FN.py

from neuromllite import (
    Network,
    Cell,
    Population,
    Synapse,
    RectangularRegion,
    RandomLayout,
)
from neuromllite import (
    Projection,
    RandomConnectivity,
    OneToOneConnector,
    Simulation,
    InputSource,
    Input,
)

from neuromllite.NetworkGenerator import check_to_generate_or_run

import sys


def generate():

    dt = 0.05
    simtime = 100

    ################################################################################
    ###   Build new network

    net = Network(id="FN")
    net.notes = "FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS"

    net.parameters = {
        "initial_w": 0.0,
        "initial_v": -1,
        "a_v": -0.3333333333333333,
        "b_v": 0.0,
        "c_v": 1.0,
        "d_v": 1,
        "e_v": -1.0,
        "f_v": 1.0,
        "time_constant_v": 1.0,
        "a_w": 1.0,
        "b_w": -0.8,
        "c_w": 0.7,
        "time_constant_w": 12.5,
        "threshold": -1.0,
        "mode": 1.0,
        "uncorrelated_activity": 0.0,
        "Iext": 0,
    }

    cellInput = Cell(id="fn", lems_source_file="FN_Definitions.xml", parameters={})
    for p in net.parameters:
        cellInput.parameters[p] = p
    net.cells.append(cellInput)

    r1 = RectangularRegion(
        id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000
    )
    net.regions.append(r1)

    pop = Population(
        id="FNpop",
        size="1",
        component=cellInput.id,
        properties={"color": "0.2 0.2 0.2", "radius": 3},
        random_layout=RandomLayout(region=r1.id),
    )
    net.populations.append(pop)

    new_file = net.to_json_file("%s.json" % net.id)

    ################################################################################
    ###   Build Simulation object & save as JSON

    sim = Simulation(
        id="Sim%s" % net.id,
        network=new_file,
        duration=simtime,
        dt=dt,
        seed=123,
        recordVariables={"V": {"all": "*"}, "W": {"all": "*"}},
        plots2D={
            "VW": {"x_axis": "%s/0/fn/V" % pop.id, "y_axis": "%s/0/fn/W" % pop.id}
        },
    )

    sim.to_json_file()

    return sim, net


if __name__ == "__main__":

    sim, net = generate()

    ################################################################################
    ###   Run in some simulators

    import sys

    check_to_generate_or_run(sys.argv, sim)