def full2DbdRNA_RM(r_m):
b1 = auto.run(start((2,2,2,2,2), (3,.05,1.0, r_m), 1, tt=800))
td = _2parFB(b1('LP1'))
td.extend(_2parFB(b1('LP2')))
if r_m >200:
npts = 10000
else:
npts = 2000
td.extend(_2parFB(b1('HB1'), npts))
b2 = auto.run(start((2,2,2,2,2), (3,2.5,1.0, r_m), 1))
tp = _2parFB(b2('HB1'), npts)
td.extend( [tp[0][:1], tp[1][:1]])
sp = mpt(td[-2][0])
a = sp['data'][td[-1][0].keys().index('PAR(2)')]
a = .89
b3 = auto.run(start((2,2,2,2,2), (3,a+.1, 1.0, r_m), 1))
periodic = auto.run(b3('HB1'), IPS=2, ICP=[1, 11], NMX=200,
DS=-0.001, DSMAX=0.01, UZR={-11:35})
homoclinicR =auto.run(periodic, IPS=9, ICP=[1,2], NPR=60,
NMX=800, STOP=['BP1', 'RG1', "LP1"], ISTART=4)
homoclinicL =auto.run(periodic, IPS=9, ICP=[1,2], NPR=60, DS=-.01,
NMX=800, STOP=['BP1', 'RG1'], ISTART=4)
td.extend([homoclinicR, homoclinicL])
#return td
#so far these are MXing.
td = reduce(__add__, td[1:], td[0])
td = auto.relabel(td)
return td
def continue_equilibrium(init, params=None, **kwargs):
"""Continue equilibrium forwards and backwards in I from init point."""
kwargs.setdefault('PAR', add_default_params(params, exclude=['I']))
equilibrium = auto.run(init, c='equilibrium', **kwargs)
equilibrium += auto.run(init, c='equilibrium', DS='-', **kwargs)
equilibrium = auto.relabel(auto.merge(equilibrium)) # get single curve with unique labels
return equilibrium
def continue_bifurcation(init, continuation_param, continuation_param_uzstop=None, params=None, **kwargs):
"""Continue bifurcation point in init for changing continuation_param. """
kwargs.setdefault('PAR', add_default_params(params, exclude=['I', continuation_param]))
kwargs.setdefault('ICP', ['I', continuation_param, 'PERIOD'])
if continuation_param_uzstop is not None:
kwargs.setdefault('UZSTOP', {'I': [-20, 100], continuation_param: continuation_param_uzstop})
bifurcation_point = auto.run(init, c='2par', **kwargs)
bifurcation_point += auto.run(init, c='2par', DS='-', **kwargs)
bifurcation_point = auto.relabel(auto.merge(bifurcation_point))
return bifurcation_point
def full2DbdYK():
b1 = auto.run(start((2,2,2), (3,.05)))
td = _2parFB(b1('LP1'))
td.extend(_2parFB(b1('LP2')))
td.extend(_2parFB(b1('HB1')))
b2 = auto.run(start((2,2,2), (3,2.5)))
td.extend( _2parFB(b2('HB1')))
b3 = auto.run(start((2,2,2), (3,.99)))
periodic = auto.run(b3("HB1"),IPS=2,ICP=[1,11],NMX=200,DS=0.01,DSMAX=0.01,UZR={-11:35})
homoclinicR =auto.run(periodic,IPS=9,ICP=[1,2],NPR=60,STOP=['BP1'],ISTART=4)
homoclinicL =auto.run(periodic,IPS=9,ICP=[1,2],NPR=60,DS=-.01,NMX=800,STOP=['BP1'],ISTART=4)
td.extend([homoclinicR, homoclinicL])
td = reduce(__add__, td[1:], td[0])
td = auto.relabel(td)
return td
def full2DbdRNA_smallr(r):
#still not quite right - the periodic orbit stop
#conditions need to be improved
b1 = auto.run(start((2,2,2,2,2), (3,.05,r), 1))
td = _2parFB(b1('LP1'))
td.extend(_2parFB(b1('LP2')))
td.extend(_2parFB(b1('HB1')))
b2 = auto.run(start((2,2,2,2,2), (3,2.5,r), 1))
td.extend( _2parFB(b2('HB1')))
hi = scanforHB(r=r)[2]
p = auto.run(hi[-1][0], IPS=2, ICP=[1,2,11], NMX=1000,
UZSTOP={1:2.35}, DS=-.001, DSMAX=0.01)
p2 = auto.run(p, IPS=2, ICP=[2,11], NMX=100, DS=-.001,
STOP=['MX1'])
homoclinicR = auto.run(p2, IPS=9, ICP=[1,2], NPR=60,
DS=-.01, NMX=800, ISTART=4)
homoclinicL = auto.run(p2, IPS=9, ICP=[1,2], NPR=60,
DS=.01, NMX=280, ISTART=4)
td.extend([homoclinicR, homoclinicL])
#return td
#so far these are MXing.
