Changes for page Code description

Last modified by galluzziandrea on 2022/06/20 12:33
From version 7.1
edited by galluzziandrea
on 2021/12/09 14:49
Change comment: There is no comment for this version
To version 14.1
edited by galluzziandrea
on 2022/01/27 17:01
Change comment: Uploaded new attachment "image-20220127170104-1.png", version {1}

Summary

Details

Page properties
Content
... ... @@ -235,9 +235,290 @@
235 235  # [.....],[],...]
236 236  {{/code}}
237 237  
238 +=== Defining general and nest.kernel parameters ===
238 238  
240 +{{code language="python"}}
241 +#############################------------------------------------------------------------------------
242 +#Clean the Network
243 +#############################------------------------------------------------------------------------
244 +nest.ResetKernel()
239 239  
246 +#############################------------------------------------------------------------------------
247 +#insert the introductory parameters of the simulation
248 +#############################------------------------------------------------------------------------
240 240  
241 -=== Results ===
242 242  
251 +dt = 0.1 # the resolution in ms
252 +StartMisure=0. # start time of measurements
253 +simtime = int(float(InfoPerseo[3])) # Simulation time in ms (200 s)
254 +if simtime<=StartMisure: # If the simulation time is less than StartMisure, it is increased by StartMisure
255 + simtime=simtime+StartMisure
256 +start=0.0 # start time of poissonian processes
257 +origin=0.0 # temporal origin
258 +
259 +#############################------------------------------------------------------------------------
260 +# Kernel parameters
261 +#############################------------------------------------------------------------------------
262 +LNT=multiprocessing.cpu_count();
263 +nest.SetKernelStatus({"local_num_threads": LNT})
264 +nest.SetKernelStatus({"resolution": dt, "print_time": True,
265 + "overwrite_files": True})
266 +
267 +#############################------------------------------------------------------------------------
268 +#"randomize" the seeds of the random generators
269 +#############################------------------------------------------------------------------------
270 +
271 +#msd = int(math.fabs(time.process_time()*1000))
272 +#N_vp = nest.GetKernelStatus(['total_num_virtual_procs'])[0]
273 +#pyrngs = [numpy.random.RandomState(s) for s in range(msd, msd+N_vp)]
274 +#nest.SetKernelStatus({"grng_seed" : msd+N_vp})
275 +#nest.SetKernelStatus({"rng_seeds" : list(range(msd+N_vp+1, msd+2*N_vp+1))})
276 +{{/code}}
277 +
278 +=== Building the network: neuronal populations , Poisson processes and spike detectors ===
279 +
280 +{{code language="python"}}
281 +#############################------------------------------------------------------------------------
282 +print("Building network")
283 +#############################------------------------------------------------------------------------
284 +
285 +startbuild = time.time() #initialize the calculation of the time used to simulate
286 +
287 +NeuronPop=[]
288 +NoisePop=[]
289 +DetectorPop=[]
290 +
291 +#define and initialize the populations of neurons with the parameters extracted from the.ini files
292 +for i in range(1,int(InfoBuild[0])+1):
293 + if int(InfoBuild[i][7])==0:
294 + app=float(InfoBuild[i][5])
295 + else:
296 + app=0.
