Optical systems

The model can represent five optical-system values via the OpticalSystem enum:

OpticalSystem	Typical signal unit(s)
ABSORBANCE	absorbance units (AU)
INTERFERENCE	fringes
FLUORESCENCE	declared instrument or calibrated units
INTENSITY	declared instrument or calibrated units
UNKNOWN	any (not judged)

Representation is not support. That the model can represent an optical system does not mean file import or scientific interpretation for that system is implemented or validated. Generic CSV/TSV import records whatever optical system the manifest declares; no vendor/instrument reader exists, and no optical system is scientifically interpreted.

Where it is recorded

OpticalSystem appears on each ScanMetadata (the system used for that scan) and on InstrumentMetadata (the run's primary system). Both default to UNKNOWN — an explicit "not stated", never inferred.

Optical-system / signal-unit consistency

Structural validation reports a well-defined incompatibility between a scan's optical system and the observations' signal unit:

Optical system	Compatible signal unit(s)
ABSORBANCE	ABSORBANCE_UNIT
INTERFERENCE	FRINGE
FLUORESCENCE	INSTRUMENT_UNIT, CALIBRATED_UNIT
INTENSITY	INSTRUMENT_UNIT, CALIBRATED_UNIT

UNKNOWN optical systems, and UNKNOWN/OTHER signal units, are never flagged — the model does not guess. A clear conflict (e.g. an ABSORBANCE scan with a FRINGE signal unit) is reported as a structural error by experiment.validate_structure().

An undeclared optical system is reported separately as a non-blocking optical_system_unknown warning, and more than one declared system in a single observation set as mixed_optical_systems. A mixture of UNKNOWN and one declared system is partial metadata, not a mix, and is not flagged as one. See validation tiers.

Phase 2 limitation: one signal unit per observation set

Observations carries a single signal_unit for the whole set. Heterogeneous signal units across scans in one set are not modelled in this phase, though each scan retains its own optical_system. This is noted in the Phase 2 development log as a known limitation.