Source files: 12

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Clones detected: 236

1928 of 5060 lines are duplicates (38.10%)

Parameters
clustering_threshold = 10
distance_threshold = 5
size_threshold = 5
hashing_depth = 1
clusterize_using_hash = False
clusterize_using_dcup = False

Time elapsed
Construction of AST : 1.45 seconds
Building statement hash : 0.01 seconds
Building patterns : 3.38 seconds
Marking similar statements : 5.24 seconds
Finding similar sequences of statements : 0.59 seconds
Refining candidates : 5.61 seconds
Total time: 16.28
Started at: Mon Aug 1 06:56:49 2016
Finished at: Mon Aug 1 06:57:01 2016

Clone # 1
Distance between two fragments = 3
Clone size = 27
Source file "report/results.py"
The first line is 3337
Source file "report/results.py"
The first line is 1567
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")
qtys['settoggles']  +=  "\\toggle%s{whackamoleappendix}\n"  %  \
  ("true"  if  whackamoleAppendix  else  "false")
qtys['confidenceLevel']  =  "%g"  %  \
  confidenceLevel  if  confidenceLevel  is  not  None  else  "NOT-SET"
qtys['confidenceLevel']  =  "%g"  %  \
  confidenceLevel  if  confidenceLevel  is  not  None  else  "NOT-SET"
qtys['linlg_pcntle'] = self.parameters['linlogPercentile'] qtys['linlg_pcntle'] = self.parameters['linlogPercentile']
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)] pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo) qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')



Clone # 2
Distance between two fragments = 2
Clone size = 26
Source file "report/results.py"
The first line is 2796
Source file "report/results.py"
The first line is 2394
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptext((".figures['%s']") % (figkey))
    return fig
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig
  if  self._LsAndGermInfoSet:
    baseStr_dict  =  self._getBaseStrDict()

    Ls  =  self.parameters['max  length  list']
    st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  col  in  box  plots
    nPlots  =  (len(Ls[st:])-1)+1  if  pixelPlotAppendix  else  1

    if  self.parameters['objective']  ==  "chi2":
      plotFnName,plotFnLatex  =  "Chi2",  "$\chi^2$"
    elif  self.parameters['objective']  ==  "logl":
      plotFnName,plotFnLatex  =  "LogL",  "$\\log(\\mathcal{L})$"
    else:
      raise  ValueError("Invalid  objective  value:  %s"  \
          %  self.parameters['objective'])

    printer.log("  --  %s  plots  (%d):  "  %  (plotFnName,  nPlots),  end='')
    with  printer.progress_logging(1):
      printer.show_progress(0,  0,  prefix='',  end='')
    fig  =  set_fig_qtys("bestEstimateColorBoxPlot",
        "best%sBoxes.png"  %  plotFnName,  printer  -  1)
    maxX  =  fig.get_extra_info()['nUsedXs']
    maxY  =  fig.get_extra_info()['nUsedYs']

  else:
    for  figkey  in  ["bestEstimateColorBoxPlot"]:
      qtys[figkey]  =  qtys["tt_"+figkey]  =  ""
  if  self._LsAndGermInfoSet:
    baseStr_dict  =  self._getBaseStrDict()

    Ls  =  self.parameters['max  length  list']
    st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  col  in  box  plots
    nPlots  =  (len(Ls[st:])-1)+1  if  pixelPlotAppendix  else  1

    if  self.parameters['objective']  ==  "chi2":
      plotFnName,plotFnLatex  =  "Chi2",  "$\chi^2$"
    elif  self.parameters['objective']  ==  "logl":
      plotFnName,plotFnLatex  =  "LogL",  "$\\log(\\mathcal{L})$"
    else:
      raise  ValueError("Invalid  objective  value:  %s"
          %  self.parameters['objective'])

    printer.log("  --  %s  plots  (%d):  "  %  (plotFnName,  nPlots),  end='')
    with  printer.progress_logging(1):
      printer.show_progress(0,  0,  prefix='',  end='')
    fig  =  set_fig_qtys("bestEstimateColorBoxPlot",
        "best%sBoxes.pdf"  %  plotFnName,  printer  -  1)
    maxX  =  fig.get_extra_info()['nUsedXs']
    maxY  =  fig.get_extra_info()['nUsedYs']

  else:
    for  figkey  in  ["bestEstimateColorBoxPlot"]:
      qtys[figkey]  =  qtys["tt_"+figkey]  =  ""



Clone # 3
Distance between two fragments = 3
Clone size = 26
Source file "report/plotting.py"
The first line is 3092
Source file "report/plotting.py"
The first line is 2911
if fidPairs is None:
    gatestringsToWhack = [((prepStr) + (gatestringToWhack)) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ]
else:
    gatestringsToWhack = [((prepStrs[i]) + (gatestringToWhack)) + (effectStrs[j]) for i, j in fidPairs ]
if fidPairs is None:
    gatestringsToWhack = [((prepStr) + (gatestringToWhack)) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ]
else:
    gatestringsToWhack = [((prepStrs[i]) + (gatestringToWhack)) + (effectStrs[j]) for i, j in fidPairs ]
whacked_indices = [allGatestringsUsedInLogLOpt.index(s) for s in gatestringsToWhack ] whacked_indices = [allGatestringsUsedInChi2Opt.index(s) for s in gatestringsToWhack ]
whacked_DlogL = _np.take(DlogL, whacked_indices, axis=1) whacked_Dchi2 = _np.take(Dchi2, whacked_indices, axis=1)
grad = (-1.0) * (_np.sum(whacked_DlogL, axis=(0, 1))) grad = (-1.0) * (_np.sum(whacked_Dchi2, axis=(0, 1)))
dx = ((whackWith) * (grad)) / (_np.dot(grad, grad)) dx = ((whackWith) * (grad)) / (_np.dot(grad, grad))
delta = _np.sum(_np.dot(DlogL, dx), axis=0) delta = _np.sum(_np.dot(Dchi2, dx), axis=0)
def mx_fn(gateStr):
    if gateStr is None:
        return (_np.nan) * (_np.zeros((len(effectStrs), len(prepStrs)), 'd'))
    if fidPairs is None:
        return _np.array([[delta[allGatestringsUsedInLogLOpt.index(((prepStr) + (gateStr)) + (effectStr))] for prepStr in prepStrs ] for effectStr in effectStrs ])
    else:
        ret = (_np.nan) * (_np.ones((len(effectStrs), len(prepStrs)), 'd'))
        for i, j in fidPairs:
            ret[j,i] = delta[allGatestringsUsedInLogLOpt.index(((prepStrs[i]) + (gateStr)) + (effectStrs[j]))]
        return ret
def mx_fn(gateStr):
    if gateStr is None:
        return (_np.nan) * (_np.zeros((len(effectStrs), len(prepStrs)), 'd'))
    if fidPairs is None:
        return _np.array([[delta[allGatestringsUsedInChi2Opt.index(((prepStr) + (gateStr)) + (effectStr))] for prepStr in prepStrs ] for effectStr in effectStrs ])
    else:
        ret = (_np.nan) * (_np.ones((len(effectStrs), len(prepStrs)), 'd'))
        for i, j in fidPairs:
            ret[j,i] = delta[allGatestringsUsedInChi2Opt.index(((prepStrs[i]) + (gateStr)) + (effectStrs[j]))]
        return ret
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  +max_abs  if  M  is  None  else  M
stdcmap = StdColormapFactory('div', n_boxes=n_boxes, vmin=m, vmax=M, dof=dof, midpoint=0) stdcmap = StdColormapFactory('div', n_boxes=n_boxes, vmin=m, vmax=M, dof=dof, midpoint=0)
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$') return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 4
Distance between two fragments = 4
Clone size = 23
Source file "report/results.py"
The first line is 859
Source file "report/results.py"
The first line is 831
expr3 = 'whack(.+?)MoleBoxesSummed' expr2 = 'whack(.+?)MoleBoxes'
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    Ls, germs, gsBest, fidPairs, _, _, baseStr_dict, strs, st = plot_setup()
    highestL = Ls[-1]
    hammerWeight = 10.0
    mpc = getMPC()
    gateLabel = _re.match(expr3, key).group(1)
    strToWhack = _gs.GateString(((gateLabel)) * (highestL))
    whackAMolePlotFn = getWhackAMolePlotFn()
    return whackAMolePlotFn(strToWhack, self.gatestring_lists['all'], Ls[st:], germs, baseStr_dict, self.dataset, gsBest, strs, '$L$', 'germ', scale=1.0, sumUp=True, title='', whackWith=hammerWeight, save_to='', minProbClipForWeighting=mpc, ticSize=20, fidPairs=fidPairs)
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    Ls, germs, gsBest, fidPairs, _, _, baseStr_dict, strs, st = plot_setup()
    highestL = Ls[-1]
    hammerWeight = 10.0
    mpc = getMPC()
    gateLabel = _re.match(expr2, key).group(1)
    strToWhack = _gs.GateString(((gateLabel)) * (highestL))
    whackAMolePlotFn = getWhackAMolePlotFn()
    return whackAMolePlotFn(strToWhack, self.gatestring_lists['all'], Ls[st:], germs, baseStr_dict, self.dataset, gsBest, strs, '$L$', 'germ', scale=1.0, sumUp=False, title='', whackWith=hammerWeight, save_to='', minProbClipForWeighting=mpc, ticSize=20, fidPairs=fidPairs)
def fn_validate(key):
    if not self._LsAndGermInfoSet:
        return []
    len1GermFirstEls = [g[0] for g in self.gatestring_lists['germs'] if len(g) == 1]
    keys = [('whack%sMoleBoxesSummed') % (gl) for gl in len1GermFirstEls ]
    if key == expr3:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._LsAndGermInfoSet:
        return []
    len1GermFirstEls = [g[0] for g in self.gatestring_lists['germs'] if len(g) == 1]
    keys = [('whack%sMoleBoxes') % (gl) for gl in len1GermFirstEls ]
    if key == expr2:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr3] = (fn, fn_validate) fns[expr2] = (fn, fn_validate)



Clone # 5
Distance between two fragments = 0
Clone size = 23
Source file "report/results.py"
The first line is 3276
Source file "report/results.py"
The first line is 1498
if tips:
    def tooltiptex(directive):
        return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('%s}') % (directive))
else:
    def tooltiptex(directive):
        return ''
if tips:
    def tooltiptex(directive):
        return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('%s}') % (directive))
else:
    def tooltiptex(directive):
        return ''
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
    +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
      else  "GSTReport"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
    +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
      else  "GSTReport"
  report_base  +=  suffix
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if title == 'auto':
    title = ('GST report for %s') % (datasetLabel)
if title == 'auto':
    title = ('GST report for %s') % (datasetLabel)



Clone # 6
Distance between two fragments = 2
Clone size = 22
Source file "report/latex.py"
The first line is 199
Source file "report/html.py"
The first line is 208
TOL = 1e-09 TOL = 1e-09
def render(x):
    if abs(x) < (5) * ((10) ** (-(precision) + (1))):
        s = ('%.0e') % (x)
    elif abs(x) < 1:
        s = ('%.*f') % ((precision, x))
    elif abs(x) <= (10) ** (precision):
        s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))
    else:
        s = ('%.0e') % (x)
    p = s.split('e')
    if len(p) == 2:
        ex = str(int(p[1]))
        s = (((p[0]) + ('\\e{')) + (ex)) + ('}')
    if '.' in s:
        while s.endswith('0'):
            s = s[:-1]
        if s.endswith('.'):
            s = s[:-1]
    return s
def render(x):
    if abs(x) < (5) * ((10) ** (-(precision) + (1))):
        s = ('%.0e') % (x)
    elif abs(x) < 1:
        s = ('%.*f') % ((precision, x))
    elif abs(x) <= (10) ** (precision):
        s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))
    else:
        s = ('%.0e') % (x)
    p = s.split('e')
    if len(p) == 2:
        ex = str(int(p[1]))
        s = (((p[0]) + ('×10')) + (ex)) + ('')
    if '.' in s:
        while s.endswith('0'):
            s = s[:-1]
        if s.endswith('.'):
            s = s[:-1]
    return s
if isinstance(el, basestring):
    return el
if isinstance(el, basestring):
    return el
if type(el) in (int, _np.int64):
    return ('%d') % (el)
if type(el) in (int, _np.int64):
    return ('%d') % (el)
if (el is None) or (_np.isnan(el)):
    return '--'
if (el is None) or (_np.isnan(el)):
    return '--'



Clone # 7
Distance between two fragments = 4
Clone size = 22
Source file "report/results.py"
The first line is 2037
Source file "report/results.py"
The first line is 2311
qtys['gofObjective']  =  "$2\\Delta\\log{\\mathcal{L}}$"  \
  if  obj  ==  "logl"  else  "$\\chi^2$"
qtys['gofObjective']  =  "$2\\Delta\\log{\\mathcal{L}}$"  \
  if  self.parameters['objective']  ==  "logl"  else  "$\\chi^2$"
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)] pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo) qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')



Clone # 8
Distance between two fragments = 2
Clone size = 23
Source file "report/results.py"
The first line is 3276
Source file "report/results.py"
The first line is 1974
if tips:
    def tooltiptex(directive):
        return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('%s}') % (directive))
else:
    def tooltiptex(directive):
        return ''
if tips:
    def tooltiptex(directive):
        return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('%s}') % (directive))
else:
    def tooltiptex(directive):
        return ''
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
   
+  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
   
  else  "GSTReport"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTBrief"
  report_base  +=  suffix
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if title == 'auto':
    title = ('GST report for %s') % (datasetLabel)
if title == 'auto':
    title = ('Brief GST report for %s') % (datasetLabel)



Clone # 9
Distance between two fragments = 2
Clone size = 23
Source file "report/results.py"
The first line is 1498
Source file "report/results.py"
The first line is 1974
if tips:
    def tooltiptex(directive):
        return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('%s}') % (directive))
else:
    def tooltiptex(directive):
        return ''
if tips:
    def tooltiptex(directive):
        return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('%s}') % (directive))
else:
    def tooltiptex(directive):
        return ''
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
   
+  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
   
  else  "GSTReport"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTBrief"
  report_base  +=  suffix
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if title == 'auto':
    title = ('GST report for %s') % (datasetLabel)
if title == 'auto':
    title = ('Brief GST report for %s') % (datasetLabel)



Clone # 10
Distance between two fragments = 1
Clone size = 20
Source file "report/results.py"
The first line is 3729
Source file "report/results.py"
The first line is 2141
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Merging into template file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex'))
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))
mainTemplate = 'report_general_main.tex' mainTemplate = 'brief_report_main.tex'
self._merge_template(qtys, mainTemplate, mainTexFilename) self._merge_template(qtys, mainTemplate, mainTexFilename)
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...') printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')
cwd = _os.getcwd() cwd = _os.getcwd()
if len(report_dir) > 0:
    _os.chdir(report_dir)
if len(report_dir) > 0:
    _os.chdir(report_dir)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
return None return None



Clone # 11
Distance between two fragments = 0
Clone size = 22
Source file "report/results.py"
The first line is 2040
Source file "report/results.py"
The first line is 3351
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)] pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo) qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')



Clone # 12
Distance between two fragments = 0
Clone size = 22
Source file "report/results.py"
The first line is 2040
Source file "report/results.py"
The first line is 1573
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)] pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo) qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')



Clone # 13
Distance between two fragments = 0
Clone size = 22
Source file "report/results.py"
The first line is 3351
Source file "report/results.py"
The first line is 2314
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)] pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo) qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')



Clone # 14
Distance between two fragments = 0
Clone size = 22
Source file "report/results.py"
The first line is 1573
Source file "report/results.py"
The first line is 2314
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)] pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
for key in sorted(list(self.parameters.keys())):
    pdfInfo.append((key, self.parameters[key]))
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo) qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')



Clone # 15
Distance between two fragments = 1
Clone size = 19
Source file "report/ppt.py"
The first line is 211
Source file "report/html.py"
The first line is 233
if isinstance(el, basestring):
    return el
if isinstance(el, basestring):
    return el
if type(el) in (int, _np.int64):
    return ('%d') % (el)
if type(el) in (int, _np.int64):
    return ('%d') % (el)
if (el is None) or (_np.isnan(el)):
    return '--'
if (el is None) or (_np.isnan(el)):
    return '--'
try:
  if  abs(el.real)  >  TOL:
    if  abs(el.imag)  >  TOL:
      if  complexAsPolar:
        r,phi  =  cmath.polar(el)
        ex  =  ("i%.1f"  %  phi)  if  phi  >=  0  else  ("-i%.1f"  %  -phi)
        s  =  "%se^{%s}"  %  (render(r),ex)
      else:
        s  =  "%s%s%si"  %  (render(el.real),'+'  if  el.imag  >  0  else  '-',  render(abs(el.imag)))
    else:
      s  =  "%s"  %  render(el.real)
  else:
    if  abs(el.imag)  >  TOL:
      s  =  "%si"  %  render(el.imag)
    else:
      s  =  "0"
except:
  #try:
  #        if  abs(el)  >  TOL:  #thows  exception  if  el  is  not  a  number
  #                s  =  "%s"  %  render(el.real)
  #        else:
  #                s  =  "0"
  #except:
  s  =  str(el)
try:
  if  abs(el.real)  >  TOL:
    if  abs(el.imag)  >  TOL:
      if  complexAsPolar:
        r,phi  =  cmath.polar(el)
        ex  =  ("i%.1f"  %  phi)  if  phi  >=  0  else  ("-i%.1f"  %  -phi)
        s  =  "%se<sup>%s</sup>"  %  (render(r),ex)
      else:
        s  =  "%s%s%si"  %  (render(el.real),'+'  if  el.imag  >  0  else  '-',  render(abs(el.imag)))
    else:
      s  =  "%s"  %  render(el.real)
  else:
    if  abs(el.imag)  >  TOL:
      s  =  "%si"  %  render(el.imag)
    else:
      s  =  "0"
except:
  #try:
  #        if  abs(el)  >  TOL:  #throw  exception  if  el  is  not  a  number
  #                s  =  "%s"  %  render(el.real)
  #        else:
  #                s  =  "0"
  #except:
  s  =  str(el)
return s return s



