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import Gaia
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@timothydmorton
timothydmorton committed May 11, 2018
1 parent ea324e1 commit d954786
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Showing 4 changed files with 68 additions and 57 deletions.
106 changes: 52 additions & 54 deletions isochrones/isochrone.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ def get_ichrone(models, bands=None, default=True):
"""
if isinstance(models, Isochrone):
return models

def actual(bands, ictype):
if default:
if bands is None:
Expand Down Expand Up @@ -82,13 +82,13 @@ class Isochrone(object):
Array of initial mass values [msun].
:type m_ini: array-like
:param age:
:param age:
log10(age) [yr]
:param feh:
Metallicity [dex]
:param m_act:
:param m_act:
Actual mass; same as m_ini if mass loss not implemented [msun]
:param logL:
Expand All @@ -100,10 +100,10 @@ class Isochrone(object):
:param logg:
log10(surface gravity) [cgs]
:param mags:
:param mags:
Dictionary of absolute magnitudes in different bands
:type mags: ``dict``
:param tri:
Triangulation object used
to initialize the interpolation functions.
Expand All @@ -115,7 +115,7 @@ class Isochrone(object):
:param minage,maxage:
If desired, a minimum or maximum age can be manually entered.
"""
def __init__(self,m_ini,age,feh,m_act,logL,Teff,logg,mags,tri=None,
minage=None, maxage=None, ext_table=False):
Expand Down Expand Up @@ -221,7 +221,7 @@ def nu_max(self, *args):
reference: https://arxiv.org/pdf/1312.3853v1.pdf, Eq (3)
"""
return 3120.* (self.mass(*args) /
return 3120.* (self.mass(*args) /
(self.radius(*args)**2 * np.sqrt(self.Teff(*args)/5777.)))

def _mag_fn(self, band):
Expand All @@ -239,7 +239,7 @@ def fn(mass, age, feh, distance=10, AV=0.0, x_ext=0., ext_table=self.ext_table):
return fn


def __call__(self, mass, age, feh,
def __call__(self, mass, age, feh,
distance=None, AV=0.0,
return_df=True, bands=None):
"""
Expand All @@ -263,12 +263,14 @@ def __call__(self, mass, age, feh,
:param bands: (optional)
List of photometric bands in which to return magnitudes.
Must be subset of ``self.bands``. If not set, then will
default to returning all available bands.
default to returning all available bands.
:return:
Either a :class:`pandas.DataFrame` or a dictionary containing
model values evaluated at input points.
"""
# Broadcast inputs to the same shape
mass, age, feh = [np.array(a) for a in np.broadcast_arrays(mass, age, feh)]
args = (mass, age, feh)
Ms = self.mass(*args)*1
Rs = self.radius(*args)*1
Expand All @@ -285,10 +287,10 @@ def __call__(self, mass, age, feh,
# for band in mags:
# A = AV*EXTINCTION[band]
# mags[band] = mags[band] + dm + A


props = {'age':age,'mass':Ms,'radius':Rs,'logL':logLs,
'logg':loggs,'Teff':Teffs,'mag':mags}
'logg':loggs,'Teff':Teffs,'mag':mags}

if not return_df:
return props
Expand All @@ -300,10 +302,7 @@ def __call__(self, mass, age, feh,
d['{}_mag'.format(m)] = props['mag'][m]
else:
d[key] = props[key]
try:
df = pd.DataFrame(d)
except ValueError:
df = pd.DataFrame(d, index=[0])
df = pd.DataFrame(d)
return df

def agerange(self, m, feh=0.0):
Expand All @@ -320,28 +319,28 @@ def evtrack(self,m,feh=0.0,minage=None,maxage=None,dage=0.02,
"""
Returns evolution track for a single initial mass and feh.
:param m:
:param m:
Initial mass of desired evolution track.
:param feh: (optional)
:param feh: (optional)
Metallicity of desired track. Default = 0.0 (solar)
:param minage, maxage: (optional)
Minimum and maximum log(age) of desired track. Will default
to min and max age of model isochrones.
to min and max age of model isochrones.
:param dage: (optional)
Spacing in log(age) at which to evaluate models. Default = 0.02
:param return_df: (optional)
Whether to return a ``DataFrame`` or dicionary. Default is ``True``.
:return:
Either a :class:`pandas.DataFrame` or dictionary
representing the evolution
track---fixed mass, sampled at chosen range of ages.
"""
if minage is None:
minage = self.minage
Expand Down Expand Up @@ -374,13 +373,13 @@ def evtrack(self,m,feh=0.0,minage=None,maxage=None,dage=0.02,
df = pd.DataFrame(d, index=[0])
return df


