arb_test.py

import arbor, dbbs_models
from patch import p
# cell = arbor.cable_cell(morph.morphology, labels, decor)
model = dbbs_models.StellateCell
cell = model.cable_cell()
neuron_cell = model()
print(neuron_cell.soma)
neuron_cell.record_soma()
neuron_time = p.time
p.celsius = 32
p.finitialize(-40)
p.continuerun(100)
# (4) Define a recipe for a single cell and set of probes upon it.
# This constitutes the corresponding generic recipe version of
# `single_cell_model.py`.
class single_recipe(arbor.recipe):
    def __init__(self, cell, probes):
        # (4.1) The base C++ class constructor must be called first, to ensure that
        # all memory in the C++ class is initialized correctly.
        arbor.recipe.__init__(self)
        self.the_cell = cell
        self.the_probes = probes
        self.the_props = arbor.cable_global_properties()
        self.the_props.set_property(Vm=-65, tempK=300, rL=35.4, cm=0.01)
        self.the_props.set_ion(ion='na', int_con=10,   ext_con=140, rev_pot=50, method='nernst/na')
        self.the_props.set_ion(ion='k',  int_con=54.4, ext_con=2.5, rev_pot=-77)
        self.the_props.set_ion(ion='ca', int_con=5e-5, ext_con=2, rev_pot=132.5)
        self.the_props.set_ion(ion='h', valence=1, int_con=5e-5, ext_con=2, rev_pot=-34)
        self.the_cat = arbor.default_catalogue()
        self.the_cat.extend(arbor.dbbs_catalogue(), "")
        self.the_props.register(self.the_cat)
    def num_cells(self):
        # (4.2) Override the num_cells method
        return 31000
    def num_sources(self, gid):
        # (4.3) Override the num_sources method
        return 0
    def cell_kind(self, gid):
        # (4.4) Override the cell_kind method
        return arbor.cell_kind.cable
    def cell_description(self, gid):
        # (4.5) Override the cell_description method
        return self.the_cell
    def probes(self, gid):
        # (4.6) Override the probes method
        return self.the_probes
    def global_properties(self, kind):
        # (4.7) Override the global_properties method
        return self.the_props
# (6) Create a default execution context and a default domain decomposition.
probe = arbor.cable_probe_membrane_voltage('(proximal (tag 1))')
recipe = single_recipe(cell, [probe])
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# (7) Create and run simulation and set up 10 kHz (every 0.1 ms) sampling on the probe.
# The probe is located on cell 0, and is the 0th probe on that cell, thus has probe_id (0, 0).
sim = arbor.simulation(recipe, domains, context)
sim.record(arbor.spike_recording.all)
handle = sim.sample((0, 0), arbor.regular_schedule(0.1))
sim.run(tfinal=100)
spikes = sim.spikes()
data, meta = sim.samples(handle)[0]
if len(spikes)>0:
    print('{} spikes:'.format(len(spikes)))
    for t in spikes['time']:
        print('{:3.3f}'.format(t))
else:
    print('no spikes')
# (9) Plot the recorded voltages over time.
import plotly.graph_objs as go # You may have to pip install these.
go.Figure(
    [
        go.Scatter(x=data[:, 0], y=data[:, 1], name="arbor"),
        go.Scatter(x=list(neuron_time), y=list(neuron_cell.Vm), name="neuron"),
    ]
).show()