import glob
import json
import os
import re
from bmtk.simulator.bionet.pyfunction_cache import add_synapse_model
from neuron import h
import random
import numpy as np
scale = 10
#max_exc = 0
weight_means = {"exc": {}, "inh": {}}
def lognormal(m, s):
mean = np.log(m) - 0.5 * np.log((s/m)**2+1)
std = np.sqrt(np.log((s/m)**2 + 1))
return max(np.random.lognormal(mean, std, 1), 0.0000000001)
def Bg2Pyr(syn_params, sec_x, sec_id):
"""Create a bg2pyr synapse
:param syn_params: parameters of a synapse
:param sec_x: normalized distance along the section
:param sec_id: target section
:return: NEURON synapse object
"""
lsyn = h.bg2pyr(sec_x, sec=sec_id)
if syn_params.get('initW'):
lsyn.initW = float(syn_params['initW'])
if syn_params.get('taun1'):
lsyn.taun1 = float(syn_params['taun1'])
if syn_params.get('taun2'):
lsyn.taun2 = float(syn_params['taun2'])
if syn_params.get('gNMDAmax'):
lsyn.gNMDAmax = float(syn_params['gNMDAmax'])
if syn_params.get('enmda'):
lsyn.enmda = float(syn_params['enmda'])
if syn_params.get('taua1'):
lsyn.taua1 = float(syn_params['taua1'])
if syn_params.get('taua2'):
lsyn.taua2 = float(syn_params['taua2'])
if syn_params.get('gAMPAmax'):
lsyn.gAMPAmax = float(syn_params['gAMPAmax'])
if syn_params.get('eampa'):
lsyn.eampa = float(syn_params['eampa'])
return lsyn
def bg2pyr(syn_params, xs, secs):
"""Create a list of bg2pyr synapses
:param syn_params: parameters of a synapse
:param xs: list of normalized distances along the section
:param secs: target sections
:return: list of NEURON synpase objects
"""
syns = []
for x, sec in zip(xs, secs):
syn = Pyr2Pyr(syn_params, x, sec)
syns.append(syn)
return syns
def Pyr2Int(syn_params, sec_x, sec_id):
"""Create a pyr2int synapse
:param syn_params: parameters of a synapse
:param sec_x: normalized distance along the section
:param sec_id: target section
:return: NEURON synapse object
"""
lsyn = h.pyr2int(sec_x, sec=sec_id)
if syn_params.get('AlphaTmax_ampa'):
lsyn.AlphaTmax_ampa = float(syn_params['AlphaTmax_ampa']) # par.x(21)
if syn_params.get('Beta_ampa'):
lsyn.Beta_ampa = float(syn_params['Beta_ampa']) # par.x(22)
if syn_params.get('Cdur_ampa'):
lsyn.Cdur_ampa = float(syn_params['Cdur_ampa']) # par.x(23)
if syn_params.get('gbar_ampa'):
lsyn.gbar_ampa = float(syn_params['gbar_ampa']) # par.x(24)
if syn_params.get('Erev_ampa'):
lsyn.Erev_ampa = float(syn_params['Erev_ampa']) # par.x(16)
if syn_params.get('AlphaTmax_nmda'):
lsyn.AlphaTmax_nmda = float(syn_params['AlphaTmax_nmda']) # par.x(25)
if syn_params.get('Beta_nmda'):
lsyn.Beta_nmda = float(syn_params['Beta_nmda']) # par.x(26)
if syn_params.get('Cdur_nmda'):
lsyn.Cdur_nmda = float(syn_params['Cdur_nmda']) # par.x(27)
if syn_params.get('gbar_nmda'):
lsyn.gbar_nmda = float(syn_params['gbar_nmda']) # par.x(28)
if syn_params.get('Erev_nmda'):
lsyn.Erev_nmda = float(syn_params['Erev_nmda']) # par.x(16)
if syn_params.get('initW'):
lsyn.initW = float(syn_params['initW']) * random.uniform(0.5,1.0) # par.x(0) * rC.uniform(0.5,1.0)//rand.normal(0.5,1.5) //`rand.repick()
if syn_params.get('Wmax'):
lsyn.Wmax = float(syn_params['Wmax']) * lsyn.initW # par.x(1) * lsyn.initW
if syn_params.get('Wmin'):
lsyn.Wmin = float(syn_params['Wmin']) * lsyn.initW # par.x(2) * lsyn.initW
#delay = float(syn_params['initW']) # par.x(3) + delayDistance
