def from_ini(cls, folder='.',
ini_file='fpp.ini', recalc=False, refit_trap=False,
star_ini_file='star.ini', ichrone=DARTMOUTH,
**kwargs):
"""
To enable simple usage, initializes a FPPCalculation from a .ini file
By default, a file called ``fpp.ini`` will be looked for in the
current folder. Also present must be a ``star.ini`` file that
contains the observed properties of the target star.
``fpp.ini`` must be of the following form::
name = k2oi
ra = 11:30:14.510
dec = +07:35:18.21
period = 32.988 #days
rprs = 0.0534 #Rp/Rstar
photfile = lc_k2oi.csv
[constraints]
maxrad = 10 #exclusion radius [arcsec]
secthresh = 0.001 #maximum allowed secondary signal depth
#This variable defines contrast curves
#ccfiles = Keck_J.cc, Lick_J.cc
Photfile must be a text file with columns ``(days_from_midtransit,
flux, flux_err)``. Both whitespace- and comma-delimited
will be tried, using ``np.loadtxt``. Photfile need not be there
if there is a pickled :class:`TransitSignal` saved in the same
directory as ``ini_file``, named ``trsig.pkl`` (or another name
as defined by ``trsig`` keyword in ``.ini`` file).
``star.ini`` should look something like the following::
B = 15.005, 0.06
V = 13.496, 0.05
g = 14.223, 0.05
r = 12.858, 0.04
i = 11.661, 0.08
J = 9.763, 0.03
H = 9.135, 0.03
K = 8.899, 0.02
W1 = 8.769, 0.023
W2 = 8.668, 0.02
W3 = 8.552, 0.025
Kepler = 12.473
#Teff = 3503, 80
#feh = 0.09, 0.09
#logg = 4.89, 0.1
Any star properties can be defined; if errors are included
then they will be used in the :class:`isochrones.StarModel`
MCMC fit.
Spectroscopic parameters (``Teff, feh, logg``) are optional.
If included, then they will also be included in
:class:`isochrones.StarModel` fit. A magnitude for the
band in which the transit signal is observed (e.g., ``Kepler``)
is required, though need not have associated uncertainty.
:param folder:
Folder to find configuration files.
:param ini_file:
Input configuration file.
:param star_ini_file:
Input config file for :class:`isochrones.StarModel` fits.
:param recalc:
Whether to re-calculate :class:`PopulationSet`, if a
``popset.h5`` file is already present
:param **kwargs:
Keyword arguments passed to :class:`PopulationSet`.
Creates:
* ``trsig.pkl``: the pickled :class:`vespa.TransitSignal` object.
* ``starfield.h5``: the TRILEGAL field star simulation
* ``starmodel.h5``: the :class:`isochrones.StarModel` fit
* ``popset.h5``: the :class:`vespa.PopulationSet` object
representing the model population simulations.
"""
if not os.path.isabs(ini_file):
config = ConfigObj(os.path.join(folder,ini_file))
else:
config = ConfigObj(ini_file)
folder = os.path.abspath(folder)
#required items
name = config['name']
ra, dec = config['ra'], config['dec']
period = float(config['period'])
rprs = float(config['rprs'])
#load starmodels if there;
# if not, create them.
if 'starmodel_basename' not in config:
starmodel_basename = 'dartmouth_starmodel'
else:
starmodel_basename = config['starmodel_basename']
single_starmodel_file = os.path.join(folder,'{}_single.h5'.format(starmodel_basename))
binary_starmodel_file = os.path.join(folder,'{}_binary.h5'.format(starmodel_basename))
triple_starmodel_file = os.path.join(folder,'{}_triple.h5'.format(starmodel_basename))
#Single
try:
single_starmodel = StarModel.load_hdf(single_starmodel_file)
logging.info('Single StarModel loaded from {}'.format(single_starmodel_file))
except:
single_starmodel = StarModel.from_ini(ichrone, folder,
ini_file=star_ini_file)
logging.info('Fitting single StarModel to {}...'.format(single_starmodel.properties))
single_starmodel.fit()
single_starmodel.save_hdf(single_starmodel_file)
triangle_base = os.path.join(folder, '{}_triangle_single'.format(starmodel_basename))
single_starmodel.triangle_plots(triangle_base)
logging.info('StarModel fit done.')
