diff --git a/manual/develop/en/.buildinfo b/manual/develop/en/.buildinfo index 9de48e36..13933b44 100644 --- a/manual/develop/en/.buildinfo +++ b/manual/develop/en/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: e015b6dc9bfc7443fb19c91af7441403 +config: 3acbb30cac794629572a38a5d72c4acc tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/manual/develop/en/_modules/index.html b/manual/develop/en/_modules/index.html index bfb8bab6..b32c94d8 100644 --- a/manual/develop/en/_modules/index.html +++ b/manual/develop/en/_modules/index.html @@ -1,18 +1,22 @@ - + - Overview: module code — PHYSBO 1.2-dev documentation - - + Overview: module code — PHYSBO 1.1.1 documentation + + + + - - - + + + + + @@ -31,7 +35,7 @@ PHYSBO
- 1.2 + 1.1
diff --git a/manual/develop/en/_modules/physbo/blm/basis/fourier.html b/manual/develop/en/_modules/physbo/blm/basis/fourier.html index 51f4d423..eb18c9af 100644 --- a/manual/develop/en/_modules/physbo/blm/basis/fourier.html +++ b/manual/develop/en/_modules/physbo/blm/basis/fourier.html @@ -1,18 +1,22 @@ - + - physbo.blm.basis.fourier — PHYSBO 1.2-dev documentation - - + physbo.blm.basis.fourier — PHYSBO 1.1.1 documentation + + + + - - - + + + + + @@ -31,7 +35,7 @@ PHYSBO
- 1.2 + 1.1
@@ -81,7 +85,9 @@

Source code for physbo.blm.basis.fourier

 import numpy as np
 
 
-
[docs]class fourier:
+

+[docs]
+class fourier:
     """
     random feature maps
     ``Psi(X; W,b) = cos[X * Wt + b] * alpha``
@@ -124,7 +130,9 @@ 
Source code for physbo.blm.basis.fourier
         self.params = params
         self.nbasis = self.params[1].shape[0]
 
-
[docs]    def get_basis(self, X, params=None):
+

+[docs]
+    def get_basis(self, X, params=None):
         """
         compute the value of basis
 
@@ -153,7 +161,10 @@ 
Source code for physbo.blm.basis.fourier
 
         return np.cos(np.dot(X, params[0].transpose()) + params[1]) * params[2]

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         update basis parameters
 
@@ -167,7 +178,10 @@ 
Source code for physbo.blm.basis.fourier
         self._check_len_params(params)
         self.params = params

 
-
[docs]    def show(self):
+
+

+[docs]
+    def show(self):
         """
         print parameters
         """
@@ -175,6 +189,7 @@ 
Source code for physbo.blm.basis.fourier
         print("b = ", self.params[1])
         print("alpha = ", self.params[2])

 
+
     def _check_params(self, params):
         """
         Parameters
@@ -218,6 +233,7 @@ 
Source code for physbo.blm.basis.fourier
             else:
                 if isinstance(params[2], str):
                     raise ValueError("The third entry of <params> must be a scalar.")

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/blm/core/model.html b/manual/develop/en/_modules/physbo/blm/core/model.html
index d96f6314..87010757 100644
--- a/manual/develop/en/_modules/physbo/blm/core/model.html
+++ b/manual/develop/en/_modules/physbo/blm/core/model.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.blm.core.model — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.blm.core.model — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -81,7 +85,9 @@ 
Source code for physbo.blm.core.model
 from .. import inf
 
 
-
[docs]class model:
+

+[docs]
+class model:
     """
     Baysean Linear Model
 
@@ -107,7 +113,9 @@ 
Source code for physbo.blm.core.model
         self._set_options(options)
         self.stats = ()
 
-
[docs]    def prepare(self, X, t, Psi=None):
+

+[docs]
+    def prepare(self, X, t, Psi=None):
         """
         initializes model by using the first training dataset
 
@@ -129,7 +137,10 @@ 
Source code for physbo.blm.core.model
         else:
             pass

 
-
[docs]    def update_stats(self, x, t, psi=None):
+
+

+[docs]
+    def update_stats(self, x, t, psi=None):
         """
         updates model by using another training data
 
@@ -151,7 +162,10 @@ 
Source code for physbo.blm.core.model
         else:
             pass

 
-
[docs]    def get_post_params_mean(self):
+
+

+[docs]
+    def get_post_params_mean(self):
         """
         calculates posterior mean of weights
 
@@ -166,7 +180,10 @@ 
Source code for physbo.blm.core.model
         if self.method == "exact":
             self.lik.linear.params = inf.exact.get_post_params_mean(blm=self)

 
-
[docs]    def get_post_fmean(self, X, Psi=None, w=None):
+
+

+[docs]
+    def get_post_fmean(self, X, Psi=None, w=None):
         """
         calculates posterior mean of model (function)
 
@@ -189,7 +206,10 @@ 
Source code for physbo.blm.core.model
             pass
         return fmu

 
-
[docs]    def sampling(self, w_mu=None, N=1, alpha=1.0):
+
+

+[docs]
+    def sampling(self, w_mu=None, N=1, alpha=1.0):
         """
         draws samples of weights
 
@@ -221,7 +241,10 @@ 
Source code for physbo.blm.core.model
             pass
         return w_hat

 
-
[docs]    def post_sampling(self, Xtest, Psi=None, N=1, alpha=1.0):
+
+

+[docs]
+    def post_sampling(self, Xtest, Psi=None, N=1, alpha=1.0):
         """
         draws samples of mean value of model
 
@@ -247,7 +270,10 @@ 
Source code for physbo.blm.core.model
         w_hat = self.sampling(N=N, alpha=alpha)
         return Psi.dot(w_hat) + self.lik.linear.bias

 
-
[docs]    def predict_sampling(self, Xtest, Psi=None, N=1):
+
+

+[docs]
+    def predict_sampling(self, Xtest, Psi=None, N=1):
         """
         draws samples from model
 
@@ -272,7 +298,10 @@ 
Source code for physbo.blm.core.model
         A = np.random.randn(Xtest.shape[0], N)
         return fmean + np.sqrt(self.lik.cov.sigma2) * A

 
-
[docs]    def get_post_fcov(self, X, Psi=None, diag=True):
+
+

+[docs]
+    def get_post_fcov(self, X, Psi=None, diag=True):
         """
         calculates posterior covariance of model
 
@@ -301,6 +330,7 @@ 
Source code for physbo.blm.core.model
             pass
         return fcov

 
+
     def _set_options(self, options):
         """
         read options
@@ -327,6 +357,7 @@ 
Source code for physbo.blm.core.model
         if prior is None:
             prior = prior.gauss(self.nbasis)
         self.prior = prior

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/blm/inf/exact.html b/manual/develop/en/_modules/physbo/blm/inf/exact.html
index f6b6efd4..ea72d3ed 100644
--- a/manual/develop/en/_modules/physbo/blm/inf/exact.html
+++ b/manual/develop/en/_modules/physbo/blm/inf/exact.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.blm.inf.exact — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.blm.inf.exact — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -83,7 +87,9 @@ 
Source code for physbo.blm.inf.exact
 import physbo.misc as misc
 
