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A spatial network in 3D with Gaussian connection probabilities

Hans Ekkehard Plesser, UMB

import nest
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D


pos = nest.spatial.free(nest.random.uniform(-0.5, 0.5), extent=[1.5, 1.5, 1.5])

l1 = nest.Create('iaf_psc_alpha', 1000, positions=pos)

# visualize

# extract position information, transpose to list of x, y and z positions
xpos, ypos, zpos = zip(*nest.GetPosition(l1))
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(xpos, ypos, zpos, s=15, facecolor='b')

# Gaussian connections in full box volume [-0.75,0.75]**3
nest.Connect(l1, l1,
             {'rule': 'pairwise_bernoulli',
              'p': nest.spatial_distributions.gaussian(nest.spatial.distance, std=0.25),
              'allow_autapses': False,
              'mask': {'box': {'lower_left': [-0.75, -0.75, -0.75],
                               'upper_right': [0.75, 0.75, 0.75]}}})

# show connections from center element
# sender shown in red, targets in green
ctr = nest.FindCenterElement(l1)
xtgt, ytgt, ztgt = zip(*nest.GetTargetPositions(ctr, l1)[0])
xctr, yctr, zctr = nest.GetPosition(ctr)
ax.scatter([xctr], [yctr], [zctr], s=40, facecolor='r')
ax.scatter(xtgt, ytgt, ztgt, s=40, facecolor='g', edgecolor='g')

tgts = nest.GetTargetNodes(ctr, l1)[0]
distances = nest.Distance(ctr, l1)
tgt_distances = [d for i, d in enumerate(distances) if i + 1 in tgts]

plt.hist(tgt_distances, 25)

Total running time of the script: ( 0 minutes 0.000 seconds)

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