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)
gs_lgst4 = pygsti.do_lgst(ds, self.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst6 = pygsti.do_lgst(ds, self.specs, self.gateset, svdTruncateTo=6, verbosity=0)
sys.stdout.flush()
self.runSilent(pygsti.do_lgst, ds, self.specs, self.gateset, svdTruncateTo=6, verbosity=4) # test verbose prints
chiSq4 = pygsti.chi2(ds, gs_lgst4, self.lgstStrings, minProbClipForWeighting=1e-4)
chiSq6 = pygsti.chi2(ds, gs_lgst6, 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
gs_lsgst = self.runSilent(pygsti.do_iterative_mc2gst_with_model_selection, ds, gs_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, gs_lsgst_wts = self.runSilent(pygsti.do_iterative_mc2gst_with_model_selection, ds, gs_lgst4,
1, tuple_strings, verbosity=10, minProbClipForWeighting=1e-3,
probClipInterval=(-1e5,1e5), gatestringWeightsDict={ ('Gx',): 2.0 },
returnAll=True, returnErrorVec=True)
# Do non-iterative to cover GateString->tuple conversion
gs_non_iterative = self.runSilent( pygsti.do_mc2gst_with_model_selection, ds,
gs_lgst4, 1, self.lsgstStrings[0],
verbosity=10, probClipInterval=(-1e5,1e5) )
# RUN BELOW LINES TO SEED SAVED GATESET FILES
#pygsti.io.write_gateset(gs_lsgst,compare_files + "/lsgstMS.gateset", "Saved LSGST Gateset with model selection")
gs_lsgst_compare = pygsti.io.load_gateset(compare_files + "/lsgstMS.gateset")
gs_lsgst_go = pygsti.optimize_gauge(gs_lsgst, 'target', targetGateset=gs_lsgst_compare, spamWeight=1.0)
self.assertAlmostEqual( gs_lsgst_go.frobeniusdist(gs_lsgst_compare), 0, places=5)
def runAnalysis(obj, myspecs, mygerms, gsTarget, seed,
maxLs = [1,2,4,8],
nSamples=1000, useFreqWeightedChiSq=False,
minProbClipForWeighting=1e-4, fidPairList=None,
comm=None, distributeMethod="gatestrings"):
rhoStrs, EStrs = pygsti.construction.get_spam_strs(myspecs)
lgstStrings = pygsti.construction.list_lgst_gatestrings(
myspecs, gsTarget.gates.keys())
lsgstStrings = pygsti.construction.make_lsgst_lists(
gsTarget.gates.keys(), rhoStrs, EStrs, mygerms, maxLs, fidPairList )
print len(myspecs[0]), " rho specifiers"
print len(myspecs[1]), " effect specifiers"
print len(mygerms), " germs"
print len(lgstStrings), " total LGST gate strings"
print len(lsgstStrings[-1]), " LSGST strings before thinning"
lsgstStringsToUse = lsgstStrings
allRequiredStrs = pygsti.remove_duplicates(lgstStrings + lsgstStrings[-1])
gs_dataGen = gsTarget.depolarize(gate_noise=0.1)
dsFake = pygsti.construction.generate_fake_data(
gs_dataGen, allRequiredStrs, nSamples, sampleError="multinomial",
seed=seed)
#Run LGST to get starting gate set
gs_lgst = pygsti.do_lgst(dsFake, myspecs, gsTarget,
svdTruncateTo=gsTarget.dim, verbosity=3)
gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",
targetGateset=gs_dataGen)
#Run full iterative LSGST
tStart = time.time()
if obj == "chi2":
all_gs_lsgst = pygsti.do_iterative_mc2gst(
dsFake, 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(
dsFake, 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, gs_dataGen
def test_eLGST(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.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",targetGateset=self.gateset, spamWeight=1.0, gateWeight=1.0)
gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
gs_single_exlgst = pygsti.do_exlgst(ds, gs_clgst, self.elgstStrings[0], self.specs,
self.gateset, regularizeFactor=1e-3, svdTruncateTo=4,
verbosity=0)
gs_single_exlgst_verb = self.runSilent(pygsti.do_exlgst, ds, gs_clgst, self.elgstStrings[0], self.specs,
self.gateset, regularizeFactor=1e-3, svdTruncateTo=4,
verbosity=10)
gs_exlgst = pygsti.do_iterative_exlgst(ds, gs_clgst, self.specs, self.elgstStrings,
targetGateset=self.gateset, svdTruncateTo=4, verbosity=0)
all_minErrs, all_gs_exlgst_tups = pygsti.do_iterative_exlgst(
