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...	...	@@ -323,6 +323,213 @@
323	323	endbuild = time.time()
324	324	{{/code}}
325	325
326		-=== Results ===
	326	+=== [[image:image-20220127165908-2.png||height="659" width="1149"]] ===
327	327
	328	+=== Connecting the network nodes: neuronal populations, Poisson processes and spike detectors ===
	329	+
	330	+{{code language="python"}}
	331	+#############################------------------------------------------------------------------------
	332	+print("Connecting ")
	333	+#############################------------------------------------------------------------------------
	334	+
	335	+startconnect = time.time()
	336	+Connessioni=[]
	337	+Medie=[]
	338	+
	339	+#create and define the connections between the populations of neurons and the poisson generators
	340	+#and between the populations of neurons and the spike detectors with the parameters extracted from the.ini files
	341	+
	342	+for i in range(0,int(InfoBuild[0])):
	343	+ nest.Connect(NoisePop[i], NeuronPop[i], syn_spec={'synapse_model': 'static_synapse_hpc',
	344	+ 'delay': dt,
	345	+ 'weight': nest.math.redraw(nest.random.normal(mean=float(InfoConnectNoise[i+1][0]),
	346	+ std=(float(InfoConnectNoise[i+1][1])*float(InfoConnectNoise[i+1][0]))),
	347	+ min=0., max=float('Inf'))
	348	+ })
	349	+ nest.Connect(NeuronPop[i][:int(InfoBuild[i+1][0])], DetectorPop[i], syn_spec={"weight": 1.0, "delay": dt})
	350	+
	351	+#create and define the connections between the populations of neurons with the parameters extracted from the.ini files
	352	+
	353	+for i in range(0,len(InfoConnectPop[1:])):
	354	+
	355	+ conn=nest.Connect(NeuronPop[int(InfoConnectPop[i+1][1])], NeuronPop[int(InfoConnectPop[i+1][0])],
	356	+ {'rule': 'pairwise_bernoulli',
	357	+ 'p':float(InfoConnectPop[i+1][2]) },
	358	+ syn_spec={'synapse_model': 'static_synapse_hpc',
	359	+ 'delay':nest.math.redraw(nest.random.exponential(beta=float(1./(2.99573227355/(float(InfoConnectPop[i+1][4])-float(InfoConnectPop[i+1][3]))))),
	360	+ min= numpy.max([dt,float(1./float(InfoConnectPop[i+1][4]))]),
	361	+ max= float(1./(float(InfoConnectPop[i+1][3])-dt/2))),
	362	+
	363	+ 'weight':nest.random.normal(mean=float(InfoConnectPop[i+1][6]),
	364	+ std=math.fabs(float(InfoConnectPop[i+1][6])*float(InfoConnectPop[i+1][7])))})
	365	+
	366	+
	367	+endconnect = time.time()
	368	+{{/code}}
	369	+
	370	+=== ===
	371	+
	372	+=== ===
	373	+
	374	+(% class="wikigeneratedid" %)
	375	+=== [[image:image-20220127170104-1.png||height="630" width="1430"]] ===
	376	+
	377	+(% class="wikigeneratedid" %)
	378	+=== ===
	379	+
	380	+(% class="wikigeneratedid" %)
	381	+=== ===
	382	+
	383	+=== Simulating: neuronal time evolution. ===
	384	+
	385	+=== ===
	386	+
	387	+{{code language="python"}}
	388	+ #############################------------------------------------------------------------------------
	389	+ print("Simulating")
	390	+ #############################------------------------------------------------------------------------
	391	+ ###################################################################################################################################################################
	392	+ if Salva:
	393	+ print("I m going to save the data")
	394	+ #x=str(iterazioni)
	395	+ f = open(FileName,"w")
	396	+ if len(InfoProtocol):
	397	+ print("I m going to split the simulation")
	398	+ tempo=0
	399	+ for contatore in range(0,len(InfoProtocol)):
	400	+ appoggio1=int((tempo+InfoProtocol[contatore][0])/1000.)
	401	+ appoggio2=int(tempo/1000.)
	402	+ appoggio3=tempo+InfoProtocol[contatore][0]
	403	+ if (appoggio1-appoggio2)>=1:
	404	+ T1=(1+appoggio2)*1000-tempo
	405	+ nest.Simulate(T1)
	406	+ #Save the Data!!!!
