def test_create_segments_around_linemasks(self):
#---Create segments around linemasks -------------------------------------------
line_regions = ispec.read_line_regions(ispec_dir +
"/input/regions/fe_lines.txt")
segments = ispec.create_segments_around_lines(line_regions,
margin=0.25)
self.assertEqual(len(segments), 132)
self.assertAlmostEqual(segments['wave_base'][0], 480.01937)
self.assertAlmostEqual(segments['wave_top'][0], 481.08295)
def test_determine_loggf_line_by_line_using_synth_spectra(self):
code = "spectrum"
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
#--- Radial Velocity determination with template -------------------------------
# - Read synthetic template
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Arcturus.372_926nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Sun.372_926nm/template.txt.gz")
template = ispec.read_spectrum(
ispec_dir +
"/input/spectra/templates/NARVAL.Sun.370_1048nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Synth.Sun.300_1100nm/template.txt.gz")
models, ccf = ispec.cross_correlate_with_template(star_spectrum, template, \
lower_velocity_limit=-200, upper_velocity_limit=200, \
velocity_step=1.0, fourier=False)
# Number of models represent the number of components
components = len(models)
# First component:
rv = np.round(models[0].mu(), 2) # km/s
rv_err = np.round(models[0].emu(), 2) # km/s
#--- Radial Velocity correction ------------------------------------------------
star_spectrum = ispec.correct_velocity(star_spectrum, rv)
#--- Resolution degradation ----------------------------------------------------
# NOTE: The line selection was built based on a solar spectrum with R ~ 47,000 and GES/VALD atomic linelist.
from_resolution = 80000
to_resolution = 47000
star_spectrum = ispec.convolve_spectrum(star_spectrum, to_resolution,
from_resolution)
#--- Continuum fit -------------------------------------------------------------
model = "Splines" # "Polynomy"
degree = 2
nknots = None # Automatic: 1 spline every 5 nm
from_resolution = to_resolution
# Strategy: Filter first median values and secondly MAXIMUMs in order to find the continuum
order = 'median+max'
median_wave_range = 0.05
max_wave_range = 1.0
star_continuum_model = ispec.fit_continuum(star_spectrum, from_resolution=from_resolution, \
nknots=nknots, degree=degree, \
median_wave_range=median_wave_range, \
max_wave_range=max_wave_range, \
model=model, order=order, \
automatic_strong_line_detection=True, \
strong_line_probability=0.5, \
use_errors_for_fitting=True)
#--- Normalize -------------------------------------------------------------
normalized_star_spectrum = ispec.normalize_spectrum(
star_spectrum,
star_continuum_model,
consider_continuum_errors=False)
# Use a fixed value because the spectrum is already normalized
star_continuum_model = ispec.fit_continuum(star_spectrum,
fixed_value=1.0,
model="Fixed value")
#--- Model spectra ----------------------------------------------------------
# Parameters
initial_teff = 5771.0
initial_logg = 4.44
initial_MH = 0.00
initial_alpha = 0.00
initial_vmic = ispec.estimate_vmic(initial_teff, initial_logg,
initial_MH)
initial_vmac = ispec.estimate_vmac(initial_teff, initial_logg,
initial_MH)
initial_vsini = 1.60 # Sun
initial_limb_darkening_coeff = 0.6
initial_R = to_resolution
initial_vrad = 0
max_iterations = 6
# 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"
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"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(
atomic_linelist_file,
wave_base=np.min(star_spectrum['waveobs']),
wave_top=np.max(star_spectrum['waveobs']))
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)
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Free parameters
#free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
#free_params = ["vrad"]
free_params = []
# Free individual element abundance (WARNING: it should be coherent with the selected line regions!)
chemical_elements_file = ispec_dir + "/input/abundances/chemical_elements_symbols.dat"
chemical_elements = ispec.read_chemical_elements(
chemical_elements_file)
# Line regions
line_regions_with_atomic_data = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_synth_good_for_params_all_extended.txt"
.format(code))
#line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all_extended.txt".format(code))
# Select only the lines to get abundances from
line_regions_with_atomic_data = line_regions_with_atomic_data[:5]
line_regions_with_atomic_data = ispec.adjust_linemasks(
normalized_star_spectrum,
line_regions_with_atomic_data,
max_margin=0.5)
output_dirname = "example_loggf_line_by_line_%s" % (code, )
#ispec.mkdir_p(output_dirname)
for i, line in enumerate(line_regions_with_atomic_data):
# Directory and file names
#element_name = "_".join(line['element'].split())
element_name = "_".join(line['note'].split())
common_filename = "example_" + code + "_individual_" + element_name + "_%.4f" % line[
'wave_peak']
