def fitspec():
s=read_fits.read_fits_spectrum1d('E5_1_004.fits',dispersion_unit='Angstrom')
wave_range = [21000,24000]
good = np.where((s.wavelength.value > wave_range[0]) & (s.wavelength.value < wave_range[1]))[0]
s = Spectrum1D.from_array(s.wavelength[good],s.flux[good]/np.median(s.flux[good]), dispersion_unit = s.wavelength.unit)
snr = 40
s.uncertainty = (np.zeros(len(s.flux.value))+1.0/snr)*s.flux.unit
#g=load_grid('phoenix_20000_k.h5')
g = load_grid('phoenix_r20000_1.9-2.5_k.h5')
my_model = assemble_model(g, vrad=0, vrot=0,R=20000,spectrum=s,normalize_npol=4)
wave,flux = my_model()
plt.clf()
plt.plot(s.wavelength,s.flux)
plt.plot(wave,flux)
teff_prior = priors.UniformPrior(3000,8000)
logg_prior = priors.UniformPrior(0.0,4.4)
mh_prior = priors.UniformPrior(-1.5,1.0)
alpha_prior = priors.UniformPrior(-0.2,1.2)
vrot_prior = priors.UniformPrior(0,20)
vrad_prior = priors.UniformPrior(-300,300)
R_prior = priors.GaussianPrior(5400,600)
ll = Chi2Likelihood(s)
my_model = my_model | ll
fitobj = MultiNest(my_model, [teff_prior, logg_prior, mh_prior, alpha_prior, vrot_prior, vrad_prior, R_prior])
result = fitobj.run()
return result
def run_multinest_fit_rv_constrained(fit_model, vrad, vrad_err):
teff_prior = priors.UniformPrior(1000, 6000)
logg_prior = priors.UniformPrior(0.1, 4.0)
mh_prior = priors.UniformPrior(-2.0, 1.0)
alpha_prior = priors.UniformPrior(-0.25, 0.5)
vrot_prior = priors.UniformPrior(0, 350.0)
#vrad_prior1 = priors.FixedPrior(vrad)
vrad_prior1 = priors.UniformPrior(vrad - 3. * vrad_err,
vrad + 3. * vrad_err)
#R_prior1 = priors.UniformPrior(1500,5000)
R_prior1 = priors.FixedPrior(24000)
# make a MultiNest fitting object with the model and the prior
gc_fitobj = MultiNest(fit_model, [
teff_prior, logg_prior, mh_prior, alpha_prior, vrot_prior, vrad_prior1,
R_prior1
])
# Run the fit using the MultiNest sampler.
# Will take about 5-10 minutes to run for high resolution Phoenix grid
gc_result = gc_fitobj.run()
# summary statistics like the mean and median can be accessed as dictionaries
print(gc_result.median)
print(gc_result.mean), "end"
# can also compute 1 sigma intervals (or arbitrary)
gc_result.calculate_sigmas(1)
return gc_result
def fit_star_multi_order(starname,
g,
specdir='/group/data/nirspec/spectra/',
savedir='../nirspec_fits/',
snr=30.0,
nnorm=2,
teff_range=[2500, 6000],
vrad_range=[-600, 600],
logg_range=[0., 4.5],
mh_range=[-2., 1.0],
vrot_range=[0, 20],
R=40000,
verbose=True,
alpha_range=[-1., 1.],
r_range=[15000.0, 40000.0],
R_fixed=None,
logg_fixed=None,
l1norm=False):
# fit a spectrum of a star with multiple orders that can have different velocities
file1 = glob.glob(specdir + starname + '_order34*.dat')
file2 = glob.glob(specdir + starname + '_order35*.dat')
file3 = glob.glob(specdir + starname + '_order36*.dat')
starspectrum34 = read_fits_file.read_nirspec_dat(
file1, desired_wavelength_units='Angstrom', wave_range=[2.245, 2.275])
starspectrum34.uncertainty = (
np.zeros(len(starspectrum34.flux.value)) +
1.0 / np.float(snr)) * starspectrum34.flux.unit
starspectrum35 = read_fits_file.read_nirspec_dat(
file2, desired_wavelength_units='Angstrom', wave_range=[2.181, 2.2103])
starspectrum35.uncertainty = (
