def test_mist_basic(bands='JHK'):
ic = MIST_Isochrone(bands)
_basic_ic_checks(ic)
assert np.isclose(ic.logg(632, 7.55, -1.75), 2.4117770214014103) # Grid point
assert np.isclose(ic.logg(355, 9.653, 0.0), 4.4124675)
assert np.isclose(ic.logg(700, 9.3, -0.03), 2.24831956)
def test_mist_basic(bands='JHK'):
ic = MIST_Isochrone(bands)
_basic_ic_checks(ic)
assert np.isclose(ic.logg(632, 7.55, -1.75), 2.4117770214014103) # Grid point
assert np.isclose(ic.logg(355, 9.653, 0.0), 4.4124675)
assert np.isclose(ic.logg(700, 9.3, -0.03), 2.24831956)
def test_mist_basic(bands=['J']):
ic = MIST_Isochrone(bands, version='1.0')
ic2 = MIST_Isochrone(bands + ['TESS', 'BP', 'RP'], version='1.1')
_basic_ic_checks(ic)
_basic_ic_checks(ic2)
assert np.isclose(ic.radius(1.0, 9.5, 0.0), 0.9764494078461442)
assert np.isclose(ic.radius(1.01, 9.72, 0.02), 1.0671791635014685)
assert np.isclose(ic.radius(1.21, 9.38, 0.11), 1.2963342261673843)
assert np.isclose(ic.radius(0.61, 9.89, -0.22), 0.5873830516268735)
assert np.isclose(ic2.radius(1.0, 9.5, 0.0), 0.9765234978729515)
assert np.isclose(ic2.radius(1.01, 9.72, 0.02), 1.0671845393364638)
assert np.isclose(ic2.radius(1.21, 9.38, 0.11), 1.2963536270911573)
assert np.isclose(ic2.radius(0.61, 9.89, -0.22), 0.5873849015685695)
def get_ichrone(models,
bands=None,
default=False,
tracks=False,
basic=False,
**kwargs):
"""Gets Isochrone Object by name, or type, with the right bands
If `default` is `True`, then will set bands
to be the union of bands and default_bands
"""
if not bands:
bands = None
if isinstance(models, ModelGridInterpolator):
return models
if type(models) is type(type):
ichrone = models(bands)
elif models == 'mist':
if tracks:
from isochrones.mist import MIST_EvolutionTrack
ichrone = MIST_EvolutionTrack(bands=bands, **kwargs)
else:
if basic:
from isochrones.mist import MISTBasic_Isochrone
ichrone = MISTBasic_Isochrone(bands=bands, **kwargs)
else:
from isochrones.mist import MIST_Isochrone
ichrone = MIST_Isochrone(bands=bands, **kwargs)
else:
raise ValueError('Unknown stellar models: {}'.format(models))
return ichrone
def HRD_plot(teff, abs_gmag):
# dar = Dartmouth_Isochrone()
mist = MIST_Isochrone()
iso_300 = mist.isochrone(age=np.log10(300e6), feh=0.0, AV=0.0)
counts, xbins, ybins = np.histogram2d(teff, abs_gmag, bins=100)
# Make temperature cuts
lower_lim, upper_lim = 3200, 8000
m = (lower_lim < teff) * (teff < upper_lim)
plt.clf()
# Plot points + contours
plt.scatter(teff[m], abs_gmag[m], c=teff[m], s=2, cmap="viridis_r",
zorder=0)
plt.colorbar(label="$T_{\mathrm{eff}}$")
plt.contour(counts.transpose(),
extent=[xbins.min(), xbins.max(), ybins.min(), ybins.max()],
linewidths=.5, colors='white', linestyles='solid')
# Plot isochrones
plt.plot(iso_300.Teff[:100], iso_300.G_mag[:100]+1, "k", lw=.5)
plt.plot(iso_300.Teff[:100], iso_300.G_mag[:100]-1, "k", lw=.5)
# Select stars between isochrones
fup = interp1d(iso_300.Teff[:100], iso_300.G_mag[:100] + 1)
flo = interp1d(iso_300.Teff[:100], iso_300.G_mag[:100] - 1)
inds = []
for i, G in enumerate(abs_gmag[m]):
upper_G_at_this_teff = fup(teff[m][i])
lower_G_at_this_teff = flo(teff[m][i])
