Package index • hyperspectR

Data I/O

Read and write hyperspectral data cubes

hsi_cube(): Create an HSI Cube Object
print(<hsi_cube>): Print an hsi_cube Object
summary(<hsi_cube>): Summarize an hsi_cube Object
dim(<hsi_cube>): Get Dimensions of an hsi_cube
`[`(<hsi_cube>): Subset an hsi_cube Object
as.data.frame(<hsi_cube>): Convert hsi_cube to Data Frame
as_tibble.hsi_cube(): Convert hsi_cube to Tibble
hs_read_cube(): Read a Hyperspectral Data Cube from Any Supported Format
hs_read_envi(): Read an ENVI Hyperspectral Image File
hs_read_tiff(): Read a Multi-Channel TIFF File
hs_read_cubert(): Read a Cubert .cu3s Session File
hs_write_envi(): Write an HSI Cube to ENVI Format
hs_write_tiff(): Write an HSI Cube to Multi-Band TIFF
hs_export_png(): Export a Single-Band Image as PNG

Calibration

Radiometric calibration and correction

hs_calibrate(): Calibrate Raw HSI Data to Reflectance
hs_dark_correct(): Apply Dark Current Correction
hs_white_normalize(): Apply White Reference Normalization
hs_fix_bad_pixels(): Detect and Correct Bad Pixels

Preprocessing

Spectral smoothing, normalization, and transformation

hs_smooth(): Savitzky-Golay Spectral Smoothing
hs_snv(): Standard Normal Variate Correction
hs_msc(): Multiplicative Scatter Correction
hs_derivative(): Spectral Derivative
hs_absorbance(): Convert Reflectance to Absorbance
hs_continuum_removal(): Continuum Removal
hs_resample(): Resample Spectra to New Wavelength Grid

Biomedical Indices

Clinical tissue indices for surgical HSI

hs_sto2(): Compute Tissue Oxygen Saturation (StO2)
hs_npi(): Compute Near-Infrared Perfusion Index (NPI)
hs_thi(): Compute Tissue Hemoglobin Index (THI)
hs_twi(): Compute Tissue Water Index (TWI)
hs_ndi(): Compute Normalized Difference Index (General Purpose)
hs_clinical_indices(): Compute All Available Clinical Indices

Analysis

Dimensionality reduction, classification, and unmixing

hs_pca(): PCA on Hyperspectral Cube
hs_mnf(): Minimum Noise Fraction Transform
hs_umap(): UMAP Embedding of Spectral Data
hs_sam(): Spectral Angle Mapper Classification
hs_classify_svm(): SVM Pixel Classification
hs_classify_rf(): Random Forest Pixel Classification
hs_unmix_nnls(): Linear Spectral Unmixing via NNLS
hs_beer_lambert(): Beer-Lambert Chromophore Fitting
hs_endmembers(): Extract Endmember Spectra from a Cube

ROI Analysis

Region-of-interest tools

hs_roi_rect(): Define Rectangular ROI
hs_roi_polygon(): Define Polygon ROI
hs_roi_stats(): Compute ROI Statistics

Visualization

Plotting and clinical display

autoplot(<hsi_cube>): Plot an hsi_cube Object
hs_plot_spectra(): Plot Spectral Profiles
hs_plot_image(): Plot Single-Band Spatial Image
hs_plot_rgb(): Synthesize RGB Image from Spectral Cube
hs_plot_clinical(): TIVITA-Style Clinical Panel Display
hs_plot_index(): Plot Index Map with Clinical Color Scale
scale_color_wavelength() scale_colour_wavelength(): Wavelength-to-Color Scale for Spectral Plots
theme_hsi(): Minimalist HSI Theme

Reference Data

Chromophore spectra and simulation

hs_chromophore_data(): Get Chromophore Extinction Coefficient Spectra
hs_simulate_cube(): Generate a Synthetic HSI Cube for Testing and Examples
hs_example_cube(): Get Example HSI Cube
hs_example_files(): Write Example ENVI Files to a Temporary Directory

Shiny Application

Interactive HSI explorer

hs_run_app(): Launch Interactive Hyperspectral Image Explorer