# Free individual element abundance (WARNING: it should be coherent with the selected line regions!)
free_abundances = None
# Line by line
individual_line_regions = line_regions_with_atomic_data[
i:i + 1] # Keep recarray structure
linelist_free_loggf = line_regions_with_atomic_data[
i:i + 1] # Keep recarray structure
# Filter the line that we want to determine the loggf from the global atomic linelist
lfilter = atomic_linelist['element'] == linelist_free_loggf[
'element'][0]
for key in [
'wave_nm', 'lower_state_eV', 'loggf', 'stark', 'rad',
'waals'
]:
lfilter = np.logical_and(
lfilter,
np.abs(atomic_linelist[key] - linelist_free_loggf[key][0])
< 1e-9)
# Segment
segments = ispec.create_segments_around_lines(
individual_line_regions, margin=0.25)
wfilter = ispec.create_wavelength_filter(
normalized_star_spectrum,
regions=segments) # Only use the segment
obs_spec, modeled_synth_spectrum, params, errors, abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum[wfilter], star_continuum_model, \
modeled_layers_pack, atomic_linelist[~lfilter], isotopes, solar_abundances, free_abundances, linelist_free_loggf, initial_teff, \
initial_logg, initial_MH, initial_alpha, initial_vmic, initial_vmac, initial_vsini, \
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params, segments=segments, \
linemasks=individual_line_regions, \
enhance_abundances=True, \
use_errors = True, \
vmic_from_empirical_relation = False, \
vmac_from_empirical_relation = False, \
max_iterations=max_iterations, \
tmp_dir = None, \
code=code)
self.assertAlmostEqual(loggf_found['loggf'][0],
-1.0743873027191777)
self.assertAlmostEqual(loggf_found['eloggf'][0],
0.11414696354921147)
self.assertEqual(len(loggf_found['loggf']), 1)
self.assertEqual(individual_line_regions['lower_state_eV'][0],
loggf_found['linelist']['lower_state_eV'][0])
break
def test_determine_astrophysical_parameters_using_grid(self):
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
#star_spectrum = ispec.read_spectrum(ispec_dir + "/input/spectra/examples/NARVAL_Arcturus.txt.gz")
#star_spectrum = ispec.read_spectrum(ispec_dir + "/input/spectra/examples/NARVAL_muCas.txt.gz")
#star_spectrum = ispec.read_spectrum(ispec_dir + "/input/spectra/examples/NARVAL_muLeo.txt.gz")
#star_spectrum = ispec.read_spectrum(ispec_dir + "/input/spectra/examples/HARPS.GBOG_Procyon.txt.gz")
#--- Radial Velocity determination with template -------------------------------
# - Read synthetic template
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Arcturus.372_926nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Sun.372_926nm/template.txt.gz")
template = ispec.read_spectrum(
ispec_dir +
"/input/spectra/templates/NARVAL.Sun.370_1048nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Synth.Sun.300_1100nm/template.txt.gz")
models, ccf = ispec.cross_correlate_with_template(star_spectrum, template, \
lower_velocity_limit=-200, upper_velocity_limit=200, \
velocity_step=1.0, fourier=False)
# Number of models represent the number of components
components = len(models)
# First component:
rv = np.round(models[0].mu(), 2) # km/s
rv_err = np.round(models[0].emu(), 2) # km/s
#--- Radial Velocity correction ------------------------------------------------
star_spectrum = ispec.correct_velocity(star_spectrum, rv)
#--- Resolution degradation ----------------------------------------------------
# NOTE: The line selection was built based on a solar spectrum with R ~ 47,000 and GES/VALD atomic linelist.
from_resolution = 80000
to_resolution = 47000
star_spectrum = ispec.convolve_spectrum(star_spectrum, to_resolution,
from_resolution)
#--- Continuum fit -------------------------------------------------------------
model = "Splines" # "Polynomy"
degree = 2
nknots = None # Automatic: 1 spline every 5 nm
from_resolution = to_resolution
# Strategy: Filter first median values and secondly MAXIMUMs in order to find the continuum
order = 'median+max'
median_wave_range = 0.05
max_wave_range = 1.0
star_continuum_model = ispec.fit_continuum(star_spectrum, from_resolution=from_resolution, \
nknots=nknots, degree=degree, \
median_wave_range=median_wave_range, \
max_wave_range=max_wave_range, \
model=model, order=order, \
automatic_strong_line_detection=True, \
strong_line_probability=0.5, \
use_errors_for_fitting=True)
#--- Normalize -------------------------------------------------------------
normalized_star_spectrum = ispec.normalize_spectrum(
star_spectrum,
star_continuum_model,
consider_continuum_errors=False)
# Use a fixed value because the spectrum is already normalized
star_continuum_model = ispec.fit_continuum(star_spectrum,
fixed_value=1.0,
model="Fixed value")
#--- Model spectra ----------------------------------------------------------
# Parameters
initial_teff = 5750.0
initial_logg = 4.5
initial_MH = 0.00
initial_alpha = 0.00
initial_vmic = ispec.estimate_vmic(initial_teff, initial_logg,
initial_MH)
initial_vmac = ispec.estimate_vmac(initial_teff, initial_logg,
initial_MH)
initial_vsini = 2.0
initial_limb_darkening_coeff = 0.6
initial_R = to_resolution
initial_vrad = 0
max_iterations = 20
code = "grid"
precomputed_grid_dir = ispec_dir + "/input/grid/SPECTRUM_MARCS.GES_GESv6_atom_hfs_iso.480_680nm_light/"
atomic_linelist = None
isotopes = None
modeled_layers_pack = None
solar_abundances = None
free_abundances = None
linelist_free_loggf = None
# Free parameters (vmic cannot be used as a free parameter when using a spectral grid)
#free_params = ["teff", "logg", "MH", "alpha", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
free_params = ["teff", "logg", "MH", "alpha", "vmic", "R"]
# Line regions
line_regions = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_synth_good_for_params_all.txt".format(
code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/{}_synth_good_for_params_all_extended.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all_extended.txt".format(code))
## Select only some lines to speed up the execution (in a real analysis it is better not to do this)
#line_regions = line_regions[np.logical_or(line_regions['note'] == 'Ti 1', line_regions['note'] == 'Ti 2')]
#line_regions = ispec.adjust_linemasks(normalized_star_spectrum, line_regions, max_margin=0.5)
