Description of problem
I’m getting the difficult to debug error when I try to run the code included below. The error message is not very informative.
Minimal code to reproduce problem
tau_e=5 * ms # excitatory synaptic time constant
tau_i=10 * ms # inhibitory synaptic time constant
tau_Ia = 1000*ms # adaptation current
tau_ref = 2 * ms, # refractory time
SFA = 0.1 * nS, # conductance adaptation
Vr=-60 * mV # resting potential
VT=-35 * mV # spike threshold
DeltaT=1 * mV
g_l = 5 * nS # leak conductance
E_l = -60 * mV
E_e = 0 * mV # excitatory synaptic potential
E_i = -75 * mV # inhibitory synaptic potential
E_Ia = -90*mV
C_m = 100 * pF # capacitance
start_scope()
eqs = '''
dv/dt = (g_l*(E_l-v) + g_e*(E_e-v) - g_i*(E_i-v) - g_Ia*(E_Ia-v))/C_m : volt (unless refractory)
dg_e/dt = -g_e/tau_e : siemens
dg_i/dt = -g_i/tau_i : siemens
dg_Ia/dt = -g_Ia/tau_Ia : siemens
'''
G = NeuronGroup(10,
eqs,
threshold='v > VT',
reset='''v = Vr; g_Ia-=SFA''',
refractory = tau_ref)
G.v = -30 * mV
M = StateMonitor(G, 'v', record=True)
run(duration = 100*ms)
plot(M.t/ms, M.v[0])
xlabel('Time (ms)')
ylabel('v')
What you have aready tried
I tried to use Equations.
Full traceback of error (if relevant)
File ~/anaconda3/envs/brian/lib/python3.10/re.py:240, in findall(pattern, string, flags)
233 """Return a list of all non-overlapping matches in the string.
234
235 If one or more capturing groups are present in the pattern, return
(...)
238
239 Empty matches are included in the result."""
--> 240 return _compile(pattern, flags).findall(string)
TypeError: expected string or bytes-like object
The above exception was the direct cause of the following exception:
BrianObjectException Traceback (most recent call last)
Input In [69], in <module>
33 G.v = -60 * mV
35 M = StateMonitor(G, 'v', record=True)
---> 37 run(duration = 100*ms)
39 plot(M.t/ms, M.v[0])
40 xlabel('Time (ms)')
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/units/fundamentalunits.py:2428, in check_units.<locals>.do_check_units.<locals>.new_f(*args, **kwds)
2421 error_message = (f"Function '{f.__name__}' "
2422 f"expected a quantitity with unit "
2423 f"{unit} for argument '{k}' but got "
2424 f"'{value}'")
2425 raise DimensionMismatchError(error_message,
2426 get_dimensions(newkeyset[k]))
-> 2428 result = f(*args, **kwds)
2429 if 'result' in au:
2430 if isinstance(au['result'], Callable) and au['result'] != bool:
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/core/magic.py:373, in run(duration, report, report_period, namespace, profile, level)
310 @check_units(duration=second, report_period=second)
311 def run(duration, report=None, report_period=10*second, namespace=None,
312 profile=None, level=0):
313 """
314 run(duration, report=None, report_period=10*second, namespace=None, level=0)
315
(...)
371 intended use. See `MagicNetwork` for more details.
372 """
--> 373 return magic_network.run(duration, report=report, report_period=report_period,
374 namespace=namespace, profile=profile, level=2+level)
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/core/magic.py:230, in MagicNetwork.run(self, duration, report, report_period, namespace, profile, level)
227 def run(self, duration, report=None, report_period=10*second,
228 namespace=None, profile=None, level=0):
229 self._update_magic_objects(level=level+1)
--> 230 Network.run(self, duration, report=report, report_period=report_period,
231 namespace=namespace, profile=profile, level=level+1)
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/core/base.py:293, in device_override.<locals>.device_override_decorator.<locals>.device_override_decorated_function(*args, **kwds)
291 return getattr(curdev, name)(*args, **kwds)
292 else:
--> 293 return func(*args, **kwds)
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/units/fundamentalunits.py:2428, in check_units.<locals>.do_check_units.<locals>.new_f(*args, **kwds)
2421 error_message = (f"Function '{f.__name__}' "
2422 f"expected a quantitity with unit "
2423 f"{unit} for argument '{k}' but got "
2424 f"'{value}'")
2425 raise DimensionMismatchError(error_message,
2426 get_dimensions(newkeyset[k]))
-> 2428 result = f(*args, **kwds)
2429 if 'result' in au:
2430 if isinstance(au['result'], Callable) and au['result'] != bool:
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/core/network.py:1006, in Network.run(self, duration, report, report_period, namespace, profile, level)
1003 if namespace is None:
1004 namespace = get_local_namespace(level=level+3)
-> 1006 self.before_run(namespace)
1008 if len(all_objects) == 0:
1009 return # TODO: raise an error? warning?
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/core/base.py:293, in device_override.<locals>.device_override_decorator.<locals>.device_override_decorated_function(*args, **kwds)
291 return getattr(curdev, name)(*args, **kwds)
292 else:
--> 293 return func(*args, **kwds)
File ~/anaconda3/envs/brian/lib/python3.10/site-packages/brian2/core/network.py:894, in Network.before_run(self, run_namespace)
892 obj.before_run(run_namespace)
893 except Exception as ex:
--> 894 raise BrianObjectException("An error occurred when preparing an object.", obj) from ex
896 # Check that no object has been run as part of another network before
897 for obj in all_objects:
BrianObjectException: Error encountered with object named 'neurongroup_17_stateupdater'.
Object was created here (most recent call only, full details in debug log):
File '/var/folders/zt/s4rb4_kj4pnbmcqw7xyw52hw0000gn/T/ipykernel_88701/1728005146.py', line 28, in <module>
G = NeuronGroup(10,
Clearly I made a mistake somewhere, not sure where?