ds, gs_clgst, self.specs, [ [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.specs, self.elgstStrings,
targetGateset=self.gateset, svdTruncateTo=4, verbosity=10)
gs_exlgst_reg = pygsti.do_iterative_exlgst(ds, gs_clgst, self.specs, 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.specs, 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.specs, 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_go = pygsti.optimize_gauge(gs_exlgst, 'target', targetGateset=gs_exlgst_compare, spamWeight=1.0)
gs_exlgst_reg_go = pygsti.optimize_gauge(gs_exlgst_reg, 'target', targetGateset=gs_exlgst_reg_compare, spamWeight=1.0)
self.assertAlmostEqual( gs_exlgst_go.frobeniusdist(gs_exlgst_compare), 0, places=5)
self.assertAlmostEqual( gs_exlgst_reg_go.frobeniusdist(gs_exlgst_reg_compare), 0, places=5)
def test_LGST_1overSqrtN_dependence(self):
my_datagen_gateset = self.gateset.depolarize(gate_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)
gs_lgst = pygsti.do_lgst(ds, self.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",targetGateset=my_datagen_gateset,
spamWeight=1.0, gateWeight=1.0)
diffs.append( my_datagen_gateset.frobeniusdist(gs_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 setUp(self):
#Set GateSet objects to "strict" mode for testing
pygsti.objects.GateSet._strict = True
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 = 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="cmp_chk_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("cmp_chk_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)
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
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.optimize_gauge(gs_lgst,"target",
targetGateset=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
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lgstStrings, nSamples=1000,
# sampleError='binomial', seed=None)
gs_lgst = pygsti.do_lgst(ds, self.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_verb = self.runSilent(pygsti.do_lgst, ds, self.specs, self.gateset, svdTruncateTo=4, verbosity=10)
self.assertAlmostEqual(gs_lgst.frobeniusdist(gs_lgst_verb),0)
gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",targetGateset=self.gateset, spamWeight=1.0, gateWeight=1.0)
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)
self.assertAlmostEqual( gs_lgst_go.frobeniusdist(gs_lgst_go_compare), 0)
self.assertAlmostEqual( gs_clgst.frobeniusdist(gs_clgst_compare), 0)
#Check for error conditions
with self.assertRaises(ValueError):
gs_lgst = pygsti.do_lgst(ds, self.specs, None, svdTruncateTo=4, verbosity=0) #no gate labels
with self.assertRaises(ValueError):
gs_lgst = pygsti.do_lgst(ds, self.specs, None, gateLabels=list(self.gateset.gates.keys()),
svdTruncateTo=4, verbosity=0) #no spam dict
with self.assertRaises(ValueError):
gs_lgst = pygsti.do_lgst(ds, self.specs, 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_specs = pygsti.construction.build_spam_specs(
pygsti.construction.gatestring_list([('Gx',),('Gx',),('Gx',),('Gx',)]), effect_labels=['E0'])
gs_lgst = pygsti.do_lgst(ds, bad_specs, self.gateset, svdTruncateTo=4, verbosity=0) # bad specs (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.specs, 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.specs, self.gateset,
svdTruncateTo=4, verbosity=0)
def test_gaugeopt_and_contract(self):
ds = self.ds_lgst
#pygsti.construction.generate_fake_data(self.datagen_gateset, self.lgstStrings,
# nSamples=10000,sampleError='binomial', seed=100)
gs_lgst = pygsti.do_lgst(ds, self.specs, self.gateset, svdTruncateTo=4, verbosity=0)
#Gauge Opt to Target
gs_lgst_target = self.runSilent(pygsti.optimize_gauge, gs_lgst,"target",targetGateset=self.gateset,verbosity=10)
#Gauge Opt to Target using non-frobenius metrics
gs_lgst_targetAlt = self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"target",targetGateset=self.gateset,
