def normaliseContinuum(spec):
"""
Based on example.py
normalize_whole_spectrum_strategy1_ignoring_prefixed_strong_lines function
"""
model = 'Splines'
degree = 2
nknots = None
from_resolution = INSTRUMENT[args.instrument]['RESOLUTION']
# continuum fit
order = 'median+max'
median_wave_range = 0.01
max_wave_range = 1.0
strong_lines = ispec.read_line_regions(strongLines)
continuum_model = ispec.fit_continuum(spec, \
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)
# continuum normalisation
spec_norm = ispec.normalize_spectrum(spec, \
continuum_model, \
consider_continuum_errors=False)
return spec_norm
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_normalize_whole_spectrum_ignoring_prefixed_strong_lines(self):
"""
Use the whole spectrum but ignoring some strong lines, strategy 'median+max'
"""
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
#--- Continuum fit -------------------------------------------------------------
model = "Splines" # "Polynomy"
degree = 2
nknots = None # Automatic: 1 spline every 5 nm
from_resolution = 80000
# 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
strong_lines = ispec.read_line_regions(
ispec_dir + "/input/regions/strong_lines/absorption_lines.txt")
star_continuum_model = ispec.fit_continuum(star_spectrum, from_resolution=from_resolution, \
ignore=strong_lines, \
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)
#--- Continuum normalization ---------------------------------------------------
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")
np.testing.assert_equal(star_spectrum['waveobs'],
normalized_star_spectrum['waveobs'])
self.assertAlmostEqual(star_spectrum['flux'][0], 0.67077)
self.assertAlmostEqual(star_spectrum['flux'][-1], 2.2169)
self.assertAlmostEqual(star_spectrum['err'][0], 0.0021259)
self.assertAlmostEqual(star_spectrum['err'][-1], 0.0043878)
self.assertAlmostEqual(normalized_star_spectrum['flux'][0],
0.8005567874185445)
self.assertAlmostEqual(normalized_star_spectrum['flux'][-1],
0.9874528805693361)
self.assertAlmostEqual(normalized_star_spectrum['err'][0],
0.0025372388067043607)
self.assertAlmostEqual(normalized_star_spectrum['err'][-1],
0.0019544164145257493)
self.assertTrue(
np.all(star_continuum_model(star_spectrum['waveobs']) == 1))
def test_normalize_whole_spectrum_with_template(self):
"""
Use a template to normalize the whole spectrum
"""
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
synth_spectrum = ispec.read_spectrum(
ispec_dir +
"/input/spectra/templates/Synth.Sun.300_1100nm/template.txt.gz")
#--- Continuum fit -------------------------------------------------------------
model = "Template"
nknots = None # Automatic: 1 spline every 5 nm (in this case, used to apply a gaussian filter)
from_resolution = 80000
median_wave_range = 5.0
#strong_lines = ispec.read_line_regions(ispec_dir + "/input/regions/strong_lines/absorption_lines.txt")
strong_lines = ispec.read_line_regions(
ispec_dir + "/input/regions/relevant/relevant_line_masks.txt")
#strong_lines = None
star_continuum_model = ispec.fit_continuum(star_spectrum, from_resolution=from_resolution, \
ignore=strong_lines, \
nknots=nknots, \
median_wave_range=median_wave_range, \
model=model, \
template=synth_spectrum)
#--- Continuum normalization ---------------------------------------------------
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")
np.testing.assert_equal(star_spectrum['waveobs'],
normalized_star_spectrum['waveobs'])
self.assertAlmostEqual(star_spectrum['flux'][0], 0.67077)
self.assertAlmostEqual(star_spectrum['flux'][-1], 2.2169)
self.assertAlmostEqual(star_spectrum['err'][0], 0.0021259)
self.assertAlmostEqual(star_spectrum['err'][-1], 0.0043878)
self.assertAlmostEqual(normalized_star_spectrum['flux'][0],
0.7964201448878107)
self.assertAlmostEqual(normalized_star_spectrum['flux'][-1],
0.997168332612696)
self.assertAlmostEqual(normalized_star_spectrum['err'][0],
0.002524128368914824)
self.assertAlmostEqual(normalized_star_spectrum['err'][-1],
0.0019736457259407225)
self.assertTrue(
np.all(star_continuum_model(star_spectrum['waveobs']) == 1))
def normalize_spectrum(star_spectrum,
res=80000,
model="Splines",
degree=2,
nknots=None):
'''
Fit continuum ignoring strong lines and using fe lines template,
strategy 'median+max'
