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+"""
+Parameter Identification from Noncontiguous Measurements with Bias and Noise
+============================================================================
+
+In parameter estimation it is common to collect measurements of a system's
+trajectories from distinct experiments. For example, if you are identifying the
+parameters of a mass-spring-damper system, you may excite the system with
+different initial conditions multiple times and measure the position of the
+mass. The data cannot simply be stacked end-to-end in time and the
+identification run because the measurement data would be discontinuous between
+each measurement trial.
+
+A workaround in opty is to create a set of differential equations with unique
+state variables for each measurement trial that all share the same constant
+parameters. You can then identify the parameters from all measurement trials
+simultaneously by passing the uncoupled differential equations to opty.
+This idea is due to Jason Moore.
+
+In addition, for each measurement, one may create a set of differential
+equations with unique state variables that again share the same constant
+parameters. In addition, one adds noise to these equations. (Intuitively this
+noise corresponds to a force acting on the system).
+This idea is due to Huawei Wang and A. J. van den Bogert.
+
+So, if one has *number_of_measurements* measurements, and one creates
+*number_of_repeats* differential equations for each measurement, one will have
+*number_of_measurements* * *number_of_repeats* uncoupled differential equations,
+all sharing the same constant parameters.
+
+Mass-spring-damper-friction Example
+===================================
+
+The position of a simple system consisting of a mass connected to a fixed point
+by a spring and a damper and subject to friction is simulated and recorded as
+noisy measurements. The spring constant, the damping coefficient
+and the coefficient of friction will be identified.
+
+**State Variables**
+
+- :math:`x_{i, j}`: position of the mass of the i-th measurement trial [m]
+- :math:`u_{i, j}`: speed of the mass of the i-th measurement trial [m/s]
+
+
+**Parameters**
+
+- :math:`m`: mass [kg]
+- :math:`c`: linear damping coefficient [Ns/m]
+- :math:`k`: linear spring constant [N/m]
+- :math:`l_0`: natural length of the spring [m]
+- :math:`friction`: friction coefficient [N]
+- :math:`n_{i, j}`: noise added [N]
+
+"""
+import sympy as sm
+import sympy.physics.mechanics as me
+import numpy as np
+from scipy.integrate import solve_ivp
+from opty import Problem
+from opty.utils import parse_free
+import matplotlib.pyplot as plt
+
+# %%
+# Equations of Motion.
+# --------------------
+#
+# Basic data may be set here
+number_of_measurements = 4
+number_of_repeats = 3
+t0, tf = 0.0, 10.0
+num_nodes = 500
+noise_scale = 1.0
+#
+m, c, k, l0, friction = sm.symbols('m, c, k, l0, friction')
+
+t = me.dynamicsymbols._t
+x = sm.Matrix([me.dynamicsymbols([f'x{i}_{j}' for j in range(number_of_repeats)])
+        for i in range(number_of_measurements)])
+u = sm.Matrix([me.dynamicsymbols([f'u{i}_{j}' for j in range(number_of_repeats)])
+        for i in range(number_of_measurements)])
+
+n = sm.Matrix([me.dynamicsymbols([f'n{i}_{j}' for j in range(number_of_repeats)])
+        for i in range(number_of_measurements)])
+
+xh, uh = me.dynamicsymbols('xh, uh')
+
+# %%
+# Form the equations of motion, I use Kane's method here.
+#
+def kd_eom_rh(xh, uh, m, c, k, l0, friction):
+    """" sets up the eoms for the system"""
+    N = me.ReferenceFrame('N')
+    O, P = sm.symbols('O, P', cls=me.Point)
+    O.set_vel(N, 0)
+
+    P.set_pos(O, xh*N.x)
+    P.set_vel(N, uh*N.x)
+    bodies = [me.Particle('part', P, m)]
+    # :math:`\tanh(\alpha \cdot x) \approx sign(x)` for large :math:`\alpha`, and
+    # is differentiale everywhere.
+    forces = [(P, -c*uh*N.x - k*(xh-l0)*N.x - friction * sm.tanh(60*uh)*N.x)]
+    kd = sm.Matrix([uh - xh.diff(t)])
+    KM = me.KanesMethod(N,
+                        q_ind=[xh],
+                        u_ind=[uh],
+                        kd_eqs=kd
+    )
+    fr, frstar = KM.kanes_equations(bodies, forces)
+    rhs = KM.rhs()
+    return (kd, fr + frstar, rhs)
+
+kd, fr_frstar, rhs = kd_eom_rh(xh, uh, m, c, k, l0, friction)
+
+# %%
+# Stack the equations such that the first number_of_repeats equations
+# belong to the first measurement, the second number_of_repeats equations belong
+# to the second measurement, and so on.
