paper-figure-generate

name	paper-figure-generate
description	Generates publication-quality figures and diagrams from output/PAPER_PLAN.md for GIScience, GeoAI, and remote sensing journals (IJGIS, ISPRS JPRS, RSE, TGIS). Decides per-figure whether to produce reproducible code-generated plots/maps or structured prompts for external image-generation models (nano banana, ChatGPT image). Produces figure files, source scripts, captions, manifest, and prompt artifacts. Never fabricates results — uses only evidence from project files.
argument-hint	["figure-number-or-\"all\"-or-plan-path"]
allowed-tools	Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply

Skill: paper-figure-generate

You turn the figure plan in output/PAPER_PLAN.md into manuscript-ready figures for $ARGUMENTS. For each figure you decide between a code-generated artifact (plots, maps, quantitative panels) and a prompt-generated artifact (workflow, architecture, conceptual diagrams) and produce the right deliverable with captions and provenance.

This skill is used when the manuscript needs:

• standard plots for spatial data science studies,
• a heterogeneous mix of figure types (maps + architecture + ablations + graphical abstract),
• diagrams better produced by an external image model,
• figure planning artifacts while some experiments are still in flight.

---

Constants

• PLAN_PATH = output/PAPER_PLAN.md — source of truth for figure inventory.
• FIG_DIR = output/figures/ — all figure artifacts.
• SCRIPT_DIR = output/figures/scripts/ — reproducible figure source code.
• PROMPT_DIR = output/figures/prompts/ — external-image-model prompts and design notes.
• MANIFEST = output/figures/FIGURE_MANIFEST.md — master index of all figures.
• CAPTIONS = output/figures/FIGURE_CAPTIONS.md — manuscript-ready captions.
• TARGET_VENUE — read from output/PAPER_PLAN.md header, else research_contract.md, else default IJGIS.
• EXPORT_FORMATS = png, pdf — default raster + vector. Add svg if diagram will be edited by hand.
• DPI = 300 — for raster exports.
• FIG_WIDTH_SINGLE = 3.5in / 89mm — single-column.
• FIG_WIDTH_DOUBLE = 7.2in / 183mm — double-column.

Override via argument (e.g., /paper-figure-generate Fig03 — venue: ISPRS, formats: png,pdf,svg).

---

Core Philosophy

1. Evidence over aesthetics. Never invent metrics, coordinates, or labels. If the evidence is not in the project files, produce a specification stub and stop — do not fill with plausible-looking data.
2. Two honest pathways. Every figure is either reproducible (code + data → image) or schematic (prompt → image). Pick one deliberately per figure; justify in the manifest.
3. Publication discipline. Restrained typography, consistent palette, legible at print size, grayscale-readable where feasible. No marketing gloss.
4. Consistency across the paper. Same fonts, line widths, terminology, dataset names, and notation as the manuscript.
5. Graceful degradation. Missing data → stub + TODO; partial system knowledge → draft prompt + assumptions list. Never silent guesses.

---

Phase 1 — Read and Interpret PAPER_PLAN.md

1. Read output/PAPER_PLAN.md fully. Locate:

   • the Figure Plan table (IDs, types, priorities),
   • the Hero Figure description,
   • the Claims-Evidence Matrix / memory/APPROVED_CLAIMS.md,
   • Methods and Results sections that reference specific figures/tables,
   • any figure draft notes, mockups, or placeholder captions.

2. Resolve the target venue from the plan header (e.g., Target: IJGIS). Apply venue norms (column width, grayscale-safe palette, line-figure vs. color policy).

3. Build an internal figure registry. For each figure extract:

   Field	Notes
   id	Fig01, Fig02, … — zero-padded.
   title	Short, manuscript-ready.
   purpose	Scientific message, one sentence.
   key_message	What a skim reader should take away.
   claim_refs	IDs from APPROVED_CLAIMS.md (if any).
   data_source	Path(s) or MISSING.
   figure_type	From the taxonomy below.
   pathway	code or prompt (Phase 3).
   priority	HIGH / MEDIUM / LOW from plan.
   status	ready / stub / draft-prompt / blocked.
   annotations	Labels, arrows, callouts required.
   dependencies	Tables, experiments, scripts it depends on.

   Persist this registry inline in the manifest (Phase 6). Do not write it to a separate JSON unless the user asks.

4. If PAPER_PLAN.md is missing or incomplete, attempt in order:

   • read linked result files (output/results/, output/spatial-analysis/, output/reports/),
   • read memory/APPROVED_CLAIMS.md + memory/OUTLINE.md,
   • infer the smallest defensible figure set, and mark every inferred row with assumption: inferred from <source> in the manifest.

---

Phase 2 — Figure Type Taxonomy

Choose the type that best serves the scientific message, not the one that looks nicest.