td = reduce(__add__, td[1:], td[0])
td = auto.relabel(td)
return td
def cont_WB_temperature_f(hb_continuation, outputname, gK, gNa):
#Input parameters:
# hb_continuation: What do we want to do?
# 0: Cont Hopf in Cm
# 1: Cont Hopf in T
# 2: Cont Hopf in gK
# 3: Cont Hopf in gK, followed by several conts in gNa
# 4: Cont Hopf in gNa
# outputname: Name of resultfiles that will be written
import matplotlib
import ipdb
#matplotlib.use("Agg")
import pylab, brian2, brianutils, os, json, sympy, scipy, sys, \
datetime, shelve, autoutils, auto, contextlib, inibrian
from sympy import S
########### Get initial condition through brian ###########
bifpar = {
"I": ["0.0* uA/cm2"],
"Cm": [
"1.0*uF/cm2", "1.1*uF/cm2", "1.4*uF/cm2", "1.41*uF/cm2",
"1.42*uF/cm2"
],
"dT": ["0. * kelvin"],
"gK": [str(gK) + " * msiemens/cm2"],
"gNa": [str(gNa) + " * msiemens/cm2"] #,
#"q_gk": ["1.2 * kelvin/kelvin"]
}
unames, pnames, ini, autobifpar = inibrian.find_ini_brian(
'wangBuzsaki_brian_temperature.json', 'model2', bifpar, 'wbtemp')
autobifpar['Cm'] = 1
autobifpar['gK'] = gK
autobifpar['gNa'] = gNa
################# CONT FP & LC ############################
calc_period = 0 #do we want to calculate orbits?
refine_hb = 0 #do we want to get the HB position even more exactly? (Not needed and also not really working :))
directionlist = [1, -1]
r1_fwd = auto.run(
ini,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I'],
ISP=1,
ILP=1,
SP=['LP', 'HB', 'BP'],
PAR=autobifpar,
ITNW=17,
NWTN=13,
NMX=100000,
NPR=100000, #NMX=113500, NPR=5000,
DS=directionlist[0] * 1e-3,
DSMAX=directionlist[0] * 1e-2,
STOP=['HB1'],
UZSTOP={})
r1_bwd = auto.run(
ini,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I'],
ISP=1,
ILP=1,
SP=['LP', 'HB', 'BP'],
PAR=autobifpar,
ITNW=17,
NWTN=13,
NMX=3000,
NPR=3000, #NMX=113500, NPR=5000,
DS=directionlist[1] * 1e-3,
DSMAX=directionlist[1] * 1e-2,
STOP=['HB1'],
UZSTOP={})
r1 = r1_fwd + r1_bwd
s1HB = r1_fwd.getLabel('HB')[0]
#s1LP = r1.getLabel('LP')[0]
#s1UZ = r1.getLabel('EP')[0]
################# Optional: continue orbit #######################
if calc_period:
r1_period = auto.run(s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I', 'period'],
ILP=1,
ISW=1,
IPS=2,
ITNW=7,
NWTN=3,
NMX=1000,
NPR=1000,
DS=1e-3,
DSMAX=1e-2,
NTST=300,
SP=['BT', 'LP', 'HB', 'BP', 'CP'],
UZSTOP={})
r1_withperiod = r1 + r1_period
s1HB = r1_withperiod.getLabel('HB')[0]
################# Optional: refine HB ############################
if refine_hb:
try:
r21 = auto.run(s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I', 'Cm', 'period'],
ISP=1,
ILP=1,
SP=['LP', 'HB', 'BP'],
ITNW=17,
NWTN=13,
NMX=10000,
NPR=10000,
DS=-1e-5,
DSMAX=-1e-4,
STOP=['HB1'],
IID=3)
r22 = auto.run(s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I', 'Cm', 'period'],
ISP=1,
ILP=1,
SP=['LP', 'HB', 'BP'],
ITNW=17,
NWTN=13,
NMX=10000,
NPR=10000,
DS=1e-5,
DSMAX=1e-4,
STOP=['HB1'],
IID=3)
r2 = r21 + r22
s2HB = r2.getLabel('HB')[0]
r31 = auto.run(s2HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I', 'Cm', 'period'],
ISP=1,
ILP=1,
SP=['LP', 'HB', 'BP'],
ITNW=17,
NWTN=13,
NMX=10000,
NPR=10000,
DS=-1e-5,
DSMAX=-1e-4,
STOP=['HB1'],
IID=3)
r32 = auto.run(s2HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['I', 'Cm', 'period'],
ISP=1,
ILP=1,
SP=['LP', 'HB', 'BP'],
ITNW=17,
NWTN=13,
NMX=10000,
NPR=10000,
DS=1e-5,
DSMAX=1e-4,
STOP=['HB1'],
IID=3)
r3 = r31 + r32
s3HB = r3.getLabel('HB')[0]
s1HB = s3HB
except:
print(
"Could not refine position: Bifurcation point not found. Continuing with unrefined HB."
