Figures and Reports

Figures & Reports

golgi turns any study into publication-grade figures and a single multi-page PDF report, from the same registry of plots the GUI shows. Everything is exportable per-panel, in bulk, or as a report.

Source: golgi/figures/ — registry.py (catalog), export.py (presets/formats), report.py (PDF), render3d.py (off-screen 3-D capture), plus the per-figure builders.

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The figure registry

registry.py is the single source of truth for "what figures exist in this project right now." Each entry (FigureSpec) has an id, title, category, and a source — either a 2-D plotly figure or an off-screen 3-D render variant — and an availability predicate so only computable figures are offered. Categories span the pipeline:

Category	Examples
Mesh	surface-quality and tet-quality histograms
FEM	axis-line Vₑ, slice Vₑ, activating function, impedance bars
Single fiber	pulse, propagation, waterfall, CNAP
Population	diameter KDE, cross-section recruitment, propagation, CNAP
Conductivity	Cole–Cole σ(f)
Sweep	recruitment curve, threshold-vs-diameter, activation heatmap
Selectivity	Veraart-SI bars
3-D renders	electrode, mesh (per region), fibers, FEM field, Vₑ on endo/epi/fibers, E-field streamlines, cuff zooms

The 3-D variants render off-screen with a caller-supplied camera so all variants of a category share one viewpoint.

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Export presets & formats

export.py defines export presets (e.g. screen and publication at higher DPI with serif fonts) and renders to PNG, PDF, SVG, EPS, JPG for figures and CSV for the underlying data. Colour-blind-safe palettes are available (cividis-based viridis-cb, the ibm-cb 5-colour palette, and a grayscale fallback) so output is accessible by default.

Three ways to export:

• Per-panel — an export button beside each plot (format + preset popover) → a single file.
• Bulk — the Export figures drawer: pick a format + preset, tick figures by category, and Export to ZIP (figures + a data/ folder of CSVs).
• Report — see below.

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The PDF report

Export ▸ Export report opens the Generate Report dialog. You tick which sections to include; golgi assembles a single multi-page PDF with:

1. Cover — project name, timestamp, author, golgi version, and mesh/FEM hashes.
2. Table of contents.
3. Per-domain sections (optional) — electrode design, mesh (with quality histogram), fiber trajectories (branch summary), FEM (axis/slice/activating-function), single-fiber, population, and sweep, each with a 3-D snapshot and the relevant figures + parameter tables.
4. Auto-included appendices — the conductivity table + σ(f) plot, a reproducibility appendix (hashes + frozen requirements + active config files), a bibliography (citations from the active population preset), and an audit excerpt.

Because the report captures the 3-D viewport once, position the camera before generating. All output respects the chosen export preset.

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See also

Recruitment Sweeps & Selectivity · Reproducible Study Bundles · GUI Walkthrough · Reproducing the Paper