#Binary
try:
binary_starmodel = BinaryStarModel.load_hdf(binary_starmodel_file)
logging.info('BinaryStarModel loaded from {}'.format(binary_starmodel_file))
except:
binary_starmodel = BinaryStarModel.from_ini(ichrone, folder,
ini_file=star_ini_file)
logging.info('Fitting BinaryStarModel to {}...'.format(binary_starmodel.properties))
binary_starmodel.fit()
binary_starmodel.save_hdf(binary_starmodel_file)
triangle_base = os.path.join(folder, '{}_triangle_binary'.format(starmodel_basename))
binary_starmodel.triangle_plots(triangle_base)
logging.info('BinaryStarModel fit done.')
#Triple
try:
triple_starmodel = TripleStarModel.load_hdf(triple_starmodel_file)
logging.info('TripleStarModel loaded from {}'.format(triple_starmodel_file))
except:
triple_starmodel = TripleStarModel.from_ini(ichrone, folder,
ini_file=star_ini_file)
logging.info('Fitting TripleStarModel to {}...'.format(triple_starmodel.properties))
triple_starmodel.fit()
triple_starmodel.save_hdf(triple_starmodel_file)
triangle_base = os.path.join(folder, '{}_triangle_triple'.format(starmodel_basename))
triple_starmodel.triangle_plots(triangle_base)
logging.info('TripleStarModel fit done.')
if 'popset' in config:
popset_file = config['popset']
if not os.path.isabs(popset_file):
popset_file = os.path.join(folder, popset_file)
else:
popset_file = os.path.join(folder,'popset.h5')
if 'starfield' in config:
trilegal_file = config['starfield']
if not os.path.isabs(trilegal_file):
trilegal_file = os.path.join(folder, trilegal_file)
else:
trilegal_file = os.path.join(folder,'starfield.h5')
if 'trsig' in config:
trsig_file = config['trsig']
if not os.path.isabs(trsig_file):
trsig_file = os.path.join(folder, trsig_file)
else:
trsig_file = os.path.join(folder,'trsig.pkl')
#create TransitSignal
if os.path.exists(trsig_file):
logging.info('Loading transit signal from {}...'.format(trsig_file))
trsig = pickle.load(open(trsig_file,'rb'))
else:
if 'photfile' not in config:
raise AttributeError('If transit pickle file (trsig.pkl) '+
'not present, "photfile" must be'+
'defined.')
if not os.path.isabs(config['photfile']):
photfile = os.path.join(folder,config['photfile'])
else:
photfile = config['photfile']
logging.info('Reading transit signal photometry ' +
'from {}...'.format(photfile))
try:
ts, fs, dfs = np.loadtxt(photfile, unpack=True)
except:
ts, fs, dfs = np.loadtxt(photfile, delimiter=',', unpack=True)
trsig = TransitSignal(ts, fs, dfs, P=period, name=name)
logging.info('Fitting transitsignal with MCMC...')
trsig.MCMC()
trsig.save(trsig_file)
#create PopulationSet
try:
if recalc:
if os.path.exists(popset_file):
os.remove(popset_file)
raise RuntimeError #just to get to except block
try:
popset = PopulationSet.load_hdf(popset_file)
except HDF5ExtError:
os.remove(popset_file)
logging.warning('{} file corrupted; removing.'.format(popset_file))
raise RuntimeError #to get to except block
for m in DEFAULT_MODELS:
popset[m] #should there be a better way to check this? (yes)
if refit_trap:
os.remove(popset_file)
for pop in popset.poplist:
logging.info('Re-fitting trapezoids for {}...'.format(pop.model))
pop.fit_trapezoids()
pop.save_hdf(popset_file, pop.modelshort,
append=True)
popset = PopulationSet.load_hdf(popset_file)
logging.info('PopulationSet loaded from {}'.format(popset_file))
except:
if recalc:
do_only = DEFAULT_MODELS
else:
try:
popset = PopulationSet.load_hdf(popset_file)
do_only = []
for m in DEFAULT_MODELS:
try:
popset[m]
except:
do_only.append(m)
except:
do_only = DEFAULT_MODELS
if os.path.exists(popset_file):
logging.warning('{} exists, but regenerating Population Set ({})...'.format(popset_file, do_only),
exc_info=True)
popset = PopulationSet(period=period, mags=single_starmodel.mags,
ra=ra, dec=dec,
trilegal_filename=trilegal_file,
starmodel=single_starmodel,
binary_starmodel=binary_starmodel,
triple_starmodel=triple_starmodel,
rprs=rprs, do_only=do_only,
savefile=popset_file, **kwargs)
fpp = cls(trsig, popset, folder=folder)
#############
# Apply constraints
# Exclusion radius
maxrad = float(config['constraints']['maxrad'])
fpp.set_maxrad(maxrad)
if 'secthresh' in config['constraints']:
secthresh = float(config['constraints']['secthresh'])
if not np.isnan(secthresh):
fpp.apply_secthresh(secthresh)
# Odd-even constraint
diff = 3 * np.max(trsig.depthfit[1])
fpp.constrain_oddeven(diff)
#apply contrast curve constraints if present
if 'ccfiles' in config['constraints']:
ccfiles = config['constraints']['ccfiles']
if isinstance(ccfiles, basestring):
ccfiles = [ccfiles]
for ccfile in ccfiles:
if not os.path.isabs(ccfile):
ccfile = os.path.join(folder, ccfile)
m = re.search('(\w+)_(\w+)\.cc',os.path.basename(ccfile))
if not m:
logging.warning('Invalid CC filename ({}); '.format(ccfile) +
'skipping.')
