def test_dartmouth_basic(bands=['J']):
dar = Dartmouth_Isochrone(bands)
_basic_ic_checks(dar)
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 obs_to_starmodel(obs, iso=None):
""" Given an Observation, return a StarModel object """
if iso is None:
iso = Dartmouth_Isochrone()
mags = obs_to_mags(obs)
parallax = (obs.tgas_source.parallax, obs.tgas_source.parallax_error)
model = StarModel(iso, use_emcee=True, parallax=parallax, **mags)
model.set_bounds(mass=(0.01, 20),
feh=(-1, 1),
distance=(0, 300),
AV=(0, 1))
return model
def isochrones(name):
dar = Dartmouth_Isochrone()
Teff, logg, feh, vsini, vmag = parameters(name)
model = StarModel(
dar,
Teff=Teff,
feh=feh,
logg=logg,
V=vmag,
)
outfn = os.path.join(OUTPUTDIR, '{}_isochrones.hdf'.format(name))
print "performing isochrones analysis on {}".format(name)
model.fit(overwrite=True)
columns = 'Teff logg feh mass radius age distance'.split()
print "performing isochrones analysis on {}".format(name)
print model.samples[columns].quantile([0.15, 0.5, 0.85]).T.to_string()
model.save_hdf(outfn)
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
def __init__(self,
koi,
recalc=False,
use_JRowe=True,
trsig_kws=None,
tag=None,
starmodel_mcmc_kws=None,
**kwargs):
koi = koiname(koi)
#if saved popset exists, load
folder = os.path.join(KOI_FPPDIR, koi)
if tag is not None:
folder += '_{}'.format(tag)
if not os.path.exists(folder):
os.makedirs(folder)
if trsig_kws is None:
trsig_kws = {}
#first check if pickled signal is there to be loaded
trsigfile = os.path.join(folder, 'trsig.pkl')
if os.path.exists(trsigfile):
trsig = pickle.load(open(trsigfile, 'rb'))
else:
if use_JRowe:
trsig = JRowe_KeplerTransitSignal(koi, **trsig_kws)
else:
trsig = KeplerTransitSignal(koi, **trsig_kws)
popsetfile = os.path.join(folder, 'popset.h5')
if os.path.exists(popsetfile) and not recalc:
popset = PopulationSet(popsetfile, **kwargs)
else:
koinum = koiname(koi, koinum=True)
kepid = ku.DATA.ix[koi, 'kepid']
if 'mass' not in kwargs:
kwargs['mass'] = koi_propdist(koi, 'mass')
if 'radius' not in kwargs:
kwargs['radius'] = koi_propdist(koi, 'radius')
if 'feh' not in kwargs:
kwargs['feh'] = koi_propdist(koi, 'feh')
if 'age' not in kwargs:
try:
kwargs['age'] = koi_propdist(koi, 'age')
except:
kwargs['age'] = (9.7, 0.1) #default age
if 'Teff' not in kwargs:
kwargs['Teff'] = kicu.DATA.ix[kepid, 'teff']
if 'logg' not in kwargs:
kwargs['logg'] = kicu.DATA.ix[kepid, 'logg']
if 'rprs' not in kwargs:
if use_JRowe:
kwargs['rprs'] = trsig.rowefit.ix['RD1', 'val']
else:
kwargs['rprs'] = ku.DATA.ix[koi, 'koi_ror']
#if stellar properties are determined spectroscopically,
# fit stellar model
if 'starmodel' not in kwargs:
if re.match('SPE', kicu.DATA.ix[kepid, 'teff_prov']):
logging.info(
'Spectroscopically determined stellar properties.')
#first, see if there already is a starmodel to load
#fit star model
Teff = kicu.DATA.ix[kepid, 'teff']
e_Teff = kicu.DATA.ix[kepid, 'teff_err1']
logg = kicu.DATA.ix[kepid, 'logg']
e_logg = kicu.DATA.ix[kepid, 'logg_err1']
feh = kicu.DATA.ix[kepid, 'feh']
e_feh = kicu.DATA.ix[kepid, 'feh_err1']
logging.info(
'fitting StarModel (Teff=({},{}), logg=({},{}), feh=({},{}))...'
