matlab-analyze-spectral-images

# Spectral Imaging Skill

Generate MATLAB code for working with hyperspectral and multispectral data using the Hyperspectral Imaging Library for Image Processing Toolbox. Requires desktop MATLAB (not MATLAB Online or MATLAB Mobile) and the Hyperspectral Imaging Library add-on.

## When to Use

- Reading/writing hyperspectral or multispectral images (ENVI, NITF, GeoTIFF, TIFF, ASTER, Sentinel-2, Landsat)
- Reading ECOSTRESS spectral library signatures (`readEcostressSig`)
- Creating hypercube/multicube objects, band selection, cropping, block processing
- Radiometric calibration, atmospheric correction, spectral correction
- Denoising, sharpening, dimensionality reduction (PCA, MNF)
- Endmember extraction, spectral unmixing, abundance estimation
- Spectral matching, target detection, anomaly detection
- Computing spectral indices (NDVI, EVI, custom)
- Segmentation (spectral clustering, superpixels, ISODATA)
- Labeling with the Spectral Image Labeler app
- Creating ground truth objects for spectral labeling
- Deep learning classification or unmixing of spectral images
- Semantic segmentation of multispectral satellite imagery (DeepLabV3+ with multi-channel input)

## When NOT to Use

- General image reading/writing (use `imread`/`imwrite`)
- Non-spectral 3-D volume data (use Medical Imaging or Image Processing Toolbox)
- General image classification not involving spectral cubes (use Deep Learning Toolbox)
- Non-spectral semantic segmentation of RGB/grayscale images (use Computer Vision Toolbox)
- Point spectra or spectral libraries without spatial dimensions

## Prerequisite Check

If you suspect the Hyperspectral Imaging Library might not be installed (e.g., user reports errors), verify with `exist('imhypercube','file')`. If not installed, suggest installing via Add-On Explorer and fall back to `multibandread`/`imread`. Do NOT run this check if you are confident the library is available.

## Quick Start

```matlab
% Read hyperspectral data
hcube = imhypercube("scene.hdr");

% Visualize — colorize syntax (NO name-value for basic usage):
falseColor = colorize(hcube);              % false-colored image (default, 3 most informative bands)
rgb = colorize(hcube, Method="rgb");       % true RGB (hypercube ONLY — needs R/G/B wavelengths)
cir = colorize(hcube, Method="cir");       % color infrared (hypercube ONLY)
custom = colorize(hcube, [30 20 10]);      % false color from specific band INDICES (not wavelengths)
imshow(falseColor)

% Radiometric pipeline
hcube = dn2radiance(hcube);
hcube = radiance2Reflectance(hcube);
hcube = fastInScene(hcube);

% Compute NDVI
ndviMap = ndvi(hcube);

% Endmember extraction and unmixing
numEM = countEndmembersHFC(hcube);
endmembers = nfindr(hcube, numEM);
abundance = estimateAbundanceLS(hcube, endmembers, Method="fcls");

% Anomaly detection
rxScore = anomalyRX(hcube);

% Segmentation
L = hyperseganchor(hcube, 8);

% Launch viewer app
hyperspectralViewer(hcube)

% Launch labeler app (Since R2026a)
spectralImageLabeler(hcube)
```

## Essential Syntax (use without reading reference files)

### colorize — Visualization
```matlab
% HYPERCUBE (supports Method, 2 outputs, ContrastStretching default=false)
falseColor = colorize(hcube)                        % false-colored (default)
rgb = colorize(hcube, Method="rgb")                 % true color RGB
cir = colorize(hcube, Method="cir")                 % color infrared
custom = colorize(hcube, [b1 b2 b3])               % 3 band indices
[img, indices] = colorize(hcube)                    % also get band indices used
img = colorize(hcube, ContrastStretching=true)      % with CLAHE

% MULTICUBE (NO Method param, 1 output, ContrastStretching default=true)
rgb = colorize(mcube)                               % true RGB (auto-selects by wavelength)
custom = colorize(mcube, [b1 b2 b3])               % false color from band indices
img = colorize(mcube, ContrastStretching=false)     % disable contrast stretching
```

### I/O and Band Management
```matlab
hcube = imhypercube("file.hdr");                    % read ENVI/NITF/TIFF
mcube = immulticube("MTL.txt");                     % read Landsat (pass *_MTL.txt file)
mcube = immulticube("manifest.safe");              % read Sentinel-2 (pass manifest.safe file, NOT .SAFE folder)
mcube = immulticube("AST_L1T.hdf");                % read ASTER HDF
cropped = cropData(hcube, 30:110, 30:110);          % row indices, col indices (NOT [x y w h])
vnir = selectBands(hcube, Wavelength=[400 1000]);   % by wavelength range
subset = selectBands(hcube, BandNumber=[1 10 20]);  % by band index
cleaned = removeBands(hcube, Wavelength=[1350 1450]); % remove wavelength range
data = gather(hcube);                               % get M-by-N-by-C numeric array

% ACCESSING DIMENSIONS — NO NumRows/NumColumns/NumBands properties exist:
height = hcube.Metadata.Height;                     % number of rows (M)
width  = hcube.Metadata.Width;                      % number of columns (N)
bands  = hcube.Metadata.Bands;                      % number of spectral bands (C)
% For multicube: use mcube.BandSize(1,1) for height, mcube.BandSize(1,2) for width

% RESAMPLING vs SELECTING (multicube only):
mcubeUniform = resampleBands(mcube, 30);                       % RESAMPLE all bands TO 30m (keeps ALL bands, changes spatial size)
mcubeUniform = resampleBands(mcube, 30, Method="bilinear");    % interpolation: "nearest"(default),"bilinear","cubic"
mcube30m = selectBands(mcube, "DataResolution", 30);           % KEEP only bands already at 30m (DISCARDS others)
% When asked to "resample" or "match resolution" → use resampleBands
% When asked to "select" or "filter" bands by resolution → use selectBands
```

### Spectral Indices (NEVER compute manually — use built-in functions)
```matlab
% NDVI — use built-in ndvi() function (supports block processing natively)
ndviMap = ndvi(spcube);                             % direct numeric M-by-N output, range [-1,1]
ndviMap = ndvi(spcube, BlockSize=[512 512]);        % with block pr