Example6.py

from neuromllite import Network, Cell, Population, Simulation, Synapse
from neuromllite import RectangularRegion, RandomLayout
from neuromllite import Projection, RandomConnectivity, OneToOneConnector

import sys


def generate(ref="Example6_PyNN", add_inputs=True):
    ################################################################################
    ###   Build new network

    net = Network(id=ref, notes="Another network for PyNN - work in progress...")

    net.parameters = {
        "N_scaling": 0.005,
        "layer_height": 400,
        "width": 100,
        "depth": 100,
        "input_weight": 0.1,
    }

    cell = Cell(id="CorticalCell", pynn_cell="IF_curr_exp")
    cell.parameters = {
        "cm": 0.25,  # nF
        "i_offset": 0.0,  # nA
        "tau_m": 10.0,  # ms
        "tau_refrac": 2.0,  # ms
        "v_reset": -65.0,  # mV
        "v_rest": -65.0,  # mV
        "v_thresh": -50.0,  # mV
    }
    net.cells.append(cell)

    if add_inputs:
        input_cell = Cell(id="InputCell", pynn_cell="SpikeSourcePoisson")
        input_cell.parameters = {"start": 0, "duration": 10000000000, "rate": 150}
        net.cells.append(input_cell)

    e_syn = Synapse(
        id="ampa",
        pynn_receptor_type="excitatory",
        pynn_synapse_type="curr_exp",
        parameters={"tau_syn": 0.5},
    )
    net.synapses.append(e_syn)
    i_syn = Synapse(
        id="gaba",
        pynn_receptor_type="inhibitory",
        pynn_synapse_type="curr_exp",
        parameters={"tau_syn": 0.5},
    )
    net.synapses.append(i_syn)

    N_full = {
        "L23": {"E": 20683, "I": 5834},
        "L4": {"E": 21915, "I": 5479},
        "L5": {"E": 4850, "I": 1065},
        "L6": {"E": 14395, "I": 2948},
    }

    scale = 0.1

    pops = []
    input_pops = []
    pop_dict = {}

    layers = ["L23"]
    layers = ["L23", "L4", "L5", "L6"]

    for l in layers:
        i = 3 - layers.index(l)
        r = RectangularRegion(
            id=l,
            x=0,
            y=i * net.parameters["layer_height"],
            z=0,
            width=net.parameters["width"],
            height=net.parameters["layer_height"],
            depth=net.parameters["depth"],
        )
        net.regions.append(r)

        for t in ["E", "I"]:
            try:
                import opencortex.utils.color as occ

                if l == "L23":
                    if t == "E":
                        color = occ.L23_PRINCIPAL_CELL
                    if t == "I":
                        color = occ.L23_INTERNEURON
                if l == "L4":
                    if t == "E":
                        color = occ.L4_PRINCIPAL_CELL
                    if t == "I":
                        color = occ.L4_INTERNEURON
                if l == "L5":
                    if t == "E":
                        color = occ.L5_PRINCIPAL_CELL
                    if t == "I":
                        color = occ.L5_INTERNEURON
                if l == "L6":
                    if t == "E":
                        color = occ.L6_PRINCIPAL_CELL
                    if t == "I":
                        color = occ.L6_INTERNEURON

            except:
                color = ".8 0 0" if t == "E" else "0 0 1"

            pop_id = "%s_%s" % (l, t)
            pops.append(pop_id)
            ref = "l%s%s" % (l[1:], t.lower())
            exec(
                ref
                + " = Population(id=pop_id, size='int(%s*N_scaling)'%N_full[l][t], component=cell.id, properties={'color':color, 'type':t})"
            )
            exec("%s.random_layout = RandomLayout(region = r.id)" % ref)
            exec("net.populations.append(%s)" % ref)
            exec("pop_dict['%s'] = %s" % (pop_id, ref))

            if add_inputs:
                color = ".8 .8 .8"
                input_id = "%s_%s_input" % (l, t)
                input_pops.append(input_id)
                input_ref = "l%s%s_i" % (l[1:], t.lower())
                exec(
                    input_ref
                    + " = Population(id=input_id, size='int(%s*N_scaling)'%N_full[l][t], component=input_cell.id, properties={'color':color})"
                )
                exec("%s.random_layout = RandomLayout(region = r.id)" % input_ref)
                exec("net.populations.append(%s)" % input_ref)