# Read segments if we have them or...
#segments = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
# ... or we can create the segments on the fly:
segments = ispec.create_segments_around_lines(line_regions,
margin=0.25)
## Add also regions from the wings of strong lines:
# H beta
hbeta_lines = ispec.read_line_regions(ispec_dir +
"input/regions/wings_Hbeta.txt")
hbeta_segments = ispec.read_segment_regions(
ispec_dir + "input/regions/wings_Hbeta_segments.txt")
line_regions = np.hstack((line_regions, hbeta_lines))
segments = np.hstack((segments, hbeta_segments))
# H alpha
halpha_lines = ispec.read_line_regions(
ispec_dir + "input/regions/wings_Halpha.txt")
halpha_segments = ispec.read_segment_regions(
ispec_dir + "input/regions/wings_Halpha_segments.txt")
line_regions = np.hstack((line_regions, halpha_lines))
segments = np.hstack((segments, halpha_segments))
# Magnesium triplet
mgtriplet_lines = ispec.read_line_regions(
ispec_dir + "input/regions/wings_MgTriplet.txt")
mgtriplet_segments = ispec.read_segment_regions(
ispec_dir + "input/regions/wings_MgTriplet_segments.txt")
line_regions = np.hstack((line_regions, mgtriplet_lines))
segments = np.hstack((segments, mgtriplet_segments))
obs_spec, modeled_synth_spectrum, params, errors, abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum, star_continuum_model, \
modeled_layers_pack, atomic_linelist, isotopes, solar_abundances, free_abundances, linelist_free_loggf, initial_teff, \
initial_logg, initial_MH, initial_alpha, initial_vmic, initial_vmac, initial_vsini, \
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params, segments=segments, \
linemasks=line_regions, \
enhance_abundances=False, \
use_errors = True, \
vmic_from_empirical_relation = False, \
vmac_from_empirical_relation = True, \
max_iterations=max_iterations, \
tmp_dir = None, \
code=code, precomputed_grid_dir=precomputed_grid_dir)
expected_params = {
'teff': 5848.516352941799,
'logg': 4.47140586507073,
'MH': 0.021745200217247945,
'alpha': 0.0,
'vmic': 0.5617098008018283,
'vmac': 4.5,
'vsini': 2.0,
'limb_darkening_coeff': 0.6,
'R': 78395.52968455742
}
for k, v in list(expected_params.items()):
self.assertAlmostEqual(params[k], v)
expected_errors = {
'teff': 16.061649602869444,
'logg': 0.028408456932473077,
'MH': 0.007324730574204324,
'alpha': 0.007733907152934892,
'vmic': 0.043996803165640905,
'vmac': 0.0,
'vsini': 0.0,
'limb_darkening_coeff': 0.0,
'R': 3898.724894322937
}
for k, v in list(expected_errors.items()):
self.assertAlmostEqual(errors[k], v)
self.assertEqual(len(stats_linemasks), 337)
def test_determine_astrophysical_parameters_using_synth_spectra(self):
code = "spectrum"
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
#--- Radial Velocity determination with template -------------------------------
# - Read synthetic template
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Arcturus.372_926nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Sun.372_926nm/template.txt.gz")
template = ispec.read_spectrum(
ispec_dir +
"/input/spectra/templates/NARVAL.Sun.370_1048nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Synth.Sun.300_1100nm/template.txt.gz")
models, ccf = ispec.cross_correlate_with_template(star_spectrum, template, \
lower_velocity_limit=-200, upper_velocity_limit=200, \
velocity_step=1.0, fourier=False)
# Number of models represent the number of components
components = len(models)
# First component:
rv = np.round(models[0].mu(), 2) # km/s
rv_err = np.round(models[0].emu(), 2) # km/s
#--- Radial Velocity correction ------------------------------------------------
star_spectrum = ispec.correct_velocity(star_spectrum, rv)
#--- Resolution degradation ----------------------------------------------------
# NOTE: The line selection was built based on a solar spectrum with R ~ 47,000 and GES/VALD atomic linelist.
from_resolution = 80000
to_resolution = 47000
star_spectrum = ispec.convolve_spectrum(star_spectrum, to_resolution,
from_resolution)
#--- Continuum fit -------------------------------------------------------------
model = "Splines" # "Polynomy"
degree = 2
nknots = None # Automatic: 1 spline every 5 nm
from_resolution = to_resolution
# Strategy: Filter first median values and secondly MAXIMUMs in order to find the continuum
order = 'median+max'
median_wave_range = 0.05
max_wave_range = 1.0
star_continuum_model = ispec.fit_continuum(star_spectrum, from_resolution=from_resolution, \
nknots=nknots, degree=degree, \
median_wave_range=median_wave_range, \
max_wave_range=max_wave_range, \
model=model, order=order, \
automatic_strong_line_detection=True, \
strong_line_probability=0.5, \
use_errors_for_fitting=True)
#--- Normalize -------------------------------------------------------------
normalized_star_spectrum = ispec.normalize_spectrum(
star_spectrum,
star_continuum_model,
consider_continuum_errors=False)
# Use a fixed value because the spectrum is already normalized
star_continuum_model = ispec.fit_continuum(star_spectrum,
fixed_value=1.0,
model="Fixed value")
#--- Model spectra ----------------------------------------------------------
# Parameters
initial_teff = 5750.0
initial_logg = 4.5
initial_MH = 0.00
initial_alpha = ispec.determine_abundance_enchancements(initial_MH)
initial_vmic = ispec.estimate_vmic(initial_teff, initial_logg,
initial_MH)
initial_vmac = ispec.estimate_vmac(initial_teff, initial_logg,
initial_MH)
initial_vsini = 2.0
initial_limb_darkening_coeff = 0.6
initial_R = to_resolution
initial_vrad = 0
max_iterations = 6
# 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"
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"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(
atomic_linelist_file,
wave_base=np.min(star_spectrum['waveobs']),
wave_top=np.max(star_spectrum['waveobs']))
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)
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Free parameters
#free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
free_params = ["teff", "logg", "MH", "vmic", "R"]
# Free individual element abundance
free_abundances = None
linelist_free_loggf = None
# Line regions
line_regions = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_synth_good_for_params_all.txt".format(
code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/{}_synth_good_for_params_all_extended.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all_extended.txt".format(code))
## Select only some lines to speed up the execution (in a real analysis it is better not to do this)
line_regions = line_regions[np.logical_or(
line_regions['note'] == 'Ti 1', line_regions['note'] == 'Ti 2')]
line_regions = ispec.adjust_linemasks(normalized_star_spectrum,
line_regions,
max_margin=0.5)
