def sum_squared_diff_moments(theta, model, est_par, data):
par = model.par
#Update parameters
par = updatepar(par, est_par, theta)
# Solve the model
model.create_grids()
model.solve()
# Simulate the momemnts
moments = np.nan + np.zeros((data.moments.size, par.moments_numsim))
for s in range(par.moments_numsim):
# Simulate
model.simulate()
#Calculate moments
moments[:, s] = calc_moments(par, model.sim)
# Mean of moments
moments = np.mean(moments, 1)
# Objective function
if hasattr(par, 'weight_mat'):
weight_mat_inv = np.linalg.inv(par.weight_mat)
else:
weight_mat_inv = np.eye(moments.size) # The identity matrix and I^-1=I
diff = (moments - data.moments).reshape(moments.size, 1)
return (diff.T @ weight_mat_inv @ diff).ravel()
def parallel_init(model_copy):
'''parallel_init(model_copy) --> None
parallel initilization of a pool of processes. The function takes a
pickle safe copy of the model and resets the script module and the compiles
the script and creates function to set the variables.
'''
global model, par_funcs
model = model_copy
model._reset_module()
model.simulate()
(par_funcs, start_guess, par_min, par_max) = model.get_fit_pars()
def update(self, dt):
for model in self.models:
model.simulate()
if self.SAVE_TO_IMAGES:
a = [0] * (self.window.width * self.window.height * 3)
a = (GLuint * len(a))(*a)
glReadPixels(0, 0, self.window.width, self.window.height, GL_RGB, GL_UNSIGNED_BYTE, a)
a = np.array(a)
a = a.reshape((self.window.height, self.window.width, 3))
image = Image.fromarray(a, "RGB")
image = image.transpose(Image.FLIP_TOP_BOTTOM)
image.save("/Users/tanatanoi/Documents/university/CGRA409/project/vid/" + str(self.models[0].count)+".jpg")
def stimulus_ISI_calculator(cellparams, stimulus, tlength=10):
"""
Calculate ISI for a given cell and stimulus
Parameters
----------
cellparams: dictionary
The model parameters of the cells
stimulus: 1-D array
The stimulus of interest.
tlength: Float
Length of the stimulus time in seconds
Returns
-------
spiketimes: 1D array
The timestamp of the spike times
spikeISI: 1D array
The ISI values for the spikes
meanspkfr: float
The average spiking rate
"""
#Get the stimulus response of the model
cellparams['v_zero'] = np.random.rand()
spiketimes = mod.simulate(stimulus, **cellparams)
spikeISI = np.diff(spiketimes)
meanspkfr = len(spiketimes) / tlength #mean spike firing rate per second
print('mean spike firing rate (averaged over stimulus time) is %.3f' %
(meanspkfr))
return spiketimes, spikeISI, meanspkfr
def worker(weights, seed, train_mode_int=1, max_len=-1):
train_mode = (train_mode_int == 1)
model.set_model_params(weights)
reward_list, t_list = simulate(model, train_mode=train_mode, render_mode=False, num_episode=num_episode, seed=seed, max_len=max_len)
if batch_mode == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, t
def on_key_press(self, symbol, modifiers):
if(symbol == key.Q):
self.r_x += 0.3
elif(symbol == key.E):
self.r_x -= 0.3
elif(symbol == key.S):
self.z -= 50
elif(symbol == key.W):
self.z += 50
elif(symbol == key.A):
self.x += 200
elif(symbol == key.D):
self.x -= 200
elif(symbol == key.Z):
self.r_x += 90
elif(symbol == key.R):
if(self.models[0].wind_magnitude == 0):
for model in self.models:
model.wind_magnitude = 1
for model in self.models:
model.wind_magnitude *= 1.5
print("Wind magnitude is ", self.models[0].wind_magnitude)
elif(symbol == key.T):
if(abs(self.models[0].wind_magnitude) < 1):
for model in self.models:
model.wind_magnitude = 0
for model in self.models:
model.wind_magnitude /= 1.5
print("Wind magnitude is ", self.models[0].wind_magnitude)