+#
+kd_total = sm.Matrix([])
+eom_total = sm.Matrix([])
+rhs_total = sm.Matrix([])
+
+for i in range(number_of_measurements):
+    for j in range(number_of_repeats):
+        eom_h = fr_frstar.subs({xh: x[i, j], uh: u[i, j],
+            uh.diff(t): u[i, j].diff(t), xh.diff(t): u[i, j]}) + \
+            sm.Matrix([n[i, j]])
+        kd_h = kd.subs({xh: x[i, j], uh: u[i, j]})
+        rhs_h = sm.Matrix([rhs[1].subs({xh: x[i, j], uh: u[i, j]})])
+
+        kd_total = kd_total.col_join(kd_h)
+        eom_total = eom_total.col_join(eom_h)
+        rhs_total = rhs_total.col_join(rhs_h)
+
+eom = kd_total.col_join(eom_total)
+
+uh =sm.Matrix([u[i, j] for i in range(number_of_measurements)
+    for j in range(number_of_repeats)])
+rhs = uh.col_join(rhs_total)
+
+for i in range(number_of_repeats):
+    sm.pprint(eom[i])
+for i in range(3):
+    print('.........')
+for i in range(number_of_repeats):
+    sm.pprint(eom[-(number_of_repeats-i)])
+
+# %%
+# Generate Noisy Measurement
+# --------------------------
+# Create 'number_of_measurements' sets of measurements with different initial
+# conditions. To get the measurements, the equations of motion are integrated,
+# and then noise is added to each point in time of the solution.
+#
+
+states = [x[i, j] for i in range(number_of_measurements)
+                for j in range(number_of_repeats)] + \
+        [u[i, j] for i in range(number_of_measurements)
+                for j in range(number_of_repeats)]
+
+parameters = [m, c, k, l0, friction]
+par_vals = [1.0, 0.25, 2.0, 1.0, 0.5]
+
+eval_rhs = sm.lambdify(states + parameters, rhs)
+
+times = np.linspace(t0, tf, num=num_nodes)
+
+measurements = []
+# %%
+# Integrate the differential equations. If np.random.seed(seed) is used, the
+# seed must be changed for every measurement to ensure they are independent.
+#
+for i in range(number_of_measurements):
+    seed = 1234*(i+1)
+    np.random.seed(seed)
+
+    x0 = 3.0*np.random.randn(2*number_of_measurements * number_of_repeats)
+    sol = solve_ivp(lambda t, x, p: eval_rhs(*x, *p).squeeze(),
+            (t0, tf), x0, t_eval=times, args=(par_vals,))
+
+    seed = 10000 + 12345*(i+1)
+    np.random.seed(seed)
+    measurements.append(sol.y[0, :] + 1.0*np.random.randn(num_nodes))
+
+measurements = np.array(measurements)
+print('shape of measurement array', measurements.shape)
+print('shape of solution array   ', sol.y.shape)
+
+# %%
+# Setup the Identification Problem
+# --------------------------------
+#
+# The goal is to identify the damping coefficient :math:`c`, the spring
+# constant :math:`k` and the coefficient of friction :math:`friction`.
+# The objective :math:`J` is to minimize the least square
+# difference in the optimal simulation as compared to the measurements.  If
+# some measurement is considered more reliable, its weight :math:`w` may be
+# increased relative to the other measurements.
+#
+#
+# objective = :math:`\int_{t_0}^{t_f} \sum_{i=1}^{\text{number_of_measurements}} \left[ \sum_{s=1}^{\text{number_of_repeats}} (w_i (x_{i, s} - x_{i,s}^m)^2 \right] \hspace{2pt} dt`
+#
+interval_value = (tf - t0) / (num_nodes - 1)
+
+w =[1 for _ in range(number_of_measurements)]
+
+nm = number_of_measurements
+nr = number_of_repeats
+def obj(free):
+    sum = 0.0
+    for i in range(nm):
+        for j in range(nr):
+            sum += np.sum((w[i]*(free[(i*nr+j)*num_nodes:(i*nr+j+1)*num_nodes] -
+                measurements[i])**2))
+    return sum
+
+def obj_grad(free):
+    grad = np.zeros_like(free)
+    for i in range(nm):
+        for j in range(nr):
+            grad[(i*nr+j)*num_nodes:(i*nr+j+1)*num_nodes] = 2*w[i]*interval_value*(
+                free[(i*nr+j)*num_nodes:(i*nr+j+1)*num_nodes] - measurements[i]
+            )
+    return grad
+
+
+# %%
+# By not including :math:`c`, :math:`k`, :math:`friction`
+# in the parameter map, they will be treated as unknown parameters.
