## 3 Materials and Methods
The AVIRIS hyperspectral sensor has 224 bands with 10 nm FWHM in the 365 to 2500 nm range. Spatial resolution of the AVIRIS IFOV depends on flight altitude. Modified from [[https://landsat.gsfc.nasa.gov](https://landsat.gsfc.nasa.gov)]([https://landsat.gsfc.nasa.gov](https://landsat.gsfc.nasa.gov)). Figure 2: False color composite images of the five AVIRIS flight lines used in this study. A wide range of agriculture in the Great Central Valley of California is sampled in both summer and fall. Bare rock substrates are present in the Sierra and Coast Ranges. Non-photosynthetic vegetation (NPV) is present in both agricultural and natural land cover regimes. Cloud contamination near the ends of the Delta, Davis, and Coast Ranges lines was excluded from the remainder of the analysis. Wetlands are sampled in the Delta line and the San Joaquin line. Spectrally complex salt ponds are present in the South Bay portion of the Davis line. Sun glint is present in some water bodies. The five AVIRIS flight lines were subdivided into seven spatial subsets of 5000 \(\times\) 700 pixels each. Coincident multispectral Landsat images were coregistered to match the hyperspectral subsets using nearest neighbor spectral resampling. All individual AVIRIS pixels were preserved without pixel averaging or interpolation. Because the spatial resolution of the AVIRIS data used in this study is somewhat higher (15 m to 17 m) than the 30 m resolution of Landsat 8, no direct pixel-to-pixel comparisons are attempted. Fortunately, the spatial scale of the land cover features of interest is generally coarse enough to allow a comparison of multipixel means of homogenous targets. The total areal coverage of the seven spatial subsets is approximately 9800 km\({}^{2}\). Bad and no data pixels present in either dataset were flagged and removed from the analysis. AVIRIS channels 108-133 (1363 to 1423 nm), 154-167 (1827 to 1927 nm), and 223-224 (2480 to 2500 nm) were excluded from subsequent analysis because of a large number of pixels with nonphysical reflectance values (i.e., high amplitude positive and negative spikes). Landsat 8 OLI coastal aerosol and cirrus bands (1 and 9) were excluded from this analysis because land cover is the focus of this study. The Landsat 8 panchromatic band was not used. Image statistics were then computed for the remaining 181 channels of the AVIRIS image and PC rotations of all the AVIRIS spectra were computed based on both the image covariance and correlation matrices. Eigenvalues were normalized by their sum to compute the fraction of variance present in each dimension. The same procedure was repeated for the six band Landsat 8 pixels. A Minimum Noise Fraction (MNF) transform [43] was also used for comparison, but yielded similar EMs to the PC-derived feature space. For comparison with pure substrate EMs, 161 laboratory spectra of rocks and soils from the Johns Hopkins University (JHU) spectral library were used for a PC analysis, as described above. For more details on the JHU spectral library, see: [[https://speclib.jpl.nasa.gov/documents/jhu_desc](https://speclib.jpl.nasa.gov/documents/jhu_desc)]([https://speclib.jpl.nasa.gov/documents/jhu_desc](https://speclib.jpl.nasa.gov/documents/jhu_desc)).