continue
else:
band = m.group(2)
inst = m.group(1)
name = '{} {}-band'.format(inst, band)
cc = ContrastCurveFromFile(ccfile, band, name=name)
fpp.apply_cc(cc)
#apply "velocity contrast curve" if present
if 'vcc' in config['constraints']:
dv = float(config['constraints']['vcc'][0])
dmag = float(config['constraints']['vcc'][1])
vcc = VelocityContrastCurve(dv, dmag)
fpp.apply_vcc(vcc)
return fpp
kepfolder = 'fits/' + args.keplernumber
fitfolder = kepfolder +'/' + args.folder
ini_file = fitfolder + '/' + 'congfig.ini'
config = ConfigObj(ini_file)
#convert strings to ints where necessary
config['koinum'] = int(config['koinum'])
config['planets'] = [int(i) for i in config['planets']]
#reassign to make code easier to read
koinum = config['koinum']
planets = config['planets']
planets = [int(i) for i in planets]
which = config['which']
#star model h5 file is in the kepfolder
starmodel = kepfolder + '/dartmouth_starmodel_binary.h5'
#load the star model from isochrones
starmod = BinaryStarModel.load_hdf(starmodel)
#create density and dilution samples
rhostarA = density_samples(starmod)
rhostarB = density_samples(starmod,'B')
dilution = dilution_samples(starmod)
#build light curve and grab Kepler data, save to file
lc = BinaryKeplerLightCurve(int(koinum),planets,rhostarA,rhostarB,dilution)
lc.save_hdf(fitfolder+'/'+str(koinum)+'_lc.h5')
#makedirs('fits/{}/{}/chains/'.format(args.keplernumber,args.folder))
def get_mod_special(self, ic, folder):
return BinaryStarModel(ic, folder=folder)
def from_ini(cls,
folder='.',
ini_file='fpp.ini',
recalc=False,
refit_trap=False,
star_ini_file='star.ini',
ichrone=DARTMOUTH,
**kwargs):
"""
To enable simple usage, initializes a FPPCalculation from a .ini file
By default, a file called ``fpp.ini`` will be looked for in the
current folder. Also present must be a ``star.ini`` file that
contains the observed properties of the target star.
``fpp.ini`` must be of the following form::
name = k2oi
ra = 11:30:14.510
dec = +07:35:18.21
period = 32.988 #days
rprs = 0.0534 #Rp/Rstar
photfile = lc_k2oi.csv
[constraints]
maxrad = 10 #exclusion radius [arcsec]
secthresh = 0.001 #maximum allowed secondary signal depth
#This variable defines contrast curves
#ccfiles = Keck_J.cc, Lick_J.cc
Photfile must be a text file with columns ``(days_from_midtransit,
flux, flux_err)``. Both whitespace- and comma-delimited
will be tried, using ``np.loadtxt``. Photfile need not be there
if there is a pickled :class:`TransitSignal` saved in the same
directory as ``ini_file``, named ``trsig.pkl`` (or another name
as defined by ``trsig`` keyword in ``.ini`` file).
``star.ini`` should look something like the following::
B = 15.005, 0.06
V = 13.496, 0.05
g = 14.223, 0.05
r = 12.858, 0.04
i = 11.661, 0.08
J = 9.763, 0.03
H = 9.135, 0.03
K = 8.899, 0.02
W1 = 8.769, 0.023
W2 = 8.668, 0.02
W3 = 8.552, 0.025
Kepler = 12.473
#Teff = 3503, 80
#feh = 0.09, 0.09
#logg = 4.89, 0.1
Any star properties can be defined; if errors are included
then they will be used in the :class:`isochrones.StarModel`
MCMC fit.
