Reproducing the Paper

Reproducing the Paper

The paper_figs/ directory holds the scripts that regenerate every figure in the golgi papers, plus the tooling that packages the figure simulations as replay-verified study bundles for the Zenodo deposit.

Where the data lives. paper_figs/io_paths.py defines a shared ROOT and output layout (out/figures/{png,pdf,svg}, out/tables, out/data). The git repository ships source only — the multi-gigabyte meshes, FEM results, micro-CT cohort, and rendered figures live outside it. To regenerate figures you need the source data and a configured ROOT (or, for verification, the published study bundles below). io_paths.save_fig(fig, name) writes PNG+PDF+SVG for each figure.

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Figure → script map

The authoritative mapping is the output filename each script writes (docstring figure numbers in a few files lag a mid-draft renumbering — trust the filenames) and the curated KEEP_PAPERFIGS allowlist in make_release_package.py.

Figure	Script(s)	Content · species
Fig 2	fig3_setup.py, fig3_render.py	Modeling setup & FEM solution (cuff, multi-region mesh, cuff-designer, Vₑ & |E| cross-sections, along-fiber Vₑ + activating function) · swine
Fig 4	fig_validation_full.py (assembles comsol_validation_fig, validate_fig, fig_nrv, fig_bucksot)	Integrated validation: analytic/COMSOL, dog-VNS, NRV LIFE, Bucksot
Fig 5	fig_species.py (+ fig5_population.py, fig5_thresholds.py, fig06_selectivity.py)	7-panel per-species result · swine cervical vagus
Fig 6	fig_species.py (human half); fig06_selectivity.py	7-panel per-species result · human cervical vagus
Fig 7	rabbit_selectivity_fig.py	Superior-cardiac-branch-selective stim, 4×5 ring cuff + position×config sweep · real-3-D rabbit
Fig 8	new_human_selectivity_fig.py	SCB-selective stim, 4×5 ring cuff + position×config sweep · real-3-D human

Supplements / tables: validate_fig.py (→ supp_foundations, the S8 fiber-model foundations), validate_mrg.py (MRG vs McIntyre discrete), comsol_validation_fig.py (→ supp_comsol_validation, S15), fig_supp_cohort.py (cohort gallery), cohort_table.py + gen_s1_table.py (the S1 cohort table). Rendering scripts (render_*.py) make the cel-shaded PyVista presentation renders.

Per-figure pipelines

Each species result is produced by a sequence of pipeline-driver scripts that mesh, solve, seed fibers, and sweep — for example the human SCB / Fig 8 chain:

new_human3d_prep → new_human3d_traj → new_human_mesh → new_human_fem
   → new_human_sweep → new_human_tripole_sweep_build → new_human_tripole_analyze
   → new_human_steer_opt → new_human_xsec_contours

with parallel rabbit_* (Fig 7) and human_bundle_* (Fig 6) chains. Threshold sweeps for the selectivity panels run through fig5_thresholds.py (golgi's exact PyFibers/NEURON bisection path) and the run_*_tripole_sweep_thr.sh drivers. Species covered across the paper: swine, human, rabbit, dog (dog-VNS), and cat (NRV LIFE).

Packaging for Zenodo

• make_study_bundles.py packages the Fig 4–8 simulations as hashed, replay-verified .golgi bundles (each re-checked byte-for-byte via golgi.projects.replay) into paper_figs/out/study_bundles/ with a BUNDLES.json + CHECKSUMS.sha256. Bundle IDs: fig04a_dogvns_validation, fig04c_bucksot_validation, fig05_swine_cervical_vagus, fig06_human_cervical_vagus, fig07_rabbit_branching, fig08_human_scb_branching (fig04b NRV-LIFE ships cached figure data, as the synthetic LIFE geometry isn't re-meshable).

  python paper_figs/make_study_bundles.py            # all figures
  python paper_figs/make_study_bundles.py fig07       # one figure

• make_release_package.py assembles the full paper deliverable (both manuscripts, the curated code subset, the reproduction bundles + checksums, and a top-level README). The KEEP_PAPERFIGS list in it (≈lines 53–95) is the definitive index of which script produces which figure.

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See also

Validation · Reproducible Study Bundles · Pipeline Overview · License & Citation