/
duplicated_algorithms.html
1277 lines (1268 loc) · 61.5 KB
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duplicated_algorithms.html
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<HTML>
<HEAD>
<TITLE> CloneDigger Report </TITLE>
<script type="text/javascript">
function unhide(divID) {
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item.className=(item.className=='hidden')?'unhidden':'hidden';
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<style type="text/css">
.hidden { display: none; }
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.preformatted {
border: 1px dashed #3c78b5;
font-size: 11px;
font-family: Courier;
margin: 10px;
line-height: 13px;
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background-color: #f0f0f0;
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<!--
<div class="preformatted"><div class="preformattedContent">
<pre>Clone Digger
</pre>
</div></div>
-->
</style>
</HEAD>
<BODY>
<P>Source files: 6</P>
<a href = "javascript:unhide('files');">Click here to show/hide file names</a><div id="files" class="hidden"><P><B>Source files:</B><BR>algorithms/fiducialpairreduction.py, <BR>algorithms/__init__.py, <BR>algorithms/grammatrix.py, <BR>algorithms/fiducialselection.py, <BR>algorithms/core.py, <BR>algorithms/germselection.py</P></div>
<P>Clones detected: 36</P>
<P>442 of 1927 lines are duplicates (22.94%) </P>
<P>
<B>Parameters<BR> </B>
clustering_threshold = 10<BR>
distance_threshold = 5<BR>
size_threshold = 5<BR>
hashing_depth = 1<BR>
clusterize_using_hash = False<BR>
clusterize_using_dcup = False<BR>
</P>
<B>Time elapsed</B><BR>Construction of AST : 0.41 seconds<BR>
Building statement hash : 0.01 seconds<BR>
Building patterns : 1.08 seconds<BR>
Marking similar statements : 1.41 seconds<BR>
Finding similar sequences of statements : 0.18 seconds<BR>
Refining candidates : 0.39 seconds<BR>
Total time: 3.47<BR>
Started at: Mon Aug 1 06:55:02 2016<BR>
Finished at: Mon Aug 1 06:55:06 2016
<P><B>Clone # 1</B><BR>Distance between two fragments = 0 <BR>Clone size = 18<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1026</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1998</TD></TR><TR>
<TD>
if maxEvalSubTreeSize is not None:<BR>
evTree.split(maxEvalSubTreeSize, None)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if maxEvalSubTreeSize is not None:<BR>
evTree.split(maxEvalSubTreeSize, None)</TD>
</TR>
<TR>
<TD>
if comm is not None:<BR>
nprocs = comm.Get_size()<BR>
if distributeMethod == 'gatestrings':<BR>
if not evTree.is_split():<BR>
evTree.split(None, nprocs)<BR>
else:<BR>
assert maxEvalSubTreeSize is not None<BR>
if len(evTree.get_sub_trees()) < nprocs:<BR>
evTree.split(None, nprocs)<BR>
if any([len(sub) > maxEvalSubTreeSize for sub in evTree.get_sub_trees() ]):<BR>
evTree.split(maxEvalSubTreeSize, None)<BR>
elif distributeMethod == 'deriv':<BR>
pass<BR>
else:<BR>
raise ValueError(('Invalid distribute method: %s') % (distributeMethod))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if comm is not None:<BR>
nprocs = comm.Get_size()<BR>
if distributeMethod == 'gatestrings':<BR>
if not evTree.is_split():<BR>
evTree.split(None, nprocs)<BR>
else:<BR>
assert maxEvalSubTreeSize is not None<BR>
if len(evTree.get_sub_trees()) < nprocs:<BR>
evTree.split(None, nprocs)<BR>
if any([len(sub) > maxEvalSubTreeSize for sub in evTree.get_sub_trees() ]):<BR>
evTree.split(maxEvalSubTreeSize, None)<BR>
elif distributeMethod == 'deriv':<BR>
pass<BR>
else:<BR>
raise ValueError(('Invalid distribute method: %s') % (distributeMethod))</TD>
</TR>
<TR>
<TD>
if ((comm is None) or (comm.Get_rank() == 0)) and (evTree.is_split()):<BR>
printer.log('Memory limit and/or MPI has imposed a division of the evaluation tree:', 2)<BR>
evTree.print_analysis()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if ((comm is None) or (comm.Get_rank() == 0)) and (evTree.is_split()):<BR>
printer.log('Memory limit and/or MPI has imposed a division of the evaluation tree:', 2)<BR>
evTree.print_analysis()</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 2</B><BR>Distance between two fragments = 1 <BR>Clone size = 16<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1456</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1418</TD></TR><TR>
<TD>