Clone # 16
Distance between two fragments = 0
Clone size = 18
Source file "report/results.py"
The first line is 2338
Source file "report/results.py"
The first line is 2745
D = (report_base) + ('_files') D = (report_base) + ('_files')
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
if not _os.path.isdir(_os.path.join(report_dir, D)):
    _os.mkdir(_os.path.join(report_dir, D))
printer.log('*** Generating tables ***') printer.log('*** Generating tables ***')
std_tables = ('targetSpamTable', 'targetGatesTable', 'datasetOverviewTable', 'bestGatesetSpamTable', 'bestGatesetSpamParametersTable', 'bestGatesetGatesTable', 'bestGatesetChoiTable', 'bestGatesetDecompTable', 'bestGatesetRotnAxisTable', 'bestGatesetVsTargetTable', 'bestGatesetErrorGenTable') std_tables = ('targetSpamTable', 'targetGatesTable', 'datasetOverviewTable', 'bestGatesetSpamTable', 'bestGatesetSpamParametersTable', 'bestGatesetGatesTable', 'bestGatesetChoiTable', 'bestGatesetDecompTable', 'bestGatesetRotnAxisTable', 'bestGatesetVsTargetTable', 'bestGatesetErrorGenTable')
ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable') ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable')
tables_to_compute = std_tables tables_to_compute = std_tables
tables_to_blank = [] tables_to_blank = []
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables



Clone # 17
Distance between two fragments = 0
Clone size = 17
Source file "report/results.py"
The first line is 3442
Source file "report/results.py"
The first line is 1665
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
maxW, maxH = (6.5, 9.0) maxW, maxH = (6.5, 9.0)
def incgr(figFilenm, W=None, H=None):
    if W is None:
        W = maxW
    if H is None:
        H = maxH
    return (('\\includegraphics[width=%.2fin,height=%.2fin') % ((W, H))) + ((',keepaspectratio]{%s/%s}') % ((D, figFilenm)))
def incgr(figFilenm, W=None, H=None):
    if W is None:
        W = maxW
    if H is None:
        H = maxH
    return (('\\includegraphics[width=%.2fin,height=%.2fin') % ((W, H))) + ((',keepaspectratio]{%s/%s}') % ((D, figFilenm)))
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig



Clone # 18
Distance between two fragments = 4
Clone size = 17
Source file "report/results.py"
The first line is 2289
Source file "report/results.py"
The first line is 1548
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true"  )
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false"  )
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")
qtys['settoggles']  +=  "\\toggle%s{debuggingaidsappendix}\n"  %  \
  ("true"  if  debugAidsAppendix  else  "false"  )
qtys['settoggles']  +=  "\\toggle%s{debuggingaidsappendix}\n"  %  \
  ("true"  if  debugAidsAppendix  else  "false")
qtys['settoggles']  +=  "\\toggle%s{pixelplotsappendix}\n"  %  \
  ("true"  if  pixelPlotAppendix  else  "false"  )
qtys['settoggles']  +=  "\\toggle%s{gaugeoptappendix}\n"  %  \
  ("true"  if  gaugeOptAppendix  else  "false")
qtys['settoggles']  +=  "\\toggle%s{whackamoleappendix}\n"  %  \
  ("true"  if  whackamoleAppendix  else  "false"  )
qtys['settoggles']  +=  "\\toggle%s{pixelplotsappendix}\n"  %  \
  ("true"  if  pixelPlotAppendix  else  "false")



Clone # 19
Distance between two fragments = 3
Clone size = 16
Source file "report/results.py"
The first line is 3737
Source file "report/results.py"
The first line is 2558
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))
mainTemplate = 'report_general_main.tex' mainTemplate = 'slides_main.tex'
self._merge_template(qtys, mainTemplate, mainTexFilename) self._merge_template(qtys, mainTemplate, mainTexFilename)
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...') printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')
cwd = _os.getcwd() cwd = _os.getcwd()
if len(report_dir) > 0:
    _os.chdir(report_dir)
if len(report_dir) > 0:
    _os.chdir(report_dir)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
return None return None



Clone # 20
Distance between two fragments = 3
Clone size = 16
Source file "report/results.py"
The first line is 2558
Source file "report/results.py"
The first line is 2148
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex'))
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))
mainTemplate = 'slides_main.tex' mainTemplate = 'brief_report_main.tex'
self._merge_template(qtys, mainTemplate, mainTexFilename) self._merge_template(qtys, mainTemplate, mainTexFilename)
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...') printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')
cwd = _os.getcwd() cwd = _os.getcwd()
if len(report_dir) > 0:
    _os.chdir(report_dir)
if len(report_dir) > 0:
    _os.chdir(report_dir)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
return None return None



Clone # 21
Distance between two fragments = 2
Clone size = 17
Source file "report/results.py"
The first line is 3289
Source file "report/results.py"
The first line is 2258
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
   
+  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
   
  else  "GSTReport"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if title == 'auto':
    title = ('GST report for %s') % (datasetLabel)
if title == 'auto':
    title = ('GST on %s') % (datasetLabel)
best_gs = self.gatesets['final estimate'] best_gs = self.gatesets['final estimate']



Clone # 22
Distance between two fragments = 4
Clone size = 15
Source file "report/results.py"
The first line is 2525
Source file "report/results.py"
The first line is 2505
  with  printer.progress_logging(1):
    for  i,germ  in  enumerate(len1Germs):
      #  printer.log("%d  "  %  (len(len1Germs)+i+1),  end='')
      printer.show_progress(i,  len(len1Germs)  -  1,  prefix='',  end='')

      fig  =  self.figures.get(
"whack%sMoleBoxesSummed"  %  germ[0],
       
verbosity=printer  -  1)
      fig.save_to(_os.path.join(report_dir,  D,"whack%sMoleBoxesSummed.pdf"  %  germ[0]))

      whackamoleplots  +=  "\n"
      whackamoleplots  +=  "\\begin{frame}\n"
      whackamoleplots  +=  "\\frametitle{Summed  whack-a-%s-mole  plot  for  $\mathrm{%s}^{%d}$}"  %  (plotFnLatex,germ[0],highestL)
      whackamoleplots  +=  "\\begin{figure}\n"
      whackamoleplots  +=  "\\begin{center}\n"
      #whackamoleplots  +=  "\\adjustbox{max  height=\\dimexpr\\textheight-5.5cm\\relax,  max  width=\\textwidth}{"
      whackamoleplots  +=  "\\includegraphics[width=%.2fin,height=%.2fin,keepaspectratio]{%s/whack%sMoleBoxesSummed.pdf}\n"  %  (maxW,maxH,D,germ[0])
      #FUTURE:  add  caption  and  conditional  tooltip?
      whackamoleplots  +=  "\\end{center}\n"
      whackamoleplots  +=  "\\end{figure}\n"
      whackamoleplots  +=  "\\end{frame}\n"
  with  printer.progress_logging(1):
    for  i,germ  in  enumerate(len1Germs):
      printer.show_progress(i,  len(len1Germs)  -  1,  prefix='',  end='')

      fig  =  self.figures.get
("whack%sMoleBoxes"  %  germ[0],verbosity=printer  -  1)
      fig.save_to(_os.path.join(report_dir,  D,"whack%sMoleBoxes.pdf"
     
  %  germ[0]))

      whackamoleplots  +=  "\n"
      whackamoleplots  +=  "\\begin{frame}\n"
      whackamoleplots  +=  "\\frametitle{Whack-a-%s-mole  plot  for  $\mathrm{%s}^{%d}$}"  %  (plotFnLatex,germ[0],highestL)
      whackamoleplots  +=  "\\begin{figure}\n"
      whackamoleplots  +=  "\\begin{center}\n"
      #whackamoleplots  +=  "\\adjustbox{max  height=\\dimexpr\\textheight-5.5cm\\relax,  max  width=\\textwidth}{"
      whackamoleplots  +=  "\\includegraphics[width=%.2fin,height=%.2fin,keepaspectratio]{%s/whack%sMoleBoxes.pdf}\n"  %  (maxW,maxH,D,germ[0])
      #FUTURE:  add  caption  and  conditional  tooltip?
      whackamoleplots  +=  "\\end{center}\n"
      whackamoleplots  +=  "\\end{figure}\n"
      whackamoleplots  +=  "\\end{frame}\n"



Clone # 23
Distance between two fragments = 0
Clone size = 15
Source file "report/results.py"
The first line is 2085
Source file "report/results.py"
The first line is 2364
for key in tables_to_compute:
    qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
    qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))
for key in tables_to_compute:
    qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
    qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))
for key in tables_to_blank:
    qtys[key] = _generation.get_blank_table().render('latex', longtables=self.options.long_tables)
    qtys[('tt_') + (key)] = ''
for key in tables_to_blank:
    qtys[key] = _generation.get_blank_table().render('latex', longtables=self.options.long_tables)
    qtys[('tt_') + (key)] = ''
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 24
Distance between two fragments = 2
Clone size = 15
Source file "report/plotting.py"
The first line is 508
Source file "report/plotting.py"
The first line is 529
input_values = _np.linspace(0.0, 1.0, N) input_values = _np.linspace(0.0, 1.0, N)
scaled_values = _np.linspace(low_val, high_val, N) scaled_values = _np.linspace(low_val, high_val, N)
colors = cmap(input_values) colors = cmap(input_values)
prev_r, prev_g, prev_b, prev_a = prev_cmap(1.0) prev_r, prev_g, prev_b, prev_a = prev_cmap(1.0)
r, g, b, a = colors[0] r, g, b, a = colors[0]
red_list.append((low_val, prev_r, r)) red_list.append((low_val, prev_r, r))
green_list.append((low_val, prev_g, g)) green_list.append((low_val, prev_g, g))
blue_list.append((low_val, prev_b, b)) blue_list.append((low_val, prev_b, b))
alpha_list.append((low_val, prev_a, a)) alpha_list.append((low_val, prev_a, a))
for  color,  value  in  zip(colors[1:-1],  scaled_values[1:-1]):
  r,  g,  b,  a  =  color
  red_list.append((value,  r,  r))
  green_list.append((value,  g,  g))
  blue_list.append((value,  b,  b))
  alpha_list.append((value,  a,  a))
for  color,  value  in  zip(colors[1:],  scaled_values[1:]):
  r,  g,  b,  a  =  color
  red_list.append((value,  r,  r))
  green_list.append((value,  g,  g))
  blue_list.append((value,  b,  b))
  alpha_list.append((value,  a,  a))



Clone # 25
Distance between two fragments = 2
Clone size = 16
Source file "report/results.py"
The first line is 2258
Source file "report/results.py"
The first line is 1511
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
   
+  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
   
  else  "GSTReport"
  report_base  +=  suffix
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if title == 'auto':
    title = ('GST on %s') % (datasetLabel)
if title == 'auto':
    title = ('GST report for %s') % (datasetLabel)



Clone # 26
Distance between two fragments = 2
Clone size = 14
Source file "report/results.py"
The first line is 2258
Source file "report/results.py"
The first line is 1985
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTBrief"
  report_base  +=  suffix
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if datasetLabel == 'auto':
    if default_base is not None:
        datasetLabel = _latex.latex_escaped(default_base)
    else:
        datasetLabel = '$\\mathcal{D}$'
if title == 'auto':
    title = ('GST on %s') % (datasetLabel)
if title == 'auto':
    title = ('Brief GST report for %s') % (datasetLabel)



Clone # 27
Distance between two fragments = 1
Clone size = 14
Source file "report/plotting.py"
The first line is 3069
Source file "report/plotting.py"
The first line is 2889
prepStrs, effectStrs = strs prepStrs, effectStrs = strs
spamLabels = gateset.get_spam_labels() spamLabels = gateset.get_spam_labels()
spam_lbl_rows  =  {  sl:i  for  (i,sl)  in  enumerate(spamLabels)  } spam_lbl_rows  =  {  sl:i  for  (i,sl)  in  enumerate(spamLabels)  }
vec_gs_len = gateset.num_params() vec_gs_len = gateset.num_params()
N = _np.empty(len(allGatestringsUsedInLogLOpt)) N = _np.empty(len(allGatestringsUsedInChi2Opt))
f = _np.empty((len(spamLabels), len(allGatestringsUsedInLogLOpt))) f = _np.empty((len(spamLabels), len(allGatestringsUsedInChi2Opt)))
probs = _np.empty((len(spamLabels), len(allGatestringsUsedInLogLOpt))) probs = _np.empty((len(spamLabels), len(allGatestringsUsedInChi2Opt)))
dprobs = _np.empty((len(spamLabels), len(allGatestringsUsedInLogLOpt), vec_gs_len)) dprobs = _np.empty((len(spamLabels), len(allGatestringsUsedInChi2Opt), vec_gs_len))
for i, gateStr in enumerate(allGatestringsUsedInLogLOpt):
    N[i] = float(dataset[gateStr].total())
    for k, sl in enumerate(spamLabels):
        f[k,i] = dataset[gateStr].fraction(sl)
for i, gateStr in enumerate(allGatestringsUsedInChi2Opt):
    N[i] = float(dataset[gateStr].total())
    for k, sl in enumerate(spamLabels):
        f[k,i] = dataset[gateStr].fraction(sl)
evTree = gateset.bulk_evaltree(allGatestringsUsedInLogLOpt) evTree = gateset.bulk_evaltree(allGatestringsUsedInChi2Opt)
gateset.bulk_fill_dprobs(dprobs, spam_lbl_rows, evTree, prMxToFill=probs) gateset.bulk_fill_dprobs(dprobs, spam_lbl_rows, evTree, prMxToFill=probs)



Clone # 28
Distance between two fragments = 3
Clone size = 13
Source file "report/plotting.py"
The first line is 2247
Source file "report/plotting.py"
The first line is 2408
def direct_chi2_boxplot(xvals, yvals, xy_gatestring_dict, dataset, directGatesets, strs, xlabel='', ylabel='', scale=1.0, prec='compact', title='Direct $\\chi^2$', sumUp=False, boxLabels=True, histogram=False, histBins=50, minProbClipForWeighting=0.0001, save_to=None, ticSize=20, invert=False, fidPairs=None, linlg_pcntle=0.05):
    prepStrs, effectStrs = strs
    def mx_fn(gateStr):
        return direct_chi2_matrix(gateStr, dataset, directGatesets.get(gateStr, None), strs, minProbClipForWeighting, fidPairs)
    xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
    stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
    return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')
def direct_logl_boxplot(xvals, yvals, xy_gatestring_dict, dataset, directGatesets, strs, xlabel='', ylabel='', scale=1.0, prec='compact', title='Direct $\\log(\\mathcal{L})$', sumUp=False, boxLabels=True, histogram=False, histBins=50, minProbClipForWeighting=0.0001, save_to=None, ticSize=20, invert=False, fidPairs=None, linlg_pcntle=0.05):
    prepStrs, effectStrs = strs
    def mx_fn(gateStr):
        return direct_logl_matrix(gateStr, dataset, directGatesets.get(gateStr, None), strs, minProbClipForWeighting, fidPairs)
    xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
    stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
    return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 29
Distance between two fragments = 0
Clone size = 13
Source file "report/results.py"
The first line is 2307
Source file "report/results.py"
The first line is 2727
qtys['confidenceLevel']  =  "%g"  %  confidenceLevel  \
  if  confidenceLevel  is  not  None  else  "NOT-SET"
qtys['confidenceLevel']  =  "%g"  %  confidenceLevel  \
  if  confidenceLevel  is  not  None  else  "NOT-SET"
qtys['objective']  =  "$\\log{\\mathcal{L}}$"  \
  if  self.parameters['objective']  ==  "logl"  else  "$\\chi^2$"
qtys['objective']  =  "$\\log{\\mathcal{L}}$"  \
  if  self.parameters['objective']  ==  "logl"  else  "$\\chi^2$"
qtys['gofObjective']  =  "$2\\Delta\\log{\\mathcal{L}}$"  \
  if  self.parameters['objective']  ==  "logl"  else  "$\\chi^2$"
qtys['gofObjective']  =  "$2\\Delta\\log{\\mathcal{L}}$"  \
  if  self.parameters['objective']  ==  "logl"  else  "$\\chi^2$"
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'



Clone # 30
Distance between two fragments = 0
Clone size = 13
Source file "report/results.py"
The first line is 3758
Source file "report/results.py"
The first line is 1886
self._merge_template(qtys, mainTemplate, mainTexFilename) self._merge_template(qtys, mainTemplate, mainTexFilename)
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...') printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')
cwd = _os.getcwd() cwd = _os.getcwd()
if len(report_dir) > 0:
    _os.chdir(report_dir)
if len(report_dir) > 0:
    _os.chdir(report_dir)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
return None return None



Clone # 31
Distance between two fragments = 0
Clone size = 13
Source file "report/results.py"
The first line is 2562
Source file "report/results.py"
The first line is 1886
self._merge_template(qtys, mainTemplate, mainTexFilename) self._merge_template(qtys, mainTemplate, mainTexFilename)
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...') printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')
cwd = _os.getcwd() cwd = _os.getcwd()
if len(report_dir) > 0:
    _os.chdir(report_dir)
if len(report_dir) > 0:
    _os.chdir(report_dir)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
return None return None



Clone # 32
Distance between two fragments = 0
Clone size = 13
Source file "report/results.py"
The first line is 2152
Source file "report/results.py"
The first line is 1886
self._merge_template(qtys, mainTemplate, mainTexFilename) self._merge_template(qtys, mainTemplate, mainTexFilename)
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...') printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')
cwd = _os.getcwd() cwd = _os.getcwd()
if len(report_dir) > 0:
    _os.chdir(report_dir)
if len(report_dir) > 0:
    _os.chdir(report_dir)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
try:
    try:
    self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)
except _subprocess.CalledProcessError, e:
    printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))
finally:
    _os.chdir(cwd)
return None return None



Clone # 33
Distance between two fragments = 4
Clone size = 13
Source file "report/results.py"
The first line is 770
Source file "report/results.py"
The first line is 783
fns['blankSummedBoxPlot'] = (fn, validate_LsAndGerms) fns['directLGSTColorBoxPlot'] = (fn, validate_LsAndGerms)
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    directPlotFn = getDirectPlotFn()
    mpc = getMPC()
    Ls, germs, _, fidPairs, _, _, baseStr_dict, strs, st = plot_setup()
    directLGST = self._specials.get('direct_lgst_gatesets', verbosity=vb)
    return directPlotFn(Ls[st:], germs, baseStr_dict, self.dataset, directLGST, strs, '$L$', 'germ', scale=1.0, sumUp=False, title='', minProbClipForWeighting=mpc, fidPairs=fidPairs, save_to='', ticSize=20, linlg_pcntle=(float(self.parameters['linlogPercentile'])) / (100))
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    directPlotFn = getDirectPlotFn()
    mpc = getMPC()
    Ls, germs, _, fidPairs, _, _, baseStr_dict, strs, st = plot_setup()
    directLongSeqGST = self._specials.get('DirectLongSeqGatesets', verbosity=vb)
    return directPlotFn(Ls[st:], germs, baseStr_dict, self.dataset, directLongSeqGST, strs, '$L$', 'germ', scale=1.0, sumUp=False, title='', minProbClipForWeighting=mpc, fidPairs=fidPairs, save_to='', ticSize=20, linlg_pcntle=(float(self.parameters['linlogPercentile'])) / (100))
fns['directLGSTColorBoxPlot'] = (fn, validate_LsAndGerms) fns['directLongSeqGSTColorBoxPlot'] = (fn, validate_LsAndGerms)



