def makeTelluricModel(lsf, alpha, flux_offset, wave_offset0, data=data): """ Make a telluric model as a function of LSF, alpha, and flux offset. """ data2 = copy.deepcopy(data) data2.wave = data2.wave + wave_offset0 #data2.wave = data2.wave * (1 + wave_offset1) + wave_offset0 telluric_model = nsp.convolveTelluric(lsf, data2, alpha=alpha) if data.order == 35: from scipy.optimize import curve_fit data_flux_avg = np.average(data2.flux) popt, pcov = curve_fit(nsp.voigt_profile,data2.wave[0:-10], data2.flux[0:-10], p0=[21660,data_flux_avg,0.1,0.1,0.01,0.1,10000,1000], maxfev=10000) #model = nsp.continuum(data=data2, mdl=telluric_model, deg=2) model = telluric_model max_model_flux = np.max(nsp.voigt_profile(data2.wave, *popt)) model.flux *= nsp.voigt_profile(data2.wave, *popt)/max_model_flux model = nsp.continuum(data=data2, mdl=model, deg=2) else: model = nsp.continuum(data=data2, mdl=telluric_model, deg=2) model.flux += flux_offset return model
def bestParams2(theta, data): i, alpha, c2, c0, c1 = theta data2 = copy.deepcopy(data) data2.wave = data2.wave*c1 + c0 telluric_model = nsp.convolveTelluric(i, data2, alpha=alpha) model = nsp.continuum(data=data2, mdl=telluric_model) return np.sum(data.flux - (model.flux + c2))**2
def makeTelluricModel(lsf, airmass, pwv, flux_offset, wave_offset, data): """ Make a telluric model as a function of LSF, alpha, and flux offset. """ data2 = copy.deepcopy(data) data2.wave = data2.wave + wave_offset telluric_model = convolveTelluric(lsf, airmass, pwv, data2) model = nsp.continuum(data=data2, mdl=telluric_model, deg=2) model.flux += flux_offset return model
def bestParams(data, i, alpha, c2, c0): data2 = copy.deepcopy(data) data2.wave = data2.wave + c0 telluric_model = nsp.convolveTelluric(i, data2, alpha=alpha) model = nsp.continuum(data=data2, mdl=telluric_model) #plt.figure(2) #plt.plot(model.wave, model.flux+c2, 'r-', alpha=0.5) #plt.plot(data.wave*c1+c0, data.flux, 'b-', alpha=0.5) #plt.close() #plt.show() #sys.exit() return model.flux + c2
def getLSF2(telluric_data, continuum=True, test=False, save_path=None): """ Return a best LSF value from a telluric data. """ data = copy.deepcopy(telluric_data) def bestParams(data, i, alpha, c2, c0): data2 = copy.deepcopy(data) data2.wave = data2.wave + c0 telluric_model = nsp.convolveTelluric(i, data2, alpha=alpha) model = nsp.continuum(data=data2, mdl=telluric_model) #plt.figure(2) #plt.plot(model.wave, model.flux+c2, 'r-', alpha=0.5) #plt.plot(data.wave*c1+c0, data.flux, 'b-', alpha=0.5) #plt.close() #plt.show() #sys.exit() return model.flux + c2 def bestParams2(theta, data): i, alpha, c2, c0, c1 = theta data2 = copy.deepcopy(data) data2.wave = data2.wave*c1 + c0 telluric_model = nsp.convolveTelluric(i, data2, alpha=alpha) model = nsp.continuum(data=data2, mdl=telluric_model) return np.sum(data.flux - (model.flux + c2))**2 from scipy.optimize import curve_fit, minimize popt, pcov = curve_fit(bestParams, data, data.flux, p0=[4.01, 1.01, 0.01, 1.01], maxfev=1000000, epsfcn=0.1) #nll = lambda *args: bestParams2(*args) #results = minimize(nll, [3., 1., 0.1, -10., 1.], args=(data)) #popt = results['x'] data.wave = data.wave+popt[3] telluric_model = nsp.convolveTelluric(popt[0], data, alpha=popt[1]) model = nsp.continuum(data=data, mdl=telluric_model) #model.flux * np.e**(-popt[2]) + popt[3] model.flux + popt[2] return popt[0]
def makeModel(teff, logg, z, vsini, rv, alpha, wave_offset, flux_offset,
**kwargs):
"""
Return a forward model.
