HyPyRameter

Spectral parameters (band depths, band areas, slopes, ratios, peaks and indices) for hyperspectral reflectance data: the CRISM parameter set of Viviano-Beck et al. (2014) plus additions for terrestrial and laboratory spectra. Works on image cubes, tables of spectra or a single spectrum.

Installation

pip install hypyrameter            # or:  uv add hypyrameter
pip install "hypyrameter[browse]"  # + PNG browse products (imageio)
pip install "hypyrameter[denoise]" # + the IOVF denoiser

Requires Python 3.10 or newer. The only hard dependencies are numpy, scipy, pandas and spectral (for ENVI files).

Usage

Core API

import numpy as np
from hypyrameter import compute, valid_parameters, PARAMETERS
from hypyrameter.io import read_envi, write_envi

cube, wavelengths, metadata = read_envi("scene.hdr")   # (rows, cols, bands), nm

names = valid_parameters(wavelengths)      # every parameter the range supports
params = compute(cube, wavelengths, names, progress=lambda f, n: print(f"{f:4.0%} {n}"))
write_envi("scene_params.hdr", params, names, base_metadata=metadata)

# or just a few, on any array with the wavelength axis last:
bd = compute(cube, wavelengths, ["BD2290", "BD1900_2", "RPEAK1"])
one = compute(cube[10, 20], wavelengths, ["BD2290"])   # a single spectrum

• wavelengths may be in nm or µm (values below 10 are taken as µm).
• Missing data is NaN in and NaN out. Fill bad bands first with hypyrameter.fill_nans_along_spectrum if you want a parameter whose window straddles them.
• PARAMETERS maps each name to its wavelength range, description and group; valid_parameters(wavelengths, tolerance=5) filters by range.
• Parameters that depend on another (BDI1000VIS needs RPEAK1) compute what they need automatically.

Browse products

from hypyrameter.browse import BROWSE_PRODUCTS, browse_image, write_browse_products

layers = {name: params[..., i] for i, name in enumerate(names)}
rgb = browse_image(layers, "PHY")                   # (rows, cols, 3) uint8
write_browse_products(layers, "browse/")            # a PNG per valid product

BROWSE_PRODUCTS holds the 18 CRISM MTRDR browse products with the channels the PDS products' labels name (CRISM Data Product SIS, §3.12.3; Viviano-Beck et al. 2014): TRU, VNA, FEM, FM2, FAL, IRA, MAF, HYD, PHY, PFM, PAL, HYS, ICE, IC2, CHL, CAR, CR2 and TAN; and HyPyRameter's own BIO, FM3, HEM, HYD2, HYD3, PLG, SED and SUL. browse_image stretches each channel by the scene's statistics (stretch), not by the PDS products' fixed ranges.

The 0.2.x classes

cubeParamCalculator and pointParamCalculator still exist as thin wrappers over the core and behave as before, minus the interactive prompts when you give them their inputs:

from hypyrameter.paramCalculator import cubeParamCalculator, pointParamCalculator

pc = cubeParamCalculator(in_file="scene.hdr", outdir="out/")   # dialogs if omitted
pc.run()                       # writes out/scene_params.hdr and browse PNGs

ppc = pointParamCalculator(data_path="spectra.csv")   # or df=..., or a .sed glob
table = ppc.run()              # DataFrame: parameters (rows) x spectra (columns)

Both accept parameters=[...] to compute a subset. See the notebooks in hypyrameter/ for worked examples.

