fixed implementation of linesource method

[espenhgn]

I found an ugly bug in the linesource implementation, such that somatic currents were not correctly accounted for when computing the potential in proximity to the soma. I fixed now this implementation. The output of the different methods can be compared like this:

#!/usr/bin/env python
'''compare methods for LFPy.RecExtElectrode class'''
import LFPy
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from matplotlib.collections import PolyCollection
import neuron

################################################################################
# Main script, set parameters and create cell, synapse and electrode objects
################################################################################

# clear out old section references in NEURON
neuron.h('forall delete_section()')

cellParameters = {
    'morphology' : 'dipole.hoc',
    'tstartms' : 0.,
    'tstopms' : 10.,
    'timeres_python' : 0.1,
    'timeres_NEURON' : 0.1,
    'pt3d' : True,    
}

cell = LFPy.Cell(**cellParameters)
cell.set_pos(zpos=-15)

synapseParameters = {
    'idx' : 0,
    'e' : 0,
    'syntype' : 'Exp2Syn',
    'tau1' : 0.1,
    'tau2' : 1.,
    'weight' : 0.01,
    'record_current' : True
}
synapse = LFPy.Synapse(cell, **synapseParameters)
synapse.set_spike_times(np.array([2.]))

# compute potentials on a grid in x-z plane at a y-depth of 5 um
dx = 5 # spatial resolution
x = np.arange(-80., 80.+dx, dx)
z = np.arange(-150., 150.+dx, dx)
X, Z = np.meshgrid(x, z)
electrodeParameters = {
    'x' : X.flatten(),
    'y' : np.zeros(X.size)-5,
    'z' : Z.flatten(),
    'sigma' : 0.3,
}

# compute cell response and extracellular potentials
cell.simulate(rec_imem=True, rec_isyn=True)

methods = ['pointsource', 'linesource', 'som_as_point']
electrodes = [LFPy.RecExtElectrode(cell=cell, method=method, **electrodeParameters) for method in methods]
for electrode in electrodes:
    electrode.calc_lfp()


########################
# Figure
########################
fig = plt.figure(figsize=(16, 9))
fig.subplots_adjust(left=0.02, right=0.98)
gs = GridSpec(1, 3, left=0.02, right=0.98)
axes = [fig.add_subplot(gs[0, i], aspect='equal') for i in range(len(methods))]

#morphology - line sources for panels A and B
zips = []
xz = cell.get_idx_polygons()
for x, z in xz:
    zips.append(zip(x, z))
for ax, method, electrode in zip(axes, methods, electrodes):
    polycol = PolyCollection(zips,
                             linewidths=(0.5),
                             edgecolors='k',
                             facecolors='none',
                             zorder=-5)
    ax.add_collection(polycol)

    #morphology mid points
    ax.plot(cell.xmid, cell.zmid, 'o', mec='none', mfc='k',
             markersize=3, zorder=0)
    
    # mark synapse location
    ax.plot(synapse.x, synapse.z, '> ', mec='r', mfc='r', markersize=5, zorder=1)

    t_max = abs(synapse.i) == abs(synapse.i).max()
    vmax = 0.005
    im = ax.contourf(X, Z, electrode.LFP[:, t_max].reshape(X.shape),
                      levels=np.linspace(-vmax, vmax, 51),
                      cmap=plt.get_cmap('PRGn'), zorder=-10,
                      vmin=-vmax,
                      vmax=vmax)
    ax.set_title(method)
    bbox = np.array(ax.get_position())
    cax = fig.add_axes([bbox[0][0]+(bbox[1][0]-bbox[0][0])/4, bbox[0][1]-0.05, (bbox[1][0]-bbox[0][0])/2, 0.015])
    axcb = fig.colorbar(im, cax=cax, orientation='horizontal')
    axcb.outline.set_visible(False)
    axcb.set_label('$\phi$ (mV)')
    axcb.set_ticks(np.arange(-np.round(vmax), np.round(vmax)+0.001, 0.001))

Corresponding morphology file:

/* ----------------------------------------------------
dipole.hoc
-----------------------------------------------------*/
create soma[1]
create dend[1]
soma[0] {
    pt3dadd(0, 0, 0, 10)
    pt3dadd(0, 0, 30, 10)
}
dend[0] {
    pt3dadd(0, 0, 30, 10)
    pt3dadd(0, 0, 60, 10)
}
connect dend[0](0), soma[0](1)

I also added an assertion that the number of x,y,z-coordinate values for electrodes are identical

[torbjone]

Fix confirmed. I have a few trivial suggestions for style improvements, but I'll make a separate pull request for that soon.

[espenhgn]

Fine, will merge.