figcrop 0.1.0__tar.gz

figcrop-0.1.0/AGENTS.md

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+# Agent Guide
+
+Use this repo to extract publication figures from PDFs. Keep changes small and
+verify outputs visually: figure extraction is geometry-heavy and regressions are
+often only visible in the saved JPEGs.
+
+## Important Paths
+
+- Main tool: `figtools.py`
+- Local venv on the development machine: `.venv\Scripts\python.exe`
+- Output manifest: `figures.json` in each extraction output directory
+- Model cache/IR: `models/`
+
+## Common Commands
+
+Windows:
+
+```powershell
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto figs=1,2
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto caption=include
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto trim=whiteband
+.\.venv\Scripts\python.exe figtools.py serve auto
+```
+
+Linux/macOS:
+
+```bash
+.venv/bin/python figtools.py extract paper.pdf out auto
+.venv/bin/python figtools.py serve auto
+```
+
+HTTP server request:
+
+```bash
+curl -s -X POST http://127.0.0.1:8077/extract \
+  -H "Content-Type: application/json" \
+  -d '{"pdf":"paper.pdf","out_dir":"out","figs":[1,2],"caption_mode":"include"}'
+```
+
+## Extraction Options
+
+- `figs=1,2`: extract real figure numbers found from PDF text captions.
+- `top=N`: fallback to the first N visual regions per page.
+- `panels=true`: output detected regions/panels separately.
+- `trim=mask`: default fast trim mode.
+- `trim=whiteband`: slower local whitespace snap around the detector bbox.
+- `caption=include`: include the matched caption text below the figure.
+
+## Verification
+
+Always inspect JPEG outputs, not just command success. At minimum:
+
+1. Open a montage or representative outputs with `view_image`.
+2. Check for cut-off axes, table borders, panel labels, and caption text.
+3. Check for neighbor figure/table frame lines, section headings, or unrelated
+   fallback regions.
+4. For `caption=include`, check that the caption is complete and that nearby
+   frame rules were not included.
+5. Run `python -m py_compile figtools.py` after code changes.
+
+Small one-shot extractions usually finish in a few seconds after model setup.
+Use the server when repeatedly extracting from many PDFs or iterating on trim
+logic.
+
+## Implementation Notes
+
+- Layout detection uses MinerU PP-DocLayoutV2. The OpenVINO IR has static
+  800x800 input, so detector edge errors are handled by trimming, not by raising
+  detector resolution.
+- Numbering is local logic: PDF text captions are matched to nearby visual
+  regions. It is not MinerU's full reading-order pipeline.
+- Default output is one crop per `Fig.N`; `panels=true` opts into region-level
+  output.
+- `caption=include` first trims the figure body, then unions it with a tight
+  caption text-ink rectangle from the PDF text block. Long horizontal/vertical
+  caption-adjacent rules are ignored for the caption bbox.
+- Very dense pages can still need `figs=`, `top=`, or manual review.
+
+## Commit Attribution
+
+If Codex makes commits in this repo, include:
+
+```text
+Co-authored-by: Codex <noreply@openai.com>
+```
+
+Do not add Codex attribution to commits that were authored by another agent or
+by the user. If rewriting already-pushed history, create a backup branch first
+and use `git push --force-with-lease`, never plain `--force`.

figcrop-0.1.0/CLAUDE.md

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+# figcrop Guide for Claude Code
+
+This repository contains a single-file tool, `figtools.py`, for extracting
+figures from research-paper PDFs by real `Fig.N` / `Table N` captions.
+
+Prefer the existing implementation style. The core behavior is geometry-heavy,
+so do not judge changes only by tests or command success: render crops and look
+at the images.
+
+## Quick Commands
+
+Windows development environment:
+
+```powershell
+.\.venv\Scripts\python.exe figtools.py help
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto figs=1,2
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto caption=include
+.\.venv\Scripts\python.exe figtools.py extract paper.pdf out auto trim=whiteband
+.\.venv\Scripts\python.exe figtools.py serve auto
+```
+
+Server request:
+
+```bash
+curl -s -X POST http://127.0.0.1:8077/extract \
+  -H "Content-Type: application/json" \
+  -d '{"pdf":"paper.pdf","out_dir":"out","figs":[1,2],"caption_mode":"include"}'
+```
+
+## Options
+
+- `figs=1,2`: extract real figure numbers from PDF text captions.
+- `top=N`: fallback to first N visual regions per page.
+- `panels=true`: output detected regions/panels separately.
+- `trim=mask`: default fast trim mode.
+- `trim=whiteband`: slower local whitespace snap mode.
+- `caption=include`: include matched caption text below the figure.
+
+API fields are `pdf`, `out_dir`, `figs`, `top`, `panels`, `trim_mode`, and
+`caption_mode`.
+
+## Verification Workflow
+
+After any code change:
+
+```powershell
+.\.venv\Scripts\python.exe -m py_compile figtools.py
+```
+
+For behavior changes, extract at least one dense PDF and inspect a montage or
+representative JPEGs. Look for:
+
+- clipped axes, table borders, panel labels, or captions
+- neighbor frame-line bleed
+- page furniture, section headings, or fallback regions mixed into crops
+- incomplete captions when `caption=include`
+
+Known useful local PDFs on the development machine include:
+
+- `C:\pf2\ye_p3.pdf`
+- `C:\pf2\ye_full.pdf`
+- `C:\pf2\attn.pdf`
+- `C:\pf2\t_isscc.pdf`
+- `C:\pf2\t_jssc.pdf`
+- `C:\pf2\t_ncomm.pdf`
+
+## Implementation Notes
+
+- MinerU PP-DocLayoutV2 detects `image`, `chart`, and `table` regions.
+- OpenVINO IR input is static 800x800, so edge mistakes are handled in trim
+  logic instead of increasing detector resolution.
+- PDF text captions are read directly from `page.get_text("dict")`; figure
+  numbering and region-to-caption assignment are local logic.
+- Default output is one whole-figure crop per `Fig.N`. Use `panels=true` only
+  when region-level output is desired.
+- `caption=include` first trims the figure body, then unions it with a tight
+  caption text-ink rectangle from the same PDF text block. Long caption-adjacent
+  horizontal/vertical rules are ignored for the caption bbox.
+- Always preserve user changes in the worktree. Avoid unrelated refactors.
+
+## Commit Attribution
+
+If Claude Code makes commits, keep its normal attribution conventions. If Codex
+made the commit, include:
+
+```text
+Co-authored-by: Codex <noreply@openai.com>
+```
+
+Do not add Codex attribution to Claude/user commits. If rewriting pushed
+history, create a backup branch first, verify the tree diff is empty, and use
+`git push --force-with-lease`, not plain `--force`.