Parameters

Parameter	Range (nm)	Description
R440	440–440	Reflectance at 440 nm (5-band median)
R463	463–463	Reflectance at 463 nm (5-band median)
R530	530–530	Reflectance at 530 nm (5-band median)
R550	550–550	Reflectance at 550 nm (5-band median)
R600	600–600	Reflectance at 600 nm (5-band median)
R637	637–637	Reflectance at 637 nm (5-band median)
R770	770–770	Reflectance at 770 nm (5-band median)
R1080	1080–1080	Reflectance at 1080 nm (5-band median)
R1330	1330–1330	Reflectance at 1330 nm (11-band median)
R1506	1506–1506	Reflectance at 1506 nm (5-band median)
R2529	2529–2529	Reflectance at 2529 nm (5-band median)
R3920	3920–3920	Reflectance at 3920 nm (5-band median)
HCPINDEX2	1690–2530	High-calcium pyroxene index: weighted continuum-relative depths between 2120 and 2460 nm (continuum 1690-2530 nm)
LCPINDEX2	1560–2450	Low-calcium pyroxene index: weighted continuum-relative depths between 1690 and 1870 nm (continuum 1560-2450 nm)
OLINDEX3	1210–1862	Olivine index: weighted continuum-relative depths between 1210 and 1330 nm (continuum 1750-1862 nm)
ESINDEX	420–950	Elemental sulfur index: steep 420-500 nm slope minus
SINDEX2	2120–2400	Sulfate index: inverted band depth at 2290 nm (2120-2400 nm)
GINDEX	1440–1570	Gypsum index: minimum of the 1447, 1491 and 1540 nm band depths
CPLINDEX	600–710	Chlorophyll index: minimum of the 626 and 678 nm band depths
CHLORINDEX	1800–2450	Chlorite index: weighted 2347, 2254, 2000 and 1921 nm depths and 2105 nm shoulder, minus BD2210_2
BD530_2	440–614	530 nm band depth (ferric oxides)
BD670	620–745	670 nm band depth (custom; hematite/chlorophyll)
BD875	747–980	875 nm band depth (custom; ferric minerals)
BD905	750–1300	905 nm band depth
BD920_2	807–984	920 nm band depth (ferric minerals)
BD1200	1115–1260	1200 nm band depth
BD1300	1080–1750	1300 nm band depth (plagioclase)
BD1400	1330–1467	1400 nm band depth (hydration)
BD1450	1340–1535	1450 nm band depth (hydration)
BD1750	1688–1820	1750 nm band depth (gypsum)
BD1900_2	1850–2067	1930 nm band depth (H2O)
BD2100_2	1930–2250	2130 nm band depth (monohydrated sulfates)
BD2100_3	2016–2220	2100 nm band depth
BD2165	2120–2230	2165 nm band depth (kaolinite group)
BD2190	2120–2250	2190 nm band depth (beidellite, allophane)
BD2210_2	2165–2290	2210 nm band depth (Al-OH phyllosilicates)
BD2250	2120–2340	2250 nm band depth
BD2265	2120–2340	2265 nm band depth (jarosite)
BD2290	2250–2350	2290 nm band depth (Fe/Mg phyllosilicates)
BD2443	2320–2480	2443 nm band depth (nitrate)
BD2355	2300–2450	2355 nm band depth (Fe/Mg phyllosilicates)
BD2600	2530–2630	2600 nm band depth (H2O)
BD1435	1370–1470	1435 nm band depth (CO2 ice, some hydrated minerals)
BD1500_2	1367–1808	1525 nm band depth (H2O ice)
BD2500_2	2364–2570	2480 nm band depth (Mg-carbonate overtone)
BD1900r2	1815–2132	1900 nm band depth, ratio form: mean continuum-relative reflectance at 1908-1941 nm over that at 1862-1875 and 2112-2126 nm (continuum 1815-2132 nm)
BDCARB	2230–2600	Carbonate band depth: geometric mean of the 2330 and 2530 nm band depths
BA1200	1115–1260	1200 nm band area
BA1450	1340–1535	1450 nm band area
BA1900	1850–2067	1900 nm band area
SH600_2	533–716	600 nm shoulder height: 1 - continuum (533-716 nm) / R600 (select ferric minerals)
SH460	420–520	460 nm shoulder height (inverted band depth)
D460	420–520	Alias of SH460 (point-spectra name)
D700	630–830	700 nm drop-off (chlorophyll red edge): continuum-relative 690-720 nm over 740-770 nm (continuum 630-830 nm)
D2200	1815–2430	2200 nm drop-off: continuum-relative 2210 and 2230 nm over 2165 nm (continuum 1815-2430 nm)
D2300	1815–2530	2300 nm drop-off: continuum-relative 2290-2330 nm over 2120-2210 nm (continuum 1815-2530 nm)
MIN2295_2480	2165–2570	Minimum of the 2295 and 2480 nm band depths (Mg carbonate)
MIN2250	2165–2350	Minimum of the 2210 and 2265 nm band depths (opal)
MIN2345_2537	2250–2602	Minimum of the 2345 and 2537 nm band depths (Ca/Fe carbonate)
BH1500	1250–1750	1500 nm band height (inverted band depth)
RPEAK1	442–989	Wavelength (µm) of the reflectance peak of a 5th-order polynomial through 13 anchors between 442 and 989 nm
RPEAK1_2	500–1150	Wavelength (µm) of the reflectance peak between 500 and 1150 nm after Savitzky-Golay smoothing
BDI1000VIS	833–1023	Integrated 1000 nm band depth (VIS): the integral (µm) over 833-1023 nm of 1 - R/RPEAK1, the reflectance normalised by the RPEAK1 peak, through a 4th-order polynomial fit
SLOPE420_500	420–500	Spectral slope 420-500 nm (reflectance per µm); >5 suggests elemental sulfur
SLOPE1815_2530	1815–2530	Spectral slope 1815-2530 nm (reflectance per µm)
ISLOPE	1815–2530	Inverse spectral slope 1815-2530 nm: -SLOPE1815_2530 (point-spectra name)
ISLOPE1	1815–2530	Spectral slope 1: (R1815 - R2530) / (W2530 - W1815), wavelengths in µm (ferric coating on dark rock); the CRISM name of ISLOPE
BD3000	2210–3000	3 µm H2O band depth: 1 - R3000 / (R2530 x R2530 / R2210), allowing for the spectral slope (bound H2O)
CINDEX2	3450–3875	Carbonate index: 1 - continuum (3450-3875 nm) / R3610, the convexity at 3.6 µm between the 3.4 and 3.9 µm carbonate bands
BR800	800–997	Band ratio R800 / R997
BR2530	2210–2530	Band ratio R2530 / R2210
IRR2	2210–2530	Alias of BR2530 (point-spectra name)
BR3500	3390–3500	Band ratio R3500 / R3390
NDVI	665–833	Normalised difference vegetation index (833, 665 nm)
NDWI	560–833	Normalised difference water index (560, 833 nm)
NDMI	833–1670	Normalised difference moisture index (833, 1670 nm)

Denoising

hypyrameter.iovf_generic.iovf is the iterative outlier voting filter of Phillips et al. (2023); it is slow and optional (pip install "hypyrameter[denoise]"). ngMeet_denoiser.m is a MATLAB script for the NGMeet algorithm.

Development

git clone git@github.com:Michael-S-Phillips/HyPyRameter.git
cd HyPyRameter
uv sync --group dev
uv run pytest
uv run ruff check . && uv run ruff format .

Releases: bump version in pyproject.toml, add a CHANGELOG entry, tag vX.Y.Z and push the tag; CI tests, builds and publishes to PyPI.

License

CC BY 4.0. Please cite the associated Planetary Science Journal publication (Phillips et al.).