netpyne.analysis.lfp_orig

Module for analyzing and plotting LFP-related results

Functions:

plotLFP([timeRange, electrodes, plots, ...])

Function for plotting local field potentials (LFP)
netpyne.analysis.lfp_orig.plotLFP(timeRange=None, electrodes=['avg', 'all'], plots=['timeSeries', 'PSD', 'spectrogram', 'locations'], inputLFP=None, NFFT=256, noverlap=128, nperseg=256, minFreq=1, maxFreq=100, stepFreq=1, smooth=0, separation=1.0, includeAxon=True, logx=False, logy=False, normSignal=False, normPSD=False, normSpec=False, filtFreq=False, filtOrder=3, detrend=False, transformMethod='morlet', maxPlots=8, overlay=False, colors=None, figSize=(8, 8), fontSize=14, lineWidth=1.5, dpi=200, saveData=None, saveFig=None, showFig=True)[source]

Function for plotting local field potentials (LFP)

Parameters:

  • timeRange (list [start, stop]) – Time range to plot. Default: None plots entire time range

  • electrodes (list) – List of electrodes to include; 'avg' is the average of all electrodes; 'all' is each electrode separately. Default: ['avg', 'all']

  • plots (list) – List of plot types to show. Default: ['timeSeries', 'PSD', 'spectrogram', 'locations']

  • NFFT (int (power of 2)) – Number of data points used in each block for the PSD and time-freq FFT. Default: 256

  • noverlap (int (<nperseg)) – Number of points of overlap between segments for PSD and time-freq. Default: 128

  • nperseg (int) – Length of each segment for time-freq. Default: 256

  • minFreq (float) – Minimum frequency shown in plot for PSD and time-freq. Default: 1

  • maxFreq (float) – Maximum frequency shown in plot for PSD and time-freq. Default: 100

  • stepFreq (float) – Step frequency. Default: 1

  • smooth (int) – Window size for smoothing LFP; no smoothing if 0 Default: 0

  • separation (float) – Separation factor between time-resolved LFP plots; multiplied by max LFP value. Default: 1.0

  • includeAxon (bool) – Whether to show the axon in the location plot. Default: True

  • logx (bool) – Whether to make x-axis logarithmic Default: False Options: <option> <description of option>

  • logy (bool) – Whether to make y-axis logarithmic Default: False

  • normSignal (bool) – Whether to normalize the signal. Default: False

  • normPSD (bool) – Whether to normalize the power spectral density. Default: False

  • normSpec (bool) – Needs documentation. Default: False

  • filtFreq (int or list) – Frequency for low-pass filter (int) or frequencies for bandpass filter in a list: [low, high] Default: False does not filter the data

  • filtOrder (int) – Order of the filter defined by filtFreq. Default: 3

  • detrend (bool) – Whether to detrend. Default: False

  • transformMethod (str) – Transform method. Default: 'morlet' Options: 'fft'

  • maxPlots (int) – Maximum number of subplots. Currently unused. Default: 8

  • overlay (bool) – Whether to overlay plots or use subplots. Default: False overlays plots.

  • colors (list) – List of normalized RGB colors to use. Default: None uses standard colors

  • figSize (list [width, height]) – Size of figure in inches. Default: (10, 8)

  • fontSize (int) – Font size on figure. Default: 14

  • lineWidth (int) – Line width. Default: 1.5

  • dpi (int) – Resolution of figure in dots per inch. Default: 100

  • saveData (bool or str) – Whether and where to save the data used to generate the plot. Default: False Options: True autosaves the data, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.pkl' and '.json'

  • saveFig (bool or str) – Whether and where to save the figure. Default: False Options: True autosaves the figure, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.png', '.jpg', '.eps', and '.tiff'

  • showFig (bool) – Shows the figure if True. Default: True

Returns:

A tuple consisting of the Matplotlib figure handles and a dictionary containing the plot data

Return type:

(figs, dict)

See also

iplotLFP