def get_phi(self, params):
"""Return wideband timing-model prior."""
# get DMEFAC- and DMEQUAD-adjusted DMX errors
dme = self.get_dme(params)
# initialize the timing-model "infinite" prior
phi = KernelMatrix(1e40 * np.ones(self._npars, "d"))
# fill the DMX slots with weighted errors
for index, which in zip(self._dmindex, self._dmwhich):
phi.set(1.0 / np.sum(1.0 / dme[which] ** 2), index)
return phi
class BasisGP(signal_base.Signal):
signal_type = "basis"
signal_name = name
signal_id = name
basis_combine = combine
def __init__(self, psr):
super(BasisGP, self).__init__(psr)
self.name = self.psrname + "_" + self.signal_id
self._do_selection(psr, priorFunction, basisFunction, coefficients, selection)
def _do_selection(self, psr, priorfn, basisfn, coefficients, selection):
sel = selection(psr)
self._keys = sorted(sel.masks.keys())
self._masks = [sel.masks[key] for key in self._keys]
self._prior, self._bases = {}, {}
self._params, self._coefficients = {}, {}
for key, mask in zip(self._keys, self._masks):
pnames = [psr.name, name, key]
pname = "_".join([n for n in pnames if n])
self._prior[key] = priorfn(pname, psr=psr)
self._bases[key] = basisfn(pname, psr=psr)
for par in itertools.chain(self._prior[key]._params.values(), self._bases[key]._params.values()):
self._params[par.name] = par
if coefficients:
# we can only create GPCoefficients parameters if the basis
# can be constructed with default arguments
# (and does not change size)
self._construct_basis()
for key in self._keys:
pname = "_".join([n for n in [psr.name, name, key] if n])
chain = itertools.chain(self._prior[key]._params.values(), self._bases[key]._params.values())
priorargs = {par.name: self._params[par.name] for par in chain}
logprior = parameter.Function(functools.partial(self._get_coefficient_logprior, key), **priorargs)
size = self._slices[key].stop - self._slices[key].start
cpar = parameter.GPCoefficients(logprior=logprior, size=size)(pname + "_coefficients")
self._coefficients[key] = cpar
self._params[cpar.name] = cpar
@property
def basis_params(self):
"""Get any varying basis parameters."""
ret = []
for basis in self._bases.values():
ret.extend([pp.name for pp in basis.params])
return ret
@signal_base.cache_call("basis_params")
def _construct_basis(self, params={}):
basis, self._labels = {}, {}
for key, mask in zip(self._keys, self._masks):
basis[key], self._labels[key] = self._bases[key](params=params, mask=mask)
nc = sum(F.shape[1] for F in basis.values())
self._basis = np.zeros((len(self._masks[0]), nc))
# TODO: should this be defined here? it will cache phi
self._phi = KernelMatrix(nc)
self._slices = {}
nctot = 0
for key, mask in zip(self._keys, self._masks):
Fmat = basis[key]
nn = Fmat.shape[1]
self._basis[mask, nctot : nn + nctot] = Fmat
self._slices.update({key: slice(nctot, nn + nctot)})
nctot += nn
# this class does different things (and gets different method
# definitions) if the user wants it to model GP coefficients
# (e.g., for a hierarchical likelihood) or if they do not
if coefficients:
def _get_coefficient_logprior(self, key, c, **params):
self._construct_basis(params)
phi = self._prior[key](self._labels[key], params=params)
if phi.ndim == 1:
return -0.5 * np.sum(c * c / phi) - 0.5 * np.sum(np.log(phi)) - 0.5 * len(phi) * np.log(2 * np.pi)
# note: (2*pi)^(n/2) is not in signal_base likelihood
else:
# TO DO: this code could be embedded in KernelMatrix
phiinv, logdet = KernelMatrix(phi).inv(logdet=True)
return -0.5 * np.dot(c, np.dot(phiinv, c)) - 0.5 * logdet - 0.5 * phi.shape[0] * np.log(2 * np.pi)
# MV: could assign this to a data member at initialization
@property
def delay_params(self):
return [pp.name for pp in self.params if "_coefficients" in pp.name]
@signal_base.cache_call(["basis_params", "delay_params"])
def get_delay(self, params={}):
self._construct_basis(params)
c = np.zeros(self._basis.shape[1])
for key, slc in self._slices.items():
p = self._coefficients[key]
c[slc] = params[p.name] if p.name in params else p.value
return np.dot(self._basis, c)
def get_basis(self, params={}):
return None
def get_phi(self, params):
return None
def get_phiinv(self, params):
return None
else:
@property
def delay_params(self):
return []
def get_delay(self, params={}):
return 0
def get_basis(self, params={}):
self._construct_basis(params)
return self._basis
def get_phi(self, params):
self._construct_basis(params)
for key, slc in self._slices.items():
phislc = self._prior[key](self._labels[key], params=params)
self._phi = self._phi.set(phislc, slc)
return self._phi
def get_phiinv(self, params):
return self.get_phi(params).inv()