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Last modified by galluzziandrea on 2022/06/20 12:33
From version 17.1
edited by galluzziandrea
on 2022/01/27 17:07
Change comment: Uploaded new attachment "image-20220127170722-1.png", version {1}
To version 8.1
edited by galluzziandrea
on 2021/12/09 14:58
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... ... @@ -323,213 +323,6 @@
323 323  endbuild = time.time()
324 324  {{/code}}
325 325  
326 -=== [[image:image-20220127165908-2.png||height="659" width="1149"]] ===
326 +=== Results ===
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 -
535 535  ==== ====
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