if (lower_G_at_this_teff < G) and (G < upper_G_at_this_teff):
inds.append(i)
# plt.scatter(teff[m][inds], abs_gmag[m][inds], c="k", s=2, zorder=1)
plt.xlabel("$T_{\mathrm{eff}}$")
plt.ylabel("$M_G$")
plt.ylim(10, -7)
plt.xlim(upper_lim, lower_lim)
plt.subplots_adjust(left=.15, bottom=.15)
plt.savefig("HRD")
plt.savefig("HRD.pdf")
return m, inds
def test_mist_basic(bands=['G','B','V','J','H','K','W1','W2','W3']):
ic = MIST_Isochrone(bands)
_basic_ic_checks(ic)
print('{} ({})'.format(ic.radius(1.0, 9.5, 0.0), 0.9764494078461442))
assert np.isclose(ic.radius(1.0, 9.5, 0.0), 0.9764494078461442)
assert np.isclose(ic.radius(1.01, 9.72, 0.02), 1.0671791635014685)
assert np.isclose(ic.radius(1.21, 9.38, 0.11), 1.2836469028034225)
assert np.isclose(ic.radius(0.61, 9.89, -0.22), 0.59475269177846402)
def get_ichrone(models, bands=None, default=False, **kwargs):
"""Gets Isochrone Object by name, or type, with the right bands
If `default` is `True`, then will set bands
to be the union of bands and default_bands
"""
if isinstance(models, Isochrone):
return models
def actual(bands, ictype):
if bands is None:
return list(ictype.default_bands)
elif default:
return list(set(bands).union(set(ictype.default_bands)))
else:
return bands
if type(models) is type(type):
ichrone = models(actual(bands, models))
elif models == 'dartmouth':
from isochrones.dartmouth import Dartmouth_Isochrone
ichrone = Dartmouth_Isochrone(bands=actual(bands, Dartmouth_Isochrone),
**kwargs)
elif models == 'dartmouthfast':
from isochrones.dartmouth import Dartmouth_FastIsochrone
ichrone = Dartmouth_FastIsochrone(bands=actual(
bands, Dartmouth_FastIsochrone),
**kwargs)
elif models == 'mist':
from isochrones.mist import MIST_Isochrone
ichrone = MIST_Isochrone(bands=actual(bands, MIST_Isochrone), **kwargs)
elif models == 'padova':
from isochrones.padova import Padova_Isochrone
ichrone = Padova_Isochrone(bands=actual(bands, Padova_Isochrone),
**kwargs)
elif models == 'basti':
from isochrones.basti import Basti_Isochrone
ichrone = Basti_Isochrone(bands=actual(bands, Basti_Isochrone),
**kwargs)
else:
raise ValueError('Unknown stellar models: {}'.format(models))
return ichrone
#!/usr/bin/python3
import os
import sys
import numpy as np
import pandas as pd
import h5py
import tqdm
import emcee
from isochrones.mist import MIST_Isochrone
from isochrones import StarModel
mist = MIST_Isochrone()
import stardate as sd
from stardate.lhf import lnprob
from multiprocessing import Pool
# Necessary to add cwd to path when script run
# by SLURM (since it executes a copy)
sys.path.append(os.getcwd())
# def infer_stellar_age(row):
# df = row[1]
def infer_stellar_age(df):
# Small observational uncertainties are needed (even though the stars
# weren't simulated with any) in order to get a good fit.
}
labels = {
'G': r'$G$',
'J': r'$J$',
'H': r'$H$',
'K': r'$K$',
'PanSTARRS_g': r'$g_\mathrm{PS}$',
'PanSTARRS_r': r'$r_\mathrm{PS}$',
'PanSTARRS_i': r'$i_\mathrm{PS}$',
'PanSTARRS_z': r'$z_\mathrm{PS}$',
'PanSTARRS_y': r'$y_\mathrm{PS}$',
}
mist = MIST_Isochrone(bands=[
'G', 'J', 'H', 'K', 'PanSTARRS_g', 'PanSTARRS_r', 'PanSTARRS_i',
'PanSTARRS_z', 'PanSTARRS_y'
])