+#
+par_map = {m: par_vals[0], l0: par_vals[3]}
+
+bounds = {
+    c: (0.01, 2.0),
+    k: (0.1, 10.0),
+    friction: (0.1, 10.0),
+}
+# %%
+# Set up the known trajectory map. If np.random.seed(seed) is used, the
+# seed must be changed for every map to ensure they are idependent.
+# noise_scale gives the 'strength' of the noise.
+#
+known_trajectory_map = {}
+for i in range(number_of_measurements):
+    for j in range(number_of_repeats):
+        seed = 10000 + 12345*(i+1)*(j+1)
+        np.random.seed(seed)
+        known_trajectory_map = (known_trajectory_map |
+            {n[i, j]: noise_scale*np.random.randn(num_nodes)})
+
+# %%
+# Set up the problem.
+#
+problem = Problem(
+    obj,
+    obj_grad,
+    eom,
+    states,
+    num_nodes,
+    interval_value,
+    known_parameter_map=par_map,
+    time_symbol=me.dynamicsymbols._t,
+    integration_method='midpoint',
+    bounds=bounds,
+    known_trajectory_map=known_trajectory_map
+)
+# %%
+# This give the sequence of the unknown parameters at the tail of solution.
+print(problem.collocator.unknown_parameters)
+# %%
+# Create an Initial Guess
+# -----------------------
+#
+# It is reasonable to use the measurements as initial guess for the states
+# because they would be available. Here, only the measurements of the position
+# are used and the speeds are set to zero. The last values are the guesses
+# for :math:`c`, :math:`friction` and :math:`k`, respectively.
+#
+initial_guess = np.array([])
+for i in range(number_of_measurements):
+    for j in range(number_of_repeats):
+        initial_guess = np.concatenate((initial_guess, measurements[i, :]))
+initial_guess = np.hstack((initial_guess,
+                np.zeros(number_of_measurements*number_of_repeats*num_nodes),
+                [0.1, 3.0, 2.0]))
+
+# %%
+# Solve the Optimization Problem
+# ------------------------------
+#
+solution, info = problem.solve(initial_guess)
+print(info['status_msg'])
+print(f'final value of the objective function is {info['obj_val']:.2f}' )
+
+# %%
+problem.plot_objective_value()
+
+# %%
+problem.plot_constraint_violations(solution)
+
+
+# %%
+# The identified parameters are:
+# ------------------------------
+#
+print(f'Estimate of damping coefficient is      {solution[-3]: 1.2f}' +
+      f' Percentage error is {(solution[-3]-par_vals[1])/solution[-3]*100:1.2f} %')
+print(f'Estimate of the spring constant is      {solution[-1]: 1.2f}' +
+      f' Percentage error is {(solution[-1]-par_vals[2])/solution[-1]*100:1.2f} %')
+print(f'Estimate of the friction coefficient is {solution[-2]: 1.2f}'
+      f' Percentage error is {(solution[-2]-par_vals[-1])/solution[-2]*100:1.2f} %')
+
+# %%
+# Plot the measurements and the trajectories calculated
+#------------------------------------------------------
+#
+sol_parsed, _, _ = parse_free(solution, len(states), 0, num_nodes )
+if number_of_measurements > 1:
+    fig, ax = plt. subplots(number_of_measurements, 1,
+        figsize=(6.4, 1.25*number_of_measurements), sharex=True, constrained_layout=True)
+
+    for i in range(number_of_measurements):
+        ax[i].plot(times, sol_parsed[i*number_of_repeats, :], color='red')
+        ax[i].plot(times, measurements[i], color='blue', lw=0.5)
+        ax[i].set_ylabel(f'{states[number_of_repeats* i]}')
+    ax[-1].set_xlabel('Time [s]')
+    ax[0].set_title('Trajectories')
+
+else:
+    fig, ax = plt. subplots(1, 1, figsize=(6.4, 1.25))
+    ax.plot(times, sol_parsed[0, :], color='red')
+    ax.plot(times, measurements[0], color='blue', lw=0.5)
+    ax.set_ylabel(f'{states[0]}')
+    ax.set_xlabel('Time [s]')
+    ax.set_title('Trajectories')
+
+
+prevent_output = True
+
+# %%
+#Plot the Trajectories
+#
+problem.plot_trajectories(solution)
+# %%
+#
+# sphinx_gallery_thumbnail_number = 3
+#
+plt.show()