 
-
[docs]def prepare(blm, X, t, Psi=None):
+

+[docs]
+def prepare(blm, X, t, Psi=None):
     """
     initializes auxiaialy parameters for quick sampling
 
@@ -111,7 +117,10 @@ 
Source code for physbo.blm.inf.exact
     blm.stats = (U, b, alpha)

 
 
-
[docs]def update_stats(blm, x, t, psi=None):
+
+

+[docs]
+def update_stats(blm, x, t, psi=None):
     """
     calculates new auxiaialy parameters for quick sampling by fast-update
 
@@ -144,7 +153,10 @@ 
Source code for physbo.blm.inf.exact
     return (U, b, alpha)

 
 
-
[docs]def sampling(blm, w_mu=None, N=1, alpha=1.0):
+
+

+[docs]
+def sampling(blm, w_mu=None, N=1, alpha=1.0):
     """
     draws samples of weights
 
@@ -180,7 +192,10 @@ 
Source code for physbo.blm.inf.exact
     return (invUz.transpose() + w_mu).transpose()

 
 
-
[docs]def get_post_params_mean(blm):
+
+

+[docs]
+def get_post_params_mean(blm):
     """
     calculates mean of weight
 
@@ -195,7 +210,10 @@ 
Source code for physbo.blm.inf.exact
     return blm.stats[2] * blm.lik.cov.prec

 
 
-
[docs]def get_post_fmean(blm, X, Psi=None, w=None):
+
+

+[docs]
+def get_post_fmean(blm, X, Psi=None, w=None):
     """
     calculates posterior mean of model
 
@@ -223,7 +241,10 @@ 
Source code for physbo.blm.inf.exact
     return Psi.dot(w) + blm.lik.linear.bias

 
 
-
[docs]def get_post_fcov(blm, X, Psi=None, diag=True):
+
+

+[docs]
+def get_post_fcov(blm, X, Psi=None, diag=True):
     """
     calculates posterior covariance of model
 
@@ -262,6 +283,7 @@ 
Source code for physbo.blm.inf.exact
         fcov = np.dot(RT, R)
 
     return fcov

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/blm/lik/gauss.html b/manual/develop/en/_modules/physbo/blm/lik/gauss.html
index 61240582..1e1f9ef3 100644
--- a/manual/develop/en/_modules/physbo/blm/lik/gauss.html
+++ b/manual/develop/en/_modules/physbo/blm/lik/gauss.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.blm.lik.gauss — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.blm.lik.gauss — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.blm.lik.gauss
 import numpy as np
 
 
-
[docs]class gauss:
+

+[docs]
+class gauss:
     """
     Gaussian
 
@@ -97,7 +103,9 @@ 
Source code for physbo.blm.lik.gauss
         self.cov = cov
         self.stats = ()
 
-
[docs]    def get_cov(self, N, params=None):
+

+[docs]
+    def get_cov(self, N, params=None):
         """
         Returns covariance matrix
 
@@ -119,7 +127,10 @@ 
Source code for physbo.blm.lik.gauss
 
         return self.cov.get_cov(N, params)

 
-
[docs]    def get_prec(self, N, params=None):
+
+

+[docs]
+    def get_prec(self, N, params=None):
         """
         Returns precision matrix
 
@@ -142,7 +153,10 @@ 
Source code for physbo.blm.lik.gauss
 
         return self.cov.get_cov(N, params)

 
-
[docs]    def get_basis(self, X):
+
+

+[docs]
+    def get_basis(self, X):
         """
         calculates value of basis function at input
 
@@ -157,7 +171,10 @@ 
Source code for physbo.blm.lik.gauss
         """
         return self.linear.basis.get_basis(X)

 
-
[docs]    def get_mean(self, X, Psi=None, params=None, bias=None):
+
+

+[docs]
+    def get_mean(self, X, Psi=None, params=None, bias=None):
         """
         calculates mean value
 
@@ -178,19 +195,28 @@ 
Source code for physbo.blm.lik.gauss
         """
         return self.linear.get_mean(X, Psi, params, bias)

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         sets parameters
         """
         self.linear.set_params(params)

 
-
[docs]    def set_bias(self, bias):
+
+

+[docs]
+    def set_bias(self, bias):
         """
         sets bias
         """
         self.linear.set_bias(bias)

 
-
[docs]    def sampling(self, fmean):
+
+

+[docs]
+    def sampling(self, fmean):
         """
         draws samples
 
@@ -205,7 +231,9 @@ 
Source code for physbo.blm.lik.gauss
         """
         num_data = fmean.shape[0]
         eps = np.sqrt(self.cov.sigma2) * np.random.randn(num_data)
-        return fmean + eps

+        return fmean + eps

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/blm/lik/linear.html b/manual/develop/en/_modules/physbo/blm/lik/linear.html
index 236aecdd..0d3e5f14 100644
--- a/manual/develop/en/_modules/physbo/blm/lik/linear.html
+++ b/manual/develop/en/_modules/physbo/blm/lik/linear.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.blm.lik.linear — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.blm.lik.linear — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.blm.lik.linear
 import numpy as np
 
 
-
[docs]class linear:
+

+[docs]
+class linear:
     """
 
     Attributes
@@ -106,7 +112,9 @@ 
Source code for physbo.blm.lik.linear
             self.params = np.zeros(self.nbasis)
         self.nparams = self.nbasis
 
-
[docs]    def get_mean(self, X, Psi=None, params=None, bias=None):
+

+[docs]
+    def get_mean(self, X, Psi=None, params=None, bias=None):
         """
         calculate mean values
 
@@ -140,7 +148,10 @@ 
Source code for physbo.blm.lik.linear
 
         return Psi.dot(params) + bias

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         set parameters
 
@@ -150,7 +161,10 @@ 
Source code for physbo.blm.lik.linear
         """
         self.params = params

 
-
[docs]    def set_bias(self, bias):
+
+

+[docs]
+    def set_bias(self, bias):
         """
         set bias
 
@@ -160,7 +174,10 @@ 
Source code for physbo.blm.lik.linear
         """
         self.bias = bias

 
-
[docs]    def _init_params(self, params):
+
+

+[docs]
+    def _init_params(self, params):
         """
         initialize parameters
 
@@ -174,6 +191,7 @@ 
Source code for physbo.blm.lik.linear
 
         self.params = params

 
+
     def _init_bias(self, bias):
         """
         initialize bias
@@ -187,6 +205,7 @@ 
Source code for physbo.blm.lik.linear
             self.bias = 0
 
         self.bias = bias

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/blm/predictor.html b/manual/develop/en/_modules/physbo/blm/predictor.html
index fad0b2b5..a03a2b7a 100644
--- a/manual/develop/en/_modules/physbo/blm/predictor.html
+++ b/manual/develop/en/_modules/physbo/blm/predictor.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.blm.predictor — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.blm.predictor — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.blm.predictor
 import physbo.predictor
 
 
-
[docs]class predictor(physbo.predictor.base_predictor):
+

+[docs]
+class predictor(physbo.predictor.base_predictor):
     """Predictor using Baysean linear model
 