def isochrone(self,age,feh=0.0,minm=None,maxm=None,dm=0.02,
return_df=True,distance=None,AV=0.0):
"""
Returns stellar models at constant age and feh, for a range of masses
:param age:
:param age:
log10(age) of desired isochrone.
:param feh: (optional)
Expand All @@ -394,17 +393,17 @@ def isochrone(self,age,feh=0.0,minm=None,maxm=None,dm=0.02,
:param return_df: (optional)
Whether to return a :class:``pandas.DataFrame`` or dictionary. Default is ``True``.
:param distance:
Distance in pc. If passed, then mags will be converted to
apparent mags based on distance (and ``AV``).
:param AV:
V-band extinction (magnitudes).
V-band extinction (magnitudes).
:return:
:class:`pandas.DataFrame` or dictionary containing results.
"""
if minm is None:
minm = self.minmass
Expand All @@ -428,8 +427,8 @@ def isochrone(self,age,feh=0.0,minm=None,maxm=None,dm=0.02,
mags[band] = mags[band] + dm + A

props = {'M':Ms,'R':Rs,'logL':logLs,'logg':loggs,
'Teff':Teffs,'mag':mags}
'Teff':Teffs,'mag':mags}

if not return_df:
return props
else:
Expand All @@ -445,7 +444,7 @@ def isochrone(self,age,feh=0.0,minm=None,maxm=None,dm=0.02,
except ValueError:
df = pd.DataFrame(d, index=[0])
return df

def random_points(self,n,minmass=None,maxmass=None,
minage=None,maxage=None,
minfeh=None,maxfeh=None):
Expand All @@ -464,7 +463,7 @@ def random_points(self,n,minmass=None,maxmass=None,
:param minfehs, maxfeh: (optional)
Desired allowed range. Default is feh range of ``self``.
:return:
:class:`np.ndarray` arrays of randomly selected mass, log10(age),
and feh values
Expand Down Expand Up @@ -521,7 +520,7 @@ def __init__(self, ic, band, icol):
if self.ext_table:
self.AAV = EXTINCTION[self.band]
else:
self.AAV = ext(LAMBDA_EFF[self.band])
self.AAV = ext(LAMBDA_EFF[self.band])

def __call__(self, mass, age, feh, distance=10, AV=0.0, x_ext=None, ext_table=False):
if x_ext is not None:
Expand All @@ -533,7 +532,7 @@ def __call__(self, mass, age, feh, distance=10, AV=0.0, x_ext=None, ext_table=Fa
if ext_table:
AAV = EXTINCTION[self.band]
else:
AAV = ext(LAMBDA_EFF[self.band])
AAV = ext(LAMBDA_EFF[self.band])
else:
AAV = self.AAV

Expand All @@ -545,15 +544,15 @@ def __call__(self, mass, age, feh, distance=10, AV=0.0, x_ext=None, ext_table=Fa
class FastIsochrone(Isochrone):
"""Alternative isochrone implementation for large grids, faster likelihoods
This implementation allows faster point interpolations than
This implementation allows faster point interpolations than
the triangulation method in the base :class:`Isochrone` class;
however, for simulating large populations (passing arrays of parameters
at a time), the base :class:`Isochrone` is still faster. This is
also the go-to implementation for grids that are too large to make the
at a time), the base :class:`Isochrone` is still faster. This is
also the go-to implementation for grids that are too large to make the
Delaunay method feasible (e.g., significantly over 100,000 points in the grid.)
However, edge effects might be a bit more problematic here than in the base class,
meaning fitting very evolved stars might be an issue. Also, don't trust this subclass
meaning fitting very evolved stars might be an issue. Also, don't trust this subclass
for the :function:`Isochrone.agerange` function, for the same reason.
Subclasses must set the appropriate attributes, and then things should work.
Expand Down Expand Up @@ -581,7 +580,7 @@ def __init__(self, bands=None, x_ext=0., ext_table=False, debug=False):
self.ext_table = ext_table
self.debug = debug