####
#### ASSUMING DEFAULT VALUES FOR:
#### RESOLUTION, MODEL FOR CONTINUUM, DEGREE OF MODEL, NKNOTS!!!!
#### TAKE CARE!!!!
####
returns normalized star spectrum object and continumm model
'''
from_resolution = res #define 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
# read continuum regions from Fe lines and strong lines
continuum_regions = ispec.read_continuum_regions(\
ispec_dir + "/input/regions/fe_lines_continuum.txt")
strong_lines = ispec.read_line_regions(\
ispec_dir + "/input/regions/strong_lines/absorption_lines.txt")
star_continuum_model = ispec.fit_continuum(star_spectrum,\
from_resolution=from_resolution, ignore=strong_lines,\
continuum_regions=continuum_regions, 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)
#--- Continuum normalization -----------------------------------------------
logging.info("Continuum normalization...")
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
#you need continuum model to be able to synt or interpolate params from grid
star_continuum_model = ispec.fit_continuum(star_spectrum, \
fixed_value=1.0, model="Fixed value")
return normalized_star_spectrum, star_continuum_model
def test_adjust_line_masks(self):
star_spectrum = ispec.read_spectrum(
ispec_dir + "/input/spectra/examples/NARVAL_Sun_Vesta-1.txt.gz")
#--- Adjust line masks ---------------------------------------------------------
resolution = 80000
smoothed_star_spectrum = ispec.convolve_spectrum(
star_spectrum, resolution)
line_regions = ispec.read_line_regions(ispec_dir +
"/input/regions/fe_lines.txt")
linemasks = ispec.adjust_linemasks(smoothed_star_spectrum,
line_regions,
max_margin=0.5)
self.assertAlmostEqual(line_regions['wave_base'][0], 480.26937)
self.assertAlmostEqual(line_regions['wave_top'][0], 480.28771)
self.assertEqual(len(linemasks), 315)
np.testing.assert_equal(line_regions['wave_peak'],
linemasks['wave_peak'])
self.assertAlmostEqual(linemasks['wave_base'][0], 480.269365109)
self.assertAlmostEqual(linemasks['wave_top'][0], 480.319964199)
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 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_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_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 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 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
def _determine_abundances_from_ew(self, code):
use_ares = False
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)
#--- Telluric velocity shift determination from spectrum --------------------------
# - Telluric
telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
telluric_linelist = ispec.read_telluric_linelist(
telluric_linelist_file, minimum_depth=0.0)
models, ccf = ispec.cross_correlate_with_mask(star_spectrum, telluric_linelist, \
lower_velocity_limit=-100, upper_velocity_limit=100, \
velocity_step=0.5, mask_depth=0.01, \
fourier = False,
only_one_peak = True)
vel_telluric = np.round(models[0].mu(), 2) # km/s
vel_telluric_err = np.round(models[0].emu(), 2) # km/s
#--- 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 = 80000
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")
#telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
#telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.01)
#vel_telluric = 17.79 # km/s
#telluric_linelist = None
#vel_telluric = None
#--- Read lines and adjust them ------------------------------------------------
if code in ['width', 'moog']:
line_regions_with_atomic_data = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_ew_ispec_good_for_params_all_extended.txt"
.format(code))
#line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_ew_ispec_good_for_params_all_extended.txt".format(code))
else:
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 iron lines
