def simulateModel(self):
"""
Simulates model
Returns
-------
SimConfig
generated SimConfig
"""
sim.setupRecording()
sim.simulate()
sim.saveData()
return sim
import time
from netpyne import sim # import netpyne init module
from neuron import h
simConfig, netParams = sim.readCmdLineArgs('cfg.py', 'netParams.py')
sim.create(simConfig=simConfig, netParams=netParams)
seed = int(time.time() * 1e7) & 0xffffffff
rndm = sim.h.Random()
rndm.Random123(
sim.rank, 0, 0
) #initialize with seed as second argument to achieve different results for each run
for TCsoma in [
x.secs.soma for x in sim.net.cells if x.tags['cellType'] == 'TC'
]:
TCsoma.hObj.ghbar_iar = rndm.normal(17.5, 0.0008) * 1e-6
TCsoma.pointps.kleak_0.hObj.gmax = rndm.normal(40, 0.003) * 1e-4
sim.simulate()
sim.analyze()
def simulateNetPyNEModel(self):
with redirect_stdout(sys.__stdout__):
sim.setupRecording()
sim.simulate()
sim.saveData()
return sim
def run():
sim.simulate()
def run (): sim.simulate() def plot (): sim.analysis.plotData()
sim.saveData() # save params, cell info and sim output to file (pickle,mat,txt,etc)
sim.analysis.plotData() # plot spike raster
# ###############################################################################
# # INTERACTING WITH INSTANTIATED NETWORK
# ###############################################################################
# modify conn weights
sim.net.modifyConns({'conds': {'label': 'hop->hop'}, 'weight': 0.5})
sim.runSim() # run parallel Neuron simulation
sim.gatherData() # gather spiking data and cell info from each node
sim.saveData() # save params, cell info and sim output to file (pickle,mat,txt,etc)
sim.analysis.plotData() # plot spike raster
# modify cells geometry
sim.net.modifyCells({'conds': {'popLabel': 'hop'},
'secs': {'soma': {'geom': {'L': 160}}}})
sim.simulate()
sim.analysis.plotRaster(syncLines=True)
sim.analysis.plotTraces(include = [1])
from netpyne import sim from itertools import product from npvec import npvec import numpy as np import matplotlib.pyplot as plt cfg, netParams = sim.readCmdLineArgs() sim.create(simConfig=cfg, netParams=netParams) sim.simulate() # calls runSim() and gatherData() sim.analyze()
def _run_in_same_process(self):
logging.debug('Running single core simulation')
sim.setupRecording()
sim.simulate()
sim.saveData()
