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Last modified by galluzziandrea on 2022/06/20 12:33
From version 9.1
edited by galluzziandrea
on 2021/12/09 15:04
Change comment: There is no comment for this version
To version 8.1
edited by galluzziandrea
on 2021/12/09 14:58
Change comment: There is no comment for this version

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... ... @@ -323,197 +323,6 @@
323 323  endbuild = time.time()
324 324  {{/code}}
325 325  
326 -=== Connecting the network nodes: neuronal populations, Poisson processes and spike detectors ===
327 -
328 -{{code language="python"}}
329 -#############################------------------------------------------------------------------------
330 -print("Connecting ")
331 -#############################------------------------------------------------------------------------
332 -
333 -startconnect = time.time()
334 -Connessioni=[]
335 -Medie=[]
336 -
337 -#create and define the connections between the populations of neurons and the poisson generators
338 -#and between the populations of neurons and the spike detectors with the parameters extracted from the.ini files
339 -
340 -for i in range(0,int(InfoBuild[0])):
341 - nest.Connect(NoisePop[i], NeuronPop[i], syn_spec={'synapse_model': 'static_synapse_hpc',
342 - 'delay': dt,
343 - 'weight': nest.math.redraw(nest.random.normal(mean=float(InfoConnectNoise[i+1][0]),
344 - std=(float(InfoConnectNoise[i+1][1])*float(InfoConnectNoise[i+1][0]))),
345 - min=0., max=float('Inf'))
346 - })
347 - nest.Connect(NeuronPop[i][:int(InfoBuild[i+1][0])], DetectorPop[i], syn_spec={"weight": 1.0, "delay": dt})
348 -
349 -#create and define the connections between the populations of neurons with the parameters extracted from the.ini files
350 -
351 -for i in range(0,len(InfoConnectPop[1:])):
352 -
353 - conn=nest.Connect(NeuronPop[int(InfoConnectPop[i+1][1])], NeuronPop[int(InfoConnectPop[i+1][0])],
354 - {'rule': 'pairwise_bernoulli',
355 - 'p':float(InfoConnectPop[i+1][2]) },
356 - syn_spec={'synapse_model': 'static_synapse_hpc',
357 - 'delay':nest.math.redraw(nest.random.exponential(beta=float(1./(2.99573227355/(float(InfoConnectPop[i+1][4])-float(InfoConnectPop[i+1][3]))))),
358 - min= numpy.max([dt,float(1./float(InfoConnectPop[i+1][4]))]),
359 - max= float(1./(float(InfoConnectPop[i+1][3])-dt/2))),
360 -
361 - 'weight':nest.random.normal(mean=float(InfoConnectPop[i+1][6]),
362 - std=math.fabs(float(InfoConnectPop[i+1][6])*float(InfoConnectPop[i+1][7])))})
363 -
364 -
365 -endconnect = time.time()
366 -{{/code}}
367 -
368 -=== ===
369 -
370 -=== ===
371 -
372 -=== Simulating: neuronal time evolution. ===
373 -
374 -=== ===
375 -
376 -{{code language="python"}}
377 - #############################------------------------------------------------------------------------
378 - print("Simulating")
379 - #############################------------------------------------------------------------------------
380 - ###################################################################################################################################################################
381 - if Salva:
382 - print("I m going to save the data")
383 - #x=str(iterazioni)
384 - f = open(FileName,"w")
385 - if len(InfoProtocol):
386 - print("I m going to split the simulation")
387 - tempo=0
388 - for contatore in range(0,len(InfoProtocol)):
389 - appoggio1=int((tempo+InfoProtocol[contatore][0])/1000.)
390 - appoggio2=int(tempo/1000.)
391 - appoggio3=tempo+InfoProtocol[contatore][0]
392 - if (appoggio1-appoggio2)>=1:
393 - T1=(1+appoggio2)*1000-tempo
394 - nest.Simulate(T1)
395 - #Save the Data!!!!