targetGatesMetric='fidelity', verbosity=10)
gs_lgst_targetAlt = self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"target",targetGateset=self.gateset,
targetGatesMetric='tracedist', verbosity=10)
gs_lgst_targetAlt = self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"target",targetGateset=self.gateset,
targetSpamMetric='fidelity', verbosity=10)
gs_lgst_targetAlt = self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"target",targetGateset=self.gateset,
targetSpamMetric='tracedist', verbosity=10)
with self.assertRaises(ValueError):
self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"target",targetGateset=self.gateset,
targetGatesMetric='foobar', verbosity=10) #bad targetGatesMetric
with self.assertRaises(ValueError):
self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"target",targetGateset=self.gateset,
targetSpamMetric='foobar', verbosity=10) #bad targetSpamMetric
with self.assertRaises(ValueError):
self.runSilent(pygsti.optimize_gauge, gs_lgst_target,"foobar",targetGateset=self.gateset,
targetSpamMetric='target', verbosity=10) #bad toGetTo
#Contractions
gs_clgst_tp = self.runSilent(pygsti.contract, gs_lgst_target, "TP",verbosity=10, tol=10.0)
gs_clgst_cp = self.runSilent(pygsti.contract, gs_lgst_target, "CP",verbosity=10, tol=10.0)
gs_clgst_cptp = self.runSilent(pygsti.contract, gs_lgst_target, "CPTP",verbosity=10, tol=10.0)
gs_clgst_cptp2 = self.runSilent(pygsti.contract, gs_lgst_target, "CPTP",verbosity=10, useDirectCP=False)
gs_clgst_cptp3 = self.runSilent(pygsti.contract, gs_lgst_target, "CPTP",verbosity=10, tol=10.0, maxiter=0)
gs_clgst_xp = self.runSilent(pygsti.contract, gs_lgst_target, "XP", ds,verbosity=10, tol=10.0)
gs_clgst_xptp = self.runSilent(pygsti.contract, gs_lgst_target, "XPTP", ds,verbosity=10, tol=10.0)
gs_clgst_vsp = self.runSilent(pygsti.contract, gs_lgst_target, "vSPAM",verbosity=10, tol=10.0)
gs_clgst_none = self.runSilent(pygsti.contract, gs_lgst_target, "nothing",verbosity=10, tol=10.0)
#test bad effect vector cases
gs_bad_effect = gs_lgst_target.copy()
gs_bad_effect.effects['E0'] = [100.0,0,0,0] # E eigvals all > 1.0
self.runSilent(pygsti.contract, gs_bad_effect, "vSPAM",verbosity=10, tol=10.0)
gs_bad_effect.effects['E0'] = [-100.0,0,0,0] # E eigvals all < 0
self.runSilent(pygsti.contract, gs_bad_effect, "vSPAM",verbosity=10, tol=10.0)
with self.assertRaises(ValueError):
self.runSilent(pygsti.contract, gs_lgst_target, "foobar",verbosity=10, tol=10.0) #bad toWhat
#More gauge optimizations
gs_lgst_target_cp = self.runSilent(pygsti.optimize_gauge, gs_clgst_cptp,"target",targetGateset=self.gateset,
constrainToCP=True,constrainToTP=True,constrainToValidSpam=True,verbosity=10)
gs_lgst_cptp = self.runSilent(pygsti.optimize_gauge, gs_lgst,"CPTP",verbosity=10)
gs_lgst_cptp_tp = self.runSilent(pygsti.optimize_gauge, gs_lgst,"CPTP",verbosity=10, constrainToTP=True)
gs_lgst_tp = self.runSilent(pygsti.optimize_gauge, gs_lgst,"TP",verbosity=10)
gs_lgst_tptarget = self.runSilent(pygsti.optimize_gauge, gs_lgst,"TP and target",targetGateset=self.gateset,verbosity=10)
gs_lgst_cptptarget = self.runSilent(pygsti.optimize_gauge, gs_lgst,"CPTP and target",targetGateset=self.gateset,verbosity=10)
gs_lgst_cptptarget2= self.runSilent(pygsti.optimize_gauge, gs_lgst,"CPTP and target",targetGateset=self.gateset,
verbosity=10, constrainToTP=True)
gs_lgst_cd = self.runSilent(pygsti.optimize_gauge, gs_lgst,"Completely Depolarized",targetGateset=self.gateset,verbosity=10)
#TODO: check output lies in space desired
# big kick that should land it outside XP, TP, etc, so contraction
# routines are more tested
gs_bigkick = gs_lgst_target.kick(absmag=1.0)
gs_badspam = gs_bigkick.copy()
gs_badspam.effects['E0'] = np.array( [[2],[0],[0],[4]], 'd') #set a bad evec so vSPAM has to work...
