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b/arm_model/analysis.py |
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import numpy as np |
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import pylab as plt |
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import matplotlib as mpl |
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# from mpl_toolkits.mplot3d import Axes3D |
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import pandas as pd |
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from util import to_np_mat, plot_corr_ellipses, \ |
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convex_bounded_vertex_enumeration, nullspace |
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from logger import Logger |
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# ------------------------------------------------------------------------ |
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# FeasibleMuscleSetAnalysis |
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# ------------------------------------------------------------------------ |
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def construct_muscle_space_inequality(NR, fm_par, Fmax): |
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"""Construct the feasible muscle space Z f_m0 <= B . |
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Parameters |
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---------- |
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NR: moment arm null space matrix |
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fm_par: particular muscle forces |
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Fmax: maximum muscle force |
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""" |
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Z0 = -NR |
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Z1 = NR |
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B0 = fm_par |
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B1 = np.asmatrix(np.diag(Fmax)).reshape(Fmax.shape[0], 1) - fm_par |
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Z = np.concatenate((Z0, Z1), axis=0) |
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B = np.concatenate((B0, B1), axis=0) |
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return Z, B |
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class FeasibleMuscleSetAnalysis: |
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"""Feasible muscle set analysis. |
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The required command along with the state of the system are recorded. Then |
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this information is used to compute the feasible muscle null space and |
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visualize it. |
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""" |
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def __init__(self, model, simulation_reporter): |
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""" |
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""" |
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self.logger = Logger('FeasibleMuscleSetAnalsysis') |
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self.model = model |
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self.simulation_reporter = simulation_reporter |
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def visualize_simple_muscle(self, t, ax=None): |
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"""Visualize the feasible force set at a particular time instance for a linear |
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muscle. |
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Parameters |
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---------- |
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t: time |
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ax: 1 x 3 axis |
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""" |
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m = self.model.md |
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q, Z, B, NR, fm_par = self.calculate_simple_muscles(t) |
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x_max = np.max(to_np_mat(self.model.Fmax)) |
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fm_set = self.generate_solutions(Z, B, NR, fm_par) |
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dataframe = pd.DataFrame(fm_set, columns=['$m_' + str(i) + '$' for i in |
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range(1, m + 1)]) |
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# box plot |
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if ax is None or ax.shape[0] < 3: |
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fig, ax = plt.subplots(1, 3, figsize=(15, 5)) |
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# box plot |
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dataframe.plot.box(ax=ax[0]) |
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ax[0].set_xlabel('muscle id') |
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ax[0].set_ylabel('force $(N)$') |
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ax[0].set_title('Muscle-Force Box Plot') |
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ax[0].set_ylim([0, 1.1 * x_max]) |
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# correlation matrix |
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cmap = mpl.cm.jet |
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norm = mpl.colors.Normalize(vmin=-1, vmax=1) |
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corr = dataframe.corr() |
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m = plot_corr_ellipses(corr, ax=ax[1], norm=norm, cmap=cmap) |
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cb = plt.colorbar(m, ax=ax[1], orientation='vertical', norm=norm, |
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cmap=cmap) |
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cb.set_label('Correlation Coefficient') |
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ax[1].margins(0.1) |
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ax[1].set_xlabel('muscle id') |
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ax[1].set_ylabel('muscle id') |
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ax[1].set_title('Correlation Matrix') |
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ax[1].axis('equal') |
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# draw model |
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self.model.draw_model(q, False, ax[2], scale=0.7, text=False) |
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def calculate_simple_muscles(self, t): |
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"""Construct Z f_m0 <= B for the case of a linear muscle model for a particular |
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time instance. |
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Parameters |
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---------- |
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t: time |
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""" |
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# find nearesrt index corresponding to t |
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idx = np.abs(np.array(self.simulation_reporter.t) - t).argmin() |
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t = self.simulation_reporter.t[idx] |
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q = self.simulation_reporter.q[idx] |
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u = self.simulation_reporter.u[idx] |
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tau = self.simulation_reporter.tau[idx] |
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pose = self.model.model_parameters(q=q, u=u) |
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n = self.model.nd |
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# calculate required variables |
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R = to_np_mat(self.model.R.subs(pose)) |
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RBarT = np.asmatrix(np.linalg.pinv(R.T)) |
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# reduce to independent columns to avoid singularities (proposition 3) |
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NR = nullspace(R.transpose()) |
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fm_par = np.asmatrix(-RBarT * tau.reshape((n, 1))) |
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Fmax = to_np_mat(self.model.Fmax) |
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Z, B = construct_muscle_space_inequality(NR, fm_par, Fmax) |
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return q, Z, B, NR, fm_par |
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def generate_solutions(self, A, b, NR, fm_par): |
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"""Sample the solution space that satisfy A x <= b. |
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Parameters |
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---------- |
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A: matrix A |
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b: column vector |
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NR: moment arm nullspace |
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fm_par: particular solution |
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Returns |
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------- |
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muscle forces: a set of solutions that satisfy the problem |
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""" |
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feasible_set = [] |
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fm0_set = convex_bounded_vertex_enumeration(np.array(A), |
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np.array(b).flatten(), 0) |
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n = fm0_set.shape[0] |
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for i in range(0, n): |
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fm = fm_par + NR * np.matrix(fm0_set[i, :]).reshape(-1, 1) |
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feasible_set.append(fm) |
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return np.array(feasible_set).reshape(n, -1) |
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def test_feasible_set(model): |
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feasible_set = FeasibleMuscleSetAnalysis(model) |
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n = model.nd |
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m = model.md |
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feasible_set.record(1, |
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np.random.random((m, 1)), |
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np.random.random((m, m)), |
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np.random.random((n, 1))) |
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fig, ax = plt.subplots(2, 3, figsize=(10, 10)) |
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feasible_set.visualize_simple_muscle(1, ax[0]) |
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feasible_set.visualize_simple_muscle(1, ax[1]) |
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plt.show() |