     Attributes
@@ -106,7 +112,9 @@ 
Source code for physbo.blm.predictor
         super(predictor, self).__init__(config, model)
         self.blm = None
 
-
[docs]    def fit(self, training, num_basis=None):
+

+[docs]
+    def fit(self, training, num_basis=None):
         """
         fit model to training dataset
 
@@ -126,7 +134,10 @@ 
Source code for physbo.blm.predictor
         self.blm = self.model.export_blm(num_basis)
         self.delete_stats()

 
-
[docs]    def prepare(self, training):
+
+

+[docs]
+    def prepare(self, training):
         """
         initializes model by using training data set
 
@@ -137,13 +148,19 @@ 
Source code for physbo.blm.predictor
         """
         self.blm.prepare(training.X, training.t, training.Z)

 
-
[docs]    def delete_stats(self):
+
+

+[docs]
+    def delete_stats(self):
         """
         resets model
         """
         self.blm.stats = None

 
-
[docs]    def get_basis(self, X):
+
+

+[docs]
+    def get_basis(self, X):
         """
         calculates feature maps Psi(X)
 
@@ -159,7 +176,10 @@ 
Source code for physbo.blm.predictor
         """
         return self.blm.lik.get_basis(X)

 
-
[docs]    def get_post_fmean(self, training, test):
+
+

+[docs]
+    def get_post_fmean(self, training, test):
         """
         calculates posterior mean value of model
 
@@ -178,7 +198,10 @@ 
Source code for physbo.blm.predictor
             self.prepare(training)
         return self.blm.get_post_fmean(test.X, test.Z)

 
-
[docs]    def get_post_fcov(self, training, test):
+
+

+[docs]
+    def get_post_fcov(self, training, test):
         """
         calculates posterior variance-covariance matrix of model
 
@@ -197,7 +220,10 @@ 
Source code for physbo.blm.predictor
             self.prepare(training)
         return self.blm.get_post_fcov(test.X, test.Z)

 
-
[docs]    def get_post_params(self, training, test):
+
+

+[docs]
+    def get_post_params(self, training, test):
         """
         calculates posterior weights
 
@@ -216,7 +242,10 @@ 
Source code for physbo.blm.predictor
             self.prepare(training)
         return self.blm.get_post_params_mean()

 
-
[docs]    def get_post_samples(self, training, test, N=1, alpha=1.0):
+
+

+[docs]
+    def get_post_samples(self, training, test, N=1, alpha=1.0):
         """
         draws samples of mean values of model
 
@@ -241,7 +270,10 @@ 
Source code for physbo.blm.predictor
             self.prepare(training)
         return self.blm.post_sampling(test.X, Psi=test.Z, N=N, alpha=alpha)

 
-
[docs]    def get_predict_samples(self, training, test, N=1):
+
+

+[docs]
+    def get_predict_samples(self, training, test, N=1):
         """
         draws samples of values of model
 
@@ -266,7 +298,10 @@ 
Source code for physbo.blm.predictor
             self.prepare(training)
         return self.blm.predict_sampling(test.X, Psi=test.Z, N=N).transpose()

 
-
[docs]    def update(self, training, test):
+
+

+[docs]
+    def update(self, training, test):
         """
         updates the model.
 
@@ -307,7 +342,9 @@ 
Source code for physbo.blm.predictor
                 if test.Z is None:
                     self.blm.update_stats(test.X[n, :], test.t[n])
                 else:
-                    self.blm.update_stats(test.X[n, :], test.t[n], psi=test.Z[n, :])

+                    self.blm.update_stats(test.X[n, :], test.t[n], psi=test.Z[n, :])

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/blm/prior/gauss.html b/manual/develop/en/_modules/physbo/blm/prior/gauss.html
index 5f8eb159..4414208a 100644
--- a/manual/develop/en/_modules/physbo/blm/prior/gauss.html
+++ b/manual/develop/en/_modules/physbo/blm/prior/gauss.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.blm.prior.gauss — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.blm.prior.gauss — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.blm.prior.gauss
 import numpy as np
 
 
-
[docs]class cov_const:
+

+[docs]
+class cov_const:
     """
     isotropic variance-covariance
 
@@ -108,7 +114,9 @@ 
Source code for physbo.blm.prior.gauss
             self.params = np.log(1)
         self.sigma2, self.prec = self._trans_params(params)
 
-
[docs]    def get_cov(self, nbasis, params=None):
+

+[docs]
+    def get_cov(self, nbasis, params=None):
         """
         computes the covariance
 
@@ -130,7 +138,10 @@ 
Source code for physbo.blm.prior.gauss
         sigma2, prec = self._trans_params(params)
         return np.identity(nbasis) * sigma2

 
-
[docs]    def get_prec(self, nbasis, params=None):
+
+

+[docs]
+    def get_prec(self, nbasis, params=None):
         """
         computes the precision
 
@@ -152,7 +163,10 @@ 
Source code for physbo.blm.prior.gauss
         sigma2, prec = self._trans_params(params)
         return np.identity(nbasis) * prec

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         sets params
 
@@ -164,6 +178,7 @@ 
Source code for physbo.blm.prior.gauss
         self.params = params
         self.sigma2, self.prec = self._trans_params(params)

 
+
     def _trans_params(self, params=None):
         """
         calculates variance and precise from params
@@ -190,7 +205,10 @@ 
Source code for physbo.blm.prior.gauss
         return sigma2, prec

 
 
-
[docs]class gauss:
+
+

+[docs]
+class gauss:
     """
     Gaussian prior
 
@@ -214,7 +232,9 @@ 
Source code for physbo.blm.prior.gauss
         self._init_cov(cov)
         self.nbasis = nbasis
 
-
[docs]    def get_mean(self, params=None):
+

+[docs]
+    def get_mean(self, params=None):
         """
         calculates the mean value of priors
 
@@ -230,7 +250,10 @@ 
Source code for physbo.blm.prior.gauss
         """
         return np.zeros(self.nbasis)

 
-
[docs]    def get_cov(self, params=None):
+
+

+[docs]
+    def get_cov(self, params=None):
         """
         calculates the variance-covariance matrix of priors
 
@@ -246,7 +269,10 @@ 
Source code for physbo.blm.prior.gauss
         """
         return self.cov.get_cov(self.nbasis, params)

 
-
[docs]    def get_prec(self, params=None):
+
+

+[docs]
+    def get_prec(self, params=None):
         """
         calculates the precise matrix of priors
 
@@ -262,7 +288,10 @@ 
Source code for physbo.blm.prior.gauss
         """
         return self.cov.get_prec(self.nbasis, params)

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         sets params
 
@@ -273,6 +302,7 @@ 
Source code for physbo.blm.prior.gauss
         """
         self.cov.set_params(params)

 
+
     def _init_cov(self, cov):
         """
         initialize covariance
@@ -285,6 +315,7 @@ 
Source code for physbo.blm.prior.gauss
         self.cov = cov
         if cov is None:
             self.cov = cov_const()

