def test_MPI_gaugeopt(comm):
#Gauge Opt to Target
mdl_other = std.target_model().depolarize(op_noise=0.01, spam_noise=0.01)
mdl_other['Gx'].rotate( (0,0,0.01) )
mdl_other['Gy'].rotate( (0,0,0.01) )
mdl_gopt = pygsti.gaugeopt_to_target(mdl_other, std.target_model(), verbosity=10, comm=comm)
#use a method that isn't parallelized with non-None comm (warning is given)
mdl_gopt_slow = pygsti.gaugeopt_to_target(mdl_other, std.target_model(), verbosity=10, method="BFGS", comm=comm)
def test_MPI_gatestrings_logl(comm):
#Create dataset for serial and parallel runs
ds, lsgstStrings = create_fake_dataset(comm)
#Individual processors
my1ProcResults = runOneQubit("logl", ds, lsgstStrings)
#Using all processors
myManyProcResults = runOneQubit("logl", ds, lsgstStrings, comm,
"gatestrings")
for i, (gs1, gs2) in enumerate(zip(my1ProcResults, myManyProcResults)):
assertGatesetsInSync(gs1, comm)
assertGatesetsInSync(gs2, comm)
gs2_go = pygsti.gaugeopt_to_target(gs2, gs1, {
'gates': 1.0,
'spam': 1.0
})
print("Frobenius distance %d (rank %d) = " % (i, comm.Get_rank()),
gs1.frobeniusdist(gs2_go))
if gs1.frobeniusdist(gs2_go) >= 1e-5:
print("DIFF (%d) = " % comm.Get_rank(), gs1.strdiff(gs2_go))
assert (gs1.frobeniusdist(gs2_go) < 1e-5)
return
def test_LGST_1overSqrtN_dependence(self):
my_datagen_gateset = self.model.depolarize(op_noise=0.05, spam_noise=0)
# !!don't depolarize spam or 1/sqrt(N) dependence saturates!!
nSamplesList = np.array([16, 128, 1024, 8192])
diffs = []
for nSamples in nSamplesList:
ds = pygsti.construction.generate_fake_data(my_datagen_gateset,
self.lgstStrings,
nSamples,
sampleError='binomial',
seed=100)
mdl_lgst = pygsti.do_lgst(ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,
my_datagen_gateset, {
'spam': 1.0,
'gate': 1.0
},
checkJac=True)
diffs.append(my_datagen_gateset.frobeniusdist(mdl_lgst_go))
diffs = np.array(diffs, 'd')
a, b = polyfit(np.log10(nSamplesList), np.log10(diffs), deg=1)
#print "\n",nSamplesList; print diffs; print a #DEBUG
self.assertLess(a + 0.5, 0.05)
def mdl_lgst_go(self):
return pygsti.gaugeopt_to_target(self.mdl_lgst,
self.model, {
'spam': 1.0,
'gates': 1.0
},
checkJac=True)
def test_LGST_no_sample_error(self):
#change rep-count type so dataset can hold fractional counts for sampleError = 'none'
oldType = pygsti.objects.dataset.Repcount_type
pygsti.objects.dataset.Repcount_type = np.float64
ds = pygsti.construction.generate_fake_data(self.datagen_gateset,
self.lgstStrings,
nSamples=10000,
sampleError='none')
pygsti.objects.dataset.Repcount_type = oldType
mdl_lgst = pygsti.do_lgst(ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=0)
print("DATAGEN:")
print(self.datagen_gateset)
print("\nLGST RAW:")
print(mdl_lgst)
mdl_lgst = pygsti.gaugeopt_to_target(mdl_lgst,
self.datagen_gateset, {
'spam': 1.0,
'gates': 1.0
},
checkJac=False)
print("\nAfter gauge opt:")
print(mdl_lgst)
print(mdl_lgst.strdiff(self.datagen_gateset))
self.assertAlmostEqual(mdl_lgst.frobeniusdist(self.datagen_gateset),
0,
places=4)
def main():
gs, gs_target = load()
#envSettings = dict(MKL_NUM_THREADS=1, NUMEXPR_NUM_THREADS=1, OMP_NUM_THREADS=1)
with timed_block('TP penalty gauge opt'):
gs_gaugeopt = pygsti.gaugeopt_to_target(gs, gs_target,
item_weights={'spam' : 0.0001, 'gates':1.0},
TPpenalty=1.0)
def runAnalysis(obj,
ds,
myspecs,
gsTarget,
lsgstStringsToUse,
useFreqWeightedChiSq=False,
minProbClipForWeighting=1e-4,
fidPairList=None,
comm=None,
distributeMethod="gatestrings"):
#Run LGST to get starting gate set
assertGatesetsInSync(gsTarget, comm)
gs_lgst = pygsti.do_lgst(ds,
myspecs,
gsTarget,
svdTruncateTo=gsTarget.dim,
verbosity=3)
assertGatesetsInSync(gs_lgst, comm)
gs_lgst_go = pygsti.gaugeopt_to_target(gs_lgst, gsTarget)
assertGatesetsInSync(gs_lgst_go, comm)
#Run full iterative LSGST
tStart = time.time()
if obj == "chi2":
all_gs_lsgst = pygsti.do_iterative_mc2gst(
ds,
gs_lgst_go,
lsgstStringsToUse,
minProbClipForWeighting=minProbClipForWeighting,
probClipInterval=(-1e5, 1e5),
verbosity=1,
memLimit=3 * (1024)**3,
returnAll=True,
useFreqWeightedChiSq=useFreqWeightedChiSq,
comm=comm,
distributeMethod=distributeMethod)
elif obj == "logl":
all_gs_lsgst = pygsti.do_iterative_mlgst(
ds,
gs_lgst_go,
lsgstStringsToUse,
minProbClip=minProbClipForWeighting,
probClipInterval=(-1e5, 1e5),
verbosity=1,
memLimit=3 * (1024)**3,
returnAll=True,
useFreqWeightedChiSq=useFreqWeightedChiSq,
comm=comm,
distributeMethod=distributeMethod)
tEnd = time.time()
print("Time = ", (tEnd - tStart) / 3600.0, "hours")
return all_gs_lsgst
def test_LGST(self):
ds = self.ds
print("GG0 = ", self.model.default_gauge_group)
mdl_lgst = pygsti.do_lgst(ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=0)
mdl_lgst_verb = self.runSilent(pygsti.do_lgst,
ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=10)
self.assertAlmostEqual(mdl_lgst.frobeniusdist(mdl_lgst_verb), 0)
print("GG = ", mdl_lgst.default_gauge_group)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,
self.model, {
'spam': 1.0,
'gates': 1.0
},
checkJac=True)
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if regenerate_references():
pygsti.io.write_model(
mdl_lgst, compare_files + "/lgst.model",
"Saved LGST Model before gauge optimization")
pygsti.io.write_model(mdl_lgst_go,
compare_files + "/lgst_go.model",
"Saved LGST Model after gauge optimization")
pygsti.io.write_model(
mdl_clgst, compare_files + "/clgst.model",
"Saved LGST Model after G.O. and CPTP contraction")
mdl_lgst_compare = pygsti.io.load_model(compare_files + "/lgst.model")
mdl_lgst_go_compare = pygsti.io.load_model(compare_files +
"/lgst_go.model")
mdl_clgst_compare = pygsti.io.load_model(compare_files +
"/clgst.model")
self.assertAlmostEqual(mdl_lgst.frobeniusdist(mdl_lgst_compare),
0,
places=5)
self.assertAlmostEqual(mdl_lgst_go.frobeniusdist(mdl_lgst_go_compare),
0,
places=5)
self.assertAlmostEqual(mdl_clgst.frobeniusdist(mdl_clgst_compare),
0,
places=5)
def main():
gs, gs_target = load()
with timed_block('Gauge opt with CP Penalty:'):
gs_gaugeopt = pygsti.gaugeopt_to_target(gs,
gs_target,
itemWeights={
'spam': 0.0001,
'gates': 1.0
},
CPpenalty=1.0,
validSpamPenalty=1.0)
def test_model_selection(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lsgstStrings[-1],
# nSamples=1000,sampleError='binomial', seed=100)
mdl_lgst4 = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=4, verbosity=0)
mdl_lgst6 = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=6, verbosity=0)
sys.stdout.flush()
self.runSilent(pygsti.do_lgst, ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=6, verbosity=4) # test verbose prints
chiSq4 = pygsti.chi2(mdl_lgst4, ds, self.lgstStrings, minProbClipForWeighting=1e-4)
chiSq6 = pygsti.chi2(mdl_lgst6, ds, self.lgstStrings, minProbClipForWeighting=1e-4)
print("LGST dim=4 chiSq = ",chiSq4)
print("LGST dim=6 chiSq = ",chiSq6)
#self.assertAlmostEqual(chiSq4, 174.061524953) #429.271983052)
#self.assertAlmostEqual(chiSq6, 267012993.861, places=1) #1337.74222467) #Why is this so large??? -- DEBUG later
# Least squares GST with model selection
mdl_lsgst = self.runSilent(pygsti.do_iterative_mc2gst_with_model_selection, ds, mdl_lgst4, 1, self.lsgstStrings[0:3],
verbosity=10, minProbClipForWeighting=1e-3, probClipInterval=(-1e5,1e5))
# Run again with other parameters
tuple_strings = [ list(map(tuple, gsList)) for gsList in self.lsgstStrings[0:3] ] #to test tuple argument
errorVecs, mdl_lsgst_wts = self.runSilent(pygsti.do_iterative_mc2gst_with_model_selection, ds, mdl_lgst4,
1, tuple_strings, verbosity=10, minProbClipForWeighting=1e-3,
probClipInterval=(-1e5,1e5), circuitWeightsDict={ ('Gx',): 2.0 },
returnAll=True, returnErrorVec=True)
# Do non-iterative to cover Circuit->tuple conversion
mdl_non_iterative = self.runSilent( pygsti.do_mc2gst_with_model_selection, ds,
mdl_lgst4, 1, self.lsgstStrings[0],
verbosity=10, probClipInterval=(-1e5,1e5) )
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if os.environ.get('PYGSTI_REGEN_REF_FILES','no').lower() in ("yes","1","true"):
pygsti.io.write_model(mdl_lsgst,compare_files + "/lsgstMS.model", "Saved LSGST Model with model selection")
mdl_lsgst_compare = pygsti.io.load_model(compare_files + "/lsgstMS.model")
mdl_lsgst_go = pygsti.gaugeopt_to_target(mdl_lsgst, mdl_lsgst_compare, {'spam':1.0}, checkJac=True)
self.assertAlmostEqual( mdl_lsgst_go.frobeniusdist(mdl_lsgst_compare), 0, places=4)
def test_MPI_mlgst_forcefn(comm):
fiducials = std.fiducials
target_model = std.target_model()
lgstStrings = pygsti.construction.list_lgst_circuits(fiducials, fiducials,
list(target_model.operations.keys()))
#Create dataset on root proc
if comm is None or comm.Get_rank() == 0:
datagen_gateset = target_model.depolarize(op_noise=0.01, spam_noise=0.01)
ds = pygsti.construction.generate_fake_data(datagen_gateset, lgstStrings,
nSamples=10000, sampleError='binomial', seed=100)
ds = comm.bcast(ds, root=0)
else:
ds = comm.bcast(None, root=0)
