Merge pull request #2225 from junpenglao/bugfixed_get_variable_name

fixed_ get_variable_name

Author: fonnesbeck

pymc3/distributions/continuous.py

@@ -376,7 +376,7 @@ def __init__(self, mu=None, lam=None, phi=None, alpha=0., *args, **kwargs):
         self.alpha = alpha = tt.as_tensor_variable(alpha)
         self.mu = mu = tt.as_tensor_variable(mu)
         self.lam = lam = tt.as_tensor_variable(lam)
-        self.phi = phi =tt.as_tensor_variable(phi)
+        self.phi = phi = tt.as_tensor_variable(phi)
 
         self.mean = self.mu + self.alpha
         self.mode = self.mu * (tt.sqrt(1. + (1.5 * self.mu / self.lam)**2)
@@ -1501,11 +1501,9 @@ def __init__(self, lower=0, upper=1, c=0.5,
                  *args, **kwargs):
         super(Triangular, self).__init__(*args, **kwargs)
 
-        self.c = c
-        self.lower = lower
-        self.upper = upper
-        self.mean = c
-        self.median = self.mean
+        self.median = self.mean = self.c = c  = tt.as_tensor_variable(c)
+        self.lower = lower = tt.as_tensor_variable(lower)
+        self.upper = upper = tt.as_tensor_variable(upper)
 
     def random(self, point=None, size=None):
         c, lower, upper = draw_values([self.c, self.lower, self.upper],

pymc3/distributions/discrete.py

@@ -4,6 +4,7 @@
 import theano.tensor as tt
 from scipy import stats
 
+from pymc3.util import get_variable_name
 from .dist_math import bound, factln, binomln, betaln, logpow
 from .distribution import Discrete, draw_values, generate_samples, reshape_sampled
 from pymc3.math import tround
@@ -205,8 +206,8 @@ class DiscreteWeibull(Discrete):
     def __init__(self, q, beta, *args, **kwargs):
         super(DiscreteWeibull, self).__init__(*args, defaults=['median'], **kwargs)
 
-        self.q = q
-        self.beta = beta
+        self.q = q = tt.as_tensor_variable(q)
+        self.beta = beta = tt.as_tensor_variable(beta)
 
         self.median = self._ppf(0.5)
 

pymc3/distributions/mixture.py

@@ -1,6 +1,7 @@
 import numpy as np
 import theano.tensor as tt
 
+from pymc3.util import get_variable_name
 from ..math import logsumexp
 from .dist_math import bound
 from .distribution import Discrete, Distribution, draw_values, generate_samples
@@ -41,7 +42,7 @@ class Mixture(Distribution):
     def __init__(self, w, comp_dists, *args, **kwargs):
         shape = kwargs.pop('shape', ())
 
-        self.w = w
+        self.w = w = tt.as_tensor_variable(w)
         self.comp_dists = comp_dists
 
         defaults = kwargs.pop('defaults', [])
@@ -167,7 +168,8 @@ class NormalMixture(Mixture):
     def __init__(self, w, mu, *args, **kwargs):
         _, sd = get_tau_sd(tau=kwargs.pop('tau', None),
                            sd=kwargs.pop('sd', None))
-
+        self.mu = mu = tt.as_tensor_variable(mu)
+        self.sd = sd = tt.as_tensor_variable(sd)
         super(NormalMixture, self).__init__(w, Normal.dist(mu, sd=sd),
                                             *args, **kwargs)
 
