c302_MusclesSine.py

import c302
import sys
import importlib


def setup(
    parameter_set,
    generate=False,
    duration=1000,
    dt=0.05,
    target_directory="examples",
    data_reader="SpreadsheetDataReader",
    param_overrides={},
    config_param_overrides={},
    verbose=True,
):
    ParameterisedModel = getattr(
        importlib.import_module("c302.parameters_%s" % parameter_set),
        "ParameterisedModel",
    )
    params = ParameterisedModel()

    params.set_bioparameter(
        "unphysiological_offset_current", "0pA", "Disabling offset current", "0"
    )

    # params.set_bioparameter("exc_syn_conductance", ".20 nS", "BlindGuess", "0.1")
    params.set_bioparameter("chem_exc_syn_decay", "5 ms", "BlindGuess", "0.1")

    # params.set_bioparameter("inh_syn_conductance", ".35 nS", "BlindGuess", "0.1")
    params.set_bioparameter("chem_inh_syn_decay", "200 ms", "BlindGuess", "0.1")

    # params.set_bioparameter("elec_syn_gbase", "0.001 nS", "BlindGuess", "0.1")

    # Any neurons connected to muscles

    cells = [
        "AS1",
        "AS10",
        "AS11",
        "AS2",
        "AS3",
        "AS4",
        "AS5",
        "AS6",
        "AS7",
        "AS8",
        "AS9",
        "AVFL",
        "AVFR",
        "AVKR",
        "AVL",
        "CEPVL",
        "CEPVR",
        "DA1",
        "DA2",
        "DA3",
        "DA4",
        "DA5",
        "DA6",
        "DA7",
        "DA8",
        "DA9",
        "DB1",
        "DB2",
        "DB3",
        "DB4",
        "DB5",
        "DB6",
        "DB7",
        "DD1",
        "DD2",
        "DD3",
        "DD4",
        "DD5",
        "DD6",
        "DVB",
        "HSNL",
        "HSNR",
        "IL1DL",
        "IL1DR",
        "IL1L",
        "IL1R",
        "IL1VL",
        "IL1VR",
        "PDA",
        "PDB",
        "PVNL",
        "PVNR",
        "RID",
        "RIML",
        "RIMR",
        "RIVL",
        "RIVR",
        "RMDDL",
        "RMDDR",
        "RMDL",
        "RMDR",
        "RMDVL",
        "RMDVR",
        "RMED",
        "RMEL",
        "RMER",
        "RMEV",
        "RMFL",
        "RMGL",
        "RMGR",
        "RMHL",
        "RMHR",
        "SMBDL",
        "SMBDR",
        "SMBVL",
        "SMBVR",
        "SMDDL",
        "SMDDR",
        "SMDVL",
        "SMDVR",
        "URADL",
        "URADR",
        "URAVL",
        "URAVR",
        "VA1",
        "VA10",
        "VA11",
        "VA12",
        "VA2",
        "VA3",
        "VA4",
        "VA5",
        "VA6",
        "VA7",
        "VA8",
        "VA9",
        "VB1",
        "VB10",
        "VB11",
        "VB2",
        "VB3",
        "VB4",
        "VB5",
        "VB6",
        "VB7",
        "VB8",
        "VB9",
        "VC1",
        "VC2",
        "VC3",
        "VC4",
        "VC5",
        "VC6",
        "VD1",
        "VD10",
        "VD11",
        "VD12",
        "VD13",
        "VD2",
        "VD3",
        "VD4",
        "VD5",
        "VD6",
        "VD7",
        "VD8",
        "VD9",
    ]

    cells += ["AVAL", "AVAR", "AVBL", "AVBR", "AVDL", "AVDR", "PVCL", "PVCR"]
    # cells=None  # implies all cells...

    ## Some random set of neurons
    # probability = 0.1
    cells_to_stimulate = []
    """
    for cell in cells:
        #if random.random()<probability:
        #    cells_to_stimulate.append(cell)
        if cell.startswith("xxVB") or cell.startswith("DB"):
            cells_to_stimulate.append(cell)"""
    # cells_to_stimulate = ['DB1', 'VB1']

    # cells_to_stimulate = ['PVCL', 'AVBL']
    # cells_to_stimulate.extend(['DB1', 'VB1'])
    # cells_to_stimulate = ['PVCL','PVCR']
    # cells_to_stimulate = ['PLML','PLMR']
    cells_to_stimulate = ["AVBL", "AVBR"]

    # Plot some directly stimulated & some not stimulated
    # cells_to_plot      = ['AS1', 'AS10', 'AVFL', 'DA1','DB1','DB4','DB7','IL1DL','RID', 'RIML','SMBDL', 'SMBDR', 'VB1', 'VB5', 'VB10','VC1', 'VC2']
    cells_to_plot = [
        "AVBL",
        "AVBR",
        "PVCL",
        "PVCR",
        "DB1",
        "DB2",
        "VB1",
        "VB2",
        "DD1",
        "DD2",
        "VD1",
        "VD2",
    ]

    reference = "c302_%s_MusclesSine" % parameter_set

    muscles_to_include = True  # includes all muscles in plots
    nml_doc = None

    if generate:
        nml_doc = c302.generate(
            reference,
            params,
            cells=cells,
            cells_to_plot=cells_to_plot,
            cells_to_stimulate=cells_to_stimulate,
            muscles_to_include=muscles_to_include,
            duration=duration,
            dt=dt,
            target_directory=target_directory,
            param_overrides=param_overrides,
            verbose=verbose,
            data_reader=data_reader,
        )

    # Import from libNeuroML
    from neuroml import SineGenerator, InputList, Input
    import neuroml.writers as writers

    # Create the sine wave current generator & add to NeuroML document
    sw_input = SineGenerator(
        id="NewSineWaveInput",
        delay="100ms",
        phase="0",
        duration="800ms",
        amplitude="4.5pA",
        period="200ms",
    )

    nml_doc.sine_generators.append(sw_input)

    # Which cell to stimulate
    cell = "AVBL"

    # create an InputList and add one Input to that cell
    input_list = InputList(
        id="Input_%s_%s" % (cell, sw_input.id),
        component=sw_input.id,
        populations="%s" % cell,
    )
    input_list.input.append(
        Input(id=0, target="../%s/0/GenericNeuronCell" % cell, destination="synapses")
    )
    nml_doc.networks[0].input_lists.append(input_list)

    # Write over network file created already...
    nml_file = target_directory + "/" + reference + ".net.nml"
    writers.NeuroMLWriter.write(nml_doc, nml_file)

    c302.print_("(Re)written network file to: " + nml_file)

    return cells, cells_to_stimulate, params, muscles_to_include, nml_doc


if __name__ == "__main__":
    parameter_set = sys.argv[1] if len(sys.argv) == 2 else "A"

    setup(parameter_set, generate=True)