mdl_lgst = pygsti.do_lgst(ds, fiducials, fiducials, target_model, svdTruncateTo=4, verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,target_model, {'spam':1.0, 'gates': 1.0})
forcingfn_grad = np.ones((1,mdl_lgst_go.num_params()), 'd')
mdl_lsgst_chk_opts3 = pygsti.algorithms.core._do_mlgst_base(
ds, mdl_lgst_go, lgstStrings, verbosity=3,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
forcefn_grad=forcingfn_grad, comm=comm)
def test_MLGST(self):
ds = self.ds
mdl_lgst = pygsti.do_lgst(ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,
self.model, {
'spam': 1.0,
'gates': 1.0
},
checkJac=True)
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
mdl_clgst = mdl_clgst.depolarize(
op_noise=0.02, spam_noise=0.02
) # just to avoid infinity objective funct & jacs below
CM = profiler._get_mem_usage()
mdl_single_mlgst = pygsti.do_mlgst(ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
verbosity=0)
#this test often gives an assetion error "finite Jacobian has inf norm!" on Travis CI Python 3 case
try:
mdl_single_mlgst_cpsp = pygsti.do_mlgst(
ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
cptp_penalty_factor=1.0,
spam_penalty_factor=1.0,
verbosity=10) #uses both penalty factors w/verbosity > 0
except ValueError:
pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
try:
mdl_single_mlgst_cp = pygsti.do_mlgst(ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
cptp_penalty_factor=1.0,
verbosity=10)
except ValueError:
pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
try:
mdl_single_mlgst_sp = pygsti.do_mlgst(ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
spam_penalty_factor=1.0,
verbosity=10)
except ValueError:
pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
mdl_mlegst = pygsti.do_iterative_mlgst(ds,
mdl_clgst,
self.lsgstStrings,
verbosity=0,
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
memLimit=CM + 1024**3)
maxLogL, all_gs_mlegst_tups = pygsti.do_iterative_mlgst(
ds,
mdl_clgst,
[[mdl.tup for mdl in gsList] for gsList in self.lsgstStrings],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
returnAll=True,
returnMaxLogL=True)
mdl_mlegst_verb = self.runSilent(pygsti.do_iterative_mlgst,
ds,
mdl_clgst,
self.lsgstStrings,
verbosity=10,
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
memLimit=CM + 1024**3)
self.assertAlmostEqual(mdl_mlegst.frobeniusdist(mdl_mlegst_verb),
0,
places=5)
self.assertAlmostEqual(mdl_mlegst.frobeniusdist(
all_gs_mlegst_tups[-1]),
0,
places=5)
#Run internal checks on less max-L values (so it doesn't take forever)
mdl_mlegst_chk = pygsti.do_iterative_mlgst(ds,
mdl_clgst,
self.lsgstStrings[0:2],
verbosity=0,
minProbClip=1e-4,
probClipInterval=(-1e2,
1e2),
check=True)
#Forcing function used by linear response error bars
forcingfn_grad = np.ones((1, mdl_clgst.num_params()), 'd')
mdl_lsgst_chk_opts3 = pygsti.algorithms.core._do_mlgst_base(
ds,
mdl_clgst,
self.lsgstStrings[0],
verbosity=0,
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
forcefn_grad=forcingfn_grad)
with self.assertRaises(NotImplementedError):
# Non-poisson picture needs support for a non-leastsq solver (not impl yet)
mdl_lsgst_chk_opts4 = pygsti.algorithms.core._do_mlgst_base(
ds,
mdl_clgst,
self.lsgstStrings[0],
verbosity=0,
poissonPicture=False,
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
forcefn_grad=forcingfn_grad) # non-poisson picture
#Check with small but ok memlimit -- not anymore since new mem estimation uses current memory, making this non-robust
#self.runSilent(pygsti.do_mlgst, ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-6,
# probClipInterval=(-1e2,1e2), verbosity=4, memLimit=curMem+8500000) #invoke memory control
#non-Poisson picture - should use (-1,-1) model for consistency?
with self.assertRaises(NotImplementedError):
# Non-poisson picture needs support for a non-leastsq solver (not impl yet)
pygsti.do_mlgst(ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
verbosity=0,
poissonPicture=False)
try:
pygsti.do_mlgst(
ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-1, # 1e-1 b/c get inf Jacobians...
probClipInterval=(-1e2, 1e2),
verbosity=0,
poissonPicture=False,
spam_penalty_factor=1.0,
cptp_penalty_factor=1.0)
except ValueError:
pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
#Check errors:
with self.assertRaises(MemoryError):
pygsti.do_mlgst(ds,
mdl_clgst,
self.lsgstStrings[0],
minProbClip=1e-4,
probClipInterval=(-1e2, 1e2),
verbosity=0,
memLimit=1)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if regenerate_references():
pygsti.io.write_model(mdl_mlegst, compare_files + "/mle_gst.model",
"Saved MLE-GST Model")
mdl_mle_compare = pygsti.io.load_model(compare_files +
"/mle_gst.model")
mdl_mlegst_go = pygsti.gaugeopt_to_target(mdl_mlegst,
mdl_mle_compare,
{'spam': 1.0},
checkJac=True)
self.assertAlmostEqual(mdl_mlegst_go.frobeniusdist(mdl_mle_compare),
0,
places=4)
def test_MC2GST(self):
ds = self.ds
mdl_lgst = pygsti.do_lgst(ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,
self.model, {
'spam': 1.0,
'gates': 1.0
},
checkJac=True)
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
CM = profiler._get_mem_usage()
mdl_lsgst = pygsti.do_iterative_mc2gst(ds,
mdl_clgst,
self.lsgstStrings,
verbosity=0,
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6, 1e6),
memLimit=CM + 1024**3)
all_minErrs, all_gs_lsgst_tups = pygsti.do_iterative_mc2gst(
ds,
mdl_clgst,
[[mdl.tup for mdl in gsList] for gsList in self.lsgstStrings],
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6, 1e6),
returnAll=True,
returnErrorVec=True)
mdl_lsgst_verb = self.runSilent(pygsti.do_iterative_mc2gst,
ds,
mdl_clgst,
self.lsgstStrings,
verbosity=10,
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6, 1e6),
memLimit=CM + 1024**3)
mdl_lsgst_reg = self.runSilent(pygsti.do_iterative_mc2gst,
ds,
mdl_clgst,
self.lsgstStrings,
verbosity=10,
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6, 1e6),
regularizeFactor=10,
memLimit=CM + 1024**3)
self.assertAlmostEqual(mdl_lsgst.frobeniusdist(mdl_lsgst_verb), 0)
self.assertAlmostEqual(mdl_lsgst.frobeniusdist(all_gs_lsgst_tups[-1]),
0)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if regenerate_references():
pygsti.io.write_model(mdl_lsgst, compare_files + "/lsgst.model",
"Saved LSGST Model")
pygsti.io.write_model(mdl_lsgst_reg,
compare_files + "/lsgst_reg.model",
"Saved LSGST Model w/Regularization")
mdl_lsgst_compare = pygsti.io.load_model(compare_files +
"/lsgst.model")
mdl_lsgst_reg_compare = pygsti.io.load_model(compare_files +
"/lsgst_reg.model")
mdl_lsgst_go = pygsti.gaugeopt_to_target(mdl_lsgst,
mdl_lsgst_compare,
{'spam': 1.0},
checkJac=True)
mdl_lsgst_reg_go = pygsti.gaugeopt_to_target(mdl_lsgst_reg,
mdl_lsgst_reg_compare,
{'spam': 1.0},
checkJac=True)
self.assertAlmostEqual(mdl_lsgst_go.frobeniusdist(mdl_lsgst_compare),
0,
places=4)
self.assertAlmostEqual(
mdl_lsgst_reg_go.frobeniusdist(mdl_lsgst_reg_compare), 0, places=4)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if regenerate_references():
mdl_lsgst_go = pygsti.gaugeopt_to_target(mdl_lsgst, self.model,
{'spam': 1.0})
pygsti.io.write_model(mdl_lsgst_go,
compare_files + "/analysis.model",
"Saved LSGST Analysis Model")
print("DEBUG: analysis.model = ")
print(mdl_lgst_go)
def test_eLGST(self):
ds = self.ds
assert (pygsti.obj.Model._pcheck)
mdl_lgst = pygsti.do_lgst(ds,
self.fiducials,
self.fiducials,
self.model,
svdTruncateTo=4,
verbosity=0)
#mdl_lgst._check_paramvec() #will fail, but OK, since paramvec is computed only when *needed* now
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,
self.model, {
'spam': 1.0,
'gates': 1.0
},
checkJac=True)
mdl_lgst_go._check_paramvec()
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
mdl_clgst.to_vector() # to make sure we're in sync
mdl_clgst._check_paramvec()
self.model._check_paramvec()
_, mdl_single_exlgst = pygsti.do_exlgst(ds,
mdl_clgst,
self.elgstStrings[0],
self.fiducials,
self.fiducials,
self.model,
regularizeFactor=1e-3,
svdTruncateTo=4,
verbosity=0)
mdl_single_exlgst._check_paramvec()
_, mdl_single_exlgst_verb = self.runSilent(pygsti.do_exlgst,
ds,
mdl_clgst,
self.elgstStrings[0],
self.fiducials,
self.fiducials,
self.model,
regularizeFactor=1e-3,
svdTruncateTo=4,
verbosity=10)
mdl_single_exlgst_verb._check_paramvec()
self.assertAlmostEqual(
mdl_single_exlgst.frobeniusdist(mdl_single_exlgst_verb), 0)
mdl_exlgst = pygsti.do_iterative_exlgst(ds,
mdl_clgst,
self.fiducials,
self.fiducials,
self.elgstStrings,
targetModel=self.model,
svdTruncateTo=4,
verbosity=0)
all_minErrs, all_gs_exlgst_tups = pygsti.do_iterative_exlgst(
ds,
mdl_clgst,
self.fiducials,
self.fiducials,
[[mdl.tup for mdl in gsList] for gsList in self.elgstStrings],
targetModel=self.model,
svdTruncateTo=4,
verbosity=0,
returnAll=True,
returnErrorVec=True)
mdl_exlgst_verb = self.runSilent(pygsti.do_iterative_exlgst,
ds,
mdl_clgst,
self.fiducials,
self.fiducials,
self.elgstStrings,
targetModel=self.model,
svdTruncateTo=4,
verbosity=10)
