Source code for bmtk.simulator.bionet.nrn

# Copyright 2017. Allen Institute. All rights reserved
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import sys
import os
import glob
from pathlib import Path
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()




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





def clear_gids():
    pc.gid_clear()
    pc.barrier()





def load_neuron_modules(mechanisms_dir, templates_dir, default_templates=True, use_old_import3d=False):
    """

    :param mechanisms_dir:
    :param templates_dir:
    :param default_templates:
    """
    bionet_dir = os.path.dirname(__file__)
    
    h.load_file('stdgui.hoc')   
    
    if use_old_import3d:
        # Older versions of BMTK used a modified import3d.hoc that is saved in the current directory which
        # due to being out-of-date can have issues with newer HOC models. Should be replaced fully, but 
        # until we know the side-effects have a flag to use the old "import3d.hoc" file
        h.load_file(os.path.join(bionet_dir, 'import3d.hoc').replace("\\","/"))  
    else:
        # This will load the import3d.hoc that is saved as a part of nrniv.
        h.load_file('import3d.hoc')
    
    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)





def load_templates(templates):
    """Load all templates to be available in the hoc namespace for instantiating cells"""
    cwd = os.getcwd()
    templates_list = templates if isinstance(templates, (list, tuple)) else [templates]
    for templates_cont in templates_list:
        if Path(templates_cont).is_dir():
            # If string is a path to a directory, find all hoc files and load them in one at a time.
            # TODO: Add option to sort before loading
            os.chdir(templates_cont)
            hoc_templates = glob.glob("*.hoc")
            for hoc_template in hoc_templates:
                h.load_file(str(hoc_template))
            os.chdir(cwd)
            
        elif Path(templates_cont).is_file():
            # Otherwise if just a file, eg .hoc, load it in separartly.
            h.load_file(str(templates_cont))
        else:
            io.log_warning(f'Unable to find and load {templates_cont} templates. Please ensure it is a valid directory or hoc file!', display_once=True)





def reset():
    pc.gid_clear()
    pc.barrier()