Bugfix reparameterize

pygsti/modelmembers/povms/__init__.py

@@ -547,7 +547,7 @@ def convert(povm, to_type, basis, ideal_povm=None, flatten_structure=False, cp_p
                 #It is often the case that there are more error generators than physical degrees of freedom in the POVM
                 #We define a function which finds linear comb. of errgens that span these degrees of freedom.
                 #This has been called "the trivial gauge", and this function is meant to avoid it
-                def calc_physical_subspace(dense_ideal_povm, epsilon = 1e-9):
+                def calc_physical_subspace(dense_ideal_povm, epsilon = 1e-4):
 
                     degrees_of_freedom = (dense_ideal_povm.shape[0] - 1) * dense_ideal_povm.shape[1]
                     errgen = _LindbladErrorgen.from_error_generator(povm.state_space.dim, parameterization=to_type)
@@ -578,11 +578,11 @@ def calc_physical_subspace(dense_ideal_povm, epsilon = 1e-9):
                         J[:,i] = vectorized_povm
 
                     _,S,Vt = _np.linalg.svd(J)
+
                     #Only return nontrivial singular vectors
-                    non_zero_mask = _np.abs(S) > 1e-13
-                    non_trivial_vecs = Vt[non_zero_mask]
-                    non_trivial_vecs = non_trivial_vecs.reshape(-1, Vt.shape[1])  # Reshape to ensure it's 2D
-                    return non_trivial_vecs
+                    Vt = Vt[S > 1e-13, :].reshape((-1, Vt.shape[1]))
+                    return Vt
+
 
                 phys_directions = calc_physical_subspace(dense_ideal_povm)
 

pygsti/modelmembers/states/__init__.py

@@ -270,7 +270,7 @@ def convert(state, to_type, basis, ideal_state=None, flatten_structure=False, cp
 
                     #GLND for states suffers from "trivial gauge" freedom. This function identifies
                     #the physical directions to avoid this gauge.
-                    def calc_physical_subspace(ideal_prep, epsilon = 1e-9):
+                    def calc_physical_subspace(ideal_prep, epsilon = 1e-4):
                         errgen = _LindbladErrorgen.from_error_generator(2**(2*num_qubits), parameterization=to_type)
                         num_errgens = errgen.num_params
 
@@ -289,10 +289,8 @@ def calc_physical_subspace(ideal_prep, epsilon = 1e-9):
                         _,S,Vt = _np.linalg.svd(J)
 
                         #Only return nontrivial singular vectors
-                        non_zero_mask = _np.abs(S) > 1e-13
-                        non_trivial_vecs = Vt[non_zero_mask]
-                        non_trivial_vecs = non_trivial_vecs.reshape(-1, Vt.shape[1])  # Reshape to ensure it's 2D
-                        return non_trivial_vecs
+                        Vt = Vt[S > 1e-13, :].reshape((-1, Vt.shape[1]))
+                        return Vt
 
                     phys_directions = calc_physical_subspace(dense_state)
 

pygsti/models/explicitmodel.py

@@ -349,12 +349,12 @@ def convert_members_inplace(self, to_type, categories_to_convert='all', labels_t
             for lbl, prep in self.preps.items():
                 if labels_to_convert == 'all' or lbl in labels_to_convert:
                     ideal = ideal_model.preps.get(lbl, None) if (ideal_model is not None) else None
-                    self.preps[lbl] = _state.convert(prep, to_type, self.basis, spam_cp_penalty, ideal, flatten_structure)
+                    self.preps[lbl] = _state.convert(prep, to_type, self.basis, ideal, flatten_structure, cp_penalty=spam_cp_penalty)
         if any([c in categories_to_convert for c in ('all', 'povms')]):
             for lbl, povm in self.povms.items():
                 if labels_to_convert == 'all' or lbl in labels_to_convert:
                     ideal = ideal_model.povms.get(lbl, None) if (ideal_model is not None) else None
-                    self.povms[lbl] = _povm.convert(povm, to_type, self.basis, spam_cp_penalty, ideal, flatten_structure)
+                    self.povms[lbl] = _povm.convert (povm, to_type, self.basis, ideal, flatten_structure, cp_penalty=spam_cp_penalty)
 
         self._clean_paramvec()  # param indices were probabaly updated
         if set_default_gauge_group:

test/unit/objects/test_model.py

@@ -405,15 +405,15 @@ def setUpClass(cls):
         cls.gatestring1 = ('Gx', 'Gy')
         cls.gatestring2 = ('Gx', 'Gy', 'Gy')
         cls._expected_probs = {
-            cls.gatestring1: np.transpose(cls._model.povms['Mdefault']['0'].to_dense()) @
+            cls.gatestring1: (np.transpose(cls._model.povms['Mdefault']['0'].to_dense()) @
                                     cls._model['Gy'].to_dense() @
                                            cls._model['Gx'].to_dense() @
-                                                  cls._model.preps['rho0'].to_dense().reshape(-1)[0],
-            cls.gatestring2: np.transpose(cls._model.povms['Mdefault']['0'].to_dense()) @
+                                                  cls._model.preps['rho0'].to_dense()).reshape(-1)[0],
+            cls.gatestring2: (np.transpose(cls._model.povms['Mdefault']['0'].to_dense()) @
                                     cls._model['Gy'].to_dense() @
                                            cls._model['Gy'].to_dense() @
                                                   cls._model['Gx'].to_dense() @
-                                                         cls._model.preps['rho0'].to_dense().reshape(-1)[0]
+                                                         cls._model.preps['rho0'].to_dense()).reshape(-1)[0]
         }
         # TODO expected dprobs & hprobs