input:
  paths:
    - "~/Pictures"
  patterns:
    - "SCR-*.png"
    - "*.jpg"
    - "*.jpeg"
    - "*.tiff"
    - "*.bmp"
  recursive: true
  exclude_patterns:
    - "*.photoslibrary/*"

ocr:
  engine: "paddleocr"
  languages: ["en", "latin"]
  use_gpu: false
  use_angle_cls: true
  det_db_thresh: 0.3
  det_db_box_thresh: 0.6
  det_db_unclip_ratio: 1.5
  rec_batch_num: 6
  cpu_threads: 4

processing:
  workers: 4
  batch_size: 10
  retry_attempts: 2
  timeout_per_image: 120
  skip_existing: true

detectors:
  figures:
    enabled: true
    model: "lp://PubLayNet/faster_rcnn_R_50_FPN_3x/config"
    confidence_threshold: 0.7
  tables:
    enabled: true
    model: "microsoft/table-transformer-detection"
    confidence_threshold: 0.7
  captions:
    enabled: true
    model: "lp://PubLayNet/faster_rcnn_R_50_FPN_3x/config"
    confidence_threshold: 0.5

entities:
  enabled: true
  model: "en_core_sci_lg"
  types:
    - "GENE"
    - "PROTEIN"
    - "CHEMICAL"
    - "SPECIES"
    - "DISEASE"
    - "CELL_LINE"
    - "ORGANISM"
    - "CELL_TYPE"
  merge_entities: true

citations:
  regex_enabled: true
  grobid_enabled: false
  grobid_url: "http://localhost:8070"
  grobid_timeout: 30

chunking:
  chunk_size: 1000
  chunk_overlap: 200
  separators: ["\n\n", "\n", ". ", " ", ""]
  keep_separator: true

output:
  write_consolidated: true
  consolidated_filename: "all_ocr.md"
  # Uses platformdirs default: ~/.local/share/ocr-pipeline (Linux), ~/Library/Application Support/ocr-pipeline (macOS), %LOCALAPPDATA%\ocr-pipeline (Windows)
  format: "markdown"
  organize_by: "date_run"
  frontmatter:
    fields:
      - "source_path"
      - "source_hash"
      - "timestamp"
      - "ocr_engine"
      - "ocr_confidence_mean"
      - "language"
      - "detected_entities"
      - "has_figures"
      - "has_tables"
      - "citations_found"
      - "chunk_index"
      - "total_chunks"
    include_raw_text: false

watch:
  enabled: true
  debounce_seconds: 5
  # Uses platform-aware defaults from config.py
  # ignore_patterns:
  #   - ".DS_Store"
  #   - "*.tmp"
  #   - "*.partial"
  #   - "*.crdownload"
  poll_interval: 1.0