line_regions_with_atomic_data = line_regions_with_atomic_data[
np.logical_or(line_regions_with_atomic_data['note'] == "Fe 1",
line_regions_with_atomic_data['note'] == "Fe 2")]
smoothed_star_spectrum = ispec.convolve_spectrum(
star_spectrum, 2 * to_resolution)
line_regions_with_atomic_data = ispec.adjust_linemasks(
smoothed_star_spectrum,
line_regions_with_atomic_data,
max_margin=0.5)
#--- Fit the lines but do NOT cross-match with any atomic linelist since they already have that information
linemasks = ispec.fit_lines(line_regions_with_atomic_data, normalized_star_spectrum, star_continuum_model, \
atomic_linelist = None, \
max_atomic_wave_diff = 0.005, \
telluric_linelist = telluric_linelist, \
check_derivatives = False, \
vel_telluric = vel_telluric, discard_gaussian=False, \
smoothed_spectrum=None, \
discard_voigt=True, \
free_mu=True, crossmatch_with_mu=False, closest_match=False)
# Discard bad masks
flux_peak = normalized_star_spectrum['flux'][linemasks['peak']]
flux_base = normalized_star_spectrum['flux'][linemasks['base']]
flux_top = normalized_star_spectrum['flux'][linemasks['top']]
bad_mask = np.logical_or(
linemasks['wave_peak'] <= linemasks['wave_base'],
linemasks['wave_peak'] >= linemasks['wave_top'])
bad_mask = np.logical_or(bad_mask, flux_peak >= flux_base)
bad_mask = np.logical_or(bad_mask, flux_peak >= flux_top)
linemasks = linemasks[~bad_mask]
# Exclude lines with EW equal to zero
rejected_by_zero_ew = (linemasks['ew'] == 0)
linemasks = linemasks[~rejected_by_zero_ew]
# Exclude lines that may be affected by tellurics
rejected_by_telluric_line = (linemasks['telluric_wave_peak'] != 0)
linemasks = linemasks[~rejected_by_telluric_line]
linemasks = linemasks[:20]
if use_ares:
# Replace the measured equivalent widths by the ones computed by ARES
old_linemasks = linemasks.copy()
### Different rejection parameters (check ARES papers):
## - http://adsabs.harvard.edu/abs/2007A%26A...469..783S
## - http://adsabs.harvard.edu/abs/2015A%26A...577A..67S
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="0.995", tmp_dir=None, verbose=0)
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="3;5764,5766,6047,6052,6068,6076", tmp_dir=None, verbose=0)
snr = 50
linemasks = ispec.update_ew_with_ares(normalized_star_spectrum,
linemasks,
rejt="%s" % (snr),
tmp_dir=None,
verbose=0)
#--- Determining abundances by EW of the previously fitted lines ---------------
# Parameters
teff = 5777.0
logg = 4.44
MH = 0.00
alpha = 0.00
microturbulence_vel = 1.0
# Selected model amtosphere 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/"
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)
# 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)
spec_abund, normal_abund, x_over_h, x_over_fe = ispec.determine_abundances(atmosphere_layers, \
teff, logg, MH, alpha, linemasks, solar_abundances, microturbulence_vel = microturbulence_vel, \
verbose=1, code=code)
return linemasks, x_over_h
def test_find_linemasks(self):
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)
#--- Telluric velocity shift determination from spectrum --------------------------
# - Telluric
telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
telluric_linelist = ispec.read_telluric_linelist(
telluric_linelist_file, minimum_depth=0.0)
models, ccf = ispec.cross_correlate_with_mask(star_spectrum, telluric_linelist, \
lower_velocity_limit=-100, upper_velocity_limit=100, \
velocity_step=0.5, mask_depth=0.01, \
fourier = False,
only_one_peak = True)
vel_telluric = np.round(models[0].mu(), 2) # km/s
vel_telluric_err = np.round(models[0].emu(), 2) # km/s
#--- Continuum fit -------------------------------------------------------------
model = "Splines" # "Polynomy"
degree = 2
nknots = None # Automatic: 1 spline every 5 nm
from_resolution = 80000