297 + app2= nest.Create("aeif_psc_exp", int(InfoBuild[i][0]),params={"C_m": 1.0,
298 + "g_L": 1.0/float(InfoBuild[i][3]),
299 + "t_ref": float(InfoBuild[i][6]),
300 + "E_L": 0.0,
301 + "V_reset": float(InfoBuild[i][5]),
302 + "V_m": app,
303 + "V_th": float(InfoBuild[i][4]),
304 + "Delta_T": 0.,
305 + "tau_syn_ex": 1.0,
306 + "tau_syn_in": 1.0,
307 + "a": 0.0,
308 + "b": float(InfoBuild[i][10]),
309 + "tau_w": float(InfoBuild[i][9]),
310 + "V_peak":float(InfoBuild[i][4])+10.0})
311 + NeuronPop.append(app2)
312 +
313 +#define and initialize the poisson generators and the spike detectors with the parameters extracted from the.ini files
314 +
315 +for i in range(1,int(InfoBuild[0])+1):
316 + app3= nest.Create("poisson_generator",params={"rate": float(InfoBuild[i][1]*InfoBuild[i][2]),
317 + 'origin':0.,
318 + 'start':start})
319 + NoisePop.append(app3)
320 + app4 = nest.Create("spike_recorder",params={ "start":StartMisure})
321 + DetectorPop.append(app4)
322 +
323 +endbuild = time.time()
324 +{{/code}}
325 +
326 +(% class="wikigeneratedid" %)
327 +=== [[image:image-20220127165908-2.png||height="659" width="1149"]] ===
328 +
329 +=== Connecting the network nodes: neuronal populations, Poisson processes and spike detectors ===
330 +
331 +{{code language="python"}}
332 +#############################------------------------------------------------------------------------
333 +print("Connecting ")
334 +#############################------------------------------------------------------------------------
335 +
336 +startconnect = time.time()
337 +Connessioni=[]
338 +Medie=[]
339 +
340 +#create and define the connections between the populations of neurons and the poisson generators
341 +#and between the populations of neurons and the spike detectors with the parameters extracted from the.ini files
342 +
343 +for i in range(0,int(InfoBuild[0])):
344 + nest.Connect(NoisePop[i], NeuronPop[i], syn_spec={'synapse_model': 'static_synapse_hpc',
345 + 'delay': dt,
346 + 'weight': nest.math.redraw(nest.random.normal(mean=float(InfoConnectNoise[i+1][0]),
347 + std=(float(InfoConnectNoise[i+1][1])*float(InfoConnectNoise[i+1][0]))),
348 + min=0., max=float('Inf'))
349 + })
350 + nest.Connect(NeuronPop[i][:int(InfoBuild[i+1][0])], DetectorPop[i], syn_spec={"weight": 1.0, "delay": dt})
351 +
352 +#create and define the connections between the populations of neurons with the parameters extracted from the.ini files
353 +
354 +for i in range(0,len(InfoConnectPop[1:])):
355 +
356 + conn=nest.Connect(NeuronPop[int(InfoConnectPop[i+1][1])], NeuronPop[int(InfoConnectPop[i+1][0])],
357 + {'rule': 'pairwise_bernoulli',
358 + 'p':float(InfoConnectPop[i+1][2]) },
359 + syn_spec={'synapse_model': 'static_synapse_hpc',
360 + 'delay':nest.math.redraw(nest.random.exponential(beta=float(1./(2.99573227355/(float(InfoConnectPop[i+1][4])-float(InfoConnectPop[i+1][3]))))),
361 + min= numpy.max([dt,float(1./float(InfoConnectPop[i+1][4]))]),
362 + max= float(1./(float(InfoConnectPop[i+1][3])-dt/2))),
363 +
364 + 'weight':nest.random.normal(mean=float(InfoConnectPop[i+1][6]),
365 + std=math.fabs(float(InfoConnectPop[i+1][6])*float(InfoConnectPop[i+1][7])))})
366 +
367 +
368 +endconnect = time.time()
369 +{{/code}}
370 +
371 +=== ===
372 +
373 +=== ===
374 +
375 +=== Simulating: neuronal time evolution. ===
376 +
377 +=== ===
378 +
379 +{{code language="python"}}
380 + #############################------------------------------------------------------------------------
381 + print("Simulating")
382 + #############################------------------------------------------------------------------------
383 + ###################################################################################################################################################################
384 + if Salva:
385 + print("I m going to save the data")
386 + #x=str(iterazioni)
387 + f = open(FileName,"w")
388 + if len(InfoProtocol):
389 + print("I m going to split the simulation")
390 + tempo=0
391 + for contatore in range(0,len(InfoProtocol)):
392 + appoggio1=int((tempo+InfoProtocol[contatore][0])/1000.)
393 + appoggio2=int(tempo/1000.)
394 + appoggio3=tempo+InfoProtocol[contatore][0]
395 + if (appoggio1-appoggio2)>=1:
396 + T1=(1+appoggio2)*1000-tempo
397 + nest.Simulate(T1)
398 + #Save the Data!!!!
