def align_with_O2(spectra, O2_spectra, R=5000):
# Convert to ispec structures
spectra = ispec.create_spectrum_structure(spectra.T[0], spectra.T[1],
spectra.T[2])
O2_spectra = ispec.create_spectrum_structure(O2_spectra.T[0],
O2_spectra.T[1],
O2_spectra.T[2])
# Now normalise
normed_spectra, spectra_continuum_model = normalize_whole_spectrum(spectra)
#wfilter = ispec.create_wavelength_filter(normed_spectra, wave_base=np.min(O2_spectra['waveobs']) - 3, wave_top=np.max(O2_spectra['waveobs']) + 3)
wfilter = ispec.create_wavelength_filter(normed_spectra,
wave_base=684,
wave_top=690)
normed_spectra = normed_spectra[wfilter]
params = Parameters()
params.add('rv', value=0, min=-100, max=100)
params.add('strength', value=1, min=0.7, max=1.3)
params.add('zp', value=1., min=0.9, max=1.1, vary=False)
mini = Minimizer(lmfit_func,
params,
fcn_args=(np.copy(normed_spectra), np.copy(O2_spectra),
False))
lmfit_minimize_result = mini.minimize()
printfuncs.report_fit(lmfit_minimize_result, min_correl=0.5)
corrected_spectra, o2_model = lmfit_func(lmfit_minimize_result.params,
normed_spectra,
O2_spectra,
return_model=True)
f = plt.figure()
plt.plot(normed_spectra['waveobs'], normed_spectra['flux'], 'k', alpha=0.3)
plt.plot(corrected_spectra['waveobs'],
corrected_spectra['flux'],
'k',
label='Corrected solution')
plt.plot(O2_spectra['waveobs'], O2_spectra['flux'], 'r', alpha=0.3)
plt.plot(O2_spectra['waveobs'], o2_model, 'r', label='O2 model')
plt.gca().set(title='RV = {:.3f} +- {:.3f}'.format(
lmfit_minimize_result.params['rv'].value,
lmfit_minimize_result.params['rv'].stderr),
xlabel='Wavelength [nm]',
ylabel='Normalized flux')
plt.legend()
plt.xlim(685, 690)
corrected = ispec.correct_velocity(
np.copy(spectra), lmfit_minimize_result.params['rv'].value)
return f, np.array(
[corrected['waveobs'], corrected['flux'],
corrected['err']]).T, lmfit_minimize_result.params[
'rv'].value, lmfit_minimize_result.params['rv'].stderr
def loadtemplatespectrum(filename, resolution, telluric_linelist, ccf_mask, velocity_step, wavemask):
spc = Spectrum(filename)
if wavemask :
spc.applyMask(wavemask)
barycentricTime = spc.barycentricTime()
barycentric_vel = barycentric_velocity(spc)
spc.continuumOrderByOrder(binsize = 30, overlap = 10)
spc.normalizeByContinuum(constant=10.0)
spc.binningOrderByOrder(rvsampling_kps=2.4, median=False)
spc.sortByWavelength()
ispectrum = ispec.create_spectrum_structure(spc.wl,spc.flux)
smoothed_spectrum = ispec.convolve_spectrum(ispectrum, resolution)
tel_models, tel_ccf = ispec.cross_correlate_with_mask(smoothed_spectrum, telluric_linelist, \
lower_velocity_limit=-10, upper_velocity_limit=10, \
velocity_step=0.1, mask_depth=0.01, \
fourier = False, only_one_peak = True)
tel_rv = tel_models[0].mu()
min_vel = -30.0
max_vel = +30.0
# Only the 25% of the deepest ones:
dfilter = telluric_linelist['depth'] > np.percentile(telluric_linelist['depth'], 75)
tfilter = ispec.create_filter_for_regions_affected_by_tellurics(smoothed_spectrum['waveobs'], \
telluric_linelist[dfilter], min_velocity=-tel_rv+min_vel, \
max_velocity=-tel_rv+max_vel)
clean_spectrum = smoothed_spectrum[~tfilter]
corrected_spectrum = ispec.correct_velocity(clean_spectrum, tel_rv - barycentric_vel)
models, ccf = ispec.cross_correlate_with_mask(clean_spectrum, ccf_mask, \
lower_velocity_limit=-100, upper_velocity_limit=100, \
velocity_step=velocity_step, mask_depth=0.01, \
fourier=False)
rv = models[0].mu()
clean_corrected_spectrum = ispec.correct_velocity(corrected_spectrum, rv)
return clean_corrected_spectrum
def synthesize_spectrum(theta):
teff, logg, MH = theta
# alpha = ispec.determine_abundance_enchancements(MH)
# microturbulence_vel = ispec.estimate_vmic(teff, logg, MH)
# macroturbulence = ispec.estimate_vmac(teff, logg, MH)
microturbulence_vel = 1.23
macroturbulence = 3.70
alpha = 0
limb_darkening_coeff = 0.6
resolution = 47000
vsini = 2.4
code = "grid"
precomputed_grid_dir = ispec_dir + "/input/grid/SPECTRUM_MARCS.GES_GESv6_atom_hfs_iso.480_680nm/"
grid = ispec.load_spectral_grid(precomputed_grid_dir)
atomic_linelist = None
isotopes = None
modeled_layers_pack = None
solar_abundances = None
fixed_abundances = None
abundances = None
atmosphere_layers = None
if not ispec.valid_interpolated_spectrum_target(
grid, {
'teff': teff,
'logg': logg,
'MH': MH,
'alpha': alpha,
'vmic': microturbulence_vel
}):
msg = "The specified effective temperature, gravity (log g) and metallicity [M/H] \
fall out of the spectral grid limits."