mdl_exlgst_reg = pygsti.do_iterative_exlgst(ds,
mdl_clgst,
self.fiducials,
self.fiducials,
self.elgstStrings,
targetModel=self.model,
svdTruncateTo=4,
verbosity=0,
regularizeFactor=10)
self.assertAlmostEqual(mdl_exlgst.frobeniusdist(mdl_exlgst_verb), 0)
self.assertAlmostEqual(
mdl_exlgst.frobeniusdist(all_gs_exlgst_tups[-1]), 0)
#Run internal checks on less max-L values (so it doesn't take forever)
mdl_exlgst_chk = pygsti.do_iterative_exlgst(ds,
mdl_clgst,
self.fiducials,
self.fiducials,
self.elgstStrings[0:2],
targetModel=self.model,
svdTruncateTo=4,
verbosity=0,
check_jacobian=True)
mdl_exlgst_chk_verb = self.runSilent(pygsti.do_iterative_exlgst,
ds,
mdl_clgst,
self.fiducials,
self.fiducials,
self.elgstStrings[0:2],
targetModel=self.model,
svdTruncateTo=4,
verbosity=10,
check_jacobian=True)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if regenerate_references():
pygsti.io.write_model(mdl_exlgst, compare_files + "/exlgst.model",
"Saved Extended-LGST (eLGST) Model")
pygsti.io.write_model(
mdl_exlgst_reg, compare_files + "/exlgst_reg.model",
"Saved Extended-LGST (eLGST) Model w/regularization")
mdl_exlgst_compare = pygsti.io.load_model(compare_files +
"/exlgst.model")
mdl_exlgst_reg_compare = pygsti.io.load_model(compare_files +
"/exlgst_reg.model")
mdl_exlgst.set_all_parameterizations(
"full"
) # b/c ex-LGST sets spam to StaticSPAMVec objects (b/c they're not optimized)
mdl_exlgst_reg.set_all_parameterizations(
"full"
) # b/c ex-LGST sets spam to StaticSPAMVec objects (b/c they're not optimized)
mdl_exlgst_go = pygsti.gaugeopt_to_target(mdl_exlgst,
mdl_exlgst_compare,
{'spam': 1.0},
checkJac=True)
mdl_exlgst_reg_go = pygsti.gaugeopt_to_target(mdl_exlgst_reg,
mdl_exlgst_reg_compare,
{'spam': 1.0},
checkJac=True)
def testIntermediateMeas(self):
# Mess with the target model to add some error to the povm and instrument
self.assertEqual(self.target_model.num_params(), 92) # 4*3 + 16*5 = 92
mdl = self.target_model.depolarize(op_noise=0.01, spam_noise=0.01)
gs2 = self.target_model.depolarize(
max_op_noise=0.01, max_spam_noise=0.01,
seed=1234) #another way to depolarize
mdl.povms['Mdefault'].depolarize(0.01)
# Introducing a rotation error to the measurement
Uerr = pygsti.rotation_gate_mx(
[0, 0.02, 0]) # input angles are halved by the method
E = np.dot(mdl.povms['Mdefault']['0'].T,
Uerr).T # effect is stored as column vector
Erem = self.povm_ident - E
mdl.povms['Mdefault'] = pygsti.obj.UnconstrainedPOVM({
'0': E,
'1': Erem
})
# Now add the post-measurement gates from the vector E0 and remainder = id-E0
Gmz_plus = np.dot(
E, E.T) #since E0 is stored internally as column spamvec
Gmz_minus = np.dot(Erem, Erem.T)
mdl.instruments['Iz'] = pygsti.obj.Instrument({
'plus': Gmz_plus,
'minus': Gmz_minus
})
self.assertEqual(mdl.num_params(), 92) # 4*3 + 16*5 = 92
#print(mdl)
germs = std.germs
fiducials = std.fiducials
max_lengths = [1] #,2,4,8]
glbls = list(mdl.operations.keys()) + list(mdl.instruments.keys())
lsgst_list = pygsti.construction.make_lsgst_experiment_list(
glbls, fiducials, fiducials, germs, max_lengths)
lsgst_list2 = pygsti.construction.make_lsgst_experiment_list(
mdl, fiducials, fiducials, germs, max_lengths) #use mdl as source
self.assertEqual(lsgst_list, lsgst_list2)
mdl_datagen = mdl
ds = pygsti.construction.generate_fake_data(mdl, lsgst_list, 1000,
'none') #'multinomial')
pygsti.io.write_dataset(temp_files + "/intermediate_meas_dataset.txt",
ds)
ds2 = pygsti.io.load_dataset(temp_files +
"/intermediate_meas_dataset.txt")
for opstr, dsRow in ds.items():
for lbl, cnt in dsRow.counts.items():
self.assertAlmostEqual(cnt, ds2[opstr].counts[lbl], places=2)
#print(ds)
#LGST
mdl_lgst = pygsti.do_lgst(
ds, fiducials, fiducials,
self.target_model) #, guessModelForGauge=mdl_datagen)
self.assertTrue("Iz" in mdl_lgst.instruments)
mdl_opt = pygsti.gaugeopt_to_target(mdl_lgst,
mdl_datagen) #, method="BFGS")
print(mdl_datagen.strdiff(mdl_opt))
print("Frobdiff = ", mdl_datagen.frobeniusdist(mdl_lgst))
print("Frobdiff after GOpt = ", mdl_datagen.frobeniusdist(mdl_opt))
self.assertAlmostEqual(mdl_datagen.frobeniusdist(mdl_opt),
0.0,
places=4)
#print(mdl_lgst)
#print(mdl_datagen)
#DEBUG compiling w/dataset
#dbList = pygsti.construction.make_lsgst_experiment_list(self.target_model,fiducials,fiducials,germs,max_lengths)
##self.target_model.simplify_circuits(dbList, ds)
#self.target_model.simplify_circuits([ pygsti.obj.Circuit(None,stringrep="Iz") ], ds )
#assert(False),"STOP"
#LSGST
results = pygsti.do_long_sequence_gst(ds, self.target_model, fiducials,
fiducials, germs, max_lengths)
#print(results.estimates['default'].models['go0'])
mdl_est = results.estimates['default'].models['go0']
mdl_est_opt = pygsti.gaugeopt_to_target(mdl_est, mdl_datagen)
print("Frobdiff = ", mdl_datagen.frobeniusdist(mdl_est))
print("Frobdiff after GOpt = ", mdl_datagen.frobeniusdist(mdl_est_opt))
self.assertAlmostEqual(mdl_datagen.frobeniusdist(mdl_est_opt),
0.0,
places=4)
#LGST w/TP gates
mdl_targetTP = self.target_model.copy()
mdl_targetTP.set_all_parameterizations("TP")
self.assertEqual(mdl_targetTP.num_params(), 71) # 3 + 4*2 + 12*5 = 71
#print(mdl_targetTP)
resultsTP = pygsti.do_long_sequence_gst(ds, mdl_targetTP, fiducials,
fiducials, germs, max_lengths)
mdl_est = resultsTP.estimates['default'].models['go0']
mdl_est_opt = pygsti.gaugeopt_to_target(mdl_est, mdl_datagen)
print("TP Frobdiff = ", mdl_datagen.frobeniusdist(mdl_est))
print("TP Frobdiff after GOpt = ",
mdl_datagen.frobeniusdist(mdl_est_opt))
self.assertAlmostEqual(mdl_datagen.frobeniusdist(mdl_est_opt),
0.0,
places=4)
def test_LGST(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lgstStrings, nSamples=1000,
# sampleError='binomial', seed=None)
print("GG0 = ",self.model.default_gauge_group)
mdl_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=4, verbosity=0)
mdl_lgst_verb = self.runSilent(pygsti.do_lgst, ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=4, verbosity=10)
self.assertAlmostEqual(mdl_lgst.frobeniusdist(mdl_lgst_verb),0)
print("GG = ",mdl_lgst.default_gauge_group)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,self.model, {'spam':1.0, 'gates': 1.0}, checkJac=True)
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if os.environ.get('PYGSTI_REGEN_REF_FILES','no').lower() in ("yes","1","true"):
pygsti.io.write_model(mdl_lgst,compare_files + "/lgst.model", "Saved LGST Model before gauge optimization")
pygsti.io.write_model(mdl_lgst_go,compare_files + "/lgst_go.model", "Saved LGST Model after gauge optimization")
pygsti.io.write_model(mdl_clgst,compare_files + "/clgst.model", "Saved LGST Model after G.O. and CPTP contraction")
mdl_lgst_compare = pygsti.io.load_model(compare_files + "/lgst.model")
mdl_lgst_go_compare = pygsti.io.load_model(compare_files + "/lgst_go.model")
mdl_clgst_compare = pygsti.io.load_model(compare_files + "/clgst.model")
self.assertAlmostEqual( mdl_lgst.frobeniusdist(mdl_lgst_compare), 0, places=5)
self.assertAlmostEqual( mdl_lgst_go.frobeniusdist(mdl_lgst_go_compare), 0, places=5)
self.assertAlmostEqual( mdl_clgst.frobeniusdist(mdl_clgst_compare), 0, places=5)
#Check for error conditions
with self.assertRaises(ValueError):
mdl_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, None, svdTruncateTo=4, verbosity=0) #no target model
with self.assertRaises(ValueError):
mdl_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, None, opLabels=list(self.model.operations.keys()),
svdTruncateTo=4, verbosity=0) #no spam dict
#No need for identity vector anymore
#with self.assertRaises(ValueError):
# mdl_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, None, opLabels=list(self.model.operations.keys()),
# spamDict=self.model.get_reverse_spam_defs(),
# svdTruncateTo=4, verbosity=0) #no identity vector
with self.assertRaises(ValueError):
bad_fids =pygsti.construction.circuit_list([('Gx',),('Gx',),('Gx',),('Gx',)])
mdl_lgst = pygsti.do_lgst(ds, bad_fids, bad_fids, self.model, svdTruncateTo=4, verbosity=0) # bad fiducials (rank deficient)
with self.assertRaises(KeyError): # AB-matrix construction error
incomplete_strings = self.lgstStrings[5:] #drop first 5 strings...
bad_ds = pygsti.construction.generate_fake_data(
self.datagen_gateset, incomplete_strings,
nSamples=10, sampleError='none')
mdl_lgst = pygsti.do_lgst(bad_ds, self.fiducials, self.fiducials, self.model,
svdTruncateTo=4, verbosity=0)
# incomplete dataset
with self.assertRaises(KeyError): # X-matrix construction error
incomplete_strings = self.lgstStrings[:-5] #drop last 5 strings...
bad_ds = pygsti.construction.generate_fake_data(
self.datagen_gateset, incomplete_strings,
nSamples=10, sampleError='none')
mdl_lgst = pygsti.do_lgst(bad_ds, self.fiducials, self.fiducials, self.model,
svdTruncateTo=4, verbosity=0)
def setUpClass(cls):
"""
Handle all once-per-class (slow) computation and loading,
to avoid calling it for each test (like setUp). Store
results in class variable for use within setUp.