Family	Types
Maps	study-area map, choropleth, spatial distribution, bivariate map, hot-spot (LISA/Gi*), error/residual map, change map, inset panels.
Quantitative plots	bar, grouped bar, line, scatter, scatter-with-fit, box, violin, ECDF, heatmap, confusion matrix, calibration plot.
Ablation / sensitivity	ablation bars with reference line, sensitivity heatmap, tornado plot.
Remote sensing panels	multi-band image grid, before/after, multi-temporal stack, ground-truth vs. prediction panel.
Qualitative case studies	image+label panels, attention/overlay visualizations.
Diagrams (prompt-friendly)	system architecture, workflow/pipeline, conceptual framework, module interaction, graphical abstract, layered platform schematic, human-in-the-loop diagram, data-engine-model-output pipeline.

Map defaults (any map family): scale bar, north arrow, projection + EPSG in caption, legend with units, inset showing regional context, classification scheme stated (quantile / Jenks / equal-interval), class count justified.

---

Phase 3 — Decide Production Pathway (code vs. prompt)

Apply this decision rule per figure. Record the reason in the manifest.

Use code when any of these hold:

• the figure depicts real metrics, distributions, or coordinates,
• results must be reproducible from script + data,
• reviewers may ask to regenerate with new data or parameters,
• the figure shows spatial patterns tied to actual geography,
• the figure is a table rendered as a figure.

Use prompt when all of these hold:

• the figure is primarily structural, conceptual, or schematic,
• no numeric plotting is required,
• the content is labels + boxes + arrows + grouping + style,
• a clean, journal-styled rendering from an image model will be faster than laboriously drawing it in matplotlib / graphviz / TikZ, and editorially acceptable for the target venue.

Hybrid exception. If the diagram needs both schematic structure and a small embedded real chart (e.g., architecture + mini accuracy bars), generate the chart in code, export as a transparent PNG, and note in the prompt that the rendered diagram should leave a placeholder region for it.

Venue caveat: some venues require vector, hand-editable figures. If so, default prompt outputs to prompt + hand-traceable: produce the prompt for ideation, but also emit a skeleton mermaid / graphviz / TikZ file the author can tidy into vector form.

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Phase 4 — Produce Code-Generated Figures

For each code figure:

1. Locate evidence. Grep the paths in data_source. If missing, switch status = stub and skip to the stub template (Phase 4c).
2. Prefer existing tooling. Before writing new code, check whether output/figures/scripts/visualize.py (used by paper-figure) already supports the figure type. Reuse it with explicit CLI arguments.
3. Otherwise write a focused script at output/figures/scripts/{id}_{slug}.py:
   • single purpose, < ~120 lines,
   • reads data by explicit path (no hard-coded magic),
   • exports to FIG_DIR/{id}_{slug}.png and .pdf at DPI,
   • sets figure width from FIG_WIDTH_SINGLE or FIG_WIDTH_DOUBLE,
   • uses the palette/typography defaults below.
4. Run the script from repo root: python output/figures/scripts/{id}_{slug}.py.
5. Verify output exists, has non-trivial size, opens without error.
6. Record the script path and command in the manifest row.

4a. Style defaults for code figures

• Font: a single sans-serif (e.g., Arial, Helvetica, DejaVu Sans) at 8–10 pt for body, 10–12 pt for title, 7–8 pt for tick labels.
• Line weights: 0.8–1.2 pt for axes, 1.2–1.8 pt for data lines.
• Palette: colorblind-safe, ≤ 6 hues. For maps prefer ColorBrewer sequential / diverging appropriate to the variable. Avoid rainbow.
• Grayscale test: if the figure loses meaning in grayscale, add a second channel (line style, marker shape, hatching).
• Whitespace: no unnecessary frames. Remove top/right spines unless they carry meaning.
• Legends: inside the axes when possible, single column, no redundant titles.
• Units: always in axis labels and colorbar labels.

4b. Map-specific checks

• Projection and EPSG stated in caption.
• Scale bar, north arrow, legend, inset — add or log a TODO if any is missing.
• Classification: state method + number of classes. Avoid 7+ classes for categorical color.
• No classification scheme that creates misleading clusters (e.g., equal-interval on highly skewed data).

4c. Stub template (data missing)

When data_source = MISSING, write a specification stub to SCRIPT_DIR/{id}_{slug}.py containing:

• a module docstring describing the intended figure,
• a TODO list of required inputs,
• a commented pandas.read_* call with the expected schema,
• a matplotlib skeleton that raises NotImplementedError("data required: ...") when run.

Also emit FIG_DIR/{id}_{slug}_SPEC.md with: purpose, required data, expected axes, legend, and a short rationale for why the stub cannot be filled yet.

Set status = stub in the manifest and list the blocker in missing_inputs.

