def createExportNeuroML2(netParams=None,
simConfig=None,
reference=None,
connections=True,
stimulations=True,
output=False):
''' Sequence of commands to create and export network to NeuroML2 '''
import __main__ as top
if not netParams: netParams = top.netParams
if not simConfig: simConfig = top.simConfig
sim.initialize(
netParams,
simConfig) # create network object and set cfg and net params
pops = sim.net.createPops() # instantiate network populations
cells = sim.net.createCells(
) # instantiate network cells based on defined populations
conns = sim.net.connectCells(
) # create connections between cells based on params
stims = sim.net.addStims(
) # add external stimulation to cells (IClamps etc)
simData = sim.setupRecording(
) # setup variables to record for each cell (spikes, V traces, etc)
sim.exportNeuroML2(
reference, connections,
stimulations) # export cells and connectivity to NeuroML 2 format
if output: return (pops, cells, conns, stims, simData)
def load(filename,
simConfig=None,
output=False,
instantiate=True,
createNEURONObj=True):
''' Sequence of commands load, simulate and analyse network '''
import sim
sim.initialize() # create network object and set cfg and net params
sim.cfg.createNEURONObj = createNEURONObj
sim.loadAll(filename,
instantiate=instantiate,
createNEURONObj=createNEURONObj)
if simConfig:
sim.setSimCfg(simConfig) # set after to replace potentially loaded cfg
if len(sim.net.cells) == 0 and instantiate:
pops = sim.net.createPops() # instantiate network populations
cells = sim.net.createCells(
) # instantiate network cells based on defined populations
conns = sim.net.connectCells(
) # create connections between cells based on params
stims = sim.net.addStims(
) # add external stimulation to cells (IClamps etc)
simData = sim.setupRecording(
) # setup variables to record for each cell (spikes, V traces, etc)
if output:
try:
return (pops, cells, conns, stims, simData)
except:
pass