"""
super(ReportBaseCase, cls).setUpClass()
orig_cwd = os.getcwd()
os.chdir(os.path.abspath(os.path.dirname(__file__)))
os.chdir('..') # The test_packages directory
target_model = std.target_model()
datagen_gateset = target_model.depolarize(op_noise=0.05, spam_noise=0.1)
datagen_gateset2 = target_model.depolarize(op_noise=0.1, spam_noise=0.05).rotate((0.15,-0.03,0.03))
#cls.specs = pygsti.construction.build_spam_specs(std.fiducials, effect_labels=['E0'])
# #only use the first EVec
op_labels = std.gates
cls.lgstStrings = pygsti.circuits.create_lgst_circuits(std.fiducials, std.fiducials, op_labels)
cls.maxLengthList = [1,2,4,8]
cls.lsgstStrings = pygsti.circuits.create_lsgst_circuit_lists(
op_labels, std.fiducials, std.fiducials, std.germs, cls.maxLengthList)
cls.lsgstStructs = pygsti.circuits.make_lsgst_structs(
op_labels, std.fiducials, std.fiducials, std.germs, cls.maxLengthList)
# RUN BELOW LINES TO GENERATE ANALYSIS DATASET (SAVE)
if regenerate_references():
ds = pygsti.data.simulate_data(datagen_gateset, cls.lsgstStrings[-1], num_samples=1000,
sample_error='binomial', seed=100)
ds.save(compare_files + "/reportgen.dataset")
ds2 = pygsti.data.simulate_data(datagen_gateset2, cls.lsgstStrings[-1], num_samples=1000,
sample_error='binomial', seed=100)
ds2.save(compare_files + "/reportgen2.dataset")
cls.ds = pygsti.data.DataSet(file_to_load_from=compare_files + "/reportgen.dataset")
cls.ds2 = pygsti.data.DataSet(file_to_load_from=compare_files + "/reportgen2.dataset")
mdl_lgst = pygsti.run_lgst(cls.ds, std.fiducials, std.fiducials, target_model, svd_truncate_to=4, verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst, target_model, {'gates': 1.0, 'spam': 0.0})
cls.mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
cls.mdl_clgst_tp = pygsti.contract(cls.mdl_clgst, "vSPAM")
cls.mdl_clgst_tp.set_all_parameterizations("full TP")
#Compute results for MC2GST
lsgst_gatesets_prego, *_ = pygsti.run_iterative_gst(
cls.ds, cls.mdl_clgst, cls.lsgstStrings,
optimizer={'tol': 1e-5},
iteration_objfn_builders=['chi2'],
final_objfn_builders=[],
resource_alloc=None,
verbosity=0
)
experiment_design = pygsti.protocols.StandardGSTDesign(
target_model.create_processor_spec(), std.fiducials, std.fiducials, std.germs, cls.maxLengthList
)
data = pygsti.protocols.ProtocolData(experiment_design, cls.ds)
protocol = pygsti.protocols.StandardGST()
cls.results = pygsti.protocols.gst.ModelEstimateResults(data, protocol)
cls.results.add_estimate(pygsti.protocols.estimate.Estimate.create_gst_estimate(
cls.results, target_model, cls.mdl_clgst,lsgst_gatesets_prego,
{'objective': "chi2",
'min_prob_clip_for_weighting': 1e-4,
'prob_clip_interval': (-1e6,1e6), 'radius': 1e-4,
'weights': None, 'defaultDirectory': temp_files + "",
'defaultBasename': "MyDefaultReportName"}
))
gaugeOptParams = collections.OrderedDict([
('model', lsgst_gatesets_prego[-1]), #so can gauge-propagate CIs
('target_model', target_model), #so can gauge-propagate CIs
('cptp_penalty_factor', 0),
('gates_metric',"frobenius"),
('spam_metric',"frobenius"),
('item_weights', {'gates': 1.0, 'spam': 0.001}),
('return_all', True) ])
_, gaugeEl, go_final_gateset = pygsti.gaugeopt_to_target(**gaugeOptParams)
gaugeOptParams['_gaugeGroupEl'] = gaugeEl #so can gauge-propagate CIs
cls.results.estimates['default'].add_gaugeoptimized(gaugeOptParams, go_final_gateset)
cls.results.estimates['default'].add_gaugeoptimized(gaugeOptParams, go_final_gateset, "go_dup")
#Compute results for MLGST with TP constraint
# Use run_long_sequence_gst with a non-mark dataset to trigger data scaling
tp_target = target_model.copy(); tp_target.set_all_parameterizations("full TP")
cls.ds3 = cls.ds.copy_nonstatic()
cls.ds3.add_counts_from_dataset(cls.ds2)
cls.ds3.done_adding_data()
cls.results_logL = pygsti.run_long_sequence_gst(cls.ds3, tp_target, std.fiducials, std.fiducials,
std.germs, cls.maxLengthList, verbosity=0,
advanced_options={'tolerance': 1e-6, 'starting_point': 'LGST',
'on_bad_fit': ["robust","Robust","robust+","Robust+"],
'bad_fit_threshold': -1.0,
'germ_length_limits': {('Gx','Gi','Gi'): 2} })
#OLD
#lsgst_gatesets_TP = pygsti.do_iterative_mlgst(cls.ds, cls.mdl_clgst_tp, cls.lsgstStrings, verbosity=0,
# min_prob_clip=1e-4, prob_clip_interval=(-1e6,1e6),
# returnAll=True) #TP initial model => TP output models
#cls.results_logL = pygsti.objects.Results()
#cls.results_logL.init_dataset(cls.ds)
#cls.results_logL.init_circuits(cls.lsgstStructs)
#cls.results_logL.add_estimate(target_model, cls.mdl_clgst_tp,
# lsgst_gatesets_TP,
# {'objective': "logl",
# 'min_prob_clip': 1e-4,
# 'prob_clip_interval': (-1e6,1e6), 'radius': 1e-4,
# 'weights': None, 'defaultDirectory': temp_files + "",
# 'defaultBasename': "MyDefaultReportName"})
#
#tp_target = target_model.copy(); tp_target.set_all_parameterizations("full TP")
#gaugeOptParams = gaugeOptParams.copy() #just to be safe
#gaugeOptParams['model'] = lsgst_gatesets_TP[-1] #so can gauge-propagate CIs
#gaugeOptParams['target_model'] = tp_target #so can gauge-propagate CIs
#_, gaugeEl, go_final_gateset = pygsti.gaugeopt_to_target(**gaugeOptParams)
#gaugeOptParams['_gaugeGroupEl'] = gaugeEl #so can gauge-propagate CIs
#cls.results_logL.estimates['default'].add_gaugeoptimized(gaugeOptParams, go_final_gateset)
#
##self.results_logL.options.precision = 3
##self.results_logL.options.polar_precision = 2
os.chdir(orig_cwd)
def test_MC2GST(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lsgstStrings[-1],
# nSamples=1000, sampleError='binomial', seed=100)
gs_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_go = pygsti.gaugeopt_to_target(gs_lgst,self.gateset, {'spam':1.0, 'gates': 1.0}, checkJac=True)
gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
CM = pygsti.baseobjs.profiler._get_mem_usage()
gs_single_lsgst = pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0) #uses regularizeFactor
gs_single_lsgst_cp = pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
verbosity=0) #uses cptp_penalty_factor
gs_single_lsgst_sp = pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), spam_penalty_factor=1.0,
verbosity=0) #uses spam_penalty_factor
gs_single_lsgst_cpsp = pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
spam_penalty_factor=1.0, verbosity=0) #uses both penalty factors
gs_single_lsgst_cpsp = self.runSilent(pygsti.do_mc2gst, ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
spam_penalty_factor=1.0, verbosity=10) #uses both penalty factors w/verbosity high
gs_single_lsgst_cp = self.runSilent(pygsti.do_mc2gst, ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
verbosity=10) #uses cptp_penalty_factor w/verbosity high
gs_single_lsgst_sp = self.runSilent(pygsti.do_mc2gst, ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), spam_penalty_factor=1.0,
verbosity=10) #uses spam_penalty_factor w/verbosity high
gs_lsgst = pygsti.do_iterative_mc2gst(ds, gs_clgst, self.lsgstStrings, verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
memLimit=CM + 1024**3)
all_minErrs, all_gs_lsgst_tups = pygsti.do_iterative_mc2gst(
ds, gs_clgst, [ [gs.tup for gs in gsList] for gsList in self.lsgstStrings],
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6), returnAll=True, returnErrorVec=True)
gs_lsgst_verb = self.runSilent(pygsti.do_iterative_mc2gst, ds, gs_clgst, self.lsgstStrings, verbosity=10,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
memLimit=CM + 1024**3)
gs_lsgst_reg = self.runSilent(pygsti.do_iterative_mc2gst,ds, gs_clgst,
self.lsgstStrings, verbosity=10,
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6),
regularizeFactor=10, memLimit=CM + 1024**3)
self.assertAlmostEqual(gs_lsgst.frobeniusdist(gs_lsgst_verb),0)
self.assertAlmostEqual(gs_lsgst.frobeniusdist(all_gs_lsgst_tups[-1]),0)
#Run internal checks on less max-L values (so it doesn't take forever)
gs_lsgst_chk = pygsti.do_iterative_mc2gst(ds, gs_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
check=True, check_jacobian=True)
gs_lsgst_chk_verb = self.runSilent(pygsti.do_iterative_mc2gst, ds, gs_clgst, self.lsgstStrings[0:2], verbosity=10,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
check=True, check_jacobian=True, memLimit=CM + 1024**3)
#Other option variations - just make sure they run at this point
gs_lsgst_chk_opts = pygsti.do_iterative_mc2gst(ds, gs_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
useFreqWeightedChiSq=True, gateStringSetLabels=["Set1","Set2"],
gatestringWeightsDict={ ('Gx',): 2.0 } )
aliased_list = [ pygsti.obj.GateString( [ (x if x != "Gx" else "GA1") for x in gs]) for gs in self.lsgstStrings[0] ]
gs_withA1 = gs_clgst.copy(); gs_withA1.gates["GA1"] = gs_clgst.gates["Gx"]
del gs_withA1.gates["Gx"] # otherwise gs_withA1 will have Gx params that we have no knowledge of!