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/core/learning.html b/manual/develop/en/_modules/physbo/gp/core/learning.html
index a019d708..3d6c5cef 100644
--- a/manual/develop/en/_modules/physbo/gp/core/learning.html
+++ b/manual/develop/en/_modules/physbo/gp/core/learning.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.core.learning — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.core.learning — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -82,7 +86,9 @@ 
Source code for physbo.gp.core.learning
 import scipy.optimize
 
 
-
[docs]class batch(object):
+

+[docs]
+class batch(object):
     """
     basis class for batch learning
     """
@@ -99,7 +105,9 @@ 
Source code for physbo.gp.core.learning
         self.gp = gp
         self.config = config
 
-
[docs]    def run(self, X, t):
+

+[docs]
+    def run(self, X, t):
         """
         Performing optimization using the L-BFGS-B algorithm
 
@@ -130,7 +138,10 @@ 
Source code for physbo.gp.core.learning
         params = self.one_run(params, sub_X, sub_t)
         return params

 
-
[docs]    def one_run(self, params, X, t, max_iter=None):
+
+

+[docs]
+    def one_run(self, params, X, t, max_iter=None):
         """
 
         Parameters
@@ -172,7 +183,10 @@ 
Source code for physbo.gp.core.learning
 
         return res.x

 
-
+

 
 
-
[docs]class online(object):
+
+

+[docs]
+class online(object):
     """
     base class for online learning
     """
@@ -222,7 +240,9 @@ 
Source code for physbo.gp.core.learning
         self.config = config
         self.num_iter = 0
 
-
[docs]    def run(self, X, t):
+

+[docs]
+    def run(self, X, t):
         """
         Run initial search and hyper parameter running.
 
@@ -262,7 +282,10 @@ 
Source code for physbo.gp.core.learning
 
         return params

 
-
[docs]    def one_run(self, params, X, t, max_epoch=None, is_disp=False):
+
+

+[docs]
+    def one_run(self, params, X, t, max_epoch=None, is_disp=False):
         """
 
         Parameters
@@ -319,7 +342,10 @@ 
Source code for physbo.gp.core.learning
         self.reset()
         return params

 
-
[docs]    def disp_marlik(self, params, eval_X, eval_t, num_epoch=None):
+
+

+[docs]
+    def disp_marlik(self, params, eval_X, eval_t, num_epoch=None):
         """
         Displaying marginal likelihood
 
@@ -346,7 +372,10 @@ 
Source code for physbo.gp.core.learning
 
         print("marginal likelihood", marlik)

 
-
+
 
 
-
[docs]class adam(online):
+

+[docs]
+class adam(online):
     """default"""
 
     def __init__(self, gp, config):
@@ -407,12 +443,17 @@ 
Source code for physbo.gp.core.learning
         self.m = np.zeros(self.gp.num_params)
         self.v = np.zeros(self.gp.num_params)
 
-
[docs]    def reset(self):
+

+[docs]
+    def reset(self):
         self.m = np.zeros(self.gp.num_params)
         self.v = np.zeros(self.gp.num_params)
         self.num_iter = 0

 
-
[docs]    def get_one_update(self, params, X, t):
+
+

+[docs]
+    def get_one_update(self, params, X, t):
         """
 
         Parameters
@@ -433,7 +474,9 @@ 
Source code for physbo.gp.core.learning
         self.v = self.v * self.gamma + grad**2 * (1 - self.gamma)
         hat_m = self.m / (1 - self.beta ** (self.num_iter))
         hat_v = self.v / (1 - self.gamma ** (self.num_iter))
-        return -self.alpha * hat_m / (np.sqrt(hat_v) + self.epsilon)

+        return -self.alpha * hat_m / (np.sqrt(hat_v) + self.epsilon)

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/core/model.html b/manual/develop/en/_modules/physbo/gp/core/model.html
index eb653bc6..5a9b13ce 100644
--- a/manual/develop/en/_modules/physbo/gp/core/model.html
+++ b/manual/develop/en/_modules/physbo/gp/core/model.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.core.model — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.core.model — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -85,7 +89,9 @@ 
Source code for physbo.gp.core.model
 from physbo.gp.core.prior import prior
 
 
-
[docs]class model:
+

+[docs]
+class model:
     def __init__(self, lik, mean, cov, inf="exact"):
         """
 
@@ -103,7 +109,9 @@ 
Source code for physbo.gp.core.model
         self.params = self.cat_params(self.lik.params, self.prior.params)
         self.stats = ()
 
-
[docs]    def cat_params(self, lik_params, prior_params):
+

+[docs]
+    def cat_params(self, lik_params, prior_params):
         """
         Concatinate the likelihood and prior parameters
 
@@ -121,7 +129,10 @@ 
Source code for physbo.gp.core.model
         params = np.append(lik_params, prior_params)
         return params

 
-
[docs]    def decomp_params(self, params=None):
+
+

+[docs]
+    def decomp_params(self, params=None):
         """
         decomposing the parameters to those of likelifood and priors
 
@@ -142,7 +153,10 @@ 
Source code for physbo.gp.core.model
         prior_params = params[self.lik.num_params :]
         return lik_params, prior_params

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         Setting parameters
 
@@ -156,7 +170,10 @@ 
Source code for physbo.gp.core.model
         self.lik.set_params(lik_params)
         self.prior.set_params(prior_params)

 
-
[docs]    def sub_sampling(self, X, t, N):
+
+

+[docs]
+    def sub_sampling(self, X, t, N):
         """
         Make subset for sampling
 
@@ -184,7 +201,10 @@ 
Source code for physbo.gp.core.model
             subt = t
         return subX, subt

 
-
[docs]    def export_blm(self, num_basis):
+
+

+[docs]
+    def export_blm(self, num_basis):
         """
         Exporting the blm(Baysean linear model) predictor
 
@@ -210,7 +230,10 @@ 
Source code for physbo.gp.core.model
 
         return blr

 
-
[docs]    def eval_marlik(self, params, X, t, N=None):
+
+

+[docs]
+    def eval_marlik(self, params, X, t, N=None):
         """
         Evaluating marginal likelihood.
 
@@ -238,7 +261,10 @@ 
Source code for physbo.gp.core.model
 
         return marlik

 
-
[docs]    def get_grad_marlik(self, params, X, t, N=None):
+
+

+[docs]
+    def get_grad_marlik(self, params, X, t, N=None):
         """
         Evaluating gradiant of marginal likelihood.
 
@@ -264,7 +290,10 @@ 
Source code for physbo.gp.core.model
             grad_marlik = inf.exact.get_grad_marlik(self, subX, subt, params=params)
         return grad_marlik

 
-
[docs]    def get_params_bound(self):
+
+

+[docs]
+    def get_params_bound(self):
         """
         Getting boundary of the parameters.
 
