Source code for netpyne.plotting.plotLFPLocations

# Generate plots of LFP (local field potentials) and related analyses

import math
from ..analysis.utils import exception  # , loadData
from import loadData
from .plotter import LinesPlotter
from .plotter import ImagePlotter
from .plotter import MetaFigure
import numpy as np

[docs] @exception def plotLFPLocations(sim=None, axis=None, electrodes=['all'], includeAxon=True, returnPlotter=False, **kwargs): """Function to produce a plot of LFP electrode locations NetPyNE Options --------------- sim : NetPyNE sim object The *sim object* from which to get data. *Default:* ``None`` uses the current NetPyNE sim object Parameters ---------- axis : matplotlib axis The axis to plot into, allowing overlaying of plots. *Default:* ``None`` produces a new figure and axis. electrodes : list A *list* of the electrodes to plot from. *Default:* ``['all']`` plots each electrode includeAxon : bool Whether to include axons. *Default:* ``True`` returnPlotter : bool Whether to return the figure or the NetPyNE MetaFig object. *Default:* ``False`` returns the figure. Plot Options ------------ showFig : bool Whether to show the figure. *Default:* ``False`` saveFig : bool Whether to save the figure. *Default:* ``False`` overwrite : bool whether to overwrite existing figure files. *Default:* ``True`` overwrites the figure file *Options:* ``False`` adds a number to the file name to prevent overwriting Returns ------- LFPLocationsPlot : *matplotlib figure* By default, returns the *figure*. If ``returnPlotter`` is ``True``, instead returns the NetPyNE MetaFig. """ print('Plotting LFP electrode locations...') if 'sim' not in kwargs: from .. import sim else: sim = kwargs['sim'] if 'rcParams' in kwargs: rcParams = kwargs['rcParams'] else: rcParams = None # electrode selection if 'all' in electrodes: electrodes.remove('all') electrodes.extend(list(range(int( cvals = [] # used to store total transfer resistance for cell in trSegs = list( np.sum( * 1e3, axis=0) ) # convert from Mohm to kilohm if not includeAxon: i = 0 for secName, sec in cell.secs.items(): nseg = sec['hObj'].nseg # .geom.nseg if 'axon' in secName: for j in range(i, i + nseg): del trSegs[j] i += nseg cvals.extend(trSegs) includePost = [c.gid for c in] fig, data = sim.plotting.plotShape( axis=axis, includePost=includePost, showElectrodes=electrodes, cvals=cvals, includeAxon=includeAxon, kind='LFPLocations', **kwargs ) if returnPlotter: return fig.metafig else: return fig