gs_lsgst_chk_opts2 = pygsti.do_mc2gst(ds, gs_withA1, aliased_list, minProbClipForWeighting=1e-6,
probClipInterval=(-1e2,1e2), verbosity=10,
gateLabelAliases={ 'GA1': ('Gx',) })
#Check with small but ok memlimit -- not anymore since new mem estimation uses current memory, making this non-robust
#self.runSilent(pygsti.do_mc2gst,ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
# probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
# verbosity=10, memLimit=CM + 1024**3)
#Check errors:
with self.assertRaises(MemoryError):
pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0, memLimit=1)
with self.assertRaises(AssertionError):
pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0, cptp_penalty_factor=1.0) #can't specify both cptp_penalty_factor and regularizeFactor
# RUN BELOW LINES TO SEED SAVED GATESET FILES
#pygsti.io.write_gateset(gs_lsgst,compare_files + "/lsgst.gateset", "Saved LSGST Gateset")
#pygsti.io.write_gateset(gs_lsgst_reg,compare_files + "/lsgst_reg.gateset", "Saved LSGST Gateset w/Regularization")
gs_lsgst_compare = pygsti.io.load_gateset(compare_files + "/lsgst.gateset")
gs_lsgst_reg_compare = pygsti.io.load_gateset(compare_files + "/lsgst_reg.gateset")
gs_lsgst_go = pygsti.gaugeopt_to_target(gs_lsgst, gs_lsgst_compare, {'spam':1.0}, checkJac=True)
gs_lsgst_reg_go = pygsti.gaugeopt_to_target(gs_lsgst_reg, gs_lsgst_reg_compare, {'spam':1.0}, checkJac=True)
self.assertAlmostEqual( gs_lsgst_go.frobeniusdist(gs_lsgst_compare), 0, places=4)
self.assertAlmostEqual( gs_lsgst_reg_go.frobeniusdist(gs_lsgst_reg_compare), 0, places=4)
def test_LGST(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lgstStrings, nSamples=1000,
# sampleError='binomial', seed=None)
print("GG0 = ",self.gateset.default_gauge_group)
gs_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_verb = self.runSilent(pygsti.do_lgst, ds, self.fiducials, self.fiducials, self.gateset, svdTruncateTo=4, verbosity=10)
self.assertAlmostEqual(gs_lgst.frobeniusdist(gs_lgst_verb),0)
print("GG = ",gs_lgst.default_gauge_group)
gs_lgst_go = pygsti.gaugeopt_to_target(gs_lgst,self.gateset, {'spam':1.0, 'gates': 1.0}, checkJac=True)
gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
# RUN BELOW LINES TO SEED SAVED GATESET FILES
#pygsti.io.write_gateset(gs_lgst,compare_files + "/lgst.gateset", "Saved LGST Gateset before gauge optimization")
#pygsti.io.write_gateset(gs_lgst_go,compare_files + "/lgst_go.gateset", "Saved LGST Gateset after gauge optimization")
#pygsti.io.write_gateset(gs_clgst,compare_files + "/clgst.gateset", "Saved LGST Gateset after G.O. and CPTP contraction")
gs_lgst_compare = pygsti.io.load_gateset(compare_files + "/lgst.gateset")
gs_lgst_go_compare = pygsti.io.load_gateset(compare_files + "/lgst_go.gateset")
gs_clgst_compare = pygsti.io.load_gateset(compare_files + "/clgst.gateset")
self.assertAlmostEqual( gs_lgst.frobeniusdist(gs_lgst_compare), 0, places=5)
self.assertAlmostEqual( gs_lgst_go.frobeniusdist(gs_lgst_go_compare), 0, places=5)
self.assertAlmostEqual( gs_clgst.frobeniusdist(gs_clgst_compare), 0, places=5)
#Check for error conditions
with self.assertRaises(ValueError):
gs_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, None, svdTruncateTo=4, verbosity=0) #no target gateset
with self.assertRaises(ValueError):
gs_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, None, gateLabels=list(self.gateset.gates.keys()),
svdTruncateTo=4, verbosity=0) #no spam dict
#No need for identity vector anymore
#with self.assertRaises(ValueError):
# gs_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, None, gateLabels=list(self.gateset.gates.keys()),
# spamDict=self.gateset.get_reverse_spam_defs(),
# svdTruncateTo=4, verbosity=0) #no identity vector
with self.assertRaises(ValueError):
bad_fids =pygsti.construction.gatestring_list([('Gx',),('Gx',),('Gx',),('Gx',)])
gs_lgst = pygsti.do_lgst(ds, bad_fids, bad_fids, self.gateset, svdTruncateTo=4, verbosity=0) # bad fiducials (rank deficient)
with self.assertRaises(KeyError): # AB-matrix construction error
incomplete_strings = self.lgstStrings[5:] #drop first 5 strings...
bad_ds = pygsti.construction.generate_fake_data(
self.datagen_gateset, incomplete_strings,
nSamples=10, sampleError='none')
gs_lgst = pygsti.do_lgst(bad_ds, self.fiducials, self.fiducials, self.gateset,
svdTruncateTo=4, verbosity=0)
# incomplete dataset
with self.assertRaises(KeyError): # X-matrix construction error
incomplete_strings = self.lgstStrings[:-5] #drop last 5 strings...
bad_ds = pygsti.construction.generate_fake_data(
self.datagen_gateset, incomplete_strings,
nSamples=10, sampleError='none')
gs_lgst = pygsti.do_lgst(bad_ds, self.fiducials, self.fiducials, self.gateset,
svdTruncateTo=4, verbosity=0)
def test_MLGST(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lsgstStrings[-1],
# nSamples=1000, sampleError='binomial', seed=100)
mdl_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=4, verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,self.model, {'spam':1.0, 'gates': 1.0}, checkJac=True)
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
mdl_clgst = mdl_clgst.depolarize(op_noise=0.02, spam_noise=0.02) # just to avoid infinity objective funct & jacs below
CM = pygsti.baseobjs.profiler._get_mem_usage()
mdl_single_mlgst = pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-4,
probClipInterval=(-1e2,1e2), verbosity=0)
#this test often gives an assetion error "finite Jacobian has inf norm!" on Travis CI Python 3 case
try:
mdl_single_mlgst_cpsp = pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-4,
probClipInterval=(-1e2,1e2), cptp_penalty_factor=1.0,
spam_penalty_factor=1.0, verbosity=10) #uses both penalty factors w/verbosity > 0
except ValueError: pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
try:
mdl_single_mlgst_cp = pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-4,
probClipInterval=(-1e2,1e2), cptp_penalty_factor=1.0,
verbosity=10)
except ValueError: pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
try:
mdl_single_mlgst_sp = pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-4,
probClipInterval=(-1e2,1e2), spam_penalty_factor=1.0,
verbosity=10)
except ValueError: pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
mdl_mlegst = pygsti.do_iterative_mlgst(ds, mdl_clgst, self.lsgstStrings, verbosity=0,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
memLimit=CM + 1024**3)
maxLogL, all_gs_mlegst_tups = pygsti.do_iterative_mlgst(
ds, mdl_clgst, [ [mdl.tup for mdl in gsList] for gsList in self.lsgstStrings],
minProbClip=1e-4, probClipInterval=(-1e2,1e2), returnAll=True, returnMaxLogL=True)
mdl_mlegst_verb = self.runSilent(pygsti.do_iterative_mlgst, ds, mdl_clgst, self.lsgstStrings, verbosity=10,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
memLimit=CM + 1024**3)
self.assertAlmostEqual(mdl_mlegst.frobeniusdist(mdl_mlegst_verb),0, places=5)
self.assertAlmostEqual(mdl_mlegst.frobeniusdist(all_gs_mlegst_tups[-1]),0,places=5)
#Run internal checks on less max-L values (so it doesn't take forever)
mdl_mlegst_chk = pygsti.do_iterative_mlgst(ds, mdl_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
check=True)
#Other option variations - just make sure they run at this point
mdl_mlegst_chk_opts = pygsti.do_iterative_mlgst(ds, mdl_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
circuitSetLabels=["Set1","Set2"], useFreqWeightedChiSq=True,
circuitWeightsDict={ (L('Gx'),): 2.0 } )
aliased_list = [ pygsti.obj.Circuit( [ (x if x != L("Gx") else L("GA1")) for x in mdl]) for mdl in self.lsgstStrings[0] ]
mdl_withA1 = mdl_clgst.copy(); mdl_withA1.operations["GA1"] = mdl_clgst.operations["Gx"]
del mdl_withA1.operations["Gx"] # otherwise mdl_withA1 will have Gx params that we have no knowledge of!
mdl_mlegst_chk_opts2 = pygsti.do_mlgst(ds, mdl_withA1, aliased_list, minProbClip=1e-4,
probClipInterval=(-1e2,1e2), verbosity=10,
opLabelAliases={ L('GA1'): (L('Gx'),) })
#Other option variations - just make sure they run at this point
mdl_mlegst_chk_opts3 = pygsti.do_iterative_mlgst(ds, mdl_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
circuitSetLabels=["Set1","Set2"], useFreqWeightedChiSq=True,
circuitWeightsDict={ (L('Gx'),): 2.0 }, alwaysPerformMLE=True )
#Forcing function used by linear response error bars
forcingfn_grad = np.ones((1,mdl_clgst.num_params()), 'd')
mdl_lsgst_chk_opts3 = pygsti.algorithms.core._do_mlgst_base(
ds, mdl_clgst, self.lsgstStrings[0], verbosity=0,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
forcefn_grad=forcingfn_grad)
with self.assertRaises(NotImplementedError):
# Non-poisson picture needs support for a non-leastsq solver (not impl yet)
mdl_lsgst_chk_opts4 = pygsti.algorithms.core._do_mlgst_base(
ds, mdl_clgst, self.lsgstStrings[0], verbosity=0, poissonPicture=False,
minProbClip=1e-4, probClipInterval=(-1e2,1e2),
forcefn_grad=forcingfn_grad) # non-poisson picture
#Check with small but ok memlimit -- not anymore since new mem estimation uses current memory, making this non-robust
#self.runSilent(pygsti.do_mlgst, ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-6,
# probClipInterval=(-1e2,1e2), verbosity=4, memLimit=curMem+8500000) #invoke memory control
#non-Poisson picture - should use (-1,-1) model for consistency?
with self.assertRaises(NotImplementedError):
# Non-poisson picture needs support for a non-leastsq solver (not impl yet)
pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-4,
probClipInterval=(-1e2,1e2), verbosity=0, poissonPicture=False)
try:
pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-1, # 1e-1 b/c get inf Jacobians...
probClipInterval=(-1e2,1e2), verbosity=0, poissonPicture=False,
spam_penalty_factor=1.0, cptp_penalty_factor=1.0)
except ValueError: pass # ignore when assertions in customlm.py are disabled
except AssertionError:
pass # just ignore for now. FUTURE: see what we can do in custom LM about scaling large jacobians...