np.zeros(len(starspectrum35.flux.value)) +
1.0 / np.float(snr)) * starspectrum35.flux.unit
starspectrum36 = read_fits_file.read_nirspec_dat(
file3, desired_wavelength_units='Angstrom', wave_range=[2.1168, 2.145])
starspectrum36.uncertainty = (
np.zeros(len(starspectrum36.flux.value)) +
1.0 / np.float(snr)) * starspectrum36.flux.unit
interp1 = Interpolate(starspectrum34)
convolve1 = InstrumentConvolveGrating.from_grid(g, R=24000)
rot1 = RotationalBroadening.from_grid(g, vrot=np.array([10.0]))
norm1 = Normalize(starspectrum34, nnorm)
interp2 = Interpolate(starspectrum35)
convolve2 = InstrumentConvolveGrating.from_grid(g, R=24000)
#rot2 = RotationalBroadening.from_grid(g,vrot=np.array([10.0]))
norm2 = Normalize(starspectrum35, nnorm)
interp3 = Interpolate(starspectrum36)
convolve3 = InstrumentConvolveGrating.from_grid(g, R=24000)
#rot3 = RotationalBroadening.from_grid(g,vrot=np.array([10.0]))
norm3 = Normalize(starspectrum36, nnorm)
model = g | rot1 | Splitter3() | DopplerShift(vrad=0) & DopplerShift(vrad=0) & DopplerShift(vrad=0) | \
convolve1 & convolve2 & convolve3 | interp1 & interp2 & interp3 | \
norm1 & norm2 & norm3
w1, f1, w2, f2, w3, f3 = model()
plt.clf()
plt.plot(w1, f1)
plt.plot(starspectrum34.wavelength, starspectrum34.flux)
plt.plot(w2, f2)
plt.plot(starspectrum35.wavelength, starspectrum35.flux)
plt.plot(w3, f3)
plt.plot(starspectrum36.wavelength, starspectrum36.flux)
# likelihoods
if l1norm:
like1 = L1Likelihood(starspectrum34)
like2 = L1Likelihood(starspectrum35)
like3 = L1Likelihood(starspectrum36)
else:
like1 = Chi2Likelihood(starspectrum34)
like2 = Chi2Likelihood(starspectrum35)
like3 = Chi2Likelihood(starspectrum36)
fit_model = model | like1 & like2 & like3 | Combiner3()
print fit_model.__class__
print fit_model()
teff_prior = priors.UniformPrior(*teff_range)
if logg_fixed is not None:
logg_prior = priors.FixedPrior(logg_fixed)
else:
logg_prior = priors.UniformPrior(*logg_range)
mh_prior = priors.UniformPrior(*mh_range)
alpha_prior = priors.UniformPrior(*alpha_range)
vrot_prior = priors.UniformPrior(*vrot_range)
vrad_prior1 = priors.UniformPrior(*vrad_range)
vrad_prior2 = priors.UniformPrior(*vrad_range)
vrad_prior3 = priors.UniformPrior(*vrad_range)
# R_prior1 = priors.FixedPrior(R)
# R_prior2 = priors.FixedPrior(R)
# R_prior3 = priors.FixedPrior(R)
# R_prior4 = priors.FixedPrior(R)
if R_fixed is not None:
R_prior1 = priors.FixedPrior(R_fixed)
R_prior2 = priors.FixedPrior(R_fixed)
R_prior3 = priors.FixedPrior(R_fixed)
else:
R_prior1 = priors.UniformPrior(*r_range)
R_prior2 = priors.UniformPrior(*r_range)
R_prior3 = priors.UniformPrior(*r_range)
fitobj = MultiNest(fit_model, [teff_prior, logg_prior, mh_prior, alpha_prior, vrot_prior, \
vrad_prior1,vrad_prior2,vrad_prior3,R_prior1,R_prior2,\
R_prior3])
fitobj.run(verbose=verbose,
importance_nested_sampling=False,
n_live_points=400)
result = fitobj.result
if l1norm:
like_str = '_l1norm'
else:
like_str = ''
result.to_hdf(
os.path.join(savedir, 'unmasked_' + starname + '_order34-36' +
like_str + '.h5'))
print result.calculate_sigmas(1)
print result.median
# save the individual model spectra with the max posterior value
model.teff_0 = result.maximum['teff_0']
