Source code for bmtk.simulator.bionet.nrn

# Copyright 2017. Allen Institute. All rights reserved
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import sys
import os
import glob
import neuron
from neuron import h

from bmtk.simulator.bionet.pyfunction_cache import py_modules
from bmtk.simulator.bionet.pyfunction_cache import load_py_modules
from bmtk.simulator.bionet.pyfunction_cache import synapse_model, synaptic_weight, cell_model
from bmtk.simulator.bionet.io_tools import io


pc = h.ParallelContext()



[docs]def quit_execution(): # quit the execution with a message
    pc.done()
    sys.exit()
    return




[docs]def clear_gids():
    pc.gid_clear()
    pc.barrier()




[docs]def load_neuron_modules(mechanisms_dir, templates_dir, default_templates=True):
    """

    :param mechanisms_dir:
    :param templates_dir:
    :param default_templates:
    """
    h.load_file('stdgui.hoc')

    bionet_dir = os.path.dirname(__file__)
    h.load_file(os.path.join(bionet_dir, 'import3d.hoc').replace("\\","/"))  # customized import3d.hoc to supress warnings
    h.load_file(os.path.join(bionet_dir,'default_templates',  'advance.hoc').replace("\\","/"))

    if isinstance(mechanisms_dir, list):
        for mdir in mechanisms_dir:
            try:
                neuron.load_mechanisms(str(mdir))
            except RuntimeError as rte:
                io.log_warning('Unable to load NEURON mechanisms.', display_once=True)

    elif mechanisms_dir is not None:
        try:
            neuron.load_mechanisms(str(mechanisms_dir))
        except RuntimeError as rte:
            io.log_warning('Unable to load NEURON mechanisms.', display_once=True)

    if default_templates:
        load_templates(os.path.join(bionet_dir, 'default_templates'))

    if templates_dir:
        load_templates(templates_dir)




[docs]def load_templates(template_dir):
    """Load all templates to be available in the hoc namespace for instantiating cells"""
    cwd = os.getcwd()
    os.chdir(template_dir)

    hoc_templates = glob.glob("*.hoc")

    for hoc_template in hoc_templates:
        h.load_file(str(hoc_template))

    os.chdir(cwd)




[docs]def reset():
    pc.gid_clear()
    pc.barrier()