def initialize(self, key):
# Run through the standard initialization
super().initialize(key)
# for now, start with white noise
self.data_mat = self.sigma_mat.copy()
self.data_mat_last = self.data_mat.copy()
#Set up p0 and the independent sampler
fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
phi = PhiParam.load(fname)
# Set the regions to None, since we don't want to include them even if they
# are there
phi.regions = None
#Loading file that was previously output
# Convert PhiParam object to an array
self.p0 = phi.toarray()
jump = Starfish.config["Phi_jump"]
cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
cov = np.diag(cov_arr)
def lnfunc(p):
# Convert p array into a PhiParam object
ind = self.npoly
if self.chebyshevSpectrum.fix_c0:
ind -= 1
cheb = p[0:ind]
sigAmp = p[ind]
ind+=1
logAmp = p[ind]
ind+=1
l = p[ind]
par = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)
self.update_Phi(par)
# sigAmp must be positive (this is effectively a prior)
# See https://github.com/iancze/Starfish/issues/26
if not (0.0 < sigAmp):
self.lnprob_last = self.lnprob
lnp = -np.inf
self.logger.debug("sigAmp was negative, returning -np.inf")
self.lnprob = lnp # Same behavior as self.evaluate()
else:
lnp = self.evaluate()
self.logger.debug("Evaluated Phi parameters: {} {}".format(par, lnp))
return lnp
def rejectfn():
self.logger.debug("Calling Phi revertfn.")
self.revert_Phi()
self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
def initialize(self, key):
super().initialize(key)
# for now, just use white noise
self.data_mat = self.sigma_mat.copy()
self.data_mat_last = self.data_mat.copy()
#Set up p0 and the independent sampler
fname = Starfish.specfmt.format(self.spectrum_id,
self.order) + "phi.json"
phi = PhiParam.load(fname)
self.p0 = phi.cheb
cov = np.diag(Starfish.config["cheb_jump"]**2 * np.ones(len(self.p0)))
def lnfunc(p):
# turn this into pars
self.update_Phi(p)
lnp = self.evaluate()
self.logger.debug("Evaluated Phi parameters: {} {}".format(p, lnp))
return lnp
def rejectfn():
self.logger.debug("Calling Phi revertfn.")
self.revert_Phi()
self.sampler = StateSampler(lnfunc,
self.p0,
cov,
query_lnprob=self.get_lnprob,
rejectfn=rejectfn,
debug=True)
def initialize(self, key):
super().initialize(key)
# for now, just use white noise
self.data_mat = self.sigma_mat.copy()
self.data_mat_last = self.data_mat.copy()
#Set up p0 and the independent sampler
fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
phi = PhiParam.load(fname)
self.p0 = phi.cheb
cov = np.diag(Starfish.config["cheb_jump"]**2 * np.ones(len(self.p0)))
def lnfunc(p):
# turn this into pars
self.update_Phi(p)
lnp = self.evaluate()
self.logger.debug("Evaluated Phi parameters: {} {}".format(p, lnp))
return lnp
def rejectfn():
self.logger.debug("Calling Phi revertfn.")
self.revert_Phi()
self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
def initialize(self, key):
# Run through the standard initialization
super().initialize(key)
# for now, start with white noise
self.data_mat = self.sigma_mat.copy()
self.data_mat_last = self.data_mat.copy()
#Set up p0 and the independent sampler
fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
phi = PhiParam.load(fname)
# Set the regions to None, since we don't want to include them even if they
# are there
phi.regions = None
#Loading file that was previously output
# Convert PhiParam object to an array
self.p0 = phi.toarray()
jump = Starfish.config["Phi_jump"]
cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
cov = np.diag(cov_arr)
def lnfunc(p):
# Convert p array into a PhiParam object
ind = self.npoly
if self.chebyshevSpectrum.fix_c0:
ind -= 1
cheb = p[0:ind]
sigAmp = p[ind]
ind+=1
logAmp = p[ind]
ind+=1
l = p[ind]
par = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)
self.update_Phi(par)
# sigAmp must be positive (this is effectively a prior)
# See https://github.com/iancze/Starfish/issues/26
if not (0.0 < sigAmp):
self.lnprob_last = self.lnprob
lnp = -np.inf
self.logger.debug("sigAmp was negative, returning -np.inf")
self.lnprob = lnp # Same behavior as self.evaluate()
else:
lnp = self.evaluate()
self.logger.debug("Evaluated Phi parameters: {} {}".format(par, lnp))
return lnp
def rejectfn():
self.logger.debug("Calling Phi revertfn.")