# MIST ages are in 0.05 dex increment, but the values are not exact.
# So if I query `mist.df.loc[0, 8.7]` for feh=0, age=8.7 it will incur
# index not found error because the actual value is 8.7000...1, which is kind of stupid.
def get_isodf(feh, logage):
"""Get sub-dataframe for given feh and logage"""
iage = np.abs(mist.ages - logage).argmin()
return mist.df.loc[feh, mist.ages[iage]]
def plotcmd_mist_isochrones(band1,
band2,
feh,
def main(index, overwrite=False):
# First make sure paths exist:
# os.makedirs('../cache', exist_ok=True)
# os.makedirs('../plots/isochrones', exist_ok=True)
# Load the DECam photometry
decam = load_data('../data/decam_apw.fits')
iso = MIST_Isochrone(['PanSTARRS_g', 'PanSTARRS_i', 'SkyMapper_u'])
row = decam[index]
name = 'lmcla-{0}-'.format(row['index'])
model_file = '../cache/starmodels-{0}.hdf5'.format(str(row['index']))
if path.exists(model_file) and not overwrite:
print('skipping {0} - already exists'.format(name))
sys.exit(0)
# This is our "anchor star": it was identified as being near the turnoff,
# bright, and positionally consistent with being in the LA cluster:
j1, = np.where(decam['index'] == 24365)[0]
j2 = index
if j1 == j2:
print('skipping anchor-anchor pair')
sys.exit(0)
# To fit pairs as resolved binaries, we have to construct the observation
# tree manually:
tree = ObservationTree()
for b in ['PanSTARRS_g', 'PanSTARRS_i', 'SkyMapper_u']:
survey, band = b.split('_')
if band == 'u' and decam[band.capitalize() + 'MAG'][j2] > 21:
extra_s = 0.2
else:
extra_s = 0.005
o = Observation(survey, b, 1.)
s0 = Source(
decam[band.capitalize() + 'MAG'][j1],
np.sqrt(0.005**2 + decam[band.capitalize() + 'ERR'][j1]**2))
s1 = Source(decam[band.capitalize() + 'MAG'][j2],
np.sqrt(extra_s**2 +
decam[band.capitalize() + 'ERR'][j2]**2),
separation=100.)
o.add_source(s0)
o.add_source(s1)
tree.add_observation(o)
model = StarModel(ic=iso, obs=tree, N=[1, 2])
# model = StarModel(ic=iso, obs=tree)
print('setting priors')
dist_bounds = [1 * 1e3, 100 * 1e3] # pc
# model._priors['distance'] = FlatPrior(dist_bounds)
model._priors['distance'] = GaussianPrior(30 * 1e3,
10 * 1e3,
bounds=dist_bounds)
model.set_bounds(distance=dist_bounds) # 1 to 100 kpc
feh_bounds = (-2., 0.5)
model.set_bounds(feh=feh_bounds)
# model._priors['feh'] = FlatPrior(feh_bounds)
model._priors['feh'] = GaussianPrior(-1.1, 0.5, bounds=feh_bounds)
AV_bounds = (0, 1)
model.set_bounds(AV=AV_bounds)
model._priors['AV'] = PowerLawPrior(-1.1, (1e-3, 1))
# model._priors['AV'] = GaussianPrior(0.2, 0.1, bounds=AV_bounds)
age_bounds = (7, 9.5)
model.set_bounds(age=age_bounds)
# model._priors['age'] = GaussianPrior(8, 0.5, bounds=age_bounds)
model._priors['age'] = FlatPrior(age_bounds)
print('sampling star {0}'.format(row['index']))
model.fit_multinest(basename=name,
refit=overwrite,
overwrite=overwrite,
n_live_points=2048)
# model.fit_mcmc(nwalkers=nwalkers,
# p0=np.array([350., 8., -0.5, 30000., 0.1]),
# nburn=1024, niter=2048)
model.save_hdf(model_file)
fig = model.corner_physical()
fig.savefig('../plots/isochrones/{0}-physical.png'.format(row['index']),
dpi=200)
plt.close(fig)
fig = model.corner_observed()
fig.savefig('../plots/isochrones/{0}-observed.png'.format(row['index']),
dpi=200)
plt.close(fig)
# model._samples = model.samples[::1024]
# model.save_hdf(sm_model_file)
sys.exit(0)
import tempfile
import os, shutil, glob
