NEWS

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hyperspectR 0.2.0.9000

• Corrected cube dimensions, masks, wavelength/FWHM alignment, spatial plotting, TIFF/ENVI pixel order, truncated ENVI input and unsupported integer exports.
• SG smoothing now returns full-window center bands consistently across explicit backends; derivatives use wavelength units. Calibration validates reference compatibility and bad-pixel repair uses immutable valid neighbors.
• Replaced generated hemoglobin fitting references with a pinned tabulated source. Beer-Lambert fitting requires an explicit domain and separates coefficients from concentrations requiring optical pathlength. Default StO2 is a research model fraction. The former ratio method errors; relative indices are unscaled.
• Added equality-constrained nonnegative unmixing with convergence diagnostics, optional residual storage and chunk equivalence. PCA/MNF respect masks and rank limits and expose reusable transforms.
• Repaired explorer initialization, stale results, paired uploads, TIFF metadata entry and complete archive downloads; added cancellable background computations.
• Added processing recipes, resumable manifest analysis, reusable classifier prediction, group-separated evaluation and group-level uncertainty summaries.
• Expanded exact-value regressions, browser and minimal-dependency validation, reference sensitivity reports, and performance measurements. Clinical claims remain outside the evidence supplied by synthetic tests. See MIGRATION.md for breaking changes and planning/implementation-status.md for release evidence.

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.