# Read segments if we have them or...
#segments = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
# ... or we can create the segments on the fly:
segments = ispec.create_segments_around_lines(line_regions,
margin=0.25)
### Add also regions from the wings of strong lines:
## H beta
#hbeta_lines = ispec.read_line_regions(ispec_dir + "input/regions/wings_Hbeta.txt")
#hbeta_segments = ispec.read_segment_regions(ispec_dir + "input/regions/wings_Hbeta_segments.txt")
#line_regions = np.hstack((line_regions, hbeta_lines))
#segments = np.hstack((segments, hbeta_segments))
## H alpha
#halpha_lines = ispec.read_line_regions(ispec_dir + "input/regions/wings_Halpha.txt")
#halpha_segments = ispec.read_segment_regions(ispec_dir + "input/regions/wings_Halpha_segments.txt")
#line_regions = np.hstack((line_regions, halpha_lines))
#segments = np.hstack((segments, halpha_segments))
## Magnesium triplet
#mgtriplet_lines = ispec.read_line_regions(ispec_dir + "input/regions/wings_MgTriplet.txt")
#mgtriplet_segments = ispec.read_segment_regions(ispec_dir + "input/regions/wings_MgTriplet_segments.txt")
#line_regions = np.hstack((line_regions, mgtriplet_lines))
#segments = np.hstack((segments, mgtriplet_segments))
obs_spec, modeled_synth_spectrum, params, errors, abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum, star_continuum_model, \
modeled_layers_pack, atomic_linelist, isotopes, solar_abundances, free_abundances, linelist_free_loggf, initial_teff, \
initial_logg, initial_MH, initial_alpha, initial_vmic, initial_vmac, initial_vsini, \
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params, segments=segments, \
linemasks=line_regions, \
enhance_abundances=True, \
use_errors = True, \
vmic_from_empirical_relation = False, \
vmac_from_empirical_relation = True, \
max_iterations=max_iterations, \
tmp_dir = None, \
code=code)
expected_params = {
'teff': 5696.144535300913,
'logg': 4.35386512625295,
'MH': -0.117924251886487,
'alpha': 0.047169700754594805,
'vmic': 1.1383979614486783,
'vmac': 4.04,
'vsini': 2.0,
'limb_darkening_coeff': 0.6,
'R': 49936.32725781359
}
for k, v in list(expected_params.items()):
self.assertAlmostEqual(params[k], v)
expected_errors = {
'teff': 66.38643184730074,
'logg': 0.10101410057739481,
'MH': 0.07728877921624414,
'alpha': 0.0,
'vmic': 0.10922339131594937,
'vmac': 0.0,
'vsini': 0.0,
'limb_darkening_coeff': 0.0,
'R': 3496.439438356713
}
for k, v in list(expected_errors.items()):
self.assertAlmostEqual(errors[k], v)
self.assertEqual(len(stats_linemasks), 30)
def test_determine_abundances_using_synth_spectra(self):
code = "spectrum"
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
#--- Radial Velocity determination with template -------------------------------
# - Read synthetic template
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Arcturus.372_926nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Atlas.Sun.372_926nm/template.txt.gz")
template = ispec.read_spectrum(
ispec_dir +
"/input/spectra/templates/NARVAL.Sun.370_1048nm/template.txt.gz")
#template = ispec.read_spectrum(ispec_dir + "/input/spectra/templates/Synth.Sun.300_1100nm/template.txt.gz")
models, ccf = ispec.cross_correlate_with_template(star_spectrum, template, \
lower_velocity_limit=-200, upper_velocity_limit=200, \
velocity_step=1.0, fourier=False)
# Number of models represent the number of components
components = len(models)
# First component:
rv = np.round(models[0].mu(), 2) # km/s
rv_err = np.round(models[0].emu(), 2) # km/s
#--- Radial Velocity correction ------------------------------------------------
star_spectrum = ispec.correct_velocity(star_spectrum, rv)
#--- Resolution degradation ----------------------------------------------------
# NOTE: The line selection was built based on a solar spectrum with R ~ 47,000 and GES/VALD atomic linelist.
from_resolution = 80000
to_resolution = 47000
star_spectrum = ispec.convolve_spectrum(star_spectrum, to_resolution,
from_resolution)
#--- Continuum fit -------------------------------------------------------------
model = "Splines" # "Polynomy"
degree = 2
nknots = None # Automatic: 1 spline every 5 nm
from_resolution = to_resolution
# Strategy: Filter first median values and secondly MAXIMUMs in order to find the continuum
order = 'median+max'
median_wave_range = 0.05
max_wave_range = 1.0
star_continuum_model = ispec.fit_continuum(star_spectrum, from_resolution=from_resolution, \
nknots=nknots, degree=degree, \
median_wave_range=median_wave_range, \
max_wave_range=max_wave_range, \
model=model, order=order, \
automatic_strong_line_detection=True, \
strong_line_probability=0.5, \
use_errors_for_fitting=True)
#--- Normalize -------------------------------------------------------------
normalized_star_spectrum = ispec.normalize_spectrum(
star_spectrum,
star_continuum_model,
consider_continuum_errors=False)
# Use a fixed value because the spectrum is already normalized
star_continuum_model = ispec.fit_continuum(star_spectrum,
fixed_value=1.0,
model="Fixed value")
#--- Model spectra ----------------------------------------------------------
# Parameters
initial_teff = 5771.0
initial_logg = 4.44
initial_MH = 0.00
initial_alpha = 0.00
initial_vmic = ispec.estimate_vmic(initial_teff, initial_logg,
initial_MH)
initial_vmac = ispec.estimate_vmac(initial_teff, initial_logg,
initial_MH)
initial_vsini = 1.60 # Sun
initial_limb_darkening_coeff = 0.6
initial_R = to_resolution
initial_vrad = 0
max_iterations = 6
# 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"
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"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(
atomic_linelist_file,
wave_base=np.min(star_spectrum['waveobs']),
wave_top=np.max(star_spectrum['waveobs']))
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)
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Free parameters
#free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
free_params = ["vrad"]
#free_params = []
