Classification of Hyperspectral Data with Ordinary Least Squares in Python

In this tutorial, we will learn to classify spectral data using the Ordinary Least Squares method.

Classification with Ordinary Least Squares solves the 2-class least squares problem.

First, we load the required packages and set initial variables.

import numpy as np
import matplotlib
import matplotlib.pyplot as mplt
from scipy import linalg
from scipy import io


### Ordinary Least Squares
### SOLVES 2-CLASS LEAST SQUARES PROBLEM

### LOAD DATA ###
### IF LoadClasses IS True, THEN LOAD DATA FROM FILES ###
### OTHERSIE, RANDOMLY GENERATE DATA ###
LoadClasses    = True
TrainOutliers  = False
TestOutliers   = False
NOut           = 20
NSampsClass    = 200
NSamps         = 2*NSampsClass

Next, we read in the example data. Note that you will need to update the filepaths below to work on your machine.

if LoadClasses:

    ### GET FILENAMES %%%
    ### THESE ARE THE OPTIONS ###
    ### LinSepC1, LinSepC2,LinSepC2Outlier (Still Linearly Separable) ###
    ### NonLinSepC1, NonLinSepC2, NonLinSepC22 ###


    ## You will need to update these filepaths for your machine:
    InFile1          = '/Users/olearyd/Git/data/RSDI2017-Data-SpecClass/NonLinSepC1.mat'
    InFile2          = '/Users/olearyd/Git/data/RSDI2017-Data-SpecClass/NonLinSepC2.mat'
    C1Dict           = io.loadmat(InFile1)
    C2Dict           = io.loadmat(InFile2)
    C1               = C1Dict['NonLinSepC1']
    C2               = C2Dict['NonLinSepC2']

    if TrainOutliers:
        ### Let's Make Some Noise ###
        Out1        = 2*np.random.rand(NOut,2)-0.5
        Out2        = 2*np.random.rand(NOut,2)-0.5
        C1          = np.concatenate((C1,Out1),axis=0)
        C2          = np.concatenate((C2,Out2),axis=0)
        NSampsClass = NSampsClass+NOut
        NSamps      = 2*NSampsClass
else:
    ### Randomly Generate Some Data
    ### Make a covariance using a diagonal array and rotation matrix
    pi      = 3.141592653589793
    Lambda1 = 0.25
    Lambda2 = 0.05
    DiagMat = np.array([[Lambda1, 0.0],[0.0, Lambda2]])
    RotMat  = np.array([[np.sin(pi/4), np.cos(pi/4)], [-np.cos(pi/4), np.sin(pi/4)]])
    mu1     = np.array([0,0])
    mu2     = np.array([1,1])
    Sigma   = np.dot(np.dot(RotMat.T, DiagMat), RotMat)
    C1      = np.random.multivariate_normal(mu1, Sigma, NSampsClass)
    C2      = np.random.multivariate_normal(mu2, Sigma, NSampsClass)
    print(Sigma)
    print(C1.shape)
    print(C2.shape)

Now we can plot the data.

### PLOT DATA ###
matplotlib.pyplot.figure(1)
matplotlib.pyplot.plot(C1[:NSampsClass, 0], C1[:NSampsClass, 1], 'bo')
matplotlib.pyplot.plot(C2[:NSampsClass, 0], C2[:NSampsClass, 1], 'ro')
matplotlib.pyplot.show()

### SET UP TARGET OUTPUTS ###
TargetOutputs          = np.ones((NSamps,1))
TargetOutputs[NSampsClass:NSamps] = -TargetOutputs[NSampsClass:NSamps]

### PLOT TARGET OUTPUTS ###
matplotlib.pyplot.figure(2)
matplotlib.pyplot.plot(range(NSampsClass),         TargetOutputs[range(NSampsClass)],   'b-')
matplotlib.pyplot.plot(range(NSampsClass, NSamps), TargetOutputs[range(NSampsClass, NSamps)], 'r-')
matplotlib.pyplot.show()

### FIND LEAST SQUARES SOLUTION ###
AllSamps     = np.concatenate((C1,C2),axis=0)
AllSampsBias = np.concatenate((AllSamps, np.ones((NSamps,1))), axis=1)
Pseudo       = linalg.pinv2(AllSampsBias)
w            = Pseudo.dot(TargetOutputs)

w

array([[ 1.00766843],
       [ 1.16641088],
       [-0.29237104]])

### COMPUTE OUTPUTS ON TRAINING DATA ###
y = AllSampsBias.dot(w)

### PLOT OUTPUTS FROM TRAINING DATA ###
matplotlib.pyplot.figure(3)
matplotlib.pyplot.plot(range(NSamps), y, 'm')
matplotlib.pyplot.plot(range(NSamps),np.zeros((NSamps,1)), 'b')
matplotlib.pyplot.plot(range(NSamps), TargetOutputs, 'k')
matplotlib.pyplot.title('TrainingOutputs (Magenta) vs Desired Outputs (Black)')
matplotlib.pyplot.show()

