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]
inh_type = sys.argv[-2]
else:
raise Exception("no work" + str(sys.argv[-1]))
# df = pd.read_csv("Segments.csv")
# types = np.array(df["Type"])
# xs = np.array(df["X"])
# ids = np.array(df["Sec ID"])
# distances = np.array(df["Distance"])
# dendrites = np.where(((types == "dend") | (types == "apic")) & (distances >= 50))[0]
# N = len(dendrites)
N = int(inp)
proportions = {"Perisomatic": [150/256, 106/256, 0, 0],
"Basal": [0, 0, 1, 0],
"Apical": [0, 0, 0, 1]}
#inh_type = "Perisomatic"
props = proportions[inh_type]
n_soma = int(N * props[0])
n_close_dend = int(N * props[1])
n_far_dend = int(N * props[2])
n_apic = int(N * props[3])
np.random.seed(2129)
#np.random.seed(42)
synapses.load()
syn = synapses.syn_params_dicts()
net = NetworkBuilder("biophysical")
net.add_nodes(N=n_soma, pop_name='Soma',
potental='exc',
model_type='biophysical',
model_template='hoc:L5PCtemplate',
morphology = None)
net.add_nodes(N=n_close_dend, pop_name='Close Dend',
potental='exc',
model_type='biophysical',
model_template='hoc:L5PCtemplate',
morphology = None)
net.add_nodes(N=n_far_dend, pop_name='Far Dend',
potental='exc',
model_type='biophysical',
model_template='hoc:L5PCtemplate',
morphology = None)
net.add_nodes(N=n_apic, pop_name='Apic',
potental='exc',
model_type='biophysical',
model_template='hoc:L5PCtemplate',
morphology = None)
inh_stim = NetworkBuilder('inh_stim')
inh_stim.add_nodes(N=1,
pop_name='inh_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'])
def norm_connect(source, target, m, s, low, high):
return int(min(max(np.random.normal(m, s), low), high))
# Create connections on the soma
net.add_edges(source=inh_stim.nodes(), target=net.nodes(pop_name="Soma"),
connection_rule=norm_connect,
connection_params={"m":2.8, "s":1.9, "low":1, "high":5},
syn_weight=1,
target_sections=['soma'],
delay=0.1,
distance_range=[0, 2000],#(2013, Pouille et al.)
dynamics_params='INT2PN.json',
model_template=syn['INT2PN.json']['level_of_detail'])
# Create connections on dendrites <50 um from the soma
net.add_edges(source=inh_stim.nodes(), target=net.nodes(pop_name="Close Dend"),
connection_rule=norm_connect,
connection_params={"m":2.8, "s":1.9, "low":1, "high":5},
syn_weight=1,
target_sections=['dend'],
delay=0.1,
distance_range=[0, 50],#(2013, Pouille et al.)
dynamics_params='INT2PN.json',
model_template=syn['INT2PN.json']['level_of_detail'])
# Create connections on dendrites >50 um from the soma
net.add_edges(source=inh_stim.nodes(), target=net.nodes(pop_name="Far Dend"),
connection_rule=norm_connect,
connection_params={"m":2.7, "s":1.6, "low":1, "high":5},
syn_weight=1,
target_sections=['dend'],
delay=0.1,
distance_range=[50, 2000],#(2013, Pouille et al.)
dynamics_params='INT2PN.json',
model_template=syn['INT2PN.json']['level_of_detail'])
# Create connections on apical dendrites
net.add_edges(source=inh_stim.nodes(), target=net.nodes(pop_name="Apic"),
connection_rule=norm_connect,
connection_params={"m":12, "s":3, "low":6, "high":18},
syn_weight=1,
target_sections=['apic'],
delay=0.1,
distance_range=[50, 2000],#(2013, Pouille et al.)
dynamics_params='INT2PN.json',
model_template=syn['INT2PN.json']['level_of_detail'])
# Build and save our networks
net.build()
net.save_nodes(output_dir='network')
net.save_edges(output_dir='network')
inh_stim.build()
inh_stim.save_nodes(output_dir='network')
import h5py
f = h5py.File('inh_stim_spikes.h5', 'w')
f.create_group('spikes')
f['spikes'].create_group('inh_stim')
f['spikes']['inh_stim'].create_dataset("node_ids", data=[0])
f['spikes']['inh_stim'].create_dataset("timestamps", data=[400])
f.close()
from bmtk.utils.sim_setup import build_env_bionet
holding_v = -80
build_env_bionet(base_dir='./',
network_dir='./network',
tstop=500.0, dt = 0.1,
report_vars=['v'],
spikes_threshold=-10,
clamp_reports=['se'],#Records se clamp currents.
se_voltage_clamp={
"amps":[[holding_v, holding_v, holding_v]],
"durations": [[500, 0, 0]],
'gids': "all",
'rs': [0.01 for _ in range(N)],
},
spikes_inputs=[('inh_stim', 'inh_stim_spikes.h5')],
components_dir='../biophys_components',
compile_mechanisms=True)