Clone # 34
Distance between two fragments = 1
Clone size = 12
Source file "report/generation.py"
The first line is 477
Source file "report/generation.py"
The first line is 344
qtys_to_compute = [('%s %s') % ((gl, qty)) for qty in qtyNames for gl in gateLabels ] qtys_to_compute = [('%s %s') % ((gl, qty)) for qty in qtyNames for gl in gateLabels ]
qtys = _cr.compute_gateset_gateset_qtys(qtys_to_compute, gateset, targetGateset, confidenceRegionInfo) qtys = _cr.compute_gateset_gateset_qtys(qtys_to_compute, gateset, targetGateset, confidenceRegionInfo)
table = _ReportTable(colHeadings, formatters) table = _ReportTable(colHeadings, formatters)
formatters = ([None]) + ((['PiErrorBars']) * (len(qtyNames))) formatters = ([None]) + ((['ErrorBars']) * (len(qtyNames)))
for gl in gateLabels:
    if confidenceRegionInfo is None:
        rowData = ([gl]) + ([(qtys[('%s %s') % ((gl, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([gl]) + ([qtys[('%s %s') % ((gl, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
for gl in gateLabels:
    if confidenceRegionInfo is None:
        rowData = ([gl]) + ([(qtys[('%s %s') % ((gl, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([gl]) + ([qtys[('%s %s') % ((gl, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
table.finish() table.finish()
return table return table



Clone # 35
Distance between two fragments = 3
Clone size = 12
Source file "report/plotting.py"
The first line is 1384
Source file "report/plotting.py"
The first line is 1279
def logl_boxplot(xvals, yvals, xy_gatestring_dict, dataset, gateset, strs, xlabel='', ylabel='', scale=1.0, prec='compact', title='$\\log(\\mathcal{L})$', linlg_pcntle=0.05, sumUp=False, boxLabels=True, histogram=False, histBins=50, minProbClipForWeighting=0.0001, save_to=None, ticSize=20, invert=False, fidPairs=None):
    prepStrs, effectStrs = strs
    def mx_fn(gateStr):
        return logl_matrix(gateStr, dataset, gateset, strs, minProbClipForWeighting, fidPairs)
    xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
    stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
    return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')
def chi2_boxplot(xvals, yvals, xy_gatestring_dict, dataset, gateset, strs, xlabel='', ylabel='', scale=1.0, prec='compact', title='$\\chi^2$', linlg_pcntle=0.05, sumUp=False, boxLabels=True, histogram=False, histBins=50, minProbClipForWeighting=0.0001, save_to=None, ticSize=20, invert=False, fidPairs=None):
    prepStrs, effectStrs = strs
    def mx_fn(gateStr):
        return chi2_matrix(gateStr, dataset, gateset, strs, minProbClipForWeighting, fidPairs)
    xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
    stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
    return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 36
Distance between two fragments = 3
Clone size = 13
Source file "report/plotting.py"
The first line is 2016
Source file "report/plotting.py"
The first line is 1883
direct_lgst = gateset_with_lgst_gatestring_estimates([gateStringToEstimate], dataset, specs, targetGateset, True, None, None, [gateStringLabel], svdTruncateTo, verbosity) direct_lgst = gateset_with_lgst_gatestring_estimates([gateStringToEstimate], dataset, specs, targetGateset, True, None, None, [gateStringLabel], svdTruncateTo, verbosity)
prepStrs, effectStrs = _construction.get_spam_strs(specs) prepStrs, effectStrs = _construction.get_spam_strs(specs)
gatestrings = ((prepStrs) + (effectStrs)) + ([(prepStr) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ]) gatestrings = ((prepStrs) + (effectStrs)) + ([(prepStr) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ])
for gateLabel in direct_lgst.gates:
    gatestrings.extend([((prepStr) + (_objs.GateString((gateLabel), bCheck=False))) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ])
for gateLabel in direct_lgst.gates:
    gatestrings.extend([((prepStr) + (_objs.GateString((gateLabel), bCheck=False))) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ])
_, direct_mlegst = _alg.do_mlgst(dataset, direct_lgst, gatestrings, minProbClip=minProbClip, probClipInterval=probClipInterval, verbosity=verbosity, gateLabelAliases={gateStringLabel: gateStringToEstimate}) _, direct_lsgst = _alg.do_mc2gst(dataset, direct_lgst, gatestrings, minProbClipForWeighting=minProbClipForWeighting, probClipInterval=probClipInterval, verbosity=verbosity, gateLabelAliases={gateStringLabel: gateStringToEstimate})
return direct_mlegst return direct_lsgst



Clone # 37
Distance between two fragments = 3
Clone size = 11
Source file "report/generation.py"
The first line is 174
Source file "report/generation.py"
The first line is 1210
gateLabels = list(gateset.gates.keys()) gateLabels = list(gateset.gates.keys())
mxBasis = gateset.get_basis_name() basisNm = gateset.get_basis_name()
mxBasisDim = gateset.get_basis_dimension() basisDims = gateset.get_basis_dimension()
basisNm = _tools.basis_longname(mxBasis, mxBasisDim) basisLongNm = _tools.basis_longname(basisNm, basisDims)
if confidenceRegionInfo is None:
    colHeadings = ('Gate', ('Superoperator (%s basis)') % (basisNm))
    formatters = (None, None)
else:
    colHeadings = ('Gate', ('Superoperator (%s basis)') % (basisNm), ('%g%% C.I. half-width') % (confidenceRegionInfo.level))
    formatters = (None, None, 'Conversion')
if confidenceRegionInfo is None:
    colHeadings = ('Gate', ('Superoperator (%s basis)') % (basisLongNm))
    formatters = (None, None)
else:
    colHeadings = ('Gate', ('Superoperator (%s basis)') % (basisLongNm), ('%g%% C.I. half-width') % (confidenceRegionInfo.level))
    formatters = (None, None, 'Conversion')
table = _ReportTable(colHeadings, formatters) table = _ReportTable(colHeadings, formatters)



Clone # 38
Distance between two fragments = 0
Clone size = 11
Source file "report/results.py"
The first line is 3451
Source file "report/results.py"
The first line is 2388
def incgr(figFilenm, W=None, H=None):
    if W is None:
        W = maxW
    if H is None:
        H = maxH
    return (('\\includegraphics[width=%.2fin,height=%.2fin') % ((W, H))) + ((',keepaspectratio]{%s/%s}') % ((D, figFilenm)))
def incgr(figFilenm, W=None, H=None):
    if W is None:
        W = maxW
    if H is None:
        H = maxH
    return (('\\includegraphics[width=%.2fin,height=%.2fin') % ((W, H))) + ((',keepaspectratio]{%s/%s}') % ((D, figFilenm)))
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig



Clone # 39
Distance between two fragments = 0
Clone size = 11
Source file "report/results.py"
The first line is 2388
Source file "report/results.py"
The first line is 1674
def incgr(figFilenm, W=None, H=None):
    if W is None:
        W = maxW
    if H is None:
        H = maxH
    return (('\\includegraphics[width=%.2fin,height=%.2fin') % ((W, H))) + ((',keepaspectratio]{%s/%s}') % ((D, figFilenm)))
def incgr(figFilenm, W=None, H=None):
    if W is None:
        W = maxW
    if H is None:
        H = maxH
    return (('\\includegraphics[width=%.2fin,height=%.2fin') % ((W, H))) + ((',keepaspectratio]{%s/%s}') % ((D, figFilenm)))
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig



Clone # 40
Distance between two fragments = 0
Clone size = 11
Source file "report/results.py"
The first line is 3326
Source file "report/results.py"
The first line is 2289
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true"  )
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false"  )



Clone # 41
Distance between two fragments = 0
Clone size = 11
Source file "report/results.py"
The first line is 3326
Source file "report/results.py"
The first line is 1548
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")



Clone # 42
Distance between two fragments = 4
Clone size = 11
Source file "report/results.py"
The first line is 806
Source file "report/results.py"
The first line is 796
fns['directLGSTDeviationColorBoxPlot'] = (fn, validate_LsAndGerms) fns['directLongSeqGSTColorBoxPlot'] = (fn, validate_LsAndGerms)
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    Ls, germs, gsBest, _, _, _, baseStr_dict, _, st = plot_setup()
    directLongSeqGST = self._specials.get('DirectLongSeqGatesets', verbosity=vb)
    return _plotting.direct_deviation_boxplot(Ls[st:], germs, baseStr_dict, self.dataset, gsBest, directLongSeqGST, '$L$', 'germ', scale=1.0, prec=-1, title='', save_to='', ticSize=20)
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    Ls, germs, gsBest, _, _, _, baseStr_dict, _, st = plot_setup()
    directLGST = self._specials.get('direct_lgst_gatesets', verbosity=vb)
    return _plotting.direct_deviation_boxplot(Ls[st:], germs, baseStr_dict, self.dataset, gsBest, directLGST, '$L$', 'germ', scale=1.0, prec=-1, title='', save_to='', ticSize=20)
fns['directLongSeqGSTDeviationColorBoxPlot'] = (fn, validate_LsAndGerms) fns['directLGSTDeviationColorBoxPlot'] = (fn, validate_LsAndGerms)



Clone # 43
Distance between two fragments = 4
Clone size = 10
Source file "report/results.py"
The first line is 482
Source file "report/results.py"
The first line is 488
fns['bestGatesetSpamBriefTable'] = (fn, validate_essential) fns['bestGatesetSpamParametersTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_parameters_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_gates_table(gsBest, cri)
fns['bestGatesetSpamParametersTable'] = (fn, validate_essential) fns['bestGatesetGatesTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_gates_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_choi_table(gsBest, cri)



Clone # 44
Distance between two fragments = 4
Clone size = 10
Source file "report/results.py"
The first line is 482
Source file "report/results.py"
The first line is 494
fns['bestGatesetSpamBriefTable'] = (fn, validate_essential) fns['bestGatesetGatesTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_parameters_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_choi_table(gsBest, cri)
fns['bestGatesetSpamParametersTable'] = (fn, validate_essential) fns['bestGatesetChoiTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_gates_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_decomp_table(gsBest, cri)



Clone # 45
Distance between two fragments = 4
Clone size = 11
Source file "report/results.py"
The first line is 530
Source file "report/results.py"
The first line is 524
fns['bestGatesetVsTargetTable'] = (fn, validate_essential) fns['bestGatesetClosestUnitaryTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_spam_vs_target_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_table(gsBest, gsTgt, cri)
fns['bestGatesetSpamVsTargetTable'] = (fn, validate_essential) fns['bestGatesetVsTargetTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_err_gen_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_spam_vs_target_table(gsBest, gsTgt, cri)



Clone # 46
Distance between two fragments = 4
Clone size = 12
Source file "report/results.py"
The first line is 536
Source file "report/results.py"
The first line is 524
fns['bestGatesetSpamVsTargetTable'] = (fn, validate_essential) fns['bestGatesetClosestUnitaryTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_err_gen_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_table(gsBest, gsTgt, cri)
fns['bestGatesetErrorGenTable'] = (fn, validate_essential) fns['bestGatesetVsTargetTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_angles_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_spam_vs_target_table(gsBest, gsTgt, cri)



Clone # 47
Distance between two fragments = 4
Clone size = 10
Source file "report/reportables.py"
The first line is 470
Source file "report/reportables.py"
The first line is 431
decompDict = _tools.decompose_gate_matrix(closestUGateMx) decompDict = _tools.decompose_gate_matrix(gate)
if decompDict['isValid']:
    angleQty = _getGateQuantity(decomp_cu_angle, gateset, label, eps, confidenceRegionInfo)
    diagQty = _getGateQuantity(decomp_cu_decay_diag, gateset, label, eps, confidenceRegionInfo)
    offdiagQty = _getGateQuantity(decomp_cu_decay_offdiag, gateset, label, eps, confidenceRegionInfo)
    errBarDict = {'pi rotations': angleQty.get_err_bar(), 'decay of diagonal rotation terms': diagQty.get_err_bar(), 'decay of off diagonal rotation terms': offdiagQty.get_err_bar()}
    decompQty = ReportableQty(decompDict, errBarDict)
else:
    decompQty = ReportableQty({})
if decompDict['isValid']:
    angleQty = _getGateQuantity(decomp_angle, gateset, label, eps, confidenceRegionInfo)
    diagQty = _getGateQuantity(decomp_decay_diag, gateset, label, eps, confidenceRegionInfo)
    offdiagQty = _getGateQuantity(decomp_decay_offdiag, gateset, label, eps, confidenceRegionInfo)
    errBarDict = {'pi rotations': angleQty.get_err_bar(), 'decay of diagonal rotation terms': diagQty.get_err_bar(), 'decay of off diagonal rotation terms': offdiagQty.get_err_bar()}
    decompQty = ReportableQty(decompDict, errBarDict)
else:
    decompQty = ReportableQty({})



Clone # 48
Distance between two fragments = 4
Clone size = 11
Source file "report/table.py"
The first line is 120
Source file "report/table.py"
The first line is 95
if (self._customHeadings is not None) and ('ppt' in self._customHeadings):
    raise ValueError(('custom headers unsupported for ') + ('powerpoint format'))
if (self._customHeadings is not None) and ('text' in self._customHeadings):
    raise ValueError('custom headers unsupported for text format')
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'ppt')
else:
    colHeadings_formatted = self._headings['ppt']
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'text')
else:
    colHeadings_formatted = self._headings['text']
ppt = {'column names': colHeadings_formatted, 'row data': []} text = {'column names': colHeadings_formatted, 'row data': []}



Clone # 49
Distance between two fragments = 2
Clone size = 10
Source file "report/results.py"
The first line is 3421
Source file "report/results.py"
The first line is 2371
for key in tables_to_blank:
    qtys[key] = _generation.get_blank_table().render('latex', longtables=self.options.long_tables)
    qtys[('tt_') + (key)] = ''
for key in tables_to_blank:
    qtys[key] = _generation.get_blank_table().render('latex', longtables=self.options.long_tables)
    qtys[('tt_') + (key)] = ''
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
maxW, maxH = (6.5, 9.0) maxW, maxH = (4.0, 3.0)



Clone # 50
Distance between two fragments = 3
Clone size = 10
Source file "report/results.py"
The first line is 2439
Source file "report/results.py"
The first line is 1731
fig = self.figures.get(('estimateForLIndex%dColorBoxPlot') % (i), verbosity=(printer) - (1)) fig = self.figures.get(('estimateForLIndex%dColorBoxPlot') % (i), verbosity=printer)
fig.save_to(_os.path.join(report_dir, D, ('L%d_%sBoxes.pdf') % ((i, plotFnName)))) fig.save_to(_os.path.join(report_dir, D, ('L%d_%sBoxes.pdf') % ((i, plotFnName))))
lx = fig.get_extra_info()['nUsedXs'] lx = fig.get_extra_info()['nUsedXs']
ly = fig.get_extra_info()['nUsedYs'] ly = fig.get_extra_info()['nUsedYs']
W = ((float((lx) + (1))) / (float((maxX) + (1)))) * (maxW) W = ((float((lx) + (1))) / (float((maxX) + (1)))) * (maxW)
H = ((float(ly)) / (float(maxY))) * (maxH) H = ((float(ly)) / (float(maxY))) * (maxH)
pixplots += '\n' pixplots += '\n'
pixplots += '\\begin{frame}\n' pixplots += '\\begin{figure}\n'



Clone # 51
Distance between two fragments = 3
Clone size = 10
Source file "report/plotting.py"
The first line is 2396
Source file "report/plotting.py"
The first line is 2236
logLMx = _np.zeros((len(strs[1]), len(strs[0])), 'd') chiSqMx = _np.zeros((len(strs[1]), len(strs[0])), 'd')
if sigma is None:
    return (_np.nan) * (logLMx)
if sigma is None:
    return (_np.nan) * (chiSqMx)
cntMx = total_count_matrix(sigma, dataset, strs, fidPairs) cntMx = total_count_matrix(sigma, dataset, strs, fidPairs)
gs_direct = directGateset gs_direct = directGateset
for sl in gs_direct.get_spam_labels():
    probMx = probability_matrix(_objs.GateString(('GsigmaLbl')), gs_direct, sl, strs, fidPairs)
    freqMx = frequency_matrix(sigma, dataset, sl, strs, fidPairs)
    logLMx += _tools.two_delta_loglfn(cntMx, probMx, freqMx, minProbClip)
for sl in gs_direct.get_spam_labels():
    probMx = probability_matrix(_objs.GateString(('GsigmaLbl')), gs_direct, sl, strs, fidPairs)
    freqMx = frequency_matrix(sigma, dataset, sl, strs, fidPairs)
    chiSqMx += _tools.chi2fn(cntMx, probMx, freqMx, minProbClipForWeighting)
return logLMx return chiSqMx



Clone # 52
Distance between two fragments = 0
Clone size = 9
Source file "report/plotting.py"
The first line is 1170
Source file "report/plotting.py"
The first line is 1121
histdata_finite = _np.take(histdata, _np.where(_np.isfinite(histdata)))[0] histdata_finite = _np.take(histdata, _np.where(_np.isfinite(histdata)))[0]
histMin  =  min(  histdata_finite  )  if  cmapFactory.vmin  is  None  else  cmapFactory.vmin histMin  =  min(  histdata_finite  )  if  cmapFactory.vmin  is  None  else  cmapFactory.vmin
histMax  =  max(  histdata_finite  )  if  cmapFactory.vmax  is  None  else  cmapFactory.vmax histMax  =  max(  histdata_finite  )  if  cmapFactory.vmax  is  None  else  cmapFactory.vmax
_plt.hist(_np.clip(histdata_finite, histMin, histMax), histBins, range=[histMin, histMax], facecolor='gray', align='mid') _plt.hist(_np.clip(histdata_finite, histMin, histMax), histBins, range=[histMin, histMax], facecolor='gray', align='mid')
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(_makeHistFilename(save_to))
    _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(_makeHistFilename(save_to))
    _plt.close(fig)