minErr, gs = do_mc2gst(dataset, curStartGateset, gateStringsToUse, maxiter, maxfev, tol, cptp_penalty_factor, minProbClipForWeighting, probClipInterval, useFreqWeightedChiSq, regularizeFactor, (printer) - (1), check, check_jacobian, gatestringWeights, None, memLimit, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
minErr, gs = do_mc2gst(dataset, curStartGateset, gateStringsToUse, maxiter, maxfev, tol, cptp_penalty_factor, minProbClipForWeighting, probClipInterval, useFreqWeightedChiSq, regularizeFactor, (printer) - (1), check, check_jacobian, gatestringWeights, None, memLimit, comm)</TD>
</TR>
<TR>
<TD>
chiSq = sum([(x) ** (2) for x in minErr ])</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
chiSq = sum([(x) ** (2) for x in minErr ])</TD>
</TR>
<TR>
<TD>
chi2diff = (chiSq) - (chiSqBest)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
chi2diff = (chiSq) - (chiSqBest)</TD>
</TR>
<TR>
<TD>
paramDiff = (nParams) - (nParamsBest)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
paramDiff = (nParams) - (nParamsBest)</TD>
</TR>
<TR>
<TD>
if (chiSqBest) - (chiSq) > (2) * ((nParams) - (nParamsBest)):<BR>
bestGS, bestMinErr, chiSqBest, nParamsBest = (gs, minErr, chiSq, nParams)<BR>
msResult = 'Selected'<BR>
else:<BR>
msResult = 'Rejected'<BR>
<span style="color: rgb(255, 0, 0);">tryIncreasedDim</span> = False</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if (chiSqBest) - (chiSq) > (2) * ((nParams) - (nParamsBest)):<BR>
bestGS, bestMinErr, chiSqBest, nParamsBest = (gs, minErr, chiSq, nParams)<BR>
msResult = 'Selected'<BR>
else:<BR>
msResult = 'Rejected'<BR>
<span style="color: rgb(255, 0, 0);">tryDecreasedDim</span> = False</TD>
</TR>
<TR>
<TD>
printer.log(('%s dim %d: chi^2 = %g (%+g w.r.t. expected mean of %d strings - %d params = %d) (dChi^2=%d, 2*dParams=%d)') % ((msResult, curDim, chiSq, (chiSq) - ((nStrings) - (nParams)), nStrings, nParams, (nStrings) - (nParams), chi2diff, (2) * (paramDiff))))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log(('%s dim %d: chi^2 = %g (%+g w.r.t. expected mean of %d strings - %d params = %d) (dChi^2=%d, 2*dParams=%d)') % ((msResult, curDim, chiSq, (chiSq) - ((nStrings) - (nParams)), nStrings, nParams, (nStrings) - (nParams), chi2diff, (2) * (paramDiff))))</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 3</B><BR>Distance between two fragments = 0 <BR>Clone size = 13<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 971</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1948</TD></TR><TR>
<TD>
if gateLabelAliases is not None:<BR>
dsGateStringsToUse = []<BR>
for s in gateStringsToUse:<BR>
for label, expandedStr in gateLabelAliases.items():<BR>
while label in tuple(s):<BR>
i = tuple(s).index(label)<BR>
s = ((tuple(s)[:i]) + (tuple(expandedStr))) + (tuple(s)[(i) + (1):])<BR>
dsGateStringsToUse.append(s)<BR>
else:<BR>
dsGateStringsToUse = gateStringsToUse</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if gateLabelAliases is not None:<BR>
dsGateStringsToUse = []<BR>
for s in gateStringsToUse:<BR>
for label, expandedStr in gateLabelAliases.items():<BR>
while label in tuple(s):<BR>
i = tuple(s).index(label)<BR>
s = ((tuple(s)[:i]) + (tuple(expandedStr))) + (tuple(s)[(i) + (1):])<BR>
dsGateStringsToUse.append(s)<BR>
else:<BR>
dsGateStringsToUse = gateStringsToUse</TD>
</TR>
<TR>
<TD>
evTree = gs.bulk_evaltree(gateStringsToUse)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
evTree = gs.bulk_evaltree(gateStringsToUse)</TD>
</TR>
<TR>
<TD>
ns = len(spamLabels)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
ns = len(spamLabels)</TD>
</TR>
<TR>
<TD>
ng = len(gateStringsToUse)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
ng = len(gateStringsToUse)</TD>
</TR>
<TR>
<TD>
ne = gs.num_params()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
ne = gs.num_params()</TD>
</TR>
<TR>
<TD>
gd = gs.get_dimension()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gd = gs.get_dimension()</TD>
</TR>
<TR>
<TD>
C = (1.0) / ((1024.0) ** (3))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
C = (1.0) / ((1024.0) ** (3))</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 4</B><BR>Distance between two fragments = 2 <BR>Clone size = 11<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 3025</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2992</TD></TR><TR>
<TD>
print_obj_func = _opt.create_obj_func_printer(objective_func)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