elif(symbol == key.Y):
for model in self.models:
model.wind_magnitude *= -1
print("Wind magnitude is ", self.models[0].wind_magnitude)
elif(symbol == key.SPACE):
for model in self.models:
model.simulate()
elif(symbol == key.F):
self.DRAW_LINES = not self.DRAW_LINES
elif(symbol == key.ESCAPE): # escape
exit()
def worker(weights, seed, max_len, new_model, train_mode_int = 1):
# print('WORKER working on environment {}'.format(_new_model.env_name))
train_mode = (train_mode_int == 1)
new_model.set_model_params(weights)
reward_list, t_list = simulate(new_model,
train_mode = train_mode, render_mode = False, num_episode = num_episode, seed = seed, max_len = max_len)
if batch_mode == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, t
def worker(weights, seed, max_len, new_model, train_mode_int=1):
train_mode = (train_mode_int == 1)
new_model.set_model_params(weights)
reward_list, t_list = simulate(new_model,
train_mode=train_mode, render_mode=True, num_episode=config.NUM_EPISODE, seed=seed,
max_len=max_len)
if config.BATCH_MODE == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, t
def worker(weights, seed, max_len, new_model, train_mode_int=1):
#print('WORKER working on environment {}'.format(_new_model.env_name))
train_mode = (train_mode_int == 1)
new_model.set_model_params(weights)
reward_list, t_list = simulate(new_model,
train_mode=train_mode, render_mode=False, num_episode=num_episode, seed=seed, max_len=max_len)
if batch_mode == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, t
def main():
import pandas as pd
df = pd.read_csv("customer-data.csv")
summary, holdout = reformat.reformat(df)
print(summary.head())
pareto, mbg = model.model(holdout)
print(pareto.params_)
print(mbg.summary['coef'])
pred_purchases_pareto, pred_purchases_mbg = model.predictions(
pareto, mbg, summary)
pred_clv_pareto, pred_clv_mbg = model.clv(pareto, mbg, summary)
model.simulate(pareto, mbg)
visuals.future_prediction_plot(pareto, holdout, n=50)
visuals.future_prediction_plot(mbg, holdout, n=50)
visuals.transaction_plot(pareto)
visuals.transaction_plot(mbg)
def worker(weights, seed, max_len, new_model, train_mode_int=1):
#print('WORKER working on environment {}'.format(_new_model.env_name))
train_mode = (train_mode_int == 1)
new_model.set_model_params(weights)
#KOE: Render_mode false below results in a static image of each individual. True shows actual behavior.
#What I really want is to turn rendering completely off. Haven't figured that out yet.
reward_list, t_list = simulate(new_model,
train_mode=train_mode, render_mode=True, num_episode=num_episode, seed=seed, max_len=max_len) #KOE: Debugging. changed rendermode from false to true
if batch_mode == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, t
def power_spectrum_transfer_function(frequency,
t,
contrast,
fAMs,
kernel,
nperseg,
amp=1,
**cellparams):
"""
Calculate the transfer function for a given set of AM (amplitude modulation) frequencies and cell model
Parameters
----------
frequency: float
The stimulus sine frequency
t: 1-D array
The time aray
contrast: float
The AM strength (can be between 0 and inf)
fAMs: 1-D array
The array containing the AM frequencies
kernel: 1-D array
The kernel array for convolution
nperseg: float
The power spectrum nperseg variable
amp: float
The amplitude of the sinus wave, set to 1 by default.
*stimulusparams: list
List of stimulus parameters.
**cellparams: dictionary
Dictionary containing parameters of the cell model
Returns
-------
tfAMs: 1-D array
The array containing the transfer function values for the given array of fAMs.
