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Last modified by galluzziandrea on 2022/06/20 12:33
From version 8.1
edited by galluzziandrea
on 2021/12/09 14:58
Change comment: There is no comment for this version
To version 16.1
edited by galluzziandrea
on 2022/01/27 17:03
Change comment: There is no comment for this version

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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  ==== ====
image-20220127165822-1.png
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