def threecycle_stimulus(tau):
"""
Applies the 3-cycle stimulus protocol for a given tau
Arguments
----------
tau : float
period of oscillation
"""
# pre-pulse
y0 = [0.99996874, 0.10023398, 0]
param[3] = tau
kron = lc.Oscillator(model(null_I), param, y0)
kron.intoptions['constraints'] = None
dsol_pre = kron.int_odes(10.4)
dts_pre = kron.ts
y0_pulse = dsol_pre[-1]
dsol_pulses = [dsol_pre]
dts_pulses = [dts_pre]
for i in range(3):
# during pulse
kron = lc.Oscillator(model(I_pulse), param, y0_pulse)
kron.intoptions['constraints'] = None
dsol_dur = kron.int_odes(5)
dts_dur = kron.ts
# after pulse
kron = lc.Oscillator(model(null_I), param, dsol_dur[-1])
kron.intoptions['constraints'] = None
dsol_post = kron.int_odes(19)
dts_post = kron.ts
y0_pulse = dsol_post[-1]
dts_pulses.append(dts_dur + dts_pulses[-1][-1])
dts_pulses.append(dts_post + dts_pulses[-1][-1])
dsol_pulses.append(dsol_dur)
dsol_pulses.append(dsol_post)
final_dist = np.sqrt(np.sum(dsol_dur[-1][:2]**2))
dsol_pulses = np.vstack(dsol_pulses)
dts_pulses = np.hstack(dts_pulses)
return dts_pulses, dsol_pulses, final_dist
def mpc_problem(init_phi, ts, ref_phis, pred_horizon):
"""
uses MPC to track the reference phis, using a stepsize and a predictive horizon.
ts should be separated by stepsize.
"""
# set up the system it gets applied to
y0mpc = pmodel.lc(init_phi * pmodel.T / (2 * np.pi) + start_time)
# get step size, current phase, etc
stepsize = ts[1] - ts[0]
u_input = []
sys_state = y0mpc
sys_phis = []
for idx, inst_time in enumerate(ts):
#get the ref phase at the time, compare to system phase at the time
ref_phi = ref_phis[idx]
# remember, phi0 is defined as when the 0-cross happens
sys_phi = (pmodel.phase_of_point(sys_state) -
pmodel._t_to_phi(start_time)) % (2 * np.pi)
sys_phis.append(sys_phi)
# phase error
phi_diff = np.angle(np.exp(1j * sys_phi)) - np.angle(
np.exp(1j * ref_phi))
delta_phi_f = -phi_diff % (
2 * np.pi) # the desired shift is to make up that angle
if np.abs(phi_diff) > 0.1: #this value may be changed as desired
# calculate the optimal inputs
us_opt = mpc_pred_horiz(sys_phi, delta_phi_f, stepsize,
pred_horizon)
u_apply = us_opt[0]
else:
u_apply = 0
print delta_phi_f, u_apply
# move forward a step
u_input.append(u_apply)
mpc_param = np.copy(param)
mpc_param[15] = mpc_param[15] - u_apply
mpc_sys = lco.Oscillator(model(), mpc_param, sys_state)
sys_progress = mpc_sys.int_odes(stepsize)
sys_state = sys_progress[-1]
return ts, sys_phis, u_input
def solutions_from_us(us, stepsize, init_phi):
""" takes a set of us, a stepsize, and a phi0; returns the trajectories of the solutions """
pred_horiz = len(us)
phases = []
ref_phases = []
states = []
times = []
running_time = 0
phi0 = init_phi
y0mpc = pmodel.lc(phi0 * pmodel.T / (2 * np.pi) + start_time)
sys_state = y0mpc
for u_apply in us:
mpc_param = np.copy(param)
mpc_param[15] = mpc_param[15] - u_apply
mpc_sys = lco.Oscillator(model(), mpc_param, sys_state)
sys_progress = mpc_sys.int_odes(stepsize, numsteps=10)
# append new times and phases
times = times + list(mpc_sys.ts[:-1] + running_time)
phases = phases + [
pmodel.phase_of_point(state) for state in sys_progress[:-1]
]
#update for next step
sys_state = sys_progress[-1]
running_time = running_time + mpc_sys.ts[-1]
u0_phases = init_phi + np.asarray(times) * 2 * np.pi / pmodel.T
return {
'u0_phases': np.asarray(u0_phases),
'times': np.asarray(times),
'phases': np.asarray(phases),
'us': np.asarray(us)
}
def threecycle_targeted_stimulus(tau, phase_target):
"""
Applies the 3-cycle stimulus protocol for a given tau
Arguments
----------
tau : float