gs_clgst_tp = self.runSilent(pygsti.contract,gs_bigkick, "TP", verbosity=10, tol=10.0)
gs_clgst_cp = self.runSilent(pygsti.contract,gs_bigkick, "CP", verbosity=10, tol=10.0)
gs_clgst_cptp = self.runSilent(pygsti.contract,gs_bigkick, "CPTP", verbosity=10, tol=10.0)
gs_clgst_xp = self.runSilent(pygsti.contract,gs_bigkick, "XP", ds, verbosity=10, tol=10.0)
gs_clgst_xptp = self.runSilent(pygsti.contract,gs_bigkick, "XPTP", ds, verbosity=10, tol=10.0)
gs_clgst_vsp = self.runSilent(pygsti.contract,gs_badspam, "vSPAM", verbosity=10, tol=10.0)
gs_clgst_none = self.runSilent(pygsti.contract,gs_bigkick, "nothing", verbosity=10, tol=10.0)
#TODO: check output lies in space desired
#Check Errors
with self.assertRaises(ValueError):
pygsti.optimize_gauge(gs_lgst,"FooBar",verbosity=0) # bad toGetTo argument
with self.assertRaises(ValueError):
pygsti.contract(gs_lgst_target, "FooBar",verbosity=0) # bad toWhat argument
def test_MLGST(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.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",targetGateset=self.gateset, spamWeight=1.0, gateWeight=1.0)
gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
gs_single_mlgst = pygsti.do_mlgst(ds, gs_clgst, self.lsgstStrings[0], minProbClip=1e-6,
probClipInterval=(-1e2,1e2), verbosity=0)
gs_mlegst = pygsti.do_iterative_mlgst(ds, gs_clgst, self.lsgstStrings, verbosity=0,
minProbClip=1e-6, probClipInterval=(-1e2,1e2),
memLimit=1000*1024**2)
maxLogL, all_gs_mlegst_tups = pygsti.do_iterative_mlgst(
ds, gs_clgst, [ [gs.tup for gs in gsList] for gsList in self.lsgstStrings],
minProbClip=1e-6, probClipInterval=(-1e2,1e2), returnAll=True, returnMaxLogL=True)
gs_mlegst_verb = self.runSilent(pygsti.do_iterative_mlgst, ds, gs_clgst, self.lsgstStrings, verbosity=10,
minProbClip=1e-6, probClipInterval=(-1e2,1e2),
memLimit=10*1024**2)
self.assertAlmostEqual(gs_mlegst.frobeniusdist(gs_mlegst_verb),0)
self.assertAlmostEqual(gs_mlegst.frobeniusdist(all_gs_mlegst_tups[-1]),0)
#Run internal checks on less max-L values (so it doesn't take forever)
gs_mlegst_chk = pygsti.do_iterative_mlgst(ds, gs_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClip=1e-6, probClipInterval=(-1e2,1e2),
check=True)
#Other option variations - just make sure they run at this point
gs_mlegst_chk_opts = pygsti.do_iterative_mlgst(ds, gs_clgst, self.lsgstStrings[0:2], verbosity=0,
minProbClip=1e-6, probClipInterval=(-1e2,1e2),
gateStringSetLabels=["Set1","Set2"], useFreqWeightedChiSq=True )
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"]
gs_mlegst_chk_opts2 = pygsti.do_mlgst(ds, gs_withA1, aliased_list, minProbClip=1e-6,
probClipInterval=(-1e2,1e2), verbosity=0,
gateLabelAliases={ 'GA1': ('Gx',) })
#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 } )
self.runSilent(pygsti.do_mlgst, ds, gs_clgst, self.lsgstStrings[0], minProbClip=1e-6,
probClipInterval=(-1e2,1e2), verbosity=4, memLimit=300000) #invoke memory control
pygsti.do_mlgst(ds, gs_clgst, self.lsgstStrings[0], minProbClip=1e-6,
probClipInterval=(-1e2,1e2), verbosity=0, poissonPicture=False)
#non-Poisson picture - should use (-1,-1) gateset for consistency?