@@ -283,7 +312,10 @@ 
Source code for physbo.gp.core.model
             bound.extend(self.prior.cov.get_params_bound())
         return bound

 
-
[docs]    def prepare(self, X, t, params=None):
+
+

+[docs]
+    def prepare(self, X, t, params=None):
         """
 
         Parameters
@@ -304,7 +336,10 @@ 
Source code for physbo.gp.core.model
         else:
             pass

 
-
[docs]    def get_post_fmean(self, X, Z, params=None):
+
+

+[docs]
+    def get_post_fmean(self, X, Z, params=None):
         """
         Calculating posterior mean of model (function)
 
@@ -328,7 +363,10 @@ 
Source code for physbo.gp.core.model
 
         return post_fmu

 
-
[docs]    def get_post_fcov(self, X, Z, params=None, diag=True):
+
+

+[docs]
+    def get_post_fcov(self, X, Z, params=None, diag=True):
         """
         Calculating posterior covariance matrix of model (function)
 
@@ -356,7 +394,10 @@ 
Source code for physbo.gp.core.model
 
         return post_fcov

 
-
[docs]    def post_sampling(self, X, Z, params=None, N=1, alpha=1):
+
+

+[docs]
+    def post_sampling(self, X, Z, params=None, N=1, alpha=1):
         """
         draws samples of mean value of model
 
@@ -382,7 +423,10 @@ 
Source code for physbo.gp.core.model
         fcov = self.get_post_fcov(X, Z, params=None, diag=False)
         return np.random.multivariate_normal(fmean, fcov * alpha**2, N)

 
-
[docs]    def predict_sampling(self, X, Z, params=None, N=1):
+
+

+[docs]
+    def predict_sampling(self, X, Z, params=None, N=1):
         """
 
         Parameters
@@ -415,7 +459,10 @@ 
Source code for physbo.gp.core.model
 
         return np.random.multivariate_normal(fmean, fcov, N)

 
-
[docs]    def print_params(self):
+
+

+[docs]
+    def print_params(self):
         """
         Printing parameters
         """
@@ -429,7 +476,10 @@ 
Source code for physbo.gp.core.model
         print("covariance parameter in GP prior: ", self.prior.cov.params)
         print("\n")

 
-
[docs]    def get_cand_params(self, X, t):
+
+

+[docs]
+    def get_cand_params(self, X, t):
         """
         Getting candidate for parameters
 
@@ -464,7 +514,10 @@ 
Source code for physbo.gp.core.model
 
         return params

 
-
[docs]    def fit(self, X, t, config):
+
+

+[docs]
+    def fit(self, X, t, config):
         """
         Fitting function (update parameters)
 
@@ -489,7 +542,9 @@ 
Source code for physbo.gp.core.model
             bfgs = learning.batch(self, config)
             params = bfgs.run(X, t)
 
-        self.set_params(params)

+        self.set_params(params)

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/core/prior.html b/manual/develop/en/_modules/physbo/gp/core/prior.html
index 5527fbe3..c65007b3 100644
--- a/manual/develop/en/_modules/physbo/gp/core/prior.html
+++ b/manual/develop/en/_modules/physbo/gp/core/prior.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.core.prior — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.core.prior — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -81,7 +85,9 @@ 
Source code for physbo.gp.core.prior
 import scipy
 
 
-
[docs]class prior:
+

+[docs]
+class prior:
     """prior of gaussian process"""
 
     def __init__(self, mean, cov):
@@ -99,7 +105,9 @@ 
Source code for physbo.gp.core.prior
         self.num_params = self.cov.num_params + self.mean.num_params
         self.params = self.cat_params(self.mean.params, self.cov.params)
 
-
[docs]    def cat_params(self, mean_params, cov_params):
+

+[docs]
+    def cat_params(self, mean_params, cov_params):
         """
 
         Parameters
@@ -114,7 +122,10 @@ 
Source code for physbo.gp.core.prior
         """
         return np.append(mean_params, cov_params)

 
-
[docs]    def decomp_params(self, params):
+
+

+[docs]
+    def decomp_params(self, params):
         """
         decomposing the parameters to those of mean values and covariance matrix for priors
 
@@ -135,7 +146,10 @@ 
Source code for physbo.gp.core.prior
         cov_params = params[self.mean.num_params :]
         return mean_params, cov_params

 
-
[docs]    def get_mean(self, num_data, params=None):
+
+

+[docs]
+    def get_mean(self, num_data, params=None):
         """
         Calculating the mean value of priors
 
@@ -153,7 +167,10 @@ 
Source code for physbo.gp.core.prior
             params = np.copy(self.params)
         return self.mean.get_mean(num_data, params[0 : self.mean.num_params])

 
-
[docs]    def get_cov(self, X, Z=None, params=None, diag=False):
+
+

+[docs]
+    def get_cov(self, X, Z=None, params=None, diag=False):
         """
         Calculating the variance-covariance matrix of priors
 
@@ -176,7 +193,10 @@ 
Source code for physbo.gp.core.prior
 
         return self.cov.get_cov(X, Z, params=params[self.mean.num_params :], diag=diag)

 
-
[docs]    def get_grad_mean(self, num_data, params=None):
+
+

+[docs]
+    def get_grad_mean(self, num_data, params=None):
         """
         Calculating the gradiant of mean values of priors
 
@@ -198,7 +218,10 @@ 
Source code for physbo.gp.core.prior
         mean_params, cov_params = self.decomp_params(params)
         return self.mean.get_grad(num_data, params=mean_params)

 
-
[docs]    def get_grad_cov(self, X, params=None):
+
+

+[docs]
+    def get_grad_cov(self, X, params=None):
         """
         Calculating the covariance matrix priors
 
@@ -219,7 +242,10 @@ 
Source code for physbo.gp.core.prior
         mean_params, cov_params = self.decomp_params(params)
         return self.cov.get_grad(X, params=cov_params)

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         Setting parameters
 
@@ -232,7 +258,10 @@ 
Source code for physbo.gp.core.prior
         self.set_mean_params(mean_params)
         self.set_cov_params(cov_params)

 
-
[docs]    def set_mean_params(self, params):
+
+

+[docs]
+    def set_mean_params(self, params):
         """
         Setting parameters for mean values of priors
 
@@ -245,7 +274,10 @@ 
Source code for physbo.gp.core.prior
             self.params[0 : self.mean.num_params] = params
             self.mean.set_params(params)

 
-
[docs]    def set_cov_params(self, params):
+
+

+[docs]
+    def set_cov_params(self, params):
         """
         Setting parameters for covariance matrix of priors
 
@@ -257,7 +289,10 @@ 
Source code for physbo.gp.core.prior
         self.params[self.mean.num_params :] = params
         self.cov.set_params(params)

 
-
[docs]    def sampling(self, X, N=1):
+
+

+[docs]
+    def sampling(self, X, N=1):
         """
         Sampling from GP prior
 
@@ -276,7 +311,9 @@ 
Source code for physbo.gp.core.prior
         G = self.get_cov(X) + 1e-8 * np.identity(num_data)
         U = scipy.linalg.cholesky(G, check_finite=False)
         Z = np.random.randn(N, num_data)
-        return np.dot(Z, U) + self.get_mean(num_data)

+        return np.dot(Z, U) + self.get_mean(num_data)

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/cov/gauss.html b/manual/develop/en/_modules/physbo/gp/cov/gauss.html
index d45319c4..30cfbbff 100644
--- a/manual/develop/en/_modules/physbo/gp/cov/gauss.html
+++ b/manual/develop/en/_modules/physbo/gp/cov/gauss.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.cov.gauss — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.cov.gauss — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -83,7 +87,9 @@ 
Source code for physbo.gp.cov.gauss
 from ._src.enhance_gauss import grad_width64
 
