from mrj.model.experiment import Experiment
from mrj.model.experiment import Neuron_passive_parameter
from mrj.model.experiment import plot
swc_parser = SwcParser()
m_swc = swc_parser.parse("../../../Data/test.swc") #slow swc_parser.parse("../../Data/MSO_Neurone/P09/ohne_axon_SkeletonTree_0015_2-1G.swc")
m_swc.neuron_create() # initialisiert die Synapse in NEURON
compartment = m_swc.compartments[5]
s = Synapse(compartment, 0.5, syntimes=getSynapticActivity(f=200, duration=5, sigma=0, fireing_rate=1, delay=0))#TODO: ??delta_time > 5
s.neuron_create()
clamp = IClamp(compartment=compartment, position=0.5, delay=1,amplitude=0,duration=3)#VClamp
neuron_passive_parameter = \
Neuron_passive_parameter(Ra=1, g=0.004, e=-60, nseg=10)
f = Experiment(m_swc, clamp, neuron_passive_parameter,
description='passive channels')
f.neuron_create()
r_in, tau_eff = f.run_simulation(duration=20,dt=0.001)
tau_eff_fit = f.tau_fit()
#TODO: ?why can linfit fail?
import math
if math.isnan(tau_eff_fit):
tau_eff_fit = 1
print (tau_eff, tau_eff_fit)
#print (r_in, tau_eff, f.tau_fit());
#f.plot_fit(r_in, tau_eff, tau_eff_fit, save=False)
plot( [f] );#[e] works, (e) is flattend
morphology = db.load_morphology( 256 ) print morphology #morphology.create_tree() clamp = IClamp(morphology.root.children[0]) neuron_passive_parameter = Neuron_passive_parameter(Ra=80) experiment = Experiment(morphology, clamp, neuron_passive_parameter) print experiment db.store( experiment ) #TODO: change compartments needs group group mapping #c = m.getCompartment( 5 ) #c = m.getCompartment( 7 ) experiment.neuron_create() experiment.run_simulation() result = experiment.get_result() print result db.store( result ) e = db.load_experiment( experiment.experiment_key ) print e e.run_simulation() r = e.get_result() print r experiment.plot_fit(r.r_in, r.tau_eff, r.tau_eff_fit) plot( [experiment] ) # [e] works, (e) is flattend