pybic.BicAn

class pybic.BicAn(inData, **kwargs)

Main class of pybic module, i.e., Bicoherence Analyzer.

pybic.BicAn(inData,**kwargs)

A typical usage is

# Import pybic module
import pybic as bic
# Create time series to analyze
x,t,fS = bic.TestSignal('circle')
# Analyze!
b = bic.BicAn(x,SampRate=fS)

Note

When using the __init__ method (i.e., pybic.BicAn(...)), keywords are case insensitive! For example, BicAn(inData,samprate=fS), BicAn(inData,SAMPRATE=fS), and BicAn(inData,sAmPrAtE=fS) are all valid means of setting the SampRate attribute upon initialization.

However, the direct augmentation of attributes is case sensitive, i.e., b.samprate = 100.0 will throw an error!

Parameters:

• inData (ndarray or str) – Time series to be analyzed or TestSignal() string. Using 'input' opens FileDialog() window to choose a local file for input.

• **kwargs – Keyword-argument pairs to set attributes (see BicAn attributes for more info).

Returns:

Output object.

Return type:

BicAn

Attributes

AlphaExp	CWT alpha exponent (see ApplyCWT()).
AxHands	List of axes handles.
BicOfTime	Calculate bispectrum/bicoherence spectrum for selected PlotSlice.
BicVec	Integers representing desired time series for cross-bispectrum.
Bispectro	Calculate bispectrogram.
CMap	Colormap for plots.
COILim	Cone of influence logarithmic cutoff (see BicAn.SpectroWavelet()).
CalcCOI	Calculate cone of influence (COI) for CWT (see BicAn.SpectroWavelet()).
CalcHist	Calculate histogram of amplitude from time series (see CalcHistVsT()).
CaxHands	List of colorbar axes handles.
CbarNorth	Place colorbar above plot.
Cross	Calculate cross-spectrum/cross-coherence.
Date	Date when pybic is loaded.
Detrend	Detrend input time series before analysis.
DistLevel	Y-axis limit for bicoherence uncertainty analysis.
Epsilon	Small value in polycoherence calculations.
ErrLim	Threshold for mean of time-frequency representation (TFR) over all frequency bins.
FScale	Log scale for frequency labels (see ScaleToString()).
Figure	Used for BicAn.PlotGUI() functionality.
Filter	Desired filter.
FontSize	Plot font size in points.
FreqRes	Frequency resolution in Hz.
InCOI	Input cone of influence (see BicAn.SpectroWavelet()).
InstFreq	Estimated instantaneous frequency of time-series.
InstFreqFlag	Toggle behavior of user clicks in BicAn.PlotGUI().
JustSpec	Limit calculation to time-frequency representation (TFR), ie, no polyspectral analysis.
LilGuy	Duplicate of BicAn.Epsilon for back-compatability.
LimFreq	Maximum frequency of CWT given by pybic.SampRate/LimFreq.
LineColor	Line color in plots.
LineWidth	Plot linewidths in points.
NFreq	Number of frequency bins.
NewGUICax	Flag for creating new colorbar axes.
NormBic	Normalize bicoherence spectrum when using BicAn.PlotBispec().
Note	User note.
PlotDPI	Dots per inch of plots.
PlotIt	Run BicAn.PlotGUI() after analysis is complete.
PlotSig	Selected time series to plot when using BicAn.PlotSpectro().
PlotSlice	Selected slice of TFR to plot when using BicAn.PlotPowerSpec() and BicAn.PlotMeanHist().
PlotType	Desired bispectral quantity to plot (see BicAn.PlotBispec() and BicAn.PlotPointOut()).
Processed	Processed input data.
RandLevel	Level of randomization in bicoherence uncertainty analysis.
Raw	Raw input data.
SampRate	Sampling rate in Hz.
Samples	Number of samples in processed data.
ScaleAxes	Desired axis scaling.
Sigma	CWT time-frequency resolution parameter (see ApplyCWT()).
SizeWarn	Display warning for large TFRs.
Smooth	Smoothing factor in samples.
SpecType	Desired time-frequency representation (TFR).
SpecVLim	Spectrogram colorbar limits as [vmin,vmax].
Step	STFT step in samples.
SubInt	STFT subinterval size in samples.
TLineCol	Colormap for automatic calls to PlotTimeline().
TScale	Log scale for time labels (see ScaleToString()).
TZero	Initial time.
TickLabel	Tick label customization.
Trispec	Calculate trispectrum.
Vector	Plot linewidths.
Window	STFT window function (see HannWindow() and FlatTopWindow()).
ZPad	Pad time series with zeros to avoid truncation for STFT.
bc	Bicoherence spectrum.
bg	Bispectrogram.
bs	Bispectrum.
bv	Bin vector of input signal histogram.
cc	Cross-coherence.
cg	Coherence spectrum (or 'coherogram').
cs	Cross-spectrum.
er	Mean & std dev of FFT.
ff	Full frequency vector
ft	Fourier amplitudes
fv	Frequency vector associated with time-frequency representation
hg	Histogram of input signal amplitudes.
ht	Time vector of input signal histogram.
mb	Mean bicoherence.
mh	Input signal histogram averaged over time.
sb	Std dev of bicoherence spectrum.
sg	Spectrogram (complex)
tc	Tricoherence spectrum.
tkRoot	Root window for tkinter.
tkVar	Variable for tkinter.
ts	Trispectrum (complex).
tv	Time vector associated with time-frequency representation