 
-
[docs]class gauss:
+

+[docs]
+class gauss:
     """gaussian kernel"""
 
     def __init__(
@@ -138,7 +144,9 @@ 
Source code for physbo.gp.cov.gauss
         params = self.cat_params(self.width, self.scale)
         self.set_params(params)
 
-
[docs]    def print_params(self):
+

+[docs]
+    def print_params(self):
         """
         show the current kernel parameters
 
@@ -150,7 +158,10 @@ 
Source code for physbo.gp.cov.gauss
         print(" scale2 = ", +self.scale**2)
         print(" \n")

 
-
[docs]    def prepare(self, params=None):
+
+

+[docs]
+    def prepare(self, params=None):
         """
         Setting parameters
 
@@ -176,7 +187,10 @@ 
Source code for physbo.gp.cov.gauss
 
         return params, width, scale

 
-
[docs]    def get_grad(self, X, params=None):
+
+

+[docs]
+    def get_grad(self, X, params=None):
         """
         Getting gradiant values of X
 
@@ -206,7 +220,10 @@ 
Source code for physbo.gp.cov.gauss
         grad[-1, :, :] = 2 * G
         return grad

 
-
[docs]    def get_cov(self, X, Z=None, params=None, diag=False):
+
+

+[docs]
+    def get_cov(self, X, Z=None, params=None, diag=False):
         """
         compute the covariant matrix
         Parameters
@@ -247,7 +264,10 @@ 
Source code for physbo.gp.cov.gauss
 
         return G

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         set kernel parameters
 
@@ -261,7 +281,10 @@ 
Source code for physbo.gp.cov.gauss
         self.params = params
         self.width, self.scale = self.decomp_params(params)

 
-
[docs]    def supp_params(self, params):
+
+

+[docs]
+    def supp_params(self, params):
         """
         Set maximum (minimum) values for parameters when the parameter is greater(less) than this value.
 
@@ -290,7 +313,10 @@ 
Source code for physbo.gp.cov.gauss
 
         return params

 
-
[docs]    def decomp_params(self, params):
+
+

+[docs]
+    def decomp_params(self, params):
         """
         decompose the parameters defined on the log region
         into width and scale parameters
@@ -310,7 +336,10 @@ 
Source code for physbo.gp.cov.gauss
         scale = np.exp(params[-1])
         return width, scale

 
-
[docs]    def save(self, file_name):
+
+

+[docs]
+    def save(self, file_name):
         """
         save the gaussian kernel
 
@@ -334,7 +363,10 @@ 
Source code for physbo.gp.cov.gauss
         with open(file_name, "wb") as f:
             np.savez(f, **kwarg)

 
-
[docs]    def load(self, file_name):
+
+

+[docs]
+    def load(self, file_name):
         """
         Recovering the Gaussian kernel from file
         Parameters
@@ -354,7 +386,10 @@ 
Source code for physbo.gp.cov.gauss
         params = temp["params"]
         self.set_params(params)

 
-
[docs]    def get_params_bound(self):
+
+

+[docs]
+    def get_params_bound(self):
         """
         Getting boundary array.
 
@@ -375,7 +410,10 @@ 
Source code for physbo.gp.cov.gauss
         bound.append((self.min_ln_scale, self.max_ln_scale))
         return bound

 
-
[docs]    def cat_params(self, width, scale):
+
+

+[docs]
+    def cat_params(self, width, scale):
         """
         Taking the logarithm of width and scale parameters
         and concatinate them into one ndarray
@@ -395,7 +433,10 @@ 
Source code for physbo.gp.cov.gauss
         params[-1] = np.log(scale)
         return params

 
-
[docs]    def rand_expans(self, num_basis, params=None):
+
+

+[docs]
+    def rand_expans(self, num_basis, params=None):
         """
         Kernel Expansion
 
@@ -417,7 +458,10 @@ 
Source code for physbo.gp.cov.gauss
         b = np.random.rand(num_basis) * 2 * np.pi
         return (W, b, amp)

 
-
[docs]    def get_cand_params(self, X, t):
+
+

+[docs]
+    def get_cand_params(self, X, t):
         """
         Getting candidate parameters.
 
@@ -462,7 +506,9 @@ 
Source code for physbo.gp.cov.gauss
             width = dist[(2 * n + 1) * tmp]
             scale = np.std(t)
             params = np.append(np.log(width + 1e-8), np.log(scale))
-        return params

+        return params

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/inf/exact.html b/manual/develop/en/_modules/physbo/gp/inf/exact.html
index b218a240..d165545f 100644
--- a/manual/develop/en/_modules/physbo/gp/inf/exact.html
+++ b/manual/develop/en/_modules/physbo/gp/inf/exact.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.inf.exact — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.inf.exact — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -83,7 +87,9 @@ 
Source code for physbo.gp.inf.exact
 from copy import deepcopy
 
 
-
[docs]def eval_marlik(gp, X, t, params=None):
+

+[docs]
+def eval_marlik(gp, X, t, params=None):
     """
     Evaluating marginal likelihood.
 
@@ -125,7 +131,10 @@ 
Source code for physbo.gp.inf.exact
     return marlik

 
 
-
[docs]def get_grad_marlik(gp, X, t, params=None):
+
+

+[docs]
+def get_grad_marlik(gp, X, t, params=None):
     """
     Evaluating gradiant of marginal likelihood.
 
@@ -189,7 +198,10 @@ 
Source code for physbo.gp.inf.exact
     return grad_marlik

 
 
-
[docs]def prepare(gp, X, t, params=None):
+
+

+[docs]
+def prepare(gp, X, t, params=None):
     """
 
     Parameters
@@ -228,7 +240,10 @@ 
Source code for physbo.gp.inf.exact
     return stats

 
 
-
[docs]def get_post_fmean(gp, X, Z, params=None):
+
+

+[docs]
+def get_post_fmean(gp, X, Z, params=None):
     """
     Calculating the mean of posterior
 
@@ -261,7 +276,10 @@ 
Source code for physbo.gp.inf.exact
     return G.dot(alpha) + fmu

 
 
-
[docs]def get_post_fcov(gp, X, Z, params=None, diag=True):
+
+

+[docs]
+def get_post_fcov(gp, X, Z, params=None, diag=True):
     """
     Calculating the covariance of posterior
 
@@ -301,6 +319,7 @@ 
Source code for physbo.gp.inf.exact
         post_cov = K - np.dot(invUG.transpose(), invUG)
 
     return post_cov

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/lik/gauss.html b/manual/develop/en/_modules/physbo/gp/lik/gauss.html
index 17780110..2d0c0a0b 100644
--- a/manual/develop/en/_modules/physbo/gp/lik/gauss.html
+++ b/manual/develop/en/_modules/physbo/gp/lik/gauss.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.lik.gauss — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.lik.gauss — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -81,7 +85,9 @@ 
Source code for physbo.gp.lik.gauss
 import numpy as np
 
 
-
[docs]class gauss:
+

+[docs]
+class gauss:
     """Gaussian likelihood function"""
 
     def __init__(self, std=1, max_params=1e6, min_params=1e-6):
@@ -105,7 +111,9 @@ 
Source code for physbo.gp.lik.gauss
         self.params = np.log(std)
         self.set_params(self.params)
 
-
[docs]    def supp_params(self, params=None):
+

+[docs]
+    def supp_params(self, params=None):
         """
         Set maximum (minimum) values for parameters when the parameter is greater(less) than this value.
 