@@ -176,8 +178,8 @@ def _repr_latex_(self, name=None, dist=None):
             dist = self
         mu = dist.mu
         w = dist.w
-        sigma = dist.sigma
+        sd = dist.sd
         return r'${} \sim \text{{NormalMixture}}(\mathit{{w}}={}, \mathit{{mu}}={}, \mathit{{sigma}}={})$'.format(name,
                                                 get_variable_name(w),
                                                 get_variable_name(mu),
-                                                get_variable_name(sigma))
+                                                get_variable_name(sd))

pymc3/distributions/multivariate.py

@@ -16,6 +16,7 @@
 from pymc3.math import tround
 from pymc3.theanof import floatX
 from . import transforms
+from pymc3.util import get_variable_name
 from .distribution import Continuous, Discrete, draw_values, generate_samples
 from ..model import Deterministic
 from .continuous import ChiSquared, Normal
@@ -291,7 +292,7 @@ class MvStudentT(Continuous):
     def __init__(self, nu, Sigma, mu=None, *args, **kwargs):
         super(MvStudentT, self).__init__(*args, **kwargs)
         self.nu = nu = tt.as_tensor_variable(nu)
-        self.mu = tt.zeros(Sigma.shape[0]) if mu is None else tt.as_tensor_variable(mu)
+        mu = tt.zeros(Sigma.shape[0]) if mu is None else tt.as_tensor_variable(mu)
         self.Sigma = Sigma = tt.as_tensor_variable(Sigma)
 
         self.mean = self.median = self.mode = self.mu = mu
@@ -593,9 +594,9 @@ def __init__(self, nu, V, *args, **kwargs):
                       'on the issues surrounding the Wishart see here: '
                       'https://github.com/pymc-devs/pymc3/issues/538.',
                       UserWarning)
-        self.nu = nu
-        self.p = p = V.shape[0]
-        self.V = V
+        self.nu = nu = tt.as_tensor_variable(nu)
+        self.p = p = tt.as_tensor_variable(V.shape[0])
+        self.V = V = tt.as_tensor_variable(V)
         self.mean = nu * V
         self.mode = tt.switch(1 * (nu >= p + 1),
                               (nu - p - 1) * V,
@@ -695,7 +696,7 @@ def WishartBartlett(name, S, nu, is_cholesky=False, return_cholesky=False, testv
     c = tt.sqrt(ChiSquared('c', nu - np.arange(2, 2 + n_diag), shape=n_diag,
                            testval=diag_testval))
     pm._log.info('Added new variable c to model diagonal of Wishart.')
-    z = Normal('z', 0, 1, shape=n_tril, testval=tril_testval)
+    z = Normal('z', 0., 1., shape=n_tril, testval=tril_testval)
     pm._log.info('Added new variable z to model off-diagonals of Wishart.')
     # Construct A matrix
     A = tt.zeros(S.shape, dtype=np.float32)

pymc3/distributions/timeseries.py

@@ -1,8 +1,9 @@
 import theano.tensor as tt
 from theano import scan
 
+from pymc3.util import get_variable_name
+from .continuous import get_tau_sd, Normal, Flat
 from . import multivariate
-from . import continuous
 from . import distribution
 
 __all__ = [
@@ -29,20 +30,20 @@ class AR1(distribution.Continuous):
 
     def __init__(self, k, tau_e, *args, **kwargs):
         super(AR1, self).__init__(*args, **kwargs)
-        self.k = k
-        self.tau_e = tau_e
+        self.k = k = tt.as_tensor_variable(k)
+        self.tau_e = tau_e = tt.as_tensor_variable(tau_e)
         self.tau = tau_e * (1 - k ** 2)
-        self.mode = 0.
+        self.mode = tt.as_tensor_variable(0.)
 
     def logp(self, x):
         k = self.k
         tau_e = self.tau_e
 
         x_im1 = x[:-1]
         x_i = x[1:]
-        boundary = continuous.Normal.dist(0, tau_e).logp
+        boundary = Normal.dist(0., tau=tau_e).logp
 
-        innov_like = continuous.Normal.dist(k * x_im1, tau_e).logp(x_i)
+        innov_like = Normal.dist(k * x_im1, tau=tau_e).logp(x_i)
         return boundary(x[0]) + tt.sum(innov_like) + boundary(x[-1])
 
     def _repr_latex_(self, name=None, dist=None):
@@ -71,14 +72,15 @@ class GaussianRandomWalk(distribution.Continuous):
         distribution for initial value (Defaults to Flat())
     """
 