period of oscillation
phase_target : float
phase at which we want to apply the pulse
"""
# set up parameters for first time
y0 = [0.99996874, 0.10023398, 0]
param[3] = tau
dsol_total = [[y0]]
dts_total = [[0]]
for pulsecount in range(3):
# set up oscillator
kron = lc.Oscillator(model(null_I), param, y0)
kron.intoptions['constraints'] = None
phase = skron.phase_of_point(y0[:-1])
# move forward when it's before the pulse time, or after the pulse
while np.logical_or(phase < phase_target,
phase > phase_target + 3 / tau * 2 * np.pi):
# perform the integration
dsol_pre = kron.int_odes(0.5, numsteps=100)
dts_pre = kron.ts
yend = dsol_pre[-1]
phase = skron.phase_of_point(yend[:-1])
kron.y0 = yend
# append the integration
dsol_total.append(dsol_pre)
dts_total.append(dts_pre + dts_total[-1][-1])
# when it's time, apply the pulse
kron = lc.Oscillator(model(I_pulse), param, yend)
kron.intoptions['constraints'] = None
dsol_dur = kron.int_odes(5)
dts_dur = kron.ts
y0 = dsol_dur[-1]
dts_total.append(dts_dur + dts_total[-1][-1])
dsol_total.append(dsol_dur)
# residual 15h period after pulse - no need to try to target here
kron = lc.Oscillator(model(null_I), param, dsol_dur[-1])
kron.intoptions['constraints'] = None
dsol_post = kron.int_odes(15)
dts_post = kron.ts
dts_total.append(dts_post + dts_total[-1][-1])
dsol_total.append(dsol_post)
final_dist = np.sqrt(np.sum(dsol_dur[-1][:2]**2))
dsol_total = np.vstack(dsol_total)
dts_total = np.hstack(dts_total)
return dts_total, dsol_total, final_dist
""" from __future__ import division import numpy as np import casadi as cs import matplotlib.pyplot as plt from matplotlib import Grid from LocalImports import LimitCycle as lc from LocalImports import PlotOptions as plo from LocalModels.kronauer_model import model, param, EqCount, y0in, null_I import LocalModels.simplified_kronauer_model as skm # set-up way to get the phase of a point using the simpler model skron = lc.Oscillator(skm.model(), skm.param, skm.y0in) skron.intoptions['constraints'] = None skron.calc_y0() skron.limit_cycle() # figure out phase at which the pulse occurs for the 24.6h case, since that # one is the most effective y0 = [0.99996874, 0.10023398, 0] param[3] = 24.6 kron = lc.Oscillator(model(null_I), param, y0) kron.intoptions['constraints'] = None dsol_pre = kron.int_odes(10.4) dts_pre = kron.ts y0_pulse = dsol_pre[-1] pulse_phase = skron.phase_of_point(y0_pulse[:-1]) # should give ~2.66
import numpy as np from scipy import integrate, optimize, stats import matplotlib.pyplot as plt from matplotlib import gridspec import casadi as cs from pyswarm import pso import brewer2mpl as colorbrewer #local imports from LocalModels.hirota2012 import model, param, y0in from LocalImports import LimitCycle as lco from LocalImports import PlotOptions as plo from LocalImports import Utilities as ut pmodel = lco.Oscillator(model(), param, y0in) pmodel.calc_y0() pmodel.corestationary() pmodel.limit_cycle() pmodel.find_prc() # start at negative prc region times = np.linspace(0, pmodel.T, 10001) roots = pmodel.pPRC_interp.splines[15].root_offset() neg_start_root = roots[0] # for when region becomes positive pos_start_root = roots[1] # for when region becomes negative umax = 0.06 # define a periodic spline for the start_time = pos_start_root prc_pos = stats.threshold(-pmodel.pPRC_interp(times + start_time)[:, 15],
def mpc_problem_fig2(shift_value):
"""
function for parallelization. returns the max time at which there is an
error in phase greater than 0.1rad
"""
print str(shift_value) + ' started'
shift_val = shift_value * pmodel.T / 24.
