hyperspectR 0.1.0
Initial release
Data I/O
-
hs_read_envi(): Read ENVI .hdr + binary hyperspectral cubes (BSQ/BIL/BIP). -
hs_read_tiff(): Read multi-channel TIFF files. -
hs_read_cubert(): Read Cubert .cu3s session files via Python bridge (optional). -
hs_read_cube(): Auto-detect format and dispatch to correct reader. -
hs_write_envi(),hs_write_tiff(),hs_export_png(): Export functions.
Calibration
-
hs_calibrate(): Full calibration workflow (dark + white reference). -
hs_fix_bad_pixels(): Statistical bad pixel detection and interpolation.
Preprocessing
-
hs_smooth(): Savitzky-Golay smoothing and derivatives. -
hs_snv(): Standard Normal Variate correction. -
hs_msc(): Multiplicative Scatter Correction. -
hs_absorbance(): Reflectance to absorbance conversion. -
hs_continuum_removal(),hs_resample().
Biomedical Indices
-
hs_sto2(): Tissue oxygen saturation (500-815 nm). -
hs_npi(): Near-infrared perfusion index (655-910 nm). -
hs_thi(): Tissue hemoglobin index (530-825 nm). -
hs_twi(): Tissue water index (adapted for Cubert range). -
hs_ndi(): Generic normalized difference index. -
hs_clinical_indices(): Compute all available indices.
Analysis
-
hs_pca(),hs_mnf(): Dimensionality reduction. -
hs_umap(): UMAP spectral embedding (optional, requires uwot). -
hs_sam(): Spectral Angle Mapper classification. -
hs_classify_svm(),hs_classify_rf(): Machine learning classification. -
hs_unmix_nnls(): Linear spectral unmixing via NNLS. -
hs_beer_lambert(): Chromophore concentration fitting.
Visualization
-
autoplot.hsi_cube(): Plot RGB, single band, or spectra. -
hs_plot_clinical(): TIVITA-style clinical panel display. -
hs_plot_index(): Pseudocolor index map with clinical palette. -
hs_plot_spectra(): Spectral profile plots with mean +/- SD. -
scale_color_wavelength(),theme_hsi().
Shiny Application
-
hs_run_app(): Interactive 6-tab HSI explorer.
Data
-
hs_example_cube(): Synthetic 30x30 tissue cube (430-910 nm, 61 bands). -
hs_simulate_cube(): Configurable synthetic cube generator. -
hs_chromophore_data(): Published HbO2/Hb extinction coefficients.