model.logg_0 = result.maximum['logg_0']
model.mh_0 = result.maximum['mh_0']
model.alpha_0 = result.maximum['alpha_0']
model.vrot_1 = result.maximum['vrot_1']
model.vrad_3 = result.maximum['vrad_3']
model.vrad_4 = result.maximum['vrad_4']
model.vrad_5 = result.maximum['vrad_5']
model.R_7 = result.maximum['R_6']
model.R_8 = result.maximum['R_7']
model.R_9 = result.maximum['R_8']
w1, f1, w2, f2, w3, f3 = model()
comment1 = 'teff %f,logg %f,mh %f,alpha %f,vrot %f,vrad %f,R %f' % \
(model.teff_0.value,model.logg_0.value,model.mh_0.value,model.alpha_0.value,
model.vrot_1.value,model.vrad_3.value,model.R_7.value)
comment2 = 'teff %f,logg %f,mh %f,alpha %f,vrot %f,vrad %f,R %f' % \
(model.teff_0.value,model.logg_0.value,model.mh_0.value,model.alpha_0.value,
model.vrot_1.value,model.vrad_4.value,model.R_8.value)
comment3 = 'teff %f,logg %f,mh %f,alpha %f,vrot %f,vrad %f,R %f' % \
(model.teff_0.value,model.logg_0.value,model.mh_0.value,model.alpha_0.value,
model.vrot_1.value,model.vrad_5.value,model.R_9.value)
file1 = os.path.join(savedir, starname + '_order34_model.txt')
file2 = os.path.join(savedir, starname + '_order35_model.txt')
file3 = os.path.join(savedir, starname + '_order36_model.txt')
write_spectrum.write_txt(w1, f1, file1, comments=comment1)
write_spectrum.write_txt(w2, f2, file2, comments=comment2)
write_spectrum.write_txt(w3, f3, file3, comments=comment3)
teff_prior = priors.UniformPrior(1000,6000) logg_prior = priors.UniformPrior(0.1,4.0) mh_prior = priors.UniformPrior(-2.0,1.0) alpha_prior = priors.UniformPrior(-0.25,0.5) vrot_prior = priors.UniformPrior(0,350.0) vrad_prior1 = priors.UniformPrior(-1000,1000) #R_prior1 = priors.UniformPrior(1500,5000) R_prior1 = priors.FixedPrior(24000) # make a MultiNest fitting object with the model and the prior gc_fitobj = MultiNest(fit_model, [teff_prior, logg_prior, mh_prior, alpha_prior,vrot_prior, vrad_prior1,R_prior1]) # Run the fit using the MultiNest sampler. # Will take about 5-10 minutes to run for high resolution Phoenix grid gc_result = gc_fitobj.run() # after fitting, save the results to an HDF5 file gc_result.to_hdf(savefile) print "here" # load from the HDF5 file in case the fit was not run gc_result = MultiNestResult.from_hdf5(savefile)
def fit(input_file,
spectrum=None,
teff_prior=[10000.0, 35000.0],
logg_prior=[2.0, 5.0],
mh_prior=[-1.0, 0.8],
alpha_prior=[-0.25, 0.5],
vrot_prior=[0, 350.0],
vrad_prior=[-5000, 5000],
R_prior=4000.0,
wave_range=None,
outdir='./',
snr=30.0,
norm_order=2,
g=None,
molecfit=False,
wavelength_units='micron',
debug=False,
**kwargs):
'''
Given a fits file, read in and fit the spectrum using a grid
Passes keyword arguements into read_fits_file using **kwargs
'''
if g is None:
print('need to input grid in g keyword')
return 0
teff_prior1 = priors.UniformPrior(teff_prior[0], teff_prior[1])
logg_prior1 = priors.UniformPrior(logg_prior[0], logg_prior[1])
mh_prior1 = priors.UniformPrior(-1.0, 0.8)
alpha_prior1 = priors.UniformPrior(-0.25, 0.5)
vrot_prior1 = priors.UniformPrior(0, 350.0)
vrad_prior1 = priors.UniformPrior(-5000, 5000)
#R_prior1 = priors.UniformPrior(1500,10000)
R_prior1 = priors.FixedPrior(R_prior)
# wavelength range for the fit
#wave_range = None
