Human-L2-3-Cortical-Microcircuit/NeuroML2/cellmorph2nml.py

#!/usr/bin/env python3
"""
Convert cell morphology to NeuroML.

We only export morphologies here. We add the biophysics manually.

File: NeuroML2/scripts/cell2nml.py

Copyright 2022 Ankur Sinha
Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
"""

import os
import sys

import pyneuroml
from pyneuroml.neuron import export_to_neuroml2
from neuron import h


def main(acell):
    """Main runner method.

    :param acell: name of cell
    :returns: None

    """
    loader_hoc_file = f"{acell}_loader.hoc"
    loader_hoc_file_txt = f"""
    /*load_file("nrngui.hoc")*/
    load_file("stdrun.hoc")

    //=================== creating cell object ===========================
    load_file("import3d.hoc")
    objref newcell

    strdef morphology_file
    morphology_file = "../L23Net/morphologies/{acell}.swc"

    load_file("../L23Net/models/NeuronTemplate.hoc")
    newcell = new NeuronTemplate(morphology_file)

    define_shape()
    """

    with open(loader_hoc_file, 'w') as f:
        print(loader_hoc_file_txt, file=f)

    export_to_neuroml2(loader_hoc_file, f"{acell}.morph.cell.nml",
                       includeBiophysicalProperties=False, validate=False)

    os.remove(loader_hoc_file)


if __name__ == "__main__":
    if len(sys.argv) != 2:
        print("This script only accepts one argument.")
        sys.exit(1)
    main(sys.argv[1])