self._fehs = None
self._ages = None
self._Nfeh = None
Expand All @@ -593,7 +592,7 @@ def __init__(self, bands=None, x_ext=0., ext_table=False, debug=False):
self._maxmass = None
self._minfeh = None
self._maxfeh = None

n_common_cols = len(self.modelgrid.common_columns)
self._mag_cols = {b:n_common_cols+i for i,b in enumerate(self.bands)}
self.mag = {b: MagFunction(self, b, i)
Expand All @@ -602,7 +601,7 @@ def __init__(self, bands=None, x_ext=0., ext_table=False, debug=False):
#organized array
self._grid = None
self._grid_Ns = None

def _initialize(self):
for attr in ['df','Ncols','fehs','ages','Nfeh','Nage',
'minage','maxage','minfeh','maxfeh','minmass','maxmass']:
Expand All @@ -614,17 +613,17 @@ def df(self):
if self._df is None:
self._df = self.modelgrid(self.bands).df
return self._df

@property
def Ncols(self):
return self.df.shape[1]

@property
def fehs(self):
if self._fehs is None:
self._fehs = self.df.iloc[:, self.feh_col].unique()
return self._fehs

@property
def ages(self):
if self._ages is None:
Expand All @@ -642,13 +641,13 @@ def Nage(self):
if self._Nage is None:
self._Nage = len(self.ages)
return self._Nage

@property
def minage(self):
if self._minage is None:
self._minage = self.ages.min()
return self._minage

@property
def maxage(self):
if self._maxage is None:
Expand All @@ -660,7 +659,7 @@ def minfeh(self):
if self._minfeh is None:
self._minfeh = self.fehs.min()
return self._minfeh

@property
def maxfeh(self):
if self._maxfeh is None:
Expand All @@ -672,12 +671,12 @@ def minmass(self):
if self._minmass is None:
self._minmass = self.df.iloc[:, self.mass_col].min()
return self._minmass

@property
def maxmass(self):
if self._maxmass is None:
self._maxmass = self.df.iloc[:, self.mass_col].max()
return self._maxmass
return self._maxmass

def logTeff(self, mass, age, feh):
return self.interp_value(mass, age, feh, self.loggTeff_col)
Expand All @@ -699,16 +698,16 @@ def grid(self):
if self._grid is None:
self._make_grid()
return self._grid

@property
def grid_Ns(self):
if self._grid_Ns is None:
self._make_grid()
return self._grid_Ns

@property
def _npz_filename(self):
return os.path.join(ISOCHRONES, self.name, '{}.npz'.format('-'.join(self.bands)))
return os.path.join(ISOCHRONES, self.name, '{}.npz'.format('-'.join(self.bands)))

def _make_grid(self, recalc=False):
# Read from file if available.
Expand All @@ -718,7 +717,7 @@ def _make_grid(self, recalc=False):
self._grid_Ns = d['grid_Ns']
else:
df_list = [[self.df.ix[f,a] for f in self.fehs] for a in self.ages]
lens = np.array([[len(df_list[i][j]) for j in range(self.Nfeh)]
lens = np.array([[len(df_list[i][j]) for j in range(self.Nfeh)]
for i in range(self.Nage)]).T #just because
data = np.zeros((self.Nfeh, self.Nage, lens.max(), self.Ncols))

Expand All @@ -731,7 +730,7 @@ def _make_grid(self, recalc=False):
np.savez(self._npz_filename, grid=data, grid_Ns=lens)
self._grid = data
self._grid_Ns = lens

def interp_value(self, mass, age, feh, icol): # 4 is log_g
if self._ages is None:
self._initialize()
Expand All @@ -752,4 +751,3 @@ def interp_value(self, mass, age, feh, icol): # 4 is log_g
return interp_values(mass, age, feh, icol,
self.grid, self.mass_col,
self.ages, self.fehs, self.grid_Ns)

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