"""
pfAMs = np.zeros(len(fAMs))
for idx, fAM in enumerate(fAMs):
stimulus = amp * np.sin(2 * np.pi * frequency * t) * (
1 + contrast * np.sin(2 * np.pi * fAM * t))
spiketimes = mod.simulate(stimulus, **cellparams)
f, p, __ = power_spectrum(stimulus, spiketimes, t, kernel, nperseg)
power_interpolator = interpolate(f, p)
pfAMs[idx] = power_interpolator(fAM)
tfAMs = np.sqrt(pfAMs) / contrast #transfer function value
return tfAMs
def worker(weights, seed, train_mode_int=1, max_len=-1):
behaviour_char = np.zeros(BC_SIZE)
train_mode = (train_mode_int == 1)
model.set_model_params(weights)
reward_list, bc_list, t_list = simulate(model, train_mode=train_mode, render_mode=False, num_episode=num_episode,
novelty_search=novelty_search, novelty_mode=novelty_mode, seq_len=BC_SEQ_LENGTH,
seed=seed, max_len=max_len)
if novelty_search:
# bc_list shape (n_episodes, bc_size)
behaviour_char = np.array(bc_list).mean(axis=0)
if batch_mode == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, behaviour_char, t # bc_list shape (bc_size,)
def main():
# tiny example program:
example_cell_idx = 20
# load model parameter:
parameters = load_models("models.csv")
model_params = parameters[example_cell_idx]
cell = model_params.pop('cell')
EODf = model_params.pop('EODf')
print("Example with cell:", cell)
# generate EOD-like stimulus with an amplitude step:
deltat = model_params["deltat"]
stimulus_length = 2.0 # in seconds
time = np.arange(0, stimulus_length, deltat)
# baseline EOD with amplitude 1:
stimulus = np.sin(2 * np.pi * EODf * time)
# amplitude step with given contrast:
t0 = 0.5
t1 = 1.5
contrast = 0.3
stimulus[int(t0 // deltat):int(t1 // deltat)] *= (1.0 + contrast)
# integrate the model:
spikes = simulate(stimulus, **model_params)
# some analysis an dplotting:
freq = calculate_isi_frequency(spikes, deltat)
freq_time = np.arange(spikes[0], spikes[-1], deltat)
fig, axs = plt.subplots(2, 1, sharex="col")
axs[0].plot(time, stimulus)
axs[0].set_title("Stimulus")
axs[0].set_ylabel("Amplitude in mV")
axs[1].plot(freq_time, freq)
axs[1].set_title("Model Frequency")
axs[1].set_ylabel("Frequency in Hz")
axs[1].set_xlabel("Time in s")
plt.show()
plt.close()
def run(Bnum, indexing):
prefix = "BUOY_"
bname = prefix + Bnum
path = "../../generated_data/" + bname
PD = model.readposveldata(path)
s = settings.settings()
h = s['h']
trate = s['trate']
forcevec = settings.forcevec
(forcenam, folname) = gf.forcedetail(forcevec, trate, h)
#creation of the folder for storing the simulated data.
path = path + '/' + folname
gf.mkdir_p(path)
## description of consant ice thickness or not in the simulation.
[forcevecn, trate] = gf.icethicktyp(forcevec, trate)
s['trate'] = trate
logging.info("Model simulation started.")
PD = model.simulate(s, Bnum, indexing, forcevecn, PD)
logging.info("Model Simulations done.")
Xib = PD['Xib']
Yib = PD['Yib']
Uibvec = PD['Uibvec']
hvec = PD['hvec']
Tib = PD['Tib']
Xis = PD['Xis']
Yis = PD['Yis']
Uisvec = PD['Uisvec']
## We will do elaborate plotting part later in postprocessing.
logging.info("Plotting started")
plots.plticepos(Xib, Yib, Xis, Yis, path)
logging.info("Plotting completed for the buoy path.")
## Statistic computation.
(XD, YD) = statscompute(s, Xib, Yib, Xis, Yis)
(UD, VD) = statscompute(s, Uibvec[:, 0], Uibvec[:, 1], Uisvec[:, 0],
Uisvec[:, 1])
logging.info("Statistics computation done.")
# simdata2excel(path,Bnum,forcenam,XD,YD,UD,VD,PD)
simdata2excl(s, path, Bnum, forcenam, XD, YD, UD, VD, PD)
logging.info("Excel data file created for simulated data.")
logging.info("Processing completed for buoy: " + bname)
gf.logcopy(path)
logging.shutdown()
def worker(weights, seed, train_mode, max_len=-1):
model.set_model_params(weights)
if train_mode == 2:
model.env.start_accumulate_trajs()
reward_list, t_list = simulate(model,
train_mode=train_mode == 1,
render_mode=False,
num_episode=num_episode,
seed=seed,
max_len=max_len)
if train_mode == 2:
model.env.end_accumulate_trajs()
if batch_mode == 'min':
reward = np.min(reward_list)
else:
reward = np.mean(reward_list)
t = np.mean(t_list)
return reward, t
t) * (1 + contrast * np.sin(2 * np.pi * contrastf * t))
#kernel parameters
kernelparams = {
'sigma': 0.0001,
'lenfactor': 5,
'resolution': t_delta
} #kernel is muhc shorter for power spectrum
#create kernel
kernel, kerneltime = helpers.spike_gauss_kernel(**kernelparams)
#power spectrum parameters:
nperseg = 2**15
spiketimes = mod.simulate(stimulus, **cellparams)
fexample, pexample, meanspkfr = helpers.power_spectrum(
stimulus, spiketimes, t, kernel, nperseg)
pdB = helpers.decibel_transformer(pexample)
power_interpolator_decibel = interpolate(fexample, pdB)
#stimulus power spectrum
fexamplestim, pexamplestim = welch(
np.abs(stimulus - np.mean(stimulus)), nperseg=nperseg,
fs=1 / t_delta) #zero peak of power spectrum is part of the stimulus,
#which stays even when stimulus mean is substracted.