self.revert_Phi()
self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
def test_load(self):
load = PhiParam.load(Starfish.specfmt.format(0, 22) + "phi_test.json")
print(load.spectrum_id)
print(load.order)
print(load.fix_c0)
print(load.cheb)
print(load.sigAmp)
print(load.logAmp)
print(load.l)
print(load.regions)
def test_load(self):
load = PhiParam.load(Starfish.specfmt.format(0, 22) + "phi_test.json")
print(load.spectrum_id)
print(load.order)
print(load.fix_c0)
print(load.cheb)
print(load.sigAmp)
print(load.logAmp)
print(load.l)
print(load.regions)
def initialize(self, key):
'''
Initialize to the correct chunk of data (echelle order).
:param key: (spectrum_id, order_key)
:param type: (int, int)
This method should only be called after all subprocess have been forked.
'''
self.id = key
spectrum_id, self.order_key = self.id
# Make sure these are ints
self.spectrum_id = int(spectrum_id)
self.instrument = Instruments[self.spectrum_id]
self.dataSpectrum = DataSpectra[self.spectrum_id]
self.wl = self.dataSpectrum.wls[self.order_key]
self.fl = self.dataSpectrum.fls[self.order_key]
self.sigma = self.dataSpectrum.sigmas[self.order_key]
self.ndata = len(self.wl)
self.mask = self.dataSpectrum.masks[self.order_key]
self.order = int(self.dataSpectrum.orders[self.order_key])
self.logger = logging.getLogger("{} {}".format(self.__class__.__name__, self.order))
if self.debug:
self.logger.setLevel(logging.DEBUG)
else:
self.logger.setLevel(logging.INFO)
self.logger.info("Initializing model on Spectrum {}, order {}.".format(self.spectrum_id, self.order_key))
self.npoly = Starfish.config["cheb_degree"]
self.chebyshevSpectrum = ChebyshevSpectrum(self.dataSpectrum, self.order_key, npoly=self.npoly)
# If the file exists, optionally initiliaze to the chebyshev values
fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
if os.path.exists(fname):
self.logger.debug("Loading stored Chebyshev parameters.")
phi = PhiParam.load(fname)
self.chebyshevSpectrum.update(phi.cheb)
#self.resid_deque = deque(maxlen=500) #Deque that stores the last residual spectra, for averaging
self.counter = 0
self.emulator = Emulator.open()
self.emulator.determine_chunk_log(self.wl)
self.pca = self.emulator.pca
self.wl_FFT = self.pca.wl
# The raw eigenspectra and mean flux components
self.EIGENSPECTRA = np.vstack((self.pca.flux_mean[np.newaxis,:], self.pca.flux_std[np.newaxis,:], self.pca.eigenspectra))
self.ss = np.fft.rfftfreq(self.pca.npix, d=self.emulator.dv)
self.ss[0] = 0.01 # junk so we don't get a divide by zero error
# Holders to store the convolved and resampled eigenspectra
self.eigenspectra = np.empty((self.pca.m, self.ndata))
self.flux_mean = np.empty((self.ndata,))
self.flux_std = np.empty((self.ndata,))
self.flux_scalar = None
self.sigma_mat = self.sigma**2 * np.eye(self.ndata)
self.mus, self.C_GP, self.data_mat = None, None, None
self.Omega = None
self.lnprior = 0.0 # Modified and set by NuisanceSampler.lnprob
# self.nregions = 0
# self.exceptions = []
# Update the outdir based upon id
self.noutdir = Starfish.routdir + "{}/{}/".format(self.spectrum_id, self.order)
except:
print("Don't you want to use a user defined prior??")