print_obj_func = _opt.create_obj_func_printer(objective_func)</TD>
</TR>
<TR>
<TD>
if objective_func(gs.to_vector()) < 1e-08:<BR>
printer.log(<span style="color: rgb(255, 0, 0);">'Already in CP - no contraction necessary'</span>, 1)<BR>
return (0.0, gs)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if objective_func(gs.to_vector()) < 1e-08:<BR>
printer.log(<span style="color: rgb(255, 0, 0);">'Already in XP - no contraction necessary'</span>, 1)<BR>
return (0.0, gs)</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">optSol = _opt.minimize(objective_func,gs.to_vector(),<BR>
method=method, tol=tol, maxiter=maxiter,<BR>
callback = print_obj_func if printer.verbosity > 2 else None)<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="font-family: monospace;">optSol = _opt.minimize(objective_func,gs.to_vector(),<BR>
method=method, tol=tol, maxiter=maxiter,<BR>
callback = print_obj_func if printer.verbosity > 2 else None)<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
gs.from_vector(optSol.x)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gs.from_vector(optSol.x)</TD>
</TR>
<TR>
<TD>
if optSol.fun >= CLIFF:<BR>
_warnings.warn(<span style="color: rgb(255, 0, 0);">'Failed to contract gateset to CP'</span>)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if optSol.fun >= CLIFF:<BR>
_warnings.warn(<span style="color: rgb(255, 0, 0);">'Failed to contract gateset to XP'</span>)</TD>
</TR>
<TR>
<TD>
printer.log(('The closest legal point found was distance: ') + (str(optSol.fun)), 1)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log(('The closest legal point found was distance: ') + (str(optSol.fun)), 1)</TD>
</TR>
<TR>
<TD>
return (optSol.fun, gs)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
return (optSol.fun, gs)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 5</B><BR>Distance between two fragments = 2 <BR>Clone size = 11<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2656</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2753</TD></TR><TR>
<TD>
if constrainToTP:<BR>
tpGateset = gateset<BR>
tpGaugeMx = _np.identity(gateDim, 'd')<BR>
else:<BR>
_, tpGaugeMx, tpGateset = optimize_gauge(gateset, <span style="color: rgb(255, 0, 0);">'TP'</span>, maxiter, maxfev, tol, 'L-BFGS-B', targetGateset, targetFactor, constrainToTP, constrainToCP, constrainToValidSpam, True, gateWeight, spamWeight, itemWeights, (printer) - (1))</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if constrainToTP:<BR>
tpGateset = gateset<BR>
tpGaugeMx = _np.identity(gateDim, 'd')<BR>
else:<BR>
_, tpGaugeMx, tpGateset = optimize_gauge(gateset, <span style="color: rgb(255, 0, 0);">'TP and target'</span>, maxiter, maxfev, tol, 'L-BFGS-B', targetGateset, targetFactor, constrainToTP, constrainToCP, constrainToValidSpam, True, gateWeight, spamWeight, itemWeights, (printer) - (1))</TD>
</TR>
<TR>
<TD>
printer.log('', 2)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('', 2)</TD>
</TR>
<TR>
<TD>
printer.log((<span style="color: rgb(255, 0, 0);">'--- Gauge Optimization to CPTP w/valid SPAM (%s) ---'</span>) % (method), 1, indentOffset=-1)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
printer.log((<span style="color: rgb(255, 0, 0);">'--- Gauge Optimization to CPTP and target w/valid SPAM (%s) ---'</span>) % (method), 1, indentOffset=-1)</TD>
</TR>
<TR>
<TD>
constrainToTP = True</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
constrainToTP = True</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 6</B><BR>Distance between two fragments = 2 <BR>Clone size = 10<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 946</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1931</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
gs = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gs = startGateset.copy()</TD>
</TR>
<TR>
<TD>
if maxfev is None:<BR>
maxfev = maxiter</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if maxfev is None:<BR>
maxfev = maxiter</TD>
</TR>
<TR>
<TD>
printer.log('', 2)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('', 2)</TD>
</TR>
<TR>
<TD>
printer.log(<span style="color: rgb(255, 0, 0);">'--- Minimum Chi^2 GST ---'</span>, 1, indentOffset=-1)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
printer.log(<span style="color: rgb(255, 0, 0);">'--- MLGST ---'</span>, 1, indentOffset=-1)</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">if comm is not None:<BR>
