"""Contains the general function run_network used to run a bmtk simulation.
"""
import os,sys,inspect
currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
parentdir = os.path.dirname(currentdir)
#sys.path.insert(0, parentdir)
sys.path.insert(0, currentdir)
from bmtk.simulator import bionet
import numpy as np
from neuron import h
import pandas as pd
[docs]def run_network(callbacks, v_report_all=False, quit_execution=True, random_seed = 42):
"""Runs the standard bmtk simulation and call the given callbacks right before running the simulation.
Parameters
----------
callbacks : list
list of functions to be called before sim.run().
each function will be called with (graph, sim)
v_report_all : bool
whether the v_report should be set to record every section
quit_execution : bool
whether to call bionet.nrn.quit_execution()
return: list
list of returns of the given callbacks
"""
np.random.seed(random_seed)
config_file = 'simulation_config.json'
conf = bionet.Config.from_json(config_file, validate=True)
if v_report_all:
conf["reports"]["v_report"]["sections"] = "all"
conf.build_env()
graph = bionet.BioNetwork.from_config(conf)
sim = bionet.BioSimulator.from_config(conf, network=graph)
callback_returns = []
for c in callbacks:
callback_returns.append(c(graph, sim))
sim.run()
if (quit_execution):
bionet.nrn.quit_execution()
return callback_returns