Mixed network and from-scatch morgphology network vis

[michaeldeistler]

This allows networks which consist of mixed SWC and from-scratch morphologies:

import matplotlib.pyplot as plt

import jaxley as jx
from jaxley.synapses import GlutamateSynapse


cell1 = jx.read_swc("jaxley_experiments/nex/ca1net/morphologies/n120/n120.CNG.swc", nseg=4)
cell2 = jx.read_swc("jaxley_experiments/nex/ca1net/morphologies/n121/n121.CNG.swc", nseg=4)

comp = jx.Compartment()
branch = jx.Branch(comp, 4)
cell3 = jx.Cell(branch, parents=[-1, 0, 0, 1, 1])
cell4 = jx.Cell(branch, parents=[-1, 0, 0, 1, 1])

conns = [
        jx.Connectivity(
            GlutamateSynapse(),
            [jx.Connection(0, 0, 0.0, 1, 0, 0.0), jx.Connection(0, 0, 0.0, 2, 0, 0.0)],
        )
    ]

net = jx.Network([cell1, cell2, cell3, cell4], conns)

net.compute_xyz()

net.cell(1).move(0, 800)
net.cell(2).move(0, -800)
net.cell(3).move(0, -1200)

fig, ax = plt.subplots(1, 1, figsize=(4, 4))
ax = net.vis(detail="full", ax=ax)