README.md

pyspc-unmix: Python package for unmixing hyperspectral data

Installation

pip install git+https://github.com/r-hyperspec/pyspc-unmix

Available alogrithms

• N-FINDR

Example

Prepare pure-mixture dataset

Generate pure signals

import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
from sklearn.decomposition import PCA
from pyspc_unmix import NFINDR

# Prepare pure signals
x = np.arange(0, 20, 0.01)
y1 = stats.norm.pdf(x, 7, 1)
y2 = stats.norm.pdf(x, 10, 1)
y3 = stats.norm.pdf(x, 13, 1)

# Plot the signals
fig, ax = plt.subplots()
ax.plot(x, y1, "r-.")
ax.plot(x, y2, "g-.")
ax.plot(x, y3, "b-.")
plt.show()

Mix the pure signals

y1_coefs = [0, 0.5, 1, 1.5, 2]
y2_coefs = [0, 0.5, 1, 1.5, 2]
y3_coefs = [0, 0.5, 1, 1.5, 2]

# Make all possible combination of the coefficients
true_coefs = np.array(np.meshgrid(y1_coefs, y2_coefs, y3_coefs)).T.reshape(-1, 3)
# Replace (0,0,0) point to avoid zero division
true_coefs[0, :] = [0.1, 0.1, 0.1]
# Normalize coefficients so the sum is always 1
true_coefs = (true_coefs.T / np.sum(true_coefs.T, 0)).T
np.random.shuffle(true_coefs)

print(np.round(true_coefs[:5,:],2))
# array([[0.5 , 0.  , 0.5 ],
#        [0.57, 0.  , 0.43],
#        [0.67, 0.33, 0.  ],
#        [0.2 , 0.6 , 0.2 ],
#        [0.4 , 0.  , 0.6 ]])


# Plot the mixtures
mixtures = true_coefs @ np.vstack((y1, y2, y3))
fig, ax = plt.subplots()
for i in range(len(mixtures)):
    ax.plot(x, mixtures[i, :])
plt.show()

Apply NFINDR: Basic example

# First, reduce dimension with PCA
x = PCA(n_components=2).fit_transform(mixtures)

# Apply NFINDR to find pure components and the concentrations
# Set random state for reproducible results
nf = NFINDR(n_endmembers=3, random_state=21)
nf.fit(x)

# See found endmembers
print(true_coefs[nf.endmember_indices_,:])
# array([[0., 0., 1.], 
#       [1., 0., 0.], 
#       [0., 1., 0.]])

print(np.round(nf.endmembers_,2))
# [[-3.76 -2.01]
#  [ 3.76 -2.01]
#  [-0.    4.02]]

# Calculate the coefficients/concetrations
nfindr_coefs = nf.transform(x)

# The values correspond to true concentrations
print(np.round(nfindr_coefs[:5,:],2))
# array([[0.5 , 0.5 , 0.  ],
#        [0.43, 0.57, 0.  ],
#        [0.  , 0.67, 0.33],
#        [0.2 , 0.2 , 0.6 ],
#        [0.6 , 0.4 , 0.  ]])

Apply NFINDR: Pipline interface

from sklearn.pipeline import Pipeline

p=3
pca_nfindr_pipe = Pipeline([('pca', PCA(n_components=p-1)), ('nfindr', NFINDR(n_endmembers=p, random_state=21))])
nfindr_coefs = pca_nfindr_pipe.fit_transform(mixtures)

print(np.round(nfindr_coefs[:5,:],2))
# array([[0.5 , 0.5 , 0.  ],
#        [0.43, 0.57, 0.  ],
#        [0.  , 0.67, 0.33],
#        [0.2 , 0.2 , 0.6 ],
#        [0.6 , 0.4 , 0.  ]])

Apply NFINDR: Out-of-simplex points and Barycentric vs. NNLS

Using NFINDR algorithm one should take care of the points out of the simplex since in real-world application the data rarely looks like a perfect simplex. In the following examples it will be demonstrated how the two availalbe transformations (barycentric and NNLS) behave in those cases.

# Prepare a simple simplex and points to unmix
vertices = np.array([
    [0, 0],
    [1, 0],
    [0, 1],
])
new_points = np.array([
    [0.2, 0.3],  # Inside of the simplex
    [5.0, 5.0],       # Outside of the simplex
])

# Apply NFINDR
nf = NFINDR().fit(vertices)

# Transform with Barycentric (default)
barycentric_concentrations = nf.transform(new_points)
# # The total sum of contrations/coefficients is always 1. Howerver,
# # The coefficients are not in the range [0,1], if a point is outside of the simplex
# array([
#     [ 0.5,  0.2,  0.3],   
#     [-9. ,  5. ,  5. ]
# ])


# Transform with NNLS
nnls_concentrations = nf.transform(new_points, method="nnls")
# # Each coefficient is always non-negative. Howerver,
# # it does not have to be less than 1. Also, the total sum
# # is not always equal to 1.
# array([
#     [ 0.0,  0.2,  0.3],   
#     [ 0.0,  5. ,  5. ]
# ])

Currently, there is not clear way of dealing with out-of-simplex points. However one of workarounds can be application of NNLS and normalizing to row sums (see the example below). This approach allows to keep all concentrations in range [0, 1] with total sum of 1. However, one should always take into account that such transformation increases the error of restoring data and does not necesseray prepresent the true coefficients as barycentric coordinates.

nnls_concentrations = nf.transform(new_points, method="nnls")
nnls_concentrations /= nnls_concentrations.sum(1).reshape(len(nnls_concentrations),-1)
# # The values were normalized to have 1 a sto a total sum 
# array([
#     [ 0.0,  0.4,  0.6],   
#     [ 0.0,  0.5,  0.5]
# ])