Cropfig

<Purpose> Three-step pipeline that produces, from a `.key` or `.pptx` deck, both manuscript-ready vector PDFs and outline-ready raster PNGs of the figure-only content (top label and bottom caption stripped), and uploads both into the right places. Both image artifacts derive from the same cropped PDF so they cannot drift; the outline embed is idempotent (re-running replaces the link rather than duplicating). </Purpose>

<Use_When>

• You author figures in Keynote/PowerPoint and need (a) vector PDFs to drop into a LaTeX manuscript and (b) low-resolution PNGs to embed into an outline doc that already carries caption text.
• The /sync command needs to embed figure-only PNGs into an outline document at each result section.
• Preparing figures for slides / social-media / a reviewer response where the caption is supplied separately. </Use_When>

<Do_Not_Use_When>

• The caller wants the slide with its caption / label intact (the full-slide PDFs are intermediate and discarded — only cropped artifacts are saved).
• The deck has no consistent "Figure N. Title" top label or trailing caption (the heuristic still tight-bboxes whitespace, so this is safe but wasted effort).
• You need a different crop policy (e.g. keep top label, drop bottom only) — the band-classification heuristic is symmetric and not configurable per-side. </Do_Not_Use_When>

<Configuration> Required inputs: the deck path + (for func 3) the manuscript dir and outline file. Cropping outputs land next to the deck by default; func 3 reads from there and copies into the manuscript + outline-parent figures dirs.

Variable	Default	Used by	Purpose
DECK_FILE	(required)	func 1, 2, 3	Path to a .key or .pptx deck. Step 1 + 2 read it directly; step 3 derives <deck_parent>/pdf/ and <deck_parent>/png/ from it.
MANUSCRIPT_DIR	paper	func 3	LaTeX manuscript root. Cropped PDFs land in <MANUSCRIPT_DIR>/figures/figureNN.pdf. Matches /omcr-setup's default.
OUTLINE_FILE	outline.md	func 3	Outline markdown file. PNGs land in <dirname(OUTLINE_FILE)>/figures/figureNN.png; image links are inserted into the outline itself.
RESULT_PATTERN	^### Result (\d+)	func 3	Regex with a single capture group = figure number. Used to find result headings in the outline.
CROPFIG_PROBE_DPI	100	func 2	DPI used for the probe rasterization that drives crop-bound detection. Higher = slower but slightly tighter crops.
CROPFIG_PNG_DPI	120	func 2	Output DPI for the outline PNGs. Raise for sharper outline review (and larger docx); lower for slimmer docx.

Output locations.

<dirname($DECK_FILE)>/
├── <deck>.key|pptx               # the deck itself
├── pdf/figureNN.pdf              # func 2 writes (manuscript-grade vector)
└── png/figureNN.png              # func 2 writes (outline-grade raster)

$MANUSCRIPT_DIR/
└── figures/figureNN.pdf          # func 3 copies here for the .tex

dirname($OUTLINE_FILE)/
├── $OUTLINE_FILE                 # func 3 inserts/updates ![Figure N](...) links
└── figures/figureNN.png          # func 3 copies here for the markdown

These defaults match /omcr-setup's conventions (Manuscript dir: paper/, Outline file: outline.md, Result pattern: ^### Result (\d+)). See wiki/Configuration.md for the CLAUDE.md Research-stack schema.

On first invocation with no DECK_FILE and no project Deck file in CLAUDE.md, ask the user for the deck path then offer to persist it to the project's CLAUDE.md. </Configuration>

<Steps>

Step 1 — Export deck to per-slide PDFs (export_deck.py)

Run the exporter with a temp staging directory:

STAGE=$(mktemp -d)
python3 "$CLAUDE_PLUGIN_ROOT"/skills/cropfig/export_deck.py "$DECK_FILE" "$STAGE"

Dispatch inside export_deck.py — each format uses its native app to avoid cross-format import drift:

• .key → macOS Keynote via AppleScript → single deck PDF.
• .pptx → macOS PowerPoint via AppleScript when /Applications/Microsoft PowerPoint.app is present; otherwise LibreOffice headless (soffice --convert-to pdf).

