PDF Extract

Source: https://github.com/aipoch/medical-research-skills

Validation Shortcut

Run this minimal command first to verify the supported execution path:

python scripts/extract_pdf.py --help

When to Use

• Converting a PDF report/paper into Markdown while preserving page structure (## Page XX) for easy navigation.
• Preparing PPT or design materials where you need both extracted text and page screenshots/blocks (tables, figures, diagrams).
• Reviewing scanned or mixed PDFs and filtering out "text-only" screenshots to keep only meaningful visuals.
• Building a dataset for downstream analysis where each page's text and images must be linked and traceable.
• Creating a lightweight "PDF-to-Markdown" archive with per-page headings and image references.

Key Features

• Extracts selectable PDF text and normalizes paragraphs (collapses line breaks into readable paragraphs).
• Writes Markdown with a document title and per-page sections (# <filename>, ## Page XX).
• Supports multiple image extraction modes:
  • segment (default): renders segmented page blocks (useful for tables/figures).
  • embedded: extracts embedded images from the PDF.
  • page: renders full pages as images.
• Optional post-filters to reduce noisy images:
  • Filter text-heavy images via OCR (--filter-text).
  • Drop images that match extracted page text (likely screenshots of text) (--filter-match).
  • Drop images overlapping PDF text blocks without OCR (--filter-pdf-text).
• Produces stable, per-page image links in Markdown for easy referencing.

Dependencies

• pdfplumber (version not specified)
• pymupdf (version not specified)
• pytesseract (version not specified; required only when --filter-text on or --filter-match on)

Example Usage

python scripts/extract_pdf.py \
  --input input.pdf \
  --output output.md \
  --image-dir images \
  --image-mode segment \
  --filter-text on \
  --text-threshold 0.25 \
  --text-lang eng \
  --filter-match on \
  --match-lang eng \
  --match-min-len 30 \
  --filter-pdf-text on \
  --pdf-text-threshold 0.1

Expected Markdown structure:

• Document title: # <filename>
• Per-page section: ## Page XX
• Text paragraphs (normalized)
• Image links, depending on mode:
  • Segmented blocks: ![page-XX](images/page-XX-block-YY.png) with --image-mode segment
  • Embedded images: ![page-XX](images/page-XX-img-YY.png) with --image-mode embedded
  • Full page render: ![page-XX](images/page-XX.png) with --image-mode page

Implementation Details

• Text extraction and normalization

  • Extracts selectable text from the PDF and collapses line breaks to form coherent paragraphs.
  • Headings are inferred using font-size heuristics (larger font sizes are treated as heading markers).

• Image extraction modes

  • segment (default): renders page segments/blocks to capture localized content (tables/figures) rather than entire pages.
  • embedded: extracts images embedded in the PDF content stream.
  • page: renders each full page as a single image (not recommended if you need cropped screenshots/blocks).

• Filtering options

  • --filter-text on: runs OCR on extracted images and removes images whose OCR text density exceeds --text-threshold (e.g., 0.25).
  • --filter-match on: removes images whose OCR text substantially matches the page's extracted text; controlled by --match-min-len and language via --match-lang.
  • --filter-pdf-text on: removes images that overlap PDF text blocks using PDF layout information (no OCR); controlled by --pdf-text-threshold (e.g., 0.1).

• Output writing

  • Writes a single Markdown file with ## Page XX sections and image links pointing to files saved under --image-dir.

When Not to Use

• Do not use this skill when the required source data, identifiers, files, or credentials are missing.
• Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
• Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

• A clearly specified task goal aligned with the documented scope.
• All required files, identifiers, parameters, or environment variables before execution.
• Any domain constraints, formatting requirements, and expected output destination if applicable.