def load_positions(timestamp, gj_conn_type, trial):
positions = np.loadtxt(utils.cs_cell_positions_file(timestamp, gj_conn_type, trial),
delimiter=",")
return positions
for gj_conn_type in ['2010', '2012']:
sim_config_name = 'coupling_strength_' + gj_conn_type + 'gap'
sim_config = project.simConfigInfo.getSimConfig(sim_config_name)
project.neuronSettings.setNoConsole()
for trial in range(n_trials):
print('=====new trial: regenerating network=====')
# generate
nC_seed = Long(random.getrandbits(32))
pm.doGenerate(sim_config_name, nC_seed)
while pm.isGenerating():
time.sleep(0.02)
print('network generated')
##=== save network structure ===
cell_positions_file = open(
utils.cs_cell_positions_file(timestamp, gj_conn_type, trial), 'wb')
edge_list_file = open(
utils.cs_edge_list_file(timestamp, gj_conn_type, trial), 'wb')
cell_positions_writer = csv.writer(cell_positions_file)
edge_list_writer = csv.writer(edge_list_file)
# extract connectivity structure
if gj_conn_type == '2010':
conn_names = ['GJ2010_reduced_TTX']
elif gj_conn_type == '2012':
conn_names = [
'GJ_reduced_TTX_GCL', 'GJ_reduced_TTX_ML1',
'GJ_reduced_TTX_ML2', 'GJ_reduced_TTX_ML3'
]
syn_conns = [
project.generatedNetworkConnections.getSynapticConnections(conn)
for conn in conn_names
for gj_conn_type in ['2010', '2012']:
sim_config_name = 'coupling_strength_' + gj_conn_type + 'gap'
sim_config = project.simConfigInfo.getSimConfig(sim_config_name)
project.neuronSettings.setNoConsole()
for trial in range(n_trials):
print('=====new trial: regenerating network=====')
# generate
nC_seed = Long(random.getrandbits(32))
pm.doGenerate(sim_config_name, nC_seed)
while pm.isGenerating():
time.sleep(0.02)
print('network generated')
##=== save network structure ===
cell_positions_file = open(utils.cs_cell_positions_file(timestamp,
gj_conn_type,
trial),
'wb')
edge_list_file = open(utils.cs_edge_list_file(timestamp,
gj_conn_type,
trial),
'wb')
cell_positions_writer = csv.writer(cell_positions_file)
edge_list_writer = csv.writer(edge_list_file)
# extract connectivity structure
if gj_conn_type == '2010':
conn_names = ['GJ2010_reduced_TTX']
elif gj_conn_type == '2012':
conn_names = ['GJ_reduced_TTX_GCL',
'GJ_reduced_TTX_ML1',
'GJ_reduced_TTX_ML2',
def load_positions(timestamp, gj_conn_type, trial):
positions = np.loadtxt(utils.cs_cell_positions_file(
timestamp, gj_conn_type, trial),
delimiter=",")
return positions