OCR-to-RAG pipeline for life science screenshots

PaddleOCR with preprocessing, scispaCy NER, figure/table detection, citation extraction, and chunked Markdown output with frontmatter. Includes watch mode and notebook reprocessing.
2026-07-18 19:34:22 +00:00
parent 012549b4bc
commit a32b7508c7
68 changed files with 8708 additions and 0 deletions
--- a/src/ocr_pipeline.egg-info/PKG-INFO
+++ b/src/ocr_pipeline.egg-info/PKG-INFO
@@ -0,0 +1,276 @@
+Metadata-Version: 2.4
+Name: ocr-pipeline
+Version: 0.1.0
+Summary: OCR pipeline for life science screenshots - RAG ready
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: typer[all]>=0.9.0
+Requires-Dist: pydantic>=2.6.0
+Requires-Dist: pydantic-settings>=2.2.0
+Requires-Dist: pyyaml>=6.0.1
+Requires-Dist: structlog>=24.1.0
+Requires-Dist: rich>=13.7.0
+Requires-Dist: tqdm>=4.66.0
+Requires-Dist: opencv-python-headless>=4.9.0
+Requires-Dist: pillow>=10.2.0
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: scikit-image>=0.22.0
+Requires-Dist: paddleocr>=2.7.0
+Requires-Dist: pytesseract>=0.3.10
+Requires-Dist: torch>=2.2.0
+Requires-Dist: torchvision>=0.17.0
+Requires-Dist: transformers>=4.38.0
+Requires-Dist: layoutparser>=0.3.0
+Requires-Dist: langchain-text-splitters>=0.0.2
+Requires-Dist: spacy>=3.7.0
+Requires-Dist: sqlite-utils>=3.37.0
+Requires-Dist: watchdog>=3.0.0
+Requires-Dist: python-slugify>=8.0.0
+Requires-Dist: xxhash>=3.4.0
+Requires-Dist: python-magic>=0.4.27
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.12.0; extra == "dev"
+Requires-Dist: ruff>=0.2.0; extra == "dev"
+Requires-Dist: mypy>=1.8.0; extra == "dev"
+Requires-Dist: pre-commit>=3.6.0; extra == "dev"
+Provides-Extra: grobid
+Requires-Dist: grobid-client>=0.8.0; extra == "grobid"
+Provides-Extra: full
+Requires-Dist: ocr-pipeline[dev]; extra == "full"
+Requires-Dist: ocr-pipeline[grobid]; extra == "full"
+
+# OCR Pipeline for Life Science Screenshots
+
+A production-ready OCR pipeline that extracts text from scientific screenshots and converts them into RAG-ready Markdown files with rich metadata.
+
+## Features
+
+- **Multi-engine OCR**: PaddleOCR (primary) with Tesseract fallback
+- **Image preprocessing**: Deskewing, denoising, CLAHE contrast enhancement, line removal
+- **Parallel processing**: Multi-process worker pool for throughput
+- **Scientific entity recognition**: Genes, proteins, chemicals, species, diseases, cell lines via scispaCy
+- **Figure & table detection**: LayoutParser + Table Transformer
+- **Citation extraction**: DOI, PMID, arXiv, PMC, ISBN via regex + optional GROBID
+- **Semantic chunking**: LangChain recursive splitter optimized for scientific text
+- **RAG-ready output**: Markdown with YAML frontmatter (source, hash, timestamp, entities, confidence)
+- **Watch mode**: File system monitoring with SQLite persistence for incremental processing
+- **Notebook migration**: Reprocess screenshots from existing Jupyter notebooks
+- **Life-science focused**: Handles scientific notation, units, gene symbols, chemical formulas
+
+## Quick Start
+
+```bash
+# Install with uv (recommended)
+uv sync
+
+# Or with pip
+pip install -e .
