netpyne.analysis.lfp_orig
Module for analyzing and plotting LFP-related results
Functions:
|
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 rangeelectrodes (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 datafiltOrder (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 colorsfigSize (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