# Error massage from SpikeGeneratorGroup

**URL:** <https://brian.discourse.group/t/error-massage-from-spikegeneratorgroup/622>\
**Category:** Support\
**Created:** [5 March 2022 19:41 UTC](https://brian.discourse.group/t/error-massage-from-spikegeneratorgroup/622 "2022-03-05T19:41:28Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![rth](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/rth/32/16_2.png) [@rth](https://brian.discourse.group/u/rth)\
**Post date:** [5 March 2022 19:41 UTC](https://brian.discourse.group/t/error-massage-from-spikegeneratorgroup/622/1 "2022-03-05T19:41:28Z")

</div>

# Description of problem

I’m trying to feed a simple cortical model with spike time of LGN neurons. Spike times are in 2D array with 2 columns time and neuron index [dLGNspk.npz](https://storage.r-a-r.org/index.php/s/DWX98eXZyQPD3rg)

# Minimal code to reproduce problem

```auto
from brian2 import *
from numpy import random as rnd

with load("dLGNspk.npz") as npd:
    LGNspk = npd["arr_0"]
nLGN = int(ceil(amax(LGNspk[:,1])))+1
print(" > Checking that all interspike intervals that are longer than 2 simulation steps")
lastspike = zeros(nLGN)
for xid,(spt,spi) in enumerate(LGNspk):
    if abs(lastspike[int(spi)]-spt) < 0.5 :
        print(f" > LGN neuron #{spi} still have ISI shorter than two simulation steps: {lastspike[int(spi)]}, {spt}")
        exit(1)
    lastspike[int(spi)]=spt
#savez("dLGNspk.npz",LGNspk)
print(" > All ISI are linger than 2 simulation steps")

lgnminsyn,lgnmaxsyn = 107,267
print(f"Range for number of synapses from one lgn neuron [{lgnminsyn},{lgnmaxsyn}]")
connectivity=array([
    [s,rnd.randint(0,600)]
    for s in range(nLGN) for p in range(lgnminsyn,lgnmaxsyn)
]).astype(int)
ninputs = zeros(600)
for l,c in connectivity:
    ninputs[c] += 1
print(f"Minimal number of connections per CX neuron {amin(ninputs)}")
print(f"Mean+-std number of connections per CX neuron {mean(ninputs)}+-{std(ninputs)}")
print(f"Maximal number of connections per CX neuron {amax(ninputs)}")

Esyn = 0. * mV
tau_sr = 0.5 * ms
tau_sd = 2 * ms

#prepostSTDP params: 
Altp = 14e-5* mS
Altd = 8e-5* mS
thetad = -70.6 * mV
thetap = -45.3 * mV 
uref2 = 0.95e-3 #Murata and Colonnese • Thalamic Control of Cortical State Development 0.95 spike/sec
tau_u2 = 1000*ms

tau_xp = 15*ms
tau_p = 7*ms
tau_m = 10*ms
wmin,wmax = 0*mS, 200*nS
#defaultclock.dt = 1*ms

# Adex Parameters
C = 281 * pF
gL = 30 * nS
taum = C / gL
EL = -70.6 * mV
DeltaT = 2 * mV
vti = -50.4 * mV
tauvt = 50 * ms
taua = 144.*ms
a = 4 * nS
b = 0.805*pA
vtrest = -5 * mV
VTmax = 18 * mV

tauw, c, b, Vr = 144 * ms, 4 * nS, 0.0805 * nA, -70.6 * mV # Regular spiking (as in the paper)

eqs_neuron = """
dvm/dt=(gL*(EL-vm)+gL*DeltaT*exp((vm-vt)/DeltaT)+gs*(Esyn-vm)*(sd-sr)*ms/(tau_sd-tau_sr)-va )/C : volt
dvt/dt=-(vt-vti)/tauvt : volt # Threshold votage
dva/dt =(a*(vm-EL)-va)/taua : amp # voltage adaptation current
dsr/dt=-sr/tau_sr : 1 # synaptic conductance rise
dsd/dt=-sd/tau_sd : 1 # synaptic conductance decay
dud/dt=(vm-ud)/tau_m : volt # depression voltage low-pass filter u-
# du2/dt=(ud-u2)/tau_u2 : volt # depression second voltage low-pass filter u--
dup/dt=(vm-up)/tau_p : volt # potentiation voltage low-pass filter u+
dxp/dt=-xp/tau_xp : 1 # potentiation spike low-pass filter x+
du2/dt=(xp-u2)/tau_u2 : 1 # depression second spike low-pass filter (change in the model)

gs : siemens
"""

lgninput = SpikeGeneratorGroup(nLGN,LGNspk[:,1].flatten().astype(int),LGNspk[:,0]*ms)
neurons = NeuronGroup(600, model=eqs_neuron, threshold='vm>vt', reset="vm=Vr;a+=b;vt=VTmax;x+=1")
neurons.vt = vtrest
neurons.vm = EL
model='''dw/dt=Altp*xp_pre*clip((vm_pre-tetap)/mV,0,inf)*clip((up_pre-tetad)/mV,0,inf)-Altd*u2_post**2/uref2*clip((ud_pre-tetad)/mV,0,inf) : siemens (event-driven)'''
syn = Synapses(lgninput, neurons, model, on_pre="w=clip(w,wmin,wmax): siemens; gs_post = w : siemens (summed)")
syn.connect(i=connectivity[:,0].flatten(), j=connectivity[:,1].flatten())

SM = SpikeMonitor(neurons)
VM = StateMonitor(neurons, 'vm', record=[0,49,99])

    
run(2e4*ms,report="txt")

