Bugfixes for PGG FPR and Germ Selection

pygsti/algorithms/fiducialpairreduction.py

@@ -19,22 +19,20 @@
 import scipy.linalg as _sla
 
 from math import ceil
-import time
 
 from pygsti import baseobjs as _baseobjs
 from pygsti import circuits as _circuits
 
 from pygsti.circuits import circuitconstruction as _gsc
 from pygsti.modelmembers.operations import EigenvalueParamDenseOp as _EigenvalueParamDenseOp
-from pygsti.tools import apply_aliases_to_circuits as _apply_aliases_to_circuits
 from pygsti.tools import remove_duplicates as _remove_duplicates
 from pygsti.tools import slicetools as _slct
 from pygsti.tools.legacytools import deprecate as _deprecated_fn
+from pygsti.forwardsims import MatrixForwardSimulator as _MatrixForwardSimulator
 
-from pygsti.algorithms.germselection import construct_update_cache, minamide_style_inverse_trace, compact_EVD, compact_EVD_via_SVD, germ_set_spanning_vectors
+from pygsti.algorithms.germselection import construct_update_cache, minamide_style_inverse_trace, compact_EVD, germ_set_spanning_vectors
 from pygsti.algorithms import scoring as _scoring
 
-from pygsti.tools.matrixtools import print_mx
 
 import warnings
 
@@ -1658,6 +1656,10 @@ def find_sufficient_fiducial_pairs_per_germ_global(target_model, prep_fiducials,
         `prep_fiducials` and `meas_fiducials`).
     """
 
+    if not isinstance(target_model.sim, _MatrixForwardSimulator):
+        target_model = target_model.copy()
+        target_model.sim = 'matrix'
+
     printer = _baseobjs.VerbosityPrinter.create_printer(verbosity)
 
     #if no germ_vector_spanning_set is passed in compute it here.
@@ -1674,7 +1676,7 @@ def find_sufficient_fiducial_pairs_per_germ_global(target_model, prep_fiducials,
             if germ_set_spanning_kwargs is not None:
                 used_kwargs.update(germ_set_spanning_kwargs)
 
-            germ_vector_spanning_set = germ_set_spanning_vectors(target_model, germs, 
+            germ_vector_spanning_set, _ = germ_set_spanning_vectors(target_model, germs, 
                                                                  float_type=float_type, 
                                                                  evd_tol = evd_tol,
                                                                  verbosity=verbosity,

pygsti/algorithms/germselection.py

@@ -409,15 +409,17 @@ def find_germs(target_model, randomize=True, randomization_strength=1e-2,
     #force the line labels on each circuit to match the state space labels for the target model.
     #this is suboptimal for many-qubit models, so will probably want to revisit this. #TODO
     finalGermList = []
-    for ckt in germList:
-        if ckt._static:
-            new_ckt = ckt.copy(editable=True)
-            new_ckt.line_labels = target_model.state_space.state_space_labels
-            new_ckt.done_editing()
-            finalGermList.append(new_ckt)
-        else:
-            ckt.line_labels = target_model.state_space.state_space_labels
-            finalGermList.append(ckt)
+    if germList is not None:
+        for ckt in germList:
+            if ckt._static:
+                new_ckt = ckt.copy(editable=True)
+                new_ckt.line_labels = target_model.state_space.state_space_labels
+                new_ckt.done_editing()
+                finalGermList.append(new_ckt)
+            else:
+                ckt.line_labels = target_model.state_space.state_space_labels
+                finalGermList.append(ckt)
+
     return finalGermList
 
 
@@ -4531,6 +4533,10 @@ def germ_set_spanning_vectors(target_model, germ_list, assume_real=False, float_
         amplificational properties of the reduced vector set. 
     """
     printer = _baseobjs.VerbosityPrinter.create_printer(verbosity)
+
+    if not isinstance(target_model.sim, _MatrixForwardSimulator):
+        target_model = target_model.copy()
+        target_model.sim = 'matrix'
 
     #Add some checks related to the option to switch up data types:
     if not assume_real:

pygsti/modelmembers/operations/lindbladcoefficients.py

@@ -4,17 +4,23 @@
 import collections as _collections
 import copy as _copy
 import warnings as _warnings
-
 from pygsti.tools import lindbladtools as _lt
 from pygsti.tools import matrixtools as _mt
 from pygsti.tools import optools as _ot
-from pygsti.tools import fastcalc as _fc
 from pygsti.baseobjs.basis import Basis as _Basis, BuiltinBasis as _BuiltinBasis
 from pygsti.modelmembers import term as _term
 from pygsti.baseobjs.polynomial import Polynomial as _Polynomial
 from pygsti.baseobjs.nicelyserializable import NicelySerializable as _NicelySerializable
-
 from functools import lru_cache
+try:
+    from pygsti.tools import fastcalc as _fc
+    triu_indices = _fc.fast_triu_indices
+except ImportError:
+    msg = 'Could not import cython module `fastcalc`. This may indicate that your cython extensions for pyGSTi failed to.'\
+          +'properly build. Lack of cython extensions can result in significant performance degredation so we recommend trying to rebuild them.'\
+           'Falling back to numpy implementation for triu_indices.'
+    _warnings.warn(msg)
+    triu_indices = _np.triu_indices
 
 IMAG_TOL = 1e-7  # tolerance for imaginary part being considered zero
 
@@ -814,7 +820,7 @@ def from_vector(self, v):
 
                 cache_mx = self._cache_mx
 
-                params_upper_indices = _fc.fast_triu_indices(num_bels) 
+                params_upper_indices = triu_indices(num_bels) 
                 params_upper = 1j*params[params_upper_indices]
                 params_lower = (params.T)[params_upper_indices]
 
@@ -837,7 +843,7 @@ def from_vector(self, v):
 
             elif self._param_mode == "elements":  # params mx stores block_data (hermitian) directly
                 #params holds block_data real and imaginary parts directly
-                params_upper_indices = _fc.fast_triu_indices(num_bels) 
+                params_upper_indices = triu_indices(num_bels) 
                 params_upper = -1j*params[params_upper_indices]
                 params_lower = (params.T)[params_upper_indices]
 

test/unit/algorithms/test_germselection.py

@@ -147,7 +147,8 @@ class GenerateGermsTester(GermSelectionData, BaseCase):
     def test_generate_germs_with_candidate_germ_counts(self):
         germs = germsel.find_germs(
             self.mdl_target_noisy, randomize=False,
-            candidate_germ_counts={3: 'all upto', 4: 10, 5: 10, 6: 10}
+            candidate_germ_counts={3: 'all upto', 4: 10, 5: 10, 6: 10},
+            candidate_seed=1234
         )
         # TODO assert correctness