laue_index

The Python orchestration for LaueMatching, packaged as typed pipeline stages around the C/CUDA indexer (REFACTOR_PLAN). Mirrors the in-repo laue_torch conventions (curated __init__, single-responsibility modules, typed records) but stays independent of the paper-tied packages (laue_torch / laue_jax / jax_cpfem) — shared pure math is duplicated with # TODO(unify-after-publish).

Modules

Module	Responsibility
`records.py`	`Solution` typed record + `parse_solutions(source, fmt)` + `SolutionFormat` column maps (runimage / stream) — replaces positional column "magic numbers".
`geometry.py`	Pure CSL/disorientation helpers (`disorientation_deg_axis`, `is_csl_related`, cubic ops, CSL table).
`filtering.py`	`calculate_unique_spots`, `filter_orientations`, `filter_orientations_robust` + `OrientationFilter` strategies (`LegacyUniqueSpotFilter`, `RobustCSLAwareFilter`). Single source of truth.
`thresholds.py`	`ThresholdStrategy` classes (`NoiseFloorThreshold`/adaptive, `Percentile`, `Otsu`, `Fixed`) + `apply_threshold` dispatch.
`preprocess.py`	Image pipeline (background → threshold → components → blur) + `Preprocessor`.
`indexer.py`	Thin wrapper around the C indexing binary (`run_indexer`).
`postprocess.py`	`PostProcessor`: unique-spots → sort → filter → spot-filter.
`output.py`	HDF5 result writer.
`config_schema.py`	One declarative `SCHEMA` table driving config parse + write.
`cli.py`	`laue-index` console entry: `parse` (summarise a solutions table) and `filter` (re-run post-processing on existing C output, no re-indexing).

Relationship to `scripts/`

The legacy scripts/laue_stream_utils.py is now a thin shim that re-exports from this package, so RunImage.py, laue_postprocess.py, and laue_image_server.py keep working unchanged while the implementation lives here. RunImage.py is the orchestrator wiring the stages together.

Testing

pytest (from the repo root) runs the unit suite — golden-anchored characterization tests pin behaviour through the refactor. The full end-to-end test (tests/test_char_e2e.py) is opt-in: set LAUE_E2E=1 with the orientation DB, the built C binary, and a prebuilt forward cache present; otherwise it skips, so CI is safe with SKIP_DOWNLOAD=1 (no 6.7 GB database needed for units).

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