from bmtk.builder import NetworkBuilder
import numpy as np
import sys
import synapses
import pandas as pd
if __name__ == '__main__':
if __file__ != sys.argv[-1]:
inp = sys.argv[-1]
else:
raise Exception("no work" + str(sys.argv[-1]))
N = int(inp)
np.random.seed(2129)
#np.random.seed(42)
synapses.load()
syn = synapses.syn_params_dicts()
net = NetworkBuilder("biophysical")
net.add_nodes(N=1, pop_name='Pyrc',
potental='exc',
model_type='biophysical',
model_template='hoc:L5PCtemplate',
morphology = None)
exc_stim = NetworkBuilder('exc_stim')
exc_stim.add_nodes(N=1,
pop_name='exc_stim',
potential='exc',
model_type='virtual')
# def connection(source, target, id):
# if target.node_id == id:
# return 1
# else:
# return 0
# for i in range(N):
# #import pdb; pdb.set_trace()
# net.add_edges(source=exc_stim.nodes(), target=net.nodes(),
# connection_rule=connection,
# connection_params={"id":i},
# syn_weight = 1,
# sec_id = ids[dendrites][i],
# delay=0.1,
# sec_x = xs[dendrites][i],
# dynamics_params='PN2PN.json',
# model_template=syn['PN2PN.json']['level_of_detail'])
# Create connections between Exc --> Pyr cells
net.add_edges(source=exc_stim.nodes(), target=net.nodes(),
connection_rule=N,
syn_weight=1,
target_sections=['apic'],
delay=0.1,
#distance_range=[149.0, 151.0], #0.348->0.31, 0.459->0.401
distance_range=[635, 2000],#(2013, Pouille et al.)
#distance_range=[1250,2000],
#distance_range=[-500, 500],
dynamics_params='PN2PN.json',
model_template=syn['PN2PN.json']['level_of_detail'])
# Build and save our networks
net.build()
net.save_nodes(output_dir='network')
net.save_edges(output_dir='network')
exc_stim.build()
exc_stim.save_nodes(output_dir='network')
import h5py
f = h5py.File('exc_stim_spikes.h5', 'w')
f.create_group('spikes')
f['spikes'].create_group('exc_stim')
f['spikes']['exc_stim'].create_dataset("node_ids", data=[0, 0, 0])
f['spikes']['exc_stim'].create_dataset("timestamps", data=[350, 370, 390])
f.close()
from bmtk.utils.sim_setup import build_env_bionet
build_env_bionet(base_dir='./',
network_dir='./network',
tstop=500.0, dt = 0.1,
report_vars=['v'],
spikes_threshold=-10,
spikes_inputs=[('exc_stim', 'exc_stim_spikes.h5')],
components_dir='../biophys_components',
compile_mechanisms=True)