396 - ###########################################################
397 - Equilibri=[]
398 - for i in range(0,int(InfoBuild[0])):
399 - Equilibri.append([])
400 - a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
401 - if len(a)>0:
402 - Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
403 - hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
404 - Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
405 - else:
406 - Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
407 - hist=numpy.zeros(200)
408 - Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
409 - Equilibri[i]=hist
410 - nest.SetStatus(DetectorPop[i],{'n_events':0})
411 - for j in range(0,len(hist)):
412 - f.write(str(Tbin[j])+" ")
413 - for i in range(0,int(InfoBuild[0])):
414 - f.write(str(Equilibri[i][j])+" ")
415 - f.write("\n ")
416 - ###########################################################
417 - tempo=tempo+T1
418 - for contatore2 in range(1,(appoggio1-appoggio2)):
419 - nest.Simulate(1000.)
420 - #Save the Data!!!!
421 - ###########################################################
422 - Equilibri=[]
423 - for i in range(0,int(InfoBuild[0])):
424 - Equilibri.append([])
425 - a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
426 - if len(a)>0:
427 - Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
428 - hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
429 - Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
430 - else:
431 - Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
432 - hist=numpy.zeros(200)
433 - Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
434 - Equilibri[i]=hist
435 - nest.SetStatus(DetectorPop[i],{'n_events':0})
436 - for j in range(0,len(hist)):
437 - f.write(str(Tbin[j])+" ")
438 - for i in range(0,int(InfoBuild[0])):
439 - f.write(str(Equilibri[i][j])+" ")
440 - f.write("\n ")
441 - tempo=tempo+1000.
442 - T2=appoggio3-tempo
443 - nest.Simulate(T2);
444 - tempo=tempo+T2;
445 - else:
446 - nest.Simulate(InfoProtocol[contatore][0])
447 - temp=InfoProtocol[contatore][0]
448 - tempo=tempo+temp
449 - if InfoProtocol[contatore][2]==4:
450 - nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
451 - if InfoProtocol[contatore][2]==12:
452 - nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
453 - else:
454 - nest.Simulate(simtime)
455 - tempo=simtime
456 - if (simtime-tempo)>0.:
457 - nest.Simulate(simtime-tempo)
458 -
459 -
460 - endsimulate = time.time()
461 - f.close()
462 - else:
463 - if len(InfoProtocol):
464 - tempo=0
465 - for contatore in range(0,len(InfoProtocol)):
466 - nest.Simulate(InfoProtocol[contatore][0])
467 - temp=InfoProtocol[contatore][0]
468 - tempo=tempo+temp
469 - if InfoProtocol[contatore][2]==4:
470 - nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
471 - #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
472 - if InfoProtocol[contatore][2]==12:
473 - nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
474 - #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
475 -
476 - else:
477 - nest.Simulate(simtime)
478 - tempo=simtime
479 - if (simtime-tempo)>0.:
480 - nest.Simulate(simtime-tempo)
481 - endsimulate = time.time()
482 -
483 -
484 - ###################################################################################################################################################################
485 -
486 - #############################------------------------------------------------------------------------
487 - #print some information from the simulation
488 - #############################------------------------------------------------------------------------
489 -
490 - num_synapses = nest.GetDefaults('static_synapse_hpc')["num_connections"]
491 - build_time = endbuild - startbuild
492 - connect_time = endconnect - startconnect
493 - sim_time = endsimulate - endconnect
494 -
495 - N_neurons=0
496 - for i in range(0,int(InfoBuild[0])):
497 - N_neurons=N_neurons+int(InfoBuild[i+1][0])
498 -
499 - print(" Network simulation (Python) neuron type:",InfoPerseo[0])
500 - print("Number of neurons : {0}".format(N_neurons))
501 - print("Number of synapses: {0}".format(num_synapses))
502 - print("Building time : %.2f s" % build_time)
503 - print("Connecting time : %.2f s" % connect_time)
504 - print("Simulation time : %.2f s" % sim_time)
505 -
506 -Fine=time.time()
507 -print ("Total Simulation time : %.2f s" % (Fine-Inizio))
508 -{{/code}}
509 -
510 -=== ===
511 -
512 512  === Results ===
513 513  
514 -
515 -
516 -
517 -
518 -
519 519  ==== ====