        # l23i = Population(id='L23_I', size=int(100*scale), component=cell.id, properties={'color':})
        # l23ei = Population(id='L23_E_input', size=int(100*scale), component=input_cell.id)
        # l23ii = Population(id='L23_I_input', size=int(100*scale), component=input_cell.id)

    # net.populations.append(l23e)
    # net.populations.append(l23ei)
    # net.populations.append(l23i)
    # net.populations.append(l23ii)

    conn_probs = [
        [0.1009, 0.1689, 0.0437, 0.0818, 0.0323, 0.0, 0.0076, 0.0],
        [0.1346, 0.1371, 0.0316, 0.0515, 0.0755, 0.0, 0.0042, 0.0],
        [0.0077, 0.0059, 0.0497, 0.135, 0.0067, 0.0003, 0.0453, 0.0],
        [0.0691, 0.0029, 0.0794, 0.1597, 0.0033, 0.0, 0.1057, 0.0],
        [0.1004, 0.0622, 0.0505, 0.0057, 0.0831, 0.3726, 0.0204, 0.0],
        [0.0548, 0.0269, 0.0257, 0.0022, 0.06, 0.3158, 0.0086, 0.0],
        [0.0156, 0.0066, 0.0211, 0.0166, 0.0572, 0.0197, 0.0396, 0.2252],
        [0.0364, 0.001, 0.0034, 0.0005, 0.0277, 0.008, 0.0658, 0.1443],
    ]

    if add_inputs:
        for p in pops:
            proj = Projection(
                id="proj_input_%s" % p,
                presynaptic="%s_input" % p,
                postsynaptic=p,
                synapse=e_syn.id,
                delay=2,
                weight="input_weight",
            )
            proj.one_to_one_connector = OneToOneConnector()
            net.projections.append(proj)

    for pre_i in range(len(pops)):
        for post_i in range(len(pops)):
            pre = pops[pre_i]
            post = pops[post_i]
            prob = conn_probs[post_i][pre_i]  #######   TODO: check!!!!
            weight = 1
            syn = e_syn
            if prob > 0:
                if "I" in pre:
                    weight = -1
                    syn = i_syn
                proj = Projection(
                    id="proj_%s_%s" % (pre, post),
                    presynaptic=pre,
                    postsynaptic=post,
                    synapse=syn.id,
                    delay=1,
                    weight=weight,
                )
                proj.random_connectivity = RandomConnectivity(probability=prob)
                net.projections.append(proj)

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

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

    record_traces = {}
    record_spikes = {}

    from neuromllite.utils import evaluate

    for p in pops:
        forecast_size = evaluate(pop_dict[p].size, net.parameters)
        record_traces[p] = list(range(min(2, forecast_size)))
        record_spikes[p] = "*"
    for ip in input_pops:
        record_spikes[ip] = "*"

    sim = Simulation(
        id="Sim%s" % net.id,
        network=new_file,
        duration="100",
        dt="0.025",
        seed=1234,
        record_traces=record_traces,
        record_spikes=record_spikes,
    )

    sim.to_json_file()

    return sim, net


if __name__ == "__main__":
    if "-noinputs" in sys.argv:
        sim, net = generate("Example6_PyNN_noinputs", False)
    else:
        sim, net = generate("Example6_PyNN", True)

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

    from neuromllite.NetworkGenerator import check_to_generate_or_run

    check_to_generate_or_run(sys.argv, sim)