@@ -129,7 +137,10 @@ 
Source code for physbo.gp.lik.gauss
 
         return params

 
-
[docs]    def trans_params(self, params=None):
+
+

+[docs]
+    def trans_params(self, params=None):
         """
         Get exp[params].
 
@@ -149,7 +160,10 @@ 
Source code for physbo.gp.lik.gauss
         std = np.exp(params)
         return std

 
-
[docs]    def get_params_bound(self):
+
+

+[docs]
+    def get_params_bound(self):
         """
         Get boundary array.
 
@@ -161,7 +175,10 @@ 
Source code for physbo.gp.lik.gauss
         bound = [(self.min_params, self.max_params) for i in range(0, self.num_params)]
         return bound

 
-
[docs]    def get_cov(self, num_data, params=None):
+
+

+[docs]
+    def get_cov(self, num_data, params=None):
         """
         Get a covariance matrix
 
@@ -181,7 +198,10 @@ 
Source code for physbo.gp.lik.gauss
         var = std**2
         return var * np.identity(num_data)

 
-
[docs]    def get_grad(self, num_data, params=None):
+
+

+[docs]
+    def get_grad(self, num_data, params=None):
         """
         Get a gradient matrix
 
@@ -201,7 +221,10 @@ 
Source code for physbo.gp.lik.gauss
         var = std**2
         return var * np.identity(num_data) * 2

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         Set parameters.
 
@@ -218,7 +241,10 @@ 
Source code for physbo.gp.lik.gauss
         self.params = self.supp_params(params)
         self.std = self.trans_params(params)

 
-
[docs]    def get_cand_params(self, t):
+
+

+[docs]
+    def get_cand_params(self, t):
         """
         Getting candidate parameters.
 
@@ -234,8 +260,11 @@ 
Source code for physbo.gp.lik.gauss
         """
         return np.log(np.std(t) / 10)

 
+
     # [TODO] Check: This function seems not to be used.
-
[docs]    def sampling(self, fmean):
+

+[docs]
+    def sampling(self, fmean):
         """
         Sampling by adding noise
 
@@ -249,7 +278,9 @@ 
Source code for physbo.gp.lik.gauss
         """
         num_data = fmean.shape[0]
         eps = self.std * np.random.randn(num_data)
-        return fmean + eps

+        return fmean + eps

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/mean/const.html b/manual/develop/en/_modules/physbo/gp/mean/const.html
index 30a3e3b2..8c78f0a1 100644
--- a/manual/develop/en/_modules/physbo/gp/mean/const.html
+++ b/manual/develop/en/_modules/physbo/gp/mean/const.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.mean.const — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.mean.const — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.gp.mean.const
 import numpy as np
 
 
-
[docs]class const:
+

+[docs]
+class const:
     """constant"""
 
     def __init__(self, params=None, max_params=1e12, min_params=-1e12):
@@ -101,7 +107,9 @@ 
Source code for physbo.gp.mean.const
         self.init_params(params)
         self.num_params = 1
 
-
[docs]    def supp_params(self, params):
+

+[docs]
+    def supp_params(self, params):
         """
         Setting maximum and minimum value of parameters.
 
@@ -122,7 +130,10 @@ 
Source code for physbo.gp.mean.const
 
         return params

 
-
[docs]    def get_params_bound(self):
+
+

+[docs]
+    def get_params_bound(self):
         """
         Getting the boundary list for parameters
 
@@ -135,7 +146,10 @@ 
Source code for physbo.gp.mean.const
         bound = [(self.min_params, self.max_params) for i in range(0, self.num_params)]
         return bound

 
-
[docs]    def get_mean(self, num_data, params=None):
+
+

+[docs]
+    def get_mean(self, num_data, params=None):
         """
 
         Parameters
@@ -153,7 +167,10 @@ 
Source code for physbo.gp.mean.const
             params = np.copy(self.params)
         return params * np.ones(num_data)

 
-
[docs]    def get_grad(self, num_data, params=None):
+
+

+[docs]
+    def get_grad(self, num_data, params=None):
         """
         Returning a new array of (num_data), filled with ones.
 
@@ -170,7 +187,10 @@ 
Source code for physbo.gp.mean.const
         """
         return np.ones(num_data)

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         Setting parameters defined in const class.
 
@@ -185,7 +205,10 @@ 
Source code for physbo.gp.mean.const
         """
         self.params = params

 
-
[docs]    def init_params(self, params):
+
+

+[docs]
+    def init_params(self, params):
         """
         Initializing parameters
 
@@ -204,7 +227,10 @@ 
Source code for physbo.gp.mean.const
         else:
             self.params = self.supp_params(params)

 
-
[docs]    def get_cand_params(self, t):
+
+

+[docs]
+    def get_cand_params(self, t):
         """
         Getting the median array of candidates.
 
@@ -219,7 +245,9 @@ 
Source code for physbo.gp.mean.const
             A new array holding the result.
 
         """
-        return np.median(t)

+        return np.median(t)

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/mean/zero.html b/manual/develop/en/_modules/physbo/gp/mean/zero.html
index fd294b63..31bda1de 100644
--- a/manual/develop/en/_modules/physbo/gp/mean/zero.html
+++ b/manual/develop/en/_modules/physbo/gp/mean/zero.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.mean.zero — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.mean.zero — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,14 +84,18 @@ 
Source code for physbo.gp.mean.zero
 import numpy as np
 
 
-
[docs]class zero:
+

+[docs]
+class zero:
     """zero"""
 
     def __init__(self):
         self.num_params = 0
         self.params = np.array([])
 
-
[docs]    def get_mean(self, num_data, params=None):
+

+[docs]
+    def get_mean(self, num_data, params=None):
         """
         Returning numpy.zeros(num_data)
 
@@ -105,7 +113,10 @@ 
Source code for physbo.gp.mean.zero
         """
         return np.zeros(num_data)

 
-
[docs]    def get_grad(self, num_data, params=None):
+
+

+[docs]
+    def get_grad(self, num_data, params=None):
         """
         Returning empty numpy.ndarray
 
@@ -123,7 +134,10 @@ 
Source code for physbo.gp.mean.zero
         """
         return np.array([])

 
-
[docs]    def set_params(self, params):
+
+

+[docs]
+    def set_params(self, params):
         """
         Not defined
 
@@ -135,7 +149,9 @@ 
Source code for physbo.gp.mean.zero
         -------
 
         """
-        pass

+        pass

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/gp/predictor.html b/manual/develop/en/_modules/physbo/gp/predictor.html
index a8da2f95..1ad9d88b 100644
--- a/manual/develop/en/_modules/physbo/gp/predictor.html
+++ b/manual/develop/en/_modules/physbo/gp/predictor.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.gp.predictor — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.gp.predictor — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.gp.predictor
 import physbo.predictor
 
