def sindy(n, p, a, thres):
if n == 2:
functions = [
lambda x1, y1, x2, y2: (x2 - x1) / (
(x2 - x1)**2 + (y2 - y1)**2)**(3 / 2), lambda x1, y1, x2, y2:
(y2 - y1) / ((x2 - x1)**2 + (y2 - y1)**2)**(3 / 2)
]
lib_custom = CustomLibrary(library_functions=functions)
optimizer = ps.STLSQ(threshold=thres)
t = np.arange(0, p.shape[0], 1)
model = ps.SINDy(feature_library=lib_custom,
optimizer=optimizer,
feature_names=['x0', 'y0', 'x1', 'y1', 'x2', 'y2'])
model.fit(p, t=t, x_dot=a)
model.print(lhs=["x0''", "y0''", "x1''", "y1''"])
coef = model.coefficients()
print(coef)
return coef
elif n == 3:
functions = [
lambda x0, y0, x1, y1, x2, y2: (x1 - x0) / ((x1 - x0)**2 +
(y1 - y0)**2)**(3 / 2),
lambda x0, y0, x1, y1, x2, y2: (y1 - y0) / ((x1 - x0)**2 +
(y1 - y0)**2)**(3 / 2),
lambda x0, y0, x1, y1, x2, y2: (x2 - x0) / ((x2 - x0)**2 +
(y2 - y0)**2)**(3 / 2),
lambda x0, y0, x1, y1, x2, y2: (y2 - y0) / ((x2 - x0)**2 +
(y2 - y0)**2)**(3 / 2),
lambda x0, y0, x1, y1, x2, y2: (x2 - x1) / ((x2 - x1)**2 +
(y2 - y1)**2)**(3 / 2),
lambda x0, y0, x1, y1, x2, y2: (y2 - y1) / ((x2 - x1)**2 +
(y2 - y1)**2)**(3 / 2)
]
lib_custom = CustomLibrary(library_functions=functions)
optimizer = ps.STLSQ(threshold=thres)
t = np.arange(0, p.shape[0], 1)
model = ps.SINDy(feature_library=lib_custom,
optimizer=optimizer,
feature_names=['x0', 'y0', 'x1', 'y1', 'x2', 'y2'])
model.fit(p, t=t, x_dot=a)
model.print(lhs=["x0''", "y0''", "x1''", "y1''", "x2''", "y2''"])
coef = model.coefficients()
print(coef)
return coef
else:
print('Number of bodies not supported')
def test_default_5d_model(self):
contents = read_file("random_5d.csv", "")
time_series, dt, contents, variable_names = clean_contents(contents)
model = ps.SINDy(feature_names=variable_names)
model.fit(contents, t=dt)
_ = model.coefficients()
actual_score = model.score(contents, t=time_series)
# expected_coefficients should be incomprehensible
expected_score_max = 0.1 # model is expected to fail
# assert (pytest.approx(actual_co, 0.1) == expected_co)
assert actual_score < expected_score_max # model is expected to score poorly (less than 0.1)
def train(self, trajs, xdot=None, silent=False):
X = [traj.obs for traj in trajs]
U = [traj.ctrls for traj in trajs]
#basis_funcs = [get_constant_basis_func(), get_identity_basis_func()]
basis_funcs = [get_identity_basis_func()]
if self.trig_basis:
for freq in range(1,self.trig_freq+1):
basis_funcs += get_trig_basis_funcs(freq)
if self.trig_interaction:
basis_funcs += get_trig_interaction_terms(freq)
if self.poly_basis:
for deg in range(2,self.poly_degree+1):
basis_funcs.append(get_poly_basis_func(deg))
if self.poly_cross_terms:
for deg in range(2,self.poly_degree+1):
basis_funcs += get_cross_term_basis_funcs(deg)
library_functions = [basis.func for basis in basis_funcs]
function_names = [basis.name_func for basis in basis_funcs]
library = ps.CustomLibrary(library_functions=library_functions,
function_names=function_names)
self.basis_funcs = basis_funcs
if self.time_mode == "continuous":
sindy_model = ps.SINDy(feature_library=library,
discrete_time=False,
optimizer=ps.STLSQ(threshold=self.threshold))
sindy_model.fit(X, u=U, multiple_trajectories=True,
t=self.system.dt, x_dot=xdot)
elif self.time_mode == "discrete":
sindy_model = ps.SINDy(feature_library=library,
discrete_time=True,
optimizer=ps.STLSQ(threshold=self.threshold))
sindy_model.fit(X, u=U, multiple_trajectories=True)
self.model = sindy_model
def test_default_lorenz_model(self):
contents = read_file("data_Lorenz3d.csv", "")
time_series, dt, contents, variable_names = clean_contents(contents)
model = ps.SINDy(feature_names=variable_names)
model.fit(contents, t=dt)
actual_co = model.coefficients()
actual_score = model.score(contents, t=time_series)
expected_co = [[0.0, -10.0, 10.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 28.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, -2.666, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0]]
expected_score = 1.0
assert (pytest.approx(actual_co, 0.1) == expected_co)
assert (pytest.approx(actual_score, 0.01) == expected_score)
def make_model(data, calculate_derivatives=True):
"""
constructs SINDy model
...