prediction_window = 2
# set up times, and phases
days = 7
shift_day = 1.75
times = np.linspace(0, days * 23.7, days * 1200 + 1)
def phase_of_time(times):
return (times * 2 * np.pi / pmodel.T) % (2 * np.pi)
def shift_time(ts, shift_t=shift_day * pmodel.T, shift_val=shift_val):
if np.size(ts) is 1:
if ts >= shift_t:
return ts + shift_val
else:
return ts
elif np.size(ts) > 1:
ts = np.copy(ts)
ts[np.where(ts >= shift_t)] += shift_val
return np.asarray(ts)
else:
print "unknown type supplied"
# create the ref and uncontrolled traj
unpert_p = pmodel.lc(times)[:, 0]
pert_p = pmodel.lc(pmodel._phi_to_t(phase_of_time(shift_time(times))))[:,
0]
# control inputs
control_vectors = [pmodel.pdict['vdCn']]
prcs = pmodel.pPRC_interp
# set up the discretization
control_dur = 23.7 / 12 # 2hr
time_steps = np.arange(0, days * 23.7, 2 * 23.7 / 24)
tstep_len = time_steps[1]
control_inputs = np.zeros(
[len(time_steps) - prediction_window,
len(control_vectors) + 1])
single_step_ts = np.linspace(0, tstep_len, 100)
# initialize the problem
segment_ystart = y0in
mpc_ts = []
mpc_ps = []
mpc_phis = []
mpc_pts = []
pred_phis = [0.]
errors = []
continuous_phases = []
tphases = []
for idx, time in enumerate(time_steps[:-prediction_window]):
#calculate current phase of oscillator
mpc_phi = None
while mpc_phi is None:
# this sometimes fails to converge and I do not know why
try:
mpc_phi = pmodel.phase_of_point(segment_ystart)
except:
mpc_phi = 0
print segment_ystart
mpc_phis.append(mpc_phi)
mpc_pts.append(segment_ystart)
mpc_time_start = pmodel._phi_to_t(
mpc_phi) # used for calculating steps
control_inputs[idx, 0] = time
# get the absolute times, external times, external phases, and predicted
# phases. predicted phases are what's used for the mpc
abs_times = time_steps[idx:idx + prediction_window + 1]
abs_phases = phase_of_time(abs_times)
ext_times = shift_time(abs_times)
ext_phases = phase_of_time(ext_times)
# the next predicted phases do not anticipate the shift
pred_ext_times = ext_times[0] + time_steps[1:prediction_window + 1]
pred_ext_phases = pmodel._t_to_phi(pred_ext_times) % (2 * np.pi)
# calculate the error in phase at the current step
p1 = mpc_phi
p2 = ext_phases[0]
diff = np.min([(p1 - p2) % (2 * np.pi), (p2 - p1) % (2 * np.pi)])
errors.append(diff**2)
print idx, diff**2
# only calculate if the error matters
if diff**2 > 0.01:
# define the objective fcn
def err(parameter_shifts, future_ext_phases, mpc_time):
# assert that args are good
assert len(parameter_shifts)==len(future_ext_phases), \
"length mismatch between u, phi_ext"
osc_phases = np.zeros(len(parameter_shifts) + 1)
osc_phases[0] = mpc_phi
for i, pshift in enumerate(parameter_shifts):
# next oscilltor phase = curr phase + norm prog +integr pPRC
def dphidt(phi, t0):
return 2 * np.pi / (pmodel.T) + pshift * prcs(
pmodel._phi_to_t(phi))[:, control_vectors[0]]
osc_phases[i + 1] = integrate.odeint(
dphidt, osc_phases[i], single_step_ts)[-1]
#calc difference
p1 = osc_phases[1:]
p2 = future_ext_phases
differences = np.asarray([(p1 - p2) % (2 * np.pi),
(p2 - p1) % (2 * np.pi)]).min(0)
differences = stats.threshold(differences, threshmin=0.1)
#quadratic cost in time
weights = (np.arange(len(differences)) + 1)
return np.sum(weights * differences**2) + 0.001 * np.sum(
parameter_shifts**2)
# the sys functions here stop the swarm from printing its results
xopt, fopt = pso(err, [-0.1] * prediction_window,
