weightfun=weightFunction,
weightargs=weightArguments[i][j],
minweight=minweight,
delayfun=delayFunction,
delayargs=delayArguments[i][j],
mindelay=mindelay,
multapsefun=multapseFunction,
multapseargs=multapseArguments[i][j],
syn_pos_args=synapsePositionArguments[i][j],
save_connections=False,
)
# set up extracellular recording device.
# Here `cell` is set to None as handles to cell geometry is handled
# internally
electrode = RecExtElectrode(cell=None, **electrodeParameters)
# set up recording of current dipole moments. Ditto with regards to
# `cell` being set to None
current_dipole_moment = CurrentDipoleMoment(cell=None)
# run simulation:
SPIKES = network.simulate(probes=[electrode, current_dipole_moment],
**networkSimulationArguments)
# collect somatic potentials across all RANKs to RANK 0:
if RANK == 0:
somavs = []
for i, name in enumerate(population_names):
somavs_pop = None # avoid undeclared variable
for j, cell in enumerate(network.populations[name].cells):
connectivity=connectivity,
syntype=synapseModel,
synparams=synapseParameters[i][j],
weightfun=np.random.normal,
weightargs=weightArguments[i][j],
minweight=minweight,
delayfun=delayFunction,
delayargs=delayArguments[i][j],
mindelay=mindelay,
multapsefun=multapseFunction,
multapseargs=multapseArguments[i][j],
syn_pos_args=synapsePositionArguments[i][j],
)
# set up extracellular recording device:
electrode = RecExtElectrode(**electrodeParameters)
# run simulation:
SPIKES, OUTPUT, DIPOLEMOMENT = network.simulate(
electrode=electrode,
**networkSimulationArguments
)
# collect somatic potentials across all RANKs to RANK 0:
if RANK == 0:
somavs = []
for i, name in enumerate(population_names):
somavs.append([])
somavs[i] += [cell.somav
for cell in network.populations[name].cells]
for j in range(1, SIZE):
post=post,
connectivity=connectivity,
syntype=synapseModel,
synparams=synapseParameters[i][j],
weightfun=np.random.normal,
weightargs=weightArguments[i][j],
minweight=minweight,
delayfun=delayFunction,
delayargs=delayArguments[i][j],
mindelay=mindelay,
multapsefun=multapseFunction,
multapseargs=multapseArguments[i][j],
syn_pos_args=synapsePositionArguments[i][j],
save_connections=False, # Creates synapse_positions.h5
)
electrode = RecExtElectrode(**electrodeParameters)
EEG_electrode_params = dict(x=0, y=0, z=90000., method="soma_as_point")
EEG_electrode = RecExtElectrode(**EEG_electrode_params)
# run simulation:
SPIKES2, OUTPUT2, DIPOLEMOMENT2 = network.simulate(
electrode=electrode,
# electrode = EEG_electrode,
**networkSimulationArguments,
)
# collect somatic potentials across all RANKs to RANK 0:
if RANK == 0:
somavs = []
for i, name in enumerate(population_names):
somavs.append([])