# Free individual element abundance (WARNING: it should be coherent with the selected line regions!)
chemical_elements_file = ispec_dir + "/input/abundances/chemical_elements_symbols.dat"
chemical_elements = ispec.read_chemical_elements(
chemical_elements_file)
element_name = "Ca"
free_abundances = ispec.create_free_abundances_structure(
[element_name], chemical_elements, solar_abundances)
free_abundances['Abund'] += initial_MH # Scale to metallicity
linelist_free_loggf = None
# Line regions
line_regions = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_synth_good_for_params_all.txt".format(
code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/{}_synth_good_for_params_all_extended.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all_extended.txt".format(code))
# Select only the lines to get abundances from
line_regions = line_regions[np.logical_or(
line_regions['note'] == element_name + ' 1',
line_regions['note'] == element_name + ' 2')]
line_regions = ispec.adjust_linemasks(normalized_star_spectrum,
line_regions,
max_margin=0.5)
# Read segments if we have them or...
#segments = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
# ... or we can create the segments on the fly:
segments = ispec.create_segments_around_lines(line_regions,
margin=0.25)
obs_spec, modeled_synth_spectrum, params, errors, abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum, star_continuum_model, \
modeled_layers_pack, atomic_linelist, isotopes, solar_abundances, free_abundances, linelist_free_loggf, initial_teff, \
initial_logg, initial_MH, initial_alpha, initial_vmic, initial_vmac, initial_vsini, \
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params, segments=segments, \
linemasks=line_regions, \
enhance_abundances=True, \
use_errors = True, \
vmic_from_empirical_relation = False, \
vmac_from_empirical_relation = False, \
max_iterations=max_iterations, \
tmp_dir = None, \
code=code)
expected_params = {
'teff': 5771.0,
'logg': 4.44,
'MH': 0.0,
'alpha': 0.0,
'vmic': 1.07,
'vmac': 4.19,
'vsini': 1.6,
'limb_darkening_coeff': 0.6,
'R': 47000.0,
'vrad0000': -0.009293697395991595,
'vrad0001': -0.06018526081728252,
'vrad0002': -0.015666491320596353,
'vrad0003': -0.055193632795656256,
'vrad0004': -0.1567689404172516,
'vrad0005': -0.22508061064189286,
'vrad0006': -0.20359311863771612,
'vrad0007': -0.16078450322612126
}
for k, v in list(expected_params.items()):
self.assertAlmostEqual(params[k], v)
expected_errors = {
'teff': 0.0,
'logg': 0.0,
'MH': 0.0,
'alpha': 0.0,
'vmic': 0.0,
'vmac': 0.0,
'vsini': 0.0,
'limb_darkening_coeff': 0.0,
'R': 0.0,
'vrad0000': 2.2914331925224816,
'vrad0001': 0.6770488621090028,
'vrad0002': 0.2767472596825708,
'vrad0003': 1.0820599330375968,
'vrad0004': 0.47734411482243877,
'vrad0005': 0.2585031799872256,
'vrad0006': 0.46187116575854853,
'vrad0007': 0.23921192411257394
}
for k, v in list(expected_errors.items()):
self.assertAlmostEqual(errors[k], v)
self.assertEqual(len(stats_linemasks), 8)
self.assertEqual(abundances_found['element'][0], 'Ca')
self.assertAlmostEqual(abundances_found['[X/H]'][0],
-0.0020078068382556324)
self.assertAlmostEqual(abundances_found['[X/Fe]'][0],
-0.0020078068382556324)
self.assertAlmostEqual(abundances_found['e[X/H]'][0],
0.027149612080779945)
self.assertAlmostEqual(abundances_found['e[X/Fe]'][0],
0.027149612080779945)
def determine_abundances(spec_id, species, params):
multiprocessing.current_process().daemon=False
#code = "synthe"
code = "spectrum"
star_spectrum = ispec.read_spectrum(spec_id)
# Use a fixed value because the spectrum is already normalized
star_continuum_model = ispec.fit_continuum(star_spectrum, fixed_value=1.0, model="Fixed value")
#--- Model spectra ----------------------------------------------------------
# Parameters
initial_teff = params[1]
initial_logg = params[5]
initial_MH = params[4]
initial_vmic = params[2]
initial_vmac = params[0]
initial_vsini = params[3]
initial_limb_darkening_coeff = params[7]
initial_R = params[6]
initial_vrad = 0
max_iterations = 6
# Selected model amtosphere, linelist and solar abundances
#model = ispec_dir + "/input/atmospheres/MARCS/modeled_layers_pack.dump"
model = ispec_dir + "/input/atmospheres/MARCS.GES/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/MARCS.APOGEE/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.APOGEE/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Castelli/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Kurucz/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Kirby/modeled_layers_pack.dump"
#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/GESv5_atom_hfs_iso.420_920nm/atomic_lines.tsv"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/GESv5_atom_nohfs_noiso.420_920nm/atomic_lines.tsv"
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/Grevesse.1998/stdatom.dat"
#solar_abundances_file = ispec_dir + "/input/abundances/Anders.1989/stdatom.dat"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(atomic_linelist_file, wave_base=np.min(star_spectrum['waveobs']), wave_top=np.max(star_spectrum['waveobs']))
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)
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Free parameters
#free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
#free_params = ["vrad"]
free_params = []