#lcon = new NetCon(&v(0.5), lsyn, 0, delay, 1)
if syn_params.get('lambda1'):
lsyn.lambda1 = float(syn_params['lambda1']) # par.x(6)
if syn_params.get('lambda2'):
lsyn.lambda2 = float(syn_params['lambda2']) # par.x(7)
if syn_params.get('threshold1'):
lsyn.threshold1 = float(syn_params['threshold1']) # par.x(8)
if syn_params.get('threshold2'):
lsyn.threshold2 = float(syn_params['threshold2']) # par.x(9)
if syn_params.get('tauD1'):
lsyn.tauD1 = float(syn_params['tauD1']) # par.x(10)
if syn_params.get('d1'):
lsyn.d1 = float(syn_params['d1']) # par.x(11)
if syn_params.get('tauD2'):
lsyn.tauD2 = float(syn_params['tauD2']) # par.x(12)
if syn_params.get('d2'):
lsyn.d2 = float(syn_params['d2']) # par.x(13)
if syn_params.get('tauF'):
lsyn.tauF = float(syn_params['tauF']) # par.x(14)
if syn_params.get('f'):
lsyn.f = float(syn_params['f']) # par.x(15)
if syn_params.get('bACH'):
lsyn.bACH = float(syn_params['bACH']) # par.x(17)
if syn_params.get('aDA'):
lsyn.aDA = float(syn_params['aDA']) # par.x(18)
if syn_params.get('bDA'):
lsyn.bDA = float(syn_params['bDA']) # par.x(19)
if syn_params.get('wACH'):
lsyn.wACH = float(syn_params['wACH']) # par.x(20)
return lsyn
def pyr2int(syn_params, xs, secs):
"""Create a list of pyr2int synapses
:param syn_params: parameters of a synapse
:param xs: list of normalized distances along the section
:param secs: target sections
:return: list of NEURON synpase objects
"""
syns = []
for x, sec in zip(xs, secs):
syn = Pyr2Int(syn_params, x, sec)
syns.append(syn)
return syns
def Int2Pyr(syn_params, sec_x, sec_id):
"""Create a int2pyr synapse
:param syn_params: parameters of a synapse
:param sec_x: normalized distance along the section
:param sec_id: target section
:return: NEURON synapse object
"""
trg_cell_nid = int(str(sec_id).split("[")[1].split("]")[0])
# if trg_cell_nid > 0:
# import pdb; pdb.set_trace()
if trg_cell_nid in weight_means["inh"].keys():
mean_weight = weight_means["inh"][trg_cell_nid]
else:
weight_means["inh"][trg_cell_nid] = mean_weight = np.random.uniform(0.2, 0.35)
lsyn = h.int2pyr(sec_x, sec=sec_id)
if syn_params.get('AlphaTmax_ampa'):
lsyn.AlphaTmax_ampa = float(syn_params['AlphaTmax_ampa']) # par.x(21)
if syn_params.get('Beta_ampa'):
lsyn.Beta_ampa = float(syn_params['Beta_ampa']) # par.x(22)
if syn_params.get('Cdur_ampa'):
lsyn.Cdur_ampa = float(syn_params['Cdur_ampa']) # par.x(23)
if syn_params.get('gbar_ampa'):
lsyn.gbar_ampa = float(syn_params['gbar_ampa']) # par.x(24)
if syn_params.get('Erev_ampa'):
lsyn.Erev_ampa = float(syn_params['Erev_ampa']) # par.x(16)
if syn_params.get('AlphaTmax_nmda'):
lsyn.AlphaTmax_nmda = float(syn_params['AlphaTmax_nmda']) # par.x(25)
if syn_params.get('Beta_nmda'):
lsyn.Beta_nmda = float(syn_params['Beta_nmda']) # par.x(26)
if syn_params.get('Cdur_nmda'):
lsyn.Cdur_nmda = float(syn_params['Cdur_nmda']) # par.x(27)
if syn_params.get('gbar_nmda'):
lsyn.gbar_nmda = float(syn_params['gbar_nmda']) # par.x(28)
if syn_params.get('Erev_nmda'):
lsyn.Erev_nmda = float(syn_params['Erev_nmda']) # par.x(16)
if syn_params.get('initW'):
#lsyn.initW = float(syn_params['initW']) * random.uniform(0.5,1.0) # par.x(0) * rC.uniform(0.5,1.0)//rand.normal(0.5,1.5) //`rand.repick()
lsyn.initW = float(min(lognormal(mean_weight, 0.1), 5) * scale)