#Check errors:
with self.assertRaises(MemoryError):
pygsti.do_mlgst(ds, gs_clgst, self.lsgstStrings[0], minProbClip=1e-6,
probClipInterval=(-1e2,1e2),verbosity=0, memLimit=1)
# RUN BELOW LINES TO SEED SAVED GATESET FILES
#pygsti.io.write_gateset(gs_mlegst,compare_files + "/mle_gst.gateset", "Saved MLE-GST Gateset")
gs_mle_compare = pygsti.io.load_gateset(compare_files + "/mle_gst.gateset")
gs_mlegst_go = pygsti.optimize_gauge(gs_mlegst, 'target', targetGateset=gs_mle_compare, spamWeight=1.0)
self.assertAlmostEqual( gs_mlegst_go.frobeniusdist(gs_mle_compare), 0, places=5)
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.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst_go = pygsti.optimize_gauge(gs_lgst,"target",targetGateset=self.gateset, spamWeight=1.0, gateWeight=1.0)
gs_clgst = pygsti.contract(gs_lgst_go, "CPTP")
gs_single_lsgst = pygsti.do_mc2gst(ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=0)
gs_lsgst = pygsti.do_iterative_mc2gst(ds, gs_clgst, self.lsgstStrings, verbosity=0,
minProbClipForWeighting=1e-6, probClipInterval=(-1e6,1e6),
memLimit=1000*1024**2)
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=10*1024**2)
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=100*1024**2)
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=100*1024**2)
#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 } )
#Check with small but ok memlimit
self.runSilent(pygsti.do_mc2gst,ds, gs_clgst, self.lsgstStrings[0], minProbClipForWeighting=1e-6,
probClipInterval=(-1e6,1e6), regularizeFactor=1e-3,
verbosity=10, memLimit=300000)
#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(NotImplementedError):
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) #cptp pentalty not implemented yet
# 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.optimize_gauge(gs_lsgst, 'target', targetGateset=gs_lsgst_compare, spamWeight=1.0)
gs_lsgst_reg_go = pygsti.optimize_gauge(gs_lsgst_reg, 'target', targetGateset=gs_lsgst_reg_compare, spamWeight=1.0)
self.assertAlmostEqual( gs_lsgst_go.frobeniusdist(gs_lsgst_compare), 0, places=5)
self.assertAlmostEqual( gs_lsgst_reg_go.frobeniusdist(gs_lsgst_reg_compare), 0, places=5)
def test_LGST_no_sample_error(self):
ds = pygsti.construction.generate_fake_data(self.datagen_gateset, self.lgstStrings,
nSamples=1000, sampleError='none')
gs_lgst = pygsti.do_lgst(ds, self.specs, self.gateset, svdTruncateTo=4, verbosity=0)
gs_lgst = pygsti.optimize_gauge(gs_lgst, "target", targetGateset=self.datagen_gateset, gateWeight=1.0, spamWeight=1.0)
self.assertAlmostEqual( gs_lgst.frobeniusdist(self.datagen_gateset), 0)
def setUp(self):
#Set GateSet objects to "strict" mode for testing
pygsti.objects.GateSet._strict = True
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 = 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="cmp_chk_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("cmp_chk_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)
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)
lsgst_gatesets = [ pygsti.optimize_gauge(gs, "target", targetGateset=self.targetGateset,
gateWeight=1,spamWeight=0.001) for gs in lsgst_gatesets_prego]
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, False, None, lsgst_gatesets_prego)
self.results.parameters.update({'minProbClip': 1e-6, 'minProbClipForWeighting': 1e-4,
'probClipInterval': (-1e6,1e6), 'radius': 1e-4,
'weights': None, 'defaultDirectory': "temp_test_files",
'defaultBasename': "MyDefaultReportName" } )
#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)
lsgst_gatesets_TP = [ pygsti.optimize_gauge(gs, "target", targetGateset=self.targetGateset, constrainToTP=True,
gateWeight=1,spamWeight=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, True)
def test_bootstrap(self):
ds = pygsti.objects.DataSet(fileToLoadFrom=compare_files + "/drivers.dataset")
specs = self.runSilent(pygsti.construction.build_spam_specs, std.fiducials)
gs = pygsti.do_lgst(ds, specs, targetGateset=std.gs_target, svdTruncateTo=4, verbosity=0)
bootds_p = pygsti.drivers.make_bootstrap_dataset(
ds,'parametric', gs, seed=1234 )
bootds_np = pygsti.drivers.make_bootstrap_dataset(
ds,'nonparametric', seed=1234 )
with self.assertRaises(ValueError):
pygsti.drivers.make_bootstrap_dataset(ds,'foobar', seed=1)
#bad generationMethod
with self.assertRaises(ValueError):
pygsti.drivers.make_bootstrap_dataset(ds,'parametric', seed=1)
# must specify gateset for parametric mode
with self.assertRaises(ValueError):
pygsti.drivers.make_bootstrap_dataset(ds,'nonparametric',gs,seed=1)
# must *not* specify gateset for nonparametric mode
maxLengths = [0] #just do LGST strings to make this fast...