print(msg)
regions = None
# Interpolation
synth_spectrum = ispec.create_spectrum_structure(x)
# interpolated_spectrum = ispec.create_spectrum_structure(np.arange(wave_base, wave_top, wave_step))
synth_spectrum['flux'] = ispec.generate_spectrum(synth_spectrum['waveobs'], \
atmosphere_layers, teff, logg, MH, alpha, atomic_linelist, isotopes, abundances, \
fixed_abundances, microturbulence_vel = microturbulence_vel, \
macroturbulence=macroturbulence, vsini=vsini, limb_darkening_coeff=limb_darkening_coeff, \
R=resolution, regions=regions, verbose=1,
code=code, grid=grid)
return synth_spectrum
print "Error: check usage with App_iSpecTest.py -h "; sys.exit(1);
if options.verbose:
print 'Input spectrum: ', options.input
print 'Output wavelength range: ', options.wlrange
print 'Spectrum type: ', options.spectype
print 'Polar option: ', options.polar
print 'Telluric correction: ', options.telluric
print 'Heliocentric correction: ', options.helio
spc = Spectrum(options.input, options.spectype, options.polar, options.telluric, options.helio)
spc.continuumOrderByOrder(binsize = 30, overlap = 10)
spc.normalizeByContinuum(constant=10.0)
spc.binningOrderByOrder(rvsampling_kps=2.5, median=False)
spc.sortByWavelength()
ispectrum = ispec.create_spectrum_structure(spc.wl,spc.flux)
resolution = 80000
smoothed_star_spectrum = ispec.convolve_spectrum(ispectrum, resolution)
mask_file = ispec_dir + "input/linelists/CCF/Narval.Sun.370_1048nm/mask.lst"
ccf_mask = ispec.read_cross_correlation_mask(mask_file)
models, ccf = ispec.cross_correlate_with_mask(smoothed_star_spectrum, ccf_mask, \
lower_velocity_limit=-50, upper_velocity_limit=50, \
velocity_step=0.05, mask_depth=0.01, \
fourier=False)
components = len(models)
rv = np.round(models[0].mu(), 3) # km/s
def _synthesize_spectrum(self, code):
#--- Synthesizing spectrum -----------------------------------------------------
# Parameters
teff = 5771.0
logg = 4.44
MH = 0.00
alpha = ispec.determine_abundance_enchancements(MH)
microturbulence_vel = ispec.estimate_vmic(teff, logg, MH) # 1.07
macroturbulence = ispec.estimate_vmac(teff, logg, MH) # 4.21
vsini = 1.60 # Sun
limb_darkening_coeff = 0.6
resolution = 300000
wave_step = 0.001
# Wavelengths to synthesis
#regions = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
regions = None
wave_base = 515.0 # Magnesium triplet region
wave_top = 525.0
# Selected model amtosphere, linelist and solar abundances
#model = ispec_dir + "/input/atmospheres/MARCS/"
model = ispec_dir + "/input/atmospheres/MARCS.GES/"
#model = ispec_dir + "/input/atmospheres/MARCS.APOGEE/"
#model = ispec_dir + "/input/atmospheres/ATLAS9.APOGEE/"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Castelli/"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Kurucz/"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Kirby/"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/VALD.300_1100nm/atomic_lines.tsv"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/VALD.1100_2400nm/atomic_lines.tsv"
atomic_linelist_file = ispec_dir + "/input/linelists/transitions/GESv6_atom_hfs_iso.420_920nm/atomic_lines.tsv"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/GESv6_atom_nohfs_noiso.420_920nm/atomic_lines.tsv"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(atomic_linelist_file,
wave_base=wave_base,
wave_top=wave_top)
atomic_linelist = atomic_linelist[
atomic_linelist['theoretical_depth'] >=
0.01] # Select lines that have some minimal contribution in the sun
isotopes = ispec.read_isotope_data(isotope_file)
if "ATLAS" in model:
solar_abundances_file = ispec_dir + "/input/abundances/Grevesse.1998/stdatom.dat"
else:
# MARCS
solar_abundances_file = ispec_dir + "/input/abundances/Grevesse.2007/stdatom.dat"
#solar_abundances_file = ispec_dir + "/input/abundances/Asplund.2005/stdatom.dat"
#solar_abundances_file = ispec_dir + "/input/abundances/Asplund.2009/stdatom.dat"
#solar_abundances_file = ispec_dir + "/input/abundances/Anders.1989/stdatom.dat"
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
## Custom fixed abundances
#fixed_abundances = ispec.create_free_abundances_structure(["C", "N", "O"], chemical_elements, solar_abundances)
#fixed_abundances['Abund'] = [-3.49, -3.71, -3.54] # Abundances in SPECTRUM scale (i.e., x - 12.0 - 0.036) and in the same order ["C", "N", "O"]
## No fixed abundances
fixed_abundances = None
# Validate parameters
if not ispec.valid_atmosphere_target(modeled_layers_pack, {
'teff': teff,
'logg': logg,
'MH': MH,
'alpha': alpha
}):
msg = "The specified effective temperature, gravity (log g) and metallicity [M/H] \
fall out of theatmospheric models."