+
+# Install pre-commit hooks
+pre-commit install
+
+# Run on your screenshots
+ocr-pipeline run
+
+# Watch for new screenshots
+ocr-pipeline watch
+
+# Reprocess from notebook
+ocr-pipeline reprocess ocr_sc.ipynb
+
+# Check status
+ocr-pipeline status
+```
+
+## Configuration
+
+Edit `config.yaml`:
+
+```yaml
+input:
+  paths: ["~/Pictures", "/mnt/storage3/aman/screenshots"]
+  patterns: ["SCR-*.png", "*.jpg", "*.jpeg", "*.tiff"]
+  recursive: true
+
+ocr:
+  engine: "paddleocr"  # paddleocr | tesseract | auto
+  languages: ["en", "latin"]
+  use_gpu: false
+  preprocess:
+    deskew: true
+    denoise: true
+    clahe: true
+    adaptive_threshold: true
+    remove_lines: true
+
+processing:
+  workers: 4
+  batch_size: 10
+  retry_attempts: 2
+
+detectors:
+  figures:
+    enabled: true
+    confidence_threshold: 0.7
+  tables:
+    enabled: true
+    confidence_threshold: 0.7
+
+entities:
+  enabled: true
+  model: "en_core_sci_lg"  # scispaCy large model
+
+citations:
+  regex_enabled: true
+  grobid_enabled: false  # Set true if running GROBID server
+
+chunking:
+  chunk_size: 1000
+  chunk_overlap: 200
+
+output:
+  base_directory: "./data/ocr_output"
+  organize_by: "date_run"  # date_run | source_dir | flat
+  frontmatter:
+    - source_path
+    - source_hash
+    - timestamp
+    - ocr_engine
+    - ocr_confidence_mean
+    - language
+    - detected_entities
+    - has_figures
+    - has_tables
+    - citations_found
+    - chunk_index
+    - total_chunks
+
+watch:
+  enabled: true
+  debounce_seconds: 5
+  db_path: "./data/processed_files.db"
+```
+
+## Output Format
+
+Each chunk produces a Markdown file with YAML frontmatter:
+
+```markdown
+---
+source_path: "/Users/Aman/Pictures/SCR-20250115-gel.png"
+source_hash: "a1b2c3d4e5f6..."
+timestamp: "2025-01-15T10:30:00Z"
+ocr_engine: "paddleocr"
+ocr_confidence_mean: 0.91
+language: "en"
+detected_entities: ["GENE", "PROTEIN", "CHEMICAL"]
+has_figures: true
+has_tables: false
+citations_found: ["DOI:10.1038/nature12345", "PMID:12345678"]
+chunk_index: 0
+total_chunks: 2
+---
+
+# Screenshot: SCR-20250115-gel.png
+
+## Figures
+
+### Figure 1
+- **BBox**: [100, 200, 800, 600]
+- **Confidence**: 0.92
+- **Caption**: "Western blot showing BRCA1 expression..."
+
+## Detected Entities
+
+- BRCA1
+- CRISPR
+- β-actin
+
+## Citations
+
+- DOI: 10.1038/nature12345
+- PMID: 12345678
+
+## Extracted Text
+
+**Western Blot Analysis of BRCA1 Expression**
+
+Lane 1: WT control
+Lane 2: BRCA1 KO (CRISPR)
+Lane 3: BRCA1 KO + pBRCA1-WT rescue
+Lane 4: BRCA1 KO + pBRCA1-C61G mutant
+
+Anti-BRCA1 (1:1000), Anti-β-actin (1:5000)
+```
+
+## Directory Structure
+
+```
+data/ocr_output/
+├── 2025-01-15/
+│   ├── run_001/
+│   │   ├── SCR-20250115-gel_chunk_000.md
+│   │   └── SCR-20250115-gel_chunk_001.md
+│   └── run_002/
+│       └── ...
+└── 2025-01-16/
+    └── run_001/
+        └── ...
+```
+
+## Docker
+
+```bash
+# Build
+docker build -t ocr-pipeline .
+
+# Run once
+docker run -v ~/Pictures:/data/screenshots -v ./data:/app/data ocr-pipeline run
+
+# Watch mode
+docker run -v ~/Pictures:/data/screenshots -v ./data:/app/data ocr-pipeline watch
+```
+
+## Life Science Optimizations
+
+| Feature | Implementation |
+|---------|----------------|
+| Gene/Protein names | scispaCy `en_core_sci_lg` NER |
+| Chemical formulas | Regex + unit normalization (µM, ng/mL, kb, etc.) |
+| Scientific notation | `1.5×10⁻³` → `1.5×10^-3` |
+| Gel/blot lanes | Figure detection + caption extraction |
+| Citations | DOI, PMID, arXiv, PMC, ISBN patterns |
+| Units | µM, ng/mL, kb/Mb/Gb, °C, ×g, etc. |
+
+## Development
+
+```bash
+# Install dev dependencies
+uv sync --dev
+
+# Run tests
+pytest
+
+# Lint
+ruff check .