The single deck PDF is then split into figure01.pdf, figure02.pdf, … using PyMuPDF. These per-slide PDFs are vector (text and lines stay sharp at any zoom) and feed Step 2.

Guard: if export fails (missing tool, permission denied, headless env), surface the error and stop.

Step 2 — Crop + emit both artifacts (crop_figures.py)

python3 "$CLAUDE_PLUGIN_ROOT"/skills/cropfig/crop_figures.py "$STAGE"
rm -rf "$STAGE"

This writes to <dirname($DECK_FILE)>/pdf/ and <dirname($DECK_FILE)>/png/. To write elsewhere, pass positional output dirs:

python3 "$CLAUDE_PLUGIN_ROOT"/skills/cropfig/crop_figures.py "$STAGE" "$PDF_OUT" "$PNG_OUT"

For each slide PDF, the script:

1. Renders a CROPFIG_PROBE_DPI probe and runs find_crop_bounds from crop_bounds.py (band-classification heuristic on top + bottom; tight-bbox on remaining content).
2. Maps the pixel bounds back to PDF point coordinates and applies them as a CropBox on a copy of the slide — output stays vector.
3. Writes the cropped PDF next to the deck under pdf/figureNN.pdf.
4. Re-rasterizes the cropped PDF at CROPFIG_PNG_DPI → png/figureNN.png next to the deck.

Both outputs share the same crop decision because the PNG is a downsampled view of the manuscript PDF.

Step 3 — Upload to manuscript + outline (upload_figures.py)

python3 "$CLAUDE_PLUGIN_ROOT"/skills/cropfig/upload_figures.py

Reads from <deck_parent>/pdf/ and <deck_parent>/png/ (so func 2 must have run first). Does two things:

3a. Manuscript copy. For each figureNN.pdf, copies to $MANUSCRIPT_DIR/figures/figureNN.pdf. The .tex is not modified — \includegraphics{figures/figureNN} is author content.

3b. Outline embed. For each figureNN.png:

1. Copy to <dirname($OUTLINE_FILE)>/figures/figureNN.png.
2. Scan the outline for lines matching $RESULT_PATTERN. For each match, the captured N is the figure number; insert (or replace, if previously inserted by this script) the link ![Figure N](figures/figureNN.png) immediately after the heading (skipping blank lines).

The embed is idempotent — re-running replaces the existing link line with the same content rather than appending a new one. Result heading without a matching figure is reported as missing; figure with no matching result heading is reported as orphan.

Step 4 — Report

## Cropfig run — YYYY-MM-DD

- Deck: $DECK_FILE (N slides)
- Manuscript PDFs: <dirname($DECK_FILE)>/pdf/ (N files)
- Outline PNGs:    <dirname($DECK_FILE)>/png/ (N files, $CROPFIG_PNG_DPI DPI)
- Top label removed: A / N
- Bottom caption removed: B / N

Upload:
- $MANUSCRIPT_DIR/figures/: N PDF(s) copied
- $OUTLINE_FILE: M heading(s) updated  (missing: ..., orphan: ...)

Slides where heuristic skipped a side (still tight-bboxed):
- <filename> — <which side>

If Step 1 failed, report only that and skip the rest. Steps 2 and 3 can run independently if a prior staging dir or PDF/PNG dir already exists.

</Steps>

<Output_Contract>

Path	Owner	Content	Used by
<dirname($DECK_FILE)>/pdf/figureNN.pdf	func 2	cropped vector PDF (no top label, no bottom caption, tight-bbox); page CropBox set	source of truth — func 3 reads here for the manuscript copy
<dirname($DECK_FILE)>/png/figureNN.png	func 2	rasterized view of the same cropped PDF at CROPFIG_PNG_DPI	source of truth — func 3 reads here for the outline copy
$MANUSCRIPT_DIR/figures/figureNN.pdf	func 3 (copy)	identical to the source PDF	\includegraphics{figures/figureNN} in the .tex
<dirname($OUTLINE_FILE)>/figures/figureNN.png	func 3 (copy)	identical to the source PNG	 in the outline
$OUTLINE_FILE	func 3 (modifies)	image link inserted after each result heading	outline rendering (GitHub, VS Code preview, Pandoc → docx)

Filenames mirror across the four image locations so callers can pair figureNN.pdf with figureNN.png. The staging dir from Step 1 is ephemeral and deleted at the end of the run; no uncropped intermediate is persisted.

