class SampleThetaCheb(Order):
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 update_Phi(self, p):
'''
Update the Chebyshev coefficients only.
'''
self.chebyshevSpectrum.update(p)
def finish(self, *args):
super().finish(*args)
fname = Starfish.routdir + Starfish.specfmt.format(
self.spectrum_id, self.order) + "/mc.hdf5"
self.sampler.write(fname=fname)
class SampleThetaCheb(Order):
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 update_Phi(self, p):
'''
Update the Chebyshev coefficients only.
'''
self.chebyshevSpectrum.update(p)
def finish(self, *args):
super().finish(*args)
fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
self.sampler.write(fname=fname)
class SampleThetaPhiLines(Order):
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 update_Phi(self, phi):
self.logger.debug("Updating nuisance parameters to {}".format(phi))
# Read off the Chebyshev parameters and update
self.chebyshevSpectrum.update(phi.cheb)
# Check to make sure the global covariance parameters make sense
if phi.sigAmp < 0.1:
raise C.ModelError("sigAmp shouldn't be lower than 0.1, something is wrong.")
max_r = 6.0 * phi.l # [km/s]
# Create a partial function which returns the proper element.
k_func = make_k_func(phi)
# Store the previous data matrix in case we want to revert later
self.data_mat_last = self.data_mat
self.data_mat = get_dense_C(self.wl, k_func=k_func, max_r=max_r) + phi.sigAmp*self.sigma_mat + self.region_mat
def finish(self, *args):
super().finish(*args)
fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
self.sampler.write(fname=fname)
class SampleThetaPhi(Order):
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 update_Phi(self, p):
self.logger.debug("Updating nuisance parameters to {}".format(p))
# Read off the Chebyshev parameters and update
self.chebyshevSpectrum.update(p.cheb)
# Check to make sure the global covariance parameters make sense
#if p.sigAmp < 0.1:
# raise C.ModelError("sigAmp shouldn't be lower than 0.1, something is wrong.")
max_r = 6.0 * p.l # [km/s]
# Create a partial function which returns the proper element.
k_func = make_k_func(p)
# Store the previous data matrix in case we want to revert later
self.data_mat_last = self.data_mat
self.data_mat = get_dense_C(self.wl, k_func=k_func, max_r=max_r) + p.sigAmp*self.sigma_mat
def finish(self, *args):
super().finish(*args)
fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
self.sampler.write(fname=fname)
print("No optimal jump matrix found, using diagonal jump matrix.")
sampler = StateSampler(lnprob,
p0,
cov,
query_lnprob=query_lnprob,
acceptfn=acceptfn,
rejectfn=rejectfn,
debug=True,
outdir=Starfish.routdir)
p, lnprob, state = sampler.run_mcmc(p0,
N=args.samples,
incremental_save=args.incremental_save)
print("Final", p)
sampler.write()
# Kill all of the orders
for pconn in pconns.values():
pconn.send(("FINISH", None))
pconn.send(("DIE", None))
# Join on everything and terminate
for p in ps.values():
p.join()
p.terminate()
import sys
sys.exit()
class SampleThetaPhiLines(Order):
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 update_Phi(self, phi):
self.logger.debug("Updating nuisance parameters to {}".format(phi))
# Read off the Chebyshev parameters and update
self.chebyshevSpectrum.update(phi.cheb)
# Check to make sure the global covariance parameters make sense
if phi.sigAmp < 0.1:
raise C.ModelError(
"sigAmp shouldn't be lower than 0.1, something is wrong.")
max_r = 6.0 * phi.l # [km/s]
# Create a partial function which returns the proper element.
k_func = make_k_func(phi)
# Store the previous data matrix in case we want to revert later
self.data_mat_last = self.data_mat
self.data_mat = get_dense_C(
self.wl, k_func=k_func,
max_r=max_r) + phi.sigAmp * self.sigma_mat + self.region_mat
def finish(self, *args):
super().finish(*args)
fname = Starfish.routdir + Starfish.specfmt.format(
self.spectrum_id, self.order) + "/mc.hdf5"
self.sampler.write(fname=fname)
print("Calling rejectfn")
for ((spectrum_id, order_id), pconn) in pconns.items():
pconn.send(("DECIDE", False))
from Starfish.samplers import StateSampler
start = Starfish.config["Theta"]
p0 = np.array(start["grid"] + [start["vz"], start["vsini"], start["logOmega"]])
jump = Starfish.config["Theta_jump"]
cov = np.diag(np.array(jump["grid"] + [jump["vz"], jump["vsini"], jump["logOmega"]])**2)
sampler = StateSampler(lnprob, p0, cov, query_lnprob=query_lnprob, acceptfn=acceptfn, rejectfn=rejectfn, debug=True, outdir=Starfish.routdir)
p, lnprob, state = sampler.run_mcmc(p0, N=args.samples)
print("Final", p)
sampler.write()
# Kill all of the orders
for pconn in pconns.values():
pconn.send(("FINISH", None))
pconn.send(("DIE", None))
# Join on everything and terminate
for p in ps.values():
p.join()
p.terminate()
import sys;sys.exit()
class SampleThetaPhi(Order):
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 update_Phi(self, p):
self.logger.debug("Updating nuisance parameters to {}".format(p))
# Read off the Chebyshev parameters and update
self.chebyshevSpectrum.update(p.cheb)
# Check to make sure the global covariance parameters make sense
#if p.sigAmp < 0.1:
# raise C.ModelError("sigAmp shouldn't be lower than 0.1, something is wrong.")
max_r = 6.0 * p.l # [km/s]
# Create a partial function which returns the proper element.
k_func = make_k_func(p)
# Store the previous data matrix in case we want to revert later
self.data_mat_last = self.data_mat
self.data_mat = get_dense_C(self.wl, k_func=k_func, max_r=max_r) + p.sigAmp*self.sigma_mat
def finish(self, *args):
super().finish(*args)
fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
self.sampler.write(fname=fname)