added print m and print m.all differentiation

GPy/core/model.py

@@ -397,13 +397,17 @@ class Model(Parameterized):
             return np.nan
         return 0.5 * self._get_params().size * np.log(2 * np.pi) + self.log_likelihood() - hld
 
-    def __str__(self):
-        s = Parameterized.__str__(self).split('\n')
+    def __str__(self, names=None):
+        if names is None:
+            names = self._get_print_names()
+        s = Parameterized.__str__(self, names=names).split('\n')
         # add priors to the string
         if self.priors is not None:
             strs = [str(p) if p is not None else '' for p in self.priors]
         else:
-            strs = [''] * len(self._get_params())
+            strs = [''] * len(self._get_param_names())
+        name_indices = self.grep_param_names("|".join(names))
+        strs = np.array(strs)[name_indices]
         width = np.array(max([len(p) for p in strs] + [5])) + 4
 
         log_like = self.log_likelihood()

GPy/core/parameterized.py

@@ -27,6 +27,9 @@ class Parameterized(object):
 
     def _get_param_names(self):
         raise NotImplementedError, "this needs to be implemented to use the Parameterized class"
+    def _get_print_names(self):
+        """ Override for which names to print out, when using print m """
+        return self._get_param_names()
 
     def pickle(self, filename, protocol=None):
         if protocol is None:
@@ -333,19 +336,26 @@ class Parameterized(object):
         n = [nn for i, nn in enumerate(n) if not i in remove]
         return n
 
-    def __str__(self, nw=30):
+    @property
+    def all(self):
+        return self.__str__(self._get_param_names())
+
+
+    def __str__(self, names=None, nw=30):
         """
         Return a string describing the parameter names and their ties and constraints
         """
-        names = self._get_param_names()
+        if names is None:
+            names = self._get_print_names()
+        name_indices = self.grep_param_names("|".join(names))
         N = len(names)
 
         if not N:
             return "This object has no free parameters."
         header = ['Name', 'Value', 'Constraints', 'Ties']
-        values = self._get_params() # map(str,self._get_params())
+        values = self._get_params()[name_indices] # map(str,self._get_params())
         # sort out the constraints
-        constraints = [''] * len(names)
+        constraints = [''] * len(self._get_param_names())
         for i, t in zip(self.constrained_indices, self.constraints):
             for ii in i:
                 constraints[ii] = t.__str__()

GPy/core/sparse_gp.py

@@ -194,6 +194,9 @@ class SparseGP(GPBase):
         return sum([['iip_%i_%i' % (i, j) for j in range(self.Z.shape[1])] for i in range(self.Z.shape[0])], [])\
             + self.kern._get_param_names_transformed() + self.likelihood._get_param_names()
 
+    def _get_print_names(self):
+        return self.kern._get_param_names_transformed() + self.likelihood._get_param_names()
+
     def update_likelihood_approximation(self):
         """
         Approximates a non-gaussian likelihood using Expectation Propagation

GPy/models/bayesian_gplvm.py

@@ -57,6 +57,7 @@ class BayesianGPLVM(SparseGP, GPLVM):
         return SparseGP.getstate(self) + [self.init]
 
     def setstate(self, state):
+        self._const_jitter = None
         self.init = state.pop()
         SparseGP.setstate(self, state)
 
@@ -65,6 +66,9 @@ class BayesianGPLVM(SparseGP, GPLVM):
         S_names = sum([['X_variance_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
         return (X_names + S_names + SparseGP._get_param_names(self))
 
+    def _get_print_names(self):
+        return SparseGP._get_print_names(self)
+
     def _get_params(self):
         """
         Horizontally stacks the parameters in order to present them to the optimizer.

GPy/models/mrd.py

@@ -163,17 +163,28 @@ class MRD(Model):
         self._init_X(initx, self.likelihood_list)
         self._init_Z(initz, self.X)
 
-    def _get_param_names(self):
-        # X_names = sum([['X_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
-        # S_names = sum([['X_variance_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
+    def _get_latent_param_names(self):
         n1 = self.gref._get_param_names()
         n1var = n1[:self.NQ * 2 + self.MQ]
+        return n1var
+
+
+    def _get_kernel_names(self):
         map_names = lambda ns, name: map(lambda x: "{1}_{0}".format(*x),
                                          itertools.izip(ns,
                                                         itertools.repeat(name)))
-        return list(itertools.chain(n1var, *(map_names(\
-                SparseGP._get_param_names(g)[self.MQ:], n) \
-                for g, n in zip(self.bgplvms, self.names))))
+        kernel_names = (map_names(SparseGP._get_param_names(g)[self.MQ:], n) for g, n in zip(self.bgplvms, self.names))
+        return kernel_names
+
+    def _get_param_names(self):
+        # X_names = sum([['X_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
+        # S_names = sum([['X_variance_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])
+        n1var = self._get_latent_param_names()
+        kernel_names = self._get_kernel_names()
+        return list(itertools.chain(n1var, *kernel_names))
+
+    def _get_print_names(self):
+        return list(itertools.chain(*self._get_kernel_names()))
 
     def _get_params(self):
         """
@@ -329,7 +340,9 @@ class MRD(Model):
         """
         if titles is None:
             titles = [r'${}$'.format(name) for name in self.names]
+        ymax = reduce(max, [numpy.ceil(max(g.input_sensitivity())) for g in self.bgplvms])
         def plotf(i, g, ax):
+            ax.set_ylim([0,ymax])
             g.kern.plot_ARD(ax=ax, title=titles[i], *args, **kwargs)
         fig = self._handle_plotting(fignum, ax, plotf, sharex=sharex, sharey=sharey)
         return fig