gs_cmp = comm.bcast(gs if (comm.Get_rank() == 0) else None, root=0)<BR>
if gs.frobeniusdist(gs_cmp) > 1e-6:<BR>
raise ValueError("MPI ERROR: *different* M<span style="color:rgb(255,0,0);">C2</span>GST start gatesets" +<BR>
" given to different processors!")<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="font-family: monospace;">if comm is not None:<BR>
gs_cmp = comm.bcast(gs if (comm.Get_rank() == 0) else None, root=0)<BR>
if gs.frobeniusdist(gs_cmp) > 1e-6:<BR>
raise ValueError("MPI ERROR: *different* M<span style="color:rgb(255,0,0);">L</span>GST start gatesets" +<BR>
" given to different processors!")<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 7</B><BR>Distance between two fragments = 3 <BR>Clone size = 9<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2361</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1602</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">mleGatesets</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">lsgstGatesets</span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">maxLogLs</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">mleGateset</span> = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">lsgstGateset</span> = startGateset.copy()</TD>
</TR>
<TR>
<TD>
nIters = len(gateStringLists)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nIters = len(gateStringLists)</TD>
</TR>
<TR>
<TD>
tRef = _time.time()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
tRef = _time.time()</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 8</B><BR>Distance between two fragments = 0 <BR>Clone size = 9<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2733</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2711</TD></TR><TR>
<TD>
matM = vectorM.reshape((gateDim, gateDim))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
matM = vectorM.reshape((gateDim, gateDim))</TD>
</TR>
<TR>
<TD>
gs = gateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gs = gateset.copy()</TD>
</TR>
<TR>
<TD>
gs.transform(matM)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gs.transform(matM)</TD>
</TR>
<TR>
<TD>
tpPenalty = 0</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
tpPenalty = 0</TD>
</TR>
<TR>
<TD>
for gate in list(gs.gates.values()):<BR>
tpPenalty += ((1.0) - (gate[0,0])) ** (2)<BR>
for k in range(1, gate.shape[1]):<BR>
tpPenalty += (gate[0,k]) ** (2)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for gate in list(gs.gates.values()):<BR>
tpPenalty += ((1.0) - (gate[0,0])) ** (2)<BR>
for k in range(1, gate.shape[1]):<BR>
tpPenalty += (gate[0,k]) ** (2)</TD>
</TR>
<TR>
<TD>
for rhoVec in list(gs.preps.values()):<BR>
tpPenalty += ((rhoVecFirstEl) - (rhoVec[0])) ** (2)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for rhoVec in list(gs.preps.values()):<BR>
tpPenalty += ((rhoVecFirstEl) - (rhoVec[0])) ** (2)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 9</B><BR>Distance between two fragments = 2 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 791</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1768</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">elgstGatesets</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">lsgstGatesets</span> = []</TD>
</TR>
<TR>
<TD>
minErrs = []</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
minErrs = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">elgstGateset</span> = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">lsgstGateset</span> = startGateset.copy()</TD>
</TR>
<TR>
<TD>
nIters = len(gateStringLists)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nIters = len(gateStringLists)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 10</B><BR>Distance between two fragments = 3 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 791</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2361</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">elgstGatesets</span></span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">mleGatesets</span></span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">maxLogLs</span></span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">elgstGateset</span></span> = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">mleGateset</span></span> = startGateset.copy()</TD>
</TR>
<TR>
<TD>