#float(lognormal(3.171729, 0.5173616067) * scale * 20)
#lsyn.initW = float(lognormal(mean_weight, 0.5173616067) * scale)
#lsyn.initW = min(float(lognormal(mean_weight, 1)), 11) * scale
#lsyn.initW = 3.171729*10
if syn_params.get('Wmax'):
lsyn.Wmax = float(syn_params['Wmax']) * lsyn.initW # par.x(1) * lsyn.initW
if syn_params.get('Wmin'):
lsyn.Wmin = float(syn_params['Wmin']) * lsyn.initW # par.x(2) * lsyn.initW
#delay = float(syn_params['initW']) # par.x(3) + delayDistance
#lcon = new NetCon(&v(0.5), lsyn, 0, delay, 1)
if syn_params.get('lambda1'):
lsyn.lambda1 = float(syn_params['lambda1']) # par.x(6)
if syn_params.get('lambda2'):
lsyn.lambda2 = float(syn_params['lambda2']) # par.x(7)
if syn_params.get('threshold1'):
lsyn.threshold1 = float(syn_params['threshold1']) # par.x(8)
if syn_params.get('threshold2'):
lsyn.threshold2 = float(syn_params['threshold2']) # par.x(9)
if syn_params.get('tauD1'):
lsyn.tauD1 = float(syn_params['tauD1']) # par.x(10)
if syn_params.get('d1'):
lsyn.d1 = float(syn_params['d1']) # par.x(11)
if syn_params.get('tauD2'):
lsyn.tauD2 = float(syn_params['tauD2']) # par.x(12)
if syn_params.get('d2'):
lsyn.d2 = float(syn_params['d2']) # par.x(13)
if syn_params.get('tauF'):
lsyn.tauF = float(syn_params['tauF']) # par.x(14)
if syn_params.get('f'):
lsyn.f = float(syn_params['f']) # par.x(15)
return lsyn
def int2pyr(syn_params, xs, secs):
"""Create a list of int2pyr synapses
:param syn_params: parameters of a synapse
:param xs: list of normalized distances along the section
:param secs: target sections
:return: list of NEURON synpase objects
"""
syns = []
for x, sec in zip(xs, secs):
syn = Int2Pyr(syn_params, x, sec)
syns.append(syn)
return syns
def Pyr2Pyr(syn_params, sec_x, sec_id):
"""Create a pyr2pyr synapse
:param syn_params: parameters of a synapse
:param sec_x: normalized distance along the section
:param sec_id: target section
:return: NEURON synapse object
"""
#import pdb; pdb.set_trace()
trg_cell_nid = int(str(sec_id).split("[")[1].split("]")[0])
# if trg_cell_nid > 0:
# import pdb; pdb.set_trace()
if trg_cell_nid in weight_means["exc"].keys():
mean_weight = weight_means["exc"][trg_cell_nid]
else:
weight_means["exc"][trg_cell_nid] = mean_weight = np.random.uniform(0.435, 0.5)
#weight_means["exc"][trg_cell_nid] = mean_weight = np.random.uniform(0.18181829517744805 + 0.32, 0.18181829517744805 + 0.35)
lsyn = h.pyr2pyr(sec_x, sec=sec_id)
if syn_params.get('AlphaTmax_ampa'):
lsyn.AlphaTmax_ampa = float(syn_params['AlphaTmax_ampa']) # par.x(21)
if syn_params.get('Beta_ampa'):
lsyn.Beta_ampa = float(syn_params['Beta_ampa']) # par.x(22)
if syn_params.get('Cdur_ampa'):
lsyn.Cdur_ampa = float(syn_params['Cdur_ampa']) # par.x(23)
if syn_params.get('gbar_ampa'):
lsyn.gbar_ampa = float(syn_params['gbar_ampa']) # par.x(24)
if syn_params.get('Erev_ampa'):
lsyn.Erev_ampa = float(syn_params['Erev_ampa']) # par.x(16)
if syn_params.get('AlphaTmax_nmda'):
lsyn.AlphaTmax_nmda = float(syn_params['AlphaTmax_nmda']) # par.x(25)
if syn_params.get('Beta_nmda'):
lsyn.Beta_nmda = float(syn_params['Beta_nmda']) # par.x(26)
if syn_params.get('Cdur_nmda'):
lsyn.Cdur_nmda = float(syn_params['Cdur_nmda']) # par.x(27)
if syn_params.get('gbar_nmda'):
lsyn.gbar_nmda = float(syn_params['gbar_nmda']) # par.x(28)
