Classify Hyperspectral Image Using Library Signatures and SAM

This example shows how to classify pixels in a hyperspectral image by using the spectral angle mapper (SAM) classification algorithm. This algorithm classifies each pixel in the test data by computing the spectral match score between the spectrum of a pixel and the pure spectral signatures read from the ECOSTRESS spectral library. This example uses a data sample from the Jasper Ridge dataset as the test data. The test data contains four endmembers latent, consisting of roads, soil, water, and trees. In this example, you will:

1. Generate a score map for different regions present in the test data by computing the SAM spectral match score between the spectrum of each test pixel and a pure spectrum. The pure spectra are from the ECOSTRESS spectral library.

2. Classify the regions by using minimum score criteria, and assign a class label for each pixel in the test data.

This example requires the Hyperspectral Imaging Library for Image Processing Toolbox™. You can install the Hyperspectral Imaging Library for Image Processing Toolbox from Add-On Explorer. For more information about installing add-ons, see Get and Manage Add-Ons. The Hyperspectral Imaging Library for Image Processing Toolbox requires desktop MATLAB®, as MATLAB® Online™ and MATLAB® Mobile™ do not support the library.

Read Test Data

Read test data from the Jasper Ridge dataset by using the hypercube function. The function returns a hypercube object, which stores the hyperspectral data cube and the corresponding wavelength and metadata information read from the test data. The test data has 198 spectral bands and their wavelengths range from 399.4 nm to 2457 nm. The spectral resolution is up to 9.9 nm and the spatial resolution of each band image is 100-by-100.

hcube = hypercube('jasperRidge2_R198.img')

hcube = 
  hypercube with properties:

      DataCube: "[100x100x198 int16]"
    Wavelength: [198x1 double]
      Metadata: [1x1 struct]
     BlockSize: [100 100]

Estimate an RGB image from the data cube. Apply contrast stretching to enhance the contrast of the output RGB image.

rgbImg = colorize(hcube,'Method','rgb','ContrastStretching',true);

Display the RGB image of the test data.

figure
imagesc(rgbImg);
axis image off
title('RGB Image of Data Cube')

Read Signatures from ECOSTRESS Spectral Library

The ECOSTRESS spectral library consists of pure spectral signatures for individual surface materials. If the spectrum of a pixel matches a signature from the ECOSTRESS library, the pixel consists entirely of that single surface material. The library is a compilation of over 3400 spectral signatures for both natural and manmade materials. Since you know the endmembers latent in the test data, choose the ECOSTRESS spectral library files related to those four endmembers.

Read spectral files related to water, vegetation, soil, and concrete from the ECOSTRESS spectral library. Use the spectral signatures of these types:

• Manmade to classify roads and highway structures

• Soil to classify sand, silt, and clay regions

• Vegetation to classify tree regions

• Water to classify water regions

filenames = ["water.seawater.none.liquid.tir.seafoam.jhu.becknic.spectrum.txt",...
    "vegetation.tree.eucalyptus.maculata.vswir.jpl087.jpl.asd.spectrum.txt",...
    "soil.utisol.hapludult.none.all.87p707.jhu.becknic.spectrum.txt",...
    "soil.mollisol.cryoboroll.none.all.85p4663.jhu.becknic.spectrum.txt",...    
    "manmade.concrete.pavingconcrete.solid.all.0092uuu_cnc.jhu.becknic.spectrum.txt"];
lib = readEcostressSig(filenames)

lib=1×5 struct array with fields:
    Name
    Type
    Class
    SubClass
    ParticleSize
    Genus
    Species
    SampleNo
    Owner
    WavelengthRange
    Origin
    CollectionDate
    Description
    Measurement
    FirstColumn
    SecondColumn
    WavelengthUnit
    DataUnit
    FirstXValue
    LastXValue
    NumberOfXValues
    AdditionalInformation
    Wavelength
    Reflectance
      ⋮

Extract the class names from the library structure.

classNames = [lib.Class];

Plot the pure spectral signatures read from the ECOSTRESS spectral library.

