<reponame>emmanuelle/multi-diffusion
"""
Fitting multidiffusion profiles for three components
====================================================

A typical fitting procedure is shown in this example. Synthetic diffusion
profiles are generated for a system with three components, and three different
different exchange experiments. Uphill diffusion is observed for one of the
exchange experiments. For a moderate noise, we see that the fitting procedure
results in an accurate estimate of the diffusion matrix.
"""

import numpy as np
import matplotlib.pyplot as plt
from multidiff import compute_diffusion_matrix, create_diffusion_profiles

############################################################################
# First we generate synthetic data, with three components. The diffusion
# matrix has two eigenvalues with quite different magnitudes. Exchange vectors
# correspond to the exchange of the three possible pairs of components
# (meaning that each endmember is enriched in one component and poorer in
# another, compared to the other endmember).

n_comps = 2

diags = np.array([1, 5])
P = np.matrix([[1, 1], [-1, 0]])

############################################################################
# It is possible to have different measurement points for the different
# experiments. Also note that measurement points don't have to be symmetric
# around 0.
xpoints_exp1 = np.linspace(-10, 10, 100)
xpoints_exp2 = np.linspace(-12, 10, 100)
xpoints_exp3 = np.linspace(-8, 10, 120)
x_points = [xpoints_exp1, xpoints_exp2, xpoints_exp3]

############################################################################
# Let us now define the exchange vectors. Each column corresponds to an
# experiment: e.g. the first column represents the exchange of the first two
# components.

exchange_vectors = np.array([[0, 1, 1], 
               [1, -1, 0],
               [-1, 0, -1]])


concentration_profiles = create_diffusion_profiles((diags, P), x_points,
                                                    exchange_vectors,
                                                    noise_level=0.0)


############################################################################
# The algorithm needs an initial guess for the diffusion matrix. Here we give
# an initialization that is quite far from the looked-for diffusion matrix.
# Nevertheless, the result of the fit is quite good.

diags_init = np.array([1, 1])
P_init = np.eye(2)
diags_res, eigvecs, _, _, _ = compute_diffusion_matrix((diags_init, P_init), 
                               x_points,
                               concentration_profiles, plot=True)

print("True eigenvalues: ", diags)

print("Fitted eigenvalues: ", diags_res)

print("True eigenvectors: ", P)

print("Fitted eigenvalues: ", eigvecs)

plt.show()

"""
Fitting multidiffusion profiles for three components
====================================================

A typical fitting procedure is shown in this example. Synthetic diffusion
profiles are generated for a system with three components, and three different
different exchange experiments. Uphill diffusion is observed for one of the
exchange experiments. For a moderate noise, we see that the fitting procedure
results in an accurate estimate of the diffusion matrix.
"""

import numpy as np
import matplotlib.pyplot as plt
from multidiff import compute_diffusion_matrix, create_diffusion_profiles

############################################################################
# First we generate synthetic data, with three components. The diffusion
# matrix has two eigenvalues with quite different magnitudes. Exchange vectors
# correspond to the exchange of the three possible pairs of components
# (meaning that each endmember is enriched in one component and poorer in
# another, compared to the other endmember).

n_comps = 2

diags = np.array([1, 5])
P = np.matrix([[1, 1], [-1, 0]])

############################################################################
# It is possible to have different measurement points for the different
# experiments. Also note that measurement points don't have to be symmetric
# around 0.
xpoints_exp1 = np.linspace(-10, 10, 100)
xpoints_exp2 = np.linspace(-12, 10, 100)
xpoints_exp3 = np.linspace(-8, 10, 120)
x_points = [xpoints_exp1, xpoints_exp2, xpoints_exp3]

############################################################################
# Let us now define the exchange vectors. Each column corresponds to an
# experiment: e.g. the first column represents the exchange of the first two
# components.

exchange_vectors = np.array([[0, 1, 1], 
               [1, -1, 0],
               [-1, 0, -1]])


concentration_profiles = create_diffusion_profiles((diags, P), x_points,
                                                    exchange_vectors,
                                                    noise_level=0.0)


############################################################################
# The algorithm needs an initial guess for the diffusion matrix. Here we give
# an initialization that is quite far from the looked-for diffusion matrix.
# Nevertheless, the result of the fit is quite good.

diags_init = np.array([1, 1])
P_init = np.eye(2)
diags_res, eigvecs, _, _, _ = compute_diffusion_matrix((diags_init, P_init), 
                               x_points,
                               concentration_profiles, plot=True)

print("True eigenvalues: ", diags)

print("Fitted eigenvalues: ", diags_res)

print("True eigenvectors: ", P)

print("Fitted eigenvalues: ", eigvecs)

plt.show()
Fitting multidiffusion profiles for three components ====================================================  A typical fitting procedure is shown in this example. Synthetic diffusion profiles are generated for a system with three components, and three different different exchange experiments. Uphill diffusion is observed for one of the exchange experiments. For a moderate noise, we see that the fitting procedure results in an accurate estimate of the diffusion matrix. ############################################################################ # First we generate synthetic data, with three components. The diffusion # matrix has two eigenvalues with quite different magnitudes. Exchange vectors # correspond to the exchange of the three possible pairs of components # (meaning that each endmember is enriched in one component and poorer in # another, compared to the other endmember). ############################################################################ # It is possible to have different measurement points for the different # experiments. Also note that measurement points don't have to be symmetric # around 0. ############################################################################ # Let us now define the exchange vectors. Each column corresponds to an # experiment: e.g. the first column represents the exchange of the first two # components. ############################################################################ # The algorithm needs an initial guess for the diffusion matrix. Here we give # an initialization that is quite far from the looked-for diffusion matrix. # Nevertheless, the result of the fit is quite good.