Error in passive_cable.getting_started()

[diegogcerdas]

While running the introductory code for exercises 5:
import brian2 as b2 import matplotlib.pyplot as plt from neurodynex3.cable_equation import passive_cable from neurodynex3.tools import input_factory import numpy as np %matplotlib inline passive_cable.getting_started()

I get the following error trace:

_cython_magic_15f462c2d8ad86b6857db74f110ed9a8.cpp
C:\Users\dgcxb\anaconda3\envs\bmnn\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
Creating library C:\Users\dgcxb.cython\brian_extensions\Users\dgcxb.cython\brian_extensions_cython_magic_15f462c2d8ad86b6857db74f110ed9a8.cp38-win_amd64.lib and object C:\Users\dgcxb.cython\brian_extensions\Users\dgcxb.cython\brian_extensions_cython_magic_15f462c2d8ad86b6857db74f110ed9a8.cp38-win_amd64.exp
Generating code
Finished generating code
_cython_magic_963f4ad1402bd5c688206467215aef7b.cpp
C:\Users\dgcxb\anaconda3\envs\bmnn\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
Creating library C:\Users\dgcxb.cython\brian_extensions\Users\dgcxb.cython\brian_extensions_cython_magic_963f4ad1402bd5c688206467215aef7b.cp38-win_amd64.lib and object C:\Users\dgcxb.cython\brian_extensions\Users\dgcxb.cython\brian_extensions_cython_magic_963f4ad1402bd5c688206467215aef7b.cp38-win_amd64.exp
Generating code
Finished generating code
_cython_magic_7208c94ddee8df5b2361722452059636.cpp
C:\Users\dgcxb\anaconda3\envs\bmnn\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
Creating library C:\Users\dgcxb.cython\brian_extensions\Users\dgcxb.cython\brian_extensions_cython_magic_7208c94ddee8df5b2361722452059636.cp38-win_amd64.lib and object C:\Users\dgcxb.cython\brian_extensions\Users\dgcxb.cython\brian_extensions_cython_magic_7208c94ddee8df5b2361722452059636.cp38-win_amd64.exp
Generating code
Finished generating code

Error compiling Cython file:

...
cdef double area
# namespace for function current
global _namespace_timedarray_4_values
global _namespace_num_timedarray_4_values
cdef _numpy.ndarray[double, ndim=1, mode='c'] _buf__timedarray_4_values = _namespace['_timedarray_4_values']
_namespace_timedarray_4_values = <double *> _buf__timedarray_4_values.data
^

C:\Users\dgcxb.cython\brian_extensions_cython_magic_36fb1bcd5ee8fe59860441ce2aa93114.pyx:221:37: Cannot convert 'double *' to Python object
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9025 : overriding '/W3' with '/w'

ZeroDivisionError Traceback (most recent call last)
~\anaconda3\envs\bmnn\lib\site-packages\brian2\codegen\runtime\cython_rt\cython_rt.py in run_block(self, block)
159 try:
--> 160 return compiled_code.main(self.namespace)
161 except Exception as exc:

_cython_magic_a4e948818012e0811dae587a5d0fef77.pyx in _cython_magic_a4e948818012e0811dae587a5d0fef77.main()

ZeroDivisionError: float division

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

BrianObjectException Traceback (most recent call last)
in
----> 1 passive_cable.getting_started()

~\anaconda3\envs\bmnn\lib\site-packages\neurodynex3\cable_equation\passive_cable.py in getting_started()
106 """
107 current = input_factory.get_step_current(500, 510, unit_time=b2.us, amplitude=3. * b2.namp)
--> 108 voltage_monitor, cable_model = simulate_passive_cable(
109 length=0.5 * b2.mm, current_injection_location=[0.1 * b2.mm], input_current=current,
110 nr_compartments=100, simulation_time=2 * b2.ms)

~\anaconda3\envs\bmnn\lib\site-packages\neurodynex3\cable_equation\passive_cable.py in simulate_passive_cable(current_injection_location, input_current, length, diameter, r_longitudinal, r_transversal, e_leak, initial_voltage, capacitance, nr_compartments, simulation_time)
98 # set initial values and run for 1 ms
99 cable_model.v = initial_voltage
--> 100 b2.run(simulation_time)
101 return monitor_v, cable_model
102

~\anaconda3\envs\bmnn\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
2383 get_dimensions(newkeyset[k]))
2384
-> 2385 result = f(*args, **kwds)
2386 if 'result' in au:
2387 if au['result'] == bool:

~\anaconda3\envs\bmnn\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
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)
375 run.module = name

~\anaconda3\envs\bmnn\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
229 namespace=None, profile=False, level=0):
230 self._update_magic_objects(level=level+1)
--> 231 Network.run(self, duration, report=report, report_period=report_period,
232 namespace=namespace, profile=profile, level=level+1)
233

~\anaconda3\envs\bmnn\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
276 return getattr(curdev, name)(*args, **kwds)
277 else:
--> 278 return func(*args, **kwds)
279
280 device_override_decorated_function.doc = func.doc

~\anaconda3\envs\bmnn\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
2383 get_dimensions(newkeyset[k]))
2384
-> 2385 result = f(*args, **kwds)
2386 if 'result' in au:
2387 if au['result'] == bool:

~\anaconda3\envs\bmnn\lib\site-packages\brian2\core\network.py in run(self, duration, report, report_period, namespace, profile, level)
1074 else:
1075 for obj in active_objects:
-> 1076 obj.run()
1077
1078 timestep[0] += 1

~\anaconda3\envs\bmnn\lib\site-packages\brian2\core\base.py in run(self)
179 def run(self):
180 for codeobj in self._code_objects:
--> 181 codeobj()
182
183 contained_objects = property(fget=lambda self:self._contained_objects,

~\anaconda3\envs\bmnn\lib\site-packages\brian2\codegen\codeobject.py in call(self, **kwds)
105 self.namespace.update(**kwds)
106
--> 107 return self.run()
108
109 def run_block(self, block):

~\anaconda3\envs\bmnn\lib\site-packages\brian2\codegen\codeobject.py in run(self)
133 defined during the call of CodeGenerator.code_object.
134 '''
--> 135 return self.run_block('run')
136
137 def after_run(self):

~\anaconda3\envs\bmnn\lib\site-packages\brian2\codegen\runtime\cython_rt\cython_rt.py in run_block(self, block)
162 message = ('An exception occured during the execution of the {} '
163 'block of code object {}.\n').format(block, self.name)
--> 164 raise BrianObjectException(message, self.owner) from exc
165
166 def _insert_func_namespace(self, func):

BrianObjectException: Error encountered with object named "spatialneuron_1".
Object was created here (most recent call only, full details in debug log):
File "C:\Users\dgcxb\anaconda3\envs\bmnn\lib\site-packages\neurodynex3\cable_equation\passive_cable.py", line 85, in simulate_passive_cable
cable_model = b2.SpatialNeuron(morphology=cable_morphology, model=eqs, Cm=capacitance, Ri=r_longitudinal)

An exception occured during the execution of the run block of code object spatialneuron_1_spatialstateupdater_codeobject.
(See above for original error message and traceback.)