bootgs_p = self.runSilent(pygsti.drivers.make_bootstrap_gatesets,
2, ds, 'parametric', std.fiducials, std.fiducials,
std.germs, maxLengths, inputGateSet=gs, constrainToTP=True,
returnData=False)
default_maxLens = [0]+[2**k for k in range(10)]
gateStrings = pygsti.construction.make_lsgst_experiment_list(
self.gateLabels, self.fiducials, self.fiducials, self.germs,
default_maxLens, fidPairs=None, truncScheme="whole germ powers")
ds_defaultMaxLens = pygsti.construction.generate_fake_data(
gs, gateStrings, nSamples=1000, sampleError='round')
bootgs_p_defaultMaxLens = self.runSilent(
pygsti.drivers.make_bootstrap_gatesets,
2, ds_defaultMaxLens, 'parametric', std.fiducials, std.fiducials,
std.germs, None, inputGateSet=gs, constrainToTP=True,
returnData=False) #test when maxLengths == None
bootgs_np, bootds_np2 = self.runSilent(
pygsti.drivers.make_bootstrap_gatesets,
2, ds, 'nonparametric', std.fiducials, std.fiducials,
std.germs, maxLengths, targetGateSet=gs,
constrainToTP=True, returnData=True)
with self.assertRaises(ValueError):
pygsti.drivers.make_bootstrap_gatesets(
2, ds, 'parametric', std.fiducials, std.fiducials,
std.germs, maxLengths, constrainToTP=True,
returnData=False)
#must specify either inputGateSet or targetGateSet
with self.assertRaises(ValueError):
pygsti.drivers.make_bootstrap_gatesets(
2, ds, 'parametric', std.fiducials, std.fiducials,
std.germs, maxLengths, inputGateSet=gs, targetGateSet=gs,
constrainToTP=True, returnData=False)
#cannot specify both inputGateSet and targetGateSet
self.runSilent(pygsti.drivers.gauge_optimize_gs_list,
bootgs_p, std.gs_target, constrainToTP=True,
gateMetric = 'frobenius', spamMetric = 'frobenius',
plot=False)
#Test plotting -- seems to work.
self.runSilent(pygsti.drivers.gauge_optimize_gs_list,
bootgs_p, std.gs_target, constrainToTP=True,
gateMetric = 'frobenius', spamMetric = 'frobenius',
plot=True)
#Test utility functions -- just make sure they run for now...
def gsFn(gs):
return gs.get_dimension()
tp_target = std.gs_target.copy()
tp_target.set_all_parameterizations("TP")
pygsti.drivers.gs_stdev(gsFn, bootgs_p)
pygsti.drivers.gs_mean(gsFn, bootgs_p)
pygsti.drivers.gs_stdev1(gsFn, bootgs_p)
pygsti.drivers.gs_mean1(gsFn, bootgs_p)
pygsti.drivers.to_vector(bootgs_p[0])
pygsti.drivers.to_mean_gateset(bootgs_p, tp_target)
pygsti.drivers.to_std_gateset(bootgs_p, tp_target)
pygsti.drivers.to_rms_gateset(bootgs_p, tp_target)
pygsti.drivers.gateset_jtracedist(bootgs_p[0], tp_target)
pygsti.drivers.gateset_process_fidelity(bootgs_p[0], tp_target)
pygsti.drivers.gateset_diamonddist(bootgs_p[0], tp_target)
pygsti.drivers.gateset_decomp_angle(bootgs_p[0])
pygsti.drivers.gateset_decomp_decay_diag(bootgs_p[0])
pygsti.drivers.gateset_decomp_decay_offdiag(bootgs_p[0])
pygsti.drivers.spamrameter(bootgs_p[0])
