Synthetic Experiment Suite

These guides are working synthetic replacements for first Luxnode lab data. Each scenario generates sample/reference/dark arrays, runs the real Lux algorithms, and renders an interactive Plotly dashboard. Replace the synthetic arrays with Luxnode captures when the hardware is on the bench.

Run every scenario locally:

python -m lux.experiments --list
python -m lux.experiments plant-water-stress --json
python -m lux.experiments --write-docs-data docs/assets/data/synthetic-experiments.json

Use this pattern when real data arrives:

from luxspec import SerialLuxNode
from lux.pipeline import process_absorbance, process_reflectance

with SerialLuxNode("/dev/tty.usbmodem1101") as node:
    dark = node.capture("dark")
    reference = node.capture("white")      # or "blank" for cuvette absorbance
    sample = node.capture("raw")

# Reflectance guide:
processed = process_reflectance(sample.wavelengths_nm, sample.counts, reference.counts, dark.counts)

# Absorbance guide:
processed = process_absorbance(sample.wavelengths_nm, sample.counts, reference.counts, dark.counts)

The dashboards below are intentionally deterministic. If an incoming real scan breaks a synthetic expectation, keep the same pipeline but update calibration, integration time, reference geometry, and local spectral libraries before changing the science logic.

Experiment Guides

Guide	Module	What it proves
Plant water stress	Plants	Reflectance correction, red edge, stress scoring, plant library search.
Leaf chlorophyll proxy	Plants	Chlorophyll loss and nitrogen-deficiency style reflectance.
Plant pigment extract	Plants / molecules	VIS cuvette absorbance, peak ID, pigment matching.
Nitrate UV assay	UV chemistry	Quartz cuvette UV correction, nitrate matching, A220 correction.
Caffeine and polyphenols	Food / UV	Molecule matching and concentration proxies.
Beer color and haze	Brewing	SRM/EBC and haze proxies.
Kombucha fermentation	Kombucha	Color, turbidity, fermentation trend features.
Hematite mineral ID	Minerals	VIS mineral database matching.
Clay and iron mixture	Minerals	Future VIS/NIR mixture fitting and hydration proxy.
Element emission	Elements	Peak picking against an element line database.
Stellar classification	Astronomy	Telescope adapter spectra, Balmer features, and stellar template matching.
UV mercury calibration	Calibration	Known-line wavelength calibration and residuals.
TDDFT riboflavin	Simulation	Broadened oscillator-strength comparison against synthetic TDDFT spectra.