."))
jd = ephem.julian_date(obs_time.replace("T", " ").split(".")[0])
host_rv = pl_rv_array(jd, *host_params[0:6])[0]
print("host_rv", host_rv, "km/s")
offset = -host_rv
# offset = 0
_berv_corrected_observed_spectra = barycorr_crires_spectrum(observed_spectra, offset) # Issue with air/vacuum
# This introduces nans into the observed spectrum
berv_corrected_observed_spectra.wav_select(*berv_corrected_observed_spectra.xaxis[
np.isfinite(berv_corrected_observed_spectra.flux)][[0, -1]])
# Shift to star RV
plot_obs_with_model(berv_corrected_observed_spectra, host_spectrum_model,
companion_spectrum_model, title="After BERV Correction")
# print("\nWarning!!!\n BERV is not good have added a offset to get rest working\n")
# Chisquared fitting
alphas = 10 ** np.linspace(-4, 0.1, 100)
rvs = np.arange(-50, 50, 0.05)
# chisqr_store = np.empty((len(alphas), len(rvs)))
observed_limits = [np.floor(berv_corrected_observed_spectra.xaxis[0]),
np.ceil(berv_corrected_observed_spectra.xaxis[-1])]
print("Observed_limits ", observed_limits)
n_jobs = 1
if n_jobs is None:
n_jobs = mprocess.cpu_count() - 1
start_time = dt.now()
if np.all(np.isnan(host_spectrum_model.flux)):
print("Host spectrum is all Nans")
if np.all(np.isnan(companion_spectrum_model.flux)):
print("Companion spectrum is all Nans")
print("Now performing the Chisqr grid analaysis")
obs_chisqr_parallel = parallel_chisqr(alphas, rvs, berv_corrected_observed_spectra, alpha_model2,
(host_spectrum_model, companion_spectrum_model,
observed_limits, berv_corrected_observed_spectra), n_jobs=n_jobs)
# chisqr_parallel = parallel_chisqr(alphas, rvs, simlulated_obs, alpha_model, (org_star_spec,
# org_bd_spec, new_limits), n_jobs=4)
end_time = dt.now()
print("Time to run parallel chisquared = {}".format(end_time - start_time))
# Plot memmap
# plt.subplot(2, 1, 1)
x, y = np.meshgrid(rvs, alphas)
fig = plt.figure(figsize=(7, 7))
cf = plt.contourf(x, y, np.log10(obs_chisqr_parallel.reshape(len(alphas), len(rvs))), 100)
fig.colorbar(cf)
plt.title("Sigma chisquared")
plt.ylabel("Flux ratio")
plt.xlabel("RV (km/s)")
plt.show()
# Locate minimum and plot resulting model next to observation
def find_min_chisquared(x, y, z):
"""Find minimum vlaue in chisqr grid."""
min_loc = np.argmin(z)
print("min location", min_loc)
x_sol = x.ravel()[min_loc]
y_sol = y.ravel()[min_loc]
z_sol = z.ravel()[min_loc]
return x_sol, y_sol, z_sol, min_loc
rv_solution, alpha_solution, min_chisqr, min_loc = find_min_chisquared(x, y, obs_chisqr_parallel)
print("Minium Chisqr value {2}\n RV sol = {0}\nAlpha Sol = {1}".format(rv_solution, alpha_solution, min_chisqr))
solution_model = alpha_model2(alpha_solution, rv_solution, host_spectrum_model, companion_spectrum_model,
observed_limits)
# alpha_model2(alpha, rv, host, companion, limits, new_x=None):
plt.plot(solution_model.xaxis, solution_model.flux, label="Min chisqr solution")
plt.plot(berv_corrected_observed_spectra.xaxis, berv_corrected_observed_spectra.flux, label="Observation")
plt.legend(loc=0)
plt.show()
# Dump the results into a pickle file
pickle_path = "/home/jneal/.chisqrpickles/"
pickle_name = "Chisqr_results_{0}_{1}_chip_{2}.pickle".format(star, obsnum, chip)
with open(os.path.join(pickle_path, pickle_name), "wb") as f:
# Pickle all the necessary parameters to store.
pickle.dump((rvs, alphas, berv_corrected_observed_spectra, host_spectrum_model, companion_spectrum_model,
rv_solution, alpha_solution, min_chisqr, min_loc, solution_model), f)
def plot_transit_and_rv(t,f,trv,rv,rv_err,parameters,ld_law,rv_jitter,transit_instruments,rv_instruments,\
resampling = False, phase_max = 0.025, texp = 0.01881944, N_resampling = 5):
# Extract parameters:
P = parameters['P']['object'].value
inc = parameters['inc']['object'].value
a = parameters['a']['object'].value
p = parameters['p']['object'].value
t0 = parameters['t0']['object'].value
q1 = parameters['q1']['object'].value
q2 = parameters['q2']['object'].value
K = parameters['K']['object'].value
ecc = parameters['ecc']['object'].value
omega = parameters['omega']['object'].value
all_rv_instruments, all_rv_instruments_idxs, n_data_rvs = count_instruments(
rv_instruments)
if len(all_rv_instruments) > 1:
mu = {}
for instrument in all_rv_instruments:
mu[instrument] = parameters['mu_' + instrument]['object'].value
else:
mu = parameters['mu']['object'].value
# Get data phases:
phases = get_phases(t, P, t0)
# Generate model times by super-sampling the times:
model_t = np.linspace(np.min(t), np.max(t), len(t) * 2)
model_phase = get_phases(model_t, P, t0)
# Initialize the parameters of the transit model,
# and prepare resampling data if resampling is True:
if resampling:
idx_resampling = np.where((model_phase > -phase_max)
& (model_phase < phase_max))[0]
t_resampling = np.array([])
for i in range(len(idx_resampling)):
tij = np.zeros(N_resampling)
for j in range(1, N_resampling + 1):
# Eq (35) in Kipping (2010)
tij[j - 1] = model_t[idx_resampling[i]] + (
(j - ((N_resampling + 1) / 2.)) *
(texp / np.double(N_resampling)))
t_resampling = np.append(t_resampling, np.copy(tij))
idx_resampling_pred = np.where((phases > -phase_max)
& (phases < phase_max))[0]
t_resampling_pred = np.array([])
for i in range(len(idx_resampling_pred)):
tij = np.zeros(N_resampling)
for j in range(1, N_resampling + 1):
tij[j - 1] = t[idx_resampling_pred[i]] + (
(j - ((N_resampling + 1) / 2.)) *
(texp / np.double(N_resampling)))
t_resampling_pred = np.append(t_resampling_pred, np.copy(tij))
params, m = init_batman(t_resampling, law=ld_law)
params2, m2 = init_batman(t_resampling_pred, law=ld_law)
transit_flat = np.ones(len(model_t))
transit_flat[idx_resampling] = np.zeros(len(idx_resampling))
transit_flat_pred = np.ones(len(t))
transit_flat_pred[idx_resampling_pred] = np.zeros(
len(idx_resampling_pred))
else:
params, m = init_batman(model_t, law=ld_law)
params2, m2 = init_batman(t, law=ld_law)
coeff1, coeff2 = reverse_ld_coeffs(ld_law, q1, q2)
params.t0 = t0
params.per = P
params.rp = p
params.a = a
params.inc = inc
params.ecc = ecc
params.omega = omega
params.u = [coeff1, coeff2]
# Generate model and predicted lightcurves:
if resampling:
model = m.light_curve(params)
for i in range(len(idx_resampling)):
transit_flat[idx_resampling[i]] = np.mean(
model[i * N_resampling:N_resampling * (i + 1)])
model_lc = transit_flat
model = m2.light_curve(params)
for i in range(len(idx_resampling_pred)):
transit_flat_pred[idx_resampling_pred[i]] = np.mean(
model[i * N_resampling:N_resampling * (i + 1)])
model_pred = transit_flat_pred
else:
model_lc = m.light_curve(params)
model_pred = m2.light_curve(params)
# Now plot:
plt.style.use('ggplot')
plt.subplot(211)
#plt.xlabel('Phase')
plt.title('exonailer final fit + data')
plt.ylabel('Relative flux')
idx = np.argsort(model_phase)
plt.plot(phases, f, '.', color='black', alpha=0.4)
plt.plot(model_phase[idx], model_lc[idx])
plt.plot(phases,
f - model_pred + (1 - 1.8 * (p**2)),
'.',
color='black',
alpha=0.4)
plt.subplot(212)
plt.ylabel('Radial velocity (m/s)')
plt.xlabel('Phase')
model_rv = rv_model.pl_rv_array(model_t, 0.0, K, omega * np.pi / 180., ecc,
t0, P)
if len(all_rv_instruments) > 1:
for i in range(len(all_rv_instruments)):
rv_phases = get_phases(trv[all_rv_instruments_idxs[i]], P, t0)
plt.errorbar(
rv_phases,
(rv[all_rv_instruments_idxs[i]] - mu[all_rv_instruments[i]]) *
1e3,
yerr=rv_err[all_rv_instruments_idxs[i]] * 1e3,
fmt='o',
label='RVs from ' + all_rv_instruments[i])
plt.legend()
else:
rv_phases = get_phases(trv, P, t0)
plt.errorbar(rv_phases, (rv - mu) * 1e3, yerr=rv_err * 1e3, fmt='o')
plt.plot(model_phase[idx], (model_rv[idx]) * 1e3)
plt.show()
opt = raw_input('\t Save lightcurve and RV data and models? (y/n)')
if opt == 'y':
fname = raw_input('\t Output filename (without extension): ')
fout = open('results/' + fname + '_lc_data.dat', 'w')
fout.write('# Time Phase Normalized flux \n')
for i in range(len(phases)):
fout.write(
str(t[i]) + ' ' + str(phases[i]) + ' ' + str(f[i]) + '\n')
fout.close()
fout = open('results/' + fname + '_lc_model.dat', 'w')
fout.write('# Phase Normalized flux \n')
for i in range(len(model_phase[idx])):
fout.write(
str(model_phase[idx][i]) + ' ' + str(model_lc[idx][i]) + '\n')
fout.close()
fout = open('results/' + fname + '_rvs_data.dat', 'w')
fout.write('# Phase RV (m/s) Error (m/s) Instrument\n')
for i in range(len(all_rv_instruments)):
rv_phases = get_phases(trv[all_rv_instruments_idxs[i]], P, t0)
for j in range(len(rv_phases)):
fout.write(str(rv_phases[j])+' '+str(((rv[all_rv_instruments_idxs[i]]-mu[all_rv_instruments[i]])*1e3)[j])+\
' '+str(((rv_err[all_rv_instruments_idxs[i]])*1e3)[j])+\
' '+all_rv_instruments[i]+'\n')
fout.close()
fout = open('results/' + fname + '_rvs_model.dat', 'w')
fout.write('# Phase RV (m/s) \n')
for i in range(len(model_phase[idx])):
fout.write(
str(model_phase[idx][i]) + ' ' +
str(((model_rv[idx]) * 1e3)[i]) + '\n')
fout.close()