print(msg)
# Prepare atmosphere model
atmosphere_layers = ispec.interpolate_atmosphere_layers(
modeled_layers_pack, {
'teff': teff,
'logg': logg,
'MH': MH,
'alpha': alpha
},
code=code)
# Synthesis
synth_spectrum = ispec.create_spectrum_structure(
np.arange(wave_base, wave_top, wave_step))
synth_spectrum['flux'] = ispec.generate_spectrum(synth_spectrum['waveobs'], \
atmosphere_layers, teff, logg, MH, alpha, atomic_linelist, isotopes, solar_abundances, \
fixed_abundances, microturbulence_vel = microturbulence_vel, \
macroturbulence=macroturbulence, vsini=vsini, limb_darkening_coeff=limb_darkening_coeff, \
R=resolution, regions=regions, verbose=1,
code=code)
return synth_spectrum
def test_interpolate_spectrum(self):
#--- Synthesizing spectrum -----------------------------------------------------
# Parameters
#teff = 5771.0
teff = 4025.0
logg = 4.44
MH = 0.00
alpha = ispec.determine_abundance_enchancements(MH)
microturbulence_vel = ispec.estimate_vmic(teff, logg, MH) # 1.07
macroturbulence = ispec.estimate_vmac(teff, logg, MH) # 4.21
vsini = 1.60 # Sun
limb_darkening_coeff = 0.6
resolution = 300000
wave_step = 0.001
# Wavelengths to synthesis
wave_base = 515.0 # Magnesium triplet region
wave_top = 525.0
code = "grid"
precomputed_grid_dir = ispec_dir + "/input/grid/SPECTRUM_MARCS.GES_GESv6_atom_hfs_iso.480_680nm_light/"
grid = ispec.load_spectral_grid(precomputed_grid_dir)
atomic_linelist = None
isotopes = None
modeled_layers_pack = None
solar_abundances = None
fixed_abundances = None
abundances = None
atmosphere_layers = None
regions = None
# Validate parameters
if not ispec.valid_interpolated_spectrum_target(
grid, {
'teff': teff,
'logg': logg,
'MH': MH,
'alpha': alpha,
'vmic': microturbulence_vel
}):
msg = "The specified effective temperature, gravity (log g) and metallicity [M/H] \
fall out of the spectral grid limits."
print(msg)
# Interpolation
interpolated_spectrum = ispec.create_spectrum_structure(
np.arange(wave_base, wave_top, wave_step))
interpolated_spectrum['flux'] = ispec.generate_spectrum(interpolated_spectrum['waveobs'], \
atmosphere_layers, teff, logg, MH, alpha, atomic_linelist, isotopes, abundances, \
fixed_abundances, microturbulence_vel = microturbulence_vel, \
macroturbulence=macroturbulence, vsini=vsini, limb_darkening_coeff=limb_darkening_coeff, \
R=resolution, regions=regions, verbose=1,
code=code, grid=grid)
np.testing.assert_almost_equal(
interpolated_spectrum['flux'][:10],
np.array([
1.0000000e-10, 9.3509103e-01, 9.2898036e-01, 9.2100053e-01,
9.1271230e-01, 9.0331793e-01, 8.9166097e-01, 8.7667336e-01,
8.5752275e-01, 8.3368807e-01
]))
np.testing.assert_almost_equal(
interpolated_spectrum['waveobs'][:10],
np.array([
515., 515.001, 515.002, 515.003, 515.004, 515.005, 515.006,
515.007, 515.008, 515.009
]))
def run_synspec(starname, teff, logg, feh, alpha, outdir, mode = "MR", \
arms = ['blue','red','nir']):
## Custom abundance e.g., to change C, N, O abundances to the desired values
solar_abundances_file = ispec_dir + "/input/abundances/Asplund.2009/stdatom.dat"
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
chemical_elements_file = ispec_dir + "/input/abundances/chemical_elements_symbols.dat"
chemical_elements = ispec.read_chemical_elements(chemical_elements_file)
#fixed_abundances = ispec.create_free_abundances_structure(["C", "N", "O"], chemical_elements, solar_abundances)
#fixed_abundances['Abund'] = [-3.49, -3.71, -3.54] # Abundances in SPECTRUM scale (i.e., x - 12.0 - 0.036) and in the same order ["C", "N", "O"]
fixed_abundances = None
## Synthesize a spectrum with the code "turbospectrum"
spectrum_wave = []
spectrum_flux = []