nIters = len(gateStringLists)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nIters = len(gateStringLists)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 11</B><BR>Distance between two fragments = 2 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 791</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1602</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">elgstGatesets</span></span></span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGatesets</span></span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">elgstGateset</span></span></span> = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGateset</span></span> = startGateset.copy()</TD>
</TR>
<TR>
<TD>
nIters = len(gateStringLists)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nIters = len(gateStringLists)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 12</B><BR>Distance between two fragments = 3 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1768</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2361</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGatesets</span></span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">mleGatesets</span></span></span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">maxLogLs</span></span></span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGateset</span></span> = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">mleGateset</span></span></span> = startGateset.copy()</TD>
</TR>
<TR>
<TD>
nIters = len(gateStringLists)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nIters = len(gateStringLists)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 13</B><BR>Distance between two fragments = 0 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1768</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1602</TD></TR><TR>
<TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)</TD>
</TR>
<TR>
<TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (len(gateStringSetsToUseInEstimation) > 0) and (len(gateStringSetsToUseInEstimation[0]) > 0) and (isinstance(gateStringSetsToUseInEstimation[0][0], _objs.GateString)):<BR>
gateStringLists = [[gstr.tup for gstr in gsList ] for gsList in gateStringSetsToUseInEstimation ]<BR>
else:<BR>
gateStringLists = gateStringSetsToUseInEstimation</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGatesets</span></span> = []</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGatesets</span></span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="color: rgb(255, 0, 0);">minErrs</span> = []</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGateset</span></span> = startGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">lsgstGateset</span></span> = startGateset.copy()</TD>
</TR>
<TR>
<TD>
nIters = len(gateStringLists)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nIters = len(gateStringLists)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 14</B><BR>Distance between two fragments = 0 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2131</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2153</TD></TR><TR>
<TD>
pos_probs = _np.where(probs < min_p, min_p, probs)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pos_probs = _np.where(probs < min_p, min_p, probs)</TD>
</TR>
<TR>
<TD>
S = (minusCntVecMx) / (min_p)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
S = (minusCntVecMx) / (min_p)</TD>
</TR>
<TR>
<TD>
S2 = ((-0.5) * (minusCntVecMx)) / ((min_p) ** (2))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
S2 = ((-0.5) * (minusCntVecMx)) / ((min_p) ** (2))</TD>
</TR>
<TR>
<TD>
v = (freqTerm) + ((minusCntVecMx) * (_np.log(pos_probs)))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = (freqTerm) + ((minusCntVecMx) * (_np.log(pos_probs)))</TD>
</TR>
<TR>
<TD>
v = _np.maximum(v, 0)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.maximum(v, 0)</TD>
</TR>
<TR>
<TD>
v = _np.where(probs < min_p, ((v) + ((S) * ((probs) - (min_p)))) + ((S2) * (((probs) - (min_p)) ** (2))), v)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.where(probs < min_p, ((v) + ((S) * ((probs) - (min_p)))) + ((S2) * (((probs) - (min_p)) ** (2))), v)</TD>
</TR>
<TR>
<TD>
v = _np.where(minusCntVecMx == 0, 0.0, v)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.where(minusCntVecMx == 0, 0.0, v)</TD>
</TR>
<TR>
<TD>