#take absolute value to get the envelope
pdBstim = helpers.decibel_transformer(pexamplestim)
def plot_selected():
import model
cd = pathlib.Path(__file__).absolute().parent
path_weight_list = [(cd / "param_q1_opt_1E-6.npy", "1E-6"),
(cd / "param_q2_opt_1E-6.npy", "1E-6"),
(cd / "param_q1_opt_1E-5.npy", "1E-5"),
(cd / "param_q2_opt_1E-5.npy", "1E-5"),
(cd / "param_q1_opt_1E-4.npy", "1E-4"),
(cd / "param_q2_opt_1E-4.npy", "1E-4"),
(cd / "param_q1_opt_1E-3.npy", "1E-3"),
(cd / "param_q2_opt_1E-3.npy", "1E-3")]
param_pair_weight_list = [
(numpy.load(p1), numpy.load(p2), w)
for (p1, w), (p2, _) in make_pair_list(path_weight_list)
]
x_ticks = [w for _, _, w in param_pair_weight_list]
pc_vars = numpy.array(
[get_var(p1, p2) for p1, p2, _ in param_pair_weight_list])
pc_q1_std = numpy.sqrt(pc_vars[:, 0])
pc_q2_std = numpy.sqrt(pc_vars[:, 1])
tau_ises = numpy.array([
get_tau_ises(*get_taus(p1, p2)) for p1, p2, _ in param_pair_weight_list
])
tau_ises_npy_path = cd / "tau_ises.npy"
if not tau_ises_npy_path.exists():
numpy.save(tau_ises_npy_path, tau_ises)
tau1_ises = tau_ises[:, 0]
tau2_ises = tau_ises[:, 1]
height = 55 / 25.4
width = 84 / 25.4
f = plt.figure(figsize=(width, height))
plt.subplots_adjust(top=0.784,
bottom=0.207,
left=0.202,
right=0.792,
hspace=0.2,
wspace=0.2)
plt.plot(x_ticks,
pc_q1_std,
linestyle="none",
marker="o",
markerfacecolor="#00000000",
markeredgecolor="#000000ff",
label=r"$\theta_1$")
plt.plot(x_ticks,
pc_q2_std,
linestyle="none",
marker="x",
markerfacecolor="#00000000",
markeredgecolor="#000000ff",
label=r"$\theta_2$")
plt.xlabel(r"$w_{\tau}$")
plt.ylabel(r"Std. dev. of $\theta_1, \theta_2$ [deg]")
plt.legend()
plt.gca().twinx()
plt.plot(x_ticks,
tau1_ises,
linestyle="none",
marker="^",
markerfacecolor="#00000000",
markeredgecolor="#000000ff",
label=r"$\tau_1$")
plt.plot(x_ticks,
tau2_ises,
linestyle="none",
marker="^",
markerfacecolor="#000000ff",
markeredgecolor="#000000ff",
label=r"$\tau_2$")
plt.ylabel(r"Int. Sq. of torque [N${}^2$m${}^2$]")
plt.legend()
f.savefig("angle_and_torque.svg")
f = plt.figure(figsize=(width, height))
plt.subplots_adjust(top=0.975,
bottom=0.21,
left=0.185,
right=0.975,
hspace=0.2,
wspace=0.2)
tlist = numpy.linspace(0, 1, 1001)
p1, p2, w = param_pair_weight_list[3]
tau1, tau2 = get_tau(p1, p2)
plt.plot(tlist,
tau1,
linestyle="-",
color="black",
label=r"$\tau_{{1}}$ ({})".format(w))
plt.plot(tlist,
tau2,
linestyle="-.",
color="black",
label=r"$\tau_{{2}}$ ({})".format(w))
p1, p2, w = param_pair_weight_list[1]
tau1, tau2 = get_tau(p1, p2)
plt.plot(tlist,
tau1,
linestyle="--",
color="black",
label=r"$\tau_{{1}}$ ({})".format(w))
plt.plot(tlist,
tau2,
linestyle=":",
color="black",
label=r"$\tau_{{2}}$ ({})".format(w))
plt.xlabel(r"Time [s]")
plt.ylabel(r"Torque [Nm]")
plt.yticks([-25.0, 0.0, 25.0, 50.0])
plt.grid()
f.savefig("torque_series.svg")
f = plt.figure(figsize=(width, height))
plt.subplots_adjust(top=0.975,