# 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)
#--- Find linemasks ------------------------------------------------------------
#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"
telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
# Read
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
#telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.01)
#vel_telluric = 17.79 # km/s
#telluric_linelist = None
#vel_telluric = None
resolution = 80000
smoothed_star_spectrum = ispec.convolve_spectrum(
star_spectrum, resolution)
min_depth = 0.05
max_depth = 1.00
star_linemasks = ispec.find_linemasks(star_spectrum, star_continuum_model, \
atomic_linelist=atomic_linelist, \
max_atomic_wave_diff = 0.005, \
telluric_linelist=telluric_linelist, \
vel_telluric=vel_telluric, \
minimum_depth=min_depth, maximum_depth=max_depth, \
smoothed_spectrum=smoothed_star_spectrum, \
check_derivatives=False, \
discard_gaussian=False, discard_voigt=True, \
closest_match=False)
# Exclude lines that have not been successfully cross matched with the atomic data
# because we cannot calculate the chemical abundance (it will crash the corresponding routines)
rejected_by_atomic_line_not_found = (star_linemasks['wave_nm'] == 0)
star_linemasks = star_linemasks[~rejected_by_atomic_line_not_found]
# Exclude lines with EW equal to zero
rejected_by_zero_ew = (star_linemasks['ew'] == 0)
star_linemasks = star_linemasks[~rejected_by_zero_ew]
# Select only iron lines
iron = star_linemasks['element'] == "Fe 1"
iron = np.logical_or(iron, star_linemasks['element'] == "Fe 2")
iron_star_linemasks = star_linemasks[iron]
self.assertEqual(len(star_linemasks), 1732)
self.assertEqual(len(iron_star_linemasks), 883)
self.assertAlmostEqual(iron_star_linemasks['ew'][0], 15.82970157775808)
self.assertAlmostEqual(iron_star_linemasks['ew'][-1],
15.545342323635188)
self.assertAlmostEqual(iron_star_linemasks['ew_err'][0],
1.1187509030236669)
self.assertAlmostEqual(iron_star_linemasks['ew_err'][-1],
1.3221015426240295)
tmp_filename = tempfile.mktemp()
# Write regions with masks limits, cross-matched atomic data and fit data
ispec.write_line_regions(star_linemasks, tmp_filename, extended=True)
recover_star_linemasks = ispec.read_line_regions(tmp_filename)
os.remove(tmp_filename)
# Write regions with masks limits and cross-matched atomic data (fit data fields are zeroed)
zeroed_star_linemasks = ispec.reset_fitted_data_fields(star_linemasks)
np.testing.assert_almost_equal(star_linemasks['wave_nm'],
recover_star_linemasks['wave_nm'])
np.testing.assert_almost_equal(star_linemasks['ew'],
recover_star_linemasks['ew'],
decimal=1)
np.testing.assert_almost_equal(star_linemasks['wave_base'],
recover_star_linemasks['wave_base'],
decimal=4)
np.testing.assert_almost_equal(star_linemasks['wave_top'],
recover_star_linemasks['wave_top'],
decimal=4)
np.testing.assert_almost_equal(star_linemasks['wave_peak'],
recover_star_linemasks['wave_peak'],
decimal=4)
self.assertTrue(np.all(zeroed_star_linemasks['ew'] == 0))
def test_determine_astrophysical_parameters_from_ew(self):
code = "moog"
use_ares = False
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)
#--- Telluric velocity shift determination from spectrum --------------------------
# - Telluric
telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
telluric_linelist = ispec.read_telluric_linelist(
telluric_linelist_file, minimum_depth=0.0)
models, ccf = ispec.cross_correlate_with_mask(star_spectrum, telluric_linelist, \
lower_velocity_limit=-100, upper_velocity_limit=100, \
velocity_step=0.5, mask_depth=0.01, \
fourier = False,
only_one_peak = True)
vel_telluric = np.round(models[0].mu(), 2) # km/s
vel_telluric_err = np.round(models[0].emu(), 2) # km/s
#--- 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 = 80000
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")
#telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
#telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.01)
#vel_telluric = 17.79 # km/s
#telluric_linelist = None
#vel_telluric = None
#--- Read lines and adjust them ------------------------------------------------
if code in ['width', 'moog']:
line_regions_with_atomic_data = ispec.read_line_regions(
ispec_dir +
"/input/regions/47000_GES/{}_ew_ispec_good_for_params_all_extended.txt"
.format(code))
#line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/{}_ew_ispec_good_for_params_all_extended.txt".format(code))
else:
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 iron lines
line_regions_with_atomic_data = line_regions_with_atomic_data[
np.logical_or(line_regions_with_atomic_data['note'] == "Fe 1",
line_regions_with_atomic_data['note'] == "Fe 2")]
smoothed_star_spectrum = ispec.convolve_spectrum(
star_spectrum, 2 * to_resolution)
line_regions_with_atomic_data = ispec.adjust_linemasks(
smoothed_star_spectrum,
line_regions_with_atomic_data,
max_margin=0.5)
#--- Fit the lines but do NOT cross-match with any atomic linelist since they already have that information
linemasks = ispec.fit_lines(line_regions_with_atomic_data, normalized_star_spectrum, star_continuum_model, \
atomic_linelist = None, \
max_atomic_wave_diff = 0.005, \
telluric_linelist = telluric_linelist, \
check_derivatives = False, \
vel_telluric = vel_telluric, discard_gaussian=False, \
smoothed_spectrum=None, \
discard_voigt=True, \
free_mu=True, crossmatch_with_mu=False, closest_match=False)
# Discard bad masks
flux_peak = normalized_star_spectrum['flux'][linemasks['peak']]
flux_base = normalized_star_spectrum['flux'][linemasks['base']]
flux_top = normalized_star_spectrum['flux'][linemasks['top']]
bad_mask = np.logical_or(
linemasks['wave_peak'] <= linemasks['wave_base'],
linemasks['wave_peak'] >= linemasks['wave_top'])
bad_mask = np.logical_or(bad_mask, flux_peak >= flux_base)
bad_mask = np.logical_or(bad_mask, flux_peak >= flux_top)
linemasks = linemasks[~bad_mask]
# Exclude lines with EW equal to zero
rejected_by_zero_ew = (linemasks['ew'] == 0)
linemasks = linemasks[~rejected_by_zero_ew]
# Exclude lines that may be affected by tellurics
rejected_by_telluric_line = (linemasks['telluric_wave_peak'] != 0)
linemasks = linemasks[~rejected_by_telluric_line]
if use_ares:
# Replace the measured equivalent widths by the ones computed by ARES
old_linemasks = linemasks.copy()
### Different rejection parameters (check ARES papers):
## - http://adsabs.harvard.edu/abs/2007A%26A...469..783S
## - http://adsabs.harvard.edu/abs/2015A%26A...577A..67S
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="0.995", tmp_dir=None, verbose=0)
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="3;5764,5766,6047,6052,6068,6076", tmp_dir=None, verbose=0)
snr = 50
linemasks = ispec.update_ew_with_ares(normalized_star_spectrum,
linemasks,
rejt="%s" % (snr),
tmp_dir=None,
verbose=0)
#--- Model spectra from EW --------------------------------------------------
# Parameters
initial_teff = 5777.0
initial_logg = 4.44
initial_MH = 0.00
initial_alpha = 0.00
initial_vmic = ispec.estimate_vmic(initial_teff, initial_logg,
initial_MH)
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/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"
# Load model atmospheres
modeled_layers_pack = ispec.load_modeled_layers_pack(model)
# Load SPECTRUM abundances
solar_abundances = ispec.read_solar_abundances(solar_abundances_file)
# Validate parameters
if not ispec.valid_atmosphere_target(
modeled_layers_pack, {
'teff': initial_teff,
'logg': initial_logg,
'MH': initial_MH,
'alpha': initial_alpha
}):
msg = "The specified effective temperature, gravity (log g) and metallicity [M/H] \
fall out of theatmospheric models."