Parameters
----------
data: Data object
training data object constructed using Data class
calculate_derivatives: bool
if False, precalculated derivative values will be used.
Otherwise, they will be calculated during training (differentiation method can be specified)
Returns
-------
model: SINDy model object
trained SINDy model
"""
optimizer = ps.SR3(threshold=0.01,
thresholder='l1',
normalize=True,
max_iter=1000) # ?
feature_lib = ps.PolynomialLibrary(degree=2) # ?
model = ps.SINDy(optimizer,
feature_library=feature_lib,
feature_names=FEATURES + COMMANDS)
if calculate_derivatives:
model.fit(x=data.x,
u=data.u,
t=data.t,
multiple_trajectories=data.multiple_trajectories)
else:
model.fit(x=data.x,
x_dot=data.x_dot,
u=data.u,
t=data.t,
multiple_trajectories=data.multiple_trajectories)
return model
def test_default_lorenz_plot(self):
contents = read_file("data_Lorenz3d.csv", "")
time_series, dt, contents, variable_names = clean_contents(contents)
model = ps.SINDy(feature_names=variable_names)
model.fit(contents, t=dt)
coefs = model.coefficients()
feats = model.get_feature_names(
) # Get the feature names from the obtained model
conds = np.array(
[float(val) for val in contents[0]]
) # Convert the system's initial conditions into a numpy array of float values as this is what is expected by the model.simulate() function
sim_data = model.simulate(
conds, time_series
) # Create the forward simulated data. This uses the original initial conditions evolved with the model output equations to obtain new data
fig, _ = create_plot(time_series, contents, variable_names, coefs,
feats, sim_data)
return fig
# DX_K = np.copy(x_dot)
# DX_K[:, 0] = x_dot[:, 0] - a*X[:, 0]
# DX_K[:, 1] = x_dot[:, 1] - c*X[:, 1]
# print(DX_K.shape)
# plt.plot(tt, DX_K)
# %%
differentiation_method = ps.FiniteDifference(order=2)
optimizer = ps.STLSQ(threshold=th)
feature_library = ps.PolynomialLibrary(degree=2)
# %%
model = ps.SINDy(
differentiation_method=differentiation_method,
feature_library=feature_library,
optimizer=optimizer,
feature_names=feature_names
)
dt= t_end/(X.shape[0]-1)
print("PySINDy nominal")
model.fit(X, x_dot=DX_, t=dt, multiple_trajectories=False)
%time model.print()
%time p_ident_nominal = model.coefficients().T
calc_param_ident_error(p_nom, p_ident_nominal)
print("PySINDy zentral")
%time model.fit(X, x_dot=x_dot, t=dt, multiple_trajectories=False)
%time model.print()
%time p_ident_zentral = model.coefficients().T
calc_param_ident_error(p_nom, p_ident_zentral)
def fit_model_cb(sender, data):
df = get_data(cfg.CSV)
# Get x data
x_names = get_data(cfg.X_NAMES)
X = df[x_names].to_numpy()
add_data(cfg.X, X)
# Get der data
# Get input data
u_names = get_data(cfg.U_NAMES)
if len(u_names) > 0:
U = df[u_names].to_numpy()
else:
U = None
add_data(cfg.U, U)
# Get time data
if get_value("Method##time") == "Constant Step":
dt = get_value("Step size##time")
time = np.arange(0, X.shape[0]) * dt
else:
time_channel = get_value("Channel##combo##time")
if time_channel == None or time_channel == "":
