Alignment configuration

tomojax.alignment provides the building blocks behind tj.align and tomojax align.

• AlignConfig: every solver setting. Its fields are also the keys of a tomojax align --config TOML file.
• alignment_plan(mode, grid, quality=..., levels=..., freeze=...): the configuration and coarse-to-fine levels tj.align runs for a mode. Change a field with dataclasses.replace(plan.config, ...) and pass the result as tj.align(scan, mode=..., config=...).
• align_multires: the array-level solver.

tj.align(scan, checkpoint="align.ckpt") saves progress after each outer iteration and resumes an interrupted run from it. Without expert overrides, tj.align chooses centre estimation for axial parallel scans and guarded setup, support and motion selection for unposed laminography; its result records conditional outcomes and limitations. Explicit mode="pose" selects per-view corrections (five parameters, six in a cone beam). Smooth pose models, setup stages and mixed schedules remain available explicitly. See the alignment guide.

Joint alignment retries without its derivative cache before skipping a level that does not fit GPU memory. The result records factors_skipped and factors_skipped_reason; a completed checkpoint retains that reason on resume.

Import from tomojax.alignment or tomojax.alignment.api.