Clone # 53
Distance between two fragments = 1
Clone size = 9
Source file "report/results.py"
The first line is 1689
Source file "report/results.py"
The first line is 2808
Ls = self.parameters['max length list'] Ls = self.parameters['max length list']
st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  column  in  plots st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  col  in  box  plots
nPlots  =  (len(Ls[st:])-1)+2  if  pixelPlotAppendix  else  2 nPlots  =  (len(Ls[st:])-1)+1  if  pixelPlotAppendix  else  1
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))



Clone # 54
Distance between two fragments = 1
Clone size = 9
Source file "report/results.py"
The first line is 1689
Source file "report/results.py"
The first line is 2405
Ls = self.parameters['max length list'] Ls = self.parameters['max length list']
st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  column  in  plots st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  col  in  box  plots
nPlots  =  (len(Ls[st:])-1)+2  if  pixelPlotAppendix  else  2 nPlots  =  (len(Ls[st:])-1)+1  if  pixelPlotAppendix  else  1
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))



Clone # 55
Distance between two fragments = 0
Clone size = 9
Source file "report/results.py"
The first line is 2276
Source file "report/results.py"
The first line is 2712
if title == 'auto':
    title = ('GST on %s') % (datasetLabel)
if title == 'auto':
    title = ('GST on %s') % (datasetLabel)
best_gs = self.gatesets['final estimate'] best_gs = self.gatesets['final estimate']
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel



Clone # 56
Distance between two fragments = 0
Clone size = 9
Source file "report/results.py"
The first line is 2258
Source file "report/results.py"
The first line is 2694
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix



Clone # 57
Distance between two fragments = 1
Clone size = 11
Source file "report/results.py"
The first line is 3289
Source file "report/results.py"
The first line is 2694
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
   
+  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
   
  else  "GSTReport"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix



Clone # 58
Distance between two fragments = 1
Clone size = 11
Source file "report/results.py"
The first line is 2694
Source file "report/results.py"
The first line is 1511
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  \
   
+  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  \
   
  else  "GSTReport"
  report_base  +=  suffix



Clone # 59
Distance between two fragments = 1
Clone size = 9
Source file "report/results.py"
The first line is 2694
Source file "report/results.py"
The first line is 1985
default_dir = self.parameters['defaultDirectory'] default_dir = self.parameters['defaultDirectory']
default_base = self.parameters['defaultBasename'] default_base = self.parameters['defaultBasename']
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTSlides"
  report_base  +=  suffix
if  filename  !=  "auto":
  report_dir  =  _os.path.dirname(filename)
  report_base  =  _os.path.splitext(  _os.path.basename(filename)  )[0]  +  suffix
else:
  cwd  =  _os.getcwd()
  report_dir    =  default_dir    if  (default_dir    is  not  None)  else  cwd
  report_base  =  default_base  if  (default_base  is  not  None)  else  "GSTBrief"
  report_base  +=  suffix



Clone # 60
Distance between two fragments = 2
Clone size = 9
Source file "report/generation.py"
The first line is 818
Source file "report/generation.py"
The first line is 736
gate = gateset.gates[gl] gate = gateset.gates[gl]
targetGate = targetGateset.gates[gl] targetGate = targetGateset.gates[gl]
fig = _plotting.polar_eigenval_plot(gate, targetGate, title=gl, save_to='', showNormal=False, showRelative=True) fig = _plotting.polar_eigenval_plot(gate, targetGate, title=gl, save_to='', showNormal=True, showRelative=False)
sz = min((0.95) * ((maxHeight) / (nRows)), ((0.95) * (0.75)) * ((maxWidth) - (0.5))) sz = min((0.95) * ((maxHeight) / (nRows)), ((0.95) * (0.75)) * ((maxWidth) - (0.5)))
sz = min(sz, 2.0) sz = min(sz, 2.0)
nm = ((figFilePrefix) + ('_')) + (gl) nm = ((figFilePrefix) + ('_')) + (gl)
figInfo = (fig, nm, sz, sz) figInfo = (fig, nm, sz, sz)



Clone # 61
Distance between two fragments = 3
Clone size = 10
Source file "report/plotting.py"
The first line is 265
Source file "report/plotting.py"
The first line is 221
prepStrs, effectStrs = strs prepStrs, effectStrs = strs
logLMx = _np.zeros((len(effectStrs), len(prepStrs)), 'd') chiSqMx = _np.zeros((len(effectStrs), len(prepStrs)), 'd')
if gateString is None:
    return (_np.nan) * (logLMx)
if gateString is None:
    return (_np.nan) * (chiSqMx)
cntMx = total_count_matrix(gateString, dataset, strs, fidPairs) cntMx = total_count_matrix(gateString, dataset, strs, fidPairs)
for sl in gateset.get_spam_labels():
    probMx = probability_matrix(gateString, gateset, sl, strs, fidPairs)
    freqMx = frequency_matrix(gateString, dataset, sl, strs, fidPairs)
    logLMx += _tools.two_delta_loglfn(cntMx, probMx, freqMx, minProbClip)
for sl in gateset.get_spam_labels():
    probMx = probability_matrix(gateString, gateset, sl, strs, fidPairs)
    freqMx = frequency_matrix(gateString, dataset, sl, strs, fidPairs)
    chiSqMx += _tools.chi2fn(cntMx, probMx, freqMx, minProbClipForWeighting)
return logLMx return chiSqMx



Clone # 62
Distance between two fragments = 3
Clone size = 9
Source file "report/results.py"
The first line is 3331
Source file "report/results.py"
The first line is 2026
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")
qtys['settoggles']  +=  "\\toggle%s{goodnessSection}\n"  %  \
  ("true"  if  goodnessOfFitSection  else  "false")
qtys['confidenceLevel']  =  "%g"  %  \
 
confidenceLevel  if  confidenceLevel  is  not  None  else  "NOT-SET"
qtys['confidenceLevel']  =  "%g"  %  confidenceLevel  \
  if  confidenceLevel  is  not  None  else  "NOT-SET"



Clone # 63
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 286
Source file "report/results.py"
The first line is 282
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.gatestring_lists.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatesets.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .tables -- a dict of ReportTable objects w/keys:\n' s += ' .gatestring_lists -- a dict of GateString lists w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.tables.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatestring_lists.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .figures -- a dict of ReportFigure objects w/keys:\n' s += ' .tables -- a dict of ReportTable objects w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'



Clone # 64
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 290
Source file "report/results.py"
The first line is 282
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.tables.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatesets.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .figures -- a dict of ReportFigure objects w/keys:\n' s += ' .gatestring_lists -- a dict of GateString lists w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.figures.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatestring_lists.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .parameters -- a dict of simulation parameters:\n' s += ' .tables -- a dict of ReportTable objects w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'



Clone # 65
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 294
Source file "report/results.py"
The first line is 282
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.figures.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatesets.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .parameters -- a dict of simulation parameters:\n' s += ' .gatestring_lists -- a dict of GateString lists w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.parameters.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatestring_lists.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .options -- a container of display options:\n' s += ' .tables -- a dict of ReportTable objects w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'



Clone # 66
Distance between two fragments = 3
Clone size = 9
Source file "report/generation.py"
The first line is 403
Source file "report/generation.py"
The first line is 392
formatters = (['Effect']) + ((['ErrorBars']) * (len(qtyNames))) formatters = (['Rho']) + ((['ErrorBars']) * (len(qtyNames)))
qtys_to_compute = [('%s effect %s') % ((l, qty)) for qty in qtyNames for l in effectLabels ] qtys_to_compute = [('%s prep %s') % ((l, qty)) for qty in qtyNames for l in prepLabels ]
qtys = _cr.compute_gateset_gateset_qtys(qtys_to_compute, gateset, targetGateset, confidenceRegionInfo) qtys = _cr.compute_gateset_gateset_qtys(qtys_to_compute, gateset, targetGateset, confidenceRegionInfo)
for l in effectLabels:
    if confidenceRegionInfo is None:
        rowData = ([l]) + ([(qtys[('%s effect %s') % ((l, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([l]) + ([qtys[('%s effect %s') % ((l, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
for l in prepLabels:
    if confidenceRegionInfo is None:
        rowData = ([l]) + ([(qtys[('%s prep %s') % ((l, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([l]) + ([qtys[('%s prep %s') % ((l, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)



Clone # 67
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 2037
Source file "report/results.py"
The first line is 2731
qtys['gofObjective']  =  "$2\\Delta\\log{\\mathcal{L}}$"  \
  if  obj  ==  "logl"  else  "$\\chi^2$"
qtys['gofObjective']  =  "$2\\Delta\\log{\\mathcal{L}}$"  \
  if  self.parameters['objective']  ==  "logl"  else  "$\\chi^2$"
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'



Clone # 68
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 921
Source file "report/results.py"
The first line is 901
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('targetGateBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr5:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('bestGateErrGenBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr4:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr5] = (fn, fn_validate) fns[expr4] = (fn, fn_validate)
expr6 = 'bestEstimatePolar(.+?)EvalPlot' expr5 = 'targetGateBoxes(.+)'



Clone # 69
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 921
Source file "report/results.py"
The first line is 940
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('targetGateBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr5:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('bestEstimatePolar%sEvalPlot') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr6:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr5] = (fn, fn_validate) fns[expr6] = (fn, fn_validate)
expr6 = 'bestEstimatePolar(.+?)EvalPlot' expr7 = 'pauliProdHamiltonianDecompBoxes(.+)'



Clone # 70
Distance between two fragments = 4
Clone size = 9
Source file "report/results.py"
The first line is 901
Source file "report/results.py"
The first line is 940
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('bestGateErrGenBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr4:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('bestEstimatePolar%sEvalPlot') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr6:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr4] = (fn, fn_validate) fns[expr6] = (fn, fn_validate)
expr5 = 'targetGateBoxes(.+)' expr7 = 'pauliProdHamiltonianDecompBoxes(.+)'



Clone # 71
Distance between two fragments = 1
Clone size = 9
Source file "report/generation.py"
The first line is 1065
Source file "report/generation.py"
The first line is 1007
pv = (1.0) - (_stats.chi2.cdf(twoDeltaLogL, k)) pv = (1.0) - (_stats.chi2.cdf(chi2, k))
if (twoDeltaLogL) - (k) < _np.sqrt((2) * (k)):
    rating = 5
elif (twoDeltaLogL) - (k) < (2) * (k):
    rating = 4
elif (twoDeltaLogL) - (k) < (5) * (k):
    rating = 3
elif (twoDeltaLogL) - (k) < (10) * (k):
    rating = 2
else:
    rating = 1
if (chi2) - (k) < _np.sqrt((2) * (k)):
    rating = 5
elif (chi2) - (k) < (2) * (k):
    rating = 4
elif (chi2) - (k) < (5) * (k):
    rating = 3
elif (chi2) - (k) < (10) * (k):
    rating = 2
else:
    rating = 1
table.addrow((str(L), twoDeltaLogL, k, (twoDeltaLogL) - (k), _np.sqrt((2) * (k)), pv, Ns, Np, ('') * (rating)), (None, 'Normal', 'Normal', 'Normal', 'Normal', 'Rounded', 'Normal', 'Normal', 'Conversion')) table.addrow((str(L), chi2, k, (chi2) - (k), _np.sqrt((2) * (k)), pv, Ns, Np, ('') * (rating)), (None, 'Normal', 'Normal', 'Normal', 'Normal', 'Rounded', 'Normal', 'Normal', 'Conversion'))



Clone # 72
Distance between two fragments = 0
Clone size = 9
Source file "report/generation.py"
The first line is 193
Source file "report/generation.py"
The first line is 253
intervalVec = confidenceRegionInfo.get_profile_likelihood_confidence_intervals(gl)[None:None,None] intervalVec = confidenceRegionInfo.get_profile_likelihood_confidence_intervals(gl)[None:None,None]
if isinstance(gateset.gates[gl], _objs.FullyParameterizedGate):
    gate_dim = gateset.get_dimension()
    intervalMx = intervalVec.reshape(gate_dim, gate_dim)
elif isinstance(gateset.gates[gl], _objs.TPParameterizedGate):
    gate_dim = gateset.get_dimension()
    intervalMx = _np.concatenate((_np.zeros((1, gate_dim), 'd'), intervalVec.reshape((gate_dim) - (1), gate_dim)), axis=0)
else:
    intervalMx = intervalVec
if isinstance(gateset.gates[gl], _objs.FullyParameterizedGate):
    gate_dim = gateset.get_dimension()
    intervalMx = intervalVec.reshape(gate_dim, gate_dim)
elif isinstance(gateset.gates[gl], _objs.TPParameterizedGate):
    gate_dim = gateset.get_dimension()
    intervalMx = _np.concatenate((_np.zeros((1, gate_dim), 'd'), intervalVec.reshape((gate_dim) - (1), gate_dim)), axis=0)
else:
    intervalMx = intervalVec



Clone # 73
Distance between two fragments = 0
Clone size = 9
Source file "report/results.py"
The first line is 2092
Source file "report/results.py"
The first line is 3421
for key in tables_to_blank:
    qtys[key] = _generation.get_blank_table().render('latex', longtables=self.options.long_tables)
    qtys[('tt_') + (key)] = ''
for key in tables_to_blank:
    qtys[key] = _generation.get_blank_table().render('latex', longtables=self.options.long_tables)
    qtys[('tt_') + (key)] = ''
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 74
Distance between two fragments = 3
Clone size = 9
Source file "report/results.py"
The first line is 2839
Source file "report/results.py"
The first line is 1729
printer.show_progress(i, (len(Ls)) - (2), prefix='', end='') printer.show_progress(i, (len(Ls)) - (2), prefix='', end='')
fig = self.figures.get(('estimateForLIndex%dColorBoxPlot') % (i), verbosity=(printer) - (1)) fig = self.figures.get(('estimateForLIndex%dColorBoxPlot') % (i), verbosity=printer)
fig.save_to(_os.path.join(report_dir, D, ('L%d_%sBoxes.png') % ((i, plotFnName)))) fig.save_to(_os.path.join(report_dir, D, ('L%d_%sBoxes.pdf') % ((i, plotFnName))))
lx = fig.get_extra_info()['nUsedXs'] lx = fig.get_extra_info()['nUsedXs']
ly = fig.get_extra_info()['nUsedYs'] ly = fig.get_extra_info()['nUsedYs']
W = ((float((lx) + (1))) / (float((maxX) + (1)))) * (maxW) W = ((float((lx) + (1))) / (float((maxX) + (1)))) * (maxW)
H = ((float(ly)) / (float(maxY))) * (maxH) H = ((float(ly)) / (float(maxY))) * (maxH)



Clone # 75
Distance between two fragments = 0
Clone size = 9
Source file "report/plotting.py"
The first line is 1239
Source file "report/plotting.py"
The first line is 1084
def val_filter(vals):
    formatted_vals = []
    for val in vals:
        if (type(val) in (tuple, _objs.GateString)) and (all([type(el) == str for el in val ])):
            if len(val) == 0:
                formatted_vals.append('$\\{\\}$')
            else:
                formatted_vals.append((('$') + ('\\cdot'.join([('\\mathrm{%s}') % (el) for el in val ]))) + ('$'))
        else:
            formatted_vals.append(val)
    return formatted_vals
def val_filter(vals):
    formatted_vals = []
    for val in vals:
        if (type(val) in (tuple, _objs.GateString)) and (all([type(el) == str for el in val ])):
            if len(val) == 0:
                formatted_vals.append('$\\{\\}$')
            else:
                formatted_vals.append((('$') + ('\\cdot'.join([('\\mathrm{%s}') % (el) for el in val ]))) + ('$'))
        else:
            formatted_vals.append(val)
    return formatted_vals



Clone # 76
Distance between two fragments = 3
Clone size = 8
Source file "report/generation.py"
The first line is 830
Source file "report/generation.py"
The first line is 748
if confidenceRegionInfo is None:
    rel_evals = qtys[('%s relative eigenvalues') % (gl)].get_value()
    rel_evals = rel_evals.reshape((rel_evals.size) // (2), 2)
    rowData = [gl, (rel_evals, None), figInfo]
else:
    rel_evals, rel_evalsEB = qtys[('%s relative eigenvalues') % (gl)].get_value_and_err_bar()
    rel_evals = rel_evals.reshape((rel_evals.size) // (2), 2)
    rowData = [gl, (rel_evals, rel_evalsEB), figInfo]
if confidenceRegionInfo is None:
    evals = qtys[('%s eigenvalues') % (gl)].get_value()
    evals = evals.reshape((evals.size) // (2), 2)
    rowData = [gl, (evals, None), figInfo]
else:
    evals, evalsEB = qtys[('%s eigenvalues') % (gl)].get_value_and_err_bar()
    evals = evals.reshape((evals.size) // (2), 2)
    rowData = [gl, (evals, evalsEB), figInfo]
table.addrow(rowData, formatters) table.addrow(rowData, formatters)



Clone # 77
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 557
Source file "report/results.py"
The first line is 566
fns['bestGatesetGaugeOptParamsTable'] = (fn, validate_essential) fns['chi2ProgressTable'] = (fn, validate_LsAndGerms)
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_chi2_progress_table(self.parameters['max length list'], self.gatesets['iteration estimates'], self.gatestring_lists['iteration'], self.dataset)
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_logl_progress_table(self.parameters['max length list'], self.gatesets['iteration estimates'], self.gatestring_lists['iteration'], self.dataset)
fns['chi2ProgressTable'] = (fn, validate_LsAndGerms) fns['logLProgressTable'] = (fn, validate_LsAndGerms)



Clone # 78
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 754
Source file "report/results.py"
The first line is 762
fns[expr1] = (fn, fn_validate) fns['blankBoxPlot'] = (fn, validate_LsAndGerms)
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    Ls, germs, _, _, _, _, baseStr_dict, strs, st = plot_setup()
    return _plotting.blank_boxplot(Ls[st:], germs, baseStr_dict, strs, '$L$', 'germ', scale=1.0, title='', sumUp=False, save_to='', ticSize=20)
def fn(key, confidenceLevel, vb):
    noConfidenceLevelDependence(confidenceLevel)
    Ls, germs, _, _, _, _, baseStr_dict, strs, st = plot_setup()
    return _plotting.blank_boxplot(Ls[st:], germs, baseStr_dict, strs, '$L$', 'germ', scale=1.0, title='', sumUp=True, save_to='', ticSize=20)
fns['blankBoxPlot'] = (fn, validate_LsAndGerms) fns['blankSummedBoxPlot'] = (fn, validate_LsAndGerms)



Clone # 79
Distance between two fragments = 0
Clone size = 8
Source file "report/results.py"
The first line is 2352
Source file "report/results.py"
The first line is 1616
ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable') ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable')
tables_to_compute = std_tables tables_to_compute = std_tables
tables_to_blank = [] tables_to_blank = []
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables



Clone # 80
Distance between two fragments = 1
Clone size = 8
Source file "report/results.py"
The first line is 2352
Source file "report/results.py"
The first line is 3395
ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable') ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germList2ColTable', 'progressTable')
tables_to_compute = std_tables tables_to_compute = std_tables
tables_to_blank = [] tables_to_blank = []
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables



Clone # 81
Distance between two fragments = 0
Clone size = 8
Source file "report/results.py"
The first line is 2759
Source file "report/results.py"
The first line is 1616
ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable') ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable')
tables_to_compute = std_tables tables_to_compute = std_tables
tables_to_blank = [] tables_to_blank = []
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables



Clone # 82
Distance between two fragments = 1
Clone size = 8
Source file "report/results.py"
The first line is 2759
Source file "report/results.py"
The first line is 3395
ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable') ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germList2ColTable', 'progressTable')
tables_to_compute = std_tables tables_to_compute = std_tables
tables_to_blank = [] tables_to_blank = []
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables



Clone # 83
Distance between two fragments = 1
Clone size = 8
Source file "report/results.py"
The first line is 1616
Source file "report/results.py"
The first line is 3395
ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germListTable', 'progressTable') ls_and_germs_tables = ('fiducialListTable', 'prepStrListTable', 'effectStrListTable', 'germList2ColTable', 'progressTable')
tables_to_compute = std_tables tables_to_compute = std_tables
tables_to_blank = [] tables_to_blank = []
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables
if self._LsAndGermInfoSet:
    tables_to_compute += ls_and_germs_tables
else:
    tables_to_blank += ls_and_germs_tables



Clone # 84
Distance between two fragments = 0
Clone size = 8
Source file "report/results.py"
The first line is 1172
Source file "report/results.py"
The first line is 666
baseStr_dict = self._getBaseStrDict() baseStr_dict = self._getBaseStrDict()
strs = (self.gatestring_lists['prep fiducials'], self.gatestring_lists['effect fiducials']) strs = (self.gatestring_lists['prep fiducials'], self.gatestring_lists['effect fiducials'])
germs = self.gatestring_lists['germs'] germs = self.gatestring_lists['germs']
gsBest = self.gatesets['final estimate'] gsBest = self.gatesets['final estimate']
fidPairs = self.parameters['fiducial pairs'] fidPairs = self.parameters['fiducial pairs']
Ls = self.parameters['max length list'] Ls = self.parameters['max length list']
st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  column  in  plots st  =  1  if  Ls[0]  ==  0  else  0  #start  index:  skip  LGST  column  in  plots



Clone # 85
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 295
Source file "report/results.py"
The first line is 291
s += ((' ') + ('\n '.join(list(self.figures.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.tables.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .parameters -- a dict of simulation parameters:\n' s += ' .figures -- a dict of ReportFigure objects w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.parameters.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.figures.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .options -- a container of display options:\n' s += ' .parameters -- a dict of simulation parameters:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'



Clone # 86
Distance between two fragments = 2
Clone size = 8
Source file "report/results.py"
The first line is 962
Source file "report/results.py"
The first line is 940
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('pauliProdHamiltonianDecompBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr7:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('bestEstimatePolar%sEvalPlot') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr6:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr7] = (fn, fn_validate) fns[expr6] = (fn, fn_validate)



Clone # 87
Distance between two fragments = 2
Clone size = 8
Source file "report/results.py"
The first line is 962
Source file "report/results.py"
The first line is 921
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('pauliProdHamiltonianDecompBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr7:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('targetGateBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr5:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr7] = (fn, fn_validate) fns[expr5] = (fn, fn_validate)



Clone # 88
Distance between two fragments = 2
Clone size = 8
Source file "report/results.py"
The first line is 962
Source file "report/results.py"
The first line is 901
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('pauliProdHamiltonianDecompBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr7:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
def fn_validate(key):
    if not self._bEssentialResultsSet:
        return []
    keys = [('bestGateErrGenBoxes%s') % (gl) for gl in self.gatesets['final estimate'].gates ]
    if key == expr4:
        return keys
    elif key in keys:
        return [key]
    else:
        return []
fns[expr7] = (fn, fn_validate) fns[expr4] = (fn, fn_validate)



Clone # 89
Distance between two fragments = 4
Clone size = 8
Source file "report/reportables.py"
The first line is 341
Source file "report/reportables.py"
The first line is 336
def decomp_cu_decay_diag(gate):
    closestUGateMx = _alg.find_closest_unitary_gatemx(gate)
    decomp = _tools.decompose_gate_matrix(closestUGateMx)
    return decomp.get('decay of diagonal rotation terms', 0)
def decomp_cu_angle(gate):
    closestUGateMx = _alg.find_closest_unitary_gatemx(gate)
    decomp = _tools.decompose_gate_matrix(closestUGateMx)
    return decomp.get('pi rotations', 0)
def decomp_cu_decay_offdiag(gate):
    closestUGateMx = _alg.find_closest_unitary_gatemx(gate)
    decomp = _tools.decompose_gate_matrix(closestUGateMx)
    return decomp.get('decay of off diagonal rotation terms', 0)
def decomp_cu_decay_diag(gate):
    closestUGateMx = _alg.find_closest_unitary_gatemx(gate)
    decomp = _tools.decompose_gate_matrix(closestUGateMx)
    return decomp.get('decay of diagonal rotation terms', 0)



Clone # 90
Distance between two fragments = 2
Clone size = 9
Source file "report/results.py"
The first line is 2909
Source file "report/results.py"
The first line is 2898
  with  printer.progress_logging(1):
    for  i,germ  in  enumerate(len1Germs):
      printer.show_progress(i,  len(len1Germs)  -  1,  prefix='',  end='')
      #  printer.log("%d  "  %  (len(len1Germs)+i+1),  end='')

      fig  =  self.figures.get("whack%sMoleBoxesSummed"  %  germ[0],
         
verbosity=printer  -  1)
      fig.save_to(_os.path.join(
       
report_dir,  D,  "whack%sMoleBoxesSummed.png"  %  germ[0]))
      whackamoleplots.append(  _os.path.join(
        report_dir,  D,"whack%sMoleBoxesSummed.png"  %  germ[0])  )
  with  printer.progress_logging(1):
    for  i,germ  in  enumerate(len1Germs):
      printer.show_progress(i,  len(len1Germs)  -  1,  prefix='',  end='')

      fig  =  self.figures.get("whack%sMoleBoxes"  %  germ[0],verbosity=printer  -1)
      fig.save_to(_os.path.join(report_dir,  D,"whack%sMoleBoxes.png"
       
  %  germ[0]))
      whackamoleplots.append(  _os.path.join(
        report_dir,  D,  "whack%sMoleBoxes.png"  %  germ[0])  )



Clone # 91
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 1085
Source file "report/results.py"
The first line is 1083
ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetDecompTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 92
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 1093
Source file "report/results.py"
The first line is 1091
ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetDecompTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetVsTargetTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetErrorGenTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetVsTargetTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 93
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 1087
Source file "report/results.py"
The first line is 1083
ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetDecompTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 94
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 1089
Source file "report/results.py"
The first line is 1083
ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetDecompTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 95
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 1091
Source file "report/results.py"
The first line is 1083
ret[('best%sGatesetDecompTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetVsTargetTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 96
Distance between two fragments = 4
Clone size = 8
Source file "report/results.py"
The first line is 1093
Source file "report/results.py"
The first line is 1083
ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetVsTargetTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetErrorGenTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetChoiTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 97
Distance between two fragments = 1
Clone size = 8
Source file "report/results.py"
The first line is 2842
Source file "report/results.py"
The first line is 2439
fig = self.figures.get(('estimateForLIndex%dColorBoxPlot') % (i), verbosity=(printer) - (1)) fig = self.figures.get(('estimateForLIndex%dColorBoxPlot') % (i), verbosity=(printer) - (1))
fig.save_to(_os.path.join(report_dir, D, ('L%d_%sBoxes.png') % ((i, plotFnName)))) fig.save_to(_os.path.join(report_dir, D, ('L%d_%sBoxes.pdf') % ((i, plotFnName))))
lx = fig.get_extra_info()['nUsedXs'] lx = fig.get_extra_info()['nUsedXs']
ly = fig.get_extra_info()['nUsedYs'] ly = fig.get_extra_info()['nUsedYs']
W = ((float((lx) + (1))) / (float((maxX) + (1)))) * (maxW) W = ((float((lx) + (1))) / (float((maxX) + (1)))) * (maxW)
H = ((float(ly)) / (float(maxY))) * (maxH) H = ((float(ly)) / (float(maxY))) * (maxH)



Clone # 98
Distance between two fragments = 4
Clone size = 8
Source file "report/ppt.py"
The first line is 50
Source file "report/latex.py"
The first line is 51
d = 0 d = 0
for l in x.shape:
    if l > 1:
        d += 1
for l in x.shape:
    if l > 1:
        d += 1
x = _np.squeeze(x) x = _np.squeeze(x)
if d == 0:
    return ppt_value(x, precision=precision, polarprecision=polarprecision)
if d == 0:
    return latex_value(x, precision=precision, polarprecision=polarprecision)
if d == 1:
    return ppt_vector(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 1:
    return latex_vector(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 2:
    return ppt_matrix(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 2:
    return latex_matrix(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
raise ValueError(("I don't know how to render a rank %d numpy array as ppt") % (d)) raise ValueError(("I don't know how to render a rank %d numpy array as latex") % (d))



Clone # 99
Distance between two fragments = 4
Clone size = 8
Source file "report/ppt.py"
The first line is 50
Source file "report/html.py"
The first line is 51
d = 0 d = 0
for l in x.shape:
    if l > 1:
        d += 1
for l in x.shape:
    if l > 1:
        d += 1
x = _np.squeeze(x) x = _np.squeeze(x)
if d == 0:
    return ppt_value(x, precision=precision, polarprecision=polarprecision)
if d == 0:
    return html_value(x, precision=precision, polarprecision=polarprecision)
if d == 1:
    return ppt_vector(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 1:
    return html_vector(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 2:
    return ppt_matrix(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 2:
    return html_matrix(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
raise ValueError(("I don't know how to render a rank %d numpy array as ppt") % (d)) raise ValueError(("I don't know how to render a rank %d numpy array as html") % (d))



Clone # 100
Distance between two fragments = 4
Clone size = 8
Source file "report/latex.py"
The first line is 51
Source file "report/html.py"
The first line is 51
d = 0 d = 0
for l in x.shape:
    if l > 1:
        d += 1
for l in x.shape:
    if l > 1:
        d += 1
x = _np.squeeze(x) x = _np.squeeze(x)
if d == 0:
    return latex_value(x, precision=precision, polarprecision=polarprecision)
if d == 0:
    return html_value(x, precision=precision, polarprecision=polarprecision)
if d == 1:
    return latex_vector(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 1:
    return html_vector(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 2:
    return latex_matrix(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
if d == 2:
    return html_matrix(x, brackets=brackets, precision=precision, polarprecision=polarprecision)
raise ValueError(("I don't know how to render a rank %d numpy array as latex") % (d)) raise ValueError(("I don't know how to render a rank %d numpy array as html") % (d))



Clone # 101
Distance between two fragments = 0
Clone size = 8
Source file "report/latex.py"
The first line is 202
Source file "report/ppt.py"
The first line is 190
if abs(x) < (5) * ((10) ** (-(precision) + (1))):
    s = ('%.0e') % (x)
elif abs(x) < 1:
    s = ('%.*f') % ((precision, x))
elif abs(x) <= (10) ** (precision):
    s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))
else:
    s = ('%.0e') % (x)
if abs(x) < (5) * ((10) ** (-(precision) + (1))):
    s = ('%.0e') % (x)
elif abs(x) < 1:
    s = ('%.*f') % ((precision, x))
elif abs(x) <= (10) ** (precision):
    s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))
else:
    s = ('%.0e') % (x)
p = s.split('e') p = s.split('e')



Clone # 102
Distance between two fragments = 0
Clone size = 8
Source file "report/html.py"
The first line is 211
Source file "report/ppt.py"
The first line is 190
if abs(x) < (5) * ((10) ** (-(precision) + (1))):
    s = ('%.0e') % (x)
elif abs(x) < 1:
    s = ('%.*f') % ((precision, x))
elif abs(x) <= (10) ** (precision):
    s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))
else:
    s = ('%.0e') % (x)
if abs(x) < (5) * ((10) ** (-(precision) + (1))):
    s = ('%.0e') % (x)
elif abs(x) < 1:
    s = ('%.*f') % ((precision, x))
elif abs(x) <= (10) ** (precision):
    s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))
else:
    s = ('%.0e') % (x)
p = s.split('e') p = s.split('e')



Clone # 103
Distance between two fragments = 2
Clone size = 8
Source file "report/results.py"
The first line is 1563
Source file "report/results.py"
The first line is 2301
qtys['settoggles']  +=  "\\toggle%s{gaugeoptappendix}\n"  %  \
  ("true"  if  gaugeOptAppendix  else  "false")
qtys['settoggles']  +=  "\\toggle%s{debuggingaidsappendix}\n"  %  \
  ("true"  if  debugAidsAppendix  else  "false"  )
qtys['settoggles']  +=  "\\toggle%s{pixelplotsappendix}\n"  %  \
  ("true"  if  pixelPlotAppendix  else  "false")
qtys['settoggles']  +=  "\\toggle%s{pixelplotsappendix}\n"  %  \
  ("true"  if  pixelPlotAppendix  else  "false"  )
qtys['settoggles']  +=  "\\toggle%s{whackamoleappendix}\n"  %  \
  ("true"  if  whackamoleAppendix  else  "false")
qtys['settoggles']  +=  "\\toggle%s{whackamoleappendix}\n"  %  \
  ("true"  if  whackamoleAppendix  else  "false"  )
qtys['confidenceLevel']  =  "%g"  %  \
 
confidenceLevel  if  confidenceLevel  is  not  None  else  "NOT-SET"
qtys['confidenceLevel']  =  "%g"  %  confidenceLevel  \
  if  confidenceLevel  is  not  None  else  "NOT-SET"



Clone # 104
Distance between two fragments = 0
Clone size = 8
Source file "report/generation.py"
The first line is 1568
Source file "report/generation.py"
The first line is 1462
cri = _objs.ConfidenceRegion(gateset, hessian, confidenceLevel, hessianProjection, nonMarkRadiusSq=nonMarkRadiusSq) cri = _objs.ConfidenceRegion(gateset, hessian, confidenceLevel, hessianProjection, nonMarkRadiusSq=nonMarkRadiusSq)
Np_check = gateset.num_nongauge_params() Np_check = gateset.num_nongauge_params()
if Np_check != cri.nNonGaugeParams:
    _warnings.warn(('Number of non-gauge parameters in gateset and confidence region do ') + (' not match. This indicates an internal logic error.'))
if Np_check != cri.nNonGaugeParams:
    _warnings.warn(('Number of non-gauge parameters in gateset and confidence region do ') + (' not match. This indicates an internal logic error.'))
return cri return cri



Clone # 105
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 1156
Source file "report/results.py"
The first line is 1147
mpc = self.parameters['minProbClip'] mpc = self.parameters['minProbClipForWeighting']
return _plotting.direct_mlgst_gatesets(baseStrs, self.dataset, direct_specs, gsTarget, svdTruncateTo=gsTarget.get_dimension(), minProbClip=mpc, probClipInterval=self.parameters['probClipInterval'], verbosity=0) return _plotting.direct_mc2gst_gatesets(baseStrs, self.dataset, direct_specs, gsTarget, svdTruncateTo=gsTarget.get_dimension(), minProbClipForWeighting=mpc, probClipInterval=self.parameters['probClipInterval'], verbosity=0)



Clone # 106
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 543
Source file "report/results.py"
The first line is 536
fns['bestGatesetErrorGenTable'] = (fn, validate_essential) fns['bestGatesetSpamVsTargetTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_angles_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_err_gen_table(gsBest, gsTgt, cri)
fns['bestGatesetVsTargetAnglesTable'] = (fn, validate_essential) fns['bestGatesetErrorGenTable'] = (fn, validate_essential)



Clone # 107
Distance between two fragments = 4
Clone size = 7
Source file "report/results.py"
The first line is 441
Source file "report/results.py"
The first line is 448
fns['fiducialListTable'] = (fn, validate_LsAndGerms) fns['prepStrListTable'] = (fn, validate_LsAndGerms)
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_gatestring_table(self.gatestring_lists['prep fiducials'], 'Preparation Fiducial')
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_gatestring_table(self.gatestring_lists['effect fiducials'], 'Measurement Fiducial')
fns['prepStrListTable'] = (fn, validate_LsAndGerms) fns['effectStrListTable'] = (fn, validate_LsAndGerms)



Clone # 108
Distance between two fragments = 1
Clone size = 7
Source file "report/results.py"
The first line is 2246
Source file "report/results.py"
The first line is 2669
printer = VerbosityPrinter.build_printer(verbosity) printer = VerbosityPrinter.build_printer(verbosity)
assert self._bEssentialResultsSet assert self._bEssentialResultsSet
self.confidence_level = confidenceLevel self.confidence_level = confidenceLevel
self._comm = comm self._comm = comm
v = verbosity v = verbosity
def tooltiptex(directive):
    return ''
def tooltiptext(directive):
    return ''



Clone # 109
Distance between two fragments = 3
Clone size = 7
Source file "report/html.py"
The first line is 172
Source file "report/html.py"
The first line is 129
if brackets:
    return (((('
')) + ('
 ') + ('')) + ('\n'.join(lines))) + ('
 
\n')
else:
    return (((('
')) + ('
') + ('')) + ('\n'.join(lines))) + ('
\n')
if brackets:
    return (((('
')) + ('
 ') + ('
')) + ('
'.join(lines))) + ('
 
\n')
else:
    return (((('
')) + ('
') + ('
')) + ('
'.join(lines))) + ('
\n')



Clone # 110
Distance between two fragments = 0
Clone size = 7
Source file "report/results.py"
The first line is 1855
Source file "report/results.py"
The first line is 3727
qtys['whackamole_plot_figures'] = whackamoleplots qtys['whackamole_plot_figures'] = whackamoleplots
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Merging into template file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex'))
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))



Clone # 111
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 2026
Source file "report/results.py"
The first line is 2294
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true"  )
qtys['settoggles']  +=  "\\toggle%s{goodnessSection}\n"  %  \
  ("true"  if  goodnessOfFitSection  else  "false")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false"  )