print(msg)
# Reduced equivalent width
# Filter too weak/strong lines
# * Criteria presented in paper of GALA
#efilter = np.logical_and(linemasks['ewr'] >= -5.8, linemasks['ewr'] <= -4.65)
efilter = np.logical_and(linemasks['ewr'] >= -6.0,
linemasks['ewr'] <= -4.3)
# Filter high excitation potential lines
# * Criteria from Eric J. Bubar "Equivalent Width Abundance Analysis In Moog"
efilter = np.logical_and(efilter, linemasks['lower_state_eV'] <= 5.0)
efilter = np.logical_and(efilter, linemasks['lower_state_eV'] >= 0.5)
## Filter also bad fits
efilter = np.logical_and(efilter, linemasks['rms'] < 1.00)
# no flux
noflux = normalized_star_spectrum['flux'][linemasks['peak']] < 1.0e-10
efilter = np.logical_and(efilter, np.logical_not(noflux))
unfitted = linemasks['fwhm'] == 0
efilter = np.logical_and(efilter, np.logical_not(unfitted))
results = ispec.model_spectrum_from_ew(linemasks[efilter], modeled_layers_pack, \
solar_abundances, initial_teff, initial_logg, initial_MH, initial_alpha, initial_vmic, \
free_params=["teff", "logg", "vmic"], \
adjust_model_metalicity=True, \
max_iterations=max_iterations, \
enhance_abundances=True, \
#outliers_detection = "robust", \
#outliers_weight_limit = 0.90, \
outliers_detection = "sigma_clipping", \
#sigma_level = 3, \
tmp_dir = None, \
code=code)
params, errors, status, x_over_h, selected_x_over_h, fitted_lines_params, used_linemasks = results
expected_params = {
'teff': 5825.366401775263,
'logg': 4.3929210834771535,
'MH': 0.03500000000000014,
'alpha': 0.0,
'vmic': 1.1670939448402673
}
for k, v in list(expected_params.items()):
self.assertAlmostEqual(params[k], v)
expected_errors = {
'teff': 59.030776466850426,
'logg': 0.08775700534919817,
'MH': 0.0606561589029185,
'alpha': 0.0,
'vmic': 0.03900548810240552
}
for k, v in list(expected_errors.items()):
self.assertAlmostEqual(errors[k], v)
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 test_fit_lines_determine_ew_and_crossmatch_with_atomic_data(self):
use_ares = False
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)
#--- Telluric velocity shift determination from spectrum --------------------------
# - Telluric
telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.0)
models, ccf = ispec.cross_correlate_with_mask(star_spectrum, telluric_linelist, \
lower_velocity_limit=-100, upper_velocity_limit=100, \
velocity_step=0.5, mask_depth=0.01, \
fourier = False,
only_one_peak = True)
vel_telluric = np.round(models[0].mu(), 2) # km/s
vel_telluric_err = np.round(models[0].emu(), 2) # km/s
#--- 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 = 80000
# 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")
#--- Fit lines -----------------------------------------------------------------
#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"
# Read
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
#telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
#telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.01)
#vel_telluric = 17.79 # km/s
#telluric_linelist = None
#vel_telluric = None
line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/moog_synth_good_for_params_all.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/width_synth_good_for_params_all.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/moog_synth_good_for_params_all.txt")
#line_regions = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/width_synth_good_for_params_all.txt")
line_regions = ispec.adjust_linemasks(normalized_star_spectrum, line_regions, max_margin=0.5)