import logging
import numpy as np
from isochrones.dartmouth import Dartmouth_Isochrone
from isochrones.mist import MIST_Isochrone
from isochrones import StarModel, get_ichrone
DAR = Dartmouth_Isochrone()
MIST = MIST_Isochrone()
def test_dartmouth_basic(bands=['z', 'B', 'W3', 'LSST_r', 'J', 'UK_J']):
dar = Dartmouth_Isochrone(bands)
_basic_ic_checks(dar)
print('{} ({})'.format(dar.radius(1., 9.5, 0.0), 0.95409593462955189))
assert np.isclose(dar.radius(1., 9.5, 0.0), 0.95409593462955189)
assert np.isclose(dar.radius(1.01, 9.72, 0.02), 1.0435559519926865)
assert np.isclose(dar.radius(1.21, 9.38, 0.11), 1.2762022494652547)
assert np.isclose(dar.radius(0.61, 9.89, -0.22), 0.5964945760402941)
def test_mist_basic(bands=['G','B','V','J','H','K','W1','W2','W3']):
ic = MIST_Isochrone(bands)
_basic_ic_checks(ic)
print('{} ({})'.format(ic.radius(1.0, 9.5, 0.0), 0.9764494078461442))
assert np.isclose(ic.radius(1.0, 9.5, 0.0), 0.9764494078461442)
assert np.isclose(ic.radius(1.01, 9.72, 0.02), 1.0671791635014685)
assert np.isclose(ic.radius(1.21, 9.38, 0.11), 1.2836469028034225)
assert np.isclose(ic.radius(0.61, 9.89, -0.22), 0.59475269177846402)
def __init__(self, bands, age, Av, distance, feh=0.001, maxm=18.25, **kwargs):
super(IsochromeLayer, self).__init__(**kwargs)
from isochrones.mist import MIST_Isochrone
MIST = MIST_Isochrone(bands)
iso = MIST.isochrone(age=np.log10(age), feh=feh, AV=Av, distance=distance, maxm=maxm)
def test_mist_basic(bands=['G', 'B', 'V', 'J', 'H', 'K', 'W1', 'W2', 'W3']):
ic = MIST_Isochrone(bands)
_basic_ic_checks(ic)
def fit_star(star, verbose=False):
output_filename = "{0}.h5".format(star.kepid)
logging.info("Output filename: {0}".format(output_filename))
if os.path.exists(output_filename):
return
time.sleep(30)
return
strt = time.time()
# The KIC parameters
mean_log_mass = np.log(star.mass)
sigma_log_mass = (np.log(star.mass + star.mass_err1) -
np.log(star.mass + star.mass_err2)
) # double the kic value
mean_feh = star.feh
sigma_feh = star.feh_err1 - star.feh_err2 # double the kic value
min_distance, max_distance = 0.0, 3000.0
# Other bands
other_bands = dict()
if np.isfinite(star.tgas_w1gmag):
other_bands = dict(
W1=(star.tgas_w1gmag, star.tgas_w1gmag_error),
W2=(star.tgas_w2gmag, star.tgas_w2gmag_error),
W3=(star.tgas_w3gmag, star.tgas_w3gmag_error),
)
if np.isfinite(star.tgas_Vmag):
other_bands["V"] = (star.tgas_Vmag, star.tgas_e_Vmag)
if np.isfinite(star.tgas_Bmag):
other_bands["B"] = (star.tgas_Bmag, star.tgas_e_Bmag)
if np.isfinite(star.tgas_gpmag):
other_bands["g"] = (star.tgas_gpmag, star.tgas_e_gpmag)
if np.isfinite(star.tgas_rpmag):
other_bands["r"] = (star.tgas_rpmag, star.tgas_e_rpmag)
if np.isfinite(star.tgas_ipmag):
other_bands["i"] = (star.tgas_ipmag, star.tgas_e_ipmag)
# Build the model
mist = MIST_Isochrone()
mod = StarModel(mist,
J=(star.jmag, star.jmag_err),
H=(star.hmag, star.hmag_err),
K=(star.kmag, star.kmag_err),
parallax=(star.tgas_parallax, star.tgas_parallax_error),
**other_bands)
# Initialize
nwalkers = 500
ndim = 5
lnpost_init = -np.inf + np.zeros(nwalkers)
coords_init = np.empty((nwalkers, ndim))
m = ~np.isfinite(lnpost_init)
while np.any(m):
K = m.sum()
# Mass
coords_init[m, 0] = np.exp(mean_log_mass +
sigma_log_mass * np.random.randn(K))
# Age
u = np.random.rand(K)
coords_init[m,
1] = np.log((np.exp(mist.maxage) - np.exp(mist.minage)) *