.format(Teff, e_Teff, logg, e_logg, feh, e_feh))
dar = Dartmouth_Isochrone()
starmodel = StarModel(dar,
Teff=(Teff, e_Teff),
logg=(logg, e_logg),
feh=(feh, e_feh))
if starmodel_mcmc_kws is None:
starmodel_mcmc_kws = {}
starmodel.fit_mcmc(**starmodel_mcmc_kws)
logging.info('Done.')
kwargs['starmodel'] = starmodel
if 'mags' not in kwargs:
kwargs['mags'] = ku.KICmags(koi)
if 'ra' not in kwargs:
kwargs['ra'], kwargs['dec'] = ku.radec(koi)
if 'period' not in kwargs:
kwargs['period'] = ku.DATA.ix[koi, 'koi_period']
if 'pl_kws' not in kwargs:
kwargs['pl_kws'] = {}
if 'fp_specific' not in kwargs['pl_kws']:
rp = kwargs['radius'].mu * kwargs['rprs'] * RSUN / REARTH
kwargs['pl_kws']['fp_specific'] = fp_fressin(rp)
#trilegal_filename = os.path.join(folder,'starfield.h5')
trilegal_filename = kepler_starfield_file(koi)
popset = PopulationSet(trilegal_filename=trilegal_filename,
**kwargs)
#popset.save_hdf('{}/popset.h5'.format(folder), overwrite=True)
lhoodcachefile = os.path.join(folder, 'lhoodcache.dat')
self.koi = koi
FPPCalculation.__init__(self, trsig, popset, folder=folder)
self.save()
self.apply_default_constraints()
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 get_isochrone_params(stars, modeldir, overwrite=False):
"""Fill out parameter table with values obtained from isochrone package
Args:
stars (pd.DataFrame): parameter table
modeldir (str): directory to save fitted models
overwrite (bool, optional): whether to use existing models or overwrite
Returns:
stars (pd.DataFrame): updated parameter table
"""
dar = Dartmouth_Isochrone()
num_stars = len(stars)
current_star = 1
for idx, row in stars.iterrows():
print("Getting isochrone parameters for star {0} of {1}".format(
current_star, num_stars))
current_star += 1
# get known stellar properties
lib_props = {}
for p in library.Library.STAR_PROPS:
if not np.isnan(row[p]):
# (value, uncertainty)
lib_props[p] = (row[p], row['u_' + p])
# if all properties are known, we don't need to use the model
if len(lib_props) == 6:
continue
if modeldir is None:
model = StarModel(dar, **lib_props)
model.fit(overwrite=True, verbose=False)
else:
# check if fitting has already been done
modelfile = os.path.join(modeldir,
"{0}_model.h5".format(row['cps_name']))
if os.path.exists(modelfile) and not overwrite:
model = StarModel.load_hdf(modelfile)
# otherwise perform the fit
else:
model = StarModel(dar, **lib_props)
model.fit(overwrite=True, verbose=False)
model.save_hdf(modelfile)
N_SIGMA = 2
MAX_PERCENTILE = 0.95
MIN_PERCENTILE = 0.05
# fill out unknown parameters
for p in library.Library.STAR_PROPS:
value = model.samples[p].quantile(0.5)
upper_bound = model.samples[p].quantile(MAX_PERCENTILE)
lower_bound = model.samples[p].quantile(MIN_PERCENTILE)
# If a property is already known, check for model consistency
if p in lib_props:
# check if 2-sigma bounds fail to overlap
if (row[p] + N_SIGMA * row['u_'+p]) < lower_bound \
or (row[p] - N_SIGMA * row['u_'+p]) > upper_bound:
warningstr = "Warning: Inconisistent {0} for star {1}\n"\
.format(p, row['cps_name'])
warningstr += "\tLibrary values: {0:.2f} +/- {1:.2f}\n"\
.format(row[p], row['u_'+p])
warningstr += "\tModel values: {0:.2f}, ".format(value)
warningstr += "{0:d}-sigma = ({1:.2f}, {2:.2f})\n".format(
N_SIGMA, lower_bound, upper_bound)
print(warningstr)
# Save error messages to file
errpath = os.path.join(modeldir, 'errors.txt')
with open(errpath, 'a') as f:
f.write(warningstr)
# Insert the unknown values if we don't already know them
else:
stars.loc[idx, p] = np.around(value, 2)
stars.loc[idx, 'u_'+p] = \
np.around((upper_bound - lower_bound) / 2, 2)
return stars
# useful links: # http://slittlefair.staff.shef.ac.uk/teaching/phy241/resources/plotting_isochrones.html # https://isochrones.readthedocs.io/en/latest/ # https://isochrones.readthedocs.io/en/latest/_modules/isochrones/isochrone.html #catalog_name = "./isochronetest_ngc7062.csv" #df = pd.read_csv(catalog_name) #g = df['phot_g_mean_mag'] #bp = df['phot_bp_mean_mag'] #rp = df['phot_rp_mean_mag'] #padoviso = Padova_Isochrone(bands=['B','V']) #padoviso = Padova_Isochrone() #mist = MIST_Isochrone() iso = Dartmouth_Isochrone(bands=['B', 'V']) #sys.exit(0) #print(padoviso.bands) #print(mist.radius(1.0, 9.7, 0.0)) #M/Msun, log10(age), Fe/H #print(mist.bands) #mass, age, feh, distance, AV = (0.95, 9.61, -0.2, 200, 0.2) #print(mist.mag['g'](mass, age, feh, distance, AV)) #print(iso.bands) #model = iso.isochrone(9.235) # log10 of the age #print(type(model))
def test_dartmouth_basic(bands=['z', 'B', 'W3', 'LSST_r', 'J', 'UK_J']):
dar = Dartmouth_Isochrone(bands)
_basic_ic_checks(dar)
from __future__ import print_function, division
import pandas as pd
import numpy as np
import logging
from scipy.stats import poisson
from numba import jit
from isochrones.dartmouth import Dartmouth_Isochrone
from .utils import draw_powerlaw
from .utils import get_duration, get_a, get_delta, get_pgeom
dar = Dartmouth_Isochrone()
#because
dar.radius(1,9.8,0.0)
R_EARTH = 0.009171 # in solar units
# Some default ranges
P_RANGE = (50, 300)
R_RANGE = (0.75, 20)
def sim_binaries(stars, fB=0.5, gamma=0.3,
qmin=0.1, minmass=None, band='Kepler', ic=dar):
"""
Generates binary companions to stars
import numpy as np
import emcee
from tqdm import tqdm
# Package
from comoving_rv.log import logger
from comoving_rv.db import Session, Base, db_connect
from comoving_rv.db.model import (Run, Observation, TGASSource, SimbadInfo,
GroupToObservations, SpectralLineInfo,
SpectralLineMeasurement, RVMeasurement)
from isochrones import StarModel
# from isochrones.mist import MIST_Isochrone
# iso = MIST_Isochrone() # interpolation issues with MIST isochrones
from isochrones.dartmouth import Dartmouth_Isochrone
iso = Dartmouth_Isochrone()
def main():
# TODO: bad, hard-coded...
# base_path = '/Volumes/ProjectData/gaia-comoving-followup/'
base_path = '../../data/'
db_path = path.join(base_path, 'db.sqlite')
engine = db_connect(db_path)
session = Session()
chain_path = path.abspath('./isochrone_chains')
os.makedirs(chain_path, exist_ok=True)
# Check out the bottom of "Color-magnitude diagram.ipynb":
interesting_group_ids = [1500, 1229, 1515]
from isochrones.dartmouth import Dartmouth_Isochrone
from isochrones.utils import addmags
import numpy as np
import pandas as pd
file = open('/tigress/np5/true_params.txt','a')
for n in range(6000,7000,1):
index = str(n)
file.write('test: ' + index + '\n')
dar = Dartmouth_Isochrone()
array = np.random.rand(2) + 0.5
if array[0] > array[1]:
M1 = array[1]
M2 = array[0]
else:
M1 = array[0]
M2 = array[1]
feh1,feh2 = 0.7*np.random.rand(2) - 0.5
random1, random2 = np.random.rand(2)
age_low, age_high = dar.agerange(M1,feh1)
age_low = max(age_low, dar.minage)
age_high = min(age_high, dar.maxage)
age_low = 10**age_low
age_high = 10**age_high
def main():
args = _parser()
path = os.path.expanduser('~/.SWEETCat/')
_sc = os.path.join(path, 'sweetcat.csv')
if os.path.isdir(path):
if not os.path.isfile(_sc):
print('Downloading SWEET-Cat...')