figcrop-0.1.0/CONNECTORS.md

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+# AI Connectors
+
+figcrop can be exposed to AI tools in two practical ways:
+
+1. **OpenAPI / REST** via the built-in FastAPI server.
+2. **MCP** via the optional `figcrop_mcp.py` stdio server.
+
+Use OpenAPI when an AI product wants an HTTP schema. Use MCP when Claude,
+Codex, or another local agent can run a tool server on the same machine as the
+PDF files.
+
+## OpenAPI / REST
+
+Start the server:
+
+```powershell
+.\.venv\Scripts\python.exe figtools.py serve auto
+```
+
+Discovery endpoints:
+
+- `GET http://127.0.0.1:8077/`
+- `GET http://127.0.0.1:8077/openapi.json`
+- `GET http://127.0.0.1:8077/health`
+
+Extraction request:
+
+```bash
+curl -s -X POST http://127.0.0.1:8077/extract \
+  -H "Content-Type: application/json" \
+  -d '{"pdf":"paper.pdf","out_dir":"out","figs":[1,2],"caption_mode":"include"}'
+```
+
+Important request fields:
+
+- `pdf`: path to the input PDF on the machine running the server
+- `out_dir`: output directory for JPEG crops and `figures.json`
+- `figs`: optional real figure numbers
+- `top`: optional positional fallback
+- `panels`: output panels/regions separately
+- `trim_mode`: `mask` or `whiteband`
+- `caption_mode`: `exclude` or `include`
+
+The server is local by default (`127.0.0.1`). Remote AI products cannot call it
+unless you intentionally expose it through a secure tunnel or hosted deployment.
+
+## MCP
+
+If installed with pipx from GitHub, the MCP command is available directly:
+
+```powershell
+pipx install git+https://github.com/tadalab-keio/figcrop.git
+figcrop-mcp
+```
+
+For a source checkout created with `setup.ps1` / `setup.sh`, install the optional
+MCP dependency:
+
+```powershell
+uv pip install --python .\.venv\Scripts\python.exe -r requirements-mcp.txt
+```
+
+Run the MCP server:
+
+```powershell
+.\.venv\Scripts\python.exe figcrop_mcp.py
+```
+
+The MCP tool is named `extract_figures` and accepts:
+
+```json
+{
+  "pdf": "paper.pdf",
+  "out_dir": "out",
+  "figs": [1, 2],
+  "top": null,
+  "panels": false,
+  "trim_mode": "mask",
+  "caption_mode": "include",
+  "device": "auto"
+}
+```
+
+It returns the output directory, crop count, `figures.json` path, and manifest
+entries.
+
+### Example Local MCP Config
+
+Use absolute paths when configuring external clients:
+
+```json
+{
+  "mcpServers": {
+    "figcrop": {
+      "command": "figcrop-mcp",
+      "args": []
+    }
+  }
+}
+```
+
+If the client does not inherit the pipx command PATH, use the absolute path
+printed by `pipx list` for `figcrop-mcp`.
+
+Keep the server local unless you have a clear security model. PDFs and output
+paths may contain private research material.
+
+## AI-Side Verification
+
+An AI agent should treat extraction as incomplete until it has inspected the
+images. Recommended flow:
+
+1. Run extraction.
+2. Read `figures.json`.
+3. Create or open a montage of JPEGs.
+4. Check for clipped axes/captions and neighbor frame lines.
+5. Retry with `figs=`, `top=`, `panels=true`, or `trim=whiteband` if needed.

figcrop-0.1.0/LICENSE

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figcrop-0.1.0/MANIFEST.in

@@ -0,0 +1,4 @@
+include AGENTS.md
+include CLAUDE.md
+include CONNECTORS.md
+include requirements-mcp.txt

figcrop-0.1.0/NOTICE

@@ -0,0 +1,19 @@
+figcrop
+Copyright 2026 TadaLab (Keio University)
+
+Licensed under the Apache License, Version 2.0.
+
+This product depends on and is built upon third-party software:
+
+- MinerU (https://github.com/opendatalab/MinerU)
+  Licensed under the "MinerU Open Source License" (based on Apache 2.0 with
+  additional terms). figcrop uses MinerU's layout model (PP-DocLayoutV2) and
+  adapts a small portion of MinerU's detection post-processing logic and its
+  class-label list into figtools.py (the OpenVINO path). MinerU itself is not
+  redistributed here; it is installed as a dependency.
+
+- OpenVINO (https://github.com/openvinotoolkit/openvino) — Apache License 2.0.
+- PyMuPDF (https://github.com/pymupdf/PyMuPDF).
+
+Model weights (PP-DocLayoutV2 etc.) are downloaded at runtime from Hugging Face
+and are governed by their own licenses; they are not included in this repository.