log_error("Time channel must be selected", logger="logger##main")
return
time = df[time_channel].to_numpy()
add_data(cfg.TIME, time)
# Get Optimizer
if get_value("Methods##Optimizers") == "STLSQ":
threshold = get_value("threshold##optimizers")
alpha = get_value("alpha##optimizers")
max_iter = get_value("max_iter##optimizers")
optimizer = ps.STLSQ(threshold=threshold,
alpha=alpha,
max_iter=max_iter)
elif get_value("Methods##Optimizers") == "Lasso":
alpha = get_value("alpha##optimizers")
max_iter = get_value("max_iter##optimizers")
optimizer = Lasso(alpha=alpha, max_iter=max_iter, fit_intercept=False)
else:
optimizer = None
##############################
# Feature libraries
##############################
libs = []
if get_value("Enable##polynomial##libraries") == True:
degree = get_value("Degree##polynomial##libraries")
include_interaction = not (get_value("Type##polynomial##libraries")
== "Only states")
interaction_only = get_value(
"Type##polynomial##libraries") == "Only interaction"
include_bias = get_value("Include bias terms##polynomial##libraries")
log_debug(
f'degree: {degree}, include_interaction: {include_interaction}, interaction_only: {interaction_only}, include_bias: {include_bias}'
)
libs.append(
ps.PolynomialLibrary(degree=degree,
include_interaction=include_interaction,
interaction_only=interaction_only,
include_bias=include_bias))
if get_value("Enable##fourier##libraries") == True:
n_frequencies = get_value("n_frequencies##fourier##libraries")
include_sin = get_value("Include sin##fourier##libraries")
include_cos = get_value("Include cos##fourier##libraries")
try:
fourierlib = ps.FourierLibrary(n_frequencies=n_frequencies,
include_sin=include_sin,
include_cos=include_cos)
libs.append(fourierlib)
except ValueError as err:
log_error(err, "logger##main")
return
if get_value("Enable##identity##libraries") == True:
libs.append(ps.IdentityLibrary())
# Handle the case if nothing's selected
if not libs:
libs.append(ps.PolynomialLibrary())
log_debug(libs, logger="logger##main")
# Get "feature_library" by reducing the "libs" list
feature_library = functools.reduce(lambda a, b: a + b, libs)
try:
model = ps.SINDy(optimizer=optimizer, feature_library=feature_library)
model.fit(X, t=time, u=U)
log_info(f"Model fitted.", logger="logger##main")
except ValueError as err:
log_error(err, logger="logger##main")
return
model_eqs = []
for i, eq in enumerate(model.equations()):
model_eqs.append(f"der(x{i}) = {eq}")
model_text = "\n".join(model_eqs)
set_value("Score##fitting", model.score(X, time, u=U))
set_value("Equations##fitting", model_text)
add_data(cfg.MODEL, model)
# clear X_fit listbox
configure_item("X_fit##fitting", items=[])
# Training data
t_fine = np.linspace(0, Tf, N_fine + 1)
X_fine = odeint_jax(LV, x0, t_fine, alpha, beta, gamma, delta)
X_fine_noise = X_fine + noise * X_fine.std(0) * random.normal(
key, X_fine.shape)
t = t_fine[onp.array(list(range(0, N_fine + 1, N_fine // N)))]
X_train = X_fine_noise[list(range(0, N_fine + 1, N_fine // N)), :]
gap = 4