Methods

ApplyZPad()	Apply zero padding to Raw data.
Bicoherence()	Class wrapper for bispectral analysis.
CalcMean([Ntrials])	Calculate mean of bicoherence spectrum across the full bi-frequency space.
CheckCouple(f[, checkdiff])	Check nth order coupling for a given test vector of freqs.
ClickPlot(event)	Callback for BicAn.PlotGUI() clicks.
Coherence()	Class wrapper for SpecToCoherence().
FindMaxInRange(FxLo, FxHi, FyLo, FyHi[, useb2])	Finds maximum bicoherence in given range.
HistogramSig([Nbins])	Class wrapper for CalcHistVsT().
InstAmpFreq(j[, calc_type, fband, realBPF, ...])	Perform instantaneous amplitude and frequency analysis.
InstDiffFreq(j, k[, fband, fwindow, dist, ...])	Plot the instantaneous difference frequency vs normalized bispectral modulus.
MonteCarloMax([N, Nrolls, critCoh, plot, ...])	Identifies maxima in N-coherence spectra with random restart hillclimb.
ParseInput(inData, kwargs)	Parse inputs for BicAn constructor.
PlotBispec(*args[, normb2, plot3d, squeezeAxes])	Plots bispectrum or bicoherence spectrum.
PlotCoherence(*args[, crossSpec, vLim])	Plots cross-coherence spectrum cc or cross-spectrum cs.
PlotGUI([SaveAs, subplotType])	Main graphical interface for exploring BicAn data.
PlotHelper(whatPlot, X, Y[, IsFreq, ...])	Estimate and plot distribution of bispectrum/bicoherence for single point.
PlotHisto(*args[, vLim])	Plots data histogram vs time.
PlotInstFreq(j, k[, diff_freq, freq_type, ...])	Perform instantaneous frequency analysis.
PlotMeanHist(*args[, vLim])	Plots time average (or slice) of data histogram.
PlotPhaseDist(j, k[, ylim, SaveAs])	Plots phase distribution of single point in bifrequency space.
PlotPointOut(X, Y[, IsFreq, PlotAll, ...])	Wraps BicAn.PlotHelper() for BicAn.PlotGUI().
PlotPowerSpec(*args[, vLim])	Plots time average (or slice) of spectrogram.
PlotSpectro(*args[, vLim, maxLine])	Plots absolute value of spectrogram.
PlotTrispec([Tval, colorTricoh, elev, azim, ...])	Plots trispectrum or tricoherence spectrum.
ProcessData()	Main processing loop (see source code).
RefreshGUI([SaveAs])	Refreshes GUI as initiated by BicAn.PlotGUI().
SizeWarnPrompt(n)	Modal warning about large FFT size.
SpectroSTFT()	Class wrapper for ApplySTFT().
SpectroWavelet()	Class method for CWT analysis.
SwitchCMap()	Interactive colormap selection.
SwitchCMapClick()	Callback function for BicAn.SwitchCMap().
SwitchPlot(event)	Callback for BicAn.PlotGUI() keypresses.
Tricoherence()	Class wrapper for trispectral analysis (SpecToTrispec()).
WhichPlot([local])	Assists plotting functions with data and labeling.