if syn_params.get('Erev_nmda'):
lsyn.Erev_nmda = float(syn_params['Erev_nmda']) # par.x(16)
global max_exc
if syn_params.get('initW'):
#lsyn.initW = float(syn_params['initW']) * random.uniform(0.5,1.0) # par.x(0) * rC.uniform(0.5,1.0)//rand.normal(0.5,1.5) //`rand.repick()
lsyn.initW = float(lognormal(mean_weight, 0.14) * scale)
#lsyn.initW = 5
# if (lsyn.initW > max_exc):
# max_exc = lsyn.initW
#lsyn.initW = float(lognormal(mean_weight, 0.13993260156705545) * scale)
#lsyn.initW = float(min(lognormal(mean_weight, 0.22), 1.20) * scale)
#lsyn.initW = 0.18181829517744805 * 10
#print(lsyn.initW)
if syn_params.get('Wmax'):
lsyn.Wmax = 8#float(syn_params['Wmax']) * lsyn.initW # par.x(1) * lsyn.initW
if syn_params.get('Wmin'):
lsyn.Wmin = float(syn_params['Wmin']) * lsyn.initW # par.x(2) * lsyn.initW
#delay = float(syn_params['initW']) # par.x(3) + delayDistance
#lcon = new NetCon(&v(0.5), lsyn, 0, delay, 1)
if syn_params.get('lambda1'):
lsyn.lambda1 = float(syn_params['lambda1']) # par.x(6)
if syn_params.get('lambda2'):
lsyn.lambda2 = float(syn_params['lambda2']) # par.x(7)
if syn_params.get('threshold1'):
lsyn.threshold1 = float(syn_params['threshold1']) # par.x(8)
if syn_params.get('threshold2'):
lsyn.threshold2 = float(syn_params['threshold2']) # par.x(9)
if syn_params.get('tauD1'):
lsyn.tauD1 = float(syn_params['tauD1']) # par.x(10)
if syn_params.get('d1'):
lsyn.d1 = float(syn_params['d1']) # par.x(11)
if syn_params.get('tauD2'):
lsyn.tauD2 = float(syn_params['tauD2']) # par.x(12)
if syn_params.get('d2'):
lsyn.d2 = float(syn_params['d2']) # par.x(13)
if syn_params.get('tauF'):
lsyn.tauF = float(syn_params['tauF']) # par.x(14)
if syn_params.get('f'):
lsyn.f = float(syn_params['f']) # par.x(15)
if syn_params.get('bACH'):
lsyn.bACH = float(syn_params['bACH']) # par.x(17)
if syn_params.get('aDA'):
lsyn.aDA = float(syn_params['aDA']) # par.x(18)
if syn_params.get('bDA'):
lsyn.bDA = float(syn_params['bDA']) # par.x(19)
if syn_params.get('wACH'):
lsyn.wACH = float(syn_params['wACH']) # par.x(20)
return lsyn
def pyr2pyr(syn_params, xs, secs):
"""Create a list of pyr2pyr synapses
:param syn_params: parameters of a synapse
:param xs: list of normalized distances along the section
:param secs: target sections
:return: list of NEURON synpase objects
"""
syns = []
for x, sec in zip(xs, secs):
syn = Pyr2Pyr(syn_params, x, sec)
syns.append(syn)
return syns
def load():
#import pdb; pdb.set_trace()
add_synapse_model(Bg2Pyr, 'bg2pyr', overwrite=False)
add_synapse_model(Bg2Pyr, overwrite=False)
add_synapse_model(Pyr2Pyr, 'pyr2pyr', overwrite=False)
add_synapse_model(Pyr2Pyr, overwrite=False)
add_synapse_model(Pyr2Int, 'pyr2int', overwrite=False)
add_synapse_model(Pyr2Int, overwrite=False)
add_synapse_model(Int2Pyr, 'int2pyr', overwrite=False)
#import pdb; pdb.set_trace()
add_synapse_model(Int2Pyr, overwrite=False)
#import pdb; pdb.set_trace()
return
def syn_params_dicts(syn_dir='../biophys_components/synaptic_models'):
"""
returns: A dictionary of dictionaries containing all
properties in the synapse json files
"""
files = glob.glob(os.path.join(syn_dir,'*.json'))
data = {}
for fh in files:
with open(fh) as f:
data[os.path.basename(fh)] = json.load(f) #data["filename.json"] = {"prop1":"val1",...}
return data