	407	+ ###########################################################
	408	+ Equilibri=[]
	409	+ for i in range(0,int(InfoBuild[0])):
	410	+ Equilibri.append([])
	411	+ a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
	412	+ if len(a)>0:
	413	+ Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
	414	+ hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
	415	+ Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
	416	+ else:
	417	+ Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
	418	+ hist=numpy.zeros(200)
	419	+ Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
	420	+ Equilibri[i]=hist
	421	+ nest.SetStatus(DetectorPop[i],{'n_events':0})
	422	+ for j in range(0,len(hist)):
	423	+ f.write(str(Tbin[j])+" ")
	424	+ for i in range(0,int(InfoBuild[0])):
	425	+ f.write(str(Equilibri[i][j])+" ")
	426	+ f.write("\n ")
	427	+ ###########################################################
	428	+ tempo=tempo+T1
	429	+ for contatore2 in range(1,(appoggio1-appoggio2)):
	430	+ nest.Simulate(1000.)
	431	+ #Save the Data!!!!
	432	+ ###########################################################
	433	+ Equilibri=[]
	434	+ for i in range(0,int(InfoBuild[0])):
	435	+ Equilibri.append([])
	436	+ a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
	437	+ if len(a)>0:
	438	+ Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
	439	+ hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
	440	+ Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
	441	+ else:
	442	+ Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
	443	+ hist=numpy.zeros(200)
	444	+ Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
	445	+ Equilibri[i]=hist
	446	+ nest.SetStatus(DetectorPop[i],{'n_events':0})
	447	+ for j in range(0,len(hist)):
	448	+ f.write(str(Tbin[j])+" ")
	449	+ for i in range(0,int(InfoBuild[0])):
	450	+ f.write(str(Equilibri[i][j])+" ")
	451	+ f.write("\n ")
	452	+ tempo=tempo+1000.
	453	+ T2=appoggio3-tempo
	454	+ nest.Simulate(T2);
	455	+ tempo=tempo+T2;
	456	+ else:
	457	+ nest.Simulate(InfoProtocol[contatore][0])
	458	+ temp=InfoProtocol[contatore][0]
	459	+ tempo=tempo+temp
	460	+ if InfoProtocol[contatore][2]==4:
	461	+ nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
	462	+ if InfoProtocol[contatore][2]==12:
	463	+ nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
	464	+ else:
	465	+ nest.Simulate(simtime)
	466	+ tempo=simtime
	467	+ if (simtime-tempo)>0.:
	468	+ nest.Simulate(simtime-tempo)
	469	+
	470	+
	471	+ endsimulate = time.time()
	472	+ f.close()
	473	+ else:
	474	+ if len(InfoProtocol):
	475	+ tempo=0
	476	+ for contatore in range(0,len(InfoProtocol)):
	477	+ nest.Simulate(InfoProtocol[contatore][0])
	478	+ temp=InfoProtocol[contatore][0]
	479	+ tempo=tempo+temp
	480	+ if InfoProtocol[contatore][2]==4:
	481	+ nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
	482	+ #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
	483	+ if InfoProtocol[contatore][2]==12:
	484	+ nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
	485	+ #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
	486	+
	487	+ else:
	488	+ nest.Simulate(simtime)
	489	+ tempo=simtime
	490	+ if (simtime-tempo)>0.:
	491	+ nest.Simulate(simtime-tempo)
	492	+ endsimulate = time.time()
	493	+
	494	+
	495	+ ###################################################################################################################################################################
	496	+
	497	+ #############################------------------------------------------------------------------------
	498	+ #print some information from the simulation
	499	+ #############################------------------------------------------------------------------------
	500	+
	501	+ num_synapses = nest.GetDefaults('static_synapse_hpc')["num_connections"]
	502	+ build_time = endbuild - startbuild
	503	+ connect_time = endconnect - startconnect
	504	+ sim_time = endsimulate - endconnect
	505	+
	506	+ N_neurons=0
	507	+ for i in range(0,int(InfoBuild[0])):
	508	+ N_neurons=N_neurons+int(InfoBuild[i+1][0])
	509	+
	510	+ print(" Network simulation (Python) neuron type:",InfoPerseo[0])
	511	+ print("Number of neurons : {0}".format(N_neurons))
	512	+ print("Number of synapses: {0}".format(num_synapses))
	513	+ print("Building time : %.2f s" % build_time)
	514	+ print("Connecting time : %.2f s" % connect_time)
	515	+ print("Simulation time : %.2f s" % sim_time)
	516	+
	517	+Fine=time.time()
	518	+print ("Total Simulation time : %.2f s" % (Fine-Inizio))
	519	+{{/code}}
	520	+
	521	+=== ===
	522	+
	523	+(% class="wikigeneratedid" %)
	524	+=== [[image:image-20220127170155-2.png||height="682" width="1439"]] ===
	525	+
	526	+=== Results: ===
	527	+
	528	+the output of this simulationo is...
	529	+
	530	+
	531	+
	532	+
	533	+
	534	+
328	328	==== ====

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