# Free individual element abundance (WARNING: it should be coherent with the selected line regions!)
chemical_elements_file = ispec_dir + "/input/abundances/chemical_elements_symbols.dat"
chemical_elements = ispec.read_chemical_elements(chemical_elements_file)
element_name = species[:-2]
free_abundances = ispec.create_free_abundances_structure([element_name], chemical_elements, solar_abundances)
free_abundances['Abund'] += initial_MH # Scale to metallicity
linelist_free_loggf = None
linemask_id = species.replace(" ", "_") + "_linemasks.txt"
# Line regions
line_regions = ispec.read_line_regions(linemask_id)
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/limited_but_with_missing_elements_spectrum_synth_good_for_abundances_all_extended.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/limited_but_with_missing_elements_turobspectrum_synth_good_for_abundances_all_extended.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/limited_but_with_missing_elements_sme_synth_good_for_abundances_all_extended.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/limited_but_with_missing_elements_moog_synth_good_for_abundances_all_extended.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/limited_but_with_missing_elements_synthe_synth_good_for_abundances_all_extended.txt")
# Select only the lines to get abundances from
#line_regions = line_regions[np.logical_or(line_regions['note'] == element_name+' 1', line_regions['note'] == element_name+' 2')]
#line_regions = ispec.adjust_linemasks(normalized_star_spectrum, line_regions, max_margin=0.5)
# Read segments if we have them or...
#segments = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
# ... or we can create the segments on the fly:
segments = ispec.create_segments_around_lines(line_regions, margin=0.25)
obs_spec, modeled_synth_spectrum, params, errors, abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(star_spectrum, star_continuum_model, \
modeled_layers_pack, atomic_linelist, isotopes, solar_abundances, free_abundances, linelist_free_loggf, initial_teff, \
initial_logg, initial_MH, initial_vmic, initial_vmac, initial_vsini, \
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params, segments=segments, \
linemasks=line_regions, \
enhance_abundances=True, \
use_errors = True, \
vmic_from_empirical_relation = False, \
vmac_from_empirical_relation = False, \
max_iterations=max_iterations, \
tmp_dir = None, \
code=code)
abundance = str(abundances_found)
results = abundance.split()
del results[0:4]
del results[1:3]
del results[2:5]
for i in range(0, len(results)):
results[i] = float(results[i].replace(",",""))
return results
def determine_parameters(spec_id, lines_id):
#code = "synthe"
code = "spectrum"
star_spectrum = ispec.read_spectrum(spec_id)
# Use a fixed value because the spectrum is already normalized
star_continuum_model = ispec.fit_continuum(star_spectrum, fixed_value=1.0, model="Fixed value")
normalized_star_spectrum = ispec.normalize_spectrum(star_spectrum, star_continuum_model, consider_continuum_errors=False)
#--- Model spectra ----------------------------------------------------------
params = []
with open('config.txt', 'r') as cfile:
for line in cfile:
params.append(float(str(line)[:-1]))
# Parameters
initial_teff = params[0]
initial_logg = params[1]
initial_MH = params[2]
initial_vmic = params[3]
initial_vmac = params[4]
initial_vsini = params[5]
initial_limb_darkening_coeff = params[6]
initial_R = params[7]
initial_vrad = params[8]
max_iterations = params[9]
# Selected model amtosphere, linelist and solar abundances
#model = ispec_dir + "/input/atmospheres/MARCS/modeled_layers_pack.dump"
model = ispec_dir + "/input/atmospheres/MARCS.GES/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/MARCS.APOGEE/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.APOGEE/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Castelli/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Kurucz/modeled_layers_pack.dump"
#model = ispec_dir + "/input/atmospheres/ATLAS9.Kirby/modeled_layers_pack.dump"
#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/GESv5_atom_hfs_iso.420_920nm/atomic_lines.tsv"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/GESv5_atom_nohfs_noiso.420_920nm/atomic_lines.tsv"
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/Grevesse.1998/stdatom.dat"
#solar_abundances_file = ispec_dir + "/input/abundances/Anders.1989/stdatom.dat"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(atomic_linelist_file, wave_base=np.min(star_spectrum['waveobs']), wave_top=np.max(star_spectrum['waveobs']))
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)
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Free parameters
#free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini"]
# Free individual element abundance
free_abundances = None
linelist_free_loggf = None
# Line regions
line_regions = ispec.read_line_regions(lines_id)
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/spectrum_synth_turbospectrum_synth_sme_synth_moog_synth_synthe_synth_good_for_params_all_extended.txt")
# Select only some lines to speed up the execution (in a real analysis it is better not to do this)
#line_regions = line_regions[np.logical_or(line_regions['note'] == 'Ti 1', line_regions['note'] == 'Ti 2')]
#line_regions = ispec.adjust_linemasks(normalized_star_spectrum, line_regions, max_margin=0.5)
# Read segments if we have them or...
#segments = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
# ... or we can create the segments on the fly:
segments = ispec.create_segments_around_lines(line_regions, margin=0.25)
obs_spec, modeled_synth_spectrum, params, errors, abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum, star_continuum_model, \
modeled_layers_pack, atomic_linelist, isotopes, solar_abundances, free_abundances, linelist_free_loggf, initial_teff, \
initial_logg, initial_MH, initial_vmic, initial_vmac, initial_vsini, \
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params, segments=segments, \
linemasks=line_regions, \
enhance_abundances=True, \
use_errors = True, \
vmic_from_empirical_relation = False, \
vmac_from_empirical_relation = False, \
max_iterations=max_iterations, \
tmp_dir = None, \
code=code)
##--- Save results -------------------------------------------------------------
logging.info("Saving results...")