#Check errors:
with self.assertRaises(MemoryError):
pygsti.do_mlgst(ds, mdl_clgst, self.lsgstStrings[0], minProbClip=1e-4,
probClipInterval=(-1e2,1e2),verbosity=0, memLimit=1)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if os.environ.get('PYGSTI_REGEN_REF_FILES','no').lower() in ("yes","1","true"):
pygsti.io.write_model(mdl_mlegst,compare_files + "/mle_gst.model", "Saved MLE-GST Model")
mdl_mle_compare = pygsti.io.load_model(compare_files + "/mle_gst.model")
mdl_mlegst_go = pygsti.gaugeopt_to_target(mdl_mlegst, mdl_mle_compare, {'spam':1.0}, checkJac=True)
self.assertAlmostEqual( mdl_mlegst_go.frobeniusdist(mdl_mle_compare), 0, places=4)
def test_eLGST(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lsgstStrings[-1],
# nSamples=1000,sampleError='binomial', seed=100)
assert(pygsti.obj.GateSet._pcheck)
gs_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst._check_paramvec()
gs_lgst_go = pygsti.gaugeopt_to_target(gs_lgst,self.gateset, {'spam':1.0, 'gates': 1.0}, checkJac=True)
gs_lgst_go._check_paramvec()
gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
gs_clgst._check_paramvec()
self.gateset._check_paramvec()
_,gs_single_exlgst = pygsti.do_exlgst(ds, gs_clgst, self.elgstStrings[0], self.fiducials, self.fiducials,
self.gateset, regularizeFactor=1e-3, svdTruncateTo=4,
verbosity=0)
gs_single_exlgst._check_paramvec()
_,gs_single_exlgst_verb = self.runSilent(pygsti.do_exlgst, ds, gs_clgst, self.elgstStrings[0], self.fiducials, self.fiducials,
self.gateset, regularizeFactor=1e-3, svdTruncateTo=4,
verbosity=10)
gs_single_exlgst_verb._check_paramvec()
self.assertAlmostEqual(gs_single_exlgst.frobeniusdist(gs_single_exlgst_verb),0)
gs_exlgst = pygsti.do_iterative_exlgst(ds, gs_clgst, self.fiducials, self.fiducials, self.elgstStrings,
targetGateset=self.gateset, svdTruncateTo=4, verbosity=0)
all_minErrs, all_gs_exlgst_tups = pygsti.do_iterative_exlgst(
ds, gs_clgst, self.fiducials, self.fiducials, [ [gs.tup for gs in gsList] for gsList in self.elgstStrings],
targetGateset=self.gateset, svdTruncateTo=4, verbosity=0, returnAll=True, returnErrorVec=True)
gs_exlgst_verb = self.runSilent(pygsti.do_iterative_exlgst, ds, gs_clgst, self.fiducials, self.fiducials, self.elgstStrings,
targetGateset=self.gateset, svdTruncateTo=4, verbosity=10)
gs_exlgst_reg = pygsti.do_iterative_exlgst(ds, gs_clgst, self.fiducials, self.fiducials, self.elgstStrings,
targetGateset=self.gateset, svdTruncateTo=4, verbosity=0,
regularizeFactor=10)
self.assertAlmostEqual(gs_exlgst.frobeniusdist(gs_exlgst_verb),0)
self.assertAlmostEqual(gs_exlgst.frobeniusdist(all_gs_exlgst_tups[-1]),0)
#Run internal checks on less max-L values (so it doesn't take forever)
gs_exlgst_chk = pygsti.do_iterative_exlgst(ds, gs_clgst, self.fiducials, self.fiducials, self.elgstStrings[0:2],
targetGateset=self.gateset, svdTruncateTo=4, verbosity=0,
check_jacobian=True)
gs_exlgst_chk_verb = self.runSilent(pygsti.do_iterative_exlgst,ds, gs_clgst, self.fiducials, self.fiducials, self.elgstStrings[0:2],
targetGateset=self.gateset, svdTruncateTo=4, verbosity=10,
check_jacobian=True)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
#pygsti.io.write_gateset(gs_exlgst,compare_files + "/exlgst.gateset", "Saved Extended-LGST (eLGST) Gateset")
#pygsti.io.write_gateset(gs_exlgst_reg,compare_files + "/exlgst_reg.gateset", "Saved Extended-LGST (eLGST) Gateset w/regularization")
gs_exlgst_compare = pygsti.io.load_gateset(compare_files + "/exlgst.gateset")
gs_exlgst_reg_compare = pygsti.io.load_gateset(compare_files + "/exlgst_reg.gateset")
gs_exlgst.set_all_parameterizations("full") # b/c ex-LGST sets spam to StaticSPAMVec objects (b/c they're not optimized)
gs_exlgst_reg.set_all_parameterizations("full") # b/c ex-LGST sets spam to StaticSPAMVec objects (b/c they're not optimized)
gs_exlgst_go = pygsti.gaugeopt_to_target(gs_exlgst,gs_exlgst_compare, {'spam':1.0 }, checkJac=True)
gs_exlgst_reg_go = pygsti.gaugeopt_to_target(gs_exlgst_reg,gs_exlgst_reg_compare, {'spam':1.0 }, checkJac=True)
'updnup': ('rho0', 'E2'),
'updndn': ('rho0', 'E3'),
'dnupup': ('rho0', 'E4'),
'dnupdn': ('rho0', 'E5'),
'dndnup': ('rho0', 'E6'),
'dndndn': ('rho0', 'remainder')
},
basis="pp")
#print gs_target.num_params()
# In[3]:
#Test Gauge optimization
gs_depol = gs_target.copy().depolarize(max_gate_noise=0.05,
spam_noise=0.1,
seed=1200)
gs_kicked = gs_depol.kick(absmag=0.25, seed=1200)
# In[ ]:
t0 = time.time()
gs_go = pygsti.gaugeopt_to_target(gs_kicked, gs_target, tol=1e-10, verbosity=3)
print("%g sec" % (time.time() - t0))
print(gs_go.frobeniusdist(gs_target))
# In[ ]:
pickle.dump(results, open("3qbit_results.pkl", "wb"))
# In[ ]:
def setUpClass(cls):
"""
Handle all once-per-class (slow) computation and loading,
to avoid calling it for each test (like setUp). Store
results in class variable for use within setUp.
"""
super(ReportBaseCase, cls).setUpClass()
orig_cwd = os.getcwd()
os.chdir(os.path.abspath(os.path.dirname(__file__)))
os.chdir('..') # The test_packages directory
targetGateset = std.gs_target
datagen_gateset = targetGateset.depolarize(gate_noise=0.05,
spam_noise=0.1)
datagen_gateset2 = targetGateset.depolarize(gate_noise=0.1,
spam_noise=0.05).rotate(
(0.15, -0.03, 0.03))
#cls.specs = pygsti.construction.build_spam_specs(std.fiducials, effect_labels=['E0'])
# #only use the first EVec
gateLabels = std.gates
cls.lgstStrings = pygsti.construction.list_lgst_gatestrings(
std.fiducials, std.fiducials, gateLabels)
cls.maxLengthList = [1, 2, 4, 8]
cls.lsgstStrings = pygsti.construction.make_lsgst_lists(
gateLabels, std.fiducials, std.fiducials, std.germs,
cls.maxLengthList)
cls.lsgstStructs = pygsti.construction.make_lsgst_structs(
gateLabels, std.fiducials, std.fiducials, std.germs,
cls.maxLengthList)
try:
basestring #Only defined in Python 2
cls.versionsuffix = "" #Python 2
except NameError:
cls.versionsuffix = "v3" #Python 3
# RUN BELOW LINES TO GENERATE ANALYSIS DATASET
#ds = pygsti.construction.generate_fake_data(datagen_gateset, cls.lsgstStrings[-1], nSamples=1000,
# sampleError='binomial', seed=100)
#ds.save(compare_files + "/reportgen.dataset%s" % cls.versionsuffix)
#ds2 = pygsti.construction.generate_fake_data(datagen_gateset2, cls.lsgstStrings[-1], nSamples=1000,
# sampleError='binomial', seed=100)
#ds2.save(compare_files + "/reportgen2.dataset%s" % cls.versionsuffix)
cls.ds = pygsti.objects.DataSet(
fileToLoadFrom=compare_files +
"/reportgen.dataset%s" % cls.versionsuffix)
cls.ds2 = pygsti.objects.DataSet(
fileToLoadFrom=compare_files +
"/reportgen2.dataset%s" % cls.versionsuffix)
gs_lgst = pygsti.do_lgst(cls.ds,
std.fiducials,
std.fiducials,
targetGateset,
svdTruncateTo=4,
verbosity=0)
gs_lgst_go = pygsti.gaugeopt_to_target(gs_lgst, targetGateset, {
'gates': 1.0,
'spam': 0.0
})
cls.gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
cls.gs_clgst_tp = pygsti.contract(cls.gs_clgst, "vSPAM")
cls.gs_clgst_tp.set_all_parameterizations("TP")
#Compute results for MC2GST
lsgst_gatesets_prego = pygsti.do_iterative_mc2gst(
cls.ds,
cls.gs_clgst,
cls.lsgstStrings,
verbosity=0,
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6, 1e6),
returnAll=True)
cls.results = pygsti.objects.Results()
cls.results.init_dataset(cls.ds)
cls.results.init_gatestrings(cls.lsgstStructs)
cls.results.add_estimate(
targetGateset, cls.gs_clgst, lsgst_gatesets_prego, {
'objective': "chi2",
'minProbClipForWeighting': 1e-4,
'probClipInterval': (-1e6, 1e6),
'radius': 1e-4,
'weights': None,
'defaultDirectory': temp_files + "",
'defaultBasename': "MyDefaultReportName"
})
gaugeOptParams = collections.OrderedDict([
('gateset', lsgst_gatesets_prego[-1]), #so can gauge-propagate CIs