Clone # 112
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 2026
Source file "report/results.py"
The first line is 1553
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  =    "\\toggle%s{confidences}\n"  %  \
  ("false"  if  confidenceLevel  is  None  else  "true")
qtys['settoggles']  +=  "\\toggle%s{goodnessSection}\n"  %  \
  ("true"  if  goodnessOfFitSection  else  "false")
qtys['settoggles']  +=  "\\toggle%s{LsAndGermsSet}\n"  %  \
  ("true"  if  self._LsAndGermInfoSet  else  "false")



Clone # 113
Distance between two fragments = 4
Clone size = 7
Source file "report/results.py"
The first line is 296
Source file "report/results.py"
The first line is 280
s += '\n' s += ' .dataset -- the DataSet used to generate these results\n\n'
s += ' .parameters -- a dict of simulation parameters:\n' s += ' .gatesets -- a dictionary of GateSet objects w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'
s += ((' ') + ('\n '.join(list(self.parameters.keys())))) + ('\n') s += ((' ') + ('\n '.join(list(self.gatesets.keys())))) + ('\n')
s += '\n' s += '\n'
s += ' .options -- a container of display options:\n' s += ' .gatestring_lists -- a dict of GateString lists w/keys:\n'
s += ' ---------------------------------------------------------\n' s += ' ---------------------------------------------------------\n'



Clone # 114
Distance between two fragments = 4
Clone size = 7
Source file "report/reportables.py"
The first line is 98
Source file "report/reportables.py"
The first line is 82
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Gate quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Prep quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
df, f0 = confidenceRegionInfo.get_prep_fn_confidence_interval(fnOfPrep, prepLabel, eps, returnFnVal=True, verbosity=verbosity) df, f0 = confidenceRegionInfo.get_gate_fn_confidence_interval(fnOfGate, gateLabel, eps, returnFnVal=True, verbosity=verbosity)
return ReportableQty(f0, df) return ReportableQty(f0, df)



Clone # 115
Distance between two fragments = 0
Clone size = 7
Source file "report/results.py"
The first line is 2812
Source file "report/results.py"
The first line is 3508
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
printer.log((' -- %s plots (%d): ') % ((plotFnName, nPlots)), end='') printer.log((' -- %s plots (%d): ') % ((plotFnName, nPlots)), end='')



Clone # 116
Distance between two fragments = 0
Clone size = 7
Source file "report/results.py"
The first line is 2409
Source file "report/results.py"
The first line is 3508
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
printer.log((' -- %s plots (%d): ') % ((plotFnName, nPlots)), end='') printer.log((' -- %s plots (%d): ') % ((plotFnName, nPlots)), end='')



Clone # 117
Distance between two fragments = 3
Clone size = 7
Source file "report/generation.py"
The first line is 485
Source file "report/generation.py"
The first line is 407
for gl in gateLabels:
    if confidenceRegionInfo is None:
        rowData = ([gl]) + ([(qtys[('%s %s') % ((gl, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([gl]) + ([qtys[('%s %s') % ((gl, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
for l in effectLabels:
    if confidenceRegionInfo is None:
        rowData = ([l]) + ([(qtys[('%s effect %s') % ((l, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([l]) + ([qtys[('%s effect %s') % ((l, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
table.finish() table.finish()
return table return table



Clone # 118
Distance between two fragments = 3
Clone size = 7
Source file "report/generation.py"
The first line is 407
Source file "report/generation.py"
The first line is 352
for l in effectLabels:
    if confidenceRegionInfo is None:
        rowData = ([l]) + ([(qtys[('%s effect %s') % ((l, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([l]) + ([qtys[('%s effect %s') % ((l, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
for gl in gateLabels:
    if confidenceRegionInfo is None:
        rowData = ([gl]) + ([(qtys[('%s %s') % ((gl, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([gl]) + ([qtys[('%s %s') % ((gl, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
table.finish() table.finish()
return table return table



Clone # 119
Distance between two fragments = 0
Clone size = 9
Source file "report/results.py"
The first line is 3351
Source file "report/results.py"
The first line is 2734
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'



Clone # 120
Distance between two fragments = 0
Clone size = 9
Source file "report/results.py"
The first line is 1573
Source file "report/results.py"
The first line is 2734
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'
if confidenceLevel is not None:
    cri = self._get_confidence_region(confidenceLevel)
    qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)
    qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)
else:
    cri = None
    qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'
    qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'



Clone # 121
Distance between two fragments = 2
Clone size = 7
Source file "report/results.py"
The first line is 1837
Source file "report/results.py"
The first line is 1819
printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='') printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='')
fig = self.figures.get(('whack%sMoleBoxesSummed') % (germ[0]), verbosity=(printer) - (1)) fig = self.figures.get(('whack%sMoleBoxes') % (germ[0]), verbosity=(printer) - (1))
fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxesSummed.pdf') % (germ[0]))) fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxes.pdf') % (germ[0])))
whackamoleplots += '\n' whackamoleplots += '\n'
whackamoleplots += '\\begin{figure}\n' whackamoleplots += '\\begin{figure}\n'
whackamoleplots += '\\begin{center}\n' whackamoleplots += '\\begin{center}\n'



Clone # 122
Distance between two fragments = 0
Clone size = 7
Source file "report/results.py"
The first line is 3326
Source file "report/results.py"
The first line is 2719
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel



Clone # 123
Distance between two fragments = 0
Clone size = 7
Source file "report/results.py"
The first line is 1548
Source file "report/results.py"
The first line is 2719
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
if not self._LsAndGermInfoSet:
    debugAidsAppendix = False
    pixelPlotAppendix = False
    whackamoleAppendix = False
qtys = {} qtys = {}
qtys['title'] = title qtys['title'] = title
qtys['datasetLabel'] = datasetLabel qtys['datasetLabel'] = datasetLabel



Clone # 124
Distance between two fragments = 2
Clone size = 7
Source file "report/results.py"
The first line is 146
Source file "report/results.py"
The first line is 243
self.dataset = dataset self.dataset = dataset
self.parameters['objective'] = objective self.parameters['objective'] = objective
self.parameters['constrainToTP'] = constrainToTP self.parameters['constrainToTP'] = constrainToTP
if gatesetEstimate_noGaugeOpt is not None:
    self.gatesets['iteration estimates pre gauge opt'] = [gatesetEstimate_noGaugeOpt]
if gatesetsByL_noGaugeOpt is not None:
    self.gatesets['iteration estimates pre gauge opt'] = gatesetsByL_noGaugeOpt
self._bEssentialResultsSet = True self._bEssentialResultsSet = True



Clone # 125
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3640
Source file "report/plotting.py"
The first line is 3440
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 126
Distance between two fragments = 2
Clone size = 6
Source file "report/results.py"
The first line is 1665
Source file "report/results.py"
The first line is 2378
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
maxW, maxH = (6.5, 9.0) maxW, maxH = (4.0, 3.0)



Clone # 127
Distance between two fragments = 1
Clone size = 6
Source file "report/results.py"
The first line is 3457
Source file "report/results.py"
The first line is 2796
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptext((".figures['%s']") % (figkey))
    return fig



Clone # 128
Distance between two fragments = 1
Clone size = 6
Source file "report/results.py"
The first line is 2796
Source file "report/results.py"
The first line is 1680
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptext((".figures['%s']") % (figkey))
    return fig
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):
    fig = self.figures.get(figkey, verbosity=v)
    fig.save_to(_os.path.join(report_dir, D, figFilenm))
    qtys[figkey] = incgr(figFilenm, W, H)
    qtys[('tt_') + (figkey)] = tooltiptex((".figures['%s']") % (figkey))
    return fig



Clone # 129
Distance between two fragments = 3
Clone size = 6
Source file "report/plotting.py"
The first line is 526
Source file "report/plotting.py"
The first line is 491
prev_cmap = cmaps[-2] cmap = cmaps[0]
N = cmap.N N = cmap.N
low_val, high_val = ranges[-1] low_val, high_val = ranges[0]
input_values = _np.linspace(0.0, 1.0, N) input_values = _np.linspace(0.0, 1.0, N)
scaled_values = _np.linspace(low_val, high_val, N) scaled_values = _np.linspace(low_val, high_val, N)
colors = cmap(input_values) colors = cmap(input_values)



Clone # 130
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 604
Source file "report/results.py"
The first line is 598
fns['bestGatesetErrGenBoxTable'] = (fn, validate_essential) fns['targetGatesBoxTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    return _generation.get_gateset_eigenval_table(gsBest, gsTgt, 'bestEvalPolarPlt')
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    return _generation.get_gates_vs_target_err_gen_boxes_table(gsBest, gsTgt, 'bestErrgenBoxes')
fns['bestGatesetEvalTable'] = (fn, validate_essential) fns['bestGatesetErrGenBoxTable'] = (fn, validate_essential)



Clone # 131
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 610
Source file "report/results.py"
The first line is 598
fns['bestGatesetEvalTable'] = (fn, validate_essential) fns['targetGatesBoxTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    return _generation.get_gateset_relative_eigenval_table(gsBest, gsTgt, 'bestRelEvalPolarPlt')
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    return _generation.get_gates_vs_target_err_gen_boxes_table(gsBest, gsTgt, 'bestErrgenBoxes')
fns['bestGatesetRelEvalTable'] = (fn, validate_essential) fns['bestGatesetErrGenBoxTable'] = (fn, validate_essential)



Clone # 132
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 494
Source file "report/results.py"
The first line is 500
fns['bestGatesetGatesTable'] = (fn, validate_essential) fns['bestGatesetChoiTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_choi_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_decomp_table(gsBest, cri)
fns['bestGatesetChoiTable'] = (fn, validate_essential) fns['bestGatesetDecompTable'] = (fn, validate_essential)



Clone # 133
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 468
Source file "report/results.py"
The first line is 482
fns['germList2ColTable'] = (fn, validate_LsAndGerms) fns['bestGatesetSpamBriefTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_parameters_table(gsBest, cri)
fns['bestGatesetSpamTable'] = (fn, validate_essential) fns['bestGatesetSpamParametersTable'] = (fn, validate_essential)



Clone # 134
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 468
Source file "report/results.py"
The first line is 488
fns['germList2ColTable'] = (fn, validate_LsAndGerms) fns['bestGatesetSpamParametersTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_gates_table(gsBest, cri)
fns['bestGatesetSpamTable'] = (fn, validate_essential) fns['bestGatesetGatesTable'] = (fn, validate_essential)



Clone # 135
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 482
Source file "report/results.py"
The first line is 500
fns['bestGatesetSpamBriefTable'] = (fn, validate_essential) fns['bestGatesetChoiTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_parameters_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_decomp_table(gsBest, cri)
fns['bestGatesetSpamParametersTable'] = (fn, validate_essential) fns['bestGatesetDecompTable'] = (fn, validate_essential)



Clone # 136
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 543
Source file "report/results.py"
The first line is 512
fns['bestGatesetErrorGenTable'] = (fn, validate_essential) fns['bestGatesetRotnAxisTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_angles_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_eigenval_table(gsBest, gsTgt, cri)
fns['bestGatesetVsTargetAnglesTable'] = (fn, validate_essential) fns['bestGatesetEvalTable'] = (fn, validate_essential)



Clone # 137
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 468
Source file "report/results.py"
The first line is 494
fns['germList2ColTable'] = (fn, validate_LsAndGerms) fns['bestGatesetGatesTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_choi_table(gsBest, cri)
fns['bestGatesetSpamTable'] = (fn, validate_essential) fns['bestGatesetChoiTable'] = (fn, validate_essential)



Clone # 138
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 536
Source file "report/results.py"
The first line is 512
fns['bestGatesetSpamVsTargetTable'] = (fn, validate_essential) fns['bestGatesetRotnAxisTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_err_gen_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_eigenval_table(gsBest, gsTgt, cri)
fns['bestGatesetErrorGenTable'] = (fn, validate_essential) fns['bestGatesetEvalTable'] = (fn, validate_essential)



Clone # 139
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 468
Source file "report/results.py"
The first line is 500
fns['germList2ColTable'] = (fn, validate_LsAndGerms) fns['bestGatesetChoiTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_table(gsBest, cri)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_decomp_table(gsBest, cri)
fns['bestGatesetSpamTable'] = (fn, validate_essential) fns['bestGatesetDecompTable'] = (fn, validate_essential)



Clone # 140
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 530
Source file "report/results.py"
The first line is 512
fns['bestGatesetVsTargetTable'] = (fn, validate_essential) fns['bestGatesetRotnAxisTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_spam_vs_target_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_eigenval_table(gsBest, gsTgt, cri)
fns['bestGatesetSpamVsTargetTable'] = (fn, validate_essential) fns['bestGatesetEvalTable'] = (fn, validate_essential)



Clone # 141
Distance between two fragments = 3
Clone size = 7
Source file "report/results.py"
The first line is 543
Source file "report/results.py"
The first line is 524
fns['bestGatesetErrorGenTable'] = (fn, validate_essential) fns['bestGatesetClosestUnitaryTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_angles_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_table(gsBest, gsTgt, cri)
fns['bestGatesetVsTargetAnglesTable'] = (fn, validate_essential) fns['bestGatesetVsTargetTable'] = (fn, validate_essential)



Clone # 142
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 524
Source file "report/results.py"
The first line is 512
fns['bestGatesetClosestUnitaryTable'] = (fn, validate_essential) fns['bestGatesetRotnAxisTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gates_vs_target_table(gsBest, gsTgt, cri)
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_eigenval_table(gsBest, gsTgt, cri)
fns['bestGatesetVsTargetTable'] = (fn, validate_essential) fns['bestGatesetEvalTable'] = (fn, validate_essential)



Clone # 143
Distance between two fragments = 4
Clone size = 7
Source file "report/results.py"
The first line is 441
Source file "report/results.py"
The first line is 455
fns['fiducialListTable'] = (fn, validate_LsAndGerms) fns['effectStrListTable'] = (fn, validate_LsAndGerms)
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_gatestring_table(self.gatestring_lists['prep fiducials'], 'Preparation Fiducial')
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_gatestring_table(self.gatestring_lists['germs'], 'Germ')
fns['prepStrListTable'] = (fn, validate_LsAndGerms) fns['germListTable'] = (fn, validate_LsAndGerms)



Clone # 144
Distance between two fragments = 2
Clone size = 6
Source file "report/plotting.py"
The first line is 2755
Source file "report/plotting.py"
The first line is 1641
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  0  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  max_abs  if  M  is  None  else  M



Clone # 145
Distance between two fragments = 3
Clone size = 6
Source file "report/plotting.py"
The first line is 2755
Source file "report/plotting.py"
The first line is 2637
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  +max_abs  if  M  is  None  else  M



Clone # 146
Distance between two fragments = 3
Clone size = 6
Source file "report/plotting.py"
The first line is 2755
Source file "report/plotting.py"
The first line is 3118
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  +max_abs  if  M  is  None  else  M



Clone # 147
Distance between two fragments = 3
Clone size = 6
Source file "report/plotting.py"
The first line is 2755
Source file "report/plotting.py"
The first line is 2937
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  +max_abs  if  M  is  None  else  M



Clone # 148
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 2637
Source file "report/plotting.py"
The first line is 3118
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  +max_abs  if  M  is  None  else  M



Clone # 149
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 2637
Source file "report/plotting.py"
The first line is 2937
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  -max_abs  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m
M  =  +max_abs  if  M  is  None  else  M M  =  +max_abs  if  M  is  None  else  M



Clone # 150
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3640
Source file "report/plotting.py"
The first line is 3267
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 151
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3640
Source file "report/plotting.py"
The first line is 1263
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 152
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3640
Source file "report/plotting.py"
The first line is 828
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 153
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3440
Source file "report/plotting.py"
The first line is 3267
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 154
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3440
Source file "report/plotting.py"
The first line is 1263
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 155
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3440
Source file "report/plotting.py"
The first line is 828
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 156
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3267
Source file "report/plotting.py"
The first line is 1263
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 157
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 3267
Source file "report/plotting.py"
The first line is 828
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 158
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 1263
Source file "report/plotting.py"
The first line is 828
rptFig = _ReportFigure(axes) rptFig = _ReportFigure(axes)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
if save_to is not None:
    if len(save_to) > 0:
        _plt.savefig(save_to, bbox_extra_artists=(axes), bbox_inches='tight')
    if fig is not None:
        _plt.close(fig)
return rptFig return rptFig



Clone # 159
Distance between two fragments = 4
Clone size = 7
Source file "report/plotting.py"
The first line is 2081
Source file "report/plotting.py"
The first line is 1950
with  printer.progress_logging(1):
  for  i,sigma  in  enumerate(gateStrings):
    printer.show_progress(i,  len(gateStrings)  -  1,  prefix="---  Computing  gateset  for  string  ",  suffix="---")
    directMLEGSTgatesets[sigma]  =  direct_mlgst_gateset(  sigma,  "GsigmaLbl",  dataset,  specs,  targetGateset,
      svdTruncateTo,  minProbClip,  probClipInterval,  verbosity)
with  printer.progress_logging(1):
  for  i,sigma  in  enumerate(gateStrings):
    printer.show_progress(i,  len(gateStrings)  -  1,  prefix="---  Computing  gateset  for  string-",  suffix='---')
    directLSGSTgatesets[sigma]  =  direct_mc2gst_gateset(  sigma,  "GsigmaLbl",  dataset,  specs,  targetGateset,
      svdTruncateTo,  minProbClipForWeighting,
   
  probClipInterval,  verbosity)
return directMLEGSTgatesets return directLSGSTgatesets



Clone # 160
Distance between two fragments = 4
Clone size = 6
Source file "report/reportables.py"
The first line is 734
Source file "report/reportables.py"
The first line is 741
key = ('%s Frobenius diff') % (gateLabel) key = ('%s Jamiolkowski trace dist') % (gateLabel)
possible_qtys.append(key) possible_qtys.append(key)
if key in qtynames:
    def fro_diff(gate):
        return _tools.frobeniusdist(gate, gateset2.gates[gateLabel])
    ret[key] = _getGateQuantity(fro_diff, gateset1, gateLabel, eps, confidenceRegionInfo)
if key in qtynames:
    def jt_diff(gate):
        return _tools.jtracedist(gate, gateset2.gates[gateLabel])
    ret[key] = _getGateQuantity(jt_diff, gateset1, gateLabel, eps, confidenceRegionInfo)
key = ('%s Jamiolkowski trace dist') % (gateLabel) key = ('%s diamond norm') % (gateLabel)
possible_qtys.append(key) possible_qtys.append(key)



Clone # 161
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 3727
Source file "report/results.py"
The first line is 2549
qtys['whackamole_plot_figures'] = whackamoleplots qtys['whackamole_plot_slides'] = whackamoleplots
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Merging into template file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))