figure
hold on
for idx = 1:numel(lib)
    plot(lib(idx).Wavelength,lib(idx).Reflectance,'LineWidth',2)
end
axis tight
box on
title('Pure Spectral Signatures from ECOSTRESS Library')
xlabel('Wavelength (\mum)')
ylabel('Reflectance (%)')
legend(classNames,'Location','northeast')
title(legend,'Class Names')
hold off

Compute Score Map for Pixels in Test Data

Find the spectral match score between each pixel spectrum and the library signatures by using the spectralMatch function. By default, the spectralMatch function computes the degree of similarity between two spectra by using the SAM classification algorithm. The function returns an array with the same spatial dimensions as the hyperspectral data cube and channels equal to the number of library signatures specified. Each channel contains the score map for a single library signature. In this example, there are five ECOSTRESS spectral library files specified for comparison, and each band of the hyperspectral data cube has spatial dimensions of 100-by-100 pixels. The size of the output array of score maps thus is 100-by-100-by-5.

scoreMap = spectralMatch(lib,hcube);

Display the score maps.

figure
montage(scoreMap,'Size',[1 numel(lib)],'BorderSize',10)
title('Score Map Obtained for Each Pure Spectrum','FontSize',14)
colormap(jet);
colorbar

Classify Pixels Using Minimum Score Criteria

Lower SAM values indicate higher spectral similarity. Use the minimum score criteria to classify the test pixels by finding the best match for each pixel among the library signatures. The result is a pixel-wise classification map in which the value of each pixel is the index of library signature file in lib for which that pixel exhibits the lowest SAM value. For example, if the value of a pixel in the classification map is 1, the pixel exhibits high similarity to the first library signature in lib.

[~,classMap] = min(scoreMap,[],3);

Create a class table that maps the classification map values to the ECOSTRESS library signatures used for spectral matching.

classTable = table((min(classMap(:)):max(classMap(:)))',classNames',...
             'VariableNames',{'Classification map value','Matching library signature'})

classTable=5×2 table
    Classification map value    Matching library signature
    ________________________    __________________________

               1                       "Sea Water"        
               2                       "Tree"             
               3                       "Utisol"           
               4                       "Mollisol"         
               5                       "Concrete"         

Display the RGB image of the hyperspectral data and the classification results. Visual inspection shows that spectral matching classifies each pixel effectively.

fig = figure('Position',[0 0 700 300]);
axes1 = axes('Parent',fig,'Position',[0.04 0 0.4 0.9]);
imagesc(rgbImg,'Parent',axes1);
axis off
title('RGB Image of Data Cube')
axes2 = axes('Parent',fig,'Position',[0.47 0 0.45 0.9]);
imagesc(classMap,'Parent',axes2)
axis off
colormap(jet(numel(lib)))
title('Pixel-wise Classification Map')
ticks = linspace(1.4,4.8,numel(lib));
colorbar('Ticks',ticks,'TickLabels',classNames)     

References

[1] Kruse, F.A., A.B. Lefkoff, J.W. Boardman, K.B. Heidebrecht, A.T. Shapiro, P.J. Barloon, and A.F.H. Goetz. “The Spectral Image Processing System (SIPS)—Interactive Visualization and Analysis of Imaging Spectrometer Data.” Remote Sensing of Environment 44, no. 2–3 (May 1993): 145–63. https://doi.org/10.1016/0034-4257(93)90013-N.

[2] ECOSTRESS Spectral Library: https://speclib.jpl.nasa.gov

[3] Meerdink, Susan K., Simon J. Hook, Dar A. Roberts, and Elsa A. Abbott. “The ECOSTRESS Spectral Library Version 1.0.” Remote Sensing of Environment 230 (September 2019): 111196. https://doi.org/10.1016/j.rse.2019.05.015.

[4] Baldridge, A.M., S.J. Hook, C.I. Grove, and G. Rivera. “The ASTER Spectral Library Version 2.0.” Remote Sensing of Environment 113, no. 4 (April 2009): 711–15. https://doi.org/10.1016/j.rse.2008.11.007.