('targetGateset', targetGateset), #so can gauge-propagate CIs
('cptp_penalty_factor', 0),
('gatesMetric', "frobenius"),
('spamMetric', "frobenius"),
('itemWeights', {
'gates': 1.0,
'spam': 0.001
}),
('returnAll', True)
])
_, gaugeEl, go_final_gateset = pygsti.gaugeopt_to_target(
**gaugeOptParams)
gaugeOptParams['_gaugeGroupEl'] = gaugeEl #so can gauge-propagate CIs
cls.results.estimates['default'].add_gaugeoptimized(
gaugeOptParams, go_final_gateset)
cls.results.estimates['default'].add_gaugeoptimized(
gaugeOptParams, go_final_gateset, "go_dup")
#Compute results for MLGST with TP constraint
# Use do_long_sequence_gst with a non-mark dataset to trigger data scaling
tp_target = targetGateset.copy()
tp_target.set_all_parameterizations("TP")
cls.ds3 = cls.ds.copy_nonstatic()
cls.ds3.add_counts_from_dataset(cls.ds2)
cls.ds3.done_adding_data()
cls.results_logL = pygsti.do_long_sequence_gst(
cls.ds3,
tp_target,
std.fiducials,
std.fiducials,
std.germs,
cls.maxLengthList,
verbosity=0,
advancedOptions={
'tolerance': 1e-6,
'starting point': 'LGST',
'onBadFit': ["robust", "Robust", "robust+", "Robust+"],
'badFitThreshold': -1.0,
'germLengthLimits': {
('Gx', 'Gi', 'Gi'): 2
}
})
#OLD
#lsgst_gatesets_TP = pygsti.do_iterative_mlgst(cls.ds, cls.gs_clgst_tp, cls.lsgstStrings, verbosity=0,
# minProbClip=1e-4, probClipInterval=(-1e6,1e6),
# returnAll=True) #TP initial gateset => TP output gatesets
#cls.results_logL = pygsti.objects.Results()
#cls.results_logL.init_dataset(cls.ds)
#cls.results_logL.init_gatestrings(cls.lsgstStructs)
#cls.results_logL.add_estimate(targetGateset, cls.gs_clgst_tp,
# lsgst_gatesets_TP,
# {'objective': "logl",
# 'minProbClip': 1e-4,
# 'probClipInterval': (-1e6,1e6), 'radius': 1e-4,
# 'weights': None, 'defaultDirectory': temp_files + "",
# 'defaultBasename': "MyDefaultReportName"})
#
#tp_target = targetGateset.copy(); tp_target.set_all_parameterizations("TP")
#gaugeOptParams = gaugeOptParams.copy() #just to be safe
#gaugeOptParams['gateset'] = lsgst_gatesets_TP[-1] #so can gauge-propagate CIs
#gaugeOptParams['targetGateset'] = tp_target #so can gauge-propagate CIs
#_, gaugeEl, go_final_gateset = pygsti.gaugeopt_to_target(**gaugeOptParams)
#gaugeOptParams['_gaugeGroupEl'] = gaugeEl #so can gauge-propagate CIs
#cls.results_logL.estimates['default'].add_gaugeoptimized(gaugeOptParams, go_final_gateset)
#
##self.results_logL.options.precision = 3
##self.results_logL.options.polar_precision = 2
os.chdir(orig_cwd)
def testIntermediateMeas(self):
# Mess with the target gateset to add some error to the povm and instrument
self.assertEqual(self.gs_target.num_params(), 92) # 4*3 + 16*5 = 92
gs = self.gs_target.depolarize(gate_noise=0.01, spam_noise=0.01)
gs2 = self.gs_target.depolarize(max_gate_noise=0.01,
max_spam_noise=0.01,
seed=1234) #another way to depolarize
gs.povms['Mdefault'].depolarize(0.01)
# Introducing a rotation error to the measurement
Uerr = pygsti.rotation_gate_mx(
[0, 0.02, 0]) # input angles are halved by the method
E = np.dot(gs.povms['Mdefault']['0'].T,
Uerr).T # effect is stored as column vector
Erem = self.povm_ident - E
gs.povms['Mdefault'] = pygsti.obj.UnconstrainedPOVM({
'0': E,
'1': Erem
})
# Now add the post-measurement gates from the vector E0 and remainder = id-E0
Gmz_plus = np.dot(
E, E.T) #since E0 is stored internally as column spamvec
Gmz_minus = np.dot(Erem, Erem.T)
gs.instruments['Iz'] = pygsti.obj.Instrument({
'plus': Gmz_plus,
'minus': Gmz_minus
})
self.assertEqual(gs.num_params(), 92) # 4*3 + 16*5 = 92
#print(gs)
germs = std.germs
fiducials = std.fiducials
max_lengths = [1] #,2,4,8]
glbls = list(gs.gates.keys()) + list(gs.instruments.keys())
lsgst_list = pygsti.construction.make_lsgst_experiment_list(
glbls, fiducials, fiducials, germs, max_lengths)
lsgst_list2 = pygsti.construction.make_lsgst_experiment_list(
gs, fiducials, fiducials, germs, max_lengths) #use gs as source
self.assertEqual(lsgst_list, lsgst_list2)
gs_datagen = gs
ds = pygsti.construction.generate_fake_data(gs, lsgst_list, 1000,
'none') #'multinomial')
pygsti.io.write_dataset(temp_files + "/intermediate_meas_dataset.txt",
ds)
ds2 = pygsti.io.load_dataset(temp_files +
"/intermediate_meas_dataset.txt")
for gstr, dsRow in ds.items():
for lbl, cnt in dsRow.counts.items():
self.assertAlmostEqual(cnt, ds2[gstr].counts[lbl], places=2)
#print(ds)
#LGST
gs_lgst = pygsti.do_lgst(
ds, fiducials, fiducials,
self.gs_target) #, guessGatesetForGauge=gs_datagen)
self.assertTrue("Iz" in gs_lgst.instruments)
gs_opt = pygsti.gaugeopt_to_target(gs_lgst,
gs_datagen) #, method="BFGS")
print(gs_datagen.strdiff(gs_opt))
print("Frobdiff = ", gs_datagen.frobeniusdist(gs_lgst))
print("Frobdiff after GOpt = ", gs_datagen.frobeniusdist(gs_opt))
self.assertAlmostEqual(gs_datagen.frobeniusdist(gs_opt), 0.0, places=4)
#print(gs_lgst)
#print(gs_datagen)
#LSGST
results = pygsti.do_long_sequence_gst(ds, self.gs_target, fiducials,
fiducials, germs, max_lengths)
#print(results.estimates['default'].gatesets['go0'])
gs_est = results.estimates['default'].gatesets['go0']
gs_est_opt = pygsti.gaugeopt_to_target(gs_est, gs_datagen)
print("Frobdiff = ", gs_datagen.frobeniusdist(gs_est))
print("Frobdiff after GOpt = ", gs_datagen.frobeniusdist(gs_est_opt))
self.assertAlmostEqual(gs_datagen.frobeniusdist(gs_est_opt),
0.0,
places=4)
#LGST w/TP gates
gs_targetTP = self.gs_target.copy()
gs_targetTP.set_all_parameterizations("TP")
self.assertEqual(gs_targetTP.num_params(), 71) # 3 + 4*2 + 12*5 = 71
#print(gs_targetTP)
resultsTP = pygsti.do_long_sequence_gst(ds, gs_targetTP, fiducials,
fiducials, germs, max_lengths)
gs_est = resultsTP.estimates['default'].gatesets['go0']
gs_est_opt = pygsti.gaugeopt_to_target(gs_est, gs_datagen)
print("TP Frobdiff = ", gs_datagen.frobeniusdist(gs_est))
print("TP Frobdiff after GOpt = ",
gs_datagen.frobeniusdist(gs_est_opt))
self.assertAlmostEqual(gs_datagen.frobeniusdist(gs_est_opt),
0.0,
places=4)
def setUp(self):
super(ReportBaseCase, self).setUp()
self.targetGateset = std.gs_target
datagen_gateset = self.targetGateset.depolarize(gate_noise=0.05, spam_noise=0.1)
self.fiducials = std.fiducials
self.germs = std.germs
self.specs = pygsti.construction.build_spam_specs(self.fiducials, effect_labels=['E0']) #only use the first EVec
self.gateLabels = list(self.targetGateset.gates.keys()) # also == std.gates
self.lgstStrings = pygsti.construction.list_lgst_gatestrings(self.specs, self.gateLabels)
self.maxLengthList = [0,1,2,4,8]
self.lsgstStrings = pygsti.construction.make_lsgst_lists(
self.gateLabels, self.fiducials, self.fiducials, self.germs, self.maxLengthList)
self.ds = pygsti.objects.DataSet(fileToLoadFrom=compare_files + "/reportgen.dataset")
# RUN BELOW LINES TO GENERATE ANALYSIS DATASET
#ds = pygsti.construction.generate_fake_data(datagen_gateset, lsgstStrings[-1], nSamples=1000,
# sampleError='binomial', seed=100)
#ds.save(compare_files + "/reportgen.dataset")
gs_lgst = pygsti.do_lgst(self.ds, self.specs, self.targetGateset, svdTruncateTo=4, verbosity=0)
#gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",targetGateset=self.targetGateset,gateWeight=1.0,spamWeight=0.0) #DEPRECATED
gs_lgst_go = pygsti.gaugeopt_to_target(gs_lgst, self.targetGateset, {'gates': 1.0, 'spam': 0.0})
self.gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
self.gs_clgst_tp = pygsti.contract(self.gs_clgst, "vSPAM")
self.gs_clgst_tp.set_all_parameterizations("TP")
try:
import pptx
self.have_python_pptx = True
except ImportError:
warnings.warn("**** IMPORT: Cannot import pptx (python-pptx), and so" +
" Powerpoint slide generation tests have been disabled.")