+ruff format .
+
+# Type check
+mypy src/
+```
+
+## Model Downloads
+
+First run downloads models automatically:
+- PaddleOCR detection/recognition models (~200MB)
+- scispaCy `en_core_sci_lg` (~800MB)
+- Table Transformer (~500MB)
+- LayoutParser PubLayNet (~300MB)
+
+Cache location: `~/.cache/ocr_pipeline/`
+
+## License
+
+MIT
--- a/src/ocr_pipeline.egg-info/SOURCES.txt
+++ b/src/ocr_pipeline.egg-info/SOURCES.txt
@@ -0,0 +1,35 @@
+README.md
+pyproject.toml
+src/ocr_pipeline/__init__.py
+src/ocr_pipeline/cli.py
+src/ocr_pipeline/config.py
+src/ocr_pipeline/pipeline.py
+src/ocr_pipeline/watch.py
+src/ocr_pipeline.egg-info/PKG-INFO
+src/ocr_pipeline.egg-info/SOURCES.txt
+src/ocr_pipeline.egg-info/dependency_links.txt
+src/ocr_pipeline.egg-info/entry_points.txt
+src/ocr_pipeline.egg-info/requires.txt
+src/ocr_pipeline.egg-info/top_level.txt
+src/ocr_pipeline/citations/__init__.py
+src/ocr_pipeline/citations/extractor.py
+src/ocr_pipeline/citations/regex_extractor.py
+src/ocr_pipeline/detectors/__init__.py
+src/ocr_pipeline/detectors/figures.py
+src/ocr_pipeline/detectors/tables.py
+src/ocr_pipeline/ocr/__init__.py
+src/ocr_pipeline/ocr/engine.py
+src/ocr_pipeline/ocr/parallel.py
+src/ocr_pipeline/output/__init__.py
+src/ocr_pipeline/output/markdown.py
+src/ocr_pipeline/postprocess/__init__.py
+src/ocr_pipeline/postprocess/chunk.py
+src/ocr_pipeline/postprocess/clean.py
+src/ocr_pipeline/postprocess/entities.py
+src/ocr_pipeline/utils/__init__.py
+src/ocr_pipeline/utils/db.py
+src/ocr_pipeline/utils/logging.py
+src/ocr_pipeline/utils/migrate.py
+src/ocr_pipeline/watch/__init__.py
+src/ocr_pipeline/watch/watcher.py
+tests/test_postprocess.py
--- a/src/ocr_pipeline.egg-info/dependency_links.txt
+++ b/src/ocr_pipeline.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
--- a/src/ocr_pipeline.egg-info/entry_points.txt
+++ b/src/ocr_pipeline.egg-info/entry_points.txt
@@ -0,0 +1,2 @@
+[console_scripts]
+ocr-pipeline = ocr_pipeline.cli:app
--- a/src/ocr_pipeline.egg-info/requires.txt
+++ b/src/ocr_pipeline.egg-info/requires.txt
@@ -0,0 +1,39 @@
+typer[all]>=0.9.0
+pydantic>=2.6.0
+pydantic-settings>=2.2.0
+pyyaml>=6.0.1
+structlog>=24.1.0
+rich>=13.7.0
+tqdm>=4.66.0
+opencv-python-headless>=4.9.0
+pillow>=10.2.0
+numpy>=1.26.0
+scikit-image>=0.22.0
+paddleocr>=2.7.0
+pytesseract>=0.3.10
+torch>=2.2.0
+torchvision>=0.17.0
+transformers>=4.38.0
+layoutparser>=0.3.0
+langchain-text-splitters>=0.0.2
+spacy>=3.7.0
+sqlite-utils>=3.37.0
+watchdog>=3.0.0
+python-slugify>=8.0.0
+xxhash>=3.4.0
+python-magic>=0.4.27
+
+[dev]
+pytest>=8.0.0
+pytest-cov>=4.1.0
+pytest-mock>=3.12.0
+ruff>=0.2.0
+mypy>=1.8.0
+pre-commit>=3.6.0
+
+[full]
+ocr-pipeline[dev]
+ocr-pipeline[grobid]
+
+[grobid]
+grobid-client>=0.8.0
--- a/src/ocr_pipeline.egg-info/top_level.txt
+++ b/src/ocr_pipeline.egg-info/top_level.txt
@@ -0,0 +1 @@
+ocr_pipeline