v = _np.sqrt(v)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.sqrt(v)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 15</B><BR>Distance between two fragments = 0 <BR>Clone size = 8<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2066</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2089</TD></TR><TR>
<TD>
pos_probs = _np.where(probs < min_p, min_p, probs)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pos_probs = _np.where(probs < min_p, min_p, probs)</TD>
</TR>
<TR>
<TD>
S = ((minusCntVecMx) / (min_p)) + (totalCntVec[None,None:None])</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
S = ((minusCntVecMx) / (min_p)) + (totalCntVec[None,None:None])</TD>
</TR>
<TR>
<TD>
S2 = ((-0.5) * (minusCntVecMx)) / ((min_p) ** (2))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
S2 = ((-0.5) * (minusCntVecMx)) / ((min_p) ** (2))</TD>
</TR>
<TR>
<TD>
v = ((freqTerm) + ((minusCntVecMx) * (_np.log(pos_probs)))) + ((totalCntVec[None,None:None]) * (pos_probs))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = ((freqTerm) + ((minusCntVecMx) * (_np.log(pos_probs)))) + ((totalCntVec[None,None:None]) * (pos_probs))</TD>
</TR>
<TR>
<TD>
v = _np.maximum(v, 0)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.maximum(v, 0)</TD>
</TR>
<TR>
<TD>
v = _np.where(probs < min_p, ((v) + ((S) * ((probs) - (min_p)))) + ((S2) * (((probs) - (min_p)) ** (2))), v)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.where(probs < min_p, ((v) + ((S) * ((probs) - (min_p)))) + ((S2) * (((probs) - (min_p)) ** (2))), v)</TD>
</TR>
<TR>
<TD>
v = _np.where(minusCntVecMx == 0, (totalCntVec[None,None:None]) * (_np.where(probs >= a, probs, ((((-1.0) / ((3) * ((a) ** (2)))) * ((probs) ** (3))) + (((probs) ** (2)) / (a))) + ((a) / (3.0)))), v)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.where(minusCntVecMx == 0, (totalCntVec[None,None:None]) * (_np.where(probs >= a, probs, ((((-1.0) / ((3) * ((a) ** (2)))) * ((probs) ** (3))) + (((probs) ** (2)) / (a))) + ((a) / (3.0)))), v)</TD>
</TR>
<TR>
<TD>
v = _np.sqrt(v)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
v = _np.sqrt(v)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 16</B><BR>Distance between two fragments = 2 <BR>Clone size = 7<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1456</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1388</TD></TR><TR>
<TD>
minErr, gs = do_mc2gst(dataset, <span style="color: rgb(255, 0, 0);">curStartGateset</span>, gateStringsToUse, maxiter, maxfev, tol, cptp_penalty_factor, minProbClipForWeighting, probClipInterval, useFreqWeightedChiSq, regularizeFactor, (printer) - (1), check, check_jacobian, gatestringWeights, None, memLimit, comm)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
minErr, gs = do_mc2gst(dataset, <span style="color: rgb(255, 0, 0);">startGateset</span>, gateStringsToUse, maxiter, maxfev, tol, cptp_penalty_factor, minProbClipForWeighting, probClipInterval, useFreqWeightedChiSq, regularizeFactor, (printer) - (1), check, check_jacobian, gatestringWeights, None, memLimit, comm)</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">chiSq</span> = sum([(x) ** (2) for x in minErr ])</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">chiSqBest</span> = sum([(x) ** (2) for x in minErr ])</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 17</B><BR>Distance between two fragments = 2 <BR>Clone size = 7<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1418</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1388</TD></TR><TR>
<TD>
minErr, gs = do_mc2gst(dataset, <span style="color: rgb(255, 0, 0);">curStartGateset</span>, gateStringsToUse, maxiter, maxfev, tol, cptp_penalty_factor, minProbClipForWeighting, probClipInterval, useFreqWeightedChiSq, regularizeFactor, (printer) - (1), check, check_jacobian, gatestringWeights, None, memLimit, comm)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
minErr, gs = do_mc2gst(dataset, <span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">startGateset</span></span>, gateStringsToUse, maxiter, maxfev, tol, cptp_penalty_factor, minProbClipForWeighting, probClipInterval, useFreqWeightedChiSq, regularizeFactor, (printer) - (1), check, check_jacobian, gatestringWeights, None, memLimit, comm)</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">chiSq</span> = sum([(x) ** (2) for x in minErr ])</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">chiSqBest</span></span> = sum([(x) ** (2) for x in minErr ])</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 18</B><BR>Distance between two fragments = 2 <BR>Clone size = 7<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/germselection.py"<BR>The first line is 296</TD><TD></TD><TD>Source file "algorithms/fiducialselection.py"<BR>The first line is 159</TD></TR><TR>