raise
# Insert the prior here
def lnprob(p):
lp = lnprior(p)
if not np.isfinite(lp):
return -np.inf
return lp + lnlike(p)
import emcee
start = Starfish.config["Theta"]
fname = Starfish.specfmt.format(model.spectrum_id, model.order) + "phi.json"
phi0 = PhiParam.load(fname)
ndim, nwalkers = 8, 40
p0 = np.array(start["grid"] + [start["vz"], start["vsini"], start["logOmega"]] +
[phi0.sigAmp, phi0.logAmp, phi0.l])
p0_std = [5, 0.02, 0.5, 0.5, 0.01, 0.01, 0.001, 0.5]
if args.resume:
p0_ball = np.load("emcee_chain.npy")[:,-1,:]
else:
p0_ball = emcee.utils.sample_ball(p0, p0_std, size=nwalkers)
n_threads = multiprocessing.cpu_count()
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, threads=n_threads)
def initialize(self, key):
# Run through the standard initialization
super().initialize(key)
# for now, start with white noise
self.data_mat = self.sigma_mat.copy()
self.data_mat_last = self.data_mat.copy()
#Set up p0 and the independent sampler
fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
phi = PhiParam.load(fname)
# print("Phi.regions", phi.regions)
# import sys
# sys.exit()
# Get the regions matrix
region_func = make_k_func_region(phi)
max_r = 4.0 * np.max(phi.regions, axis=0)[2]
self.region_mat = get_dense_C(self.wl, k_func=region_func, max_r=max_r)
print(self.region_mat)
# Then set phi to None
phi.regions = None
#Loading file that was previously output
# Convert PhiParam object to an array
self.p0 = phi.toarray()
jump = Starfish.config["Phi_jump"]
cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
cov = np.diag(cov_arr)
def lnfunc(p):
# Convert p array into a PhiParam object
ind = self.npoly
if self.chebyshevSpectrum.fix_c0:
ind -= 1
cheb = p[0:ind]
sigAmp = p[ind]
ind+=1
logAmp = p[ind]
ind+=1
l = p[ind]
phi = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)
self.update_Phi(phi)
lnp = self.evaluate()
self.logger.debug("Evaluated Phi parameters: {} {}".format(phi, lnp))
return lnp
def rejectfn():
self.logger.debug("Calling Phi revertfn.")
self.revert_Phi()
self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
def initialize(self, key):
'''
Initialize to the correct chunk of data (echelle order).
:param key: (spectrum_id, order_key)
:param type: (int, int)
This method should only be called after all subprocess have been forked.
'''
self.id = key
spectrum_id, self.order_key = self.id
# Make sure these are ints
self.spectrum_id = int(spectrum_id)
self.instrument = Instruments[self.spectrum_id]
self.dataSpectrum = DataSpectra[self.spectrum_id]
self.wl = self.dataSpectrum.wls[self.order_key]
self.fl = self.dataSpectrum.fls[self.order_key]
self.sigma = self.dataSpectrum.sigmas[self.order_key]
self.ndata = len(self.wl)
self.mask = self.dataSpectrum.masks[self.order_key]
self.order = int(self.dataSpectrum.orders[self.order_key])
self.logger = logging.getLogger("{} {}".format(self.__class__.__name__, self.order))
if self.debug:
self.logger.setLevel(logging.DEBUG)
else:
self.logger.setLevel(logging.INFO)
self.logger.info("Initializing model on Spectrum {}, order {}.".format(self.spectrum_id, self.order_key))
self.npoly = Starfish.config["cheb_degree"]
self.chebyshevSpectrum = ChebyshevSpectrum(self.dataSpectrum, self.order_key, npoly=self.npoly)
# If the file exists, optionally initiliaze to the chebyshev values
fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
if os.path.exists(fname):
self.logger.debug("Loading stored Chebyshev parameters.")