399 + ###########################################################
400 + Equilibri=[]
401 + for i in range(0,int(InfoBuild[0])):
402 + Equilibri.append([])
403 + a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
404 + if len(a)>0:
405 + Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
406 + hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
407 + Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
408 + else:
409 + Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
410 + hist=numpy.zeros(200)
411 + Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
412 + Equilibri[i]=hist
413 + nest.SetStatus(DetectorPop[i],{'n_events':0})
414 + for j in range(0,len(hist)):
415 + f.write(str(Tbin[j])+" ")
416 + for i in range(0,int(InfoBuild[0])):
417 + f.write(str(Equilibri[i][j])+" ")
418 + f.write("\n ")
419 + ###########################################################
420 + tempo=tempo+T1
421 + for contatore2 in range(1,(appoggio1-appoggio2)):
422 + nest.Simulate(1000.)
423 + #Save the Data!!!!
424 + ###########################################################
425 + Equilibri=[]
426 + for i in range(0,int(InfoBuild[0])):
427 + Equilibri.append([])
428 + a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
429 + if len(a)>0:
430 + Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
431 + hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
432 + Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
433 + else:
434 + Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
435 + hist=numpy.zeros(200)
436 + Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
437 + Equilibri[i]=hist
438 + nest.SetStatus(DetectorPop[i],{'n_events':0})
439 + for j in range(0,len(hist)):
440 + f.write(str(Tbin[j])+" ")
441 + for i in range(0,int(InfoBuild[0])):
442 + f.write(str(Equilibri[i][j])+" ")
443 + f.write("\n ")
444 + tempo=tempo+1000.
445 + T2=appoggio3-tempo
446 + nest.Simulate(T2);
447 + tempo=tempo+T2;
448 + else:
449 + nest.Simulate(InfoProtocol[contatore][0])
450 + temp=InfoProtocol[contatore][0]
451 + tempo=tempo+temp
452 + if InfoProtocol[contatore][2]==4:
453 + nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
454 + if InfoProtocol[contatore][2]==12:
455 + nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
456 + else:
457 + nest.Simulate(simtime)
458 + tempo=simtime
459 + if (simtime-tempo)>0.:
460 + nest.Simulate(simtime-tempo)
461 +
462 +
463 + endsimulate = time.time()
464 + f.close()
465 + else:
466 + if len(InfoProtocol):
467 + tempo=0
468 + for contatore in range(0,len(InfoProtocol)):
469 + nest.Simulate(InfoProtocol[contatore][0])
470 + temp=InfoProtocol[contatore][0]
471 + tempo=tempo+temp
472 + if InfoProtocol[contatore][2]==4:
473 + nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
474 + #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
475 + if InfoProtocol[contatore][2]==12:
476 + nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
477 + #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
478 +
479 + else:
480 + nest.Simulate(simtime)
481 + tempo=simtime
482 + if (simtime-tempo)>0.:
483 + nest.Simulate(simtime-tempo)
484 + endsimulate = time.time()
485 +
486 +
487 + ###################################################################################################################################################################
488 +
489 + #############################------------------------------------------------------------------------
490 + #print some information from the simulation
491 + #############################------------------------------------------------------------------------
492 +
493 + num_synapses = nest.GetDefaults('static_synapse_hpc')["num_connections"]
494 + build_time = endbuild - startbuild
495 + connect_time = endconnect - startconnect
496 + sim_time = endsimulate - endconnect
497 +
498 + N_neurons=0
499 + for i in range(0,int(InfoBuild[0])):
500 + N_neurons=N_neurons+int(InfoBuild[i+1][0])
501 +
502 + print(" Network simulation (Python) neuron type:",InfoPerseo[0])
503 + print("Number of neurons : {0}".format(N_neurons))
504 + print("Number of synapses: {0}".format(num_synapses))
505 + print("Building time : %.2f s" % build_time)
506 + print("Connecting time : %.2f s" % connect_time)
507 + print("Simulation time : %.2f s" % sim_time)
508 +
509 +Fine=time.time()
510 +print ("Total Simulation time : %.2f s" % (Fine-Inizio))
511 +{{/code}}
512 +
513 +=== ===
514 +
515 +=== Results: ===
516 +
517 +the output of this simulationo is...
518 +
519 +
520 +
521 +
522 +
523 +
243 243  ==== ====
image-20220127165822-1.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.galluzziandrea
Size
... ... @@ -1,0 +1,1 @@
1 +237.6 KB
Content
image-20220127165908-2.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.galluzziandrea
Size
... ... @@ -1,0 +1,1 @@
1 +106.6 KB
Content
image-20220127170104-1.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.galluzziandrea
Size
... ... @@ -1,0 +1,1 @@
1 +149.6 KB
Content