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()