Spectroscopic parameters (``Teff, feh, logg``) are optional.
If included, then they will also be included in
:class:`isochrones.StarModel` fit. A magnitude for the
band in which the transit signal is observed (e.g., ``Kepler``)
is required, though need not have associated uncertainty.
:param folder:
Folder to find configuration files.
:param ini_file:
Input configuration file.
:param star_ini_file:
Input config file for :class:`isochrones.StarModel` fits.
:param recalc:
Whether to re-calculate :class:`PopulationSet`, if a
``popset.h5`` file is already present
:param **kwargs:
Keyword arguments passed to :class:`PopulationSet`.
Creates:
* ``trsig.pkl``: the pickled :class:`vespa.TransitSignal` object.
* ``starfield.h5``: the TRILEGAL field star simulation
* ``starmodel.h5``: the :class:`isochrones.StarModel` fit
* ``popset.h5``: the :class:`vespa.PopulationSet` object
representing the model population simulations.
"""
if not os.path.isabs(ini_file):
config = ConfigObj(os.path.join(folder, ini_file))
else:
config = ConfigObj(ini_file)
folder = os.path.abspath(folder)
#required items
name = config['name']
ra, dec = config['ra'], config['dec']
period = float(config['period'])
rprs = float(config['rprs'])
#load starmodels if there;
# if not, create them.
if 'starmodel_basename' not in config:
starmodel_basename = 'dartmouth_starmodel'
else:
starmodel_basename = config['starmodel_basename']
single_starmodel_file = os.path.join(
folder, '{}_single.h5'.format(starmodel_basename))
binary_starmodel_file = os.path.join(
folder, '{}_binary.h5'.format(starmodel_basename))
triple_starmodel_file = os.path.join(
folder, '{}_triple.h5'.format(starmodel_basename))
#Single
try:
single_starmodel = StarModel.load_hdf(single_starmodel_file)
logging.info('Single StarModel loaded from {}'.format(
single_starmodel_file))
except:
single_starmodel = StarModel.from_ini(ichrone,
folder,
ini_file=star_ini_file)
logging.info('Fitting single StarModel to {}...'.format(
single_starmodel.properties))
single_starmodel.fit()
single_starmodel.save_hdf(single_starmodel_file)
triangle_base = os.path.join(
folder, '{}_triangle_single'.format(starmodel_basename))
single_starmodel.triangle_plots(triangle_base)
logging.info('StarModel fit done.')
#Binary
try:
binary_starmodel = BinaryStarModel.load_hdf(binary_starmodel_file)
logging.info(
'BinaryStarModel loaded from {}'.format(binary_starmodel_file))
except:
binary_starmodel = BinaryStarModel.from_ini(ichrone,
folder,
ini_file=star_ini_file)
logging.info('Fitting BinaryStarModel to {}...'.format(
binary_starmodel.properties))
binary_starmodel.fit()
binary_starmodel.save_hdf(binary_starmodel_file)
triangle_base = os.path.join(
folder, '{}_triangle_binary'.format(starmodel_basename))
binary_starmodel.triangle_plots(triangle_base)
logging.info('BinaryStarModel fit done.')
#Triple
try:
triple_starmodel = TripleStarModel.load_hdf(triple_starmodel_file)
logging.info(
'TripleStarModel loaded from {}'.format(triple_starmodel_file))
except:
triple_starmodel = TripleStarModel.from_ini(ichrone,
folder,
ini_file=star_ini_file)
logging.info('Fitting TripleStarModel to {}...'.format(
triple_starmodel.properties))
triple_starmodel.fit()
triple_starmodel.save_hdf(triple_starmodel_file)
triangle_base = os.path.join(
folder, '{}_triangle_triple'.format(starmodel_basename))
triple_starmodel.triangle_plots(triangle_base)
logging.info('TripleStarModel fit done.')