#dump_file = "example_results_synth_%s.dump" % (code)
#ispec.save_results(dump_file, (params, errors, abundances_found, loggf_found, status, stats_linemasks))
# If we need to restore the results from another script:
#params, errors, abundances_found, loggf_found, status, stats_linemasks = ispec.restore_results(dump_file)
#logging.info("Saving synthetic spectrum...")
#synth_filename = "example_modeled_synth_%s.fits" % (code)
#ispec.write_spectrum(modeled_synth_spectrum, synth_filename)
parameters = "\n" + str(params)
parameter_errors = "\n" + str(errors)
file_id = spec_id + "_info.txt"
with open(file_id, "w") as savefile:
savefile.write(parameters)
savefile.write(parameter_errors)
def abund_line_by_line(star_spectrum,
param,
star_continuum_model,
object_id,
code="grid"):
''' more or less same function as one above but i created wraper
just to make things clear;
The idea is that we use grid interpolation but only free param is metalicity
and to fix everything else from previously derived model atmh;
Drawback is it only returns metalicity, not abundance of elements
because you cant interpolate abundances in grid
But with line mask and fitting by segment, metalicity you get is bassicaly
abundance for that spectral line; One elements creates multiple line
so just take averages afterwards and you can use that for rough estimate'''
normalized_star_spectrum = star_spectrum
precomputed_grid_dir = ispec_dir + "/input/grid/SPECTRUM_MARCS.GES_GESv5_atom_hfs_iso.480_680nm_light/"
#--- Model spectra ----------------------------------------------------------
# Parameters
initial_teff = param['teff']
initial_logg = param['logg']
initial_MH = param['MH']
initial_alpha = param['alpha']
initial_vmic = param['vmic']
initial_vmac = param['vmac']
initial_vsini = param['vsini']
initial_limb_darkening_coeff = param['limb_darkening_coeff']
initial_R = param['R']
initial_vrad = 0
max_iterations = 10
# 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/GESv5_atom_hfs_iso.420_920nm/atomic_lines.tsv"
#atomic_linelist_file = ispec_dir + "/input/linelists/transitions/GESv5_atom_nohfs_noiso.420_920nm/atomic_lines.tsv"
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/Grevesse.1998/stdatom.dat"
#solar_abundances_file = ispec_dir + "/input/abundances/Anders.1989/stdatom.dat"
isotope_file = ispec_dir + "/input/isotopes/SPECTRUM.lst"
# Load chemical information and linelist
atomic_linelist = ispec.read_atomic_linelist(\
atomic_linelist_file, wave_base=np.min(star_spectrum['waveobs']),\
wave_top=np.max(star_spectrum['waveobs']))
# Select lines that have some minimal contribution in the sun
atomic_linelist = atomic_linelist[
atomic_linelist['theoretical_depth'] >= 0.01]
isotopes = ispec.read_isotope_data(isotope_file)
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Free parameters
#free_params = ["teff", "logg", "MH", "vmic", "vmac", "vsini", "R", "vrad", "limb_darkening_coeff"]
#free_params = ["vrad"]
free_params = ["MH"]
#this is where we fix drawback; if we use synth we could use abundances
free_abundances = None
# Free individual element abundance (WARNING: it should be coherent with the selected line regions!)
chemical_elements_file = ispec_dir + "/input/abundances/chemical_elements_symbols.dat"
chemical_elements = ispec.read_chemical_elements(chemical_elements_file)
# Line regions
line_regions = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/grid_synth_good_for_params_all.txt".format(
code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/{}_synth_good_for_params_all_extended.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all_extended.txt".format(code))
# Select only the lines to get abundances from
#line_regions = line_regions[0:5]
line_regions = ispec.adjust_linemasks(normalized_star_spectrum,
line_regions,
max_margin=0.5)
output_dirname = "example_abundance_line_by_line_%s" % (code, )
ispec.mkdir_p(output_dirname)
abund_array = np.array(())
#create empty text file
for i, line in enumerate(line_regions):
# Directory and file names
#element_name = "_".join(line['element'].split())
element_name = "_".join(line['note'].split())
common_filename = "example_" + code + "_individual_" + element_name + "_%.4f" % line[
'wave_peak']
print("=========ELEMENT NAME==============")
print(element_name)
linelist_free_loggf = None
# Line by line
individual_line_regions = line_regions[i:i +
1] # Keep recarray structure
# Segment
segments = ispec.create_segments_around_lines(individual_line_regions,
margin=0.25)
wfilter = ispec.create_wavelength_filter(
normalized_star_spectrum, regions=segments) # Only use the segment
#skip this line if flux is 0 somewhere in region or there is no data
if len(normalized_star_spectrum[wfilter]) == 0 or np.any(
normalized_star_spectrum[wfilter] == 0):
continue
#this sometimes fails for different reasons
#if it does, lets ignore this line
try:
obs_spec, modeled_synth_spectrum, derived_params, errors,\
abundances_found, loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum[wfilter],\
star_continuum_model, modeled_layers_pack, atomic_linelist,\
isotopes, solar_abundances, free_abundances, linelist_free_loggf,\
initial_teff, initial_logg, initial_MH, initial_alpha, initial_vmic,\
initial_vmac, initial_vsini, initial_limb_darkening_coeff, initial_R,\
initial_vrad, free_params, segments=segments,\
linemasks=individual_line_regions,enhance_abundances=True,\
use_errors = True, vmic_from_empirical_relation = False,\
vmac_from_empirical_relation = False, max_iterations=max_iterations,\
tmp_dir = None, code=code, precomputed_grid_dir=precomputed_grid_dir)
except Exception:
continue
#Write every element abundance to separate file
#We use tihs ugly stuff here because if model_spectrum fails
#it raises exception and i dont currently know how to handle it
abundances_file = open(
output_dirname + "/abd/%s_%s_abundances.txt" %
(object_id, element_name), "a")
abundances_file.write("%f\t%f\n" %
(derived_params['MH'], errors['MH']))
abundances_file.close()
##--- Save results -------------------------------------------------------------
dump_file = output_dirname + "/" + 'dumps' + '/' + common_filename + ".dump"
logging.info("Saving results...")