Clone # 162
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 1855
Source file "report/results.py"
The first line is 2549
qtys['whackamole_plot_figures'] = whackamoleplots qtys['whackamole_plot_slides'] = whackamoleplots
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Merging into template file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))



Clone # 163
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 304
Source file "report/table.py"
The first line is 188
s += '\n' s += '\n'
s += "NOTE: passing 'tips=True' to create_full_report_pdf or\n" s += 'Access row and column data by indexing into this object\n'
s += ' create_brief_report_pdf will add markup to the resulting\n' s += ' as a dictionary using the column header followed by the\n'
s += ' PDF indicating how tables and figures in the PDF correspond\n' s += ' value of the first element of each row, i.e.,\n'
s += ' to the values of .tables[ ] and .figures[ ] listed above.\n' s += ' tableObj[][].\n'
return s return s



Clone # 164
Distance between two fragments = 3
Clone size = 7
Source file "report/reportables.py"
The first line is 148
Source file "report/reportables.py"
The first line is 131
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Spam quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('GateSet quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
df, f0 = confidenceRegionInfo.get_spam_fn_confidence_interval(fnOfSpamVecs, eps, returnFnVal=True, verbosity=verbosity) df, f0 = confidenceRegionInfo.get_gateset_fn_confidence_interval(fnOfGateSet, eps, returnFnVal=True, verbosity=verbosity)
return ReportableQty(f0, df) return ReportableQty(f0, df)



Clone # 165
Distance between two fragments = 0
Clone size = 6
Source file "report/plotting.py"
The first line is 1229
Source file "report/plotting.py"
The first line is 807
if title is not None:
    axes.set_title(title, fontsize=(ticSize) + (4))
if title is not None:
    axes.set_title(title, fontsize=(ticSize) + (4))
if xlabel is not None:
    axes.set_xlabel(xlabel, fontsize=(ticSize) + (4))
if xlabel is not None:
    axes.set_xlabel(xlabel, fontsize=(ticSize) + (4))
if ylabel is not None:
    axes.set_ylabel(ylabel, fontsize=(ticSize) + (4))
if ylabel is not None:
    axes.set_ylabel(ylabel, fontsize=(ticSize) + (4))



Clone # 166
Distance between two fragments = 4
Clone size = 7
Source file "report/reportables.py"
The first line is 115
Source file "report/reportables.py"
The first line is 98
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Effect quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Gate quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
df, f0 = confidenceRegionInfo.get_effect_fn_confidence_interval(fnOfEffect, effectLabel, eps, returnFnVal=True, verbosity=verbosity) df, f0 = confidenceRegionInfo.get_prep_fn_confidence_interval(fnOfPrep, prepLabel, eps, returnFnVal=True, verbosity=verbosity)
return ReportableQty(f0, df) return ReportableQty(f0, df)



Clone # 167
Distance between two fragments = 4
Clone size = 7
Source file "report/reportables.py"
The first line is 115
Source file "report/reportables.py"
The first line is 82
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Effect quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
if gateset.frobeniusdist(confidenceRegionInfo.get_gateset()) > 1e-06:
    raise ValueError(('Prep quantity confidence region is being requested for ') + ('a different gateset than the given confidenceRegionInfo'))
df, f0 = confidenceRegionInfo.get_effect_fn_confidence_interval(fnOfEffect, effectLabel, eps, returnFnVal=True, verbosity=verbosity) df, f0 = confidenceRegionInfo.get_gate_fn_confidence_interval(fnOfGate, gateLabel, eps, returnFnVal=True, verbosity=verbosity)
return ReportableQty(f0, df) return ReportableQty(f0, df)



Clone # 168
Distance between two fragments = 0
Clone size = 6
Source file "report/results.py"
The first line is 1857
Source file "report/results.py"
The first line is 2141
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Merging into template file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex'))
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))



Clone # 169
Distance between two fragments = 0
Clone size = 6
Source file "report/results.py"
The first line is 1693
Source file "report/results.py"
The first line is 3508
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))
if self.parameters['objective'] == 'chi2':
    plotFnName, plotFnLatex = ('Chi2', '$\\chi^2$')
elif self.parameters['objective'] == 'logl':
    plotFnName, plotFnLatex = ('LogL', '$\\log(\\mathcal{L})$')
else:
    raise ValueError(('Invalid objective value: %s') % (self.parameters['objective']))



Clone # 170
Distance between two fragments = 0
Clone size = 6
Source file "report/results.py"
The first line is 2364
Source file "report/results.py"
The first line is 3412
for key in tables_to_compute:
    qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
    qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))
for key in tables_to_compute:
    qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
    qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))



Clone # 171
Distance between two fragments = 0
Clone size = 6
Source file "report/results.py"
The first line is 2085
Source file "report/results.py"
The first line is 3412
for key in tables_to_compute:
    qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
    qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))
for key in tables_to_compute:
    qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
    qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))



Clone # 172
Distance between two fragments = 4
Clone size = 6
Source file "report/reportables.py"
The first line is 324
Source file "report/reportables.py"
The first line is 328
def decomp_angle(gate):
    decomp = _tools.decompose_gate_matrix(gate)
    return decomp.get('pi rotations', 0)
def decomp_decay_diag(gate):
    decomp = _tools.decompose_gate_matrix(gate)
    return decomp.get('decay of diagonal rotation terms', 0)
def decomp_decay_diag(gate):
    decomp = _tools.decompose_gate_matrix(gate)
    return decomp.get('decay of diagonal rotation terms', 0)
def decomp_decay_offdiag(gate):
    decomp = _tools.decompose_gate_matrix(gate)
    return decomp.get('decay of off diagonal rotation terms', 0)



Clone # 173
Distance between two fragments = 4
Clone size = 6
Source file "report/plotting.py"
The first line is 538
Source file "report/plotting.py"
The first line is 497
for  color,  value  in  zip(colors[1:],  scaled_values[1:]):
  r,  g,  b,  a  =  color
  red_list.append((value,  r,  r))
  green_list.append((value,  g,  g))
  blue_list.append((value,  b,  b))
  alpha_list.append((value,  a,  a))
for  color,  value  in  zip(colors[:-1],  scaled_values[:-1]):
  r,  g,  b,  a  =  color
  red_list.append((value,  r,  r))
  green_list.append((value,  g,  g))
  blue_list.append((value,  b,  b))
  alpha_list.append((value,  a,  a))



Clone # 174
Distance between two fragments = 2
Clone size = 6
Source file "report/plotting.py"
The first line is 517
Source file "report/plotting.py"
The first line is 497
for  color,  value  in  zip(colors[1:-1],  scaled_values[1:-1]):
  r,  g,  b,  a  =  color
  red_list.append((value,  r,  r))
  green_list.append((value,  g,  g))
  blue_list.append((value,  b,  b))
  alpha_list.append((value,  a,  a))
for  color,  value  in  zip(colors[:-1],  scaled_values[:-1]):
  r,  g,  b,  a  =  color
  red_list.append((value,  r,  r))
  green_list.append((value,  g,  g))
  blue_list.append((value,  b,  b))
  alpha_list.append((value,  a,  a))



Clone # 175
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 1095
Source file "report/results.py"
The first line is 1091
ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetDecompTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetVsTargetTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetRotnAxisTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetErrorGenTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 176
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 1095
Source file "report/results.py"
The first line is 1083
ret[('best%sGatesetClosestUnitaryTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetVsTargetTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetSpamParametersTable') % (gaugeKey)] = _generation.get_blank_table()
ret[('best%sGatesetErrorGenTable') % (gaugeKey)] = _generation.get_blank_table() ret[('best%sGatesetGatesTable') % (gaugeKey)] = _generation.get_blank_table()



Clone # 177
Distance between two fragments = 1
Clone size = 6
Source file "report/results.py"
The first line is 2528
Source file "report/results.py"
The first line is 1837
printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='') printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='')
fig = self.figures.get(('whack%sMoleBoxesSummed') % (germ[0]), verbosity=(printer) - (1)) fig = self.figures.get(('whack%sMoleBoxesSummed') % (germ[0]), verbosity=(printer) - (1))
fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxesSummed.pdf') % (germ[0]))) fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxesSummed.pdf') % (germ[0])))
whackamoleplots += '\n' whackamoleplots += '\n'
whackamoleplots += '\\begin{frame}\n' whackamoleplots += '\\begin{figure}\n'



Clone # 178
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 2528
Source file "report/results.py"
The first line is 1819
printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='') printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='')
fig = self.figures.get(('whack%sMoleBoxesSummed') % (germ[0]), verbosity=(printer) - (1)) fig = self.figures.get(('whack%sMoleBoxes') % (germ[0]), verbosity=(printer) - (1))
fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxesSummed.pdf') % (germ[0]))) fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxes.pdf') % (germ[0])))
whackamoleplots += '\n' whackamoleplots += '\n'
whackamoleplots += '\\begin{frame}\n' whackamoleplots += '\\begin{figure}\n'



Clone # 179
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 2507
Source file "report/results.py"
The first line is 1837
printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='') printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='')
fig = self.figures.get(('whack%sMoleBoxes') % (germ[0]), verbosity=(printer) - (1)) fig = self.figures.get(('whack%sMoleBoxesSummed') % (germ[0]), verbosity=(printer) - (1))
fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxes.pdf') % (germ[0]))) fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxesSummed.pdf') % (germ[0])))
whackamoleplots += '\n' whackamoleplots += '\n'
whackamoleplots += '\\begin{frame}\n' whackamoleplots += '\\begin{figure}\n'



Clone # 180
Distance between two fragments = 1
Clone size = 6
Source file "report/results.py"
The first line is 2507
Source file "report/results.py"
The first line is 1819
printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='') printer.show_progress(i, (len(len1Germs)) - (1), prefix='', end='')
fig = self.figures.get(('whack%sMoleBoxes') % (germ[0]), verbosity=(printer) - (1)) fig = self.figures.get(('whack%sMoleBoxes') % (germ[0]), verbosity=(printer) - (1))
fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxes.pdf') % (germ[0]))) fig.save_to(_os.path.join(report_dir, D, ('whack%sMoleBoxes.pdf') % (germ[0])))
whackamoleplots += '\n' whackamoleplots += '\n'
whackamoleplots += '\\begin{frame}\n' whackamoleplots += '\\begin{figure}\n'



Clone # 181
Distance between two fragments = 0
Clone size = 6
Source file "report/results.py"
The first line is 1139
Source file "report/results.py"
The first line is 1115
baseStrs = [] baseStrs = []
fullDict = self.parameters['L,germ tuple base string dict'] fullDict = self.parameters['L,germ tuple base string dict']
for L in self.parameters['max length list']:
    for germ in self.gatestring_lists['germs']:
        if fullDict[(L, germ)] not in baseStrs:
            baseStrs.append(fullDict[(L, germ)])
for L in self.parameters['max length list']:
    for germ in self.gatestring_lists['germs']:
        if fullDict[(L, germ)] not in baseStrs:
            baseStrs.append(fullDict[(L, germ)])



Clone # 182
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2099
Source file "report/results.py"
The first line is 2783
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 183
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2099
Source file "report/results.py"
The first line is 1665
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 184
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2783
Source file "report/results.py"
The first line is 3442
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 185
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2783
Source file "report/results.py"
The first line is 2378
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 186
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2783
Source file "report/results.py"
The first line is 1665
printer.log('*** Generating plots ***') printer.log('*** Generating plots ***')
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False
if _matplotlib.is_interactive():
    _matplotlib.pyplot.ioff()
    bWasInteractive = True
else:
    bWasInteractive = False



Clone # 187
Distance between two fragments = 4
Clone size = 5
Source file "report/results.py"
The first line is 2892
Source file "report/results.py"
The first line is 1809
allGateStrings = self.gatestring_lists['all'] highestL = Ls[-1]
hammerWeight = 10.0 hammerWeight = 10.0
len1Germs = [g for g in self.gatestring_lists['germs'] if len(g) == 1] len1Germs = [g for g in self.gatestring_lists['germs'] if len(g) == 1]
printer.log((' -- Whack-a-mole plots (%d): ') % ((2) * (len(len1Germs))), end='') printer.log((' -- Whack-a-mole plots (%d): ') % ((2) * (len(len1Germs))), end='')



Clone # 188
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 2892
Source file "report/results.py"
The first line is 2497
highestL = Ls[-1] highestL = self.parameters['max length list'][-1]
allGateStrings = self.gatestring_lists['all'] allGateStrings = self.gatestring_lists['all']
hammerWeight = 10.0 hammerWeight = 10.0
len1Germs = [g for g in self.gatestring_lists['germs'] if len(g) == 1] len1Germs = [g for g in self.gatestring_lists['germs'] if len(g) == 1]
printer.log((' -- Whack-a-mole plots (%d): ') % ((2) * (len(len1Germs))), end='') printer.log((' -- Whack-a-mole plots (%d): ') % ((2) * (len(len1Germs))), end='')



Clone # 189
Distance between two fragments = 4
Clone size = 5
Source file "report/results.py"
The first line is 1809
Source file "report/results.py"
The first line is 2498
highestL = Ls[-1] allGateStrings = self.gatestring_lists['all']
hammerWeight = 10.0 hammerWeight = 10.0
len1Germs = [g for g in self.gatestring_lists['germs'] if len(g) == 1] len1Germs = [g for g in self.gatestring_lists['germs'] if len(g) == 1]
printer.log((' -- Whack-a-mole plots (%d): ') % ((2) * (len(len1Germs))), end='') printer.log((' -- Whack-a-mole plots (%d): ') % ((2) * (len(len1Germs))), end='')



Clone # 190
Distance between two fragments = 0
Clone size = 5
Source file "report/plotting.py"
The first line is 2509
Source file "report/plotting.py"
The first line is 1482
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof) stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$') return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 191
Distance between two fragments = 0
Clone size = 5
Source file "report/plotting.py"
The first line is 2509
Source file "report/plotting.py"
The first line is 1377
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof) stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$') return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 192
Distance between two fragments = 0
Clone size = 5
Source file "report/plotting.py"
The first line is 2348
Source file "report/plotting.py"
The first line is 1482
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof) stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$') return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 193
Distance between two fragments = 0
Clone size = 5
Source file "report/plotting.py"
The first line is 2348
Source file "report/plotting.py"
The first line is 1377
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof) stdcmap = StdColormapFactory('linlog', n_boxes=n_boxes, linlg_pcntle=linlg_pcntle, dof=dof)
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$') return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')



Clone # 194
Distance between two fragments = 3
Clone size = 5
Source file "report/results.py"
The first line is 612
Source file "report/results.py"
The first line is 606
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    return _generation.get_gateset_relative_eigenval_table(gsBest, gsTgt, 'bestRelEvalPolarPlt')
def fn(key, confidenceLevel, vb):
    gsTgt, gsBest = setup()
    return _generation.get_gateset_eigenval_table(gsBest, gsTgt, 'bestEvalPolarPlt')
fns['bestGatesetRelEvalTable'] = (fn, validate_essential) fns['bestGatesetEvalTable'] = (fn, validate_essential)



Clone # 195
Distance between two fragments = 4
Clone size = 5
Source file "report/results.py"
The first line is 590
Source file "report/results.py"
The first line is 411
fns['progressTable'] = (fn, validate_LsAndGerms) fns['targetSpamBriefTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, _ = setup()
    return _generation.get_gateset_gate_boxes_table(gsTgt, 'targetGatesBoxes')
def fn(key, confidenceLevel, vb):
    gsTgt, _ = setup()
    return _generation.get_unitary_gateset_gates_table(gsTgt, None)



Clone # 196
Distance between two fragments = 4
Clone size = 6
Source file "report/results.py"
The first line is 399
Source file "report/results.py"
The first line is 411
fns['blankTable'] = (fn, validate_none) fns['targetSpamBriefTable'] = (fn, validate_essential)
def fn(key, confidenceLevel, vb):
    gsTgt, _ = setup()
    return _generation.get_gateset_spam_table(gsTgt, None)
def fn(key, confidenceLevel, vb):
    gsTgt, _ = setup()
    return _generation.get_unitary_gateset_gates_table(gsTgt, None)
fns['targetSpamTable'] = (fn, validate_essential) fns['targetGatesTable'] = (fn, validate_essential)



Clone # 197
Distance between two fragments = 3
Clone size = 5
Source file "report/results.py"
The first line is 478
Source file "report/results.py"
The first line is 508
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_spam_table(gsBest, cri, False)
def fn(key, confidenceLevel, vb):
    _, gsBest = setup()
    cri = self._get_confidence_region(confidenceLevel)
    return _generation.get_gateset_rotn_axis_table(gsBest, cri, True)
fns['bestGatesetSpamBriefTable'] = (fn, validate_essential) fns['bestGatesetRotnAxisTable'] = (fn, validate_essential)



Clone # 198
Distance between two fragments = 3
Clone size = 6
Source file "report/results.py"
The first line is 450
Source file "report/results.py"
The first line is 457
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_gatestring_table(self.gatestring_lists['effect fiducials'], 'Measurement Fiducial')
def fn(key, confidenceLevel, vb):
    setup()
    return _generation.get_gatestring_table(self.gatestring_lists['germs'], 'Germ')
fns['effectStrListTable'] = (fn, validate_LsAndGerms) fns['germListTable'] = (fn, validate_LsAndGerms)



Clone # 199
Distance between two fragments = 4
Clone size = 5
Source file "report/plotting.py"
The first line is 1641
Source file "report/plotting.py"
The first line is 2637
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  0  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m



Clone # 200
Distance between two fragments = 4
Clone size = 5
Source file "report/plotting.py"
The first line is 1641
Source file "report/plotting.py"
The first line is 3118
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  0  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m



Clone # 201
Distance between two fragments = 4
Clone size = 5
Source file "report/plotting.py"
The first line is 1641
Source file "report/plotting.py"
The first line is 2937
xvals, yvals, subMxs, _, _ = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, True) xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ]) max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])
m  =  0  if  m  is  None  else  m m  =  -max_abs  if  m  is  None  else  m



Clone # 202
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 1967
Source file "report/results.py"
The first line is 2669
printer = VerbosityPrinter.build_printer(verbosity) printer = VerbosityPrinter.build_printer(verbosity)
assert self._bEssentialResultsSet assert self._bEssentialResultsSet
self.confidence_level = confidenceLevel self.confidence_level = confidenceLevel
self._comm = comm self._comm = comm
v = verbosity v = verbosity