```

# Actual output (if relevant)

```bash
python brianDB.py 
 > Checking that all interspike intervals that are longer than 2 simulation steps
   > All ISI are linger than 2 simulation steps
Range for number of synapses from one lgn neuron [107,267]
Minimal number of connections per CX neuron 16.0
Mean+-std number of connections per CX neuron 29.866666666666667+-5.038738819276991
Maximal number of connections per CX neuron 45.0
INFO No numerical integration method specified for group 'neurongroup', using method 'euler' (took 0.02s, trying other methods took 0.18s). [brian2.stateupdaters.base.method_choice]
ERROR Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at <http://brian.discourse.group/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /tmp/brian_debug_fa9271y8.log Additionally, you can also include a copy of the script that was run, available at: /tmp/brian_script_033f24m6.py You can also include a copy of the redirected std stream outputs, available at '/tmp/brian_stdout_bkulmqx1.log' and '/tmp/brian_stderr_xwxarr18.log'. Thanks! [brian2]
Traceback (most recent call last):
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/network.py", line 892, in before_run
    obj.before_run(run_namespace)
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/input/spikegeneratorgroup.py", line 197, in before_run
    raise ValueError(f"Using a dt of {self.dt!s}, some neurons of "
ValueError: Using a dt of <spikegeneratorgroup.dt: 100. * usecond>, some neurons of SpikeGeneratorGroup 'spikegeneratorgroup' spike more than once during a time step.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/media/rth/rth-master/rth/simulations/Th20Hz/CorticalInmputs/brianDB.py", line 93, in <module>
    run(2e4*ms,report="txt")
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/units/fundamentalunits.py", line 2428, in new_f
    result = f(*args, **kwds)
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/magic.py", line 373, in run
    return magic_network.run(duration, report=report, report_period=report_period,
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/magic.py", line 230, in run
    Network.run(self, duration, report=report, report_period=report_period,
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/base.py", line 293, in device_override_decorated_function
    return func(*args, **kwds)
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/units/fundamentalunits.py", line 2428, in new_f
    result = f(*args, **kwds)
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/network.py", line 1006, in run
    self.before_run(namespace)
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/base.py", line 293, in device_override_decorated_function
    return func(*args, **kwds)
  File "/home/rth/.local/lib/python3.9/site-packages/brian2/core/network.py", line 894, in before_run
    raise BrianObjectException("An error occurred when preparing an object.", obj) from ex
brian2.core.base.BrianObjectException: Error encountered with object named 'spikegeneratorgroup'.
Object was created here (most recent call only, full details in debug log):
  File '/media/rth/rth-master/rth/simulations/Th20Hz/CorticalInmputs/brianDB.py', line 81, in <module>
    lgninput = SpikeGeneratorGroup(nLGN,LGNspk[:,1].flatten().astype(int),LGNspk[:,0]*ms)

An error occurred when preparing an object. (See above for original error message and traceback.)

```

As you can see above, that the input sequence pass the test, and there are no neurons with ISI less 0.5 ms

```auto
 > Checking that all interspike intervals that are longer than 2 simulation steps
   > All ISI are linger than 2 simulation steps

```

However, `brain` returns an error,

```auto
ValueError: Using a dt of <spikegeneratorgroup.dt: 100. * usecond>, some neurons of SpikeGeneratorGroup 'spikegeneratorgroup' spike more than once during a time step.

```

---

<div class="post-metadata">

**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\
**Post date:** [8 March 2022 16:56 UTC](https://brian.discourse.group/t/error-massage-from-spikegeneratorgroup/622/2 "2022-03-08T16:56:23Z")

</div>

Hi @rth. Your test assumes that all spike times in the matrix are in ascending order, but there are at least a number of zero values violating this assumption (which of course all end up in the first time step):

```nohighlight
>>> print(LGNspk[LGNspk[:, 1] == 0,0][:20])
[ 95856.62498666 96012.94998662 96281.97498656 0.
 209069.6000511 209500.9250515 209939.55005191 210185.02505214
 210664.12505258 210878.80005278 211067.90005296 211490.92505335
      0. 271149.67510892 273379.10011099 348083.62518057
 348457.67518091 348812.22518124 349201.42518161 349938.80018229]

```

Even after removing the zeros, there are still a number of places where the times are not in order:

```nohighlight
>>> print(LGNspk[(LGNspk[:, 1] == 0) & (LGNspk[:, 0] != 0.), :][610:613, :])
[[1751156.30273884 0.]
 [1653799.40275253 0.]
 [1862511.0028033 0.]]

```

It is of course still possible that Brian does something wrong, but at the first sight I’d say that Brian is correct in complaining about the provided spike times/indices.

---

<div class="post-metadata">

**Author:** ![rth](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/rth/32/16_2.png) [@rth](https://brian.discourse.group/u/rth)\
**Post date:** [8 March 2022 17:34 UTC](https://brian.discourse.group/t/error-massage-from-spikegeneratorgroup/622/3 "2022-03-08T17:34:20Z")

</div>

@mstimberg thank you for looking into my problem!  
Oh, I thought I’d caught all ‘strange’ behavior of spike sorting.