def run_once(self, job_dir, ** kwargs):
from neuromllite.utils import print_v
from neuromllite.utils import load_simulation_json,load_network_json
from neuromllite.NetworkGenerator import generate_and_run
from pyneuroml.pynml import get_value_in_si
print_v('Running NeuroMLlite simulation in dir: %s...'%job_dir)
sim = load_simulation_json(self.nmllite_sim)
import random
sim.id = '%s%s'%(sim.id, '_%s'%kwargs['reference'] if 'reference' in kwargs else '')
network = load_network_json(self.base_dir+'/'+sim.network)
for a in kwargs:
if a in network.parameters:
print_v(' Setting %s to %s in network...'%(a, kwargs[a]))
network.parameters[a] = kwargs[a]
elif a in sim.fields:
print_v(' Setting %s to %s in simulator...'%(a, kwargs[a]))
setattr(sim,a,kwargs[a])
else:
print_v(' Cannot set parameter %s to %s in network or simulator...'%(a, kwargs[a]))
traces, events = generate_and_run(sim,
simulator = self.simulator,
network = network,
return_results = True,
base_dir = self.base_dir,
target_dir = job_dir)
print_v("Returned traces: %s, events: %s"%(traces.keys(), events.keys()))
return traces, events
def runSimulation(self):
"""Run a simulation in the chosen simulator"""
simulator = str(self.simulatorComboBox.currentText())
print(
"Run button was clicked. Running simulation %s in %s with %s"
% (self.simulation.id, self.sim_base_dir, simulator)
)
self.tabs.setCurrentWidget(self.simTab)
self.update_net_sim()
from neuromllite.NetworkGenerator import generate_and_run
# return
try:
self.current_traces, self.current_events = generate_and_run(
self.simulation,
simulator=simulator,
network=self.network,
return_results=True,
base_dir=self.sim_base_dir,
)
self.replotSimResults()
except Exception as e:
self.dialog_popup("Error: %s" % e)
def showLemsView(self):
"""Generate lemsView button has been pressed"""
print_v("lemsView button was clicked.")
self.update_net_sim()
self.tabs.setCurrentWidget(self.all_tabs[self.LEMS_VIEW_TAB])
self.update_net_sim()
from neuromllite.NetworkGenerator import generate_neuroml2_from_network
from neuromllite.NetworkGenerator import generate_and_run
lems_file_name = generate_and_run(self.simulation,
simulator='jNeuroML_norun',
network=self.network,
return_results=True,
base_dir=self.sim_base_dir)
post_args = "-graph"
from pyneuroml.pynml import run_jneuroml
run_jneuroml("",
lems_file_name,
post_args,
verbose = True)
lems_view_file = lems_file_name.replace('.xml','.png')
self.add_image(lems_view_file, self.LEMS_VIEW_TAB)
mod_graph = model.graphs[0]
print("Loaded Graph:")
print_summary(mod_graph)
print("------------------")
nmllite_file = example.replace(".json", ".nmllite.json")
net, sim = mdf_to_neuroml(mod_graph,
save_to=nmllite_file,
format=model.format,
run_duration_sec=2)
if run:
sf = "%s.json" % sim.id
print("Running the model: %s" % sf)
from neuromllite.NetworkGenerator import generate_and_run
simulator = "jNeuroML"
traces, events = generate_and_run(
sim,
simulator,
network=net,
return_results=True,
base_dir=None,
target_dir=None,
num_processors=1,
)
for t in traces:
if t != "t": # the time array
print(" {} = {}".format(t, traces[t][-1]))