---

Phase 5 — Produce Prompt-Generated Figures

For each prompt figure, write three artifacts:

1. output/figures/prompts/{id}_prompt.md — the authoritative design document (see template below).
2. output/figures/prompts/{id}_prompt.txt — the final ready-to-paste prompt text (no front matter, no explanation).
3. output/figures/prompts/{id}_design_notes.md — assumptions, revision checklist, second-pass prompt guidance.

Save the rendered image (once the user supplies it) at FIG_DIR/{id}_{slug}.png. Do not fabricate renders.

5a. Required prompt contents

Every prompt must include, in order:

1. Objective — one sentence on what the figure communicates.
2. Figure type — e.g., "system architecture diagram", "workflow schematic", "conceptual framework".
3. Target journal style — e.g., "IJGIS — restrained, two-column compatible, print-legible".
4. Audience — e.g., "GIScience / GeoAI researchers".
5. Layout instructions — number of layers / columns / rows, grouping panels, reading order, aspect ratio (e.g., 16:9 widescreen or 3:2).
6. Element inventory — every box, node, module, lane, or panel, with exact labels.
7. Relationships — every arrow / line, its direction, and what it means.
8. Text labels to include — verbatim; the model must render them as shown.
9. Style constraints — background, palette, line weights, box shapes, icon policy.
10. Rendering constraints — resolution, aspect ratio, margin, language (English).
11. Negative prompt / avoidance — bullets of what the render must not do.
12. Short prompt version — ≤ 60 words, for quick iteration.
13. Long prompt version — detailed, paste-ready.

5b. Prompt style defaults (bias the model toward these)

• Clean white or subtle neutral background; no decorative gradient.
• Restrained scientific palette — 3–5 muted hues + one accent color for emphasis.
• Rounded rectangles with thin 1–1.5 pt strokes; no drop shadows, no 3-D bevels.
• Sans-serif labels, medium weight, high contrast.
• Explicit arrow directions; no ambiguous double-headed arrows unless the relationship is symmetric.
• Grouping via light-tinted background panels or subtle dashed borders — not saturated color blocks.
• Widescreen layout for architecture/workflow figures; portrait for graphical abstracts.
• Journal-suitable, not marketing-suitable.

5c. Required negative prompt

Always include variants of:

• no 3-D shiny icons, no glossy buttons, no reflective surfaces;
• no cartoon or comic styling;
• no stock-photo people;
• no decorative backgrounds, no world-map wallpaper;
• no invented numbers, metrics, or chart-like decorations inside the diagram;
• no unreadable micro-labels;
• no random geographic symbols unrelated to the paper;
• no text in languages other than the manuscript language;
• no watermark, no vendor logo, no signature.

5d. Assumptions and iteration

{id}_design_notes.md must contain:

• Assumptions — every label, grouping, or relationship inferred from context rather than stated explicitly in PAPER_PLAN.md. Tag each with the source file + section.
• Revision checklist — boxes to tighten, labels to shorten, arrows to reposition once the first render is seen.
• Second-pass prompt hook — a placeholder the user fills in after viewing pass 1 ("after render: check that module X is upstream of Y; if not, …").
• Confirmation list — modules, datasets, or relationships the author should verify before the figure ships.

If the system/workflow is only partially documented, produce a conservative draft prompt (only structure that is clearly supported) and surface the rest as needs_confirmation. Do not invent modules to make the diagram look complete.

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Phase 6 — Captions, Manifest, Provenance

6a. FIGURE_CAPTIONS.md

For each figure (code or prompt), append a manuscript-ready caption:

**Figure N.** [What is shown]. [Data source / experiment ID / CRS + EPSG if a map]. [One sentence of key takeaway that states the finding or structural message, aligned with claim IDs if applicable].

Captions must:

• be self-contained (readable without the body text),
• state CRS/EPSG for every map,
• cite dataset names consistent with the Methods section,
• state sample size / time period where relevant,
• never contain numbers that are not in APPROVED_CLAIMS.md or the source file.

6b. FIGURE_MANIFEST.md

Maintain a single manifest with one row per figure:

| ID | Title | Type | Pathway | Priority | Status | Data Source | Script / Prompt | Claims | Missing Inputs | Notes |
|---|---|---|---|---|---|---|---|---|---|---|
| Fig01 | NORA system architecture | architecture | prompt | HIGH | draft-prompt | - | prompts/Fig01_prompt.md | C1,C2 | - | widescreen, 4 layers |
| Fig02 | Study area, CONUS counties | choropleth map | code | HIGH | ready | data/processed/counties.geojson | scripts/Fig02_study_area.py | C1 | - | EPSG:5070 |
| Fig03 | Local R² by county | choropleth map | code | HIGH | stub | output/results/mgwr_results.json | scripts/Fig03_local_r2.py | C3 | mgwr_results.json | blocked on experiment |

Also include a short prose summary at the top: venue, total figures, counts by pathway, counts by status, outstanding blockers.

