How to reset network monitors?

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@rth please try this.

Note: This structure writes on the memory. If you’re dealing with gigantic data or have a very old hard drive, this operation may be the bottleneck of your whole simulation!

from brian2 import *
import numpy as np

start_scope()
thr = -10
v_reset = -60 

# lets' make some populations
nPops = 3
pops = []
for n in range(nPops):
    pop = NeuronGroup(
            N = 5, 
            model= """
            dv/dt = (-v + I)/tau : 1
            I: 1
            tau: second
            """,
            threshold="v>thr", 
            reset="v=v_reset", 
            method="euler",
            )
            
    pop.tau[:] = abs(np.random.normal(10, 3))*ms
    pop.v[:] = np.random.normal(-75, 3)
    pop.I[:] = 1*(pop.i+1)
    pops.append(pop)

# and connect them all together with synapses
syns = []
for l in range(nPops):
    for m in range(nPops):
        syn = Synapses(source = pops[l], target = pops[m],
                        model = """w : 1""", 
                        on_pre = """v += w""",
                        method = 'euler',
                        )
        syn.connect(condition = 'i!=j', p=0.1)
        syn.w = np.random.normal(0.5,0.02, size=len(syn))

        syns.append(syn)

net = Network(collect())  # collects nothing
net.add(pops) 
net.add(syns)

# this function redefines the monitor objects conveniently 
def monitor_maker(syns):
    monitors = []
    for syn in syns:
        monitor = StateMonitor(syn, 'w', record=True)
        monitors.append(monitor)
    return monitors

# and this one just saves the recorded vars on the hard disk
def intra_sim_process(monitors, chunk_id):
    for monitor in monitors:
        np.save('w_'+str(chunk_id)+'.npy', monitor.w)

# let's a run simulation of total duration 1 second. We break it down
# to 10 subsimulation of duration 100 ms to avoid memory cloggage 
for chunk in range(10):
    print("*"*10 + " CHUNK ID : {} ".format(chunk)+ "*"*10 + "\n")
    # add monitors
    monitors = monitor_maker(syns)
    net.add(monitors)
    net.run(100*ms, report='text', report_period=20*ms)
    intra_sim_process(monitors, chunk) 
    net.remove(monitors)

If you spotted anything wrong or saw potential improvements, please don’t hesitate to leave it as a reply below. I’d be thankful.

Arash

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