### CALCULATE AND PLOT LINEAR DISCRIMINANT ###
Slope     = -w[1]/w[0]
Intercept = -w[2]/w[0]
Domain    = np.linspace(-1.1, 1.1, 60)  # set up the descision surface domain, -1.1 to 1.1 (looking at the data), do it 60 times
Disc      = Slope*Domain+Intercept

matplotlib.pyplot.figure(4)
matplotlib.pyplot.plot(C1[:NSampsClass, 0], C1[:NSampsClass, 1], 'bo')
matplotlib.pyplot.plot(C2[:NSampsClass, 0], C2[:NSampsClass, 1], 'ro')
matplotlib.pyplot.plot(Domain, Disc, 'k-')
matplotlib.pyplot.ylim([-1.1,1.3])
matplotlib.pyplot.title('Ordinary Least Squares')
matplotlib.pyplot.show()

RegConst      = 0.1
AllSampsBias  = np.concatenate((AllSamps, np.ones((NSamps,1))), axis=1)
AllSampsBiasT = AllSampsBias.T
XtX           = AllSampsBiasT.dot(AllSampsBias)
AllSampsReg   = XtX + RegConst*np.eye(3)
Pseudo        = linalg.pinv2(AllSampsReg)
wr            = Pseudo.dot(AllSampsBiasT.dot(TargetOutputs))

Slope     = -wr[1]/wr[0]
Intercept = -wr[2]/wr[0]
Domain    = np.linspace(-1.1, 1.1, 60)
Disc      = Slope*Domain+Intercept

matplotlib.pyplot.figure(5)
matplotlib.pyplot.plot(C1[:NSampsClass, 0], C1[:NSampsClass, 1], 'bo')
matplotlib.pyplot.plot(C2[:NSampsClass, 0], C2[:NSampsClass, 1], 'ro')
matplotlib.pyplot.plot(Domain, Disc, 'k-')
matplotlib.pyplot.ylim([-1.1,1.3])
matplotlib.pyplot.title('Ridge Regression')
matplotlib.pyplot.show()

Save this project with the name: OLSandRidgeRegress2DPGader. Make a New Project for Spectra.

### COMPUTE OUTPUTS ON TRAINING DATA ###
yr = AllSampsBias.dot(wr)

### PLOT OUTPUTS FROM TRAINING DATA ###
matplotlib.pyplot.figure(6)
matplotlib.pyplot.plot(range(NSamps), yr, 'm')
matplotlib.pyplot.plot(range(NSamps),np.zeros((NSamps,1)), 'b')
matplotlib.pyplot.plot(range(NSamps), TargetOutputs, 'k')
matplotlib.pyplot.title('TrainingOutputs (Magenta) vs Desired Outputs (Black)')
matplotlib.pyplot.show()

y1 = y[range(NSampsClass)]
y2 = y[range(NSampsClass, NSamps)]
Corr1 = np.sum([y1>0])
Corr2 = np.sum([y2<0])

y1r = yr[range(NSampsClass)]
y2r = yr[range(NSampsClass, NSamps)]
Corr1r = np.sum([y1r>0])
Corr2r = np.sum([y2r<0])

print('Result for Ordinary Least Squares')
CorrClassRate=(Corr1+Corr2)/NSamps
print(Corr1 + Corr2, 'Correctly Classified for a ', round(100*CorrClassRate), '% Correct Classification \n')

print('Result for Ridge Regression')
CorrClassRater=(Corr1r+Corr2r)/NSamps
print(Corr1r + Corr2r, 'Correctly Classified for a ', round(100*CorrClassRater), '% Correct Classification \n')

Result for Ordinary Least Squares
397 Correctly Classified for a  99 % Correct Classification 

Result for Ridge Regression
397 Correctly Classified for a  99 % Correct Classification 

### Make Confusion Matrices ###
NumClasses = 2;
Cm         = np.zeros((NumClasses,NumClasses))
Cm[(0,0)]  = Corr1/NSampsClass
Cm[(0,1)]  = (NSampsClass-Corr1)/NSampsClass
Cm[(1,0)]  = (NSampsClass-Corr2)/NSampsClass
Cm[(1,1)]  = Corr2/NSampsClass
Cm           = np.round(100*Cm)
print('Confusion Matrix for OLS Regression \n', Cm, '\n')

Cm           = np.zeros((NumClasses,NumClasses))
Cm[(0,0)]    = Corr1r/NSampsClass
Cm[(0,1)]    = (NSampsClass-Corr1r)/NSampsClass
Cm[(1,0)]    = (NSampsClass-Corr2r)/NSampsClass
Cm[(1,1)]    = Corr2r/NSampsClass
Cm           = np.round(100*Cm)
print('Confusion Matrix for Ridge Regression \n', Cm, '\n')

Confusion Matrix for OLS Regression 
 [[100.   0.]
 [  1.  99.]] 

Confusion Matrix for Ridge Regression 
 [[100.   0.]
 [  1.  99.]] 

EXERCISE: Run Ordinary Least Squares and Ridge Regression on Spectra and plot the weights