organon-mueller 1.0.0

Symbolic engine for the Stokes-Mueller algebra of polarization optics: Mueller-matrix decomposition, certified identity discovery (equality saturation + exact symbolic proof), coupled-dipole modelling, and evidence-labelled LaTeX reporting.

organon-mueller

A symbolic engine for the Stokes–Mueller algebra of polarization optics: it decomposes depolarizing Mueller matrices into nondepolarizing components, discovers and certifies algebraic identities of the underlying state algebra, models coupled oriented dipoles, and reports every result as evidence-labelled LaTeX — with each mathematical statement gated by a written verification contract.

Status: experimental research software. Results are labelled by evidence class — verified (machine-checked against published equations/tables: symbolic-exact or seeded-numeric) or candidate (beyond the published results; no novelty or physics claim — that judgement is left to human experts, per docs/novelty-protocol.md).

Released under the MIT License.

What it does

• Represents a pure polarization state in six isomorphic ways — Jones matrix J, Mueller matrix M = ZZ*, covariance matrix H, covariance vector |h⟩ = (τ, α, β, γ), Z-matrix, and biquaternion — with exact, symbolically proven conversions between all of them [1, 2, 3].
• Decomposes depolarizing Mueller matrices into symmetry-conditioned nondepolarizing components: the six fundamental variants and three composite types of the symmetry-conditioned decomposition [4], derived from rank-1 minor conditions (not transcribed from the published tables), plus a rank-3 three-term zone that goes beyond the published cases.
• Discovers algebraic identities by equality saturation over a covariance-vector term language (egglog), with every candidate certified by engine-independent symbolic proof; guarded atoms open a Horn-conditional channel (P(x) → t₁ = t₂).
• Models coupled oriented dipoles [5, 6, 7]: the three-term scattering decomposition as a theorem, mode hybridization, optical activity, Perrin reciprocity, and ensemble statistics — bridged back to the decomposition layer through the covariance representation.
• Reports any of the above as deterministic, evidence-labelled LaTeX.

Installation

Requires Python ≥ 3.10 (the discovery engine needs ≥ 3.11).

pip install -e ".[test]"                # base
pip install -e ".[test,discovery]"      # + discovery engine (egglog)
pip install -e ".[test,discovery,mcp]"  # + MCP server surface
pip install -e ".[test,ui]"             # + local web interface

python -m pytest -q                     # full suite: 306 tests collected (discovery self-skips on py3.10)

Quickstart

Interactive (no code) — the local web interface:

organon-ui       # opens http://127.0.0.1:7860 (needs the ui extra)

As a library:

from organon_mueller import HVector

h = HVector.generic("a")   # generic complex (tau, alpha, beta, gamma)
M = h.to_mueller()         # M = Z Z*
Z = h.to_z()
q = h.to_quaternion()      # tau*1 + i*alpha*i + i*beta*j + i*gamma*k

import numpy as np
from organon_mueller.decomposition import decompose

# a depolarizing Mueller matrix -> a symmetric + a generic pure component
result = decompose(mueller=my_4x4_matrix, symmetry="type1")
print(result.alpha1, result.m1, result.m2)

Full demonstration (decomposition against a published worked example, rank-3 recovery, the hypothesis bridge, the dipole engine):

python examples/demo.py

Usage surfaces

Surface	For	Entry
Python package	scripting / integration	import organon_mueller
Local web UI	interactive use, no code (localhost only)	docs/README-ui.md
MCP server	tool use from an assistant	docs/README-mcp.md
Static web viewer	reading results in a browser (no terminal)	web/index.html

Nothing is hosted or exposed by the project. The local web UI binds to 127.0.0.1 only (no tunnel, no public link); the MCP server and static viewer are code + tests only — running them is your decision.

Verification contract (the trust anchor)

No mathematical statement reaches main without passing the layers in docs/VERIFICATION.md: exact symbolic proof · seeded numeric checks · regression against the 21 identities of the known-identity library (each tied to a published equation) · engine-independent certification of every discovery candidate · an independent adversarial review of every change set (each reviewer re-derives the mathematics from scratch) · a 3-version CI matrix. Numeric confidence is never a substitute for a passing test.

Architecture

Layered, with one-way dependencies: algebra → identities/conditions → discovery / decomposition / dipoles → reporting → mcp_server → web / ui, plus a safe_parse security layer guarding deserialization. See docs/architecture.md for the layer map and the index of design decisions, and docs/user-guide.md for a task-oriented walkthrough.

Every change lands with a written spec (specs/) and a closing report (reports/); nothing untested reaches main.

References

The algorithms implement, verify against, and extend results from:

1. E. Kuntman, M. A. Kuntman, O. Arteaga, Vector and matrix states for Mueller matrices of nondepolarizing optical media, J. Opt. Soc. Am. A 34, 80 (2017).
2. E. Kuntman, M. A. Kuntman, O. Arteaga, Quaternion algebra for Stokes–Mueller formalism, arXiv:1705.07147 (2017).
3. E. Kuntman, M. A. Kuntman, J. Sancho-Parramon, O. Arteaga, Formalism of optical coherence and polarization based on material media states, Phys. Rev. A 95, 063819 (2017).
4. E. Kuntman, O. Arteaga, Decomposition of a depolarizing Mueller matrix into its nondepolarizing components by using symmetry conditions, Appl. Opt. 55, 2543 (2016).
5. M. A. Kuntman, E. Kuntman, J. Sancho-Parramon, O. Arteaga, Light scattering by coupled oriented dipoles: decomposition of the scattering matrix, Phys. Rev. B 98, 045410 (2018).
6. M. A. Kuntman, E. Kuntman, O. Arteaga, Asymmetric scattering and reciprocity in a plasmonic dimer, Symmetry 12, 1790 (2020).
7. M. A. Kuntman, E. Kuntman, Plasmonic dimers in a solution: a theoretical approach to the optical activity in an ensemble of randomly oriented chiral and achiral plasmonic dimers, preprint.

License

MIT.