[0.0] * prediction_window,
args=(pred_ext_phases, mpc_time_start),
maxiter=300,
swarmsize=100,
minstep=1e-4,
minfunc=1e-4)
opt_shifts = xopt
opt_first_step = opt_shifts[0]
else:
# no action necessary
opt_shifts = np.zeros(prediction_window)
opt_first_step = opt_shifts[0]
# simulate everything forward for one step
control_inputs[idx, 1] = opt_first_step
mpc_opt_param = np.copy(param)
mpc_opt_param[pmodel.pdict['vdCn']] += opt_first_step
mpc_model = lco.Oscillator(model(), mpc_opt_param, segment_ystart)
sol = mpc_model.int_odes(tstep_len, numsteps=500)
tsol = mpc_model.ts
# add the step results to the overall results
segment_ystart = sol[-1]
mpc_ts += list(tsol + time)
mpc_ps += list(sol[:, 0])
phases = [pmodel.phase_of_point(pt) for pt in sol[::60]]
tphases += list(tsol[::60] + time)
continuous_phases += list(phases)
abs_err = np.sqrt(errors)
ext_phis_output = phase_of_time(shift_time(time_steps))
simulation_results = [
control_inputs, errors, time_steps, mpc_phis, ext_phis_output, mpc_ps,
mpc_ts, tphases, continuous_phases
]
print str(shift_value) + ' completed'
return simulation_results
@author: abel
This file plots the ARC of the Kronauer model toward driving it to 0.
"""
from __future__ import division
import numpy as np
import casadi as cs
import matplotlib.pyplot as plt
from LocalImports import LimitCycle as lc
from LocalImports import PlotOptions as plo
from LocalModels.simplified_kronauer_model import model, param, EqCount, y0in
kron = lc.Oscillator(model(), param, y0in)
kron.intoptions['constraints'] = None
# get the PRC and ARC for this model
kron.calc_y0()
kron.limit_cycle()
kron.find_prc()
kron.findARC_whole()
# plot PRC, ARC
plt.figure()
plt.plot(kron.arc_ts, kron.pPRC_interp(kron.arc_ts)[:, 4])
plt.vlines(12.9, -0.4, 0.3, 'k')
plt.xlabel('time (h), CBTmin = 12.9')
plt.ylabel('pPRC $\hat B$')
dts_pulses.append(dts_post)
dsol_pulses.append(dsol_dur)
dsol_pulses.append(dsol_post)
final_dist = np.sqrt(np.sum(dsol_dur[-1][:2]**2))
dsol_pulses = np.vstack(dsol_pulses)
dts_pulses = np.hstack(dts_pulses)
return dts_pulses, dsol_pulses, final_dist
dts_pulses, dsol_pulses, final_dist = threecycle_stimulus(24.2)
# comparison lc
y0 = [0.99996874, 0.10023398, 0]
kron = lc.Oscillator(model(null_I), param, y0)
kron.intoptions['constraints'] = None
dsol_lc = kron.int_odes(25)
dts_lc = kron.ts
plt.figure()
# limit cycle plot
plt.plot(dsol_lc[:, 0], dsol_lc[:, 1], 'k', label='LC')
plt.plot(dsol_pre[:, 0], dsol_pre[:, 1], 'r--', label='Pre-Stim')
plt.plot(dsol_pulses[:, 0], dsol_pulses[:, 1], 'b--', label='During')
plt.plot(dsol_post[:, 0], dsol_post[:, 1], 'g', label='Post')
plt.xlabel('$x$')
plt.ylabel('$x_c$')
plt.ylim([-1.4, 1.1])
get, full pulse form 10-15h.
"""
from __future__ import division
import numpy as np
import casadi as cs
import matplotlib.pyplot as plt
from LocalImports import LimitCycle as lc
from LocalImports import PlotOptions as plo
from LocalModels.kronauer_model import model, param, EqCount, y0in, null_I
# pre-pulse
y0 = [0.99996874, 0.10023398, 0]
kron = lc.Oscillator(model(null_I), param, y0)
kron.intoptions['constraints'] = None
dsol_pre = kron.int_odes(3)
dts_pre = kron.ts
# during pulse
def I_pulse(t):
""" returns just max """
return 9500
kron = lc.Oscillator(model(I_pulse), param, dsol_pre[-1])
kron.intoptions['constraints'] = None
dsol_dur = kron.int_odes(5)
dts_dur = kron.ts