)
################# CONT HB ############################
if (hb_continuation == 0):
runHB = [0 for item in directionlist]
for counter, direction in enumerate(directionlist):
runHB[counter] = auto.run(
s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['Cm', 'I'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=10000,
NPR=1000, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={})
elif (hb_continuation == 1):
runHB = [0 for item in directionlist]
for counter, direction in enumerate(directionlist):
runHB[counter] = auto.run(
s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['dT', 'I'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=10000,
NPR=1000, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={'dT': direction * 90})
runHB_fwdbwd = runHB[0] + runHB[1]
elif (hb_continuation == 2):
runHB = [0 for item in directionlist]
for counter, direction in enumerate(directionlist):
runHB[counter] = auto.run(
s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['gK', 'I'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=1000,
NPR=100, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={})
runHB_fwdbwd = runHB[0] + runHB[1]
elif (hb_continuation == 3):
runHB_gk = [0 for item in directionlist]
runHB_gna = [0 for item in directionlist]
#continue in gk
for counter, direction in enumerate(directionlist):
runHB_gk[counter] = auto.run(
s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['gK', 'I', 'gNa'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=1000,
NPR=100, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={'gK': direction * 75})
runHB_gna[counter] = auto.run(
s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['gNa', 'I', 'gK'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=1000,
NPR=100, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={'gNa': direction * 75})
#take every gk point and continue it in gN
runHB_fwdbwd_gk = runHB_gk[0] + runHB_gk[1]
runHB_fwdbwd_gk = auto.relabel(runHB_fwdbwd_gk)
start_idxs = runHB_fwdbwd_gk.getLabels()
for pointcounter, startpoint in enumerate(start_idxs):
for listcounter, direction in enumerate(directionlist):
runHB_fwdbwd_gk += auto.run(
runHB_fwdbwd_gk.getLabel(startpoint),
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['gNa', 'I', 'gK'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=1000,
NPR=100, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={'gK': 0.1})
#oppsite: take every gna point and cont it in gK
runHB_fwdbwd_gna = runHB_gna[0] + runHB_gna[1]
runHB_fwdbwd_gna = auto.relabel(runHB_fwdbwd_gna)
start_idxs = runHB_fwdbwd_gna.getLabels()
#run_gkna = [0 for i in range(len(start_idxs)*2)]
for pointcounter, startpoint in enumerate(start_idxs):
for listcounter, direction in enumerate(directionlist):
runHB_fwdbwd_gna += auto.run(
runHB_fwdbwd_gna.getLabel(startpoint),
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['gK', 'I', 'gNa'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=1000,
NPR=100, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={'gK': 0.1})
runHB_fwdbwd = runHB_fwdbwd_gk + runHB_fwdbwd_gna
test0 = runHB_fwdbwd['I']
test1 = runHB_fwdbwd['gNa']
runHB_fwdbwd = auto.klb(runHB_fwdbwd)
runHB_fwdbwd = auto.dlb(runHB_fwdbwd)
#take every gna point and continue it in gK
elif (hb_continuation == 4):
runHB = [0 for item in directionlist]
#continue in gk
for counter, direction in enumerate(directionlist):
runHB[counter] = auto.run(
s1HB,
e='wbtemp',
c='wbtemp',
parnames=pnames,
unames=unames,
ICP=['gNa', 'I', 'gK'], #IPS = 1
ISP=2,
ILP=
1, # SP=['LP','HB','BP'], # ISP: Bifurcation detection; 0=off, 1=BP(FP), 3=BP(PO,BVP), 2=all | ILP: Fold detection; 1=on, 0=off
ISW=
2, # ISW: Branch switching; 1=normal, -1=switch branch (BP, HB, PD), 2=switch to two-parameter continuation (LP, BP, HB, TR), 3=switch to three-parameter continuation (BP)
ITNW=17,
NWTN=13,
NMX=1000,
NPR=100, #Not sure if needed: PAR=autobifpar,
DS=direction * 1e-2,
DSMAX=direction *
1e-1, #IID = 5, RL1=0.58, EPSL = 1e+1, EPSU = 1e+1, EPSS = 10, NTST = 500,
UZSTOP={'gNa': direction * 75})
runHB_fwdbwd = runHB[0] + runHB[1]
else:
print("Please specify HB cont mode!")
rhbt = runHB_fwdbwd + r1
auto.save(rhbt, outputname) #for "Run HB temperature"
ipdb.set_trace()