if 'popset' in config:
popset_file = config['popset']
if not os.path.isabs(popset_file):
popset_file = os.path.join(folder, popset_file)
else:
popset_file = os.path.join(folder, 'popset.h5')
if 'starfield' in config:
trilegal_file = config['starfield']
if not os.path.isabs(trilegal_file):
trilegal_file = os.path.join(folder, trilegal_file)
else:
trilegal_file = os.path.join(folder, 'starfield.h5')
if 'trsig' in config:
trsig_file = config['trsig']
if not os.path.isabs(trsig_file):
trsig_file = os.path.join(folder, trsig_file)
else:
trsig_file = os.path.join(folder, 'trsig.pkl')
#create TransitSignal
if os.path.exists(trsig_file):
logging.info(
'Loading transit signal from {}...'.format(trsig_file))
trsig = pickle.load(open(trsig_file, 'rb'))
else:
if 'photfile' not in config:
raise AttributeError('If transit pickle file (trsig.pkl) ' +
'not present, "photfile" must be' +
'defined.')
if not os.path.isabs(config['photfile']):
photfile = os.path.join(folder, config['photfile'])
else:
photfile = config['photfile']
logging.info('Reading transit signal photometry ' +
'from {}...'.format(photfile))
try:
ts, fs, dfs = np.loadtxt(photfile, unpack=True)
except:
ts, fs, dfs = np.loadtxt(photfile, delimiter=',', unpack=True)
trsig = TransitSignal(ts, fs, dfs, P=period, name=name)
logging.info('Fitting transitsignal with MCMC...')
trsig.MCMC()
trsig.save(trsig_file)
#create PopulationSet
try:
if recalc:
if os.path.exists(popset_file):
os.remove(popset_file)
raise RuntimeError #just to get to except block
try:
popset = PopulationSet.load_hdf(popset_file)
except HDF5ExtError:
os.remove(popset_file)
logging.warning(
'{} file corrupted; removing.'.format(popset_file))
raise RuntimeError #to get to except block
for m in DEFAULT_MODELS:
popset[m] #should there be a better way to check this? (yes)
if refit_trap:
os.remove(popset_file)
for pop in popset.poplist:
logging.info('Re-fitting trapezoids for {}...'.format(
pop.model))
pop.fit_trapezoids()
pop.save_hdf(popset_file, pop.modelshort, append=True)
popset = PopulationSet.load_hdf(popset_file)
logging.info('PopulationSet loaded from {}'.format(popset_file))
except:
if recalc:
do_only = DEFAULT_MODELS
else:
try:
popset = PopulationSet.load_hdf(popset_file)
do_only = []
for m in DEFAULT_MODELS:
try:
popset[m]
except:
do_only.append(m)
except:
do_only = DEFAULT_MODELS
if os.path.exists(popset_file):
logging.warning(
'{} exists, but regenerating Population Set ({})...'.
format(popset_file, do_only),
exc_info=True)
popset = PopulationSet(period=period,
mags=single_starmodel.mags,
ra=ra,
dec=dec,
trilegal_filename=trilegal_file,
starmodel=single_starmodel,
binary_starmodel=binary_starmodel,
triple_starmodel=triple_starmodel,
rprs=rprs,
do_only=do_only,
savefile=popset_file,
**kwargs)
fpp = cls(trsig, popset, folder=folder)
#############
# Apply constraints
# Exclusion radius
maxrad = float(config['constraints']['maxrad'])
fpp.set_maxrad(maxrad)
if 'secthresh' in config['constraints']:
secthresh = float(config['constraints']['secthresh'])
if not np.isnan(secthresh):
fpp.apply_secthresh(secthresh)
# Odd-even constraint
diff = 3 * np.max(trsig.depthfit[1])
fpp.constrain_oddeven(diff)
#apply contrast curve constraints if present
if 'ccfiles' in config['constraints']:
ccfiles = list(config['constraints']['ccfiles'])
for ccfile in ccfiles:
if not os.path.isabs(ccfile):
ccfile = os.path.join(folder, ccfile)
m = re.search('(\w+)_(\w+)\.cc', os.path.basename(ccfile))
if not m:
logging.warning('Invalid CC filename ({}); ' +
'skipping.'.format(ccfile))
continue
else:
band = m.group(2)
inst = m.group(1)
name = '{} {}-band'.format(inst, band)
cc = ContrastCurveFromFile(ccfile, band, name=name)
fpp.apply_cc(cc)
#apply "velocity contrast curve" if present
if 'vcc' in config['constraints']:
dv = float(config['constraints']['vcc'][0])
dmag = float(config['constraints']['vcc'][1])
vcc = VelocityContrastCurve(dv, dmag)
fpp.apply_vcc(vcc)
return fpp