</Output_Contract>

<Failure_Modes>

Symptom	Cause	Action
ModuleNotFoundError: fitz	PyMuPDF not installed	python3 -m pip install pymupdf
ModuleNotFoundError: numpy / PIL	bare environment	python3 -m pip install numpy pillow
ERROR: .key export requires macOS + Keynote	running on non-macOS with a .key deck	run on macOS, or re-save the deck as .pptx and retry
Keynote export failed: ...	Keynote not installed, deck password-protected, or AppleScript permission denied	grant System Settings → Privacy & Security → Automation → Terminal/your shell → Keynote
PowerPoint export failed: ...	PowerPoint not licensed/signed in, deck password-protected, or AppleScript permission denied	grant System Settings → Privacy & Security → Automation → Terminal/your shell → Microsoft PowerPoint. Failures are no longer silently swallowed — there is no auto-fallback when PowerPoint IS installed.
PowerPoint export failed: ... -9074	Office sandbox refused to write to the staging path	the script already stages under ~/Library/Caches/cropfig/ to satisfy Office sandbox; if you see this anyway, check that ~/Library/Caches/ is writable and Office has been granted Full Disk Access if your deck is on a network volume
LibreOffice (soffice) not on PATH	Linux/PowerPoint-not-installed path with no LibreOffice	brew install --cask libreoffice (mac) / apt install libreoffice (linux)
Top label or bottom caption NOT removed on a slide	band thinner than MIN_LABEL_HEIGHT=30 rows, or contains a colored element (heuristic treats it as figure content)	accept — tight-bbox still removes whitespace; don't globally lower the threshold to catch one slide
Cropped PDF still shows label when opened in some viewers	viewer ignores CropBox and renders MediaBox	use a viewer that honors CropBox (Preview, Acrobat, most LaTeX rasterizers do); the PNG path is unaffected
Output PNG looks blurry in docx	CROPFIG_PNG_DPI too low	raise to 150 / 180 (file sizes grow proportionally)
func 3 reports headings without matching figure: #N	outline has more ### Result N headings than the deck has slides for	either add the missing slide to the deck, or trim the outline heading; func 3 will not invent a figure
func 3 reports orphan figures: figureN	deck has more slides than the outline has result headings	extend the outline with ### Result N, or accept the orphan if those slides are non-result (concept, schematic, appendix)
WARN (3b copy): PNG source dir not found	func 2 has not run yet, or wrote to a different location	run func 1 + 2 first; verify <dirname($DECK_FILE)>/png/ exists

</Failure_Modes>

<Files> - `SKILL.md` — this file. - `export_deck.py` — func 1: deck → per-slide vector PDFs. Dispatches by extension: `.key` → Keynote AppleScript, `.pptx` → PowerPoint AppleScript when installed, else LibreOffice headless. Splits the resulting deck PDF via PyMuPDF. Stages under `~/Library/Caches/cropfig/` on macOS so Office sandbox can write. - `crop_figures.py` — func 2: per-slide PDF → cropped PDF (vector, manuscript) + raster PNG (outline). Both share one crop decision. - `upload_figures.py` — func 3: copies cropped PDFs to `$MANUSCRIPT_DIR/figures/`, copies cropped PNGs to `<dirname($OUTLINE_FILE)>/figures/`, inserts/updates `` links in the outline after each `$RESULT_PATTERN` match. Idempotent. - `crop_bounds.py` — pure heuristic module. `find_top_cut`, `find_bottom_cut`, `find_crop_bounds(arr)` — used by `crop_figures.py`. Tune constants at the top if your slide-deck layout changes (most likely tweak: `MIN_LABEL_HEIGHT` for shorter labels). </Files>