netpyne.plotting.plotCSD module

netpyne.plotting.plotCSD.getPaddedCSD(CSDData, pad)[source]
netpyne.plotting.plotCSD.plotCSD(CSDData=None, LFPData=None, pop=None, timeRange=None, dt=None, sampr=None, spacing_um=None, fontSize=12, ymax=None, figSize=(8, 8), overlay=None, hlines=False, layerBounds=None, stimTimes=None, saveFig=True, dpi=200, showFig=False, smooth=True, colorbar=True, pad=1, **kwargs)[source]

Function to plot CSD values extracted from simulated LFP data

Parameters:

  • CSDData (list or array) – CSDData for plotting. Default: None

  • LFPData (list or numpy array) – LFP data provided by user (mV). Each element of the list/array must be a list/array containing LFP data for an electrode. Default: None pulls the data from the current NetPyNE sim object.

  • pop (str) – Plot CSD data from a specific cell population Default: ``None``plots overall CSD data

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

  • dt (float) – Time between recording points (ms). Default: None uses sim.cfg.recordStep from the current NetPyNE sim object.

  • sampr (float) – Sampling rate for data recording (Hz). Default: None uses 1.0/sim.cfg.recordStep from the current NetPyNE sim object.

  • spacing_um (float) – Electrode contact spacing in units of microns. Default: None pulls the information from the current NetPyNE sim object. If the data is empirical, defaults to 100 (microns).

  • fontSize (int) – Default: 12

  • ymax (float) – The upper y-limit. Default: None

  • figSize (tuple) – Size of CSD plot figure Default: (8,8)

  • overlay (str) – Option to include LFP data overlaid on CSD color map plot. Default: None provides no overlay OPTIONS are ‘LFP’ or ‘CSD’

  • hlines (bool) – Option to include horizontal lines on plot to indicate electrode positions. Default: False

  • layerBounds (dict #### <-- SHOULD FIX THIS SO L1 IS A LIST) – Dictionary containing layer labels as keys, and layer boundaries as values, e.g. {‘L1’:100, ‘L2’: 160, ‘L3’: 950, ‘L4’: 1250, ‘L5A’: 1334, ‘L5B’: 1550, ‘L6’: 2000} Default: None

  • stimTimes (list OR float / int) – Time(s) when stimulus is applied (ms) Default: None does not add anything to plot Options: Adds vertical dashed line(s) to the plot at stimulus onset(s)

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

  • dpi (int) – Resolution for saving figures. Default: 200

  • showFig (bool) – Whether to show the figure. Default: True

  • smooth (bool) – Whether or not to plot the smoothed interpoloation Default: True

  • colorbar (bool) – Whether or not to plot the colorbar Default: True

  • pad (int) – Amount to pad CSDData on top/bottom for more accurate interpolation at edges Default: 1