<TD>
if scoreFunc == 'all':<BR>
def list_score(input_array):<BR>
return sum((1.0) / (input_array))<BR>
elif scoreFunc == 'worst':<BR>
def list_score(input_array):<BR>
return (1.0) / (min(input_array))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if scoreFunc == 'all':<BR>
def list_score(input_array):<BR>
return sum((1.0) / (input_array))<BR>
elif scoreFunc == 'worst':<BR>
def list_score(input_array):<BR>
return (1.0) / (min(input_array))</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">gateset</span> = <span style="color: rgb(255, 0, 0);">gateset</span>.<span style="color: rgb(255, 0, 0);">copy</span>()</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">dimRho</span> = <span style="color: rgb(255, 0, 0);">gateset</span>.<span style="color: rgb(255, 0, 0);">get_dimension</span>()</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 19</B><BR>Distance between two fragments = 2 <BR>Clone size = 7<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/fiducialselection.py"<BR>The first line is 563</TD><TD></TD><TD>Source file "algorithms/germselection.py"<BR>The first line is 688</TD></TR><TR>
<TD>
printer.log(('score = %s') % (score))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log(('score = %s') % (score))</TD>
</TR>
<TR>
<TD>
printer.log(('weights = %s') % (weights))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log(('weights = %s') % (weights))</TD>
</TR>
<TR>
<TD>
printer.log(('L1(weights) = %s') % (sum(weights)))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log(('L1(weights) = %s') % (sum(weights)))</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">goodFidList</span> = []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">goodGermsList</span> = []</TD>
</TR>
<TR>
<TD>
for index, val in enumerate(weights):<BR>
if val == 1:<BR>
<span style="color: rgb(255, 0, 0);">goodFidList</span>.append(<span style="color: rgb(255, 0, 0);">fidList</span>[index])</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
for index, val in enumerate(weights):<BR>
if val == 1:<BR>
<span style="color: rgb(255, 0, 0);">goodGermsList</span>.append(<span style="color: rgb(255, 0, 0);">germsList</span>[index])</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 20</B><BR>Distance between two fragments = 0 <BR>Clone size = 7<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 1787</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1623</TD></TR><TR>
<TD>
if (stringsToEstimate is None) or (len(stringsToEstimate) == 0):<BR>
continue</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (stringsToEstimate is None) or (len(stringsToEstimate) == 0):<BR>
continue</TD>
</TR>
<TR>
<TD>
if gatestringWeightsDict is not None:<BR>
gatestringWeights = _np.ones(len(stringsToEstimate), 'd')<BR>
for gatestr, weight in gatestringWeightsDict.items():<BR>
if gatestr in stringsToEstimate:<BR>
gatestringWeights[stringsToEstimate.index(gatestr)] = weight<BR>
else:<BR>
gatestringWeights = None</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if gatestringWeightsDict is not None:<BR>
gatestringWeights = _np.ones(len(stringsToEstimate), 'd')<BR>
for gatestr, weight in gatestringWeightsDict.items():<BR>
if gatestr in stringsToEstimate:<BR>
gatestringWeights[stringsToEstimate.index(gatestr)] = weight<BR>
else:<BR>
gatestringWeights = None</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 21</B><BR>Distance between two fragments = 0 <BR>Clone size = 7<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2678</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 2767</TD></TR><TR>
<TD>
vectorM = _np.concatenate((firstRowForTP, vectorM))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
vectorM = _np.concatenate((firstRowForTP, vectorM))</TD>
</TR>
<TR>
<TD>
matM = vectorM.reshape((gateDim, gateDim))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
matM = vectorM.reshape((gateDim, gateDim))</TD>
</TR>
<TR>
<TD>
gs = tpGateset.copy()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gs = tpGateset.copy()</TD>