_download_sweetcat(_sc)
else:
os.mkdir(path)
print('%s Created' % path)
print('Downloading SWEET-Cat...')
_download_sweetcat(_sc)
df = _read_sweetcat(_sc)
if args.sweetcat:
df = df[df.source == True]
df['x'] = df[args.x]
df['y'] = df[args.y]
if (args.x == 'age') or (args.y == 'age') or (args.z == 'age'):
from isochrones.dartmouth import Dartmouth_Isochrone
dar = Dartmouth_Isochrone()
age = np.zeros(df.shape[0])
for i, (mass, feh) in enumerate(df[['mass', 'feh']].values):
tmp = dar.agerange(mass, feh)
age[i] = (10**(tmp[0]-9) + 10**(tmp[1]-9))/2
df['age'] = pd.Series(age)
if args.z:
if args.iz:
z = 1/df[args.z].values
else:
z = df[args.z].values
color = df[args.z].values
u = z[~np.isnan(z)]
size = (z-u.min())/(u.max()-u.min())*100
size[np.argmin(size)] = 10 # Be sure to show the "smallest" point
plt.scatter(df['x'], df['y'], c=color, s=size) #, cmap=cm.viridis)
else:
plt.scatter(df['x'], df['y'], s=40)
labels = {'teff': r'$T_\mathrm{eff}$ [K]',
'tefferr': r'$\sigma T_\mathrm{eff}$ [K]',
'logg': r'$\log(g)$ [cgs]',
'loggerr': r'$\sigma \log(g)$ [cgs]',
'logglc': r'$\log(g)$ [cgs]',
'logglcerr': r'$\sigma \log(g)$ [cgs]',
'feh': '[Fe/H]',
'feherr': r'$\sigma$ [Fe/H]',
'vt': r'$\xi_\mathrm{micro}$ [km/s]',
'vterr': r'$\sigma\xi_\mathrm{micro}$ [km/s]',
'lum': r'$L_\odot$',
'mass': r'$M_\odot$',
'masserr': r'$\sigma M_\odot$',
'radius': r'$R_\odot$',
'radiuserr': r'$\sigma R_\odot$',
'age': r'Age $[Gyr]$',
'par': r'$\pi$ [mas]',
'parerr': r'$\sigma \pi$ [mas]',
'vmag': 'V magnitude',
'vmagerr': r'$\sigma$ V magnitude'}
plt.xlabel(labels[args.x])
plt.ylabel(labels[args.y])
if args.z:
cbar = plt.colorbar()
cbar.set_label(labels[args.z])
if args.s:
sun = {'teff': 5777,
'tefferr': 1,
'logg': 4.44,
'loggerr': 0.01,
'feh': 0.00,
'feherr': 0.01,
'vt': 1.00,
'vterr': 0.01,
'lum': 1,
'mass': 1,
'masserr': 0.01,
'radius': 1,
'radiuserr': 0.01,
'age': 4.567}
plt.scatter(sun[args.x], sun[args.y], marker='*', s=200, alpha=0.8)
if args.ix:
plt.xlim(plt.xlim()[::-1])
if args.iy:
plt.ylim(plt.ylim()[::-1])
if args.lx:
plt.xscale('log')
df['x'] = np.log(df['x'])
if args.ly:
y1, y2 = plt.ylim()
plt.yscale('log')
plt.ylim(max(y1, 0.01), y2)
df['y'] = np.log(df['y'])
if args.l:
p = np.polyfit(df['x'], df['y'], deg=1)
print(' y=%.3f*x+%.3f' % (p[0], p[1]))
x1, x2 = df.x.min(), df.x.max()
yfit = np.poly1d(p)([x1, x2])
if args.lx and args.ly:
plt.plot(np.exp([x1, x2]), np.exp(yfit), '-k')
elif args.lx and not args.ly:
plt.plot(np.exp([x1, x2]), yfit, '-k')
elif not args.lx and args.ly:
plt.plot([x1, x2], np.exp(yfit), '-k')
else:
plt.plot([x1, x2], yfit, '-k')
plt.tight_layout()
plt.show()
def iso_age(teff, logg, feh):
dar = Dartmouth_Isochrone()
mod = StarModel(dar, Teff=(teff, 80), Logg=(logg, 0.10), Feh=(feh, 0.1))
logage, _, _ = mod.maxlike()
age = np.exp(logage)
return age