forked from lbologna/olfactory_bulb_utils
/
params.py
189 lines (142 loc) · 4.24 KB
/
params.py
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# import args
# -*- coding: cp1252 -*-
# bulb spatial definition
bulbCenter = [ 50., 1275., 0. ]
bulbAxis = [ 2100., 2800., 2100.]
glomAxis = [ bulbAxis[i]+300 for i in range(3) ]
granAxisUp = [ bulbAxis[i]-700 for i in range(3) ]
granAxisDw = [ bulbAxis[i]-1500 for i in range(3) ]
GLOM_RADIUS = 50.
# coreneuron parameters
coreneuron = False
gpu = False
filemode = False
"""
try:
from neuron import h
h.celsius = 35
except:
pass
filename = 'cfg27'
def load_params(_filename):
global filename
global stream_last
global stream_orn_w
global stream_orn_act
filename = _filename
try:
module = __import__(filename)
globals().update(vars(module))
stream_last = stream_last_fixed+stream_ods_shift
stream_orn_w = stream_last; stream_last += 6
stream_orn_act = stream_last; stream_last += 1
glom2blanes = []
with open('blanes_exc_conn.txt', 'r') as fi:
l = fi.readline()
while l:
tk = l.split()
glom2blanes.append((int(tk[0]), int(tk[1])))
l = fi.readline()
except:
print('error during params import')
from copy import copy
from math import pi, sqrt
use_fi_stdp = False # FastInhibSTDP vs FastInhib
#plasticity
mc_fi_tau1 = 1
mc_fi_tau2 = 5
mt_fi_tau1 = 1
mt_fi_tau2 = 5
"""
gran_voxel = 17 #19
gran_connect_radius = 41.
mean_synapse_invl = 10.0
glomRealCoords = []
with open('realgloms.txt', 'r') as fi:
line = fi.readline()
while line:
token = line.split()
glomRealCoords.append([ float(token[0]), float(token[1]), float(token[2]) ])
line = fi.readline()
glomRealCoords = glomRealCoords[:127]
# cell numbers
Ngloms = len(glomRealCoords) # glomeruli
# mitral
gid_mitral_begin = 0
Nmitral_per_glom = 5 # mitral per glomerolus
Nmitral = Ngloms * Nmitral_per_glom
# middle tufted
gid_mtufted_begin = gid_mitral_begin+Nmitral
Nmtufted_per_glom = 2*Nmitral_per_glom # twice than mitral!
Nmtufted = Ngloms * Nmtufted_per_glom
gid_granule_begin = gid_mtufted_begin + Nmtufted
import granules
granules.init(bulbCenter, granAxisUp, granAxisDw, gran_voxel, gid_granule_begin)
Ngranule = len(granules.ggid2pos)
gid_blanes_begin = gid_granule_begin+Ngranule
NBlanes_per_glom = 3
NBlanes = Ngloms*NBlanes_per_glom
gid_mbs_begin = gid_blanes_begin+NBlanes
gid_bc2gc_begin = gid_mbs_begin+Nmtufted*NBlanes
# reciprocal synapse
gid_mgrs_begin = gid_bc2gc_begin+NBlanes*Ngranule
if gid_mgrs_begin % 2 != 0:
gid_mgrs_begin += 1
# Random123 secondary stream identifiers
# note: the primary stream index is the "gid" which is ordered as
# Nmitral, Ngranule, synapses
# Not all secondary identifiers are used for all types
"""
stream_last=1
stream_soma = stream_last; stream_last += 1
stream_dend = stream_last; stream_last += 1
stream_apic = stream_last; stream_last += 1
stream_tuft = stream_last; stream_last += 1
stream_latdendconnect = stream_last; stream_last += 1000 #allows per dendrite stream
stream_dsac = stream_last; stream_last += Nmitral+Nmtufted
stream_granule_diam = stream_last; stream_last += 1
stream_granule_type = stream_last; stream_last += 1
stream_granule_dsac = stream_last; stream_last += 8
stream_gap_junction = stream_last; stream_last += 1
stream_blanes = stream_last+Ngranule+Nmtufted; stream_last += 1
stream_blanes_conn = stream_last+Ngranule; stream_last += 1
stream_last_fixed = stream_last
# for the odorstim
stream_last = stream_last_fixed
stream_orn_w = stream_last; stream_last += 6
stream_orn_act = stream_last; stream_last += 1
stream_sniff_delay = stream_last; stream_last += 1
granule_rn_mean = 603.2
granule_rn_std = 363.4/10.
#granule_rn_mean = 728.7
#granule_rn_std = 293.06/10
def ranstream(id1, id2):
r = h.Random()
r.Random123(id1, id2)
return r
# learning
orn_g_mc_std = 1e-4
orn_g_mt_std = 1e-4
if False:
orn_g_mc_baseline = 0
orn_g_mc_max = 15e-3
orn_g_mt_baseline = 0
orn_g_mt_max = 15e-3
else:
orn_g_mc_baseline = 5e-4
orn_g_mc_max = 4e-3
orn_g_mt_baseline = 5e-4
orn_g_mt_max = 10e-3
scrambled_weights = False
gap_junctions_active = True
glomerular_layer = 2
load_params('cfg27')
gc_type3_prob=0
vclamp = []
args = args.parse_arguments()
tstop = args.tstop
coreneuron = args.coreneuron
gpu = args.gpu
filemode = args.filemode
filename = args.filename
"""