Parameters
----------
params : a dictionary that specifies the parameters such as teff, logg, z.
data : an input science data used for continuum correction
Returns
-------
model: a synthesized model
"""
# read in the parameters
order = kwargs.get('order', 33)
modelset = kwargs.get('modelset', 'btsettl08')
lsf = kwargs.get('lsf', 6.0) # instrumental LSF
tell = kwargs.get('tell', True) # apply telluric
data = kwargs.get('data', None) # for continuum correction and resampling
if data is not None:
order = data.order
# read in a model
#model = nsp.Model(teff=teff, logg=logg, feh=z, order=order, modelset=modelset)
model = nsp.Model()
model.wave, model.flux = InterpModel(teff,
logg,
modelset=modelset,
order=order)
model.wave *= 10000
# wavelength offset
#model.wave += wave_offset
# apply vsini
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux,
vbroad=vsini,
rotate=True,
gaussian=False)
# apply rv (including the barycentric correction)
model.wave = nsp.rvShift(model.wave, rv=rv)
# apply telluric
if tell is True:
model = nsp.applyTelluric(model=model, alpha=alpha, airmass='1.5')
# NIRSPEC LSF
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux,
vbroad=lsf,
rotate=False,
gaussian=True)
# add a fringe pattern to the model
#model.flux *= (1+amp*np.sin(freq*(model.wave-phase)))
# wavelength offset
model.wave += wave_offset
# integral resampling
if data is not None:
model.flux = np.array(
nsp.integralResample(xh=model.wave, yh=model.flux, xl=data.wave))
model.wave = data.wave
# contunuum correction
model = nsp.continuum(data=data, mdl=model)
# flux offset
model.flux += flux_offset
#model.flux **= (1 + flux_exponent_offset)
return model
# apply telluric
model = nsp.applyTelluric(model=model, alpha=alpha)
# NIRSPEC LSF
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux,
vbroad=lsf,
rotate=False,
gaussian=True)
# integral resampling
model.flux = np.array(
nsp.integralResample(xh=model.wave, yh=model.flux, xl=data.wave))
model.wave = data.wave
# contunuum correction
model, cont_factor = nsp.continuum(data=data, mdl=model, prop=True)
# NIRSPEC LSF
model_notell.flux = nsp.broaden(wave=model_notell.wave,
flux=model_notell.flux,
vbroad=lsf,
rotate=False,
gaussian=True)
# integral resampling
model_notell.flux = np.array(
nsp.integralResample(xh=model_notell.wave,
yh=model_notell.flux,
xl=data.wave))
model_notell.wave = data.wave
model_notell.flux *= cont_factor
def makeModel(teff, logg, z, vsini, rv, wave_offset, flux_offset, **kwargs):
"""
Return a forward model.