phi = PhiParam.load(fname)
self.chebyshevSpectrum.update(phi.cheb)
self.resid_deque = deque(maxlen=500) #Deque that stores the last residual spectra, for averaging
self.counter = 0
self.emulator = Emulator.open()
self.emulator.determine_chunk_log(self.wl)
self.pca = self.emulator.pca
self.wl_FFT = self.pca.wl
# The raw eigenspectra and mean flux components
self.EIGENSPECTRA = np.vstack((self.pca.flux_mean[np.newaxis,:], self.pca.flux_std[np.newaxis,:], self.pca.eigenspectra))
self.ss = np.fft.rfftfreq(self.pca.npix, d=self.emulator.dv)
self.ss[0] = 0.01 # junk so we don't get a divide by zero error
# Holders to store the convolved and resampled eigenspectra
self.eigenspectra = np.empty((self.pca.m, self.ndata))
self.flux_mean = np.empty((self.ndata,))
self.flux_std = np.empty((self.ndata,))
self.sigma_mat = self.sigma**2 * np.eye(self.ndata)
self.mus, self.C_GP, self.data_mat = None, None, None
self.lnprior = 0.0 # Modified and set by NuisanceSampler.lnprob
# self.nregions = 0
# self.exceptions = []
# Update the outdir based upon id
self.noutdir = Starfish.routdir + "{}/{}/".format(self.spectrum_id, self.order)
from Starfish import utils
# Determine all of the orders we will be fitting
spectra = Starfish.data["files"]
orders = Starfish.data["orders"]
for spectrum_id in range(len(spectra)):
for order in orders:
npoly = Starfish.config["cheb_degree"]
if order == orders[-1]:
# Use cheb degree - 1 for the last order
npoly -= 1
fname_phi = Starfish.specfmt.format(spectrum_id, order) + "phi.json"
phi = PhiParam.load(fname_phi)
fname_mc = args.rundir + "/" + Starfish.specfmt.format(
spectrum_id, order) + "/mc.hdf5"
flatchain = utils.h5read(fname_mc)
pars = flatchain[-1, :]
phi.cheb = pars[:npoly]
phi.sigAmp = float(pars[npoly])
phi.logAmp = float(pars[npoly + 1])
phi.l = float(pars[npoly + 2])
phi.save()
def initialize(self, key):
# Run through the standard initialization
super().initialize(key)
# for now, start with white noise
self.data_mat = self.sigma_mat.copy()
self.data_mat_last = self.data_mat.copy()
#Set up p0 and the independent sampler
fname = Starfish.specfmt.format(self.spectrum_id,
self.order) + "phi.json"
phi = PhiParam.load(fname)
# print("Phi.regions", phi.regions)
# import sys
# sys.exit()
# Get the regions matrix
region_func = make_k_func_region(phi)
max_r = 4.0 * np.max(phi.regions, axis=0)[2]
self.region_mat = get_dense_C(self.wl, k_func=region_func, max_r=max_r)
print(self.region_mat)
# Then set phi to None
phi.regions = None
#Loading file that was previously output
# Convert PhiParam object to an array
self.p0 = phi.toarray()
jump = Starfish.config["Phi_jump"]
cheb_len = (self.npoly -
1) if self.chebyshevSpectrum.fix_c0 else self.npoly
cov_arr = np.concatenate(
(Starfish.config["cheb_jump"]**2 * np.ones((cheb_len, )),
np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2))
cov = np.diag(cov_arr)
def lnfunc(p):
# Convert p array into a PhiParam object
ind = self.npoly
if self.chebyshevSpectrum.fix_c0:
ind -= 1
cheb = p[0:ind]
sigAmp = p[ind]
ind += 1
logAmp = p[ind]
ind += 1
l = p[ind]
phi = PhiParam(self.spectrum_id, self.order,
self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp,
l)
self.update_Phi(phi)
lnp = self.evaluate()
self.logger.debug("Evaluated Phi parameters: {} {}".format(
phi, lnp))
return lnp
def rejectfn():
self.logger.debug("Calling Phi revertfn.")
self.revert_Phi()
self.sampler = StateSampler(lnfunc,
self.p0,
cov,
query_lnprob=self.get_lnprob,
rejectfn=rejectfn,
debug=True)
fname = Starfish.specfmt.format(spectrum_id, order) + "regions.json"
f = open(fname, "r")
read = json.load(f) # read is a dictionary
f.close()
mus = np.array(read["mus"])
assert spectrum_id == read["spectrum_id"], "Spectrum/Order mismatch"
assert order == read["order"], "Spectrum/Order mismatch"
# Load the guesses for the global parameters from the .json
# If the file exists, optionally initiliaze to the chebyshev values
fname = Starfish.specfmt.format(spectrum_id, order) + "phi.json"
try:
phi = PhiParam.load(fname)
except FileNotFoundError:
print("No order parameter file found (e.g. sX_oXXphi.json), please run `star.py --initPhi` first.")
raise
# Puposely set phi.regions to none for this exercise, since we don't care about existing regions, and likely we want to overwrite them.
phi.regions = None
def optimize_region_residual(wl, residuals, sigma, mu):
'''
Determine the optimal parameters for the line kernels by fitting a Gaussian directly to the residuals.
'''
# Using sigma0, truncate the wavelength vector and residulas to include
# only those portions that fall in the range [mu - sigma, mu + sigma]
ind = (wl > mu - args.sigma0) & (wl < mu + args.sigma0)
wl = wl[ind]