## - Wavelength coverage defined at
## https://pfs.ipmu.jp/research/parameters.html
## - Mergins of 10nm are applied if possible.
## - Overlaps in wavelength between neighboring arms are removed.
for arm in arms:
if arm != 'nir':
if arm == 'blue':
wmin = 370.
wmax = 650.
R = 2300
elif arm == 'red':
if mode == 'MR':
wmin = 700.
wmax = 895.
R = 5000.
else:
wmin = 650.
wmax = 970.
R = 3000.
synthesize_spectrum(code = "turbospectrum", teff = teff, logg = logg, MH = feh, \
vsini = 0.0, wave_base = wmin, wave_top = wmax, R=R, fixed_abundances = fixed_abundances)
spectrum_tmp = ispec.read_spectrum('outflux.txt')
spectrum_wave = np.hstack((spectrum_wave, spectrum_tmp['waveobs']))
spectrum_flux = np.hstack((spectrum_flux, spectrum_tmp['flux']))
elif arm == 'nir':
for i in range(0, 2):
if i==0:
if mode == "MR":
wmin_tmp = 930.
else:
wmin_tmp = 970.
wmax_tmp = 1100.
else:
wmin_tmp = 1100.
wmax_tmp = 1270.
R = 4300.
synthesize_spectrum(code = "turbospectrum", teff = teff, logg = logg, MH = feh, \
vsini = 0.0, wave_base = wmin_tmp, wave_top = wmax_tmp, R=R, fixed_abundances = fixed_abundances)
spectrum_tmp = ispec.read_spectrum('outflux.txt')
spectrum_wave = np.hstack((spectrum_wave, spectrum_tmp['waveobs']))
spectrum_flux = np.hstack((spectrum_flux, spectrum_tmp['flux']))
synth_spectrum = ispec.create_spectrum_structure(spectrum_wave)
synth_spectrum['flux'] = spectrum_flux
ispec.write_spectrum(synth_spectrum, outdir + '/' + starname + '.txt')
return()
def synthesize_spectrum(theta, code="moog"):
teff, logg, MH, vsini = theta
resolution = 48000
microturbulence_vel = ispec.estimate_vmic(teff, logg, MH)
macroturbulence = ispec.estimate_vmac(teff, logg, MH)
limb_darkening_coeff = 0.6
regions = None
wave_base = 609.0
wave_top = 620.0
model = ispec_dir + "/input/atmospheres/ATLAS9.Castelli/"
atomic_linelist_file = ispec_dir + "/input/linelists/transitions/VALD.300_1100nm/atomic_lines.tsv"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/GESv5_atom_hfs_iso.420_920nm/atomic_lines.tsv"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
alpha = ispec.determine_abundance_enchancements(MH)
atomic_linelist = ispec.read_atomic_linelist(atomic_linelist_file,
wave_base=wave_base,
wave_top=wave_top)
atomic_linelist = atomic_linelist[
atomic_linelist['theoretical_depth'] >= 0.01]
isotopes = ispec.read_isotope_data(isotope_file)
solar_abundances_file = ispec_dir + "/input/abundances/Asplund.2009/stdatom.dat"
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
fixed_abundances = None
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
atmosphere_layers = ispec.interpolate_atmosphere_layers(
modeled_layers_pack, {
'teff': teff,
'logg': logg,
'MH': MH,
'alpha': alpha
},
code=code)
synth_spectrum = ispec.create_spectrum_structure(x)
synth_spectrum['flux'] = ispec.generate_spectrum(
synth_spectrum['waveobs'],
atmosphere_layers,
teff,
logg,
MH,
alpha,
atomic_linelist,
isotopes,
solar_abundances,
fixed_abundances,
microturbulence_vel=microturbulence_vel,
macroturbulence=macroturbulence,
vsini=vsini,
limb_darkening_coeff=limb_darkening_coeff,
R=resolution,
regions=regions,
verbose=0,
code=code)
return synth_spectrum