Parameters
----------
teff : effective temperature
data : an input science data used for continuum correction
Optional Parameters
-------------------
Returns
-------
model: a synthesized model
"""
# read in the parameters
order = kwargs.get('order', 33)
modelset = kwargs.get('modelset', 'btsettl08')
instrument = kwargs.get('instrument', 'nirspec')
lsf = kwargs.get('lsf', 6.0) # instrumental LSF
tell = kwargs.get('tell', True) # apply telluric
data = kwargs.get('data', None) # for continuum correction and resampling
if data is not None and instrument == 'nirspec':
order = data.order
# read in a model
#print('teff ',teff,'logg ',logg, 'z', z, 'order', order, 'modelset', modelset)
#print('teff ',type(teff),'logg ',type(logg), 'z', type(z), 'order', type(order), 'modelset', type(modelset))
model = nsp.Model(teff=teff,
logg=logg,
feh=z,
order=order,
modelset=modelset,
instrument=instrument)
elif data is not None and instrument == 'apogee':
model = nsp.Model(teff=teff,
logg=logg,
feh=z,
modelset=modelset,
instrument=instrument)
# wavelength offset
#model.wave += wave_offset
# apply vsini
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux,
vbroad=vsini,
rotate=True,
gaussian=False)
# apply rv (including the barycentric correction)
model.wave = nsp.rvShift(model.wave, rv=rv)
# instrumental LSF
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux,
vbroad=lsf,
rotate=False,
gaussian=True)
# add a fringe pattern to the model
#model.flux *= (1+amp*np.sin(freq*(model.wave-phase)))
# wavelength offset
model.wave += wave_offset
# integral resampling
if data is not None:
model.flux = np.array(
nsp.integralResample(xh=model.wave, yh=model.flux, xl=data.wave))
model.wave = data.wave
# contunuum correction
model = nsp.continuum(data=data, mdl=model)
# flux offset
model.flux += flux_offset
#model.flux **= (1 + flux_exponent_offset)
return model
labels=ylabels,
truths=[lsf_mcmc[0],
alpha_mcmc[0],
A_mcmc[0],
B_mcmc[0]],
quantiles=[0.16, 0.84],
label_kwargs={"fontsize": 20})
plt.minorticks_on()
fig.savefig(save_to_path+'/triangle.png', dpi=300, bbox_inches='tight')
#plt.show()
plt.close()
data2 = copy.deepcopy(data)
data2.wave = data2.wave + B_mcmc[0]
telluric_model = nsp.convolveTelluric(lsf_mcmc[0], data, alpha=alpha_mcmc[0])
model, pcont = nsp.continuum(data=data, mdl=telluric_model, deg=2, tell=True)
model.flux += A_mcmc[0]
plt.tick_params(labelsize=20)
fig = plt.figure(figsize=(20,8))
ax1 = fig.add_subplot(111)
ax1.plot(model.wave, model.flux, c='C3', ls='-', alpha=0.5)
ax1.plot(model.wave, np.polyval(pcont, model.wave) + A_mcmc[0], c='C1', ls='-', alpha=0.5)
ax1.plot(data.wave, data.flux, 'k-', alpha=0.5)
ax1.plot(data.wave, data.flux-(model.flux+A_mcmc[0]),'k-', alpha=0.5)
ax1.minorticks_on()
plt.figtext(0.89,0.86,"{} O{}".format(tell_data_name, order),
color='k',
horizontalalignment='right',
verticalalignment='center',
fontsize=12)
def makeModel(teff,logg,z,vsini,rv,alpha,wave_offset,flux_offset,**kwargs):
"""
Return a forward model.
Parameters
----------
teff : effective temperature
data : an input science data used for continuum correction
Optional Parameters
-------------------
Returns
-------
model: a synthesized model
"""
# read in the parameters
order = kwargs.get('order', 33)
modelset = kwargs.get('modelset', 'btsettl08')
instrument = kwargs.get('instrument', 'nirspec')
lsf = kwargs.get('lsf', 6.0) # instrumental LSF
tell = kwargs.get('tell', True) # apply telluric
data = kwargs.get('data', None) # for continuum correction and resampling
output_stellar_model = kwargs.get('output_stellar_model', False)
if data is not None and instrument == 'nirspec':
order = data.order
# read in a model
#print('teff ',teff,'logg ',logg, 'z', z, 'order', order, 'modelset', modelset)