ispec.save_results(dump_file,
(derived_params, errors, abundances_found,
loggf_found, status, stats_linemasks))
# If we need to restore the results from another script:
# params, errors, abundances_found, loggf_found, status, stats_linemasks = ispec.restore_results(dump_file)
logging.info("Saving synthetic spectrum...")
synth_filename = output_dirname + "/" + common_filename + ".fits"
ispec.write_spectrum(modeled_synth_spectrum, synth_filename)
return abund_array
def param_using_grid(normalized_star_spectrum, star_continuum_model, object_id,\
resolution=80000, p0 = [5750.0, 4.5, 0, 0, 2, 0.6, 0], max_iter = 10):
''' Derive spectroscopic parameters using grid model
p0 are initial values list:
teff, logg, MH, alpha, vsini, limb_darkening coef, vrad
Returns params, errors and ispec_pectrum object with spectra form best fit
'''
#--- Model spectra --------------------------------------------------------
# Parameters initiall values
initial_teff = p0[0]
initial_logg = p0[1]
initial_MH = p0[2]
initial_alpha = p0[3]
initial_vmic = ispec.estimate_vmic(initial_teff, initial_logg, initial_MH)
initial_vmac = ispec.estimate_vmac(initial_teff, initial_logg, initial_MH)
initial_vsini = p0[4]
initial_limb_darkening_coeff = p0[5]
initial_R = resolution
initial_vrad = p0[6]
max_iterations = max_iter
#load grid
code = "grid"
precomputed_grid_dir = ispec_dir + "/input/grid/SPECTRUM_MARCS.GES_GESv5_atom_hfs_iso.480_680nm_light/"
atomic_linelist = None
isotopes = None
modeled_layers_pack = None
solar_abundances = None
free_abundances = None
linelist_free_loggf = None
# Free parameters (vmic cannot be used as a free parameter when using a spectral grid)
free_params = ["teff", "logg", "MH", "alpha", "R"]
# Line regions
line_regions = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_synth_good_for_params_all.txt".format(
code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/{}_synth_good_for_params_all_extended.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all.txt".format(code))
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_synth_good_for_params_all_extended.txt".format(code))
## Select only some lines to speed up the execution (in a real analysis it is better not to do this)
#line_regions = line_regions[np.logical_or(line_regions['note'] == 'Ti 1', line_regions['note'] == 'Ti 2')]
#line_regions = ispec.adjust_linemasks(normalized_star_spectrum, line_regions, max_margin=0.5)
# Read segments if we have them or...
#segments = ispec.read_segment_regions(ispec_dir + "/input/regions/fe_lines_segments.txt")
# ... or we can create the segments on the fly:
segments = ispec.create_segments_around_lines(line_regions, margin=0.25)
## Add also regions from the wings of strong lines:
# H beta
hbeta_lines = ispec.read_line_regions(ispec_dir +
"/input/regions/wings_Hbeta.txt")
hbeta_segments = ispec.read_segment_regions(
ispec_dir + "/input/regions/wings_Hbeta_segments.txt")
line_regions = np.hstack((line_regions, hbeta_lines))
segments = np.hstack((segments, hbeta_segments))
# H alpha
halpha_lines = ispec.read_line_regions(ispec_dir +
"/input/regions/wings_Halpha.txt")
halpha_segments = ispec.read_segment_regions(
ispec_dir + "/input/regions/wings_Halpha_segments.txt")
line_regions = np.hstack((line_regions, halpha_lines))
segments = np.hstack((segments, halpha_segments))
# Magnesium triplet
mgtriplet_lines = ispec.read_line_regions(
ispec_dir + "/input/regions/wings_MgTriplet.txt")
mgtriplet_segments = ispec.read_segment_regions(
ispec_dir + "/input/regions/wings_MgTriplet_segments.txt")
line_regions = np.hstack((line_regions, mgtriplet_lines))
segments = np.hstack((segments, mgtriplet_segments))
# run model spectra from grid!
obs_spec, modeled_synth_spectrum, params, errors, abundances_found,\
loggf_found, status, stats_linemasks = \
ispec.model_spectrum(normalized_star_spectrum, star_continuum_model,\
modeled_layers_pack, atomic_linelist, isotopes, solar_abundances,\
free_abundances, linelist_free_loggf, initial_teff, initial_logg,\
initial_MH, initial_alpha, initial_vmic, initial_vmac, initial_vsini,\
initial_limb_darkening_coeff, initial_R, initial_vrad, free_params,\
segments=segments, linemasks=line_regions, enhance_abundances=False,\
use_errors = True, vmic_from_empirical_relation = False,\
vmac_from_empirical_relation = True, max_iterations=max_iterations,\
tmp_dir = None, code=code, precomputed_grid_dir=precomputed_grid_dir)
##--- Save results ---------------------------------------------------------
#logging.info("Saving results...")
dump_file = "example_results_synth_grid_%s.dump" % (object_id)
#logging.info("Saving results...")
ispec.save_results(dump_file, (params, errors, abundances_found,
loggf_found, status, stats_linemasks))
# If we need to restore the results from another script:
# params, errors, abundances_found, loggf_found, status, stats_linemasks = ispec.restore_results(dump_file)
#logging.info("Saving synthetic spectrum...")
synth_filename = "example_modeled_synth_grid_%s.fits" % (object_id)
ispec.write_spectrum(modeled_synth_spectrum, synth_filename)
return params, errors, modeled_synth_spectrum