linemasks = ispec.fit_lines(line_regions, normalized_star_spectrum, star_continuum_model, \
atomic_linelist = atomic_linelist, \
#max_atomic_wave_diff = 0.005, \
max_atomic_wave_diff = 0.00, \
telluric_linelist = telluric_linelist, \
smoothed_spectrum = None, \
check_derivatives = False, \
vel_telluric = vel_telluric, discard_gaussian=False, \
discard_voigt=True, \
free_mu=True, crossmatch_with_mu=False, closest_match=False)
# Discard lines that are not cross matched with the same original element stored in the note
linemasks = linemasks[linemasks['element'] == line_regions['note']]
# Exclude lines that have not been successfully cross matched with the atomic data
# because we cannot calculate the chemical abundance (it will crash the corresponding routines)
rejected_by_atomic_line_not_found = (linemasks['wave_nm'] == 0)
linemasks = linemasks[~rejected_by_atomic_line_not_found]
# Exclude lines with EW equal to zero
rejected_by_zero_ew = (linemasks['ew'] == 0)
linemasks = linemasks[~rejected_by_zero_ew]
# Exclude lines that may be affected by tellurics
rejected_by_telluric_line = (linemasks['telluric_wave_peak'] != 0)
linemasks = linemasks[~rejected_by_telluric_line]
if use_ares:
# Replace the measured equivalent widths by the ones computed by ARES
old_linemasks = linemasks.copy()
### Different rejection parameters (check ARES papers):
## - http://adsabs.harvard.edu/abs/2007A%26A...469..783S
## - http://adsabs.harvard.edu/abs/2015A%26A...577A..67S
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="0.995", tmp_dir=None, verbose=0)
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="3;5764,5766,6047,6052,6068,6076", tmp_dir=None, verbose=0)
snr = 50
linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="%s" % (snr), tmp_dir=None, verbose=0)
self.assertEqual(len(linemasks), 281)
self.assertAlmostEqual(linemasks['ew'][0], 68.48284589709996)
self.assertAlmostEqual(linemasks['ew'][-3], 46.17583047097995)
self.assertEqual(linemasks['element'][0], 'Fe 1')
self.assertEqual(linemasks['element'][-3], 'Si 1')
self.assertAlmostEqual(linemasks['loggf'][0], -1.028)
self.assertAlmostEqual(linemasks['loggf'][-3], -1.062)
def test_fit_lines_already_crossmatched_with_atomic_data_and_determine_ew(self):
use_ares = False
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)
#--- Telluric velocity shift determination from spectrum --------------------------
# - Telluric
telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.0)
models, ccf = ispec.cross_correlate_with_mask(star_spectrum, telluric_linelist, \
lower_velocity_limit=-100, upper_velocity_limit=100, \
velocity_step=0.5, mask_depth=0.01, \
fourier = False,
only_one_peak = True)
vel_telluric = np.round(models[0].mu(), 2) # km/s
vel_telluric_err = np.round(models[0].emu(), 2) # km/s
#--- 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")
#--- Read lines with atomic data ------------------------------------------------
line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/moog_synth_good_for_params_all_extended.txt")
#line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_GES/width_synth_good_for_params_all_extended.txt")
#line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/moog_synth_good_for_params_all_extended.txt")
#line_regions_with_atomic_data = ispec.read_line_regions(ispec_dir + "/input/regions/47000_VALD/width_synth_good_for_params_all_extended.txt")
smoothed_star_spectrum = ispec.convolve_spectrum(star_spectrum, 2*to_resolution)
line_regions_with_atomic_data = ispec.adjust_linemasks(smoothed_star_spectrum, line_regions_with_atomic_data, max_margin=0.5)