 
-
[docs]class predictor(physbo.predictor.base_predictor):
+

+[docs]
+class predictor(physbo.predictor.base_predictor):
     """predictor"""
 
     def __init__(self, config, model=None):
@@ -94,7 +100,9 @@ 
Source code for physbo.gp.predictor
         """
         super(predictor, self).__init__(config, model)
 
-
[docs]    def fit(self, training, num_basis=None):
+

+[docs]
+    def fit(self, training, num_basis=None):
         """
         Fitting model to training dataset
 
@@ -110,7 +118,10 @@ 
Source code for physbo.gp.predictor
         self.model.fit(training.X, training.t, self.config)
         self.delete_stats()

 
-
[docs]    def get_basis(self, *args, **kwds):
+
+

+[docs]
+    def get_basis(self, *args, **kwds):
         """
 
         Parameters
@@ -124,7 +135,10 @@ 
Source code for physbo.gp.predictor
         """
         pass

 
-
[docs]    def get_post_params(self, *args, **kwds):
+
+

+[docs]
+    def get_post_params(self, *args, **kwds):
         """
 
         Parameters
@@ -138,10 +152,16 @@ 
Source code for physbo.gp.predictor
         """
         pass

 
-
[docs]    def update(self, training, test):
+
+

+[docs]
+    def update(self, training, test):
         self.prepare(training)

 
-
[docs]    def prepare(self, training):
+
+

+[docs]
+    def prepare(self, training):
         """
         Initializing model by using training data set
 
@@ -153,10 +173,16 @@ 
Source code for physbo.gp.predictor
         """
         self.model.prepare(training.X, training.t)

 
-
[docs]    def delete_stats(self):
+
+

+[docs]
+    def delete_stats(self):
         self.model.stats = None

 
-
[docs]    def get_post_fmean(self, training, test):
+
+

+[docs]
+    def get_post_fmean(self, training, test):
         """
         Calculating posterior mean value of model
 
@@ -176,7 +202,10 @@ 
Source code for physbo.gp.predictor
             self.prepare(training)
         return self.model.get_post_fmean(training.X, test.X)

 
-
[docs]    def get_post_fcov(self, training, test, diag=True):
+
+

+[docs]
+    def get_post_fcov(self, training, test, diag=True):
         """
         Calculating posterior variance-covariance matrix of model
 
@@ -197,7 +226,10 @@ 
Source code for physbo.gp.predictor
             self.prepare(training)
         return self.model.get_post_fcov(training.X, test.X, diag=diag)

 
-
[docs]    def get_post_samples(self, training, test, alpha=1):
+
+

+[docs]
+    def get_post_samples(self, training, test, alpha=1):
         """
         Drawing samples of mean values of model
 
@@ -218,7 +250,10 @@ 
Source code for physbo.gp.predictor
             self.prepare(training)
         return self.model.post_sampling(training.X, test.X, alpha=alpha)

 
-
[docs]    def get_predict_samples(self, training, test, N=1):
+
+

+[docs]
+    def get_predict_samples(self, training, test, N=1):
         """
         Drawing samples of values of model
 
@@ -239,7 +274,9 @@ 
Source code for physbo.gp.predictor
         """
         if self.model.stats is None:
             self.prepare(training)
-        return self.model.predict_sampling(training.X, test.X, N=N)

+        return self.model.predict_sampling(training.X, test.X, N=N)

+

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/misc/centering.html b/manual/develop/en/_modules/physbo/misc/centering.html
index 0966b1b2..ae1d90c7 100644
--- a/manual/develop/en/_modules/physbo/misc/centering.html
+++ b/manual/develop/en/_modules/physbo/misc/centering.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.misc.centering — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.misc.centering — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -80,7 +84,9 @@ 
Source code for physbo.misc.centering
 import numpy as np
 
 
-
[docs]def centering(X):
+

+[docs]
+def centering(X):
     """
     Normalize the mean and standard deviation along the each column of X to 0 and 1, respectively
 
@@ -98,6 +104,7 @@ 
Source code for physbo.misc.centering
     index = np.where(stdX != 0)
     X_normalized = (X[:, index[0]] - np.mean(X[:, index[0]], 0)) / stdX[index[0]]
     return X_normalized

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/misc/gauss_elim.html b/manual/develop/en/_modules/physbo/misc/gauss_elim.html
index 6b4ef53a..7e2976cd 100644
--- a/manual/develop/en/_modules/physbo/misc/gauss_elim.html
+++ b/manual/develop/en/_modules/physbo/misc/gauss_elim.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.misc.gauss_elim — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.misc.gauss_elim — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -81,7 +85,9 @@ 
Source code for physbo.misc.gauss_elim
 import scipy
 
 
-
[docs]def gauss_elim(U, t):
+

+[docs]
+def gauss_elim(U, t):
     """
     Calculate alpha using scipy.linalg.solve_triangular.
     alpha = (U^T U)^-1 t = U^-1 [(U^T)-1 t]
@@ -105,6 +111,7 @@ 
Source code for physbo.misc.gauss_elim
         U, alpha, lower=False, overwrite_b=False, check_finite=False
     )
     return alpha

+
 

 
            

diff --git a/manual/develop/en/_modules/physbo/misc/set_config.html b/manual/develop/en/_modules/physbo/misc/set_config.html
index be3dea07..cd94bb5b 100644
--- a/manual/develop/en/_modules/physbo/misc/set_config.html
+++ b/manual/develop/en/_modules/physbo/misc/set_config.html
@@ -1,18 +1,22 @@
 
-
+
 
   
   
-  physbo.misc.set_config — PHYSBO 1.2-dev documentation
-      
-      
+  physbo.misc.set_config — PHYSBO 1.1.1 documentation
+      
+      
+
+  
   
   
-        
-        
-        
+        
+        
+        
+        
+        
         
     
     
@@ -31,7 +35,7 @@
             PHYSBO
           
               

-                1.2
+                1.1
               

 

   
@@ -81,7 +85,9 @@ 
Source code for physbo.misc.set_config
 import configparser
 
 
-
[docs]class set_config:
+

+[docs]
+class set_config:
     def __init__(self, search_config=None, learning_config=None):
         """
         Setting configuration for search and learning.
@@ -100,7 +106,9 @@ 
Source code for physbo.misc.set_config
             learning_config = adam()
         self.learning = learning_config
 
-
[docs]    def show(self):
+

+[docs]
+    def show(self):
         """
         Showing information of search and learning objects.
 
@@ -111,7 +119,10 @@ 
Source code for physbo.misc.set_config
         self.search.show()
         self.learning.show()

 
-
[docs]    def load(self, file_name="config.ini"):
+
+

+[docs]
+    def load(self, file_name="config.ini"):
         """
         Loading information of configuration.
 
@@ -141,15 +152,21 @@ 
Source code for physbo.misc.set_config
         if method in ("bfgs", "batch"):
             learning_config = batch()
             self.learning = learning_config
-            self.learning.load(config)

+            self.learning.load(config)

+

+
 
 
-