-    def __init__(self, tau=None, init=continuous.Flat.dist(), sd=None, mu=0.,
+    def __init__(self, tau=None, init=Flat.dist(), sd=None, mu=0.,
                  *args, **kwargs):
         super(GaussianRandomWalk, self).__init__(*args, **kwargs)
-        self.tau = tau
-        self.sd = sd
-        self.mu = mu
+        tau, sd = get_tau_sd(tau=tau, sd=sd)
+        self.tau = tau = tt.as_tensor_variable(tau)
+        self.sd = sd = tt.as_tensor_variable(sd)
+        self.mu = mu = tt.as_tensor_variable(mu)
         self.init = init
-        self.mean = 0.
+        self.mean = tt.as_tensor_variable(0.)
 
     def logp(self, x):
         tau = self.tau
@@ -89,7 +91,7 @@ def logp(self, x):
         x_im1 = x[:-1]
         x_i = x[1:]
 
-        innov_like = continuous.Normal.dist(mu=x_im1 + mu, tau=tau, sd=sd).logp(x_i)
+        innov_like = Normal.dist(mu=x_im1 + mu, sd=sd).logp(x_i)
         return init.logp(x[0]) + tt.sum(innov_like)
 
     def _repr_latex_(self, name=None, dist=None):
@@ -124,15 +126,15 @@ class GARCH11(distribution.Continuous):
         initial_vol >= 0, distribution for initial volatility, sigma_0
     """
 
-    def __init__(self, omega=None, alpha_1=None, beta_1=None,
-                 initial_vol=None, *args, **kwargs):
+    def __init__(self, omega, alpha_1, beta_1,
+                 initial_vol, *args, **kwargs):
         super(GARCH11, self).__init__(*args, **kwargs)
 
-        self.omega = omega
-        self.alpha_1 = alpha_1
-        self.beta_1 = beta_1
+        self.omega = omega = tt.as_tensor_variable(omega)
+        self.alpha_1 = alpha_1 = tt.as_tensor_variable(alpha_1)
+        self.beta_1 = beta_1 = tt.as_tensor_variable(beta_1)
         self.initial_vol = initial_vol
-        self.mean = 0
+        self.mean = tt.as_tensor_variable(0.)
 
     def get_volatility(self, x):
         x = x[:-1]
@@ -149,7 +151,7 @@ def volatility_update(x, vol, w, a, b):
 
     def logp(self, x):
         vol = self.get_volatility(x)
-        return tt.sum(continuous.Normal.dist(0, sd=vol).logp(x))
+        return tt.sum(Normal.dist(0., sd=vol).logp(x))
 
     def _repr_latex_(self, name=None, dist=None):
         if dist is None:
@@ -178,7 +180,7 @@ class EulerMaruyama(distribution.Continuous):
     """
     def __init__(self, dt, sde_fn, sde_pars, *args, **kwds):
         super(EulerMaruyama, self).__init__(*args, **kwds)
-        self.dt = dt
+        self.dt = dt = tt.as_tensor_variable(dt)
         self.sde_fn = sde_fn
         self.sde_pars = sde_pars
 
@@ -187,7 +189,7 @@ def logp(self, x):
         f, g = self.sde_fn(x[:-1], *self.sde_pars)
         mu = xt + self.dt * f
         sd = tt.sqrt(self.dt) * g
-        return tt.sum(continuous.Normal.dist(mu=mu, sd=sd).logp(x[1:]))
+        return tt.sum(Normal.dist(mu=mu, sd=sd).logp(x[1:]))
 
     def _repr_latex_(self, name=None, dist=None):
         if dist is None:
@@ -210,7 +212,7 @@ class MvGaussianRandomWalk(distribution.Continuous):
     init : distribution
         distribution for initial value (Defaults to Flat())
     """
-    def __init__(self, mu=0., cov=None, init=continuous.Flat.dist(),
+    def __init__(self, mu=0., cov=None, init=Flat.dist(),
                  *args, **kwargs):
         super(MvGaussianRandomWalk, self).__init__(*args, **kwargs)
         if cov is None:
@@ -220,9 +222,9 @@ def __init__(self, mu=0., cov=None, init=continuous.Flat.dist(),
         if cov.ndim != 2:
             raise ValueError('cov must be two dimensional.')
         self.cov = cov
-        self.mu = mu
+        self.mu = mu = tt.as_tensor_variable(mu)
         self.init = init
-        self.mean = 0.
+        self.mean = tt.as_tensor_variable(0.)
 