Clone # 203
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 1967
Source file "report/results.py"
The first line is 2246
printer = VerbosityPrinter.build_printer(verbosity) printer = VerbosityPrinter.build_printer(verbosity)
assert self._bEssentialResultsSet assert self._bEssentialResultsSet
self.confidence_level = confidenceLevel self.confidence_level = confidenceLevel
self._comm = comm self._comm = comm
v = verbosity v = verbosity



Clone # 204
Distance between two fragments = 4
Clone size = 5
Source file "report/plotting.py"
The first line is 3426
Source file "report/plotting.py"
The first line is 3417
r = _np.absolute(rel_evals10) r = _np.absolute(target_evals)
theta = _np.angle(rel_evals10) theta = _np.angle(target_evals)
axes.plot(theta, r, linestyle='None', marker='o', color='g', markersize=5) axes.plot(theta, r, linestyle='None', marker='o', color='k', markersize=8)
r = _np.absolute(rel_evals) r = _np.absolute(evals)
theta = _np.angle(rel_evals) theta = _np.angle(evals)



Clone # 205
Distance between two fragments = 2
Clone size = 5
Source file "report/generation.py"
The first line is 802
Source file "report/generation.py"
The first line is 720
gateLabels = list(gateset.gates.keys()) gateLabels = list(gateset.gates.keys())
colHeadings = ('Gate', 'Relative Evals', 'Polar Plot') colHeadings = ('Gate', 'Eigenvalues', 'Polar Plot')
formatters = ([None]) * (3) formatters = ([None]) * (3)
qtyNames = ('relative eigenvalues') qtyNames = ('eigenvalues')
qtys_to_compute = [('%s %s') % ((gl, qty)) for qty in qtyNames for gl in gateLabels ] qtys_to_compute = [('%s %s') % ((gl, qty)) for qty in qtyNames for gl in gateLabels ]



Clone # 206
Distance between two fragments = 4
Clone size = 5
Source file "report/reportables.py"
The first line is 485
Source file "report/reportables.py"
The first line is 447
closestU_qtys[('%s closest unitary choi matrix') % (label)] = closeUJMxQty gate_qtys[('%s choi trace') % (label)] = choiTrQty
closestU_qtys[('%s closest unitary decomposition') % (label)] = decompQty gate_qtys[('%s decomposition') % (label)] = decompQty
for qtyname in qtynames:
    if qtyname in closestU_qtys:
        ret[qtyname] = closestU_qtys[qtyname]
for qtyname in qtynames:
    if qtyname in gate_qtys:
        ret[qtyname] = gate_qtys[qtyname]



Clone # 207
Distance between two fragments = 2
Clone size = 5
Source file "report/results.py"
The first line is 953
Source file "report/results.py"
The first line is 890
noConfidenceLevelDependence(confidenceLevel) noConfidenceLevelDependence(confidenceLevel)
gateLabel = _re.match(expr7, key).group(1) gateLabel = _re.match(expr4, key).group(1)
gate = self.gatesets['final estimate'].gates[gateLabel] gate = self.gatesets['final estimate'].gates[gateLabel]
target_gate = self.gatesets['target'].gates[gateLabel] targetGate = self.gatesets['target'].gates[gateLabel]
basisNm = self.gatesets['final estimate'].get_basis_name() basisNm = self.gatesets['final estimate'].get_basis_name()



Clone # 208
Distance between two fragments = 0
Clone size = 5
Source file "report/ppt.py"
The first line is 211
Source file "report/latex.py"
The first line is 223
if isinstance(el, basestring):
    return el
if isinstance(el, basestring):
    return el
if type(el) in (int, _np.int64):
    return ('%d') % (el)
if type(el) in (int, _np.int64):
    return ('%d') % (el)
if (el is None) or (_np.isnan(el)):
    return '--'
if (el is None) or (_np.isnan(el)):
    return '--'



Clone # 209
Distance between two fragments = 4
Clone size = 5
Source file "report/results.py"
The first line is 3727
Source file "report/results.py"
The first line is 2925
qtys['whackamole_plot_figures'] = whackamoleplots qtys['whackamole_plot_slides'] = whackamoleplots
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Assembling PPT file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainPPTFilename = _os.path.join(report_dir, (report_base) + ('.pptx'))



Clone # 210
Distance between two fragments = 3
Clone size = 5
Source file "report/results.py"
The first line is 2549
Source file "report/results.py"
The first line is 2925
qtys['whackamole_plot_slides'] = whackamoleplots qtys['whackamole_plot_slides'] = whackamoleplots
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Assembling PPT file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainPPTFilename = _os.path.join(report_dir, (report_base) + ('.pptx'))



Clone # 211
Distance between two fragments = 4
Clone size = 5
Source file "report/results.py"
The first line is 1855
Source file "report/results.py"
The first line is 2925
qtys['whackamole_plot_figures'] = whackamoleplots qtys['whackamole_plot_slides'] = whackamoleplots
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Assembling PPT file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainPPTFilename = _os.path.join(report_dir, (report_base) + ('.pptx'))



Clone # 212
Distance between two fragments = 4
Clone size = 5
Source file "report/results.py"
The first line is 304
Source file "report/results.py"
The first line is 277
s += '\n' s += '\n'
s += "NOTE: passing 'tips=True' to create_full_report_pdf or\n" s += 'I can create reports for you directly, via my create_XXX\n'
s += ' create_brief_report_pdf will add markup to the resulting\n' s += 'functions, or you can query me for result data via members:\n\n'
s += ' PDF indicating how tables and figures in the PDF correspond\n' s += ' .dataset -- the DataSet used to generate these results\n\n'
s += ' to the values of .tables[ ] and .figures[ ] listed above.\n' s += ' .gatesets -- a dictionary of GateSet objects w/keys:\n'



Clone # 213
Distance between two fragments = 4
Clone size = 5
Source file "report/table.py"
The first line is 188
Source file "report/results.py"
The first line is 277
s += '\n' s += '\n'
s += 'Access row and column data by indexing into this object\n' s += 'I can create reports for you directly, via my create_XXX\n'
s += ' as a dictionary using the column header followed by the\n' s += 'functions, or you can query me for result data via members:\n\n'
s += ' value of the first element of each row, i.e.,\n' s += ' .dataset -- the DataSet used to generate these results\n\n'
s += ' tableObj[][].\n' s += ' .gatesets -- a dictionary of GateSet objects w/keys:\n'



Clone # 214
Distance between two fragments = 2
Clone size = 5
Source file "report/results.py"
The first line is 2141
Source file "report/results.py"
The first line is 2551
if bWasInteractive:
    _matplotlib.pyplot.ion()
if bWasInteractive:
    _matplotlib.pyplot.ion()
printer.log('*** Merging into template file ***') printer.log('*** Merging into template file ***')
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex')) mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex')) pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))



Clone # 215
Distance between two fragments = 3
Clone size = 5
Source file "report/generation.py"
The first line is 485
Source file "report/generation.py"
The first line is 396
for gl in gateLabels:
    if confidenceRegionInfo is None:
        rowData = ([gl]) + ([(qtys[('%s %s') % ((gl, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([gl]) + ([qtys[('%s %s') % ((gl, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
for l in prepLabels:
    if confidenceRegionInfo is None:
        rowData = ([l]) + ([(qtys[('%s prep %s') % ((l, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([l]) + ([qtys[('%s prep %s') % ((l, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)



Clone # 216
Distance between two fragments = 3
Clone size = 5
Source file "report/generation.py"
The first line is 352
Source file "report/generation.py"
The first line is 396
for gl in gateLabels:
    if confidenceRegionInfo is None:
        rowData = ([gl]) + ([(qtys[('%s %s') % ((gl, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([gl]) + ([qtys[('%s %s') % ((gl, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)
for l in prepLabels:
    if confidenceRegionInfo is None:
        rowData = ([l]) + ([(qtys[('%s prep %s') % ((l, qty))].get_value(), None) for qty in qtyNames ])
    else:
        rowData = ([l]) + ([qtys[('%s prep %s') % ((l, qty))].get_value_and_err_bar() for qty in qtyNames ])
    table.addrow(rowData, formatters)



Clone # 217
Distance between two fragments = 1
Clone size = 5
Source file "report/table.py"
The first line is 43
Source file "report/table.py"
The first line is 71
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'latex')
else:
    colHeadings_formatted = self._headings['latex']
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'html')
else:
    colHeadings_formatted = self._headings['html']



Clone # 218
Distance between two fragments = 1
Clone size = 5
Source file "report/table.py"
The first line is 125
Source file "report/table.py"
The first line is 71
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'ppt')
else:
    colHeadings_formatted = self._headings['ppt']
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'html')
else:
    colHeadings_formatted = self._headings['html']



Clone # 219
Distance between two fragments = 1
Clone size = 5
Source file "report/table.py"
The first line is 125
Source file "report/table.py"
The first line is 43
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'ppt')
else:
    colHeadings_formatted = self._headings['ppt']
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'latex')
else:
    colHeadings_formatted = self._headings['latex']



Clone # 220
Distance between two fragments = 1
Clone size = 5
Source file "report/table.py"
The first line is 99
Source file "report/table.py"
The first line is 71
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'text')
else:
    colHeadings_formatted = self._headings['text']
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'html')
else:
    colHeadings_formatted = self._headings['html']



Clone # 221
Distance between two fragments = 1
Clone size = 5
Source file "report/table.py"
The first line is 99
Source file "report/table.py"
The first line is 43
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'text')
else:
    colHeadings_formatted = self._headings['text']
if self._headingFormatters is not None:
    colHeadings_formatted = formatSet.formatList(self._headings, self._headingFormatters, 'latex')
else:
    colHeadings_formatted = self._headings['latex']



Clone # 222
Distance between two fragments = 1
Clone size = 5
Source file "report/generation.py"
The first line is 476
Source file "report/generation.py"
The first line is 807
qtyNames = ('angle btwn rotn axes') qtyNames = ('relative eigenvalues')
qtys_to_compute = [('%s %s') % ((gl, qty)) for qty in qtyNames for gl in gateLabels ] qtys_to_compute = [('%s %s') % ((gl, qty)) for qty in qtyNames for gl in gateLabels ]
qtys = _cr.compute_gateset_gateset_qtys(qtys_to_compute, gateset, targetGateset, confidenceRegionInfo) qtys = _cr.compute_gateset_gateset_qtys(qtys_to_compute, gateset, targetGateset, confidenceRegionInfo)
table = _ReportTable(colHeadings, formatters) table = _ReportTable(colHeadings, formatters)



Clone # 223
Distance between two fragments = 4
Clone size = 5
Source file "report/formatter.py"
The first line is 272
Source file "report/formatter.py"
The first line is 257
FormatSet.formatDict['Precision'] = {'html': _PrecisionFormatter(html_value), 'latex': _PrecisionFormatter(latex_value), 'text': _no_format, 'ppt': _PrecisionFormatter(ppt_value)} FormatSet.formatDict['Normal'] = {'html': _PrecisionFormatter(html), 'latex': _PrecisionFormatter(latex), 'text': _no_format, 'ppt': _PrecisionFormatter(ppt)}



Clone # 224
Distance between two fragments = 2
Clone size = 5
Source file "report/reportables.py"
The first line is 843
Source file "report/reportables.py"
The first line is 812
FQty = _getEffectQuantity(fidelity, gateset1, effectLabel, eps, confidenceRegionInfo) FQty = _getPrepQuantity(fidelity, gateset1, prepLabel, eps, confidenceRegionInfo)
InFQty = ReportableQty((1.0) - (FQty.get_value()), FQty.get_err_bar()) InFQty = ReportableQty((1.0) - (FQty.get_value()), FQty.get_err_bar())
if key in qtynames:
    ret[key] = FQty
if key in qtynames:
    ret[key] = FQty
if key2 in qtynames:
    ret[key2] = InFQty
if key2 in qtynames:
    ret[key2] = InFQty



Clone # 225
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 3413
Source file "report/results.py"
The first line is 1631
qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision) qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key)) qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))



Clone # 226
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2365
Source file "report/results.py"
The first line is 1631
qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision) qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key)) qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))



Clone # 227
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 2086
Source file "report/results.py"
The first line is 1631
qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision) qtys[key] = self.tables.get(key, verbosity=(printer) - (1)).render('latex', longtables=self.options.long_tables, scratchDir=D, precision=self.options.precision, polarprecision=self.options.polar_precision)
qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key)) qtys[('tt_') + (key)] = tooltiptex((".tables['%s']") % (key))



Clone # 228
Distance between two fragments = 0
Clone size = 5
Source file "report/results.py"
The first line is 982
Source file "report/results.py"
The first line is 386
def  validate_essential(key):
  return  [key]  if  self._bEssentialResultsSet  else  []
def  validate_essential(key):
  return  [key]  if  self._bEssentialResultsSet  else  []
def  validate_LsAndGerms(key):
  return  [key]  if  (self._bEssentialResultsSet  and
    self._LsAndGermInfoSet)  else  []
def  validate_LsAndGerms(key):
  return  [key]  if  (self._bEssentialResultsSet  and
    self._LsAndGermInfoSet)  else  []



Clone # 229
Distance between two fragments = 4
Clone size = 5
Source file "report/reportables.py"
The first line is 257
Source file "report/reportables.py"
The first line is 159
def compute_gateset_qty(qtyname, gateset, confidenceRegionInfo=None):
    ret = compute_gateset_qtys([qtyname], gateset, confidenceRegionInfo)
    if qtyname is None:
        return ret
    elif qtyname in ret:
        return ret[qtyname]
    else:
        return None
def compute_dataset_qty(qtyname, dataset, gatestrings=None):
    ret = compute_dataset_qtys([qtyname], dataset, gatestrings)
    if qtyname is None:
        return ret
    elif qtyname in ret:
        return ret[qtyname]
    else:
        return None



Clone # 230
Distance between two fragments = 2
Clone size = 5
Source file "report/formatter.py"
The first line is 380
Source file "report/formatter.py"
The first line is 372
FormatSet.formatDict['VecErrorBars'] = {'html': _EB_html, 'latex': _VEB_latex, 'text': _EB_text, 'ppt': _EB_ppt} FormatSet.formatDict['ErrorBars'] = {'html': _EB_html, 'latex': _EB_latex, 'text': _EB_text, 'ppt': _EB_ppt}



Clone # 231
Distance between two fragments = 3
Clone size = 5
Source file "report/reportables.py"
The first line is 843
Source file "report/reportables.py"
The first line is 705
FQty = _getEffectQuantity(fidelity, gateset1, effectLabel, eps, confidenceRegionInfo) FQty = _getGateQuantity(process_fidelity, gateset1, gateLabel, eps, confidenceRegionInfo)
InFQty = ReportableQty((1.0) - (FQty.get_value()), FQty.get_err_bar()) InFQty = ReportableQty((1.0) - (FQty.get_value()), FQty.get_err_bar())
if key in qtynames:
    ret[key] = FQty
if key in qtynames:
    ret[key] = FQty
if key2 in qtynames:
    ret[key2] = InFQty
if key2 in qtynames:
    ret[key2] = InFQty



Clone # 232
Distance between two fragments = 3
Clone size = 5
Source file "report/reportables.py"
The first line is 812
Source file "report/reportables.py"
The first line is 705
FQty = _getPrepQuantity(fidelity, gateset1, prepLabel, eps, confidenceRegionInfo) FQty = _getGateQuantity(process_fidelity, gateset1, gateLabel, eps, confidenceRegionInfo)
InFQty = ReportableQty((1.0) - (FQty.get_value()), FQty.get_err_bar()) InFQty = ReportableQty((1.0) - (FQty.get_value()), FQty.get_err_bar())
if key in qtynames:
    ret[key] = FQty
if key in qtynames:
    ret[key] = FQty
if key2 in qtynames:
    ret[key2] = InFQty
if key2 in qtynames:
    ret[key2] = InFQty



Clone # 233
Distance between two fragments = 3
Clone size = 5
Source file "report/results.py"
The first line is 637
Source file "report/results.py"
The first line is 643
def getPlotFn():
    obj = self.parameters['objective']
    assert obj in ('chi2', 'logl')
    if obj == 'chi2':
        return _plotting.chi2_boxplot
    elif obj == 'logl':
        return _plotting.logl_boxplot
def getDirectPlotFn():
    obj = self.parameters['objective']
    assert obj in ('chi2', 'logl')
    if obj == 'chi2':
        return _plotting.direct_chi2_boxplot
    elif obj == 'logl':
        return _plotting.direct_logl_boxplot



Clone # 234
Distance between two fragments = 3
Clone size = 5
Source file "report/results.py"
The first line is 643
Source file "report/results.py"
The first line is 649
def getDirectPlotFn():
    obj = self.parameters['objective']
    assert obj in ('chi2', 'logl')
    if obj == 'chi2':
        return _plotting.direct_chi2_boxplot
    elif obj == 'logl':
        return _plotting.direct_logl_boxplot
def getWhackAMolePlotFn():
    obj = self.parameters['objective']
    assert obj in ('chi2', 'logl')
    if obj == 'chi2':
        return _plotting.whack_a_chi2_mole_boxplot
    elif obj == 'logl':
        return _plotting.whack_a_logl_mole_boxplot



Clone # 235
Distance between two fragments = 3
Clone size = 5
Source file "report/results.py"
The first line is 637
Source file "report/results.py"
The first line is 649
def getPlotFn():
    obj = self.parameters['objective']
    assert obj in ('chi2', 'logl')
    if obj == 'chi2':
        return _plotting.chi2_boxplot
    elif obj == 'logl':
        return _plotting.logl_boxplot
def getWhackAMolePlotFn():
    obj = self.parameters['objective']
    assert obj in ('chi2', 'logl')
    if obj == 'chi2':
        return _plotting.whack_a_chi2_mole_boxplot
    elif obj == 'logl':
        return _plotting.whack_a_logl_mole_boxplot



Clone # 236
Distance between two fragments = 2
Clone size = 5
Source file "report/results.py"
The first line is 3013
Source file "report/results.py"
The first line is 3026
tf = table.cell(0, i).text_frame tf = table.cell(i, j).text_frame
tf.vertical_anchor = MSO_ANCHOR.MIDDLE tf.vertical_anchor = MSO_ANCHOR.MIDDLE
tf.auto_size = MSO_AUTO_SIZE.SHAPE_TO_FIT_TEXT tf.auto_size = MSO_AUTO_SIZE.SHAPE_TO_FIT_TEXT
tf.word_wrap = False tf.word_wrap = False
tf.paragraphs[0].alignment = PP_ALIGN.CENTER tf.paragraphs[0].alignment = PP_ALIGN.CENTER



Clone Digger is aimed to find software clones in Python and Java programs. It is provided under the GPL license and can be downloaded from the site http://clonedigger.sourceforge.net