# ESSD Manuscript Scripts

This folder contains the scripts used to regenerate the ESSD manuscript
numbers, diagnostics, and figures from the released SeismicX-Cont files.

## Main Entry Points

- `reproduce_manuscript_outputs.sh` is the one-command entry point for
  regenerating the ESSD manuscript audit files, tables, and figures from the
  released data products and evaluation outputs.
- `audit_manuscript_numbers.py` regenerates the key inventory, annotation,
  waveform-coverage, operational-diagnostic, consensus-audit, and appendix-table
  values reported in the manuscript.
- `check_manuscript_consistency.py` checks the regenerated inventory,
  period-summary, consensus-audit, and appendix baseline-table values against
  `essd/template.tex`.
- `plot_dataset_overview.py` regenerates `figures/dataset_overview.pdf`.
- `plot_monitoring_regime_characterization.py` regenerates the monitoring
  regime characterization figure and writes JSON/text summaries under
  `essd_scripts/outputs/`.
- `plot_essd_qc_figures.py` regenerates the workflow, coverage,
  continuous-output, residual, and appendix diagnostic figures.
- `evaluate_picks.py` matches automatic picker JSONL outputs to reference labels
  and writes `summary.json`, `summary.tsv`, and `matches.jsonl`.
- `compare_associated_events.py` evaluates associated-event JSONL outputs
  against the reference catalog.

## Quick Checks

```bash
./essd_scripts/reproduce_manuscript_outputs.sh
python essd_scripts/audit_manuscript_numbers.py --format text
python essd_scripts/audit_manuscript_numbers.py --format latex-baseline
python essd_scripts/check_manuscript_consistency.py
python essd_scripts/plot_dataset_overview.py
python essd_scripts/plot_monitoring_regime_characterization.py
python essd_scripts/plot_essd_qc_figures.py
```

The one-command script runs the manuscript-number audit first, exports JSON and
LaTeX-ready table rows, checks the manuscript against the regenerated numbers
when `essd/template.tex` is present, then rebuilds the overview,
monitoring-regime characterization, and QC figures. Outputs are written to
`essd_scripts/outputs/` and `figures/`.

The plotting scripts write manuscript figures under `figures/`. The audit script
is read-only unless its output is redirected by the caller.

## Manuscript Coverage

The scripts cover the manuscript outputs as follows:

| Manuscript output | Reproduction source |
|---|---|
| Fig. 1, data-product workflow | `plot_essd_qc_figures.py`, using the released HDF5 directory, SQLite index, and annotation JSON for the displayed counts |
| Fig. 2, inventory and monitoring-regime overview | `plot_dataset_overview.py`, using the annotation JSON, SQLite index, and HDF5 waveform files |
| Fig. 3, waveform coverage matrix | `plot_essd_qc_figures.py`, using the SQLite waveform index |
| Fig. 4, monitoring-regime characterization | `plot_monitoring_regime_characterization.py`, using the annotation JSON and SQLite waveform index |
| Fig. 5, label coverage and provenance | `plot_essd_qc_figures.py`, using `eval_picks/eval_phasenet/matches.jsonl` and annotation metadata |
| Fig. 6, continuous-output diagnostics | `plot_essd_qc_figures.py`, using the distributed baseline-output summaries |
| Fig. 7, residual diagnostics | `plot_essd_qc_figures.py`, using matched baseline-output residuals |
| Appendix Fig. A1, baseline reuse space | `plot_essd_qc_figures.py`, using baseline-output summaries |
| Core inventory, monitoring-period, validation, consensus, and appendix baseline statistics | `audit_manuscript_numbers.py` and `check_manuscript_consistency.py` |

The baseline-output summaries are included as data-product usability validation
and interoperability checks. They should not be read as a model-performance
ranking or leaderboard.