u + np.exp(mist.minage))
# Fe/H
coords_init[m, 2] = mean_feh + sigma_feh * np.random.randn(K)
# Distance
u = np.random.rand(K)
coords_init[m, 3] = (u * (max_distance**3 - min_distance**3) +
min_distance**3)**(1. / 3)
# Av
coords_init[m, 4] = np.random.rand(K)
lnpost_init[m] = np.array(list(map(mod.lnpost, coords_init[m])))
m = ~np.isfinite(lnpost_init)
class ICModel(emcee3.Model):
def compute_log_prior(self, state):
state.log_prior = mod.lnprior(state.coords)
return state
def compute_log_likelihood(self, state):
state.log_likelihood = mod.lnlike(state.coords)
return state
sampler = emcee3.Sampler(emcee3.moves.KDEMove())
ensemble = emcee3.Ensemble(ICModel(), coords_init)
chunksize = 200
targetn = 3
for iteration in range(100):
if verbose:
print("Iteration {0}...".format(iteration + 1))
sampler.run(ensemble, chunksize, progress=verbose)
mu = np.mean(sampler.get_coords(), axis=1)
try:
tau = emcee3.autocorr.integrated_time(mu, c=1)
except emcee3.autocorr.AutocorrError:
continue
tau_max = tau.max()
neff = ((iteration + 1) * chunksize / tau_max - 2.0)
if verbose:
print("Maximum autocorrelation time: {0}".format(tau_max))
print("N_eff: {0}\n".format(neff * nwalkers))
if neff > targetn:
break
burnin = int(2 * tau_max)
ntot = 5000
if verbose:
print("Discarding {0} samples for burn-in".format(burnin))
print("Randomly choosing {0} samples".format(ntot))
samples = sampler.get_coords(flat=True, discard=burnin)
total_samples = len(total_samples)
inds = np.random.choice(np.arange(len(samples)), size=ntot, replace=False)
samples = samples[inds]
fit_parameters = np.empty(len(samples),
dtype=[
("mass", float),
("log10_age", float),
("feh", float),
("distance", float),
("av", float),
])
computed_parameters = np.empty(len(samples),
dtype=[
("radius", float),
("teff", float),
("logg", float),
])
if verbose:
prog = tqdm.tqdm
else:
prog = lambda f, *args, **kwargs: f
for i, p in prog(enumerate(samples), total=len(samples)):
ic = mod.ic(*p)
fit_parameters[i] = p
computed_parameters[i] = (ic["radius"], ic["Teff"], ic["logg"])
total_time = time.time() - strt
logging.info("emcee3 took {0} sec".format(total_time))
with h5py.File(output_filename, "w") as f:
f.attrs["kepid"] = int(star.kepid)
f.attrs["neff"] = neff * nwalkers
f.attrs["runtime"] = total_time
f.create_dataset("fit_parameters", data=fit_parameters)
f.create_dataset("computed_parameters", data=computed_parameters)
# Plot
fig = corner.corner(samples)
fig.savefig("corner-{0}.png".format(star.kepid))
plt.close(fig)
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from tqdm import tqdm, trange
import emcee
import read_mist_models
from isochrones.mist import MIST_Isochrone
from isochrones import StarModel
from stardate.lhf import gyro_model_rossby, gyro_model, sigma, calc_rossby_number
bands = ["B", "V", "J", "H", "K", "BP", "RP", "G"]
mist = MIST_Isochrone(bands)
mist.initialize()
def color_err(c):
c_err = np.zeros(len(c))
bright = c < 13
medium = (13 < c) * (c < 17)
faint = 17 <= c
c_err[bright] = np.ones(len(c_err[bright])) * .002
c_err[medium] = np.ones(len(c_err[medium])) * .01
c_err[faint] = np.ones(len(c_err[faint])) * .2
return c_err
def photometric_noise(G, bp, rp):
"""
Calculates the noise on Gaia G, bp, rp and parallax.
def get_isochrone(logage, feh):
"""Retrieve isochrone for given age and feh."""
mist = MIST_Isochrone()
iso = mist.isochrone(logage, feh)
return iso