     def logp(self, x):
         cov = self.cov
@@ -259,13 +261,13 @@ class MvStudentTRandomWalk(distribution.Continuous):
     init : distribution
         distribution for initial value (Defaults to Flat())
     """
-    def __init__(self, nu, mu=0., cov=None, init=continuous.Flat.dist(),
+    def __init__(self, nu, mu=0., cov=None, init=Flat.dist(),
                  *args, **kwargs):
         super(MvStudentTRandomWalk, self).__init__(*args, **kwargs)
-        self.mu = mu
-        self.nu = nu
+        self.mu = mu = tt.as_tensor_variable(mu)
+        self.nu = nu = tt.as_tensor_variable(nu)
         self.init = init
-        self.mean = 0.
+        self.mean = tt.as_tensor_variable(0.)
 
         if cov is None:
             raise ValueError('A covariance matrix must be provided as cov argument.')

pymc3/tests/test_distributions.py

@@ -7,9 +7,9 @@
 from ..model import Model, Point, Potential
 from ..blocking import DictToVarBijection, DictToArrayBijection, ArrayOrdering
 from ..distributions import (DensityDist, Categorical, Multinomial, VonMises, Dirichlet,
-                             MvStudentT, MvNormal, ZeroInflatedPoisson,
+                             MvStudentT, MvNormal, ZeroInflatedPoisson, GaussianRandomWalk,
                              ZeroInflatedNegativeBinomial, Constant, Poisson, Bernoulli, Beta,
-                             BetaBinomial, HalfStudentT, StudentT, Weibull, Pareto,
+                             BetaBinomial, HalfStudentT, StudentT, Weibull, Pareto, NormalMixture,
                              InverseGamma, Gamma, Cauchy, HalfCauchy, Lognormal, Laplace,
                              NegativeBinomial, Geometric, Exponential, ExGaussian, Normal,
                              Flat, LKJCorr, Wald, ChiSquared, HalfNormal, DiscreteUniform,
@@ -822,3 +822,17 @@ def ref_pdf(value):
                     )
 
                 self.pymc3_matches_scipy(TestedInterpolated, R, {}, ref_pdf)
+
+
+def test_repr_latex_():
+    with Model():
+        x0 = Binomial('Discrete', p=.5, n=10)
+        x1 = Normal('Continuous', mu=0., sd=1.)
+        x2 = GaussianRandomWalk('Timeseries', mu=x1, sd=1., shape=2)
+        x3 = MvStudentT('Multivariate', nu=5, mu=x2, Sigma=np.diag(np.ones(2)), shape=2)
+        x4 = NormalMixture('Mixture', w=np.array([.5, .5]), mu=x3, sd=x0)
+    assert x0._repr_latex_()=='$Discrete \\sim \\text{Binomial}(\\mathit{n}=10, \\mathit{p}=0.5)$'
+    assert x1._repr_latex_()=='$Continuous \\sim \\text{Normal}(\\mathit{mu}=0.0, \\mathit{sd}=1.0)$'
+    assert x2._repr_latex_()=='$Timeseries \\sim \\text{GaussianRandomWalk}(\\mathit{mu}=Continuous, \\mathit{sd}=1.0)$'
+    assert x3._repr_latex_()=='$Multivariate \\sim \\text{MvStudentT}(\\mathit{nu}=5, \\mathit{mu}=Timeseries, \\mathit{Sigma}=array)$'
+    assert x4._repr_latex_()=='$Mixture \\sim \\text{NormalMixture}(\\mathit{w}=array, \\mathit{mu}=Multivariate, \\mathit{sigma}=f(Discrete))$'