file_part = os.path.splitext(os.path.split(input_file)[-1])[0]
file_part = os.path.join(outdir, file_part)
extension = os.path.splitext(input_file)[-1]
spectrum_file = file_part + extension
fit_file = file_part + '.h5'
plot_file = file_part + '.pdf'
corner_file = file_part + '_corner.pdf'
model_file = file_part + '_model.txt' # best fit model
print('copying file from %s to %s' % (input_file, spectrum_file))
shutil.copyfile(input_file, spectrum_file)
# read in the spectrum and set the uncertainty as 1/SNR
if spectrum is None:
if molecfit:
spectrum = read_fits_file.read_txt_file(
spectrum_file,
desired_wavelength_units=wavelength_units,
wave_range=wave_range,
molecfit=True)
else:
if (extension == '.csv') or (extension == '.txt'):
if extension == '.csv':
delimiter = ','
else:
delimiter = None
spectrum = read_fits_file.read_txt_file(
spectrum_file,
desired_wavelength_units='angstrom',
delimiter=delimiter,
wave_range=wave_range,
wavelength_units=wavelength_units,
**kwargs)
else:
spectrum = read_fits_file.read_fits_file(
spectrum_file,
desired_wavelength_units='angstrom',
wavelength_units=wavelength_units,
wave_range=wave_range)
spectrum.uncertainty = np.zeros(len(spectrum.flux)) + 1.0 / snr
# setup the model
interp1 = Interpolate(spectrum)
convolve1 = InstrumentConvolveGrating.from_grid(g, R=R_prior)
rot1 = RotationalBroadening.from_grid(g, vrot=np.array([10.0]))
norm1 = Normalize(spectrum, norm_order)
model = g | rot1 | DopplerShift(vrad=0) | convolve1 | interp1 | norm1
# add likelihood parts
like1 = Chi2Likelihood(spectrum)
#like1_l1 = SpectralL1Likelihood(spectrum)
fit_model = model | like1
fitobj = MultiNest(fit_model, [
teff_prior1, logg_prior1, mh_prior1, alpha_prior1, vrot_prior1,
vrad_prior1, R_prior1
])
fitobj.run(verbose=debug)
result = fitobj.result
logging.info('saving results to: ' + fit_file)
result.to_hdf(fit_file)
# print some of the results into the log
m = result.maximum
sig = result.calculate_sigmas(1)
for k in sig.keys():
print('%s\t %f\t %f\t %f\t %f' % (k, m[k], sig[k][0], sig[k][1],
(sig[k][1] - sig[k][0]) / 2.0))
# evaluating the model
model.teff_0 = result.maximum.teff_0
model.logg_0 = result.maximum.logg_0
model.mh_0 = result.maximum.mh_0
model.vrot_1 = result.maximum.vrot_1
model.vrad_2 = result.maximum.vrad_2
model.R_3 = result.maximum.R_3
model_wave, model_flux = model()
logging.info('saving model spectrum to: ' + model_file)
save_spectrum(model_wave, model_flux, model_file)
plt.figure(figsize=(12, 6))
plt.plot(model_wave, model_flux, label='Best Fit Model')
plt.plot(spectrum.wavelength, spectrum.flux, label='Data')
plt.ylim(
np.nanmin(spectrum.flux.value) - 0.2,
np.nanmax(spectrum.flux.value) + 0.2)
plt.xlabel('Wavelength (Angstrom)')
plt.ylabel('Flux')
plt.title(spectrum_file)
plt.legend()
plt.savefig(plot_file)
result.plot_triangle(
parameters=['teff_0', 'logg_0', 'mh_0', 'alpha_0', 'vrot_1', 'vrad_2'])
logging.info('saving corner plot to: ' + corner_file)
plt.savefig(corner_file)
# try to free up memory
fitobj = 0
fit_model = 0
return result
def run_fit(self, spectral_grid):
likelihood = spectral_grid | self.model
mn = MultiNest(likelihood, self.priors)
return mn.run(**self.multinest_kwargs)