validate & status: pre-flight checks and a dataset progress report

[bbarad]

Two read-only utility commands for setting up and tracking a dataset.

morphometrics validate config.yml

Pre-flights a config + folder setup before a run:

• seg_dir exists (error) and tomo_dir exists (warning only — tomograms are needed only for density sampling, thickness, and refinement);
• each segmentation has a matching tomogram under the pipeline's shared-prefix naming, and flags tomograms with no matching segmentation — so a name mismatch shows up here instead of as a silently skipped tomogram;
• which configured segmentation_values labels actually appear in each segmentation (flags segmentations where none appear, or where an unmapped label value is present).

Exits non-zero on errors; warnings do not fail. Label scan reads slice-by-slice via mmap (~0.6 s for a 1000×1000×200 segmentation).

morphometrics status config.yml

Prints a per-segmentation, per-surface summary of what has been computed — mesh, curvature, refinement (and the accepted iteration), and which self/inter distances, verticality, and thickness measurements exist. Everything is derived from the files in work_dir and the per-surface CSV column headers, so it always reflects reality with no state to maintain. --output PATH also writes the summary to a text file.

YTC041_1_lam4_2_ts_002_labels   [tomogram ✓]
  IMM   mesh ✓  curv ✓  refine accepted@iter4  self-dist ✓  vert ✓  inter OMM  thickness ✓
  OMM   mesh ✓  curv ✓  refine accepted@iter4  self-dist ✓  vert ✓  inter IMM  thickness ✓

The one non-derivable piece — which refinement iteration was accepted — is now recorded by accept_refinement as a one-line {surface}.accepted_iter marker; older datasets without it report accepted (step unknown) from the .orig.bak backups.

Notes

• Both are light Setup subcommands (no graph-tool); registered in --help.
• Tests: 11 (6 status incl. the accepted-iter marker + dry-run, 5 validate).
• Docs already landed on main (commit d423a8e) ahead of this merge.

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