feat: diagnostic and analysis scripts

[FIrgolitsch]

Stacked PR 3/22 — review order: #115 → #97 → #98 → #99 → #100 → #101 → #108 → #106 → #107 → #87 → #116 → #110 → #111 → #40 → #112 → #113 → #117 → #118 → #120 → #121 → #122 → #123 → #124 → #125

Base: pr-f-gpu-acceleration. Retargets to main as upstream PRs merge.

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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 feat: motor stacking, auto-exclude, refined stitching #98 and interpolation gates in 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

Notes

• Several scripts consume outputs from feat: motor stacking, auto-exclude, refined stitching #98 (motor stacking) and feat: Allen atlas improvements and RAS alignment #101 (RAS alignment); all callable standalone but most useful after those stages run