feat: diagnostic and analysis scripts

[FIrgolitsch]

PR #100 — Diagnostic & Analysis Scripts

Collection of per-stage diagnostics and an end-of-pipeline HTML report generator. Two commits: the initial set and a refinement that adds stitch-affine analysis and significantly expands slice-quality assessment and the report generator.

New scripts

• linum_diagnose_pipeline.py — runs lightweight checks across an entire pipeline output tree (presence of expected files, schema of slice_config.csv, pyramid integrity)
• linum_diagnose_reconstruction.py — reconstruction-stage diagnostics (shift magnitudes, outlier detection, motor vs. registered drift)
• linum_generate_pipeline_report.py — HTML report aggregating all diagnostics, interpolation fragments, and slice-quality scores; the final artefact of the Nextflow pipeline
• linum_assess_slice_quality.py — per-slice quality assessment (SSIM vs. neighbours, edge score, foreground fraction); feeds auto-exclude in PR feat: motor stacking, auto-exclude, refined stitching #98 and interpolation gates in PR feat: slice interpolation for missing sections (z-morph) #87
• linum_analyze_shifts.py — statistics over pairwise shifts
• linum_analyze_registration_transforms.py — analysis of registration affine transforms
• linum_analyze_acquisition_rotation.py — acquisition-rotation analysis
• linum_analyze_tile_dilation.py — per-tile dilation / deformation analysis
• linum_aggregate_dilation_analysis.py — aggregates per-tile dilation into per-slice summaries
• linum_analyze_stitch_affine.py — analyse and visualise the affine transforms produced by refined 3D stitching (scale / shear / rotation per slice)
• linum_suggest_params.py — parameter suggestion tool based on observed per-stage metrics

Commits

1. feat: diagnostic and analysis scripts — initial 10 scripts
2. feat(diag): add stitch-affine analyzer and refine diagnostics — adds linum_analyze_stitch_affine.py, substantially expands linum_assess_slice_quality.py and linum_generate_pipeline_report.py, tightens linum_diagnose_pipeline.py

Dependencies

• Stacked on PR feat: utility modules, preprocessing improvements, galvo correction #97 (utility/preprocessing) → PR build: migrate to uv, add ruff/ty, format all files #95 (build tooling)
• Several scripts consume outputs from PR feat: motor stacking, auto-exclude, refined stitching #98 (motor stacking) and PR feat: Allen atlas improvements and RAS alignment #101 (RAS alignment); all callable standalone but most useful after those stages run