ind_t = np.array([0])
ind_t = np.concatenate([ind_t[:, None], np.arange(gap + 1, N + 1)[:, None]])
ind_t = ind_t[:, 0]
t_grid = onp.array(t[ind_t])
print('case_1_as_GP_NODE', t_grid, t_grid.shape)
model_GP_ODE = ps.SINDy(feature_library=custom_library)
model_GP_ODE.fit(onp.array(X_train[ind_t, :]), t=t_grid)
print('case_1_as_GP_NODE:')
model_GP_ODE.print()
x_test_sim = model_GP_ODE.simulate(x0_onp, t_grid_test)
plt.figure(figsize=(12, 6.5))
plt.xticks(fontsize=22)
plt.yticks(fontsize=22)
plt.plot(t_grid_test,
data_test[:, 0],
'r-',
label="True trajectory of $x_1(t)$")
plt.plot(t_grid, X_train[ind_t, 0], 'ro', label="Training data of $x_1(t)$")
plt.plot(t_grid_test,
x_test_sim[:, 0],
# fit Koopman operator
# model = ps.SINDy()
# model.fit(Vtilde[:1000, :-1], t=.01)
# model.print()
# linear regression:
# reg = linear_model.LinearRegression()
# reg.fit(Vtilde[100:600, :-1], dVtilde_dt[100:600, :-1])
# A = reg.coef_
# fig, ax = plt.subplots()
# ax = sns.heatmap(A, center=0)
#
# dVtilde_dt_pred = reg.predict(Vtilde[600:, :-1])
model = ps.SINDy()
model.fit(Vtilde, t=0.01)
model.print()
#
# fig, ax = plt.subplots()
# ax.plot(dVtilde_dt_pred[:, 0], alpha=0.6, c='k', linestyle='--', label="pred")
# ax.plot(dVtilde_dt[500:, 0], alpha=0.6, lw=1, label="true")
# ax.legend()
#
# # runge-kutta integration
# y = first_order_kutta_runge(dx_dt=dVtilde_dt_pred, x=Vtilde, starting_point=600)
#
# # plot the predicted 1st component
# fig, ax = plt.subplots()
# ax.plot(y.T[0], alpha=0.6, lw=1, label="pred")
# ax.legend()
functions = [lambda x,y : x/(x**2+y**2)**(3/2), lambda x,y : y/(x**2+y**2)**(3/2)] # The specific functions we're looking for
lib_custom = CustomLibrary(library_functions=functions) # defines the custom library we want to use
# ## Model identification
#
# The following cell includes the model optimization and model identification.
# In[6]:
optimizer = ps.STLSQ(threshold=1)
model = ps.SINDy(
feature_library = lib_custom,
optimizer=optimizer,
feature_names = ['x', 'y'])
xd = np.gradient(x[:, 0], t)
yd = np.gradient(x[:, 1], t)
dot = np.array([xd, yd]).T # .T is to transpose the array
model.fit(x, t=t, x_dot=a)
model.print()
coef = model.coefficients()
print(coef)
# ## Data analysis
# LPF?
# DO[1, :] = 10 * DO[1, :]
# DO = stats.zscore(DO,axis=1)
coeff_gram = []
model_scores = []
skips = 10
length_window = int(1 / dt * 30)
sample_vect = np.arange(DO.shape[1])
for tt in sample_vect[::skips]:
if tt + length_window > DO.shape[1]:
continue
model = ps.SINDy(optimizer=optimizer, feature_library=lib_generalized)
DO_snip = DO[:, tt:tt + length_window]
model.fit(DO_snip.T, t=dt)
coeff_gram.append(model.coefficients())
model_scores.append(model.score(DO_snip.T))
coeff_grams[pt] = np.array(coeff_gram)
#%%
dyn_feat_names = lib_generalized.get_feature_names()
split_dyn_feat_names = ["L: " + a for a in dyn_feat_names
] + ["R: " + a for a in dyn_feat_names]
x_0_coeffs = [a for a in split_dyn_feat_names if a.find("x0") != -1]
x_1_coeffs = [a for a in split_dyn_feat_names if a.find("x1") != -1]