def evaluateSimulation(traj):
rid = traj.id
logging.info("Running run id {}".format(rid))
model = evolution.getModelFromTraj(traj)
model.params["dt"] = 0.2
model.params["duration"] = 2 * 1000.0
model.run()
# -------- fitness evaluation here --------
# example: get dominant frequency of activity
frs, powers = func.getPowerSpectrum(
model.rates_exc[:, -int(1000 / model.params["dt"]):],
model.params["dt"],
)
domfr = frs[np.argmax(powers)]
fitness = abs(domfr - 25) # let's try to find a 25 Hz oscillation
fitness_tuple = ()
fitness_tuple += (fitness, )
return fitness_tuple, model.outputs
def evaluateSimulation(traj):
model = evolution.getModelFromTraj(traj)
model.run()
# compute power spectrum
frs, powers = func.getPowerSpectrum(
model.x[:, -int(1000 / model.params["dt"]):],
dt=model.params["dt"])
# find the peak frequency
domfr = frs[np.argmax(powers)]
# fitness evaluation: let's try to find a 25 Hz oscillation
fitness = abs(domfr - 25)
# deap needs a fitness *tuple*!
fitness_tuple = ()
# more fitness values could be added
fitness_tuple += (fitness, )
# we need to return the fitness tuple and the outputs of the model
return fitness_tuple, model.outputs
def test_getPowerSpectrum(self):
fr, pw = func.getPowerSpectrum(self.model.rates_exc[0, :],
dt=self.model.params["dt"])