</TR>
<TR>
<TD>
gs.transform(matM)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
gs.transform(matM)</TD>
</TR>
<TR>
<TD>
cpPenalties = _tools.sums_of_negative_choi_evals(gs)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
cpPenalties = _tools.sums_of_negative_choi_evals(gs)</TD>
</TR>
<TR>
<TD>
cpPenalty = sum(cpPenalties)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
cpPenalty = sum(cpPenalties)</TD>
</TR>
<TR>
<TD>
spamPenalty = sum([_tools.prep_penalty(rhoVec) for rhoVec in list(gs.preps.values()) ])</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
spamPenalty = sum([_tools.prep_penalty(rhoVec) for rhoVec in list(gs.preps.values()) ])</TD>
</TR>
<TR>
<TD>
spamPenalty += sum([_tools.effect_penalty(EVec) for EVec in list(gs.effects.values()) ])</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
spamPenalty += sum([_tools.effect_penalty(EVec) for EVec in list(gs.effects.values()) ])</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 22</B><BR>Distance between two fragments = 2 <BR>Clone size = 6<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/germselection.py"<BR>The first line is 693</TD><TD></TD><TD>Source file "algorithms/fiducialselection.py"<BR>The first line is 487</TD></TR><TR>
<TD>
for index, val in enumerate(weights):<BR>
if val == 1:<BR>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">goodGermsList</span></span>.append(<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">germsList</span></span>[index])</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
for index, val in enumerate(weights):<BR>
if val == 1:<BR>
<span style="color: rgb(255, 0, 0);">goodFidList</span>.append(<span style="color: rgb(255, 0, 0);">fidList</span>[index])</TD>
</TR>
<TR>
<TD>
if returnAll:<BR>
return (<span style="color: rgb(255, 0, 0);">goodGermsList</span>, weights, scoreD)<BR>
else:<BR>
return <span style="color: rgb(255, 0, 0);">goodGermsList</span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if returnAll:<BR>
return (<span style="color: rgb(255, 0, 0);">goodFidList</span>, weights, scoreD)<BR>
else:<BR>
return <span style="color: rgb(255, 0, 0);">goodFidList</span></TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 23</B><BR>Distance between two fragments = 1 <BR>Clone size = 6<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/fiducialselection.py"<BR>The first line is 171</TD><TD></TD><TD>Source file "algorithms/fiducialselection.py"<BR>The first line is 408</TD></TR><TR>
<TD>
if prepOrMeas == 'prep':<BR>
fidArrayList = make_prep_mxs(gateset, fidList)<BR>
elif prepOrMeas == 'meas':<BR>
fidArrayList = make_meas_mxs(gateset, fidList)<BR>
else:<BR>
raise Exception(<span style="color: rgb(255, 0, 0);">'Invalid value for prepOrMeas (must be "prep" or "meas")!'</span>)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if prepOrMeas == 'prep':<BR>
fidArrayList = make_prep_mxs(gateset, fidList)<BR>
elif prepOrMeas == 'meas':<BR>
fidArrayList = make_meas_mxs(gateset, fidList)<BR>
else:<BR>
raise Exception(<span style="color: rgb(255, 0, 0);">'prepOrMeas must be specified!'</span>)</TD>
</TR>
<TR>
<TD>
numMxs = len(fidArrayList)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
numMxs = len(fidArrayList)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 24</B><BR>Distance between two fragments = 0 <BR>Clone size = 6<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "algorithms/core.py"<BR>The first line is 2193</TD><TD></TD><TD>Source file "algorithms/core.py"<BR>The first line is 1256</TD></TR><TR>
<TD>
nGateStrings = len(gateStringsToUse)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nGateStrings = len(gateStringsToUse)</TD>
</TR>
<TR>
<TD>
nDataParams = (nGateStrings) * ((len(dataset.get_spam_labels())) - (1))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
nDataParams = (nGateStrings) * ((len(dataset.get_spam_labels())) - (1))</TD>
</TR>
<TR>
<TD>
try:<BR>
nModelParams = gs.num_nongauge_params()<BR>
except:<BR>
printer.warning('Could not obtain number of *non-gauge* parameters - using total params instead')<BR>
nModelParams = gs.num_params()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
try:<BR>
nModelParams = gs.num_nongauge_params()<BR>
except:<BR>
printer.warning('Could not obtain number of *non-gauge* parameters - using total params instead')<BR>