#print('teff ',type(teff),'logg ',type(logg), 'z', type(z), 'order', type(order), 'modelset', type(modelset))
model = nsp.Model(teff=teff, logg=logg, feh=z, order=order, modelset=modelset, instrument=instrument)
#elif data is not None and instrument == 'apogee':
elif instrument == 'apogee':
model = nsp.Model(teff=teff, logg=logg, feh=z, modelset=modelset, instrument=instrument)
elif data is None and instrument == 'nirspec':
model = nsp.Model(teff=teff, logg=logg, feh=z, order=order, modelset=modelset, instrument=instrument)
# wavelength offset
#model.wave += wave_offset
# apply vsini
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux, vbroad=vsini, rotate=True, gaussian=False)
# apply rv (including the barycentric correction)
model.wave = rvShift(model.wave, rv=rv)
if output_stellar_model:
stellar_model = copy.deepcopy(model)
# apply telluric
if tell is True:
model = nsp.applyTelluric(model=model, alpha=alpha, airmass='1.5')
# instrumental LSF
model.flux = nsp.broaden(wave=model.wave,
flux=model.flux, vbroad=lsf, rotate=False, gaussian=True)
if output_stellar_model:
stellar_model.flux = nsp.broaden(wave=stellar_model.wave,
flux=stellar_model.flux, vbroad=lsf, rotate=False, gaussian=True)
# add a fringe pattern to the model
#model.flux *= (1+amp*np.sin(freq*(model.wave-phase)))
# wavelength offset
model.wave += wave_offset
if output_stellar_model: stellar_model.wave += wave_offset
# integral resampling
if data is not None:
model.flux = np.array(nsp.integralResample(xh=model.wave,
yh=model.flux, xl=data.wave))
model.wave = data.wave
if output_stellar_model:
stellar_model.flux = np.array(nsp.integralResample(xh=stellar_model.wave,
yh=stellar_model.flux, xl=data.wave))
stellar_model.wave = data.wave
# contunuum correction
if data.instrument == 'nirspec':
if output_stellar_model:
model, cont_factor = nsp.continuum(data=data, mdl=model, prop=True)
stellar_model.flux *= cont_factor
else:
model = nsp.continuum(data=data, mdl=model)
elif data.instrument == 'apogee' and data.datatype =='apvisit':
## set the order in the continuum fit
deg = 5
## because of the APOGEE bands, continuum is corrected from three pieces of the spectra
data0 = copy.deepcopy(data)
model0 = copy.deepcopy(model)
range0 = np.where((data0.wave >= data.oriWave0[0][-1]) & (data0.wave <= data.oriWave0[0][0]))
data0.wave = data0.wave[range0]
data0.flux = data0.flux[range0]
data0.noise = data0.noise[range0]
model0.wave = model0.wave[range0]
model0.flux = model0.flux[range0]
model0 = nsp.continuum(data=data0, mdl=model0, deg=deg)
data1 = copy.deepcopy(data)
model1 = copy.deepcopy(model)
range1 = np.where((data1.wave >= data.oriWave0[1][-1]) & (data1.wave <= data.oriWave0[1][0]))
data1.wave = data1.wave[range1]
data1.flux = data1.flux[range1]
data1.noise = data1.noise[range1]
model1.wave = model1.wave[range1]
model1.flux = model1.flux[range1]
model1 = nsp.continuum(data=data1, mdl=model1, deg=deg)
data2 = copy.deepcopy(data)
model2 = copy.deepcopy(model)
range2 = np.where((data2.wave >= data.oriWave0[2][-1]) & (data2.wave <= data.oriWave0[2][0]))
data2.wave = data2.wave[range2]
data2.flux = data2.flux[range2]
data2.noise = data2.noise[range2]
model2.wave = model2.wave[range2]
model2.flux = model2.flux[range2]
model2 = nsp.continuum(data=data2, mdl=model2, deg=deg)
model.flux = np.array( list(model0.flux) + list(model1.flux) + list(model2.flux) )
model.wave = np.array( list(model0.wave) + list(model1.wave) + list(model2.wave) )
elif data.instrument == 'apogee' and data.datatype =='apstar':
model = nsp.continuum(data=data, mdl=model)
# flux offset
model.flux += flux_offset
if output_stellar_model: stellar_model.flux += flux_offset
#model.flux **= (1 + flux_exponent_offset)
if output_stellar_model:
return model, stellar_model
else:
return model