self.have_python_pptx = False
#Compute results for MC2GST
lsgst_gatesets_prego = pygsti.do_iterative_mc2gst(self.ds, self.gs_clgst, self.lsgstStrings, verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
returnAll=True)
gaugeOptParams = collections.OrderedDict([
('TPpenalty', 0),
('CPpenalty', 0),
('gatesMetric',"frobenius"),
('spamMetric',"frobenius"),
('itemWeights', {'gates': 1.0, 'spam': 0.001}) ])
lsgst_gatesets = []
for gs in lsgst_gatesets_prego:
lsgst_gatesets.append( pygsti.gaugeopt_to_target(gs,self.targetGateset,
**gaugeOptParams) )
self.results = pygsti.report.Results()
self.results.init_Ls_and_germs("chi2", self.targetGateset, self.ds, self.gs_clgst,
self.maxLengthList, self.germs,
lsgst_gatesets, self.lsgstStrings, self.fiducials, self.fiducials,
pygsti.construction.repeat_with_max_length, None, lsgst_gatesets_prego)
self.results.parameters.update({'minProbClip': 1e-6, 'minProbClipForWeighting': 1e-4,
'probClipInterval': (-1e6,1e6), 'radius': 1e-4,
'weights': None, 'defaultDirectory': temp_files + "",
'defaultBasename': "MyDefaultReportName",
'gaugeOptParams': gaugeOptParams} )
self.results.options.precision = 3
self.results.options.polar_precision = 2
#Compute results for MLGST with TP constraint
lsgst_gatesets_TP = pygsti.do_iterative_mlgst(self.ds, self.gs_clgst_tp, self.lsgstStrings, verbosity=0,
minProbClip=1e-4, probClipInterval=(-1e6,1e6),
returnAll=True) #TP initial gateset => TP output gatesets
tp_target = self.targetGateset.copy(); tp_target.set_all_parameterizations("TP")
lsgst_gatesets_TP = [ pygsti.gaugeopt_to_target(gs, tp_target, {'gates': 1.0, 'spam': 0.001})
for gs in lsgst_gatesets_TP ]
self.results_logL = pygsti.report.Results()
self.results_logL.init_Ls_and_germs("logl", self.targetGateset, self.ds, self.gs_clgst_tp, self.maxLengthList, self.germs,
lsgst_gatesets_TP, self.lsgstStrings, self.fiducials, self.fiducials,
pygsti.construction.repeat_with_max_length)
self.results_logL.options.precision = 3
self.results_logL.options.polar_precision = 2
try:
basestring #Only defined in Python 2
self.versionsuffix = "" #Python 2
except NameError:
self.versionsuffix = "v3" #Python 3
def test_MC2GST(self):
ds = self.ds
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lsgstStrings[-1],
# nSamples=1000, sampleError='binomial', seed=100)
mdl_lgst = pygsti.do_lgst(ds, self.fiducials, self.fiducials, self.model, svdTruncateTo=4, verbosity=0)
mdl_lgst_go = pygsti.gaugeopt_to_target(mdl_lgst,self.model, {'spam':1.0, 'gates': 1.0}, checkJac=True)
mdl_clgst = pygsti.contract(mdl_lgst_go, "CPTP")
CM = pygsti.baseobjs.profiler._get_mem_usage()
mdl_single_lsgst = pygsti.do_mc2gst(ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0) #uses regularizeFactor
mdl_single_lsgst_cp = pygsti.do_mc2gst(ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
verbosity=0) #uses cptp_penalty_factor
mdl_single_lsgst_sp = pygsti.do_mc2gst(ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), spam_penalty_factor=1.0,
verbosity=0) #uses spam_penalty_factor
mdl_single_lsgst_cpsp = pygsti.do_mc2gst(ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
spam_penalty_factor=1.0, verbosity=0) #uses both penalty factors
mdl_single_lsgst_cpsp = self.runSilent(pygsti.do_mc2gst, ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
spam_penalty_factor=1.0, verbosity=10) #uses both penalty factors w/verbosity high
mdl_single_lsgst_cp = self.runSilent(pygsti.do_mc2gst, ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), cptp_penalty_factor=1.0,
verbosity=10) #uses cptp_penalty_factor w/verbosity high
mdl_single_lsgst_sp = self.runSilent(pygsti.do_mc2gst, ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-4,
probClipInterval=(-1e6,1e6), spam_penalty_factor=1.0,
verbosity=10) #uses spam_penalty_factor w/verbosity high
mdl_lsgst = pygsti.do_iterative_mc2gst(ds, mdl_clgst, self.lsgstStrings, verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
memLimit=CM + 1024**3)
all_minErrs, all_gs_lsgst_tups = pygsti.do_iterative_mc2gst(
ds, mdl_clgst, [ [mdl.tup for mdl in gsList] for gsList in self.lsgstStrings],
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6), returnAll=True, returnErrorVec=True)
mdl_lsgst_verb = self.runSilent(pygsti.do_iterative_mc2gst, ds, mdl_clgst, self.lsgstStrings, verbosity=10,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
memLimit=CM + 1024**3)
mdl_lsgst_reg = self.runSilent(pygsti.do_iterative_mc2gst,ds, mdl_clgst,
self.lsgstStrings, verbosity=10,
minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6),
regularizeFactor=10, memLimit=CM + 1024**3)
self.assertAlmostEqual(mdl_lsgst.frobeniusdist(mdl_lsgst_verb),0)
self.assertAlmostEqual(mdl_lsgst.frobeniusdist(all_gs_lsgst_tups[-1]),0)
#Run internal checks on less max-L values (so it doesn't take forever)
mdl_lsgst_chk = pygsti.do_iterative_mc2gst(ds, mdl_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
check=True, check_jacobian=True)
mdl_lsgst_chk_verb = self.runSilent(pygsti.do_iterative_mc2gst, ds, mdl_clgst, self.lsgstStrings[0:2], verbosity=10,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
check=True, check_jacobian=True, memLimit=CM + 1024**3)
#Other option variations - just make sure they run at this point
mdl_lsgst_chk_opts = pygsti.do_iterative_mc2gst(ds, mdl_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
useFreqWeightedChiSq=True, circuitSetLabels=["Set1","Set2"],
circuitWeightsDict={ ('Gx',): 2.0 } )
aliased_list = [ pygsti.obj.Circuit( [ (x if x != L("Gx") else L("GA1")) for x in mdl]) for mdl in self.lsgstStrings[0] ]
mdl_withA1 = mdl_clgst.copy(); mdl_withA1.operations["GA1"] = mdl_clgst.operations["Gx"]
del mdl_withA1.operations["Gx"] # otherwise mdl_withA1 will have Gx params that we have no knowledge of!
mdl_lsgst_chk_opts2 = pygsti.do_mc2gst(ds, mdl_withA1, aliased_list, minProbClipForWeighting=1e-6,
probClipInterval=(-1e2,1e2), verbosity=10,
opLabelAliases={ L('GA1'): (L('Gx'),) })
#Check with small but ok memlimit -- not anymore since new mem estimation uses current memory, making this non-robust
#self.runSilent(pygsti.do_mc2gst,ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
# probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
# verbosity=10, memLimit=CM + 1024**3)
#Check errors:
with self.assertRaises(MemoryError):
pygsti.do_mc2gst(ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0, memLimit=1)
with self.assertRaises(AssertionError):
pygsti.do_mc2gst(ds, mdl_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0, cptp_penalty_factor=1.0) #can't specify both cptp_penalty_factor and regularizeFactor
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if os.environ.get('PYGSTI_REGEN_REF_FILES','no').lower() in ("yes","1","true"):
pygsti.io.write_model(mdl_lsgst,compare_files + "/lsgst.model", "Saved LSGST Model")
pygsti.io.write_model(mdl_lsgst_reg,compare_files + "/lsgst_reg.model", "Saved LSGST Model w/Regularization")
mdl_lsgst_compare = pygsti.io.load_model(compare_files + "/lsgst.model")
mdl_lsgst_reg_compare = pygsti.io.load_model(compare_files + "/lsgst_reg.model")
mdl_lsgst_go = pygsti.gaugeopt_to_target(mdl_lsgst, mdl_lsgst_compare, {'spam':1.0}, checkJac=True)
mdl_lsgst_reg_go = pygsti.gaugeopt_to_target(mdl_lsgst_reg, mdl_lsgst_reg_compare, {'spam':1.0}, checkJac=True)
self.assertAlmostEqual( mdl_lsgst_go.frobeniusdist(mdl_lsgst_compare), 0, places=4)
self.assertAlmostEqual( mdl_lsgst_reg_go.frobeniusdist(mdl_lsgst_reg_compare), 0, places=4)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
if os.environ.get('PYGSTI_REGEN_REF_FILES','no').lower() in ("yes","1","true"):
mdl_lsgst_go = pygsti.gaugeopt_to_target(mdl_lsgst, self.model, {'spam':1.0})
pygsti.io.write_model(mdl_lsgst_go,compare_files + "/analysis.model", "Saved LSGST Analysis Model")
print("DEBUG: analysis.model = "); print(mdl_lgst_go)
def mdl_lsgst_go(self):
# Was previously written to disk as 'analysis.model'
return pygsti.gaugeopt_to_target(self.mdl_lsgst, self.model, {'spam': 1.0})
def main():
gs_target = std1Q_XYI.gs_target
fiducials = std1Q_XYI.fiducials
germs = std1Q_XYI.germs
maxLengths = [1, 2, 4]
#maxLengths = [1, 2, 4, 8, 16, 32, 64]
#Generate some data
gs_datagen = gs_target.depolarize(gate_noise=0.1, spam_noise=0.001)
gs_datagen = gs_datagen.rotate(rotate=0.04)
listOfExperiments = pygsti.construction.create_lsgst_circuits(
gs_target, fiducials, fiducials, germs, maxLengths)
ds = pygsti.construction.simulate_data(gs_datagen,
listOfExperiments,
n_samples=1000,
sample_error="binomial",
seed=1234)
#Run GST
gs_target.set_all_parameterizations("TP") #TP-constrained
results = pygsti.run_long_sequence_gst(ds,
gs_target,
fiducials,
fiducials,
germs,
maxLengths,
verbosity=0)
with open('data/example_report_results.pkl', 'wb') as outfile:
pickle.dump(results, outfile, protocol=2)
# Case1: TP-constrained GST
tpTarget = gs_target.copy()
tpTarget.set_all_parameterizations("TP")
results_tp = pygsti.run_long_sequence_gst(ds,
tpTarget,
fiducials,
fiducials,
germs,
maxLengths,
gauge_opt_params=False,
verbosity=0)
# Gauge optimize
est = results_tp.estimates['default']
gsFinal = est.gatesets['final iteration estimate']
gsTarget = est.gatesets['target']
for spamWt in [1e-4, 1e-3, 1e-2, 1e-1, 1.0]:
gs = pygsti.gaugeopt_to_target(gsFinal, gsTarget, {
'gates': 1,
'spam': spamWt
})
est.add_gaugeoptimized({'item_weights': {
'gates': 1,
'spam': spamWt
}}, gs, "Spam %g" % spamWt)
#Case2: "Full" GST
fullTarget = gs_target.copy()
fullTarget.set_all_parameterizations("full")
results_full = pygsti.run_long_sequence_gst(ds,
fullTarget,
fiducials,
fiducials,
germs,
maxLengths,
gauge_opt_params=False,
verbosity=0)
#Gauge optimize
est = results_full.estimates['default']
gsFinal = est.gatesets['final iteration estimate']
gsTarget = est.gatesets['target']
for spamWt in [1e-4, 1e-3, 1e-2, 1e-1, 1.0]:
gs = pygsti.gaugeopt_to_target(gsFinal, gsTarget, {
'gates': 1,
'spam': spamWt
})
est.add_gaugeoptimized({'item_weights': {
'gates': 1,
'spam': spamWt
}}, gs, "Spam %g" % spamWt)
with open('data/full_report_results.pkl', 'wb') as outfile:
pickle.dump((results_tp, results_full), outfile, protocol=2)