bottom=0.21,
left=0.185,
right=0.975,
hspace=0.2,
wspace=0.2)
tlist = numpy.linspace(0, 1, 1001)
p1, p2, w = param_pair_weight_list[3]
tau1, tau2 = get_tau(p1, p2)
q1, q2, _, _ = model.simulate(tau1, tau2, 0)
plt.plot(tlist,
q1 * 180 / numpy.pi,
linestyle="-",
color="black",
label=r"$\theta_{{1}}$ ({})".format(w))
plt.plot(tlist,
q2 * 180 / numpy.pi,
linestyle="-.",
color="black",
label=r"$\theta_{{2}}$ ({})".format(w))
p1, p2, w = param_pair_weight_list[1]
tau1, tau2 = get_tau(p1, p2)
q1, q2, _, _ = model.simulate(tau1, tau2, 0)
plt.plot(tlist,
q1 * 180 / numpy.pi,
linestyle="--",
color="black",
label=r"$\theta_{{1}}$ ({})".format(w))
plt.plot(tlist,
q2 * 180 / numpy.pi,
linestyle=":",
color="black",
label=r"$\theta_{{2}}$ ({})".format(w))
plt.xlabel(r"Time [s]")
plt.ylabel(r"Posture angle [deg]")
plt.yticks([-60.0, 0.0, 60.0, 120.0])
plt.grid()
f.savefig("angle_series.svg")
plt.show()
from model import simulate
import random
from csv import writer
random.seed(97)
size = 50
unblock_input = list(range(1, size**2 + 1))
number_of_observation = 10000
header = ["edge_size", "total_sites", "unblocked_sites"]
with open("data.csv", "w") as data_file:
file_writer = writer(data_file)
file_writer.writerow(header)
with open("data.csv", "a") as data_file:
file_writer = writer(data_file)
for i in range(number_of_observation):
new_row = [size, size**2]
random.shuffle(unblock_input)
new_row.append(simulate(size, unblock_input))
file_writer.writerow(new_row)
for key, val in solver_settings.items():
getattr(solver.optimizer, key)(val)
#update mask info
model.data = copy.deepcopy(model.data_original)
[each.apply_mask() for each in model.data]
if RAXS_FIT:
raxs_tag, all_tag = get_data_type_tag(model)
for i in range(len(raxs_tag)):
model = set_model(model, int(raxs_tag[i] - 100),
all_tag.index(raxs_tag[i]))
#simulate the model first
print(
'Starting the RAXS fit, trial {} of {} trials in total'.format(
i, len(raxs_tag)))
print("Simulating the model now ...")
model.simulate()
print("Start the fit...")
solver.StartFit()
model.save(each_file)
else:
#simulate the model first
print("Simulating the model now ...")
model.simulate()
print("Start the fit...")
solver.StartFit()
model.save(each_file)
cov = solver.optimizer.return_covariance_matrix(fom_level=0.2)
model.save_addition('covariance_matrix', cov)
sensitivity = solver.optimizer.return_sensitivity(max_epoch=200,
epoch_step=0.1)
model.save_addition('sensitivity', str(list(sensitivity)))
Test
----
Main testing file for model.
"""
import numpy as np
import numpy.testing as npt
import model
p = model.parameter_set(beta=1.0, gamma=0.4)
x0 = np.array([0.99, 0.01])
T = 20
ts, result = model.simulate(p, x0, T=T, dt=0.01)
def test_parameters_set():
"""
Test that parameter set works correctly.
"""
beta = 0.1
gamma = 0.2
p = model.parameter_set(beta=beta, gamma=gamma)
npt.assert_equal(beta, p['beta'])
npt.assert_equal(gamma, p['gamma'])