6c. Filename conventions

• Figures: FIG_DIR/{id}_{slug}.{png,pdf,svg} — id is Fig01 etc., slug is short kebab-case.
• Scripts: SCRIPT_DIR/{id}_{slug}.py.
• Prompts: PROMPT_DIR/{id}_prompt.md, {id}_prompt.txt, {id}_design_notes.md, optional {id}_assumptions.md if long.
• Specs (stubs): FIG_DIR/{id}_{slug}_SPEC.md.

6d. Consistency pass (always run before finishing)

After all figures are produced, do one pass across the set and verify:

• figure numbering is contiguous and matches PAPER_PLAN.md,
• typography, line widths, and palette are shared across code figures,
• terminology (model names, dataset names, metric names, region names) matches the manuscript and APPROVED_CLAIMS.md,
• diagram labels in prompt figures match code figure axis labels,
• every caption in FIGURE_CAPTIONS.md has a manifest row and vice versa,
• no caption contains a number absent from APPROVED_CLAIMS.md.

Log any inconsistencies at the top of the manifest under ## Consistency Issues.

---

Decision Rules (quick reference)

Situation	Action
Plan lists a figure but no data exists	Emit stub script + _SPEC.md, set status=stub, list blocker.
Plan lists a conceptual/system figure	Use prompt pathway.
Plan lists a hero figure mixing schematic + real metrics	Hybrid: code chart + prompt diagram with placeholder region.
Venue requires vector	Default prompt figures to produce a companion mermaid/graphviz skeleton.
Map without CRS/scale info	Add TODO in caption; do not silently omit.
Finding needed for caption not in APPROVED_CLAIMS.md	Write caption without the number and tag [NEEDS CLAIM].
Plan missing entirely	Infer minimum viable figure set from claims + results; mark all as inferred.
User asks for a single figure ID	Restrict work to that ID; do not regenerate others.

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Guardrails

• Never fabricate results, coordinates, metrics, dataset names, or module names.
• Never classify a map in a way that visually amplifies a pattern not supported by the data (e.g., custom breaks that manufacture clusters).
• Never produce flashy, 3-D, or marketing-styled renders. If the prompt tends that way, strengthen the negative prompt.
• Never overload a figure with text — if a panel has more than ~8 labels, split it.
• Never let diagram labels conflict with PAPER_PLAN.md. If the plan says "Agent A" and the architecture says "Scout", pick one and update the other.
• Never skip the consistency pass (Phase 6d).
• Never delete an existing FIGURE_MANIFEST.md or FIGURE_CAPTIONS.md — append / edit in place so provenance is preserved.
• Never run destructive shell commands and never modify files outside FIG_DIR, SCRIPT_DIR, PROMPT_DIR, and output/ generally.

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Outputs

• output/figures/{id}_{slug}.png and .pdf (and .svg when justified) — rendered code figures.
• output/figures/scripts/{id}_{slug}.py — reproducible figure source.
• output/figures/{id}_{slug}_SPEC.md — specification stubs when data are missing.
• output/figures/prompts/{id}_prompt.md / .txt / _design_notes.md — prompt artifacts for external image models.
• output/figures/FIGURE_MANIFEST.md — master index + consistency log.
• output/figures/FIGURE_CAPTIONS.md — manuscript-ready captions.
• Update memory/OUTLINE.md Figures section with paths and status.
• Append a one-line entry per generated figure to output/PROJ_NOTES.md (e.g., Fig03 stub — waiting on mgwr_results.json).

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Relationship to Other Skills

• paper-plan produces PAPER_PLAN.md (this skill's input). If the plan is missing, invoke paper-plan first rather than fabricating one.
• paper-figure handles the standard spatial-regression figure pipeline via visualize.py. When the paper is a pure spatial-regression study, prefer paper-figure. Use paper-figure-generate for mixed / systems / GeoAI / benchmark papers and whenever diagram prompts are needed.
• result-to-claim is the safety gate: do not place a number in a caption unless it is in memory/APPROVED_CLAIMS.md.
• submit-check consumes FIGURE_MANIFEST.md and FIGURE_CAPTIONS.md — keep them in journal-ready shape.

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Invocation

/paper-figure-generate                      # generate / refresh all figures in PAPER_PLAN.md
/paper-figure-generate Fig03                # generate a single figure
/paper-figure-generate "all — venue: ISPRS" # override venue
/paper-figure-generate prompts-only         # only regenerate prompt artifacts
/paper-figure-generate code-only            # only regenerate code figures

See templates/prompt_template.md and templates/manifest_template.md in this skill folder for the canonical artifact shapes.