#telluric_linelist_file = ispec_dir + "/input/linelists/CCF/Synth.Tellurics.500_1100nm/mask.lst"
#telluric_linelist = ispec.read_telluric_linelist(telluric_linelist_file, minimum_depth=0.01)
#vel_telluric = 17.79 # km/s
#telluric_linelist = None
#vel_telluric = None
#--- Fit the lines but do NOT cross-match with any atomic linelist since they already have that information
linemasks = ispec.fit_lines(line_regions_with_atomic_data, normalized_star_spectrum, star_continuum_model, \
atomic_linelist = None, \
max_atomic_wave_diff = 0.005, \
telluric_linelist = telluric_linelist, \
check_derivatives = False, \
vel_telluric = vel_telluric, discard_gaussian=False, \
smoothed_spectrum=None, \
discard_voigt=True, \
free_mu=True, crossmatch_with_mu=False, closest_match=False)
# Discard bad masks
flux_peak = normalized_star_spectrum['flux'][linemasks['peak']]
flux_base = normalized_star_spectrum['flux'][linemasks['base']]
flux_top = normalized_star_spectrum['flux'][linemasks['top']]
bad_mask = np.logical_or(linemasks['wave_peak'] <= linemasks['wave_base'], linemasks['wave_peak'] >= linemasks['wave_top'])
bad_mask = np.logical_or(bad_mask, flux_peak >= flux_base)
bad_mask = np.logical_or(bad_mask, flux_peak >= flux_top)
linemasks = linemasks[~bad_mask]
# Exclude lines with EW equal to zero
rejected_by_zero_ew = (linemasks['ew'] == 0)
linemasks = linemasks[~rejected_by_zero_ew]
# Exclude lines that may be affected by tellurics
rejected_by_telluric_line = (linemasks['telluric_wave_peak'] != 0)
linemasks = linemasks[~rejected_by_telluric_line]
if use_ares:
# Replace the measured equivalent widths by the ones computed by ARES
old_linemasks = linemasks.copy()
### Different rejection parameters (check ARES papers):
## - http://adsabs.harvard.edu/abs/2007A%26A...469..783S
## - http://adsabs.harvard.edu/abs/2015A%26A...577A..67S
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="0.995", tmp_dir=None, verbose=0)
#linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="3;5764,5766,6047,6052,6068,6076", tmp_dir=None, verbose=0)
snr = 50
linemasks = ispec.update_ew_with_ares(normalized_star_spectrum, linemasks, rejt="%s" % (snr), tmp_dir=None, verbose=0)
self.assertEqual(len(linemasks), 281)
self.assertAlmostEqual(linemasks['ew'][0], 68.62459244466727)
self.assertAlmostEqual(linemasks['ew'][-3], 46.23135207295078)
self.assertEqual(linemasks['element'][0], 'Fe 1')
self.assertEqual(linemasks['element'][-3], 'Si 1')
self.assertAlmostEqual(linemasks['loggf'][0], -1.028)
self.assertAlmostEqual(linemasks['loggf'][-3], -1.062)
except Exception as e:
print "Continuum file", filenames[
'continuum'], "has an incompatible format!"
sys.exit(2)
## Validations
if np.any((continuum['wave_top'] - continuum['wave_base']) < 0):
raise Exception(
"Continuum: wave_top cannot be smaller than wave_base")
else:
continuum = np.zeros((0, ),
dtype=[('wave_base', '<f8'), ('wave_top', '<f8')])
if filenames['lines'] != None:
try:
lines = ispec.read_line_regions(filenames['lines'])
except Exception as e:
print "Lines file", filenames[
'lines'], "has an incompatible format!"
sys.exit(2)
## Validations
if np.any((lines['wave_top'] - lines['wave_base']) < 0):
raise Exception("Lines: wave_top cannot be smaller than wave_base")
if np.any((lines['wave_top'] - lines['wave_peak']) < 0):
raise Exception("Lines: wave_top cannot be smaller than wave_peak")
if np.any((lines['wave_peak'] - lines['wave_base']) < 0):
raise Exception(
"Lines: wave_peak cannot be smaller than wave_base")
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